bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular calculations with the nonempirical ab initioMODPOT, VRDDO, and MODPOT/VRDDO procedures. IX. Carcinogenic benzo(a)pyrene and its metabolites using a MERGE technique
Authors: Kaufman Joyce J. , Popkie Herbert E. , Palalikit Surat , Hariharan P. C. 
Published: December 2004

AbstractAb initio MODPOT/VRDDO calculations have been carried out on carcinogenic benzo(a)pyrene and its metabolites. The MODPOT/VRDDO method incorporates two very desirable options into our fast ab initio Gaussian programs: MODPOT—ab initio effective core model potentials—and a charge‐conserving integral prescreening approximation which we named VRDDO (variable retention of diatomic differential overlap). For orbital energies and population analyses the MODPOT/VRDDO results agree to essentially three decimal places with completely ab initio calculations using the same valence atomic basis set. For this series of very closely related congeners a new MERGE technique was implemented that allows reuse of integrals of a common skeletal fragment. Since our program computes integrals efficiently by blocks, reusing information common to the block, it was more difficult to implement a MERGE technique than for integral programs which calculate the integrals one‐byone. The MODPOT/VRDDO calculations were performed for benzo(a)pyrene (BP), BP oxides, BP dihydrodiols, and BP dihydrodiol epoxides. The metabolites investigated were BP‐7,8‐oxide, BP‐4,5‐oxide, BP‐7,8‐dihydrodiol [cis(e, a), cis(a, e), trans(e, e), and trans(a, a)], and BP‐7,8‐dihydrodiol‐9,10‐epoxide [β,β,β (the most stable), β,β,α; α,α,β, and α,α,α all derived from cis‐BP‐7,8‐dihydrodiol and β,α,β; α,β,β and α,β,β derived from trans‐BP‐7,8‐dihydrodiol]. Several different conformations were calculated for each of the BP dihydrodiols and BP dihydrodiol epoxides. Calculations were carried out for the opening of the C9—O—C10 epoxide ring both toward C9 and C10 for the, most stable β,β,β isomer of BP‐7,8‐dihydrodiol‐9,10‐epoxide. Opening the epoxide ring between C10 and O leads to a more stable intermediate than opening the epoxide ring between C9 and C10. However, there is no buildup of positive charge in C10 as has been postulated by some cancer researchers, but rather the C10 becomes slightly more negative. Nor is there a buildup of negative charge on the O atom. rather it becomes slightly less negative. As the epoxide ring is opened further than 90° for the O—C9—C10 or O—C10—C9 angles, there appears to be a possible mixing of configurations that is being investigated further.
Perturbation treatment of multiple site reactivity. II. Additivity in trimolecular interactions
Authors: Chang Shih Y. , Weinstein Harel 
Published: December 2004

AbstractA multiple perturbation method for the study of molecular reactivity following multiple site interactions has been extended to trimolecular systems. The theory is reformulated by the many‐body diagrammatic method. While adding no new physical content to the previous theory, the present formulation allows for a systematic way of evaluating higher‐order energies. The additivity of perturbation contributions to the modification of molecular reactivity is tested on dihydrated adenine. The results compare favorably with supermolecule calculations.
Optimum geometries and relative energies for cytosine, thymine, uracil, the imino tautomer of cytosine, the enol tautomer of thymine, and the enol tautomer of uracil by the MINDO/2 SCF MO method
Authors: Zielinski Theresa Julia , Rein Robert 
Published: December 2004

AbstractA MINDO/2 SCF MO geometry optimization of cytosine (C), thymine (T), uracil (U), the imino tautomer of cytosine (C*), the enol tautomer of thymine (T*), and the enol tautomer of uracil (U*)was made. The optimized geometries for cytosine, thymine, and uracil agree well with crystallographic data. The optimized geometries for the tautomers show the correct trends in bond lengthening and bond angle except for the C4—O4 length and C4—O4—H angle of T* and U*. The energies of tautomerization were found to be 10.3, −9.0, and −14.2 kcal/mol for C⇌C*, T⇌T*, and U⇌U*, respectively, when optimized geometries are used. The overestimation of the C4—O4—H angle is speculated to arise because of an inadequacy in the parametrization of the one‐center integrals in MINDO/2.
Variable basis sets in perturbation theory: Numerical finite perturbation versus analytic approach
Authors: Epstein Saul T. , Sadlej Andrzej J. 
Published: December 2004

AbstractWe consider the problem of determining variational, external‐field‐dependent corrections to nonoptimal zero‐field nonlinear parameters. Both a direct analytic perturbation analysis and finite perturbation methods are described in a general way and in detail for the SCF approximation. The abstract theory is illustrated by reference to the results of several explicit calculations. Also, the sensitivity of the results to the choice of zero‐field values is discussed.
Semiempirical MO study on the abnormal bond orders of large networks of highly branched polyenes
Authors: Kanazawa Tomoko , Hosoya Haruo , Iwata Suehiro 
Published: December 2004

AbstractThe π‐electronic structures of the ground state of linear and highly branched polyenes with up to 80 π‐electrons are calculated with particular reference to the alternation of the bond orders. The MO methods adopted are HMO, PPP, variable‐β, γ, and its improved version. The effect of the electron correlation through singly and doubly excited configurations is estimated with a second‐order perturbation calculation. The calculated bond orders systematically vary with the degree of approximation used. Most of the bond order values can be grouped into either a single or double bond region. In certain series of highly branched polyenes the bond orders of double and single bonds at the root of branching, respectively, get smaller and larger as the size of the molecule increases and sometimes their difference gets diminishingly small. The origin of these abnormal bond orders is discussed in terms of the π‐electron flow networks.
Conformational possibilities of double‐helical nucleic acids: Theory and experiment
Authors: Ivanov V. I. , Zhurkin V. B. , Zavriev S. K. , Lysov Yu. P. , Minchenkova L. E. , Minyat E. E. , Frank‐Kamenetskii M. D. , Schyolkina A. K. 
Published: December 2004

AbstractThis survey covers the following topics: (1) Theoretical calculation of the total multitude of the energetically permitted regular DNA helices. (2) Theoretical study of flexibility of the double helix with emphasis on nucleosome structure. (3) Experimental data on the properties of the B to A transition of DNA in solution: the degree of cooperativity and influence of sequence. (4) The B‐A transition and its possible role in genes activation.
Ab initiocalculations and absolute rate theory. Critical test for a series of elementary gas‐phase reactions
Authors: Čársky P. , Zahradník R. 
Published: December 2004

AbstractAbsolute rate theory (ART) was applied to a series of reactions of the type A+BC → AB+C containing H, F, HF, H2, and F2,trans–cisisomerization of dideuteroethylene, and processes H + CH4→ H2+ CH3and H′+CH4→ H′CH3+ H. Geometries and energies of activated complexes were taken from the bestab initiostudies reported in the literature in which at least a DZ + P basis set was used and a large portion of the correlation energy was included. Vibrational frequencies needed for the zero‐point energies and vibrational partition functions were estimated from the reported potential surfaces (HHF and HFF) or evaluated fromSCF4‐31G calculations (HFH, FHF, twisted C2H4, and CH5complexes). Compatability of calculated rate constants with the experimental data was examined.
Ab initio calculations including electron correlation for the minimum energy path of the (1A1) CH2+(1Σ)H2→ (1A1) CH4 insertion reaction
Authors: Jeziorek Danuta , Żurawski Bronisław 
Published: December 2004

AbstractAb initio calculations on the SCF level and with the inclusion of valence shell electron correlation in the IEPA–PNO (independent electron pair approximation with pair natural orbitals), the PNO–CI (pair‐natural‐orbital configuration interaction) and the CEPA–PNO (coupled electron pair approximation with pair natural orbitals) schemes with Gaussian lobe functions of “double zeta quality” have been performed for the minimum energy path of the insertion of singlet (1A1) methylene to the (1Σ)H2 molecule to yield methane. The energy was minimized on the SCF level to all geometrical parameters for various values of the “approximate” reaction coordinate. The energy along the reaction path decreases monotonically without a barrier and the curves representing the total energy of the system as a function of approximate reaction coordinates obtained at different levels of approximations have the same shape. From the physical point of view three phases of the reaction can be distinguished (chemically two steps) with different geometrical arrangements and different internal geometries of the partners.
Electronic structural properties and photosynthesis
Authors: Christoffersen Ralph E. 
Published: December 2004

AbstractA review of recent theoretical studies of molecules of interest to photosynthesis is given, in which the results of ab initio self‐consistent‐field plus configuration‐interaction studies are discussed. Ground‐state and low‐lying excited singlet and triplet state descriptions are presented for six molecules, including Mg‐porphine, Mg‐chlorin, ethyl chlorophyllide a, and their corresponding magnesium‐free analogs. The data are then used to rationalize a variety of observed properties, including molecular orbital structure, ionization potentials, chemical reactivity, Franck‐Condon transition energies, oscillator strengths, transition polarizations, and other properties. As a result, relatively comprehensive and complete descriptions of the electronic structural features of chlorophyll a and related molecules are obtained, which are in general in good agreement with available experimental data, but which also provide new concepts and reinterpretation of existing data in several instances.
Model studies on the active site of carbonic anhydrase: Ligand properties and CO2 binding
Authors: Pullman A. , Demoulin D. 
Published: December 2004

AbstractIn view of building a workable molecular model of tetraliganded zinc at the active site of carbonic anhydrase, an ab initio SCF study using pseudopotentials is performed on Zn2+(OH2)n from n = 2 to 6, Zn2+(NH3)n−1 (OH2) for n = 2 and 4, Zn2+(NH3)2 (imidazole) (OH2), and their ionized species involving OH− or imidazolate, considering in particular the evolution of the properties of the ligands and of the bound cation upon increasing n and upon replacement of one ligand by another. (Comparison of NH3 and imidazole binding was made in a full SCF calculation.) The results obtained in the tetraliganded complex confirm that zinc binding facilitates water deprotonation more than imidazole deprotonation, so as to reverse the order of their intrinsic ease of ionization. A study of the approach of CO2 toward the active site is made in an electrostatic approximation using as models the most representative of the computed four‐ligand complexes.
Interaction of water with DNA single and double helix in the B conformation
Authors: Clementi E. , Corongiu G. 
Published: December 2004

AbstractThe interaction energy between water and B‐DNA in the single and double helix is computed at a number of planar cross sections perpendicular to the helix long axis and for a few cylindrical surfaces enclosing the helix. In addition, Monte Carlo simulations are presented for a small cluster of water around regions of energy minima. On the base of these simulations the structure of water for B‐DNA in solution, the quaternary structure of B‐DNA, is proposed and discussed. The intermolecular interaction used in the Monte Carlo computation has been derived from ab initio computations of complexes between water and the DNA bases, diethylphosphate, a ribose derivative, and other model compounds.
On the validity range of the qualitative theory of chemical reactivity
Authors: Basilevsky M. V. , Weinberg N. N. 
Published: December 2004

AbstractAn attempt is made to refine the physical background underlying qualitative quantum‐chemical concepts that are an essential component of the modern theory of chemical reactivity. The energy of electron delocalization in a transition state (stabilization energy, SE) is used as a measure of chemical reactivity. Using Coulson's integral representation for bond order matrix enables one to present the Woodward–Hoffmann rules and the effects of conjugated substitutents as theorems for a Hückel SE in alternant systems. A part of the results are extended to heteroatomic systems. The validity of the present treatment is discussed in terms of the SCF PPP theory.
Fock coordinate function method for separation of spin variables in transition density matrices
Authors: Klimko G. T. , Mestechkin M. M. , Whyman G. E. 
Published: December 2004

AbstractThe Fock generating function method is employed for the separation of spin variables into two‐particle transition density matrices. Their spatial components introduced by McWeeny are expressed through Schrödinger's coordinate wave functions. Some nontrivial integral relations between these components and the charge and transition spin density matrices are obtained. The interrelation between the mentioned spatial components and the Matsen–Poshusta symmetrized density matrices of an arbitrary spatial function is found.
Asymptotic forms of atomic scattering factors and momentum densities
Authors: Yusaf M. S. , Lawes G. P. , March N. H. 
Published: December 2004

AbstractWithin the framework of the nonrelativistic Schrödinger equation, the Coulomb field case is used to assess the range of validity of the Thomas–Fermi statistical theory of atoms. In particular, attention is focused on (a) the x‐ray scattering factor, which is the Fourier transform of the electron density; and (b) the momentum density. In each case the predictions of the statistical theory are compared with the exact results for the Coulomb potential. These can conveniently be calculated using earlier work of Fock. Some assessment is also made of the accuracy of the statistical approximation for the kinetic energy density; this is of interest in connection with the density functional approach. Finally, some brief comments are made on the relation between the self‐consistent Thomas–Fermi method and the Hartree theory for atoms.
Energy levels for perturbed Morse oscillators
Authors: Requena A. , Peña R. , Serna A. 
Published: December 2004

AbstractThe energy levels and perturbation expansions for the expectation values of arbitrary powers of position for a perturbed Morse oscillator are obtained by application of the hypervirial and Hellmann–Feynman theorems, solely in terms of the unperturbed energy. We obtain expressions for the first‐order corrections for (1 − e−aq )m for 4 ⩽ m ⩽ 8 and the expressions to second and third order for the quartic perturbation. A numerical application to the CO molecule is made.
Behavior of molecular potential energy curves for large nuclear separations
Authors: Morgan John D. , Simon Barry 
Published: December 2004

AbstractWe prove by elementary geometric methods and within the Born–Oppenheimer approximation that as the nuclei of a molecule are dissociated into spatially separated clusters, the discrete molecular energies approach sums of the energies of isolated subsystems. Our methods also show that the spectral projections associated with the discrete molecular spectrum asymptotically approach direct sums of suitable spectral projections for the isolated subsystems. These results apply to any system of particles interacting by asymptotically vanishing pair potentials. We prove that the 1/R expansion for discrete molecular potential curves is asymptotic as R → ∞, and we discuss the behavior of the coefficients of the 1/R expansion for the ground state of H2+.
Effect of substituents on electron energy redistribution in uracil derivatives and their ionization in polar solvents
Authors: Blagoy Y. U. P. , Sheina G. G. , Luzanov A. V. , Silina L. K. , Pedash V. F. , Rubin Y. U. V. , Leibina E. A. 
Published: December 2004

AbstractIt is assumed that the chemical reactivity may be described in terms of the appropriate energy density calculated for each atom. Indices of energy density for deprotonization of uracil, 5‐nitro‐ and 5‐aminouracil are presented. The results of a quantum chemical calculation of the deprotonization energy are in qualitative agreement with experimental pK and ΔH values.
Permutational–symmetry‐adapted powers of representations of the point groups deduced from the unitary group
Authors: Flurry R. L. , Siddall T. H. 
Published: December 2004

AbstractThe construction of symmetrized powers of representations of the point groups can be deduced by decomposing the appropriate representation of the unitary group into the representations of the group of the sphere, and then mapping these representations onto the point group. The method is generally simpler than the traditional method based on the character tables of the symmetric group. As an example, the symmetry‐adapted powers (N) of the representations of the icosahedral group are presented for 2≤N≤5.
One‐center expansion method with model potentials. I. Formulation and test calculations
Authors: Tindimubona Alex R. 
Published: December 2004

AbstractThe one‐center expansion (OCE) method is extended to evaluate molecular wave functions for molecules with heavy off‐center nuclei. This extension is achieved through the use of model potentials (MP) to approximate the highly bound core orbitals. The remaining diffuse valence charge distribution is then rather easy to simulate using OCE. The formulation of the method is described. New molecular integrals are solved to a high degree of accuracy. Successful results are reported for H2O, H2S, and N2. The valence electron distributions and orbital energies are in good agreement with those obtained from more complete calculations. The method combines the computational economy of both OCE and MP procedures, resulting in a potentially useful package for further chemical applications.
Orbital contributions to some two‐electron properties
Authors: Largo‐Cabrerizo J. , Calvo F. M. Duque 
Published: December 2004

AbstractAnalytical formulas are given for the orbital contributions to two‐electron properties such as 〈r〉, with n = −2, −1, 1, 2, 3, and 4, for atomic systems in which orbitals are expanded as linear combinations of Gaussian functions. Numerical values for all possible contributions in the atoms Li to Ne have been calculated at the Hartree–Fock level. These quantities are compared and discussed to show what kind of information can be obtained from such quantities. The influence of the basis set size has also been considered.
Semiempirical molecular‐orbital studies on the problem of nonclassical resonance in the homoallylic cation
Authors: Murthy A. S. N. , Ranganathan Shoba 
Published: December 2004

AbstractThe quantum‐mechanical methods (EHT and CNDO/2) have been applied to the homoallylic cation. Both methods successfully predict that the ion need not be represented as a nonclassical structure.
Many‐body calculation of the electric field gradient in the hydrogen molecule
Authors: Itagaki T. , Saika A. 
Published: December 2004

AbstractThe electric field gradient in the hydrogen molecule has been calculated by diagrammatic many‐body perturbation theory (MBPT) in Gaussian basis sets. The procedure through third order in electron correlation gives a value for the field gradient of 0.34041 a.u., which is 0.8% greater than the accurate value. The result is discussed in terms of the completeness of the basis sets and the convergence of the perturbation expansion.
Study of correlation holes. II. CI calculations on model polyatomic systems
Authors: Cimiraglia Renzo , Resta Raffaele 
Published: December 2004

AbstractThe shape of correlation holes in many‐electron systems is at present scarcely known, even where correlated wave functions are available. We investigate here the kind of electron correlation brought about by configuration interaction (CI), within a given basis set, in the wavefunction of a polyatomic system. The model ring system H6 (in two different bonding circumstances) and H14 have been chosen for a detailed study, because of their paradigmatic importance. We set out the equal‐spin and different‐spin correlation holes as obtained from complete CI calculations in H6 and partial ct in H14, both within a minimal basis set. We basically find the spinless correlation as being short range, while the spin‐dependent correlation holes show long‐range oscillations of antiferromagnetic character. We also present a natural spin‐geminal analysis of the two‐body reduced density matrices in these systems; we find a peculiarity possibly related to the long‐range correlation discussed above. Finally, we compare the electron correlation as given from our CI wavefunction to other pictures of electron correlation, as obtained essentially from alternant molecular orbital wave functions and from the electron–gas literature.
Antisymmetric product of geminals in the context of the method of moments
Authors: Røeggen I. 
Published: December 2004

AbstractA scheme for obtaining approximate solutions of the electronic Schrödinger equation is formulated within the context of the method of moments. The flexibility of the method of moments is utilized in the construction of a model based on an antisymmetric product of geminals (APG). This APG model is compared with a model based on an antisymmetric product of strongly orthogonal geminals (APSG). As a test example the advocated APG model is applied to the ground state of ammonia. Our best APG function recovers 37% of the total molecular correlation energy to be compared with an estimated 31% for the best APSG function.
Electronic structure of the metabolites of cyclophosphamide
Authors: Ulmer W. 
Published: December 2004

AbstractSome physical and chemical properties of the metabolites of the cancerostat cyclophosphamide (trade name: ENDOXAN) have been calculated with an appropriately prepared CNDO/S‐CI method. The ground state properties (e.g., charge densities and free valences) do not indicate a significant change, compared with the results of cyclophosphamide, and the same fact is also true for the energy levels of the two lowest excited singlet and triplet states. With respect to the dipole transition moments only the metabolite N‐mustard‐diamido‐phosphoric acid (Friedman acid) differs drastically from cyclophosphamide and the other metabolites. The chemical reactivity has been considered under the aspect of singlet–triplet transitions between quasidegenerate singlet and triplet states. Again Friedman acid behaves quite differently from the other compounds, and only this metabolite exhibits the remarkable ability to act as an alkylating agent via splitting off chloride ions.
Direct energy minimization of self‐consistent electron pair by an orthogonal transformation of the basis
Authors: Fantucci Piercarlo , Polezzo Stefano , Trombetta Laura 
Published: December 2004

AbstractIn the frame of direct minimization of MC–SCF energy by an orthogonal transformation of the basis, a new procedure for iteratively solving the orbital equations is presented, in which the orthogonal matrix is calculated by the singular value and vector decomposition of a nonsymmetric matrix. The procedure is applied to the self‐consistent electron pair theory and tested on LiH molecule. Convergence rate and numerical stability are found to be satisfactory.
Three‐body potential energy terms for methane trimers
Authors: Novaro O. , Castillo S. , Kołos W. , Leś A. 
Published: December 2004

AbstractAn SCF LCAO MO calculation on the methane–methane–methane system is presented, in order to analyze the deviation from pairwise additivity of the interaction energy. Three‐body terms are shown to be remarkably similar to those of noble gas trimers both in magnitude and in their dependence on the geometrical arrangements of the three molecules.