bluuebunny/crossref_metadata_2025 huggingface dataset:
Monte Carlo simulations of pure liquid substituted benzenes with OPLS potential functions
Authors: Jorgensen William L. , Laird Ellen R. , Nguyen Toan B. , Tirado‐Rives Julian
Published: January 2005

Intermolecular potential functions have been developed for use in computer simulations of substituted benzenes. Previously reported optimized potentials for liquid simulations (OPLS) for benzene and organic functional groups were merged and tested in Monte Carlo statistical mechanics simulations for the pure liquids of toluene, m‐cresol, anisole, aniline, and benzonitrile at 25°C at 1 atm. The merged potential functions yielded acceptable thermodynamic results for the liquids except in the case of aniline, for which the error in the heat of vaporization was 12%. This was remedied by enhancing the polarity of the model to be more consistent with the observed dipole moment of aniline. Overall, the average errors in computed heats of vaporization and densities were then 2 and 1%, respectively. The structures of the liquids were characterized through energy and radial distribution functions. For m‐cresol and aniline, the molecules participate in averages of 1.6 and 1.4 hydrogen bonds, respectively. Condensed phase effects on the torsional energies for anisole, m‐cresol, and aniline were found to be small; m‐cresol has a slightly enhanced tendency to be nonplanar in the liquid than in the gas phase, while anisole shows the opposite pattern. © 1993 John Wiley & Sons, Inc.
Fast generation of molecular surfaces from 3D data fields with an enhanced “marching cube” algorithm
Authors: Heiden W. , Goetze T. , Brickmann J.
Published: January 2005

An improved version of the “marching cubes” algorithm [W. Lorensen and H. Cline, Comp. Graph. 21, (1987)] for the generation of isosurfaces from 3D data fields is presented and applied to molecular surfaces. The new algorithm avoids inconsistent pattern definitions of the original one, which lead to artificial gaps. The advantage of a logarithmic interpolation procedure, in particular for data fields typically occurring in molecular science, is demonstrated. An example is the generation of molecular surfaces based upon electron density data. © 1993 John Wiley & Sons, Inc.
Vibrational molecular force field of model compounds with biologic interest. II. Harmonic dynamics of both anomers of glucose in the crystalline state
Authors: Dauchez Manuel , Derreumaux Philippe , Vergoten Gérard
Published: January 2005

Combining the modified Urey–Bradley–Shimanouchi intramolecular potential energy function with an appropriate intermolecular energy function, normal coordinate calculations have been performed for both α and β anomers of glucose and for some deuterated analogs in the crystalline state. The overall agreement between the observed and calculated frequencies leads to an average error on the order of 3 and 5 cm−1 for α and β glucose, respectively. In both cases, it is shown that the intermolecular potential energy terms are essential to reproduce perfectly the whole spectra, in particular for the hydroxyl stretching region, the anomeric and crystalline spectral regions, and the low‐frequency range. Moreover, the intermolecular interactions have a nonnegligible influence on the value of the intramolecular force constants. But, the potential energy distribution of vibrational modes are in accord with previous works performed for an isolated molecule. It is also important to point out that approximately the same set of force constants has been used for both molecules, differences existing only for the atoms involved in the anomeric configuration. Likewise, different charge distributions have been calculated and tested with different value of the dielectric constant. Charges determined by the AM1 quantum mechanical procedure with a value of 3 for the dielectric constant have the merit to reproduce quite well the whole spectra and in particular the frequency range below 200 cm−1. © 1993 John Wiley & Sons, Inc.
Fitting of nonlinear regressions by orthogonalized power series
Authors: Randić Milan
Published: January 2005

We outline a procedure that resolves ambiguities in fitting nonlinear data by power series. As is well known, the coefficients in the regression equations depend upon the truncation of the power series. We outline the procedure in which the coefficients of the regression using a power expansion are independent of the degree of the polynomials used. This is achieved by considering mutual regression of descriptors and using residuals as novel variables. The derived regression equations show unusual numerical stability, i.e., the coefficients of the regression equations are constant and independent of the truncation of the power series. The process is illustrated in an example to show all details and facilitate duplicating the process for interested readers. The method described here complements recently outlined procedures for construction of orthogonal descriptors for use in multivariate regression analysis. © 1993 John Wiley & Sons, Inc.
Loop closure via bond scaling and relaxation
Authors: Zheng Qiang , Rosenfeld Rakefet , Vajda Sandor , Delisi Charles
Published: January 2005

We describe, test, and apply a new computational algorithm for generating protein loop conformations subject to distance and secondary structure constraints. The algorithm is based upon initial scaling and subsequent relaxation of covalent bond lengths. The scaling‐relaxation procedure needs no additional energy terms and can be readily incorporated into existing molecular modeling packages. The algorithm uses an all‐atom energy function from the outset in a straightforward way so that about 60% of the generated loop conformations are free of severe distortions of covalent bond lengths and angles. An extensive application to the major loop conformations of TFIIIA‐type zinc fingers (Zif268 and ADR1) is presented, as well as preliminary calculations on hypervariable loops of two immunoglobulins (MCPC603 and Bence‐Jones). © 1993 John Wiley & Sons, Inc.
FORTRAN routine to compute Born–Oppenheimer potential energy curves directly from spectroscopic data
Authors: Battaglia Franco , Gallicchio Emilio
Published: January 2005

A computer program that calculates Born–Oppenheimer potential energy curves of diatomic molecules directly from spectroscopic data is presented. Rather than performing the usual preliminary fitting of the experimental data to a single polynomial in the variable (v + 1/2), where v is the vibrational quantum number, the program contains an accurate built‐in interpolation routine by which each experimental input point belongs to its own polynomial. The program is tested on the ground state of the H2 molecule and results are compared with the most accurate ab initio calculations available. © 1993 John Wiley & Sons, Inc.
Comparison of methods to estimate the free energy of solvation:Importance in the modulation of the affinity of 3‐benzazepines for the D1receptor
Authors: Alkorta Ibon , Villar Hugo O. , Perez Juan J.
Published: January 2005

We computed the free energy of solvation for a series of ions and neutral molecules using two different continuum approaches. First, we used the AM1–SM1 technique, where the AM1 Fock matrix is modified to include a generalized Born contribution. Second, we applied the DelPhi approach, where the electrostatic component of the free energy of solvation is evaluated by resolving the Poisson–Boltzman equation by a finite difference method. Both methods appear equally reliable for ionic systems. For neutral compounds, AM1–SM1 performs better than DelPhi; however, the differences become less pronounced for compounds with larger free energies of solvation. In parallel, both methods were applied to study the influence of the solvation process in the overall drug receptor interaction for a series of closely related ligands for the D1 dopamine receptor. An inverse linear relationship was found between the free energy of solvation and the logarithm of the affinity of the ligands; nevertheless, electrostatic properties are likely to modulate affinity as well. © 1993 John Wiley & Sons, Inc.
Treatment of hydrogen bonding in SINDO1
Authors: Jug Karl , Geudtner Gerald
Published: January 2005

For the treatment of hydrogen bonding in SINDO1, 2p orbitals are introduced on hydrogen. The optimization of the orbital exponent together with the generation of approximate formulas for the core attraction integrals is sufficient to obtain good geometries and binding energies in hydrogen bonded systems. The method is applied to the dimers (H2O)2, (NH3)2, (HF)2, (HCOOH)2, (HCN)2, (H2S)2, and (HCI)2, mixed dimers NH3 · H2O and H2O · HCN, and cyclic polymers (HF)n(n = 3, 4, 6). © 1993 John Wiley & Sons, Inc.
Theoretical study of “protonated pyruvate”: A methylhydroxycarbene—carbon dioxide complex—implications for the decarboxylation of pyruvic acid
Authors: Norris Kathryn E. , Bacskay George B. , Gready Jill E.
Published: January 2005

Two conformers of protonated pyruvate, CH3C+(OH)COO, with the OH group either trans or cis to the methyl group and the carboxylate group in the CCC plane have been studied using the ab initio SCF/3‐21G method, as well as by some semiempirical AM1 calculations. Both ab initio SCF and AM1 curves for the potential energy as a function of the CCOO distance exhibit a minimum corresponding to a complex of methylhydroxycarbene, CH3COH, associated with carbon dioxide, but only the AM1 curves predict an inner minimum corresponding to a covalently bonded protonated pyruvate molecule with a CCOO distance of 1.6–1.7 Å. The two models also disagree on the dissociation pathway for pyruvic acid, with the AM1 calculations predicting formation of acetyl and HOCO radicals while the ab initio method predicts dissociation into methylhydroxycarbene and carbon dioxide following an initial intramolecular proton transfer. The weakly bound complexes of methylhydroxycarbene and carbon dioxide have been studied in some detail using ab initio SCF and MP2 methods in conjunction with 6‐311G** basis sets, obtaining equilibrium geometries and vibrational frequencies. In addition, the lactone‐type isomer of protonated pyruvate, which contains a CCO ring, was also studied. The conclusions of these calculations are consistent with those from earlier work using the smaller 3‐21G basis set. The most stable complex is predicted to occur between trans‐methylhydroxycarbene and carbon dioxide where substantial stabilization is provided by an OH ⃛ OC hydrogen bond. © 1993 John Wiley & Sons, Inc.
Comparison of the boys and Pipek–Mezey localizations in the local correlation approach and automatic virtual basis selection
Authors: Boughton James W. , Pulay Peter
Published: January 2005

Our implementation of Pipek–Mezey population localization is described. It is compared with other localization schemes and its use in the framework of the local correlation method is discussed. For such use, this localization is shown to be clearly superior to Boys in the case of physically well‐localized systems. Our current algorithm for selection of local virtual spaces is also described. © 1993 John Wiley & Sons, Inc.
Hydrolytic degradation of α‐substituted polyglycolic acids: A semiempirical computational study
Authors: Pratt Lawrence M. , Chu C.C.
Published: January 2005

The two‐step hydrolyses of substituted polyglycolic acids are modeled by the semiempirical MNDO Hamiltonian using small molecule analogs to determine the effect of the alkyl substituents on the reaction and activation enthalpies. Reaction enthalpies remain reasonably constant up to three carbons, before becoming less exothermic for large alkyl substituents. Activation enthalpies show patterns that can be explained by steric effects. © 1993 John Wiley & Sons, Inc.
Conformational analysis and molecular dynamics simulation of cellobiose and larger cellooligomers
Authors: Hardy B.J. , Sarko A.
Published: January 2005

The conformational behavior of cellobiose (D‐glc‐ß(1→4)‐D‐glc), cellotetraose, and cellooctaose was studied by a combination of energy minimization and molecular dynamics simulations in vacuo at 400 K. These diand oligosaccharide models have considerable flexibility and exhibit a variety of different motions in glycosidic and exocyclic torsions. The glycosidic ϕ, ψ torsions moved frequently between two local minima on the cellobiose energy surface in the region of known crystal structures. Transitions of the hydroxymethyl side chain were observed between gt,gg, and tg conformations accompanied by changes in intramolecular hydrogen bonding patterns. A reasonable fit to the experimental optical rotation and nuclear magnetic resonance vicinal coupling data of cellobiose in solution required a distribution of its conformations. The oligomers, although generally extended, assumed a more coiled or twisted shape than is observed in the crystalline state of cellulose and exhibited considerable backbone motion due to local ring rotations about the glycosidic bonds. Long‐lived transitions to structures having torsion angles 180° from the major minima (ring flips) introduced kinks and bends into the tetramer and octamer. While the glucose rings of the structures remained primarily in the 4C1 conformation, twist and boat structures were also observed in the tetramer and octamer structures. Reducing the simulation temperature to 300 K eliminated some of the transitions seen at 400 K. © 1993 John Wiley & Sons, Inc.
Efficient calculations of coulombic interactions in biomolecular simulations with periodic boundary conditions
Authors: Shimada Jiro , Kaneko Hiroki , Takada Toshikazu
Published: January 2005

To 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

Calculations 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

Estimating 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

New 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

A 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

Molecular 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

The 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

Computer 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

A 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

An 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

A 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

The 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

By 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

A 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

Zinc 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

We 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.
Molecular mechanics (MM3) calculations on alkyl radicals
Authors: Liu Ruifeng , Allinger Norman L.
Published: January 2005

The MM3 force field has been extended to cover alkyl radicals. Structures, conformational energies, vibrational spectra, and heats of formation have been well fit, mostly to ab initio data. © 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

Effective 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

The 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

A 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

A 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.
Shape analysis of hydrogen‐bonded networks in solvation clusters
Authors: Arteca Gustavo A.
Published: January 2005

A procedure is developed and applied to characterize the global shape of the hydrogen‐bonded networks formed in solvent and solute‐solvent clusters. The methodology combines elements of geometry and topology of molecular chains, and it provides a description of the compactness and complexity of the entanglements formed by the network of hydrogen bonds between solute and solvent molecules. This approach complements others in the literature, where the hydrogen bonding is described in terms of the spatial distribution of bonds, their energetics and lifetimes, or the length hydrogen‐bonded walks in space. The results of the present technique do not depend too strongly on the details of the molecular geometry. Therefore, one can assess the extent to which large‐scale architecture is modified by rearrangements in the nuclear configuration, information which is important in molecular dynamics when estimating the persistence of essential structural features along dynamic trajectories. In this article we discuss the methodology and illustrate its application to the study of water clusters and solvated clusters of acetic acid. Expected qualitative features in the change of shape descriptors in actual reorganizations of hydrogen‐bonding patterns are discussed briefly. © 1994 by John Wiley & Sons, Inc.
Internal dynamics of a globular protein under external force field
Authors: Yoshioki Shuzo
Published: January 2005

The inelastic neutron‐scattering experiment of a small globular protein in powder form can present the density of states as a function of the frequency. This characterizes the internal dynamics of the protein, which (especially in the case of low‐frequency internal dynamics, < 200 cm−1) is required for an improved understanding of protein function. The theoretical frequency distributions of the internal dynamics of a protein have only been calculated in vacuo using the normal mode analysis. Here we show that frequency distributions of the internal motions of a protein in different environments can be provided by changing the magnitude of external force fields acting on the protein. Our test case is bovine pancreatic trypsin inhibitor (BPTI), consisting of 58 amino acid residues. To mimic the effect of intermolecular contacts in powders, external force fields formed by surrounding water molecules are forced to act on the protein. The neutron‐derived density of states of BPTI in powders is shown to be reproduced by the external force fields. In addition, the densities of states, shifted to low frequencies, are suggested to represent that of BPTI in solution. © 1994 by John Wiley & Sons, Inc.
Fast geometry optimization using a modified extended Hückel method: Results for molecules containing H, C, N, O, and F
Authors: Dixon Steven L. , Jurs Peter C.
Published: January 2005

A semiempirically parameterized version of the extended Hückel molecular orbital method has been combined with an efficient quasi‐Newton Broyden‐Fletcher‐Goldfarb‐Shannon (BFGS) optimization algorithm to obtain accurate geometries for compounds containing H, C, N, O, and F. The requirement of only one matrix diagonalization per energy evaluation makes the EHNDO (Extended Hückel Neglect of Differential Overlap) method faster than semiempirical Hartree–Fock NDDO methods such as MNDO, AM1, and PM3. Geometrical results for EHNDO appear to be as good as or better than results for the widely used AM1 technique, and geometry optimization for EHNDO also requires only a fraction of the time. © 1994 by John Wiley & Sons, Inc.
High‐precision atomic computations from finite element techniques: Second‐order correlation energies for Be, Ca, Sr, Cd, Ba, Yb, and Hg
Authors: Flores Jesús R. , Redondo P.
Published: January 2005

We have applied the FEM‐MP2 method (an implementation of the p‐version finite element technique within the framework of second‐order Møller–Plesset perturbation theory, [J. Chem. Phys., 98, 5642 (1993), and references therein]) to calculate second‐order correlation energies for the atoms Be, Ca, Sr, Ba, Yb, Cd, and Hg and thus to complete our studies on closed‐shell elements. The FEM‐MP2 method permits the use of virtual orbitals of very high angular momentum (lmax = 12) in combination with radial basis sets which are very close to completeness, in such a way that we are able to obtain results that could be the most accurate published so far and, in some cases, the only values available in the literature. We hope they may be useful as a reference for basis set saturation tests and for new methods to calculate correlation energies. © 1994 by John Wiley & Sons, Inc.
D‐CICADA: A software for conformational PES elucidation on network of workstations
Authors: Matyska Luděk , Koča Jaroslav
Published: January 2005

The methodology of conformational potential energy (hyper)surface (PES) elucidation is the subject of this article. The decomposition of the recently developed software CICADA and its implementation in the distributed environment using PVM (parallel virtual machine) is presented. CICADA has been chosen for the parallelization because of its ability to elucidate systematically the low‐energy areas of PES in polynomial time. This makes the method applicable on larger systems which are beyond the scope of the grid search. To show the level of parallelization, conformational PES of two molecules, cyclohexane and terminally blocked alanine, have been studied by the distributed version, D‐CICADA, and results have been compared to those of the sequential version. D‐CICADA was tested on several virtual machines composed of DEC and Sun workstations. The timing shows good efficiency for both the decomposition of the original algorithm and the PVM environment. © 1994 by John Wiley & Sons, Inc.
Conformational study of dipeptides: A sensitivity analysis approach
Authors: Susnow Roberta , Schutt Clarence , Rabitz Herschel , Subramaniam Shankar
Published: January 2005

This article studies the backbone influence on the side chains of N‐methyl N′‐acetyl amides (dipeptides) of alanine, valine, phenylalanine, leucine, isoleucine, glutamine, and lysine. Several local minima corresponding to protein ϕ, ψ, and χ values for each dipeptide are determined through optimization in the MM2 force field. These local minima are located in various regions on the Ramachandran map related to particular protein secondary structures. The dipeptide backbone influence on the side chain is explored via the sensitivity of the side chain torsion angles χ with respect to the backbone ϕ and ψ angles. Sensitivity coefficients are calculated, describing the χ response to an externally imposed change in ϕ or ψ. The χ response, which depends on the backbone conformation in a particular region, is induced primarily by the van der Waals and dipole interactions between the backbone and the side chain, which change with a deviation in ϕ or ψ. Various sensitivity trends are observed in the particular Ramachandran regions, revealing the subtle relationships between the dipeptide backbone and the side chain. © 1994 by John Wiley & Sons, Inc.
On the calculation of ab initio quantum molecular similarities for large systems: Fitting the electron density
Authors: Mestres Jordi , Solà Miquel , Duran Miquel , Carbó Ramon
Published: January 2005

A set of procedures for rapid calculation of quantum molecular similarities from ab initio wave functions is discussed. In all cases a density fitting is carried out to eliminate the need of calculating costly four‐centered integrals. It is proved that this methodology can be applied to large systems to reproduce exact quantum molecular similarity measures at an extremely low computational cost. © 1994 by John Wiley & Sons, Inc.
Algorithm to infer the structures of molecular formulas within a reaction pathway
Authors: Valdés‐Pérez Raúl E.
Published: January 2005

MECHEM is a computer aid for elucidation of reaction pathways that was developed over the last 5 years. The program searches systematically and comprehensively for the simplest multistep reaction pathways (or mechanisms) that are consistent with the experimental constraints formulated by the experimentalist, any ad hoc assumptions, and the program's internal theory. Previous articles have reported the basic pathway‐generation algorithm and another algorithm that tests the structural soundness of individual steps. This article introduces an algorithm to solve another basic problem: Given a multistep pathway containing a mixture of molecular structures and formulas, assign possible structures to the formulas while obeying (and exploiting) the constraint imposed by the pathway steps. With this new algorithm, MECHEM is now approaching competence as an interactive tool for elucidating some catalytic reaction pathways, which is the current chemical focus. © 1994 by John Wiley & Sons, Inc.
Anisotropy of atom–atom repulsions
Authors: Stone A. J. , Tong C.‐S.
Published: January 2005

We describe investigations of the short‐range repulsion part of the intermolecular potential using a test particle approach. This approach provides an economical method of constructing reasonably accurate model repulsion potentials and demonstrates the importance of anisotropy in describing the short‐range repulsion. © 1994 by John Wiley & Sons, Inc.
Heats of formation of organic molecules calculated from ab initio theory and a group equivalent scheme: Alkenes
Authors: Schmitz Lawrence R. , Chen Yi Ren
Published: January 2005

A bond and group equivalent scheme that allows the calculation of heats of formation of alkenes from ab initio 6‐31G* energies has been developed. For a group of 26 compounds, the root mean square (rms) error for the calculated heat of formation was 0.78 kcal/mol. Heats of formation have been predicted for an additional nine compounds for which the experimental values are either unknown or suspect. The heats of hydrogenation of barrelene and related compounds are discussed. © 1994 by John Wiley & Sons, Inc.