bluuebunny/crossref_metadata_2025_split huggingface dataset:
Strain energy minimization study of the mechanism of, and the barrier to, conformational interconversion in five‐membered diamine chelate rings
Authors: Hambley Trevor W. 
Published: January 2005

AbstractThe method of Lagrangian multipliers is used to constrain torsion angles during molecular mechanics refinement for the purpose of plotting strain energy against a reaction coordinate. A complete two‐dimensional analysis of the conformational interconversion from δ‐ to λ‐[Co(ethane‐1,2‐diamine) (NH3)4]3+ reveals a mechanism in which the transition state geometry has an envelope conformation and an inversion barrier of 15.7 kJ mol−1. Substitution at the carbon atoms, variation of the metal‐nitrogen distance, and replacement of the amine ligands with bidentate amines only slightly alters the inversion barrier. Substitution at the nitrogen atoms of the bidentate ligand increases the inversion barrier significantly to 24.6 kJ mol−1 for (N,N,N′,N′‐tetramethylethane‐1,2‐diamine) [(NH3)4]3+.
Molecular valence calculations on cyclohexasulfur, cycloheptasulfur, and cyclooctasulfur
Authors: Laitinen Risto S. , Randolph Bruce , Pakkanen Tapani A. 
Published: January 2005

AbstractA theoretical study of homocyclic sulfur species S6, S7, and S8 was carried out using a molecular valence method involving stepwise approximations for orthogonality and core‐valence interactions. The valence shell orbitals are described at the minimal basis level. The geometries of the molecules are predicted well as compared with other theoretical studies and the experimental values. The slight overestimation of the SS bond length is typical to the nonpolarized basis sets. The energies of the valence orbitals are well in accord with the conventional all‐electron ab initio results. The trend in the stabilities of the three molecules is discussed. The present method provides an attractive possibility to study homocyclic and heterocyclic systems involving heavier chalcogens with no increase of the computing time.
Basis sets for molecular interactions. 1. Construction and tests on (HF)2 and (H2O)2
Authors: Latajka Zdzislaw , Scheiner Steve 
Published: January 2005

AbstractBasis set superposition error (BSSE) remains one of the major difficulties besetting current ab initio calculations of molecular interactions. Despite the widespread notion that lowering of the BSSE to negligible magnitude requires extremely large basis sets, we show that simple modifications of basis sets of only moderate size (e.g., 6‐31G**) can accomplish the same end at much reduced computational expense. These modifications include reoptimization of the orbital exponents within the framework of the relevant molecules, plus addition of a single diffuse shell of sp orbitals on nonhydrogen centers. Subsequent addition of a second set of d‐functions further lowers the SCF BSSE, bringing it below 0.1 kcal/mol for both (HF)2 and (H2O)2. It is notable that addition of the latter d‐functions without prior reoptimization of the valence orbitals produces the opposite effect of an increase in the BSSE. Although the MP2 BSSE is also substantially decreased by the above modifications, it appears difficult to reduce this quantity below about 0.4 kcal/mol.
The stepwise heats of hydrogenation of barrelene, an ab initio study
Authors: Schmitz Lawrence R. , Allinger Norman L. , Flurchick Kenneth M. 
Published: January 2005

AbstractAb initio Hartree‐Fock calculations at the 6–31G*//3–21G level of theory are reported for bicyclo[2.2.2]‐2,5,7‐octatriene (barrelene), 1, bicyclo[2.2.2]‐2,5‐octadiene, 2, bicyclo[2.2.2]‐2‐octene, 3, and bicyclo‐[2.2.2]octane, 4. The stepwise heats of hydrogenation of 1 were found to be 38.1, 31.8, and 28.4 kcal/mol, respectively. The unusually large heat of hydrogenation for the first double bond is attributed to the destabilizing electronic effects involving the interaction of the three double bonds of 1.
One‐center expansion for pseudopotential matrix elements
Authors: Pelissier M. , Komiha N. , Daudey J. P. 
Published: January 2005

AbstractSemilocal pseudopotential operators can be expressed as a linear combination of nonlocal (projection) operators. Pseudopotential operator integrals over a molecular basis set are therefore reduced to linear combinations of overlap integrals products. Molecular calculations indicate that sufficient precision can be achieved with a limited number of nonlocal operators. Analytic derivatives of pseudopotential integrals are easily deduced and implemented in a standard quantum chemistry program.
Quantum mechanics of pseudorotation in ring systems: An application of the MuMATH symbolic algebra system
Authors: Trindle Carl 
Published: January 2005

AbstractA variety of quantum mechanical models have guided the interpretation of the far infrared (IR) spectrum of easily deformed ring systems, but an explicit guide to such modelling would ease further analysis. The coordinates introduced by Cremer and Pople provide a starting point for description of puckering, separate from other internal motions of a ring system. For a ring of N atoms there are N‐3 puckering modes, composed of [N ‐ (2)/2] pseudorotation “amplitudes” and [(N ‐ 3)/2] “angles.” (The brackets [] mean “truncate to the integer.”) Separation of the Schroedinger equation is possible for the “free puckerer,” the “puckerer in a box,” and for puckering opposed by a separable harmonic potential; in this latter case the energy is determined and the state is labeled by a set of pseudorotation quantum numbers Mk and radial quantum numbers nk:

Here vk is the harmonic frequency for the k‐th mode, and h is Planck's constant. Since most ring systems are nonharmonic, and require a distinct “quartic‐puckering” potential for each puckering mode, a perturbation treatment of the quartic terms is required. We provide formulas and a symbolic algebra computer program to generate expressions for integrals needed for the perturbation or linear variation modeling.
The multiple minimum problem in molecular modeling. Tree searching internal coordinate conformational space
Authors: Lipton Mark , Still W. Clark 
Published: January 2005

AbstractA general algorithm is described which exhaustively searches conformational space using an internal coordinate tree search. Using only geometrical operations and a set of criteria for eliminating chemically unreasonable structures, the algorithm generates starting geometries for optimization by molecular mechanics. An implementation of this algorithm is exceedingly fast and finds all known minima, as well as several new ones, for four test alkanes. This method makes feasible global conformational searches for molecules with up to 109 conformational possibilities.
Construction of the best set of four orthonormal 2s‐2p hybrid orbitals by least‐squares methods
Authors: Laube Thomas 
Published: January 2005

AbstractA least‐squares procedure for the construction of four 2s‐2p hybrid orbital direction vectors that deviate least from four given bond vectors emanating from a tetravalent atom is described. The procedure is used as a tool for the interpretation of structural data from X‐ray diffraction, electron diffraction, and microwave experiments.
AM1 calculations of rotation around essential single bonds and preferred conformations in conjugated molecules
Authors: Fabian Walter M. F. 
Published: January 2005

AbstractEquilibrium twist angles, rotational barriers around essential single bonds, and preferred conformations for over 60 conjugated organic molecules were calculated using the semiempirical AM1 (Austin model 1) method. Comparison withab initioand experimental data shows that AM1 can be applied quite successfully to conformational problems of this type. Relatively large errors are, however, found for compounds in which lone pair–hydrogen and especially lone pair–lone pair interactions are decisive for their conformational behavior. AM1‐calculated rotational barriers in conjugated molecules, however, are found to be much too low. Moreover, AM1 does not seem to even correctly reproduce the trend of rotational barriers within a series of structurally related compounds.E/Zenergy differences obtained by AM1 are also frequently considerably too low. In contrast to rotational barriers, their trends and thus conformational preferences, however, are quite satisfactorily calculated by this method. Ionization potentials obtained by AM1 are too high by about 0.5 eV. However, trends are quite well predicted.
Numerical sensitivity of trajectories across conformational energy hypersurfaces from geometry optimized molecular orbital calculations: AM1, MNDO, and MINDO/3
Authors: Boyd Donald B. , Smith David W. , Stewart James J. P. , Wimmer Erich 
Published: January 2005

AbstractThe monocyclic β‐lactam [[4(S)‐methyl‐2‐oxo‐1‐azetidinyl]thia]acetic acid was studied by the semiempirical molecular orbital methods AM1, MNDO, and MINDO/3. Using the reaction coordinate option in the program MOPAC on VAX and Cray X‐MP computers, the potential energy curve was calculated for rotation of the C2‐N1‐S‐C torsional angle in the conformationally flexible side chain while optimizing all other geometrical variables in the molecule. The trajectory taken during geometry optimization was found to be sensitive to the computer, the program version, the convergence criteria, and the degree of code optimization used in the calculation. In order to reduce the likelihood of spurious results, conformational or reaction energy hypersurfaces need to be calculated with the more precise SCF convergence and minimization criteria available in programs for MINDO/3, MNDO, and AM1 calculations. The nitrogen in the model β‐lactam antibiotic is predicted to invert periodically as the dihedral angle to the exocyclic N‐substituent sweeps through 360°.
Computer generation of spectra of graphs: Applications to C60 clusters and other systems
Authors: Balasubramanian K. , Liu Xiaoyu 
Published: January 2005

AbstractA computer code based on the Givens–Householder matrix diagonalization method is used to calculate the spectra of graphs containing a large number of vertices. The code is most general in that it can handle graphs containing 200 or more vertices. Further, the code can be used to generate the spectra of weighted graphs. The program requires as input only the neighborhood table of the graph. The spectra of many graphs are generated for the first time in less than a few minutes of computer time. Applications to a number of chemical systems including two forms (foot and hand) of the recently synthesized C60 cluster and the effect of bond alternation on these systems are discussed. In addition, the spectra of square and honeycomb lattices and the characteristic polynomials of the foot and hand forms of the C60 cluster are obtained.
Modified MINDO/3 13C chemical shift calculations for simple hydrocarbons
Authors: Chesnut D. B. , Zhang C. 
Published: January 2005

AbstractCalculations of 13C chemical shifts in some simple hydrocarbons have been carried out using the GIAO approach in the MINDO/3 semiempirical formalism. In order to achieve reasonable agreement with experiment it is necessary to modify (increase) the vacant orbital energies in the MINDO/3 calculation in order to reduce the magnitude of the paramagnetic contribution, and to also modify this dominant term by generally reducing it as a function of the number of hydrogen and carbon atoms bonded to the resonant nucleus in question. For a set of 34 resonant nuclei of the simpler hydrocarbons, agreement with experiment of the order of 7.8 ppm is attained; however, pathological cases such as cyclopropane and some simple allenes continue to cause problems, increasing the standard deviation of the full set to 12.5 ppm. Our results indicate that the MINDO/3 approach is as viable for 13C chemical shift calculations as other semiempirical approaches, all of which seem currently to be limited to a standard deviation of the order of 10 ppm.
Fast algorithm for ring perception
Authors: Matyska Luděk 
Published: January 2005

AbstractAn algorithm for finding rings in graphs is presented. The algorithm is based on the Welch‐Assembly‐Gibbs algorithm of Wipke and Dyott but using the homeomorphically reduced pruned graph (the extension of HRG of Balaban et al). The algorithm is able to generate both the fundamental set of rings and all possible rings in a given graph. The time and storage needs are superior to both underlying algorithms. The CPU times of the old and new algorithms are given.
Rotation around the C1C2 bond of propylamine, an ab initio study
Authors: Schmitz Lawrence R. , Allinger Norman L. , Profeta Salvatore 
Published: January 2005

AbstractAb initio Hartree‐Fock calculations at the 6–31G*//6–31G* and MP3/6–31G*//6–31G* levels of theory are reported for propylamine. All ten stationary points needed in a description of the rotation around the C1–C2 bond have been located on the 6–31G* surface and each of these points has been examined at the MP3 level.
General algorithm for calculating vibrational–librational states of a rigid molecule in an external potential. Application to benzene–water complexes
Authors: Linse Per 
Published: January 2005

AbstractA general algorithm of calculating the eigenstates of a rigid molecule trapped in an external potential is reported. The wave function and the potential are expanded about a common reference configuration. The expansion coefficients of the wave function are variationally determined. Contracted basis functions may be used to restrict the number of expansion coefficients. The use of the algorithm is illustrated by calculations of intermolecular eigenstates of benzene–water complexes.
Ab initio pseudopotential study of the fluxional behavior in tetrahydroborate complexes. Many‐body contributions to the energy barriers of NaBH4, AlH2BH4, and GaH2BH4
Authors: Barone Vincenzo , Minichino Camilla , Lelj Francesco , Russo Nino 
Published: January 2005

AbstractThe relative stabilities of the bidentate and tridentate configurations of the complex hydrides NaBH4, AlH2BH4, and GaH2BH4 have been computed both at the Hartree‐Fock and post‐Hartree‐Fock levels using the ab initio pseudopotential method. For both compounds correlation effects favor the configurations with the highest coordination of the metal. The changes with respect to HF results are not very large, so that second‐order perturbative computation of correlation energy is sufficient to give accurate results.
Determination of the major solution conformation of tyrocidine A, using molecular mechanics energy minimization and NMR‐derived distance and torsion angle constraints
Authors: Tonge Alan P. , Murray‐rust Peter , Gibbons William A. , McLachlan Lesley K. 
Published: January 2005

AbstractMolecular mechanics energy calculations coupled with nuclear magnetic resonance‐determined distance and torsion angle constraints have been used to determine the three‐dimensional structure of tyrocidine A, a cyclic decapeptide which exists largely as a single conformation in solution. Two open‐chain polyalanine models were used to represent separate halves of the peptide backbone and a combinatorial method of searching conformation space used to generate candidate structures consistent with experimental distance constraints. These structures were energy‐minimized using the AMBER molecular mechanics forcefield and the resulting conformations classified by factor analysis of their Cartesian coordinates. Representative low‐energy conformers of the two halves of the backbone were fused together and two candidate conformations of the completed backbone refined by further minimization using both distance and torsional constraints. Side chains were then added as their experimentally preferred rotamers and the whole molecule minimized without constraints to give the final model structure. This shows type II' and III ß turns at residues 4–5 and 9–10, respectively, coupled by twisted antiparallel strands which show hydrogen bonds between all four pairs of opposing peptide groups. The backbone conformation of residues 2–6 closely resembles that found in the crystal structure of gramicidin S.
Electron donor‐acceptor complexes: Evaluation of MNDO as a computational tool to probe intermolecular interactions
Authors: Glauser William A. , Raber Douglas J. , Stevens Brian 
Published: January 2005

AbstractDonor‐acceptor pairs form EDA complexes that exist as conformational isomers exhibiting different ground‐state and photochemical properties. We have sought a rapid, general, and accurate quantum mechanical computational method to generate potential energy surfaces that are representative of the donor‐acceptor intermolecular interactions at the self‐consistent field (SCF) level. The semiempirical molecular orbital (MO) method MNDO has been compared to ab initio methods to assess its behavior with respect to energy, dipole moment and ionization potential shifts. MNDO correctly distinguishes between repulsive and bound EDA complex states at the SCF level and produces potential curves that are smooth and free of spurious minima or cusps. MNDO curves are systematically more repulsive than those for ab initio STO‐3G calculations; calculated interaction energies exhibit a mean absolute deviation of 2.90 kcal/mol. MNDO appears to provide a reliable qualitative estimate of the nondispersion portion of the interaction energy. Limitations and errors arising from minimal basis sets, single determinants, and neglect of dispersion are discussed.
Shape characterization of some molecular model surfaces
Authors: Arteca Gustavo A. , Mezey Paul G. 
Published: January 2005

AbstractAn algebraic method is proposed to represent and to characterize in a concise way the shape of an arbitrarily asymmetrical surface composed from spherical pieces. These surfaces include, among others, the well‐known van der Waals surfaces. The procedure is based on the computation of a hierarchy of homology groups (“shape groups”) of algebraic topology, for a family of objects defined by the original surface. The technique uses the same input information as that necessary to produce a graphical display of the molecular surface. However, the actual figure is not necessary for the computation of the shape groups. Only a classification of the points on the surface, according to their position with respect to the intersection of two or more spheres, is needed. The result is a purely algebraic characterization that can be obtained and stored by a computer, and that may prove to be useful when comparing shapes of different molecules. Illustrative examples are provided for different molecules, as well as for different conformations of the same molecule.
MC‐SCF and CI calculations on four isomers of Si6H6
Authors: Sax Alexander F. , Kalcher Josef , Janoschek Rudolf 
Published: January 2005

AbstractThe four isomers of Si6 H6, hexasilabenzene (1), hexasilaprismane (2), hexasila‐Dewar benzene (3), and tris‐(disilanediyl) (4), have been investigated, using highly correlated wavefunctions in conjunction with a local pseudopotential approach. At the Hartree‐Fock level 1 (D6h), 2 (D3h), and 3 (C2v) are established as minima by means of the harmonic vibrational frequencies. Inclusion of the most important correlation corrections via CI however, provokes a significant puckering of 1 resulting in a D3d structure, 7.1 kJ/mol below the planar conformer. The detailed analysis shows unambiguously that the propensity to puckering is due solely to the correlation contributions from the σ framework while correlation of the π electrons is of little relevance. Isomer 2 turns out to be the most stable of the investigated isomers lying 41 kJ/mol below 1 (D3d). Isomers 3 and 4 are more than 100 kJ/mol higher in energy. The SiSi bond energies of 1 and 2 are determined as 251 and 176 kJ/mol, respectively.
Ab initio calculations on large molecules: The multiplicative integral approximation
Authors: Van Alsenoy C. 
Published: January 2005

AbstractIn the multiplicative integral approximation (MIA), two‐electron integrals are evaluated using an expansion of a product of two Gaussians in terms of auxiliary functions. An estimator of the error introduced by the approximation is incorporated in the self‐consistent field (SCF) calculations and the integrals for which the error estimate is larger than a preset value are systematically corrected. In this way the results of a MIA‐assisted calculation have the same accuracy as a conventional calculation. The full exploitation of the expansion technique while constructing the Fock‐matrix allows important time savings. Results are presented for a number of test cases.
Computer assisted structure–taste studies on sulfamates by pattern recognition method using graph theoretical invariants
Authors: Okuyama Tohru , Miyashita Yoshikatsu , Kanaya Shigehiko , Katsumi Hiroyuki , Sasaki Shin‐Ichi , Randić Milan 
Published: January 2005

AbstractStructure–taste relationships for 25 acyclic and 20 cyclic carbosulfamates were investigated by means of pattern recognition using different graph theoretical invariants as molecular substituent descriptors. The SIMCA method was used to classify the compounds into sweet and nonsweet classes. All selected graph theoretical invariants that are related to the “rooted” vertex were found to give promising results. Using the weighted path numbers and self‐returning walks for the rooted atom as descriptors of substituents, we found 87% of acyclic compounds were correctly classified. Using the atomic path numbers for the rooted atom as descriptors of substituents, we found 81% of cyclic compounds were correctly classified. These results are better than previously used shape and size substituent descriptors. It may be concluded that the graph theoretical descriptors have great potential in encoding structure components in structure–activity studies (SAR) studies.
Conformational energetics of 1,3‐dichloropropane as predicted by several calculations methods
Authors: Holder Andrew J. , Wertz David L. 
Published: January 2005

AbstractTwo semiempirical methods (MNDO and AM1), a molecular mechanics technique (MM2) and two ab initio approaches (6–31G* full optimization and 3–21G/6–31G*) were used to calculate the ordering of and energy difference between conformers in 1,3‐dichloropropane. The semiempirical methods did not order the conformers properly or predict correct energy differences. Both ab initio methods ordered the conformers and predicted energy differences correctly, with the 6–31G* full optimization performing slightly better. The MM2 results were presented for calculations involving a force field with no hydrogens and a full force field of all atoms. The full force field properly ordered the conformers but did not correctly predict the energy differences. The nonhydrogen field ordered the conformers based on the Cl…Cl nonbonded distance. The data show that conformer stability is not a simple matter of maximizing the Cl…Cl nonbonded distance, but is also related to some other stabilizing interaction(s).
Computation of one and two electron spin‐orbit integrals
Authors: King Harry F. , Furlani Thomas R. 
Published: January 2005

AbstractMethods for the computation of one‐ and two‐electron spin‐orbit integrals over Gaussian‐type basis functions are presented. We show that existing nuclear‐attraction and electron‐repulsion integral codes can be readily adapted for the efficient evaluation of spin‐orbit integrals; in particular, one can take advantage of recent advances in the computation of derivative integrals. Recurrence relations for the nuclear attraction integrals are also developed.
Ab initio calculations relevant to the mechanism of chemical carcinogenesis by N‐nitrosamines. VIII. Effects of hydration on various reactions involved in the formation and metabolism of N‐nitrosamines
Authors: Bonaccorsi Rosanna , Tomasi Jocopo , Reynolds Christopher A. , Thomson C. 
Published: January 2005

AbstractA number of important reactions involved in the formation and metabolism of N‐nitrosamines have been studied using a modified reaction field method which treats the solute quantum mechanically and the solvent as a polarized dielectric.