bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementation and use of the method of prudent ascent in conformational analysis using molecular mechanics
Authors: Hooft Rob W. W. , Kanters Jan A. , Kroon Jan 
Published: January 2005

AbstractIn two‐dimensional conformational analysis the current practice is to perform an energy minimization for all possible combinations of two dihedral angles in the molecule, in a fixed order, and apply a certain dihedral angle step‐size. A newly developed method is presented in which the order of the evaluation points on the energy‐surface is not fixed, but is dependent on all previous results in a way which we call “the method of prudent ascent.” In this method the most promising calculation is carried out first, thus minimizing the risk of atomic collisions. In order to be able to take care of the many additional degrees of conformational freedom present in, e.g., carbohydrate molecules, all minimizations are performed using a set of different promising starting conformations on the basis of previous calculations, and only the lowest energy result for each point is saved. An application of the method to conformational analysis of methyl‐cellobiose and the artificial sweetener trichlorogalactosucrose is also presented.
Quantitative comparison of molecular electrostatic potentials for structure‐activity studies
Authors: Richard Ann M. 
Published: January 2005

AbstractAn approach for representing, efficiently calculating and comparing discrete three‐dimensional molecular electrostatic potentials using a quantitative similarity index (MEP‐SI) based on a Carbo‐type formalism is presented. A radial‐type (MACRA) grid representation is described that provides more efficient storage of MEP information than a cubic grid of similar range, appropriate emphasis, and a convenient means for restricting the comparison of MEP functions to a local molecule region. The MACRA based MEP‐SI formalism was used to evaluate the suitability of a variety of approximate methods for efficiently calculating the MEP for use in MEP‐SI comparison of dissimilar molecules. The Mulliken charge method was found inadequate, while the method of potential‐derived charges (PDCs), with additional charges for lone electron pairs included on sulfur, provided an efficient and sufficiently accurate representation of the MEP for this purpose. Convergence of the MEP‐SI with respect to MACRA grid extent and mesh size was demonstrated; the effect of MEP error and different grid point emphasis in the MACRA versus the cubic grid results was investigated, and MEP‐SI results were compared for different forms of the SI equation. The methodology proposed in this study provides an efficient and practical means for comparing MEP functions for two molecules and gives discriminating results for a sample series of molecular analogues consistent with expectations.
Long range nonbonded attractive constants for some charged atoms
Authors: Bartolotti Libero J. , Pedersen Lee G. , Charifson Paul S. 
Published: January 2005

AbstractEmploying the hydrodynamic formulation of time‐dependent Kohn–Sham theory, long range dispersion constants are calculated for some metal ions. We show that these quantities, when used in molecular mechanics calculations or molecular dynamics simulations, lead to excellent results.
Predicting partition coefficients for isomeric diastereoisomers of some tripeptide analogs
Authors: Bodor Nicholas , Huang Ming‐Ju 
Published: January 2005

AbstractThe octanol‐water partition coefficients (Log P) of tripeptide diastereoisomers have been calculated by our recently developed method for predicting Log P from the results of AM1 semiempirical calculations. This method can distinguish different diastereoisomers. The differences arise from variations in molecular conformation, which lead to significant differences in the dipole moment and ovality of the different diastereoisomers.
MSEED: A program for the rapid analytical determination of accessible surface areas and their derivatives
Authors: Perrot G. , Cheng B. , Gibson K.D. , Vila J. , Palmer K.A. , Nayeem A. , Maigret B. , Scheraga H.A. 
Published: January 2005

AbstractAn algorithm for the rapid analytical determination of the accessible surface areas of solute molecules is described. The accessible surface areas as well as the derivatives with respect to the Cartesian coordinates of the atoms are computed by a program called “MSEED,” which is based in part on Connolly's analytical formulas for determining surface area. Comparisons of the CPU time required for MSEED, Connolly's numerical algorithm DOT, and a program for surface area determination (ANA) based on Connolly's analytical algorithm, are presented. MSEED is shown to be as much as 70 times faster than ANA and up to 11 times faster than DOT for several proteins. The greater speed of MSEED is achieved partially because nonproductive computation of the surface areas of internal atoms is avoided. A sample minimization of an energy function, which included a term for hydration, was carried out on MET‐enkephalin using MSEED to compute the solvent‐accessible surface area and its derivatives. The potential employed was ECEPP/2 plus an empirical potential for solvation based on the solvent‐accessible surface area of the peptide. The CPU time required for 150 steps of minimization with the potential that included solvation was approximately twice as great as the CPU time required for 150 steps of minimization with the ECEPP/2 potential only.
Exploring the conformation space of cycloalkanes by linearized embedding
Authors: Crippen Gordon M. 
Published: January 2005

AbstractLinearized embedding is a variant on the usual distance geometry methods for finding atomic Cartesian coordinates given constraints on interatomic distances. Instead of dealing primarily with the matrix of interatomic distances, linearized embedding concentrates on properties of the metric matrix, the matrix of inner products between pairs of vectors defining local coordinate systems within the molecule. Here, the approach is used to explore the full conformation space allowed to small cyclic alkanes, given the constraint of exact bond lenghts and bond angles. Useful general tools developed along the way are expressions for rotation matrices in any number of dimensions and a generalization of spherical coordinates to any number of dimensions. Analytical results give some novel views of the conformation spaces of cyclopropane, cyclobutane, cyclopentane, and eyclohexane. A combination of numerical and analytical approaches gives the most comprehensive description to date of the cycloheptane conformation space with fixed bond lengths and angles. In this representation, the pseudorotation paths of cyclohexane and cycloheptane are closed curved lines on the surfaces of spheres.
Theoretical calculations of β‐lactam antibiotics. III. AM1, MNDO, and MINDO/3 calculations of hydrolysis of β‐lactam compound (azetidin‐2‐one ring)
Authors: Frau J. , Donoso J. , Muñoz F. , Blanco F. García 
Published: January 2005

AbstractSemiempirical AM1, MINDO/3, and MNDO methods have been used in the study of the alkaline hydrolysis of β‐lactam antibiotics through a base‐catalyzed, acyl‐cleavage, bimolecular mechanism. In this work, the hydroxyl ion has been chosen as nucleophilic agent and the azetidin‐2‐one ring like a model of β‐lactam antibiotic. The MINDO/3 method does not predict correctly the energies of small rings. This, together with the fact that, like MNDO, it cannot detect the occurrence of hydrogen bonds, gives rise to uncertain estimates of energy barriers. The AM1 method can be considered the most suitable for studying the hydrolysis of β‐lactam compounds.
Conformational analysis of flexible ligands in macromolecular receptor sites
Authors: Leach Andrew R. , Kuntz Irwin D. 
Published: January 2005

AbstractA computational method for exploring the orientational and conformational space of a flexible ligand within a macromolecular receptor site is presented. The approach uses a variant of the DOCK algorithm [Kuntz et al., J. Mol. Biol., 161, 288 (1982)] to determine orientations of a fragment of the ligand within the site. These positions then form the basis for exploring the conformational space of the rest of the ligand, using a systematic search algorithm. The search incorporates a method by which the ligand conformation can be modified in response to interactions with the receptor. The approach is applied to two test cases, in both of which the crystallographically determined structures are obtained. However, alternative models can also be obtained that differ significantly from those observed experimentally. The ability of a variety of measures of the intermolecular interaction to discriminate among these structures is discussed.
Semiempirical study of compounds with O‐HO intramolecular hydrogen bond
Authors: Ríos Miguel A. , Rodríguez JesúS 
Published: January 2005

AbstractApplication of MNDO, AM1, PM3, MNDO/H, and MNDO/M methods to a set of compounds with intramolecular hydrogen bonds suggested that none of these methods accurately modeled the characteristics of the hydrogen bonds. Since the MNDO/H and MNDO/M methods work well for intermolecular hydrogen bonds, we followed their example and modified MNDO for intramolecular hydrogen bonds by altering the empirical core–core repulsion energy function for all pairs of atoms involved in intramolecular O‐HO bonds. The resulting modified method models the behavior of these bonds quite well, especially as regards their geometry and the barrier to proton transfer. © 1992 by John Wiley & Sons, Inc.
Does CH prefer a C2v rather than a Cs structure?
Authors: Von Ragué Schleyer Paul , De M. Carneiro José Walkimar 
Published: January 2005

AbstractThe closely related Cs (1) and C2v (3) structures of CH have been reinvestigated at many ab initio levels using MP2/6‐31G** and MP2/6‐311 + + G(2df, 2pd) geometries. The largest basis sets employed were 6‐311G(3df, 2p), 6‐311 + + G(3df, 3pd), and the Dunning “correlation consistent” polarized triple‐split valence basis set (cc‐pVTZ). Electron correlation was probed at the MP4 level, but the QCISD method was also used with the largest basis sets. While electron correlation favors 3 over 1 by about 2 kcal/mol, the correlated relative energies with all basis sets employed range from 0.36–1.03 kcal/mol in favor of 1. The best estimate of this difference, 0.86 kcal/mol, is essentially identical with the (scaled) zero‐point energy difference, 0.84 kcal/mol, favoring 3 over 1. These results indicate that 1 and 3 have almost exactly the same energy at 0 K. Our best value for the dissociation energy of CH is 42.0 kcal/mol [QCISD(T)/6‐311 + + G(3df, 3pd)//MP2(fu)/6‐311 + + G(2df, 2pd), corrected to 298 K], which agrees very well with the experimental value. © 1992 by John Wiley & Sons, Inc.
Extended Koopmans' theorem: Approximate ionization energies from MCSCF wave functions
Authors: Morrison Robert C. , Liu Guanghua 
Published: January 2005

AbstractThe extended Koopmans' theorem has been implemented using multiconfigurational self‐consistent field wave functions calculated with the GAMESS, HONDO, and SIRIUS programs. The results of illustrative calculations are presented for the molecules HF, H2O, NH3, CH4, N2, CO, HNC, HCN, C2H2, H2CO, and B2H6. The lowest extended Koopmans' theorem ionization potentials agree well within the experimental values and the ionization potentials representing excited states of the ions show some improvements over the Koopmans' theorem values in most cases. The extended Koopmans' theorem is easily implemented and the time required to calculate the ionization energies is insignificant compared to the time required to calculate the wave function of the un‐ionized molecule. © 1992 by John Wiley & Sons, Inc.
Multicenter point charge model for high‐quality molecular electrostatic potentials from AM1 calculations
Authors: Rauhut Guntram , Clark Timothy 
Published: January 2005

AbstractThe natural atomic orbital/point charge (NAO‐PC) model based upon the AM1 wave function has been developed to calculate molecular electrostatic potentials (MEPs). Up to nine point charges (including the core charge) are used to represent heavy atoms. The positions and magnitudes of the eight charges that represent the atomic electron cloud are calculated from the natural atomic orbitals (NAOs) and their occupations. Each hybrid NAO is represented by two point charges situated at the centroid of each lobe. The positions of the centroids and the magnitudes of the charges were obtained by numerical integration of the Slater‐type hybrids and the results used to set up polynomials and look‐up tables that replace the integration step in the actual MEP calculation. The MEPs calculated using this method are found to be in better agreement with those obtained using RHF/6‐31G* than those obtained from the AM1 wave function using Coulson charges or with MOPAC‐ESP. The MEP calculations are extremely fast and have, for instance, been incorporated into an interactive graphics package. © 1993 John Wiley & Sons, Inc.
Substrate specificity of cytochrome P450cam for L‐ and D‐ norcamphor as studied by molecular dynamics simulations
Authors: Bass Michael B. , Ornstein Rick L. 
Published: January 2005

AbstractIn our earlier molecular dynamics simulations, we found that there was a discrepancy between the predicted and experimental product ratios when norcamphor is hydroxylated by cytochrome P450cam. The experimental results suggest that there is a nearly equimolar ratio between the 5‐ and 6‐hydroxynorcamphor (45% 5‐, 47% 6‐, and 8% 3‐hydroxynorcamphor) [W.M. Atkins and S.J. Sligar, J. Am. Chem. Soc., 109, 3754 (1987)]. Our previous simulations predicted predominately from 68–88% 5‐hydroxynorcamphor [M.B. Bass et al., Prot. Struct. Funct. Genet., 13, 26 (1992); M.B. Bass et al., Proc. Natl. Acad. Sci. U.S.A., submitted]. One possible explanation for this discrepancy is that the simulations were performed using D‐norcamphor while the experiments were conducted with racemic norcamphor. The suggestion that norcamphor is the D‐isomer was based upon the similarity with the native substrate D‐camphor. Indeed, the reported crystallographic structure for norcamphor‐bound P450cam models norcamphor as the D‐isomer. Unfortunately, the two stereomers have never been separated. The simulations presented here model the L‐isomer of norcamphor. Three simulations each of the L‐ and D‐isomers of norcamphor bound to cytochrome P450cam were compared to account for the effects due to substrate orientation and the assignment of random velocities. The results presented here show that the L‐isomer of norcamphor is predicted to give rise to predominately 6‐hydroxynorcamphor, while the D‐isomer gives rise to mainly 5‐hydroxynorcamphor. From this data, we infer that racemic norcamphor will give rise to nonracemic 5‐ and 6‐hydroxynorcamphors after oxidation by cytochrome P450cam. © 1993 John Wiley & Sons, Inc.
Global measure of molecular flexibility and shape fluctuations about conformational minima
Authors: Arteca Gustavo A. 
Published: January 2005

AbstractA method to characterize conformations adopted by chain and cyclic molecules, and to assess their degree of flexibility toward folding, is developed and applied. The proceudure constructs a function A0 from some simple geometric and topological properties of molecular chains. This function provides a global descriptor of the essential shape features of the molecular fold. The descriptor takes a maximum value of 1 for a completely linear or planar structure and a minimum value of 0 for an entangled or globular backbone. In this sense, the function proposed measures the compactness and degree of folding of a configuration. When one monitors the changes in this function along computer‐simulated molecular dynamics trajectories, it is possible to assess the differential stability of conformations as a function of time, temperature, and other factors. Molecules that are stable over time toward adopting conformations with radically different folds are characterized as rigid. Consequently, the procedure provides also a quantitative measure of rigidity and flexibility toward folding. In other words, the fluctuations of A0 provide a quantitative measure of stability whereas the value of A0 gives a measure of the actual type of instant folding pattern. The description is characteristic of the given conformation and not relative to the initial nuclear geometry for the dynamics. The procedure is illustrated by comparing conformations of hexane and cyclohexane at various temperatures and contrasting the dynamics of hexane and decane, both starting from similar conformational minima. © 1993 John Wiley & Sons, Inc.
Evaluation of one‐electron integrals for arbitrary operators V(r) over Cartesian Gaussians: Application to inverse‐square distance and Yukawa operators
Authors: Jensen James O. , Carrieri Arthur H. , Vlahacos Constantine P. , Zeroka Daniel , Hameka Hendrik F. , Merrow Clifton N. 
Published: January 2005

AbstractA general procedure is presented for generating one‐electron integrals over any arbitrary potential operator that is a function of radial distance only. The procedure outlines that for a nucleus centered at point C integrals over Cartesian Gaussians can be written as linear combinations of 1‐D integrals. These Cartesian Gaussian functions are expressed in a compact form involving easily computed auxiliary functions. It is well known that integrals over the Coulomb operator can be expressed in terms of Fn(T) integrals, where

By means of a substitution for Fn(T) by other simple functions, algorithms that form integrals over an arbitrary function can be generated. Formation of such integrals is accomplished with minor editing of existing code based on the McMurchie–Davidson formalism. Further, the method is applied using the inverse‐square distance and Yukawa potential operators V(r) over Cartesian Gaussian functions. Thus, the proposed methodology covers a large class of one‐electron integrals necessary for theoretical studies of molecular systems by ab initio calculations. Finally, by virtue of the procedure's recursive nature it provides us with an efficient scheme of computing the proposed class of one‐electron integrals. © 1993 John Wiley & Sons, Inc.
Accuracy of free energies of hydration for organic molecules from 6‐31g*‐derived partial charges
Authors: Carlson Heather A. , Nguyen Toan B. , Orozco Modesto , Jorgensen William L. 
Published: January 2005

AbstractAbsolute free energies of hydration have been computed for 13 diverse organic molecules using partial charges derived from ab initio 6‐31G* wave functions. Both Mulliken charges and charges fit to the electrostatic potential surface (EPS) were considered in conjunction with OPLS Lennard–Jones parameters for the organic molecules and the TIP4P model of water. Monte Carlo simulations with statistical perturbation theory yielded relative free energies of hydration. These were converted to absolute quantities through perturbations to reference molecules for which absolute free energies of hydration had been obtained previously in TIP4P water. The average errors in the computed absolute free energies of hydration are 1.1 kcal/mol for the 6‐31G* EPS charges and 4.0 kcal/mol for the Mulliken charges. For the EPS charges, the largest individual errors are under 2 kcal/mol except for acetamide, in which case the error is 3.7 kcal/mol. The hydrogen bonding between the organic solutes and water has also been characterized. © John Wiley & Sons, Inc.
General atomic and molecular electronic structure system
Authors: Schmidt Michael W. , Baldridge Kim K. , Boatz Jerry A. , Elbert Steven T. , Gordon Mark S. , Jensen Jan H. , Koseki Shiro , Matsunaga Nikita , Nguyen Kiet A. , Su Shujun , Windus Theresa L. , Dupuis Michel , Montgomery John A. 
Published: January 2005

AbstractA description of theab initioquantum chemistry package GAMESS is presented. Chemical systems containing atoms through radon can be treated with wave functions ranging from the simplest closed‐shell case up to a general MCSCF case, permitting calculations at the necessary level of sophistication. Emphasis is given to novel features of the program. The parallelization strategy used in the RHF, ROHF, UHF, and GVB sections of the program is described, and detailed speecup results are given. Parallel calculations can be run on ordinary workstations as well as dedicated parallel machines. © John Wiley & Sons, Inc.
Hydrating peptides using a sprouting technique
Authors: David Carl W. 
Published: January 2005

AbstractA scheme for generating water coordinates, whose proton orientations are random, and simultaneously generating side chain coordinates of peptides, preparatory to studying solvation of peptides using molecular dynamics schemes is presented in an X‐PLOR context. Examples from the Integrin and Tropomyosin systems are used to illustrate the procedure. © 1994 by John Wiley & Sons, Inc.
Computational study of the hydrolysis of degradable polysaccharide biomaterials: Substituent effects on the hydrolytic mechanism
Authors: Pratt Lawrence M. , Chu C. C. 
Published: January 2005

AbstractHyaluronic acid and its derivatives are absorbable polysaccharides which are used extensively in cosmetics and as biomaterials. Two possible mechanisms of degradation, involving an oxocarbenium ion and the corresponding radical cation, are examined by modeling of the saccharide ring and the effects of various ring substituents on the two possible mechanisms. © 1994 by John Wiley & Sons, Inc.
Monte Carlo simulations on short single‐stranded oligonucleotides. I. Application to RNA trimers
Authors: Ghomi Mahmoud , Victor Jean‐Marc , Henriet Charles 
Published: January 2005

AbstractMonte Carlo (MC) structural simulation of short RNA sequences has been carried out by random variations of the nucleotide conformational angles (i.e., phosphodiester chain torsional angles and sugar pucker pseudorotational angles). All of the chemical bond lengths and valence angles remained fixed during the structural simulation, except those of the sugar pucker ring. In this article we present the simulated structures of RNA trimers—r(AAA) and r(AAG)—obtained at 11°C and 70°C. The influence of various initial conformations (selected as starting points in the MC simulations) on the equilibrium conformations has been discussed. The simulated conformational angles have been compared with those estimated by nuclear magnetic resonance (NMR) spectroscopy. For both of the oligonucleotides studied here, the most stable structures are helical conformations with stacked bases, at 11°C and 70°C. However, when the starting point is a stretched chain, it is found that r(AAA) adopts a reverse‐stacked structure at low temperature (11°C), in which the A3 base is located between the A1 and A2 bases. Although the energies of these conformations (helical and reverse stacked) are very close to each other, the potential barrier between them is extremely high (close to 30 kcal/mol). This hinders the conformational transition from one structure to the other at a given temperature (and in the course of a same MC simulation). However, it is possible to simulate this structural transition by heating the reverse‐stacked structure up to 500°C and cooling down progressively to 70°C and 11°C: Canonical helical structures have been obtained by this procedure. © 1994 by john Wiley & Sons, Inc.