bluuebunny/crossref_metadata_2025_split huggingface dataset:
General quantum mechanical operators. An open‐ended approach for one‐electron integrals with Gaussian bases
Authors: Augspurger Joseph D. , Dykstra Clifford E. 
Published: January 2005

AbstractA universal computational approach for evaluating integrals over gaussian basis functions for general operators of the form

is presented. The implementation is open‐ended with respect to the types of basis functions (s, p, d, f, g, h…) and with respect to the integers that specify the operator. These one‐electron integrals comprise operators associated with electrical and magnetic properties of molecules and include those needed to find multipole polarizabilities, multipole susceptibilities, chemical shifts, and so on. The scheme also generates the usual kinetic, nuclear attraction, and overlap operators.
Ab initio study of substituent effect on the addition of hydrogen fluoride to fluoroethylenes
Authors: Solà Miquel , Lledós Agustí , Duran Miquel , Bertrán Juan , Ventura Oscar N. 
Published: January 2005

AbstractAn ab initio 3‐21G study of the direct addition of HF to C2HnF(4–n), with n = 0 to 4, has been performed to investigate the effect of the substituent on the reaction. Geometry optimization of all charge‐transfer complexes and transition states has been done. Standard analysis of activation energies of addition reactions, vibrational and thermodynamical analysis, as well as Morokuma energy decomposition, BSSE correction, PMO analysis, and Pauling bond orders were used to explain the results. A subset of the reactions, including that of C2H4 as reference one and the two most favorable cases, was also studied at the MP2/6–31G(d,p)//HF/6–31G(d,p) level. The barriers so obtained are in agreement with the indirectly found from experimental data. It was found that the effect of the substituent is not monotonic for the additions. Decomposition of the interaction energy is shown to be adequate to explain this nonmonotonic behavior. The implications for laser chemistry of the addition of hydrogen halides to fluorosubstituted olefins is briefly discussed.
Derivation of net atomic charges from molecular electrostatic potentials
Authors: Woods Robert J. , Khalil Maged , Pell Wendy , Moffat Steven H. , Smith Vedene H. 
Published: January 2005

AbstractThe dependence of net atomic charges, as derived from least‐squares fitting to electrostatic potentials, on molecular orientation and potential site location is critically examined. A unique rotationally invariant algorithm, in which the charges may be constrained to reproduce the molecular dipole moment, is presented and the results for several basis sets compared to previous work. Significant improvements in dipole moments derived from the unconstrained charges are noted.
Variable step molecular dynamics: An exploratory technique for peptides with fixed geometry
Authors: Gibson Kenneth D. , Scheraga Harold A. 
Published: January 2005

AbstractA new algorithm is presented for performing molecular dynamics simulations of peptides with fixed geometry, with the aim of simulating conformational changes and of exploring conformational space. The principle of the method is to expand the potential energy as a Taylor's series in the coordinates around the current point, retaining the force and its first two derivatives, and obtain a series solution of the resulting differential equations using a method due to Lyapunov. By choosing the time step so that the second term in the series is small compared to the first, the true solution can in principle be approximated to any desired degree of accuracy. The algorithm has been used to solve numerically Lagrange's equations of motion for N‐acetyl alanine amide and N‐acetyl methionide amide, regarded as fixed at their C‐termini, under the influence of the ECEPP/2 potential energy function, and time steps of 15–30 fsec have been achieved with little variation in the total energy. Possible directions for future development are discussed.
A new algorithm for solving large inhomogeneous linear system of algebraic equations
Authors: Ramasesha S. 
Published: January 2005

AbstractAn algorithm based on a small matrix approach to the solution of a system of inhomogeneous linear algebraic equations is developed and tested in this short communication. The solution is assumed to lie in an initial subspace and the dimension of the subspace is augmented iteratively by adding the component of the correction vector obtained from the Jacobi scheme on the coefficient matrix A (ATA, if the matrix A is nondefinite) that is orthogonal to the subspace. If the dimension of the subspace becomes inconveniently large, the iterative scheme can be restarted. The scheme is applicable to both symmetric and nonsymmetric matrices. The small matrix is symmetric (nonsymmetric), if the coefficient matrix is symmetric (nonsymmetric). The scheme has rapid convergence even for large nonsymmetric sparse systems.
Computing the electric potential of biomolecules: Application of a new method of molecular surface triangulation
Authors: Zauhar R. J. , Morgan R. S. 
Published: January 2005

AbstractA new method is presented for defining a smooth, triangulated analytic surface for biological molecules. The surface produced by the algorithm is well‐suited for use with a recently developed polarizationcharge technique1 for the computation of the electrostatic potential of solvated molecules, and may also be used for calculations of molecular surface areas and volumes. The new method employs Connolly's definitions of contact, reentrant and saddle surface,2 but includes modifications that preclude the presence of self‐interesting reentrant surface, and also insure a rigorous decomposition of contact regions into curvilinear finite elements. The triangulation algorithm may be used in conjunction with the electrostatic methods described previously to compute the electric potential of molecules of arbitrary shape in solution. Applications include the estimation of hydration enthalpies, computation of the electrostatic forces associated with solvation, estimation of interactions between separate charged species in solution, and computation of the three‐dimensional form of the molecular electric potential. Test calculations are presented for a double‐stranded dinucleotide, the polypeptide enkephalin, and the protein ferredoxin.
Adaptation of D2hab initio computer code to higher‐symmetry point groups
Authors: Earl Edward 
Published: January 2005

AbstractThe imposition of symmetry in electronic structure calculations can be plagued by artifactual symmetry‐breaking in orbital or configuration amplitudes. While most ab initio computer code is well‐developed to impose symmetry constraints in D2h and its subgroups, the problem is not nearly as tractable in higher‐symmetry point groups. This article describes the successful modification of existing D2h ab initio computer code to handle symmetry constraints in higher‐symmetry point groups. Prospects for the development of ab initio computer code that runs fully under any point group are also discussed.
On the interaction of palladium with olefinic systems
Authors: Sellers Harrell 
Published: January 2005

AbstractWe have performed all electron Hartree–Fock gradient calculations and geometry optimizations on systems composed of one to three palladium atoms and: CH3 cation and anion, C2H4, C2H3NH2, C4H4, NH3, and (NH3) + (C2H4). Several basis set considerations are discussed and the binding energies of Pd to these small molecules are reported. We find the counterpoise correction to the binding energies of these systems to be large. We also present MP2 calculations of the palladium binding energy with a large uncontracted palladium spd basis set in the PdC2H4 and PdNH3 systems. The binding interaction between ethylene and palladium results in a mixing of the 4d–π* and 5s–π orbitals, and, is dissociative to the ethylene. The palladium‐butadiene and palladium‐cyclobutene relative stabilites and structures are interesting since these molecules could form from acetylene on a palladium surface. We find the Pd‐butadiene cyclic structure to be 43 kcal/mol more stable than the Pd‐cyclobutene product.
Combinatorial models and algorithms in chemistry. The expanded Wiener number—a novel topological index
Authors: Tratch S. S. , Stankevitch M. I. , Zefirov N. S. 
Published: January 2005

AbstractAn expanded form of the Wiener number is suggested for characterization of molecular graphs and structure‐property correlations. The simple, computer‐oriented method for counting of the novel index is briefly discussed.
On the use of AM1 and MNDO wave functions to compute accurate electrostatic charges
Authors: Orozco M. , Luque F. J. 
Published: January 2005

AbstractA new strategy to evaluate accurate electrostatic charges from semiempirical wave functions is reported. The rigorous quantum mechanical molecular electrostatic potentials computed from both MNDO and AM1 wave functions are fitted to the point‐charge molecular electrostatic potential to obtain the electrostatic charges. The reliability of this strategy is tested by comparing the semiempirical electrostatic charges for 21 molecules with the semiempirical Mulliken charges and with the ab initio STO‐3G and 6‐31G* electrostatic charges. The ability of the dipoles derived from the semiempirical electrostatic and Mulliken charges as well as from the SCF charge distributions to reproduce the ab initio 6‐31G* electrostatic dipoles and the gas phase experimental values is determined. The statistical analysis clearly point out the goodness of the semiempirical electrostatic charges, specially when the MNDO method is used. The excellent relationships found between the MNDO and 6‐31G* electrostatic charges permit to define a scaling factor which allows to accurately reproduce the 6‐31G* electrostatic charge distribution as well as the experimental dipoles from the semiempirical electrostatic charges.
Electronic structure and photoelectron spectra of Sb2 and Sb4 from local‐spin‐density calculations. Model potential for Sb
Authors: Musolino V. , Toscano M. , Russo N. 
Published: January 2005

AbstractThe geometry, electronic structure, and photoelectron spectra of Sb2 and Sb4 have been investigated employing the LCGTO‐MP‐LSD method. For both molecules the geometrical and spectroscopic constants computed using the VWN potential are in very good agreement with the available experimental data. The HeI photoelectron spectra were computed with different potentials (Xα, GL, HL, BH, and VWN). The calculated spectra are in excellent agreement with the experimental ones and the use of the VWN potential gives the most accurate results. The reliable results for molecules complement those for the Sb atom and show that the proposed LSD Model Potential is able to give an accurate description of the structural and spectroscopic properties of the title molecules.
The effect of diffuse functions on minimal basis set superposition errors for H‐bonded dimers
Authors: Alagona Giuliano , Ghio Caterina 
Published: January 2005

AbstractThe effect of the addition of diffuse functions of sp type on the first row atoms (and/or of d type on phosphorus) to a MINI‐1 minimal basis set is evaluated by comparing the SCF description of the interaction energy and its decomposition, counterpoise (CP) corrected and uncorrected for basis set superposition errors (BSSEs), with that produced by extended basis sets (6‐31G** and 3‐21G+) as well as by basis sets (6‐31G** + VPS and (2d)S), previously successfully tested, designed to minimize the BSSE. The systems considered are a few anions (F−, HCOO−, H2PO−4) H‐bonded to water; the basis set performance on a different geometry (bifurcated instead of linear) of the phosphate‐water adduct was also considered. An additional comparison with the interaction energy in a neutral dimer, (HF)2, was carried out. The addition of diffuse functions to the MINI‐1 basis set, instead of resorting to extended basis sets, seems to be a sensible choice for anions. The equilibrium distance is shifted towards the reference basis set value at the CP corrected level as well as at the uncorrected one. The spread of the energy due to the basis set is hardly distinguishable when the CP corrected values are plotted. The description of the interaction energy in dimers involving phosphorus is improved using d type diffuse functions.
Comparative study of imidazole hydration: Ab initio and electrostatic calculations vs. Cambridge structural database analysis
Authors: Alagona Giuliano , Ghio Caterina , Nagy Péter , Simon Kálmán , Náray‐Szabo Gábor 
Published: January 2005

AbstractWe studied geometries and energies of complexes between water and neutral or protonated imidazole by ab initio molecular orbital calculations using the 4‐31G basis set with and without the counterpoise correction. Positions of hydration sites and relative binding energies could be also estimated by using the electrostatic field map of imidazole as calculated by our bond increment method. The reliability of the calculations is confirmed by comparing the geometries of the imidazole‐water complex to the experimental ones from the Cambridge Structural Database. These were obtained by X‐ray diffraction studies on crystals with water bound to a molecule containing the imidazole fragment.
An ab initio method for approximation of the frozen molecular fragment
Authors: Roszak S. , Hariharan P. C. , Kaufman Joyce J. 
Published: January 2005

AbstractAn ab initio method for calculation on many‐electron molecular systems with the approximation of the inactive part of a molecule by frozen molecular fragment is presented. In the following method the SCF calculations are performed in two series. First the molecular orbitals resulting from the first SCF calculation (modest basis set) are localized. In the second SCF run, the basis set is extended for the active part of the molecule, while molecular orbitals of the inactive part, selected from the localized set, are kept frozen. The results are in good agreement with the extended basis set calculation.
Four‐Index transformation on distributed‐memory parallel computers
Authors: Covick Lawrence A. , Sando Kenneth M. 
Published: January 2005

AbstractBecause it has 𝒪(N5) operations, a low computation to data transfer ratio, and is a compact piece of code, the four‐index transformation is a good test case for parallel algorithm development of electronic structure calculations. We present an algorithm primarily designed for distributed‐memory machines. Unlike the previous algorithm of Whiteside et al., ours is not designed with a particular architecture in mind. It is a general algorithm in the sense that not only can it be used on some common architectures but it can utilize some of the advantages inherent in each. In addition, we present formulas predicting that there would be a twofold decrease in communication time if our algorithm was used instead of that of Whiteside et al., on a square array of processors and up to an N‐fold decrease if the two algorithms were implemented on a hypercube.
The bond order—bond length relationship
Authors: Paolini John P. 
Published: January 2005

AbstractThe difference in length between two bond orders was reported by Pauling to be essentially the same, regardless of the atoms that make up the bond. To a first approximation these differences hold not only for bond orders 1, 2 and 3 but also for six membered aromatic rings containing all carbon, carbon‐nitrogen, nitrogen‐nitrogen, carbon‐phosphorous, carbon‐arsenic, and carbon‐antimony bonds. An equation was developed (based upon these differences) that relates bond order and bond length. The output of this equation was compared with those of Gordy and Pauling. Our equation as well as the Gordy equation (with revised constants) return a bond length of 1.4 Å for bond order 1.67 which is consistent with theory. (This bond order was not used in developing either the equation or the revised Gordy constants.)
Macromolecular dynamics on a shared‐memory multiprocessor
Authors: Skeel Robert D. 
Published: January 2005

AbstractThis is a study of the effect of data structures and algorithms on parallelism and vectorization for the molecular dynamics package GROMOS. About 80% of the computing time (for the GROMOS benchmark) is spent on the nonbonded interactions, and an important issue is the method that is used for finding all pairs of atoms (actually atom groups) which are within a given cutoff radius of each other. Favored by the authors of GROMOS is the use of the (Verlet) neighbor list with direct calculation of all distances. Substantial restructuring of their code for the nonbonded interactions has resulted in a speedup of a factor 6.9 for the eight‐processor Alliant FX/8 through the use of concurrent subroutine calls. Vectorization gave a further improvement of 30%. However, the direct calculation of all distances does not scale up linearly with the number of atoms. (Nor would neighbor lists be needed if cutoffs were abandoned in favor of such techniques as the fast multipole method). Therefore an alternative GROMOS subroutine that implements the “gridcell plus linked list” approach without a neighbor list was also rewritten and tested. This resulted in the discovery of an apparent flaw in an early study of the relative merits of the two algorithms. It is observed that actually the neighbor list version of GROMOS is not much faster.
A comparison of conformational energies calculated by molecular mechanics (MM2(85), Sybyl 5.1, Sybyl 5.21, and ChemX) and semiempirical (AM1 and PM3) methods
Authors: Gundertofte Klaus , Palm Jonas , Pettersson Ingrid , Stamvik Anders 
Published: January 2005

AbstractConformational energies of different conformers have been calculated for a series of molecules using various molecular mechanics and semiempirical methods. The quality of the force fields has also been tested by calculating barriers to rotation about carbon‐carbon bonds. The molecular mechanics force fields used are MM2(85), Sybyl 5.1, Sybyl 5.21, and ChemX, ver. Jan 89. The semiempirical methods used are AM1 and PM3. Molecules with different functional groups, for which good experimental data exist, have been selected. The semiempirical methods generally calculate barriers to rotation which are lower than the experimentally determined. The conformational energies for hydrocarbons are reasonably well reproduced by all tested methods although MM2(85) gives the quantitatively best agreement with experiments. For compounds containing oxygen, nitrogen and halogens MM2(85) gives results which are in best agreement with the experimentally determined values.
A complete shape characterization for molecular charge densities represented by Gaussian‐type functions
Authors: Walker P. Duane , Arteca Gustavo A. , Mezey Paul G. 
Published: January 2005

AbstractAn algorithm for a detailed 3‐D characterization of the shapes of molecular charge distributions is implemented, tested and applied for a family of AB2 molecules. The characterization is performed by computing a number of topological invariants (“shape groups”) associated with a continuum of molecular surfaces: the complete family of all electronic isodensity contours for the given molecules. These shape groups (the homology groups of truncated surfaces derived from isodensity contours) depend continuously on two parameters: a density value defining the density contour, and a reference curvature value, to which the local curvatures of the isodensity contours are compared. The electronic charge distribution is modeled by means of Gaussian‐type functions. The method employs an explicit form of the charge density function in order to compute the curvature properties for the molecular surfaces analytically, from which the shape groups are derived by the algorithm. No visual inspection is required for the characterization and comparison of shapes of molecular charge densities, as these are done algorithmically by the computer. However, visual inspection of the results of the shape analysis is a possible option. For a given molecule, in a given nuclear configuration, the technique provides a two‐dimensional shape map, displaying the distribution of shape groups as a function of the local curvature and the level set value (the value of the charge density at the contour). The computer program GSHAPE performs the analysis of shape maps automatically. This feature makes it potentially useful in the context of computer‐aided drug design, where unbiased, automated shape characterization methods are valuable tools. As examples, several two‐dimensional shape maps for simple systems are discussed. The changes induced in these maps by a change in the nuclear geometry, as well as by the changes of the nuclear charge, are also analyzed. The method is applicable to large biomolecules of interest if charge density information is available.
On the ab initio geometry optimization of molecular solutes
Authors: Bonaccorsi Rosanna , Cammi Roberto , Tomasi Jacopo 
Published: January 2005

AbstractWe present several variants of methods for the automatic search of optimum geometries of solutes via ab initio SCF procedures. The physical meaning of geometry optimization in solution is discussed. Advantages and disadvantages of the different variants are shown making use of calculations on the HF dimer with different basis sets, supplemented by information on the computational times. Suggestions for the most convenient strategies (which in part depend on the nature of the solute) are also done.
Construction of molecular mechanics energy functions by mathematical transformation of ab initio force fields and structures
Authors: Palmö K. , Pietilä L.‐O. , Krimm S. 
Published: January 2005

AbstractA method is presented by which ab initio (or empirical) force fields and structures can be converted to molecular mechanics energy parameters. Using Cartesian coordinates, the effect of van der Waals and other nonquadratic interactions is eliminated from the original spectroscopic force field, and molecular mechanics force constants and reference geometry parameters are derived. The computed parameters yield molecular structure and vibrational frequencies that are identical to the original ones. The transformation produces a complete general valence force field, which in most cases is impractical, and a procedure to reduce the number of force constants is therefore described. Different ways of applying the transformation are outlined.
Frequency dependent nonlinear optical properties of molecules: Formulation and implementation in the HONDO program
Authors: Karna S. P. , Dupuis M. 
Published: January 2005

AbstractThis article summarizes the detailed equations for the time‐dependent Hartree–Fock treatment of nonlinear properties for perturbations made up of a static electric field and an oscillating field. Explicit expressions for all nonlinear processes up to third order are obtained in terms of the density matrices at the same order. For processes at second and third order in perturbation, expressions in terms of lower order quantities are also obtained by applying the (2n + 1) theorem of perturbation theory. The corresponding computer implementation in the HONDO program is described.
Computation of spectroscopic properties of van der Waals systems from post‐SCF ab initio potentials including the EICP alternative counterpoise technique
Authors: Tolosa S. , Espinosa J. , del Valle F. J. Olivares 
Published: January 2005

AbstractThe basis set superposition error (BSSE) is studied using the Counterpoise (CP) technique at SCF and post‐SCF level in weakly bonded systems, with the aim of making manifest the overestimate introduced by the Boys and Bernardi method which does not facilitate a valid ab initio construction of potentials in van der Waals systems. The results show that the excess correction introduced by the CP method is to a large extent corrected using the version called the Indirect Counterpoise (ICP) method. The extension of this method to the exchange‐polarization and exchange‐charge transfer coupling terms provides good ab initio potentials from which quite satisfactory spectroscopic properties can be extracted.