bluuebunny/crossref_metadata_2025_split huggingface dataset:
An examination of intermolecular and intramolecular hydrogen bonding in biomolecules by AM1 and MNDO/M semiempirical molecular orbital studies
Authors: Khalil Maged , Woods Robert J. , Weaver Donald F. , Smith Vedene H. 
Published: January 2005

AbstractThe recent NMDO/M modification and parameterization of the MNDO molecular orbital method has been used to analyze intermolecular hydrogen bonding between amino acids and water, and intramolecular hydrogen bonding in monosaccharides. The results have been compared to AM1 calculations on the same systems. The MNDO/M calculations gave values which were similar to ab initio calculations with respect to the intermolecular interactions, but yielded significantly poorer results for the intramolecular interactions. The AM1 procedure performed better on the intramolecular interactions than the MNDO/M procedure, but frequently provided unfavorable three‐centered hydrogen bonding geometries for the intermolecular interactions.
Can the Lennard–Jones 6‐12 function replace the 10‐12 form in molecular mechanics calculations?
Authors: Ferguson David M. , Kollman Peter A. 
Published: January 2005

AbstractA protocol to replace “10‐12” hydrogen bonding function with the “6‐12” form to reproduce hydrogen bond distances, energies, and geometries in molecular mechanics calculations is described. The 6‐12 function was least‐squares fit to the normally employed 10‐12 form of the function for the hydrogen bond types of the Weiner et al. force field by iterating over the A and B coefficients. A weighting function was used to fit the curves in the most critical areas. The 6‐12 hydrogen bond model was compared with the Weiner et al. force field, OPLS/AMBER fore field, and quantum mechanical calculations on two simple systems, the water dimer and the chloride‐water interaction. The 6‐12 model produced structures, energies, and geometries that were consistent with the other molecular mechanics calculations and showed reasonable agreement to the quantum mechanical results for the water dimer. The 6‐12 model was also compared with normal calculations using a 10‐12 model on several representative systems. The results indicate that the 6‐12 function, when substituted by the procedure outlined in this work, yields structures and hydrogen bond properties that are similar to the normal 10‐12 model.
A new strategy for the evaluation of force parameters from quantum mechanical computations
Authors: Alemán Carlos , Canela Enric I. , Franco Rafael , Orozco Modesto 
Published: January 2005

AbstractA new strategy for the determination of force parameters is presented. The equilibrium values appearing in the force field equations representing the “stretching” and “bending” of bonds are directly determined from quantum mechanical calculations without geometrical restrictions. The determination of the force parameters is carried out by means of a rigorous fitting between the quantum mechanic and the molecular mechanical energy variations arising from the perturbation of the geometric variables. The strategy presented here has been incorporated into a computer program named PAPQMD, which was developed in order to provide nonquantum mechanical experts with a powerful tool for the determination of approximate force parameters. The program was developed upon the assumption that force parameters are not universal, but they strongly depend on the molecular environment. This implies that the parametrization procedure should be done in a molecular model close to the molecule or molecules to be studied by means of molecular mechanical or dynamic methods, and consequently, it is no longer supposed that the variation of one geometrical parameter does not affect the rest of the molecular geometry. PAPQMD performs the fitting between molecular mechanics and quantum mechanical energies considering all the perturbations that the modification in one geometric variable causes in all the others, enabling the parametrization even of large molecules. The ability of our method to reproduce experimentally derived force parameters is discussed and compared with the widely used Hopfinger's strategy. The study of the behavior of PAPQMD and Hopfinger's strategies for reproducing the force parameters of two complex molecules demonstrates the superiority of the methodology presented here.
On the additivity of basis set effects in some simple fluorine containing systems
Authors: Ignacio Edgar W. , Schlegel H. Bernhard 
Published: January 2005

AbstractThe reactions F + H2 → HF + H, HF → H + F, F → F+ + e− and F + e− → F− were used as simple test cases to assess the additivity of basis set effects on reaction energetics computed at the MP4 level. The 6‐31G and 6‐311G basis sets were augmented with 1, 2, and 3 sets of polarization functions, higher angular momentum polarization functions, and diffuse functions (27 basis sets from 6‐31Gd, p) to 6‐31 ++ G(3df, 3pd) and likewise for the 6‐311G series). For both series substantial nonadditivity was found between diffuse functions on the heavy atom and multiple polarization functions (e.g., 6‐31 + G(3d, 3p) vs. 6‐31 + G(d, p) and 6‐31G(3d, 3p)). For the 6‐311G series there is an extra nonadditivity between d functions on hydrogen and multiple polarization functions. Provided that these interactions are taken into account, the remaining basis set effects are additive to within ±0.5 kcal/mol for the reactions considered. Large basis set MP4 calculations can also be estimated to within ±0.5 kcal/mol using MP2 calculations, est. EMP4(6‐31 ++ G(3df, 3pd)) ≈ EMP4(6‐31G(d, p)) + EMP2(6‐31 ++ G(3df, 3pd)) – EMP2(6‐31G(d, p)) or EMP4(6‐31 + G(d, p) + EMP2(6‐31 ++ G(3df, 3pd)) – EMP2(6‐31 + G(d, p)) and likewise for the 6‐311G series.
Self‐consistent, nonorthogonal group function approximation. III. Approaches for modeling intermolecular interactions
Authors: Fülscher M. P. , Mehler E. L. 
Published: January 2005

AbstractA new program has been developed for the implementation of the self‐consistent nonorthogonal group function (NOGF) approximation for the calculation of wavefunctions between interacting systems. The NOGF approach is based on the reformulation of a single‐determinental, closed shell wavefunction into an antisymmetrized product of nonorthogonal group functions, each of which is a single determinant of doubly occupied orbitals. The group product form of the wavefunction combined with the relaxation of the orthogonality constraints and the structure of the orbital equations allows each group's orbitals to be expanded in a local basis set, and makes it possible to modify the orbital expansions or iterative process to simplify the computation. Three models for approximating the full single‐determinental wavefunction are tested: (1) different quality basis sets for orbitals belonging to different groups, (2) variation of the types of intergroup interactions included in the wavefunction, and (3) the use of frozen orbitals which have been predetermined in a subsystem and are subsequently transferred to the system of interest. These approximations are applied to the calculation of protonation energies of formate, ammonia, imidazole, and guanidine with part of the first hydration shell being represented by two water molecules hydrogen bonded to each species. The results from different basis sets are compared. Then interaction potentials between the acid and ammonia are calculated for both neutral and charged forms, again with inclusion of part of the first hydration shell. The results show that these techniques can yield reliable wavefunctions of the same quality as obtained with the standard supermolecule approach. The effect of the basis set superposition error in the NOGF approach is briefly considered, and the reduction in computing effort resulting from the three models is discussed.
MM2 study on the conformation of N‐acetyl‐L‐amino acid N′‐methylamides with aliphatic side chain and their Nα‐methyl derivatives
Authors: Hlaváček Jan , Matějka Václav , C̆ársky Petr 
Published: January 2005

Abstractφ – ψ maps have been calculated by the MM2(87) potential for the Nα‐acetyl derivatives of Gly, Ala, Val, and Tle methylamides and their Nα‐methyl substituted derivatives to interpret the 1H NMR and CD spectra of these compounds. From the critical examination of the available theoretical and experimental evidence it follows that in the series of Nα unsubstituted Ala, Val, and Tle derivatives the importance of the second lowest energy conformation (C5) is increased and that eventually it becomes the lowest energy conformation instead of C. With the Nα‐methyl substituted Ala and Val derivatives, the lowest energy conformation seems to be C. Performance of MM2(87) was tested for the φ – ψ map of the Ala derivative by comparing it with other theoretical data available in the literature.
On computation of optimal parameters for multivariate analysis of structure‐property relationship
Authors: Randić Milan 
Published: January 2005

AbstractWe outline a search for optimal parameters involving heteroatoms for use in multivariate regression analysis in structure‐property and structure‐activity studies. The problem consists of determining optimal numerical values for the diagonal elements of the adjacency matrix in graphs with atoms of different kind. In particular we consider weighted paths as the basic molecular descriptors and search for optimal parameters for carbon atom and oxygen atom in a correlation of molecular structure with isomeric variations in the boiling points of hexanols. Standard error is taken as the criterion for the selection of the optimal parameters. The weighting algorithm restricts the diagonal entries to values greater than −1. The selection of positive diagonal values leads to reducing the path numbers and the negative values lead to enlarging the role of path numbers relative to the zero diagonal values implied by simple graphs in which heteroatoms are not discriminated. A systematic search for optimal parameters for alcohols gave for carbon atom and oxygen atom diagonal entries: x = 1.50 and y = −0.85 respectively when a single path number is used as a descriptor and x = −0.15 and y = −0.94 when two path numbers are used. The parameters derived for 17 hexanols have been successively applied to 37 heptanols demonstrating thus transferability of the parameters.
The CαC internal rotation in α‐alkyl substituted carbonyls and thiocarbonyls: CH(CH3)2C(X)YH (X, Y O or S)
Authors: Teixeira‐Dias J. J. C. , Fausto R. , de Carvalho L. A. E. Batista 
Published: January 2005

AbstractThe CαC internal rotation in 2‐methylpropionic, 2‐methylthiopropionic (thiol and thion forms) and 2‐methyldithiopropionic acids was studied by the ab initio SCF‐MO method using 3‐21G and 3‐21G + d(0.65S) basis sets. Energies and structures of several conformations of these molecules, determined by gradient geometry refinement, are reported and used to assess the effects of oxygen‐by‐sulphur substitution on molecular properties. The nature and relative importance of intramolecular interactions involving both the α‐methyl substituents and the C(X)Y (X, Y O or S) fragment are also discussed.
Prescreening of two‐electron integral derivatives in SCF gradient and Hessian calculations
Authors: Horn Hans , Weiß Horst , Háser Marco , Ehrig Michael , Ahlrichs Reinhart 
Published: January 2005

AbstractThe definition and implementation of a rigorous two‐electron integral bound based on Schwarz' inequality both for gradient and hessian calculations is presented. Tests demonstrate the advantages of this easily implemented and effective bound.
A general procedure for obtaining wave functions obeying the virial theorem
Authors: Lehd Michael , Jensen Frank 
Published: January 2005

AbstractThe virial theorem for molecules is shown to have two different forms, one employing the energy gradient the other involving the Hellmann–Feynman force. While the former VT can be fulfilled by a uniform scaling of the basis set, the latter cannot be satisfied in certain basis sets, and can give unrealistic results in others. The scaling procedure is applied to molecules at nonstationary points on the potential energy surface and it is found that energy components can change substantially, especially at short bondlengths, while the change in total energy is small. The effects on molecular properties are also small.
Theoretical kinetic isotope effects for the hydride transfer from formate to carbon dioxide: A comparison of theory with experiment
Authors: Jones Jeffrey P. , Urbauer Jeffrey L. 
Published: January 2005

AbstractHeavy atom and deuterium isotope effects for the hydride transfer from formate to carbon dioxide were determined using MNDO, AM1, and PM3 semiempirical methods and the ab initio RHF/3‐21G*, 3‐21 + G, 6‐31G*, and 6‐31 + G* basis sets. Frequencies were also determined for ground state structures using 6‐31G* basis set at the MP2 level of theory. The calculated isotope effects compared favorably with the experimentally determined values of Hermes et al. (Biochemistry, 23, 5479 (1984)). The calculated ground state frequencies were high for most vibrational modes as compared with measured values, however some ab initio methods underestimate the carbon hydrogen stretching frequencies. The heavy atom isotope effects were influenced to a large extent by the excitation factor, the mass factor and the moment of inertia factor of the Bigeleisen equation.
Unimolecular rearrangements of ethylnitrene: An exploratory theoretical study
Authors: Kakkar Rita , Walia Vibha 
Published: January 2005

AbstractThe products of the rearrangement of ethylnitrene are ethylideneimine via a 1,2 hydrogen shift, N‐methyl methyleneimine via a 1,2 methyl shift, and the corresponding aziridine by cyclization. The three reactions have been studied by the semiempirical MNDO method. The charge transfer effects have been investigated. Theoretically calculated vibrational frequencies and kinetic properties have been used in calculating macroscopic thermodynamic and kinetic properties. The entropies of activation, the high pressure rate constants, k∞, and the high pressure Arrhenius parameters, A∞ and E∞, have been computed. The kinetic isotope effects have also been studied.
Analytic Löwdin alpha‐function method for two‐center electron‐repulsion integrals over slater‐type orbitals
Authors: Jones Herbert W. 
Published: January 2005

AbstractUsing the Löwdin alpha‐function method in which displaced orbitals are expanded in spherical harmonics, two‐center, two‐electron repulsion integrals of the Coulomb, hybrid, and exchange type are done analytically using Slater‐type orbitals. Computer algebra and integer arithmetic are used to obtain analytic results and avoid cancellation errors by the generation of rational matrix elements for C, E, and F matrices that are used to express the α‐function. The formula for the exchange integral is kept simple by reversing the order of integration over each part of a split quadrant. Only two basic integrals are used that are first efficiently evaluated by using look‐up tables and then used repeatedly.
The application of symbolic computing to chemical kinetic reaction schemes
Authors: Holmes Mark H. , Bell Jonathan 
Published: January 2005

AbstractGiven a reaction mechanism we show how a symbolic computation approach can be used to develop the kinetic equations by identifying the reaction scheme with an equivalent matrix. Our method is also applicable in cases where the stoichiometric matrix approach fails. The specific algorithm that is written applies to schemes where individual reactions are at most ternary, but the way to generalize the procedure is also discussed. By using symbolic computing it is possible to determine general properties of the system. We demonstrate this by showing how to use the matrix to determine the system's conservation laws, which in turn can be used to reduce the number of equations in the system. As another application it is shown how to determine some of the species which have a zero equilibrium state. To illustrate the procedure, example reaction schemes are investigated.
On the use of electrostatic potential derived charges in molecular mechanics force fields. The relative solvation free energy of cis‐ and trans‐N‐methyl‐acetamide
Authors: Cieplak Piotr , Kollman Peter 
Published: January 2005

AbstractWe have carried out free energy perturbation calculations on the relative solvation free energy of cis‐ and trans‐N‐methyl‐acetamide (NMA). Experimentally, the solvation free energy difference has been found to be near zero. Using 6‐31G* ab initio electrostatic potential derived charges for both the cis and trans conformations, we calculate a solvation free energy difference of 0.1 ± 0.1 kcal/mol. Using the 6‐31G* charges derived for the trans conformation for both the cis and trans models leads to a solvation free energy difference of 0.9 ± 0.1 kcal/mol, compared to the value of 2.2 kcal/mol determined for the OPLS model for trans‐NMA.
Topological analysis of complex molecular surfaces
Authors: Zachmann Carl‐Dieter , Heiden Wolfgang , Schlenkrich Micheal , Brickmann Jürgen 
Published: January 2005

AbstractAn algorithm for the calculation of local and global curvatures of molecular surfaces is presented. The analysis is based on a surface representation as a set of points in 3‐D space (“dotted surface” representation). The surface data are used to subdivide the surfac into domains with different curvatures. All domains are characterized by a reference point with a corresponding curvature profile specifiying the topological properties in its neighborhood. The curvature profiles provide a method for a systematic comparison of the shapes of different molecules. Such a strategy is important for the treatment of molecular recognition problems. The enzyme‐inhibitor complex trypsin/BPTI was chosen to demonstrate the scopes of the method.
Application of SINDO1 to organo‐transition metal compounds
Authors: Li Jian , Jug Karl 
Published: January 2005

AbstractThe recently extended SINDO1 method is used to study geometries, electronic structures, and chemical bonding of transition metal organometallic compounds. The optimized distances and angles between metal atoms and organic ligands are in fair agreement with experimental data and are comparable to ab initio results. The comparison of orbital energies between the current method and ab initio methods shows that the method can give a correct description of electronic structure and bonding patterns of organometallic compounds. The method is also used to calculate atomic and bond valence, which are defined in terms of appropriate combinations of first‐order density matrix elements for molecules. The valence indices provide a straightforward and easy‐to‐interpret way to analyze the magnitude of metal‐carbon and metal‐metal bonds.
A coarse‐grain parallel implementation of the direct SCF method
Authors: Lüthi Hans P. , Mertz John E. , Feyereisen Martin W. , Almlöf Jan E. 
Published: January 2005

AbstractA coarse‐grain, parallel approach to direct Hartree–Fock calculations is presented and discussed. The suggested scheme allows for a near asymptotic speedup involving a very low parallelization overhead without compromising the vector performance of vector‐parallel architectures. A shared‐memory MIMD implementation, for which very high speeds of computation have been achieved, is discussed in detail.
Ab initio evidence for the stepwise mechanism of the McLafferty rearrangement of the butanal radical cation
Authors: Liu Ruifeng , Pulay Peter 
Published: January 2005

AbstractThe mechanism of the McLafferty rearrangement of the butanal radical cation to ethylene and vinyl alcohol cation is found, by ab initio calculations, to be stepwise. The results of a previous ab initio study are inconclusive because of symmetry restriction in their geometry optimization.
Geometry optimization in Cartesian coordinates: Constrained optimization
Authors: Baker Jon 
Published: January 2005

AbstractAn efficient algorithm for constrained geometry optimization in Cartesian coordinates is presented. It incorporates mode‐following techniques within both the classical method of Lagrange multipliers and the penalty function method. Both constrained minima and transition states can be located and, unlike the standard Z‐matrix using internal coordinates, the desired constraints do not have to be satisfied in the initial structure. The algorithm is as efficient as a Z‐matrix optimization while presenting several additional advantages.
PEFF: A program for the development of empirical force fields
Authors: Dillen Jan L. M. 
Published: January 2005

AbstractPEFF is a new computer program designed to assist in the development of empirical force fields used in molecular mechanics calculations. Its main features are: constrained and unconstrained energy minimization available with four different techniques, rigid group refinement, crystal lattice summations, calculation of normal modes, thermodynamic functions and crystallographic temperature factors, vibrational corrections of calculated crystal structures, and a multidimensional driver to scan the energy hypersurface. Used in force field optimization mode, the program employs a least‐squares method to fit the force field parameters to a set of experimental data.
Representation of molecules by atomic charges: A new population analysis
Authors: Tasi Gyula , Kiricsi Imre , Förster Horst 
Published: January 2005

AbstractFor the calculation of atomic charges in molecules, a new fast procedure based on extended Mulliken population analysis is presented. The reliability of the new population analysis is tested within the AM1 approximation and the results are compared in detail with those obtained by different methods reported in the literature.
Molecular docking using shape descriptors
Authors: Shoichet Brian K. , Kuntz Irwin D. , Bodian Dale L. 
Published: January 2005

AbstractMolecular docking explores the binding modes of two interacting molecules. The technique is increasingly popular for studying protein‐ligand interactions and for drug design. A fundamental problem problem with molecular docking is that orientation space is very large and grows combinatorially with the number of degrees of freedom of the interacting molecules. Here, we describe and evaluate algorithms that improve the efficiency and accuracy of a shape‐based docking method. We use molecular organization and sampling techniques to remove the exponential time dependence on molecular size in docking calculations. The new techniques allow us to study systems that were prohibitively large for the original method. The new algorithms are tested in 10 different protein‐ligand systems, including 7 systems where the ligand is itself a protein. In all cases, the new algorithms successfully reproduce the experimentally determined configurations of the ligand in the protein.
Efficient algorithm for the reconstruction of a protein backbone from the α‐carbon coordinates
Authors: Rey Antonio , Skolnick Jeffrey 
Published: January 2005

AbstractWe present an analytical method for generating a whole protein backbone structure from the coordinates of the α‐carbons. The procedure begins by automatically positioning the β‐carbons for every residue, and then the positions of the carbonyl groups and the amide nitrogens are also computed. The method is based upon the simultaneous minimization of a number of geometrical constraints that appear in real proteins and that can be very easily formulated as a set of trigonometric relations between the coordinates of the atoms involved in the backbone reconstruction. The resulting algorithm has been tested for proteins of very different sizes and topologies, and can advantageously compete with other methods proposed for this goal both in accuracy and in computational requirements. Possible ways of further refinement of the resulting structures are discussed.