bluuebunny/crossref_metadata_2025_split huggingface dataset:
An open‐ended self‐consistent field method. A simulation of a molecular orbital technique for small memory computers
Authors: Benzel Mark A. , Dykstra Clifford E. 
Published: December 2004

AbstractThe steps in a nonconventional algorithm for self‐consistent field calculations are outlined, and calculations on cumulenes are given to demonstrate the convergence properties of the method. The approach is essentially open ended and is likely to be cost effective on computer systems with minimal core.
Empirical penetration functions and two‐center electron repulsion integrals for semiempirical calculations of electronic structure
Authors: Parry D. E. , Whitehead M. A. 
Published: December 2004

AbstractExplicit functional forms for both the two‐electron Coulomb integral, (aa∣bb), and the one‐center core–orbital integrals, Z (aa∣ZA), are derived which permit the penetration integrals to be fully derived and calculated. With these forms the 3Σ of the H2 molecule is unstable. These forms are generalized so that they are suitable for optimizing semiempirical predictions of experimental one‐electron properties.
Ab initio studies of structural features not easily amenable to experiment. 22. Structural aspects of a long‐chain hydrocarbon (n‐nonane) and a study of the transferability of electronic effects through CC single bonds
Authors: Scarsdale J. N. , Sellers H. L. , Schäfer Lothar , Allinger Norman L. 
Published: December 2004

AbstractThe molecular structure of the stretched form of n‐nonane, as a typical long‐chain hydrocarbon, was refined by geometrically unconstrained ab initio force relaxation on the 4‐21G level. The CC bonds and CH bond distances in the interior of the hydrocarbon chain are found to be longer (by about 0.001 Å and 0.002 Å, respectively) than those near the end of the chain. Similarly, interior CCC bond angles are 0.4° larger than the terminal angles. The variation of structural parameters with distance from the molecular ends levels off after the second carbon atom, and the geometry of methylene is practically constant from C3 on. However, if one end of the system is perturbed by moving the inplane methyl hydrogen away from equilibrium, the resulting destabilizing electronic effects are transmitted through the CC bond distance chain in such a way that significant perturbations are still experienced at C5. Molecular mechanics (MM2) gives a structure in which the small changes in bond lengths and angles with chain location are well reproduced.
An improved method for the evaluation of transition states
Authors: Scharfenberg Peter 
Published: December 2004

AbstractA simple but efficient coupled iteration procedure is proposed for searching saddle points and extrema along the line of constrained minimum energy paths by (analytical) calculation of the derivatives, i.e., the reduced forces and reduced force constants. The advantage of the method is shown with analytical potentials as well as a calculation of HCHHNC rearrangement, as working examples.
Dynamics of ethyl radical decomposition. II. Applicability of classical mechanics to large‐molecule unimolecular reaction dynamics
Authors: Hase William L. , Buckowski Daniel G. 
Published: December 2004

AbstractThe classical trajectory method is used to investigate the unimolecular dynamics of ethyl radical dissociation. It is found that chaotic trajectories need not be backward integrable to yield accurate lifetime, and product energy and angular momenta distributions. This allows the use of large numerical integration step sizes in trajectory calculations. The product energy and angular momenta distributions are independent of the ethyl radical lifetime, and are obtained after only 50 dissociation events. Differences between classical and quantal unimolecular dynamics are discussed, and a prognosis for future trajectory studies of large‐molecule unimolecular decompositions is given.
Conformational study of protonated, neutral, and deprotonated formamide
Authors: Zielinski Theresa Julia , Poirier Raymond Alcide , Peterson Michael Roy , Csizmadia Imre G. 
Published: December 2004

AbstractNeutral, protonated, and deprotonated formamide isomers were studied at the 3‐21G SCF level with complete geometry optimization. Ten stable structures, ten first‐order saddle points, and three second‐order saddle points (conformational maxima) are reported. [Total energies are reported in hartrees (1 hartree = 627.51 kcal/mol = 2625.5 kJ/mol) and energy differences are reported in kJ/mol (1 kJ/mol = 0.239 kcal/mol).] Rotational barriers and proton affinities are discussed and compared to isoelectronic amidine species.
A nonelectrocyclic path from the cyclobutene cation radical to the 1,3‐butadiene cation radical
Authors: Bellville Dennis J. , Chelsky Ronald , Bauld Nathan L. 
Published: December 2004

AbstractThe conversion of the cyclobutene cation radical to the 1,3‐butadiene cation radical has been studied using MINDO/3 and ab initio SCF MO methods. Not only smooth electrocyclic but also stepwise, non‐electrocyclic routes were considered. Both calculational methods agree that the preferred reaction path is a novel nonelectrocyclic one proceeding through an intermediate “cyclopropylcarbinyl cation radical.” The quantitative agreement in the activation parameters calculated by the two methods is excellent. The proposed intermediate also provides an attractive explanation for the mass spectrometric fragmentation patterns of the cyclobutene and butadiene cation radicals.
Improved SCF convergence acceleration
Authors: Pulay P. 
Published: December 2004

AbstractAn improved version of the direct inversion in the iterative subspace algorithm is developed. The method is significantly more efficient than the previous version, and is applicable to intrinsically divergent or slowly convergent cases. Comparisons indicate that the method is superior to the recently proposed quadratically convergent (QC–SCF) method of Bacskay.
Conformation analysis of small molecules with PCILO methods
Authors: Bendl János , Pretscn Ernö 
Published: December 2004

AbstractThe conformational potential of n‐butane, ethyl methyl ether, n‐propanol, methyl propyl ether, and 1,2‐dimethoxyethane was calculated with different PCILO algorithms as well as with ab‐initio SCF–LCAO–MO computations. Compared with ab‐initio calculations, the conformational potentials obtained by PCILO methods on the same geometries are too flat. In particular, the barrier at 0˚ (synperiplanar conformation) is much too low at the second‐ and third‐order level. This is mainly a consequence of the second‐order delocalization corrections. Since the PCILO algorithms are not capable of reproducing conformational potentials obtained from ab‐initio calculations, only qualitative predictions are possible.
A study by molecular mechanics of the geometric isomers of benzene hexachloride, benzene tetrachloride, and naphthalene tetrachloride
Authors: De La Mare Peter B. D. , Hall David , Pavitt Nicola 
Published: December 2004

AbstractThe MM2 molecular mechanics force field, as modified for halogens, is able to predict the structures, dipole moments, and energies of the isomers of benzene hexachloride. For benzene tetrachloride and naphthalene tetrachloride the field exaggerates the stability of conformers with axial chlorine, but gives satisfactory results if the field is modified to allow for interaction between electronegative substituents and the π electrons.
A new treatment of the vibration–Rotation eigenvalue problem for a diatomic molecule
Authors: Kobeissi Hafez , Dagher Mounzer , Korek Mahmoud , Chaalan Ahmad 
Published: December 2004

AbstractThe problem of the determination of the vibration–rotation eigenvalue in diatomic molecules is considered. An eigenvalue equation totally independent from the eigenfunction is written for any potential, analytical or numerical. This equation uses uniquely the vibration–rotation canonical functions; its resolution is reduced to that of a simple and classical numerical problem. Examples of numerical applications for analytical (Morse) and numerical potentials are presented. It is shown that the vibrational eigenvalues deduced from the eigenvalue equation are within 10–6 cm–1 of the exact values. Comparison with conventional methods are presented and discussed.
Theory of the radiative lifetime of the 3B1 state of SO2
Authors: Phillips Philip , Davidson Ernest R. 
Published: December 2004

AbstractInterchange and many‐body perturbation theory are applied to the calculation of the radiative lifetime of the 3B1 state of SO2. The radiative lifetime of 3B1 SO2 is predicted to be 7.6 msec, in excellent agreement with the experimental collision‐free phosphorescence lifetime. As a separate calculation, interchange perturbation theory is used to determine the radiative lifetime of the 1A1 state of CH2.
Isotope effects in molecular mechanics (MM2). Calculations deuterium compounds
Authors: Allinger Norman L. , Flanagan Heather L. 
Published: December 2004

AbstractParameters have been derived so as to enable the inclusion of deuterium in the MM2 molecular mechanics force field. Several compounds were studied and the results are compared with experiment. The results are never qualitatively wrong, but the accuracy ranges from excellent to only fair. They are quite good for hydrocarbons, but less so for ketones.
Three‐electron bonds. III. Phosphorus and chlorine σ* radical cations
Authors: Clark Timothy 
Published: December 2004

AbstractThe radical cations H3PPH, H3PSH, H3PClH+·, and HClClH+· have been studied by ab initio molecular‐orbital theory. An increasing tendency to adopt trigonal bipyramidal (TBP) gemoetries is observed for the phosphorus radicals with sulfur and chlorine ligands. The three‐electron bond dissociation energies are calculated to be between 7 and 31 kcal mol−1. The dependence of these bond energies on the ionization potentials for the neutral hydrides is illustrated, and the deformation of phosphorus σ* radicals towards TBP structures is discussed.
Properties of excited states of aromatic rings containing nitrogen
Authors: Jug Karl , Hahn Gerhard 
Published: December 2004

AbstractQuantum chemical calculations with the semiempirical molecular orbital (MO) method SINDO1 were performed on excited states of the following five‐ and six‐membered heterocycles containing nitrogen: imidazol, pyrazol, pyridine, pyridazine, pyrimidine, pyrazine, and s‐triazine. The geometries and adiabatic excitation energies of T1, S1, S2 were calculated. We also present charges, bond orders, and dipole moments. Consequences of these results for UV spectroscopic data are discussed.
A water‐mediated tautomerism mechanism in formamide and amidine. An ab initio study
Authors: Zielinski Theresa Julia , Poirier Raymond Alcide , Peterson Michael Roy , Csizmadia Imre G. 
Published: December 2004

AbstractFormamide, formamidic acid, and amidine water complexes were studied using 3‐21G fully optimized structures and 6–31G energies. Hydrogen bonding and a water‐mediated tautomerism mechanism were examined. The optimized complexes show that relaxation of the monomers has occurred. Hydrogen bond lengths and energies fall within the range of values found using other basis sets and other comparable systems.
Theoretical conformational analysis of the Gramicidin a transmembrane channel. I. Helix sense and energetics of head‐to‐head dimerization
Authors: Venkatachalam C. M. , Urry D. W. 
Published: December 2004

AbstractConformational energy calculations are presented for the head‐to‐head dimerized β helices for Gramicidin A transmembrane channel structures. The calculations take into account both left‐ and right‐handed β helices, and various side‐chain conformations. The energetics of the dimerization is studied by considering various docking geometries. It is concluded from these vacuum‐energy calculations that the lowest energy conformation for the channel dimer is that comprised of left‐handed β helices.
Calculations on the diphenylmethyl anion
Authors: Adams Stephen M. , Bank Shelton 
Published: December 2004

AbstractSemiempirical and ab initio calculations for the diphenylmethyl anion and related species are reported. MINDO/3 calculations indicate a coplanar anion with an enlarged bond angle of ∼139° to counteract the steric repulsions. MNDO calculations reveal an expanded bond angle with somewhat greater twist (21°). The ab initio calculations (STO‐3G level) reveal an expanded central bond angle with an intermediate degree of phenyl twist. The results are compared with experimental data for this and related anions.
The propagation of basis‐set error and geometry optimization in ab initio calculations. II. Correlation between the balance of Gaussian basis sets and calculated molecular properties
Authors: Mezey Paul G. , Hass Ernst ‐C. 
Published: December 2004

AbstractBasis‐set balance parameters, defined in terms of various projections of an abstract force vector in the space spanned by the logarithms of orbital exponents, are evaluated for a sample of 100 Gaussian basis sets. These basis sets are taken from a random Gaussian distribution of bases, centered on the best energy, fully variational uniform quality (UQ) atomic orbital (AO) basis sets. With each basis geometry optimization has been carried out for model molecule dimethyl sulfoxide, the wavefunction of which molecule is exceptionally sensitive to basis‐set errors. Correlations between the balance of basis sets and calculated molecular properties are analyzed.
Reaction path calculations for the interaction of the ethylene radical cation with triplet oxygen
Authors: Chen Chia‐Chung , Fox Marye Anne 
Published: December 2004

AbstractUMNDO reaction path calculations for trapping of the ethylene‐cation radical with ground state oxygen suggest that formation of a dioxetane radical cation proceeds through the intermediacy of a peroxycation radical. The predicted enthalpy of activation (ΔH‡ = 13.8 kcal/mol) is consistent with rapid trapping of olefinic cation radicals by triplet oxygen at room temperature.
Guidelines for development of basis sets for the first‐order intermolecular interaction energy calculations
Authors: Sokalski W. A. , Hariharan P. C. , Kaufman Joyce J. 
Published: December 2004

AbstractGeneral guidelines for development of small but efficient basis sets for intermolecular interaction calculations have been proposed and tested for simple model systems. It has been demonstrated that the use of overlap matched atomic orbitals (OMAO) leads to significant improvement in the first‐order exchange and electrostatic penetration contributions. Basis sets assuring proper charge distribution lead to a better description of the electrostatic multipole component. The ab‐initio effective‐core‐model potential technique permits a considerable reduction of basis size while having little effect on the selfconsistent field (SCF) interaction energy if basis‐set superposition error is corrected properly.
MNDO calculations of proton and methyl‐and ethyl‐cation affinities of neutral carbon, nitrogen, and oxygen bases
Authors: Ford George P. , Scribner John D. 
Published: December 2004

AbstractProton affinities (PA) of 80 neutral bases were calculated using the semiempirical molecular orbital procedure MNDO. These were compared with the corresponding experimental and, where available, ab initio STO‐3G and 4‐31G data. For the 12 bases studied which led to ions which were not hyperconjugatively stabilized, the mean absolute error between the calculated and experimental values was 7.2 kcal mol−1. However, a plot of these data revealed a clear tendency of MNDO to underestimate the PAs of the more basic molecules. Where hyperconjugative stabilization of the ion was possible, the calculated PAS were underestimated by a further 7–10 kcal mol−1 for each attached alkyl group. Calculated and observed methyl‐and ethyl‐cation affinities were compared for 18 bases with qualitatively similar results.
Ab initio studies on polymers. VII. Polyoxymethylene
Authors: Karpfen Alfred , Beyer Anton 
Published: December 2004

AbstractThe structure of an isolated, infinite polyoxymethylene chain has been investigated with the aid of the ab initio crystal orbital method applying a basis set of double‐zeta quality. Restricting the primitive unit cell to a single CH2O group, conformational potential curves as a function of the torsional angle have been evaluated. Only a single minimum closely corresponding to an all‐gauche structure was detected. The all‐trans conformation is a maximum on the energy curve for simultaneous rotation around CO single bonds. Detailed geometry optimization in the vicinity of the all‐gauche conformation led to the following structure: rCO = rOC = 1.425 Å, rCH = 1.072 Å, ∠HCH = 111.7°, ∠OCO = 110.9°, ∠COC = 115.1°, and τOCOC = 70.75°. The computed torsional angle τOCOC lies midway between the hexagonal (78.2°) and the orthorhombic (63.5°) modification of solid polyoxymethylene.
Evaluation of MNDO calculated proton affinities
Authors: Olivella Santiago , Urpi Felix , Vilarrasa Jaume 
Published: December 2004

AbstractA large set of charged species arising mainly from protonation or deprotonation of hydrocarbons, alcohols, ethers, carboxylic acids, amines, imines, and nitriles has been studied by means of the semiempirical self‐consistent‐field (SCF) molecular orbital (MO) MNDO method. From the calculated heats of formation of such charged species and those of neutral molecules, MNDO‐estimated proton affinities have been obtained and the results compared with experimental gas‐phase proton affinities. If the small size anions and acetylides, for which the method predicts heats of formation too large, are ruled out, the mean absolute error in calculated proton affinities is ca. 7 kcal/mol for hydrocarbons (22 acid‐base pairs) and ca. 8 kcal/mol for oxygen‐containing compounds (25 acid‐base pairs). For nitrogen‐containing molecules it is necessary to discard, in addition, the values corresponding to the protonation of alkylamines and imines in order to achieve a reasonable mean absolute error of 7–8 kcal/mol.
A computational study of the reaction of methane with methyl radical
Authors: Gilliom Richard D. 
Published: December 2004

AbstractThe activation energy and optimized transition‐state geometry for the abstraction of a hydrogen atom from methane by methyl radical have been calculated by the semiempirical methods MINDO/3 and MNDO. These results are compared with other semiempirical and ab initio results. The MINDO/3 method, based upon accuracy of the computed energy of activation, appears to be the computational method of greatest reliability. A method of locating the transition state on semiempirical surfaces is demonstrated.
On searching neighbors in computer simulations of macromolecular systems
Authors: van Gunsteren W. F. , Berendsen H. J. C. , Colonna F. , Perahia D. , Hollenberg J. P. , Lellouch D. 
Published: December 2004

AbstractVarious algorithms for evaluating nonbonded interactions in molecular dynamics (MD) simulations of macromolecular systems are considered, and a combination of two techniques using a space grid for finding neighbor atoms is proposed. The application of grid search techniques to nonrectangular periodic systems is discussed. Finally, the computing time required by different algorithms is compared on a Cray‐1 vector processing computer as well as on a CDC Cyber 170/760 sequential computer. Neighbor list techniques turn out to be faster than the grid search techniques for the systems considered here. However, storage requirements may exclude the use of neighbor list techniques for large systems. Finally, MD of complex macromolecular systems turned out to be about 4–14 times faster on a Cray‐1 than on a Cyber 170/760.
Use of molecular symmetry in two‐electron integral transformation An MP2 program compatible with HONDO 5
Authors: Čársky P. , Hess B. A. , Schaad L. J. 
Published: December 2004

AbstractA computer program is described which evaluates the second‐order Møller‐Plesset energy using the integral list formed by HONDO 5. In this program use may be made of full molecular symmetry for most common point groups, even if they contain two‐dimensional representations. The algorithm for the integral transformation may also be applied to other methods beyond Hartree‐Fock. Some numerical results and timings are presented.
Geometry, basis set, and correlation energy dependence of computed protonation energies of imino bases
Authors: Del Bene Janet E. 
Published: December 2004

AbstractThe nitrogen protonation energies of the imino bases HNCHR, where R is H, CH3, NH2, OH, and F, have been evaluated to determine the dependence of absolute and relative protonation energies on geometry, basis set, and correlation effects. Reliable absolute protonation energies require a basis set larger than a split‐valence plus polarization basis, the inclusion of correlation, and optimized geometries of at least Hartree–Fock 4‐31G quality. Consistent relative protonation energies can be obtained at the Hartree–Fock level with smaller basis sets. Extending the split‐valence basis set by the addition of polarization functions on all atoms decreases the computed absolute Hartree–Fock nitrogen protonation energies of the imino bases HNCHR except when R is F, but increases the oxygen protonation energies of the carbonyl bases OCHR.
Computer generation of the characteristic polynomials of chemical graphs
Authors: Balasubramanian K. 
Published: December 2004

AbstractA computer program based on the Frame method for the characteristic polynomials of graphs is developed. This program makes use of an efficient polynomial algorithm of Frame for generating the coefficients in the characteristic polynomials of graphs. This program requires as input only the set of vertices that are neighbors of a given vertex and with labels smaller than the label of that vertex. The program generates and stores only the lower triangle of the adjacency matrix in canonical ordering in a one‐dimensional array. The program is written in integer arithmetic, and it can be easily modified to real arithmetic. The coefficients in the characteristic polynomials of several graphs were generated in less than a few seconds, thus solving the difficult problem of generating characteristic polynomials of graphs. The characteristic polynomials of a number of very complicated graphs are obtained including for the first time the characteristic polynomial of an honeycomb lattice graph containing 54 vertices.