bluuebunny/crossref_metadata_2025_split huggingface dataset:
A method for modeling icosahedral virions: Rotational symmetry boundary conditions
Authors: Çağin Tahir , Holder Michael , Pettitt B. Montgomery 
Published: January 2005

AbstractWe 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 interprotomer 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.
Atom based parametrization for a conformationally dependent hydrophobic index
Authors: Kantola Angelina , Villar Hugo O. , Loew Gilda H. 
Published: January 2005

AbstractAn atomic parametrization for the determination of a hydrophobicity index that depends on the molecular conformation is presented. The hydrophobicity parameter was calculated in four alternative ways based on charge densities and atomic contributions to the total molecular surface area and depending on the approach, the molecular dipole moment. The geometries required for the computations were calculated using quantum mechanical semiempirical methods as well as molecular mechanics. The charges were computed using semiempirical methods as well as the Gasteiger method.
Bond functions, covalent potential curves, and the basis set superposition error
Authors: Wright James S. , Barclay V. J. 
Published: January 2005

AbstractIn the current practice of quantum chemistry, it is not clear whether corrections for basis set superposition errors should be applied to the calculation of potential energy curves, in order to improve agreement with experimental data. To examine this question, spectroscopic parameters derived from theoretical potential curves are reported for the homonuclear diatomics C2, N2, O2, and F2, using a configuration interaction method. Three different basis sets were used, including double zeta plus polarization, triple zeta plus double polarization, and double zeta polarization augmented by bond functions. The bond function basis sets, which were optimized in the preceding paper to obtain accurate dissociation energies, also gave the most accurate parameters. The potential curves were then corrected for basis set superposition error using the counterpoise correction, and the spectroscopic parameters were computed again. The BSSE‐corrected curves showed worse agreement with experiment for all properties than the original (uncorrected) curves. The reasons for this finding are discussed. In addition to the numerical results, some problems in the application of the BSSE correction to basis sets containing bond functions are shown. In particular, there is an overcounting of the lowering due to the bond functions, regardless of which type of correction is applied. Also, genuine BSSE affects cannot be separated from energy‐lowering effects due to basis set incompleteness, and we postulate that it is the latter which is strongly dominant in the calculation of covalent potential curves. Based on these arguments, two conclusions follow: (1) application of BSSE corrections to potential curves should not be routinely applied in situations where the bonding is strong, and (2) appropriate use of bond functions can lead to systematic improvement in the quality of potential curves.
Effects of hydration on scale factors for ab initio force constants
Authors: Williams Robert W. , Lowrey Alfred H. 
Published: January 2005

AbstractExperimentally measured vibrational frequencies from the polar groups of peptides in aqueous solutions do not agree with frequencies calculated from scaled quantum mechanical force fields (SQMFF) using differential scale factors developed for molecules in the vapor phase. Measured stretching frequencies for carbonyl groups are more than 50 wavenumbers lower than the calculated values. On the other hand, frequencies for non‐polar groups calculated using these scale factors are relatively accurate. Our goal is to develop a SQMFF that yields accurate calculated frequencies for peptides in aqueous solutions. To this end, we have calculated scale factors for ab initio force constants for formic acid, acetic acid, and acetone using a least squares fit of calculated and experimental frequencies. We compare these scale factors with changes observed in the ab initio force constants calculated for these molecules at various states of hydration. These force constants are calculated using fully optimized geometries for these hydrated molecules using the 4‐31G basis. We present a comparison of the experimental and calculated frequencies, along with their potential energy distributions, for both vapor and aqueous phases. The results indicate that scale factors can simulate the effects of solvation on molecular force constants to yield accurate scaled ab initio force fields.
A vectorized algorithm for calculating the accessible surface area of macromolecules
Authors: Wang Huajun , Levinthal Cyrus 
Published: January 2005

AbstractAn algorithm is presented for calculating the solvent accessible surface area of proteins using a three‐dimensional grid. Since it requires only calculations based on single atomic positions, the algorithm is easy to be vectorized. It has been implemented on ST100 and may also be implemented on supercomputers like the CRAY or the CYBER. Results on several proteins indicate that its deviation from that of the Shrake‐Rupley algorithm is very small while the computation time is much reduced.
A molecular mechanics study of conformational trends in simple alcohols and ethers. Part I: Geometric trends
Authors: Vázquez Saulo A. , Ríos Miguel A. , Carballeira Luis 
Published: January 2005

AbstractWe have modified the MM2(80) molecular mechanics force field for alcohols and ethers to reproduce geometric trends predicted by ab initio calculations with the 4‐21G basis set. The results obtained with the modified force field are consistent with experimental evidence.
Force field parameters for molecular mechanical simulation of dehydroamino acid residues
Authors: Alagona Giuliano , Ghio Caterina , Pratesi Claudio 
Published: January 2005

AbstractParameters suitable to describe the conformational behavior of α – β unsaturated aminoacids and peptides in the framework of an existing force field for nucleic acids and proteins (S.J. Weiner, P.A. Kollman, D.A. Case, U. Chandra Singh, C. Ghio, G. Alagona, S. Profeta, Jr., and P. Weiner, J. Am. Chem. Soc., 106, 765 (1984)) are proposed and tested. Attention is primarily focused on dehydrophenylalanine and dehydroalanine containing peptides. The values of the parameters needed were obtained from experimental measurements available in the literature and from ad hoc quantum mechanical calculations. The selected values have subsequently been adapted and refined through molecular mechanical simulations on model compounds, such as Ac‐ΔPhe‐NMe, for which it was possible to carry out STO‐3G/SCF calculations to check selected points on the ϕ,ψ conformational map, and Ac‐ΔAla‐NMe, where the comparison was carried out at the 4‐31G level. The newly determined force field was then applied to Ac‐ΔPhe‐Ala‐ΔPhe‐NMe, whose minimal energy structures allowed us to explain the different circular dichroism behavior observed in CH2Cl2 and in dioxane. Starting from two minimum energy geometries of this tripeptide, the full optimization with AM1 produced an independent guess to their structure and stability in good agreement with the molecular mechanical one.
Counterpoise corrected calculations at the correlated level: A simplified method using LMOs
Authors: Kozmutza C. , Kapuy E. 
Published: January 2005

AbstractAb initio calculations have been performed in order to investigate the counterpoise corrections, especially at the correlated level for molecular interactions. It is pointed out that, when using a localized representation, the calculations using the MBPT/MP2 method can be simplified. The H2O + H2O system was studied, with the use of 6‐31 G* basis set. The method allows one to determine the intramolecular correlation components in a simplified way. Boys' localization procedure was applied throughout, both in the occupied as well as in the virtual spaces.
Simulations of lipid crystals: Characterization of potential energy functions and parameters for lecithin molecules
Authors: Stouch Terry R. , Ward Keith B. , Altieri Amanda , Hagler Arnold T. 
Published: January 2005

AbstractWe evaluate an empirical potential energy function and associated parameters for classical molecular dynamics simulations of lecithins, a common class of lipid. The physical accuracy of the force field was tested through its application to molecular dynamics simulations of the known crystal structures of lipid molecules. Average atomic positions and molecular conformation are well maintained during the simulations despite considerable thermal motion. Calculated isotropic temperature factors correlate highly with those from experiment.
Semiempirical vibrational and electronic structures of C60 and C70
Authors: Stewart James J. P. , Coolidge Michael B. 
Published: January 2005

AbstractThe electronic and vibrational structures of C60 and C70 have been calculated at the PM3 semiempirical level. C60 has a partially delocalized structure, while C70 has both a localized set and a delocalized set of MOs. As with AM1 and MNDO, PM3 predicts the heat of formation of C70 to be greater than that of C60, and that C70 is the thermodynamically more stable species. Calculation of the normal modes was accelerated over 40 times by limited use of symmetry theory.
Toward accurate transferable electrostatic models for polypeptides: A distributed multipole study of blocked amino acid residue charge distributions
Authors: Price S. L. , Faerman C. H. , Murray C. W. 
Published: January 2005

AbstractWe have developed a method for building up accurate electrostatic models for polypeptides, based on a distributed multipole representation of the SCF charge densities for the dipeptides (CH3.CO.NH.CHR.CO.NH.CH3) of the naturally occurring amino acids. It is based on the observation that each peptide residue has almost the correct formal charge (0, ±1). We find that the variations in the backbone charge distributions (excluding proline) with sidechain have a negligible effect on the predicted electrostatic potential around the residue. However changes in the atomic multipoles with the torsion angles (ϕ, ψ, χ) are more significant, and may need to be taken into account if electrostatic potential close to the residue is required to high accuracy. This type of DMA peptide library provides more accurate, more theoretically based, estimates of the electrostatic potential around polypeptides than current models.
Generation of carbon‐cage polyhedra
Authors: Liu X. , Klein D. J. , Schmalz T. G. , Seitz W. A. 
Published: January 2005

AbstractThe problem of the generation of polyhedra with degree‐3 vertices, and faces each of which is pentagonal or hexagonal, is addressed in order to characterize carbon in order to characterize clusters of ca. 30 or more atoms. Following Eulerian type arguments such polyhedra are subcategorized in terms of numbers of different types of local structures. An algorithm to generate such polyhedra is developed, and its computer implementation is described. Results for smaller than 80‐vertex cages of subcategories anticipated to be more chemically relevant are reported. The singular position of the truncated‐icosahedron (buckminsterfullerene) structure is noted.
Vector and parallel algorithms for the molecular dynamics simulation of macromolecules on shared‐memory computers
Authors: Mertz John E. , Tobias Douglas J. , Brooks Charles L. , Singh U. C. 
Published: January 2005

AbstractA detailed description of vector/parallel algorithms for the molecular dynamics (MD) simulation of macromolecular systems on multiple processor, shared‐memory computers is presented. The algorithms encompass three computationally intensive portions of typical MD programs: (1) the evaluation of the potential energies and forces, (2) the generation of the nonbonded neighbor list, and (3) the satisfaction of holonomic constraints. We implemented the algorithms into two standard programs; CHARMM and AMBER, and obtained near linear speedups on eight processors of a Cray Y‐MP for cases (1) and (2). For case (3) the SHAKE method demonstrated a speedup of 6.0 on eight processors while the matrix inversion method demonstrated 6.4. For a system of water molecules the performance improvement over the standard scalar SHAKE subroutine in AMBER ranged from a factor of 165 to greater than 2000.
A vector processing algorithm of auxiliary integral evaluation for two‐electron Gaussian integrals
Authors: Yahiro Shuichi , Gondo Yasuhiko 
Published: January 2005

AbstractA six‐term auxiliary integral expression for the two‐electron Gaussian integral is derived on the basis of the Chebyshev polynomial approximation instead of the seven‐term Taylor expansion. This expression and the related recurrence formula enable us to perform a high‐speed calculation on a vector processing computer.
The solution of adsorption integral equations by means of the regularization method
Authors: Szombathely M.V. , Bräuer P. , Jaroniec M. 
Published: January 2005

AbstractAn overall adsorption quantity for a heterogeneous solid is usually expressed by an integral equation, which contains a distribution function that describes heterogeneous properties of this solid. The calculation of this distribution function is an ill‐posed problem. The current article shows that the difficulties arising from the ill‐posed nature of an adsorption equation can be overcome with the regularization method. This work presents general principles of regularization for solving the ill‐posed problems without detailed mathematical considerations. The application of the regularization method to calculate a distribution function from any overall adsorption functions is illustrated with both simulated and experimental adsorption isotherms.
On the evaluation of molecular electron affinities by approximate density functional theory
Authors: Ziegler T. , Gutsev G.L. 
Published: January 2005

AbstractThe ability of approximate Density Functional Theory to calculate molecular electron affinities has been probed by a series of calculations on the hydrides CH3, NH2, OH, and HC2 as well as the multibonded species CN, BO, N3, OCN, and NO2. The simple Hartree–Fock Slater scheme lacks dynamic correlations and underestimates on the average the adiabatic electron affinities (EAad) by 0.7 eV. A considerable improvement is obtained by the Local Density Approximation (LDA) in which dynamic correlation is included. Values from LDA calculation underestimate, on the average, the adiabatic electron affinities by 0.4 eV. The best agreement with experiment is obtained by the LDA/NL scheme in which a nonlocal correction recently proposed by Becke is added to the LDA energy expression. The LDA/NL method underestimates EAad by 0.2 eV. It is concluded that the LDA/NL method affords EAad's in as good agreement with experiment as ab initio techniques in which electron correlation is taken into account by extensive configuration interaction. A full geometry optimization has been carried out on the nine neutral sample molecules as well as the corresponding anions.
On the numerical solution of the multidimensional vibrational time‐independent Schroedinger equation
Authors: Alvarez‐Collado J.R. , Buenker Robert J. 
Published: January 2005

AbstractA preliminary study of the capability of the finite difference and finite element methods (FDM, FEM) to evaluate eigenvalues of one‐, two‐, and three‐dimensional self‐adjoint operators is reported with reference to applications dealing with the description of vibrational levels. Results of harmonic oscillator model potentials and ab initio PES for the water molecule are obtained by using the FDM. In spite of the large matrices used, low accuracy, nonvariational results are found. A different method, based on FEM and normal coordinates, is therefore proposed. Two nearly harmonic cases are studied and it is shown that variational results with higher accuracy can be obtained with a moderate cost. The vibrational levels of the water molecule are also calculated in order to compare the results with those of the FDM treatment.
Methods for the calculation of Voh in OHO hydrogen bonds
Authors: van Duijneveldt‐van de Rijdt Jeanne G.C.M. , van Duijneveldt Frans B. 
Published: January 2005

AbstractAb initio calculations are reported for dimerization‐induced changes, Δk, in the harmonic force constant k of the H‐bonded OH in water dimer. Two dimer geometries are considered. Δk is obtained by considering the perturbation of a given monomer OH potential by the interaction energy in the dimer in question. The interaction energy is partitioned to identify the role of the various contributions to Δk. The sensitivity of Δk to the choice of the one‐electron basis set is studied by using five different basis sets, some of which have a set of bond functions in the HO bond. At the correlated level, correction for basis set superposition error is found to be essential. A comparison is made of the correlation contribution to Δk as given by the CEPA1, MP2, MP3, and MP4 methods. Of these, MP2 gives exaggerated results. Nevertheless, for economical and reasonably accurate calculations on large systems the MP2 approach in the ESPB basis set is advocated. The most accurate calculations yield a shift Δv0‐;1 of – 121 cm−1 for the uncoupled donor O‐H vibrational frequency in water dimer.
Ab initio and molecular mechanics study of n‐phenyl phthalimide and its crystal structure
Authors: Kendrick John , Robson Elizabeth , McIntyre Sara 
Published: January 2005

AbstractAb initio molecular orbital calculations are reported on the energetics for torsional motion of N‐phenyl phthalimide using 3‐21G, 6‐31G, and 6‐31G** basis sets and incorporating electron correlation effects for selected geometries. With the largest basis set, a minimum energy is found for a torsion angle of 59.2°. Atomic charges are assigned to the molecules on the basis of a least‐squares fit to the molecular electrostatic potential. This information is then used in molecular mechanics calculations of the crystal structure, where the calculated unit cell parameters are in good agreement with those observed experimentally.
Atomic charge calculations for quantitative structure—property relationships
Authors: Dixon Steven L. , Jurs Peter C. 
Published: January 2005

AbstractA previously published empirical charge scheme has been adapted for use in studies of quantitative structure‐property relationships. New parameters have been developed to allow the inclusion of nitrates, nitriles, sulfides, thiols, thiophenes, and sulfoxides. No changes have been made to the original scheme, thus preserving all previous results. A few simple additions to the program have made it possible to calculate atomic charges in a variety of ionic structures containing a formally positive nitrogen or a formally negative oxygen. The results obtained for ions are consistent with a number of concepts surrounding the familiar inductive and resonance effects.
Protein calculations on parallel processors. I. Parallel algorithm for the potential energy
Authors: Janak J.F. , Pattnaik P.C. 
Published: January 2005

AbstractWe investigate and test an algorithm suitable for the parallel calculation of the potential energy of a protein, or its spatial gradient, when the protein atoms interact via pair potentials. This algorithm is similar to one previously proposed, but it is more efficient, having half the interprocessor communications costs. For a given protein, we show that there is an optimal number of processors that gives a maximum speedup of the potential energy calculation compared to a sequential machine. (Using more than the optimum number of processors actually increases the computation time). With the optimum number the computation time is proportional to the protein size N. This is a considerable improvement in performance compared to sequential machines, where the computation time is proportional to N2. We also show that the dependence of the maximum speedup on the message latency time is relatively weak.
Modeling a reaction path by molecular mechanics: Dimerization of carbon free radicals
Authors: Peyman Anusch , Beckhaus Hans‐Dieter 
Published: January 2005

AbstractA variable force field model for radical dimerization was developed. It uses MM2 force constants for most atoms and new parameters only for the core atoms involved in bonding changes. The change in hybridization from sp2 to sp3 is modeled using distance‐dependent switch functions. The validity of the model has been tested by calculating the minimum energy path of the dimerization of di‐tert‐butylmethyl radicals. The calculated and experimental values for the enthalpy of activation of both dimerization of the radicals and dissociation of the dimer are in excellent agreement. The model has also been successfully applied to the stereoselective dimerization of 1‐phenylneopentyl radicals: The form of the potential energy surface yields an explanation for the observed stereoselectivity. Another common feature in radical dimerization seems to be the formation of adsorption complexes prior to dimerization that can lead to increased reactivity. The results suggest that it is important to analyze the whole reaction path and not only the transition state alone.
Ab initio calculation of magnetic properties by the “direct” IGLO method
Authors: Meier Ulrich , Van Wüllen Christoph , Schindler Michael 
Published: January 2005

AbstractA direct method for the ab initio calculation of the magnetic susceptibility and chemical shielding tensors based on the individual gauge for localized molecular orbitals (IGLO) formalism is introduced. “Direct” in this context means we avoid storing the two‐electron repulsion integrals in favor of recalculating them whenever necessary. In conjunction with the Direct‐SCF package TURBOMOLE Direct IGLO (DIGLO) permits calculation of magnetic second‐order properties for large molecules by minimizing peripheral disc storage requirements. The size of the molecules to be treated is limited only by the amount of CPU time available. The performance of DIGLO is demonstrated for some selected examples.
Multicenter and multiparticle integrals for explicitly correlated cartesian gaussian‐type functions
Authors: Kozlowski Pawel M. , Adamowicz Ludwik 
Published: January 2005

AbstractAn analytical derivation of multicenter and multiparticle integrals for explicitly correlated Cartesian Gaussian‐type cluster functions is demonstrated. The evaluation method is based on the application of raising operators that transform spherical cluster Gaussian functions into Cartesian Gaussian functions.