bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generalized morse analytic function for the “true” diatomic potential of the RKR type
Authors: Dagher M. , Kobeissi H. , Kobressi M. , D'Incan J. , Effantin C. 
Published: January 2005

AbstractThe problem of the representation of the RKR (or IPA) diatomic potential by a simple analytic function is considered. This old problem has for a fairly good solution the Coxon‐Hajigeorgiou function U(x) = D[1 ‐ exp‐fn(x)]2 with fn(x) = Σ amxm. The problem of the determination of the disposable parameters a1 … an [in order that U(r) fits the given RKR potential] is reduced to that of a set of linear equations in am where a standard least‐squares technique is used. The application to several states (ground or excited) of several molecules shows that a fairly “good” fit is obtained for n ∼ 10, even for the state XOg—I2 bounded by 109 vibrational levels, for which the RKR potential is defined by the coordinates of 219 points. It is shown that the percentage deviation |U(r)RKR ‐ U(r)| throughout the range of r values is about 0.04% for XΣLi2, 0.0005% for XΣHCl, 0.06% for XOgI2, and 0.05% for BOuI2 (as examples). This approach shows the same success for deep and shallow potentials. The comparison of the computed Ev (vibrational energy) and Bv (rotational constant) with their corresponding experimental values shows that a good agreement is reached even for high vibrational levels close to the dissociation. © John Wiley & Sons, Inc.
Prediction of peptide conformation by multicanonical algorithm: New approach to the multiple‐minima problem
Authors: Hansmann Ulrich H. E. , Okamoto Yuko 
Published: January 2005

AbstractWe apply a recently developed method, the multicanonical algorithm, to the problem of tertiary structure prediction of peptides and proteins. As a simple example to test the effectiveness of the algorithm, metenkephalin is studied and the ergodicity problem, or multiple‐minima problem, is shown to be overcome by this algorithm. The lowest‐energy conformation obtained agrees with that determined by other efficient methods such as Monte Carlo simulated annealing. The superiority of the present method to simulated annealing lies in the fact that the relationship to the canonical ensemble remains exactly controlled. Once the multicanonical parameters are determined, only one simulation run is necessary to obtain the lowest‐energy conformation and further the results of this one run can be used to calculate various thermodynamic quantities at any temperature. The latter point is demonstrated by the calculation of the average potential energy and specific heat as functions of temperature. © John Wiley & Sons, Inc.
Analysis of the genetic algorithm method of molecular conformation determination
Authors: McGarrah D.B. , Judson R.S. 
Published: January 2005

AbstractMany important problems in chemistry require knowledge of the 3‐D conformation of a molecule. A commonly used computational approach is to search for a variety of low‐energy conformations. Here, we study the behavior of the genetic algorithm (GA) method as a global search technique for finding these low‐energy conformations. Our test molecule is cyclic hexaglycine. The goal of this study is to determine how to best utilize GAs to find low‐energy populations of conformations given a fixed amount of CPU time. Two measures are presented that help monitor the improvement in the GA populations and their loss of diversity. Different hybrid methods that combine coarse GA global search with local gradient minimization are evaluated. We present several specific recommendations about trade‐offs when choosing GA parameters such as population size, number of generations, rate of interaction between subpopulations, and combinations of GA and gradient minimization. In particular, our results illustrate why approaches that emphasize convergence of the GA can actually decrease its effectiveness as a global conformation search method. © John Wiley & Sons, Inc.
“Full numerical” diatomic matrix elements: Simplified shooting method
Authors: Kobeissi Hafez , Trad Chafia H. , Kobeissi Majida 
Published: January 2005

AbstractThe problem of diatomic matrix elements Mnn′ = 〈Ψn|Q|Ψn′〉 related to the anharmonic oscillator is considered for standard operators Q of the form x = r – re (r is the radial variable), powers of x, or exponentials, or combinations of such operators; the quantum numbers (n, n′) may be equal or not. A “full numerical” method to determine Mnn′ is presented for any type of the potential U, analytic like that of Morse or numerical like the RKR potential. This numerical method is a simplified version of the standard Cooley shooting method (CSM). The present simplified shooting method (SSM): (1) shoots in one direction only (instead of two); (2) avoids starting problems and matching problems; (3) determines the “end” point automatically (without prior guesses); and (4) reduces thus the number of grid points effectively needed. Examples for analytic (Morse) and RKR potentials are presented. The numerical application to a standard example used by Delgado‐Barrio et al. [J. Comp. Chem., 7, 208 (1986)] using the CSM, and by Kobeissi et al. [J. Comp. Chem., 10, 358 (1989)] using the highly accurate “Canonical Functions” method, shows that when the SSM and CSM are used with the same integrator and the same mesh size the relative discrepancy ΔMnn′(between computed and exact M) is averaged for several (n, n′) to 5.4 × 10−4 for the CSM and to 8.5 × 10−6 for the present SSM. This improvement in accuracy is supplemented by a reduction in computer time consumption. © John Wiley & Sons, Inc.
Use of molecular dynamics simulations with ab initio SCF calculations for the determination of the deuterium quadrupole coupling constant in liquid water and bond lengths in ice
Authors: Eggenberger Rolf , Gerber Stefan , Huber Hanspeter , Searles Debra , Welker Marc 
Published: January 2005

AbstractThe deuterium quadrupole coupling constant and asymmetry parameter in heavy water were determined using ab initio SCF calculations. Snapshots from a molecular dynamics simulation were used to give liquid water cluster configurations and the influence of simulation parameters on the quadrupole coupling constant was investigated. The electronic potential model and the number of molecules in the molecular dynamics simulation and the pressure of the system were found to have only a small influence on the quadrupole coupling constant. The average value of the quadrupole coupling constant at room temperature, corrected for the known deficiency of the ab initio calculation in the gas phase, yields a quadrupole coupling constant of 253 kHz, in perfect agreement with the most recent experiments. The oxygen—deuterium bond lengths in ice Ih, ice II, and ice IX were determined using experimental quadrupole coupling constants and a model equation. An averaged bond length of 98.9 pm was obtained for the Ih form, which is approximately 2 pm shorter than that determined by neutron diffraction studies, whereas the bond lengths for the four deuterium sites in ice II and the three sites in ice IX are in fair agreement with experiment. © John Wiley & Sons, Inc.
Implementation of a data parallel, logical domain decomposition method for interparticle interactions in molecular dynamics of structured molecular fluids
Authors: Young William S. , Brooks Charles L. 
Published: January 2005

AbstractIn this article, we describe a domain decomposition method for the efficient parallel computation of nonbonded forces and energies in condensed‐phase molecular systems. This decomposition is based upon the monotonic logical grid (MLG) approach of Boris [J. Boris, J. Comp. Phys., 66, 1 (1986)] and yields an efficient, scalable algorithm for interparticle interaction computation on private‐memory, single‐instruction multiple‐data (SIMD) parallel computers. We illustrate the application of this technique in a molecular dynamics kernel for rigid molecular solvents by simulating the structural and thermodynamic properties of water and methanol. The performance of this algorithm on the Thinking Machines' CM‐2, private‐memory SIMD computer, is demonstrated to be good compared to conventional vector/parallel supercomputers. However, as the fluid becomes less structured performance slightly degrades. © 1994 by John Wiley & Sons, Inc.
Applicability of the WKB method in asymmetric double wells with degenerate and nondegenerate minima
Authors: Gelabert Ricard , Moreno Miquel , Lluch José M. 
Published: January 2005

AbstractTo test the applicability of the WKB semiclassical approximation to correctly describe the tunneling frequencies and energy levels in asymmetric double wells, we have considered the cases where the asymmetry comes from the nondegeneracy of the two minima and when it comes from the asymmetry in the shape of the barrier between both minima. To do this, we compare the tunneling frequencies and energy levels obtained through the WKB method for symmetric and asymmetric cases with exact results obtained by a basis set procedure. Our results show that the semiclassical WKB approximation has to be used with caution for asymmetric double wells. © 1994 by John Wiley & Sons, Inc.
Rationalizing nuclear overhauser effect data for compounds adopting multiple‐solution conformations
Authors: Forster Mark J. , Mulloy Barbara 
Published: January 2005

AbstractAn algorithm is described for refining the populations of a set of multiple‐solution conformers using experimental nuclear Overhauser effects (nOes). The method is based upon representing the effective relaxation matrix for the set of interconverting proposed conformers as a linear combination of relaxation matrices (LCORMs) due to each conformer. The conformer population derivative of the nOe is derived from a Taylor series expression for the calculated nOe. This derivative may then be used in a standard nonlinear least‐squares refinement procedure. The LCORM nOe procedure is tested using a monosaccharide system, 1‐O‐methyl‐α‐L‐iduronate, that is known to exhibit conformational variability. The measured nOes for this system are used to refine the populations of a set of three static conformers, namely, the 1C4, 4C1, and 2S0 ring conformers. The populations thus derived are compared to those previously obtained using nuclear magnetic resonance proton‐proton coupling constant information. Two possible extensions to the method are discussed: The first uses combined nOe and coupling constant data while the second removes the restrictions that the conformers used for fitting be rigid entities. © 1994 by John Wiley & Sons, Inc.
Preconditioners for distance matrix algorithms
Authors: Glunt W. , Hayden T. L. , Raydan M. 
Published: January 2005

AbstractA recent gradient algorithm in nonlinear optimization uses a novel idea that avoids line searches. This so‐called spectral gradient algorithm works well when the spectrum of the Hessian of the function to be minimized has a small range or is clustered. In this article, we find a general preconditioning method for this algorithm. The preconditioning method is applied to the stress function, which arises in many applications of distance geometry, from statistics to finding molecular conformations. The Hessian of stress is shown to have a nice block structure. This structure yields a preconditioner which decreases the amount of computation needed to minimize stress by the spectral gradient algorithm. © 1994 by John Wiley & Sons, Inc.
Force field calculations (MM3) on glyoxal, quinones, and related compounds
Authors: Allinger Norman L. , Fan Yi 
Published: January 2005

AbstractA general force field type of calculation has been devised in connection with MM3 to treat 1,2‐ and 1,4‐diketones, both when they are not conjugated (as in derivatives of glyoxal) and when they are conjugated (as in derivatives of ortho‐ and para‐benzoquinone). The molecular structures, moments of inertia, dipole moments, and vibrational spectra have been examined for about 15 compounds, some in several conformations. Ab initio calculations (6‐31G*) have been used to determine quantities that have not been previously defined by experiment. In general, the force field permits the calculation of the structures with high accuracy, and the spectroscopic and conformational energy data with fair accuracy. © 1994 by John Wiley & Sons, Inc.
Finite‐state and reduced‐parameter representations of protein backbone conformations
Authors: Buturović Ljubomir J. , Smith Temple F. , Vajda Sandor 
Published: January 2005

AbstractThis article studies the representation of protein backbone conformations using a finite number of values for the backbone dihedral angles. We develop a combinatorial search algorithm that guarantees finding the global minima of functions over the configuration space of discrete protein conformations, and use this procedure to fit finite‐state models to the backbones of globular proteins. It is demonstrated that a finite‐state representation with a reasonably small number of states yields either a small root‐mean‐square error or a small dihedral angle deviation from the native structure, but not both at the same time. The problem can be resolved by introducing limited local optimization in each step of the combinatorial search. In addition, it is shown that acceptable approximation is achieved using a single dihedral angle as an independent variable in local optimization. Results for 11 proteins demonstrate the advantages and shortcomings of both the finite‐state and reduced‐parameter approximations of protein backbone conformations. © 1994 by John Wiley & Sons, Inc.
Molecular simulation of alkyl boronic acids: Molecular mechanics and solvation free energy calculations
Authors: Chen Xiannong , Bartolotti Libero , Ishaq Khalid , Tropsha Alexander 
Published: January 2005

AbstractThe alkyl boronic acid moiety is incorporated into many biologically interesting structures. To provide parameters for molecular mechanics and dynamics studies of compounds containing this group, we performed ab initio calculations at the 6‐31G* level to obtain bond stretching, bending, and torsion constants. The hydrodynamic formulation of the time‐dependent density functional theory was used to calculate the attractive part of van der Waals (VDW) 6–12 potential. The geometry of boronic acid moiety of the 6‐31G* optimized methyl boronic acid was similar to that of the X‐ray crystal structure of phenyl boronic acid. To test the reliability of nonbonded parameters, Monte Carlo free energy perturbation simulations and the thermodynamic cycle approach were used to estimate the differences in solvation free energy between alkyl alcohol and alkyl boronic acid, both in water and in chloroform. These free energy differences were also obtained experimentally by measuring the vapor–water and water–chloroform partition coefficients. The close agreement between experimental values and the results of our simulations suggests the reliability of new molecular mechanics force‐field parameters for alkyl boronic acids. © 1994 by John Wiley & Sons, Inc.
Variation of atomic charges during proton transfer in hydrogen bonds
Authors: FloriáN Jan , Scheiner Steve 
Published: January 2005

AbstractThe point atomic charges in a number of ionic H‐bonded systems are studied by ab initio calculations as functions of the proton transfer coordinate. In the proton‐bound complexes of water–water, ammonia–ammonia, formamide–water, formamide–ammonia, and dimethylether–ammonia, the net atomic charges were obtained using Mulliken population analysis and from the diagonal elements of the atomic polar tensors calculated at the HF/4–31G and MP2/6–31 + G** levels. The dependence of the atomic charges upon the coordinate of the transferring proton was found to be close (within an error of 0.02 e) to a linear function for intermolecular distances in the 2.5–2.8 Å range. The obtained charge and charge flux dependencies highlight the electron redistribution during the proton transfer process and provide insights into the source of the high infrared (IR) intensities of stretching modes of NH and OH bonds undergoing hydrogen bonding. © 1994 by John Wiley & Sons, Inc.
Interaction between carbon dioxide and naphthalene: A molecular modeling approach
Authors: Battersby P. , Dean J. R. , Hitchen S. M. , Tomlinson W. R. , Myers P. M. 
Published: January 2005

AbstractThe formation of a charge‐transfer complex between carbon dioxide and naphthalene was studied using a molecular modeling program, with the aim of studying the solubility of naphthalene in supercritical carbon dioxide. The orbitals involved in the formation of the complex were studied using MINDO/3 as the semi‐empirical method. A solvent cage was constructed, and the maximum number of carbon dioxide molecules to surround naphthalene was found to be 20. The heat of interaction of the complex was obtained using MINDO/3. © 1994 by John Wiley & Sons, Inc.
Structures and stabilization energies of methyl anions with main group substituents from the first five periods
Authors: El‐Nahas Ahmed M. , Schleyer Paul Von Ragué 
Published: January 2005

AbstractThe effects of substituents (X) on the structures and stabilities of CH2X− anions for groups comprised of fourth‐ and fifth‐period main group elements (X = K, CaH, GaH2, GeH3, AsH2, SeH, Br, Rb, SrH, InH2, SnH3, SbH2, TeH, and I) have been investigated by ab initio pseudopotential calculations. Full geometry optimizations have been carried out on the CH2X− anions and the corresponding neutral parent molecules, CH3X, at HF/DZP + and MP2/DZP + levels. Results for substituents from the second (X = LiF) and third (X = NaCl) periods provide comparisons of substituent effects of the main group elements of the first four rows of the periodic table on methyl anions. Frequency calculations characterize the nature of stationary points and show pyramidal CH2X− anion structures to be the most stable unless π acceptor interactions (e.g., with BH2, AlH2, GaH2, and InH2 favor planar geometries. The CH2X− stabilization energies [at QCISD(T)/DZP + /MP2/DZP + + ZPE level for X = KI and QCISD(T)/6−31 + G*/MP2/6−31 + G* + ZPE level] for X = LiCl) also show strong π‐stabilizing effects for the same substituents. With the exception of CH3 and NH2, all substituents stabilize methyl anions, although the σ stabilization by OH and F is small. The SiH3PH2SHCl, GeH3AsH2SeHBr, and SnH3SbH2TeHI sets of substituents give stabilization energies between 19 and 30 kcal/mol. The stability of methyl anions substituted by the halogens and the chalcogens (X = OH, SH, SeH, and TeH) increases down a group in accord with the increasing substituent polarizability, while for π acceptors (BH2, AlH2, GaH2, and InH2) the stability decreases down a group in line with their π‐accepting ability. © 1994 by John Wiley & Sons, Inc.
Direct search methods for the molecular conformation problem
Authors: Meza J. C. , Martinez M. L. 
Published: January 2005

AbstractAn important area of research in computational biochemistry is the design of molecules for specific applications. The design of these molecules, which depends on the accurate determination of their three‐dimensional structure, can be formulated as a global optimization problem. In this article, we present results from the application of a new conformation searching method based on direct search methods. We compare these results to some earlier results using genetic algorithms and simulated annealing. © 1994 by John Wiley & Sons, Inc.
New spherical‐cutoff methods for long‐range forces in macromolecular simulation
Authors: Steinbach Peter J. , Brooks Bernard R. 
Published: January 2005

AbstractNew atom‐ and group‐based spherical‐cutoff methods have been developed for the treatment of nonbonded interactions in molecular dynamics (MD) simulation. A new atom‐based method, force switching, leaves short‐range forces unaltered by adding a constant to the potential energy, switching forces smoothly to zero over a specified range. A simple improvement to group‐based cutoffs is presented: Switched group‐shifting shifts the group–group potential energy by a constant before being switched smoothly to zero. Also introduced are generalizations of atom‐based force shifting, which adds a constant to the Coulomb force between two charges. These new approaches are compared to existing methods by evaluating the energy of a model hydrogen‐bonding system consisting of two N‐methyl acetamide molecules and by full MD simulation. Thirty‐five 150 ps simulations of carboxymyoglobin (MbCO) hydrated by 350 water molecules indicate that the new methods and atom‐based shifting are each able to approximate no‐cutoff results when a cutoff at or beyond 12 Å is used. However, atom‐based potential‐energy switching and truncation unacceptably contaminate group–group electrostatic interactions. Group‐based potential truncation should not be used in the presence of explicit water or other mobile electrostatic dipoles because energy is not a state function with this method, resulting in severe heating (about 4 K/ps in the simulations of hydrated MbCO). The distance‐dependent dielectric (ϵ ∝︁ r) is found to alter the temperature dependence of protein dynamics, suppressing anharmonic motion at high temperatures. Force switching and force shifting are the best atom‐based spherical cutoffs, whereas switched group‐shifting is the preferred group‐based method. To achieve realistic simulations, increasing the cutoff distance from 7.5 to 12 Å or beyond is much more important than the differences among the three best cutoff methods. © 1994 by John Wiley & Sons, Inc.This article is a US Government work and, as such, is in the public domain in the United States of America.
Iterative methods for the calculation of a few of the lowest eigenvalues and corresponding eigenvectors of the AX = λBX equation with real symmetric matrices of large dimension
Authors: Mitin Alexander V. 
Published: January 2005

AbstractNew methods for the iterative calculation of a few of the lowest eigenvalues and corresponding eigenvectors of a generalized eigenvalue problem are proposed. These methods use only multiplication of the A and B matrices on a vector. © 1994 by John Wiley & Sons, Inc.
Long‐time overdamped Langevin dynamics of molecular chains
Authors: Grønbech‐jensen Niels , Doniach Sebastian 
Published: January 2005

AbstractWe present a novel algorithm of constrained, overdamped dynamics to study the long‐time properties of peptides, proteins, and related molecules. The constraints are applied to an all‐atom model of the molecule by projecting out all components of the nonbonding interactions which tend to alter fixed bond lengths and angles. Because the overdamped dynamical equations are first order in time, the constraints are satisfied by inversion of a banded matrix at each timestep, which is computationally efficient. Thermal effects are included through a Langevin noise term in the equation of motion. Because high‐frequency components of the motion have been eliminated, the timestep of the algorithm is determined by the nonbonding forces, which are two to three orders of magnitude weaker than the bonding forces. Using polyalanine as a test example, we demonstrate that trajectories simulating a microsecond of motion can be run about 103 times faster than an equivalent molecular dynamics simulation. © 1994 by John Wiley & Sons, Inc.
Decomposition analyses of the intermolecular interaction energies in two ππ stacking complexes: Quinhydrone and N,N,N′, N′‐tetramethyl‐P‐diaminobenzene‐chloranil complex
Authors: Kurita Yasuyuki , Takayama Chiyozo , Tanaka Shizuya 
Published: January 2005

AbstractAlthough there is a similarity in the orbital interaction scheme between quinhydrone and N,N,N′,N′‐tetramethyl‐p‐diaminobenzene‐chloranil complex, the stacking conformations are different from each other. The former prefers the half‐stacked conformation, whereas the latter prefers the completely stacked conformation. We have done ab initio molecular orbital calculations and decomposition analyses of the intermolecular interaction energies to clarify the origin of the different stacking conformations. It was concluded that the main origin is the difference in the steric part of the interaction energies. © 1994 by John Wiley & Sons, Inc.