bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parametrization of calcium binding site in proteins and molecular dynamics simulation on phospholipase A2
Authors: Shiratori Yasuhiko , Nakagawa Setsuko 
Published: January 2005

AbstractThe empirical energy parameters for a calcium ion and its ligands in proteins were determined within a pairwise additive framework. The interaction energies of Ca2+‐water, Ca2+‐peptide group and Ca2+‐carboxyl group systems were calculated using the ab initio molecular orbital method with basis sets of double zeta quality including polarization or diffuse functions. The resulting potential energy surfaces served as references for the determination of the nonbonded parameters in the empirical energy function. The nonadditive corrections for the Ca2+‐ligand pair potentials are incorporated implicitly in the nonbonded paremeters by treating three‐body (1:2 complex) or seven‐body (1:6 complex) systems in reference calculations. Ligand polarizations induced by Ca2+ are estimated from the partial atomic charges of two‐body (1:1 complex) systems. The charge sets were determined by scaling so as to reproduce the reference potential energy surfaces. The newly determined parameter set was used in a stochastic boundary molecular dynamics simulation of phospholipase A2. The solvated structure of the Ca2+‐binding site obtained from an X‐ray crystallographic study is well reproduced by the parameter set.
Comparison of AM1 and ab initio calculation of the carbon‐carbon bond rotation in ethylene glycol diacetate
Authors: Fagerburg David R. 
Published: January 2005

AbstractThe C‐C glycol bond rotational energy in ethylene diacetate as a polyester model was compared using the semiempirical method AM1 and an ab initio method with an STO‐3G basis set. The results were qualitatively much different depending on the method used. Ab initio calculations showed the expected minima at 180 and near 60 (69.6) degrees dihedral angle with maxima at 0 and 120 degrees. The AM1 rotational curve indicated an apparent minimum at a 90 degree dihedral angle, a shallow, apparent maximum at 180 degrees and an apparent maximum at 0 degrees which could not be confirmed as minima or maxima via frequency calculations. Ethylene diacetate analog compounds with one or two ester oxygens replacing methylene group(s) gave curves with AM1 having the general shape for ethylene diacetate by the ab initio method, indicating a parameterization problem for the otherwise very useful AM1 to correctly handle a compound with only two carbons between the two electronegative oxygen atoms thus rendering this method currently unsuitable for examination of rotational energy barriers of such polyester model compounds.
The half‐projected Hartree–Fock model for computing thermally “forbidden” pericyclic reactions
Authors: Olivella Santiago , Salvador José 
Published: January 2005

AbstractThe possible use of a half‐projected Hartree–Fock (HPHF) wavefunction correlating a single pair of electrons is investigated in relation with the computation of potential energy hypersurfaces associated to pericyclic reactions of systems with an even number of electrons, in which the orbital configuration of the lowest‐energy singlet state is not conserved during the course of the reaction. The results of calculations, within the framework of the MINDO/3 Hamiltonian, for eleven stationary points on the potential energy hypersurfaces of three prototypical thermally “forbidden” pericyclic reactions indicate that, in general, the HPHF model provides a geometrical and energetical description that is equivalent to that obtained from a conventional two‐configuration self‐consistent‐field approach.
Determination of molecular topology and atomic hybridization states from heavy atom coordinates
Authors: Meng Elaine C. , Lewis Richard A. 
Published: January 2005

AbstractA method is presented for the derivation of hybridization states and connectivity within molecules from the atomic numbers and coordinates of heavy atoms. The algorithm utilizes bond length data from studies of the Cambridge Structural Database (Allen et al., J. Chem. Soc. Perkin Trans. II, S1, (1987)). The program, IDATM, is useful for processing input to hydrogen‐adding routines and molecular mechanics programs, as it minimizes the amount of manual preprocessing required. IDATM has been tested on a range of crystallographically determined structures, including poorly determined structures, with a successful assignment of hybridization for over 99% of the atoms in the set.
Calculations of molecular vibrational frequencies using semiempirical methods
Authors: Coolidge Michael B. , Marlin John E. , Stewart James J. P. 
Published: January 2005

AbstractMINDO/3, MNDO, AM1, and PM3 calculations of molecular vibrational frequencies are reported for 61 molecules. All techniques were applied to both well‐behaved and badly behaved systems. Overall, MINDO/3 and MNDO were found to contain rather large errors whereas AM1 and PM3 were relatively accurate. Since no technique does well for all molecules, the technique used should be chosen based on the molecular vibration of interest. In general, AM1 and PM3 together provide fairly accurate results.
New method for the computation of ionic distribution around rod‐like polyelectrolytes with the helical distribution of charges. I. General approach and a nonlinearized Poisson–Boltzmann equation
Authors: Rashin Alexander A. , Malinsky Joseph 
Published: January 2005

AbstractThis article is a first step in an attempt to reevaluate the relative role of different contributions to the energetics of DNA in salt solutions. To identify individual terms yielding such contributions a new derivation is given of the generalized Poisson–Boltzmann equation, which includes correlation effects, and explicitly shows terms ignored in the regular Poisson–Boltzmann approach. A general method based on the Boundary Element Technique is discussed, which can be used to evaluate these terms in the next steps of the reevaluation. An implementation of this method for the solution of the nonlinear Poisson–Boltzmann equation is described in detail, and is used to compute the ionic atmosphere around DNAs modeled as cylinders with helical distributions of charges. In the B‐type DNA models, it is found that the ion densities in the minor and major grooves near the DNA surface differ by up to threefold. This difference is ca. 10‐fold for Z‐type DNA models. There are 20–25% differences in the magnitude of the maximum ionic charge density between DNA models of the same type. The addition of excess salt (up to 0.15 M) changes this maximum by only 10–15%. This change is not proportional to the concentration of excess salt. The contributions of different factors to the stabilization of alternative forms of DNA are evaluated. These factors are: (1) interactions between the phosphates, (2) interactions of phosphates with water, (3) interactions of phosphates with the ionic cloud, (4) interactions within the ionic cloud, (5) entropy of the ionic cloud. It is found that regardless of large variations in the counterion distributions around different DNAs, energetic contributions from these distributions are similar (−12.65 ± 0.6 kcal/mol · cell). The calculated change in stabilization per unit cell of models of B and Z‐type DNAs due to 0.15 M excess NaCl is only −0.56 ± 0.02 kcal/mol, indicating no tendency toward B‐Z transition in this concentration range. Significantly larger variations of the order of 10 kcal/mol per unit cell can result from factors 1–2. Possible effects of the realistic DNA‐solvent boundaries on the energetics of DNA solutions are discussed.
Host‐guest preorganization and complementarity: A molecular mechanics and molecular dynamics study of cation complexes of a cyclic urea‐anisole spherand
Authors: Maye P. V. , Venanzi C. A. 
Published: January 2005

AbstractMolecular mechanics and molecular dynamics calculations were carried out in vacuo for 1 and for the complexes of 1 with alkali metal cations and t‐BuNH. The calculations identify perching and nesting conformations of the complexes not available from X‐ray data. For the Li+ −1 complex, the MD simulations identify a new global minimum not found by the molecular mechanics calculation. In general, the net favorable ion‐spherand complexation energy is due to the offset of the unfavorable reorganization energy of the spherand by the overwhelmingly favorable electrostatic component of the ion‐spherand interaction energy. The host is least preorganized for the binding of Li+ and, even in its complexed conformation, presents the least steric complementarity to this ion. The complexation energy becomes significantly more favorable due to a large increase in the electrostatic complementarity of the ion binding site when the spherand adopts its complexed conformation. Correction of the calculated complexation energy by the experimental free energy of ion aqueous desolvation leads to results in line with the findings of Cram and co‐workers that K+ is the most, and Li+ the least, favorably bound by 1.
Vectorization of the general Monte Carlo classical trajectory program VENUS
Authors: Hu Xiche , Hase William L. , Pirraglia Tony 
Published: January 2005

AbstractThe general chemical dynamics computer program VENUS is used to perform classical trajectory simulations for large polyatomic systems, with many atoms and complicated potential energy functions. To simulate an ensemble of many trajectories requires a large amount of CPU time. Since each trajectory is independent, it is possible to parallel process a large set of trajectories instead of processing the trajectories by the conventional sequential approach. This enhances the vectorizability of the VENUS program, since the integration of Hamilton's equations of motion and the gradient evaluation, which comprise 97.8% of the CPU, can each be parallel processed. In this article, the vectorization and ensuing optimization of VENUS on the CRAY‐YMP and IBM‐3090 are presented in terms of both global strategies and technical details. A switching algorithm is designed to enhance the vector performance and to minimize the memory storage. A performance of 140 MFLOPS and a vector/scalar execution rate ratio of 10.6 are observed when this new version of VENUS is used to study the association of CH3 with the H(Ar)12 cluster on the CRAY‐YMP.
Efficient search for all low energy conformations of polypeptides by Monte Carlo methods
Authors: von Freyberg Berthold , Braun Werner 
Published: January 2005

AbstractThe Metropolis Monte Carlo method has been added to the program FANTOM for energy refinement of polypeptides and proteins using a Newton–Raphson minimizer in torsion angle space. With this extension, different strategies for global minimization of the semiempirical energy function ECEPP/2 by various temperature schedules and restriction of conformational space were tested for locating local minimum conformations with low energy of the pentapeptide Met‐enkephalin. In total, 1881 conformations below −10 kcal/mol were found. These conformations could be represented by 77 nonidentical conformations which were analysed for their pattern of hydrogen bonds, types of tight turn, pairwise root‐mean‐square‐deviation (rmsd), Zimmermann codes and side chain conformations. All low energy conformations below −10.4 kcal/mol show strong similarity to the global minimum conformation in the backbone structure.
Stabilities of small Ben and Bn clusters (4 ≤ n ≤ 8) by vibrational analysis
Authors: Kato Hiroshi , Tanaka Eishi 
Published: January 2005

AbstractThe stabilities Ben and Bn clusters (4 ≤ n ≤ 8) based on the vibrational analysis were investigated by ab initio MO calculations. The computations were performed by using a 3‐21G basis set at the R(U)HF level and at the R(U)MP4 level with the HF optimized structures. Spin‐multiplicities were also considered up to quintet states (n ≤ 7). Of the 120 species that were treated, half of them were considered stable and some of these stable species were obtained by the deformations of transition state and unstable species, following the imaginary normal modes. The transformation barrier between the transition state species and corresponding stable ones was presented. It was found that there were two types of stable clusters: (1) a low symmetry species with lower frequencies and lower geometrical change barriers and (2) a high symmetry one with higher frequencies. The former type was considered as a structural “soft” species and the latter as a “hard” species.
The number of spanning trees in buckminsterfullerene
Authors: Brown T. J. N. , Mallion R. B. , Pollak P. , de Castro Branca R. M. , Gomes J. A. N. F. 
Published: January 2005

AbstractThe theorem of Gutman et al. (1983) is applied to calculate the number of spanning trees in the carbon‐carbon connectivity‐network of the recently diagnosed C60‐cluster buckminsterfullerene. This “complexity” turns out to be approximately 3.75 × 1020 and it is found necessary to invoke the device of modulo arithmetic and the “Chinese Remainder Theorem” in order to evaluate it precisely on a small computer. The exact spanningtree count for buckminsterfullerene is 375 291 866 372 898 816 000, or, 225 × 34 × 53 × 115 × 193. A “ringcurrent” calculation by the method of McWeeny may be based on any desired one of this vast number of spanning trees.
A fully three‐dimensional finite element method calculation for the vibrational levels of H2O and D2O
Authors: Neto J. J. Soares , Linderberg Jan 
Published: January 2005

AbstractA finite element method approach for solving the three‐dimensional Schrödinger equation expressed in hyperspherical coordinates is applied to the calculation of rovibrational states of H2O and D2O. Comparisons to experimental values and other theoretical calculations are offered.
A comparison of distance geometry and molecular dynamics simulation techniques for conformational analysis of β‐cyclodextrin
Authors: Wertz David A. , Shi Chen‐Xi , Venanzi Carol A. 
Published: January 2005

AbstractDistance geometry and molecular dynamics simulation techniques were compared in their ability to search the conformational potential energy surface of β‐cyclodextrin. Structures generated by the DISGEO program were minimized using three different atomic point charge sets. Some of these structures were used as starting points for molecular dynamics simulation in vacuo at 298K. The distance geometry results showed that the global features of the conformational potential energy surface were generally independent of the point charge set. The distance geometry technique was able to find structures of lower energy than those obtained by direct minimization of the X‐ray or neutron diffraction structures. However, the molecular dynamics simulation technique was consistently able to find structures of lower energy than those generated by distance geometry. Root mean square fit of the trajectory structures to the starting structure showed that the simulation allowed the molecule to explore regions of the potential energy surface in the neighborhood of the starting structure. Both the distance geometry and molecular dynamics simulation techniques showed that β‐cyclodextrin can adopt a wide range of conformations in the gas phase and that these conformations are much less symmetrical than the crystalline structure.
Ab initio and molecular mechanics calculations on imine derivatives: A study of the rotational barriers and the development of MM2 parameters
Authors: Kontoyianni Maria , Hoffman Andrew J. , Bowen J. Phillip 
Published: January 2005

AbstractThe application of molecular mechanics methods for the study of structures has become a standard approach to conformational analysis. The MM2 force field has been extended to include imines. In general, a diverse group of aliphatic and aromatic imine structures can now be treated. The rotational energy profiles and barriers to N‐substituted imines about the Csp2Csp2 single bonds adjacent to CN functional group were calculated via ab initio MO theory. Information obtained from the quantum mechanical calculations at the 3‐21G, 6‐31G*, and MP4/6‐31G* //6‐31G* levels was used both to study the phenomena involved and to parameterize MM2. The syn‐anti isomerization was also studied, and the mechanistic pathways have been evaluated. In cases where the comparison with experimental data can be made, the agreements are good.
Kinetic effects of multiple charge modifications in enzyme‐substrate reactions: Brownian dynamics simulations of Cu, Zn superoxide dismutase
Authors: Sines Jacqueline J. , McCammon J. Andrew , Allison Stuart A. 
Published: January 2005

AbstractWe used Brownian dynamics simulations of substrate O encounters with the enzyme bovine erythrocyte Cu, Zn superoxide dismutase (SOD) to study the effects of multiple charge modifications in the enzyme on the kinetics of its diffusion‐controlled reaction. When the charges of two or three residues were changed, the calculated rate consant relative to that for the unmodified enzyme was usually found to be the product of relative rate constants for the enzymes with the corresponding single‐site changes. This “multiplicativity” rule may be useful in the design of enzymes that operate with diffusion‐controlled kinetics. Residues that deviate from the general rule are found in the active site channel of SOD, and the origin of these deviations is considered.
Correlation and solvation effects. IV. A systematic analysis of the influence of cavity size and shape on solvation properties in the polarizable continuum model with electron correlation
Authors: del Valle F. J. Olivares , Aguilar M.A. 
Published: January 2005

AbstractFrom the standpoint of models that use a polarizable continuum to represent the solvent in studying the phenomenon of solvation, a systematic and detailed analysis is made of the influence of the cavity size and shape on calculated energies. The solute is represented by its ab initio wavefunction, and the electronic part of the solvation energy is calculated including terms that take into account electron correlation up to third order. The analysis shows the convenience of modeling the cavity according to considerations of homogeneity, which are based fundamentally on how the solute wavefunction is constructed, i.e., the basis set used.
A systematic ab initio study of the group V trihalides MX3 and pentahalides MX5 (M = PBi, X = FI)
Authors: Breidung Jürgen , Thiel Walter 
Published: January 2005

AbstractAb initio calculations using effective core potentials and polarized split‐valence basis sets are reported for the title compounds. The calculated geometries, vibrational frequencies, infrared intensities, harmonic force fields, dipole moments, relative energies, and barriers to pseudorotation are compared with the available experimental data for the known molecules. Predictions are made for those pentahalides that are still unknown. Trends in the calculated properties are identified and discussed.
Probing the conformational space available to inhibitors in the thermolysin active site using Monte Carlo/energy minimization techniques
Authors: Guida Wayne C. , Bohacek Regine S. , Erion Mark D. 
Published: January 2005

AbstractThe conformational space available to four inhibitors of the bacterial enzyme thermolysin has been searched in the enzyme binding site using a method that combines Monte Carlo type techniques with energy minimization for exploration of the conformational potential energy hypersurface. Molecular mechanics methodology using the AMBER force field was employed for computation of the molecular energetics. Solvation energies were also included in the calculations by employing a technique that estimates hydration energies based on the exposed solvent accessible surface area for each atom of the inhibitor and active site. It was found that in each case, the crystallographically observed conformation was among the low energy conformers discovered. In fact, in three of the calculations it was the lowest energy conformation. The methodology described in this article is expected to be quite useful for studies involving computer aided design and evaluation of enzyme inhibitors.
Free energy perturbation calculations involving potential function changes
Authors: Ferguson David M. , Pearlman David A. , Swope William C. , Kollman Peter A. 
Published: January 2005

AbstractThe solvation free energies of thymine and adenine were calculated using free energy methods to examine the effect of applying Lennard–Jones 6‐12 and 10‐12 perturbations to the hydrogen‐bonding groups. The calculations were performed using a new free energy algorithm developed for the AMBER 4.0 program package that allows an interaction described by a Lennard–Jones 6‐12 potential to be changed into one described by a hydrogen bond 10‐12 potential. The algorithm applied allows this change to occur smoothly without the generation of more extrema on the potential surface. Results using this algorithm have been compared with those determined using the standard AMBER 3.0 Revision A program package, which provides for 6‐12 to 6‐12 parameter perturbations only. We have also developed a procedure to perform pyrimidine to purine nucleoside mutations to calculate the relative free energies of solvation directly. The theoretical results are compared to experimental energies derived from solvation and vaporization data taken from the literature. The free energies calculated using the new algorithm show good agreement with the derived experimental values. This is also true for the calculations that employ the 6‐12 function only, but with 6‐12 parameters modified to reflect the correct hydrogen‐bonding interactions. However, perturbation of the “standard” 6‐12 parameters without changing the functional form proves to be less effective in determining solvation free energies correctly, and demonstrates the importance of accurate hydrogen bond descriptions in free energy simulations.
Parallelization of quantum mechanical integral calculations
Authors: Kindermann S. , Michel E. , Otto P. 
Published: January 2005

AbstractIn ab initio Hartree—Fock crystal orbital calculations of chemical and physical properties of polymers, the huge number of two‐electron integrals restricts the size of the elementary cell. Therefore, the question arises how the storage and computation resources of modern parallel supercomputers can be exploited. In this work, we report the parallelization of the one‐ and two‐electron integral programs, respectively, for the parallel computer SUPRENUM. A short description of the hardware and software environment of this supercomputer is given. The results are discussed with respect to speed‐up and efficiency.
Vinyloxyborane and its isomers. An ab initio study of the C2H5BO potential energy surface, the barrier to 1,3‐shifts in β‐ketoboranes, and the mechanism of the carbonylation reaction of boranes
Authors: Ibrahim Mustafa R. , Bühl Michael , Knab Reinhard , Schleyer Paul Von Rague 
Published: January 2005

AbstractVinyloxyboranes, CH2CH;O;BR2, are shown by ab initio molecular orbital theory to be more stable than the isomeric β‐aldoboranes, R2BCH2CHO, by ca. 19 kcal/mol. The MP2/6‐31G*/6‐31G* + ZPE barrier for the [1,3] boron shift is only 10.9 kcal/mol (R  Me) relative to the aldoborane. Other C2H5BO isomers (β‐ketoboranes, boraepoxides and organoboron oxides), which are related to the proposed stages in the carbonylation reaction of boranes, are shown to be plausible intermediates. However, some of the computed barriers for methyl group migrations are unrealistically large, up to ca. 63 kcal/mol.