bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ab initio molecular calculations with pseudopotentials: calculations of double‐zeta quality on BeH2, BH3, CH4, and C2H6
Authors: Gáspár R. , Gáspáar R. 
Published: December 2004

AbstractA new form of pseudopotential for applicaiton in ab initio molecular calculations is described. A method for determining pseudopotential parameters is suggested and pseudopotential parameters of double‐zeta quality are presented for the first row atoms of the periodic table. The pseudopotential is especially well suited for incorporation into the floating‐spherical‐Gaussian‐orbital (FSGO) method, though it is not restricted to any particular method. Applications of the resulting pseudo‐FSGO method to BeH2, BH3, CH4, and C2H6 are presented.
Geometry of density matrices. III. Spin components
Authors: Harriman John E. 
Published: December 2004

AbstractA definition is given for the spin‐tensorial components of a p‐electron density matrix for arbitrary p. Certain of these are defined to be standard components, and it is shown that all others can be obtained from them by linear combinations of permutations. When the density matrix is reduced, the standard components either map into standard components of the fewer‐electron density matrix or into the origin. One‐ and two‐electron density matrices are treated in greater detail. Reducing bases are given for the spaces in which the spatial coefficients of the spin components are elements. For spin eigenstates traces of all components are determined, and the π = 1 parts of all components are determined in terms of two independent components, which are themselves determined by the two‐electron charge density matrix. Geometric consequences are investigated.
On the polarity of the amide group and its impact on dipeptide conformation
Authors: Prasad C. V. , Sundaram K. 
Published: December 2004

AbstractGiving explicit consideration to the lone pairs of the carbonyl oxygen of the amide group it is found that the polarity of the amide group resides essentially in the lone pair. As a confirmation, the lone pairs of the ester group are also found to account for most of its polarity. This localization of amide dipole affects the dipeptide conformation map only in the unallowed regions of the map, but has significant impact on the dipole moment of the dipeptide in different conformations. The experimentally observed dipole moments of dipeptides in solution are in conformity with our assignment of polarity of the amide group.
Analytic perturbation theory and localization phenomena
Authors: Brändas E. J. , Obcemea C. H. 
Published: December 2004

AbstractThis paper attempts to apply the results of analytic perturbation theory to systems exhibiting some degree of randomness in their state variables. In particular, we focus on the localization problem in the Anderson model. It is shown that this approach proves the existence of bound states as a result of the statistical treatment of the Weinberg–van Winter–Hunziker irreducible N‐particle kernel. The analysis is extended beyond the one‐particle cluster approach and the occurrence of higher‐order clusters is discussed in relation to the diluteness criterion and the conditions set on the interaction potential V.
MCSCF optimization through combined use of natural orbitals and the brillouin–levy–berthier theorem
Authors: Ruedenberg K. , Cheung L. M. , Elbert S. T. 
Published: December 2004

AbstractA novel approach is developed for optimizing molecular orbitals within the context of a multiconfiguration self‐consistent‐field problem. The MCSCF wave function is determined through a sequence of eigenvalue problems in the multiconfiguration space and the single‐excitation space. They are used to iteratively improve the natural orbitals, which in turn are related, by successively improved transformations, to the MCSCF orbitals. The mathematical problems arising out of this general concept are solved and the computational implementation is discussed. In many applications the method has proven itself as a powerful approach in forcing rapid convergence. Adaptation to spin and spatial symmetry is maintained throughout and the procedure is applicable to excited states as well as to ground states.
Electronic rearrangements during chemical reactions. II. Planar dissociation of ethylene
Authors: Cheung L. M. , Sundberg K. R. , Ruedenberg K. 
Published: December 2004

AbstractThe direct dissociation of ethylene into two methylenes is studied along the least motion reaction path by means of an ab initio multiconfiguration self‐consistent‐field (MCSCF) calculation. All eight configurations arising from those valence orbitals that form the CC bonds, seven of them singlet coupled and one triplet coupled, are taken into account. The HCH bond angle is optimized along the entire reaction path. Separate MCSCF optimizations are carried through for the lowest two states of 1Ag symmetry. The (1Agσ2π2) ethylene ground state dissociates into two (3B1σπ) ground‐state methylenes. The (1Agσ2π*2) excited state of ethylene dissociates into two (1A1σ2) excited methylenes. It is established that both these dissociations proceed without any barrier in the energy curve. In the ground state, where orbital symmetry is conserved, the π‐bond breaks before the σ‐bond, and the calculated heat of reaction agrees within 6 kcal/mol with the experimental value. In the excited state, where orbital symmetry is not conserved, the nonbonded repulsion between methylene σ2 lone pairs is found to blend into the antibonding character of the excited ethylene, yielding an energy curve that is everywhere repulsive. However, the variation of the HCH angle during the dissociation process is not simple, initially it expands and subsequently it contracts. Quantitative analytical approaches are developed which furnish conceptual interpretations of the orbital changes and configurational changes along the reaction path.
Energy of planar autoassociation of xanthine and spatial structure of poly(riboxanthylic acid)
Authors: Geller M. , Lesyng B. , Pohorille A. 
Published: December 2004

AbstractFirst‐ and second‐order perturbation theory in a polarization approximation was employed to calculate interaction energies of planar xanthine–xanthine pairs in stable configurations. Electrostatic energy was obtained in the atomic‐dipole approximation. The results provided a basis for formulation of a four‐stranded model of poly(xanthylic acid) that allows two hydrogen bonds per base. The model accounts satisfactorily for the unusual thermal stability and the observed pH transition of the polymer. The latter is due to the gradual dissociation of the N3 protons accompanying by disrupture of the weak N3H ··· O6 hydrogen bonds. However, the structure is only moderately weakened since the configuration of the coplanar bases remains stabilized by four N1H ··· O2 hydrogen bonds.
Determination of potential‐energy surface of molecules in an applied field on the basis of virial relations
Authors: Rossikhin V. V. , Voronkov E. O. , Kruglyak Yu. A. 
Published: December 2004

AbstractThe quantum‐mechanical virial theorem (in diagonal and nondiagonal forms) for molecules in an external, weak, uniform electric field is used for obtaining the analytical expression of the potentialenergy surface in the Hartree–Fock–Roothaan one‐determinantal approximation. The polarizability tensor components of the H2O molecule are computed on this basis. The dependence of basing the atomic orbitals upon the intensity of the applied field lead to good coincidence of results with the data of near Hartree–Fock calculations.
Active‐site α‐helix in papain and the stability of the ion pair RS− ··· ImH+.Ab initio molecular orbital study
Authors: van Duijnen P. Th. , Thole B. Th. , Broer Ria , Nieuwpoort W. C. 
Published: December 2004

AbstractAb initio MO calculations, using both minimal (STO‐3G) and extended (Roos–Siegbahn) basis sets are reported for the systems methanethiol–imidazole, methanethiol–imidazole–formaldehyde, and methanethiol–imidazole–formamide, which, together with a point‐change representation of a long α‐helix, form models for the active site of papain. It is shown that the large electric field exerted by the helix in the active‐site region is responsible for the presence of the essential residues Cys 25 and His 159 in the form of an ion pair RS− ··· ImH+, which is crucial for a recently proposed mechanism for the catalytic action of the enzyme. Also, an explanation is given for the anomalies in measured pK values for these residues. Detailed studies on the (sub)systems show that minimal basis sets lack the flexibility necessary for describing the type of proton transfer involved. We conclude that α‐helices are essential parts of enzymes and that they play a significant role in the catalytic process.
Possible generalization of the optimized diatomics‐in molecules theory: Further studies of the diatomic state mixing parameter adjustment
Authors: Zaitsevskii A. V. , Nemukhin A. V. , Stepanov N. F. 
Published: December 2004

AbstractA generalization of optimized diatomics‐in‐molecules method that provides an accurate treatment of overlap integrals is presented. The possibilities of the method to reproduce potential surfaces of the 4B2, 2B2, and 2A1 states of the H3 molecule are investigated. It is shown that satisfactory results can be achieved only for a single state under consideration, but not for the three states simultaneously.
“Ring currents” static hypersusceptibilities
Authors: Gayoso J. , Maouche B. , Ouamerali O. , Baba‐Ahmed A. 
Published: December 2004

AbstractThe Hückel–London theory has been applied to the calculation of the “ring currents” octopole hypersusceptibilities of a series of conjugated compounds. Our calculations have been performed using fourth‐order Rayleigh–Schrödinger perturbation technique. This is believed to be the first calculation of this kind. It is found that the values of “ring currents” hypersusceptibilities of fulvene and azulene are larger, in absolute magnitude, than the values corresponding, respectively, to benzene and naphthalene. It is found that, in most cases, the “ring currents” hypersusceptibilities are diamagnetic (negative values) for aromatic molecules and paramagnetic (positive values) for pseudoaromatic or antiaromatic compounds.
Chemical graph theory: Modeling the thermodynamic properties of molecules
Authors: Mekenyan O. , Bonchev D. , Trinajstić N. 
Published: December 2004

AbstractGraph‐ and information‐theoretical indices were recently developed as quantitative structural characteristics of molecules. In this paper they are found to correlate well with a number of molecular properties of alkylbenzenes: heats of formation, combustion (both in liquid and gas phase) and vaporization, molecular volume, boiling point, and parachor. The topological information index and the number of carbon atoms are taken as variables. The correlation coefficient was found to be equal or close to 1. In three cases the mean relative error is less than 0.1%, in another three cases it is within the range 0.2–0.4%, and for boiling points only it is 1.25%. The proposed approach is compared with the additive scheme of Tatevskii.
Calculated optical spectrum of model oxyheme complex
Authors: Loew Gilda H. , Herman Zelek S. , Zerner Michael C. 
Published: December 2004

AbstractThe optical spectrum of a model oxyheme complex has been calculated using a new intermediate neglect of differential overlap (INDO‐SCF‐CI) method that allows for the inclusion of configuration interaction and transition metals. In addition to the porphyrin π→π* transitions common to all heme proteins, four weak x,y polarized transitions observed only in oxyheme complexes have been calculated and assigned to excitations involving the lowest‐empty highly delocalized (Oπ, dπ) orbital. Two broad z‐polarized bands observed in the single‐crystal polarized absorption spectra of oxymyoglobin and hemoglobin have also been calculated. Controversy exists over the assignment of these transitions and, in particular, over the extent of involvement of the oxygen ligand. Our calculations assign the weaker near‐IR visible band mainly to the d σ dπ→ dπ* excitations and the more intense UV band mainly to a2u → dσ* excitations. While significant participation (25%) of the highly delocalized (Oπ, dπ) virtual orbital is also found, these z‐polarized transitions need not be totally unique to oxyheme complexes, in keeping with experimental observation.
Weak interactions at the photoexcited states of partially oriented aromatic chromophores in man‐made bilayer membranes
Authors: Nagamura Toshihiko , Takayanagi Takashi , Matsuo Taku 
Published: December 2004

AbstractMonoalkyl and dialkyl quarternary ammonium salt‐type cationic surfactants containing a phenoxy group as aromatic chromophores at different positions of alkyl chains were synthesized. Monoalkyl‐type surfactants formed micelles in aqueous solutions. The bilayer structure similar to that found in phospholipid liposomes was obtained in the aqueous dispersions of dialkyl‐type surfactants. The phenoxy groups were partially oriented and aligned in these molecular assemblies. The interactions of aligned phenoxy groups in micelles or bilayers resulted in luminescence with lower energy than that of the monomer fluorescence or in a radiationless deactivation of excited states. Such interactions could be effectively prevented in bilayer structures composed of surfactant molecules containing a “spacer chain” between aligned chromophores. Evidence was obtained supporting energy migrations between aligned chromophores that were separated by a dodecyl chain in the bilayer structure.
Physicochemical properties of SF 6847, a potent uncoupler of oxidative phosphorylation in mitochondria in relation to its activity
Authors: Yoshikawa Kenichi , Kumazawa Noriyuki , Terada Hiroshi , Akagi Kazuo 
Published: December 2004

AbstractThe steric and electronic structure of the most potent uncoupler of oxidative phosphorylation, SF 6847, was studied. From 1H NMR measurements, it was found that the benzylic protons meta to the hydroxyl group are equivalent in neutral form, and that these protons tend to become non‐equivalent on acid dissociation of the phenolic proton. The CNDO/2 calculation of the dimethyl derivative of SF 6847 showed that in the most stable conformation the angle of the malononitrile group with respect to the benzene ring is about 40° and that the planar form is quite unstable. Results on electronic absorption of SF 6847 in various media showed that the acid dissociation of its phenolic group is affected very much by small changes in the nature of the surrounding environment. It was also found that the calculated total energy differences between the anionic and neutral forms are correlated well with the uncoupling activities of 4‐substituted 2,6‐di‐tert‐butylphenol derivatives.
Scaled single‐zeta basis set for use with a silicon effective potential: Generalized valence bond description of disilane
Authors: Moskowitz Jules W. , Topiol Sid , Snyder Lawrence C. , Ratner Mark A. 
Published: December 2004

AbstractA compact and efficient scaled single‐zeta basis set has been developed for use in conjunction with the coreless Hartree–Fock silicon effective potential. The scale factors were determined by minimizing the electronic energy of the disilane molecule. Based upon a generalized valence bond computation using this basis, we conclude that the classical concept of localized σ bonds is adequate to fully explain the electronic structure of disilane in analogy to the ethane molecule.
Optical oscillator strengths for isoelectronic ions of nitrogen
Authors: Ganas P. S. 
Published: December 2004

AbstractAn analytic atomic active electron model potential adjusted to experimental single‐particle energy levels is used to generate wave functions for the valence and excited states of O1+, F2+, Ne3+, Na4+, and Mg5+. Using these wave functions in conjunction with the Born approximation and the LS‐coupling scheme, we calculate optical oscillator strengths for excitations from the 1s22s22p3(4S3/2) ground state. The results are compared to experimental data and other calculations. Systematic trends along the isoelectronic sequence are discussed.
Calculation of the minimum energy conformation of acetylcholine using a global optimization technique
Authors: Rao Gita Subba , Tyagi R. S. , Mishra R. K. 
Published: December 2004

AbstractThe conformational energy of acetylcholine is minimized with respect to the distances between nonbonded atoms with the help of the Bremermann method of unconstrained global optimization. The set of distances for which the energy is the absolute minimum is then used to calculate the coordinates of all the atoms and hence the conformation of the molecule. The simplest type of potential function, namely the classical potential function is chosen for the calculation. The major advantages of this method are (i) that the starting point need not be close to the actual solution, (ii) that it gives the global minimum, irrespective of the starting point, (iii) that it is very general and can be used for any type of potential function, and (iv) that it does not require the computation of gradients. The results obtained are in very good agreement with those of other workers.
Ab initio valence bond calculations. XI. Pyridine: Ground and ionized states
Authors: Tantardini Gian Franco , Simonetta Massimo 
Published: December 2004

AbstractThe ab initio valence bond method has been used to study the ground and the lowest vertical valence ionized states of pyridine. On the basis of our calculations the first two ionization potentials are assigned to π and n electron removals, respectively. The final wave functions have been interpreted in terms of valence bond structures by means of an appropriate population analysis.
Morse matrix elements: An asymptotic expansion treatment
Authors: Chakraborty B. P. 
Published: December 2004

AbstractAn asymptotic expansion method has been used to calculate the Morse matrix elements for the vibration–rotation transition. A general expression has been derived for the quartic matrix elements, which can be reduced to the expressions for the cubic, quadratic, and linear matrix elements. The results agree extremely well with those given by the factorization method outlined by Badawi et al., and are similar to those given by Coquant et al., who used quite complicated and lengthy equations based on the Dunham potential. Earlier works to calculate the electronic transition probability parameters utilizing the above mentioned asymptotic expansion technique have also been extended and modified.
Application of the theory of symmetry of nonrigid molecules to the calculation of the conformational dependences of the torsional potential and dipole moment of acetone‐related molecules
Authors: Labbe A. Toro , Maruani J. 
Published: December 2004

AbstractWe have investigated the conformational dependences of the torsional potential and dipole moment of double‐rotor molecules related to acetone, using semiempirical and ab initio calculations and expressing the results in terms of limited Fourier‐series expansions. The use of the isodynamic operations of nonrigid molecules to obtain symmetry‐adapted quasianalytic forms for the various properties helps compute the representative surfaces with a minimum number of points. Potential surfaces have been calculated for planar ground‐state acetone (CNDO/2, STO/3G, and STO/4‐31G) and both pyramidal excited‐triplet acetone and ground‐state dimethylamine (CNDO/2). For groundstate acetone STO/4‐31G brings the results obtained with STO/3G closer to those from CNDO/2 and from experiment. The potential surface of excited‐triplet acetone appears intermediate between those of ground‐state acetone and dimethylamine. For dipole moments the convergence of the harmonic expansions of the vector components is slower than that of the torsional potential whereas that of the vector magnitude is faster.
Some properties of the Lagrange multiplier μ in density functional theory
Authors: Nguyen‐Dang T. T. , Bader R. F. W. , Essén H. 
Published: December 2004

AbstractSome new properties of the Lagrange multiplier μ introduced through the normalization constraint on ρ in the variations of energy density functionals are determined. Through arguments concerning the homogeneity properties of these functionals with respect to μ, it is demonstrated that at the point of variation μ = μ0 = E0/N, where E0 is the ground state energy and N is the total particle number. It is also shown that the value of μ0 is independent of the normalization imposed on ρ. The interpretation of μ0 as a chemical potential is discussed in the light of these findings.
Large‐scale RPA calculations of chiroptical properties of organic molecules: Program RPAC
Authors: Bouman Thomas D. , Hansen Aage E. , Voigt Bjørn , Rettrup Sten 
Published: December 2004

AbstractThe computational considerations involved in calculating ordinary and rotatory intensities and electronic excitation energies in the random phase approximation (RPA) are examined. We employ a localized orbital formulation in order to analyze the results in terms of local and charge‐transfer excitations. Occupied orbitals are localized by the Foster–Boys procedure. The virtual space is transformed into a localized “valence” set that maximizes dipole strengths with the occupied counterparts, and a delocalized remainder. The two‐electron integral transformation is performed with an efficient algorithm, based on Diercksen's, that generates only the particle–hole‐type integrals required in the RPA. The lowest solutions of the RPA equations are obtained iteratively using a modification of the Davidson‐Liu simultaneous vector expansion method. This allows the inclusion of the entire set of particle–hole states supported by a basis set of up to 102 orbitals. Calculations at this level give better excitation energies and intensities than SDCI methods, at substantial savings in computational effort. Comparative timings, computed results and analysis in terms of localized orbitals are given for planar and distorted ethylene using extended atomic orbital bases including diffuse functions. The results for planar ethylene are in excellent agreement with experiment.
Isolation and characterization of a novel cDNA encoding a DNA‐binding protein (Hils1) specifically expressed in testicular haploid germ cells
Authors: Iguchi Naoko , Tanaka Hiromitsu , Yomogida Kentaro , Nishimune Yoshitake 
Published: December 2004

SummaryA cDNA encoding a protein homologous with histone H1 has been cloned from a haploid germ cell specific cDNA library. Deduced amino acid sequence (170 amino acids) showed 40% identity with histone H1 globular domain. Messenger RNA of the gene was observed exclusively in the testis, and was accumulated after post‐natal day 23. Western blotting analysis showed that the protein encoded by this gene is about 19 kDa in molecular weight, and it was exclusively recovered from the nuclei of testicular germ cells. Immunohistochemical analysis showed that the protein was localized to the nuclei of round and elongating spermatids, consistent with the results of immunoblot analysis. Thus, the gene product was named Hils1 (histone H1 like protein in spermatids 1). In vitro DNA‐binding experiments using DNA‐cellulose mini‐columns showed that Hils1 was able to bind to both double and single stranded‐DNAs in a non‐sequence‐specific manner. These findings suggest that Hils1 may play an important role in the structural changes of spermatid nuclei, such as nuclear condensation, and gene regulation of haploid germ cell differentiation.