bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ab initio study of some CH3OCXYCH2 radicals: The influence of anomeric effects on their structure and their stability
Authors: Arnaud R. 
Published: January 2005

AbstractOptimized equilibrium geometries and rotational transition structures for CH3OCH XCH2 (X = H, F, CH3, NH2) and CH3OCF2CH2 radicals are obtained by using unrestructed Hartree‐Fock (UHF) and second‐order Møller‐Plesset perturbation (UMP2) theory; a standard 6‐31G* basis set is used for geometry optmizations; single‐point energies for all stable rotamers are obtained at the UMP4/6‐31 + G*//UMP2/6‐31G* level. By analysis of rotamers, it is apparent that an anomeric effect exists for X = F and to a lesser extent for X = NH2. Several isodesmic reactions have been studied for the purpose of obtaining theoretical heats of formation and stabilization energies (SE) of these β substituted radicals and their α isomers; the examination of computed SE shows that in the case of CH3OCHFCH2 and CH3OCF2CH2 radicals, a significant extra stabilization induced by the anomeric effect occurs. The question of nO → σ negative hyperconjugation in β‐substituted radicals was explored with the aid of natural bond orbital (NBO) energetic analysis; it appears that nO → σ delocalization plays a predominant role in the conformational preference and stabilization of β fluoro derivatives; on the other hand, the stabilization arising from the oxygen lone pair into the σ orbital does not appear to be the key factor in the conformational preference of the CH3OCHNH2CH2 radical. © 1994 by John Wiley & Sons, Inc.
Variational biorthogonal valence bond descriptions of 1,3‐dipoles
Authors: Malcolm Nathaniel O. J. , McDouall Joseph J. W. 
Published: January 2005

AbstractThe variational biorthogonal valence bond method is applied to the π‐electrons of six 1,3‐dipoles (CH2N2, HCNO, CH2NHO, N2O, O3, NO2). The results are compared with those from other valence bond techniques, including a detailed comparison with the spin‐coupled valence bond approach. For CH2N2, HCNO, CH2NHO, and N2O, zwitterionic structures are predicted and it is shown that the variational biorthogonal valence bond method leads to orbitals and configuration weights which are essentially indistinguishable from those of the spin‐coupled valence bond method. However, for O3 and NO2 the techniques give contradictory results. The biorthogonal valence method predicts O3 and NO2 to be spin‐paired diradicals. Evidence from other calculations on O3 is discussed. © 1994 by John Wiley & Sons, Inc.
A rapid and efficient algorithm for packing polypeptide chains by energy minimization
Authors: Gibson Kenneth D. , Scheraga Harold A. 
Published: January 2005

AbstractAn improved algorithm for packing polypeptide chains with fixed geometry, which converges to a local energy minimum rapidly and efficiently, is described. The speed of convergence of the new algorithm is comparable to that of existing algorithms for minimizing the energies of single polypeptide chains, and it is several times greater than the speed of convergence of previous algorithms for minimizing the energy of structures consisting of several polypeptide chains. The algorithm has been used to minimize the energy of three‐stranded (L‐Ala)8 β‐sheets, three‐stranded (L‐Val)6 β‐sheets, and five‐stranded (L‐Ile)6 β‐sheets, starting from regular structures found previously; of the three‐stranded regular and truncated (Gly‐L‐Pro‐L‐Pro)4 structures used in earlier work to model collagen; and of the stacked β‐sheet (L‐Ala‐GLy)6 structures used to model silk. The antiparallel L‐Ala β‐sheet, and Gly‐Pro‐Pro triple helices, and the silk II structure remained nearly regular after energy minimization, but by contrast with results from earlier computations the other structures became significantly irregular. © 1994 by John Wiley & Sons, Inc.
Molecular mechanics (MM3) calculations on azoxy compounds
Authors: Fan Yi , Allinger Norman L. 
Published: January 2005

AbstractThe MM3 force field has been extended to include azoxy compounds and also the related amine oxides, both aliphatic and aromatic. The structures of nine molecules were all well fit. The heats of formation for the aliphatic compounds were also well fit, and the vibrational spectra of eight compounds were also fit to the accuracy expected for such calculations. Because many of the experimental data needed to derive the force field were either lacking or were inadequate, ab initio calculations on structures, optimized at the MP2/6‐31G* level, were used as needed. © 1994 by John Wiley & Sons, Inc.
Geometric molecular similarity from volume‐based distance minimization: Application to saxitoxin and tetrodotoxin
Authors: Petitjean Michel 
Published: January 2005

AbstractThe geometric molecular dissimilarity between two molecules is defined as the difference between the volume of their union minus the volume of their intersection. This dissimilarity has the mathematical properties of a distance. This distance is minimized under all rotations and translations using a discrete Broyden, Fletcher, Goldfarb & Shanno (B.F.G.S.) algorithm. The optimal geometric superimposition of saxitoxin and tetrodotoxin is discussed. © 1995 by John Wiley & Sons, Inc.
Implementation of a parallel direct SCF algorithm on distributed memory computers
Authors: Furlani Thomas R. , King Harry F. 
Published: January 2005

AbstractA parallel direct self‐consistent field (SCF) algorithm for distributed memory computers is described. Key features of the algorithm are its ability to achieve a load balance dynamically, its modest memory requirements per processor, and its ability to utilize the full eightfold index permutation symmetry of the two‐electron integrals despite the fact that entire copies of the Fock and density matrices are not present in each processor's local memory. The algorithm is scalable and, accordingly, has the potential to function efficiently on hundreds of processors. With the algorithm described here, a calculation employing several thousand basis functions can be carried out on a distributed memory machine with 100 or more processors each with just 4 MBytes of RAM and no disk. The Fock matrix build portion of the algorithm has been implemented on a 16‐node Intel iPSC/2. Results from benchmark calculations are encouraging. The algorithm shows excellent load balance when run on 4, 8, or 16 processors and displays almost ideal speed‐up in going from 4 to 16 processors. Preliminary benchmark calculations have also been carried out on an Intel Paragon. © 1995 by John Wiley & Sons, Inc.
An examination of a density functional/molecular mechanical coupled potential
Authors: Stanton Robert V. , Hartsough David S. , Merz Kenneth M. 
Published: January 2005

AbstractIn this article we describe the coupling of a density functional (DF) Hamiltonian with the molecular mechanics (MM) potential function AMBER. We examine a series of test cases in which we compare the binding energies and geometries of the complexes predicted by this coupled potential with those predicted by other theoretical methods and experiment to establish the relative accuracy of the DF/MM coupled potential. We find that the DF/MM coupled potential performs well in most cases studied and, in general, outperforms the semiempirical/MM approach. The interaction energies and structures obtained using this method appear to be insensitive to the use of nonlocal (NL) corrections to the DF method. The is fortuitous because the NL treatment is significantly more computationally expensive than the local treatment. However, NL corrections may be required to predict accurately the shape of potential energy surfaces that involve bond breaking and formation. The DF/MM method has also been applied to the determination of the solvation free energy for a series of ions using free‐energy perturbation methods. The results obtained are good and can be improved by a simple scaling of the Lennard‐Jones parameters for the ion in question. © 1995 by John Wiley & Sons, Inc.
Solving the finite‐difference, nonlinear, Poisson–Boltzmann equation under a linear approach
Authors: Zhexin Xiang , Yunyu Shi , Yinwu Xu 
Published: January 2005

AbstractElectrostatic interactions are among the key factors in determining the structure and function of biomolecules. Simulating such interactions involves solving the Poisson equation and the Poisson‐Boltzmann (P‐B) equation in the molecular interior and exterior region, respectively. The P‐B equation is a nonlinear partial differential equation. The central processing unit (CPU) time for solving the full nonlinear P‐B equation has been severalfold greater than the equivalent linear case. Here a simple method is proposed to solve the full nonlinear P‐B equation under a linear approach, which has been tested both on a spherical case and on small molecules. Results show that our method converges rapidly even under highly charged cases. With this method, the CPU time for solving the full nonlinear P‐B equation is somewhat less than the equivalent linear case in our calculations. © 1995 by John Wiley & Sons, Inc.
The geometry of pyrazole: A test for ab initio calculations
Authors: Llamas‐Saiz Antonio L. , Foces‐Foces Concepción , Mó Otilia , Yáñez Manuel , Elguero Eric , Elguero José 
Published: January 2005

AbstractAb initio calculations on the structure of pyrazole have been carried out at different levels of accuracy. At the Hartree‐Fock (HF) level, the performance of several basis sets, namely 3‐21G, 6‐31G, 6‐31G**, and 6–311G** was investigated. The influence of electron correlation effects also was studied by carrying out geometry optimizations at the MP2, MP4, and QCISD levels. The performance of a density functional method also was evaluated. We have also investigated the possible influence of the frozen core approximation on the final optimized geometry. Three different statistical analyses were considered in determining which geometry is closest to the experimental microwave geometry—namely Paul Curtin's diagrams, cluster analysis, and multidimensional scaling. From these analyses, we conclude that there is no asymptotic approach to the experimental geometry by increasing the quality of the theoretical model, although, as expected, the more reliable structures are those obtained at the MP2, MP4, and QCISD levels, as well as those obtained by the B3LYP density functional method. We have also found that the values of the rotational constants are a tight criterion to define the quality of a molecular geometry. © 1995 by John Wiley & Sons, Inc.
Small‐amplitude protein conformational dynamics: Second‐order analytic relation between cartesian coordinates and dihedral angles
Authors: Sunada Shinji , Go Nobuhiro 
Published: January 2005

AbstractAn analytic expression for protein atomic displacements in Cartesian coordinate space (CCS) against small changes in dihedral angles is derived. To study time‐dependent dynamics of a native protein molecule in CCS from dynamics in the internal coordinate space (ICS), it is necessary to convert small changes of internal coordinate variables to Cartesian coordinate variables. When we are interested in molecular motion, six degrees of freedom for translational and rotational motion of the molecule must be eliminated in this conversion, and this conversion is achieved by requiring the Eckart condition to hold. In this article, only dihedral angles are treated as independent internal variables (i.e., bond angles and bond lengths are fixed), and Cartesian coordinates of atoms are given analytically by a second‐order Taylor expansion in terms of small deviations of variable dihedral angles. Coefficients of the first‐order terms are collected in the K matrix obtained previously by Noguti and Go (1983) (see ref. 2). Coefficients of the second‐order terms, which are for the first time derived here, are associated with the (newly termed) L matrix. The effect of including the resulting quadratic terms is compared against the precise numerical treatment using the Eckart condition. A normal mode analysis (NMA) in the dihedral angle space (DAS) of the protein bovine pancreatic trypsin inhibitor (BPTI) has been performed to calculate shift of mean atomic positions and mean square fluctuations around the mean positions. The analysis shows that the second‐order terms involving the L matrix have significant contributions to atomic fluctuations at room temperature. This indicates that NMA in CCS involves significant errors when applied for such large molecules as proteins. These errors can be avoided by carrying out NMA in DAS and by considering terms up to second order in the conversion of atomic motion from DAS to CCS. © 1995 by John Wiley & Sons, Inc.
Parallel computation of the MP2 energy on distributed memory computers
Authors: Márquez Antonio M. , Dupuis Michel 
Published: January 2005

AbstractA parallel distributed implementation of the second‐order Møller‐Plesset perturbation theory method, widely used in quantum chemistry, is presented. Parallelization strategy and performance for the HONDO quantum chemistry program running on a network of Unix computers are also discussed. Superlinear speedups are obtained through a combined use of the CPU and memory of the different processors. Performance for standard and direct algorithms are presented and discussed. A superdirect algorithm that eliminates the communication bottleneck during the integral transformation step is also proposed. © 1995 by John Wiley & Sons, Inc.
SINDO1 study of the photoreaction of tetramethylene sulfone
Authors: Gerwens Heiko , Jug Karl 
Published: January 2005

AbstractThe mechanism of the photoreaction of tetramethylene sulfone (TMSO2) was investigated by the semiempirical molecular orbital (MO) method SINDO1. The relevant low‐lying potential energy surfaces, which were calculated with limited configuration interaction (CI), were studied by optimizing intermediates and transition structures and by introducing linear interpolations between these stationary points. The main initial reaction step for all important products is an α cleavage of one CS bond. This leads to an intermediate that can be classified as an excited singlet diradical. Its electronic structure is described with a two‐electron, three‐orbital model. Starting from this initially generated intermediate, the reaction branches into several pathways leading to various products. Feasible reaction pathways were established for all important products consistent with experiments. © 1995 by John Wiley & Sons, Inc.
Fast, fuzzy c‐means clustering of data sets with many features
Authors: Alsberg Bjørn K. 
Published: January 2005

AbstractA fuzzy c‐means clustering algorithm is presented which is much faster than the traditional algorithm for data sets in which the number of features is significantly larger than the number of feature vectors. The algorithm is constructed by utilizing the covariance structure of feature vectors and cluster centers. By using results from a previous clustering, modified versions of the new algorithm achieve additional reductions in floating point operations. © 1995 by John Wiley & Sons, Inc.
Force and virial of torsional‐angle‐dependent potentials
Authors: Bekker H. , Berendsen H. J. C. , van Gunsteren W. F. 
Published: January 2005

AbstractSimple expressions for the forces due to dihedral‐angle interactions are derived using first principles of mechanics. The expressions require significantly fewer numerical operations than those generally used in the literature and provide insight into the physics of dihedral‐angle interactions. It is also shown that the scalar virial due to angle‐dependent interactions is zero. © 1995 by John Wiley & Sons, Inc.
An empirical force field. I. Alkanes
Authors: Dillen Jan L. M. 
Published: January 2005

AbstractA new empirical force field for saturated hydrocarbons is presented. It is applicable to gaseous and crystalline alkanes that do not contain four‐ or three‐membered rings. The force field allows the calculation of structural, thermodynamic, and vibrational properties of both simple and highly strained molecules to an accuracy comparable to experiment. Vibrational frequencies are improved considerably as compared to MM3. © 1995 by John Wiley & Sons, Inc.
Theoretical study of the gas‐phase addition of HF and HCl to ethylene: Analysis of the catalytic action of dimeric halides
Authors: Menéndez M. I. , Suárez D. , Sordo J. A. , Sordo T. L. 
Published: January 2005

AbstractAb initioMP2/6‐31G** calculations render the same mechanism for the gas‐phase addition of HF and HCl to ethylene in contrast with previous HF/3‐21G calculations. The leading interaction is in both cases the electrophilic attachment of the hydrogen atom in the hydrogen halide to a carbon atom in ethylene. The presence of a second molecule of hydrogen halide causes a catalytic effect by allowing an alternative mechanism for electron density rearrangement through ethylene polarization. © 1995 by John Wiley & Sons, Inc.
Efficient conformational space sampling for nucleosides using internal coordinate Monte Carlo simulations and a modified furanose description
Authors: Gabb H. A. , Lavery R. , Prévost C. 
Published: January 2005

AbstractInternal coordinates can be very helpful in modeling large biomacromolecules because freezing stiffer degrees of freedom, such as bond lengths, strongly reduces the number of variables describing the system. This, however, leads to difficulties in treating flexible rings such as the furanose sugars of nucleic acids or the proline residues of proteins, for which internal coordinates are an overcomplete description. We present here a new, internal coordinate furanose model based on the pseudorotational variables phase and amplitude which avoids having to solve a ring closure problem. The choice of a two‐ rather than a four‐variable description is justified by a detailed analysis of molecular dynamic simulations. The efficiency and accuracy of the method are also demonstrated using extensive Monte Carlo simulations. This method of ring treatment is fast and well adapted to macromolecular simulations. © 1995 by John Wiley & Sons, Inc.
Potential energy function for cation–peptide interactions: An ab initio study
Authors: Roux Benoît , Karplus Martin 
Published: January 2005

AbstractA potential energy function is developed to represent the interaction of small monovalent cations, Li+, Na+, and K+, with the backbone of polypeptides. The results are based on ab initio calculations up to the 6‐31G* level of the interactions of the ions with acetamide and N‐methylacetamide. Basis set superposition errors are corrected with the counterpoise method. A systematic overestimate of the bond polarities is taken into account by an empirical scaling procedure that uses the ratio of the experimental to ab initio dipole moment. The calculated binding energies obtained with this procedure show consistent convergence with different basis sets and are in good agreement with experimental data on cation–water and cation–dimethylformamide systems. Investigations of the calculated ab initio potential energy surface indicate that the cation–peptide interaction is dominated by electrostatics and includes a nonnegligible contribution from polarization of the peptide group by the ion. The induced polarization results in a steeper‐than‐Coulombic interaction and cannot be described by fixed ion–peptide partial charges electrostatics. Atomic polarizabilities located on the atoms of the ligand molecule are introduced to account for the induced polarization in the empirical energy function. A ∼1/r4 attractive interaction appears in the potential function. The resulting radial and angular dependence of the potential energy surface is well reproduced. © 1995 by John Wiley & Sons, Inc.
Dynamic load balancing algorithms for replicated data molecular dynamics
Authors: Young William S. , Brooks Charles L. 
Published: January 2005

AbstractAlgorithms to enhance parallel performance of molecular dynamics simulations on parallel computers by dynamic load balancing are described. Load balancing is achieved by redistribution of work based on either a history of time spent computing per processor or on the number of pair interactions computed per processor. The two algorithms we detail are designed to yield optimal load balancing on both workstation clusters and parallel supercomputers. We illustrate these methods using a small molecular dynamics kernel developed for the simulation of rigid molecular solvents. In addition, we discuss our observation regarding global communications performance on workstation clusters with a fiber distributed data interface (FDDI) using a high‐speed point‐to‐point switch (Gigaswitch) and the k‐ary 3‐cube of the Cray T3D. © 1995 by John Wiley & Sons, Inc.
The electronic structure of weakly bound systems. I. Rare‐gas bimolecular cations
Authors: López Gustavo E. 
Published: January 2005

AbstractA general perspective is presented of bimolecular positive ions formed from two rare gases that share a positive charge. These species, which are important in ionospheric processes, arise when neutral van der Waals species are ionized. A general theoretical program based on standard theoretical techniques (e.g., various configuration interaction and Møller‐Plesset techniques and quadratic configuration interaction) is outlined, and results for the geometry, stability, and vibrational frequencies for a set of rare gas dimers, AB+, are presented. Specifically, the molecules HeHe+, HeNe+, HeAr+, NeNe+, NeAr+, and ArAr+ are considered; the equilibrium geometry of the ground electronic state is determined at several levels of approximation. Then binding energies are calculated in several ways, and these binding energies are compared to experimental and other sophisticated theoretical results. In general, the agreement with experiment is good, within a few kcal/mol. Harmonic vibrational frequencies at the MP2 level are also computed. © 1995 by John Wiley & Sons, Inc.
Conformational analysis of jet‐cooled tryptophan analogs and Histamine using the MM3(94) force field: Comparison with experiment
Authors: Sulkes Mark 
Published: January 2005

AbstractMM3(94) has been used to predict the conformers of nitrogen‐containing aromatic heterocycles with polar aliphatic sidechains. Computations were done for cases in which experimental gas‐phase rotational constants have been determined and include histamine and analogs of tryptophan. The agreement with experiment for the tryptophan analogs is better than earlier MM2(87) computations but still not complete. A fairly good match can be made to experimental rotational constants of four histamine conformers, but other conformers are also predicted that may not be important experimentally. A comparison can be made with ab initio calculations undertaken for histamine. Similar structures were generally predicted, but there were significant discrepancies with MM3 in relative conformer energies. © 1995 by John Wiley & Sons, Inc.
A rapid method for calculating derivatives of solvent accessible surface areas of molecules
Authors: Sridharan S. , Nicholls Anthony , Sharp Kim A. 
Published: January 2005

AbstractA novel method to calculate the derivatives of solvent accessible surface areas is presented. Unlike earlier analytic methods, which require the molecular topology and the use of global Gauss‐Bonnet theorem, this method requires only the fractional accessibilities of surface arcs. We developed an efficient numerical algorithm to calculate the surface arcs by creating a uniform set of points on the circles of intersection between surface atoms. A hierarchical point density doubling scheme led to a logarithmic dependence of Central Processing Unit (CPU) time on the number of points used. This algorithm calculated area derivatives for a 1000‐atom protein in 1.5 s on an SGI INDIGO2 which were within 2% of the analytic area derivatives calculated with the program ANAREA. This algorithm scales linearly with the number of atoms for large molecules and is easily parallelizable. © 1995 by John Wiley & Sons, Inc.