bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hamiltonian dynamics of chemical reactions. Consecutive first‐order reactions and reactions possessing one autocatalytic intermediate
Authors: Georgian T. , Halpin J. M. , Findley G. L. 
Published: January 2005

AbstractA recently proposed Hamiltonian approach to phenomenological chemical kinetics [T. Georgian and G.L. Findley, Int. J. Quantum Chem., Quantum Biol. Symp. 10, 331 (1983); T. Georgian, J.M. Halpin, and G.L. Findley, Int. J. Quantum Chem., Quantum Biol. Symp. 11, 347 (1984)] is applied to all consecutive first‐order, single‐step reactions, and to all reactions possessing one autocatalytic intermediate. The reaction Hamiltonians presented are shown to be consistent with the phenomenological rate equations and the relationship between reaction form and the form of the reaction potential is discussed. In particular, we show: (1) that the interaction between consecutive reactions manifests itself as a coupling term in the reaction potential, a term which may be eliminated via transition to “normal reaction coordinates” for the chemical system; and (2) that coupled sets of autocatalytic reactions give rise to coupling terms in the reaction Hamiltonian which are characteristic of the reaction mechanism.
Charge calculations in molecular mechanics IV: A general method for conjugated systems
Authors: Abraham Raymond J. , Smith Paul E. 
Published: January 2005

AbstractA general method for calculating pi charges based on the Hückel molecular orbital (HMO) approach is incorporated into an existing scheme for calculating partial atomic charges in saturated systems. The parametrization of the Hückel coulomb and resonance integrals is given based on (a) the CNDO pi densities and (b) the observed molecular dipole moments. The results for these two schemes are compared both with other theoretical methods and also with the observed dipole moments of a variety of conjugated and aromatic compounds. The dipole moment (DM) parametrization gives in general more consistent results and is to be preferred. The compounds studied include substituted olefins and aromatics (with substituents R, F, Cl, Br, I, OR), aldehydes, ketones, acids, esters, amides, and the heterocyclic ring systems of furan, pyrrole, pyridine, and indole.
Combinatorial models and algorithms in chemistry. Search for isomorphisms and automorphisms of molecular graphs
Authors: Stankevitch M. I. , Tratch S. S. , Zefirov N. S. 
Published: January 2005

AbstractAn algorithm for the recognition of all isomorphisms for any pair of labeled graphs as well as for generation of the graph group is described. Some results obtained with computer realization of the suggested algorithm are briefly discussed.
Conformational preferences in alkylbenzenes and aryl‐alkylamines: A comparative study using CAMSEQ, MM2 and molecular dynamics methods
Authors: Grunewald Gary L. , Creese Mary W. , Weintraub H. J. R. 
Published: January 2005

AbstractConformational preferences in a series of alkylbenzenes and protonated and neutral aryl‐alkylamines of biological interest have been examined. First, a general picture was obtained for the 25 compounds in the series by means of the CAMSEQ empirical potential software system. This provided solution as well as vacuum data. A low‐energy “folded” conformation (alkyl chain coiled toward aromatic ring) was observed in every case. The presence of an amino nitrogen atom in the alkyl chain did not significantly influence conformational preference. Secondly, a group of 14 compounds, representative of the subgroupings within the main series, was selected and the previously established (CAMSEQ) folded and extended minimum positions were further examined by means of a modified MM2 program. Energy differences between conformers were also calculated, and the presence of a stable folded form was confirmed. A feature common to many of the folded conformations is the positioning over the ring of a hydrogen atom from the terminal group of the chain. The MM2 folded/extended energy differences were in some cases smaller than those determined by CAMSEQ, with the “extended” form in many cases being about 1 or 2 kcal/mol more stable. Thirdly, three representative compounds from the series were examined by means of a molecular dynamics program which permitted the sampling of conformational space throughout the transition from extended to folded forms. This method gave energy differences between folded and extended conformations which agreed with the corresponding MM2 differences.
Calculating the electrostatic potential of molecules in solution: Method and error assessment
Authors: Gilson Michael K. , Sharp Kim A. , Honig Barry H. 
Published: January 2005

AbstractWe present a numerical method for calculating the electrostatic potential of molecules in solution, using the linearized Poisson‐Boltzmann equation. The emphasis in this work is on applications to biological macromolecules. The accuracy of the method is assessed by comparisons with analytic solutions for the case of a single charge in a dielectric sphere (Tanford‐Kirkwood theory), which serves as a model for a macromolecule. We find that the solutions are generally accurate to within 5%. Larger errors occur close to the charge and the dielectric boundary, but the maximum error found at ion‐bonding distance (3 Å) from a charge close to the boundary (1 Å deep) is only ∼15%. Several algorithmic improvements, described here, contribute to the accuracy of the method. The programs involved compose a coherent software package, called Del Phi, which goes from a Brookhaven Protein Data Bank format file to calculated electrostatic fields.
A method for calculating atomic charges in large molecules
Authors: Mullay John 
Published: January 2005

AbstractA simple electronegativity method is used to calculate atomic charges for molecules of interest to biochemistry. These include purines, pyrimidines, and amino acids. Results are compared to those obtained from other theoretical methods (ab initio and semiempirical) as well as to nuclear magnetic resonance (NMR) data. Correlation is fair with CNDO results but very good for ab initio, DelRe, and other electronegativity methods. Good correlation was also achieved with NMR data. It is shown that a correction factor may be required in some cases and that important resonance effects need to be taken into account. Because of the small amount of calculational effort involved, these results suggest that this method could be quite useful in this field.
Ab initio vibrational analysis of three rotamers of 2‐propen‐1‐imine, H2CCHHCNH, and methanimine, H2CNH
Authors: Panchenko Yurii N. , Krasnoshchiokov Sergei V. , Bock Charles W. 
Published: January 2005

AbstractThe results of complete Hartree‐Fock (HF)/6–31G geometry optimization and HF/6–31G//HF/6–31G force fields evaluations of three rotamers of the H2CCH–HCNH molecule (s‐trans–d‐trans–, s‐trans–d‐cis‐ and s‐cis–d‐trans‐2‐propen‐1‐imine) and the H2C=N–H molecule are reported. All three conformers were found to be planar with the s‐trans–d‐trans conformer lowest in energy. This was corroborated by further complete optimizations of the geometries of the s‐trans–d‐trans and s‐trans–d‐cis conformers at the HF/6–31G*(5D) level as well as single‐point MP4/6–31G*//HF/6–31G*(5D) calculations. The assignment of the vibrational frequencies of the propenimine rotamers and some isotopomers of methanimine are also reported. The majority of the experimental frequencies of propenimine in the gaseous phase are found to belong to the s‐trans–d‐trans form, but a few frequencies are attributed to the high‐energy s‐trans–d‐cis conformer.
Efficient calculation of electrically based intermolecular potentials of weakly bonded clusters
Authors: Dykstra Clifford E. 
Published: January 2005

AbstractElectrical interactions between molecules are important effects in weak and long‐range attractions. With quantum mechanical techniques now capable of yielding values of all multipole polarizabilities, hyperpolariabilities, and beyond, exhaustive treatment of electrical interaction is no longer out of the question. An efficient computational strategy is presented for the evaluation of electrical interaction energies to any desired level for small, medium, and large (ca. 100 molecules) clusters. With incorporation of repulsive, hard‐wall potentials, global surfaces may be examined. Example calculations are presented.
Basis set effects and the choice of reference geometry in ab initio calculations of vibrational spectra
Authors: Michalska D. , Schaad L. J. , C̆arsky P. , Andes Hess B. , Ewig C. S. 
Published: January 2005

AbstractTatewaki and Huzinaga's [J. Comput. Chem. 1, 205 (1980)] basis sets, constructed to minimize superposition error, were used to calculate infrared (IR) frequencies and intensities. They were found inferior to Pople bases such as 3–21G and 6–31G*. The question of whether a theoretical vibrational spectrum should be computed at experimental or theoretical bond lengths was also investigated. If the magnitude of the correlation energy increases with bond length, Hartree‐Fock bond lengths are expected to be shorter than experimental, and frequencies computed there will be higher than those computed at experimental lengths. Conversely, if this magnitude decreases with R, computed lengths should be longer than experimental and should give lower computed frequencies.
Surface model for ZnS thin films: ZnS clusters and chemisorption of ZnCl2 on ZnS surface
Authors: Lindblad Marina , Pakkanen Tapani A. 
Published: January 2005

AbstractHartree‐Fock valence calculations have been used to study small ZnxSy, (x,y = 1–13), clusters. The aim was to develop surface models for chemisorption processes on zinc sulfide. The calculations show that proper models should have closed ring systems with x = y. The description of the adsorption site is not very critical to the size of the cluster. The coordination to the nearest neighbors is more critical and must be described accurately. The electronic structure was shown to be localized and a minimal basis set treatment gives a qualitative picture of energy and electronic structure trends. Zinc chloride is calculated to chemisorb to a surface sulfur atom with an adsorption energy of 395 to 570 kJ/mol depending on the size of the surface model and on the basis set of the valence orbitals. The adsorption geometry is found bent and virtually independent on the modelling parameters. The calculations predict free rotation of the adsorbate. The study suggests that calculations even at the simplest level are sufficient to give a qualitative picture of the zinc chloride adsorption on zinc sulfide.
A fast, direct algorithm for the least‐squares fitting of two sets of atomic coordinates of macromolecular structures
Authors: Liu Zong Jie , Rapenbusch Roland Van 
Published: January 2005

AbstractBy use of rotation angle method a direct algorithm is derived, which determines the least‐squares superposition that matches two sets of atomic coordinates. The program based on this algorithm runs fast. The solution obtained by this algorithm cannot be trapped by any local minimum. Testing examples are also presented.
Shape group studies of molecular similarity and regioselectivity in chemical reactions
Authors: Arteca Gustavo A. , Jammal Victoria B. , Mezey Paul G. , Mezey Paul G. 
Published: January 2005

AbstractThe study of the qualitative and quantitative product distribution in a chemical reaction, in particular regioselectivity, is of fundamental importance. Recently, it has been shown that the regioselectivity of some Diels‐Alder cycloadditions can be explained by analyzing the interrelations between electron density contours and molecular electrostatic potentials. This problem is related to a central topic of modern theoretical chemistry and biochemistry: the analysis of molecular shape. This work deals with a rigorous, algebraic method to analyze these surfaces. The procedure is based on the computation of the shape groups (symmetry‐independent homology groups of algebraic topology) of the molecular surface, using either a fully analytical algorithm requiring no visual inspection, or a precise method for processing pictorial information if the latter is available. The method provides a concise description of the molecular contour surface, that can replace the usually intuitive, and somewhat subjective, visual characterization of density and electrostatic potential contours. The method is illustrated for the case of Diels‐Alder reactions by considering a number of monosubstituted dienes. Extensions of the analysis to dienophiles, as well as other types of reactions are also discussed.
A stable, rapidly converging conjugate gradient method for energy minimization
Authors: Watowich Stanley J. , Meyer Eric S. , Hagstrom Ray , Josephs Robert 
Published: January 2005

AbstractWe apply Shanno's conjugate gradient algorithm to the problem of minimizing the potential energy function associated with molecular mechanical calculations. Shanno's algorithm is stable with respect to roundoff errors and inexact line searches and converges rapidly to a minimum. Equally important, this algorithm can improve the rate of convergence to a minimum by a factor of 5 relative to Fletcher‐Reeves or Polak‐Ribière minimizers when used within the molecular mechanics package AMBER. Comparable improvements are found for a limited number of simulations when the Polak‐Ribière direction vector is incorporated into the Shanno algorithm.
Toward automating the process of determining polypeptide secondary structure from 1H NMR data
Authors: Brugge John A. , Buchanan Bruce G. , Jardetzky Oleg 
Published: January 2005

AbstractA computer program has been constructed to perform a qualitative analysis of nuclear magnetic resonance data on polypeptide sequences to identify α‐helical and β‐strand secondary structure segments. The criteria embodied within the program are some of those which have proven useful in studies where secondary structure was described by visual interpretation of NOESY and COSY spectra. Other rules used in these studies, however, remain implicit in the description of the analysis or are ill‐specified, so that they are not used uniformly across studies. The structure of the program presented allows the rules and assumptions of this qualitative method to be modeled explicitly and used consistently, allowing a flexible and understandable framework for investigating both proteins of interest and the method involved in the analysis. The system has been tested on data sets from twelve proteins and was in agreement with 97% of the ø‐helical regions of the proteins when compared to the reports in the literature, as well as with 95% of the residues included, and in agreement with 96% of the β‐strand regions of the proteins, as well as with 90% of the residues included in them. Over the entire primary sequence, the system was in agreement with the placement of 83% of the residues in the major secondary structures.
Analytic solutions to sets of first‐order rate equations with up to six rate constants using a symbolic computer language SMP and application to biochemical kinetics
Authors: Kreye W. C. , Batra Prem , Skinner Gordon 
Published: January 2005

AbstractA symbolic computer language SMP* is employed to analytically solve sets of first‐order linear differential equations which occur in kinetic rate‐reaction studies. The solutions studied are fully analytic functions of time and the rate constants. Two typical systems are studied: the first contains four species and four rate constants, corresponding to four parallel and consecutive first‐order reactions; and the second contains four species and six rate constants, including two additional reverse reactions. These analytic functions allow insight into the mechanism, analytic expressions for the rate constants, and more rapid and precise solutions for the species concentrations than a completely numerical solution of the differential rate equations themselves. The results of the first system are applied to a recent experimental study of enzyme kinetics in which constituent amino acid residues of an enzyme are photooxidized and the corresponding catalytic activity measured with time. A second application of the SMP gives rise to a rapid semianalytic method for obtaining the values of the four and six exponentially nonlinear rate constants from the experimental data.
A molecular mechanics study of the SiO bond and alkyl‐silanes
Authors: Abraham Raymond J. , Grant G. H. 
Published: January 2005

AbstractThe standard MM2 force field and program have been modified to include SiO groups, the force constants being derived from ab initio wavefunctions, and using partial atomic charges calculated from the empirical algorithm CHARGE2. Molecular mechanics calculations have been carried out on disiloxane, dimethoxy‐dimethylsilane, methyl silyl ether, and cyclotrisiloxane, and reasonable agreement has been obtained between the observed and calculated geometries. In addition, the energies obtained using the modified force field have been tested against experimental data on alkyl silanes where energetic and structural information is available. Again good agreement is obtained. The application of the force field to extended SiO systems will also be discussed.
Applications of the model potential method to transition metal compounds
Authors: Miyoshi Eisaku , Sakai Yoshiko 
Published: January 2005

AbstractModel potential parameters and basis sets, presented previously for the transition metal atoms Sc through Hg, are tested in calculations of the transition metal compounds (CuF, CuCl, Cu2, TiCl4, ZrCl4, CoF63−, CoF62−, AgH, AuH, CrF6, ScO, ZrO, Cr2, Mo2). Calculated values of the bond distances, vibrational frequencies, and some transition energies (for Cu2 and CoF62−) are compared with those given by all‐electron calculations with basis sets of high quality. Singlet‐triplet splittings in Cu2 and correlation energies in CrF6n− (n = 0, 1, and 2) are also examined. The satisfactory results obtained by these calculations strongly support the contention that the model potential method is a reliable and economical alternative to the ab initio Hartree‐Fock‐Roothaan method.
Validity of the Hammond postulate and constraints on general one‐dimensional reaction barriers
Authors: Arteca Gustavo A. , Mezey Paul G. 
Published: January 2005

AbstractThe Hammond postulate is a useful, qualitative tool that interrelates structural similarities between reactants, transition structures, and products with the exo‐ or endothermicity of reactions. It applies to most chemical reactions, although several exceptions are known. In this study the following problem is addressed: is it possible to formulate conditions for the validity of the quantitative Hammond postulate in terms of simple physical quantities characteristic to the molecules involved? A detailed analysis is given for the conditions of validity of the postulate, in terms of bounds on the internal forces and force constants of nuclear arrangements encountered along a reaction path. We have determined a broad class of constraints on barrier shapes that must be satisfied in order to obtain a critical situation that violates the Hammond postulate: a reactant‐like transition structure (“transition state”) for endothermic reactions, and a product‐like one for exothermic reactions. The general constraints are formulated in terms of physically meaningful quantities: (i) energy differences, (ii) restrictions on slopes (e.g., an upper bound on internal forces), and (iii) restrictions on curvatures (e.g., upper bounds on force constants) along potential curves.
A simple method for calculating reliable atomic charges in large molecules
Authors: Mullay John 
Published: January 2005

AbstractModifications are made to a previously developed scheme for calculating atomic charge which uses orbital electronegativity and which requires minimal calculational effort. The introduced changes are a result of deficiencies noted in the earlier method which were due to an inadequate accounting of effects from neighboring atom charges. Results obtained using the modified scheme for both model compounds as well as larger molecules of interest to biochemistry are compared to previous results and also to several levels of ab initio calculations. It is shown that a definite improvement is obtained and that the present method gives very good correlations with each calculational level. Comparisons are also made with other methods that use electronegativity theory. It is shown that the present scheme represents a definite improvement over alternate orbital electronegativity methods and is roughly comparable to a higher level scheme that utilizes atomic electronegativity values. A discussion comparing the latter method with the present one is included. Because of the small amount of calculational effort involved, the results indicate that the present method could be quite useful in providing reliable atomic charges for large molecular systems.
Hydration of Fe+: A Monte Carlo simulation of water clusters and of a dilute aqueous solution
Authors: González‐Lafont A. , Lluch J. M. , Oliva A. , Bertrán J. 
Published: January 2005

AbstractMonte Carlo statistical thermodynamic computer simulations are reported for several clusters Fe+ (H2O)n at different temperatures and for a dilute aqueous solution of Fe+ at 298 K. The energy of each configuration has been calculated in the pairwise additivity approximation using the MCY potential for the water–water interaction and an ab initio analytical potential built by us for the Fe+–H2O interaction. Energy and structural analysis of the generated configurations lead to the prediction of a coordination number of six for the first hydration shell of the Fe+ ion, both in clusters and in dilute solution. Finally, the variation in the distance to the Fe+ ion of the energy and orientation of water molecules in the solution are discussed.
The MT‐MSXα(R) method: Applications to Li2, F2, and N2 molecules
Authors: Kao S. C. , Tseng T. J. 
Published: January 2005

AbstractThe multiple scattering Xα(R) method with the scaling parameter α expressed as a function of the internuclear distance is applied to the Li2, N2, and F2 molecules. Compared with the results obtained by the Xα method, the calculated Xα(R) equilibrium distances are smaller, the total energies are lower, and the dissociation energies are larger.
Note on the role of vibrational modes in molecular electronic transitions
Authors: Gordon R. L. 
Published: January 2005

AbstractA simple application of a readily available quantum chemistry program (AMPAC) permits an illuminating presentation of the role of vibrational modes in electronic transitions. A direct comparison of modal surfaces for different electronic states of the same molecule can be made by using a perspective plot of the Duschinsky matrix for the transition with mode indices or eigenvalue sequence, as the planar axes. The sum of squares of the off‐diagonal elements of the Duschinsky matrix can be used to give a measure of the difference between vibrational modes of the initial and final states. Calculations indicate that, in biacetyl, the triplet state is closer vibrationally to the anion ground state than either the singlet or the neutral ground state, while in glyoxal the ground state neutral has greater vibrational similarity to the anion ground state. The measure also indicates little change in vibrational modes upon intersystem crossing in formaldehyde.
Computer generation of edge groups and edge colorings of graphs
Authors: Liu Xiaoyu , Balasubramanian K. 
Published: January 2005

AbstractA computer code and nonnumerical algorithm are developed to construct the edge group of a graph and to enumerate the edge colorings of graphs of chemical interest. The edge colorings of graphs have many applications in nuclear magnetic resonance (NMR), multiple quantum NMR, enumeration of structural isomers of unsaturated organic compounds, and in the construction of configurational integral expansion series in statistical mechanics. The code developed is applied to many NMR graphs, complete graphs containing up to 10 vertices, and the Petersen graph.