bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular orbital theory of the properties of inorganic and organometallic compounds 4. Extended basis sets for third‐and fourth‐row, main‐group elements
Authors: Dobbs K. D. , Hehre W. J. 
Published: January 2005

AbstractTwo new series of efficient basis sets for third‐ and fourth‐row, main‐group elements have been developed. Split‐valence 3‐21G basis sets have been formulated from the minimal expansions by Huzinaga, in which each atomic orbital has been represented by a sum of three Gaussians. The original expansions for s− and p−type orbitals (except those for 1s) have been replaced by new combinations in which the two sets of orbitals (of the same n quantum number) share Gaussian exponents. The Huzinaga expansions for 1s, 3d and 4d (fourth‐row elements only) have been employed without further alteration. The valence atomic functions 4s, 4p for third‐row elements; 5s, 5p for fourth‐row elements have been split into two and one Gaussian parts. Supplemented 3‐21G(*) representations have been formed from the 3‐21G basis sets by the addition of a set of single d−type Gaussian functions.The performance of 3‐21G and 3‐21G(*) basis sets is examined with regard to the calculation of equilibrium geometries, normal mode vibrational frequencies, reaction energies, and electric dipole moments involving a variety of normal and hypervalent compounds containing third‐ and fourth‐row, main‐group elements. The supplementary functions incorporated into the 3‐21G(*) basis sets are generally found to be important, especially for the proper description of equilibrium bond lengths and electric dipole moments. 3‐21G(*) representations are recommended for general use in lieu of the unsupplemented 3‐21G basis sets.
An SCF and CI Study of the 1,3 Shift in the HXCHY⇌XCHYH Isoelectronic Series: X, YCH2, NH, and O
Authors: Poirier Raymond A. , Majlessi Dariush , Zielinski Theresa J. 
Published: January 2005

AbstractAb initio molecular orbital calculations at SCF level with the 3‐21G, 6‐31G, and 6‐31G** basis sets and CI level with the 6‐31G basis set have been carried out for an isoelectronic series HXCHY and XCHYH, where X, Y can be CH2, NH, and O. Optimized structures (3‐21G and 6‐31G**) for both tautomers and the 1,3 hydrogen shift transition states are reported. The relative stabilities of the isomers and the barriers of the 1,3 shift are discussed in terms of proton affinities and bond orders. It is shown that both the relative stabilities of the tautomers and the relative barrier heights can be explained qualitatively using simple proton affinity arguments and that the barrier heights are quantitatively related to bond orders.
Optimization of the Generalized Valence Bond Method for Vector Processors
Authors: Bair Raymond A. 
Published: January 2005

AbstractThe Generalized Valence Bond [GVB(pp)] multiconfiguration self‐consistent field wave function optimization program has undergone substantial revision in migration from serial scalar computers (like IBM and VAX) to the FPS‐164, a minisupercomputer. Many of the code optimization strategies applied to the GVB program are portable and applicable to a wide range of scientific application codes. In benchmark calculations, the optimized FPS‐164 program, GVB164, is 6.5 times faster than the initial FPS‐164 implementation, both programs storing the two‐electron integral list on disk. GVB164 runs 30 times faster in wall time (limited by the FPS‐164 disk access speed) than a reference version of GVB2P5 on the VAX 11/780. The performance of GVB164 nearly doubles again when all of the two‐electron integrals can be stored in main memory.
A Strategy for the Regional Characterization of Potential Energy Surfaces
Authors: Yeh You‐Hsing , Fink William H. 
Published: January 2005

AbstractThe problem of characterization of a region of an n‐dimensional potential energy surface with maximization of the quality of representation for a given amount of computational effort is examined with the aid of well known theorems from numerical analysis. A choice of nonlinear grid and a representation of the potential expanded in Chebyshev polynomials is shown to be efficient. The strategy was applied to a two‐dimensional analytical representation of a transition state and to the ground‐state equilibrium geometry region of the Hartree‐Fock potential energy surface obtained with split‐valence basis sets for H2O, H2S, and H2Se. Results are reported for the equilibrium geometries and force constants for these molecules. Results are comparable to those obtained by others for H2O and H2S. A full set of values is reported for H2Se.
Offcenter Molecular Charge Distribution Corrections to Born Equation Electrostatic Solvation Energies
Authors: Ehrenson S. 
Published: January 2005

AbstractUse of simple model charge distributions and classical multipolar dielectric theory has allowed investigation of the corrections appropriate to the Born equation for structured ion solutes. Among the results obtained for centrosymmetric charge distributions, but presumably of general consequence, are the demonstration of nonlinear dependence and great sensitivity of polarization to charge‐cavity boundary proximity, rapid falloff of effects upon continued subdivision of charge, and the significance of solvation energy differences for 2‐ and 3‐dimensional charge distributions. That 50% or greater corrections to the Born energy may readily be obtained in real ion systems, and the lack of sensitivity of such corrections to the dielectric of the medium for ε > 10 are also results of general interest. Analytical approximations for the electrostatic work equations appropriate to high dielectric solvation are included, and how uncertainties in charge magnitude and position for real ions might affect the analysis are also briefly considered.
On calculations of intermolecular potentials
Authors: Bhanuprakash K. , Kulkarni G. V. , Chandra Asish K. 
Published: January 2005

AbstractAb initio MO calculations of intermolecular potentials using conventional Gaussian basis set have a tendency to over emphasize binding due to underestimation of exchange repulsion. A modified semi‐empirical method has been suggested and results are found to be reliable at medium‐ and long‐range separation.
Recursion formulae for calculation of overlap integrals
Authors: Datta N. C. , Sen B. 
Published: January 2005

AbstractMulti‐ζ Slater‐type orbitals are frequently used in molecular orbital calculations. Master formulae and numerical tables are available in literature for overlap integrals between s, p, and d atomic orbitals up to principal quantum number (n) = 3 and for some other selected quantum numbers. However, no master formula or numerical table is available for quantum numbers n = 5 and above and involving ƒ orbitals. In this article recursion formulae have been presented for the calculation of the overlap integral between any two s, p, d, and ƒ atomic orbitals formed by a linear combination of Slater‐type orbitals. These formulae, when expanded, would give rise to all the master formulae reported in the literature as well as formulae hitherto unreported.
Recent advances in multireference second order perturbation CI: The CIPSI method revisited
Authors: Cimiraglia Renzo , Persico Maurizio 
Published: January 2005

AbstractThe evolution of the CIPSI method, with the latest modifications recently implemented in our laboratory, is described. A new version, based on a diagrammatic technique, is presented. Test calculations which have been run on water, ethylene, and transacrolein, show that the new method is a powerful tool for the study of medium‐size molecular systems.
Character tables and symmetry eigenvectors for two C3v rotor molecular systems
Authors: Smeyers Yves G. , Niño A. 
Published: January 2005

AbstractThe character tables of the Altmann groups for the double internal rotation of C3v rotor molecules of different symmetries were determined. These symmetries were those of para‐xylene, trans‐1,2‐dimethylcyclopropane, cis‐N‐methylethylidenimine, dimethylamine, and a dimethylated asymmetrical molecule. From these character tables, the symmetry eigenvectors, which block diagonalize the Hamiltonian matrix, were deduced. The symmetry eigenvectors were derived with the help of a small computer.
Computer enumeration and generation of physical trees
Authors: Knop J. V. , Müller W. R. , Szymanski K. , Kroto H. W. , Trinajstić N. 
Published: January 2005

AbstractA computer‐oriented method for the enumeration and generation of physical trees is presented. Physical trees depict acyclic chemical structures, but the term physical is used to stress the process by which the structures are produced.
A study of basis set effects on structures and electronic structures of phosphine oxide and fluorophosphine oxide
Authors: Streitwieser Andrew , McDowell Robert S. , Glaser Rainer 
Published: January 2005

AbstractA variety of basis sets have been used for geometric and electronic structure studies. Electronic effects were measured using integrated spatial electron populations (ISEP). The two largest basis sets used, 6‐31G* and DZ+P, give significantly different results. Use of two d‐orbital sets (6‐31G*[dd]) or decontraction of the 2sp shell on phosphorus has little further effect. d‐Orbitals on oxygen are required for consistent electronic structure results, and d‐orbitals on fluorine have a small but significant effect. Use of diffuse functions, required for anions, is not recommended with small basis sets on neutral molecules. Large negative charges (≈−1.5) on oxygen are given by all of the larger basis sets by the ISEP procedure and indicate that the PO bond in these compounds is largely semi‐polar. The best simple symbolic representation of phosphine oxide is H3P+0−, rather than H3P0.
Basis set and correlation effects on computed positive ion hydrogen bond energies of the complexes AHn · AHn + 1+1: AHn = NH3, OH2, and FH
Authors: Del Bene Janet E. 
Published: January 2005

AbstractBasis set expansion and correlation effects on computed hydrogen bond energies of the positive ion complexes AHn · AHn + 1+1, for AHn = NH3, OH2 and FH, have been evaluated. The addition of diffuse functions on nonhydrogen atoms is the single most important enhancement of split‐valence plus polarization basis sets for computing hydrogen bond energies. Basis set enhancement effects appear to be additive in these systems. The correlation energy contribution to the stabilization energies of these complexes is significant, with the second order term being the largest term and having a stabilizing effect. The third order term is smaller and of opposite sign, while the fourth order term is smaller yet and stabilizing. As a result, computed MP4 stabilization energies are bracketed by the MP2 and MP3 energies. The overall effect of basis set enhancement is to decrease hydrogen bond energies, whereas the addition of electron correlation increases stabilization energies.
Revised algorithms for the build‐up procedure for predicting protein conformations by energy minimization
Authors: Gibson K. D. , Scheraga H. A. 
Published: January 2005

AbstractThe build‐up procedure for predicting low‐energy conformations of polypeptides has been extended to cover the case of peptides in aqueous solutions. The revised procedure consists of five steps to be applied to each stage of the build‐up. I. All low‐energy minima of each of the two fragments to be joined are combined as starting points for energy minimization of the enlarged fragment, and those minima of the enlarged fragment within a certain upper bound of the lowest energy are retained. II. Whenever one of the combinations in Step I leads to an atomic overlap, the minimization is started again using a pseudoenergy function which remains finite everywhere and becomes equal to the standard energy function when no atoms overlap. III. The minima generated in Steps I and II are culled by ignoring side‐chain conformations and retaining only those minima whose backbone conformations differ significantly. IV. The rotameric states of the side chains are optimized, by testing their energy of interaction with the rest of the molecule, and subjecting the whole molecule to a further round of energy minimization if the test indicates that this would reduce the energy. V. The energies of all minima are recomputed with inclusion of a term for solvation and with a smaller upper bound as the criterion for retention. The original build‐up procedure consisted of Steps I and III only. Examples are presented showing the effectiveness of the new Steps II and IV in locating low‐energy minima, and the problems that remain to be solved, chiefly concerning Step V, are discussed.
Atomic charges derived from electrostatic potentials: A detailed study
Authors: Chirlian Lisa Emily , Francl Michelle Miller 
Published: January 2005

AbstractA new algorithm for fitting atomic charges to molecular electrostatic potentials is presented. This method is non‐iterative and rapid compared to previous work. Results from a variety of gaussian basis sets, including STO‐3G, 3‐21G and 6‐31G*, are presented. Charges for a representative collection of molecules, comprising both first and second row atoms and anions are tabulated. The effects of using experimental and optimized geometries are explored. Charges derived from these fits are found to adequately reproduce SCF dipole moments. A small split valence representation, 3‐21G, appears to yield consistently good results in a reasonable amount of time.
Computer enumeration of polyhexes using the compact naming approach
Authors: Cioslowski J. 
Published: January 2005

AbstractThe enumeration of polyhexes can be easily carried out by utilizing a compact name (CN) approach to code chemical structures. The Fortran program performing generation of benzenoid hydrocarbons with 1–10 rings is presented. The computed structures are divided into various classes according to their cata‐ or peri‐ as well and non‐ or radicaloid character. Use of the additive nodal increments (ANI) approach leads to algorithm producing representative samples of the polyhexes' sets which can be applicable in testing of various topological formulae.
On color polynomials of Fibonacci graphs
Authors: El‐Basil Sherif 
Published: January 2005

AbstractA recursion exists among the coefficients of the color polynomials of some of the families of graphs considered in recent work of Balasubramanian and Ramaraj. Such families of graphs have been called Fibonacci graphs. Application to king patterns of lattices is given. The method described here applies only to the so called Fibonacci graphs.
An efficient newton‐like method for molecular mechanics energy minimization of large molecules
Authors: Ponder Jay W. , Richards Frederic M. 
Published: January 2005

AbstractTechniques from numerical analysis and crystallographic refinement have been combined to produce a variant of the Truncated Newton nonlinear optimization procedure. The new algorithm shows particular promise for potential energy minimization of large molecular systems. Usual implementations of Newton's method require storage space proportional to the number of atoms squared (i.e., O(N2)) and computer time of O(N3). Our suggested implementation of the Truncated Newton technique requires storage of less than O(N1.5) and CPU time of less than O(N2) for structures containing several hundred to a few thousand atoms. The algorithm exhibits quadratic convergence near the minimum and is also very tolerant of poor initial structures. A comparison with existing optimization procedures is detailed for cyclohexane, arachidonic acid, and the small protein crambin. In particular, a structure for crambin (662 atoms) has been refined to an RMS gradient of 3.6 × 10−6 kcal/mol/Å per atom on the MM2 potential energy surface. Several suggestions are made which may lead to further improvement of the new method.
A powerful truncated Newton method for potential energy minimization
Authors: Schlick Tamar , Overton Michael 
Published: January 2005

AbstractWith advances in computer architecture and software, Newton methods are becoming not only feasible for large‐scale nonlinear optimization problems, but also reliable, fast and efficient. Truncated Newton methods, in particular, are emerging as a versatile subclass. In this article we present a truncated Newton algorithm specifically developed for potential energy minimization. The method is globally convergent with local quadratic convergence. Its key ingredients are: (1) approximation of the Newton direction far away from local minima, (2) solution of the Newton equation iteratively by the linear Conjugate Gradient method, and (3) preconditioning of the Newton equation by the analytic second‐derivative components of the “local” chemical interactions: bond length, bond angle and torsional potentials. Relaxation of the required accuracy of the Newton search direction diverts the minimization search away from regions where the function is nonconvex and towards physically interesting regions. The preconditioning strategy significantly accelerates the iterative solution for the Newton search direction, and therefore reduces the computation time for each iteration. With algorithmic variations, the truncated Newton method can be formulated so that storage and computational requirements are comparable to those of the nonlinear Conjugate Gradient method. As the convergence rate of nonlinear Conjugate Gradient methods is linear and performance less predictable, the application of the truncated Newton code to potential energy functions is promising.
Refined ab initio 6‐31G split‐valence basis set optimization of the molecular structures of biphenyl in twisted, planar, and perpendicular conformations
Authors: Häfelinger Günter , Regelmann Claus 
Published: January 2005

AbstractImproved full ab initio optimizations of the molecular structure of biphenyl in twisted minimum energy, coplanar, and perpendicular conformations by use of Poles's GAUSSIAN 82 program have been performed in the 6‐31G basis set. These lead to geometries and energies of much higher reliability than our earlier STO‐3G results. The torsional angle Φmin obtained now is 45.41° in close agreement with the recent experimental value of 44.4° ± 1.2°. Calculated CC distances may be converted to experimental ED rg‐values by means of independently determined linear regression correlations with very high statistical confidence, although they agree better with experimental x ray data for coplanar biphenyl without this correction. Calculated intramolecular angles are very similar for both STO‐3G and 6‐31G basis sets. The calculated torsional energy barrier towards Φ = 90° (ΔE90) is 6.76 kJ/mol in close agreement with the experimental‐31G value of 6.5 ± 2.0 kJ/mol. For coplanar biphenyl with D2h‐symmetry the calculated torsional energy barrier ΔE0 is 13.26 kJ/mol which is surprisingly much higher than the experimental value of 6.0 ± 2.1 kJ/mol. This discrepancy could not be resolved by optimizations assumed for two kinds of distortions of planarity of orthohydrogens from the molecular plane of the coplanar carbon atoms. But for the twisted minimum energy conformation asymmetric bending of ortho‐H atoms lead to a torsional angle Φmin = 44.74° together with a dihedral angle towards ortho‐H of 1.22°, and consequently even to an increase of torsional energy barriers to ΔE0 = 13.51 and ΔE90 = 6.91 kJ/mol.
A force field for allenes and for nonlinear acetylenes within the MM2 approximation
Authors: Allinger Norman L. , Pathiaseril Ahammadunny 
Published: January 2005

AbstractGeometries and heats of formation for allenes may now be calculated with an extended version of MM2. The torsional barriers about bonds in an acetylenic unit are much more complicated than originally thought, if the unit is nonlinear. Ab initio calculations have been used to show just what these torsional barriers are, and the MM2 force field has been adapted to this information.
Molecular mechanics and molecular shape. V. on the computation of the bare surface area of molecules
Authors: Meyer A. Y. 
Published: January 2005

AbstractThis article examines the numerical estimation of molecular surface areas within the model of overlapping atomic spheres. One has the choice of either basing the estimate on all elements that contribute to the surface, or of ignoring systematically some elements in the interatomic clefts. It is argued that the second choice, even though more approximate, implicitly improves on the model and is to be preferred. Since surface areas are not measurable, the demonstration is unavoidably roundabout, relying mostly on correlation analysis. Among the regressors occur two compounded parameters. One, ratio of the surface area of the equivalent sphere to the surface area, is interpreted as a measure of molecular globularity. It reflects the molecular axis‐ratio and surface convolution. The other, ratio of the surface area to the volume, is interpreted as a measure of the global congestion of a chemical residue. Together with a measure of the local congestion at the point of attachment, it affects the steric hindrance that a residue offers. The relation between the surface area and the number of valence electrons is also discussed.
Application of SINDO1 to silicon, aluminum, and magnesium compounds
Authors: Jug Karl , Iffert Rüdiger 
Published: January 2005

AbstractSINDO1 calculations are presented for ground state geometries, heats of formation, ionization potentials and dipole moments of silicon, aluminum and magnesium compounds. These calculations are based on a new parametrization of SINDO1 for second‐row elements. Important features are the inclusion of 3d orbitals and the explicit evaluation of zero point energies. A comparison with MNDO data is presented.
Explorations on the multidimensional potential energy surface of a chiral stationary phase
Authors: Lipkowitz Kenny B. , Demeter David A. , Landwer Jo. M. , Parish Carol A. , Darden Thomas 
Published: January 2005

AbstractThe multidimensional potential energy surface for a soluble analog of a chiral phase is computed with MM2 and MNDO. Minimum energy conformations are located. The minimum energy reaction pathway between these forms is located, and the templating ability of these phases is described.
The rigorous computation of the molecular electric potential
Authors: Zauhar R. J. , Morgan R. S. 
Published: January 2005

AbstractA method is presented for the rigorous computation of the electric potential of molecules of arbitrary shape, under the assumption of continuous linear dielectric media. The computational technique involves finding the distribution of induced polarization charge on the molecular surface, and proceeds by an application of the method of boundary elements. The surface, which separates the molecular interior (of low dielectric constant) from the highly polar solvent, is given a piece‐wise analytic representation as a collection of curvilinear elements. Given a set of internal fixed charges, the distribution of polarization‐charge is found as a continuous function over the surface elements, and the electric potential (including all polarization effects) is then easily computed at any point. The method is applied to a spherical interface, and to several small molecules of biological interest, including a hexapeptide. The resulting potentials show good convergence in all cases. The future application of the method to macromolecules is discussed.