bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modification of the NDO model in semiempirical MO theory
Authors: Basilevsky M. V. , Shamov A. G. 
Published: December 2004

AbstractWe suggest the explicit transformation of the parametrized atomic ϕ‐basis semiempirical Hamiltonian to the Löwdin λ basis. A nontrivial problem then arises concerning the transformation of the four‐index electron interaction matrix Γ, for which parametrization is given in the ϕ basis, whereas the NDO approximation is introduced in the λ basis. The main result is that under the CNDO assumption the two‐index Coulomb matrix can be transformed independently of other integrals of Γ. The explicit form of the transformation between the Coulomb matrix γ of parameters given in the ϕ basis and the Coulomb matrix λγ in the λ basis is found. The λγ calculated by this method differs only slightly from the result of the exact complicated four‐index transformation. On the other hand the elements of γ and λγ may differ by several eV when overlap is significant.
Interactions and self‐organization of nucleic bases, nucleotides, and polynucleotides into ordered structures. Effect of ionization and solvent salt composition
Authors: Sukhorukov B. I. , Gukovsky I. Ya. , Petrov A. I. , Gukovskaya A. S. , Mayevsky A. A. , Gusenkova N. M. 
Published: December 2004

AbstractThis paper summarizes our findings on the effects of protons and neutral salt ions on intermolecular interactions and the self‐organization of nucleotide systems in aqueous media, both at monomer and polymer levels. To gain quantitative information about these processes, methods were developed to determine the thermodynamic parameters of monomer association from the data obtained by various experimental techniques (NMR, UV spectroscopy, and spin labeling) and to estimate the individual contributions of base stacking and H‐bonding in ordered structures of polynucleotides and their complexes. The main results obtained using these methods are as follows. (i) A difference was discovered in the effects of positive and negative charges on the stacking interaction between ionized and neutral molecules of nucleic heterocycles. Protonation strongly decreases the heterocycle ability to form ordered stacks whereas deprotonation slightly affects stacking. (ii) Base–phosphate interaction, which has not yet really been investigated, was studied. This interaction, along with base stacking, governs nucleotide association in water media. It appears upon protonation of the base moiety and increases with decreasing ionic strength. (iii) Base stacking was found to become stronger under the action of salt anions stabilizing the water structure and it became weaker under the action of destabilizing salt anions, both in monomer and polymer systems, which is indicative of an indirect mechanism of the anionic effects. It is essential that small salt ion additives acting by such a “distance” mechanism can affect the formation of ordered structures in nucleotide systems as strong as the direct interaction of the bases with protons. (iv) The results obtained suggest that an increase in solvent entropy upon the self‐organization of nucleotide systems in aqueous media may be an important factor promoting these processes. (v) As follows from our data, specific weakening or strengthening of intermolecular interactions by protons and salt ions at small, physiological‐range changes in pH or solvent salt composition seems to be an effective regulatory mechanism for the functioning of nucleotide systems.
Density of non‐Bloch electron states in perfect cubic crystals
Authors: Bulski T. , Olszewski S. , Wierzbicki A. 
Published: December 2004

AbstractThis paper gives an abbreviated method for the calculation of the density of states of a crystal on the basis of that band theory in which the crystal electron states are represented by the standinglike wave functions classified according to the point‐group symmetry species. The crystal is a large but finite sphere filled regularly with atoms, and the wave functions are quantized at the boundary of the sphere. The Bloch theorem is not satisfied in this theory since the wave functions are not basis functions of the irreducible representations of the translation subgroup. On the other hand, a theorem is established that the density of states can be made up of contributions given by all irreducible representations of the crystal point group, any contribution being proportional to the square of the dimension of the irreducible representation. In distinction to a former approach, the band structure is calculated solely from the energy eigenvalues obtained with the aid of the diagonalization process of the Wannier–Slater differential operator. A simple cubic lattice with an s atomic orbital on each lattice site is taken as an example, and the results are compared with Bloch's theory.
Slater‐orbital molecular integrals by numerical Fourier‐transform methods. II. Four‐center integrals over is orbitals
Authors: Graovac Ante , Kovačević Krešimir , Maksi Zvonimir B. , Veseli Ahmet 
Published: December 2004

AbstractThe four‐center nonplanar electron repulsion integrals over 1s Slater‐type atomic orbitals are considered by a numerical Fourier‐transform method. It is shown that the highly oscillating integrand appearing in the Fourier inversion formula could be successfully treated by using Tchebyscheff quadrature. The resulting formulas are thoroughly discussed with particular emphasis on their numerical features and convergence properties. It follows that the aforementioned integrals may be calculated with a good accuracy with a moderate amount of computing time.
Absorption UV spectroscopy and electronic structure of ionic and tautomeric forms of hydroxy and methoxy derivatives of cytosine and adenine, and of some 5‐substituted analogs of pyrimidines
Authors: Borodavkin A. V. , Chekhov V. O. , Dolin Yu. S. , Morozov Yu. V. , Savin F. A. , Budowsky E. I. , Yakovlev D. Yu. 
Published: December 2004

AbstractThe individual absorption spectra of various ionic and tautomeric species of some derivatives of nucleic‐acid components have been determined by computer handling of the summary spectra of these compounds measured at different pH values. These individual spectra have been decomposed into separate bands represented by log‐normal curves and corresponding to different electronic transitions. Using the parameter system calculated earlier for the molecules of the vitamin B6 family, the calculation of the electronic spectra and electronic structure of various ionic and tautomeric species of the molecules studied have been carried out in the π‐electron approximation. These properties have also been calculated by the all‐valence electronic method CNDOS. The calculated results correlate well with both approximations and with our experimental spectral data. The localization of the molecular electronic excitation studied on the transition to the S1 and T1 states is considered in connection with the reactivity in these states.
New derivation and a k‐particle generalization of SCF‐type theories
Authors: Kutzelnigg Werner 
Published: December 2004

AbstractA hierarchy of necessary conditions that an exact density matrix of a pure state or an ensemble has to satisfy is derived, namely the hermiticity of certain operators F(k). For k = 1 this reduces to the well‐known Hartree‐Fock condition. It is then shown that the kth set of conditions is equivalent to stationarity of the energy with respect to unitary k‐particle transformations. k‐Particle generalizations of Hartree‐Fock theory are then discussed both in the spirit of k‐particle pseudoeigenvalue equations and in the framework of a Newton–Raphson‐type constructive scheme.
Modified virtual orbitals of Hartree–Fock method in calculation of second‐order perturbation energy
Authors: Hiroike Eiko 
Published: December 2004

AbstractAn advantage of modified virtual orbitals of Hartree–Fock method is discussed in the calculation of the second‐order perturbation energy. All the modified virtual orbitals can be fitted for the intermediate virtual states in the perturbation expansion, only if the molecular orbitals are expanded in terms of infinite basis functions and the set of molecular orbitals is infinite and complete. If the molecular orbitals are expanded in terms of finite basis functions, only the modified virtual orbitals with lower energies are appropriate to describe the intermediate virtual states, but the modified virtual orbitals with higher energies become inadequate. To explain the usefulness of the modified virtual orbitals, the calculation by the modified Hartree–Fock method without CI are compared with the calculation by the traditional Hartree–Fock method with complete CI.
Conservation of intrinsic dual and single symmetries of molecular orbitals
Authors: Au‐Chin Tang , Chia‐Chung Sun 
Published: December 2004

AbstractIn this paper, a fresh attempt has been made to discuss dual‐symmetry groups by which the supra–antarafacial cycloaddition and the chelatropic reactions can be correctly described, as a direct consequence of which the corresponding energy correlation diagrams are successfully constructed. Furthermore, the energy correlation diagrams of sigmatropic reactions are also established by the use of another kind of single‐symmetry group.
Comparison between the symmetry‐correlation examination and the perturbation method
Authors: Lee Tieh‐Sheng , Chu San‐Yan 
Published: December 2004

AbstractA comparison between the construction of symmetry‐correlation diagrams and the perturbation method for studying chemical reactions is carried out. The perturbation method consists of decomposing the system Hamiltonian H into a sum, H = H0 + H′. Various symmetry correlation schemes appearing in the literature may be explained by the nonuniqueness of the decomposition scheme. All symmetry selection rules may be viewed as the varieties. By examining the symmetry‐correlation diagrams, processes under investigation may be called “forbidden” or “allowed,” depending on the topological feature. Of particular importance is the topology associated with the “avoided crossing.” By making the comparison, we can establish the correspondence of the two methods and conclude that the perturbation order furnishes the origin of the “forbiddenness” of a process.
CNDO calculation of the diamagnetic susceptibilities of cyclic conjugated molecules
Authors: Boucekkine A. 
Published: December 2004

AbstractWe present the results obtained within the CNDO/2 method for the diamagnetic susceptibilities of a series of conjugated molecules including benzene, fulvene, pyridine, pyrrole, and furan. The calculations have been carried out, according to Bley's method, in the framework of coupled Hartree–Fock perturbation theory, using gauge invariant atomic orbitals and the London approximation. The two usual CNDO parametrizations, due respectively to Pople, Santry, and Segal and to Del Bene and Jaffe, did not enable one to obtain the principal susceptibilities of the molecules under consideration. We investigated the effect of the CNDO parametrizations on the different contributions to the susceptibility, and gave a first improvement to Bley's method, which permits the calculation of the mean susceptibility of conjugated molecules with less than 9% error.
Theoretical study of photochemical reactions: Electron assignment and the state correlation diagram
Authors: Yamabe Shinichi , Minato Tsutomu , Osamura Yoshihiro 
Published: December 2004

AbstractA general way for drawing the state correlation diagram and seeking the reaction path is presented. If a high‐symmetry reacting system is given, its least‐motion path that maintains the symmetry is primarily examined. For a given state, it is judged whether the least‐motion path is symmetry allowed or forbidden. If allowed, it is called the direct process. If forbidden, the symmetry imposed on the system should be relaxed, resulting in the mixing of MO's. Then, the energy barrier of the avoided crossing for some excited states is removed and the possible reaction path is found. After this procedure, the symmetry‐allowed paths may be sought by the geometry optimization with a suitable wave function. By the use of such a procedure, the dissociation of diazomethane and (3H‐)diazirine is found to proceed via the Cs and C2 symmetries.
Field correlation effects on the resonant light scattering
Authors: Kôno H. , Fujimura Y. , Nakajima T. 
Published: December 2004

AbstractEffects of incident photon field coherence on resonant light scattering have been investigated. In order to obtain the scattering intensity and the photon counting rate, an expression for the reduced density matrix for the scattered field has been derived. The expression involves the first‐order correlation function of the incident field. The relation between the line shape of the scattered light and the bandwidth of the incident field has been clarified. Model calculations of the photon counting rate have been performed in the case of an incident field without first‐order coherence. In our treatment, the transverse and longitudinal relaxation constants have been taken into account by using the impact approximation.
SCF CI MO calculations on the base–base interactions in dinucleoside monophosphates
Authors: Gumbinger H. G. , Kaiser P. M. 
Published: December 2004

AbstractIn order to elucidate further details of RNA conformations we have studied base stacking in dinucleoside monophosphates (DNP's) using UV difference spectra and the hypochromic effect. SCF CI MO calculations according to PPP and MIM approximations were carried out for six pyrimidine‐containing DNP's in each of several stacking geometries. The calculated and plotted difference spectra were fitted to the experimental spectra. Different DNP's showed distinct geometries in the range of the helix angle of 35°. From our results we conclude that there is a microstructure in the helix. This would imply an additional content of information in this macromolecule, a higher precision in nucleic acid interactions, and make possible the prediction of the conformation of polynucleotides.
MO Study of flavin–protein interactions in flavodoxin catalysis
Authors: Teitell Murray F. , Fox J. Lawrence 
Published: December 2004

AbstractMINDO/3 calculations have been performed on the Clostridium MP flavodoxin active site (a complex of the redox active coenzyme flavin mononucleotide sandwiched between the side chains of methionine and tryptophan) at various redox levels using coordinates derived from x‐ray diffraction studies of the holoenzyme. Frontier orbital indices were calculated and indicate that reduction of the flavin is accompanied by induced polar states in the amino acid side chains. This stabilization of charge by the amino acid side chains could account for the reaction rate enhancement of flavin reduction catalyzed by flavodoxin. Frontier orbitals for free flavin, for the flavodoxin bound flavin without the amino acid side chains, and for the oxidized Desulfovibrio vulgaris flavodoxin active site were computed for comparison.
MO Study of the photochemical behavior of the imine bond
Authors: Osamura Yoshihiro , Yamabe Shinichi , Nishimoto Kichisuke 
Published: December 2004

AbstractThe photoisomerization of imine compounds is studied in terms of an ab initio MO CI calculation. The potential curves of the syn‐anti isomerization via the rotation and the inversion are examined for benzaldimine. It is suggested that the photoisomerization is initiated through the rotation around the CN bond in both singlet and triplet states. The ease of the photoisomerization is found to be determined by both the conformation of phenyl ring in the ground state and the energy difference of vertically excited states between two isomers.
MO Study on the photochemical isomerization of isoxazole
Authors: Tanaka H. , Matsushita T. , Osamura Y. , Nishimoto K. 
Published: December 2004

AbstractThe reaction mechanism of photoisomerization of isoxazoles to oxazoles through azirine intermediates is investigated theoretically by means of ab initio MO CI calculations. Azirine intermediates in S1 state [(n →*) state of the carbonyl chromophore] cause the CN bond rupture of azirine ring and transform to isoxazoles via intersystem crossing to T1 state. On the other hand, azirine intermediates in S2 state [(n →*) state of the ketimine chromophore] lead to the CC bond rupture of azirine ring and convert to oxazoles via intersystem crossing to T1 state.
Ab initio molecular orbital studies of polyethylene deformation
Authors: Brower A. L. , Sabin J. R. , Crist B. , Ratner M. A. 
Published: December 2004

AbstractA molecular LCAO Hartree‐Fock procedure was used to calculate total energies of axially stretched normal paraffins containing up to nine carbon atoms. The results are used to model the mechanical properties of polyethylene.
Gaussian matrix elements of the operator X: Reduction to confluent hypergeometric functions
Authors: Niukkanen A. W. 
Published: December 2004

AbstractA new method has been proposed for calculating the Gaussian matrix elements of the interaction operator represented by an arbitrary degree of interelectron distance X. The method is based on the expansion of two‐electron integrals as the sum of one‐electron integrals which in turn admit compact operator representation in terms of confluent hypergeometric functions. The generating differential operator has been shown to be related to the modified Hermitian polynomials. The standard structure of the special functions encountered in this approach is useful in studying the analytical behavior of the integrals and makes it possible to obtain for these integrals recurrence relations, direct algebraic expressions in the forms of finite sum of confluent hypergeometric functions, integral representations, and asymptotic properties. Unlike the usual methods based on integral transformation of the interaction operator, the proposed approach has a wider field of application, and in addition, leads to compact and convenient analytical expressions. The idea of using differential properties of integrals to simplify the integrand structure gives the proposed approach a certain resemblance to that suggested by Boys but not developed in detail in his pioneer work.
Evaluation of MINDO/3 calculations in simple amides, ureas, and heterocycles of biological interest
Authors: Defina J. A. , Andrews P. R. 
Published: December 2004

AbstractThe performance of the MINDO/3 method has been evaluated in simple heteroatomic molecules that are representative of several important biological systems. Molecular geometries are accurate to within 0.04 Å for bond lengths, and 3° for most bond angles. Dipole moments and charge distributions are estimated satisfactorily, and ionization potentials are predicted to an accuracy of 0.5 eV. The method is less accurate in estimating the ionization of some upper level σ orbitals. The overall evaluation shows that MINDO/3 provides a good description of the geometries and electronic properties of the molecules studied. The results of MINDO/3 calculations in several other chemical systems are also reviewed.
Simple technique to obtain correlated energy curves: LiH calculations
Authors: Moscardó Federico , Delgado‐Barrio Gerardo 
Published: December 2004

AbstractThe possibility of applying the half‐projected Hartree–Fock method together with the Coulomb hole model to obtain cofrelated potential‐energy curves is investigated. Here we report calculations performed on the LiH molecule. The results show that this combined technique can provide potential curves very near to the experimental ones with a similar effort to that involved in the Hartree–Fock calculations.
Coupled perturbation theory within the antisymmetrized product of separated geminals (APSG) framework
Authors: Dmitriev Yu. , Peinel G. 
Published: December 2004

AbstractA coupled perturbation theory for the antisymmetrized product of separated geminals (APSG) approximation is derived. The variational principle for the APSG wave function in an external oscillating field is employed and a set of equations of the form analogous to the normal RPA is obtained. At this level the reduced resolvent in the form of a spectral expansion is written and it is used for the evaluation of the second‐order properties.
Structures, stabilities, and energies of isomerization of some alkyl cyanides and isocyanides and their corresponding α‐cyanocarbonium and α‐isocyanocarbonium ions
Authors: Moffat J. B. 
Published: December 2004

AbstractAb initio STO‐3G geometry‐optimized calculations have been performed on methyl, ethyl, and isopropyl cyanides and isocyanides, and the cations formed on abstraction of an α‐hydride ion. Stabilization energies of the cations and cyanide–isocyanide isomerization energies have been calculated and correlated with structural features and population analyses.
Ghost orbitals in semiempirical methods. Estimation of basis set superposition error
Authors: Lipiński Józef , Chojnacki Henryk 
Published: December 2004

AbstractBased on the all‐valence ZDO SCF approximation a procedure for estimating the basis set superposition error (BSSE) in semiempirical CNDO/INDO methods has been proposed. The results of the calculation show that the BSSE effect may improve the results obtained from the standard CNDO/INDO supermolecule calculation. The estimated BSSE effect enables one to explain some recently reported artificial structures for water and ethylene dimers.
A possible basis for structure–function relationship of estrogens
Authors: Durani S. , Anand Nitya 
Published: December 2004

AbstractIt is well known that a wide variety of molecules compete for binding to the estrogen receptor and act as estrogens and/or antiestrogens. These molecules such as estradiol, diethylstilbestrol, doisynolic acid, the triarylethylenes, and cyclofenyl apparently share little resemblance which could account for their interaction with a common estrogen binding site. Knowledge of the receptor binding of triarylethylene and cyclofenyl prototypes, in particular, relative to that of the other estrogens is critical for understanding their structure‐function relationship. We have carried out a study on the receptor binding specificity of triarylethylene and cyclofenyl prototypes. This study has revealed that these molecular types share considerable resemblance in their receptor binding specificity and differ from estradiol and other similar molecules in some important respects. However, comparison of their substructural binding specificities reveals the possibility that the triarylethylene and estradiol prototypes may interact with at least some common regions of the estrogen binding site. Based on this reasoning the comparative receptor binding of estrogens has been rationalized on the basis of a subsite hypothesis for the estrogen binding site. According to this hypothesis, the composite estrogen binding site is composed of essentially five subsites, and that the structurally different estrogenic prototypes can interact with different set of subsites, and thus differ in their binding orientation. The essential difference in the activity profile of estradiol prototypes and the triarylethylene antiestrogens reveals the possibility of a causal relationship between the binding orientation of a ligand and its activity profile. This model for receptor site can thus serve as a working hypothesis to rationalize the structure‐function relationship of estrogens.