bluuebunny/crossref_metadata_2025 huggingface dataset:
Studies in hydrogen bonding: Association within small clusters of water, methanol, and ammonia molecules using Jorgensen's intermolecular pair potentials
Authors: Brink George , Glasser Leslie
Published: December 2004

The geometries of the dimer, trimer, and tetramer hydrogen‐bonded clusters of water, methanol, and ammonia molecules have been derived using previously published intermolecular pair potentials containing constants optimized from ab initio calculations. The lowest energy forms for the dimers of all three types of molecules have an open structure, while the trimers and tetramers have cyclic structures. The results are compared with those previously described using another empirical potential, EPEN.
A semiempirical formulation for the study of molecular interactions
Authors: Fraga Serafin
Published: December 2004

The coefficients of a 1/R expansion (containing long‐range electrostatic interaction, medium‐range electrostatic‐induced dipole attraction, short‐range dispersive attraction, and very short overlap interaction terms) have been determined, within a semiempirical approach, from the results of a priori calculations. The formulation has been applied to the study of the stable conformations of benzene complexes.
Spin–orbit and dispersion energy effects in XeF
Authors: Krauss M. , Stevens W. J. , Julienne P. S.
Published: December 2004

Spin–orbit and dispersion energy contributions to the energy curves of XeF are examined. A rapid variation in the spin–orbit coupling with internuclear separation is found for both the ground and excited states. This result can explain the experimentally observed ordering of the ionic excited states when the spin–orbit perturbation couples 2σ and 2π energy curves obtained by both all‐electron and effective core potential (ECP) calculations at the first‐order configuration interaction (FOCI) level of accuracy. Damped dispersion energy contributions to the ground‐state energy curve are shown to be comparable to the charge transfer contribution. The energy curve for XeF is in reasonable agreement with experimental results and a calculation of the analogous XeCl curve confirms the qualitative correctness of the calculation. The energy curves and transition moments were then applied to two problems related to the efficiency of the XeF laser. Photodissociation of the X state provides a means of removing a bottlenecked vibrational level but a calculation of the radiative transition probability between the X and A states finds the cross section is too small to yield rates competitive with collisional deactivation. The bottlenecked state may also be removed by electron dissociative attachment but the calculated energy curves for the X states of XeF and XeF− do not cross at a low energy indicating a small cross section.
Strain energies of some bridgehead olefins as calculated with the MM2 force field
Authors: Warner Philip M. , Peacock Stephen
Published: December 2004

The MM2 force field has been used to calculate the strain energies of a representative series of bridgehead alkenes, and the results compared to similar previous calculations using the MM1 force field. The new results roughly parallel the old ones, although the strain energy of a given compound is normally higher with MM2 than MM1. These differences are largely negated, however, when the OS (olefinic strain) value is considered.
Orbital topology. III. Orbital mapping of unsymmetrical molecules. A survey of the thermal ring opening of isoelectronically substituted cyclobutenes and benzocyclobutenes
Authors: Kelsey Donald R.
Published: December 2004

Orbital mapping analysis based on CNDO/2 molecular orbitals has been used to survey the thermal ring‐opening isomerizations of cyclobutenes and benzocyclobutenes. Isoelectronic substitutions within the molecular framework of cyclobutene (e.g., CH2 replaced by CH−, OH+, NH, NH2+) result in ground‐state orbital correlations via both conrotatory and disrotatory pathways in several cases, in contrast to the parent hydrocarbon conrotatory stereochemistry. The results substantiate the heteroatom effects previously revealed by orbital mapping for the disrotatory thermal isomerizations of isoelectronic Dewar benzenes. Qualitative patterns, such as nodal shifts in the butadiene π orbital, are discussed in relation to the mapping correlations. The isoelectronic benzocyclobutenes give ground‐state orbital correlations via conrotatory pathways only, which suggests that delocalization may reduce the heteroatom perturbation.
The structure and stability of the acetylene dication
Authors: Pople John A. , Frisch Michael J. , Raghavachari Krishnan , Schleyer Paul V. R.
Published: December 2004

The dication C2H has been investigated by ab initio molecular orbital theory. It is found to have a linear (D∞h), structure with a triplet (3σ−g) ground state. Deprotonation to C2H+ is exothermic by 9.8 kcal/mol, but this process is hindered by a large barrier of 65 kcal/mol.
Acceleration of convergence in Monte Carlo simulations of aqueous solutions using the metropolis algorithm. Hydrophobic hydration of methane
Authors: Kincaid Robert H. , Scheraga Harold A.
Published: December 2004

Convergence problems encountered in the computer simulations of aqueous solutions are discussed. Solute–solvent radial distribution functions are shown to converge very poorly when the standard Metropolis Monte Carlo procedure is applied. To overcome this difficulty, several modifications are made in the Metropolis method. Optimum maximum step sizes are determined for simulations of liquid water. A scheme is employed for preferential sampling of both the solvent and the solute molecules. To test these modifications, a simulation is carried out for pure liquid water, treating a single water molecule as a “solute.” The convergence of the radial distribution functions is found to be accelerated significantly. A further test is made by simulating an aqueous solution of methane, consisting of one methane molecule (using the EPEN/2 potential for methane–water interactions) and 124 water molecules (using the MCY potential for water–water interactions). Again, the convergence of solute–solvent radial distribution functions is found to be accelerated. The computation of partial molar thermodynamic quantities, however, still suffers from convergence difficulties. This problem is discussed in detail. The EPEN/2 potential is found to yield structural and thermodynamic features of hydrophobic hydration that are consistent with available experimental and theoretical results for aqueous solutions of methane.
Substituent effects on the charge density in the formyl group
Authors: Eisenstein M. , Hirshfeld F. L.
Published: December 2004

SCF wavefunctions with similar extended Gaussian bases for the series HCOX with X = H, OH (syn and anti), NH2, CN, and F yield closely similar charge deformation density maps in the formyl region of all six molecules. The differences, measured by moments of partitioned atomic deformation densities, correlate almost linearly with the Hammett substituent parameters σI and σR of the several substituents X. However, systematic deviations, especially in the carbon fragment, suggest the need for modified values of the inductive parameters σI for the correlation of these molecular charge densities.
Restricted Hartree–Fock approximation. I. Techniques for the energy minimization
Authors: Rico J. Fernández , De La Vega J. M. Garcia , Alonso J. I. Fernández , Fantucci P.
Published: December 2004

We present a new procedure for direct minimization of the RHF energy, which presents advantages over SCF methods with respect to convergence rate and computational cost. In this procedure we combine several techniques with the aim of obtaining best directions and step lengths for the iterative search for a minimum of the energy. In this article we develop the theory. Therefore, we analyze the variational function; we present a short description of the minimization techniques and we discuss in detail the way in which they are to be used. The computational aspects of the procedure will be treated in the following article.
Dipole polarizability derivatives calculated by the Kirkwood method
Authors: Bishop David M. , Cartier Alain
Published: December 2004

Derivatives, with respect to the symmetry coordinates, of the components of the dipole polarizabilities of HF, H2O, and CH4 are calculated using the Kirkwood method and a generalization of that method. The results for the bond‐stretching derivatives are in reasonable agreement with those found by finite field calculations; those for angle changes are of the correct sign, but their magnitudes are in poor agreement with the finite field ones. The results are also analyzed using a four‐parameter bond polarizability model.
Energetics and structure of the hydrated gaseous halide anions
Authors: Gowda B. Thimme , Benson Sidney W.
Published: December 2004

Energetics and geometries for the hydrated gaseous halide anions have been computed from a simple model in which the molecular dipole of water was composed of two parts, one due to a lone pair on oxygen (60%) and the rest to formal charges on the nuclei. The calculations were made for both the symmetric and nonsymmetric structures. A variety of structures were used to compute potential energies and distances with up to six water molecules. The total energy consisted of a sum of electrostatic, polarization, dispersion, and repulsion terms. Various sets of repulsive potential parameters, ranging from those determined from molecular beam experiments to those determined using experimental ion–water distances or energies, have been employed to compute repulsive interaction energies. It was found that the range parameters play a significant role in deciding the magnitudes of the distances and energies, as the latter are most sensitive to them. It was also shown that with a simple correlation scheme the consistency of the experimental energies and distances can be tested separately without using repulsive potential parameters from other sources. It also suggests that a range of parameters can be used to compute repulsion energies. Despite the fact that the model is greatly simplified, the agreement of both the predicted ion‐oxygen distances and energies with both experiment and other calculations is excellent. A detailed analysis of our calculation suggests that the negative ion clusters with one to three water molecules contain symmetric orientation of water molecules, while those with more than three may contain asymmetric orientations of water molecules or a mixture of both. From the log–log plots of hydration energies versus (R + radius of water molecule), we have proposed empirical expressions of the type ΔEn−1,n = 10·0x (R + 1.38)−y with both Pauling's and Ladd's radii for univalent ions with which stepwise hydration energies of the latter can be predicted if we know thier radii. The values predicted for the alkali cations are in excellent agreement with the experimental and theoretical values, indicating the consistency of the simple model.
Computer generation of the symmetry elements of nonrigid molecules
Authors: Balasubramanian K.
Published: December 2004

Algorithms and computer programs are developed for generating the symmetry elements of nonrigid molecules. These programs are based on the wreath product formalism for the symmetry groups of nonrigid molecules developed by the present author. Several examples are given to illustrate the procedures. Applications to weakly bound van der Waal complexes synthesized by supersonic beam expansion are also presented.
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

An 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

The 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

We 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

The 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

A 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

Formulas 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

We 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

We 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

The 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

The 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

The 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

A 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

The 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.
Generic solvent sites in a crystal
Authors: Mezei Mihaly , Beveridge David L.
Published: December 2004

A numerical procedure is described and tested for the determination of solvent sites in a crystal hydrate from computer simulation results. The method does not require the computation of density distributions.
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

Three 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

The 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

We 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

Repulsion 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

General 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

Third‐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

We 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

Optimized 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

A 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.
Pseudopotential calculations on Si2H6 and Si2H4
Authors: Sax Alexander F.
Published: December 2004

Local pseudopotential calculations have been performed for the ground state of disilane as well as for the lowest singlet and triplet states of disilene and silylsilylene. Comparison with all‐electron calculations shows good agreement for geometries and relative stabilities.
Computation of reequilibration data in solids
Authors: Morin François
Published: December 2004

Reequilibration 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

A 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

An 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.
Determination of the Wiener molecular branching index for the general tree
Authors: Canfield E. R. , Robinson R. W. , Rouvray D. H.
Published: December 2004

The many applications of the distance matrix, D(G), and the Wiener branching index, W(G), in chemistry are briefly outlined. W(G) is defined as one half the sum of all the entries in D(G). A recursion formula is developed enabling W(G) to be evaluated for any molecule whose graph G exists in the form of a tree. This formula, which represents the first general recursion formula for trees of any kind, is valid irrespective of the valence of the vertices of G or of the degree of branching in G. Several closed expressions giving W(G) for special classes of tree molecules are derived from the general formula. One illustrative worked example is also presented. Finally, it is shown how the presence of an arbitrary number of heteroatoms in tree‐like molecules can readily be accommodated within our general formula by appropriately weighting the vertices and edges of G.
Structural features of benzylic carbanions. A theoretical study
Authors: Lipkowitz Kenny B. , Uhegbu Christopher , Naylor Adel M. , Vance Robert
Published: December 2004

Benzylic anions were studied with the semiempirical MNDO molecular orbital method. Structural changes were analyzed as metal counterions and solvents were allowed to interact with the benzylic carbon. Generally, benzylic carbanions were found to be trigonal planar but became pyramidal or bent when metals were included in the calculation.
Interaction energy studies of pyrrolopyrimidine nucleoside antibiotics: Tubercidin
Authors: Sanyal Nitish K. , Ojha Rajendra Prasad , Roychoudhury M.
Published: December 2004

On the basis of intermolecular interaction energy studies, the possibility of incorporation of a pyrrolopyrimidine nucleoside analog has been examined. Both stacking as well as in‐plane (hydrogen bonding) interactions have been considered for computing the association energy of analogous base (tubercidin) with nucleic acid bases and base pairs. The molecular charge distribution has been computed by CNDO/2 method while the interaction energy has been computed using second‐order perturbation theory. The energy values and the sites of association of the tubercidin base in the complex formation, obtained from the minimum energy configurations, have been compared with the corresponding energy values as well as the sites of association of nucleic acid bases in the transcription process. The theoretical results thus obtained have been discussed in the light of a model developed earlier, and an attempt has been made to correlate the results with the observed biological activity of tubercidin.
Symmetry properties of chemical graphs. IX. The valence tautomerism in the P73− skeleton
Authors: Randić Milan , Oakland David O. , Klein Douglas J.
Published: December 2004

We investigate the intramolecular rearrangement of the P73− ion in which PP bonds are continuously broken and reestablished resulting in a dynamic structure with all seven phosphorus atoms being chemically equivalent. This leads to 7/3 = 1680 valence tautomers. The P73− ion is a typical fluctuating molecule, distantly related to C10H10 bullvalene. In order to determine the symmetry of the process we first consider the problem of the construction of the rearrangement graph. Initial steps toward this goal are illustrated, and additional characterizations of the graph are derived after its construction by computer. A number of properties of this rather complicated graph having 1680 vertices and 2520 edges are discussed: in particular the occurrence of various cycles, the maximal distance between vertices, the count of neighbors at different distance, and finally its symmetry.
Mindo/3 and mndo calculations of closed‐ and open‐shell cations containing C, H, N, and O
Authors: Halim Herman , Heinrich Nikolaus , Koch Wolfram , Schmidt Jochen , Frenking Gernot
Published: December 2004

Heats of formation of 119 closed‐ and open‐shell carbocations calculated by the semiempirical quantum chemical methods MINDO/3 and MNDO are reported and compared with experimental data. With proper consideration of failures in specific areas, both methods can be used for the thermodynamics of carbocations containing C, H, N, and O. MINDO/3 predicts unrealistic values for nitrogen containing cations with nitrogen multiple bonds and is not suited for closed‐shell cations containing oxygen. Saturated acyclic hydrocarbon radical cations often are computed with abnormally long CC bonds by MNDO. Otherwise, the standard deviation of the two methods is not very different, being in the range of ±13 kcal/mol. MINDO/3 tends to overestimate the cation stabilities, whereas MNDO calculates cations usually too high in energy. Some of the errors which were found in the calculations of the ions are related to the computed values for the parent neutral structures, but others are not.
A method for the machine detection of near equivalence of major substructures in a molecule
Authors: Bersohn Malcolm , Fujiwara Shizuo , Fujiwara Yuzuru
Published: December 2004

The use of the concept of near equivalence of substructures in a computer program concerned with organic synthesis requires a concrete definition of «nearness» and an efficient method for implementing the concept. Such a method has been devised and its use is described and examples are given.
Molecular mechanics and molecular shape. III. Surface area and cross‐sectional areas of organic molecules
Authors: Meyer A. Y.
Published: December 2004

A nonanalytical procedure is proposed to calculate the surface area and cross‐sectional areas of molecules. Results are reviewed for about 70 species comprising alkanes, acyclic and cyclic, alkyl halides, and alcohols. By regression analysis, relationships are detected between surface areas or segment areas and physical properties. Computed cross‐sectional areas are confronted with adsorption values. Four ways are proposed to define quantitatively the intuitive notion of «molecular globularity».
Comparison of sequences as a method for evaluation of the molecular similarity
Authors: Jerman‐Blaẑiĉ B. , Fabiĉ I. , Randić M.
Published: December 2004

String comparison techniques were developed and applied for measuring the molecular similarity of chemical structures. The molecular structures were encoded as a sequence of numbers representing counts of paths of different lengths. The similarity index between two compounds was calculated as the difference between the gains of information derived through comparison of the corresponding molecular path sequences. Ranks between the structures of the studied data base obtained according to this similarity were used as basic data for deriving correspondences between the elements of the set of compounds. The method was applied on a group of 41 barbiturates. Correlation equations were calculated for different groups of compounds grouped according to the displayed similarity. The correlation equations and the corresponding statistics were obtained using standard computer programs. Special algorithm for computing the similarity index and the correlation matrix (outlined very briefly) was developed and implemented on VAX 11/750.
Vectorization of a classical trajectory code on a floating point systems, Inc. Model 164 attached processor
Authors: Kraus Wayne A. , Wagner Albert F.
Published: December 2004

A triatomic classical trajectory code has been modified by extensive vectorization of the algorithms to achieve much improved performance on an FPS 164 attached processor. Extensive timings on both the FPS 164 and a VAX 11/780 with floating point accelerator are presented as a function of the number of trajectories simultaneously run. The timing tests involve a potential energy surface of the LEPS variety and trajectories with 1000 time steps. The results indicate that vectorization results in timing improvements on both the VAX and the FPS. For larger numbers of trajectories run simultaneously, up to a factor of 25 improvement in speed occurs between VAX and FPS vectorized code.
Rate constants for the bimolecular self‐reaction of tertbutyl radicals in nalkane solvents
Authors: Schuh H. , Fischer H.
Published: December 2004

Rate constants for the self‐reaction of tertbutyl radicals in six nalkanes are determined as functions of temperature by kinetic electron‐spin resonance spectroscopy and from rates of product formation. They are well described by a Smoluchowski–Stokes–Einstein treatment including effects of microfriction and spin statistical factors, indicating complete diffusion control. The ratio of disproportionation to combination products is found to depend on temperature and solvent. This is tentatively ascribed to reorientational effects in the encounter pairs.
Rate constants for the reaction of O(3P) atoms with CH2 = CHF, CH2 = CHCl, and CH2 = CHBr at 298 ± 2°K
Authors: Atkinson R. , Pitts J. N.
Published: December 2004

Absolute rate constants for the reaction of O(3P) atoms with CH2 = CHF, CH2 = CHCl, and CH2 = CHBr have been obtained at 298 ± 2°K using a modulation phase shift technique. The rate constants (k2 × 10−8 l./mole · sec) obtained are: CH2 = CHF (1.61 ± 0.20), CH2 = CHCl (2.54 ± 0.26), and CH2 = CHBr (2.45 ± 0.25). These rate constants are lower than those determined by discharge flow techniques, but that for CH2 = CHF is in good agreement with relative rate measurements.
Deuterium isotope cage effects in the dismutation of alkoxyl radicals. Significance for the mode of alkylperoxyl termination
Authors: Mendenhall G. D. , Quinga E. M. Y.
Published: December 2004

Decomposition of (R1R2CXON=)2 (R1 = R2 = Ph; R1 = R2 = pClC6H4; R1 = Ph, R2 = CH3; X = H or D) in hydrocarbon solvents at 31–75°C afforded R1R2CO in 6–8% lower yield when X = D than when X = H. This result is ascribed to cage escape of secondary alkoxyl radicals in competition with dismutation. Deuterium isotope effects for alkoxyl cage dismutation of 1.35–2.4 are estimated from the data. It is suggested that this same competition may account for the experimentally slower termination rate constants in solution of primary and secondary alkylperoxyl radicals on α‐deuteration.
Über den Einfluß der Wärmebehandlung auf die Korrosionsbeständigkeit der Magnesium‐Aluminiumlegierung Mg‐Al 7
Authors: Bulian W.
Published: December 2004

Es wurde der Einfluß der Wärmebehandlung, und zwar sowohl einer Homogenisierungsglühung wie auch einer Warmaushärtung auf die Korrosionseigenschaften der Mg‐Knetlegierung Mg‐Al 7 untersucht. Die Korrosionsversuche wurden mit der Eudiometerprobe angestellt, geprüft wurde mit 0,6 %iger wäßriger NaCl‐Lösung.
Schmierung und Oberflächenbehandlung mit reinstem Molybdändisulfid
Authors: Weiss F.
Published: December 2004

Reinheits‐ und Zerteilungsgrad als wesentliche Kriterien der Wirksamkeit bei extremen Beanspruchungen—Schmierwirkung bedingt durch den lamellaren Aufbau der gitterförmigen kristalle — Hohe chemische und thermische Stabilität — Herstellung festhaftender Molybdänsulfid‐Überzüge durch Verwendung verschiedener Träger.

Es wurden Beispiele aus der Praxis über die Anwendung der MOLYKOTE‐Produkte gegeben und dabei die Art der Aufbringung des Schmierfilms auf die verschiedensten Bauelemente beschrieben. — Je intensiver solche Schmierfilme aufgebracht werden können, desto wirksamer sind sie. — In vielen Fällen hat ein Einarbeiten von MOLYKOTE‐Pulver in die Werkstoffe, z. B. Sintermetalle, Kunststoffe usw. eine Herabsetzung des Reibungskoeffizienten und Verminderung des Verschleißes herbeigeführt. — Die eigentlichen Einsatzgebiete dieser neuen Schmierstoffe liegen vor allen auf dem Gebiete der Grenz‐ bzw. Teilschmierung dort, wo unter extremen Druck‐ und Temperaturbedingungen die üblichen Schmiermittel auf Öl‐ und Fettbasis naturbedingt nicht voll befriedigen können.
Über die Oxydations‐ und Korrosionsbeständigkeit von Zirkonium
Authors: Köhler Walther
Published: December 2004

Zirkonium, das als Oxydationsmittel, Legierungselement und Röhrenbaustoff zunehmende Verwendung findet, zeichnet sich, ähnlich wie Titan, durch hohe Oxydations‐ und Korrosionsbeständigkeit aus. Die Arbeit gibt an Hand des neueren amerikanischen Schrifttums einen zeitgemäßen Überblick über die wichtigsten physikalischen Eigenschaften von Zirkonium, insbesondere über den Einfluß von Verformung und Glühbehandlung im Verlaufe der Halbzeugfertigung sowie über die thermische und chemische Beständigkeit des Zirkoniums gegen etwa 45 verschiedene angreifende Mittel.