bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal use of the recurrence relations for the evaluation of molecular integrals over Cartesian Gaussian basis functions
Authors: Ryu Ungsik , Kim Myeongcheol , Lee Yoon Sup 
Published: January 2005

AbstractWe consider the tree search problem for the recurrence relation that appears in the evaluation of molecular integrals over Cartesian Gaussian basis functions. A systematic way of performing tree search is shown. By applying the result of tree searching to the LRL2 method of Lindh, Ryu, and Liu (LRL) (J. Chem. Phys., 95, 5889 1991), which is an auxiliary function‐based method, we obtain significant reductions of the floating point operations (FLOPS) counts in the K4 region. The resulting FLOPS counts in the K4 region are comparable up to [dd|dd] angular momentum cases to the LRL1 method of LRL, currently the method requiring least FLOPS for [dd|dd] and higher angular momentum basis functions. For [ff|ff], [gg|gg], [hh|hh], and [ii|ii] cases, the required FLOPS are 24, 40, 51, and 59%, respectively, less than the LRL1 method in the K4 region. These are the best FLOPS counts available in the literature for high angular momentum cases. Also, there will be no overhead in either the K2 or K0 region in implementing the present scheme. This should lead to more efficient codes of integral evaluations for higher angular momentum cases than any other existing codes. © 1993 John Wiley & Sons, Inc.
Molecular conformations from distance matrices
Authors: Glunt W. , Hayden T.L. , Raydan M. 
Published: January 2005

AbstractTwo algorithms are introduced that show exceptional promise in finding molecular conformations using distance geometry on nuclear magnetic resonance data. The first algorithm is a gradient version of the majorization algorithm from multidimensional scaling. The main contribution is a large decrease in CPU time. The second algorithm is an iterative algorithm between possible conformations obtained from the first algorithm and permissible data points near the configuration. These ideas are similar to alternating least squares or alternating projections on convex sets. The iterations significantly improve the conformation from the first algorithm when applied to the small peptide E. coli STh enterotoxin. © 1993 John Wiley & Sons, Inc.
Conformational analysis of bradykinin by annealed molecular dynamics and comparison to NMR‐derived conformations
Authors: Salvino Joseph M. , Seoane Peter R. , Dolle Roland E. 
Published: January 2005

AbstractConformational analysis of bradykinin (BK), a nonapeptide of the sequence RPPGFSPFR, was accomplished using annealed molecular dynamics (AMD) at 1000 K in BIOGRAF 2.2. One hundred anneal cycles produced 100 conformations over approximately 2000 ps. These conformations were compared to structures derived by nuclear magnetic resonance (NMR) methods for similar shape and energy. Energy minimization of relevant conformations using both BIOGRAF 2.2 and AMBER 3.0a revealed that the AMD‐determined conformations are in the same energy range as the NMR‐determined structures. Also, the shape of the relevant conformations appeared similar, suggesting that AMD is a good tool for the conformational analysis of small peptide ligands. © 1993 John Wiley & Sons, Inc.
Improved solutions to the one‐center McMurchie—Davidson tree search problem
Authors: Cisneros Gerardo 
Published: January 2005

AbstractWe present an improvement to Johnson, Gill, and Pople's results for reducing the cost of using the McMurchie–Davidson RNLM recurrence relation for one‐center integrals. Recursive replacement of singly referenced and single‐term auxiliary integrals results in floating point operation (FLOP) savings of up to 11% and explicit auxiliary integral calculation reductions of up to 76% with respect to the full list and up to 46% with respect to FLOP‐reduced lists with no replacement. The programs are written in the string‐manipulation language Convert; one of the programs automatically generates a FORTRAN subroutine given an integral list. © 1993 John Wiley & Sons, Inc.
Theoretical comparison of conformational properties of molecules: Conformational probability maps and similarity index
Authors: Bagińki Maciej , Piela Lucjan 
Published: January 2005

AbstractThe conformational analysis for a molecule is often performed by assuming that the total conformational energy is a function of two dihedral angles. The resulting conformational energy map is sometimes not easy to interpret because what counts is not energy differences but rather the probability distribution map at a given temperature. In the present article, an algorithm to calculate such a map is given. An example concerning N‐substituted amino sugars shows how the conformational probability map may be interpreted. In addition, a similarity index is proposed to get a measure of similarity of the conformational properties of two molecules. The index is based upon the analysis of the conformational probability maps for both molecules. © 1993 John Wiley & Sons, Inc.
Conformational analysis of 2,3,6,7‐tetrahydroazepines with implications for D1‐selective benzazepines
Authors: Alkorta Ibon , Villar Hugo O. , Cachau Raul E. 
Published: January 2005

AbstractA conformational study of the 2,3,6,7‐tetrahydroazepine (THA) and closely related systems has been carried out using MM3 and CHARMm molecular mechanics, AM1 semiempirical, as well as Hartree‐Fock and local density functional (LDF) ab initio methods. For THA, all methods give similar optimal geometries; however, only MM3 agrees with the Hartree‐Fock calculations using a 6‐31G* basis set and LDF in the rank order of energies and nature of the stationary points characterized. AM1 shows serious disagreements with those results. Tetrahydrobenzazepines and a D1 receptor agonist containing the THA nucleus were studied using CHARMm, MM3, and AM1 calculations. All methods provide similar descriptions of the geometries of the conformations accessible to these compounds. However, the same disparities in the rank order of energies are observed. © 1993 John Wiley & Sons, Inc.
Molecular interaction potential: A new tool for the theoretical study of molecular reactivity
Authors: Orozco Modesto , Luque F.J. 
Published: January 2005

AbstractA new methodology to compute molecular interaction potentials (MIPs) is developed and tested. The calculation of the MIP is based upon the generalization of the rigorous quantum mechanical molecular electrostatic potential (MEP) and further addition of a classical repulsion‐dispersion term. As a result, the MIP is able to represent not only with high accuracy electrostatic interactions but also represent in a suitable way steric effects. The analysis of the results obtained for different molecules demonstrates the superiority of the MIP with regard to the standard MEP to describe nonbonded interactions, in particular hydrogen bonds. The comparison of results calculated at the ab initio I 6‐31G* and semiempirical AM1 levels points out the suitability of semiempirical calculations to qualitatively reproduce the most relevant reactive features of the molecules. Finally, possible applications of the MIP in different fields are discussed. © 1993 John Wiley & Sons, Inc.
Model calculations for small closed‐ring CdS clusters and chemisorption processes by a quantum chemical cluster approach
Authors: Tóth Katalin , Pakkanen Tapani A. 
Published: January 2005

AbstractChemisorption on small, closed‐ring CdS clusters and the electronic structure of the surface were studied using Hartree–Fock valence calculations based upon stepwise density matrix approximations. Detailed valence calculations gave stabilization energies similar to the all‐electron results for the small CdS clusters, verifying our valence method in which the approximations of the density matrices were fitted against the atomic calculations. Chemisorption studies have shown that the 4d shell relaxation on the Cd atom plays a crucial role even though the 4d does not participate directly in the substrate–adsorbate bonds. Thus, the CdCl2 was found unbound to the surface in the case of implicit description of the 4d orbital of the Cd whereas treating the Cd 4d orbital explicitly in the variational calculation the CdCl2 bonds to the surface with the calculated adsorption energy of 107.4 kJ/mol. © 1993 John Wiley & Sons, Inc.
Path integral theory: An improved simulation for the forces in semiclassic systems
Authors: Morales Juan J. 
Published: January 2005

AbstractA method is proposed for calculating the forces in path integral theory and tested on semiclassic systems. It takes the range of the classic and quantum interactions into account and uses a second table within the neighbors table for the nearest neighbors. This method is found to be much more efficient than either the standard direct method or the traditional neighbors table, the efficiency increasing with the size of the system. The method can also be applied to clusters whose interaction centers are much farther apart than the distances between two consecutive members of the cluster. © 1993 John Wiley & Sons, Inc.
A critical comparison of search algorithms applied to the optimization of protein side‐chain conformations
Authors: Tufféry P. , Etchebest C. , Hazout S. , Lavery R. 
Published: January 2005

AbstractThree different optimization algorithms are applied to solving the problem of finding the best side‐chain conformations with a test set of 14 globular proteins having known crystallographic conformations. It is shown that simulated annealing, simple and modified genetic algorithms, and a heuristic combinatorial approach achieve similar optimal solutions, with the exception of simulated annealing applied to the largest proteins. The efficiency of the different algorithms, however, shows wide variations. General conclusions are drawn concerning the optimal approach to such problems. © 1993 John Wiley & Sons, Inc.
Conformational dependence of electrostatic potential‐derived charges: Studies of the fitting procedure
Authors: Stouch Terry R. , Williams Donald E. 
Published: January 2005

AbstractAtomic monopole “point charges” are routinely determined through a least squares fit to molecular electrostatic potentials [potential‐derived (PD) charges]. Previously, it has been shown that these charges vary with variation in molecular conformation. Also, it has been observed that these swings in charges are highly correlated between neighboring atoms. Here, we examine the least squares variance–covariance data matrices for a set of data in the literature and find further indications of high colinearity within the data. These colinearities effectively reduce the dimensionality of the data to a value well below the number of atoms in the molecules. This suggests that the data is not of sufficient dimensionality to support calculation of the charges for all of the atoms in a statistically significant way. We experiment with fixing the charges of atoms whose PD charges reflect large errors in the fit. The resulting estimates of fit of the remaining charges are little degraded from the estimates of fit when the charges of all of the atoms are fit. In addition, the charges that are fit take what would be considered more reasonable and “chemically intuitive” values, often of smaller magnitude. Although most of the free charges continue to vary with molecular conformation, their range is no larger than when all charges were fit and, in some cases, the ranges of the charges for the fit atoms is actually reduced over those that are found when all of the atoms take part in the fitting procedure. The errors of fit are lower and the unconstrained charges appear more reasonable when more chemically “reasonable” charges are used for the fixed values. This suggests that in many cases charges are transferable between molecules. Further, it shows a way to justifiably reduce the large fluctuations in PD charges that occur with variations in conformation. © 1993 John Wiley & Sons, Inc.
Molecular dynamics of 18‐crown‐6 complexes with alkali–metal cations and urea: Prediction of their conformations and comparison with data from the cambridge structural database
Authors: Leuwerink E.T.H. , Harkema S. , Briels W.J. , Feil D. 
Published: January 2005

AbstractComplexes of 18‐crown‐6 with alkali–metal cations (Na+, K+, and Rb+), urea, and the uncomplexed crown ether were studied in vacuo with the molecular dynamics method. Conformational data from these calculations (simulation times in the range from 6–15 ns) was compared with information from the Cambridge Structural Database. Despite the differences in condition between the simulations and the solid state, a number of interesting similarities are observed. © 1993 John Wiley & Sons, Inc.
AQUARIUS2: Knowledge‐based modeling of solvent sites around proteins
Authors: Pitt William R. , Murray‐Rust Judith , Goodfellow Julia M. 
Published: January 2005

AbstractThe program AQUARIUS2 calculates probable positions for water molecules within the first hydration shell of any protein for which atomic coordinates are known. Like its predecessor, AQUARIUS, it uses a knowledge of water molecules sites from crystallographically determined protein structures. Energy calculations are not employed. It differs substantially from the original program in that a 3‐D probability map (for solvent sites) is generated around the surface of the protein instead of the previously used discrete points. The accuracy of the program has been gauged by comparison with experimentally derived water molecule positions for proteins not used in the knowledge base of the program. It has also been tested by combining the probability density maps with crystallographically determined electron density maps for the protein porphobilinogen deaminase. This procedure filters the most likely solvent electron density peaks from the background noise and has been used in the determination of the solvent structure around the protein nerve growth factor. © John Wiley & Sons, Inc.
Quantification of substituent and ligand size by the use of solid angles
Authors: White David , Taverner B. Craig , Leach P.G.L. , Coville Neil J. 
Published: January 2005

AbstractA new, generalized, method for measuring the steric size of ligands and substituents has been developed. The method is based on the solid angle concept, the solid angle being generated by the pairwise addition of spheres (atoms). The problem of overlapping spheres (atoms) has been solved analytically and the algorithm provided permits evaluation of the steric space occupied by any combination of spheres (atoms). A range of solid angles for commonly encountered ligands and substituents has been determined and compared to literature values for linear cone angles. © John Wiley & Sons, Inc.
LIN: A new algorithm to simulate the dynamics of biomolecules by combining implicit‐integration and normal mode techniques
Authors: Zhang Guihua , Schlick Tamar 
Published: January 2005

AbstractA central goal in molecular dynamics simulations is increasing the integration time‐step to allow the capturing of biomolecular motion on biochemically interesting time frames. We previously made a step in that direction by developing the Langevin/implicit–Euler scheme. Here, we present a modified Langevin/implicit–Euler formulation for molecular dynamics. The new method still maintains the major advantage of the original scheme, namely, stability over a wide range of time‐steps. However, it substantially reduces the damping effect of the high‐frequency modes inherent in the original implicit scheme. The new formulation involves separation of the solution into two components, one of which is solved exactly using normal‐mode techniques, the other of which is solved by implicit numerical integration. In this way, the high‐frequency and fast‐varying components are well resolved in the analytic solution component, while the remaining components of the motion are obtained by a large time‐step integration phase. Full details of the new scheme are presented, accompanied by illustrative examples for a simple pendulum system. An application to liquid butane demonstrates stability of the simulations at time‐steps up to 50 fs, still with activation of the high‐frequency modes. © John Wiley & Sons, Inc.
Optimization and application of lithium parameters for PM3
Authors: Anders Ernst , Koch Rainer , Freunscht Peter 
Published: January 2005

AbstractLithium parameters have been optimized for Stewart's standard PM3 method. The average deviation of the heats of formation calculated for 18 reference compounds is 6.2 kcal/mol from the experimental or high‐level ab initio data; the average deviation with Li/MNDO is 18.9 kcal/mol. The average error in bond lengths is also reduced by a factor of two to three. Ionization potentials and dipole moments are reproduced with comparable accuracy than Li/MNDO. However, the mean deviation for the heats of formation of both methods increases when being applied to other systems, especially to small inorgnic molecules. The applicability of the new parameter set is demonstrated further for various compounds not included in the reference set, for the calculation of the activation barriers of several lithiation reactions, as well as for the estimation of oligomerization energies of methyl lithium (including the tetramer). Li/PM3 gives reliable results even for large dimeric complexes, like [{4‐(CH3CR)C5H4N}Li]2, containing TMEDA or THF as coligands and reproduces the haptotropic interaction between Li+ and π‐systems (e.g., in benzyl lithium) as well as the relative energies and structural features of compounds with “hypervalent” atoms (e.g., in lithiated sulfones). © John Wiley & Sons, Inc.
Comparison of atomic charges derived via different procedures
Authors: Wiberg Kenneth B. , Rablen Paul R. 
Published: January 2005

AbstractAtomic charges were obtained fromab initiomolecular orbital calculations using a variety of procedures to compare them and assess their utility. Two procedures based on the molecular orbitals were examined, the Mulliken population analysis and the Weinhold–Reed Natural Population Analysis. Two procedures using the charge density distribution were included; the Hirshfeld procedure and Bader's Atoms in Molecules method. Charges also were derived by fitting the electrostatic potential (CHELPG) and making use of the atomic polar tensors (GAPT). The procedures were first examined for basis set independence, and then applied to a group of hydrocarbons. The dipole moments for these molecules were computed from the various atomic charges and compared to the total SCF dipole moments. This was followed by an examination of a series of substituted methanes, simple hydrides, and a group of typical organic compounds such as carbonyl derivatives, nitriles, and nitro compounds. In some cases, the ability of the charges to reproduce electrostatic potentials was examined. © John Wiley & Sons, Inc.
Comparison of NDDO and quasi‐ab initio approaches to compute semiempirical molecular electrostatic potentials
Authors: Alhambra C. , Luque F. J. , Orozco Modesto 
Published: January 2005

AbstractThe suitability of the two most widely used strategies to compute semiempirical MEPs is examined. For this purpose, MEP minima, electrostatic charges, and dipoles for a large number of molecules were computed at the AM1, MNDO, and PM3 levels using both the NDDO strategy developed by Ferenczy, Reynolds, and Richards and our own quasi‐ab initio method. Results demonstrate that the quasi‐ab initio is preferred over the NDDO method for the computation of MEP minima. It is also found that the best set of semiempirical charges and dipoles are obtained using either the AM1 NDDO or the MNDO quasi‐ab initio methods. In these two cases, the quality of the results is fully comparable with 6‐31G* values. © 1994 by John Wiley & Sons, Inc.
Display of the flow of energy in molecules
Authors: Schwieters Charles D. , Rabitz Herschel 
Published: January 2005

AbstractIn this article, we develop a method to graphically display the flow of energy within molecules. An energy continuity equation is derived leading to a molecular energy flux vector field. Computation of the flux calls for the intramolecular potential, any external interactions, and the phase space trajectories of the molecular motion. The flux provides a means to display energy flow in still frames and as a tool to visualize hitherto undiscovered dynamic pathways in molecules. Examples are presented that show energy flow in three molecular systems and illustrate the point that depiction of energy flux patterns has increasing utility and meaning as one moves to larger molecules. Simple extensions to this work would also allow visualization of the flux of such quantities as linear and angular momentum. © 1994 by John Wiley & Sons, Inc.
Conformation and reactivity of α‐oxo‐ketenes: Ab initio and semiempirical (AM1, PM3) calculations
Authors: Janoschek Rudolf , Fabian Walter M. F. , Kollenz Gert , Oliver Kappe C. 
Published: January 2005

AbstractAb initio MP2/6‐31G*//MP2/6‐31G* and semiempirical AM1 and PM3 calculations on a series of differently substituted α‐oxo‐ketenes are used to investigate E/Z‐isomerism and rotational barriers in these molecules. Sterically crowded derivatives are found to exist solely as s‐E conformers. The unusual stability of these derivatives thus can be attributed to their inability to adopt the s‐Z conformation required for the normal α‐oxo‐ketene reactions. With respect to structures and energies, the PM3 method (especially in the case of highly crowded molecules) is found to be less reliable than AM1. Ab initio HF/3‐21G and PM3 vibrational frequencies appear to be of sufficient accuracy for a distinction between s‐Z and s‐E conformers. In this respect, the AM1 method appears less reliable. © 1994 by John Wiley & Sons, Inc.
Parallel algorithm for calculating ro‐vibrational states of diatomic molecules
Authors: Neto J. J. Soares 
Published: January 2005

AbstractIn this article, we develop and implement an algorithm for calculating the rovbrational states of diatomic molecules optimized for multiple instructions multiple data computers of distributed memory. The method is based upon the p‐version of the finite element method and has been implemented on an INTEL iPSC/2 machine with 16 processors. © 1994 by John Wiley & Sons, Inc.
Free energy of solvation of a small Lennard–Jones particle
Authors: Lin Ching‐Lung , Wood Robert H. 
Published: January 2005

AbstractIn molecular dynamics (MD) and Monte Carlo (MC) free energy calculations, the choices of the thermodynamic paths from state a to state b affect the accuracy of the result and the efficiency of the programs. Most of the problems occur at the initial stages of growing in a new particle into a solvent. Based on statistical mechanical perturbation theory, an accurate and efficient direct calculation of inserting a small Lennard–Jones particle into solvent is derived. This eliminates the need for calculation of the initial stages of growing in a new particle by MD or MC simulation. Examples are given to show the utility of direct calculation. The recommended procedure is to use direct calculation for a small Lennard–Jones particle and then use MD or MC simulations to calculate the ΔG of changing the small Lennard–Jones particle into the target molecule. © 1994 by John Wiley & Sons, Inc.