bluuebunny/crossref_metadata_2025_split huggingface dataset:
Theoretical study of water‐pyridine complexes using intermolecular potentials
Authors: Genest Monique 
Published: January 2005

AbstractIntermolecular potential functions have been used to determine the equilibrium structures of the water‐pyridine complexes. The dimer and symmetrical 2:1 water pyridine systems have been studied. Three water models, ST2, TIPS2, and EMPWI have been combined with two different Lennard Jones nonbonded parameters and various charge distributions for the pyridine molecule to describe the systems. For the dimer, results show two distinguishable classes of preferential hydration sites, which are specific sites corresponding to hydrogen‐bonded dimer and nonspecific sites located near the hydrophobic regions. Calculations performed on hydrogen‐bonded symmetrical complexes show that the planar complex is generally less stable than the complex with water molecules perpendicular to the pyridine plane. For these complexes, the major factor that influences the hydrogen‐bonded configurations is the choice of the water model. The importance of atomic charge distributions for the solute over the choice of potential parameters is pointed out. Finally, the effective lone pair representation on the aromatic nitrogen atom is shown to improve the hydrogen bond geometry and the stability of the complexes.
Polarization counterpoise corrections to correlated hydrogen bond interaction energies
Authors: Loushin Sharilyn K. , Dykstra Clifford E. 
Published: January 2005

AbstractBasis set superposition error in hydrogen‐bonded systems can exaggerate attraction calculated from self‐consistent field energies as well as from electron correlation energies. One cause of this error is the basis set deficiency in describing the charge polarization of one constituent molecule when its bonding partner approaches. That constituent molecule's description is improved partly because of the proximity of the partner's basis functions, independent of real attraction. That polarization‐related error is shown to occur primarily at the SCF level and not at correlated levels.
Ab initio calculations on the effect of polarization functions on disiloxane
Authors: Grigoras Stelian , Lane Thomas H. 
Published: January 2005

AbstractThe effect of polarization functions for ab initio molecular orbital calculations at the 3‐21G* level has been studied for disiloxane. Calculated molecular geometry, dipole moment, and the linearization barrier variation were analyzed for different uncontracted polarization functions. It was concluded that variation of the polarization function on oxygen has only a minor influence on the molecular properties of disiloxane, but its presence is required to obtain a bent geometry for the disiloxane bond. The calculated molecular properties of disiloxane are greatly influenced when the polarization function on silicon is varied. Two different values (0.3 and 0.9) for the exponent of the silicon polarization function provide results comparable to the experimental values for disiloxane. The only significant differences between the results obtained from ab initio calculations using the two polarization functions are in net atomic charges. The uncontracted polarization function of silicon with a value of 0.3 for its exponent is transferable to other organosilicon compounds. Calculated molecular geometries of flexible or rigid structures are in very good agreement with the experimental values.
Transition structure in a diabatic surface formalism
Authors: Bernardi Fernando , McDouall Joseph J.W. , Robb Michael A. 
Published: January 2005

AbstractThe theory of an implementation of the diabatic surface model within the Heitler–London valence bond approach is described. It is shown that the HL–VB wave function can be obtained from a Van‐Vleck transformation of an MC–SCF wave function which has been built from atom‐localized orbitals. This wave function is built from a superposition of two diabatic components, reactantlike and productlike. The transition structure is then obtained as the minimum of the seam of intersection of the diabatic surfaces and the algorithm for performing this constrained optimization is described. Several areas of application are also discussed.
Analysis of the π‐electronic structure of infinitely large networks. I. Some remarks on the characteristic polynomial and density of states of large polycyclic aromatic hydrocarbons
Authors: Hosoya Haruo , Aida Misako , Kumagai Reiko , Watanabe Kazu 
Published: January 2005

AbstractGeneral expressions of the characteristic polynomials of various series of cyclic and linear polymers of polycyclic aromatic hydrocarbons are presented, i.e., polyacene, zigzag‐polyacene, 1,4‐dimethylbenzene polymer, polyperylene, etc. The densities of states of cyclic and linear polymers with the same repetitive units are shown. In some cases the allowed region of the energy levels of these polymers is found not to be the same. Several related problems are discussed.
The density amplitude ρ½ and the potential which generates it
Authors: March N. H. 
Published: January 2005

AbstractThe square root of the density ρ½ satisfies a Schrödinger equation with an effective local potential 𝒱(r). The form of this potential is obtained for (a) the ground state of the Be atom, (b) neutral atoms in the limit of very large atomic number from the statistical theory, and (c) almost spherical molecules XH4, again in the limit of many electrons. Some comments are made on the possibility of relativistic generalization of this method.
PERTURB: A special‐purpose algebraic manipulation program for classical perturbation theory
Authors: Fried Laurence E. , Ezra Gregory S. 
Published: January 2005

AbstractClassical perturbation theory provides a particularly promising route to EBK quantization of nonseparable systems. However, the number of terms generated when implementing perturbation theory for systems with more than two degrees of freedom can prove too large for general purpose symbolic manipulators to handle. We describe PERTURB, a specialized algebraic manipulation program written in C for quantization of multidimensional systems. A review of operator based classical perturbation theory is given, and the relationship between this type of perturbation theory and quantum mechanical Van Vleck perturbation theory discussed. The relative performance of the Dragt–Finn and Lie transform algorithms is assessed.
The shape of molecular charge distributions: Group theory without symmetry
Authors: Mezey Paul G. 
Published: January 2005

AbstractA group theoretical framework is proposed for a detailed characterization of the shapes of electronic charge distributions of general, asymmetric molecules. The proposed shape groups are the homology and cohomology groups of charge density contour surfaces. These shape groups depend on two real parameters, the charge density value a for the contour and a curvature parameter b. The two‐parameter family of various homology groups and cohomology groups of charge density contour surfaces is independent of the symmetry properties of the molecules and gives a concise description of the dominant shape characteristics. For any fixed parameter value b these groups may change only at specific charge density values, characteristic to the given molecule. On the other hand, for a fixed‐charge density contour the group changes induced by a change in the curvature parameter b provide a description of the fine details of the shape of the electron density. The changes in the structure of these groups follow strict algebraic relations, that provide a quantitative measure for shape‐similarity between various molecules. The two‐parameter shape group method is an extension of an earlier method proposed for biochemical applications.
Stereotopological indices for a family of chemical graphs
Authors: Millett Kenneth C. 
Published: January 2005

AbstractWe describe a mathematical method that can be employed to define stereotopological indices of placements of certain graphs in space. These indices are applied to successfully distinguish between configurations in a chemically interesting family of knotted and/or linked four‐valent oriented graphs in space. The methods are fundamentally algebraic and combinatorial in nature and are most readily understood in the context of calculations and the study of several key examples that are presented.
Molecular orbital theory of the properties of inorganic and organometallic compounds 5. Extended basis sets for first‐row transition metals
Authors: Dobbs K. D. , Hehre W. J. 
Published: January 2005

AbstractA series of efficient split‐valence basis sets for first‐row transition metals, termed 3‐21G, has been constructed based on previously‐formulated minimal expansions of Huzinaga, in which each atomic orbital has been represented by a sum of three gaussians. The original Huzinaga expansions for s‐ and p‐type orbitals (except those for 1s) have been fit by least squares to new three‐gaussian combinations in which the two sets of orbitals (of the samenquantum number) share gaussian exponents. The Huzinaga three‐gaussian expansions for ls and 3d atomic orbitals have been employed without alteration. The valence description of the 3‐21G basis sets comprises 3d‐, 4s‐ and 4p‐type functions, each of which has been split into two‐ and one‐gaussian parts. 4p functions, while not populated in the ground state of the free atoms, are believed to be important to 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 normalmode vibrational frequencies for a variety of inorganic and organometallic compounds containing first‐row transition metals. Calculated equilibrium structures, while generally superior to those obtained at STO‐3G, are not as good as those for compounds containing main‐group elements only. The calculations generally underestimate the lengths of double bonds between transition metals and main‐group elements, and overestimate the lengths of single linkages. Calculated normal‐mode vibrational frequencies for metal‐containing systems are less uniform than in those for main‐group compounds.
Voronoi binding site models
Authors: Crippen Gordon M. 
Published: January 2005

AbstractA frequently occurring problem in drug design and enzymology is that the binding constants for several compounds to the same site are known, but the geometry and energetic interactions of the site are not. This paper presents in detail a novel approach to the problem which accurately but compactly represents the allowed conformation space of each ligand, accurately depicts their three‐dimensional structures, and realistically allows each ligand to adopt the conformation and positioning in the site which is most favorable energetically. The investigator supplies only the ligand structures and observed binding free energies, along with a proposed site geometry. With no further assumptions about how the ligands bind and what parts of the ligands are important in determining the binding, the algorithm fits the observed binding energies without leaving outliers, predicts exactly how each of the given ligands binds in the site, and predicts the strength and mode of binding of new compounds, regardless of chemical similarity to the original set of ligands. The method is illustrated by devising a simple site that accounts for the binding of five polychlorinated biphenyls to thyroxine binding prealbumin. This model then predicts the binding energies correctly for an additional six biphenyls, and fails on one compound.
Determination of an empirical energy function for protein conformational analysis by energy embedding
Authors: Crippen Gordon M. , Ponnuswamy P. K. 
Published: January 2005

AbstractIt is quite easy to propose an empirical potential for conformational analysis such that given crystal structures lie near local minima. What is much more difficult, is to devise a function such that the native structure lies near a relatively deep local minimum, at least in some neighborhood of the native in conformation space. An algorithm is presented for finding such a potential acting on proteins where each amino acid residue is represented by a single point. When the given structure is either an α‐helical, β‐strand, or hairpin bend segment of pancreatic trypsin inhibitor, the resulting potential function in each case possesses a deep minimum within 0.10 Å of the native conformation. The improved energy embedding algorithm locates a marginally better minimum in each case only 0.1–1.3 Å away from the respective native state. In other words, this potential function guides a conformational search toward structures very close to the native over a wide range of conformation space.
An evaluation of the performance of diffuse function‐augmented basis sets for second row elements, Na‐Cl
Authors: Spitznagel Günther W. , Clark Timothy , von Ragué Schleyer Paul , Hehre Warren J. 
Published: January 2005

AbstractThe energetic effects of the addition of diffuse functions to molecules with second‐row elements are much less dramatic than those for their first‐row counterparts. Although diffuse functions on second‐row elements have little effect on the geometries and vibrational frequencies of neutral molecules, significant changes are found for anions. While the largest basis set, 6‐31 + G*, generally performs best, the results at 3‐21 + G* are comparable, and this basis can be recommended for practical applications.
The Hylleraas‐CI method in molecular calculations: Two‐electron integrals
Authors: Largo‐Cabrerizo A. , Clementi E. 
Published: January 2005

AbstractIn the Hylleraas‐CI method, first proposed by Sims and Hagstrom, correlation factors of the type r are included into the configurations of a CI expansion. The computation of the matrix elements requires the evaluation of different two‐, three‐, and four‐electron integrals. In this article we present formulas for the two‐electron integrals over Cartesian Gaussian functions, the most used basis functions in molecular calculations. Most of the integrals have been calculated analytically in closed form (some of them in terms of the incomplete Gamma function), but in one case a numerical integration is required, although the interval for the integration is finite and the integrand well‐behaved. We have also reported on partial and preliminary computations for the H2 molecule using our four‐center general formulas; a basis set of s‐ and p‐type functions yielded at R = 1.4001 Å an energy of ‐ 1.174380 a.u. to be compared with Kolos and Wolniewicz value of ‐ 1.174475.
Application of SINDO1 to phosphorus compounds
Authors: Jug Karl , Schulz Joachim 
Published: January 2005

AbstractSINDO1 calculations are presented for ground state geometries, heats of formation, ionization potentials and dipole moments. These calculations are based on a new parametrization of SINDO1 for second‐row elements which features inclusion of 3d orbitals and zero point energies. The comparison shows an improvement over MNDO, especially for hypervalent phosphorus compounds.
Atomic physicochemical parameters for three dimensional structure directed quantitative structure‐activity relationships III: Modeling hydrophobic interactions
Authors: Ghose Arup K. , Pritchett Avis , Crippen Gordon M. 
Published: January 2005

AbstractIn an earlier article8 the need was demonstrated for atomic physicochemical properties for three dimensional structure directed quantitative structure‐activity relationships, and it was shown how atomic parameters can be developed for successfully evaluating the molecular octanol‐water partition coefficient, which is a measure of hydrophobicity. In this work we report more refined atomic values of octanol‐water partition coefficients derived from nearly twice the number of compounds. Carbon, hydrogen, oxygen, nitrogen, sulfur and halogens are divided into 110 atom types of which 94 atomic values are evaluated from 830 molecules by least squares. These values gave a standard deviation of 0.470 and a correlation coefficient of 0.931. These parameters predicted the octanol‐water partition coefficient of 125 compounds with a standard deviation of 0.520 and a correlation coefficient of 0.870. There is only a correlation coefficient of 0.432 between the atomic octanol‐water partition coefficients and the atomic contributions to molar refractivity over the 93 atom types used for both the properties. This suggests that both parameters can be used simultaneously to model intermolecular interactions. We evaluated the CNDO/2 gross atomic charge distribution over several molecules to check the validity of our classification. We found that the charge density on the heteroatoms in conjugated systems is strongly affected by the presence of similar atoms in the conjugation which suggests it should be incorporated as a separate parameter in evaluating the partition coefficient.
Integral data compression for FPS 64‐BIT processors: Improved I/O and reduced storage
Authors: Hurst G. J. B. , Dupuis M. 
Published: January 2005

AbstractCompression of two‐electron integral data is used to reduce integral storage and I/O requirements with FPS M64 Series (formerly FPS‐X64) processors. Schemes are developed and implemented in assembly language to compress floating‐point values to a fixed‐point accuracy, and unsigned integer numbers. The floating‐point scheme stores only the significant bits of the mantissa and a short, biased exponent. The unsigned integers are packed into fixed‐length fields just long enough to hold the largest value. The packing procedures are tested on FPS‐164 and FPS‐264 processors (since renamed M64/145 and M64/60 by FPS) and incorporated into HONDO to compress two‐electron integral files. Reduction factors of 0.2–0.4 are obtained for floating‐point compression and 0.3–0.5 for index packing, with typical overall factors around one‐third. The advantages of improved I/O and storage efficiency are accompanied by a small increase in processor time to perform the packing and unpacking. Timing changes for HONDO are presented, and both packing schemes dramatically reduce SCF elapsed times with FPS‐264 processors. It is concluded that compression effectively extends external storage capacities, improves I/O efficiency, and can reduce the elapsed time of I/O bound calculations.
Improved algorithm for the calculation of one‐electron two‐center integrals with STOs
Authors: Rico J. Fernández , López R. , Ramírez G. 
Published: January 2005

AbstractIn a previous article (J. Fernández Rico, R. López and G. Ramírez, J. Comp. Chem., 9, 790 (1988)) we have proposed the calculation of molecular integrals involving STOs by means of some recurrence relations which use two sets (h and H) of overlap integrals (basic matrices). In the present paper, we derive explicit expressions of these integrals employing the two‐range expansion of the 0s‐function. This approach yields equations for the elements of the two basic matrices in terms of two further matrices, k(x,y) and i(x,y), and some auxiliary functions. Relations between the elements of these matrices and the functions are thoroughly explored and numerical tests are included for illustrating the behavior of the method.
Linearized embedding: A new metric matrix algorithm for calculating molecular conformations subject to geometric constraints
Authors: Crippen Gordon M. 
Published: January 2005

AbstractThere are many methods in the literature for calculating conformations of a molecule subject to geometric constraints, such as those derived from two‐dimensional NMR experiments. One of the most general ones is the EMBED algorithm, based on distance geometry, where all constraints except chirality are converted into upper and lower bounds on interatomic distances. Here we propose a variation on this where the molecule is assumed to have fixed bond lengths, vicinal bond angles and chiral centers; and these holonomic constraints are enforced separately from the experimental constraints by being built into the mathematical structure of the problem. The advantages of this approach are: (1) for molecules having large rigid groups of atoms, there are substantially fewer variables in the problem than all the atomic coordinates; (2) rigid groups achieve in the end more accurate local geometry (e.g., planar aromatic rings are truly planar, chiral centers always have their correct absolute chirality); (3) it is easier to detect inconsistencies between the holonomic and the experimental constraints; and (4) when generating a random sampling of conformers consistent with all constraints, the probability of achieving satisfactory structures tends to be greater.
Molecular mechanics of peroxides. II. Cyclic compounds
Authors: Carballeira L. , Mosquera R. A. , Rios M. A. 
Published: January 2005

AbstractThe conformations of various cyclic peroxides have been determined using a molecular mechanics force field developed by the authors and previously applied to linear peroxides. Comparison of the results with those of experimental and ab initio studies shows that this force field may be employed without correction for cyclic compounds.
A data compression method applicable to first‐order convergent iterative procedures
Authors: Shepard Ron 
Published: January 2005

AbstractA data compression method is presented that is generally applicable to first‐order convergent iterative procedures that employ subspace expansions or extrapolations based on successive correction vectors. This method is based on the truncation of insignificant information in successive correction vectors. Although the correction vectors themselves may be severely truncated with the proposed approach, the final solution vector may be represented to arbitrary accuracy. A feature of the proposed method is that more slowly convergent iterative procedures allow the correction vectors to be more severely truncated without affecting the overall convergence rate. The method is implemented and applied to the iterative Davidson diagonalization method. If the compressed representation of the expansion vectors can be held in main computer memory, then a significant reduction in the I/O requirements is achieved.
An empirically adjusted Newton–Raphson algorithm for finding local minima on molecular potential energy surfaces
Authors: Stanton John F. , Bernholdt David E. 
Published: January 2005

AbstractA simple extension of the Newton–Raphson method is proposed that approximately accounts for anharmonicity in bond‐stretching coordinates. By modeling each bonded distance in a polyatomic molecule as a Morse oscillator with no anharmonic stretch‐stretch or stretch‐bend coupling, a multiplicative correction factor to the Newton–Raphson step is derived. Representative examples suggest that the rate of convergence of the proposed scheme is typically faster than that of the standard Newton–Raphson method.
Semiempirical AM1 electrostatic potentials and AM1 electrostatic potential derived charges: A comparison with ab initio values
Authors: Ferenczy Gyorgy G. , Reynolds Christopher A. , Richards W. Graham 
Published: January 2005

AbstractElectrostatic potentials calculated from AM1 wave functions have been compared with ab initio STO‐3G values and qualitative agreement has been found. Atomic charges derived from AM1 electrostatic potentials for both experimental and AM1 optimized geometries are of comparable quality with STO‐3G potential derived charges. These results suggest that the AM1 electrostatic potential may be useful both in its own right and also for deriving atomic charges for use in molecular dynamics studies.