bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constrained optimization in cartesian coordinates
Authors: Baker Jon , Bergeron Doreen 
Published: January 2005

AbstractModifications are made to a previously published algorithm for constrained optimization in Cartesian coordinates (J. Comp. Chem., 13, 240, 1992) to incorporate both fixed and dummy atoms. Standard distance and angle constraints can now be specified with respect to dummy atoms, greatly extending the range of constraints that can be handled. Fixed atoms can be eliminated from the optimization space and so there is no need to calculate their gradients resulting in potentially significant savings of CPU time in ab initio computations. Several examples illustrate the range and versatility of the modified algorithm. © John Wiley & Sons, Inc.
Use of locally dense basis sets for nuclear magnetic resonance shielding calculations
Authors: Chesnut D.B. , Rusiloski B.E. , Moore K.D. , Egolf D.A. 
Published: January 2005

AbstractThe locally dense basis set approach to the calculation of nuclear magnetic resonance shieldings is one in which a sufficiently large or dense set of basis functions is used for an atom or molecular fragment containing the resonant nucleus or nuclei of interest and fewer or attenuated sets of basis functions employed elsewhere. Provided the dense set is of sufficient size, this approach is capable of determining chemical shieldings nearly as well as a calculation with a balanced basis set of quality equal to the locally dense set, but with considerable savings of CPU time. Detailed comparisons are provided of locally dense and balanced calculations in the gauge including atomic orbital (GIAO) method for the individual principal values, the isotropic shieldings, and the tensor orientations for hydrogen, carbon, nitrogen, oxygen, fluorine, and phosphorus nuclei. It is seen that chemical functional groups can often define the appropriate molecular fragment to be taken locally dense. While the present test cases are for the most part small molecules, the value of the method is that it will allow calculations on systems that would otherwise presently be computationally expensive or inaccessible. © John Wiley & Sons, Inc.
Computation of the mean residence time of water in the hydration shells of biomolecules
Authors: García Angel E. , Stiller Lewis 
Published: January 2005

AbstractAn algorithm is presented within the context of the calculation of the time‐relaxation behavior of the hydration shells around atomic sites in biomolecules. We report a calculation of the time‐relaxation behavior of the first and second hydration shells of polar, hydrophobic, and charged groups in a protein, crambin. The water mean residence times around protein groups are obtained from averages over configurations sampled during a 325‐ps molecular dynamics simulation of crambin in solution. A convolution arising in the calculation of the mean relaxation time is implemented using a parallel prefix operator. A new characterization is given of the parallel prefix operator as a linear transformation, and this formulation enables us to derive efficient factorization of the convolution as a product of two parallel prefix operations. The parallel prefix operations are implemented in logarithmic time. © John Wiley & Sons, Inc.
Conformational searching methods for small molecules. II. Genetic algorithm approach
Authors: Judson R.S. , Jaeger E.P. , Treasurywala A.M. , Peterson M.L. 
Published: January 2005

AbstractWe demonstrate the use of a genetic algorithm (GA) search procedure for finding low‐energy conformations of small to medium organic molecules (1–12 rotatable bonds). GAS are in a class of biologically motivated optimization methods that evolve a population of individuals where individuals who are more “fit” have a higher probability of surviving into subsequent generations. Here, an individual is a conformation of a given molecule and the fitness is the molecule's conformational energy. In the course of a simulated evolution, the population produces conformations having increasingly lower energy. We test the GA method on a suite of 72 molecules and compare the performance against the CSEARCH algorithm in Sybyl. For molecules with more than eight rotatable bonds, the GA method is more efficient computationally and as the number of rotatable bonds increases the relative efficiency of the GA method grows. The GA method also found energies equal to or lower than the energy of the relaxed crystal structure in the large majority of cases. © John Wiley & Sons, Inc.
Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. III. Application to halogenated and aromatic molecules
Authors: Park Je Myung , Tai No Kyoung , Jhon Mu Shik , Scheraga Harold A. 
Published: January 2005

AbstractThe net atomic charge parameters for halogen atoms and the atoms in aromatic molecules have been determined by the modified partial equalization of orbital electronegativity method. The same parameters are used for the halogen atoms both in aromatic and nonaromatic systems. The calculated dipole moments of haloalkanes agree well with experiment, but those of the halogenated aromatic molecules do not reproduce the experimental values as well as those of the haloalkanes; in particular, the computed dipole moments for monohalogenated benzenes are all lower than the experimental values because of the influence of the lonepair electrons on the halogens. Within the limitations of an atom‐centered point‐charge approximation, our calculated dipole moments, both for haloalkanes and halogented aromatic molecules, agree well with experimental values. © John Wiley & Sons, Inc.
Comparison of 6‐31G*‐based MST/SCRF and FEP evaluations of the free energies of hydration for small neutral molecules
Authors: Orozco Modesto , Jorgensen William L. , Luque F.J. 
Published: January 2005

AbstractA comparison between Miertus–Scrocco–Tomasi (MST) SCRF and free energy perturbation (FEP) estimates of the free energy of hydration of eight small neutral molecules is presented. In both cases, the 6‐31G* molecular electrostatic potential is used to describe the electrostatic properties of the molecules. The results demonstrate the ability of both methodologies to provide useful theoretical estimates of the total free energy of hydration; the average errors are only 1.5 kcal/mol (FEP) and 0.8 kcal/mol (MST/SCRF). The largest errors in the FEP and MST/SCRF results are less than 1.5 kcal/mol for all molecules except acetic acid, where the FEP method overestimates the free energy of hydration by 3.3 kcal/mol. © John Wiley & Sons, Inc.
Ab initio molecular orbital studies for compounds of magnesium
Authors: Gardner Peter J. , Preston Steve R. , Siertsema Rachel , Steele Derek 
Published: January 2005

AbstractUsing a 6‐311G** basis set with estimation of correlation energy at the MP2 level, structural and energetic data for 40 molecular species containing magnesium have been calculated. For about half the species studied, further energetic data were obtained using Pople's G2 method. Enthalpy changes at 298.15 K were obtained for isogyric reactions and standard enthalpies of formation were derived from these. Comparison of the standard enthalpies of formation with the sparse literature data suggests the MP2/6‐311G** standard enthalpies of formation are accurate to ± 15 kJ mol−1 and the corresponding G2 enthalpies accurate to ± 10 kJ mol−1. The calculated ΔH [MgN, g] revealed a gross error in the currently accepted value for this function. It is intended that these results will be used to parameterize the semiempirical molecular orbital package, MOPAC, for the element magnesium. © John Wiley & Sons, Inc.
Performance of fast multipole methods for calculating electrostatic interactions in biomacromolecular simulations
Authors: Shimada Jiro , Kaneko Hiroki , Takada Toshikazu 
Published: January 2005

AbstractThe fast multipole method proposed by Greengard and Rokhlin (GR) is applied to large biomacromolecular systems. In this method, the system is divided into a hierarchy of cells, and electric field exerted on a particle is decomposed into two parts. The first part is a rapidly varying field due to nearby cells, so that it needs rigorous pairwise calculations. The second part is a slowly varying local field due to distant cells; hence, it allows rapid calculations through a multipole expansion technique. In this work, two additional possibilities for improving the performance are numerically examined. The first is an improvement of the convergence of the expansion by increasing the number of nearby cells, without including higher‐order multipole moments. The second is an acceleration of the calculations by the particle–particle and particle–mesh/multipole expansion (PPPM/MPE) method, which uses fast Fourier transform instead of the hierarchy. For this purpose, the PPPM/MPE method originally developed by the authors for a periodic system is extended to a nonperiodic isolated system. The advantages and disadvantages of the GR and PPPM/MPE methods are discussed for both periodic and isolated systems. It is numerically shown that these methods with reasonable costs can reduce the error in potential felt by each particle to 0.1–1 kcal/mol, much smaller than the 30‐kcal/mol error involved in conventional simple truncations. © 1994 by John Wiley & Sons, Inc.
General parameterization of a reaction field theory combined with the boundary element method
Authors: Furuki Takao , Umeda Akihiro , Sakurai Minoru , Inoue Yoshio , Chûjô Riichirô , Harata Kazuaki 
Published: January 2005

AbstractWe described various technical aspects in applying reaction field theories using continuum models to practical problems. It was investigated how solvent‐dependent properties of solute molecules are influenced by the following factors: difference in quantum‐chemical description of solute–solvent (continuum dielectric) interaction, difference in values of empirically determinable parameters such as atomic radii to define a size of a cavity created in a dielectric to accommodate a solute, and difference in the sophistication level of molecular orbital calculation, including electron correlation and different parameter sets (MNDO, AM1, and PM3). Through these investigations, the better parameter sets were found to evaluate accurately physicochemically important parameters such as hydration enthalpy. © 1994 by John Wiley & Sons, Inc.
Ab initio molecular orbital study of 1‐fluorosilatrane
Authors: Csonka G. I. , Hencsei P. 
Published: January 2005

AbstractThe molecular geometry of 1‐fluorosilatrane was optimized fully by restricted Hartree–Fock (HF) calculations using the 3‐21G, 3‐21G(d) and 6‐31G(d) basis sets, with the aim of locating the positions of the local minima on the energy hypersurface. The optimized geometries were compared with available experimental (X‐ray and ED) and semiempirical data. The ab initio calculations using polarized basis sets are in good agreement with those of previously reported semiempirical calculations, giving a slightly longer equilibrium SiN distance (∼ 256 pm) in the case of the endo minimum. However, the exo minimum predicted by the semiempirical methods is not supported. There was no experimental evidence for the existence of this exo minimum, and the present ab initio calculations suggest that it is highly unstable. There is considerable disagreement among the experimental results in the CN and CC bond lengths in various silatranes, their differences being as large as 13 pm. The present calculations predict that these differences may appear because the silatrane skeleton is flexible with low‐energy, large‐amplitude internal motions which introduce considerable uncertainties into the position of ring carbon atoms. © 1994 by John Wiley & Sons, Inc.
Transferable semiempirical quadratic force fields: The case of polythiophene and shorter oligomers
Authors: Ramírez F. J. , Hernández V. , Navarrete J. T. López 
Published: January 2005

AbstractThe vibrational spectra of oligomers of thiophene are treated theoretically with the main purpose of deriving information for the interpretation of the infrared and Raman spectra of the polymer and isotopic derivatives. We report the results of a series of semiempirical MNDO calculations on the structure and vibrational properties of oligothiophenes, and we compare the calculated MNDO Pulay scaled force field of the monomer with an empirical harmonic force field that we have obtained by least squares refinement on nine isotopic derivatives. The scaling factors obtained were transferred from thiophene for the computation of the vibrational spectrum and the phonon dispersion curves of the polymer. © 1994 by John Wiley & Sons, Inc.
Direct one‐index transformations in multiconfiguration response calculations
Authors: Vahtras Olav , Årgren Hans , Jensen Hans Jørgen AA. 
Published: January 2005

AbstractThe evaluation of gradient vectors of a general operator with one‐index, double‐one‐index, or higher‐order one‐index transformed integrals is a key operation in multiconfiguration response theory calculations. We describe an integral‐driven direct algorithm that carries out this operation efficiently without pretransforming the integrals. The use of this algorithm leads to a considerable reduction in disk space and timing. © 1994 by John Wiley & Sons, Inc.
X‐PLORing extraribosomal peptide folding during synthesis
Authors: David Carl W. 
Published: January 2005

AbstractAn X‐PLOR scheme for imitating the action of ribosomes in aiding synthesizing peptides to find their ultimate conformations is introduced. The scheme is tested with an example from the Delta‐Sleep‐Inducing‐Peptide mutant family. © 1994 by John Wiley & Sons, Inc.
Expanding molecular dynamics simulations to the NMR time scale. I. Studies of conformational interconversions of 1, 1‐difluoro‐4, 4‐dimethylcycloheptane using MM3‐MD
Authors: Li Fanbing , Cui Weili , Allinger Norman L. 
Published: January 2005

AbstractA molecular dynamics (MD) simulation of 35,000 picoseconds (ps) has been carried out to study the conformational interconversions of 1,1‐difluoro‐4,4‐dimethylcycloheptane at room temperature using the MM3 force field. The exchange between axial and equatorial fluorine atoms was the only conformational interconversion that occurred, and it took place via the process of pseudorotation. Ring inversions (twist–chair < twist–boat < twist–chair) were not observed. The axial‐equatorial exchange of the two fluorine atoms took place five times during the MD trajectory of 35,000 ps. The two CH3 groups occupied symmetrical positions (exchangeable by a C2‐like rotations, where C2‐like means it would be C2 if the fluorines were not present) in the MM3 structures, and during most of the time of the MD trajectory. The methyls occasionally moved off the C2‐like axis in the simulated process, mostly because the C2‐like axis was momentarily moved so that it did not pass through the ring atom to which the two CH3 groups are bonded. A C2‐like symmetry of the twist‐chair conformation was maintained approximately during most of the MD simulation. The conformational geometry with the highest energy obtained during the axial‐equatorial exchange process was found and used to locate the transition state. The energy barrier for this axial‐equatorial exchange was calculated to be 4.7 kcal/mol, and it compares with the value (5.0 kcal/mol) determined by dynamic nuclear magnetic resonance (NMR). © 1994 by John Wiley & Sons, Inc.
Normal mode analysis of oligomeric proteins: Reduction of the memory requirement by consideration of rigid geometry and molecular symmetry
Authors: Gibrat Jean‐françois , Garnier Jean , Gō Nobuhiro 
Published: January 2005

AbstractA method is presented to reduce the memory requirement of normal mode analysis applied to systems containing two or more large proteins when these systems exhibit symmetry properties. We use a rigid geometry model (i.e., only the dihedral angles of the polypeptide chain are considered as variables). This model allows a reduction by a factor of 8 on average of the number of variables with a concomitant freezing of the high‐frequency modes. The symmetry properties of the system are used to reduce further the number of variables that must be considered in the computation. Application of group theory leads to a factorization of the matrices of interest (the coefficient and the Hessian matrices) into independent blocks along the diagonal. The initial, reducible representation is thus transformed into a number of irreducible representations of smaller dimensions. In the case of the C2 symmetry group, the method leads to a reduction of the size of the matrices that must be manipulated during the computation (coefficient matrix, Hessian matrix, and eigenvectors matrix) by a factor of 256 compared with the usual normal mode analysis in Cartesian coordinate space. The method is particularly well adapted to the study of the dynamics of oligomeric proteins because these proteins often display symmetry properties (e.g., virus coat proteins, immunoglobulins, hemoglobin, etc.). In favorable cases, in conjunction with X‐ray diffuse scattering data, the study of systems showing allosteric properties might be considered. © 1994 by John Wiley & Sons, Inc.
A force field for monosaccharides and (1 → 4) linked polysaccharides
Authors: Glennon Timothy M. , Zheng Ya‐Jun , Le Grand Scott M. , Shutzberg Brad A. , Merz Kenneth M. 
Published: January 2005

AbstractA force field for monosaccharides that can be extended to (1 → 4) linked polysaccharides has been developed for the AMBER potential function. The resulting force field is consistent with the existing AMBER force field for proteins and nucleic acids. Modifications to the standard AMBER OH force constant and to the Lennard‐Jones parameters were made. Furthermore, a 10–12 nonbonded term was included between the hydroxyl hydrogen of the saccharide and the water oxygen (TIP3P, SPC/E, etc.) to reproduce better the water–saccharide intermolecular distances. STO‐3G electrostatic potential (ESP) charges were used to represent the electrostatic interactions between the saccharide and its surrounding environment. To obtain charges for polysaccharides, a scheme was developed to piece together saccharide residues through 1 → 4 connections while still retaining a net neutral charge on the molecule as a whole. Free energy perturbation (FEP) simulations of D‐glucose and D‐mannose in water were performed to test the resulting force field. The FEP simulations demonstrate that AMBER overestimates intramolecular interaction energies, suggesting that further improvements are needed in this part of the force field. To test further the reliability of the parameters, a molecular dynamics (MD) simulation of α‐D‐glucose in water was also performed. The MD simulation was able to produce structural and conformational results that are in accord with experimental evidence and previous theoretical results. Finally, a relaxed conformational map of β‐maltose was assembled and it was found that the present force field is consistent with available theoretical and experimental results. © 1994 by John Wiley & Sons, Inc.
Application of the multiple computer automated structure evaluation methodology to a quantitative structure–activity relationship study of acidity
Authors: Klopman Gilles , Fercu Dan 
Published: January 2005

AbstractWe applied the Multiple Computer Automated Structure Evaluation (Multi‐CASE) program to the analysis of the relationship between the structure of 2464 organic acids and their (first) pKa values. By using the self‐created expert dictionary of molecular attributes pertinent to acidity, the program could make successful a priori prediction of the acidity of new organic compounds. © 1994 by John Wiley & Sons, Inc.
Transition structure modeling by intersecting potential energy surfaces
Authors: Jensen Frank 
Published: January 2005

AbstractA previously proposed method of modeling force field transition structures as the lowest energy structure on the seam of two intersecting potential energy surfaces is improved with respect to the force field expression and the efficiency of the optimization algorithm. Comparison with ab initio and experimental results show that the force field method may have the potential of achieving almost quantitative results. It appears that the results from transition state modeling are currently limited by the accuracy of the underlying force field. © 1994 by John Wiley & Sons, Inc.
The effects of solvent screening in quantum mechanical calculations in protein systems
Authors: Baldridge K. , Fine R. , Hagler A. 
Published: January 2005

AbstractWe report on an implementation of quantum mechanical density functional calculations carried out in a dielectric medium. The dielectric medium is introduced by integrating the solution of the Poisson‐Boltzmann equations into the density functional calculation. The calculations are carried out for a simple amide in vacuum, in the field of an ion, and in the ion field in several dielectric environments. The environment was constructed to include a low dielectric interior embedded in a high dielectric continuum of dielectric 80 (corresponding to aqueous solution). The energies and electron densities of formamide in the ion field were calculated at various configurations in this system, including at the low dielectric–high dielectric interface. The systems were designed to simulate situations which are similar to those that occur in proteins (i.e., the protein constitutes the low dielectric medium surrounded by aqueous solution). The system mimics situations in which charges in such proteins located in various regions interact with other parts of the protein and with ligands which mainly bind to the surface. © 1994 by John Wiley & Sons, Inc.
Comparison of the molecular mechanics + generalized Born/surface area and the ab initio + Monte Carlo simulation methods in estimating conformational equilibria in aqueous solution
Authors: Nagy Peter I. , Bitar Joseph E. , Smith Douglas A. 
Published: January 2005

AbstractA method using molecular mechanics to calculate internal energies and the generalized Born/surface area (GB/SA) method for calculating solvation free energy has been compared with the corresponding terms obtained from ab initio quantum chemical calculations in the gas phase and the free energy perturbation method implemented in Monte Carlo (MC) simulations to study conformational equilibria in solution. 1,2‐Ethanediol, 2‐hydroxybenzoic acid, the neutral and protonated histamine, were considered in aqueous solution as systems capable of intramolecular hydrogen bonding. The molecular mechanics method with all atom and united atom models, using the AMBER* force field and the parameterization as implemented in the MacroModel modeling package and the GB/SA continuum solvation model, produces smaller separation in relative conformer free energies than does the ab initio + MC method in aqueous solution. The GB/SA relative solvation free energies using the charges from the AMBER* force fields were consistently smaller than the values obtained in Monte Carlo simulations. Using the charge sets from the Monte Carlo simulations and considering solute geometries with torsional angles fixed at the optimized ab initio values, the relative solvation free energies remained underestimated by up to 30% as compared to the Monte Carlo values. The AMBER*//GB/SA predicted most stable conformer for the 1,2‐ethandiol system in aqueous solution is in contrast with the ab initio + MC finding and the available experimental results. For the histamine system predictions by only the united atom AMBER*//GB/SA model agree with those by ab initio + MC and with data derived from nuclear magnetic resonance (NMR) experiments. Differences in the two methods are considered mainly due to the application of torsional parameters and atomic charges developed in the AMBER* parameter set for monofunctional polar systems. New parameters seem to be needed for quantitative description of the in‐solution conformational equilibria for organic compounds with a possible intramolecular hydrogen bond. © 1994 by John Wiley & Sons, Inc.