bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractTheoretical 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

AbstractWe 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

AbstractIn 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

AbstractThe 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

AbstractThe 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

AbstractA 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

AbstractA 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

AbstractAb 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

AbstractWe 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

AbstractAn 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

AbstractTheoretical 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

AbstractPractical 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

AbstractThe 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

AbstractThe 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

AbstractThe 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

AbstractDifferent 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

AbstractIn 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

AbstractThe 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

AbstractProlog 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

AbstractAlgorithms 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

AbstractHydrogen 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

AbstractAb 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

AbstractThe 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.