bluuebunny/crossref_metadata_2025 huggingface dataset:
AM1 calculations of rotation around essential single bonds and preferred conformations in conjugated molecules
Authors: Fabian Walter M. F.
Published: January 2005

Equilibrium 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

The 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

A 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

Calculations 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

An 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

Ab 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

A 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

The 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

Molecular 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

Donor‐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

An 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

The 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

In 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

Structure–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

Two 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

Methods 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

A 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.
Theoretical calculations of proton affinities of azines. Prediction of the relative basicities and preferred protonation sites
Authors: Sanz Javier Fernández , Anguiano Julio , Vilarrasa Jaume
Published: January 2005

Theoretical calculations at the 3‐21G and 3‐21 + G ab initio levels and at the MNDO and AM1 semiempirical levels of several six‐membered nitrogenated heterocycles and their protonated species have been carried out. The 3–21G calculated proton affinities are systematically too high, in relation to the available experimental data, and it is estimated that inclusion of electron correlation and zero‐point corrections is not sufficient to reach the desired agreement; however, additional inclusion of diffuse functions (3‐21 + G/3‐21G calculations) lowers the calculated proton affinities by 5.4–6.8 kcal/mol, a good agreement being thus obtained, at least for 1–7. On the other hand, semiempirical methods underestimate the repulsion between each pair of vicinal nitrogens; however, if a correction of ˜9 kcal/mol is added to the AM1 results for each pair of neighboring nitrogens containing lone pairs of electrons, the corresponding proton affinities match fairly well the available exoerimental data and corrected 3‐21 + G results. As expected, all methods predict that the introduction of additional nitrogens decreases the overall absolute basicity. Futhermore, comparison of the relative basicity of the isomers and of the preferred protonation site for each isomer indicates that nitrogen atoms with (only) one α‐nitrogen and without a γ‐nitrogen are more basic than any others. In benzazines, MNDO and AM1 suggest that the 2,3‐diaza arrangement has a higher intrinsic basicity than the 1,2‐diaza arrangement.
Calculation of the one‐electron two‐center integrals with STOS using recurrence‐based algorithms
Authors: Fernández Rico J. , López R. , Ramírez G.
Published: January 2005

We present a new algorithm for the calculation of two‐center one‐electron integrals with STOS based on two sets of recurrence relations. The first one enables us to calculate any of these integrals in terms of a few “basic integrals.” Furthermore, these basic integrals are written in terms of certain auxiliary functions which can be obtained through the second set of relations from only two starting values. We give also simple formulas for these starting quantities. Finally, the numerical stability, accuracy, and speed of the different steps of the algorithm are analyzed.
On the computation of stationary points on potential energy hypersurfaces
Authors: Kliesch Wolfgang , Schenk Klaus , Heidrich Dietmar , Dachsel Holger
Published: January 2005

In this article, a modification of a procedure proposed by Zirrilliet al.for solving nonlinear equations is presented. The method permits the computation of minima and saddle points of energy functionals. The Müller‐Brown test potential and the quantum chemical description of some proton transfer reactions are given as examples.
Doublet instability and the molecular structure of AlO2
Authors: Rubio J. , Ricart J. M. , Illas F.
Published: January 2005

The possible Cs, C2v, and C∞v structures of AlO2 corresponding to the two lowest electronic states which dissociate into the neutral Al(2P) and O2(3Σg−) fragments have been investigated at the ab initio self‐consistent field (SCF) and CI levels using nonempirical pseudopotentials. The most stable structure corresponds to a C2v symmetry in the 2A2 electronic state. However, this structure presents the three‐center three‐electron Hartree‐Fock instability and CASSCF calculations were necessary to unequivocally characterize it as true minimum. Moreover, only another stable structure, of C2v geometry, was found to be a minimum, corresponding to a low‐lying excited state of 2A1 symmetry. The optimized C∞v structures were not minima on the corresponding potential energy surfaces and no evidence of any stable Cs structure was found. Calculating values are compared with the different experimental data obtained from the reaction of Al and O2 in frozen gas inert matrices.
On testing difference equations for the diatomic eigenvalue problem
Authors: Kobeissi Hafez , Kobeissi Majida , Hajj Ali El
Published: January 2005

The determination of the vibration‐rotation eigenvalues (for an electronic state of a diatomic molecule) is done using various algorithms, where the differential equation y″ + f(r)y = 0 (with given initial values yo and y′o at an origin ro) is to be integrated, that is, to be replaced by a “convenient” difference equation (DE). The best known are those of: Numerov (N), Runge‐Kutta (RK), and the Taylor series expansion (TS). Each algorithm is commonly associated with an “appropriate” DE, and the conventional comparisons of algorithms and/or DE are often misleading. This work compares different DE used in the same algorithm for the same potential and with the same tests. It considers the mentioned conventional DE, and three nonconventional ones: Hajj et al. (HKN) [J. Comp. Phys., 16, 150 (1974)], Cash and Raptis (CR) [Comput. Phys. Commun., 32, 299 (1984)], and Kobeissi “integrals superposition” (IS) [J. Phys. B, 15, 693 (1982)]. A convenient test of these DE is presented and applied. It is shown that: (i) if ϵ is the average error by using Numerov DE, it is of 4ϵ for RK, 2ϵ for TS, ϵ × 10−3 for HKN, 4ϵ × 10−4 for CR and ϵ × 10−6 for IS; (ii) if τ is the average computing time by using Numerov DE, it is of 2.9τ for RK, 3.4τ for TS, 1.5τ for HKN, 2.7τ for CR and 0.9τ for IS.
Molecular mechanics of peroxides. I. Parametrization and conformational analysis of linear compounds
Authors: Carballeira Luis , Mosquera Ricardo A. , Ríos Miguel A.
Published: January 2005

A force field has been developed for use in MM2 calculations of geometric and energy data for linear peroxides R1OOR2 and tested in some of them (R1, R2 = H, Me, Et, Pri, But). The field obtained yield results that agree considerably better with experimental and ab initio data than those afforded by the only set of estimated parameters hitherto available.
A new tool for the rapid estimation of charge distribution
Authors: Houser John J. , Klopman Gilles
Published: January 2005

A method has been developed which uses a rapid connectivity‐based calculation to give a reasonable approximation of CNDO σ and π charges for most carbons in saturated and unsaturated hydrocarbons. In this calculation an appropriately parameterized Del Re method is used to calculate the σ charges, and if the molecule is unsaturated, these charges are used to modify the diagonal elements in a Hückel matrix, reducing the normally exaggerated π charges. The CNDO charges are obtained from “single point” calculations, using optimized geometries derived from molecular mechanics. The Del Re/Hückel method is most reliable where steric and hyperconjugative effects are absent.
Theoretical studies of conjugated systems containing CC and CN fragments and their alkyl and amino derivatives
Authors: Kao J.
Published: January 2005

Ab initio molecular orbital theory has been systematically employed to investigate the structures, energies, and conformations of 27 nitrogen‐containing compounds. A force field has been developed, on the basis of available experimental and theoretical data, to permit extension of the molecular orbital‐based molecular mechanics calculations to hetero‐conjugated systems. Structures, heats of formation, and conformations of more than 65 molecules were studied by the developed force field and the results were compared with the available experimental data.
Ab initio SCF MO results for the carborane isomers 3,5‐C2B6H8, 1, 7‐C2B7H9, and 1,2‐C2B7H9
Authors: Gimarc Benjamin M. , Dai Baiching , Ott Jane J.
Published: January 2005

We report the geometry‐optimized total energies and bond distances for the closo‐carborane isomers 3,5‐C2B6H8, 1,7‐C2B7H9, and 1,2‐C2B7H9 calculated by the ab initio SCF MO method using the STO‐3G basis set. Relative energies are compared with those of the other carborane isomers in the 8‐ and 9‐ atom classes. These results complete the set of calculations at the same level of theory for all deltahedral carborane isomers except for those of the 11‐atom class.
Guanidinium‐Type resonance stabilization and its biological implications. I. the guanidine and extended‐guanidine series
Authors: Williams Martin L. , Gready Jill E.
Published: January 2005

An unusual type of π‐electron delocalization in Y‐shaped molecules related to guanidine and its protonated form, the guanidinium ion, has been studied by ab initio methods at the STO‐3G and 3‐21G levels. Results are reported for tautomeric, rotameric, and protonated forms of the oxygen‐substituted guanidine series (urea, carbamic, and carbonic acids); “extended‐guanidine” (aminomethylene guanidine) including pseudocyclic forms; and simple ring systems in which the extended‐guanidine group is incorporated (3‐amino‐1,2,4‐triazole, 2,4‐diaminopyrimidine). Both the guanidine and guanidinium type stabilizations have been characterized in terms of a number of structural and energetic parameters: degree of single/double bond character from bond lengths and π‐bond orders, electron distributions, and protonation energies. The major finding is that the structural and energetic properties of the isolated extended‐guanidinium group resemble those of the group when incorporated within 6‐membered heterocyclic or heterobicyclic rings, although the details vary with the nature of the ring and possibility of reinforcement or interference with the substructure resonance from overall ring delocalization. The implications for stabilization of the protonated forms of some biologically important pteridines is discussed.
Correlation analysis of substituent effects on the acidity of benzoic acids by the AM1 method
Authors: Sotomatsu Tomoko , Murata Yoshiyuki , Fujita Toshio
Published: January 2005

Theoretical analysis of the electronic effect of aromatic substituents was done with the use of the AM1 computational procedure. The gas‐phase acidity of substituted benzoic acids was linear with the difference in the heat of formation between corresponding benzoic acids and benzoate anions, the energy of the highest occupied molecular orbital, and the net charge on the acidic oxygen atoms of the corresponding benzoate anions. The Hammett σ constant was linearly correlated with the net charge on the atoms of the acid moiety of substituted benzoic acids. The AM1 computational procedure satisfactorily reproduced the electronic properties of a wide variety of substituents.
Basis set selections for relativistic self‐consistent field calculations
Authors: Lee Yoon Sup , Baeck Kyoung Koo , McLean A. D.
Published: January 2005

Practical methods of generating reliable and economic basis sets for relativistic self‐consistent fields (RSCF) calculations are developed. Large component basis sets are generated from constrained optimizations of exponents in the nonrelativistic atomic calculations for light atoms. For heavy atoms, large component basis sets for inner core orbitals are generated by fitting numerical atomic spinors of Dirac‐Hartree‐Fock calculations with appropriate number of Slater‐type functions. Small component basis sets are obtained by using the kinetic balance condition and other computational criteria. With judicious selections of the basis sets, virtual orbitals in RSCF calculations become very similar to those in nonrelativistic calculations, implying that relativistic virtual orbitals can be used in electron correlation calculations in the same manner as the conventional nonrelativistic virtual orbitals. It is also evident that the Koopmans' theorem is also valid in RSCF results.
Stochastic search for the conformations of bicyclic hydrocarbons
Authors: Saunders Martin
Published: January 2005

The stochastic search method was used to seek all of the conformations for 32 bicyclic hydrocarbons. Since the size of the random kick used is sufficient to invert the configurations of carbon atoms, the out, out, in, out, and in, in conformations were all found in a single stochastic run for each hydrocarbon. The lowest energy conformer obtained in each category is reported. A modification of the program to prevent inversion of configuration was developed. It was found, in some cases, that in, in and out, out isomers for some bicyclic hydrocarbons were interconverted by this modified program, presumably through the “homeomorphic isomerization” process described by Park and Simmons. A statistical formula for estimating the approximate chances of finding (or missing) any conformer as a function of the number of random kicks given is derived and presented.
The gradient‐optimized geometry of haloperidol at the 4‐21G level
Authors: Van Alsenoy C. , Lenstra A. T. H. , Geise H. J.
Published: January 2005

The molecular structure of haloperidol as free base in its C(13)—C(14) trans form is optimized using Pulay's gradient method and a 4‐21G basis set without any geometrical constraints. The resulting structure is compared with the experimental structure of the free base in the C(13)—C(14) gauche form and with the experimental structure of the HBr salt of haloperidol in the C(13)—C(14) trans form. Apart from the obvious differences, the two rotameric forms of the free base show many similarities. This, together with the manner in which the differences of the two experimental structures are distributed over the haloperidol molecule, leads to the conclusion that the conspicuous differences between the experimental structures are caused by inaccuracies in the X‐ray determination of the HBr salt. Deviations of phenyl ring geometries from D6h symmetry and the asymmetry of the conformation around C(1)—C(9) could be rationalized by intramolecular effects.
MC‐SCF and CI calculations on the Si4H4 system
Authors: Sax Alexander F. , Kalcher Josef
Published: January 2005

The lowest singlet along with selected high spin states of three isomers of Si4H4 have been investigated, using highly correlated wave functions in conjunction with a local pseudopotential approach. Tetrasilabicyclo[1.1.0]but‐1(3)‐ene 1 and tetrasilatetrahedrane 3a are established as true minima by means of the harmonic vibrational frequencies. The local minimum for tetrasilacyclobutadiene is not a planar 2a but a puckered conformer 2b. Isomer 1 was found to be the most stable of the investigated isomers lying 1.96 eV below 3a and 1.04 eV below 2b. A previously examined bond stretch isomer of tetrasilatetrahedrane 3b lies only 0.2 eV above isomer 1. The SiSi bond energies of 2b, 3a, and 3b are determined as 208, 124, and 228 kJ/mol, respectively. An explanation of the bonding situation in 1 is given.
Basis set dependence, precision, and accuracy of full ab initio gradient optimizations of molecular structures of nonstrained hydrocarbons. I. CC bond lengths
Authors: Häfelinger Günter , Regelmann Claus Ulrich , Krygowski Tadeusz Marek , Wozniak Krzysztof
Published: January 2005

Different highly accurate experimental determinations of molecular structures (ED: rg and r0α, MW: r0, rs, and rz, and X‐ray distances) of 14 unstrained hydrocarbons have been linearly correlated with corresponding self‐consistent field Hartree Fock (SCF HF) ab initio full gradient‐optimized structures. From the eight applied basis sets (STO‐3G, STO‐6G; 3‐21G, 4‐31G, 6‐31G, 6‐311G; 6‐31G*, and 6‐31G**) the 6‐31G basis set, although not best regarding total energies, yields statistically the most precise regression equation, which allows the prediction of ED rg CC distances as reliable as the best experimental determinations. Surprisingly the accuracy of all calculated CC distances (measured as difference Δ between calculated CC distances and experimental ED rg values) depends linearly on bond distances, with the largest deviations being observed for triple bonds. This seems to be a clear indication of different influences of correlation effects on calculated geometries which are neglected in the applied HF treatment. The linear regression equations presented here allow the prediction of any kind of experimental CC distance parameters for each of the eight basis sets considered. Even experimentally unknown re CC distances may be predicted from these single determinantal HF optimizations.
A submatrix algorithm for the matrix‐vector multiplication of very large matrices
Authors: Lindh Roland , Malmquist Per‐Årke
Published: January 2005

In self‐consistent field (SCF) calculations the construction of the Fock matrix is most time‐consuming step. The Fock matrix construction may formally be seen as a matrix‐vector multiplication, where the matrix is the supermatrix,𝒫ijkl, and the vector is the first‐order density matrix, γij. This formalism should be optimal for vector machines. This is not, however, fully utilized in most programs running on computers with small core memory. The size of the 𝒫 matrix, typically in the order of 106–108 elements, has forced programmers to implement other nonvectorizable methods. We will present a submatrixbased algorithm which will partition the supermatrix so that vectorizable methods can be employed. The method will also reduce the input/output.
Ab initio study of the proton affinity of a number of ortho‐substituted pyridines
Authors: Martin J. M. L. , François J. P. , Gijbels R.
Published: January 2005

The proton affinity, dipole moment, and first vertical ionization potential of a number of ortho‐mono‐substituted pyridines are computed at the restricted Hartree‐Fock level, using a number of different basis sets. Some approximations concerning the geometry, the force constants, and the basis set superposition error are introduced. The effect of both the basis set and the approximations is investigated systematically. Two nonstandard basis sets, 4‐31G(*) and 4‐31+G(*), in which polarization functions are only applied to heteroatoms, are defined. A qualitative explanation for the effects of electron correlation on the proton affinity is given and underbuilt with the results of some MP2 calculations. While accuracy is maintained, computational cost is reduced very substantially.
Prolog program for subgraph enumeration and calculation of molecular connectivity indexes
Authors: Takeuchi Kei , Kuroda Chiaki , Ishida Masaru
Published: January 2005

Prolog is applied to calculate the zero‐ through the sixth‐order molecular connectivity indexes. A description of the program is given. Enumeration of substructure fragments, which is the most time‐consuming part for this calculation, can be executed quite compactly by Prolog. For this execution, molecular structures and substructures are represented by Prolog facts and rules. An example of calculation is presented for a polycyclic structure. In addition, the method to increase the calculation speed is demonstrated.
Computer generation of the character tables of the symmetric groups (Sn)
Authors: Liu Xiaoyu , Balasubramanian K.
Published: January 2005

Algorithms and codes based on the method of Schur functions and Frobenius' theorem are used to generate the character tables of the symmetric groups (Sn) containing n! elements. The codes developed can generate characters of Sn up to n = 20.
Degenerate lithium‐hydrogen exchange reactions: Ab initio models for metallation mechanisms involving H2, CH4, NH3, H2O, and HF
Authors: Kaufmann Elmar , Ragué Schleyer Paul Von
Published: January 2005

Hydrogen exchange reactions between lithium and sodium compounds, MX (M=Li: X=H, CH3, NH2, OH, F; M=Na: X=CH3), and the corresponding hydrides, HX, have been modelled by means of ab initio calculations including electron correlation and zero point energy (ZPE) corrections. Small or no activation barriers (from the initial complexes) are encountered in systems involving lone pairs (10.8, 2.4, 0.0 kcal/mol for X=NH2, OH, F, respectively). Since the association energies of the initial complexes are much larger (21.0, 20.4, 23.5 kcal/mol, respectively; MP2/6–31+G*/6–31+G* + ZPE), such exchange reactions should occur spontaneously in the gas phase. The methyl systems (X=CH3) have the largest barriers: 26.7 (M=Li) and 31.7 (M=Na) kcal/mol (MP2/6–31+G*/6–31G* + ZPE), and the initial complexes are only weakly bound. The significance of these systems as models for hydrogen exchange reactions in complexes of electropositive transition metals is discussed. However, the gegenion‐free exchange of hydrogen between CH3 and CH4 has a much lower, 11.8 kcal/mol barrier (MP2/6–31+G*/6–31+G* + ZPE). All the transition structures are highly ionic (charges on the metals > +0.8). The effect of aggregation has been considered by examining the hydrogen exchange between (LiX)2 and HX(X=H, CH3, NH2, OH). Although these dimer reactions formally involve six, instead of four electrons, no “aromatic” preference is observed.
Atomic charge models for polypeptides derived from ab initio calculations
Authors: Bellido M. N. , Rullmann J. A. C.
Published: January 2005

Ab Initio charge distributions for amino acid dipeptides are derived utilizing two medium‐sized basis sets. Peptide charges differ in two ways from those of existing force fields: the magnitude of the peptide dipole and the dependency on the residue type. The merging of charge distributions of side chain and backbone fragments within a semiclassical model including polarization is investigated. Polarization plays a small, but distinct role in improving the correspondence with ab initio data derived for the complete dipeptide. A description in terms of partly overlapping, interacting fragments correlates well with the ab initio data. The method can be used to derive the electrostatic properties of biological macromolecules by combining accurate descriptions of short range interactions (using good quality basis sets on not too small fragments) with good classical models of long range interactions (using multicenter multipole expansions and atomic polarizability tensors). Factors limiting the accuracy of the present representations are discussed.
Molecular mechanics (MM2) calculations on peptides and on the protein Crambin using the CYBER 205
Authors: Lii Jenn‐Huei , Gallion Steven , Bender Charles , Wikström Håkan , Allinger Norman L. , Flurchick Kenneth M. , Teeter M. M.
Published: January 2005

The MM2 potential functions for amides and peptides have been further extended by examining the experimental crystal structures for cyclo‐(‐Ala‐Ala‐Gly‐Gly‐Ala‐Gly‐), I, and cyclo‐(‐Ala‐Ala‐Gly‐Ala‐Gly‐Gly‐), II. The force field obtained was then applied to a study of the structure of the hydrophobic protein Crambin, for which a high resolution crystal structure is available. The energy minimization was carried out using a version of MM2 adapted to the CYBER 205.
An ab initio molecular orbital study of the structures and energies of neutral and charged bimolecular complexes of NH3 with the hydrides AHn (A = N, O, F, P, S, and Cl)
Authors: Del Bene Janet E.
Published: January 2005

Hartree‐Fock 6‐31G(d) structures for the neutral, positive ion, and negative ion bimolecular complexes of NH3 with the first‐ and second‐row hydrides AHn (AHn = NH3, OH2, FH, PH3, SH2, and ClH) have been determined. All of the stable neutral complexes except (NH3)2, the positive ion complexes with NH3 as the proton acceptor, and the negative ion complexes containing first‐row anions exhibit conventional hydrogen bonded structures with essentially linear hydrogen bonds and directed lone pairs of electrons. The positive ion complex NH4+ …︁ OH2 has the dipole moment vector of H2O instead of a lone pair directed along the intermolecular line, while the complexes of NH4+ with SH2, FH, and ClH have structures intermediate between the lone‐pair directed and dipole directed forms. The negative ion complexes containing second‐row anions have nonlinear hydrogen bonds. The addition of diffuse functions on nonhydrogen atoms to the valence double‐split plus polarization 6‐31G(d,p) basis set usually decreases the computed stabilization energies of these complexes. Splitting d polarization functions usually destabilizes these complexes, whereas splitting p polarization functions either has no effect or leads to stabilization. The overall effect of augmenting the 6‐31G(d,p) basis set with diffuse functions on nonhydrogen atoms and two sets of polarization functions is to lower computed stabilization energies. Electron correlation stabilizes all of these complexes. The second‐order Møller–Plesset correlation term is the largest term and always has a stabilizing effect, whereas the third and fourth‐order terms are smaller and often of opposite sign. The recommended level of theory for computing the stabilization energies of these complexes is MP2/6‐31+G(2d,2p), although MP2/6‐31+G(d,p) is appropriate for the negative ion complexes.
Locally dense basis sets for chemical shift calculations
Authors: Chesnut D. B. , Moore K. D.
Published: January 2005

Calculations of chemical shifts have been carried out using “locally dense” basis sets for the resonant atom of interest, and smaller, attenuated sets on other atoms in the molecule. For carbon, calculations involving a 6‐311G(d) triply split valence set with polarization on the resonant atom and 3‐21G atomic bases on other heavy atoms result in good agreement with experiment, and are virtually identical to those found employing the larger basis on all atoms. For species such as nitrogen, oxygen, and fluorine where standard balanced basis sets do not agree well with experiment, use of attenuated sets fail as well. The use of locally dense basis sets permits calculations previously impractical, and the successful application to carbon suggests that the chemical shift is most dependent on the local basis set, and less so on whether or not a balanced or unbalanced calculation is being carried out.
3S‐ Versus 1s‐type Gaussian primitives: Modifications of the 3‐21G(*) basis set for the sulfur atom
Authors: Sabio Michael , Topiol Sid
Published: January 2005

The complete set of second‐order Gaussian functions (6D) includes a totally symmetric second‐order Gaussian function (3s‐type) in addition to the five d‐type functions. This 3s‐type function in the 3–21G(*) basis set for the sulfur atom is described (1) in terms of its geometric and electronic effects observed in the sulfur atom and in four sulfur‐containing molecules and (2) by the ability of a single zero‐order 1s‐type Gaussian function (with various exponents) to replace it in ab initio Hartree–Fock calculations. The geometry of the molecules (dihydrogen sulfide, dihydrogen thioketone, dihydrogen disulfide, and methanesulfonamide) were obtained using various semiempirical and ab initio methods. It is found that the 3s‐type function lowers the energy relative to that calculated with the 3–21G(*) basis set with only five second‐order Gaussian functions by ca. 46–48 kcal/mol per sulfur atom. Only small changes in geometry are observed when the latter basis set is augmented with a 3s or 1s function. When the exponent of the 1s replacement function is chosen so that the resulting function has a location similar to that of the 3s function as measured by the degree of overlap or the coincidence of radial distribution maxima, the corresponding drop in energy is less than 8 kcal/mol per sulfur atom. However, when the shape of the radial distribution of the 1s function is similar to that of the 3s, i.e., when the value of the 1s exponent is ca. equal to that of the 3s function (a local maximum in the 1s energy profile), the energy lowering is similar to that produced with the 3s function. The electronic effects observed in the molecules differ from those in the atom, the largest deviations being found in the methanesulfonamide calculations.
Force field parameterization for the 4‐fluorophenyl group
Authors: Gregory D. H. , Gerig J. T.
Published: January 2005

Empirical intermolecular force field parameters for the fluorine atom of the 4‐fluorophenyl group have been generated for use in molecular mechanics programs. Partial charges on the ring system were obtained by Mulliken population analysis of wave functions generated by molecular orbital calculations in the STO‐3G approximation. Fluorine van der Waals parameters were obtained by non‐linear least‐squares fitting of crystallographic data following the procedure of Hagler and Lifson. The parameters developed are compared to fluorine parameters reported previously.
A simplified representation of the potential produced by Gaussian charge distributions
Authors: Fortunelli Alessandro , Salvetti Oriano
Published: January 2005

A procedure is presented which allows a more economical representation of the potential produced by orbital charge distributions in which the orbitals are expanded in terms of a finite set of polynomial Gaussian functions. The basic idea is that the products of pairs of Gaussian basis functions, on which the charge distributions are expanded, are expressed in terms of a new basis set of optimally chosen single Gaussian functions. Such a procedure has been tested in a particular case and a few possible applications have been suggested.
Free energy calculations involving NH4+ in water
Authors: Boudon Stéphane , Wipff Georges
Published: January 2005

The analysis of the hydration of NH4+ and the estimation of relative or absolute free energies of hydration by means of Monte Carlo computer simulations using different 1‐6‐12 potential functions is reported. Two electrostatic representations of NH4+ (used respectively by W.L. Jorgensen and P.A. Kollman) in conjunction with two common water models (TIP3P and TIP4P) are considered. A change in relative hydration free energies of 1.7 kcal/mol is found when the NH4+ models are mutated into each other in either TIP3P or TIP4P. The NH4+ → Na+ mutation in both solvent models leads to similar but overestimated relative hydration energies of about −28.7 kcal/mol. Similarly, the NH4+ annihilation significantly overestimates the absolute free energy of hydration.
A general Brownian dynamics simulation program for biopolymer dynamics and its implementation on a vector computer
Authors: Elvingson Christer
Published: January 2005

A Brownian dynamics simulation program for the computation of transport properties of charged polarizable macromolecules is presented. The program contains routines for simulating polymer dynamics in a gel network as well as in a quiescent fluid or in a shear field. An electric field can also be included to simulate e.g., gel electrophoresis or electric dichroism. Vector algorithms have been used where possible to obtain maximum efficiency on a vector processor. The length of the vector registers and the effect of computer memory organization have also been considered. On an IBM 3090‐150S VF, more than 1.5 · 106 steps are executed in one cpu hour for a chain with 128 subunits diffusing in a rigid gel consisting of 8828 beads.
Molecular mechanics (MM2) and conformational analysis of compounds with NCO units. Parametrization of the force field and anomeric effect
Authors: Fernández Berta , Ríos Miguel A. , Carballeira Luís
Published: January 2005

A molecular mechanics force field was developed for systems bearing the NCO unit on the basis of 6‐31G* and 4‐21G “ab initio” calculations with full optimization of the geometry and experimental heats of formation. The parameters used, which implicitly included the anomeric effect, provided good geometric and energetic results, both for the compounds on which the parametrization was based and for others on which the validity of the predictions was checked.