bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient calculations of coulombic interactions in biomolecular simulations with periodic boundary conditions
Authors: Shimada Jiro , Kaneko Hiroki , Takada Toshikazu 
Published: January 2005

AbstractTo make improved treatments of electrostatic interactions in biomacromolecular simulations, two possibilities are considered. The first is the famous particle–particle and particle–mesh (PPPM) method developed by Hockney and Eastwood, and the second is a new one developed here in their spirit but by the use of the multipole expansion technique suggested by Ladd. It is then numerically found that the new PPPM method gives more accurate results for a two‐particle system at small separation of particles. Preliminary numerical examination of the various computational methods for a single configuration of a model BPTI–water system containing about 24,000 particles indicates that both of the PPPM methods give far more accurate values with reasonable computational cost than do the conventional truncation methods. It is concluded the two PPPM methods are nearly comparable in overall performance for the many‐particle systems, although the first method has the drawback that the accuracy in the total electrostatic energy is not high for configurations of charged particles randomly generated. © 1993 John Wiley & Sons, Inc.
Computational convergence of electronic structure calculations of transition metal ligand complexes
Authors: Magnusson Eric , Moriarty Nigel W. 
Published: January 2005

AbstractCalculations of binding energies and optimum geometries of compounds of the series M(H2O)+ with M = Sc to Zn have been carried out and compared with gas‐phase experimental data and with the Rosi and Bauschlicher MCPF calculations. Hartree–Fock calculations and correlated calculations at MP2, MP4, and QCISD(T) levels were used to test the dependence of the results upon the level of correlation. A test of basis set dependence was also carried out, using parallel calculations on four basis sets ranging in size from a small DZ set to a TZ contraction. Correlation levels above MP2 and elaboration of the metal d‐function basis set to (4d/3d) size or greater were both necessary for convergence with the most uniformly reliable results obtained from QCISD(T) calculations on a basis set with a (6d/4d) contraction for the d‐function space. However, MP2 or higher‐level calculations with a contracted four or five d function set [(5d/3d) or (4d/3d)] are capable of yielding results on binding energies and geometries close to the current gas‐phase experimental uncertainty on electrostatically bound transition metal complexes. © 1993 John Wiley & Sons, Inc.
Assessment of methods used for predicting lipophilicity: Application to nucleosides and nucleoside bases
Authors: Viswanadhan Vellarkad N. , Reddy M. Rami , Bacquet Russell J. , Erion Mark D. 
Published: January 2005

AbstractEstimating log P (logarithm of “1‐octanol to water” partition coefficients) as a measure of lipophilicity for organic compounds is of considerable importance in drug discovery. Several methods have been developed for this purpose, each with its own drawbacks and advantages. In this article, a systematic comparison of three well‐documented and fully computerized methods has been attempted for a set of nucleosides and bases. The first method (BLOGP) is based on overall molecular properties derived from a molecular orbital calculation to predict log P. The second method (CLOGP) uses fragmental lipophilicity constants with correction factors and treats log P as an additive‐constitutive property. The third method (ALOGP) is based on an additivity scheme of atomic lipophilicity constants, with the constitutive factor governed by an elaborate list of atom types. However, none of these methods take into account conformational flexibility or intramolecular hydrogen bonding, which can cause substantial discrepancy between observations and predictions. A comparison of predictions from each of these methods indicates that the atomic contribution method (ALOGP with r = 0.842 and SD = 0.51) is better than other methods (with r = 0.395 and SD = 1.2 for BLOGP and r = 0.713 and SD = 0.93 for CLOGP) for this class of compounds. Our overall assessment is that we do not have, as yet, a highly reliable, fully computerized log P prediction method applicable to flexible heterocycles such as nucleoside analogs. © John Wiley & Sons, Inc.
New combining rules for rare gas van der waals parameters
Authors: Waldman Marvin , Hagler A.T. 
Published: January 2005

AbstractNew combining rules are proposed for the well depth, ϵ, and interaction distance, σ, describing nonbonded interatomic forces for rare gas pair interactions. Concepts underlying current combining rules applied in simulations of macromolecular and polymer systems are shown to be incompatible with experimental data on the rare gases. The current combining rules are compared with the new results using the experimental data. Mathematical properties of combining rules are considered, and it is shown how to reduce combining rule formulas from a two‐parameter to a single‐parameter problem. It is also shown how to graphically analyze combining rules against experimental data. We demonstrate using this analysis technique that the rare gas potentials do not obey a single combining rule for the ϵ parameter but do follow a single combining rule for the σ parameter. Finally, we demonstrate that a combining rule using both ϵ and ω can be used to predict the ϵ parameters for the mixed rare gas pairs. © John Wiley & Sons, Inc.
New approach to the rapid semiempirical calculation of molecular electrostatic potentials based on the am1 wave function: Comparison with ab initio hf/6‐31g* results
Authors: Ford George P. , Wang Bingze 
Published: January 2005

AbstractA new approach to the computation of molecular electrostatic potentials based on the AM1 wave function is described. In contrast to the prevailing philosophy, but consistent with the underlying NDDO approximation, no deorthogonalization of the wave function is carried out. The integrals required for the computation of the electronic contributions to the molecular electrostatic potential are evaluated in a manner similar to that of the AM1 core‐electron attraction integrals, while the nuclear contributions are computed using a new semiempirical function—ZA(SASA, SpSp)[1 + exp[ – ωA(RAi – δA)]]—where the atomic parameters ωA and δA are obtained by calibration against the results of ab initio HF/6‐31G* calculations. Isopotential contour maps for guanine and cytosine obtained with the new method are qualitatively almost indistinguishable from their HF/6‐31G* counterparts, while quantitative comparisons for the minima for a wide range of molecules are reproduced with an rms error of 5.2 kcal mol−1. The locations of the “lone‐pair” minima for a wide range of heterosubstituted organic molecules generally fall within 0.02 Å of the corresponding HF/6‐31G* minima while those in the π‐regions of unsaturated molecules are generally within 0.2 Å. Because of the rapid integral evaluation, the fully semiempirical method described here is extremely economical. For example, for the guanine–cytosine base pair it is >500 times faster than calculations in which the complete integral matrix is computed analytically from the deorthogonalized AM1 wave function. © John Wiley & Sons, Inc.
Stiffness and energy conservation in molecular dynamics: An improved integrator
Authors: Harrison Robert W. 
Published: January 2005

AbstractMolecular dynamics is the integration of a set of coupled differential equations describing the motion of atoms over time. These equations exhibit the unfortunate property of stiffness, that is, terms of the equations (the forces on the atoms) are defined on several scales—ranging from tens of kcal/mol/Å to thousands of kcal/mol/Å. Additional nonconservative and stiff effects occur when a distance cutoff is used for the electrostatics and nonbonded potentials. Because the first derivative at the cutoff is essentially infinite, small variations in positions will cause large variations in energy and violate conservation of energy. The effects are demonstrated in a small system of 125 isolated water molecules. It is possible to greatly reduce and nearly eliminate the stiff integration effects with an improved integrator. The nonconservative effects of the distance cutoff cannot be removed by changing the integrator. © John Wiley & Sons, Inc.
MNDO‐PM3 study on model cytochrome P450‐mediated desulfuration of thiophosphoryl trifluoride, trimethylphosphine sulfide, and trimethyl phosphorothionate
Authors: Katagi Toshiyuki 
Published: January 2005

AbstractThe reaction mechanism of the model cytochrome P450‐mediated desulfuration of thiophosphoryl trifluoride, trimethylphosphine sulfide, and trimethyl phosphorothionate was examined by the semiempirical MNDO‐PM3 molecular orbital method. The proposed pathways, involving initial formation of S‐oxide followed by rear‐rangement to a cyclic phosphoxathiirane and the successive liberation of atomic sulfur to form a phosphate derivative, wee stepwisely analyzed by using the two model active oxygen species, O(1D) and O(3P). Reaction coordinate analysis followed by refinement of transition states in each spin state strongly suggested that the desulfuration of thiophosphorus compounds by O(3P) was energetically more favorable than O(1D). The alternative triplet pathway, abstraction of sulfur by O(3P) forming phosphine and sulfur monoxide followed by recombination between phosphorus and oxygen, was found to be energetically more probable than the rearrangement pathway. © 1993 by John Wiley & Sons, Inc.
Improved strategy in analytic surface calculation for molecular systems: Handling of singularities and computational efficiency
Authors: Eisenhaber Frank , Argos Patrick 
Published: January 2005

AbstractComputer methods for analytic surface calculations of molecular systems suffer from numerical instabilities and are CPU time consuming. In this article, we present proposals toward the solution of both problems. Singularities arise when nearly collinear triples of neighboring atoms or multiple vertices are encountered during the calculation. Topological decisions in analytic surface calculation algorithms (accessibility of vertices and arcs) are based upon the comparison of distances or angles. If two such numbers are nearly equal, then currently used computer programs may not resolve this ambiguity correctly and can subsequently fail. In this article, modifications in the analytic surface calculation algorithm are described that recognize singularities automatically and treat them appropriately without restarting parts of the computation. The computing time required to execute these alterations is minimal. The basic modification consists in defining an accuracy limit within which two values may be assumed as equal. The search algorithm has been reformulated to reduce the computational effort. A new set of formulas makes it possible to avoid mostly the extraction of square roots. Tests for small‐and medium‐sized intersection circles and for pairs of vertices with small vertex height help recognize fully buried circles and vertex pairs at an early stage. The new program can compute the complete topology of the surface and accessible surface area of the protein crambin in 1.50–4.29 s (on a single R3000 processor of an SGI 4D/480) depending on the compactness of the conformation where the limits correspond to the fully extended or fully folded chain, respectively. The algorithm, implemented in a computer program, will be made available on request. © John Wiley & Sons, Inc.
Grid positioning independence and the reduction of self‐energy in the solution of the Poisson—Boltzmann equation
Authors: Bruccoleri Robert E. 
Published: January 2005

AbstractA common problem in the solution of the Poisson–Boltzmann equation using finite difference methods is the self‐energy of the system, also known as the grid energy. Because atoms are typically modeled as a point charge, the infinite self‐energy of a point charge is likewise modeled. In this article, a simple, alternate treatment of atomic charge is described where each atom is represented as a sphere of uniform charge. Unlike the point charge model, this method converges as the grid spacing is reduced. The uniform charge model generates the same electrostatic field outside the atoms. In addition, the use of fine grids reduces the variations in the potential due to variations in the position of atoms relative to the grid. Calculations of Born ion solvation energies, small‐molecule solvation energies, and the electrostatic field of superoxide dismutase are used to demonstrate that this method yields the same results as the point charge model. © John Wiley & Sons, Inc.
Algorithm to test the structural plausibility of a proposed elementary reaction
Authors: Valdés‐Pérez Raúal E. 
Published: January 2005

AbstractAn algorithm is introduced that tests whether a proposed elementary reaction can be realized within a specified number of cleavages and formations of covalent bonds. This is related to the problem of computing the minimum chemical distance of a given stoichiometry, but differs from it in important ways that are exploited in the algorithm design. One application of the algorithm is as a filter in MECHEM—a computer aid for the elucidation of reaction pathways. In that application, reaction steps implying more changes to covalent bonds than a given threshold are ruled implausible, and in practice such tests need to be carried out many thousands of times. Future applications of the algorithm can be expected because the question addressed is a fundamental one: What elementary reactions can occur? © 1993 by John Wiley & Sons,	Inc.
Estimation of pKa for organic oxyacids using calculated atomic charges
Authors: Dixon Steven L. , Jurs Peter C. 
Published: January 2005

AbstractA method for the estimation of pKa from empirically calculated atomic charges has been developed and tested on a diverse set of organic oxyacids. The approach involves a comparison of the atomic charges calculated for both the acid and the negative ion that is formed after loss of the acidic proton. These charges have been used in conjunction with the familiar concepts of induction and resonance to develop an accurate formula to predict pKa. Results for a set of 135 compounds, including alcohols, phenols, and carboxylic acids, yielded a fit of pKa with r = 0.993 and an rms error of 0.455. © John Wiley & Sons, Inc.
Bulk properties from finite cluster calculations. VIII. Benchmark calculations of the efficiency of extrapolation methods for the HF and MP2 energies of polyacenes
Authors: Cioslowski Jerzy , Weniger Ernst Joachim 
Published: January 2005

AbstractThe total energies per unit cell of both the undistorted and the Peierls‐distorted polyacene polymers are computed from the respective HF/6‐311G** and MP2/6‐311G** finite‐cluster data using 40 different extrapolation schemes. The benchmark calculations, which aim at assessing the efficiency of extrapolation methods, clearly show that the best procedure for obtaining rapidly converging bulk properties should involve computation of the energy differences, followed by rational extrapolation techniques such Wynn's p algorithm or its iteration, both with the interpolation points xn = (n + 1)2, and closely related extrapolation methods, or Wynn's ε algorithm and its close relative, Aitken's iterated Δ2 algorithm. © John Wiley & Sons, Inc.
Experiences and practical hints on using the DDRP method, illustrated by the example of the H2 + H reaction
Authors: Dömötör Gy. , Bán M.I. , Stachó L.L. 
Published: January 2005

AbstractBy using the dynamically defined reaction path (DDRP) method and starting from various initial polygons, the intrinsic reaction coordinate (IRC) of the H2 + H → H + H2 reaction has been calculated. The numerical stability of the method is illustrated by the evolution phases of the reaction path. Techniques and experiences on the parameter choice and effects of the parameter values on the stability and computer time consumption are discussed. © John Wiley & Sons, Inc.
Basis‐Modified hydrogen atoms as embedding atoms in ab initio chemisorption cluster model calculations on Si surfaces
Authors: Illas F. , Roset L. , Ricart J.M. , Rubio J. 
Published: January 2005

AbstractA comparative and systematic ab initio study of different models simulating the Si (111) surface has been carried out for a variety of embedding hydrogen atoms including unmodified hydrogen atoms and modified hydrogen atoms described with a STO‐4G basis set and a Slater exponent optimized to have the cluster atoms as neutral as possible. The study has been extended to some chemisorption processes as Ag and Al on Si (111). The main conclusion of the present work is that neither the electronic structure of the isolated cluster models nor the nature of the chemisorption bond depend on the kind of embedding hydrogen atoms used to saturate the free valences of the cluster edge atoms. © John Wiley & Sons, Inc.
Simulations of the solution structure of HIV‐1 protease in the presence and absence of bound zinc
Authors: York D. M. , Bartolotti L. J. , Darden T. A. , Pedersen L. G. , Anderson M. W. 
Published: January 2005

AbstractZinc ions have been shown to inhibit human immunodeficiency virus type 1 (HIV‐1) protease in vitro at neutral pH [Zhang et al. Biochemistry, 36, 8717 (1991)]. Kinetic data from this study support a reversible binding mechanism of zinc in the active site. Preliminary calculations of the ion–protein potential energy based on the geometry of the crystallographic structure [Wlodawer et al. Science, 245, 616 (1989)] are consistent with this proposed mechanism. To examine the structure of HIV‐1 protease with zinc bound in the active site, molecular dynamics simulations in the presence and absence of zinc at this site have been carried out to 200 ps. These simulations suggest zinc remains stably bound to the catalytic aspartate residues without disruption of the dimer or significant alteration of the active site structure. These data are consistent with those observed by Zhang et al. (1991), and together give strong evidence that this is the binding site that leads to inactivation. A proposed model of zinc binding at the active site based on quantum mechanical calculations indicates Zn+2 coordination is monodentate with each catalytic aspartate, leaving at least two ligand positions potentially free (occupied by water molecules in the calculations). © 1994 by John Wiley & Sons, Inc.
Canonical numerical methods for molecular dynamics simulations
Authors: Okunbor Daniel I. , Skeel Robert D. 
Published: January 2005

AbstractWe consider the application of canonical numerical integrators to molecular dynamics simulations. Computer experiments are done to analyze the relative merits of using canonical integrators against their noncanonical counterparts. These experiments involve the study of the properties of liquid argon utilizing the Lennard–Jones interaction potential. To accomplish this comparative study of canonical and noncanonical integrators, we computed thermodynamic and structural quantities. Our results indicate that noncanonical methods, with one exception, fail miserably to conserve energy and as a consequence give poor estimates of the other quantities. Also, higher‐order canonical methods may offer an advantage over the Störmer/Verlet method. © 1994 by John Wiley & Sons, Inc.
A comparative study of effective core potential and full‐electron calculations in Mo compounds. I. An analysis of topological properties of bond charge distribution
Authors: Sierraalta Anibal , Ruette Fernando 
Published: January 2005

AbstractEffective core potential (ECP) and full‐electron (FE) calculations for MoS4−2, MoO4−2, and MoOCl4compounds were analyzed. Geometry parameters, binding energies, charge distributions, and topological properties of the electronic density were studied for MoL bonds (L = S, O, Cl). Results clearly indicate that those approaches that include valence plus 4sand 4pelectrons (ECP2 methods) are able to reproduce the topological properties of MoL bonds, charge distributions, and geometries with respect to those obtained by FE methods. ECP methods that consider only the 4dand 5svalence electrons (ECP1) fail in the calculation of molecular properties. The use of 5pfunctions in ECP1 approaches produces a negative Mulliken charge on Mo. Bader's charges give more consistent results than Mulliken's ones. A new parameter for measuring the degree of ionicity is proposed. © 1994 by John Wiley & Sons, Inc.
Ab initio study of low‐lying electronic states of the PF2 radical
Authors: Cai Z.‐L. 
Published: January 2005

AbstractThe equilibrium geometries, excitation energies, force constants, and vibrational frequencies of the low‐lying electronic states X2B1, 2A1, 2B2, and 2A2 of the PF2 radical have been calculated at the MRSDCI level with a double zeta plus polarization basis set. Our calculated geometry, force constants, and vibrational frequencies for the X2B1 state are in good agreement with experimental data. The electronic transition moments, oscillator strengths for the 2A1 → X2B1 and 2A2 → X2B1 transitions, and radiative lifetimes for the 2A1 and 2A2 states are calculated based on the MRSDCI wave functions. © 1994 by John Wiley & Sons, Inc.
Free energy perturbation calculations on parallel computers: Demonstrations of scalable linear speedup
Authors: Debolt Stephen E. , Pearlman David A. , Kollman Peter A. 
Published: January 2005

AbstractA coarse‐grain parallel implementation of the free energy perturbation (FEP) module of the AMBER molecular dynamics program is described and then demonstrated using five different molecular systems. The difference in the free energy of (aqueous) solvation is calculated for two monovalent cations ΔΔGaq(Li+ Δ Cs+), and for the zero‐sum ethane‐to‐ethane′ perturbation ΔΔGaq(CH3methylX → XmethylCH3), where X is a ghost methyl. The difference in binding free energy for a docked HIV‐1 protease inhibitor into its ethylene mimetic is examined by mutating its fifth peptide bond, ΔG(CONH → CHCH). A potassium ion (K+) is driven outward from the center of mass of ionophore salinomycin (SAL−) in a potential of mean force calculation ΔGMeOH(SAL− · K+) carried out in methanol solvent. Parallel speedup obtained is linearly proportional to the number of parallel processors applied. Finally, the difference in free energy of solvation of phenol versus benzene, ΔΔGoct(phenol → benzene), is determined in water‐saturated octanol and then expressed in terms of relative partition coefficients, Δ log(Po/w). Because no interprocessor communication is required, this approach is scalable and applicable in general for any parallel architecture or network of machines. FEP calculations run on the nCUBE/2 using 50 or 100 parallel processors were completed in clock times equivalent to or twice as fast as a Cray Y‐MP. The difficulty of ensuring adequate system equilibrium when agradual configurational reorientation follows the mutation of the Hamiltonian is discussed and analyzed. The results of a successful protocol for overcoming this equilibration problem are presented. The types of molecular perturbations for which this method is expected to perform most efficiently are described. © 1994 by John Wiley & Sons, Inc.
On the analytical calculation of van der Waals surfaces and volumes: Some numerical aspects
Authors: Petitjean Michel 
Published: January 2005

AbstractA fast computer algorithm is presented for complete analytical calculation of van der Waals surfaces and volumes. Connolly's analytical algorithms, computing second‐ and third‐order atomic spheres overlaps, are shown to give insufficient numerical approximations of the exact van der Waals surfaces and volumes. The presented algorithm computes overlaps of any order. Practical situations frequently involve six‐order overlaps. Analytical computed surfaces and volumes of 63 chemicals are compared with Monte Carlo measured values. © 1994 by John Wiley & Sons, Inc.