bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intramolecular interaction effects and the structure of N2OS and N2O2: An Ab initio study
Authors: Bock Charles , Trachtman Mendel , Schmiedekamp Ann , George Philip , Chin Tin S. 
Published: December 2004

AbstractAn ab initio study of ONNS with full geometry optimization has been carried out to corroborate the presence of an interaction between the terminal atoms in this type of structure, which, in ONNO, apparently stabilizes the cis conformer. Using the unscaled 4–31G basis set with a full set of d functions on the sulfur, there is a potential minimun at the trans but not the cis geometry. A gauche conformer with a torsional angle of 77.2° is the most stable. With N2O2 this basis set gives potential minima at both the cis and trans geometries, but the trans conformer is slightly more stable, contrary to experiment and the results of (7,3) basis‐set calculations reported in the literature in which Gaussian lobe functions were employed. Using a (9,5) basis set there is no longer a potential minimum at the cis geometry, and a gauche structure is more stable than the cis conformer as in the case of N2OS with the less‐extended basis set. Force constants (harmonic and anharmonic), compliance constants, relaxed force constants, and interaction‐displacement coordinates for both molecules are compared for key structural elements.
Ab initio calculations on the effect of different basis sets and electron correlation on the transition state for the reactions HNC ⇌ HCN and BCN ⇌ BNC
Authors: Glidewell Christopher , Thomson Colin 
Published: December 2004

AbstractThe geometry of the ground states of the isomers and transition state for the systems HCN ⇌ HNC and BCN ⇌ BNC have been investigated using a wide variety of basis sets, both at the self‐consistent‐field (SCF) level and including correlation at the second‐, and third‐order Møller–Plesset (MP2 and MP3) levels. The barrier to isomerization and the isomerization energy were shown to be strongly dependent on the basis set and method, particularly for the BCN system.
A combinatorial algorithm for calculating ligand binding
Authors: Kuhl F. S. , Crippen G. M. , Friesen D. K. 
Published: December 2004

AbstractWe consider the problem of predicting the mode of binding of a small molecule to a receptor site on a protein. One plausible approach, given a rigid molecule and its geometry, is to search directly for the orientation in space that maximizes the degree of contact. The computation time required for such a naive procedure is proportional to n3m3, where n is the number of points in the site where binding can occur, and m is the number of atoms in the ligand. We give an alternative, combinatorial approach, in which only “contact–no‐contact” criteria are considered. We relate this problem to the well‐known combinatorial problem of finding cliques in a graph and show that we can use a solution to the clique problem not only to solve our original problem, but also the problem of avoiding energetically unfavorable matches. Our experience with this method indicates that the computation time required is proportional to nm2.8, with a lower constant of proportionality than that of the naive procedure.
Theoretical analysis of gramicidin A transmembrane channel. II. Energetics of helical librational states of the channel
Authors: Venkatachalam C. M. , Urry D. W. 
Published: December 2004

AbstractThe degrees of conformational freedom of polyL–Dβ‐helical chain are analyzed consistent with the helical parameters of gramicidin A structure. From conformational energy calculations, “helical librations” that can be sustained by this structure are described and the energy of libration as a function of the cavity size is presented. Two different modes of conformational change are identified corresponding to librations of allL–D‐peptide units or allD–L‐peptide units while retaining the helical parameters. Such helical librations are considered relative to conformational perturbations due to the presence of an ion in the channel.
Calculating the electrostatic potential of molecular models with separate evaluations by conventional, vector, and array processors
Authors: Egan John T. , MacElroy Robert D. 
Published: December 2004

AbstractA simple computational scheme for estimating the electrostatic potential about molecular models of moderate size is given. The large amount of calculations required for the evaluation of the hypersurface lends itself to treatment by high speed, unconventional computing machines. The essence of these calculations lies in Coulombic interactions that are computed between hypothetical proton test probes positioned in a gridded region surrounding the model and the partial electrostatic charges (CNDO/2) of each atom in the model. A specific scientific application is discussed which involves the recognition of amino acids and nucleotide bases. Three different evaluations of the potential hypersurface within the context of this approach were made. The first was performed on a VAX 11/780 which is a general purpose machine widely used in the scientific community; the second was performed using a pipelined Vector Processor, the FPS AP‐120B; and the third by a processor array, the ILLIAC‐IV. A comparison of the architectures and processing speeds of each class of machines is made. The computing power observed is consistent with the design and purpose of each machine. Also discussed are methods for displaying the vast amount of data that result from such calculations. It is determined that computer graphics offers an effective means for extracting information from large amounts of data. Finally, the scientific value of the calculations are briefly discussed. If caution is applied to interpreting the results, then the electrostatic potential (EP) mappings can be useful in identifying sites of potential chemical interactions.
A program for calculation of crystal conformations of flexible molecules using convergence acceleration
Authors: Pietilä Lars‐Olof , Rasmussen Kjeld 
Published: December 2004

AbstractFormulas are given for convergence‐accelerated lattice sums over all intermolecular Coulomb, London, and repulsive interactions. Their implementation in the consistent force field is described. Optimum values of convergence constant and summation limit are found for r−12, r−9, and r−1 interaction terms. Energy minimization in all degrees of freedom, also intramolecular, for crystals of Ar, KCl, and C2H6 is reported.
Vibrational predissociation of the van der Waals complex Ne ⃛ I2 (B). A quasiclassical approach
Authors: Delgado‐Barrio G. , Villarreal P. , Mareca P. , Beswick J. A. 
Published: December 2004

AbstractWe study the vibrational predissociation of the van der Waals molecule Ne ⃛ I2(B3π) by using a quasiclassical trajectory method. The potential energy surface assumed was a simple sum of pairwise atom–atom interactions. According to approximate quantal calculations, the necessary initial conditions were obtained and the relevant Hamilton equations were numerically solved. In the range of initial vibrational excitations of I 36 ⩽ v ⩽ 56, two crossover levels are found, which are reflected in the vibrational distributions of the diatomic fragment as in the halfwidth Γ for vibrational predissocoiation. Our present results for Ne ⃛ I2(B) are in agreement with the so‐called “energy gap law” when compared with similar ones for He ⃛ I2(B).
The molecular mechanics of valinomycin. I. Energy minimization calculations on the uncomplexed ionophore
Authors: Masut Remo A. , Kushick Joseph N. 
Published: December 2004

AbstractWe have used energy minimization calculations to study a number of conformations of uncomplexed valinomycin. In certain cases, x‐ray diffraction atomic coordinates were used directly as input coordinates, while in other cases, conformations were found by altering the x‐ray coordinates prior to minimization. Five calculated conformations are reported along with their relative energies. The conformation found theoretically to be the most stable is in agreement with earlier, cruder calculations, but does not correspond to the predominant conformation observed in nonpolar solvents. A possible rationale is presented.
A monotone iterative technique for solution of pth order (p < 0) reaction‐diffusion problems in permeable catalysis
Authors: Perry W. L. 
Published: December 2004

AbstractThe problem of determining the amount of reactant present in the steady state of a reaction‐diffusion problem with pth order reaction kinetics and slab geometry can be achieved by solving the boundary value problem

where u is a normalized (dimensionless) concentration, and ϕ is the Thiele modulus. By considering the related nonlinear eigenvalue problem

and constructing a sequence of functions that converges monotonically to y(x), solutions of the original boundary value problem are obtained for the negative exponent case.
The value of the π‐bond order–bond length relationship in geometry prediction and chemical bonding interpretation
Authors: Gready Jill E. 
Published: December 2004

AbstractThe π‐bond order–bond length relationship is reintroduced to the literature and extended to heteronuclear bonds by presenting graphs derived solely by theoretical methods. π‐bond order and overlap population results for carbon–carbon, carbon–nitrogen, and carbon–oxygen bonds obtained from ab initio STO‐3G calculations using theoretically‐optimized geometries are reported for a series of pteridines and for a wide range of small organic molecules. The order–length correlation graphs are used in predicting the “intrinsic” single bond lengths for sp2 – sp2 and sp – sp hybridized CC, CN, and CO bonds, and in evaluating the relative importance of hybridization, π‐electron delocalization and bond polarization effects in causing bond shortening in conjugated and hyperconjugated molecules. The calculated value of the π‐bond order for a given bond in a molecule is shown to be relatively insensitive to moderate geometry changes: Hence, a use for the correlation graphs in geometry prediction is suggested. Some results for the extended 4‐21G basis set are also presented.
Molecular vibrational constants of some simple polyatomic molecules. Methyl, silyl, and germyl halides
Authors: Mercau N. , Aroca R. , Robinson E. A. , Aron J. , Bunnell J. , Ford T. A. 
Published: December 2004

AbstractThe force constants and compliance constants of methyl, silyl, and germyl fluoride, chloride, bromide, and iodide have been calculated by the iterative consistency method. Using the force fields so obtained, centrifugal distortion constants, Coriolis coupling constants, and mean amplitudes of vibration have been computed and compared with experimental data, where available.
An appraisal of molecular force fields for the representation of polypeptides
Authors: Hall David , Pavitt Nicola 
Published: December 2004

AbstractA number of force fields of the molecular mechanics type have been tested for their ability to represent as an energy minimum, the observed crystal structure for three cyclic hexapeptides, cyclo‐(‐Ala‐Ala‐Gly‐Gly‐Ala‐Gly‐), cyclo‐(‐Ala‐Ala‐Gly‐Gly‐Ala‐Gly‐), and cyclo‐(‐D‐Ala‐D‐Ala‐Gly‐Gly‐Gly‐Gly‐). The most effective force field tested was that recently proposed by Kollman and co‐workers, notwithstanding its use of “united” atoms for CH, CH2, and CH3 groups. Fields proposed by Levitt, and adaptations of that of Scheraga and co‐workers, were also effective. Force fields in which hydrogens bonded to electronegative atoms were not specified explicitly were less accurate in representation.
Ab initio studies of structural features not easily amenable to experiment. 38. Structural and conformational investigations of propanoic, 2‐methylpropanoic, and butanoic acid
Authors: Siam K. , Klimkowski V. J. , Ewbank J. D. , Schäfer Lothar , Van Alsenoy C. 
Published: December 2004

AbstractThe structures and conformational energies of several conformations of propanoic acid, 2‐methylpropanoic acid, and butanoic acid were determined by geometrically unconstrained ab initio gradient geometry refinement on the 4‐21G level. The OCCC torsional potentials of propanoic acid and butanoic acid are found to be practically identical. There are energy minima at 0° and 120°, and maxima in the 60° region and at 180°. In 2‐methylpropanoic acid there are energy minima at HCCO dihedral angles of 0° and 120°, and maxima at 60° and 180°. The exact positions of the maxima and minima of the HCCO torsional potential of 2‐methylpropanoic acid are found to be predictable from propanoic acid rotational‐potential parameters. Some conformationally dependent, local geometry trends are discussed.
Discrimination of isomeric structures using information theoretic topological indices
Authors: Raychaudhury C. , Ray S. K. , Ghosh J. J. , Roy A. B. , Basak S. C. 
Published: December 2004

AbstractThree newly defined information theoretic topological indices, namely “degree complexity (Id),” “graph vertex complexity (HV),” and “graph distance complexity (HD)” along with three other information indices have been used to study their discriminating power of 45 trees and 19 monocyclic graphs. It is found that the newly defined indices have satisfactory discriminating power while HD has been found to be the only index to discriminate all the graphs studied.
Analytical MCSCF energy gradients: Treatment of symmetry and CASSCF applications to propadienone
Authors: Taylor Peter R. 
Published: December 2004

AbstractThe formula for the first derivative of the MCSCF energy with respect to a nuclear coordinate is reviewed. The efficient utilization of symmetry in programs employing symmetry‐adapted basis functions is described: Advantages that are also obtained for higher derivatives and for gradients of nonself‐consistent wave functions are briefly discussed. Using CASSCF wave functions, the method is applied to the question of nonlinearity in the heavy atom chain of propadienone (CH2CCO).
Energy component analysis calculations on neutral atom …︁ base interactions
Authors: Singh U. Chandra , Kollman Peter 
Published: December 2004

AbstractWe present energy component analysis calculations on alkali atom (Li,Na) hydride (H2O,NH3,H2S) interactions and compare these with corresponding (Li+ …︁ NH3) cation …︁ hydride interactions. In contrast to cation hydride interactions, the neutral atom–hydride interactions are shown to involve considerable contributions from all energy components.
Potential functions for alkali halide molecules
Authors: Thimme Gowda B. , Sherigara B. S. , Benson Sidney W. 
Published: December 2004

AbstractRepulsion and dispersion parameters for alkali–metal halide diatomic molecules were computed by ionic Rittner and truncated Rittner models with radial dependent repulsion terms. Experimental data on the bond energies, the equilibrium interionic distances, and the spectroscopic frequencies were employed for the purpose. The polarizabilities used were also computed from the experimental dipole moments of alkali–metal halides. The potential parameters obtained were compared with parameters from other sources and checked for consistency. The computed potential parameters of alkali–metal halide monomer molecules were used to predict the energetics and geometries for alkali–metal halide dimer molecules. The predicted values are in good agreement with experiment and other calculations indicating the consistency and reliability of the potential employed. Although the magnitude of repulsive and dispersive energy terms varies with potential functions employed, the difference between the two for a molecule is constant. The repulsive term is more sensitive than the attractive term. The uncertainty in the exponential repulsion results in an inaccurate representation of the attractive contribution. Introduction of the radial‐dependent repulsion term changes the relative magnitudes of repulsive and dispersive parameters and hence the relative contribution to the total potential with monomers. But this has no significant effect on the energetics and geometries of the dimers.
A generalized formalism of the quantum theory of valence and bonding
Authors: Natiello Mario A. , Reale Héctor F. , Medrano Jorge A. 
Published: December 2004

AbstractGeneral definitions of valence, degree of bonding between pairs of atoms, and atomic anisotropy and reactivity are given. They can be applied to closed‐ or open‐shell molecular wave functions (in the semiempirical, quasi or full ab initio SCF levels), as well as to GVB ones. The properties and usefulness of the definitions are discussed as well as their relation to former empirical notions. Examples of their application are also reported.
Theoretical study of the relative stabilities of H+(X)2 and H+(X)3 conformers and their clustering energies: X  CO and N2
Authors: Ikuta Shigeru 
Published: December 2004

AbstractThird‐order Møller–Plesset perturbation theory (MP3) with a 6‐31G** basis set was applied to study the relative stabilities of H+(X)2 conformations (X  CO and N2) and their clustering energies. The effect of both basis set extensions and electron correlation is not negligible on the relative stabilities of the H+(CO)2 clusters. The most stable conformation of H+(CO)2 is found to be a C∞v structure in which a carbon atom of CO bonds to the proton of H+(CO), whereas that of H+(N2)2 is a symmetry D∞h structure. The second lowest energy conformations of H+(CO)2 and H+(N2)2 lie within 2 kcal/mol above the energies of the most stable structures. Clustering energies computed using MP3 method with the 6‐31G** basis set are in good agreement with the experimental findings of Hiraoka, Saluja, and Kebarle. The low‐lying singlet conformations of H+(X)3 (X  CO and N2) have been studied by the use of the Hartree–Fock MO method with the 6‐31G** basis set and second‐order Møller–Plesset perturbation theory with a 4‐31G basis set. The most stable structure is a T‐shaped structure in which a carbon atom of CO (or a nitrogen atom of N2) attacks the proton of the most stable conformation of H+(X)2 clusters.
The molecular mechanics of valinomycin. II: Comparative studies of alkali ion binding
Authors: Masut Remo A. , Kushick Joseph N. 
Published: December 2004

AbstractWe have carried out a series of molecular mechanics calculations on the alkali ion complexes of valinomycin. For the ions Na+, K+, Rb+, and Cs+ we have found three‐fold rotationally symmetric conformations as the lowest energy structures, while for Li+ a markedly asymmetric configuration is preferred. The relative free energies of the complexes show that Li+ is by far the poorest binding partner in solution, followed by Na+, which is in turn far poorer than any of the three larger ions. The binding selectivity derives from the slower variation of the complexation free energy with ionic size than the ionic solvation free energy, so that the ionophore is unable to compete with the solvent for the smaller ions. Our calculated strain energies suggest that valinomycin's failure to form complexes with the smaller ions in solution is due partially to the rigidity of the ionophore structure, which prevents the central cavity from contracting to accommodate them. Certain geometric criteria indicate that K+ provides the best fit to the binding site, although there is some inconsistency between the energetic and geometric criteria of binding ability.
Optimized monopole expansions for the representation of the electrostatic properties of polypeptides and proteins
Authors: Zakrzewska Krystyna , Pullman Alberte 
Published: December 2004

AbstractOptimized monopole expansions for the peptide subunits of proteins are developed by a reparameterization of the Hückel–Del Re procedure designed to reproduce closely the electrostatic properties obtained with ab initio OMTP multipole expansions. It is shown that satisfactory values of both potential and field may be obtained for different conformations of the peptide backbone as well as for the common side chains. A comparison is presented for the pentadecapeptide Gramicidin A.
The effect of electronegative atoms on the structures of hydrocarbons. ab initio calculations on molecules containing fluorine or (carbonyl) oxygen
Authors: Allinger Norman L. , Schäfer Lothar , Siam K. , Klimkowski V. J. , Van Alsenoy C. 
Published: December 2004

AbstractA series of ab initio calculations have been carried out, using the 4‐21G basis set. Ethane and propane were first studied to obtain reference points. The effect of adding an electronegative atom (fluorine, or carbonyl oxygen) onto the framework was then studied as a function of the torsional angle about the single bond. Some pronounced trends in structural changes were observed, and these can in part be correlated with hyperconjugative effects. For example, fluoroethane has bond lengths which are shorter than those in ethane itself, by 0.024 Åin the CC bond, and 0.003 Åin the α CH bonds. These changes are essentially torsionally independent. On the other hand, in propionaldehyde, the CC bond length of the methyl group and the CH bond lengths of the hydrogens attached to the alpha carbon vary as a function of the torsion angle. If the methyl CC bond in the carbonyl plane is taken as a reference, the bond stretches .016 Åwhen the torsion angle is increased to 90°, an α CH bond similarly stretches up to .007 Å. Many of these geometric changes are large, well beyond the experimental errors in modern measurements.
Computation of reequilibration data in solids
Authors: Morin François 
Published: December 2004

AbstractReequilibration processes are often encountered within solids and they have long been described mathematically. However, computation of reequilibration data over entire processes is often difficult. An algorithm has been developed specifically for this purpose. It allows a fast and efficient computation of reequilibration parameters. Anisotropic diffusion can, moreover, be taken into account.
Compact basis sets for LCAO‐LSD calculations. Part I: Method and bases for Sc to Zn
Authors: Andzelm J. , Radzio E. , Salahub D. R. 
Published: December 2004

AbstractA method for preparing compact orbital and auxiliary basis sets for LCAO‐LSD calculations has been developed. The method has been applied to construct basis sets for first row transition metal atoms from Sc to Zn for the 3dn−14s1 and 3dn−24s2 configurations. The properties of different expansion patterns have been tested in atomic calculations for the chromium atom.
Unique description of chemical structures based on hierarchically ordered extended connectivities (HOC procedures). I. Algorithms for finding graph orbits and canonical numbering of atoms
Authors: Balaban Alexandru T. , Mekenyan Ovanes , Bonchev Danail 
Published: December 2004

AbstractAn iterative algorithm is described for finding topological equivalence, ordering, and canonical numbering of vertexes (atoms) in molecular graphs. Like the Morgan algorithm, it is based on extended connectivities but: (i) the latter are used hierarchically, i. e., the discrimination in the next iteration is carried out only for the vertices having the same extended connectivities (ranks) at the previous iteration; (ii) at equal extended connectivities, additional discrimination is introduced by the ranks of adjacent vertices; (iii) there is no “best name” search; (iv) three levels of complexity of chemical structures are distinguished and handled by different procedures.Two schemes of application of HOC procedures are presented: one directed towards a fast canonical numbering for coding systems, and another one yielding levels of topological equivalence allowing a unique topological representation of the molecule with possible applications to similarity search, structure‐activity correlations, etc.