bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational dependence of electrostatic potential derived charges of a lipid headgroup: Glycerylphosphorylcholine
Authors: Stouch T.R. , Williams Donald E. 
Published: January 2005

AbstractAtomic 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

AbstractFree 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

AbstractA 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

AbstractFinite‐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

AbstractThe 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

AbstractSimulations 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

AbstractInteractions 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

AbstractIn 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

AbstractAn 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

AbstractWe 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

AbstractThe 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

AbstractA 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

AbstractA 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

AbstractThe 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

AbstractA 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

AbstractIntermolecular 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

AbstractWe 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

AbstractA 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

AbstractThe 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

AbstractAM1 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.