bluuebunny/crossref_metadata_2025 huggingface dataset:
Applications of the simulated annealing method to intermolecular interactions
Authors: Nilar Shahul H.
Published: January 2005

The Simulated Annealing method using a quantum mechanical potential energy surface is used to study the interactions of molecules and the formation of clusters. The results obtained for a range of systems are in good agreement with other theoretical calculations and experimental data where available.
Simulations of lipid crystals: Characterization of potential energy functions and parameters for lecithin molecules
Authors: Stouch Terry R. , Ward Keith B. , Altieri Amanda , Hagler Arnold T.
Published: January 2005

We evaluate an empirical potential energy function and associated parameters for classical molecular dynamics simulations of lecithins, a common class of lipid. The physical accuracy of the force field was tested through its application to molecular dynamics simulations of the known crystal structures of lipid molecules. Average atomic positions and molecular conformation are well maintained during the simulations despite considerable thermal motion. Calculated isotropic temperature factors correlate highly with those from experiment.
Semiempirical vibrational and electronic structures of C60 and C70
Authors: Stewart James J. P. , Coolidge Michael B.
Published: January 2005

The electronic and vibrational structures of C60 and C70 have been calculated at the PM3 semiempirical level. C60 has a partially delocalized structure, while C70 has both a localized set and a delocalized set of MOs. As with AM1 and MNDO, PM3 predicts the heat of formation of C70 to be greater than that of C60, and that C70 is the thermodynamically more stable species. Calculation of the normal modes was accelerated over 40 times by limited use of symmetry theory.
Toward accurate transferable electrostatic models for polypeptides: A distributed multipole study of blocked amino acid residue charge distributions
Authors: Price S. L. , Faerman C. H. , Murray C. W.
Published: January 2005

We have developed a method for building up accurate electrostatic models for polypeptides, based on a distributed multipole representation of the SCF charge densities for the dipeptides (CH3.CO.NH.CHR.CO.NH.CH3) of the naturally occurring amino acids. It is based on the observation that each peptide residue has almost the correct formal charge (0, ±1). We find that the variations in the backbone charge distributions (excluding proline) with sidechain have a negligible effect on the predicted electrostatic potential around the residue. However changes in the atomic multipoles with the torsion angles (ϕ, ψ, χ) are more significant, and may need to be taken into account if electrostatic potential close to the residue is required to high accuracy. This type of DMA peptide library provides more accurate, more theoretically based, estimates of the electrostatic potential around polypeptides than current models.
Generation of carbon‐cage polyhedra
Authors: Liu X. , Klein D. J. , Schmalz T. G. , Seitz W. A.
Published: January 2005

The problem of the generation of polyhedra with degree‐3 vertices, and faces each of which is pentagonal or hexagonal, is addressed in order to characterize carbon in order to characterize clusters of ca. 30 or more atoms. Following Eulerian type arguments such polyhedra are subcategorized in terms of numbers of different types of local structures. An algorithm to generate such polyhedra is developed, and its computer implementation is described. Results for smaller than 80‐vertex cages of subcategories anticipated to be more chemically relevant are reported. The singular position of the truncated‐icosahedron (buckminsterfullerene) structure is noted.
Many‐body conjugated‐circuit computations
Authors: Klein D. J. , Liu X.
Published: January 2005

A powerful algorithm for calculating conjugated‐circuit expectations for planar graphs is enunicated. The utility for systematizing quantitative resonance‐theoretic computations on conjugated hydrocarbons, and related species, is emphasized.
Vector and parallel algorithms for the molecular dynamics simulation of macromolecules on shared‐memory computers
Authors: Mertz John E. , Tobias Douglas J. , Brooks Charles L. , Singh U. C.
Published: January 2005

A detailed description of vector/parallel algorithms for the molecular dynamics (MD) simulation of macromolecular systems on multiple processor, shared‐memory computers is presented. The algorithms encompass three computationally intensive portions of typical MD programs: (1) the evaluation of the potential energies and forces, (2) the generation of the nonbonded neighbor list, and (3) the satisfaction of holonomic constraints. We implemented the algorithms into two standard programs; CHARMM and AMBER, and obtained near linear speedups on eight processors of a Cray Y‐MP for cases (1) and (2). For case (3) the SHAKE method demonstrated a speedup of 6.0 on eight processors while the matrix inversion method demonstrated 6.4. For a system of water molecules the performance improvement over the standard scalar SHAKE subroutine in AMBER ranged from a factor of 165 to greater than 2000.
A vector processing algorithm of auxiliary integral evaluation for two‐electron Gaussian integrals
Authors: Yahiro Shuichi , Gondo Yasuhiko
Published: January 2005

A six‐term auxiliary integral expression for the two‐electron Gaussian integral is derived on the basis of the Chebyshev polynomial approximation instead of the seven‐term Taylor expansion. This expression and the related recurrence formula enable us to perform a high‐speed calculation on a vector processing computer.
The solution of adsorption integral equations by means of the regularization method
Authors: Szombathely M.V. , Bräuer P. , Jaroniec M.
Published: January 2005

An overall adsorption quantity for a heterogeneous solid is usually expressed by an integral equation, which contains a distribution function that describes heterogeneous properties of this solid. The calculation of this distribution function is an ill‐posed problem. The current article shows that the difficulties arising from the ill‐posed nature of an adsorption equation can be overcome with the regularization method. This work presents general principles of regularization for solving the ill‐posed problems without detailed mathematical considerations. The application of the regularization method to calculate a distribution function from any overall adsorption functions is illustrated with both simulated and experimental adsorption isotherms.
On the evaluation of molecular electron affinities by approximate density functional theory
Authors: Ziegler T. , Gutsev G.L.
Published: January 2005

The ability of approximate Density Functional Theory to calculate molecular electron affinities has been probed by a series of calculations on the hydrides CH3, NH2, OH, and HC2 as well as the multibonded species CN, BO, N3, OCN, and NO2. The simple Hartree–Fock Slater scheme lacks dynamic correlations and underestimates on the average the adiabatic electron affinities (EAad) by 0.7 eV. A considerable improvement is obtained by the Local Density Approximation (LDA) in which dynamic correlation is included. Values from LDA calculation underestimate, on the average, the adiabatic electron affinities by 0.4 eV. The best agreement with experiment is obtained by the LDA/NL scheme in which a nonlocal correction recently proposed by Becke is added to the LDA energy expression. The LDA/NL method underestimates EAad by 0.2 eV. It is concluded that the LDA/NL method affords EAad's in as good agreement with experiment as ab initio techniques in which electron correlation is taken into account by extensive configuration interaction. A full geometry optimization has been carried out on the nine neutral sample molecules as well as the corresponding anions.
On the numerical solution of the multidimensional vibrational time‐independent Schroedinger equation
Authors: Alvarez‐Collado J.R. , Buenker Robert J.
Published: January 2005

A preliminary study of the capability of the finite difference and finite element methods (FDM, FEM) to evaluate eigenvalues of one‐, two‐, and three‐dimensional self‐adjoint operators is reported with reference to applications dealing with the description of vibrational levels. Results of harmonic oscillator model potentials and ab initio PES for the water molecule are obtained by using the FDM. In spite of the large matrices used, low accuracy, nonvariational results are found. A different method, based on FEM and normal coordinates, is therefore proposed. Two nearly harmonic cases are studied and it is shown that variational results with higher accuracy can be obtained with a moderate cost. The vibrational levels of the water molecule are also calculated in order to compare the results with those of the FDM treatment.
Methods for the calculation of Voh in OHO hydrogen bonds
Authors: van Duijneveldt‐van de Rijdt Jeanne G.C.M. , van Duijneveldt Frans B.
Published: January 2005

Ab initio calculations are reported for dimerization‐induced changes, Δk, in the harmonic force constant k of the H‐bonded OH in water dimer. Two dimer geometries are considered. Δk is obtained by considering the perturbation of a given monomer OH potential by the interaction energy in the dimer in question. The interaction energy is partitioned to identify the role of the various contributions to Δk. The sensitivity of Δk to the choice of the one‐electron basis set is studied by using five different basis sets, some of which have a set of bond functions in the HO bond. At the correlated level, correction for basis set superposition error is found to be essential. A comparison is made of the correlation contribution to Δk as given by the CEPA1, MP2, MP3, and MP4 methods. Of these, MP2 gives exaggerated results. Nevertheless, for economical and reasonably accurate calculations on large systems the MP2 approach in the ESPB basis set is advocated. The most accurate calculations yield a shift Δv0‐;1 of – 121 cm−1 for the uncoupled donor O‐H vibrational frequency in water dimer.
Ab initio and molecular mechanics study of n‐phenyl phthalimide and its crystal structure
Authors: Kendrick John , Robson Elizabeth , McIntyre Sara
Published: January 2005

Ab initio molecular orbital calculations are reported on the energetics for torsional motion of N‐phenyl phthalimide using 3‐21G, 6‐31G, and 6‐31G** basis sets and incorporating electron correlation effects for selected geometries. With the largest basis set, a minimum energy is found for a torsion angle of 59.2°. Atomic charges are assigned to the molecules on the basis of a least‐squares fit to the molecular electrostatic potential. This information is then used in molecular mechanics calculations of the crystal structure, where the calculated unit cell parameters are in good agreement with those observed experimentally.
Atomic charge calculations for quantitative structure—property relationships
Authors: Dixon Steven L. , Jurs Peter C.
Published: January 2005

A previously published empirical charge scheme has been adapted for use in studies of quantitative structure‐property relationships. New parameters have been developed to allow the inclusion of nitrates, nitriles, sulfides, thiols, thiophenes, and sulfoxides. No changes have been made to the original scheme, thus preserving all previous results. A few simple additions to the program have made it possible to calculate atomic charges in a variety of ionic structures containing a formally positive nitrogen or a formally negative oxygen. The results obtained for ions are consistent with a number of concepts surrounding the familiar inductive and resonance effects.
Protein calculations on parallel processors. I. Parallel algorithm for the potential energy
Authors: Janak J.F. , Pattnaik P.C.
Published: January 2005

We investigate and test an algorithm suitable for the parallel calculation of the potential energy of a protein, or its spatial gradient, when the protein atoms interact via pair potentials. This algorithm is similar to one previously proposed, but it is more efficient, having half the interprocessor communications costs. For a given protein, we show that there is an optimal number of processors that gives a maximum speedup of the potential energy calculation compared to a sequential machine. (Using more than the optimum number of processors actually increases the computation time). With the optimum number the computation time is proportional to the protein size N. This is a considerable improvement in performance compared to sequential machines, where the computation time is proportional to N2. We also show that the dependence of the maximum speedup on the message latency time is relatively weak.
Modeling a reaction path by molecular mechanics: Dimerization of carbon free radicals
Authors: Peyman Anusch , Beckhaus Hans‐Dieter
Published: January 2005

A variable force field model for radical dimerization was developed. It uses MM2 force constants for most atoms and new parameters only for the core atoms involved in bonding changes. The change in hybridization from sp2 to sp3 is modeled using distance‐dependent switch functions. The validity of the model has been tested by calculating the minimum energy path of the dimerization of di‐tert‐butylmethyl radicals. The calculated and experimental values for the enthalpy of activation of both dimerization of the radicals and dissociation of the dimer are in excellent agreement. The model has also been successfully applied to the stereoselective dimerization of 1‐phenylneopentyl radicals: The form of the potential energy surface yields an explanation for the observed stereoselectivity. Another common feature in radical dimerization seems to be the formation of adsorption complexes prior to dimerization that can lead to increased reactivity. The results suggest that it is important to analyze the whole reaction path and not only the transition state alone.
Ab initio calculation of magnetic properties by the “direct” IGLO method
Authors: Meier Ulrich , Van Wüllen Christoph , Schindler Michael
Published: January 2005

A direct method for the ab initio calculation of the magnetic susceptibility and chemical shielding tensors based on the individual gauge for localized molecular orbitals (IGLO) formalism is introduced. “Direct” in this context means we avoid storing the two‐electron repulsion integrals in favor of recalculating them whenever necessary. In conjunction with the Direct‐SCF package TURBOMOLE Direct IGLO (DIGLO) permits calculation of magnetic second‐order properties for large molecules by minimizing peripheral disc storage requirements. The size of the molecules to be treated is limited only by the amount of CPU time available. The performance of DIGLO is demonstrated for some selected examples.
Multicenter and multiparticle integrals for explicitly correlated cartesian gaussian‐type functions
Authors: Kozlowski Pawel M. , Adamowicz Ludwik
Published: January 2005

An analytical derivation of multicenter and multiparticle integrals for explicitly correlated Cartesian Gaussian‐type cluster functions is demonstrated. The evaluation method is based on the application of raising operators that transform spherical cluster Gaussian functions into Cartesian Gaussian functions.
Conformational dependence of electrostatic potential derived charges of a lipid headgroup: Glycerylphosphorylcholine
Authors: Stouch T.R. , Williams Donald E.
Published: January 2005

Atomic monopoles are routinely determined through a least squares fit to molecular electrostatic potentials. We report studies of the variation in atomic monopoles with variation in conformation for the zwitterionic polar head group of lecithins, a common class of lipid. The monopole of one atom, a relatively buried carbon, varied by 1.3 electron units between different conformers. “Exterior” atoms, as seen previously, showed smaller changes in charge and smaller estimated standard deviations. The total charge of local groups of atoms varied less than the charge of individual atoms, indicating that shifts in charge occurred mostly between neighboring atoms. This effect might be reflected in the high correlations seen between charges of many neighboring atoms. These correlations, while present for many logical groupings of atoms (such as within methylene and methyl groups), are curiously absent between some bonded atoms. Monopoles were fit to multiple conformations simultaneously to provide a charge set that could optimally reproduce the electrostatic potential of all the conformers as a means of generating monopoles for molecular dynamics simulations or other studies where conformation varies. In some cases, the charges on chemically equivalent atoms (e.g., the hydrogen atoms in a methyl group) were different by more than their estimated error of fit. These studies lead to the suggestion that a minimum error in reported charges is on the order of 10%. All conformations show that the positive charge of the trimethylalkyl ammonium group is carried by the methyl hydrogens; the total charge on the nine hydrogens is over 2 electron units, counterbalanced by negative monopoles on the carbons. The presence of this diffuse cloud of substantial charge would appear to be a disindicator of the use of a “united” atoms approach for these methyl groups. The effects of the charge variation on intermolecular interactions is also examined.
Nucleoside free energy perturbation calculations: Mutation of purine‐to‐pyrimidine and pyrimidine‐to‐purine nucleosides
Authors: Wunz Timothy P.
Published: January 2005

Free energy perturbation calculations were conducted on the mutations of pyrimidine‐to‐pyrimidine, purine‐to‐purine, purine‐to‐pyrimidine, and pyrimidine‐to‐purine nucleosides. The parameters and technique required for these perturbations is presented. Each of the four nucleosides in DNA were mutated into the other three nucleosides, and the calculated change in free energy for each of the 12 mutations is reported.
Analysis of a large data base of electrostatic potential derived atomic charges
Authors: Merz Kenneth M.
Published: January 2005

A large data base of 6‐31G*, MNDO, AM1, and PM3 electrostatic potential (ESP) derived point charges of amino acids and monosaccharides is analyzed. We find that MNDO correlates well with 6‐31G* ESP derived point charges, while AM1 and PM3 do so quite poorly. Furthermore, scaling MNDO ESP derived point charges enhances the ability of MNDO to reproduce 6‐31G* results. We used our data base to attempt to derive a 6‐31G* transferable charge model at an atom‐by‐atom level. We find that it is simple to derive a transferable model for monosaccharides, but for the amino acids statistical difficulties make this a less attractive approach. The transferable charge model for the monosaccharides is slightly better than MNDO, but scaled MNDO charges perform significantly better than the transferable model. We also carried out a QMD simulation on the alanine dipeptide to assess the fluctuations that would be expected in atomic point charges during the course of an MD simulation. Relatively large charge fluctuations are observed and their impact on molecular simulation is addressed. © 1992 by John Wiley & Sons, Inc.
Electrostatic energy calculations by a Finite‐difference method: Rapid calculation of charge–solvent interaction energies
Authors: Luty Brock A. , Davis Malcolm E. , McCammon J. Andrew
Published: January 2005

Finite‐difference Poisson–Boltzmann (FDPB) methods allow a fast and accurate calculations of the reaction field (charge–solvent) energies for molecular systems. Unfortunately, the energy in the FDPB calculations includes the self‐energies and the finite‐difference approximation to the Coulombic energies as well as the reaction field energy. A second finite‐difference calculation, in a uniform dielectric, is therefore necesssary to eliminate these contributions. In this article we describe a rapid and accurate method to calculate the self energy and finite‐difference Coulombic energies in a uniform dielectric thus eliminating the need for a second finite‐difference calculation. The computational savings for this method range from a factor of 4 for a typical protein to a factor of 103 for small molecules. © 1992 by John Wiley & Sons, Inc.
Theoretical studies of organometallic compounds. I. All electron and pseudopotential calculations of Ti(CH3)nCl4 − n (n = 0–4)
Authors: Jonas Volker , Frenking Gernot , Reetz Manfred T.
Published: January 2005

The performance of effective core potentials (ECP) and model potentials (MP) has been studied by calculating the geometries and reaction energies of isodesmic reactions for the molecules Ti(CH3)nCl4 − n (n = 0–4) at the Hartree–Fock level of theory. The results are compared with data from all electron calculations and experimental results as far as available. The all electron calculations were performed with a 3‐21G basis set from Hehre and a (53321/521/41) basis set from Huzinaga. For the ECP calculations the potentials developed by Hay and Wadt, and for the MP calculations, the model potentials developed by Sakai and Huzinaga, are employed. © 1992 by John Wiley & Sons, Inc.
Derivation of fluorine and hydrogen atom parameters using liquid simulations
Authors: Gough Craig A. , Debolt Stephen E. , Kollman Peter A.
Published: January 2005

Simulations of periodic boxes of tetrafluoromethane and trifluoromethane were run to determine van der Waals parameters for fluorine and for hydrogen attached to a fluorine‐bearing carbon. The simulations of CF4 were performed first to determine the optimal van der Waals radius R* and well depth ε for fluorine by adjusting these parameters to reproduce the experimental molar volume and enthalpy of vaporization of CF4. The best values of R* and ε were determined to be 1.75 Å and 0.061 kcal/mol. Using these fluorine parameters, the simulations of CHF3 were then performed to determine if the hydrogen of this molecule required a smaller R* than that used for the “normal” hydrocarbon hydrogen determined by Spellmeyer and Kollman (results in preparation). That R* was determined by running Monte Carlo simulations on methane, ethane, propane, and butane and adjusting R* and ε for carbon and hydrogen to reproduce the experimental molar volume and enthalpy of vaporization. It was found that an Rε of 1.21 Å was optimal, significantly smaller than the R* = 1.49 Å found by Spellmeyer for “normal” hydrocarbon hydrogens. This value of R* is in good agreement with the R* for the hydrogen in CHF3 derived independently using ab initio calculations and molecular mechanics on F3CH… OH2 by Veenstra et al. © 1992 by John Wiley & Sons, Inc.
How transferable are hydrogen parameters in molecular mechanics calculations?
Authors: Veenstra David L. , Ferguson David M. , Kollman Peter A.
Published: January 2005

Interactions of water with various methyl hydrogens were studied using ab initio quantum mechanics and molecular mechanics. Our goal was to determine the effect of electronegative substituents on the nonbonded interactions of hydrogens. We found that methyl hydrogens are indeed very much affected by substituents and that standard van der Waals parameters used for these hydrogens in molecular mechanics do not reproduce these effects. Adjusted van der Waals parameters are presented that reproduce the ab initio values, and their use is discussed, as well as a general approach to van der Waals parameters on all types of hydrogens. © 1992 by John Wiley & Sons, Inc.
Monte Carlo simulation of the diabatic free energy curves for a dissociative electron transfer reaction in a polar solvent
Authors: Pérez Victor , Lluch José M. , Bertrán Juan
Published: January 2005

In the present work we have carried out a Monte Carlo simulation of a dissociative electron transfer reaction in a polar solvent. In particular, we have chosen as a very simple model the electrochemical reduction of hydrogen fluoride to give a hydrogen atom and a fluoride anion in a dipolar solvent. From a classical point of view, the electron transfer occurs at the intersection region S* of the diabatic potential hypersurfaces Hpp and Hss, corresponding to the precursor and successor complexes, respectively. We have evaluated both diabatic surfaces using potential functions that have been built up with ab initio methods by us. For each of the obtained configurations the parameter ΔE = Hss – Hpp has been calculated. This parameter is then used as the reaction coordinate for obtaining the diabatic free energy curves of the reaction. Because the activation energy is high, a suitable mapping potential along with the statistical perturbation theory is employed to force the system to evolve toward the intersection region S*. A total of 68,340,000 configurations have been generated. The main conclusion of this article is that Marcus' relationship seems to fail for this kind of inner‐sphere processes. © 1992 by John Wiley & Sons, Inc.
Algorithm to generate reaction pathways for computer‐assisted elucidation
Authors: Valdés‐Pérez Raúl E.
Published: January 2005

An algorithm is introduced that can generate reaction‐pathway hypotheses for computer‐assisted elucidation. A key aspect of the algorithm is its ability to conjecture reaction intermediates and products that are not input to the algorithm. The formal basis for the conjecture is stoichiometry, i.e., species variables are used in the construction of a pathway, and their molecular formulas are inferred when sufficient stoichiometric constraint is placed on the variables. These conjectured species have a degree of plausibility when the algorithm is used systematically to search for the simplest pathways consistent with given experimental evidence. The MECHEM system for computer‐assisted elucidation under development by the author adapts this algorithm to generate initial pathway hypotheses from experimental data. © 1992 by John Wiley & Sons, Inc.
Protein calculations on parallel processors. II. Parallel algorithm for the forces and molecular dynamics
Authors: Janak J.F. , Pattnaik P.C.
Published: January 2005

We describe two algorithms for the parallel calculation of a CHARMm‐like force field in macromolecules. For a molecule with a given number of atoms, we show that there is an optimal number of processors leading to a minimum computation time. At the optimum, both the number of processors and the computation time are proportional to the number of atoms. © 1992 by John Wiley & Sons, Inc.
Highly accurate diatomic centrifugal distortion constants for high orders and high levels
Authors: Korek Mahmoud , Kobeissi Hafez
Published: January 2005

The problem of the computation of the Centrifugal Distortion Constants (CDC) related to a diatomic potential is considered. The analytical expressions obtained from a reformulation of the Rayleigh‐Schrödinger perturbation theory are used [Kobeissi et al., J. Mol. Spectrosc., 138, 1 (1989)]; these are en+1 = 〈Φ0RΦn〉 – Σ em〈Φ0Φn−m〉 where R = 1/r2, Φ0 = ψv is the vibrational wave function (corresponding to the given energy Ev = e0) and Φ1, Φ2,…, are the “rotational corrections” to Φ0, solutions of the rotational (nonhomogeneous) Schrödinger equations. These equations are integrated by using a recent integrator using a powerful local control allowing (for Φ0) a high accuracy. The integrals are computed by using another powerful technique tailored for matrix elements between numerical wave functions [Kobeissi et al., J. Comp. Chem., 10, 358 (1989)]. This numerical treatment is applied to the model Lennard‐Jones potential and to the RKR potential of the I2 ground state. In both applications the CDC are computed up to e6 = Nv and e7 = Ov (these two are published for the first time), and up to the dissociation [up to v = 23 for the Lennard–Jones potential, and to v = 108 for the XΣ – I2 (RKR) potential]. © 1992 by John Wiley & Sons, Inc.
Conformational distribution of heptaalanine: Analysis using a new Monte Carlo chain growth method
Authors: Velikson B. , Garel T. , Niel J. ‐C. , Orland H. , Smith J.C.
Published: January 2005

A distribution of conformations of heptaalanine is obtained using a new Monte Carlo (MC) method that grows the chain atom by atom. Resulting configurations are energy minimized and a detailed analysis is performed of the minimum‐energy conformers using a method of classification that partitions ϕψ space. The MC‐generated configurations are compared with those generated from high‐temperature molecular dynamics (MD) simulations. It is found that the new method generates a wide distribution of low‐energy conformers at least 10 times more quickly than the MD. An analysis of the generated energy minima demonstrates that they can be divided into clusters in the space defined by the five pairs of ϕ—ψ angles of the inner residues. The space occupied by the minima populating each cluster is restricted. © 1992 by John Wiley & Sons, Inc.
Off‐lattice Monte Carlo method with constraints: Long‐time dynamics of a protein model without nonbonded interactions
Authors: Knapp E.W. , Irgens‐Defregger A.
Published: January 2005

A method is proposed to perform computer simulations of protein dynamics in the long‐time regime. The method is based upon a Monte Carlo technique. The only molecular degrees of freedom considered are bond rotations. All other degrees of freedom including the amide plane torsions are kept rigid. These constraints approximately account for all interactions related to chemical bonding. An individual Monte Carlo step adopts the Go and Scheraga algorithm where local conformational changes in a small window of the protein backbone are performed. By using correlated rotations, the conformation of residues outside the window remains invariant. To test the reliability of the method, the nonbonded interactions are turned off in the present application. Exact statistical averages are compared with values obtained from data of computer simulation involving 2 × 106 scans of the window along the protein backbone. Time is related to the number of scans of the window along the protein backbone. End‐to‐end distance autocorrelation functions decay to 1/e of its initial value in about 103–104 scans of the window algorithm. Time decay follows a stretched exponential Kohlrausch decay law. © 1993 John Wiley & Sons, Inc.
Force field for platinum binding to adenine
Authors: Kozelka Jir̆í , Savinelli Roger , Berthier Gaston , Flament Jean‐Pierre , Lavery Richard
Published: January 2005

The antitumor drug cis‐diamminedichloroplatinum(II) (cisplatin) binds preferentially to GpG and ApG sequences of DNA, forming N7,N7 intrastrand chelates. Molecular modeling of the intrastrand adducts have been handicapped, so far, by the lack of force‐field data describing the Pt–guanine and Pt–adenine binding. We used ab initio calculations with relativistic pseudopotentials to evaluate three important parameters for the platinum–adenine model complex [Pt(NH3)3(Ade)]2+: (1) the force constant for the PtN7 bond bending out of the adenine plane; (2) the energy profile for the torsion about PtN7; (3) a set of fractional atomic charges that reproduce the ab initio potential for a number of space points placed around the adduct. A population analysis and comparative study on the tetrammine complex [Pt(NH3)4]2+ have shown that for platinum adenine is a better σ‐donor than NH3, but its capacity as a π‐acceptor is weak. © 1993 John Wiley & Sons, Inc.
Multigrid solution of the Poisson—Boltzmann equation
Authors: Holst Michael , Saied Faisal
Published: January 2005

A multigrid method is presented for the numerical solution of the linearized Poisson–Boltzmann equation arising in molecular biophysics. The equation is discretized with the finite volume method, and the numerical solution of the discrete equations is accomplished with multiple grid techniques originally developed for twodimensional interface problems occurring in reactor physics. A detailed analysis of the resulting method is presented for several computer architectures, including comparisons to diagonally scaled CG, ICCG, vectorized ICCG and MICCG, and to SOR provided with an optimal relaxation parameter. Our results indicate that the multigrid method is superior to the preconditioned CG methods and SOR and that the advantage of multigrid grows with the problem size. © 1993 John Wiley & Sons, Inc.
Monte Carlo simulations of the hydration of substituted benzenes with OPLS potential functions
Authors: Jorgensen William L. , Nguyen Toan B.
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 by computing free energies of hydration for toluene, p‐xylene, phenol, anisole, benzonitrile, p‐cresol, hydroquinone, and p‐dicyanobenzene. The calculations featured Monte Carlo simulations at 25°C and 1 atm with statistical perturbation theory. The average difference between the computed results and experimental data for the absolute free energies of hydration is 0.5 kcal/mol. The AM1‐SM2 method is also found to perform well in predicting the free energies of hydration for the substituted benzenes. In addition, the Monte Carlo simulations provided details on the hydration of the substituted benzenes, in particular for the solute–water hydrogen bonding. © 1993 John Wiley & Sons, Inc.
Electrostatic solvent effects on the electronic structure of ground and excited states of molecules: Applications of a cavity model based upon a finite element method
Authors: Fox Thomas , Rösch Notker , Zauhar Randy J.
Published: January 2005

We present investigations on the use of dielectric continuum models for the self‐consistent description of electrostatic solvent effects on the ground state of a molecule and on excitation energies. The electronic structure calculations have been carried out in the framework of the INDO and INDO/S‐CI method, respectively. We compare the performance of three implementations of the cavity model that all allow an arbitrary shape of the solute cavity. The procedures differ in the effort spent on the description of the charge density at the cavity surface. Two procedures in the vein of Miertus̆, Scrocco, and Tomasi (MST) rely upon point charges to model the reaction field and differ in the way the cavity surface is modeled. While one implementation divides the surface into flat triangular patches, the improved version uses curved triangles. Alternatively, we investigate a finite element method (FEM) for the calculation of the surface charge density. Applications to rod‐shaped organic molecules (including their charge transfer excitations) illustrate the superiority of the improved MST formalism over the primitive one, as it exhibits faster convergence of the results with increasing node density on the cavity surface. The FEM approach, which also employs curved surface patches, leads to a further improvement as it needs less computational effort, especially in the treatment of excited states. © 1993 John Wiley & Sons, Inc.
AMBERCUBE MD, parallelization of Amber's molecular dynamics module for distributed‐memory hypercube computers
Authors: Debolt Stephen E. , Kollman Peter A.
Published: January 2005

A fully functional parallel version of the molecular dynamics (MD) module of AMBER3a has been implemented. Procedures parallelized include the calculation of the long‐range nonbonded Coulomb and Lennard–Jones interactions, generation of the pairlist, intramolecular bond, angle, dihedral, 1‐4 nonbonded interaction terms, coordinate restraints, and the SHAKE bond constraint algorithm. As far as we can determine, this is the first published description where a distributed‐memory MIMD parallel implementation of the SHAKE algorithm has been designed to treat not only hydrogen‐containing bonds but also all heavy‐atom bonds, and where “shaken” crosslinks are supported as well. We discuss the subtasking and partitioning of an MD time‐step, load balancing the nonbonded evaluations, describe in algorithmic detail how parallelization of SHAKE was accomplished, and present speedup, efficiency, and benchmarking results achieved when this hypercube adaptation of the MD module AMBER was applied to several variant molecular systems. Results are presented for speedup and efficiency obtained on the nCUBE machine, using up to 128 processors, as well as benchmarks for performance comparisons with the CRAY YMP and FPS522 vector machines. © 1993 John Wiley & Sons, Inc.
Stochastic searches for lactone and cycloalkene conformers
Authors: Saunders Martin , Jiménez‐Vázquez Hugo Alejandro
Published: January 2005

The stochastic search method coupled to MM3(92) has been used to locate as many conformers as possible for 6‐ to 11‐membered ring lactones, trans‐cycloalkenes, and cis‐cycloalkenes. A comparison was carried out between the conformers of lactones and cycloalkenes of the same ring size for each force field. These comparisons were carried out by means of (1) conformational distances, defined as the rms deviation between the dihedral angles of the conformers being compared, and (2), substitution, in which a lactone was transformed into an olefin and vice versa, trying to keep as much as possible the initial geometry, followed by reoptimization. It is found that cycloalkenes and lactones share many common characteristics. The thermodynamic information provided by MM3 was used to study the dependence of conformer population upon (1) temperature and (2) total number of conformers. © 1993 John Wiley & Sons, Inc.
Reconsideration of solvent effects calculated by semiempirical quantum chemical methods
Authors: Szafran Miroslaw , Karelson Mati M. , Katritzky Alan R. , Koput Jacek , Zerner Michael C.
Published: January 2005

AM1 and PM3 semiempirical calculations are reported for the solvent effects on the tautomeric equilibria of 2‐pyridone/2‐hydroxypyridine and 4‐pyridone/4‐hydroxypyridine in the gas phase and solution. The solvent effects on the tautomeric equilibria were investigated by self‐consistent reaction field (SCRF) theory implemented in the AMPAC and MOPAC program in two different ways: one in which all the solvent relaxation is included in the quantum mechanics and the total energy must be corrected for the solvent change in energy, method A; and a second in which the quantum mechanics directly includes this term, method B. The calculated (AM1, method A) tautomeric equilibrium constants (log K1) for 2‐pyridone in the gas phase, cyclohexane, chloroform, and acetonitrile are −0.3, 0.3, 0.8, and 1.3, respectively, in good agreement with the experimental data (−0.4, 0.24, 0.78, and 2.17, respectively). For 4‐pyridone/4‐hydroxypyridine differences between calculated log K1 for the gas phase, chloroform and acetonitrile (−6.0, −2.6, and −1.2, respectively) and experimental data (< −1, 0.11, and 0.66, respectively) are larger but the experimental values are also less certain. The experimental acetonitrile data are disturbed by specific interactions. An extension of the SCRF for aqueous solutions is reviewed. © 1993 John Wiley & Sons, Inc.
Conformational properties and homolytic bond cleavage of organic peroxides. I. An empirical approach based upon molecular mechanics and ab initio calculations
Authors: Benassi Rois , Folli Ugo , Sbardellati Silvia , Taddei Ferdinando
Published: January 2005

The conformational features of a large number of hydroperoxides ROOH and peroxides ROOR′, where R and R′ are alkyl groups of different and increasing size and phenyl rings, including ortho substituted derivatives, were obtained from molecular mechanics calculations by employing a standard package. For the molecules of small molecular size, comparison was carried out with the results of ab initio calculations. Heats of formation were also obtained from molecular mechanics for hydroperoxides and peroxides: The values are, in general, overestimated. For the molecules containing the CF3 group, the calculated values are subject to large errors and heats of formation were obtained from ab initio total energies in the “atom equivalents” scheme. To estimate the homolytic dissociation energies of the different bonds in the peroxide molecules, heats of formation of R·, ·OR, and ·OOR radicals were employed and several of them had to be calculated. Different approaches were employed—molecular mechanics calculations, ab initio energies within the atom equivalent and isodesmic reaction schemes, and Benson's group additivity rule; values consistent within the different calculation methods were chosen for estimating dissociation energies. The bond dissociation energies indicate different trends in these molecules as a function of the nature of the R and R′ groups and the possible electronic effects operating in these molecules are discussed. © 1993 John Wiley & Sons, Inc.
Comparison of a posteriori and a priori BSSE correction schemes for SCF intermolecular energies
Authors: Valiron Pierre , Vibók Ágnes , Mayer István
Published: January 2005

A systematic SCF study has been undertaken to compare the conventional a posteriori Boys–Bernardi BSSE correction scheme with our recent CHA/F method in which BSSE is excluded in a priori manner. Potential curves have been obtained for nine simple hydrogen‐bonded systems by using nine different basis sets for each. It is concluded that the difference between the a posteriori BB and the a priori CHA schemes diminishes much faster when the basis set improves than BSSE disappears from the uncorrected SCF results. This fact gives an additional confidence in the CHA results, permitting one to draw the explicit conclusion that, at the SCF level of theory, the a priori CHA/F scheme can be considered the ultimate solution of the BSSE problem for weakly bonded systems. © 1993 John Wiley & Sons, Inc.
Ab initio calculations on phosphorus compounds. II. Effects of disubstitution on ligand apicophilicity in phosphoranes
Authors: Wang Peng , Zhang Yala , Glaser Rainer , Streitwieser Andrew , Schleyer Paul von R.
Published: January 2005

Geometry optimizations at the HF/3‐21G(*) and HF/6‐31G* levels of ab initio theory have been carried out for various isomers of model disubstituted phosphoranes PH3XY(X, YOH, CH3, NH2, and SH). Reasonable agreement was obtained between the optimized geometries and available crystal structure data for analogous compounds. The isomers were further characterized by frequency calculations. The MP2/6‐31G*//6‐31G* + ZPE energy data reveal that the interactions between the ligands are relatively small (0–4 kcal mol−1) for the most stable conformations of the isomers. Hence, for these conformations the apicophilicities (based upon monosubstituted phosphoranes) are approximately additive. The less stable PH3XY conformations are in general transition states or higher‐order saddle points, and their interligand interactions are larger in magnitude (up to 10 kcal mol−1); the results with these conformations suggest that apicophilicities may not be as additive for some highly substituted phosphoranes. © 1993 John Wiley & Sons, Inc.
Application of explicitly correlated Gaussian functions for calculations of the ground state of the beryllium atom
Authors: Schwegler Eric , Kozlowski Pawel M. , Adamowicz Ludwik
Published: January 2005

The electronic energy of atoms and molecules may be evaluated accurately by the use of wave functions where the interelectronic distances are explicitly present. In particular, explicitly correlated Gaussian‐type functions make these types of calculations feasible and computationally tractable even for more extended systems. The resulting multielectron integrals may be reduced to standard one‐ and two‐electron integrals that are readily evaluated. Initial calculations have been made for the Be atom where all four electrons were correlated at the same time. The preliminary results show that accurate results may be obtained. © 1993 John Wiley & Sons, Inc.
Ab initio copper–water interaction potential for the simulation of aqueous solutions
Authors: Cordeiro M. Natália D.S. , Gomes José A.N.F.
Published: January 2005

A new ab initio effective two‐body potential that aims at mimicking the average copper–water interaction energy of the first solvation shell was developed. This new potential, together with the MCY water–water potential and a three‐body ion–water–water induction potential, is tested in simulations of gas‐phase clusters [Cu2+(H2O)20] and diluted solutions [Cu2+(H2O)200] at T = 298 K. The results of simulations with conventional ab initio pair potentials, with and without three‐body induction corrections, are also presented. The different types of copper–water interaction potentials are evaluated comparatively and the efficiency of the newly proposed effective pair potential is discussed. © 1993 John Wiley & Sons, Inc.
Molecular mechanics calculations (MM3) on sulfones
Authors: Allinger Norman L. , Fan Yi
Published: January 2005

The structures of several sulfones, including dimethyl sulfone, methyl ethyl sulfone, methyl vinyl sulfone, and diphenyl sulfone, have been fit with the MM3 force field to existing experimental data from electron diffraction and microwave spectroscopy. The vibrational spectra have also been fit for six of these compounds. The torsional parameters for the aliphatic sulfones were fit to ab initio 6‐31G data. Heats of formation were also fit. © 1993 John Wiley & Sons, Inc.
Calculation of hydrophobic interactions from molecular dynamics, surface areas, and experimental hydrocarbon solubilities
Authors: Hermann Robert B.
Published: January 2005

Using experimental solubilities and partial pressures for hydrocarbon solution in water and molecular dynamics calculations of hydrocarbon water interaction energies, hydrocarbon–water cavity potentials are obtained and then plotted vs. accessible surface area. The data used is mainly for aliphatic hydrocarbons, but benzene is included. Molecular dynamics calculations of pairs of hydrocarbon molecules together with the cavity potential curve are then used to obtain hydrophobic interaction free energies between the hydrocarbon pairs. While the cavity potential change is related to a change in surface area for hydrocarbon systems, the hydrocarbon–water interaction energy is not, so that the hydrophobic binding energy is not. The results are in agreement with previous results by a different method (R.B. Hermann, In Seventh Jerusalem Symposium on Quantum Pharmacology, E. Bergman and B. Pullman, Eds., D. Reidel, Dordrecht, 1974, p. 441) in that there is little or no solvent‐induced binding free energy between small hydrocarbon molecules in a dilute aqueous solution. It is proposed that the cavity potential vs. accessible surface area curve obtained here can be used together with OPLS parameters to calculate both hydrocarbon–water solvation free energies and hydrophobic interactions. © 1993 John Wiley & Sons, Inc.
A molecular mechanics study of alkyl peroxides
Authors: Chen Kuohsiang , Allinger Norman L.
Published: January 2005

Studies have been carried out on alkyl peroxides with MM3 that have led to a parameter set that allows the calculation of geometries, energies, vibrational frequencies, and heats of formation for alkyl hydroperoxides (ROOH) and dialkyl peroxides (R1OOR2). The results obtained are in agreement with the available experimental and theoretical data. A similar, although less good, parameter set has been developed for MM2. © 1993 John Wiley & Sons, Inc.
Linear combination of Lanczos vectors: A storage‐efficient algorithm for sparse matrix eigenvector computations
Authors: Koslowski T. , Von Niessen W.
Published: January 2005

We present a storage‐efficient and robust algorithm for the computation of eigenvectors of large sparse symmetrical matrices using a Lanczos scheme. The algorithm is based upon a linear combination of Lanczos vectors (LCLV) with a variable iteration depth. A simple method is given to determine the iteration depth before the eigenvector computation is performed. Test calculations are reported for tight‐binding models of ordered and disordered 2‐D systems. The algorithm turns out to be reliable if an eigenvector residual less than 10−4 is required. We report benchmarks for various computers. Possible fields of application are discussed. © 1993 John Wiley & Sons, Inc.