bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of parallel processing techniques to improving the efficiency of MM2 molecular mechanics calculations
Authors: Schweitzer Robert C. , Small Gary W. 
Published: January 2005

AbstractThe application of parallel processing techniques to molecular mechanics calculations is evaluated. Using the standard molecular mechanics package, MM2, four different parallel versions of the program are implemented in a four‐processor computing environment. A set of 529 test structures is used to compare the efficiency of the parallel versions of MM2 to a standard serial version of the program. Statistics describing execution times and program execution cycles are gathered and analyzed. The effects of parallel processing overhead and computer system load are explored, and the practical utility of parallel processing in molecular mechanics is estimated. The results of these parallelization experiments indicate that for geometry optimizations requiring significant amounts of computing time an improvement in program execution speed approaching 50% is realizable. © 1993 John Wiley & Sons, Inc.
Conformational searching methods for small molecules. I. Study of the sybyl search method
Authors: Ghose A.K. , Jaeger E.P. , Kowalczyk P.J. , Peterson M.L. , Treasurywala A.M. 
Published: January 2005

AbstractSeveral methods are available in the literature for the conformational analysis of small molecules. Each of these methods has some advantages and some disadvantages. Also, each of these methods may be expected to perform better or worse on different types of molecules. There is no clear calibration of each of these methods against a “standardized” set of molecules available in the literature. Such a reference work would be useful to the community because it would allow the choice of methods to be based on some facts. We attempted to provide a start to such a calibration in this article with an examination of the SYBYL SEARCH method. Methods for evaluating the performance of this method are described in detail and will be applied to all other available conformational analysis methods in future papers. © John Wiley & Sons, Inc.
Calculation of the interaction energy in a localized representation for a trimer (Ne3) system
Authors: Kozmutza C. , Kapuy E. , Evleth E.M. 
Published: January 2005

AbstractWe studied the transferability of the localized orbitals (LOs) of interacting Ne atoms using several basis sets. Both at SCF and at MP2 and MP3 levels, the contributions of the LOs have been calculated and discussed for the Ne2 and Ne3 systems. It was shown that for the LOs the transferability is satisfied to a good extent and due to the transferability the interaction energy at the correlated level can be calculated by using only the LOs of the supermolecule. The basis set superposition error (BSSE) is simply extracted from the intramolecular parts of the correlation energy. The two‐ and three‐body interaction energies have been investigated for the studied systems. © John Wiley & Sons, Inc.
Parallel direct SCF and gradient program for workstation clusters
Authors: Brode Stefan , Horn Hans , Ehrig Michael , Moldrup Diane , Rice Julia E. , Ahlrichs Reinhart 
Published: January 2005

AbstractA parallel direct SCF and gradient program for workstation clusters has been implemented on the basis of the ab initio program package TURBOMOLE. Applications on large molecular systems monitor an appreciable speedup in residence time. © John Wiley & Sons, Inc.
Divide‐and‐conquer, pattern matching, and relaxation methods in interpretation of 2‐D NMR spectra of polypeptides
Authors: Soo Von‐Wun , Hwang Jan‐Fu , Chen Tung‐Bo , Yu Chin 
Published: January 2005

AbstractOne task in the interpretation of the 2‐D nuclear magnetic resonance (NMR) spectrum is to assign its signal patterns to their corresponding amino acids in proteins or polypeptides. To carry out this task of interpretation, one requires sufficient chemical knowledge and expertise to reason from a set of highly noisy data. We present a system called RUBIDIUM (a Rule‐Based Identification in 2‐D NMR Spectrum) to formulate the expertise and automate the process of interpretation. Given a protein or polypeptide with a known amino acid sequence and the 2‐D NMR spectra (both COSY and NOESY), RUBIDIUM yields plausible assignments of lines that account for most signals observed in the spectrum and conform to prior chemical knowledge. Rules of pattern matching are used to detect plausible signal patterns. The expertise of the sequence‐specific assignment task is formulated to assign a signal pattern to amino acids. To cope with ambiguities and noise, RUBIDIUM adopts various low‐level data preprocessing techniques, the strategy of divide and conquer, and the relaxation technique to decrease the complexity and recover from overconstrained conditions. The polypeptides oxytocin and vasopressin are used to illustrate the performance of RUBIDIUM. © John Wiley & Sons, Inc.
Lattice representations of globular proteins: How good are they?
Authors: Godzik Adam , Kolinski Andrzej , Skolnick Jeffrey 
Published: January 2005

AbstractUsing a number of different lattice models of proteins, the problems introduced by the discretization of a protein backbone are discussed and examples of the most typical errors arising in low coordination number lattices presented. The geometric properties of different lattices used in the literature are compiled, and for all of them the resulting α‐carbon models of proteins are described in detail and compared to the original structures obtained from experiment. © John Wiley & Sons, Inc.
Long‐Range multicenter integrals with slater functions: Gauss transform‐based methods
Authors: Rico J. Fernández 
Published: January 2005

AbstractThe separation of the short‐ and long‐range terms in the potentials generated by pairs of Slater functions is reformulated in the context of the Gauss transform method. Analytic expressions of the long‐range potentials (in closed form) are derived for equal exponents and generalized (as expansion series) for different exponents. Additionally, the representation of these potentials from small sets of charges or lowest‐order multipoles is examined, paying special attention to their values and optimal positions. Finally, numerical tests of the formal developments are presented. It is concluded that the long‐range three‐ and four‐center integrals can be calculated with high accuracy in a simple and relatively inexpensive manner. © John Wiley & Sons, Inc.
Self‐Similarity of solvent‐accessible surfaces of biological and synthetical macromolecules
Authors: Zachmann Carl‐Dieter , Kast Stefan Michael , Sariban Alla , Brickmann Jürgen 
Published: January 2005

AbstractThe quantification of surface roughness of globular proteins and synthetical macromolecules in the globular state is discussed using the concept of fractality. The Hausdorff dimension as a measure for local and global fractality of surfaces is applied. To calculate the Hausdorff dimension of any surface at a high level of accuracy, a new algorithm is presented that is based on a triangulated solvent‐accessible molecular surface. It can be demonstrated that protein surfaces (as calculated on the basis of experimentally determined structures) as well as surfaces of globular polyethylene (PE) conformers (calculated on the basis of structural information basing on extensive Monte Carlo and molecular dynamics simulations) in fact show self‐similarity within a reasonable yardstick range, at least in a global statistical sense. The same is true for parts of a protein surface provided that these regions are not too small. The concept of self‐similarity breaks down when individual surface points are considered. The results obtained for the fractal dimension of PE surfaces (average fractal dimension D = 2.23) lead to the conclusion that protein surfaces probably do not exhibit a unique and specific degree of geometrical complexity (or surface roughness) characterized by a fractal dimension of approximately D = 2.2 as was argued in the past. It is clear that the concept of self‐similarity is helpful for the classification of surface roughness of large molecules, but it seems questionable whether this concept is useful for the identification of active sites or other questions related to the field of molecular recognition. © John Wiley & Sons, Inc.
Critical reevaluation of proximity effects in the barton oxidation and related intramolecular reactions
Authors: Smith Douglas A. , Smith Douglas A. , Vijayakumar S. 
Published: January 2005

AbstractThe limiting factor to account for the increased rate of intramolecular reactions between functional groups as opposed to their intermolecular counterparts can and has been explained both by proximity effects and by activation energy. Neither explanation has emerged as the single most important reason in all or even the majority of cases studied. We have therefore reexamined the spatiotemporal hypothesis of Menger and the transition‐state energy approach of Houk on a consistent set of compounds subjected to the Barton oxidation or related reactions in an effort to more clearly define the reasons for the proximity effect. For the 26 structures studied, neither hypothesis provides a consistent, quantitative explanation although the transitionstate energy hypothesis offered the most promise. © John Wiley & Sons, Inc.
Simulation of the electronic and vibrational structure of hydrogenated amorphous silicon using cluster models
Authors: Clare B.W. , Jennings P.J. , Cornish J.C.L. , Talukder G. , Lund C.P. , Hefter G.T. 
Published: January 2005

AbstractA set of simple models of hydrogenated amorphous silicon (a‐Si:H) consisting of hypothetical silane molecules with diamond or similar lattices was studied by the semiempirical AM1 method. Densities of states and infrared spectra were calculated for the silane molecules and similar molecules with dangling bonds disorder, and with boron or phosphorus substitution to simulate doping. Some examples are presented, and a comparison is made with experimental properties of a‐Si:H. It is proposed to use these models in a study of the Staebler–Wronski photodegradation of a‐Si:H and other aspects of amorphous silicon technology. © John Wiley & Sons, Inc.
Conformational analysis of HIV protease inhibitors. I. Rotation of the amide group adjacent to the P′1 decahydroisoquinoline ring system in ro 31‐8959 and related systems
Authors: Murcko Mark A. , Rao B. Govinda 
Published: January 2005

AbstractPipecolic acid derivatives have proven to be effective P′1 groups in a series of highly potent inhibitors of the enzyme HIV protease. One such inhibitor, Ro 31‐8959, contains the saturated bicyclic ring system decahydroisoquinoline (DIQ) in the P′1 position. The binding orientation of Ro 31‐8959 is known from X‐ray crystallography. However, the bound conformation of the S‐hydroxy diastereomer has not been studied, and for this molecule there are at least two different possible binding conformations. Specifically, the N‐alkyl substituents may be equatorial or axial and the 3‐carboxamide may be rotated into several different orientations. To gain a better understanding of the relative energies of these various conformations, ab initio molecular orbital calculations have been carried out on a series of pipecolic acid and DIQ derivatives. The results indicate that the lowest‐energy N‐equatorial rotamer is always at least 3 kcal/mol more stable than the lowest‐energy N‐axial rotamer. The presence of the second ring, as in the DIQ system, considerably raises the equatorial–axial difference to nearly 7 kcal/mol. Also, the preferred rotation angle of the amide group is different for the N‐equatorial and N‐axial cases. When the molecular dynamics‐averaged conformation of the bound S‐hydroxy inhibitor is considered, the energy difference between the N‐equatorial and N‐axial conformers drops to 4–5 kcal/mol. The preferred amide rotations in these systems are compared to those found in proline‐containing peptides. Finally, some observations are made with respect to the large conformational energy penalty necessary for binding Ro 31‐8959. © John Wiley & Sons, Inc.
Evaluation of AM1‐calculated radical cation ion‐neutral complexes
Authors: Griffin Lawrence L. , McAdoo David J. , Olivella Santiago 
Published: January 2005

AbstractAM1 semiempirical molecular orbital calculations are reported for 20 ion‐neutral complexes, including hydrogen‐bonded complexes, presumably involved in the gas‐phase unimolecular decomposition of simple organic radical cations. The systems investigated are [C2H4O2]˙+, [C2H5NO]˙+, [C2H6O]˙+, [C2H6O2]˙+, [C3H6O]˙+, [C3H6O2]˙+, [C3H8O]˙+, and [C3H8O2]˙+. The AM1 results are compared with ab initio molecular orbital calculations at different levels of theory up to MP3/6‐31G(d, p)//SCF/6‐31G(d) + ZPVE and the available experimental data. AM1 fails to predict some local minima and the equilibrium geometries calculated for several complexes are found to be qualitatively different from those predicted by the ab initio calculations. However, reasonable agreement is generally found for the stabilization energies of the complexes toward dissociation into their loosely bound components. © John Wiley & Sons, Inc.
Theoretical investigation into the potential of halogenated methanes to undergo reductive metabolism
Authors: Waller Chris L. , McKinney James D. 
Published: January 2005

AbstractThe density‐functional theory (DFT)‐based computational chemistry software package DMol was used to provide insight into the reductive potentials of a series of halomethanes. It is known that certain members of this series are readily reduced in vivo via catalysis by cytochrome P450. DMol was used to calculate the electron affinities of these molecules to be used as measures of their reduction potentials. Our results are consistent with experimental electrochemical reduction potentials and indicate that electron affinity is dependent upon the number and type of halogens present in the molecule. Calculated bond lengths and angles also compared favorably with experimental results and estimates derived from other ab initio methods of calculation. Concurrent with this study was the observation of a linear empirical relationship between electron affinity and the lowest unoccupied molecular orbital energy. It is possible that these values could be used as indicators of reductive potentials and ultimately of metabolic rates for use in PB–PK models designed to predict the dose associated with the toxicity of molecules of this and other classes. © John Wiley & Sons, Inc.
Updated Hessian matrix and the restricted step method for locating transition structures
Authors: Bofill Josep Maria 
Published: January 2005

AbstractA family of the updated Hessian matrices for locating transition structures is presented. An analysis and improvement of the restricted step algorithm described by Culot et al. is proposed. The efficiency of the latter method is compared with other well‐established methods for locating transition structures. © 1994 by John Wiley & Sons, Inc.
Free energy derivatives: A new method for probing the convergence problem in free energy calculations
Authors: Pearlman David A. 
Published: January 2005

AbstractThe convergence behavior of free energy calculations has been explored in more detail than in any previously reported work, using a model system of two neon atoms in a periodic box of water. We find that for thermodynamic integration‐type free energy calculations as much as a nanosecond or more molecular dynamics sampling is required to obtain a fully converged value for a single λ point of the integrand. The concept of “free energy derivatives” with respect to the individual parameters of the force field is introduced. This formalism allows the total convergence of the simulation to be deconvoluted into components. A determination of the statistical “sampling ratio” from these simulations indicates that for window‐type free energy calculations carried out in a periodic waterbox of typical size at least 0.6 ps of sampling should be performed at each window (0.7 ps if constraint contributions to the free energy are being determined). General methods to estimate and reduce the error in thermodynamic integration and free energy perturbation calculations are discussed. We show that the difficulty in applying such methods is determining a reliable estimate of the correlation length from a short series of data. © 1994 by John Wiley & Sons, Inc.
Utilization of shape data in molecular mechanics using a potential based on spherical harmonic surfaces
Authors: Malhotra Arun , Tan Robert K.‐Z. , Harvey Stephen C. 
Published: January 2005

AbstractThis article introduces a novel potential function that allows the use of topographical information in molecular modeling. Quantitative shape data are provided by techniques such as electron‐microscopy–based three‐dimensional image reconstruction for large macromolecular assemblies. Such data can provide important constraints for molecular mechanics. We represent topographical data by spherical harmonic surfaces, first used by Max and Getzoff21 for displaying molecular surfaces. A simple harmonic potential is used to constrain atoms within these spherical harmonic surfaces. This potential was implemented in the yammp molecular mechanics package.27 Implementation details and results of several test cases are discussed here. © 1994 by John Wiley & Sons, Inc.
Conformational sampling of hydrocarbon and lipid chains in an orienting potential
Authors: Hardy Barry J. , Pastor Richard W. 
Published: January 2005

AbstractA Distribution Biased Monte Carlo (DBMC) sampling procedure is developed for the efficient generation of chain conformations in the oriented environment of lipid membranes and other liquid crystalline systems. Conformations of the sn‐1 chain of dipalmitoyl phosphatidylcholine (DPPC) were generated by independently sampling torsion angles from continuous distributions in an orienting potential based on a Marcelja mean field; depending on the chain position, the convergence in the deuterium order parameters (SCD) was 100 to 3000 times more efficient with DBMC than with Brownian dynamics. Optimization using joint distribution and torsional potentials of mean force yielded a further threefold increase in sampling efficiency. Overall chain tilt was included using Euler angle rotations and a separate field strength for the anchor. A segmental DBMC procedure was used to generate a set of complete DPPC conformations with well‐converged conformationally averaged SCD consistent with experimental values. These conformations show considerable flexibility, not only in the hydrocarbon tails, but additionally in both the glycerol and head‐group portions of the lipid. An appendix compares DBMC with a number of other Monte Carlo and stochastic dynamics algorithms using the example of a bistable oscillator, and illustrates the tuning of parameters for optimal convergence. © 1994 by John Wiley & Sons, Inc.This article is a US Government work and, as such, is in the public domain in the United States of America.
Normal coordinates–finite elements calculation of 3D vibrational energy levels: Henon—Heiles and Eckart potentials, H molecule
Authors: Alvarez–collado J. R. 
Published: January 2005

AbstractTheoretical and numerical results related to the calculation of multidimensional vibrational levels are presented. A description of the methodological details of a very general method (normal coordinates–finite elements, NC–FEM) is provided. Several representative three‐dimensional (3D) systems (Henon–Heiles and Eckart potentials, and the H molecule) are studied, and NC–FEM results are compared with those published by other authors. For the H, a vibrational Hamiltonian expressed in terms of the three internuclear distances is integrated, and the results obtained are compared with the experimental ones. © 1994 by John Wiley & Sons, Inc.
Modulation of intramolecular proton transfer by electronic excitation and environment: 2‐Pyridone as a case study
Authors: Barone Vincenzo , Adamo Carlo 
Published: January 2005

AbstractThe kinetics and thermodynamics of lactam/lactim tautomerization in 2‐pyridone have been investigated, with special attention to direct and assisted proton transfer mechanisms in the ground and first excited electronic state. Specific interactions with a single water molecule strongly enhance the reaction rate and shift the equilibrium toward the lactam form. The effect of bulk solvent is comparatively negligible, although the lactam form is further stabilized. Electron excitation strongly destabilizes the saddle point for proton transfer and, especially, the lactim form with respect to the lactam species. As a consequence, the direct reaction barrier is increased, but the reverse barrier is lowered. Nonpotential energy effects are relatively small and do not modify the aforementioned general trends. © 1994 by John Wiley & Sons, Inc.
MRD‐CI studies of vertical excitation energies of unsaturated hydrocarbon molecules
Authors: Grimme S. 
Published: January 2005

AbstractSystematic MRD‐CI calculations using the AM1 Hamiltonian have been carried out for two polyenes and eight aromatic hydrocarbons ranging from benzene to ovalene (C32H14). Twenty singlet–singlet excitation energies in these compounds were calculated and compared with experimental data and ab initio STO‐3G results. On an absolute scale, the AM1/MRD‐CI approach underestimates the excitation energies to states with dominant covalent character by an average of 1.1 eV, whereas the errors for ionic states are between −1.0 and 1.0 eV. The STO‐3G calculated data are much too high by ≈ 1 eV and ≈ 5 eV, respectively. The inclusion of σπ‐correlation effects through second‐order Epstein–Nesbet perturbation theory combined with the use of localized orbitals leads to a significant improvement of the ab initio calculated state energies. In an analogous AM1 treatment, negligible corrections for the σπ correlations are found, which is attributed to the implicit account in the parameters and approximation of the semiempirical Hamiltonian. The possible error sources of the calculational methods are discussed. © 1994 by John Wiley & Sons, Inc.
Atomic orbital basis sets for molecular interactions
Authors: Da Costa Herbert F. M. , Micha David A. 
Published: January 2005

AbstractWe describe a general approach to the parametrization of linear combinations of Gaussian atomic orbitals, useful for atomic and molecular interactions. We use a Gaussian transform method and Gauss‐Legendre quadratures to express hydrogenic atomic orbitals, with varying effective charges, in terms of Gaussian‐type orbitals. This procedure provides well‐defined rules for calculating exponent factors and combination coefficients of the linear combinations of Gaussians in problems where nuclear distances may vary over large ranges during interactions. © 1994 by John Wiley & Sons, Inc.
An optimized AM1/MST method for the MST‐SCRF representation of solvated systems
Authors: Luque F. J. , Bachs M. , Orozco Modesto 
Published: January 2005

AbstractThe AM1/MST strategy for the computation of hydrated neutral molecules has been optimized. For this purpose, we have systematically explored the best cavity definition, the most suitable strategy to compute the molecular electrostatic potential (MEP), and the use of MEP scaling factors to correct the semiempirical MEPs. As a result, we have developed an optimized version of the AM1/MST method, which allows us to reproduce well the experimental free energies of hydration (root mean square, rms, deviation in the range of 1 kcal/mol) as well as the water‐induced dipoles computed at the 6‐31G*/MST level (rms deviations in the range of 0.3 D). © 1994 by John Wiley & Sons, Inc.