bluuebunny/crossref_metadata_2025_split huggingface dataset:
The modeling of chemical phenomena using topological indices
Authors: Rouvray Dennis H. 
Published: January 2005

AbstractA class of graph invariants known today as topological indices are being increasingly realized by chemists and others to be powerful tools in the description of chemical phenomena. Topological indices generally characterize both the size and shape of chemical species; in recent years a number of such indices have been put forward that sensitively reflect the amount of branching present in molecules. Chemists are thus able to model accurately the chemical behavior of an extensive range of chemical substances in all three thermodynamic states. In discussing the manifold applications of topological indices to the description of physicochemical properties, we present a survey of the progress to date in this area and point out some of the advantages and drawbacks of using topological indices.
Bond critical points in the electronic structures of the main group diatomic hydrides of lithium through bromine
Authors: Boyd Russell J. , Edgecombe Kenneth E. 
Published: January 2005

AbstractThe bond critical points and associated electronic properties of the diatomic hydrides of the twenty‐one main group elements from lithium to bromine have been calculated with large basis sets. As part of a systematic study of the polarity of chemical bonds, the position of the bond critical point, the charge density at the bond critical point, the Laplacian of the charge density at the bond critical point, and the molecular dipole moment of each molecule have been calculated. Particular attention has been paid to the effect of bond length elongation and contraction on the electronic properties. Variation of the bond length reveals that with atoms of low electronegativity, the bond critical point of AH tends to follow atom A, whereas with atoms of high electronegativity, the bond critical point tends to follow the hydrogen atom as the bond lengthens. Furthermore, it is shown that some properties of the diatomic hydrides vary monotonically within each row of the periodic table, while others effect a classification according to the character of the bond.
Some methods and applications of electron density distribution analysis
Authors: Ritchie James P. , Bachrach Steven M. 
Published: January 2005

AbstractAccurate and efficient integration of the electron density function over arbitrary regions has been previously achieved by exploiting a separation of variables. Recently, a computer program has been written that calculates ρ, \documentclass{article}\pagestyle{empty}\begin{document}$ \buildrel{\rightharpoonup}\over{\nabla} $\end{document}ρ, and ∇2ρ in an expeditious fashion, taking advantage of the separation of variables in the electron density function. Accurate integrations of ∇2ρ over arbitrary regions can also be accomplished. The structure of the program is suited especially to vector processors. As a result of the efficiencies of these programs, functions of the electron density, such as the density itself, the surrounding electrostatic potential, ∇ρ, and ∇2ρ have been calculated in three dimensions. Results of calculations for nitrated cubanes are presented illustrating how the effects of the nitro groups are manifested in the electron density and associated properties.
Graph generators
Authors: Randić Milan , Woodworth Wayne L. , Kleiner Alexander F. , Hosoya Haruo 
Published: January 2005

AbstractWe consider the construction of highly symmetrical vertex transitive graphs. Some such graphs represent the degenerate rearrangements in which a molecule or an ion is formed by breaking and making bonds so that the final and the initial skeleton is identical. The approach is closely related to Cayley's graphs for selected groups. We restrict the choice of generators to symmetric matrices. Successive multiplications of such matrices generate other permutation matrices of the same dimension, each new matrix representing a new vertex for a transitive graph under the construction. In particular we restrict our discussion to matrices of dimension 3 and 4 and proceed to construct systematically all transitive graphs using 4 × 4 symmetric matrices as generators.
Molecular orbital theory of the properties of inorganic and organometallic compounds. 6. Extended basis sets for second‐row transition metals
Authors: Dobbs K. D. , Hehre W. J. 
Published: January 2005

AbstractA series of efficient split‐valence basis sets for second‐row transitions metals, termed 3‐21G, has been constructed based on previously formulated minimal expansions of Huzinaga, and in a manner analogous to the previous development of 3‐21G basis sets for first‐row metals. The Huzinaga three Gaussian expansions for s‐ and p‐type orbitals of given n quantum number have been fit by least squares to new three Gaussian combinations in which the two sets of functions share the same Gaussian exponents. The original three Gaussian expansions for 1s, 3d, and 4d atomic orbitals have been employed as is. The valence description comprises 4d‐ 5s‐ and 5p‐type functions, each of which has been split into two and one Gaussian parts. 5p functions, while not populated in the ground state of the free atom, are believed to be important in the description of the bonding in molecules.The performance of the 3‐21G basis sets is examined with regard to the calculation of equilibrium geometries and normal‐mode vibrational frequencies for a variety of simple inorganic and organometallic compounds incorporating second‐row transition metals.
On the out‐of‐plane deformation of aromatic rings, and its representation by molecular mechanics
Authors: Liljefors Tommy , Tai Julia C. , Li Shusen , Allinger Norman L. 
Published: January 2005

AbstractIt has been found that the previous MM2 (or MMP2) description of out‐of‐plane deformation of aromatic rings sometimes yields distortions which are much too large. As a result, rotational barriers involving distortions of such rings may be calculated to have values which are too low. Examples are collected and discussed. An alternative formulation, which appears to significantly reduce the calculational error, is presented.
Cooperative effects in extended hydrogen bonded systems involving OH groups. Ab initio studies of the cyclic S4 water tetramer
Authors: Koehler J. E. H. , Saenger W. , Lesyng B. 
Published: January 2005

AbstractThe additional energy stabilization due to cooperative effects was calculated in extended hydrogen bonded systems OH ⃛OH ⃛OH with unidirectional (homodromic) orientation of the OH groups. Ab initio restricted Hartree Fock, MP2 and MP3 calculations with geometry optimization and BSSE correction have been performed using the GAUSSIAN 83 program package for the ground states of the linear water dimer with Cs symmetry and the cyclic water tetramer with S4 symmetry. The latter represents the smallest possible, experimentally observed cooperative structure. A new definition for a cooperativity parameter is proposed. The definition is based on the two‐body, non‐neighbour interaction energy, plus three‐ and four‐body contributions, including one‐body deformation terms in relation to the total interaction energy of the water tetramer. The advantage of this definition is its independence of the reference system, which is necessary in complicated molecular systems with an undefined number of hydrogen bonds, such as disordered or flip‐flop systems. According to this definition the energy gain based on cooperativity in the S4 water tetramer is 29% with the MP3/6‐31G** approximation, (30% with HF/4‐31G* and 46% with HF/3‐21G). The largest contribution of 18% is due to the three‐body term on the MP3/6‐31G** level, followed by the two‐body, non‐neighbour term with 11%. The four‐body term and the deformation term are in the order of 1% and cancel each other because they have opposite sign.
Nonbonded interactions. 1. Anisotropic hydrogen‐hydrogen interactions
Authors: Wiberg Kenneth B. , Murcko Mark A 
Published: January 2005

AbstractThe hydrogen‐hydrogen nonbonded potential which may be derived from the calculated interactions between hydrogen molecules has been obtained. The best three‐parameter Buckingham function gave an RMS error of 0.18 kcal/mol in fitting Price and Stone's ab initio data for 130 pairs of hydrogen molecules, which may be compared with an RMS error of 0.74 kcal/mol using the parameters in the MM2 force field. Burton's basis set is also considered. A better fit to these data requires that the angular relationship between the bonds be included. The data for hydrogen as well as experimental data for chlorine show that these atoms appear “larger” normal to the bond axis than along the axis, and this is probably also the case for other atoms. When simple angular terms are added it is possible to fit the Price and Stone data set with an RMS error of less than 0.06 kcal/mol. The preferred function was: V = [a0 + a1(sin θ1 + sin θ2)4 + a2r]e−3r − [c0 + c1(1 + sinθ1sinθ2)]/r5. Deficiencies in the current ab initio data are discussed.
Calculation of enthalpies of hydrogenation of hydrocarbons
Authors: Ibrahim Mustafa R. , Fataftah Zacharia A. , von Ragué Schleyer Paul , Stout Peter D. 
Published: January 2005

AbstractSets of hydrogen molecule equivalents have been developed which permit the calculation of hydrogenation of different types of carbon‐carbon bonds from ab initio total energies (3‐21G and 6‐31G* basis sets, and, to a more limited extent, for MP2/6‐31G* data) of reactants and products. The calculated enthalpies of hydrogenation are in good agreement with experiment for unstrained molecules, with average errors on the order of 2 kcal/mol. The 6‐31G* equivalents allow the enthalpies for strained molecules to be calculated accurately, but the 3‐21G equivalents do not. The equivalents for both basis sets have been tested by calculating the enthalpies of hydrogenation of carbon‐carbon bonds in nitrogen‐ and oxygen‐containing organic molecules, free radicals, and classical carbocations. The results are in good agreement with experiment in most cases.
MNDO Calculations on [n]metacyclophanes
Authors: Jenneskens Leonardus W. , de Kanter Franciscus J.J. , de Wolf Willem H. , Bickelhaupt Friedrich 
Published: January 2005

AbstractMNDO calculations on [n]metacyclophanes and a variety of related compounds are reported. An analysis of the strain, imposed by the oligomethylene bridge, and its distribution over the distorted benzene ring and the oligomethylene bridge is presented. The effect of strain and bending of the benzene ring on aromatic delocalization is investigated by a comparison of ΔHof of the bent benzene systems with that of a correspondingly bent, but localized 1,3,5‐cyclohexatriene. The results indicate that, even in the case of the highly bent [4]metacyclophane (1a), localization is unfavorable by about 10 kcal/mol.
Acetylcholine in water: Ab‐initio potential and Monte Carlo simulation
Authors: Margheritis C. , Corongiu G. 
Published: January 2005

AbstractAb initio SCF‐LCAO‐MO computations using a minimal basis set have been carried out on the acetylcholine ion in different conformations. The rotational barrier around the C9‐C8‐O1‐C2 dihedral angle (τ1) has been also calculated: the curve presents a broad minimum. SCF calculations have been carried out on the system Ach‐water at 468 different separations and/or orientations; the interaction energies were then fitted to a pair potential function used in Monte Carlo (MC) simulations of Ach water solution. The rdfs indicate a global first hydration shell with about 38 waters. Details about the hydration shell are presented. The overall MC results indicate that for the Ach ion in water solution at room temperature relative free rotation is possible around τ1, and that Ach is well represented as a large positively charged hydrated globe with a small mobile tail free of strong interactions with the surrounding water molecules.
The computation of floating functions and their use in force constant calculations
Authors: Hurley A. C. 
Published: January 2005

AbstractIt is shown how standard computer programs for calculating the equilibrium geometry of a molecule may be adapted to yield floating functions. These functions satisfy the Hellmann–Feynman theorem and so lead to simple electrostatic interpretations of intramolecular forces and vibrations. The theory is illustrated by detailed calculations for the water molecule.
A molecular mechanics study of neutral molecule complexation with crown ethers
Authors: Damewood Jr. James R. , Anderson Wayne P. , Urban Joseph J. 
Published: January 2005

AbstractMolecular mechanics methods are applied to the study of neutral molecule complexation with crown ethers. Protocols for the development of parameters necessary to describe these molecule‐molecule interactions are presented. Application of these methods to the study of 1:1 and 2:1 (guest:host) complexation between acetonitrile (1), nitromethane (2), malononitrile (3) and dimethylsulfone (4) reveals positive cooperativity in formation of the 2:1 complexes in isolation.
Pattern recognition in the prediction of protein structure. II. Chain conformation from a probability‐directed search procedure
Authors: Lambert Millard H. , Scheraga Harold A. 
Published: January 2005

AbstractA procedure that finds the most probable conformational states of a protein chain is described. Single‐residue conformations are represented in terms of four conformational states, α, ϵ, α*, and ϵ*. The conformation of the entire chain is represented by a sequence of single‐residue conformational states; the distinct conformations in this representation are called “chain‐states.” The first article in this series described a procedure that computes tripeptide conformational probabilities from the amino acid sequence using pattern recognition techniques. The procedure described in this article uses the tripeptide probabilities to estimate the probabilities of the chain‐states. The chain‐state probability estimator is a product of conditional and marginal probabilities (obtained from the tripeptide probabilities), with a penalty factor to eliminate conformations containing α‐helices and ϵ‐strands of excessive length. The probability estimator considers short‐range conformational information, medium‐range sequence information and some simple long‐range information (through the restrictions on helix and strand lengths). Energy minimization calculations can be carried out in the region of conformational space corresponding to a particular chain‐state. By selecting the most probable chain‐states, the search can be focused on the most probable, or “important,” regions of the conformational space. These energy calculations are described in the third article of the series. The complete procedure described by the three articles is called PRISM, for pattern recognition‐based importance sampling minimization.
Polypentapeptide of elastin: Damping of internal chain dynamics on extension
Authors: Chang D. K. , Urry D. W. 
Published: January 2005

AbstractMolecular dynamics simulations out to 100 ps have been carried out at 300 K in vacuo on the repeating pentapeptide, (VPGVG), of the elastin fiber. The structure employed in the simulation is a β‐spiral (helical structure) with 2.7 pentamers per turn and with a 9.45 Å rise per turn and 21.6 Å rise per turn in the relaxed and extended states, respectively. Large amplitude backbone torsion angle fluctuations are observed in the relaxed state, and significant damping is observed upon extension, particularly in the suspended segments of the β‐spiral structure. Accordingly the entropy change an extension was computed and found to be a substantial −1.1 entropy units per residue. The various energy components are compared for relaxed and extended states and the relevance of the results to the molecular mechanism of entropic elasticity is discussed.
Calculations of a list of neighbors in Molecular Dynamics simulations
Authors: Yip Virginia , Elber Ron 
Published: January 2005

AbstractA new algorithm is proposed for the evaluation of nonbonded interactions in Molecular Dynamics simulations. The algorithm is based on a grid search and on partitioning of the atoms into boxes rather than on calculations of distances. The effort associated with the generation of the box list grows only linearly with the number of atoms. The algorithm is particularly advantageous for solvated systems. Test calculations show significant savings in CPU time and storage compared to commonly used algorithms for systems containing in excess of ca. 600 atoms.
A concept of charge and valence for ab initio wave functions
Authors: Jug Karl , Fasold Eckhard , Gopinathan M. S. 
Published: January 2005

AbstractA modified scheme of a previously developed concept of atomic valence numbers in molecules is presented. The relation to population analysis is demonstrated. The scheme is suitable for ab initio wave functions with extended basis sets. The procedure involved a combination of symmetric orthogonalization and contraction of the basis set. The method is used for a systematic investigation of a series of compounds with first‐row atoms from Li to F. The predicted atomic charges and valence numbers are in line with results from infrared spectroscopy and multipole moment analysis.
Molecular dynamics simulations of polymers: Methods for optimal Fortran programming
Authors: Noid D. W. , Sumpter B. G. , Wunderlich B. , Pfeffer G. A. 
Published: January 2005

AbstractThe structure of the general classical trajectory FORTRAN code is discussed for use in molecular dynamics simulations of polymer processes. Substantial reductions in the number of mathematical operations in the code are achieved by using statement functions, modifying the ususal chain rule derivatives, applying appropriate vector identities, and using closure relationships among the required derivatives of the potential.
Theoretical study of the proton affinities of 2‐, 3‐, and 4‐monosubstituted phenolate ions in the gas phase by means of MINDO/3, MNDO, and AM1
Authors: Voets R. , Fraņois J.‐P. , Martin J. M. L. , Mullens J. , Yperman J. , Van Poucke L. C. 
Published: January 2005

AbstractProton affinities (PAs) of 2‐, 3‐, and 4‐monosubstituted phenolates in the gas phase are calculated using the MINDO/3, MNDO, and AM1 methods. The following substituents are considered: H, F, Cl (only MNDO and AM1), CN, CH3, OH, NO2, OCH3, COOH, and NH2. The results are compared with experimental values (high‐pressure mass spectroscopy) at 600 K. The MINDO/3 method overestimates the experimental PAs with a mean percentual error of ca. 4.3%. The MNDO results agree much better with the experimental values and are only ca. 1.3% too high. However, the best agreement is observed for the AM1 method, where the mean percentual error is only ca. 0.69% (in absolute value). The greatest disagreement is found for 2‐hydroxyphenolate (ca. +2.0%) and 2‐carboxyphenolate (ca. +2.7%). The PA of 2‐nitrophenolate is underestimated by ca. 1.6%. Correlations between the calculated proton affinities on the one hand, charge densities on the acid H atom of the phenols, charges on the O atom in the phenolate ions, and substituent parameters on the other hand are studied. Particularly good linear relationships are found for the 3‐ and 4‐monosubstituted compounds within the AM1 formlism. For the 2‐substituted phenolates, only the AM1 method is satifactory. As a general conclusion, the AM1 method appears to be distinctly superior to MNDO for the calculation of PAs, and definitely superior to MINDO/3.
Theoretical study of adsorption of hydrocarbons on graphite
Authors: Sordo T. L. , Sordo J. A. , Flórez R. 
Published: January 2005

AbstractThe adsorption of methane, ethane, propane, n‐butane, ethylene, propene, 1‐butene, 1,3‐butadiene, acetylene, benzene, toluene, naphthalene, anthracene, and pyrene on the basal plane of graphite has been studied by means of a semiempirical method proposed by Fraga based on a 1/R expansion of atom‐atom pair potentials. The energies of interaction obtained agree reasonably well with experimental data and statistical calculations. The orientation of the adsorbed molecules relative to the graphite surface rendered by Fraga's method improves the picture provided by other calculations with empirical potentials. These results display Fraga's method as an economical alternative for the study of physisorption of hydrocarbons on the graphite surface.
First and second derivative matrix elements for linear and out‐of‐plane bending motion
Authors: Miller Kenneth J. 
Published: January 2005

AbstractSimplified formulas for first and second derivatives of the internal coordinates with respect to Cartesian coordinates are reported for linear and out‐of‐plane bending motion. They are expressed in a local coordinate system and then rotated to a space‐fixed Cartesian coordinate system. For linear motion the important points are: (1) the invariance of the energy with respect to translational and rotational coordinate transformations and (2) the presentation of derivatives of the energy in terms of (α − π)2 rather than (α − π), where α is the bond angle, to avoid indeterminant forms. By factoring the second derivatives of the energy with respect to (α − π) and sinα, analysis in this local coordinate system avoids division by sinα as α → π. The formulas describe linear systems without the need to project the motion onto two perpendicular planes. When the angle is exactly π two degenerate directions arise, and the coordinate axes perpendicular to the axis of the linear sequence of atoms may be chosen arbitrarily. Further refinements and clarifications of methods reported previously to obtain matrix elements for linear and out‐of‐plane motion are presented.
Force field calculation of equilibrium thermodynamic properties: Diels–Alder reaction of 1,3‐butadiene and ethylene and Diels–Alder dimerization of 1,3‐butadiene
Authors: Lenz Terry G. , Vaughan John D. 
Published: January 2005

AbstractΔH0, ΔS0, and Kp have been calculated by force field methods for two prototype Diels–Alder reactions, the condensation of 1,3‐butadiene and ethylene, and the dimerization of 1,3‐butadiene. Three force field programs were employed, Allinger's MMP2, Warshel and Karplus' CFF/PI, and Boyd's MOLBD3 (with Anet and Yavari diene parameters). MMP2 and CFF/PI were combined to calculate reactant and product ΔH (by MMP2) and thermodynamic functions S0, C, and (H − H) by use of CFF/PI molecular geometry and vibrational frequencies. MOLBD3 was used separately to calculate these properties. The combined MMP2, CFF/PI calculations exhibited excellent agreement with available experimental equilibrium data for both reactions, despite uncertainties in the number and energies of adduct conformers in the dimerization reaction. The MOLBD3 results were less satisfying, particularly for the dimerization reaction, because the entropy of 1,3‐butadiene was overestimated by 2.5 cal mol−1 K−1.
Calculating electrostatic forces from grid‐calculated potentials
Authors: Davis M. E. , McCammon J. A. 
Published: January 2005

AbstractThe accurate calculation of forces from finite difference potentials is very important, especially in the area of Brownian dynamics simulations. Test charge methods are typically used to calculate these forces. In these methods, the potential is calculated with one group of charges present, then the force on a second set of charges is calculated as the negative of the gradient of the potential times the charge. The test charge methods for calculating forces between solute molecules have been compared with more accurate methods and then regions of validity of the test charge methods explored. The test charge methods neglect certain reaction field effects. It is found for the simple charged systems studied that beyond a center‐to‐center separation of about twice the sum of the molecular radii the test charge approximations can be quite good. For polar molecules with no net charges, however, the corrections can be significant to even longer ranges.