bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformation energy around the N(sp3)O single bond
Authors: Tronchet Jean M. J. , Komaromi Istvan 
Published: January 2005

AbstractA detailed conformational analysis was performed on simple substituted hydroxylamines using either ab initio (from HF/6‐31G* to RQCISD/6‐311G**) or popular semiempirical (MNDO, AM1, PM3) methods to ascertain the allowed conformations and to establish the influence of the level of theory on the results. All the ab initio results (provision being made for their expected divergences) are similar and show a simple twofold character for the > NO rotational energy, without any appreciable populations of the cis conformer. On the other hand, the predictive value of the semiempirical methods for structural and energetical parameters of molecules bearing > NO moieties is limited, a situation like that prevailing for peptide bonds. The inversional barriers for the methyl‐substituted hydroxylamines were also calculated and compared to the corresponding rotational energy barriers. Rotation is generally favored over inversion for hydroxylamine and its methylated derivatives. © 1994 by John Wiley & Sons, Inc.
Stable conformations of CH3CH2OCH2CH2OH: A comparison of theoretical methods
Authors: Luke Brian T. 
Published: January 2005

AbstractThis article presents the results of an extensive examination of the stable conformations of CH3CH2OCH2CH2OH at various levels of theory. In particular, 41 initial conformations are optimized using the MM2 force field in BIGSTRN‐3; the MINDO/3, MNDO, and AM1 Hamiltonians in AMPAC 2.2; the PM3 Hamiltonian in MOPAC 7.0; and at the HF/STO‐3G and HF/3‐21G levels using Gaussian 92. The optimized HF/3‐21G structures are reoptimized at the HF/6‐31G(d) level, and the unique structures are optimized again at the MP2 = FULL/6‐31G(d) level. In addition, single‐point MP2/6‐31G(d) calculations are performed using the HF/6‐31G(d) geometries. The goal is to determine the relative accuracy of each method and discuss their strengths and weaknesses. © 1994 by John Wiley & Sons, Inc.
A rapidly convergent simulation method: Mixed Monte Carlo/stochastic dynamics
Authors: Guarnieri Frank , Still W. Clark 
Published: January 2005

AbstractAlthough Monte Carlo and molecular dynamics are the primary methods used for free energy simulations of molecular systems, their application to molecules that have multiple conformations separated by energy barriers of ≥ 3 kcal/mol is problematic because of slow rates of convergence. In this article we introduce a hybrid simulation method termed MC‐SD which mixes Monte Carlo (MC) and stochastic dynamics (SD). This new method generates a canonical ensemble via alternating MC and SD steps and combines the local exploration strengths of dynamics with the barrier‐crossing ability of large‐step Monte Carlo. Using calculations on double‐well potentials and long simulations (108 steps of MC and 1 μs of SD) of the simple, conformationally flexible molecule n‐pentane, we find that MC‐SD simulations converage faster than either MC or SD alone and generate ensembles which are equivalent to those created by classical MC or SD. Using pure SD at 300 K, the conformational populations of n‐pentane are shown to be poorly converged even after a full microsecond of simulation. © 1994 by John Wiley & Sons, Inc.
Molecular mechanics calculations (MM2 and MM3) on enamines and aniline derivatives
Authors: Allinger N. L. , Yan Liqun , Chen Kuohsiang 
Published: January 2005

AbstractThe MM2 and MM3 force fields have been extended to cover this class of compounds. Structures, vibrational spectra, and other data for 13 compounds were examined and can be reproduced satisfactorily by MM3. Except for the spectra, the other data can be reproduced somewhat less well by MM2. © 1994 by John Wiley & Sons, Inc.
Atomic radii scales and electron properties deduced from the charge density
Authors: Pacios L. Fernández 
Published: January 2005

AbstractA procedure to represent Hartree‐Fock electron densities in atoms [L. Fernandez Pacios,J. Comp. Chem.,14, 410 (1993)] defines ρ(r) as a reduced expansion of exponential functions. These analytically modeled densities (AMDs) are used in this article to develop a simple computational procedure for analyzing different atomic radii scales implemented in the commercial software system MATHEMATICA. The analysis is focused on the physical information associated to a given atomic radius as deduced from calculations depending on ρ(r). The amount of electron charge contained in the sphere of the given radius as well as the distinct contributions to the potential energy integrated up to that radius are obtained within the AMD formulation for main‐group atoms H—Kr. The ASCII file needed to run the procedure within MATHEMATICA is also presented. © 1995 by John Wiley & Sons, Inc.
Geometry‐dependent atomic charges: Methodology and application to alkanes, aldehydes, ketones, and amides
Authors: Dinur U. , Hagler A. T. 
Published: January 2005

AbstractA general methodology for deriving geometry‐dependent atomic charges is presented. The main ingredient of the method is a model that describes the molecular dipole moment in terms of geometry‐dependent point charges. The parameters of the model are determined from ab initio calculations of molecular dipole moments and their Cartesian derivatives at various molecular geometries. Transferability of the parameters is built into the model by fitting ab initio calculations for various molecules simultaneously. The results show that charge flux along the bonds is a major contributing factor to the geometry dependence of the atomic charges, with additional contributions from fluxes along valence angles and adjacent bonds. Torsion flux is found to be smaller in magnitude than the bond and valence angle fluxes but is not always unimportant. A set of electrostatic parameters is presented for alkanes, aldehydes, ketones, and amides. Transferability of these parameters for a host of molecules is established to within 3 −5% error in the predicted dipole moments. A possible extension of the method to include atomic dipoles is outlined. With the inclusion of such atomic dipoles and with the set of transferable point charges and charge flux parameters, it is demonstrated that molecular electrostatic potentials as well as electrostatic forces on nuclei can be reproduced much better than is possible with other models (such as potential derived charges). © 1995 by John Wiley & Sons, Inc.
Poling: Promoting conformational variation
Authors: Smellie Andrew , Teig Steven L. , Towbin Peter 
Published: January 2005

AbstractThis article introduces several methods of assessing the extent to which a collection of conformations represents or covers conformational space. It also describes poling: a novel technique for promoting conformational variation that can be applied to any method of conformational analysis that locally minimizes a penalty or energy function. The function being minimized is modified to force similar conformers away from each other. The method is independent of the origin of the initial conformers and of the particular minimization method used. It is found that, with the modification of the penalty function, clustering of the resulting conformers is generally unnecessary because the conformers are forced to be dissimilar. The functional form of the poling function is presented, and the merits are discussed with reference to (1) efficacy at promoting variation and (2) perturbation of the unmodified function. Results will be presented using conformers obtained from distance geometry with and without poling. It will be shown that the addition of poling eliminates much redundancy in conformer generation and improves the coverage of the conformational space. © 1995 by John Wiley & Sons, Inc.
Parallel implementation of a mesh‐based density functional electronic structure code
Authors: Li Y. S. , Wrinn M. C. , Newsam J. M. , Sears M. P. 
Published: January 2005

AbstractWe describe the implementation of the mesh‐based first‐principles density functional code DMol on nCUBE 2 parallel computers. The numerical mesh nature of DMol makes it naturally suited for a massively parallel computational environment. Our parallelization strategy consists of a domain decomposition of mesh points. This evenly distributes mesh points to all available processors and leads to a substantial computational speedup with limited communication overhead and good node balancing. To achieve better performance and circumvent memory storage limitations, the torus wrap method is used to distribute both the Hamiltonian and overlap matrices, and a parallel matrix diagonalization routine is employed to calculate eigenvalues and eigenvectors. Benchmark calculations on a 128‐node nCUBE 2 are presented. © 1995 by John Wiley & Sons, Inc.
Evaluation of moment statistics for molecular modeling
Authors: Lipkowitz Kenny B. , Peterson Michael A. 
Published: January 2005

AbstractThe concept of moment statistics for evaluating conformations of molecules derived from molecular dynamics simulations is presented. A comparison of the rigidity of tetralin with benzene and cyclohexane, the effect of “tooth thickness” in geared systems, the fluctional motion of a linear alkane, and the differences between dynamical motions of hydrogen‐bonded systems in gas versus solution phases were studied. The strengths and weaknesses of implementing moment statistics as a tool for data reduction are described. © 1995 by John Wiley & Sons, Inc.
Prediction of LUMO energy and rate constant by comparative molecular field analysis (CoMFA)
Authors: Yoo Sung‐Eun , Cha Ok Ja 
Published: January 2005

AbstractWe used the comparative molecular field analysis (CoMFA) method to correlate the rate constant (log k) for the SN2 reaction of benzyl benzenesulfonates and p‐methoxybenzylamines. Molecular fields calculated with a C+ probe produced a good correlation with a small standard deviation and a high correlation coefficient with cross validation. This study demonstrated that CoMFA is an excellent method in predicting the physicochemical properties of the molecule such as LUMO energy and rate constants. © 1995 by John Wiley & Sons, Inc.
Parameterization and evaluation of a flexible water model
Authors: Ferguson David M. 
Published: January 2005

AbstractThe thermodynamic, dielectric, and dynamic properties of a newly parameterized flexible water model are studied using molecular dynamics simulations. The potential function developed is based on the popular simple point charge (SPC) rigid model with the addition of appropriate harmonic and anharmonic energy terms for stretching and bending. Care was taken to account for the self‐polarization and gas‐phase monomer energy corrections during the parameterization, which have typically been ignored in past studies. The results indicate that an increased Lennard‐Jones repulsive coefficient and slightly scaled partial charges are required when adding flexibility to the rigid model potential to reliably reproduce the experimental density, energy, and O ⃛ O radial distribution function of water at 298 K and 1 atm. Analysis of the power spectrum derived from the H‐velocity autocorrelation function allowed the water potential to be evaluated further and refined by adjusting the valence forces to fit the vibrational frequencies of the gas and liquid. Once a consistent set of parameters was determined, the static dielectric properties of the water model were calculated at two temperatures using the reaction field method to treat long‐range forces and correlations. The dielectric constant of 75 ± 7 calculated at 300 K is in good agreement with the experimental value of 78.5. The Kirkwood g factor was also examined for temperature dependence and showed the correct increasing behavior with decreasing T. As a final check of the water potential, the free energies of solvation of a flexible water molecule and neon were predicted using thermodynamic perturbation methods. The calculated solvation energies of −7.0 ± 0.8 for water and 2.7 ± 0.7 for neon are both consistent with the experimental values of −6.3 and 2.7 kcal/mol. Comparisons are made throughout the study with the results of previous rigid and flexible model simulations. © 1995 by John Wiley & Sons, Inc.
The true diatomic potential as a perturbed Morse function
Authors: Dagher Mounzer , Kobersi Mounif , Kobeissi Hafez 
Published: January 2005

AbstractThe problem of representing a diatomic (true) Rydberg‐Klein‐Rees potential Ut by an analytical function Ua is discussed. The perturbed Morse function is in the form Ua = UM + ∑bnyn, where the Morse potential is UM = Dy2, y = 1 −exp(−;a(r − re)). The problem is reduced to determination of the coefficients bn so Ua(r) = Ut(r). A standard least‐squares method is used, where the number N of bn is given and the average discrepancy ΔU = |(Ut − Ua)/Ut| is observed over the useful range of r. N is varied until ΔU is stable. A numerical application to the carbon monoxide X1∑ state is presented and compared to the results of Huffaker1 using the same function with N = 9. The comparison shows that the accuracy obtained by Huffaker is reached in one model with N = 5 only and that the best ΔU is obtained for N = 7 with a gain in accuracy. Computation of the vibrational energy Ev and the rotational constant Bv, for both potentials, shows that the present method gives values of ΔE and ΔB that are smaller than those found by Huffaker. The dissociation energy obtained here is 2.3% from the experimental value, which is an improvement over Huffaker's results. Applications to other molecules and other states show similar results. © 1995 by John Wiley & Sons, Inc.
An analytical algorithm for the rapid determination of the solvent accessibility of points in a three‐dimensional lattice around a solute molecule
Authors: You Tony , Bashford Donald 
Published: January 2005

AbstractWe address the problem of marking points on a grid lattice of arbitrary size and spacing as either accessible or inaccessible to a solvent‐sized spherical probe. It is shown that an analytical description of the solvent‐accessible volume suitable for rapidly testing a large number of lattice points can be constructed from relatively simple geometric elements. By first constructing these basic analytical elements and storing them in suitable data structures, any number of subsequent lattice markings can be carried out. This approach leads to increased computational efficiency whenever a multiple calculation using different lattice sizes and scales is necessary on the same molecular geometry. We also present an algorithm for determining the analytical volume elements. Some aspects of this algorithm, particularly the method for finding all sterically allowed probe positions in which the probe simultaneously contacts three atoms, may also be useful for improving the speed and reliability of analytical surface area calculations. An object‐oriented implementation of these algorithms written in C + + is freely available via Internet. © 1995 by John Wiley & Sons, Inc.
The fast multipole boundary element method for molecular electrostatics: An optimal approach for large systems
Authors: Bharadwaj Ranganathan , Windemuth Andreas , Sridharan S. , Honig Barry , Nicholls Anthony 
Published: January 2005

AbstractWe propose a fast implementation of the boundary element method for solving the Poisson equation, which approximately determines the electrostatic field around solvated molecules of arbitrary shape. The method presented uses computational resources of order O(N) only, where N is the number of elements representing the dielectric boundary at the molecular surface. The method is based on the Fast Multipole Algorithm by Rokhlin and Greengard, which is used to calculate the Coulombic interaction between surface elements in linear time. We calculate the solvation energies of a sphere, a small polar molecule, and a moderately sized protein. The values obtained by the boundary element method agree well with results from finite difference calculations and show a higher degree of consistency due to the absence of grid dependencies. The boundary element method can be taken to a much higher accuracy than is possible with finite difference methods and can therefore be used to verify their validity. © 1995 by John Wiley & Sons, Inc.
Molecular dynamics simulation with a continuum electrostatic model of the solvent
Authors: Gilson Michael K. , McCammon J. Andrew , Madura Jeffry D. 
Published: January 2005

AbstractThe accuracy and simplicity of the Poisson‐Boltzmann electrostatics model has led to the suggestion that it might offer an efficient solvent model for use in molecular mechanics calculations on biomolecules. We report a successful merger of the Poisson‐Boltzmann and molecular dynamics approaches, with illustrative calculations on the small solutes dichloroethane and alanine dipeptide. The algorithm is implemented within the program UHBD. Computational efficiency is achieved by the use of rather coarse finite difference grids to solve the Poisson‐Boltzmann equation. Nonetheless, the conformational distributions generated by the new method agree well with reference distributions obtained as Boltzmann distributions from energies computed with fine finite difference grids. The conformational distributions also agree well with the results of experimental measurements and conformational analyses using more detailed solvent models. We project that when multigrid methods are used to solve the finite difference problem and the algorithm is implemented on a vector supercomputer, the computation of solvent electrostatic forces for a protein of modest size will add only about 0.1 s computer time per simulation step relative to a vacuum calculation. © 1995 by John Wiley & Sons, Inc.
Internal motions of carbohydrates as probed by comparative molecular modeling and nuclear magnetic resonance of ethyl β‐lactoside
Authors: Engelsen Søren Balling , Pérez Serge , Braccini Isabelle , Du Penhoat Catherine Hervé 
Published: January 2005

AbstractThe realization that conformational flexibility must be incorporated into the description of the structural and dynamical behavior of carbohydrates has stimulated the quest for an appropriate force field and associated parameterization capable of dealing with the many specific features of these molecules. Accordingly, we set out to evaluate the capacity of very different force fields to reproduce a series of experimental spectral data such as optical rotatory dispersion, coupling constants, and nuclear Overhauser effects. NOESY volumes and long‐range homonuclear and heteronuclear vicinal coupling constants were measured at 400.13 MHz. Optical rotation measurements were also performed on ethyl β‐lactoside. The conformational behavior of ethyl β‐lactoside was investigated in three different molecular mechanics force fields leading to three complete ensembles of theoretical conformations, which were used for evaluating these statistically averaged observables. The calculations of optical rotation followed a recent model based on interacting oscillators. Coupling constants were calculated using the appropriate sets of Karplus‐type equations, and theoretical nuclear magnetic resonance (NMR) relaxation data were obtained for models which account for either slow or fast internal motions. The calculated potential energy surfaces were shown to be dependent on the type of force field, even in the case of such a simple disaccharide. They differ in several respects, including the number and location of low‐energy conformers and the shallowness of the dominant primary region. It was possible to assess the different time‐averaged orientations about the glycosidic linkage of the three force fields from the fit obtained for the interglycosidic heteronuclear coupling constants. Poor fits between theoretical and experimental NOESY volumes were observed for all three force fields when the slow internal motion model was used, while a greatly improved fit was obtained when the fast internal motions model was applied. It has been shown that the motional model established from NOESY data is analogous to the one obtained from molecular dynamics simulations. The quality of the fit for the NOESY data varies with the force fields and corroborates the classification obtained from heteronuclear coupling. © 1995 by John Wiley & Sons, Inc.
IMOMM: A new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structures and transition states
Authors: Maseras Feliu , Morokuma Keiji 
Published: January 2005

AbstractA new computational scheme integrating ab initio and molecular mechanics descriptions in different parts of the same molecule is presented. In contrast with previous approaches, this method is especially designed to allow the introduction of molecular mechanics corrections in full geometry optimizations concerning problems usually studied through ab initio calculations on model systems. The scheme proposed in this article intends to solve some of the systematic error associated with modeling through the use of molecular mechanics corrections. This method, which does not require any new parameter, evaluates explicitly the energy derivatives with respect to geometrical parameters and therefore has a straightforward application to geometry optimization. Examples of its performance on two simple cases are provided: the equilibrium geometry of cyclopropene and the energy barriers on SN2 reactions of alkyl chloride systems. Results are in satisfactory agreement with those of full ab initio calculations in both cases. © 1995 by John Wiley & Sons, Inc.
Flexible ligand docking without parameter adjustment across four ligand–receptor complexes
Authors: Clark Kevin P. , Ajay  
Published: January 2005

AbstractUnderstanding molecular recognition is one of the fundamental problems in molecular biology. Computationally, molecular recognition is formulated as a docking problem. Ideally, a molecular docking algorithm should be computationally efficient, provide reasonably thorough search of conformational space, obtain solutions with reasonable consistency, and not require parameter adjustments. With these goals in mind, we developed DIVALI (Docking wIth eVolutionary AlgorIthms), a program which efficiently and reliably searches for the possible binding modes of a ligand within a fixed receptor. We use an AMBER‐type potential function and search for good ligand conformations using a genetic algorithm (GA). We apply our system to study the docking of both rigid and flexible ligands in four different complexes. Our results indicate that it is possible to find diverse binding modes, including structures like the crystal structure, all with comparable potential function values. To achieve this, certain modifications to the standard GA recipe are essential. © 1995 John Wiley & Sons, Inc.