bluuebunny/crossref_metadata_2025 huggingface dataset:
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

The 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

A 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

The 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

Neutral, 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.
An improved description of lone pairs by a modified PCILO method
Authors: Lochmann R. , Weller Th. , Deininger D.
Published: December 2004

The inadequate description of molecular systems involving lone pairs by the original PCILO method is analyzed on some examples. A modified PCILO version for the lone‐pair description is proposed. The success of this method is represented in the same examples.
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

The 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

An 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

The 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

The 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

The 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

Interchange 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

Parameters 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

The 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

Quantum 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

Formamide, 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

Conformational 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

Semiempirical 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

Basis‐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

UMNDO 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

General 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

Proton 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

The 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

A 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

The 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

Various 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

A 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

The 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

A 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.
Rotation about the CN bond in 2‐aza‐1,3‐butadiene and the NN bond in 2,3‐diaza‐1,3 butadiene: A molecular orbital study
Authors: Bock Charles W. , George Philip , Trachtman Mendel
Published: December 2004

The geometry and energy of 2‐aza‐1,3‐butadiene and 2,3‐diaza‐1,3‐butadiene have been calculated using the 6‐31G* basis set as a function of the CNCC and CNNC dihedral angles, respectively. With the 2‐aza derivative potential minima are located at 0° (trans) and at about 130° for a gauche structure approximately 9.5 kJ mol−1 less stable than the trans. Potential maxima are at about 75° giving a gauche barrier height of approximately 19 kJ mol−1 relative to the trans structure, and at 180° (cis) giving a barrier height of approximately 14.5 kJ mol−1 relative to the 130° gauche structure. With the 2,3‐diaza derivative the gauche barrier has disappeared and there are a series of gauche structures in the region 70°–100° of almost equal energy 12.5‐15 kJ mol−1 less stable than the trans. In addition the cis barrier is much greater, nearly 70 kJ mol−1 relative to the trans structure. Inclusion of electron correlation, accounting for about 50% of the correlation energy, produces no significant changes in the shape of the potential energy curves. There are systematic and progressive changes in almost all the geometrical parameters as the CH groups in butadiene are replaced by N. The outward tilt and compression within the methylene groups show adverse steric interactions to be operative in the cis structures. The values of Vnn indicate that gauche structures of both the 2‐aza and the 2,3‐diaza derivatives near the cis structure are more compact (as with butadiene), and gauche structures of the 2‐aza derivative near the trans structure are less compact (as with butadiene). Originating in the changes in bond lengths and bond angles, rotation‐independent nuclear–nuclear interactions again play an important role.
A rotation–torsion vibronic band contour program
Authors: Leugers M. A. , Seliskar C. J.
Published: December 2004

A Fortran‐77 computer program has been written which calculates the rotation–torsion profile of a vibronic transition using an asymmetric top/free internal rotor Hamiltonian. The program is applicable to any molecule that is composed of a frame portion of C2v symmetry a free rotor portion of C3v symmetry. Rotation–torsion bands of A‐, B‐, and C‐type contours may be calculated within an assumed Boltzmann distribution of rotation–torsion level populations or within a specified non‐Boltzmann distribution of torsional level populations.
Examination of formamide, formamidic acid, amidine dimers, and the double proton transfer transition states involving these dimers
Authors: Zielinski Theresa Julia , Poirier Raymond Alcide
Published: December 2004

Structures and relative energies were obtained for the hydrogen bonded dimers of formamide and formamidic acid using the 3‐21G basis set. A double proton transfer transition state is claimed to link these two dimers. While the structure of the transition state was intermediate between those of the two dimers, the energy was only 7.6 kJ/mol greater than the less stable formamidic acid dimer. The activation energy from the formamide dimer side of the reaction was found to be 125 kJ/mol of dimer. A similar transition state was found for the amidine dimer system. The activation energy for this model reaction was found to be 66.9 kJ/mol of dimer.
Vectorization of quantum chemical algorithms: MC‐SCF procedures
Authors: Rappé A. K.
Published: December 2004

Examples of the types of algorithmic modification needed to achieve substantial enhancement for quantum chemical codes on vector processors such as the Cyber 205 are presented. Specific examples include matrix transformations, 4‐index integral transformations, and general multiconfiguration–self‐consistent‐field (MC‐SCF) codes.
On the calculation of transition moments between states described in different orbital basis
Authors: Bauschlicher Charles W.
Published: December 2004

The organization of a computer code to compute transition moments between states described in different orbital basis sets (a nonorthogonal transition moment) is described. The code is organized to minimize redundant work and allow efficient threshold checking. Three sample calculations are presented.
Critical comparison of the ab initio and spectroscopic methyl‐CH bond length difference in acetyl compounds, CH3C(O) X
Authors: Klimkowski V. J. , Pulay P. , Ewbank J. D. , McKean D. C. , Schäfer Lothar
Published: December 2004

In order to provide additional data for the relative lengths of methyl‐CH bond distances in acetyl derivatives, which are difficult to determine accurately by the conventional tools of structural chemistry, the geometries of CH3COH, CH3COF, CH3COCH3, CH3COOH, and CH3CONH2 were determined by ab initio SCF gradient optimization at the 5‐31G** level and compared with previous 4‐21G results. For acetaldehyde 6‐311G4* calculations were also performed and the correlated methyl‐CH stretching potential energy functions were determined. It is found that the calculated differences between the in‐plane and out‐of‐plane methyl‐CH bonds are practically independent of the computational scheme. The calculated results are in contrast to relative bond lengths obtained by some vibrational overtone spectroscopic studies, but are in perfect agreement with CH bond length differences determined from isolated CH stretching frequencies of partially deuterated compounds. The reliability of the latter, and other spectroscopic data concerning the assignment of the methyl‐CH vibrations are critically analyzed. On the basis of the available evidence we conclude: (1) the methyl groups of the CH3C(O)X systems here discussed contain one strong (in‐plane) and two weak (out‐of‐plane) CH bonds; (2) intensities of CH local mode spectra do not provide a reliable basis for assignment to individual bonds.
A MINDO/3 study of the hetero‐Diels–Alder reaction
Authors: Lee Ikchoon , Han Eun Sook , Choi Jae Young
Published: December 2004

The transition states involved in the hetero‐Diels–Alder reactions of acrylaldehyde–ethylene and butadiene–formaldehyde systems were characterized using an efficient method of locating a saddle point on the energy surface of two coordinates calculated with MINDO/3 method. It has been shown that parallel transition and rotation of the conjugate coordinate frame lead to the reaction and orthogonal coordinate system on the hyperbolic paraboloid energy surface. It was concluded that the method we adopted is similar to the “X‐method” but is much simpler to apply to real reaction systems.
Ab initio calculation of amine out‐of‐plane angles
Authors: Boggs James E. , Niu Zefu
Published: December 2004

Fully optimized geometries are computed at the Hartree–Fock level for formamide and methylamine with basis sets ranging up to ones that are triple‐zeta plus two sets of polarization functions in the valence shell. The effect of very diffuse s and p functions is also examined. The relation of basis set size and composition to the computed amino group out‐of‐plane angle and to the related localized molecular orbitals is systematically investigated and compared with scattered results previously reported for other systems. It is concluded that the amino group angle is the result of a delicate balance between lone pair character of the nitrogen electrons and delocalization of these electrons into other portions of the molecule. Polarization functions in the nitrogen basis set are necessary to provide for proper description of the lone pair character, but even in methylamine the delocalization is not properly described without an extensive basis set, either polarization functions or very diffuse s and p functions, on the other heavy atoms. The effect is extreme for molecules such as formamide, aniline, and PF2NH2, where very large basis sets are required to obtain the correct out‐of‐plane angle.
Ab initio studies of structural features not easily amenable to experiment. 42. Molecular geometries and conformational analysis of methylbutanoate
Authors: Schäfer Lothar , Klimkowski V. J. , Van Alsenoy C. , Ewbank J. D. , Scarsdale J. N.
Published: December 2004

Conformational energy profiles were calculated for τ1, the CCCO torsion, and τ2, the CCCC torsion, of methyl butanoate, using Pulay's ab initio gradient procedure at the 4‐21G level with geometry optimization at each point. In addition, the structures of seven conformations were fully relaxed, including the energy minima (τ1, τ2) = (0, −60), (0, 180), (120, 180), (120, −60), and the maxima (0, 0), (180, 180), and (60, −60). The calculated geometries confirm the previously formulated rule that, in saturated hydrocarbons, a CH bond trans to a CC bond (CHs) is consistently shorter than a CH bond (CHa) trans to another CH bond. Specifically, for XC(α) ( O)C(β)C(γ)C(δ) systems, the following rules can be formulated, incorporating results from previous studies of butanal, butanoic acid, and 2‐pentanone: (1) C(δ)Hs < C(δ)Ha in all the conformers in which the δ‐methyl group is remote from the ester group; whereas, in all the conformers in which nonbonded interactions are possible between the C(δ)‐methyl and the ester groups, the bonding pattern is affected by a CH ⃛OC interaction. (2) In the most stable conformers, (0, 60), C(β)Ha < C(β)Hs, and C(γ)Ha < C(γ)Hs, regardless of X. (3) The average CC bonds in the τ2 = 180° conformers are consistently shorter than those with τ2 = 60° (compared at τ1 constant). In the most stable conformations (τ1 = 0°, τ2 = 60° or 180°), the bonding sequence is consistently C(α)C(β) < C(β)C(γ) < C(γ)C(δ); whereas, when τ1 = 120°, C(α)C(β) < C(β)C(γ) > C(γ)C(δ).
Ab initioSCF MO calculations on the reactions of hydroxyl radical with imidazole and monoprotonated imidazole
Authors: Eatock Beverley G. , Waltz William L. , Mezey Paul G.
Published: December 2004

The addition reactions of hydroxyl radical with imidazole and its protonated form to yield radical adducts have been investigated by ab initio SCF MO methods using STO‐3G and 4‐31G basis sets. Analogous radical species are of importance in radiation damage to biological systems. Of the possible radical products, the calculations indicate that the allylic species are generally favored energetically over the nonallylic forms. On an energetic basis, the results show that the allylic adducts formed by addition at the C2 and C5 positions are about equally favorable. Although the C5 species is generally identified as the experimentally observed product in aqueous media for both protonated and unprotonated imidazole, some experimental evidence exists indicating the presence of other forms. Our results suggest that this other form is the C2 adduct. The calculations also point to the protonated form of imidazole being less reactive than imidazole, which is in accord with experimental observations.
On the use of perturbation theory corrections to numerically selected MRDCI calculations
Authors: Ruttink P. J. A. , Van Schaik M. M. M.
Published: December 2004

If numerical configuration selection procedures are used in MRDCI calculations, the full MRDCI energy may be estimated by adding energy corrections obtained by perturbation theory. Accurate results may then be obtained by including all selected CFs in the zero‐order function instead of only the reference CFs.
Effects of alkylation upon the proton affinities of nitrogen and oxygen bases
Authors: Redfern Paul , Scheiner Steve
Published: December 2004

The protonation energies of alkylated derivatives of NH3 and OH2 are calculated at the Hartree–Fock level with the split‐valence 4‐31G basis set. The methyl, dimethyl, and ethyl amines are studied; oxygen bases include methanol, dimethylether, and ethanol. The geometries of each molecule and its protonated analog are fully optimized. It is found that protonation leads to significant changes in the molecular structures. In particular, the bonds to the N and O atoms are substantially elongated, especially when the other atom involved is C rather than H. The calculated absolute proton affinities are somewhat larger than the experimental values. However, the differences in protonation energies of the various molecules relative to one another agree quantitatively with experiment. Replacement of one H atom of the base by a methyl group induces an increase in proton affinity of some 10 kcal/mol. If a second methyl group is added to the N or O atom, a further increment of about 70% this amount is noted. On the other hand, placement of the second C atom on the first methyl group (to form an ethyl substituent) leads to a smaller increase (∼30%). The magnitudes of these alkyl substituent effects are somewhat larger for the oxygen bases than for the amines.
A systematic preparation of new contracted Gaussian‐type orbitals. IX [54/5], [64/5], [64/6], [74/6], [74/7] and MAXI‐1–MAXI‐5 from Li to Ne
Authors: Tatewaki Hiroshi
Published: December 2004

The new contracted Gaussian‐type orbitals (CGTOs) for molecular calculations have been developed from Li to Ne. The CGTOs are minimal type, i.e. composed of two s‐type CGTOs, s1, s2, and one p‐type CGTO, p1. They are new family of CGTOs given by Tatewaki and Huzinaga, and others. In the previous works three primitive GTOs are used for s2, which is the main part of the 2s orbital, whereas four primitive GTOs are employed in the present work. The sets generated are [54/5], [64/5], [64/6], [74/6], and [74/7]. In almost all the cases the errors in the 2s and 2p orbital energies are smaller than those of DZ. The resulting 2s orbitals are close to the orbitals of the uncontracted GTO sets, (13/n) and (14/n) of Duijneveldt. It is found that the 2s and 2p orbitals given by [64/6], [74/6], and [74/7] are satisfactorily near to those of Hartree–Fock. The basis sets [54/5], [64/6], and [74/7] are applied to the N2 molecule in the split valence forms of [5211/311], [6211/3111], and [7211/4111]. Adding the d‐type polarization functions from one through three, the quality of the basis sets has been examined. All of the three sets show good behavior and the sets augmented with three d‐type polarization functions give almost entirely the same results as the very extended basis set.
A theoretical study of α‐substituted cyclopropyl and isopropyl radicals
Authors: Lien M. H. , Hopkinson A. C.
Published: December 2004

The structures of α‐X‐cyclopropyl and α‐X‐isopropyl radicals (X = H, CH3, NH2, OH, F, CN, and NC) are reported at the RHF 3‐21G level of theory. The isopropyl radicals are pyramidal with out‐of‐plane angles varying from 12° (X = CN) to 39° (X = NH2), and barriers to inversion ranging from 0.4 kcal/mol (X = H) to 4.0 kcal/mol (X = NH2). The cyclopropyl radicals have larger out‐of‐plane angles, from 39.9° (X = CN) to 49.4° (X = NH2), and their barriers to inversion, which increase with the inclusion of polarization functions, vary from 5.5 kcal/mol (X = H) to 16.7 kcal/mol (X = F). In both types of radicals the amino group is the most stabilizing substituent, while the α‐fluoro has little effect. The β‐fluoro group is weakly destabilizing in the cyclopropyl radical. The strain energies of the cyclopropyl radicals (36–43 kcal/mol) are compared with those of similarly substituted anions, cations, and cyclopropanes.
Orbital relaxation in the Rydberg series of the He atom
Authors: Chang T. C. , Pao Chien Hua , Hsue Chen‐Shiung
Published: December 2004

The orbital behavior of both the singlet and triplet Rydberg series for 1sns configurations of the He atom has been investigated using one‐ and two‐configuration Hartree–Fock wave functions. The core orbital within the triplet series changes negligibly; however, a contract trend is noticeable as the Rydberg orbital penetrates more into the core region, which is in contrast to that found in the 1s2ns 2S Rydberg series of Li atom. Although some properties of the whole atom can be calculated, the core relaxation of the singlet series can not be drawn without ambiguity because a two‐configuration correlated wave function has to be used, and thus the orbital picture is lost.
Basis set and correlation effects on computed proton affinities of some oxygen and nitrogen bases
Authors: Del Bene Janet E.
Published: December 2004

Basis set expansion and correlation effects on the computed proton affinities of the oxygen and nitrogen bases CH3OH, H2CO, CO, CH3NH2, CH2NH, and HCN have been evaluated. Basis set enhancements lead to systematic changes in computed proton affinities. These effects appear to be additive, and are greater for correlated proton affinities than for Hartree‐Fock energies. Inclusion of correlation decreases proton affinities, with fourth‐order Møller‐Plesset energies bracketed by second and third order energies.
General expressions for monocenter repulsion integrals in a basis of real atomic orbitals
Authors: François J. P. , Voets R. , Van Poucke L. C.
Published: December 2004

General expressions for monocenter electron repulsion integrals in a basis of real atomic orbitals are derived in terms of the radial integrals R. The final expressions for these integrals can be classified into five main classes which are characterized by the angular part of the real atomic orbitals. For a basis of real s, p, d, and f AO's the total number of monocenter repulsion integrals is 65536, from which 6652 are different from zero. The nonzero integrals can be classified into 430 groups which contain integrals of equal value.
Ab initioSTO‐3G optimization of planar, perpendicular, and twisted molecular structures of biphenyl
Authors: Häfelinger Günter , Regelmann Claus
Published: December 2004

The complete molecular structure of biphenyl, characterized by 12 independent parameters, has been derived by ab initio gradient techniques using a STO‐3G basis set for coplanar, perpendicular, and minimum energy conformations with the constraint of planar phenyl ring units and a C2 symmetry axis along the CC interring bond. The minimum torsional angle obtained was ϕ = 38.63° with torsional energy barriers of 8.59 and 10.04 kJ/mol for ϕ = 0° and ϕ = 90°, respectively.
Theoretical studies on pteridines. 2. Geometries, tautomer, ionization and reduction energies of substrates and inhibitors of dihydrofolate reductase
Authors: Gready Jill E.
Published: December 2004

Ab initio SCF calculations with STO‐3G and 3‐21G basis sets are reported for approximately 85 pteridines of interest to the study of the reaction and inhibition mechanisms of dihydrofolate reductase. These include tautomeric, protonated, deprotonated, reduced and 6‐substituted forms of the 2‐amino‐4‐oxo‐ and 2,4‐diamino‐pteridines, many of which are not easily amenable to experimental investigation. Full geometry optimizations at the SCF/STO‐3G level for 30 such pteridines have been performed. A step‐wise computational protocol designed to identify the minimum level of theory necessary for reliable prediction of relative tautomer, reduction and ionization energies has been developed in an effort to minimize the cost of calculations for this reasonably large N‐heterobicylic system. In general, SCF/STO‐3G results were found to be inadequate while SCF/3‐21G results obtained with STO‐3G optimized geometries agreed with all available experimental evidence with the exception of the relative acidity of 6‐methyl‐7,8‐dihydropterin. Correlation graphs relating experimental pKa's to the calculated ionization energies are presented: these are of potential predictive value. An analysis is given of the importance of resonance substructures, such as the guanidinium and extended‐guanidinium groups, in stabilizing some preferred tautomeric and ionized forms, and in explaining the observed geometry changes.
An efficient UMP2 program
Authors: Čársky P. , Fabian J. , Hess B. A. , Schaad L. J.
Published: December 2004

Timings are reported for 6‐31G*/UMP2 calculations on planar allene, twisted ethylene, cyclopropenyl anion, allyl, ethyl, isopropyl and CF3 radicals performed by means of the programs GAUSSIAN 80 and HONDO UMP2. The comparison of the two programs is used for pointing out several factors affecting the speed of MP2 calculations.
Study of a medium‐size biological molecular association by means of a pair potential semiempirical approach: β‐carboline–lumiflavin
Authors: Sánchez‐Marín J. , Ortí E. , Tomás F.
Published: December 2004

The molecular association between some substituted β‐carbolines and a model flavin, lumiflavin, has been studied by means of a semiempirical approach proposed by Fraga based on a 1/R expansion of atom‐atom pair potentials. Only stacked minima have been considered because of their possible biological interest. The calculations characterize 15 different minimum stacked conformations, most of them occurring in the complexes considered. The structural and energetic effects of 1–Me, 6–OH and 7–OH substituents of β‐carboline are discussed. An equilibrium conformation involving geometric overlap between the pteridinic portion of flavin and the indole group of β‐carboline is predicted to be the most characteristic structure of the complexes. The recognition of this feature can serve to check the effect of substituents and substitution sites of β‐carboline in its association complexes.
Computational aspects of Laplace transform inversion of thermal unimolecular rate constant
Authors: Schoenenberger Christian , Forst Wendell
Published: December 2004

The thermal limiting high‐pressure unimolecular rate constant k∞ represents, operationally, the Laplace transform of the product of microcanonical rate constant for decomposition of molecules having specified energy E [k(E)] and the density of states [N(E)]. By inversion, it is possible to recover k(E)N(E), from which one can obtain the energy dependence of k(E) and the pressure dependence of kuni, the thermal general‐pressure unimolecular rate constant. This article examines numerical aspects of three methods of inversion, their reliability and dependence on sampling, i.e., on the number of available experimental data points, by comparing exact k(E) and kuni with those obtained by inversion. It turns out that the method of steepest descents is the best all‐round performer.
Comparative studies on the reactivity of molecules by atomic valences
Authors: Jug Karl , Buss Sabine
Published: December 2004

SINDO1 calculations were performed to study the reactivity of molecules with a valence number derived from the density matrix. A comparison of valence numbers was made for selected examples of rotation barriers, substituted strained molecules, radical gas phase reactions, and acid‐base reactions. Relations between valence, geometry, and energy changes are discussed.
Compact basis sets for LCAO‐LSD calculations. Part II: Tests for Cr2 and Ni4
Authors: Radzio E. , Andzelm J. , Salahub D. R.
Published: December 2004

The compact orbital and auxiliary basis sets for LCAO‐LSD calculations introduced in Part I are tested in molecular calculations on Cr2 and Ni4. The present results for spectroscopic constants and valence orbital energies obtained using medium size orbital expansions with a double‐zeta representation for valence orbitals are in very good agreement with those previously calculated with very extended sets. Since the computational time of the present calculations is reduced severalfold compared with the extended basis set calculations, the present basis sets allow increased efficiency of the LCAO‐LSD calculations and allow the method to be extended to larger systems.
Unique description of chemical structures on hierarchically ordered extended connectivities (HOC procedures). II. Mathematical proofs for the HOC algorithm
Authors: Mekenyan Ovanes , Bonchev Danail , Balaban Alexandru T.
Published: December 2004

The basic notions and definitions, necessary for the better understanding of Part I of this series, are presented. The mathematical proof is given for sufficiency of the various HOC procedures for vertex canonical numbering and graph orbit finding.
The effect of including polarization functions on the geometrical parameters calculated for benzene, fluorobenzene and cyanobenzene
Authors: Bock Charles W. , Trachtman Mendel , George Philip
Published: December 2004

The geometrical parameters for benzene, fluorobenzene, and cyanobenzene have been calculated using the 6–31G*(5D) and 6–31G** basis sets, and, in addition, the 6–31 + G*(5D) basis set in the case of fluorobenzene. Compared to previous results obtained using the 6‐31G basis set there are minor changes in the magnitude of the bond lengths and angles in the ring, but the relative values remain unaltered. The values for the ipso angles in fluorobenzene and cyanobenzene are again somewhat less than those reported from microwave and/or electron diffraction studies. The distortion of the ring is characterized as either an elongation or a flattening with respect to the F–C1 ⃛C4 and NCC1C4 axes, and the shape is characterized as either a broadening or a narrowing across the ring just below the F and Cn group, i.e., an increase or a decrease in the C2 ⃛C6 internuclear distance, relative of the C3 ⃛C5 distance.
Theoretically derived absorption and MCD spectral data for the cellular species produced in the hydrolysis of cis‐diamminedichloroplatinum(II)
Authors: Krogh‐Jespersen Mary‐Beth
Published: December 2004

The cellular species formed in the hydrolysis of cis‐Pt(NH3)2Cl2 (DDP), namely, cis‐[Pt(NH3)2XY]n+ (X, Y = Cl−, H2O, OH−; n = 0, 1, 2) have been investigated theoretically using the relativistic and nonrelativistic extended Huckel molecular orbital method. Molecular orbital (MO) results for trans‐DDP and its hydrolysis products are also reported for comparison. Transition energies, molar absorption coefficients (ϵ), and B terms from magnetic circular dichroism (MCD) derived from theory are presented for each of the species studied. The electronic absorption and MCD spectra of all the complexes are predicted to exhibit ligand field transitions arising primarily from excitations between the occupied Pt 5d orbitals and the unoccupied Pt 5d and 6pz orbitals, respectively. The 5d → 6pz transitions are expected to yield intense absorptions in the UV spectral region. Some intensity is generated in the d → d transitions as a result of the low symmetry of these complexes. Correlation of available experimental data with theory allows spectral assignments to be made and predicted. Substituent effects in the cis‐ and trans‐isomeric species are discussed. Finally, the applicability of the EHMO method to these systems is examined.