bluuebunny/crossref_metadata_2025 huggingface dataset:
Implementation of the direct SCF and RPA methods on loosely coupled networks of workstations
Authors: Feyereisen Martin W. , Kendall Rick A. , Nichols Jeff , Dame David , Golab Joseph T.
Published: January 2005

The use of a cluster of workstations as an alternative supercomputer resource is demonstrated using the ab initio direct SCF and RPA code DISCO. DISCO was implemented using several different mechanisms to achieve the requisite parallelization. The various parallel software mechanisms are characterized based upon several different criteria, including portability, ease of use, and relative efficiency. The application of direct SCF and RPA techniques to study the static polarizability of paranitroaniline is described. © 1993 John Wiley & Sons, Inc.
Theoretical investigations on thallium halides: Relativistic and electron correlation effects in T1X and T1X3 compounds (XF, C1, Br, and I)
Authors: Schwerdtfeger Peter , Ischtwan Josef
Published: January 2005

Relativistic and electron correlation effects in thallium halides TlX and TlX3 (XF, Cl, Br, and I) are investigated by extensive ab initio configuration interaction calculations. Spin–orbit coupling is included at the Hartree–Fock level for the diatomic TlBr and TlI. At the best level of treatment of electron correlation (quadratic configuration interaction), the calculated molecular properties are in good agreement with experimental results, i.e., for the diatomic thallium halides deviations from experimental values are <0.06 Å for bond distances, <0.14 mdyn/Å for force constants, <35 kJ/mol for dissociation energies, and <0.3 D for dipole moments. The convergence of the Møller–Plesset series up to the fourth order is discussed. Two alternative structures of TlI3 are compared. At the Møller–Plesset level of theory, the trigonal planar structure with thallium in the oxidation state + 3 is the preferred gas phase arrangement compared with the bent arrangement containing a linear I unit and thallium in the oxidation state + 1, the difference being ca. 95 kJ/mol. Vibrational frequencies are predicted for all trigonal planar thallium(III) halides. © 1993 John Wiley & Sons, Inc.
Cumulative and discrete similarity analysis of electrostatic potentials and fields
Authors: Petke J.D.
Published: January 2005

A new index suitable for computing molecular similarity based upon the similarity of molecular properties such as electrostatic potentials or electrostatic fields is presented in two forms. For one form of the present index, general conditions are established for which a linear measure of similarity is obtained. An illustrative example is provided in which the electrostatic field and electrostatic potential of guanine obtained from different wave functions are compared. © 1993 John Wiley & Sons, Inc.
Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides
Authors: Sokalski W.A. , Keller D.A. , Ornstein R.L. , Rein R.
Published: January 2005

The defects in atomic monopole models of molecular charge distribution have been analyzed for several model‐blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off‐center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N‐acetyl, N′‐methylamide‐blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed. © 1993 John Wiley & Sons, Inc.
AMBER force‐field parameters for guanosine triphosphate and its imido and methylene analogs
Authors: Cannon John F.
Published: January 2005

Parameters were derived for guanosine triphosphate (GTP) and GTP analogs suitable for the AMBER force field. Electrostatically derived net atomic charges and force parameters were extracted from MNDO semiempirical calculations. The later parameters came from fitting MNDO and AMBER atom–atom forces in a manner that is extensible to other compounds that lack sufficient vibrational spectral data. The geometric parameters for these compounds were obtained from model compounds in the Cambridge crystallographic data base. Dynamic simulations of Na4 GTP and Na2 Mg GTP of 140 and 100 ps, respectively, indicated a strong preference for a syn C2′ exo conformation in solution. © 1993 John Wiley & Sons, Inc.
Ab initio study of hydrogen bonding in the phenol–water system
Authors: Feller David , Feyereisen Martin W.
Published: January 2005

Three hydrogen‐bonded minima on the phenol‐water, C6H5OH—H2O, potential energy surface were located with 3–21G and 6–31G** basis sets at both Hartree–Fock and MP2 levels of theory. MP2 binding energies were computed using large “correlation consistent” basis sets that included extra diffuse functions on all atoms. An estimate of the effect of expanding the basis set to the triple‐zeta level (multiple f functions on carbon and oxygen and multiple d functions on hydrogen) was derived from calculations on a related prototype system. The best estimates of the electronic binding energies for the three minima are –7.8, –5.0, and –2.0 kcal/mol. The consequences of uncertainties in the geometries and limitations in the level of correlation recovery are analyzed. It is suggested that our best estimates will likely underestimate the complete basis set, full CI values by 0.1–0.3 kcal/mol. Vibrational normal modes were determined for all three minima, including an MP2/6–31G** analysis for the most strongly bound complex. Computational strategies for larger phenol–water complexes are discussed. © John Wiley & Sons, Inc.
New method for the derivation of net atomic charges from the electrostatic potential
Authors: Su Zhengwei
Published: January 2005

Net atomic charges are derived from a least‐squares fitting to electrostatic potentials at atomic sites. The method treats atoms in the molecule as having spherically averaged Hartree–Fock densities, the atomic densities overlapping with one another. The method has the advantage of best reproducing the electrostatic potentials at the atomic nuclei and avoiding the arbitrariness in choosing the points used in the fitting. We have written a FORTRAN program, CHELPN92 (Z. Su, Chemistry Department, SUNY at Buffalo, Buffalo, NY, 1992), based on the method and applied it to deuterated benzene, l‐alanine, d,l‐histidine, 2‐methyl‐4‐nitroaniline, and deuterated pyridinium‐1‐dicyanomethylide using the molecular geometry and electrostatic potentials from analysis of accurate X‐ray diffraction data. The derived charges are used to calculate the molecular dipole moments. While the charges from this method are in general significantly different from those from the kappa refinement [P. Coppens, T.N. Guru Row, P. Leung, E.D. Stevens, P.J. Becker, and Y.W. Yang, Acta Cryst. A, 35, 63 (1979)], the dipole moments obtained with the new method agree well with those from the kappa refinement. © John Wiley & Sons, Inc.
Characterization of force fields for lipid molecules: Applications to crystal structures
Authors: Williams Donald E. , Stouch Terry R.
Published: January 2005

The nonbonded portion of a force field for lecithins was characterized by application to the study of the crystal packing geometry and energetics of eight different molecules. The molecules were either lecithin fragments or chosen to isolate particular intermolecular features to test the accuracy of the force field specifically for those interactions. In particular, the hydrocarbon interactions, hydrogen bonding, electrostatics, and phosphate interactions were critiqued. The results support previous findings that indicated that this force field is reasonably accurate for lecithins. For all molecules, a minimum was found near the experimentally determined crystal structure. Using D‐glucitol as an example, it is shown that the structural effect of hydrogen bonding is better represented by a nonelectrostatic force‐field model than by a purely electrostatic model. Results obtained with glycerylphosphocholine and four smaller organic phosphate molecules suggest that further study of nonbonded interactions of phosphate groups is needed. © John Wiley & Sons, Inc.
Ab initio models for multiple‐hydrogen exchange: Comparison of cyclic four‐ and six‐center systems
Authors: Heidrich Dietmar , Van Eikema Hommes Nicolaas J. R. , Von Ragué Schleyer Paul
Published: January 2005

High‐level ab initio calculations {QCISD(T)/6‐311 +G**//MP2(fu)/6‐31 +G**, with corrections for higher polarization [evaluated at MP2/6‐311 +G(3df,2p)] and ΔZPE//MP2(fu)/6‐31 +G**, i.e., comparable to Gaussian‐2 theory} indicate concerted mechanisms for double‐ and triple‐hydrogen exchange reactions in HF and HCl dimers and trimers, in mixed dimers and trimers containing one NH3, and in mixed dimers of HF, HCl, and NH3 with formic acid. All these reactions proceed via cyclic four‐ or six‐center transition structures, the latter being generally more favorable. Calculated activation barriers (ΔHd̊ at 0 K, kcal/mol) are 42.3 for (HF)2, 20.3 for (HF)3, 41.2 for (HCl)2, 25.6 for (HCl)3, 36.0 for NH3‐HF, 10.6 for NH3(HF)2, 19.9 for NH3‐HCl, 2.3 for NH3(HCl)2, 9.7 for HCO2H‐HF, 7.0 for HCO2H‐HCl, and 11.3, for HCO2H‐NH3. The barriers are lower for the more ionic systems and when more ion pair character is present. © John Wiley & Sons, Inc.
Ab initio SCF and Møller—plesset studies on hexafluorides of selenium and tellurium
Authors: Klobukowski Mariusz
Published: January 2005

SCF and Møller–Plesset calculations were done for the systems AB6 (TeF6 and SeF6) and AB6E (TeF and SeF) to determine their relative stabilities and geometric structures. The SCF calculations show that both TeF (as expected) and SeF (despite a small central atom) possess nonoctahedral shapes. However, at the Møller–Plesset level only the TeF2−6 ion, studied with a large valence basis set, retains nonoctahedral geometry. The calculated structural parameters of the ion in C3v symmetry (the bond lengths are 2.212 and 1.975 Å and the bond angles are 104.9 and 83.4 °) differ considerably from the octahedral values (2.101 Å and 90.0°), yet the corresponding total energy is only about 1 kcal/mol smaller. The results show significant dependence of the computational predictions on the basis sets used and indicate the need to include electron correlation effects in the studies devoted to establishing the stereochemical activity of the lone electron pair. © John Wiley & Sons, Inc.
Partitioning the motion in molecular dynamics simulations into characteristic modes of motion
Authors: Dauber‐Osguthorpe Pnina , Osguthorpe David J.
Published: January 2005

Molecular dynamics (MD) simulations result in a comprehensive description of molecular motion. However, to gain insight into the dynamic behavior of molecules it is important to be able to identify different types of motions and characterize them. We have developed a novel technique aimed at characterizing the motion of the system using digital signal processing techniques. The amplitudes and phases of the Fourier transform of the atomic fluctuations are used to define the characteristic modes of motion in the MD trajectory. This yields a pictorial description of the oscillatory motions in a manor analogous to normal‐mode (NM) analysis. The validity of this method has been tested on small molecules such as water, acetamide, and a blocked polyalanine in a helical conformation. The NMs obtained by diagonalizing the mass‐weighted second derivative matrix were combined to generate “NM trajectories” that served as well‐characterized test cases. Distinct characteristic modes can be extracted from both NM and MD trajectories. The modes extracted from the NM trajectories were identical to the original NMs. The modes extracted from the MD trajectories were in most cases highly correlated to the corresponding NM. However, intermixing of some of the modes occurred, particularly when conformational changes took place. This technique is flexible and can be applied to the molecular system as a whole or to a subset of atoms of interest. Fourier transform calculations are fast and therefore the analysis stage is not demanding in computational resources. Anharmonicity is included explicitly in the simulations and solvent can be included as well. © John Wiley & Sons, Inc.
Comparison of two force fields by molecular dynamics simulations of glucose crystals: Effect of using ewald sums
Authors: Kouwijzer M.L.C.E. , Van Eijck B.P. , Kroes S.J. , Kroon J.
Published: January 2005

To compare the GROMOS force field with one designed by Ha et al., molecular dynamics simulations of α‐D‐glucose anhydrate and monohydrate crystals were performed. Also, the long‐range interactions were calculated both with a cutoff approximation and with Ewald summations. The results are compared with results obtained experimentally by neutron and X‐ray diffraction. The force‐field parameters had been optimized with the cutoff approximation; this apparently led to worse results when the Ewald summations were used. However, in all simulations the symmetry was roughly preserved and the mean atomic coordinates and thermal parameters, bond angles, and dihedrals without hydrogen atoms were rather well reproduced. The dihedrals with hydrogen atoms exhibited conformational transitions, which resulted in a disordered hydrogen bonding scheme. In general, the GROMOS force field performed better than the Ha force field. © John Wiley & Sons, Inc.
Modeling of magic water clusters (H2O)20 and (H2O)21H+ with the PM3 quantum‐mechanical method
Authors: Jurema Marcus W. , Kirschner Karl N. , Shields George C.
Published: January 2005

The PM3 quantum‐mechanical method is able to model the magic water clusters (H2O)20 and (H2O)21H+. Results indicate that the H3O+ ion is tightly bound within the (H2O)20 cluster by multiple hydrogen bonds, causing deformation to the symmetric (H2O)20 pentagonal dodecahedron structure. The structures, energetics, and hydrogen bond patterns of six local minima (H2O)21H+ clusters are presented. © John Wiley & Sons, Inc.
Constrained optimization in cartesian coordinates
Authors: Baker Jon , Bergeron Doreen
Published: January 2005

Modifications are made to a previously published algorithm for constrained optimization in Cartesian coordinates (J. Comp. Chem., 13, 240, 1992) to incorporate both fixed and dummy atoms. Standard distance and angle constraints can now be specified with respect to dummy atoms, greatly extending the range of constraints that can be handled. Fixed atoms can be eliminated from the optimization space and so there is no need to calculate their gradients resulting in potentially significant savings of CPU time in ab initio computations. Several examples illustrate the range and versatility of the modified algorithm. © John Wiley & Sons, Inc.
Use of locally dense basis sets for nuclear magnetic resonance shielding calculations
Authors: Chesnut D.B. , Rusiloski B.E. , Moore K.D. , Egolf D.A.
Published: January 2005

The locally dense basis set approach to the calculation of nuclear magnetic resonance shieldings is one in which a sufficiently large or dense set of basis functions is used for an atom or molecular fragment containing the resonant nucleus or nuclei of interest and fewer or attenuated sets of basis functions employed elsewhere. Provided the dense set is of sufficient size, this approach is capable of determining chemical shieldings nearly as well as a calculation with a balanced basis set of quality equal to the locally dense set, but with considerable savings of CPU time. Detailed comparisons are provided of locally dense and balanced calculations in the gauge including atomic orbital (GIAO) method for the individual principal values, the isotropic shieldings, and the tensor orientations for hydrogen, carbon, nitrogen, oxygen, fluorine, and phosphorus nuclei. It is seen that chemical functional groups can often define the appropriate molecular fragment to be taken locally dense. While the present test cases are for the most part small molecules, the value of the method is that it will allow calculations on systems that would otherwise presently be computationally expensive or inaccessible. © John Wiley & Sons, Inc.
Computation of the mean residence time of water in the hydration shells of biomolecules
Authors: García Angel E. , Stiller Lewis
Published: January 2005

An algorithm is presented within the context of the calculation of the time‐relaxation behavior of the hydration shells around atomic sites in biomolecules. We report a calculation of the time‐relaxation behavior of the first and second hydration shells of polar, hydrophobic, and charged groups in a protein, crambin. The water mean residence times around protein groups are obtained from averages over configurations sampled during a 325‐ps molecular dynamics simulation of crambin in solution. A convolution arising in the calculation of the mean relaxation time is implemented using a parallel prefix operator. A new characterization is given of the parallel prefix operator as a linear transformation, and this formulation enables us to derive efficient factorization of the convolution as a product of two parallel prefix operations. The parallel prefix operations are implemented in logarithmic time. © John Wiley & Sons, Inc.
Conformational searching methods for small molecules. II. Genetic algorithm approach
Authors: Judson R.S. , Jaeger E.P. , Treasurywala A.M. , Peterson M.L.
Published: January 2005

We demonstrate the use of a genetic algorithm (GA) search procedure for finding low‐energy conformations of small to medium organic molecules (1–12 rotatable bonds). GAS are in a class of biologically motivated optimization methods that evolve a population of individuals where individuals who are more “fit” have a higher probability of surviving into subsequent generations. Here, an individual is a conformation of a given molecule and the fitness is the molecule's conformational energy. In the course of a simulated evolution, the population produces conformations having increasingly lower energy. We test the GA method on a suite of 72 molecules and compare the performance against the CSEARCH algorithm in Sybyl. For molecules with more than eight rotatable bonds, the GA method is more efficient computationally and as the number of rotatable bonds increases the relative efficiency of the GA method grows. The GA method also found energies equal to or lower than the energy of the relaxed crystal structure in the large majority of cases. © John Wiley & Sons, Inc.
Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. III. Application to halogenated and aromatic molecules
Authors: Park Je Myung , Tai No Kyoung , Jhon Mu Shik , Scheraga Harold A.
Published: January 2005

The net atomic charge parameters for halogen atoms and the atoms in aromatic molecules have been determined by the modified partial equalization of orbital electronegativity method. The same parameters are used for the halogen atoms both in aromatic and nonaromatic systems. The calculated dipole moments of haloalkanes agree well with experiment, but those of the halogenated aromatic molecules do not reproduce the experimental values as well as those of the haloalkanes; in particular, the computed dipole moments for monohalogenated benzenes are all lower than the experimental values because of the influence of the lonepair electrons on the halogens. Within the limitations of an atom‐centered point‐charge approximation, our calculated dipole moments, both for haloalkanes and halogented aromatic molecules, agree well with experimental values. © John Wiley & Sons, Inc.
Comparison of 6‐31G*‐based MST/SCRF and FEP evaluations of the free energies of hydration for small neutral molecules
Authors: Orozco Modesto , Jorgensen William L. , Luque F.J.
Published: January 2005

A comparison between Miertus–Scrocco–Tomasi (MST) SCRF and free energy perturbation (FEP) estimates of the free energy of hydration of eight small neutral molecules is presented. In both cases, the 6‐31G* molecular electrostatic potential is used to describe the electrostatic properties of the molecules. The results demonstrate the ability of both methodologies to provide useful theoretical estimates of the total free energy of hydration; the average errors are only 1.5 kcal/mol (FEP) and 0.8 kcal/mol (MST/SCRF). The largest errors in the FEP and MST/SCRF results are less than 1.5 kcal/mol for all molecules except acetic acid, where the FEP method overestimates the free energy of hydration by 3.3 kcal/mol. © John Wiley & Sons, Inc.
Ab initio molecular orbital studies for compounds of magnesium
Authors: Gardner Peter J. , Preston Steve R. , Siertsema Rachel , Steele Derek
Published: January 2005

Using a 6‐311G** basis set with estimation of correlation energy at the MP2 level, structural and energetic data for 40 molecular species containing magnesium have been calculated. For about half the species studied, further energetic data were obtained using Pople's G2 method. Enthalpy changes at 298.15 K were obtained for isogyric reactions and standard enthalpies of formation were derived from these. Comparison of the standard enthalpies of formation with the sparse literature data suggests the MP2/6‐311G** standard enthalpies of formation are accurate to ± 15 kJ mol−1 and the corresponding G2 enthalpies accurate to ± 10 kJ mol−1. The calculated ΔH [MgN, g] revealed a gross error in the currently accepted value for this function. It is intended that these results will be used to parameterize the semiempirical molecular orbital package, MOPAC, for the element magnesium. © John Wiley & Sons, Inc.
Performance of fast multipole methods for calculating electrostatic interactions in biomacromolecular simulations
Authors: Shimada Jiro , Kaneko Hiroki , Takada Toshikazu
Published: January 2005

The fast multipole method proposed by Greengard and Rokhlin (GR) is applied to large biomacromolecular systems. In this method, the system is divided into a hierarchy of cells, and electric field exerted on a particle is decomposed into two parts. The first part is a rapidly varying field due to nearby cells, so that it needs rigorous pairwise calculations. The second part is a slowly varying local field due to distant cells; hence, it allows rapid calculations through a multipole expansion technique. In this work, two additional possibilities for improving the performance are numerically examined. The first is an improvement of the convergence of the expansion by increasing the number of nearby cells, without including higher‐order multipole moments. The second is an acceleration of the calculations by the particle–particle and particle–mesh/multipole expansion (PPPM/MPE) method, which uses fast Fourier transform instead of the hierarchy. For this purpose, the PPPM/MPE method originally developed by the authors for a periodic system is extended to a nonperiodic isolated system. The advantages and disadvantages of the GR and PPPM/MPE methods are discussed for both periodic and isolated systems. It is numerically shown that these methods with reasonable costs can reduce the error in potential felt by each particle to 0.1–1 kcal/mol, much smaller than the 30‐kcal/mol error involved in conventional simple truncations. © 1994 by John Wiley & Sons, Inc.
General parameterization of a reaction field theory combined with the boundary element method
Authors: Furuki Takao , Umeda Akihiro , Sakurai Minoru , Inoue Yoshio , Chûjô Riichirô , Harata Kazuaki
Published: January 2005

We described various technical aspects in applying reaction field theories using continuum models to practical problems. It was investigated how solvent‐dependent properties of solute molecules are influenced by the following factors: difference in quantum‐chemical description of solute–solvent (continuum dielectric) interaction, difference in values of empirically determinable parameters such as atomic radii to define a size of a cavity created in a dielectric to accommodate a solute, and difference in the sophistication level of molecular orbital calculation, including electron correlation and different parameter sets (MNDO, AM1, and PM3). Through these investigations, the better parameter sets were found to evaluate accurately physicochemically important parameters such as hydration enthalpy. © 1994 by John Wiley & Sons, Inc.
Ab initio molecular orbital study of 1‐fluorosilatrane
Authors: Csonka G. I. , Hencsei P.
Published: January 2005

The molecular geometry of 1‐fluorosilatrane was optimized fully by restricted Hartree–Fock (HF) calculations using the 3‐21G, 3‐21G(d) and 6‐31G(d) basis sets, with the aim of locating the positions of the local minima on the energy hypersurface. The optimized geometries were compared with available experimental (X‐ray and ED) and semiempirical data. The ab initio calculations using polarized basis sets are in good agreement with those of previously reported semiempirical calculations, giving a slightly longer equilibrium SiN distance (∼ 256 pm) in the case of the endo minimum. However, the exo minimum predicted by the semiempirical methods is not supported. There was no experimental evidence for the existence of this exo minimum, and the present ab initio calculations suggest that it is highly unstable. There is considerable disagreement among the experimental results in the CN and CC bond lengths in various silatranes, their differences being as large as 13 pm. The present calculations predict that these differences may appear because the silatrane skeleton is flexible with low‐energy, large‐amplitude internal motions which introduce considerable uncertainties into the position of ring carbon atoms. © 1994 by John Wiley & Sons, Inc.
Transferable semiempirical quadratic force fields: The case of polythiophene and shorter oligomers
Authors: Ramírez F. J. , Hernández V. , Navarrete J. T. López
Published: January 2005

The vibrational spectra of oligomers of thiophene are treated theoretically with the main purpose of deriving information for the interpretation of the infrared and Raman spectra of the polymer and isotopic derivatives. We report the results of a series of semiempirical MNDO calculations on the structure and vibrational properties of oligothiophenes, and we compare the calculated MNDO Pulay scaled force field of the monomer with an empirical harmonic force field that we have obtained by least squares refinement on nine isotopic derivatives. The scaling factors obtained were transferred from thiophene for the computation of the vibrational spectrum and the phonon dispersion curves of the polymer. © 1994 by John Wiley & Sons, Inc.
Direct one‐index transformations in multiconfiguration response calculations
Authors: Vahtras Olav , Årgren Hans , Jensen Hans Jørgen AA.
Published: January 2005

The evaluation of gradient vectors of a general operator with one‐index, double‐one‐index, or higher‐order one‐index transformed integrals is a key operation in multiconfiguration response theory calculations. We describe an integral‐driven direct algorithm that carries out this operation efficiently without pretransforming the integrals. The use of this algorithm leads to a considerable reduction in disk space and timing. © 1994 by John Wiley & Sons, Inc.
Application of genetic algorithms in molecular modeling
Authors: Brodmeier Tilman , Pretsch Ernö
Published: January 2005

A genetic algorithm has been developed for molecular mechanics calculations. It has been proved to be a robust and efficient structure optimization technique. Because it uses randomly generated starting structures and stochastic operators, the resulting structures are not subjected to the chemist's bias. © 1994 by John Wiley & Sons, Inc.
X‐PLORing extraribosomal peptide folding during synthesis
Authors: David Carl W.
Published: January 2005

An X‐PLOR scheme for imitating the action of ribosomes in aiding synthesizing peptides to find their ultimate conformations is introduced. The scheme is tested with an example from the Delta‐Sleep‐Inducing‐Peptide mutant family. © 1994 by John Wiley & Sons, Inc.
Expanding molecular dynamics simulations to the NMR time scale. I. Studies of conformational interconversions of 1, 1‐difluoro‐4, 4‐dimethylcycloheptane using MM3‐MD
Authors: Li Fanbing , Cui Weili , Allinger Norman L.
Published: January 2005

A molecular dynamics (MD) simulation of 35,000 picoseconds (ps) has been carried out to study the conformational interconversions of 1,1‐difluoro‐4,4‐dimethylcycloheptane at room temperature using the MM3 force field. The exchange between axial and equatorial fluorine atoms was the only conformational interconversion that occurred, and it took place via the process of pseudorotation. Ring inversions (twist–chair < twist–boat < twist–chair) were not observed. The axial‐equatorial exchange of the two fluorine atoms took place five times during the MD trajectory of 35,000 ps. The two CH3 groups occupied symmetrical positions (exchangeable by a C2‐like rotations, where C2‐like means it would be C2 if the fluorines were not present) in the MM3 structures, and during most of the time of the MD trajectory. The methyls occasionally moved off the C2‐like axis in the simulated process, mostly because the C2‐like axis was momentarily moved so that it did not pass through the ring atom to which the two CH3 groups are bonded. A C2‐like symmetry of the twist‐chair conformation was maintained approximately during most of the MD simulation. The conformational geometry with the highest energy obtained during the axial‐equatorial exchange process was found and used to locate the transition state. The energy barrier for this axial‐equatorial exchange was calculated to be 4.7 kcal/mol, and it compares with the value (5.0 kcal/mol) determined by dynamic nuclear magnetic resonance (NMR). © 1994 by John Wiley & Sons, Inc.
Normal mode analysis of oligomeric proteins: Reduction of the memory requirement by consideration of rigid geometry and molecular symmetry
Authors: Gibrat Jean‐françois , Garnier Jean , Gō Nobuhiro
Published: January 2005

A method is presented to reduce the memory requirement of normal mode analysis applied to systems containing two or more large proteins when these systems exhibit symmetry properties. We use a rigid geometry model (i.e., only the dihedral angles of the polypeptide chain are considered as variables). This model allows a reduction by a factor of 8 on average of the number of variables with a concomitant freezing of the high‐frequency modes. The symmetry properties of the system are used to reduce further the number of variables that must be considered in the computation. Application of group theory leads to a factorization of the matrices of interest (the coefficient and the Hessian matrices) into independent blocks along the diagonal. The initial, reducible representation is thus transformed into a number of irreducible representations of smaller dimensions. In the case of the C2 symmetry group, the method leads to a reduction of the size of the matrices that must be manipulated during the computation (coefficient matrix, Hessian matrix, and eigenvectors matrix) by a factor of 256 compared with the usual normal mode analysis in Cartesian coordinate space. The method is particularly well adapted to the study of the dynamics of oligomeric proteins because these proteins often display symmetry properties (e.g., virus coat proteins, immunoglobulins, hemoglobin, etc.). In favorable cases, in conjunction with X‐ray diffuse scattering data, the study of systems showing allosteric properties might be considered. © 1994 by John Wiley & Sons, Inc.
A force field for monosaccharides and (1 → 4) linked polysaccharides
Authors: Glennon Timothy M. , Zheng Ya‐Jun , Le Grand Scott M. , Shutzberg Brad A. , Merz Kenneth M.
Published: January 2005

A force field for monosaccharides that can be extended to (1 → 4) linked polysaccharides has been developed for the AMBER potential function. The resulting force field is consistent with the existing AMBER force field for proteins and nucleic acids. Modifications to the standard AMBER OH force constant and to the Lennard‐Jones parameters were made. Furthermore, a 10–12 nonbonded term was included between the hydroxyl hydrogen of the saccharide and the water oxygen (TIP3P, SPC/E, etc.) to reproduce better the water–saccharide intermolecular distances. STO‐3G electrostatic potential (ESP) charges were used to represent the electrostatic interactions between the saccharide and its surrounding environment. To obtain charges for polysaccharides, a scheme was developed to piece together saccharide residues through 1 → 4 connections while still retaining a net neutral charge on the molecule as a whole. Free energy perturbation (FEP) simulations of D‐glucose and D‐mannose in water were performed to test the resulting force field. The FEP simulations demonstrate that AMBER overestimates intramolecular interaction energies, suggesting that further improvements are needed in this part of the force field. To test further the reliability of the parameters, a molecular dynamics (MD) simulation of α‐D‐glucose in water was also performed. The MD simulation was able to produce structural and conformational results that are in accord with experimental evidence and previous theoretical results. Finally, a relaxed conformational map of β‐maltose was assembled and it was found that the present force field is consistent with available theoretical and experimental results. © 1994 by John Wiley & Sons, Inc.
Application of the multiple computer automated structure evaluation methodology to a quantitative structure–activity relationship study of acidity
Authors: Klopman Gilles , Fercu Dan
Published: January 2005

We applied the Multiple Computer Automated Structure Evaluation (Multi‐CASE) program to the analysis of the relationship between the structure of 2464 organic acids and their (first) pKa values. By using the self‐created expert dictionary of molecular attributes pertinent to acidity, the program could make successful a priori prediction of the acidity of new organic compounds. © 1994 by John Wiley & Sons, Inc.
Transition structure modeling by intersecting potential energy surfaces
Authors: Jensen Frank
Published: January 2005

A previously proposed method of modeling force field transition structures as the lowest energy structure on the seam of two intersecting potential energy surfaces is improved with respect to the force field expression and the efficiency of the optimization algorithm. Comparison with ab initio and experimental results show that the force field method may have the potential of achieving almost quantitative results. It appears that the results from transition state modeling are currently limited by the accuracy of the underlying force field. © 1994 by John Wiley & Sons, Inc.
The effects of solvent screening in quantum mechanical calculations in protein systems
Authors: Baldridge K. , Fine R. , Hagler A.
Published: January 2005

We report on an implementation of quantum mechanical density functional calculations carried out in a dielectric medium. The dielectric medium is introduced by integrating the solution of the Poisson‐Boltzmann equations into the density functional calculation. The calculations are carried out for a simple amide in vacuum, in the field of an ion, and in the ion field in several dielectric environments. The environment was constructed to include a low dielectric interior embedded in a high dielectric continuum of dielectric 80 (corresponding to aqueous solution). The energies and electron densities of formamide in the ion field were calculated at various configurations in this system, including at the low dielectric–high dielectric interface. The systems were designed to simulate situations which are similar to those that occur in proteins (i.e., the protein constitutes the low dielectric medium surrounded by aqueous solution). The system mimics situations in which charges in such proteins located in various regions interact with other parts of the protein and with ligands which mainly bind to the surface. © 1994 by John Wiley & Sons, Inc.
Comparison of the molecular mechanics + generalized Born/surface area and the ab initio + Monte Carlo simulation methods in estimating conformational equilibria in aqueous solution
Authors: Nagy Peter I. , Bitar Joseph E. , Smith Douglas A.
Published: January 2005

A method using molecular mechanics to calculate internal energies and the generalized Born/surface area (GB/SA) method for calculating solvation free energy has been compared with the corresponding terms obtained from ab initio quantum chemical calculations in the gas phase and the free energy perturbation method implemented in Monte Carlo (MC) simulations to study conformational equilibria in solution. 1,2‐Ethanediol, 2‐hydroxybenzoic acid, the neutral and protonated histamine, were considered in aqueous solution as systems capable of intramolecular hydrogen bonding. The molecular mechanics method with all atom and united atom models, using the AMBER* force field and the parameterization as implemented in the MacroModel modeling package and the GB/SA continuum solvation model, produces smaller separation in relative conformer free energies than does the ab initio + MC method in aqueous solution. The GB/SA relative solvation free energies using the charges from the AMBER* force fields were consistently smaller than the values obtained in Monte Carlo simulations. Using the charge sets from the Monte Carlo simulations and considering solute geometries with torsional angles fixed at the optimized ab initio values, the relative solvation free energies remained underestimated by up to 30% as compared to the Monte Carlo values. The AMBER*//GB/SA predicted most stable conformer for the 1,2‐ethandiol system in aqueous solution is in contrast with the ab initio + MC finding and the available experimental results. For the histamine system predictions by only the united atom AMBER*//GB/SA model agree with those by ab initio + MC and with data derived from nuclear magnetic resonance (NMR) experiments. Differences in the two methods are considered mainly due to the application of torsional parameters and atomic charges developed in the AMBER* parameter set for monofunctional polar systems. New parameters seem to be needed for quantitative description of the in‐solution conformational equilibria for organic compounds with a possible intramolecular hydrogen bond. © 1994 by John Wiley & Sons, Inc.
Ab initio study of some CH3OCXYCH2 radicals: The influence of anomeric effects on their structure and their stability
Authors: Arnaud R.
Published: January 2005

Optimized equilibrium geometries and rotational transition structures for CH3OCH XCH2 (X = H, F, CH3, NH2) and CH3OCF2CH2 radicals are obtained by using unrestructed Hartree‐Fock (UHF) and second‐order Møller‐Plesset perturbation (UMP2) theory; a standard 6‐31G* basis set is used for geometry optmizations; single‐point energies for all stable rotamers are obtained at the UMP4/6‐31 + G*//UMP2/6‐31G* level. By analysis of rotamers, it is apparent that an anomeric effect exists for X = F and to a lesser extent for X = NH2. Several isodesmic reactions have been studied for the purpose of obtaining theoretical heats of formation and stabilization energies (SE) of these β substituted radicals and their α isomers; the examination of computed SE shows that in the case of CH3OCHFCH2 and CH3OCF2CH2 radicals, a significant extra stabilization induced by the anomeric effect occurs. The question of nO → σ negative hyperconjugation in β‐substituted radicals was explored with the aid of natural bond orbital (NBO) energetic analysis; it appears that nO → σ delocalization plays a predominant role in the conformational preference and stabilization of β fluoro derivatives; on the other hand, the stabilization arising from the oxygen lone pair into the σ orbital does not appear to be the key factor in the conformational preference of the CH3OCHNH2CH2 radical. © 1994 by John Wiley & Sons, Inc.
Variational biorthogonal valence bond descriptions of 1,3‐dipoles
Authors: Malcolm Nathaniel O. J. , McDouall Joseph J. W.
Published: January 2005

The variational biorthogonal valence bond method is applied to the π‐electrons of six 1,3‐dipoles (CH2N2, HCNO, CH2NHO, N2O, O3, NO2). The results are compared with those from other valence bond techniques, including a detailed comparison with the spin‐coupled valence bond approach. For CH2N2, HCNO, CH2NHO, and N2O, zwitterionic structures are predicted and it is shown that the variational biorthogonal valence bond method leads to orbitals and configuration weights which are essentially indistinguishable from those of the spin‐coupled valence bond method. However, for O3 and NO2 the techniques give contradictory results. The biorthogonal valence method predicts O3 and NO2 to be spin‐paired diradicals. Evidence from other calculations on O3 is discussed. © 1994 by John Wiley & Sons, Inc.
A rapid and efficient algorithm for packing polypeptide chains by energy minimization
Authors: Gibson Kenneth D. , Scheraga Harold A.
Published: January 2005

An improved algorithm for packing polypeptide chains with fixed geometry, which converges to a local energy minimum rapidly and efficiently, is described. The speed of convergence of the new algorithm is comparable to that of existing algorithms for minimizing the energies of single polypeptide chains, and it is several times greater than the speed of convergence of previous algorithms for minimizing the energy of structures consisting of several polypeptide chains. The algorithm has been used to minimize the energy of three‐stranded (L‐Ala)8 β‐sheets, three‐stranded (L‐Val)6 β‐sheets, and five‐stranded (L‐Ile)6 β‐sheets, starting from regular structures found previously; of the three‐stranded regular and truncated (Gly‐L‐Pro‐L‐Pro)4 structures used in earlier work to model collagen; and of the stacked β‐sheet (L‐Ala‐GLy)6 structures used to model silk. The antiparallel L‐Ala β‐sheet, and Gly‐Pro‐Pro triple helices, and the silk II structure remained nearly regular after energy minimization, but by contrast with results from earlier computations the other structures became significantly irregular. © 1994 by John Wiley & Sons, Inc.
Molecular mechanics (MM3) calculations on azoxy compounds
Authors: Fan Yi , Allinger Norman L.
Published: January 2005

The MM3 force field has been extended to include azoxy compounds and also the related amine oxides, both aliphatic and aromatic. The structures of nine molecules were all well fit. The heats of formation for the aliphatic compounds were also well fit, and the vibrational spectra of eight compounds were also fit to the accuracy expected for such calculations. Because many of the experimental data needed to derive the force field were either lacking or were inadequate, ab initio calculations on structures, optimized at the MP2/6‐31G* level, were used as needed. © 1994 by John Wiley & Sons, Inc.
Geometric molecular similarity from volume‐based distance minimization: Application to saxitoxin and tetrodotoxin
Authors: Petitjean Michel
Published: January 2005

The geometric molecular dissimilarity between two molecules is defined as the difference between the volume of their union minus the volume of their intersection. This dissimilarity has the mathematical properties of a distance. This distance is minimized under all rotations and translations using a discrete Broyden, Fletcher, Goldfarb & Shanno (B.F.G.S.) algorithm. The optimal geometric superimposition of saxitoxin and tetrodotoxin is discussed. © 1995 by John Wiley & Sons, Inc.
Implementation of a parallel direct SCF algorithm on distributed memory computers
Authors: Furlani Thomas R. , King Harry F.
Published: January 2005

A parallel direct self‐consistent field (SCF) algorithm for distributed memory computers is described. Key features of the algorithm are its ability to achieve a load balance dynamically, its modest memory requirements per processor, and its ability to utilize the full eightfold index permutation symmetry of the two‐electron integrals despite the fact that entire copies of the Fock and density matrices are not present in each processor's local memory. The algorithm is scalable and, accordingly, has the potential to function efficiently on hundreds of processors. With the algorithm described here, a calculation employing several thousand basis functions can be carried out on a distributed memory machine with 100 or more processors each with just 4 MBytes of RAM and no disk. The Fock matrix build portion of the algorithm has been implemented on a 16‐node Intel iPSC/2. Results from benchmark calculations are encouraging. The algorithm shows excellent load balance when run on 4, 8, or 16 processors and displays almost ideal speed‐up in going from 4 to 16 processors. Preliminary benchmark calculations have also been carried out on an Intel Paragon. © 1995 by John Wiley & Sons, Inc.
An examination of a density functional/molecular mechanical coupled potential
Authors: Stanton Robert V. , Hartsough David S. , Merz Kenneth M.
Published: January 2005

In this article we describe the coupling of a density functional (DF) Hamiltonian with the molecular mechanics (MM) potential function AMBER. We examine a series of test cases in which we compare the binding energies and geometries of the complexes predicted by this coupled potential with those predicted by other theoretical methods and experiment to establish the relative accuracy of the DF/MM coupled potential. We find that the DF/MM coupled potential performs well in most cases studied and, in general, outperforms the semiempirical/MM approach. The interaction energies and structures obtained using this method appear to be insensitive to the use of nonlocal (NL) corrections to the DF method. The is fortuitous because the NL treatment is significantly more computationally expensive than the local treatment. However, NL corrections may be required to predict accurately the shape of potential energy surfaces that involve bond breaking and formation. The DF/MM method has also been applied to the determination of the solvation free energy for a series of ions using free‐energy perturbation methods. The results obtained are good and can be improved by a simple scaling of the Lennard‐Jones parameters for the ion in question. © 1995 by John Wiley & Sons, Inc.
Solving the finite‐difference, nonlinear, Poisson–Boltzmann equation under a linear approach
Authors: Zhexin Xiang , Yunyu Shi , Yinwu Xu
Published: January 2005

Electrostatic interactions are among the key factors in determining the structure and function of biomolecules. Simulating such interactions involves solving the Poisson equation and the Poisson‐Boltzmann (P‐B) equation in the molecular interior and exterior region, respectively. The P‐B equation is a nonlinear partial differential equation. The central processing unit (CPU) time for solving the full nonlinear P‐B equation has been severalfold greater than the equivalent linear case. Here a simple method is proposed to solve the full nonlinear P‐B equation under a linear approach, which has been tested both on a spherical case and on small molecules. Results show that our method converges rapidly even under highly charged cases. With this method, the CPU time for solving the full nonlinear P‐B equation is somewhat less than the equivalent linear case in our calculations. © 1995 by John Wiley & Sons, Inc.