bmp_chem.bib
@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.}
}
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