@ARTICLE{Matcha:1978,
AUTHOR = {Matcha, Robert L. and Pettitt, Bernard M. and Meier, Paul F. and Pendergast, Phil},
TITLE = {Potential energy surface for the collinear reaction of neon and HeH+},
JOURNAL = {Journal of Chemical Physics},
VOLUME = 69,
NUMBER = 5,
PAGES = {2264-5},
NOTE = {CAN 90:29276
65-2
General Physical Chemistry
Dep. Chem.,Univ. Houston,Houston,TX,USA.
Journal
0021-9606
written in English.
12200-65-6 Role: PRP (Properties) (heat of reaction of, with helium); 7440-59-7 Role: PRP (Properties) (heat of reaction of, with neon hydride ion); 68694-95-1 Role: PRP (Properties) (potential surface for); 7440-01-9 Role: RCT (Reactant), RACT (Reactant or reagent) (reaction of, with helium-hydride, potential surface for); 17009-49-3 Role: RCT (Reactant), RACT (Reactant or reagent) (reaction of, with neon, potential surface for)},
ABSTRACT = {SCF-LCAO-MO calcns. were made for NeHHe+. The complex has a min. energy of -131.49544 hartree, corresponding to He-H and Ne-H bond distances of 1.875 and 2.05 bohr, resp. The reactions NeH+ + He -> NeHHe+ and Ne + HHe+ -> NeHHe+ are exothermic by 9.4 and 14.5 kcal/mol, resp. [on SciFinder (R)]},
KEYWORDS = {Heat of reaction (of helium-group gas hydride ion); Potential energy and function (surface of, for helium hydride ion collinear reaction with neon)
MO hydride neon helium; potential surface hydride helium neon; heat reaction helium neon hydride; energy potential helium neon hydride},
YEAR = 1978
}
@ARTICLE{Matcha:1978b,
AUTHOR = {Matcha, R. L. and Pettitt, B. M. and Ramirez, B. I. and McIntire, W. R.},
TITLE = {Theoretical Compton profile anisotropies in molecules and solids. III. Relationship of parallel-perpendicular anisotropies to charge distributions in alkali chloride molecules},
JOURNAL = {Journal of Chemical Physics},
VOLUME = 69,
NUMBER = 7,
PAGES = {3025-33},
NOTE = {CAN 90:12458
65-1
General Physical Chemistry
Dep. Chem.,Univ. Houston,Houston,TX,USA.
Journal
0021-9606
written in English.
7447-40-7; 7447-41-8; 7647-14-5 Role: PRP (Properties) (Compton profiles and anisotropy of momentum distribution of, MO calcn. of)},
ABSTRACT = {The total Compton profiles and anisotropies assocd. with momentum distribution along vectors parallel and perpendicular to bond axes in alkali chloride mols. are calcd. and related to changes in charge distributions accompanying bond formation. [on SciFinder (R)]},
KEYWORDS = {Alkali metal chlorides Role: PRP (Properties) (Compton profile anisotropy of, MO calcn. of); Bond formation (alkali metal-chlorine, Compton profile anisotropy in relation to); Molecular orbital (ab initio SCF, Compton profile anisotropy of alkali metal chlorides); Compton effect (profiles, of alkali chlorides, charge distribution in relation to, MO calcn. of)
alkali chloride Compton profile anisotropy},
YEAR = 1978
}
@ARTICLE{Matcha:1979,
AUTHOR = {Matcha, Robert L. and Pettitt, Bernard M. and Ramirez, B. I. and McIntire, William R.},
TITLE = {Theoretical Compton profile anisotropies in molecules and solids. V. Lithium and sodium bromide diatomics},
JOURNAL = {Journal of Chemical Physics},
VOLUME = 70,
NUMBER = 1,
PAGES = {558-64},
NOTE = {CAN 90:92893
65-4
General Physical Chemistry
Dep. Chem.,Univ. Houston,Houston,TX,USA.
Journal
0021-9606
written in English.
7550-35-8; 7647-15-6 Role: PRP (Properties) (Compton profile anisotropy in)},
ABSTRACT = {Anisotropies assocd. with momentum distributions along vectors parallel and perpendicular to bond axes in alkali metal bromide mols. are computed and analyzed. An attempt is made to relate these to charge cloud deformations accompanying mol. formation. The parallel profile assocd. with the valence p orbital is the dominating factor detg. the relative shapes of the total profile anisotropies in the low momenta regions Pz ? 0.5. [on SciFinder (R)]},
KEYWORDS = {Alkali metal bromides Role: PRP (Properties) (Compton profile anisotropy in); Compton effect (profiles, anisotropy of, in alkali metal bromide)
Compton profile lithium sodium bromide},
YEAR = 1979
}
@ARTICLE{Matcha:1979b,
AUTHOR = {Matcha, Robert L. and Pettitt, Bernard M.},
TITLE = {Theoretical Compton profile anisotropies in molecules and solids. VI. Compton profile anisotropies and chemical binding},
JOURNAL = {Journal of Chemical Physics},
VOLUME = 70,
NUMBER = 6,
PAGES = {3130-2},
NOTE = {CAN 90:192887
65-4
General Physical Chemistry
Dep. Chem.,Univ. Houston,Houston,TX,USA.
Journal
0021-9606
written in English.
7447-40-7; 7447-41-8; 7550-35-8; 7647-14-5; 7647-15-6; 7647-17-8; 7681-11-0; 7681-49-4; 7681-82-5; 7758-02-3; 7787-69-1; 7789-17-5; 7789-23-3; 7789-24-4; 7789-39-1; 7790-29-6; 7791-11-9; 10377-51-2; 13400-13-0; 13446-74-7 Role: PRP (Properties) (Compton profile anisotropies in)},
ABSTRACT = {An empirical relation between zero point Compton profile anisotropies DJ(0) and nuclear charges is noted. To a good approxn., DJ(0) = Nln(Zb/Za) for alkali halide mols., AB. [on SciFinder (R)]},
KEYWORDS = {Molecules (Compton profile anisotropies in); Alkali metal halides Role: PRP (Properties) (Compton profile anisotropies in); Nuclear charge (Compton profile anisotropies in relation to); Compton effect (in mols. and in solids, anisotropies of)
Compton profile mol solid; nuclear charge Compton profile; alkali halide Compton profile},
YEAR = 1979
}
@ARTICLE{Matcha:1979c,
AUTHOR = {Matcha, Robert L. and Pettitt, Bernard M. and Ramirez, B. I. and McIntire, William R.},
TITLE = {Theoretical Compton profile anisotropies in molecules and solids. IV. Parallel-perpendicular anisotropies in alkali fluoride molecules},
JOURNAL = {Journal of Chemical Physics},
VOLUME = 71,
NUMBER = 2,
PAGES = {991-6},
NOTE = {CAN 91:97019
65-4
General Physical Chemistry
Dep. Chem.,Univ. Houston,Houston,TX,USA.
Journal
0021-9606
written in English.
7681-49-4; 7789-23-3; 7789-24-4; 13446-74-7 Role: PRP (Properties) (Compton profile anisotropies in, electron configuration in relation to)},
ABSTRACT = {Calcns. of Compton profiles and parallel-perpendicular anisotropies in alkali fluorides are presented and analyzed in terms of mol. charge distributions and wave function character. The parallel profile assocd. with the valence p orbital is the principal factor detg. the relative shapes of the total profile anisotropies in the low momentum region. [on SciFinder (R)]},
KEYWORDS = {Electron configuration; Wave function (Compton profile anisotropies in alkali metal fluorides in relation to); Alkali metal fluorides Role: PRP (Properties) (Compton profile anisotropies in, electron configuration in relation to); Compton effect (anisotropies of, in alkali metal fluorides, electron configuration in relation to); Electron configuration (p-, Compton profile anisotropies in alkali metal fluorides in relation to)
Compton profile alkali metal fluoride},
YEAR = 1979
}
@ARTICLE{Matcha:1980,
AUTHOR = {Pettitt, B. M. and Jacobson, Kent and Matcha, R. L.},
TITLE = {Collinear reaction surface for atomic helium and argon hydride cation (ArH+)},
JOURNAL = {Journal of Chemical Physics},
VOLUME = 72,
NUMBER = 4,
PAGES = {2892-4},
NOTE = {CAN 92:203845
65-2
General Physical Chemistry
Dep. Chem.,Univ. Houston,Houston,TX,USA.
Journal
0021-9606
written in English.
12254-69-2; 12769-62-9; 13766-24-0; 30736-04-0 Role: PRP (Properties) (Morse potential energy of, SCF-LCAO calcns. of); 17009-49-3 Role: PRP (Properties) (heat of reaction of argon and, SCF-LCAO calcns. of); 7440-37-1 Role: PRP (Properties) (heat of reaction of hydrohelium(1+) and, SCF-LCAO calcns. of); 73716-98-0; 73716-99-1 Role: PRP (Properties) (mol. vibrations of, SCF-LCAO calcns. of); 12254-68-1 Role: PRP (Properties) (potential surface for reaction of helium and, SCF-LCAO calcns. of); 7440-59-7 Role: PRP (Properties) (potential surface for reaction of hydroargon(1+) and, SCF-LCAO calcns. of)},
ABSTRACT = {SCF-LCAO calcns. were done to obtain: (a) the optimized DIM potential-energy (PE) surface for the reaction of ArH+ and He; (b) the parameters of the Morse PE curves of ArH+, ArH, HeH+, HeH, HeAr+, and HeAr; and (c) the frequencies of the sym. and asym. stretching vibrations of 40ArHHe+, 40ArDHe+ 36ArHHe+, and 36ArDHe+. For (ArHHe)+ at the PE min., the energy is -529.7778 hartree, and the Ar-H and H-He interat. distances are 2.51 and 2.82 bohr, resp. The energies for the exothermic reactions ArH+ + He -> ArHHe+, Ar + HHe+ -> ArHHe+, and Ar + HeH+ -> ArH+ + He are 1.58, 41.4, and 39.8 kcal/mol, resp. [on SciFinder (R)]},
KEYWORDS = {Heat of reaction (of argon and hydrohelium(1+), SCF-LCAO calcns. of); Molecular vibration (of argon-helium-hydrogen and argon-deuterium-helium triat. monopos. ions, SCF-LCAO calcns. of); Potential energy and function (Morse, for diat. mols. and monopos. ions from argon and helium and hydrogen, SCF-LCAO calcns. of); Potential energy and function (surface, for helium-hydroargon(1+) reaction, SCF-LCAO calcns. of)
potential surface helium hydroargon cation; reaction helium hydroargon cation SCF; heat reaction argon hydrohelium cation; vibration triatomic argon helium hydrogen; Morse potential argon helium hydrogen; hydride argon helium Morse potential; deuterium argon helium triatomic vibration; hydrogen argon helium triatomic vibration},
YEAR = 1980
}
@ARTICLE{Matcha:1980b,
AUTHOR = {Matcha, Robert L. and Pettitt, Bernard M.},
TITLE = {Theoretical Compton profile anisotropies in molecules and solids. VII. Zero point Compton profile anisotropies and bond polarities in alkali halide diatomic molecules},
JOURNAL = {Journal of Chemical Physics},
VOLUME = 72,
NUMBER = 8,
PAGES = {4588-90},
NOTE = {CAN 92:220907
65-1
General Physical Chemistry
Dep. Chem.,Univ. Houston,Houston,TX,USA.
Journal
0021-9606
written in English.
7447-40-7; 7447-41-8; 7550-35-8; 7647-14-5; 7647-15-6; 7647-17-8; 7681-11-0; 7681-49-4; 7681-82-5; 7758-02-3; 7787-69-1; 7789-17-5; 7789-23-3; 7789-24-4; 7789-39-1; 7790-29-6; 7791-11-9; 10377-51-2; 13400-13-0; 13446-74-7 Role: PRP (Properties) (polarity and Compton profile anisotropy in)},
ABSTRACT = {A correlation between bond polarities and zero point Compton profile anisotropies is shown for alkali halide mols. The correlation derives from the fact that both quantities are detd. by mol. binding and antibonding forces and are thus functionally related to nuclear charge ratios. [on SciFinder (R)]},
KEYWORDS = {Compton effect (bond polarity in alk. metal halide in relation to); Alkali metal halides Role: PRP (Properties) (polarity and Compton profile anisotropy in); Bond (polarity of, in alk. metal halides, Compton profile anisotropy in relation to)
Compton effect bond polarity halide; alkali halide Compton bond polarity},
YEAR = 1980
}
@ARTICLE{Matcha:1980c,
AUTHOR = {Matcha, Robert L. and King, Stephen C., Jr. and Pettitt, B. M.},
TITLE = {Theory of the chemical bond. V. Bond polarities of posttransition hydrides},
JOURNAL = {Journal of Chemical Physics},
VOLUME = 73,
NUMBER = 8,
PAGES = {3944-6},
NOTE = {CAN 93:210525
65-1
General Physical Chemistry
Dep. Chem.,Univ. Houston,Houston,TX,USA.
Journal
0021-9606
written in English.},
ABSTRACT = {A classical derivation of a dipole moment model derived earlier (M. and K. 1976, 77) by a quantum mech. implicit perturbation technique is given. This model is used to det. the bond polarities of the posttransition (Groups IIIA-VIIA) hydrides. The polarity measures the extent of charge transfer in a bond. Polarities of alkali halides and posttransition hydrides are used to illustrate the gradual change in bond polarities with nuclear charge across the periodic table. [on SciFinder (R)]},
KEYWORDS = {Nuclear charge (bond polarity in hydrides in relation to); Alkali metal halides; Hydrogen halides Role: PRP (Properties) (bond polarity of); Bond (polarity of, of posttransition metal hydrides); Electric charge (transfer of, in posttransition metal hydride bond, polarity in relation to); Group IIIA element compounds; Group IVA element compounds; Group VA element compounds; Group VIA element compounds Role: PRP (Properties) (hydrides, bond polarity of); Hydrides (posttransition, bond polarity of)
bond polarity posttransition hydride; IIIA hydride bond polarity; IVA hydride bond polarity; VA hydride bond polarity; VIA hydride bond polarity; VIIA hydride bond polarity; hydrogen halide bond polarity; alkali halide bond polarity},
YEAR = 1980
}
@ARTICLE{Matcha:1980d,
AUTHOR = {Pettitt, B. Montgomery and Gadre, Shridhar R. and Matcha, Robert L.},
TITLE = {Theoretical Compton profile anisotropies in molecules and solids. VIII. Vibrational, rotational, and temperature-dependent diatomic alkali halide anisotropies},
JOURNAL = {International Journal of Quantum Chemistry, Quantum Chemistry Symposium},
VOLUME = 14,
PAGES = {697-706},
NOTE = {CAN 94:111705
73-1
Spectra by Absorption, Emission, Reflection, or Magnetic Resonance, and Other Optical Properties
Dep. Chem.,Univ. Houston,Houston,TX,USA.
Journal
0161-3642
written in English.
7447-41-8; 7550-35-8; 7681-49-4; 7789-23-3; 7789-24-4 Role: PRP (Properties) (Compton profile anisotropies in, rotational, temp., and vibrational dependence of)},
ABSTRACT = {A procedure, based on Rayleigh-Schroedinger perturbation theory, for obtaining vibrational, rotational, and temp.-dependent Compton profiles and profile anisotropies is presented and applied to H2 to test its validity. The computer vibrational-rotational dependence agrees well with the results of V. H. Smith et al. (1977) who obtained vibrational-rotational profiles for H2 by numerically integrating the Schroedinger equation for nuclear motion. The procedure is used to obtain vibrational, rotational, and temp.-dependent profiles and anisotropies for some alkali halide mols. The vibrational and temp. dependence of the parallel-perpendicular anisotropies in these mols. is substantial. [on SciFinder (R)]},
KEYWORDS = {Alkali metal halides Role: PRP (Properties) (Compton profile anisotropies in, rotational, temp., and vibrational dependence of); Molecular rotation; Molecular vibration (alkali metal halide Compton profile anisotropy dependence on); Compton effect (profiles, for alkali metal halides, anisotropies of)
alkali halide Compton profile anisotropy},
YEAR = 1980
}
@ARTICLE{Hirata:1982,
AUTHOR = {Hirata, Fumio and Pettitt, B. Montgomery and Rossky, Peter J.},
TITLE = {Application of an extended RISM equation to dipolar and quadrupolar fluids},
JOURNAL = {Journal of Chemical Physics},
VOLUME = 77,
NUMBER = 1,
PAGES = {509-20},
NOTE = {CAN 97:79058
65-1
General Physical Chemistry
Dep. Chem.,Univ. Texas,Austin,TX,USA.
Journal
0021-9606
written in English.
7647-01-0; 7726-95-6; 7727-37-9 Role: PRP (Properties) (site-site pair correlation functions of, in fluid state)},
ABSTRACT = {A generalization of the RISM (ref. interaction site model) integral equation for site-site pair correlation functions previously proposed by the authors is discussed and applied to model liqs. composed of strongly polar diat. mols. The nonuniform mol. charge distribution is represented by the introduction of charged interaction sites. The generalization consists of applying closure conditions analogous to those which are known to be reasonable for the description of at. ionic fluids, and the corresponding renormalization of the contributions arising from long range forces. The symmetry properties of the pair correlation functions in special cases and the dielec. properties implied by theory are discussed. Applications are presented for three two-site models which differ substantially in the degree of asymmetry of the non-Coulombic potential between the two sites, and for three-site models for Br2. The two sites models are compared to computer simulation results, and those for Br2 to exptl. results. The integral equation is well balanced in that in every case the qual. features of the liqs. structure which are introduced by polarity are well represented, even in cases where the site-site potentials are individually much larger than kBT. In cases where the mol. shape and polar forces are in competition, the results are of comparable accuracy to the corresponding theory for nonpolar systems. In the extreme case where changes in orientational structure can occur without interfering with packing requirements, the results appear quant. less reliable. [on SciFinder (R)]},
KEYWORDS = {Dielectric property (of dipolar and quadrupolar fluids, ref. interaction site model in); Statistical mechanics (ref. interaction site model, of dipolar and quadrupolar fluids); Distribution function (pair correlation, site-site, of dipolar and quadrupolar fluids)
statistical mechanics quadrupolar fluid; correlation function quadrupolar fluid; dielec property quadrupolar fluid},
YEAR = {1982}
}
@ARTICLE{Pettitt:1982,
AUTHOR = {Pettitt, B. Montgomery and Rossky, Peter J.},
TITLE = {Integral equation predictions of liquid state structure for waterlike intermolecular potentials},
JOURNAL = {Journal of Chemical Physics},
VOLUME = 77,
NUMBER = 3,
PAGES = {1451-7},
NOTE = {CAN 97:98839
65-7
General Physical Chemistry
Dep. Chem.,Univ. Texas,Austin,TX,USA.
Journal
0021-9606
written in English.
7732-18-5 Role: PRP (Properties) (liq. structure of, intermol. potential in)},
ABSTRACT = {An application of the authors recently developed extended RISM equation formulation (1981) to several 3-site models of H2O is presented. The site-site correlation functions are obtained and compared to available computer simulation results. Further, the variation of liq. state structure with the model site charge is examd. The anal. of these results has demonstrated that the integral equation approach provides a correct qual. description of the liq. structure, although the amplitudes of most structural features are somewhat less accurate than their positions. Comparison to earlier results for simpler models suggests that the nature of the quant. deficiencies of the approach is predictable. The charging study has shown that the development of waterlike structure with increasing site charge follows a qual. different pattern for O-O pairs, compared to those involving hydrogen. This is attributed to interference between the amplitudes characteristic of liq. water and of simple liqs. This is the origin of a relatively flat 0-0 correlation function for several models studied in the past, and, further, that such results should not be properly characterized as \"unstructured\". [on SciFinder (R)]},
KEYWORDS = {Liquid structure (waterlike intermol. potentials in); Potential energy and function (intermol., liq. structure in relation to)
liq structure potential; water liq structure},
YEAR = {1982}
}
@ARTICLE{Hirata:1983,
AUTHOR = {Hirata, Fumio and Rossky, Peter J. and Pettitt, B. Montgomery},
TITLE = {The interionic potential of mean force in a molecular polar solvent from an extended RISM equation},
JOURNAL = {Journal of Chemical Physics},
VOLUME = 78,
NUMBER = {6, Pt. 2},
PAGES = {4133-44},
NOTE = {CAN 98:167992
68-6
Phase Equilibriums, Chemical Equilibriums, and Solutions
Dep. Chem.,Univ. Texas,Austin,TX,USA.
Journal
0021-9606
written in English.},
ABSTRACT = {The generalization of a recently proposed extension of the RISM (ref. interaction site model) integral equation to infinitely dil. isolated ions and ion pairs in polar interaction site model mol. solvents is outlined. An essential element of the development is the explicit sepn. of the contributions which yield a continuum dielec. solvent model from the remainder. Thus, it is only for this correction that one relies on the integral equation. Application is made to a system consisting of a diat. polar solvent and at. ions of varied charge and radius. The results of the calcns. show that this approach produces qual. features of ionic solvation including an appropriately varying degree of solvent orientational satn. with ionic charge and radius. Correspondingly, the calcd. interionic potentials of mean force reproduce the same basic features manifest in already available studies of dipolar hard sphere solvents, including the positions of oscillatory features in the structure and the relatively short spatial range of the corrections to the continuum dielec. theory. [on SciFinder (R)]},
KEYWORDS = {Solutes (in polar solvents, interionic potential in relation to); Liquid structure (interionic potential of mean force in mol. polar solvent in relation to); Ion pairs; Ions in liquids (interionic potential of, in mol. polar solvent); Solvation (ionic, interionic potential of mean force in mol. polar solvents in relation to); Electric charge (of ions in polar solvents, interionic potential of mean force in relation to); Dielectric constant and dispersion (of polar solvent, interionic potential of mean force in relation to); Potential energy and function (interionic, of mean force in mol. polar solvent from extended from IRSM equation); Solvents (polar, mol., interionic potential of mean force in)
interionic potential mean force solvent; RISM polar solvent interionic potential},
YEAR = {1983}
}
@ARTICLE{Pettitt:1983,
AUTHOR = {Pettitt, B. Montgomery and Rossky, Peter J.},
TITLE = {The contribution of hydrogen bonding to the structure of liquid methanol},
JOURNAL = {Journal of Chemical Physics},
VOLUME = 78,
NUMBER = 12,
PAGES = {7296-9},
NOTE = {CAN 99:70127
22-13
Physical Organic Chemistry
Dep. Chem.,Univ. Texas,Austin,TX,USA.
Journal
0021-9606
written in English.
67-56-1 Role: PRP (Properties) (structure of liq., hydrogen bonding in relation to)},
ABSTRACT = {The structure of liq. MeOH was studied using the recently proposed extended RISM integral equation and Jorgensen's transferable intermol. potentials (TIPS). Results are obtained as a function of mol. polarity by scaling the partial Coulombic charges located at mol. interaction sites. At the exptl. d., packing forces are predominant in detg. many features of the liq. structure, as reflected in site-site correlation functions. The influence of H bonding is best characterized as a narrowing in the mol. distributions, resulting from an accommodation of the attractive forces within structural alternatives consistent with packing constraints. [on SciFinder (R)]},
KEYWORDS = {Hydrogen bond (in liq. methanol, structure in relation to); Liquid structure (of methanol, hydrogen bonding in relation to); Distribution function (radial, site-site, in liq. methanol)
methanol liq hydrogen bond structure},
YEAR = {1983}
}
@ARTICLE{Pettitt:1983b,
AUTHOR = {Pettitt, B. M. and Matcha, Robert L. and Ramirez, B. I.},
TITLE = {Theoretical Compton profile anisotropies in molecules and solids. IX. Chemical bonding and 0-90 anisotropies in the first-row diatomic hydrides AH},
JOURNAL = {Journal of Chemical Physics},
VOLUME = 79,
NUMBER = 6,
PAGES = {2913-17},
NOTE = {CAN 99:146452
65-5
General Physical Chemistry
Dep. Chem.,Univ. Houston,Houston,TX,USA.
Journal
0021-9606
written in English.
3315-37-5; 3352-57-6; 7580-67-8; 7664-39-3; 13597-97-2; 13766-26-2; 13774-92-0 Role: PRP (Properties) (Compton profiles of, bonding in relation to)},
ABSTRACT = {The parallel-perpendicular Compton-profile anisotropies were calcd. for the 1st-row diat. hydrides. Both the total and MO anisotropies present trends that were related to the nature of the chem. binding in the mols. [on SciFinder (R)]},
KEYWORDS = {Bond (in diat. hydrides of 1st row, Compton profiles in relation to); Compton effect (profiles, of diat. hydrides of 1st row, bonding in relation to); Hydrides Role: PRP (Properties) (diat., Compton profiles of 1st-row, bonding in relation to)
beryllium hydride Compton profile bonding; lithium hydride Compton profile bonding; diatomic hydride Compton profile bonding; hydrogen fluoride Compton profile bonding; imidogen Compton profile bonding; methylidyne Compton profile bonding; hydroxyl Compton profile bonding; borane Compton profile bonding},
YEAR = {1983}
}
@ARTICLE{Rossky:1983,
AUTHOR = {Rossky, Peter J. and Pettitt, B. Montgomery and Stell, George},
TITLE = {The coupling of long and short range correlations in ISM liquids},
JOURNAL = {Molecular Physics},
VOLUME = 50,
NUMBER = 6,
PAGES = {1263-71},
NOTE = {CAN 100:180215
65-1
General Physical Chemistry
Dep. Chem.,Univ. Texas,Austin,TX,USA.
Journal
0026-8976
written in English.},
ABSTRACT = {A simple modification of the HNC-like closure within the extended RISM equation formalism is considered which ensures that the asymptotic form of the site-site direct correlation functions is consistent with the dielec. const. The short ranged structural results obtained with the modification are compared with those following from the original closure for 3 strongly polar diat. models, and show very small differences. These results demonstrate both that the short ranged results are only weakly coupled to the asymptotic amplitudes, and that the latter can potentially be cor. in a relatively straighforward manner. [on SciFinder (R)]},
KEYWORDS = {Dielectric constant and dispersion (of mol. liqs., extended interaction site models for correlation functions in relation to); Distribution function (correlation, of mol. liqs., extended interaction site models for, dielec. const. in relation to)
interaction site model liq correlation; dielec const liq correlation function},
YEAR = {1983}
}
@INBOOK{Pettitt:1984,
AUTHOR = {Karplus, Martin and Brady, J. and Brooks, Bernard and Kushick, J. and Pettitt, B. Montgomery },
TITLE = {Entropy of Macromolecules},
BOOKTITLE = {Proceedings of the Workshop on Dynamics Methods and Protein Structure},
ADDRESS = {UNC, Chapel Hill},
YEAR = {1984}
}
@ARTICLE{Pettitt:1985,
AUTHOR = {Pettitt, B. Montgomery and Karplus, Martin},
TITLE = {Role of electrostatics in the structure, energy and dynamics of biomolecules: a model study of N-methylalanylacetamide},
JOURNAL = {Journal of the American Chemical Society},
VOLUME = 107,
NUMBER = 5,
PAGES = {1166-73},
NOTE = {CAN 102:96028
34-2
Amino Acids, Peptides, and Proteins
Dep. Chem.,Harvard Univ.,Cambridge,MA,USA.
Journal
0002-7863
written in English.
19701-83-8 Role: PRP (Properties) (electrostatic interaction in, calcn. of)},
ABSTRACT = {The contribution of electrostatic interactions to a range of structural, energetic, and dynamic properties of the alanine dipeptide is examd. An empirical energy function is employed to represent the dipeptide, and the partial at. charges are varied from zero to values used in std. models for amino acids and proteins. Although there are large differences in the abs. energy of models with different charges, the relative energies of the various dipeptide conformers are less sensitive to the charges. The min. energy structures of the conformers are only weakly dependent on the charges. A normal model anal. shows that only a few modes are sensitive to the charges and that thermodn. quantities, which represent sums over the modes, are essentially the same for all the models. Comparison of the harmonic dynamics results with those from an ensemble of mol. dynamics trajectories reveals that the electrostatic contributions to the potential surface introduce significant anharmonic effects. [on SciFinder (R)]},
KEYWORDS = {Enthalpy and Enthalpy function; Entropy; Free energy (harmonic, of alanine dipeptide); Hydrogen bond (in alanine dipeptide, electrostatic contribution in relation to); Heat capacity; Molecular dynamics; Molecular vibration (of alanine dipeptide); Molecular structure (of alanine dipeptide, electrostatic contribution in); Conformation and Conformers (of alanine dipeptide, electrostatic contribution in relation to); Potential energy and function; Potential energy surface and hypersurface (of alanine dipeptide, electrostatic contribution to); Peptides Role: PRP (Properties) (di-, alanine-contg., electrostatic interaction in, calcn. of)
alanine dipeptide electrostatic interaction; methylalanylacetamide electrostatic interaction; structure alanine dipeptide electrostatic interaction; mol dynamics alanine dipeptide; energy alanine dipeptide electrostatic interaction; thermodn alanine dipeptide electrostatic interaction; conformation alanine dipeptide electrostatic interaction},
YEAR = {1985}
}
@ARTICLE{Friesner:85,
AUTHOR = {Friesner, Richard and Pettitt, Montgomery and Jean, John M.},
TITLE = {Calculation of temperature-dependent multimode resonance Raman line shapes for harmonic potential surfaces},
JOURNAL = {Journal of Chemical Physics},
VOLUME = 82,
NUMBER = 7,
PAGES = {2918-26},
ABSTRACT = {An exact form for the time dependent resonance Raman kernel at finite temperature is derived under the assumption that the ground and excited state potential surfaces of the system are harmonic. The resultant expression can be evaluated by matrix algebra and Fourier transformed numerically to recover Raman scattering and excitation profiles.},
KEYWORDS = {Raman Spectroscopy; Line Shape; Resonance Scattering; Temperature Dependence},
YEAR = 1985
}
@ARTICLE{Pettitt:85a,
AUTHOR = {Pettitt, B. Montgomery and Karplus, Martin},
TITLE = {The potential of mean force between polyatomic molecules in polar mlecular solvents},
JOURNAL = {Journal of Chemical Physics},
VOLUME = 83,
NUMBER = 2,
PAGES = {781-89},
ABSTRACT = {Theoretical results obtained with the extended reference interaction site (XRISM) formalism are presented for site–site solute solvent correlations and solute–solute potentials of mean force for infinitely dilute polar molecular solutes in various polar solvents. The standard RISM site–site Ornstein–Zernike like equations, in a Coulomb renormalized form, with a hypernetted chain (HNC) analog closure are used to derive results for polar molecular solutes in polar molecular solvents. For a dipolar diatomic solute the difference in the solvation behavior between atomic and molecular solvents is examined. Finite concentration results are compared with the infinite dilution intermolecular site–site potentials of mean force for diatomic molecules in a simple fluid solvent.},
KEYWORDS = {Polyatomic Molecules; Solutions; Correlations; Intermolecular Forces; Liquid Structure},
YEAR = 1985
}
@ARTICLE{Pettitt:85b,
AUTHOR = {Pettitt, B. Montgomery and Karplus, Martin},
TITLE = {The potential of mean force surface for the alanine dipeptide in aqueous solution: a theoretical approach},
JOURNAL = {Chemical Physics Letters},
VOLUME = 121,
NUMBER = 3,
PAGES = {194-201},
NOTE = {CAN 103:209270
6-3
General Biochemistry
Dep. Chem.,Harvard Univ.,Cambridge,MA,USA.
Journal
0009-2614
written in English.
19701-83-8 Role: PRP (Properties) (potential energy surface of, conformation in relation to)},
ABSTRACT = {The results of an application of integral equation theory to the detn. of the intramol. potential of mean force for the alanine dipeptide, N-methylalanine acetamide, in aq. soln. are presented. The calcns. are based on Ornstein-Zernike-like equations for polar systems with an intramol. superposition approxn. The solvated free energy surface for the dipeptide as a function of the dihedral angles f and y (Ramachandran plot) is detd. and compared with the vacuum surface calcns. Conformations that are essentially forbidden in vacuum are found to be significant in aq. soln. The solvent contributions to the free energy surface are decompd. into enthalpic and entropic terms. Possible applications and extensions of the method are outlined. [on SciFinder (R)]},
KEYWORDS = {Conformation and Conformers (of methylalanine acetamide, potential energy surface calcns. in relation to); Potential energy surface and hypersurface (conformational, of methylalanine acetamide)
methylalanine acetamide potential energy surface conformation; alanine dipeptide potential energy surface conformation},
YEAR = 1985
}
@ARTICLE{Brooks:85,
AUTHOR = {Brooks III, Charles L. and Pettitt, B. Montgomery and Karplus, Martin},
TITLE = {Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids},
JOURNAL = {Journal of Chemical Physics},
VOLUME = 83,
NUMBER = 11,
PAGES = {5897-5908},
ABSTRACT = {The effects of Coulomb potential truncation schemes used in computer simulations of ionic and polar fluids are examined by use of integral equation techniques. A renormalized HNC type equation capable of describing both ionic and polar molecular fluids with truncated interactions is derived and applied to several model systems of interest. Good agreement is found between the integral equation results and Monte Carlo simulations of the same potential for dilute solutions of ions in a dielectric continuum. Very large effects on the distribution functions result from truncation of the electrostatic interaction in dilute systems. Even in comparatively dense systems, unrealistic pair correlations near the cutoff distance result from some of the proposed truncation schemes. The effect of Coulomb potential truncation for a molecular model of pure water is also studied. Significant errors appear in the second neighbor region for commonly used truncation schemes; a simple switching function that zeros the potential and its first derivative yields results closest to the Coulomb potential without truncation.},
KEYWORDS = {Computerized Simulation; Potentials; Liquids; Coulomb Field; Intermolecular Forces},
YEAR = 1985
}
@ARTICLE{Pettitt:86a,
AUTHOR = {Pettitt, B. Montgomery and Rossky, Peter J.},
TITLE = {Alkali halides in water: ion-solvent correlations and ion-ion potentials of mean force at infinite dilution},
JOURNAL = {Journal of Chemical Physics},
VOLUME = 84,
NUMBER = 10,
PAGES = {5836-44},
NOTE = {CAN 105:13111
68-6
Phase Equilibriums, Chemical Equilibriums, and Solutions
Dep. Chem.,Univ. Houston,Houston,TX,USA.
Journal
0021-9606
written in English.
7447-40-7; 7447-41-8; 7647-14-5; 7681-49-4; 7789-23-3 Role: PRP (Properties) (interionic potentials for, in aq. solns.); 16887-00-6; 16984-48-8; 17341-24-1; 17341-25-2; 24203-36-9 Role: PRP (Properties) (potential of, in aq. soln.)},
ABSTRACT = {By using the specialization of the extended RISM equation to infinitely dil. systems, correlation functions and interionic potentials of mean force were calcd. for a set of models corresponding to the first few alkali halides in water. From the results obtained at infinite diln., the lowest order corrections were calcd. to the soln. properties of the ions. Higher concns. are explored by using the interionic potentials. The results indicate that certain thermodn. properties, such as the mean activity coeffs. and osmotic pressures, are quite sensitive to the details of both the theory and the potential models. [on SciFinder (R)]},
KEYWORDS = {Alkali metal halides Role: PRP (Properties) (interionic potentials for, in aq. solns.); Activity; Osmotic pressure (ion-solvent correlations and ion-ion potentials of means force at infinite diln. in relation to); Distribution function (correlation, of alkali halides in water); Potential energy and function (interionic, of alkali halides in water)
alkali halide aq ion solvent correlation; potential infinite diln alkali halide aq},
YEAR = 1986
}
@ARTICLE{Pettitt:86b,
AUTHOR = {Pettitt, B. Montgomery and Karplus, Martin},
TITLE = {Interaction energies: their role in drug design},
JOURNAL = {Topics in Molecular Pharmacology},
VOLUME = 3,
NUMBER = {Mol. Graphics Drug Des.},
PAGES = {75-113},
NOTE = {CAN 106:112928
1-0
Pharmacology
Dep. Chem.,Harvard Univ.,Cambridge,MA,USA.
Journal; General Review
0167-7101
written in English.},
ABSTRACT = {A review with 80 refs. Energy of interaction between drugs and receptors is discussed in terms of drug design. [on SciFinder (R)]},
KEYWORDS = {Receptors Role: BIOL (Biological study) (drug interaction energies with, drug design in relation to)
review drug design interaction energy},
YEAR = 1986
}
@ARTICLE{Pettitt:86c,
AUTHOR = {Pettitt, B. Montgomery and Karplus, Martin and Rossky, Peter J.},
TITLE = {Integral equation model for aqueous solvation of polyatomic solutes: application to the determination of the free energy surface for the internal motion of biomolecules},
JOURNAL = {Journal of Physical Chemistry},
VOLUME = 90,
NUMBER = 23,
PAGES = {6335-45},
NOTE = {CAN 105:187049
9-10
Biochemical Methods
Dep. Chem.,Harvard Univ.,Cambridge,MA,USA.
Journal
0022-3654
written in English.
19701-83-8 Role: ANST (Analytical study) (solvent-modified, potential surface for)},
ABSTRACT = {A model is presented for detg. the intramol. potential of mean force for flexible polyat. mols. in aq. soln. This is an essential step in developing a reduced simulation technique for studying solvated biopolymers. The Ornstein-Zernike integral equation theory within a superposition formalism led to a convenient and efficient method for calcg. the solvent-modified intramol. potential. Solute-solvent distribution functions for the atoms (sites) composing the polyat. mol. are evaluated individually and introduced into the appropriate integral equations to obtain the site-site potentials of mean force for all distinct atom pairs in the mol. The superposition approxn. plus an empirical energy function for the internal degrees of freedom can then be employed to det. the total solvent-modified potential of mean force surface for the mol. system. An application to the evaluation of the intramol. potential of mean force surface for the alanine dipeptide (N-methylalanylacetamide) under vacuum and in aq. soln. is given to illustrate the method. [on SciFinder (R)]},
KEYWORDS = {Statistical mechanics (Ornstein-Zernike-type integral equation, solvent-modified potential surface for flexible internal degrees of freedom of biomols. construction by); Solvation (of biomols., potential surface for); Potential energy surface and hypersurface (solvent-modified, for flexible internal degrees of freedom of bimols.); Biopolymers; Peptides Role: ANST (Analytical study) (solvent-modified, potential surface for)
biomol solvation potential surface calcn; statistical mechanics potential surface peptide},
YEAR = 1986
}
@ARTICLE{Pettitt:86d,
AUTHOR = {Pettitt, B. Montgomery and Rossky, Peter J.},
TITLE = {New approaches to solvent-mediated molecular interactions},
JOURNAL = {Israel Journal of Chemistry},
VOLUME = 27,
NUMBER = 2,
PAGES = {156-62},
NOTE = {CAN 107:65514
68-0
Phase Equilibriums, Chemical Equilibriums, and Solutions
Dep. Chem.,Univ. Houston,Houston,TX,USA.
Journal; General Review
0021-2148
written in English.},
ABSTRACT = {Recently developed integral equation methods for the evaluation of intermol. and intramol. interactions in a polar solvent medium are discussed and representative applications are presented. Examples include solvent modification of interionic interactions between at. or mol. ions in water and liq. environment induced shifts in conformational equil. for both non-polar and polar flexible mols. in water. Emphasis is placed on the features of these phenomena which can be traced specifically to the molecularity of the solvent and hence cannot be adequately reproduced by a simple continuum dielec. solvent representation. 49 Refs. [on SciFinder (R)]},
KEYWORDS = {Solvent effect (on mol. interactions); Potential energy and function (solvent effects on)
review solvent mediated mol interaction},
YEAR = 1986
}
@ARTICLE{bmp-calf:87,
AUTHOR = {Pettitt, B. Montgomery and Calef, Daniel F.},
TITLE = {On the structure of high-density water at constant temperature},
JOURNAL = {Journal of Physical Chemistry},
VOLUME = 91,
NUMBER = 6,
PAGES = {1541-5},
NOTE = {CAN 106:108302
65-7
General Physical Chemistry
Dep. Chem.,Univ. Houston,Houston,TX,USA.
Journal
0022-3654
written in English.
1333-74-0 Role: PRP (Properties) (hydrogen bond, in water at high pressure); 7732-18-5 Role: PRP (Properties) (structure of high-d., at const. temp.)},
ABSTRACT = {Calcns. of the site-site correlation functions for a model of water were performed as functions of d. or pressure at fixed temp. These calcns. are discussed and compared to neutron-scattering data. They structure of liq. water at high pressure is consistent with a substantially distorted H-bonding network. Unlike MeOH, water cannot easily accommodate structures assocd. with directional attractive forces in the region of several kilobars of pressure. [on SciFinder (R)]},
KEYWORDS = {Hydrogen bond (in water at high pressure); Liquid structure (of high-d. water); Distribution function (correlation, of water, at high pressure)
water structure correlation function; hydrogen bond water},
YEAR = 1987
}
@ARTICLE{bmp:87a,
AUTHOR = {Pettitt, B. Montgomery and Karplus, Martin},
TITLE = {The structure of water surrounding a peptide: a theoretical approach},
JOURNAL = {Chemical Physics Letters},
VOLUME = 136,
NUMBER = 5,
PAGES = {383-6},
NOTE = {CAN 107:111367
6-3
General Biochemistry
Dep. Chem.,Univ. Houston,Houston,TX,USA.
Journal
0009-2614
written in English.
1333-74-0 Role: BIOL (Biological study) (hydrogen bond, water structure surrounding peptides response to, modeling of); 19701-83-8 Role: BIOL (Biological study) (structure of water around, calcn. of); 7732-18-5 (Water) Role: PRP (Properties) (structure of, around peptides, calcn. of)},
ABSTRACT = {Recently developed integral equation methods for the evaluation of correlations of polar mol. solutes in polar solvent media have been solved for the N-Me alanyl acetamide in H2O. The results are compared with simulations of similar model systems. The use of the full mol. site-site correlations detd. in this work can be used in approx. nonsuperposition theories for conformational populations in soln. [on SciFinder (R)]},
KEYWORDS = {Hydration (of peptides, model for); Peptides Role: BIOL (Biological study) (structure of water around, calcn. of); Hydrogen bond (water structure surrounding peptides response to, modeling of)
peptide water structure model; methylalanyl acetamide water structure model},
YEAR = 1987
}
@ARTICLE{Karim:87,
AUTHOR = {Karim, Omar A. and Pettitt, B. Montgomery},
TITLE = {Two-dimensional fluids in a periodic external potential: intercalation in graphite},
JOURNAL = {Chemical Physics Letters},
VOLUME = 137,
NUMBER = 1,
PAGES = {72-7},
NOTE = {CAN 107:121260
65-1
General Physical Chemistry
Dep. Chem.,Univ. Houston,Houston,TX,USA.
Journal
0009-2614
written in English.
7782-42-5D (Graphite) Role: PRP (Properties) (structure factor of)},
ABSTRACT = {An inhomogeneous anisotropic integral equation theory is used to predict the 6-fold pattern of intensity in the structure factor for graphite intercalation compds. The competition of length scales implied by particle size and the underlying lattice through the interplay of the liq. packing structure with the graphitic external field is shown to be responsible for the obsd. halo-like features in S(k). By using a d. functional motivated ansatz no explicit truncation of the angular Fourier components of the d. distributions was necessary. [on SciFinder (R)]},
KEYWORDS = {Alkali metals Role: PRP (Properties) (structure factor of graphite intercalation compds. contg.); Potential energy and function (periodic, two-dimensional fluids in); Distribution function (structure factor, of graphite intercalation compds.)
structure factor graphite intercalation compd},
YEAR = 1987
}
@ARTICLE{Dang:87a,
AUTHOR = {Dang, L. X. and Pettitt, B. M.},
TITLE = {Solvated chloride ions at contact},
JOURNAL = {Journal of Chemical Physics},
VOLUME = 86,
NUMBER = 11,
PAGES = {6560-1},
NOTE = {CAN 107:65641
68-6
Phase Equilibriums, Chemical Equilibriums, and Solutions
Chem. Dep.,Univ. Houston,Houston,TX,USA.
Journal
0021-9606
written in English.
16887-00-6 (Chloride) Role: PRP (Properties) (neg. ion pairs, simulation of, at contact)},
ABSTRACT = {Preliminary results are reported for dynamic computer free energy simulations for a pair of Cl-, ions in H2O with a near-ion-contact starting configuration. A contact min. is obsd. in which the 2 ions are able to oscillate for some time. Water mols. form bridging H bonds which stabilize the ion pair. [on SciFinder (R)]},
KEYWORDS = {Ion pairs (chloride-chloride, at contact, simulation of)
ion pair chloride chloride solvated; computer simulation chloride ion pair; contact chloride chloride ion pair},
YEAR = 1987
}
@ARTICLE{Dang:87b,
AUTHOR = {Dang, Liem X. and Pettitt, B. Montgomery},
TITLE = {Simple intramolecular model potentials for water},
JOURNAL = {Journal of Physical Chemistry},
VOLUME = 91,
NUMBER = 12,
PAGES = {3349-54},
NOTE = {CAN 106:220251
65-5
General Physical Chemistry
Dep. Chem.,Univ. Houston,Houston,TX,USA.
Journal
0022-3654
written in English.
7732-18-5 (Water) Role: PRP (Properties) (intramol. model potential for)},
ABSTRACT = {An effective intramol. potential is presented for use in conjunction with existing 3-site models of water. Two commonly used internal geometries were fit to the same form and yield slightly different parameterizations. By including a Urey-Bradley-like term in an otherwise std. mol. mechanics form, the exptl. transition frequencies of water monomer can be reproduced accurately. Good qual. agreements for spectral shifts were subsequently found for the models in condensed-phase applications. Harmonic anal. of clusters indicates good qual. agreement with exptl. environmental shifts in frequencies at low temps. for these models. This model should be useful for a wide variety of applications including simulations of biopolymers and ionic solns. [on SciFinder (R)]},
KEYWORDS = {Potential energy and function (intramol., for water)
intramol model potential water},
YEAR = 1987
}
@ARTICLE{Dang:87c,
AUTHOR = {Dang, Liem X. and Pettitt, B. Montgomery},
TITLE = {Chloride ion pairs in water},
JOURNAL = {Journal of the American Chemical Society},
VOLUME = 109,
NUMBER = 18,
PAGES = {5531-2},
NOTE = {CAN 107:102862
65-1
General Physical Chemistry
Chem. Dep.,Univ. Houston,Houston,TX,USA.
Journal
0002-7863
written in English.
16887-00-6 (Chloride) Role: PRP (Properties) (solvent-averaged potential of pair of, in water, quantum statistical mech. study of)},
ABSTRACT = {A quant. study is reported of the Cl--Cl- solvent-averaged potential in water, detd. by using the \"umbrella\" sampling method and the Hamiltonian used in a recent integral equation study. The resulting potential of mean force is compared to the result from previous approx. integral equation studies. The results display a clear contact stabilization in contrast to the predictions of continuum theory. [on SciFinder (R)]},
KEYWORDS = {Potential energy and function (pair, solvent-averaged, between two chloride ions in water, quantum statistical mech. study of); Statistical mechanics (quantum, of chloride ion pairs in water)
chloride ion pair water; potential interionic chloride water},
YEAR = 1987
}
@ARTICLE{Calef:87,
AUTHOR = {Calef, Daniel F. and Pettitt, B. Montgomery},
TITLE = {A theoretical study of the structure of shocked water},
JOURNAL = {Chemical Physics Letters},
VOLUME = 139,
NUMBER = 2,
PAGES = {129-33},
NOTE = {CAN 107:162352
65-8
General Physical Chemistry
Livermore Natl. Lab.,Univ. California,Livermore,CA,USA.
Journal
0009-2614
written in English.
7732-18-5 (Water) Role: PRP (Properties) (structure of, behind shock waves)},
ABSTRACT = {The extended ref. interaction site method is used to calc. the structure of water behind a shock front. The competing effects of increased d. and temp. modify the correlation functions in a manner that is qual. consistent with both expectation and recent exptl. results. [on SciFinder (R)]},
KEYWORDS = {Shock wave (in structure of water); Liquid structure (water, behind shock waves)
water structure shock wave effect},
YEAR = 1987
}
@INPROCEEDINGS{bmp:87b,
AUTHOR = {Pettitt, B. Montgomery },
TITLE = {Proteins},
BOOKTITLE = {Mc-Graw Hill World Book Encyclopedia 1988 Yearbook of Science and Technology},
EDITOR = {Parker, S.},
PAGES = {360--362},
YEAR = 1987
}
@ARTICLE{Lybrand:87,
AUTHOR = {Lybrand, Terry P. and Lau, Wan F. and McCammon, J. Andrew and Pettitt, B. Montgomery},
TITLE = {Molecular dynamics studies on antiviral agents: thermodynamics of solvation and binding},
JOURNAL = {UCLA Symposia on Molecular and Cellular Biology, New Series},
VOLUME = 69,
NUMBER = {Protein Struct., Folding, Des. 2},
PAGES = {227-33},
NOTE = {CAN 108:124055
1-3
Pharmacology
Dep. Chem.,Univ. Houston,Houston,TX,USA.
Journal
0735-9543
written in English.
87495-31-6 (WIN 51711); 98102-61-5 (WIN 52084) Role: BAC (Biological activity or effector, except adverse), BSU (Biological study, unclassified), THU (Therapeutic use), BIOL (Biological study), USES (Uses) (antiviral activity of, thermodn. of solvation and binding in relation to)},
ABSTRACT = {Mol. dynamics computer simulations utilizing the thermodn. cycle-perturbation method were used in preliminary calcns. of the relative free energies of binding for 2 new compds. (I and II) with antiviral activity to the coat proteins of human rhinovirus 14. The results suggest that intrinsic protein-ligand interactions dictate relative binding affinities, whereas relative desolvation energies contribute little to the net differences in the free energy of binding. These results and similar calcns. currently in progress should contribute to the design of new mols. with enhanced binding affinity for the rhinovirus coat proteins. [on SciFinder (R)]},
KEYWORDS = {Free energy (of binding, of phenoxyisoxazole to rhinovirus coat protein, by perturbation method); Solvation (of phenoxyisoxazole antiviral agents); Molecular association (of phenoxyisoxazole antiviral drugs, with rhinovirus coat proteins, thermodn. of); Process simulation (mol. dynamics, of phenoxyisoxazole antiviral agents); Virus (rhino-, coat proteins, phenoxyisoxazole inhibitors binding to, thermodn. of); Molecular structure-biological activity relationship (virucidal, of phenoxyisoxazoles)
antiviral phenoxyisoxazole mol dynamics; thermodn solvation binding phenoxyisoxazole antiviral; free energy phenoxyisoxazole},
YEAR = 1987
}
@ARTICLE{Lau:87,
AUTHOR = {Lau, Wan F. and Pettitt, B. Montgomery},
TITLE = {Conformations of the glycine dipeptide},
JOURNAL = {Biopolymers},
VOLUME = 26,
NUMBER = 11,
PAGES = {1817-31},
NOTE = {CAN 108:94927
34-3
Amino Acids, Peptides, and Proteins
Dep. Chem.,Univ. Houston,Houston,TX,USA.
Journal
0006-3525
written in English.
7606-79-3 Role: PRP (Properties) (conformation of)},
ABSTRACT = {Integral equation theory is applied to the detn. of the intramol. potential of mean force for the glycine peptide, N-acetylglycyl-N-methylamide, in aq. soln. The solvated free energy for the dipeptide as a function of the dihedral angles F and Y (Ramachandran plot) is detd. and compared with the vacuum surface. Conformations forbidden in vacuum are found to be populated in aq. soln. The results for the glycine dipeptide are compared to a parallel study on the alanine dipeptide. Solvent effects are responsible for the extent of many of glycine's properties related to flexibility. [on SciFinder (R)]},
KEYWORDS = {Conformation and Conformers; Potential energy surface and hypersurface (of glycine dipeptide); Solvent effect (on conformation of glycine dipeptide); Potential energy and function (conformational, of glycine dipeptide)
glycine dipeptide conformation},
YEAR = 1987
}
@ARTICLE{Madura:87,
AUTHOR = {Madura, Jeffry D. and Pettitt, B. Montgomery and McCammon, J. Andrew},
TITLE = {Geometric considerations in the calculation of relative free energies of activation},
JOURNAL = {Chemical Physics Letters},
VOLUME = 141,
NUMBER = {1-2},
PAGES = {83-7},
NOTE = {CAN 108:63328
67-3
Catalysis, Reaction Kinetics, and Inorganic Reaction Mechanisms
Dep. Chem.,Univ. Houston,Houston,TX,USA.
Journal
0009-2614
written in English.},
ABSTRACT = {A method that locates transition state structures homologous reactions and, with the use of the thermodn. cycle-perturbation technique, dets. the relative free energy of activation between the transition states is presented. A simple model system which displays the problem of finding condensed phase transition states is used to illustrate the method. [on SciFinder (R)]},
KEYWORDS = {Free energy of activation (between transition state structures of homologous reactions, geometric method for calcn. of); Transition state structure (location of, between homologous reactions, geometric method for detn. of)
transition state structure free energy activation},
YEAR = 1987
}
@ARTICLE{Karplus:87,
AUTHOR = {Karplus, M. and Ichiye, T. and Pettitt, B. M.},
TITLE = {Configurational entropy of native proteins},
JOURNAL = {Biophysical Journal},
VOLUME = 52,
NUMBER = 6,
PAGES = {1083-5},
NOTE = {CAN 108:126934
6-3
General Biochemistry
Dep. Chem.,Harvard Univ.,Cambridge,MA,USA.
Journal
0006-3495
written in English.
9087-70-1 (Bovine pancreatic trypsin inhibitor) Role: PRP (Properties) (configurational entropy of, simulation of)},
ABSTRACT = {Simulations of the residual configurational entropy of a protein in the native state suggest that it is nearly an order of magnitude larger than the entropy of denaturation. The implications of this result are discussed. [on SciFinder (R)]},
KEYWORDS = {Proteins Role: PRP (Properties) (configurational entropy of, simulation of); Entropy (of denaturation, of proteins, configurational entropy in relation to); Entropy (configurational, of proteins, simulation of)
protein configurational entropy},
YEAR = 1987
}
@ARTICLE{hruby88,
AUTHOR = {V. J. Hruby and L. F. Kao and B. M. Pettitt and M. Karplus},
TITLE = {The conformational properties of the delta-opioid peptide
[d-pen2,d-pen5]enkephalin in aqueous-solution determined by nmr
and energy minimization calculations},
JOURNAL = {J. Am. Chem. Soc.},
VOLUME = 110,
PAGES = {3351--3359},
YEAR = 1988
}
@ARTICLE{madura88,
AUTHOR = {J. D. Madura and B. M. Pettitt and D. F. Calef},
TITLE = {Water under high-pressure},
JOURNAL = {Mol. Phys.},
VOLUME = 64,
PAGES = {325--336},
YEAR = 1988
}
@ARTICLE{pettitt88,
AUTHOR = {B. M. Pettitt and M. Karplus},
TITLE = {Conformational free-energy of hydration for the alanine
dipeptide - thermodynamic analysis},
JOURNAL = {J. Phys. Chem.},
VOLUME = 92,
PAGES = {3994--3997},
YEAR = 1988
}
@ARTICLE{dang88,
AUTHOR = {L. X. Dang and B. M. Pettitt},
TITLE = {A theoretical-study of the inclusion complexes of
beta-quinol},
JOURNAL = {J. Chem. Phys.},
VOLUME = 89,
PAGES = {968--974},
YEAR = 1988
}
@ARTICLE{chen88,
AUTHOR = {Z. M. Chen and O. A. Karim and B. M. Pettitt},
TITLE = {A theory of the interionic structure of
graphite-intercalation synthetic metals - variations with respect
to interactions and state},
JOURNAL = {J. Chem. Phys.},
VOLUME = 89,
PAGES = {1042--1048},
YEAR = 1988
}
@ARTICLE{madura88b,
AUTHOR = {J. D. Madura and B. M. Pettitt},
TITLE = {Effects of truncating long-range interactions in aqueous
ionic solution simulations},
JOURNAL = {Chem. Phys. Lett.},
VOLUME = 150,
PAGES = {105--108},
YEAR = 1988
}
@BOOK{brooks88,
AUTHOR = {Brooks, Charles L., III and Karplus, Martin and Pettitt, B. Montgomery},
EDITOR = {Prigogine, I. and Rice, Stuart A.},
TITLE = {Advances in Chemical Physics, Vol. 71: Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics},
PUBLISHER = {John Wiley and Sons, USA},
NOTE = {CAN 110:110469
6-3
General Biochemistry
USA.
Book
written in English.},
KEYWORDS = {Proteins Role: PRP (Properties) (dynamics and structure and thermodn. of); Thermodynamics (of proteins, dynamics and structure in relation to)
protein dynamics structure thermodn book},
YEAR = {1988}
}
@ARTICLE{lau88,
AUTHOR = {Wan F. Lau and B. M. Pettitt and Terry P. Lybrand},
TITLE = {Molecular Dynamics of Coat Proteins of the Human Rhinovirus},
JOURNAL = {Molecular Simulation},
VOLUME = 1,
PAGES = {385--398},
YEAR = 1988
}
@INBOOK{hruby88b,
AUTHOR = {Hruby, V. L. and Kazmierski, W. and Pettitt, B. Montgomery and
Al-Obeidi, F.},
TITLE = {Conformational Constraints in the Design of Receptor Selective
Peptides: Conformational Analysis and Molecular Dynamics},
BOOKTITLE = {Molecular Biology of Brain and Endocrine Peptidergic Systems},
EDITOR = {Chretien, M. and McKerns, K. W.},
ADDRESS = {Plenum, New York, NY},
PAGES = {13--27},
YEAR = {1988}
}
@ARTICLE{madura89,
AUTHOR = {J. D. Madura and B. M. Pettitt and J. A. Mccammon},
TITLE = {Methods for calculating geometries of transition-states in
solution},
JOURNAL = {Chem. Phys.},
VOLUME = 129,
PAGES = {185--191},
YEAR = 1989
}
@INBOOK{hruby88c,
AUTHOR = {Hruby, V. L. and Pettitt, B. Montgomery},
TITLE = {Conformational-Biological Activity Relationships for Receptor
Selective, Conformationally Constrained Opioid Peptides},
BOOKTITLE = {Computer-Aided Drug Design},
EDITOR = {Perun, T. J. and Probst, C. L.},
ADDRESS = {Dekker, New York, NY},
PAGES = {405--452},
YEAR = {1988}
}
@INBOOK{pettitt89,
AUTHOR = {Pettitt, B. Montgomery},
TITLE = {Successes, Failures and Curiosities in Free Energy Calculations},
BOOKTITLE = {Computer Simulation of Biomolecular Systems: Theoretical and
Experimental Applications},
EDITOR = {van Gunsteren, W. F. and Weiner, P. K.},
ADDRESS = {ESCOM, Leiden},
PAGES = {94--100},
YEAR = {1989}
}
@ARTICLE{alobeidi89,
AUTHOR = {F. Alobeidi and M. E. Hadley and B. M. Pettitt and V. J.
Hruby},
TITLE = {Design of a new class of superpotent cyclic
alpha-melanotropins based on quenched dynamic simulations},
JOURNAL = {J. Am. Chem. Soc.},
VOLUME = 111,
PAGES = {3413--3416},
YEAR = 1989
}
@ARTICLE{dang89,
AUTHOR = {L. X. Dang and B. M. Pettitt},
TITLE = {Thermodynamics of diatomic guests in beta-quinol clathrates},
JOURNAL = {J. Phys. Chem.},
VOLUME = 93,
PAGES = {3794--3799},
YEAR = 1989
}
@ARTICLE{lau89,
AUTHOR = {W. F. Lau and B. M. Pettitt},
TITLE = {Dynamics of an oxazole compound bound to a common cold
virus},
JOURNAL = {J. Am. Chem. Soc.},
VOLUME = 111,
PAGES = {4111--4113},
YEAR = 1989
}
@ARTICLE{cagin89,
AUTHOR = {T. \c{C}a\v{g}in and B. M. Pettitt},
TITLE = {Elastic-constants of nickel - variations with respect to
temperature and pressure},
JOURNAL = {Phys. Rev. B},
VOLUME = 39,
PAGES = {12484--12491},
YEAR = 1989
}
@ARTICLE{lau89b,
AUTHOR = {W. F. Lau and B. M. Pettitt},
TITLE = {Selective elimination of interactions - a method for
assessing thermodynamic contributions to ligand-binding with
application to rhinovirus antivirals},
JOURNAL = {J. Medicinal Chem.},
VOLUME = 32,
PAGES = {2542--2547},
YEAR = 1989
}
@ARTICLE{rame90,
AUTHOR = {G. L. Ram\'{e} and W. F. Lau and B. M. Pettitt},
TITLE = {Flexibility of tripeptides in solution - free-energy
molecular mechanics},
JOURNAL = {Int. J. Peptide Protein Research},
VOLUME = 35,
PAGES = {315--327},
YEAR = 1990
}
@ARTICLE{dang90,
AUTHOR = {L. X. Dang and B. M. Pettitt},
TITLE = {A theoretical-study of like ion-pairs in solution},
JOURNAL = {J. Phys. Chem.},
VOLUME = 94,
PAGES = {4303--4308},
YEAR = 1990
}
@INBOOK{chen90b,
AUTHOR = {Chen, Z. M. and Pettitt, B. M.},
TITLE = {Free Energy of Intercalation: The Structure of Graphite
Intercalation Compounds},
BOOKTITLE = {Studies in Physical and Theoretical Chemistry},
EDITOR = {Rivail, J. L.},
PAGES = {103--117},
YEAR = {1990}
}
@ARTICLE{chen90,
AUTHOR = {Z. M. Chen and B. M. Pettitt},
TITLE = {Diatomic intercalation in lamellar graphite compounds},
JOURNAL = {Phys. Rev. B},
VOLUME = 42,
PAGES = {8173--8178},
YEAR = 1990
}
@ARTICLE{vanvlijmen90,
AUTHOR = {H. W. T. van Vlijmen and G. L. Ram\'{e} and B. M. Pettitt},
TITLE = {A study of model energetics and conformational properties
of polynucleotide triplexes},
JOURNAL = {Biopolymers},
VOLUME = 30,
PAGES = {517--532},
YEAR = 1990
}
@ARTICLE{rossky91,
TITLE = {Modeling of solvation effects in biopolymer solutions},
JOURNAL = {Theor. Biochem. Mol. Biophys.},
YEAR = {1991},
VOLUME = {2},
PAGES = {223-9},
NOTE = {CAN 115:202174 9-0 Biochemical Methods Chem. Dep.,Univ. Houston,Houston,TX,USA.
Conference; General Review written in English.},
ABSTRACT = {A review with 38 refs. By appropriate choice of the level of theor. treatment, the problem of accounting for the soln. environment in the modeling of biopolymer conformation and interactions is becoming accessible to direct computational evaluation. In this article, the authors summarize a no. of methods that have been recently applied
in this context, emphasizing those other than direct all-atom computer
simulation. [on SciFinder (R)]},
KEYWORDS = {Biopolymers Role: ANST (Analytical study) (conformation and interactions
of, solvation effects in, modeling of); Solvation (in biopolymer
solns., modeling of, conformation and interactions in relation to);
Conformation and Conformers (of biopolymers, solvation effects in,
modeling of); Process simulation (of solvation effects in biopolymer
soln.) review solvation effect biopolymer; conformation biopolymer
solvation effect review; process simulation biopolymer solvation
review}
}
@ARTICLE{smith91,
AUTHOR = {P. E. Smith and L. X. Dang and B. M. Pettitt},
TITLE = {Simulation of the structure and dynamics of the
bis(penicillamine) enkephalin zwitterion},
JOURNAL = {J. Am. Chem. Soc.},
VOLUME = 113,
PAGES = {67--73},
YEAR = 1991,
ABSTRACT = {We have performed a molecular dynamics simulation of the
enkephalin derivative Tyr-(D)Pen-Gly-Phe-(D)Pen (DPDPE) in aqueous
solvent. Electrostatic interactions were calculated with the Ewald
method so as to accurately model the large interactions between
the DPDPE zwitterion and the solvent and to avoid the use of
electrostatic cutoff's or neutral chemical blocking groups. DPDPE
is found to be extremely constrained with very little variation in
the main-chain dihedral angles. Flexibility found in the region of
the central glycine is greatly restricted compared with glycines
in straight-chain peptides. Several conformational transitions are
observed for the two aromatic side chains, indicating a high
degree of flexibility in the side chains and that DPDPE does not
have a single conformation in solution. This suggests that the
arrangement of the tyrosine and phenylalanine aromatic residues in
the bound conformation may be selected by the receptor
environment. The main-chair conformation of DPDPE in solution has
a parallel arrangement of peptide groups. This electrostatically
unfavorable structure is stabilized by interactions of the
carbonyls with the solvent. Solvent structure around the N
terminus is found to be considerably localized, involving short
ammonium cation to water contacts with lifetimes of the order of
50 ps or more. In comparison, water structure around the C
terminus is much more mobile with lifetimes of the order of 20 ps
or less.}
}
@ARTICLE{cagin91,
AUTHOR = {T. \c{C}a\u{g}in and B. M. Pettitt},
TITLE = {Molecular-dynamics with a variable number of molecules},
JOURNAL = {Mol. Phys.},
VOLUME = 72,
PAGES = {169--175},
YEAR = 1991,
ABSTRACT = {A computational demonstration of a form of
constant-chemical-potential molecular dynamics shows the
feasibility of the proposed method. The technique is based on
using a Lagrangian for a system that includes extension variables
to couple the number of particles with the chemical potential and
auxiliary variable allowing for the insertion of new particles and
the destruction of existing ones. Density dependence, equilibrium
and non-equilibrium properties are considered.}
}
@ARTICLE{mazor91,
TITLE = {Convergence of the Chemical Potential in Aqueous Solutions},
JOURNAL = {Molecular Simulations},
VOLUME = {6},
YEAR = {1991},
PAGES = {1--4}
}
@ARTICLE{cagin91b,
AUTHOR = {T. \c{C}a\v{g}in and B. M. Pettitt},
TITLE = {Grand Molecular Dynamics: A method for open systems},
JOURNAL = {Molecular Simulations},
VOLUME = 6,
PAGES = {5--26},
YEAR = 1991
}
@INBOOK{findsen93,
TITLE = {Time scales and fluctuations of protein dynamics: Metmyoglobin in
aqueous solution},
BOOKTITLE = {Principles of Molecular Recognition},
EDITOR = {Buckingham, A. D.},
ADDRESS = {Chapman Hall, London},
YEAR = {1993},
PAGES = {168-93},
NOTE = {CAN 122:3624 6-0 General Biochemistry Dep. Med. and Pharm. Chem.,Univ.
Toledo,Toledo,OH,USA. Conference; General Review written in English.},
ABSTRACT = {A review, with 23 refs., on a representative 150-ps mol. dynamics
simulation of metmyoglobin in water, the general methods used in
this dynamic simulation, and spatial and temporal fluctuations.
[on SciFinder (R)]},
KEYWORDS = {Myoglobins Role: PRP (Properties) (time scales and fluctuations of
metmyoglobin dynamics in aq. soln.) review metmyoglobin dynamics
soln}
}
@ARTICLE{yu91,
AUTHOR = {H. A. Yu and B. M. Pettitt and M. Karplus},
TITLE = {Aqueous solvation of n-methylacetamide conformers -
comparison of simulations and integral-equation theories},
JOURNAL = {J. Am. Chem. Soc.},
VOLUME = 113,
PAGES = {2425--2434},
YEAR = 1991,
ABSTRACT = {The aqueous solvation thermodynamics of cis- and
trans-N-methylacetamide is studied by integral equation theories
and molecular dynamics simulations and compared with Monte Carlo
results (Jorgensen, W. L.; Gao, J. J. Am. Chem. Soc. 1988, 110,
4212). Although the hypernetted chain (HNC) approximation is
generally recommended for polar systems, the solvation free energy
derived from the Gaussian fluctuation (GF) approximation gives
much better absolute solvation thermodynamics. With the same
atomic charges for the two conformers, the difference in solvation
free energy between the cis and trans conformers equals 1-2
kcal/mol from the HNC and GF approximations, in approximate
agreement with the value of 2.2 kcal/mol from a Monte Carlo
simulation with very similar parameters. The simpler superposition
approximation introduced by Pettitt and Karplus (Chem. Phys. Lett.
1985, 121, 194) gives results for the relative solvation
thermodynamics (cis versus trans conformers) that compare well
with the more exact integral equation theories.}
}
@ARTICLE{cagin91c,
AUTHOR = {T. \c{C}a\u{g}in and M. Holder and B. M. Pettitt},
TITLE = {A method for modeling icosahedral virions - rotational
symmetry boundary-conditions},
JOURNAL = {J. Computational Chem.},
VOLUME = 12,
PAGES = {627--634},
YEAR = 1991,
ABSTRACT = {We present two techniques for implementing a new method of
simulating an entire virion. Earlier computer simulations of a
capsid protein revealed large edge effects due to the use of free
standing boundaries. Because of the size of a given protomer,
conventional three-dimensional periodic boundary conditions would
be extremely wasteful. This would require an extremely large
number of solvent molecules, and therefore would be
computationally feasible for only a fragment of the entire virion.
The new method employs non-space-filling computational cells in
molecular modeling and molecular dynamics with the boundary
conditions based on the icosahedral group. The method is general
and could be used for any molecular system with a point group
symmetry. With this method, the dynamical and spatial intra and
interpromotomer correlations can be studied at atomic levels. The
technique is applicable to any virion with icosahedral symmetry. A
sample calculation involving a geometry optimization of the human
rhinovirus coat proteins is given to demonstrate the technique.}
}
@ARTICLE{smith91b,
AUTHOR = {P. E. Smith and F. Alobeidi and B. M. Pettitt},
TITLE = {Aspects of the design of conformationally constrained
peptides},
JOURNAL = {Methods In Enzymology},
VOLUME = 202,
PAGES = {411--436},
YEAR = 1991
}
@ARTICLE{smith91c,
AUTHOR = {P. E. Smith and B. M. Pettitt},
TITLE = {Effects of salt on the structure and dynamics of the
bis(penicillamine) enkephalin zwitterion - a simulation study},
JOURNAL = {J. Am. Chem. Soc.},
VOLUME = 113,
PAGES = {6029--6037},
YEAR = 1991,
ABSTRACT = {Molecular dynamics simulations of a zwitterionic
bis(penicillamine) enkephalin derivative in 1.0 M saline solution
have been performed. Two simulations produced essentially the same
average results although they differed in the initial random
placement of the salt ions. The dynamical and structural
properties from the simulations were compared with those from a
previous simulation of the peptide in pure water. The properties
of the sodium and chloride ions were compared with those from a
simulation of bulk salt solution. An inner-sphere complex between
the peptide and the chloride ions was observed in which two to
three chloride ions were associated with the NH3+ terminal
hydrogen atoms. Several chlorides associated with more than one
amide hydrogen simultaneously, and the resulting close
chloride-chloride ion contacts were additionally stabilized by
bridging water molecules. The sodium ions did not associate
directly with the peptide but formed an outer-sphere complex
surrounding the peptide-chloride ion complex. The effect of
chloride ion association on the structure and dynamics of the
peptide was investigated in detail. The spatial correlations
between salt ions and the enkephalin derivative are discussed in
relation to delta-opioid receptor binding. The implications that
the observed ion effects have on our understanding of the
Hofmeister series are also considered.}
}
@ARTICLE{durland91,
AUTHOR = {R. H. Durland and D. J. Kessler and S. Gunnell and M. Duvic
and B. M. Pettitt and M. E. Hogan},
TITLE = {Binding of triple helix forming oligonucleotides to sites
in gene promoters},
JOURNAL = {Biochem.},
VOLUME = 30,
PAGES = {9246--9255},
YEAR = 1991,
ABSTRACT = {A class of triplex-forming oligodeoxyribonucleotides (TFOs)
is described that can bind to naturally occurring sites in duplex
DNA at physiological pH in the presence of magnesium. The data are
consistent with a structure in which the TFO binds in the major
groove of double-stranded DNA to form a three-stranded complex
that is superficially similar to previously described triplexes.
The distinguishing features of this class of triplex are that TFO
binding apparently involves the formation of hydrogen-bonded G.GC
and T.AT triplets and the TFO is bound antiparallel with respect
to the more purine-rich strand of the underlying duplex. Triplex
formation is described for targets in the promoter regions of
three different genes: the human c-myc and epidermal growth factor
receptor genes and the mouse insulin receptor gene. All three
sites are relatively GC rich and have a high percentage of purine
residues on one strand. DNase I footprinting shows that individual
TFOs bind selectively to their target sites at pH 7.4-7.8 in the
presence of millimolar concentrations of magnesium.
Electrophoretic analysis of triplex formation indicates that
specific TFOs bind to their target sites with apparent
dissociation constants in the 10(-7)-10(-9) M range. Strand
orientation of the bound TFOs was confirmed by attaching eosin or
an iron-chelating group to one end of the TFO and monitoring the
pattern of damage to the bound duplex DNA. Possible
hydrogen-bonding patterns and triplex structures are discussed.}
}
@ARTICLE{pettitt91,
AUTHOR = {B. M. Pettitt and T. Matsunaga and F. Alobeidi and C.
Gehrig and V. J. Hruby and M. Karplus},
TITLE = {Dynamic search for bis-penicillamine enkephalin
conformations},
JOURNAL = {Biophys. J.},
VOLUME = {60},
PAGES = {1540--1544},
YEAR = {1991},
ABSTRACT = {Quenched molecular dynamics is used as a conformational
search technique for the constrained cyclic analog
[D-Pen2,D-Pen5]enkephalin (DPDPE) in a continuum solvent. The
results show a Gaussianlike distribution of conformations as a
function of energy, unlike the distributions found for simple
liquids which have sharp bands for different crystal forms and
broad glasslike states are found. The lowest energy conformers
have structural features in common with those obtained from
constrained searches based on energy minimization. (Hruby, V. J.,
L.-F. Kao, B. M. Pettitt, and M. Karplus. 1988. J. Am. Chem. Soc.
110:3351-3359.) Many of the low energy configurations are
amphiphilic with the carbonyl groups on one surface and the
hydrophobic groups on the other. This supports the conclusions
from the previous modeling study, which yielded amphiphilic
structures as the most probable conformations of DPDPE when NOE
data were included.}
}
@ARTICLE{smith91d,
AUTHOR = {P. E. Smith and B. M. Pettitt},
TITLE = {Peptides in ionic-solutions - a comparison of the ewald and
switching function techniques},
JOURNAL = {J. Chem. Phys.},
VOLUME = {95},
PAGES = {8430--8441},
YEAR = {1991},
ABSTRACT = {The methodological dependence of observed ion-peptide
associations in molecular dynamics simulations is investigated. We
compare the results from several simulations of a pentapeptide in
explicit solvent and salt ions which differ in the their treatment
of the long ranged electrostatic interactions. Results for both
the Ewald and switching function techniques are presented. It was
found that there were important differences between the two
methods for the water dipole-dipole temporal and spatial
correlations, total dipole moment fluctuations, and self-diffusion
constants. Electrostatic potentials calculated in the region of
the peptide are also used to illustrate the large differences that
can arise from different treatments of the electrostatic
interactions. It appears that the switching function distorts the
molecular electrostatic potential experienced by the salt ions to
such a degree that their behaviour becomes highly dependent on the
initial conditions. In summary, the use of a switching function is
not recommended for the simulation of ions and their interactions
with biomolecules.}
}
@ARTICLE{ji92,
AUTHOR = {J. Ji and T. \c{C}a\v{g}in and B. M. Pettitt},
TITLE = {Dynamic simulations of water at constant chemical-potential},
JOURNAL = {J. Chem. Phys.},
VOLUME = {96},
PAGES = {1333--1342},
YEAR = {1992},
ABSTRACT = {The grand molecular dynamics (GMD) method has been extended
and applied to examine the density dependence of the chemical
potential of a three-site water model. The method couples a
classical system to a chemical potential reservoir of particles
via an ansatz Lagrangian. Equilibrium properties such as structure
and thermodynamics, as well as dynamic properties such as time
correlations and diffusion constants, in open systems at a
constant chemical potential, are preserved with this method. The
average number of molecules converges in a reasonable amount of
computational effort and provides a way to estimate the chemical
potential of a given model force field.}
}
@ARTICLE{dang92,
AUTHOR = {L. X. Dang and B. M. Pettitt and P. J. Rossky},
TITLE = {On the correlation between like ion-pairs in water},
JOURNAL = {J. Chem. Phys.},
VOLUME = {96},
PAGES = {4046--4047},
YEAR = {1992},
ABSTRACT = {}
}
@ARTICLE{perkyns92b,
AUTHOR = {J. S. Perkyns and B. M. Pettitt},
TITLE = {A dielectrically consistent interaction site theory for
solvent electrolyte mixtures},
JOURNAL = {Chem. Phys. Lett.},
VOLUME = {190},
PAGES = {626--630},
YEAR = {1992},
ABSTRACT = {A reformulation of reference interaction site model theory
is proposed. The approach makes use of the formally correct
asymptotic form of the correlations obtained from the one-center
angular expansion technique. A modified closure, or equivalently,
a modified propagation equation for site-site correlations is
shown to incorporate the necessary information to allow dielectric
consistency in finite-concentration salt solutions. Examples of
the correlations and thermodynamics are given.}
}
@ARTICLE{cheng92,
AUTHOR = {Y. K. Cheng and B. M. Pettitt},
TITLE = {Hoogsteen versus reversed-hoogsteen base-pairing - dna
triple helices},
JOURNAL = {J. Am. Chem. Soc.},
VOLUME = {114},
PAGES = {4465--4474},
YEAR = {1992},
ABSTRACT = {Recently, oligonucleotides have been shown to inhibit
transcription in genes by triple helix or triplex formation in
vitro and in vivo. A better understanding of the forces that
stabilize triplex structures will be important in developing
applications of this method of genetic medication to arbitrary
sequences. Therefore, base pairings and strand orientations for
homogeneous d(T.A.T)27 and d(C.G.G)27 triplexes were examined. The
method was extended to triplex models formed by c-myc gene
promoter region and complementary oligonucleotides. Templates of a
single plane with three bases were constructed and used in a
simple geometric replication based on experimental geometric
parameters. Minimizations and quenched molecular dynamics
simulations were performed on the model systems. The estimated
accessibility of the major groove for counteraction coordination
was obtained by calculating the effective accessible surface areas
of backbone phosphate oxygen atoms. Free energy calculations of
the solvation/desolvation penalty on single strands, duplexes, and
the stereoisomeric triplexes have been performed. They were
combined with corresponding enthalpic term so that the results
could be discussed in a more realistic aspect. For d(T.A.T)27
triplexes, results from both the internal potential energy and
solvation free energy calculations contribute to the
experimentally known base pairing and strand orientation.
Solvation is found to determine the strand orientation for
d(C.G.G)27 triplexes with either Hoogsteen or reversed-Hoogsteen
base pairing between the two purine strands being possible. We
have compared the d(C.G.G)27 triplexes by computing the
hydrogen-hydrogen distances which may be useful in verifying these
models by future NMR/NOE studies. Using these homopolymers the
orientation of oligonucleotides bound to the c-myc gene promoter
site is shown to also be dominated by the forces of solvation.}
}
@ARTICLE{oconnor92,
AUTHOR = {S. D. Oconnor and P. E. Smith and F. Alobeidi and B. M.
Pettitt},
TITLE = {Quenched molecular-dynamics simulations of tuftsin and
proposed cyclic analogs},
JOURNAL = {J. Medicinal Chem.},
VOLUME = {35},
PAGES = {2870--2881},
YEAR = {1992},
ABSTRACT = {We have used high-temperature quenched molecular dynamics
calculations to investigate the conformational properties of
tuftsin (Thr-Lys-Pro-Arg) in solution. Conformers obtained after
quenching of the dynamical structures were sorted into families
depending on their relative energies and backbone conformations.
By examination of these families, several cyclic analogues of
tuftsin were proposed and examined theoretically by further
quenched dynamics simulations. Two of the four proposed analogues
were found to adopt essentially identical conformations to that of
linear tuftsin. It is suggested that these two derivatives
(cyclo[Thr-Lys-Pro-Arg-Gly] and cyclo[Thr-Lys-Pro-Arg-Asp]) may be
biologically active, and that the introduction of cyclic
conformational constraints should help to reduce the entropic
penalty to peptide binding.}
}
@ARTICLE{smith78,
AUTHOR = {Paul E. Smith and Pettitt, B. Montgomery},
TITLE = {Forms of Molecular Dynamics},
JOURNAL = {Landolt-B\"ornstein},
VOLUME = {},
NUMBER = {},
PAGES = {},
ABSTRACT = { },
KEYWORDS = { },
YEAR = {}
}
@ARTICLE{mohan92,
AUTHOR = {V. Mohan and M. E. Davis and J. A. Mccammon and B. M.
Pettitt},
TITLE = {Continuum model-calculations of solvation free-energies -
accurate evaluation of electrostatic contributions},
JOURNAL = {J. Phys. Chem.},
VOLUME = {96},
PAGES = {6428--6431},
YEAR = {1992},
ABSTRACT = {The electrostatic contributions to free energies of
solvation of several small molecules have been calculated,
treating the solvent as a statistical continuum. The computational
method is based on solving the linearized Poisson-Boltzmann
equation for the electrostatic potentials using the
finite-difference scheme. A careful study of convergence indicates
the importance of a fine grid spacing, as well as the short
comings of rotational averaging. The computed free energies of
solvation are in excellent agreement with the experimental results
as well as the free energy perturbation calculations. The free
energies of hydration of the natural nucleic acid bases are
calculated and shown to be somewhat sensitive to charge model.}
}
@ARTICLE{chen92,
AUTHOR = {Z. M. Chen and B. M. Pettitt and G. Reiter and S. C. Moss
and O. A. Karim},
TITLE = {Comparison of structural theories for
graphite-intercalation compounds},
JOURNAL = {Phys. Rev. B},
VOLUME = {46},
PAGES = {10476--10478},
YEAR = {1992},
ABSTRACT = {Alkali liquids intercalated in graphite are subject to a
strong periodic host potential. We compare here two theories for
the modulation induced in the alkali density that result in
different approximations for higher-order correlations, with
computer simulations and experimental data. We show these two
theories-one based on a cumulant expansion, the other on an
angular truncation of the Lovet-Mou-Buff equation-agree
analytically in the limit of weak host potential and are
numerically similar at high temperatures for a realistic
potential.}
}
@ARTICLE{lounnas92,
AUTHOR = {V. Lounnas and B. M. Pettitt and L. Findsen and S.
Subramaniam},
TITLE = {A microscopic view of protein solvation},
JOURNAL = {J. Phys. Chem.},
VOLUME = {96},
PAGES = {7157--7159},
YEAR = {1992},
ABSTRACT = {Because of difficulties associated with experimental
measurement techniques, the distribution of water density around
many proteins is not well-resolved. We present, in this paper, a
molecular dynamics approach to the general problem of comparing
the instantaneous vs average view of protein hydration via a
150-ps simulation of metmyoglobin in an explicit aqueous
environment. Densities as a function of position for both water
and myoglobin were computed by time-averaging the volume fraction
occupied at different positions in space. The picture so obtained
challenges the view of hydration taken from accessible surface
features related to the average structure. A detailed picture of
protein hydration is given that includes significant surface
penetration and transient channels, in conjunction with the
accepted concepts of a-tightly bound partial layer of water on the
surface near charged groups.}
}
@ARTICLE{smith92,
AUTHOR = {P. E. Smith and B. M. Pettitt},
TITLE = {Amino-acid side-chain populations in aqueous and saline
solution - bis-penicillamine enkephalin},
JOURNAL = {Biopolymers},
VOLUME = {32},
PAGES = {1623--1629},
YEAR = {1992},
ABSTRACT = {The potentials of mean force (pmfs) for rotation around the
chi1 aromatic side-chain dihedrals of the zwitterionic
bis-penicillamine enkephalin pentapeptide have been determined in
both aqueous and saline solution. These side chains are known to
be associated with the pharmacophore and their conformational
populations are thought to be critical for activity. It is found
that the association between chloride ions and the peptide in
saline solution simulations has profound effects on the relative
energies of the g-, g+, and t conformations, and also the barriers
between them. Using the pmfs we have also calculated the
respective Boltzmann-weighted 3J(alphabeta) vicinal coupling
constants. The agreement between the calculated and experimentally
determined coupling constants is poor for the pmf in pure water,
but substantially improved for the pmf determined in saline
solution. Reasons for these differences appear to be related to
the experimental conditions.}
}
@ARTICLE{lin92,
AUTHOR = {S. L. Lin and J. Mellorcrummey and B. M. Pettitt and G. N.
Phillips},
TITLE = {Molecular-dynamics on a distributed-memory multiprocessor},
JOURNAL = {J. Computational Chem.},
VOLUME = {13},
PAGES = {1022--1035},
YEAR = {1992},
ABSTRACT = {Dynamics simulations of molecular systems are notoriously
computationally intensive, Using parallel computers for these
simulations is important for reducing their turnaround time. In
this article we describe a parallelization of the simulation
program CHARMM for the Intel iPSC/860, a distributed memory
multiprocessor. In the parallelization, the computational work is
partitioned among the processors for core calculations including
the calculation of forces, the integration of equations of motion,
the correction of atomic coordinates by constraint, and the
generation and update of data structures used to compute nonbonded
interactions. Processors coordinate their activity using
synchronous communication to exchange data values. Key data
structures used are partitioned among the processors in nearly
equal pieces, reducing the memory requirement per node and making
it possible to simulate larger molecular systems. We examine the
effectiveness of the parallelization in the context of a case
study of a realistic molecular system. While effective speedup was
achieved for many of the dynamics calculations, other calculations
fared less well due to growing communication costs for exchanging
data among processors. The strategies we used are applicable to
parallelization of similar molecular mechanics and dynamics
programs for distributed memory multiprocessors.}
}
@ARTICLE{cheng92b,
AUTHOR = {Y. K. Cheng and B. M. Pettitt},
TITLE = {Stabilities of double-strand and triple-strand helical
nucleic-acids},
JOURNAL = {Progress In Biophys. & Mol. Biol.},
VOLUME = {58},
PAGES = {225--257},
YEAR = {1992},
ABSTRACT = {}
}
@ARTICLE{perkyns92,
AUTHOR = {J. Perkyns and B. M. Pettitt},
TITLE = {A site site theory for finite concentration saline
solutions},
JOURNAL = {J. Chem. Phys.},
VOLUME = {97},
PAGES = {7656--7666},
YEAR = {1992},
ABSTRACT = {A liquid state theory based on site-site integral equations
is constructed to have the asymptotics given by angular expansion
theory. This results in a theory which shows dielectric
consistency, e.g., the dielectric constant as viewed from the
solvent is the same as that viewed by the ions. Such consistency
is lacking in other extended reference interaction site model
(XRISM)-based theories and leads to unrealistic structural
predictions. The Kirkwood-Buff route to thermodynamics is used and
allows a physical partitioning of the terms responsible for the
solvation process. Sample results for a 1-1 salt are given.}
}
@ARTICLE{kouri92,
AUTHOR = {D. J. Kouri and W. Zhu and X. Ma and B. M. Pettitt and D.
K. Hoffman},
TITLE = {Monte-carlo evaluation of real-time feynman path-integrals
for quantal many-body dynamics - distributed approximating
functions and gaussian sampling},
JOURNAL = {J. Phys. Chem.},
VOLUME = {96},
PAGES = {9622--9630},
YEAR = {1992},
ABSTRACT = {In this paper we report the initial steps in the
development of a Monte Carlo method for evaluation of real-time
Feynman path integrals for many-particle dynamics. The approach
leads to Gaussian importance sampling for real-time dynamics in
which the sampling function is short ranged due to the occurrence
of Gaussian factors. These Gaussian factors result from the use of
a generalization of our new discrete distributed approximating
functions (DDAFs) to continuous distributed approximating
functions (CDAFs) so as to replace the exact coordinate
representation free-particle propagator by a "CDAF-class,
free-particle propagator" which is highly banded. The envelope of
the CDAF-class free propagator is the product of a "bare
Gaussian", exp[-(x'- x)2sigma2(0)/(2sigma4(0) + H2tau2/m2BAR)],
with a "shape polynomial" in (x' - x)2, where sigma(0) is a width
parameter at zero time (associated with the description of the
wavepacket in terms of Hermite functions), tau is the time step
(tau = t/N, where t is the total propagation time), and x and x'
are any two configurations of the system. The bare Gaussians are
used for Monte Carlo integration of a path integral for the
survival probability of a Gaussian wavepacket in a Morse
potential. The approach appears promising for real-time quantum
Monte Carlo studies based on the time-dependent Schrodinger
equation, the time-dependent von Neumann equation, and related
equations.}
}
@ARTICLE{mohan93,
AUTHOR = {V. Mohan and Y. K. Cheng and G. E. Marlow and B. M. Pettitt},
TITLE = {Molecular recognition of watson-crick base-pair reversals
in triple-helix formation - use of nonnatural oligonucleotide
bases},
JOURNAL = {Biopolymers},
VOLUME = {33},
PAGES = {1317--1325},
YEAR = {1993},
ABSTRACT = {We report the calculated characteristics of nonnatural
triplex-forming oligonucleotide (TFO) bases recognizing base-pair
reversals (TA --> AT) in a double-helical DNA sequence. Ab initio
and molecular mechanics calculations have been carried out to
characterize the geometric and energetic consequences at the
base-pair reversal sites. We have estimated the free energies of
solvation of the natural and proposed bases by solving the
linearized Poisson-Boltzmann equation. The calculations indicate
that the proposed TFO bases should bind with some specificity to
the duplex. Implications of the strategy used in the context of
molecular biology is discussed. (C) 1993 John Wiley & Sons, Inc.}
}
@INBOOK{ji93,
AUTHOR = {Jie, Ji and Pettitt, B. Montgomery },
TITLE = {Grand Molecular Dynamics: An application of extended system
dynamics},
BOOKTITLE = {Computer Simulation of Biomolecular Systems: Theoretical
and Experimental Applications},
EDITOR = {van Gunsteren, W. F. and Weiner, P. K., and Wilkinson, A. J.},
ADDRESS = {ES-COM, Leiden},
YEAR = {1993},
PAGES = {67--81}
}
@ARTICLE{smith93,
AUTHOR = {P. E. Smith and B. M. Pettitt},
TITLE = {Stochastic dynamics simulations of the alanine dipeptide
using a solvent-modified potential-energy surface},
JOURNAL = {J. Phys. Chem.},
VOLUME = {97},
PAGES = {6907--6913},
YEAR = {1993},
ABSTRACT = {Langevin dynamics on a potential of mean force energy
surface is used to model the effects of aqueous solvent on the
structure and dynamics of the alanine dipeptide. Conformational
transition rates obtained by correlation function analysis and
hazard plots from several simulations are compared. In particular,
averages obtained over three 25-ns runs are compared with a single
run of 100 ns. Rate constants for selected conformational
transitions are also examined. For the conformational processes
considered here (alpha to beta and the reverse), we observe two
rates, one of which is only significant for simulations of more
than 25 ns. On further decomposition of the rate process, it is
shown that the two observed rates correspond to the individual
rates for rotation around the phi and psi dihedrals. It is also
shown that, for the conformational transitions investigated here,
the transition process corresponds to an essentially uncorrelated
motion of the two dihedral angles.}
}
@ARTICLE{guhabiswas93,
AUTHOR = {M. Guhabiswas and M. Holder and B. M. Pettitt},
TITLE = {On the mechanism of hrv-14 antiviral compounds - slow
growth as a conformational search procedure},
JOURNAL = {J. Medicinal Chem.},
VOLUME = {36},
PAGES = {3489--3495},
YEAR = {1993},
ABSTRACT = {We report a novel conformational search procedure that is
used to investigate the binding mechanism of a member of the WIN
class of antiviral compounds. A simple hypothesis of important
residues in the binding site based on differences in drug-free and
drug-bound X-ray structures along with more elaborate models,
ultimately including the entire virus, is considered. Our search
method is a variant of slow-growth molecular dynamics used in free
energy simulations and gives rise to local motion in the protein
backbone of up to 3 angstrom. This technique involves the scaling
of drug-protein interaction energies over time periods of 10-100
ps and gives rise to local motion in the protein backbone. In
addition, we have used high-temperature dynamics with periodic
quenching to generate low-energy conformations with backbone
displacements in the crystallographic binding region of up to 7
angstrom from the native structure. Mechanism of binding,
hydrogen-bond stabilization of active-site conformations,
concerted drug-protein motions, and the mode of virion
stabilization are addressed in relation to our ligand induced and
high-temperature conformational search procedures. A loop-cap like
mechanism is consistent with the results of our study. A large
movement of the 'active-site'' residues is shown to be
theoretically possible and provides a greater access for entry of
the drug into its binding pocket than seen in the available
crystal structures.}
}
@ARTICLE{smith93b,
AUTHOR = {P. E. Smith and G. E. Marlow and B. M. Pettitt},
TITLE = {Peptides in ionic-solutions - a simulation study of a
bis(penicillamine) enkephalin in sodium-acetate solution},
JOURNAL = {J. Am. Chem. Soc.},
VOLUME = {115},
PAGES = {7493--7498},
YEAR = {1993},
ABSTRACT = {The bis(penicillamine) enkephalin, a small zwitterionic
pentapeptide, has been studied in explicit 1.0 M sodium acetate
solution with use of the molecular dynamics technique. During the
simulation the association of multiple acetate ions with the
positively charged N terminal region was observed. In addition,
but to a far lesser extent, sodium ion binding to backbone
carbonyl groups close to the negatively charged C terminus also
occurred. Interesting individual events, such as the simultaneous
binding of an acetate to a hydrogen of the N terminus and to
backbone NH groups, were observed. Most often acetates only
associated with the N terminal hydrogens. Subtle conformational
changes in the peptide backbone were found as a consequence of
acetate binding. These mechanistic observations are consistent
with, and may be rationalized by, the known salting in and salting
out properties of these ions and their relative positions in the
Hofmeister (lyotropic) series.}
}
@ARTICLE{mohan93b,
AUTHOR = {V. Mohan and P. E. Smith and B. M. Pettitt},
TITLE = {Evidence for a new spine of hydration - solvation of dna
triple helices},
JOURNAL = {J. Am. Chem. Soc.},
VOLUME = {115},
PAGES = {9297--9298},
YEAR = {1993},
ABSTRACT = {}
}
@ARTICLE{mohan93c,
AUTHOR = {V. Mohan and P. E. Smith and B. M. Pettitt},
TITLE = {Molecular-dynamics simulation of ions and water around
triplex dna},
JOURNAL = {J. Phys. Chem.},
VOLUME = {97},
PAGES = {12984--12990},
YEAR = {1993},
ABSTRACT = {We report the results of a 100-ps molecular dynamics
simulation study of triple helical DNA with explicit water,
counterions, and salt using periodic boundary conditions at 300 K.
The simulation involved an antiparallel reverse-Hoogsteen-like
homopolymeric CGG 7-mer triple helix, 837 water molecules, 21 Na+
ions, and 1 M NaCl. We have used the Ewald method to compute the
electrostatic interactions. Specific ion and water associations as
well as relative solvent and ion mobilities are reported. Specific
patterns of ion and water molecule associations are found which
are novel and may have implications for stability and recognition
of triplex-forming oligonucleotides by duplex DNA. Exchanges of
ions around neighboring phosphate were found to correspond to a
concerted mechanism of displacement. Comparisons are made with
available data from related systems.}
}
@ARTICLE{kouri93,
AUTHOR = {D. J. Kouri and W. Zhu and X. Ma and B. M. Pettitt and D.
K. Hoffman},
TITLE = {Monte-carlo evaluation of real-time feynman path-integrals
for quantal many-body dynamics - distributed approximating
functions and gaussian sampling - reply},
JOURNAL = {J. Phys. Chem.},
VOLUME = {97},
PAGES = {8107--8107},
YEAR = {1993},
ABSTRACT = {}
}
@ARTICLE{kessler93,
AUTHOR = {D. J. Kessler and B. M. Pettitt and Y. K. Cheng and S. R.
Smith and K. Jayaraman and H. M. Vu and M. E. Hogan},
TITLE = {Triple-helix formation at distant sites - hybrid
oligonucleotides containing a polymeric linker},
JOURNAL = {Nucleic Acids Research},
VOLUME = {21},
PAGES = {4810--4815},
YEAR = {1993},
ABSTRACT = {An oligonucleotide hybrid is described which possesses two
triple helix forming oligonucleotides which have been connected by
a flexible polymeric linker chain. As a prototype, binding of this
class of oligonucleotide to duplex DNA has been studied using a
segment of the HSV-1 D-glycoprotein promoter, which possesses a
pair of 12bp target sites for stable triple helix formation,
separated by a duplex spacer region which is one helical turn
long. Band shift and footprinting analysis show that such hybrids
can bind to both 12bp elements simultaneously, if flexible linkers
are included which are longer than 20 - 25 rotatable bonds.
Molecular modeling confirms that a flexible polymeric linker as
short as 22 rotatable bonds is enough to link the two distant
segments of triple helix, providing that the linker element
travels a path which is external to the helix grooves and parallel
to the long helix axis.}
}
@ARTICLE{marlow93,
AUTHOR = {G. E. Marlow and J. S. Perkyns and B. M. Pettitt},
TITLE = {Salt effects in peptide solutions - theory and simulation},
JOURNAL = {Chem. Rev.},
VOLUME = {93},
PAGES = {2503--2521},
YEAR = {1993},
ABSTRACT = {}
}
@ARTICLE{marlow94,
AUTHOR = {Marlow, Gail E. and Pettitt, B. Montgomery},
TITLE = {Theoretical and Experimental Studies of Salt-Peptide Solutions},
JOURNAL = {Adv. Comput. Biology},
VOLUME = {1},
NUMBER = {},
PAGES = {231--248},
YEAR = {1994}
}
@ARTICLE{mitra93,
AUTHOR = {Mitra, Rahul and Pettitt, B. Montgomery and Ram\'{e}, Graciela L.
and Blake, R. D.},
TITLE = {The relationship between mutation rates for the (C-G)-->(T-A) transition and features of T-G mispair structures in different neighbor environments, determined by free energy molecular mechanics},
JOURNAL = {Nucleic Acids Research},
VOLUME = {21},
NUMBER = {25},
PAGES = {6028--6037},
ABSTRACT = {The results of this theoretical study combining sequence analysis and minimization with integral equation liquid structural methods indicate that the local sequence context of a T-G wobble mismatch influences the local conformation of the helix, and that conformational alterations are correlated with mutational activity. Studies on the mismatch in four different 5' and 3' neighbor contexts indicate that the nature of the 5' base to the thymine of the mispair is probably the single most critical factor in determining the structural features that facilitate or discourage mutations. When cytosine is the 5' neighbor, the helix adopts a mostly BII conformation, whereas a 5' guanine preserves the canonical BI. Structures that vary little from the BI structure on the incorporation of the mismatch have sequences that correspond to lower rates of transition, whereas those with mostly BII conformations, have sequences with high mutation rates. Subtle variations in stacking patterns around the mismatch precipitate a structural Domino-effect, with a variety of changes in conformation. The helix opens at the mismatch with increased roll angle and propeller twist, causing the thymine to migrate into the major groove and the guanine into the minor groove, exposing the heteroatomic groups to the solvent in the major and minor grooves, respectively, and allowing for some unusual hydrogen bonds. These alterations show a tentative correlation with mutation rates, implying that stacking and structure around the mismatch are important features in the discrimination by proofreading activities of canonical W-C and wobble mismatch base pairs during replication-repair. Variations in the C1'-C1' distances, high propeller twists, changes in the electrostatic complementarity leading to unusual hydrogen bonding patterns probably all correlate with detectability. },
YEAR = {1993}
}
@ARTICLE{lounnas94,
AUTHOR = {V. Lounnas and B. M. Pettitt},
TITLE = {A connected cluster of hydration around myoglobin -
correlation between molecular-dynamics simulations and experiment},
JOURNAL = {Proteins-structure Function Genetics},
VOLUME = 18,
PAGES = {133--147},
YEAR = 1994,
ABSTRACT = {An analysis of a molecular dynamics simulation of
metmyoglobin in an explicit solvent environment of 3,128 water
molecules has been performed. Both statics and dynamics of the
protein-solvent interface are addressed in a comparison with
experiment. Three-dimensional density distributions, temperature
factors, and occupancy weights are computed for the solvent by
using the trajectory coordinates. Analysis of the hydration leads
to the localization of more than 500 hydration sites distributed
into multiple layers of solvation located between 2.6 and 6.8
Angstrom from the atomic protein surface. After locating the local
solvent density maxima or hydration sites we conclude that water
molecules of hydration positions and hydration sites are distinct
concepts. Both global and detailed properties of the hydration
cluster around myoglobin are compared with recent neutron and
X-ray data on myoglobin. Questions arising from differences
between X-ray and neutron data concerning the locations of the
protein-bound water are investigated. Analysis of water site
differences found from X-ray and neutron experiments compared with
our simulation shows that the simulation gives a way to unify the
hydration picture given by the two experiments. (C) 1994
Wiley-Liss, Inc.}
}
@ARTICLE{lounnas94b,
AUTHOR = {V. Lounnas and B. M. Pettitt},
TITLE = {Distribution function implied dynamics versus residence
times and correlations - solvation shells of myoglobin},
JOURNAL = {Proteins-structure Function Genetics},
VOLUME = 18,
PAGES = {148--160},
YEAR = 1994,
ABSTRACT = {The dynamics of water at the protein-solvent interface is
investigated through the analysis of a molecular dynamics
simulation of metmyoglobin in explicit aqueous environment.
Distribution implied dynamics, harmonic and quasiharmonic, are
compared with the simulated macroscopic dynamics. The distinction
between distinguishable solvent molecules and hydration sites
developed in the previous paper is used. The simulated hydration
region within 7 Angstrom from the protein surface is analyzed
using a set of 551 hydration sites characterized by occupancy
weights and temperature B-factors determined from the simulation
trajectory. The precision of the isotropic harmonic and
anisotropic harmonic models for the description of proximal
solvent fluctuations is examined. Residence times and dipole
reorientation times of water around the protein surface are
compared with NMR and ESR results. A correlation between
diffraction experiment quantities such as the occupancy weights
and temperature factors and the residence and correlation times
resulting from magnetic resonance experiments is found via
comparison with simulation. (C) 1994 Wiley-Liss, Inc.}
}
@ARTICLE{lounnas94c,
AUTHOR = {V. Lounnas and B. M. Pettitt and G. N. Phillips},
TITLE = {A global-model of the protein-solvent interface},
JOURNAL = {Biophys. J.},
VOLUME = 66,
PAGES = {601--614},
YEAR = 1994,
ABSTRACT = {The solvent structure and dynamics around myoglobin is
investigated at the microscopic level of detail by computer
simulation. We analyze a molecular dynamics trajectory in terms of
solvent mobility and probability distribution. Local events,
occurring in the protein-solvent interfacial region, which are
often masked by other approaches are thus revealed. Specifically,
the local solvent mobility is greatly enhanced for certain
locations at the protein surface and in its interior. In addition,
a strong correlation between the solvent mobility and density
emerges on both global and local scales. We propose a simple model
where the solvent distribution measured perpendicularly to the
protein surface is utilized to reconstruct the simulated network
of hydration within 6 Angstrom from the protein surface with a
relative error of only 17%. The global precision of this solvation
model matches results obtained with more complicated models
usually used in refinement procedures in x-ray and neutron
experiments but with far fewer parameters. The dramatically
improved correspondence between observed and calculated x-ray
intensities at low resolution relative to other methods both
confirms the validity of the approach used in the MD (molecular
dynamics) simulations and allows the results of this study to be
implemented in solvent studies on real systems.}
}
@ARTICLE{burgess94,
AUTHOR = {K. Burgess and K. K. Ho and B. M. Pettitt},
TITLE = {A gamma-turn structure induced by
2s,3s-2,3-methanomethionine},
JOURNAL = {J. Am. Chem. Soc.},
VOLUME = 116,
PAGES = {799--800},
YEAR = 1994
}
@ARTICLE{perkyns94,
AUTHOR = {J. Perkyns and B. M. Pettitt},
TITLE = {On the solubility of aqueous-electrolytes},
JOURNAL = {J. Phys. Chem.},
VOLUME = 98,
PAGES = {5147--5151},
YEAR = 1994,
ABSTRACT = {The existence of a high-density phase separation for
molecular and continuum solvent models of ion-water solutions are
demonstrated using the DRISM/HNC theory. The molecular lever
effects which influence solubility and the inability of continuum
models to exhibit some of these effects are discussed. The general
trends in experimental alkali halide solubilities are found to be
consistent with the present model calculations. The dependence of
the phase separation on ion size is found to be primarily entropic
in nature.}
}
@ARTICLE{ji94,
AUTHOR = {J. Ji and B. M. Pettitt},
TITLE = {Phase-transitions of water at constant excess
chemical-potential - an application of grand molecular-dynamics},
JOURNAL = {Mol. Phys.},
VOLUME = 82,
PAGES = {67--83},
YEAR = 1994,
ABSTRACT = {The grand molecular dynamics (GMD) method has been extended
and applied to examine the chemical potential and temperature
dependence of a three-site water model in dense phase. The study
demonstrates the utility of GMD in the study of phase transitions.
Cuts through the phase diagram of water in terms of temperature,
as well as excess chemical potential, are obtained. The density
maximum of water just above freezing is well reproduced.
High-pressure glass forms of solid ice are also examined.}
}
@ARTICLE{cannon94,
AUTHOR = {W. R. Cannon and B. M. Pettitt and J. A. Mccammon},
TITLE = {Sulfate anion in water - model structural, thermodynamic,
and dynamic properties},
JOURNAL = {J. Phys. Chem.},
VOLUME = 98,
PAGES = {6225--6230},
YEAR = 1994,
ABSTRACT = {Binding energies, intermolecular distances, and partial
charges from ab initio studies of SO42- + H2O were used to develop
a molecular mechanics model for SO42- in water. Structural,
dynamic, and thermodynamic properties for the resulting model used
in condensed-phase simulations agree well with experimental
estimates. Thirteen waters are found to be present in the first
solvation shell, and the residence time of these waters has been
calculated to be 23 ps. The model anion has a free energy of
solvation relative to xenon of -275 kcal mol(-1), which compares
well with the experimental estimate of -266 kcal mol(-1).}
}
@ARTICLE{perkyns94b,
AUTHOR = {J. Perkyns and B. M. Pettitt},
TITLE = {Integral-equation approaches to structure and
thermodynamics of aqueous salt-solutions},
JOURNAL = {Biophys. Chem.},
VOLUME = 51,
PAGES = {129--146},
YEAR = 1994,
ABSTRACT = {Results for free energy, entropy, enthalpy and internal
energy of solvation for monovalent ions in water have been studied
by comparing DRISM theory results to those of RISM and ARISM
theories. The greatly improved dielectric behavior in the DRISM
case enabled the examination of realistically modeled salts at
finite concentrations. The link between solvent structure and the
entropy of solvent co-spheres was examined. Finally comparison
with the Born free energy equation shows its virtues and flaws due
to ignoring cavity formation and asymmetric solvation terms which
together always contribute significantly to the free energy of
hydration of ions.}
}
@ARTICLE{weerasinghe94,
AUTHOR = {S. Weerasinghe and B. M. Pettitt},
TITLE = {Ideal chemical-potential contribution in molecular-dynamics
simulations of the grand-canonical ensemble},
JOURNAL = {Mol. Phys.},
VOLUME = 82,
PAGES = {897--912},
YEAR = 1994,
ABSTRACT = {An extended system Hamiltonian for the grand canonical
ensemble that includes the number dependence of the ideal chemical
potential is investigated. Use of the ideal contribution
explicitly in the equations of motion provides simpler and more
stable equations of motion than previous grand molecular dynamics
methods. We find the equations of motion remain quite stable even
in gaseous conditions where mean field treatments of the ideal
contribution provide a trivial result. The equations of motion are
solved in real variable space as opposed to using virtual
variables. Application of this simulation method with a
Lennard-Jones fluid in the gas, fluid and solid phases is
demonstrated.}
}
@ARTICLE{valdeavella94,
AUTHOR = {C. V. Valdeavella and J. S. Perkyns and B. M. Pettitt},
TITLE = {Investigations into the common ion effect},
JOURNAL = {J. Chem. Phys.},
VOLUME = 101,
PAGES = {5093--5109},
YEAR = 1994,
ABSTRACT = {The molecular origins of the common ion effect and the
salting out of nonpolar molecules from aqueous solutions are
investigated. Thermodynamic stability criteria for a common ion
mixture in a polar solvent are derived. Kirkwood-Buff statistical
thermodynamics is used to make the connection with the microscopic
pair correlation functions. The observed sensitivity of the
compositional stability with respect to ionic strength indicates
that a demixing transition is the primary cause of the instability
for the common ion effect for our model Lennard-Jones plus Coulomb
Hamiltonian.}
}
@ARTICLE{smith94,
AUTHOR = {P. E. Smith and B. M. Pettitt},
TITLE = {Modeling solvent in biomolecular systems},
JOURNAL = {J. Phys. Chem.},
VOLUME = 98,
PAGES = {9700--9711},
YEAR = 1994,
ABSTRACT = {Currently applied models for the treatment of solvent in
biomolecular systems are reviewed. Solvent models ranging from
purely continuum to quantum mechanical in nature are discussed,
together with their ranges of validity and the approximations
inherent to the various methods. As a potential energy surface
interpretation of thermodynamics and kinetics is a useful and
familiar tool to the physical chemist; we use the generalization
to free energy surfaces (or potentials of mean force) to unify the
discussion where possible. An example of how theory and
simulations can aid in the interpretation of experimental data for
the solvation of myoglobin is presented. It is argued that the
advent of better theories and increasingly faster computers will
provide the opportunity for the application of more rigorous
solvent models for the study of complex biomolecular solutions
with increasingly more accurate results.}
}
@ARTICLE{mertz94,
AUTHOR = {J. E. Mertz and B. M. Pettitt},
TITLE = {Molecular-dynamics at a constant ph},
JOURNAL = {Int. J. Supercomputer Applications High Performance
Computing},
VOLUME = 8,
PAGES = {47--53},
YEAR = 1994,
ABSTRACT = {The dynamic equilibrium that exists in a chemically
reacting system can be simulated using classical mechanics if the
appropriate statistical mechanical ensemble is chosen. This paper
describes a general method that makes it possible to simulate this
equilibrium in a simple chemical reaction through the use of a
recently developed grand canonical molecular dynamics method.
After a brief description of the method, an example calculation is
performed that simulates the acid-base equilibrium between acetic
acid and water. The computational demands of this application are
discussed along with a description of a new MPP algorithmic
approach to this application.}
}
@ARTICLE{burgess95,
AUTHOR = {K. Burgess and K. K. Ho and B. M. Pettitt},
TITLE = {Conformational effects of substituting methionine with
(2s,3s)-2,3-methanomethionine in phe-met-arg-phe-nh2},
JOURNAL = {J. Am. Chem. Soc.},
VOLUME = 117,
PAGES = {54--65},
YEAR = 1995,
ABSTRACT = {The conformational influences of
(2S,3S)-2,3-methanomethionine ((2S,3S)-cyclo-Met or
(2S,3S)-cyclo-M) were studied to ascertain possible effects of
substituting such constrained amino acids into small peptides. The
peptide chosen for study was the anti-opiate Phe-Met-Arg-Phe-NH2
(FMRF-NH2 using the one-letter code). Consequently, FMRF-NH2 and
F((2S,3S)-cyclo-M)RF-NH2 were prepared, and studied by NMR in
DMSO. Protons of the parent peptide had no anomalous chemical
shifts, no shallow temperature coefficients for variations of NH
chemical shifts with temperature, and no interresidue ROE
cross-peaks except for the sequential backbone signals. These
results were as expected for a random coil conformation.
Conversely, F((2S,3S)-cyclo-M)RF-NH2 gave NMR spectra with
indications of a bias toward defined secondary structures in
solution. Computer-assisted molecular simulations were carried out
to visualize these conformational biases. Thus, parameters for the
2,3-methanoamino acid were developed using literature values for
bond vectors from crystallography, and CHARMM defaults. The
validity of these parameters was accessed from Ramachandran plots
for derivatives of the type Ac-(cyclo-M)-NHMe. These parameters
were then used for a comparative quenched molecular dynamics (QMD)
study of FMRF-NH2 and F((2S,3S)-cyclo-M)RF-NH2, without invoking
constraints from the NMR data. Data (presented as phi, psi dot
plots) from the downloaded simulated conformations at 1000 K, and
for the energy-minimized forms of these conformations, could be
easily rationalized on the basis of reasonable conformational
biases about the amino acid residues. The rigidly oriented side
chains of the (E)-cyclo-Met derivative (wherein The alpha-amino
group and the side chain are trans with respect to the
cyclopropane ring) had a more severe effect on the allowable psi
values than on the psi torsions. The lowest energy structures
generated in the dynamics run after minimization were grouped into
families to give representations of related conformers. Finally,
the results from the NMR and QMD studies were compared. For
F((2S,3S)-cyclo-M)RF-NH2 a good correlation was found, indicating
a bias toward a gamma-turn structure in solution. We predict that
(E)-cyclo-Met residues in larger peptides could induce formation
of turn or 3(10)-helical structures.}
}
@ARTICLE{stenland95,
AUTHOR = {C. Stenland and B. M. Pettitt},
TITLE = {Binary-solution critical opalescence - mole fraction versus
temperature phase-diagram},
JOURNAL = {J. Chem. Education},
VOLUME = 72,
PAGES = {560--564},
YEAR = 1995
}
@ARTICLE{mccammon94,
AUTHOR = {J. A. Mccammon and B. M. Pettitt and L. R. Scott},
TITLE = {Ordinary differential-equations of molecular-dynamics},
JOURNAL = {Computers & Mathematics With Applications},
VOLUME = 28,
PAGES = {319--326},
YEAR = 1994,
ABSTRACT = {The ordinary differential equations of Newtonian dynamics
are used in atomic simulations with the method of molecular
dynamics. The basic issues are surveyed and standard algorithms
are described. Several algorithmic variants are discussed. Some
advanced ideas relating to parallel computation are considered.}
}
@ARTICLE{perkyns95,
AUTHOR = {J. S. Perkyns and B. M. Pettitt},
TITLE = {Peptide conformations are restricted by solution stability},
JOURNAL = {J. Phys. Chem.},
VOLUME = 99,
PAGES = {1--2},
YEAR = 1995,
ABSTRACT = {Thermodynamic stability and Statistical mechanical theory
are applied to a model of a zwitterionic tripeptide of sequence
Gly-Ala-Gly in high-concentration NaCl solution. It is found that
many peptide conformations cannot exist in equilibrium with the
salt-water solvent as a single liquid phase. This suggests a
single explanation for salting proteins into and out of solution,
unique biologically active protein structures, and small energy
differences between denatured and folded states, while also
implying a mechanism for the resolution to the Levinthal paradox.}
}
@INPROCEEDINGS{haacke95,
AUTHOR = {Robert Haacke and B. Montgomery Pettitt},
EDITOR = {},
TITLE = {The Scaling of Molecular Dynamics on the KSR-1},
BOOKTITLE = {I.E.E.E. Proceedings},
YEAR = {1995},
ORGANIZATION = {},
PUBLISHER = {},
ADDRESS = {},
VOLUME = {5},
NUMBER = {},
SERIES = {},
PAGES = {142-152},
KEY = {}
}
@ARTICLE{phillips95,
AUTHOR = {G. N. Phillips and B. M. Pettitt},
TITLE = {Structure and dynamics of the water around myoglobin},
JOURNAL = {Protein Science},
VOLUME = 4,
PAGES = {149--158},
YEAR = 1995,
ABSTRACT = {The interplay between simulations at various levels of
hydration and experimental observables has led to a picture of the
role of solvent in thermodynamics and dynamics of protein systems.
One of the most studied protein-solvent systems is myoglobin,
which serves as a paradigm for the development of
structure-function relationships in many biophysical studies. We
review here some aspects of the solvation of myoglobin and the
resulting implications. In particular, recent theoretical and
simulation studies unify much of the diverse set of experimental
results on water near proteins.}
}
@ARTICLE{weerasinghe95,
AUTHOR = {S. Weerasinghe and P. E. Smith and V. Mohan and Y. K. Cheng
and B. M. Pettitt},
TITLE = {Nanosecond dynamics and structure of a model dna
triple-helix in saltwater solution},
JOURNAL = {J. Am. Chem. Soc.},
VOLUME = 117,
PAGES = {2147--2158},
YEAR = 1995,
ABSTRACT = {The structure and stability of a DNA triple helix was
examined by molecular dynamics (MD) simulation using an all-atom
force field. A 1.3 ns simulation was performed on a d(CG . G)(7)
triple helix in a 1 M saltwater solution. The Ewald method was
used to calculate the electrostatic interactions of the system.
The behavior of the DNA in the saltwater solution was determined
by examining the structure, energetics, and mobility of water and
ions in the system. The simulation results for the helical
parameters support the validity of a model-built triplex-DNA
structure. A low root mean square deviation of the dynamic
structure from the initial structure demonstrates the stability of
the tripler in the salt solution. The sugar pseudorotation, the
backbone conformations, and the average helical parameters suggest
that the conformation of strands I and III is strictly neither
A-form nor B-form, whereas the conformation of strand II remains
near the A-form. A higher mobility of both the cytosine strand and
the triplex-forming guanine strand and also a longer residence
time of water molecules in the spine of hydration were observed
and are consistent with available NMR results.}
}
@ARTICLE{chen95,
AUTHOR = {Z. M. Chen and B. M. Pettitt},
TITLE = {Nonisotropic solution of an oz equation - matrix-methods
for integral-equations},
JOURNAL = {Computer Phys. Comm.},
VOLUME = 85,
PAGES = {239--250},
YEAR = 1995,
ABSTRACT = {Integral equations of the Ornstein-Zernike (OZ) type have
been useful constructs in the theory of liquids for nearly a
century. Only a limited number of model systems yield an analytic
solution; the rest must be solved numerically. For anisotropic
systems the numerical problems are heightened by the coupling of
more unknowns and equations. A matrix method for solving the full
anisotropic OZ integral equation is presented. The method is
compared in the isotropic limit with traditional approaches.
Examples are given for a 1-D fluid with a corrugated (periodic)
external potential. The full two point correlation functions for
both isotropic and anisotropic systems are given and discussed.}
}
@ARTICLE{mitra95,
AUTHOR = {R. Mitra and B. M. Pettitt and R. D. Blake},
TITLE = {Conformational states governing the rates of spontaneous
transition mutations},
JOURNAL = {Biopolymers},
VOLUME = 36,
PAGES = {169--179},
YEAR = 1995,
ABSTRACT = {We report the results of a theoretical study, combining the
results of sequence analysis and integral equation structural
methods for nucleic acids in aqueous solutions, on the effects of
nearest neighbors on the (T . G) mispair in solution, for 12
nearest neighbor contexts. Attempts have been made to classify the
structural and energetic effects of the 5' and 3' neighbors with
respect to the observed spontaneous mutation rates in vertebrates.
It is found that 5' nearest neighbor is probably the mast critical
structural factor in facilitating or discouraging mutations. Local
conformational states correlate with discrimination of bases to be
excised in mispairs. Our study confirms the role of the
flexibility of the DNA molecule in governing the rates of
spontaneous mutations. (C) 1995 John Wiley & Sons, Inc.}
}
@ARTICLE{cheng95,
AUTHOR = {Y. K. Cheng and B. M. Pettitt},
TITLE = {Solvent effects on model d(cg.g)(7) and d(ta.t)(7) dna
triple helices},
JOURNAL = {Biopolymers},
VOLUME = 35,
PAGES = {457--473},
YEAR = 1995,
ABSTRACT = {Using free energy molecular mechanics, we find that the
molecular effects of solvent are critical in determining relative
stabilities in DNA triple helices or triplexes. The continuum
solvent model is unable to differentiate the thermodynamics
reflecting the basic solvation differences around the occupied
major groove in triplexes. In order to avoid the local minimum
problem, which is a major limitation of any modeling study, we
started our computations with multiple structures rather than
relying on the optimization of a single reference structure. By
constructing triplex models with different initial helical twists,
helical rises, and sugar-pucker permutations, we explore the
potential surface and the structural preference with respect to
these variations. We find that in order to accommodate a third
strand in triplex formation, the backbone geometry of the B-DNA
duplex target has to be adjusted into A-DNA-like form with a deep
major groove. This is achieved by concerted adjustment in torsions
beta, epsilon, and zeta around the phosphate groups. However, the
sugar pucker displays a more rich variation, resulting in
conformations not usually associated with the canonical duplex
structures. (C) 1995 John Wiley & Sons, Inc.}
}
@ARTICLE{clarage95,
AUTHOR = {J. B. Clarage and T. Romo and B. K. Andrews and B. M.
Pettitt and G. N. Phillips},
TITLE = {A sampling problem in molecular-dynamics simulations of
macromolecules},
JOURNAL = {Proc. National Acad. Sciences United States Am.},
VOLUME = 92,
PAGES = {3288--3292},
YEAR = 1995,
ABSTRACT = {Correlations in low-frequency atomic displacements
predicted by molecular dynamics simulations on the order of 1 ns
are undersampled for the time scales currently accessible by the
technique. This is shown with three different representations of
the fluctuations in a macromolecule: the reciprocal space of
crystallography using diffuse x-ray scattering data, real
three-dimensional Cartesian space using covariance matrices of the
atomic displacements, and the 3N-dimensional configuration space
of the protein using dimensionally reduced projections to
visualize the extent to which phase space is sampled.}
}
@ARTICLE{smith95,
AUTHOR = {P. E. Smith and B. M. Pettitt},
TITLE = {Efficient ewald electrostatic calculations for large
systems},
JOURNAL = {Computer Phys. Comm.},
VOLUME = 91,
PAGES = {339--344},
YEAR = 1995,
ABSTRACT = {A method is described which improves the efficiency of
Ewald simulations of large condensed phase systems. This is
achieved by partitioning the real space sum into a short and long
range component. The long range component is calculated every time
the pair list is generated and included in subsequent steps using
a multiple time:step algorithm. The corresponding increase in the
effective cutoff distance results in an algorithm which is only
slightly more expensive than a traditional cutoff simulation, but
with fewer artifacts than obtained using a cutoff. The method is
tested on a 1.0M solution of sodium chloride.}
}
@ARTICLE{yang95,
AUTHOR = {L. Q. Yang and S. Weerasinghe and P. E. Smith and B. M.
Pettitt},
TITLE = {Dielectric response of triplex dna in ionic solution from
simulations},
JOURNAL = {Biophys. J.},
VOLUME = 69,
PAGES = {1519--1527},
YEAR = 1995,
ABSTRACT = {We have analyzed a 1.2-ns molecular dynamics simulation of
51 mM d(CG-G), with 21 Na+ counter-ions and 1 M NaCl in water. Via
the dipole fluctuations, the dielectric constant for the DNA is
found to be around 16, whereas that for the bases and sugars
combined is only 3. The dielectric constant for water in this
system is 41, which is much smaller than 71 for pure SPC/E water,
because of the strong restriction imposed on the motion of water
molecules by the DNA and the ions. Also addressed in the present
work are several technical issues related to the calculation of
the dipole moment of an ionic solution from molecular dynamics
simulations using periodic boundary conditions.}
}
@ARTICLE{valdeavella95,
AUTHOR = {C. V. Valdeavella and H. D. Blatt and B. M. Pettitt},
TITLE = {Simulations of conformers of tuftsin and a cyclic tuftsin
analog},
JOURNAL = {Int. J. Peptide Protein Research},
VOLUME = 46,
PAGES = {372--380},
YEAR = 1995,
ABSTRACT = {The conformational properties of the configurational
isomers of tuftsin, a linear tetrapeptide with the sequence
Thr-Lys-Pro-Arg, were investigated with six 1 ns molecular
dynamics simulations in explicit water and in a 1.0 M NaCl
solution. The average conformation of the cis isomer is a type VI
beta-turn. Our results indicate that water-peptide hydrogen
bonding, in addition to intramolecular hydrogen bonds, stabilizes
the cis conformer, The trans isomer is neither a beta- nor a
gamma-turn. Results are compared with parallel studies on a cyclic
analog of tuftsin, cyclo (Thr-Lys-Pro-Arg-Gly). The addition of
salt does not influence the backbone conformation of the peptide.
Differences between the structures are confined to the side-chain
orientations of the Lys and Arg residues. (C) Munksgaard 1995.}
}
@ARTICLE{yang96,
AUTHOR = {L. Q. Yang and B. M. Pettitt},
TITLE = {B to {A} transition of {DNA} on the nanosecond time scale},
JOURNAL = {J. Phys. Chem.},
VOLUME = 100,
PAGES = {2564--2566},
YEAR = 1996,
ABSTRACT = {A 3.5-ns atomic-level computer simulation of a DNA solution
was performed. We found that a dodecamer of DNA, which contains
the recognition site for Eco RI endonuclease, transforms from
B-form to A-form in 0.45 M salt water. This supports an earlier
proposal on the A-DNA binding site for transcription factor IIIA.}
}
@ARTICLE{perkyns96,
AUTHOR = {J. S. Perkyns and Y. Y. Wang and B. M. Pettitt},
TITLE = {Salting in peptides, conformationally dependent
solubilities and phase behavior of a tripeptide zwitterion in
electrolyte solution},
JOURNAL = {J. Am. Chem. Soc.},
VOLUME = 118,
PAGES = {1164--1172},
YEAR = 1996,
ABSTRACT = {The dielectrically consistent interaction site model theory
is applied to a model system consisting of a zwitterion tripeptide
of sequence Gly-Ala-Gly at infinite dilution in a solvent mixture
of water and sodium chloride with only the central phi,psi,
dihedrals for conformational degrees of freedom. The peptide is
found to be salted into solution by the cosolvent, with its
solubility depending strongly on conformation of the central
phi,psi pair. The distribution of cosolvent relative to the bulk
solvent mixture is examined and relatively little specific
association is found. Instead, the ionic concentration around the
peptide is increased, especially near the phase boundary, and the
increased concentration extends up to eight solvent diameters into
the bulk. The consequences of such an ionic distribution on
thermodynamic measures of association are discussed. Similarities
between this model system and the unusual solubility behavior of
beta-lactoglobulin found in experiments are shown. The molecular
distributions calculated are found to be consistent with a
separation of the solvent mixture into two non-miscible phases,
one of which contains the solute and has a higher cosolvent
concentration than the other. Since turbid solutions have been
observed in the beta-lactoglobulin system, it is suggested that a
separation into two liquid phases could be common to both systems.}
}
@ARTICLE{perkyns96b,
AUTHOR = {J. Perkyns and B. M. Pettitt},
TITLE = {Dependence of hydration free energy on solute size},
JOURNAL = {J. Phys. Chem.},
VOLUME = 100,
PAGES = {1323--1329},
YEAR = 1996,
ABSTRACT = {The dielectrically consistent reference interaction site
model theory (DRISM) was used to calculate excess chemical
potentials of solvation for the immersion of a nonpolar solute
molecule (Lennard-Jones sphere) in a molecular model of water in a
wide variety of state conditions. The chemical potential was found
to be predominantly entropic, In all cases the chemical potential
was found to consist almost entirely of a solute surface area and
a solute volume term. Both these terms were significant over a
range of solute sizes and pressure/temperature states. It was
concluded that the volume-dependent term must include
contributions in addition to that from the system pressure. An
exactly solvable lattice model of solvation was also investigated,
and the model conditions for which the chemical potential becomes
predominantly entropic were determined. One situation was shown
where a volume-dependent entropic term in the chemical potential,
other than pressure, arises.}
}
@ARTICLE{weerasinghe95b,
AUTHOR = {S. Weerasinghe and P. E. Smith and B. M. Pettitt},
TITLE = {Structure and stability of a model pyrimidine-purine-purine
{DNA} triple helix with a {GC} center dot {T} mismatch by
simulation},
JOURNAL = {Biochem.},
VOLUME = 34,
PAGES = {16269--16278},
YEAR = 1995,
ABSTRACT = {A 1.5 ns long molecular dynamics simulation was conducted
to compare the structure and stability of model DNA tripler in
saline solution with that found from experiments. The model DNA
was an antiparallel py . pu . pu (CG . G) 7-mer structure which
contained a GC . T mismatch triplet at the middle of the sequence.
The local conformation of the mismatch tripler and the effects of
this triplet on the global helical structure suggest that the GC .
T triplet forms stable hydrogen bonds and shows distortions from
an in-plane alignment. The overall rms deviation of the tripler is
similar to one without a mismatch, although the thymine base in
the mismatch triplet shows significantly higher mobility. A high
coordination probability for water between the G and T bases in
the mismatch tripler was observed to have an effect on the
stability of non-hydrogen-bonded base pairs. Average helical
parameters, sugar pucker, and backbone dihedral angles indicate
that the CG . G triplets on the 3' side of the mismatch triplet
possess different structural and dynamical properties than that of
the 5' side. These observations are consistent with recently
available experimental results and provide an interpretation of
the observed experimental structure. They also suggest that
inclusion of explicit water molecules is necessary in order to
understand and predict the interaction between the third strand
and duplex DNA.}
}
@ARTICLE{nishioka96,
AUTHOR = {K. Nishioka and J. McMurray and F. AlObeidi and B. M.
Pettitt},
TITLE = {Tuftsin and {Tuftsin} analogs: {Biology,} synthesis and
design theory},
JOURNAL = {Current Medicinal Chem.},
VOLUME = 3,
PAGES = {153--166},
YEAR = 1996,
ABSTRACT = {We have reviewed aspects of the medicinal chemistry of
Tuftsin. Biochemical and clinical aspects including physioogy and
assays are briefly accounted for. Structure-activity relationships
found in the literature provide a link between the
synthetic/design strategies and the biological response, Directed
rational design and synthetic techniques are reviewed for both
tuftsin and its analogs.}
}
@ARTICLE{makarov98,
AUTHOR = {Makarov, V. A. and Andrews, B. A. and Pettitt, B. Montgomery },
TITLE = {Comparison of Protein Hydration Elucidated by Molecular Dynamics
Simulations and X-ray Crystallography },
JOURNAL = {},
VOLUME = {},
NUMBER = {},
PAGES = {},
ABSTRACT = { },
YEAR = {1998}
}
@ARTICLE{yang96b,
AUTHOR = {L. Q. Yang and C. V. Valdeavella and H. D. Blatt and B. M.
Pettitt},
TITLE = {Salt effects on peptide conformers: {A} dielectric study of
tuftsin},
JOURNAL = {Biophys. J.},
VOLUME = 71,
PAGES = {3022--3029},
YEAR = 1996,
ABSTRACT = {Four 1-ns molecular dynamics computer simulations of
tuftsin, Thr-Lys-Pro-Arg, are analyzed: (1) cis tuftsin in water,
(2) trans tuftsin in water, (3) cis tuftsin in 1 M NaCl, and (4)
trans tuftsin in 1 M NaCl. Independently of the salt
concentration, the trans conformer has a higher dielectric
constant than the cis conformer because the former exhibits a more
widely distributed charge distribution in space. Independently of
the peptide conformation, the presence of salt reduces the
dielectric constants of both the peptide and the solvating water
molecules because ions, on binding, restrict the motion of other
atoms. In contrast to the dielectric constants, neither the
peptide conformation nor the salt concentration shows a
significant influence on the dielectric relaxation time of water
molecules.}
}
@ARTICLE{smith96,
AUTHOR = {P. E. Smith and B. M. Pettitt},
TITLE = {Ewald artifacts in liquid state molecular dynamics
simulations},
JOURNAL = {J. Chem. Phys.},
VOLUME = 105,
PAGES = {4289--4293},
YEAR = 1996,
ABSTRACT = {An investigation into the effects of the anisotropic nature
of the Ewald potential for the treatment of long range
electrostatic interactions in liquid solutions has been performed.
The rotational potential energy surface for two simple charge
distributions, and a small protein, have been studied under
conditions typically implemented in current biomolecular
simulations. A transition between hindered and free rotation is
observed which can be modeled quantitatively for simple charge
distributions. For most systems in aqueous solution, the
transition involves an energy change well below k(B)T. It is
argued that, for solvents with a reasonably high relative
permittivity Ewald artifacts will be small and in many cases may
be safely ignored. (C) 1996 American Institute of Physics.}
}
@ARTICLE{rudnicki97,
AUTHOR = {W. R. Rudnicki and B. M. Pettitt},
TITLE = {Modeling the {DNA-solvent} interface},
JOURNAL = {Biopolymers},
VOLUME = 41,
PAGES = {107--119},
YEAR = 1997,
ABSTRACT = {We extend the technique of using perpendicular distribution
functions to salt solutions around nucleic acids. Both solute
density averaged and nonaveraged reference frames are considered
and compared. Using a previous simulation of DNA in salt water of
over a nanosecond in duration, the aqueous distribution functions
were found to be well converged, whereas the salt perpendicular
distribution functions were less well determined.
Three-dimensional density reconstructions reliably showed the
prominent solvation features with transferable functions. The
number of solute atom types needed for reconstructions of a given
precision was determined in the context of the reference
simulation data set with the goal of achieving a required level of
reconstruction quality. (C) 1997 John Wiley & Sons, Inc.}
}
@ARTICLE{smith97,
AUTHOR = {P. E. Smith and H. D. Blatt and B. M. Pettitt},
TITLE = {A simple two-dimensional representation for the common
secondary structural elements of polypeptides and proteins},
JOURNAL = {Proteins-structure Function Genetics},
VOLUME = 27,
PAGES = {227--234},
YEAR = 1997,
ABSTRACT = {A simple method is presented for projecting the
conformation of extended secondary structure elements of peptides
and proteins that extend over four C-alpha atoms onto a simple
two-dimensional surface, A new set of two degrees of freedom is
defined, a pseudo-dihedral involving four sequential C-alpha
atoms, as well as the triple scalar product for the vectors
describing the orientation of the three intervening peptide
groups, The method provides a reduction in dimensionality, from
the usual combination of multiple phi,psi pairs to a single pair,
yielding valuable information concerning the structure and
dynamics of these important elements. The new two dimensional
surface is explored by reference to 63 selected protein crystal
structures together with a comparison of model built peptides
representing the common secondary structural elements, Dynamical
aspects on this new surface are examined using a molecular
dynamics trajectory of Basic Pancreatic Trypsin Inhibitor. (C)
1997 Wiley-Liss, Inc.}
}
@ARTICLE{valdeavella99,
AUTHOR = {C. V. Valdeavella and H. D. Blatt and L. Q. Yang and B. M.
Pettitt},
TITLE = {Hydration effects on the electrostatic potential around
tuftsin},
JOURNAL = {Biopolymers},
VOLUME = 50,
PAGES = {133--143},
YEAR = 1999,
ABSTRACT = {The electrostatic potential and component dielectric
constants from molecular dynamics (MD) trajectories of tuftsin, a
tetrapeptide with the amino acid sequence Thr-Lys-Pro-Arg in water
and in saline solution are presented. The results obtained from
the analysis of the MD trajectories for the total electrostatic
potential at points on a grid using the Ewald technique are
compared with the solution to the Poisson-Boltzmann (PB) equation.
The latter was solved using several sets of dielectric constant
parameters. The effects of structural averaging on the PB results
were also considered. Solute conformational mobility in
simulations gives rise to an electrostatic potential map around
the solute dominated by the solute monopole (or lowest order
multipole). The derailed spatial variation of the electrostatic
potential on the molecular surface brought about by the compounded
effects of the distribution of water and ions close to the
peptide, solvent mobility, and solute conformational mobility are
not qualitatively reproducible from a reparametrization of the
input solute and solvent dielectric constants to the PB equation
for a single structure or for structurally averaged PB
calculations. Nevertheless, by fitting the PB to the MD
electrostatic potential surfaces with the dielectric constants as
fitting parameters, we found that the values that give the best
fit are the values calculated from the MD trajectories.
Implications of using such field calculations on the design of
tuftsin peptide analogues are discussed. (C) 1999 John Wiley &
Sons, Inc.}
}
@ARTICLE{micu97,
AUTHOR = {A. M. Micu and B. Bagheri and A. V. Ilin and L. R. Scott
and B. M. Pettitt},
TITLE = {Numerical considerations in the computation of the
electrostatic free energy of interaction within the
{Poisson-Boltzmann} theory},
JOURNAL = {J. Computational Phys.},
VOLUME = 136,
PAGES = {263--271},
YEAR = 1997,
ABSTRACT = {We evaluate two different ways of calculating the
contribution of the electrostatic stress to the free energy
integral based on Sharp and Honig's method within the finite
difference nonlinear Poisson-Boltzmann equation method with the
University of Houston Brownian Dynamics program. We show that only
one of these approaches gives consistent results in the limit of
zero ionic concentration for interactions of the order of
magnitude of the hydrogen bond. The results are compared with
results from both the linear Poisson-Boltzmann equation and the
Debye-Huckel theory, for ion concentrations within the limits of
validity of these approximate methods. We demonstrate this by
application to DNA molecules. (C) 1997 Academic Press.}
}
@ARTICLE{smith97b,
AUTHOR = {P. E. Smith and H. D. Blatt and B. M. Pettitt},
TITLE = {Environmentally dependent conformational preferences of
peptides},
JOURNAL = {J. Am. Chem. Soc.},
VOLUME = 119,
PAGES = {8714--8715},
YEAR = 1997
}
@ARTICLE{smith97c,
AUTHOR = {P. E. Smith and H. D. Blatt and B. M. Pettitt},
TITLE = {On the presence of rotational {Ewald} artifacts in the
equilibrium and dynamical properties of a zwitterionic
tetrapeptide in aqueous solution},
JOURNAL = {J. Phys. Chem. B},
VOLUME = 101,
PAGES = {3886--3890},
YEAR = 1997,
ABSTRACT = {The presence of Ewald artifacts in a molecular dynamics
simulation of a zwitterionic tetrapeptide in aqueous solution has
been investigated. Both equilibrium and dynamical aspects of the
rotational behavior of the peptide were examined. The equilibrium
distribution of rotational states obtained from a 10 ns simulation
were consistent, within statistical errors, with a random
distribution free from Ewald artifacts. The rotational dynamics of
the peptide was observed to obey simple Debye diffusion with a
rotational diffusion rate in agreement with that predicted by a
simple rotational diffusion model assuming no substantial
long-lived water hydration shell. These results suggest that
rotational Ewald artifacts will be negligible for small
biomolecular simulations in solvents with high relative
permittivities. The data support the results obtained from a
previous study of simpler model systems.}
}
@ARTICLE{perkyns97,
AUTHOR = {J. Perkyns and B. M. Pettitt},
TITLE = {Computationally useful bridge diagram series for the
structure and thermodynamics of {Lennard-Jones} fluids},
JOURNAL = {Theoretical Chem. Accounts},
VOLUME = 96,
PAGES = {61--70},
YEAR = 1997,
ABSTRACT = {The first two orders of bridge diagrams, those with two and
three field points, have been calculated exactly for the
Lennard-Jones fluid for several isotherms. The method of
calculation was one of expansion in Legendre polynomials, and the
dependence of the method on the number of polynomials needed for
accurate results was investigated. Thermodynamic and structural
properties of the Lennard-Jones fluid calculated from integral
equation methods with the inclusion of bridge diagrams were found
to be systematically improved. Two attempts at predicting the
missing bridge diagrams of even higher order were discussed. The
first, which uses the functional form of those diagrams that were
calculated exactly, showed no significant improvement. The second,
a series sum based on the first two orders of calculated diagrams
and motivated by the success of a similar heuristic sum in the
case of hard spheres, was extremely successful. When the series
sum was employed, thermodynamic and structural quantities were
improved to the point where the difference between simulation
results and integral equation results was of the same order as the
error in the simulations themselves.}
}
@ARTICLE{feig97,
AUTHOR = {Feig, Michael and Pettitt, Bernard Montgomery},
TITLE = {Experiment vs Force Fields: DNA Conformation from Molecular Dynamics Simulations},
YEAR = 1997,
JOURNAL = {Journal of Physical Chemistry B},
VOLUME = 101,
NUMBER = 38,
PAGES = {7361--7363},
MONTH = {September}
}
@ARTICLE{blatt97,
AUTHOR = {H. D. Blatt and P. E. Smith and B. M. Pettitt},
TITLE = {Protonation effects on the equilibrium and dynamical
properties of the alanine tetrapeptide},
JOURNAL = {J. Phys. Chem. B},
VOLUME = 101,
PAGES = {7628--7634},
YEAR = 1997,
ABSTRACT = {The effect of terminal group charge on the structure and
dynamics of the alanine tetrapeptide has been investigated using
molecular dynamics simulations. Neutral and positive N-termini,
together with neutral and negative C-termini, were studied,
resulting in a total of four 10 ns simulations with different
terminal group charge combinations. Analysis of these simulations
indicates that the terminal group charge has only a minor effect
on the conformations sampled for the central dihedrals, but a
significant effect on the population distribution of the dihedrals
close to the terminal groups. The conformational distribution at
the C-terminus (psi 3) was also found to depend on the charge at
the N-terminus. Here, the differences result from the formation of
transient ion pairs (salt bridges) in the zwitterion case.
However, equilibrium sampling of these intramolecular ion pairs
was still not fully converged even after 10 ns.}
}
@ARTICLE{lynch97,
AUTHOR = {G. C. Lynch and B. M. Pettitt},
TITLE = {Grand canonical ensemble molecular dynamics simulations:
{Reformulation} of extended system dynamics approaches},
JOURNAL = {J. Chem. Phys.},
VOLUME = 107,
PAGES = {8594--8610},
YEAR = 1997,
ABSTRACT = {The extended system Hamiltonian for carrying out grand
canonical ensemble molecular dynamics simulations is reformulated.
This new Hamiltonian includes a generalized treatment of the
reference state partition function of the total chemical potential
that reproduces the ideal gas behavior and various previous
partitionings of ideal and excess terms. Initial calculations are
performed on a system of Lennard-Jones particles near the triple
point and on liquid water at room temperature. (C) 1997 American
Institute of Physics. [S0021-9606(97)52641-9].}
}
@ARTICLE{feig98,
AUTHOR = {M. Feig and B. M. Pettitt},
TITLE = {Structural equilibrium of {DNA} represented with different
force fields},
JOURNAL = {Biophys. J.},
VOLUME = 75,
PAGES = {134--149},
YEAR = 1998,
ABSTRACT = {We have recently indicated preliminary evidence of
different equilibrium average structures with the CHARMM and AMBER
force fields in explicit solvent molecular dynamics simulations on
the DNA duplex d(C5T5).d(A(5)G(5)) (Feig, M. and B. M. Pettitt,
1997, Experiment vs. Force fields: DNA conformation from molecular
dynamics simulations. J. Phys. Chem. B. 101:7361-7363). This paper
presents a detailed comparison of DNA structure and dynamics for
both force fields from extended simulation times of 10 ns each.
Average structures display an A-DNA base geometry with the CHARMM
force field and a base geometry that is intermediate between A-
and B-DNA with the AMBER force field. The backbone assumes B form
on both strands with the AMBER force field, while the CHARMM force
field produces heterogeneous structures with the purine strand in
A form and the pyrimidine strand in dynamical equilibrium between
A and B conformations. The results compare well with experimental
data for the cytosine/guanine part but fail to fully reproduce an
overall B conformation in the thymine/adenine tract expected from
crystallographic data, particularly with the CHARMM force field.
Fluctuations between A and B conformations are observed on the
nanosecond time scale in both simulations, particularly with the
AMBER force field. Different dynamical behavior during the first 4
ns indicates that convergence times of several nanoseconds are
necessary to fully establish a dynamical equilibrium in all
structural quantities on the time scale of the simulations
presented here.}
}
@ARTICLE{swint-kruse98,
AUTHOR = {L. Swint-Kruse and K. S. Matthews and P. E. Smith and B. M.
Pettitt},
TITLE = {Comparison of simulated and experimentally determined
dynamics for a variant of the {LacI} {DNA-binding} domain, Nlac-P},
JOURNAL = {Biophys. J.},
VOLUME = 74,
PAGES = {413--421},
YEAR = 1998,
ABSTRACT = {Recent advances in the experimentally determined structures
and dynamics of the domains within Lad provide a rare context for
evaluating dynamics calculations. A 1500-ps trajectory was
simulated for a variant of the Lad DNA-binding domain, which
consists of the first three helices in Lad and the hinge helix of
the homologous PurR. Order parameters derived from dynamics
simulations are compared to those obtained for the Lad DNA-binding
domain with N-15 relaxation NMR spectroscopy (Slijper et at.,
1997. Biochemistry. 36:249-254). The MD simulations suggest that
the unstructured loop between helices II and III does not exist in
a discrete state under the conditions of no salt and neutral pH,
but occupies a continuum of states between the DNA-bound and free
structures. Simulations also indicate that the unstructured region
between helix ill and the hinge helix is very mobile, rendering
motions of the hinge helix essentially independent of the rest of
the protein. Finally, the a-helical hydrogen bonds in the hinge
helix are broken after 1250 ps, perhaps as a prelude to helix
unfolding.}
}
@ARTICLE{al-obeidi98,
AUTHOR = {F. Al-Obeidi and S. D. O'Connor and C. Job and V. J. Hruby
and B. M. Pettitt},
TITLE = {NMR and quenched molecular dynamics studies of superpotent
linear and cyclic alpha-melanotropins},
JOURNAL = {J. Peptide Research},
VOLUME = 51,
PAGES = {420--431},
YEAR = 1998,
ENTRYDATE = {2006/04/28},
ABSTRACT = {Conformational searching, computer simulations, synthesis,
and NMR are used on a variety of alpha melanocyte-stimulating
hormone (alpha-MSH) analogues to understand the physical
characteristics required for biological potency. Peptides
I(Ac-[Nle(4),Asp(5),D-Phe(7),Lys(10)]alpha-MSH(4-10)-NH2),II(Ac-c[Nle(4)
,Asp(5),D-Phe(7),Lys(10)]alpha-MSH(4-10)-NH2) and III
(Ac-[Nle(4),Asp(5),D-Phe(7),Dap(10)]alpha-MSH(4-10)-NH2 all show
very similar conformational properties (backbone and side-chain
torsional angles), and all display high biological potencies. The
modeling results for these compounds are supported by the NMR
data. Peptide IV
(Ac-c[Nle(4),Asp(5),D-Phe(7),Dap(10)]alpha-MSH(4-10) appears to
have a markedly different conformation and has decreased
biological potency.}
}
@ARTICLE{makarov98b,
AUTHOR = {V. A. Makarov and B. K. Andrews and B. M. Pettitt},
TITLE = {Reconstructing the protein-water interface},
JOURNAL = {Biopolymers},
VOLUME = 45,
PAGES = {469--478},
YEAR = 1998,
ABSTRACT = {Using molecular dynamics simulations of fully hydrated
proteins and analysis of crystal structures contained in the
Protein Data Bank, we develop a transferable set of perpendicular
radial distribution functions for water molecules around globular
proteins. These universal functions may be used to reconstruct the
unique three-dimensional solvent density distribution around every
individual protein with a modest error. We discuss potential
applications of this solvent treatment in protein x-ray
crystallographic refinements and in theoretical modeling. We also
present a fast, grid-based algorithm for construction of the
perpendicular solvent density distributions. (C) 1998 John Wiley &
Sons, Inc.}
}
@ARTICLE{pettitt98,
AUTHOR = {B. M. Pettitt and V. A. Makarov and B. K. Andrews},
TITLE = {Protein hydration density: theory, simulations and
crystallography},
JOURNAL = {Current Opinion In Struct. Biol.},
VOLUME = 8,
PAGES = {218--221},
YEAR = 1998,
ABSTRACT = {Models of protein hydration are becoming increasingly more
accurate in comparison with experimental data. The recent success
of these models implies that the major features of the solvation
layers are dominated by local correlations and that such
correlations are universal. The excellent agreement between
theoretical and experimental solvent electron density radial
distributions marks a significant success in our ability to
accurately model macromolecular hydration.}
}
@ARTICLE{perkyns98,
AUTHOR = {Pettitt, B. Montgomery and },
TITLE = {\it{Erratum} Computational useful bridge diagram series for the
structure and thermodynamics of Lennard-Jones fluids },
JOURNAL = {Theoretical Chemistry Accounts},
VOLUME = {99},
NUMBER = {},
PAGES = {207-8},
ABSTRACT = { },
KEYWORDS = { },
YEAR = {1998}
}
@ARTICLE{makarov98c,
AUTHOR = {V. A. Makarov and M. Feig and B. K. Andrews and B. M.
Pettitt},
TITLE = {Diffusion of solvent around biomolecular solutes: {A}
molecular dynamics simulation study},
JOURNAL = {Biophys. J.},
VOLUME = 75,
PAGES = {150--158},
YEAR = 1998,
ABSTRACT = {Effects of the macromolecular solute on the translational
mobility of surrounding solvent water, and Na+ and Cl- ions are
investigated by molecular dynamics (MD) simulation. Using MD
trajectories of myoglobin and d(C5T5).d(G(5)A(5)) DNA decamer of
high quality and length, we determine the average diffusion
coefficients for all solvent species as a function of distance
from the closest solute atom. We examine solvent mobility in the
directions parallel and perpendicular to the solute surface and in
proximity to three different classes of solute atoms (oxygens,
nitrogens, and carbons). The nature and the magnitude of the
solute effects on water diffusion appear to be very similar for
protein and DNA decamer. The overall diffusion rate at the
interface is lower than in the bulk. The rate is higher than the
average in the direction parallel to the solute surface, and lower
in the direction normal to the surface, up to 15 Angstrom away
from the solute. The rate is also lower in the solvation shells of
the macromolecules, producing characteristic depressions in the
radial profiles of the diffusion coefficient that can be
correlated with peaks in the corresponding radial distribution
functions. The magnitude of these depressions is small compared to
the overall change in solvent mobility at the interface. Similar
features are observed in the radial profiles of the diffusion
coefficient of sodium and chlorine ions as well.}
}
@ARTICLE{andrews98,
AUTHOR = {B. K. Andrews and T. Romo and J. B. Clarage and B. M.
Pettitt and G. N. Phillips},
TITLE = {Characterizing global substates of myoglobin},
JOURNAL = {Struct.},
VOLUME = 6,
PAGES = {587--594},
YEAR = 1998,
ABSTRACT = {Background: The massive amount of information generated
from current molecular dynamics simulations makes the data
difficult to analyze efficiently. Principal component analysis has
been used for almost a century to detect and characterize data
relationships and to reduce the dimensionality for problems in
many fields. Here, we present an adaptation of principal component
analysis using a partial singular value decomposition (SVD) for
investigating both the localized and global motions of
macromolecules. Results: Configuration space projections from the
SVD analysis of a variety of myoglobin simulations are used to
characterize the dynamics of the protein. This technique reveals
new dynamical motifs, which quantify proposed hierarchical
structures of conformational substates for proteins and provide a
means by which configuration space sampling efficiency may be
probed. The SVD clearly shows that solvent effects facilitate
transitions between global conformational substates for myoglobin
molecular dynamics simulations. Lyapunov exponents calculated from
the configuration space divergence of 15 trajectories agree with
previous predictions for the chaotic behavior of complex protein
systems, Conclusions: Configuration space projections provide
invaluable information about protein motions that would be
extremely difficult to obtain otherwise. While the configuration
space for myoglobin is quite large, it does have structure. Our
analysis of this structure shows that the protein hops between a
number of distinct global conformational states, much like,the
local behavior observed for an individual residue.}
}
@ARTICLE{dyer01,
AUTHOR = {K. M. Dyer and J. S. Perkyns and B. M. Pettitt},
TITLE = {A reexamination of virial coefficients of the
{Lennard-Jones} fluid},
JOURNAL = {Theoretical Chem. Accounts},
VOLUME = 105,
PAGES = {244--251},
YEAR = 2001,
ABSTRACT = {The fourth-order virial coefficients have been calculated
exactly to five decimal places for pure fluids of the
Lennard-Jones potential at many points in the phase diagram. The
calculations were performed through direct evaluation of the
integrals, or diagrams, which make up the density expansion of the
radial distribution function: included were the standard fast
Fourier transform method of evaluating the simply connected
diagrams and the evaluation of the bridge diagram for the fourth
order in density by expansion in Legendre polynomials. The
polynomial-order dependence of the bridge diagram calculation and
the range dependence of the simply connected diagrams of the
fourth order are found to have more significance than was thought
from previous studies, especially in the low-temperature range.
This result was confirmed by direct evaluation of the diagrams
which construct the virial coefficients, as given by Rowlinson,
Barker, and coworkers. This calculation confirmed that numerical
convergence has not been achieved at the precision levels
previously reported in the literature. These differences, though
minor at higher temperatures, can be seen to be more significant
at the lower temperature ranges.}
}
@ARTICLE{feig99,
AUTHOR = {M. Feig and B. M. Pettitt},
TITLE = {Modeling high-resolution hydration patterns in correlation
with {DNA} sequence and conformation},
JOURNAL = {J. Mol. Biol.},
VOLUME = {286},
PAGES = {1075--1095},
YEAR = {1999},
ABSTRACT = {Hydration around the DNA fragment d(C5T5) . (A(5)G(5)) is
presented from two molecular dynamics simulations of 10 and 12 ns
total simulation time. The DNA has been simulated as a flexible
molecule with both the CHARMM and AMBER force fields in explicit
solvent including counterions and 0.8 M additional NaCl salt. From
the previous analysis of the DNA structure B-DNA conformations
were found with the AMBER force-field and A-DNA conformations with
CHARMM parameters. High-resolution hydration patterns are compared
between the two conformations and between C . G and T . A
base-pairs from the homopolymeric parts of the simulated sequence.
Crystallographic results from a statistical analysis of hydration
sites around DNA crystal structures compare very well with the
simulation results. Differences between the crystal sites and our
data are explained by variations in conformation, sequence, and
limitations in the resolution of water sites by crystal
diffraction. Hydration layers are defined from radial distribution
functions and compared with experimental results. Excellent
agreement is found when the measured experimental quantities are
compared with the equivalent distribution of water molecules in
the first hydration shell. The number of water molecules bound to
DNA was found smaller around T . A base-pairs and around A-DNA as
compared to B-DNA. This is partially offset by a larger number of
water molecules in hydrophobic contact with DNA around T . A
base-pairs and around A-DNA. The numbers of water molecules in
minor and major grooves have been correlated with helical roll,
twist, and inclination angles. The data more fully explain the
observed B --> A transition at low humidity. (C) 1999 Academic
Press.}
}
@ARTICLE{prabhu99,
AUTHOR = {N. V. Prabhu and J. S. Perkyns and H. D. Blatt and P. E.
Smith and B. M. Pettitt},
TITLE = {Comparison of the potentials of mean force for alanine
tetrapeptide between integral equation theory and simulation},
JOURNAL = {Biophys. Chem.},
VOLUME = {78},
PAGES = {113--126},
YEAR = {1999},
ABSTRACT = {The dielectrically consistent reference interaction site
model (DRISM) integral equation theory is applied to determine the
potential of mean force (PMF) for an alanine tetramer. A
stochastic dynamics simulation of the alanine tetramer using this
PMF is then compared with an explicit water molecular dynamics
simulation, In addition, comparison is also done with simulations
using other solvent models like the extended reference interaction
site: model (XRISM) theory, constant dielectric and linear
distance-dependent dielectric models. The results show that the
DRISM method offers a fairly accurate and computationally
inexpensive alternative to explicit water simulations for studies
on small peptides. (C) 1999 Elsevier Science B.V. All rights
reserved.}
}
@ARTICLE{prabhu99b,
AUTHOR = {N. V. Prabhu and J. S. Perkyns and B. M. Pettitt and V. J.
Hruby},
TITLE = {Structure and dynamics of {alpha-MSH} using {DRISM}
integral equation theory and stochastic dynamics},
JOURNAL = {Biopolymers},
VOLUME = {50},
PAGES = {255--272},
YEAR = {1999},
ABSTRACT = {The structural and dynamical features of the hormone
alpha-MSH in solution have been examined over a 100 ns time scale
by using free energy molecular mechanics models at room
temperature. The free energy surface has been modeled using
methods from integral equation theory and the dynamics by the
Langevin equation. A modification of the accessible surface area
friction drag model was used to calculate the atomic friction
coefficients. The molecule shows a stable beta-turn conformation
in the message region and a close interaction between the side
chains of His(6) Phe(7), and Trp(9). A salt bridge between Glu(5)
and Arg(8) was found not to be a preferred interaction, whereas a
Glu(5) and Lys(11) salt bridge was not sampled, presumably due to
relatively high free energy barriers. The message region was more
conformationally rigid than the N-terminal region. Several
structural features observed here agree well with experimental
results. The conformational features suggest a receptor-hormone
interaction model where the hydrophobic side chains of Phe(7) and
Trp(9) interact with the transmembrane portion of the MCl
receptor. Also, the positively charged side chain of Arg(8) and
the imidazole side chain of His(6) may interact with the
negatively charged portions of the receptor which may even be on
the receptor's extracellular loops. (C) 1999 John Wiley & Sons,
Inc.}
}
@ARTICLE{prabhu99c,
AUTHOR = {N. V. Prabhu and J. S. Perkyns and B. M. Pettitt},
TITLE = {Modeling of {alpha-MSH} conformations with implicit solvent},
JOURNAL = {J. Peptide Research},
VOLUME = {54},
PAGES = {394--407},
YEAR = {1999},
ABSTRACT = {A conformational search for the most probable structures of
the hormone alpha-MSH in aqueous solution was performed in order
to help determine the structural features necessary for biological
activity. The free-energy surface was modeled using methods from
integral equation theory, and high-temperature molecular dynamics
was used to enhance conformational sampling. Families of low
free-energy structures have been found. The minimum energy
structure shows a stable beta-turn conformation in the putative
message region that is stabilized by a salt bridge between Glu5
and Lys11. The orientation of the side chains reflects the
amphiphilic nature of the peptide, and a close interaction between
the side chains of the His6, Phe7 and Trp9 was observed. Several
structural features observed in the minimum energy structure agree
well with experimental results. The conformational features led to
a hypothesis of a receptor-hormone interaction model in which the
hydrophobic side chains of Phe7 and Trp9 interact with the
transmembrane portion of the human melanocortin (MC1) receptor.
Also, the positively charged side chain of Arg8 and the imidazole
side chain of His6 may interact with the negatively charged
portions of the receptor which may even be on the receptor's
extracellular loops.}
}
@ARTICLE{lynch99,
AUTHOR = {G. C. Lynch and J. S. Perkyns and B. M. Pettitt},
TITLE = {Kirkwood-Buff thermodynamics derived from grand canonical
molecular dynamics and {DRISM} calculations},
JOURNAL = {J. Computational Phys.},
VOLUME = {151},
PAGES = {135--145},
YEAR = {1999},
ABSTRACT = {The grand canonical ensemble techniques-both Monte Carlo
and molecular dynamics-have become very popular in recent years,
but no direct Link between the number fluctuation results from
these simulation methods and a Kirkwood-Buff theory has been
established. In this article we look at Kirkwood-Buff integrals
computed using thermodynamic averages derived from grand canonical
ensemble molecular dynamics simulations and compare them to
similar quantities derived from the dielectrically consistent
reference interaction site model many-body theory. These
calculations will be carried out for three different water models,
SPC, SPC/E, and TIP3P. (C) 1999 Academic Press.}
}
@ARTICLE{feig98b,
AUTHOR = {M. Feig and B. M. Pettitt},
TITLE = {Crystallographic water sites from a theoretical perspective},
JOURNAL = {Struct.},
VOLUME = 6,
PAGES = {1351--1354},
YEAR = 1998
}
@ARTICLE{feig99b,
AUTHOR = {M. Feig and M. Abdullah and L. Johnsson and B. M. Pettitt},
TITLE = {Large scale distributed data repository: design of a
molecular dynamics trajectory database},
JOURNAL = {Future Generation Computer Systems},
VOLUME = {16},
PAGES = {101--110},
YEAR = {1999},
ABSTRACT = {The design of a molecular dynamics trajectory database is
presented as an example of the organization of large-scale dynamic
distributed repositories for scientific data. Large scientific
datasets are usually interpreted through reduced data calculated
by analysis functions. This allows a database architecture in
which the analyzed datasets, that are kept in addition to the raw
datasets, are transferred to a database user. A flexible user
interface with a well defined Application Program Interface (API)
allows for a wide array of analysis functions and the
incorporation of user defined functions is a critical part of the
database design. An analysis function is executed only when the
requested analysis result is not available from an earlier
request. A prototype implementation used to gain initial practical
experiences with performance and scalability is presented. (C)
1999 Elsevier Science B.V. All rights reserved.}
}
@ARTICLE{feig99c,
AUTHOR = {M. Feig and B. M. Pettitt},
TITLE = {Sodium and chlorine ions as part of the {DNA} solvation
shell},
JOURNAL = {Biophys. J.},
VOLUME = {77},
PAGES = {1769--1781},
YEAR = {1999},
ABSTRACT = {The distribution of sodium and chlorine ions around DNA is
presented from two molecular dynamics simulations of the DNA
fragment d(C5T5).(A(5)G(5)) in explicit solvent with 0.8 M
additional NaCI salt. One simulation was carried out for 10 ns
with the CHARMM force field that keeps the DNA structure close to
A-DNA, the other for 12 ns with the AMBER force field that
preferentially stabilizes B-DNA conformations (Feig and Pettitt,
1998, Biophys. J. 75:134-149). From radial distributions of sodium
and chlorine ions a primary ion shell is defined. The ion counts
and residence times of ions within this shell are compared between
conformations and with experiment. Ordered sodium ion sites were
found in minor and major grooves around both A and B-DNA
conformations. Changes in the surrounding hydration structure are
analyzed and implications for the stabilization of A-DNA and B-DNA
conformations are discussed.}
}
@ARTICLE{pettitt00,
AUTHOR = {B. M. Pettitt},
TITLE = {A {Perspective} on {"Volume} and heat of hydration of ions"
- {Born} {M} (1920) {Z} {Phys} 1 : 45},
JOURNAL = {Theoretical Chem. Accounts},
VOLUME = 103,
PAGES = {171--172},
YEAR = 2000,
ABSTRACT = {Born's simple derivation of the free energy of hydration of
ions is classic. It connects the microscopic atomic properties
with the macroscopic thermodynamics in a transparent fashion.}
}
@ARTICLE{makarov00,
AUTHOR = {V. A. Makarov and B. K. Andrews and P. E. Smith and B. M.
Pettitt},
TITLE = {Residence times of water molecules in the hydration sites
of myoglobin},
JOURNAL = {Biophys. J.},
VOLUME = 79,
PAGES = {2966--2974},
YEAR = 2000,
ABSTRACT = {Hydration sites are high-density regions in the
three-dimensional time-averaged solvent structure in molecular
dynamics simulations and diffraction experiments. In a simulation
of sperm whale myoglobin, we found 294 such high-density regions.
Their positions appear to agree reasonably well with the
distributions of waters of hydration found in 38 x-ray and 1
neutron high-resolution structures of this protein. The hydration
sites are characterized by an average occupancy and a combination
of residence time parameters designed to approximate a
distribution of residence times. It appears that although the
occupancy and residence times of the majority of sites are rather
bulk-like, the residence time distribution is shifted toward the
longer components, relative to bulk. The sites with particularly
long residence times are located only in the cavities and clefts
of the protein. This indicates that other factors, such as
hydrogen bonds and hydrophobicity of underlying protein residues,
play a lesser role in determining the residence times of the
longest-lived sites.}
}
@INBOOK{Pettitt99,
AUTHOR = {B. Montgomery Pettitt and Claudia V. Valdeavella},
TITLE = {A comparison between simulation and Poisson-Boltzmann fields},
BOOKTITLE = {Simulation and Theory of Electrostatic Interactions in
Solution},
EDITOR = {L. R. Pratt and G. Hummer},
ADDRESS = {AIP Press},
YEAR = {1999}
}
@ARTICLE{feig98c,
AUTHOR = {M. Feig and B. M. Pettitt},
TITLE = {A molecular simulation picture of {DNA} hydration around
{A-} and B-DNA},
JOURNAL = {Biopolymers},
VOLUME = 48,
PAGES = {199--209},
YEAR = 1998,
ABSTRACT = {Recent results from molecular dynamics (MD) simulations on
hydration of DNA with respect to conformation are reviewed and
compared with experimental data. MD simulations of explicit
solvent around DNA can now give a derailed model of DNA that not
only matches well with the experimental data but provides
additional insight beyond current experimental limitations. Such
simulation results are analyzed with a focus on differential
hydration properties between A- and B-DNA and between C/G and A/T
base pairs. The extent of hydration is determined from the number
of waters in the primary shell and compared to experimental
numbers from different measurements. High-resolution hydration
patterns around the whole DNA are shown and correlated with the
conformations. The role of ions associating with DNA is discussed
with respect to changes in the hydration structure correlating
with DNA conformation. (C) 2000 John Wiley & Sons, Inc. Biopoly
38: 199-209, 1998.}
}
@ARTICLE{Johnsson00,
AUTHOR = {L. Johnsson and Michael Feig and Pettitt, B. Montgomery},
TITLE = {SimDB: A Problem Solving Environment for Molecular Dynamics
Simulation and Analysis},
JOURNAL = {1st EGRID Forum},
VOLUME = {},
NUMBER = {},
PAGES = {},
ABSTRACT = { },
KEYWORDS = { },
YEAR = {2000}
}
@ARTICLE{vainrub00,
AUTHOR = {A. Vainrub and B. M. Pettitt},
TITLE = {Thermodynamics of association to a molecule immobilized in
an electric double layer},
JOURNAL = {Chem. Phys. Lett.},
VOLUME = 323,
PAGES = {160--166},
YEAR = 2000,
ABSTRACT = {A thermodynamic theory of association to a molecule
immobilized near a surface has been developed. Exact equations for
the binding enthalpy, entropy and equilibrium reaction constant
for an immobilized complex are derived. Using Linear
Poisson-Boltzmann theory of the electric double-layer interaction
between an ion-penetrable sphere and a hard plate allows a closed
form evaluation. We briefly discuss application of the theory to a
DNA chip at high (1 M NaCl) and low (0.01 M NaCl) ionic strength
for dielectric and metallic substrates. Predicted strong
electrostatic effects suggest the feasibility of electronic
control of DNA hybridization and design of chips avoiding the DNA
folding problem. (C) 2000 Elsevier Science B.V. All rights
reserved.}
}
@ARTICLE{wong00,
AUTHOR = {K. Y. Wong and B. M. Pettitt},
TITLE = {A new boundary condition for computer simulations of
interfacial systems},
JOURNAL = {Chem. Phys. Lett.},
VOLUME = 326,
PAGES = {193--198},
YEAR = 2000,
ABSTRACT = {A new boundary condition for computer simulations of
interfacial systems is presented. The simulation box used in this
boundary condition is the asymmetric unit of space group Pb, and
it contains only one interface. Compared to the simulation box
using common periodic boundary conditions which contains two
interfaces, the number of particles in the simulation is reduced
by half. This boundary condition was tested against common
periodic boundary conditions in molecular dynamic simulations of
liquid water interacting with hydroxylated silica surfaces. It
yielded results essentially identical to periodic boundary
condition and consumed less CPU time for comparable statistics.
(C) 2000 Elsevier Science B.V. All rights reserved.}
}
@ARTICLE{lynch00,
AUTHOR = {G. C. Lynch and B. M. Pettitt},
TITLE = {Semi-grand canonical molecular dynamics simulation of
bovine pancreatic trypsin inhibitor},
JOURNAL = {Chem. Phys.},
VOLUME = 258,
PAGES = {405--413},
YEAR = 2000,
ABSTRACT = {In the quest to understand both the structural and
thermodynamic facets of biomolecular-solvent systems semi-grand
canonical ensemble molecular dynamics simulations of a protein in
solution are performed. In these simulations only the water
molecules in the system are allowed to fluctuate; the final number
of water molecules is determined by the chemical potential. An
unbiased sampling technique is used for the insertion/deletion
procedure of the water molecules thereby providing a benchmark
grand ensemble simulation of the hydration structure of proteins.
Three different chemical potential simulations were carried out
offering a direct route to thermodynamic information from a
molecular dynamics simulation. (C) 2000 Elsevier Science B.V. All
rights reserved.}
}
@ARTICLE{feig01,
AUTHOR = {M. Feig and R. Zacharias and B. M. Pettitt},
TITLE = {Conformations of an adenine bulge in a {DNA} octamer and
its influence on {DNA} structure from molecular dynamics
simulations},
JOURNAL = {Biophys. J.},
VOLUME = 81,
PAGES = {352--370},
YEAR = 2001,
ABSTRACT = {Molecular dynamics simulations have been applied to the DNA
octamer d(GCGCA-GAAC) (.) d(GTTCGCGC), which has an adenine bulge
at the center to determine the pathway for interconversion between
the stacked and extended forms. These forms are known to be
important in the molecular recognition of bulges. From a total of
similar to 35 ns of simulation time with the most recent CHARMM27
force field a variety of distinct conformations and
subconformations are found. Stacked and fully looped-out forms are
in excellent agreement with experimental data from NMR and x-ray
crystallography. Furthermore, in a number of conformations the
bulge base associates with the minor groove to varying degrees.
Transitions between many of the conformations are observed in the
simulations and used to propose a complete transition pathway
between the stacked and fully extended conformations. The effect
on the surrounding DNA sequence is investigated and biological
implications of the accessible conformational space and the
suggested transition pathway are discussed, in particular for the
interaction of the MS2 replicase operator RNA with its coat
protein.}
}
@ARTICLE{prabhu01,
AUTHOR = {N. V. Prabhu and S. A. Siddiqui and J. S. McMurray and B.
M. Pettitt},
TITLE = {Structural basis for the activity of pp60(c-src) protein
tyrosine kinase inhibitors},
JOURNAL = {Biopolymers},
VOLUME = 59,
PAGES = {167--179},
YEAR = 2001,
ABSTRACT = {Conformational searches on three closely related
pp60(c-src) protein tyrosine kinase inhibitors of varying
potencies were performed to determine a structural basis for their
activity. The first was a linear peptide (PDNEYAFFQf), the second
its 10-membered cyclic analogue, and the third a cyclic analogue
with a para carboxyphenylalanine irt place of one the F residues.
A common backbone conformation with an antiparallel beta
-sheet-like geometry capped by similar beta -turns was found for
all three peptides, which may be a binding conformation and gives
a candidate pharmacophore for further testing. The interaction
between some polar side chains and between some of the aromatic
rings may be important for maintaining the correct conformation.
The differences in potencies of these inhibitors may be attributed
to certain thermodynamic and chemical reasons. (C) 2001 John Wiley
& Sons, Inc.}
}
@ARTICLE{wong01,
AUTHOR = {K. Y. Wong and B. M. Pettitt},
TITLE = {A study of {DNA} tethered to surface by an all-atom
molecular dynamics simulation},
JOURNAL = {Theoretical Chem. Accounts},
VOLUME = 106,
PAGES = {233--235},
YEAR = 2001,
ABSTRACT = {In order to understand the structure of DNAs and their
interactions when on microarray surfaces, we performed the first
all-atom molecular dynamics simulation of DNA tethered to a
surface. On the surface, the binding of the DNA was enhanced, and
its average equilibrium conformation was the B form. The DNA
duplex spontaneously tilted towards its nearest neighbor and
settled in a leaning position with a interaxial distance of 2.2
nm. This close packing of the DNAs, which affects both in situ
synthesis and deposition of probes on microarray surfaces, can
thus be explained by salted-induced colloidlike DNA-DNA
attractions.}
}
@ARTICLE{juarez02,
AUTHOR = {L. H. Juarez and R. Glowinski and B. M. Pettitt},
TITLE = {Numerical simulation of the sedimentation of a tripole-like
body in an incompressible viscous fluid},
JOURNAL = {Appl. Mathematics Lett.},
VOLUME = 15,
PAGES = {743--747},
YEAR = 2002,
ABSTRACT = {In this note, we discuss the application of a methodology
combining distributed Lagrange multiplier based fictitious domain
techniques, finite-element approximations and operator splitting,
to the numerical simulation of the motion of a tripole-like rigid
body falling in a Newtonian incompressible viscous fluid. The
motion of the body is driven by the hydrodynamical forces and
gravity. The numerical simulation shows that the distribution of
mass of this rigid body and added moment of inertia compared to a
simple cylinder (circular or elliptic) plays a significant role on
the particle-fluid interaction. Apparently, for the parameters
examined, the action of the moving rigid body on the fluid is
stronger than the hydrodynamic forces acting on the rigid body.
(C) 2002 Elsevier Science Ltd. All rights reserved.}
}
@ARTICLE{marlow01,
AUTHOR = {G. E. Marlow and B. M. Pettitt},
TITLE = {Simulations of the bis-penicillamine enkephalin in sodium
chloride solution: {A} parameter study},
JOURNAL = {Biopolymers (Peptide Science)},
VOLUME = 60,
PAGES = {134--152},
YEAR = 2001,
ABSTRACT = {A simulation study of DPDPE in sodium chloride solution has
been poformed and compared with previous simulations using a
different interaction potential for the ions. Both global
thermodynamics as well as a characterization of association to
DPDPE have been calculated. We show that the parameters used for
the ions have a profound effect on the association to the peptide
in IM NaCl. The observed differences suggest that individual
associations in these and previous simulations are sensitive to
parameters. (C) 2001 John Wiley & Sons, Inc.}
}
@ARTICLE{swint-kruse02,
AUTHOR = {L. Swint-Kruse and C. Larson and B. M. Pettitt and K. S.
Matthews},
TITLE = {Fine-tuning function: {Correlation} of hinge domain
interactions with functional distinctions between {LacI} and PurR},
JOURNAL = {Protein Science},
VOLUME = 11,
PAGES = {778--794},
YEAR = 2002,
ABSTRACT = {LacI and PurR are highly homologous proteins. Their
functional units are homodimers, with ail N-terminal DNA binding
domain that comprises the helix-turn-helix (HTH), N-linker, and
hinge regions from both monomers, Hinge structural changes are
Known to occur upon DNA dissociation but are difficult to monitor
experimentally. The initial steps of hinge unfolding were
therefore examined using molecular dynamics simulations, utilizing
a truncated, chimeric protein comprising the LacI HTH/N-linker and
PurR hinge. A terminal Gly-Cys-Gly was added to allow
"dimerization" through disulfide bond formation. Simulations
indicate that differences in LacI and PurR hinge primary sequence
affect the quaternary structure of the hinge(.)hinge' interface.
However, these alternate hinge orientations would be sterically
restricted by the core domain. These results prompted detailed
comparison of recently available DNA-bound structures for LacI and
truncated LacI(1-62) with the PurR structure. Examination revealed
that different N-linker and hinge contacts to the core domain of
the partner monomer (which binds effector molecule) affect the
juxtapositions of the HTH. N-linker, and hinge regions in the DNA
binding domain. In addition. the two full-length repressors
exhibit significant differences in the interactions between the
core and the C-linker connection to the DNA binding domain. Both
linkers and the hinge have been implicated in the allosteric
response of these repressors. Intriguingly. one functional
difference between these two proteins is that they exhibit
opposite allosteric response to effector. Simulations and observed
structural distinctions are correlated with mutational analysis
and sequence information from the LacI/GaIR family to formulate a
mechanism for fine-tuning individual repressor function.}
}
@ARTICLE{perkyns02,
AUTHOR = {J. S. Perkyns and K. M. Dyer and B. M. Pettitt},
TITLE = {Computationally useful bridge diagram series. {II.}
{Diagrams} in h-bonds},
JOURNAL = {J. Chem. Phys.},
VOLUME = 116,
PAGES = {9404--9412},
YEAR = 2002,
ABSTRACT = {Equations for calculating accurate 4-point and 5-point
bridge diagrams in terms of h-bonds have been presented and solved
for various phase points of the Lennard-Jones fluid. A method of
finding a self-consistent solution for the bridge function and the
radial distribution function is demonstrated. The significance of
this result over bridge diagrams expressed as f-bonds, in terms of
its applicability to charged and dipolar models is discussed. Two
very simple phenomenological bridge diagram forms for the bridge
function for this model are examined and found to give results
almost as accurate and in some cases more accurate than previous
forms in the literature. This work represents the first use of
directly calculated 5-point bridge diagrams in terms of h-bonds,
and the many extra orders of f-bond diagrams which they include,
in an integral equation result. (C) 2002 American Institute of
Physics.}
}
@ARTICLE{dyer02,
AUTHOR = {K. Dyer and J. Perkyns and B. M. Pettitt},
TITLE = {Computationally useful bridge diagram series. {III.}
{Lennard-Jones} mixtures},
JOURNAL = {J. Chem. Phys.},
VOLUME = 116,
PAGES = {9413--9421},
YEAR = 2002,
ABSTRACT = {The first two orders of bridge diagrams for the f-bond
expansion and the h-bond expansion are calculated for a binary
mixture of Lennard-Jones spheres. The method used follows the
Legendre polynomial integration methods outlined in the first two
papers of this series. As for the pure fluid cases, the
thermodynamic results which follow from these methods are found to
be in reasonable agreement with the simulation result. Analysis of
the thermodynamic and structural results in comparison to the best
current bridge function approximations indicate that accurate
descriptions of higher order mixtures will require methods beyond
the current mean field treatments which are of utility in simple
fluids. The methods given are unfortunately not computationally
convenient at highest order; however, the lower order diagrams are
both accessible and give reasonable numerical results. (C) 2002
American Institute of Physics.}
}
@ARTICLE{makarov02,
AUTHOR = {V. Makarov and B. M. Pettitt and M. Feig},
TITLE = {Solvation and hydration of proteins and mucleic acids: {A}
theoretical view of simulation and experiment},
JOURNAL = {Accounts Chem. Research},
VOLUME = 35,
PAGES = {376--384},
YEAR = 2002,
ABSTRACT = {Many theoretical, computational, and experimental
techniques recently have been successfully used for description of
the solvent distribution around macromolecules. In this Account,
we consider recent developments in the areas of protein and
nucleic acid solvation and hydration as seen by experiment,
theory, and simulations. We find that in most cases not only the
general phenomena of solvation but even local hydration patterns
are more accurately discussed in the context of water
distributions rather than individual molecules of water. While a
few localized or high-residency waters are often associated with
macromolecules in solution (or crystals from aqueous liquors),
these are readily and accurately included in this more general
description. The goal of this Account is to review the theoretical
models used for the description of the interfacial solvent
structure on the border near DNA and protein molecules. In
particular, we hope to highlight the progress in this field over
the past five years with a focus on comparison of simulation and
experimental results.}
}
@ARTICLE{vainrub03,
AUTHOR = {A. Vainrub and B. M. Pettitt},
TITLE = {Surface electrostatic effects in oligonucleotide
microarrays: {Control} and optimization of binding thermodynamics},
JOURNAL = {Biopolymers},
VOLUME = 68,
PAGES = {265--270},
YEAR = 2003,
ABSTRACT = {We present a theoretical thermodynamic framework for the
design of more efficient oligonucleotide microarrays. A general
thermodynamic relation is derived to describe the electrostatic
surface effects on the binding of the assayed biomolecule to a
surface-tethered molecular probe. The relation is applied to
analyze how the nucleic acid target, the oligonuleotide probe, and
their DNA duplex electrostatic interactions with the surface
affect the hybridization on DNA arrays. Taking advantage of a
closed form exact solution of the linear Poisson-Boltzmann
equation for a charged ion penetrable sphere in electrolyte
solution interacting with a plane wall, we study the effects of
the surface and solution conditions. Binding free energy is found
as a function of the surface material, dielectric or metal, the
surface charge density, linker molecule length, temperature, and
added salt content. The charge or electric potential of the
dielectric or metal surface, respectively, is shown to dominate
the hybridization, especially at low added salt or short linker
length. We predict that substantial enhancement of sensitivity,
selectivity, and reliability of microarrays can be achieved by
control of the surface conditions. As examples, we discuss how to
overcome two limitations of current technologies: nonequal
sensitivity of the probes with different GC and AT bases content,
and poor match/mismatch discrimination. In addition, we suggest
the design of microarray conditions where the tested nucleic acid
is unfolded, thus making possible the screening of a larger
sequence with single nucleotide resolution. These promising
findings are discussed and further experimental tests suggested.
(C) 2003 Wiley Periodicals, Inc.}
}
@ARTICLE{vainrub02,
AUTHOR = {A. Vainrub and B. M. Pettitt},
TITLE = {Coulomb blockage of hybridization in two-dimensional {DNA}
arrays},
JOURNAL = {Phys. Rev. E},
VOLUME = 66,
YEAR = 2002,
ABSTRACT = {Experiments on DNA microarrays have revealed substantial
differences in hybridization thermodynamics between DNA free in
solution and surface tethered DNA. Here we develop a mean field
model of the Coulomb effects in two-dimensional DNA arrays to
understand the binding isotherms and thermal denaturation of the
double helix. We find that the electrostatic repulsion of the
assayed nucleic acid from the array of DNA probes dominates the
binding thermodynamics, and thus causes the Coulomb blockage of
the hybridization. The results explain, observed in DNA
microarrays, the dramatic decrease of the hybridization efficiency
and the thermal denaturation curve broadening as the probe surface
density grows. We demonstrate application of the theory for
evaluation and optimization of the sensitivity, specificity, and
the dynamic range of DNA array devices.}
}
@ARTICLE{marlow03,
AUTHOR = {G. E. Marlow and B. M. Pettitt},
TITLE = {Simulation of the bis(penicillamine) enkephalin in ammonium
chloride solution: {A} comparison with sodium chloride},
JOURNAL = {Biopolymers},
VOLUME = 68,
PAGES = {192--209},
YEAR = 2003,
ABSTRACT = {In order to quantify specific ion effects, a simulation
study of bis(penicllamine) enkephalin, also known as DPDPE, has
been performed in aqueous ammonium chloride solution and has been
compared to a previous simulation of DPDPE in aqueous sodium
chloride solution. Global thermodynamics have been calculated for
a model system and the solution environment around DPDPE has been
characterized. Associations of ions with DPDPE have been
investigated. The observed differences between sodium chloride
solution and ammonium chloride solution suggest that individual
cations affect the solvation and peptide binding properties of a
given anion. (C) 2002 Wiley Periodicals, Inc.}
}
@INBOOK{Vainrub03b,
AUTHOR = {Vainrub, Arnold and Li, Tong Bin and Fofanov, Yuriy and Pettitt, B. Montgomery},
EDITOR = {Moore Jr., James E. and Zouridakis, George},
TITLE = {Theoretical Considerations for the Efficient Design of DNA Arrays},
BOOKTITLE = {Biomedical Technology and Devices Handbook},
YEAR = 2003,
PUBLISHER = {CRC Press},
CHAPTER = 14,
PAGES = {1--12}
}
@ARTICLE{fofanov02,
AUTHOR = {Y. Fofanov and B. M. Pettitt},
TITLE = {Reconstruction of the genetic regulatory dynamics of the
rat spinal cord development: {Local} {Invariants} approach},
JOURNAL = {J. Biomedical Informatics},
VOLUME = 35,
PAGES = {343--351},
YEAR = 2002,
ABSTRACT = {Recently, many attempts have been made to describe the gene
expression temporal dynamics by using systems of differential
equations. This is fraught with difficulty, given the current
experimental level of understanding. Another way to extract useful
information regarding regulation in genetic networks can be
provided by our method of Incomplete Modeling using Local
Invariants, although at the price of not being able to construct a
complete model of the whole system. In this approach we are
looking for a set of simple models describing the algebraic or
differential relations among just a few variables, genes in this
case, which fit the experimental data with the required accuracy.
In the present work, we apply this method to gene expression time
profiles of 112 genes from rat spinal cord development
experiments. We found that many different types of Local
Invariants exist in this dataset. Moreover, some isolated
self-contained subsystems, whose behavior can be described by
closed systems of differential equations, were also found. (C)
2003 Elsevier Inc. All rights reserved.}
}
@ARTICLE{wong04,
AUTHOR = {K. Y. Wong and A. Vainrub and T. Powdrill and M. Hogan and
B. M. Pettitt},
TITLE = {A {non-Watson-Crick} motif of base-pairing on surfaces for
untethered oligonucleotides},
JOURNAL = {Mol. Simulation},
VOLUME = 30,
PAGES = {121--129},
YEAR = 2004,
ABSTRACT = {A structural view of DNA association/hybridization to a
target oligonucleotide molecule near a surface has been developed.
Recent experiments have showed a kinetically rapid hybridization
between large target DNA fragments and oligonucleotides
electrostatically immobilized (untethered) to a surface. Theory
and computer simulations have been used to investigate the nature
of the specificity and affinity in such a system. Simulations were
performed for a modified silicon dioxide surface with positively
charged groups at neutral pH. The dosing of a surface with
unattached oligonucleotide was simulated. The oligonucleotide was
found to associate with the surface in salt water in a way that
some of the bases remained stacked, and most of the bases near the
surface on average pointed preferentially toward the solution,
away from the surface. Use of an analytic solution to the linear
Poisson-Boltzmann (PB) theory of the electric double layer
interaction between DNA and a hard surface predicts tight binding
in this system. The simulation thus gives a mechanism for
specificity and the theory a mechanism for affinity. The geometry
is such that only non-helical base pairs would be accommodated
with an irregular backbone.}
}
@INBOOK{marko03,
AUTHOR = {Marko, John and Feig, Michael and Pettitt, B. Montgomery},
EDITOR = {Russo, N.},
TITLE = {Microscopic DNA Fluctuations are in accord with macroscopic DNA stretching elasticity
without strond dependence on force field choice},
BOOKTITLE = {NATO ASI Series: Metal Ligand Interactions},
YEAR = 2003,
PUBLISHER = {Kluwer Academic Press},
PAGES = {193--204}
}
@ARTICLE{vainrub03c,
AUTHOR = {A. Vainrub and B. M. Pettitt},
TITLE = {Sensitive quantitative nucleic acid detection using
oligonucleotide microarrays},
JOURNAL = {J. Am. Chem. Soc.},
VOLUME = 125,
PAGES = {7798--7799},
YEAR = 2003
}
@ARTICLE{wong04b,
AUTHOR = {K. Y. Wong and B. M. Pettitt},
TITLE = {Orientation of {DNA} on a surface from simulation},
JOURNAL = {Biopolymers},
VOLUME = 73,
PAGES = {570--578},
YEAR = 2004
}
@ARTICLE{vainrub04,
AUTHOR = {A. Vainrub and B. M. Pettitt},
TITLE = {Theoretical aspects of genomic variation screening using
{DNA} microarrays},
JOURNAL = {Biopolymers},
VOLUME = 73,
PAGES = {614--620},
YEAR = 2004,
ABSTRACT = {We present a theoretical model for typical microarray-based
single nucleotide polymorphism (SNP) assay of small genomic DNA
amount. We derived the adsorption isotherm expressing the on-array
hybridization efficiency in terms of genomic target sequence and
concentration, oligonucleotide probe sequence and surface density,
hybridization buffer, and temperature. This isotherm correctly
describes the surface probe density effects, the sensitivity peak,
and the melting temperature depression, and is in accord with
published experiments. We discuss optimization of parallel SNP
genotyping. Our estimates show that SNP detection at a single
temperature in aqueous hybridization buffer is restricted by DNA
regions that differ by less than 20% in GC content. We predict
that the variety of genotyped SNPs could be substantially,
extended using an assay design with high probe density and a large
fraction of probes hybridized. (C) 2004 Wiley Periodicals, Inc.}
}
@ARTICLE{kelley04,
AUTHOR = {C. T. Kelley and B. M. Pettitt},
TITLE = {A fast solver for the {Ornstein-Zernike} equations},
JOURNAL = {J. Computational Phys.},
VOLUME = 197,
PAGES = {491--501},
YEAR = 2004,
ABSTRACT = {In this paper, we report on the design and analysis of a
multilevel method for the solution of the Ornstein-Zernike
Equations and related systems of integro-algebraic equations. Our
approach is based on an extension of the Atkinson-Brakhage method,
with Newton-GMRES used as the coarse mesh solver. We report on
several numerical experiments to illustrate the effectiveness of
the method. The problems chosen are related to simple short ranged
fluids with continuous potentials. Speedups over traditional
methods for a given accuracy are reported. The new multilevel
method is roughly six times faster than Newton-GMRES and 40 times
faster than Picard. (C) 2003 Elsevier Inc. All rights reserved.}
}
@ARTICLE{rosgen04,
AUTHOR = {J. R\"{o}sgen and B. M. Pettitt and J. Perkyns and D. W. Bolen},
TITLE = {Statistical thermodynamic approach to the chemical
activities in two-component solutions},
JOURNAL = {J. Phys. Chem. B},
VOLUME = 108,
PAGES = {2048--2055},
YEAR = 2004,
ABSTRACT = {It is shown how the leading terms of a semi grand canonical
partition function (GCPF) can be used to develop analytic
expressions relating activity to concentrations in two-component
systems. The simple analytic expressions for activity coefficients
can be fitted to activity coefficient versus concentration data
for a wide range of aqueous solute systems. Only one or two
parameters are required to accurately describe the activity
coefficients of nonelectrolyte and electrolyte aqueous solute
systems over their entire range of solubility. These forms derive
from low-order number expressions of the GCPF that take into
account the effective solvent interactions with the solute and
between solute molecules for a variable amount of solvent. The
GCPF leading terms and fitting parameters define apparent
solute-solute oligomerization and solute packing phenomena that
increase with solute concentration. Advantages using this grand
canonical approach versus previous approaches are discussed.}
}
@ARTICLE{fofanov04,
AUTHOR = {Y. Fofanov and Y. Luo and C. Katili and J. Wang and Y.
Belosludtsev and T. Powdrill and C. Belapurkar and V. Fofanov and
T. B. Li and S. Chumakov and B. M. Pettitt},
TITLE = {How independent are the appearances of n-mers in different
genomes?},
JOURNAL = {Bioinformatics},
VOLUME = 20,
PAGES = {2421--2428},
YEAR = 2004,
ABSTRACT = {Motivation: Analysis of statistical properties of DNA
sequences is important for evolutional biology as well as for DNA
probe and PCR technologies. These technologies, in turn, can be
used for organism identification, which implies applications in
the diagnosis of infectious diseases, environmental studies, etc.
Results: We present results of the correlation analysis of
distributions of the presence/absence of short nucleotide
subsequences of different length ('n-mers', n = 5 - 20) in more
than 1500 microbial and virus genomes, together with five genomes
of multicellular organisms (including human). We calculate whether
a given n-mer is present or absent (frequency of presence) in a
given genome, which is not the usually calculated number of
appearances of n-mers in one or more genomes (frequency of
appearance). For organisms that are not close relatives of each
other, the presence/absence of different 7-20mers in their genomes
are not correlated. For close biological relatives, some
correlation of the presence of n-mers in this range appears, but
is not as strong as expected. Suppressed correlations among the
n-mers present in different genomes leads to the possibility of
using random sets of n-mers (with appropriately chosen n) to
discriminate genomes of different organisms and possibly
individual genomes of the same species including human with a low
probability of error.}
}
@ARTICLE{kurzak05,
AUTHOR = {J. Kurzak and B. M. Pettitt},
TITLE = {Communications overlapping in fast multipole particle
dynamics methods},
JOURNAL = {J. Computational Phys.},
VOLUME = 203,
PAGES = {731--743},
YEAR = 2005,
ABSTRACT = {In molecular dynamics the fast multipole method (FMM) is an
attractive alternative to Ewald summation for calculating
electrostatic interactions due to the operation counts. However
when applied to small particle systems and taken to many
processors it has a high demand for interprocessor communication.
In a distributed memory environment this demand severely limits
applicability of the FMM to systems with 0(10 K atoms). We present
an algorithm that allows for fine grained overlap of communication
and computation, while not sacrificing synchronization and
determinism in the equations of motion. The method avoids
contention in the communication subsystem making it feasible to
use the FMM for smaller systems on larger numbers of processors.
Our algorithm also facilitates application of multiple time
stepping techniques within the FMM. We present scaling at a
reasonably high level of accuracy compared with optimized Ewald
methods. (C) 2004 Elsevier Inc. All rights reserved.}
}
@TECHREPORT{Luo04,
AUTHOR = {Yi Luo and Charles Katili and Jim Wang and Yuri Y. Belosludtsev and
Thomas F. Powdrill and Viacheslav Fofanov and Sergey Chumakov and Yuriy Fofanov and
B. Mongomery Pettitt},
TITLE = {Short subsequences in genomes: How random are they?},
INSTITUTION = {Computer Science, University of Houston},
YEAR = 2004,
ADDRESS = {4800 Calhoun, Houston, TX 77205}
}
@ARTICLE{rosgen04b,
AUTHOR = {J. R\"{o}sgen and B. M. Pettitt and D. W. Bolen},
TITLE = {Uncovering the basis for nonideal behavior of biological
molecules},
JOURNAL = {Biochem.},
VOLUME = 43,
PAGES = {14472--14484},
YEAR = 2004,
ABSTRACT = {The molecular origin of the nonideal behavior for
concentrated binary solutions of biochemical compounds is
examined. The difference between activities expressed in the molar
and molal conventions can be large. Considering the range from
dilute to concentrated, we show that molar activity coefficients
can be represented by simple but rigorous equations involving
between one and three parameters only. We derive a universal
relationship interconverting the scales of molarity and molality
without requiring the density of the solution. The equations are
developed from first principles using a statistical thermodynamic
theory of molar activity coefficients. It is shown how to express
activity coefficients in different concentration scales, and the
advantages and disadvantages of using certain scales are discussed
and compared with the experimental data. Several classes of
biochemically relevant compounds, many of which are naturally
occurring osmolytes, are discussed: six saccharides (glucose,
xylose, maltose, mannose, raffinose, and sucrose), four polyols
(glycerol, mannitol, erythritol, and sorbitol), five amino acids
(glycine, alanine, sarcosine, glycine betaine, and proline), and
urea. Of the 16 solutes, 10 could be described in terms of a
single parameter that is due to pure first-order effects (packing,
hydration, or space limitation). The remaining six exhibit
significant second-order effects (solute-solute interactions) and
require two additional parameters, one typically identified with
the volume occupied per solute molecule in the pure solute
(crystal or liquid) and the other with a self-association
constant. The activity coefficients of the osmolytes roughly
display the rank order found with respect to their ability to
stabilize proteins. These findings are discussed in terms of the
physical principles that give rise to the activity coefficients.}
}
@ARTICLE{chumakov,
AUTHOR = {Chumakov, S. and Putoni, Catherine and Pettitt, B. Montgomery and Fox, George E. and
Willson, Richard C. and Fofanov, Yuriy},
TITLE = {Using Statistical Properties of Short Subsequences in Microbial Identification},
JOURNAL = {Proc. Int. Con. Math. Eng. Tech. Med. Bio. Sci.}
}
@ARTICLE{choudhury05,
AUTHOR = {N. Choudhury and B. M. Pettitt},
TITLE = {On the mechanism of hydrophobic association of nanoscopic
solutes},
JOURNAL = {J. Am. Chem. Soc.},
VOLUME = 127,
PAGES = {3556--3567},
YEAR = 2005,
ABSTRACT = {The hydration behavior of two planar nanoscopic hydrophobic
solutes in liquid water at normal temperature and pressure is
investigated by calculating the potential of mean force between
them at constant pressure as a function of the solute-solvent
interaction potential. The importance of the effect of weak
attractive interactions between the solute atoms and the solvent
on the hydration behavior is clearly demonstrated. We focus on the
underlying mechanism behind the contrasting results obtained in
various recent experimental and computational studies on water
near hydrophobic solutes. The length scale where crossover from a
solvent separated state to the contact pair state occurs is shown
to depend on the solute sizes as well as on details of the
solute-solvent interaction. We find the mechanism for attractive
mean forces between the plates is very different depending on the
nature of the solute-solvent interaction which has implications
for the mechanism of the hydrophobic effect for biomolecules.}
}
@ARTICLE{lakhno04,
AUTHOR = {V. D. Lakhno and V. B. Sultanov and B. M. Pettitt},
TITLE = {Combined hopping-superexchange model of a hole transfer in
DNA},
JOURNAL = {Chem. Phys. Lett.},
VOLUME = 400,
PAGES = {47--53},
YEAR = 2004,
ABSTRACT = {Relative hole transfer rates in DNA have been investigated
in a number of nucleotide sequences experimentally. Calculation of
the transfer rates in DNA is performed relying on the assumption
that the transfer is realized as hopping of a hole on guanine
sites, each hop being calculated on the basis of superexchange
theory. It is shown that the medium reorganization energy and free
energy changes play an important role in determining the transfer
rate and the type of a nucleotide sequence. The results of the
calculations are compared with experimental data covering a range
of available sequences. (C) 2004 Elsevier B.V. All rights
reserved.}
}
@INBOOK{pettitt05,
AUTHOR = {B. Montgomery Pettitt and Arnold Vainrub and Ka-Yiu Wong},
EDITOR = {D. Henderson and M. Holovko and A. Trokhymchuk},
TITLE = {DNA Saline Solutions Near Surfaces: Design Parameters of DNA Arrays},
BOOKTITLE = {NATO Science Series},
YEAR = 2005,
PUBLISHER = {Kluwer Academic Press},
PAGES = {381--393}
}
@ARTICLE{choudhury05b,
AUTHOR = {N. Choudhury and B. M. Pettitt},
TITLE = {Dynamics of water trapped between hydrophobic solutes},
JOURNAL = {J. Phys. Chem. B},
VOLUME = 109,
PAGES = {6422--6429},
YEAR = 2005,
ABSTRACT = {We describe the model dynamical behavior of the solvent
between two nanoscopic hydrophobic solutes. The dynamics of the
vicinal water in various sized traps is found to be significantly
different from bulk behavior. We consider the dynamics at normal
temperature and pressure at three intersolute distances
corresponding to the three solvent separated minima in the free
energy profile between the solutes with attractions. These three
states correspond to one, two, and three intervening layers of
water molecules. Results are obtained from a molecular dynamics
simulation at constant temperature and pressure (NPT) ensemble.
Translational diffusion of water molecules trapped between the two
solutes has been analyzed from the velocity correlation function
as well as from the mean square displacement of the water
molecules. The rotational behavior has been analyzed through the
reorientational dynamics of the dipole moment vector of the water
molecule by calculating both first and second rank dipole-dipole
correlation functions. Both the translational and reorientational
mobilities of water are found to be much slower at the smaller
separation and increases as the separation between solutes becomes
larger. The occupation time distribution functions calculated from
the trajectories also show that the relaxation is much slower for
the smallest intersolute separation as compared to other wider
separations. The sublinear trend in mean square displacement and
the stretched exponential decay of the relaxation of dipolar
correlation and occupation distribution function indicate that the
dynamical behavior of water in the confined region between two
large hydrophobic solutes departs from usual Brownian behavior.
This behavior is reminiscent of the behavior of water in the
vicinity of protein surface clefts or trapped between two domains
of a protein.}
}
@ARTICLE{choudhury05c,
AUTHOR = {N. Choudhury and B. M. Pettitt},
TITLE = {Local density profiles are coupled to solute size and
attractive potential for nanoscopic hydrophobic solutes},
JOURNAL = {Mol. Simulation},
VOLUME = 31,
PAGES = {457--463},
YEAR = 2005,
ABSTRACT = {We employ constant pressure molecular dynamics simulations
to investigate the effects of solute size and solute-water
dispersion interactions on the solvation behavior of nanoscopic
hydrophobic model solutes in water at normal temperature and
pressure. The hydration behavior around a single planar atomic
model solute as well as a pair of such solutes have been
considered. The hydration water structure of a model nanoscopic
solute with standard Lennard-Jones interaction is shown to be
significantly different from that of their purely repulsive
analogues. The density of water in the first solvation shell of a
Lennard-Jones solute is much higher than that of bulk water and it
remains almost unchanged with the increase of the solute
dimensions from one to a few nanometers. On the other hand, for a
purely repulsive analogue of the above model, solute hydration
behavior shows a marked solute size dependence. The contact
density of water in this case decreases with the increasing
dimension of the solute. We also demonstrate the effect of
solute-solvent attraction on the cavity formation in the inter
solute region between two solutes with an inter solute separation
of 6.8 angstrom, corresponding to the first solvent separated
minimum in the free energy profile as obtained in our earlier
work.}
}
@ARTICLE{kurzak05b,
AUTHOR = {J. Kurzak and B. M. Pettitt},
TITLE = {Massively parallel implementation of a fast multipole
method for distributed memory machines},
JOURNAL = {J. Parallel Distributed Computing},
VOLUME = 65,
PAGES = {870--881},
YEAR = 2005,
ABSTRACT = {We present a new load balanced parallel implementation of a
non-adaptive version of Greengard and Rokhlin's fast multipole
method for distributed memory architectures with focus on
applications in molecular dynamics. We introduce a novel load
balancing and communication overlapping scheme. Our implementation
includes periodic boundary conditions calculations and facilitates
multiple time stepping techniques without sacrificing determinism
of computation and scales to hundreds of processor for systems of
only O (10k) atoms. (c) 2005 Elsevier Inc. All rights reserved.}
}
@ARTICLE{dyer05,
AUTHOR = {K. M. Dyer and J. S. Perkyns and B. M. Pettitt},
TITLE = {Simple bond length dependence: {A} correspondence between
reactive fluid theories},
JOURNAL = {J. Chem. Phys.},
VOLUME = 122,
PAGES = {236101-1--236101-2},
YEAR = 2005
}
@ARTICLE{chen06,
AUTHOR = {C. Y. Chen and B. W. Beck and K. Krause and B. M. Pettitt},
TITLE = {Solvent participation in {Serratia} marcescens endonuclease
complexes},
JOURNAL = {Proteins-structure Function Bioinformatics},
VOLUME = 62,
PAGES = {982--995},
YEAR = 2006,
ABSTRACT = {The monomer and dimer of the bacterium Serratia marcescens
endonuclease (SMnase) are each catalytically active and the two
subunits of the dimer function independently of each other.
Specific interfacial waters may play a role in stability, complex
formation, and functionality. We performed molecular dynamics
simulations of both a subunit of SMnase and its model built
complex with DNA and analyzed the relation of the hydration sites
to the catalytic mechanism. It was found that the binding of DNA
has little influence on the global hydration properties of the
protein, including occupancy and water residence time
distributions. DNA and protein recognition in our model mainly
involves direct contacts by hydrogen bond and hydrophobic
interactions. Water-mediated contacts exist, but are less common.
Three interior water clusters were identified for SMnase. One
cluster around the active site in the monomer-DNA complex shows
relatively strong interactions between hydration sites as well as
between the sites and the biomolecules. The simulated cluster
properties agreed well with experimental data. The magnesium ion
shows ligand exchange. Although Mg2+ keeps six ligands during the
entire simulation, upon the binding of DNA, Asn119 loses its
coordination with Mg2+, while one nonbridging oxygen of the
phosphate of a DNA residue and two oxygen atoms of the side chain
of Glu127 become the ligands. Waters in a nearby cluster exchange
and participate in the resolvation of groups in the presence of
DNA. Water thus not only participates in the cleavage of DNA but
also can stabilize the transition state and the leaving groups in
our model.}
}
@ARTICLE{rosgen05,
AUTHOR = {J. R\"{o}sgen and B. M. Pettitt and D. W. Bolen},
TITLE = {Protein folding, stability, and solvation structure in
osmolyte solutions},
JOURNAL = {Biophys. J.},
VOLUME = 89,
PAGES = {2988--2997},
YEAR = 2005,
ABSTRACT = {An understanding of the impact of the crowded conditions in
the cytoplasm on its biomolecules is of clear importance to
biochemical, medical, and pharmaceutical science. Our previous
work on the use of small biochemical compounds to crowd protein
solutions indicates that a quantitative description of their
nonideal behavior is possible and straightforward. Here, we show
the structural origin of the nonideal solution behavior. We
discuss the consequences of these findings regarding protein
folding stability and solvation in crowded solutions through a
structural analysis of the m-value or the change in free-energy
difference of a macromolecule in solution with respect to the
concentration of a third component.}
}
@ARTICLE{dyer05b,
AUTHOR = {K. M. Dyer and J. S. Perkyns and B. M. Pettitt},
TITLE = {Effective density terms in proper integral equations},
JOURNAL = {J. Chem. Phys.},
VOLUME = 123,
PAGES = {204512-1--204512-11},
YEAR = 2005,
ABSTRACT = {Two complementary routes to a new integral equation theory
for site-site molecular fluids are presented. First, a simple
approximation to a subset of the atomic site bridge functions in
the diagrammatically proper integral equation theory is presented.
This in turn leads to a form analogous to the reactive fluid
theory, in which the normalization of the intramolecular
distribution function and the value of the off-diagonal elements
in the density matrix of the proper integral equations are the
means of propagating the bridge function approximation. Second, a
derivation from a topological expansion of a model for the
single-site activity followed by a topological reduction and
low-order truncation is given. This leads to an approximate
numerical value for the new density coefficient. The resulting
equations give a substantial improvement over the standard
construction as shown with a series of simple diatomic model
calculations. (c) 2005 American Institute of Physics.}
}
@ARTICLE{randall06,
AUTHOR = {Randall, Graham L. and Pettitt, B. Montgomery and
Buck, Gregory R. and Zechiedrich, E. Lynn},
TITLE = {Electrostatics of DNA-DNA juxtapositions: consequences for type II
topoisomerase function },
JOURNAL = {Journal of Physics: Condensed Matter},
VOLUME = {18},
NUMBER = {},
PAGES = {173--185},
ABSTRACT = {Type II topoisomerases resolve problematic DNA topologies such
as knots, catenanes, and supercoils that arise as a consequence of
DNA replication and recombination. Failure to remove problematic
DNA topologies prohibits cell division and can result in cell death
or genetic mutation. Such catastrophic consequences make
topoisomerases an effective target for antibiotics and anticancer
agents. Despite their biological and clinical importance, little
is understood about how a topoisomerase differentiates DNA
topologies in a molecule that is significantly larger than the
topoisomerase itself. It has been proposed that type II
topoisomerases recognize angle and curvature between two DNA
helices characteristic of knotted and catenated DNA to account for
the enzyme’s preference to unlink instead of link DNA. Here we
consider the electrostatic potential of DNA juxtapositions to
determine the possibility of juxtapositions occurring through
Brownian diffusion. We found that despite the large negative
electrostatic potential formed between two juxtaposed DNA helices,
a bulk counterion concentration as small as 50 mM provides
sufficient electrostatic screening to prohibit significant
interaction beyond an interhelical separation of 3 nm in both
hooked and free juxtapositions. This suggests that instead of
electrostatics, mechanical forces such as those occurring in
anaphase, knots, catenanes, or the writhe of supercoiled DNA may
be responsible for the formation of DNA juxtapositions.},
KEYWORDS = { },
YEAR = {2006}
}
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