bluuebunny/crossref_metadata_2025 huggingface dataset:
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

Tatewaki 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

Hartree‐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

By 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

The 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

We 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

A 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

A 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.
Simulation of wave‐propagation in three dimensions using fortran on the CYBER 205
Authors: Lugosi Erzsebet , Winfree Arthur T.
Published: January 2005

The description of a FORTRAN program made on CYBER 205 is presented for solving reaction‐diffusion equations.
A molecular mechanics study of the SiO bond and alkyl‐silanes
Authors: Abraham Raymond J. , Grant G. H.
Published: January 2005

The 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

Model 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

The 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

Modifications 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

Monte 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

The 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

A 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

A 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.
Stationary points on the potential energy surface of O2−HF and O2−H2O
Authors: Lopez Jesus P.
Published: January 2005

The determination of minima and saddle points on the potential energy surfaces of the hydrogen bonded species O2−HF and O2−H2O is performed with unrestricted Hartree‐Fock calculations. Geometries, electron density distributions, and relative energies for every stationary point are reported. Only one true minimum is found for O2−HF and for O2−H2O, and this approximately corresponds to a structure where the partially positive hydrogen atom is located along one of the superoxide ion electron lone‐pair directions. Calculated ΔH, ΔS, and ΔG values for the reaction between O2− and H2O are in good agreement with experimental data.
Improvements on the direct SCF method
Authors: Häser Marco , Ahlrichs Reinhart
Published: January 2005

Three improvements on the direct self‐consistent field method are proposed and tested which together increase CPU‐efficiency by about 50%: (i) selective storage of costly integral batches; (ii) improved integral bond for prescreening; (iii) decomposition of the current density matrix into a linear combination of previous density matrices—for which the two‐electron contributions to the Fock matrix are available—and a remainder ΔD, which is minimized; construction of the current Fock matrix only requires processing of the small ΔD which enhances prescreening.
The density integration approach to populations. A critical comparison of projection populations to populations defined by the theory of atoms in molecules
Authors: Glaser Rainer
Published: January 2005

The theory of atoms in molecules defines an unambiguous partitioning of the three‐dimensional electron density into atomic basins based on the zero‐flux surfaces of the gradient of the electron density, ∇(r). Integrations of the electron density within such basins yield integrated Bader populations (IBP) that have a rigorous foundation in quantum mechanics. In the density integration technique based on the two‐dimensional electron density projection function, P(x,z), integrated projection populations (IPP) are obtained by integration within regions demarked by steepest descent lines Dp of P(x,z). These density integration techniques are compared by an analysis of the electron density of diatomic molecules that is based on the properties of the zero‐flux surface that partitions the electron density between the atoms. The conventional method for the partitioning of regions of P(x,z) approximates the virial partitioning. Differences between IPP and IBP can be quantitatively described by two terms. One term reflects the error intrinsic to projection populations as a result of the loss of all information about the electron distribution in the third dimension in the calculation of P(x,z). The second term accounts for the effects of the displacement of the demarcation lines Dp toward the less polarizable atom compared with the cross‐section of the density with the plane of projection, Dd. The analysis suggests the definition of a projection population IPP2 that is based on the cross‐section Dd instead of the demarcation lines Dp. Relations between the populations IPP, IPP2, and IBP are derived for diatomic molecules and numerical results are presented for a series of diatomic molecules. Several polyatomic anions are also discussed. The values of IPP are found to be good approximations of IBP in highly polar diatomic molecules. In cases where the bonding involves comparatively little intramolecular charge transfer IPP2 is the better and equally satisfactory projection population. In the intermediate semipolar bonding situations projection populations provide qualitatively correct descriptions of the charge distributions but the numerical agreement with the IBP values is less satisfactory.
The calculation of molar polarizabilities by the CNDO/2 method: Correlation with the hydrophobic parameter, log P
Authors: Lewis David F. V.
Published: January 2005

Results of molecular orbital (MO) calculations by the complete neglect of differential overlap (CNDO/2) method on 50 small molecules are reported. The summation of calculated atomic polarizabilities are equated with molecular polarizabilities, and these are compared with experimentally determined values. It is found that there is very good agreement between calculated and experimental molecular polarizability. This provides a reliable method for the determination of molecular polarizabilities for compounds for which experimental values are not known. The relationship between log P and polarizability is discussed and analyzed in terms of contributions from electronic components to the partitioning energy.
AM1 studies on the potential energy surface for the proton transfer in protonated water clusters, H+(H2O)n
Authors: Choi Jae Young , Davidson Ernest R. , Lee Ikchoon
Published: January 2005

The potential energy surfaces for the proton transfer processes in H+(H2O)n with n=2 ∼ 11 have been studied using the semiempirical AM1 method. Two model systems were adopted: branched and linear systems. The branched system showed a tendency to form a bulk cluster, while the linear system showed a tendency toward a constant barrier height with increasing number of water molecules in the model system. The potential energy surfaces were discussed using Marcus theory. In the case of H+ (H2O)n with n=10 and 11, the intrinsic barrier to the proton transfer was found to be around 1.0 kcal/mol.
Guanidinium‐Type resonance stabilization and its biological implications. 2. The doubly‐extended‐guanidine series
Authors: Jordan Meredith J. , Gready Jill E.
Published: January 2005

π‐Electron delocalization in neutral and protonated “doubly‐extended‐guanidine,” (H2N)2CNCHN—CHNH, has been studied by ab initio methods at the self‐consistent field (SCF) STO‐3G and 3‐21G levels for a large number of tautomeric, rotameric, pseudocyclic, and monocyclic (disubstituted triazine) forms. These π systems have been characterized in terms of a number of structural and energetic parameters: degree of single/bond character from bond lengths and π bond orders, electron distributions, and tautomer, rotamer, and protonation energies. The acyclic neutral forms exhibit largely alternant single–double bond patterns as predicted by classical bonding structures but with, however, significant deviations due to conjugation. The acyclic protonated forms exhibit bond patterns consistent with resonance delocalized structures extending over the whole molecule (“doubly‐extended guanidinium”) or part of the molecule (“extended‐guanidinium”) or guanidinium . All systems showed alternant charge distributions with electron‐deficient carbons. The energy results have been analyzed in terms of possible contributions from steric interactions, lone‐pair repulsions, purportive electrostatic interactions in pseudocyclic forms, overall π‐system conformation (extended, kinked, or folded), and specific through‐space π‐overlap interactions in some pseudocyclic forms. It was found that these other interactions usually dominate the specifically π effects so that the general concept of preferential π delocalization in straight lines does not hold for the acyclic systems. Some interesting examples of pseudocyclic forms exhibiting strongly stabilizing intramolecular interactions attributed to π through‐space coupling are identified. These systems with incipient‐ring characteristics present intermediate bonding models between the acyclic and closed‐ring π systems. The extent of stabilization of the guanidinium‐type cations by resonance delocalization in cyclic systems depended on whether it reinforced or interfered with the overall ring delocalization.
Probing the anomeric effect. The diaminomethylene group: Calculations of NCN‐containing molecular systems1
Authors: Aped Pinchas , Schleifer Leah , Fuchs Benzion , Wolfe Saul
Published: January 2005

A study of systems containing the title moiety is described, with special reference to the anomeric effect. We have calculated ab initio, using Gaussian‐80 with the 3‐21G basis set, all basic conformations of methylene‐diamine (H2NCH2NH2) and its N‐methyl derivative with full geometry optimization of energy minima and barriers. The structural data thus obtained, were then employed to parameterize Allinger's MM2‐80 force field in a procedure similar to that described for oxygen derivatives, including hydrogen‐bonding effects and CN bond shortening in tertiary amines. This modification, termed MM2‐AE was then used to calculate larger molecules, including N,N′‐di‐ and N,N,N′,N′‐tetramethyl‐methylenediamine, various 1,3‐diazane systems, and 1,4,5,8‐tetraazadecalin derivatives of established (x‐ray) structures. The results are discussed in light of their verificative and predictive power and appear to validate MM2‐AE as a useful computational procedure.
Multiple solutions of unrestricted Hartree‐Fock equations: The SNH+ radical as an example
Authors: Redondo P. , Flores J. R. , Largo‐Cabrerizo J.
Published: January 2005

A case of appearance of multiple unrestricted Hartree‐Fock (UHF) solutions in the SNH+ (2A') radical is reported. This kind of solution does not arise from different electron configurations or symmetry breaking effects and seem to be exclusive of the UHF method. Three solutions are found and studied on the basis of wave function stability tests and several conclusions about their origin are given.
Solving the finite difference linearized Poisson‐Boltzmann equation: A comparison of relaxation and conjugate gradient methods
Authors: Davis M. E. , McCammon J. A.
Published: January 2005

Comparisons have been made between relaxation methods and certain preconditioned conjugate gradient techniques for solving the system of linear equations arising from the finite‐difference form of the linearized Poisson‐Boltzmann equation. The incomplete Cholesky conjugate gradient (ICCG) method of Meijerink and van der Vorst has been found to be superior to relaxation methods, with at least a factor of two improvement in speed, and only a 50% increase in storage.
The rate of convergence of the S matrix for the renormalized Numerov and log‐derivative methods
Authors: Braga J. P.
Published: January 2005

The convergence of the S matrix for the renormalized Numerov method, the original log‐derivative method, and one recent version of this method is studied. A single‐ and a two‐channel problem are analyzed and the percent relative errors for the S matrix and transition probabilities are calculated.
Theoretical study of the proton affinities of 2‐, 3‐, and 4‐monosubstituted pyridines in the gas phase by means of MINDO/3, MNDO, and AM1
Authors: Voets R. , François J.‐P. , Martin J. M. L. , Mullens J. , Yperman J. , Van Poucke L. C.
Published: January 2005

Proton affinities (PAs) of 2‐, 3‐, and 4‐monosubstituted pyridines in the gas phase are calculated using the MINDO/3, MNDO, and AM1 methods. The following substituents are considered: F, Cl, CN, CH3, CF3, CHO, NO2, NH2, N(CH3)2, OCH3, and SCH3. The results are compared with experimental values. It is found that all MINDO/3 PAs are ca. 6% too high (mean value) compared to the experimental results; on the other hand, the MNDO values are ca. 7% too low (mean value). However, a much better agreement has been observed for the AM1 method where the theoretical values are only ca. 2.4% too low (mean value). Correlations between the calculated proton affinities on one hand and the charges on the acid H atom and Hammett constants on the other hand are studied. Particularly good linear relationships are found for the 4‐monosubstituted compounds within the AM1 formalism.
Nitrogen inversion barriers in three‐membered rings. An ab initio molecular orbital study
Authors: Alcamí M. , De Paz J. L. G. , Yáñez M.
Published: January 2005

Polarization and correlation effects on the nitrogen inversion barrier of some three‐membered rings have been investigated. The characteristics of the barrier have been analyzed in terms of perturbation theory arguments. This analysis shows that the HOMO is the orbital that changes more dramatically along the inversion barrier. As a consequence, there is a good linear correlation between the destabilization undergone by the HOMO along the pyramidalization process and the barrier height. To obtain quantitatively meaningful barriers it is necessary to use polarized basis sets. Although polarization effects at the inverting center are dominant, a proper polarization of the remaining atoms of the ring seems also necessary. In general, with the only exception of 1H‐diazirine, correlation effects on the barrier height are small if a polarized basis set is used.
Monte Carlo simulations for the study of hemoglobin‐fragment conformations
Authors: Chen R. S.
Published: January 2005

Monte Carlo simulations have been performed to study the conformations of the pentapeptide fragments of normal adult (Thr‐Pro‐Glu‐Glu‐Lys) and sickle‐like anemia hemoglobin (Thr‐Pro‐Val‐Glu‐Lys). The results show that the energy optimized conformation of normal adult hemoglobin‐fragment agrees with the X‐ray experiment and the theoretically determined conformation of the sickle‐like anemia hemoglobin‐fragment is identical with the conformation of the normal adult hemoglobin‐fragment.
Calculation of number and free energy of the conformers of linear alkanes with medium and long chains. Implications for catalysis
Authors: Fǎrcaşiu Dan , Walter Patrick , Sheils Kelly
Published: January 2005

A method for calculating the number of rotamers of a linear alkane and of the number of rotamers with a given number of gauche conformations along the chain as a function of the total number of atoms in the chain, using general equations, is presented. A graphical method for generating individual rotamers was applied to the homologs up to decane, which has 1134 rotamers. The steric energies calculated by molecular mechanics (MM2 force field) were used as measures of the heat of formation for the coiled conformations relative to the anti conformer for each molecule, whereas the statistical entropy differences were calculated for classes of coiled rotamers grouped by the number of gauche bonds and steric energy. The free energy values calculated from these components show that already at 400 K hexane exists preferentially in conformations containing gauche bonds. For larger chains the free energy advantage for the coiled chains increases very steeply. The implications for the question of reactions of linear alkanes occurring on the surface or inside the channels of small‐ and medium‐pore zeolites are briefly examined.
A method for fitting a smooth ribbon to curved DNA
Authors: Darden Tom
Published: January 2005

A method for fitting a smooth ribbon representation of DNA structures is proposed. Following a review of the relevant definitions for classical linear helical DNA and generalizations to curving helices, a parameterization of smooth ribbons is given, which leads to tractable expressions. In addition it suggests a new way to define twist, tilt, and roll for a base step that is free of the ambiguities caused by noncommutativity of finite rotations. A least squares fitting criterion for ribbons is then proposed. In some cases the optimal ribbon with respect to this criterion is not unique. This problem is analyzed, and the circumstances in which it can occur are specified. To resolve the nonuniqueness problem, a variational description of the optimal ribbon is proposed, namely the ribbon of lowest elastic energy achieving a specified level of fit with respect to the least squares criterion. The appropriate level of fit is decided using distances of backbone atoms from fitted ribbon axes. Theoretical tests of the fitting methodology are presented, and as a sample application a smooth ribbon is fit to an existing experimental structure.
An ab initio distributed multipole study of the electrostatic potential around an undecapeptide cyclosporin derivative and a comparison with point charge electrostatic models
Authors: Price S. L. , Harrison R. J. , Guest M. F.
Published: January 2005

An SCF calculation has been performed on C63H113N11O12, a derivative of the immuno‐suppressive drug cyclosporin, using a 3‐21G basis set and a Direct SCF method. A distributed multipole analysis has been performed on the resulting charge density to give a set of multipoles at each atomic site, which are used to calculate the electrostatic potential around the molecule. The potential maxima and minima on the accessible surface of the molecule are compared with those predicted using the corresponding Mulliken charges, and also using a potential‐derived point‐charge model based on the force‐field of Kollman et al. The Mulliken charges give a misleading picture of the electrostatic potential around this peptide. The potential‐derived charges give results which are in far better agreement with the ab initio distributed multipole model, despite being derived from calculations on smaller molecules with different basis sets and geometries. The limitations of point‐charge models for describing the electrostatic interactions of polypeptides are discussed.
A molecular mechanics (MM2) study of Furan, Thiophene, and related compounds
Authors: Tai Julia C. , Lii Jenn‐Huei , Allinger Norman L.
Published: January 2005

The molecular mechanics calculations reported earlier for nitrogen heterocycles have now been extended to include the title compounds, and related molecules. It is in general possible to calculate these structures with an accuracy that compares favorably with experiment.
Voronoi binding site models: Calculation of binding modes and influence of drug binding data accuracy
Authors: Boulu Laurent G. , Crippen Gordon M.
Published: January 2005

A new and accurate method for calculating the geometrically allowed modes of binding of a ligand molecule to a Voronoi site model is reported. It is shown that the feasibility of the binding of a group of atoms to a Voronoi site reduces to a simple set of linear and quadratic inequalities and quadratic equalities which can be solved by minimization of a simple function. Newton's numerical method of solution coupled to a line search proved to be successful. Moreover, we have developed efficient molecular and site data bases to discard quickly infeasible binding modes without time‐consuming numerical calculation. The method is tested with a data set consisting of the binding constants for a series of biphenyls binding to prealbumin. After determination of the conformation space of the molecules and proposal of a Voronoi site geometry, the geometrically feasible modes are calculated and the energy interaction parameters determined to fit the observed binding energies to the site within experimental error ranges. We actually allowed these ranges to vary in order to study the influence of their broadness on the site geometry and found that as they increase, one can first model the receptor as a three‐region site then as a single region site, but never as a two‐region site.
Computational algorithms for matching polynomials of graphs from the characteristic polynomials of edge‐weighted graphs
Authors: Hosoya Haruo , Balasubramanian K.
Published: January 2005

Computational algorithms are described which provide for constructing the set of associated edge‐weighted directed graphs such that the average of the characteristic polynomials of the edge‐weighted graphs gives the matching polynomial of the parent graph. The weights were chosen to be unities or purely imaginary numbers so that the adjacency matrix is hermitian. The computer code developed earlier by one of the authors (K.B.) is generalized for complex hermitian matrices. Applications to bridged and spirographs, some lattices and all polycyclic graphs containing up to four cycles are considered.
Electrostatic interactions in host‐guest complexes 2
Authors: Bruning H. , Feil D.
Published: January 2005

In this article the quantum chemically calculated charge density distribution of 18‐crown‐6 and the K+ …18‐crown‐6 complex are compared with the charge density distribution of smaller molecules and corresponding complexes which can be considered as fragments of the 18‐crown‐6 molecule. An analysis of the charge density distribution in terms of atomic charge distribution according to the stockholder recipe gives accurate rules for the transferability of the charge density distribution. This gives us the possibility to construct the charge density distribution of large molecules out of accurate large basis set results on small molecules.
Interaction of Lysine‐Alanine‐Alanine tripeptide with a fragment of DNA: An empirical potential study
Authors: Hobza Pavel , Nachtigallová Dana , Havlas Zdeněk , Maloň Petr , Šponar Jaroslav
Published: January 2005

Interaction of a rigid fragment of B‐DNA (polyanionic as well as screened by Na+ cations) with the flexible tripeptide Lys‐Ala‐Ala (in both L and D configurations) were investigated with the aid of an empirical potential. The potential consists of intramolecular (MM2 potential) and intermolecular (pair potential described in reference 1) parts; hence total energy is formed by intra‐ and intermolecular components. The results demonstrate that intramolecular relaxation of the peptide results in a considerable decrease in total energy. While energies of DNA complexes with L‐Lys‐L‐Ala‐L‐Ala were comparable to those with D‐Lys‐D‐Ala‐D‐Ala the respective geometries exhibit considerable differences.
Tautomeric equilibria of heterocyclic molecules. A test of the semiempirical AM1 and MNDO‐PM3 methods
Authors: Fabian Walter M. F.
Published: January 2005

Tautomeric equilibria (mainly of the lactam‐lactim type) for a rather large number of six‐membered heterocyclic molecules are calculated by the semiempirical AM1, MNDO‐PM3, and MNDO methods. Except for compounds with adjacent pyridine‐like lone pairs both AM1 as well as MNDO‐PM3 give rather reliable predictions for relative stabilities of the various tautomeric species–comparable to quite high level ab initio calculations. The known errors associated with MNDO in the treatment of heterocyclic tautomerism are thus largely corrected in AM1 as well as MNDO‐PM3. For 2‐hydroxypyridine‐pyrid‐2(1H)‐one the effect of self‐association is less satisfactorily described by MNDO‐PM3 than by AM1. MNDO‐PM3 calculated relative stabilities of methylated derivatives are, however, in considerably closer agreement with experimental values than those obtained by AM1. Ionization potentials, especially those for lone‐pair orbitals, are overestimated by all three semiempirical methods. MNDO‐PM3 results for nitrogen lone‐pair orbital energies are slightly better than those obtained by the AM1 or MNDO method.
A critical comparison of MINDO/3, MNDO, AM1, and PM3 for a model problem: Carbon clusters C2‐C10. An ad hoc reparametrization of MNDO well suited for the accurate prediction of their spectroscopic constants
Authors: Martin J. M. L. , François J. P. , Gijbels R.
Published: January 2005

Dissociation energies and potential energy surface features for the carbon clusters C2 to C10 are compared with ab initio or experimental results for the semiempirical methods MINDO/3, MNDO, AM1, and PM3. Quite surprisingly, MINDO/3 gives a rather good account of the various structures and electronic states, unlike the other three methods. MINDO/3 tends towards systematic overestimates of binding energies, the other methods to systematic gross underestimates. Reparametrization of the diatomic parameters α, βs, and βp for exact reproduction of the experimental data for C3 results in much improved values for binding energies, but fails to correct the state splittings. Also reparametrizing Uss, Upp, ζs, and ζp to reproduce the ab initio linear‐rhombic energy difference in C4 results in a much improved description of the other states. For the linear structures, computed harmonic frequencies with the latter parameters are in surprisingly good agreement with experimental or correlated ab initio data, where available; experimental values are consistently overestimated by about 40 cm−1. Other results are comparable in quality to good ab initio treatments. The experimental IR bands at 2128 and 1892 cm−1, formerly assigned to C9, should be reassigned to linear C7. The intense 1997 cm−1 feature almost certainly belongs to C9; bands at 1952 and 1197 cm−1 both belong to linear C6. Tentative assignments of bands in the 1600–1850 cm−1 region to various cyclic structures of C6, C8, and C10 have been made. As such, this suggests a new and promising procedure for the theoretical study of large molecules in general, and of large clusters in particular.
Evaluation of PM3, AM1, and MNDO for calculation of higher energy ionization potentials
Authors: Gano James E. , Jacob E. Jean , Roesner Rebecca
Published: January 2005

Higher ionization energies were calculated with PM3, AM1, and MNDO for three series of molecules, representative small molecules, molecules containing heteroatoms, and sterically congested alkenes. Values from PM3, AM1, and MNDO were compared to experimental values. In most instances, the semiempirical calculations correctly predict the ordering of higher ionization energies. In the absence of steric hindrance, MNDO is the method of choice. Within groups of molecules, AM1 performs better on hydrocarbons, especially twisted hydrocarbons, than PM3. PM3 commonly gives sigma orbitals which are too high in energy compared to related pi orbitals. PM3 performed better than AM1 with molecules containing oxygen, but failed to give the correct geometry for hydrogen peroxide.
Where is the blood–brain barrier … really?
Authors: Ge Shujun , Song Li , Pachter Joel S.
Published: January 2005

Few terms in the biomedical lexicon are as widely recognized as the phrase blood–brain barrier (BBB). Indeed, it immediately conjures up a “barricade” between the blood and the brain, a feature often considered more obstacle than safeguard. In truth, the BBB performs in both capacities, and it is precisely this duality that imparts such a vital role to the BBB in influencing physiological and pathophysiological processes in the CNS. Although the concept is more than a century old, the BBB continues to remain enigmatic in both substance and idea, with seemingly resolved issues once again beckoning for clarification. In this regard, recent technological advancements, such as sequencing of the human genome and development of microarray analysis, have illuminated novel aspects of vascular gene expression and provoked reconsideration of the cellular and biochemical makeup of the BBB. In light of the critical impact of the BBB in the realms of science and medicine, this Mini‐Review will revisit the topic of the composition of the BBB, specifically highlighting how recent developments in endothelial biology have prompted a reevaluation of its precise vascular location. We have intentionally avoided discussing generalized features of the BBB, as these have been skillfully described elsewhere as noted. © 2005 Wiley‐Liss, Inc.
Transport of neurofilaments in growing axons requires microtubules but not actin filaments
Authors: Francis Franto , Roy Subhojit , Brady Scott T. , Black Mark M.
Published: January 2005

Neurofilament (NF) polymers are conveyed from cell body to axon tip by slow axonal transport, and disruption of this process is implicated in several neuronal pathologies. This movement occurs in both anterograde and retrograde directions and is characterized by relatively rapid but brief movements of neurofilaments, interrupted by prolonged pauses. The present studies combine pharmacologic treatments that target actin filaments or microtubules with imaging of NF polymer transport in living axons to examine the dependence of neurofilament transport on these cytoskeletal systems. The heavy NF subunit tagged with green fluorescent protein was expressed in cultured sympathetic neurons to visualize NF transport. Depletion of axonal actin filaments by treatment with 5 μM latrunculin for 6 hr had no detectable effect on directionality or transport rate of NFs, but frequency of movement events was reduced from 1/3.1 min of imaging time to 1/4.9 min. Depolymerization of axonal microtubules using either 5 μM vinblastine for 3 hr or 5 μg/ml nocodazole for 4–6 hr profoundly suppressed neurofilament transport. In 92% of treated neurons, NF transport was undetected. These observations indicate that actin filaments are not required for neurofilament transport, although they may have subtle effects on neurofilament movements. In contrast, axonal transport of NFs requires microtubules, suggesting that anterograde and retrograde NF transport is powered by microtubule‐based motors. © 2005 Wiley‐Liss, Inc.
An evaluation of conventional wisdom of the factors underlying the digital divide: a case study of the Isle of Man
Authors: Skok Walter , Ryder George
Published: January 2005

The digital divide is defined as the gap that exists between those with and those without access to the Internet. Conventional wisdom is represented by the technology optimists' view that the divide is caused by societal barriers to Internet connectivity such as low levels of education, income and proliferation of technology. The technology pessimists disagree that these barriers cause the divide or that they are important enough to justify significant expenditure by government. This paper reports on a study to evaluate the validity of the optimistic position.

The Isle of Man (IOM) was selected for this evaluation because of its size, social stability, high levels of education and income and established e‐government programme. The premise of the research was that if the optimistic view is correct, lower or similar barriers to those found in the UK should result in higher or similar levels of Internet access in the IOM.

Prime causal factors of the digital divide, as purported by the optimists, were found to marginally favour the IOM. However, the test of Internet access revealed that the IOM trailed the UK connectivity level by some 12% to 14%, which is not as expected from the optimistic viewpoint. This unexpected outcome could constitute a dilemma for the IOM government in adopting an appropriate strategy to e‐government implementation and narrowing the digital divide.

Copyright © 2004 John Wiley & Sons, Ltd.
Strategy and financial management in the football industry
Authors: Grundy Tony
Published: January 2005

The literatures on strategy and finance have developed very separately, notwithstanding the fact that they have a common economic underpinning. Whilst a number of strategic theorists have looked at how strategic management facilitates the most effective leverage of economic resource, studies of the linkages between strategy and finance literatures are relatively few.

This appears odd because finance is pivotal in making the resource allocation decision in management, especially in major business investment and divestment decisions and in the financing strategies needed to accomplish this. Both financial management as a discipline and financing strategies also play a role in influencing stakeholder behaviour, which is critical in strategy.

Rarer still are studies of how strategy, financial management, financial strategies and stakeholders interact. With continuing examples of devastating corporates such as Enron and more recently Parmalat, it would seem surprising that theorists have been relatively disinterested in this important border between these disciplines.

This paper seeks to make a contribution to our understanding of the topic by focusing on the interesting case of the football industry. Whilst an earlier paper in this journal (Grundy, 2004) dealt with techniques for appraising strategic options to exploit product/market opportunities, financing strategy options warrant separate exploration.

Copyright © 2004 John Wiley & Sons, Ltd.
Working together: innovation and export links within highly developed and embryonic wine clusters
Authors: Aylward David
Published: January 2005

This paper examines innovation and export linkages within two distinct levels of wine cluster development. The aim of the paper, using empirical data from the Australian wine industry, is to demonstrate that the association between innovation and export activity intensifies as the cluster develops.

Copyright © 2004 John Wiley & Sons, Ltd.