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doi: 10.1002/(SICI)1096-987X(19961130)17:15<1685::AID-JCC1>3.0.CO;2-Lpmid: N/A
This article describes the collisional dynamics (CD) method adapted for molecules with geometrical constraints within a description using Cartesian coordinates for the atoms. In the CD method, stochastic collisions with virtual particles are included in usual molecular dynamics simulations to couple the considered polymer molecule to a solvent. The actual presence of the solvent is not explicitly included in the simulation. The results‐of CD simulations of a polymer chain immersed in the time‐dependent elongational flow field are presented. The influence of nonbonded interactions on the coil‐stretch transition of the chain occurring in the flow is discussed. © 1996 John Wiley & Sons, Inc.
Williams, Stephen D.; Harper, Warren; Mamantov, Gleb; Tortorelli, Louis J.; Shankle, George
doi: 10.1002/(SICI)1096-987X(19961130)17:15<1696::AID-JCC2>3.0.CO;2-Kpmid: N/A
Molecular geometries were fully optimized for AlCl3, AlCl4‐, Al2Cl6, Al2Cl7‐, AlF3, AlF4‐, Al2F6, Al2F7‐, BCl3, BCl4‐, B2Cl6, B2Cl7‐, BF3, BF4‐, B2F6, and B2F7‐, as well as a few mixed halogen species, at the Hartree‐Fock (HF) level, using basis sets from STO‐3G to 6–311 + G(d). In some cases geometries were also optimized at the MP2 level. Where possible, the computed geometries were compared to known structures from electron or X‐ray diffraction. The agreement between these was quite good for the neutral species, and somewhat poorer for the anions. Vibrational frequencies were calculated for all species at the HF level with the largest basis set. The geometries were characterized as minima or transition structures. Various formation reaction enthalpies were calculated; these compare well with known values. More extensive calculations on the BF3/BF4‐ system indicate the structures and enthalpies are nearly converged with respect to basis set size and level of correlation treatment. The previously unknown species B2Cl7‐ is predicted to be energetically stable on the basis of the calculations. Some features of the 11B NMR spectra of room temperature melts consisting of mixtures of boron trichloride with 1‐methyl‐3‐ethylimidazolium chloride are presented. These features suggest that these melts may contain small amounts of B2Cl7‐ as an intermediate in an exchange reaction. © 1996 by John Wiley & Sons, Inc.
Campbell, Graham; Deng, Yuefan; Glimm, James; Wang, Yuan; Yu, Qiqing; Eisenberg, Moisés; Grollman, Arthur
doi: 10.1002/(SICI)1096-987X(19961130)17:15<1712::AID-JCC3>3.0.CO;2-Spmid: N/A
A number of essential biological functions are controlled by proteins that bind to specific sequences in genomic DNA. In this article we present a simplified model for analyzing DNA‐protein interactions mediated exclusively by hydrogen bonds. Based on this model, an optimized algorithm for geometric pattern recognition was developed. The large number of local energy minima are efficiently screened by using a geometric approach to pattern matching based on a square‐well potential. The second part of the algorithm represents a closed form solution for minimization based on a quadratic potential. A Monte Carlo method applied to a modified Lennard‐Jones potential is used as a third step to rank DNA sequences in terms of pattern matching. Using protein structures derived from four DNA‐protein complexes with three‐dimensional coordinates established by X‐ray diffraction analysis, all possible DNA sequences to which these proteins could bind were ranked in terms of binding energies. The algorithm predicts the correct DNA sequence when at least two hydrogen bonds per base pair are involved in binding to the protein, providing a partial solution to the three‐dimensional docking problem. This study lays a framework for future refinements of the algorithm in which the number of assumptions made in the present analysis are reduced. © 1996 by John Wiley & Sons, Inc.
doi: 10.1002/(SICI)1096-987X(19961130)17:15<1726::AID-JCC4>3.0.CO;2-Rpmid: N/A
A new thermodynamic integration approach to conformational free energy simulations is presented. The method is applicable both to one‐dimensional cases (reaction coordinates) and multidimensional situations (free energy surfaces). Analysis of the properties of the thermodynamic integration algorithm is used to formulate methods of calculating multidimensional free energy gradients. The method is applied to calculate the free energy profile for rotation around the central C—C bond of n‐butane in the gas and liquid phase and to generate maps of the 18‐dimensional free energy gradient with respect to all nine ϕ and nine ψ dihedrals of the decaalanine and deca‐α‐methylalanine peptides in vacuum. For n‐butane essentially no change in the gauche–trans equilibrium between the gas and liquid is predicted within the CHARMM explicit hydrogen model, with the thermodynamic integration, thermodynamic perturbation, and direct simulation methods yielding free energy profiles that are identical within errors. For the decapeptides the right‐handed helical region of conformational space is investigated. For decaalanine a minimum on the free energy surface is found in the vicinity of (ϕ, ψ) = (‐64.5°, ‐42.5°) in the α‐helix region; no minimum exists for 310‐helix‐type conformers. For deca‐α‐methylalanine free energy minima corresponding to both the α‐helix at ( ‐ 55.5°, ‐ 51.5°) and the 310‐helix at ( ‐ 54°, ‐ 29°) are found; the α‐helix state is favored by about 4 kcal/mol and the barrier for the concerted 310‐helix → α‐helix transition is about 3 kcal/mol. The α‐methylation also considerably increases the rigidity of the α‐helix with respect to deformations. The computational efficiency, ease of generalization to calculations of multidimensional gradients, and analytical capability due to component analysis of free energy differences make the method a novel, powerful tool to improve the basic understanding of conformational equilibria of flexible molecules in condensed phases. A related scheme for energy minimization in the presence of holonomic constraints is also presented, allowing generation of adiabatic energy surfaces in constrained systems. © 1996 by John Wiley & Sons, Inc.
doi: 10.1002/(SICI)1096-987X(19961130)17:15<1750::AID-JCC5>3.0.CO;2-Opmid: N/A
Monte Carlo simulations of loop‐erased self‐avoiding random walks in four and five dimensions were performed, using two distinct algorithms. We find consistency between these methods in their estimates of critical exponents. The upper critical dimension for this phenomenon is four, and it has been shown that the mean square end‐to‐end distance grows as n(log n)α. It has recently been established that the mean square end‐to‐end distance is asymptotically bounded by n(log n)1/3 (see Ref. 21). Our results show that asymptotic convergence to n(log n)1/3 in fact obtains and does so rather quickly. In five dimensions we examine the rate of asymptotic convergence to the mean‐field model. © 1996 by John Wiley & Sons, Inc.
Mizan, Tahmid I.; Savage, Phillip E.; Ziff, Robert M.
doi: 10.1002/(SICI)1096-987X(19961130)17:15<1757::AID-JCC6>3.0.CO;2-Opmid: N/A
This study investigates the differences between the predictions of various properties of rigid and flexible simple point charge water models at supercritical conditions. Molecular dynamics simulations were conducted for supercritical water in a temperature range of 773–1073 K and densities in the range 115–659 kg/m3. We present thermodynamic data, pair correlation functions, self‐diffusivity, power spectra, dielectric constants, and variaous measures of hydrogen bonding at different state conditions. The flexible water model performs better in predicting the pressures along the supercritical isotherms simulated. Agreement between experimental and calculated dielectric constants is superior for the flexible water model, particularly at high densities. The flexible model exhibits a greater degree of hydrogen bonding and more persistent hydrogen bonds than does the rigid model. The structural features of supercritical water at high densities are identical for the two water models. At low densities, however, the flexible potential exhibits pair correlation functions with enhanced peaks. Inclusion of flexibility in the potential model does not result in a significant shift in the position of the rotational/librational peak in the power spectrum. The self‐diffusivities obtained from the simulations are within the accuracy of the experimental values for both the rigid and flexible models. On balance the inclusion of flexibility improves agreement with the properties of real supercritical water while incurring little or no additional computational burden. © 1996 by John Wiley & Sons, Inc.
Laidig, Keith E.; Streitwieser, Andrew
doi: 10.1002/(SICI)1096-987X(19961130)17:15<1771::AID-JCC7>3.0.CO;2-Mpmid: N/A
The origins of the trends of relatively acidity across and between the first and second period hydrides (BH3, CH4, NH3, H2O, HF, AIH3, SiH4, PH3, H2S, and HCl) were investigated using molecular and subsystem quantum mechanics at the Hartree‐Fock (HF)/6–31 + + G **//HF/6–31 + + G ** level of theory. The total deprotonation energies, Δ Eacid, are interpreted in terms of three component processes: Δ E1; deprotonation without electronic and nuclear relaxation; Δ E2, electronic relaxation within the acid geometry; and Δ E3, nuclear relaxation. Δ E1 is given from the electrostatic potential at the acidic proton, Δ E3 + Δ E2 (= Δ E *) is given from the calculated energy of the conjugate anion at the acid geometry. The increased acidity across a given period is shown to be already mostly an inherent property of the acid. © 1996 by John Wiley & Sons, Inc.
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