bluuebunny/crossref_metadata_2025 huggingface dataset:
Expression and transport function of the glutamate transporter EAAC1 in Xenopus oocytes is regulated by syntaxin 1A
Authors: Zhu Yani , Fei Jian , Schwarz Wolfgang
Published: December 2004

The function of several membrane proteins is regulated by interaction with the SNARE protein syntaxin 1A; this includes regulation of GAT1, the transporter for the dominating inhibitory neurotransmitter γ‐aminobutyric acid (GABA). Here we demonstrate that also EAAC1, the transporter for the dominating excitatory neurotransmitter, is down‐regulated by interaction with syntaxin 1A. This is shown by coexpression of EAAC1 and syntaxin 1A in Xenopus oocytes. Total EAAC1 expression is not significantly affected by the coexpression of syntaxin 1A, but more proteins become targeted to the membrane as demonstrated by biotinylation. Colocalization by coimmunoprecipitation suggests direct interaction between the two proteins. In contrast to the number of transporters, the glutamate transport activity becomes reduced, and even stronger inhibition is observed for the EAAC1‐mediated conductance uncoupled from glutamate translocation. We conclude that the interaction of syntaxin 1A with EAAC1 particularly disrupts the structure of the conductance pathway of EAAC1. © 2004 Wiley‐Liss, Inc.
A data programme for population analysis of crystal‐band structures
Authors: Flodmark Stig
Published: December 2004

An electronic‐computer programme has been written by the author for calculations of energy bands in the tight‐binding approximation. This programme has been applied to crystals of α zirconium with and without dissolved oxygen. The resulting energy bands and orbital distributions represent an enormous amount of numerical data. Another programme has now also been written by the author for population analysis of the occupied bands. This programme will reduce the resulting output considerably, and only occupied bands are represented in a number of directions in k space. The occupation numbers are summed up for orbitals with equal quantum numbers l and |m|, and are found for each band as a function of k.
Error bounds for the overlap of approximate wave functions
Authors: Wang P. S. C.
Published: December 2004

Variational upper and lower bounds for the overlap between an approximate and the true wave function are proposed, and it is shown that the error bounds introduced recently by Gordon are special cases of the variational formulas.
Zur eindeutigkeit der darstellungen von energiehyperflachen
Authors: Preuss H.
Published: December 2004

The first part of this paper gives an introduction of different kinds of atomic associations. Furthermore it will be shown that partial systems of united atoms are not only described by their nuclear‐charge number, but additionally by their number of electrons. Both characteristics of a partial system of atomic associations may lead to an apparent multiple‐valuedness in the transitions between atomic associations. It is shown that the multiple‐valuedness of the atomic associations can be understood and eliminated within the Born–Oppenheimer‐approximation, which leads to the concept “energyhypersurface”. An example is given by the system {He, H, H, H}+.
Electrostatic corrections to extended Hückel theory
Authors: Carbó R. , Fornos J. M. , Hernández J. A. , Sanz F.
Published: December 2004

An electrostatic correction to the energy of the EH method is deduced from the Hartree energy. A recent correction, due to Anderson and Hoffmann, is easily deduced as a particular case. Some calculations show how the correction can improve the description of stretching problems by EH calculations but poor results are obtained in bending and torsion problems.
Parseval's identity for biorthonormal systems
Authors: Lathouwers Luc
Published: December 2004

Parseval's identity for orthonormal bases in Hilbert space is generalised to characterise uniquely biorthonormal bases among biorthonormal systems.
Diagrammatic perturbation theory: Potential curves for the ground state of the carbon monoxide molecule
Authors: Wilson Stephen
Published: December 2004

Diagrammatic many‐body perturbation theory is used to calculate the potential energy function for the X1 σ+ state of the CO molecule near the equilibrium nuclear configuration. Spectroscopic constants are derived from a number of curves which are obtained from calculations taken through third order in the energy. By forming [2/1] Padé approximants to the constants we obtain: re = 1.125 Å (1.128 Å), Be = 1.943 cm−1 (1.9312 cm−1), aBe = 0.0156 cm−1 (0.0175 cm−1), We = 2247 cm−1 (2170 cm−1), WeXe = 12.16 cm−1 (13.29 cm−1), where the experimental values are given in parenthesis.
PCILO calculations on hydrogen bonded complexes
Authors: Lochmann R.
Published: December 2004

The PCILO method was used to study systematically systems with the following types of intermolecular hydrogen bonds: . In all cases the PCILO method gives a correct description of the stabilization energies in a good agreement with reliable ab initio results. The PCILO calculated equilibrium distances are only somewhat smaller than the corresponding experimental or ab initio values. Qualitatively, also, the changes in the charge distributions are in accordance with the results of ab initio calculations.
Attractive‐dominant and repulsive‐dominant hydrocarbon reactions
Authors: George Philip , Bock Charles W. , Trachtman Mendel , Brett Alistair M.
Published: December 2004

The difference between the expectation values of the total electronic kinetic energy operator (ΔEK), and the operators accounting for the Coulombic interactions between the electrons and nuclei (ΔVen), between all pairs of electrons (ΔVee), and between all pairs of nuclei (ΔVnn) for the product and reactant species in a wide variety of hydrocarbon reactions are calculated using single determinant basis set data reported in the literature. Following Allen, their contributions to ΔET, the difference between the corresponding total molecular energies and thus the reaction heat, are grouped together as a repulsion energy term, ΔErep = ΔEK + ΔVee + ΔVnn, and an attraction energy term ΔEattr = ΔVen. For all but 2 of the 71 individual reactions considered in this paper, the experimental reaction heat at 0°K corrected for zero‐point energy contributions, (ΔH)zpe, is the result of near compensation between far larger ΔErep and ΔEattr terms, in sharp contrast to the much smaller ΔErep and ΔEattr terms which are characteristic of many molecular rotation processes. By matching the sign of (ΔH)zpe with that of ΔErep or ΔEattr, as the case may be, the reactions are classified as attractive‐dominant or repulsive‐dominant (46 in the former class and 23 in the latter), a property which is independent of the direction in which the reaction is written. The sign and magnitude of ΔVee, ΔVnn, and ΔVen and reaction category are discussed in relation to the various kinds of structural change involved in going from reactants to products. For the vast majority of reactions, the numerical relationship ΔVee ≈ ΔVnn has been found to hold to within a few percent.
Comparison of UHF and PHF methods for hyperfine structure calculations
Authors: Lunell Sten
Published: December 2004

The validity of two models used in comparisons of the UHF and PHF methods in hyperfine structure calculations is investigated for the lowest 2P state of Li. An improved model for the angular splitting of the core orbitals is proposed and shown to give an accurate description of both the UHF and the PHF wave functions.
Invariance properties of the multipole expansion with respect to the choice of the coordinate system
Authors: Stolarczyk Leszek Z. , Piela Lucjan
Published: December 2004

The physical interpretation of intermolecular interactions is usually based on the well‐known multipole expansion of the inverse of the interparticle distance. The interaction energy is then interpreted as a sum of terms arising from the interaction of various multipole moments of both systems. It is supposed that the interaction energy calculated via the truncated multipole expansion generally depends on the choice of local coordinate systems through the coordinate dependence of the multipole moments. In this paper we prove that each term of the multipole expansion given in the form ∑k = 1 Ck/Rk is invariant with respect to identical translations and arbitrary rotations of the local coordinate systems. The invariant form of the convergence criterion of the multipole expansion is given and discussed.
Improved uncoupled Hartree–Fock (IUCHF) perturbation methods and bounds for the second‐order energy in coupled Hartree–Fock perturbation theory
Authors: Vogler H.
Published: December 2004

Different kinds of improved uncoupled Hartree–Fock methods are proposed for the calculation of second‐order perturbation energies. Using these methods inequalities are derived for the error of the uncoupled procedure with geometric approximation.
Continuum contribution to polarizabilities and scaling
Authors: Canuto Sylvio , Goscinski Osvaldo
Published: December 2004

The role of the continuum, so important in ground‐state properties, is known to be less important and may even be negligible in the computation of polarizabilities and other higher negative moments of the oscillator strength distribution. This can be rationalized in terms of the solutions of the inhomogeneous equation generating the moments as an alternative to the dominating first term in an eigenfunction expansion. This leads in a natural form to the approximation Fϕ0(1 + w(r)) for the perturbed wave function where 1 + w(r) represents a nonuniform scaling of the unperturbed function ϕ0.
Approaches for interpreting π electronic states and π electronic transitions
Authors: Fabian J. , Mehlhorn A. , Fratev F.
Published: December 2004

Scope and limitations of different approaches which enable π electronic systems of topologically equivalent structures to be compared have been examined. Particular attention has been paid to analyses in terms of molecular subsystems.
Realization of the elementary biological function as a localized electron subsystem interaction process
Authors: Ananchenkov V. I. , Leontyev V. B.
Published: December 2004

While regarding the elementary biological function as a series of elementary acts resulting in either chemical bond formation (breakage) or a changed molecular subsystem state, we would like to focus attention on some of the most essential and general features of this process in terms of the Von Neumann theory of self‐reproducing automata.
Electron mechanism of nonequilibrium molecular vibration excitation in biological systems
Authors: Kovarskii V. A. , Chaikovskii I. A. , Popov E. A.
Published: December 2004

The electron mechanism of the nonequilibrium vibration excitation is considered in multiatom molecules with the condition that the bottleneck effect takes place. The quantum‐statistical theory states that if the simplest enzyme reaction is proposed on the basis of the vibrational energy recuperation idea, the vibrons emitted in producing the free product and enzyme activate the first stage of the formation of the Michaelis–Menten complex and the multiphonon feedback mechanism is realized. Resulting solutions are applied to explain some biochemical and genetic effects.
Conformational studies of double‐helical polynucleotides by the method of pair‐wise potential functions
Authors: Il'Icheva I. A. , Tumanyan V. G. , Kister A. E. , Dashevsky V. G.
Published: December 2004

Double‐helical polynucleotide conformations, poly(dA)·poly(dT), poly(d(A‐T))·poly(d(T‐A))·poly(dG)·poly(dC), and poly(d(G‐C))·poly(d(C‐G)) are analyzed by the atom–atom potential method. The energy optimization is carried out in the space of eight independent geometric parameters using analytical procedures for the constraints, taking into account the flexibility of the β‐D‐deoxyribose rings. At the first stage, the full screening of atomic partial charges was assumed. The structures of the calculated B and the A forms of DNA are characterized by low energy and absence of short contacts; the dihedral angles are near the average values in the monomers. With the typical energy difference of 3–5 kcal/mol nucleotide pairs in all cases, the B form is more preferable as compared to the A form. At the final step the effect of the Coulomb term is evaluated for poly(dA)·poly(dT) using various values of the effective dielectric constant (ϵ = 28, 24, 20, 18, 14, 12, 10, 8, 6, 4, and 1). If ϵ ⩽24, the energy optimization leads A to B. We discuss the stereochemical details of the intermediate conformations on the A–B path and hypothesize the nature of stability of the A and the B forms and the mechanism of the A–B transition.
Study of pair correlation in three‐electron atoms
Authors: Ho Fat D. , Sanders Frank C.
Published: December 2004

Pair correlation in the ground state of the Li isoelectronic sequence is studied through four approximate wave functions which incorporate inter‐ and intrashell pair correlation. Of these functions, two possess symmetry appropriate to a three‐electron system, while two do not. The functions are not variational functions in the usual sense. They are instead fixed linear combinations of products of orbitals and pair functions for the appropriate states of two‐electron atoms. They are considered here as zero‐order approximations to the exact wave functions, and the corresponding zero‐order Hamiltonians are obtained. The simplest of these functions is improved by the introduction of a screening parameter for the “outer” electron. This latter function is found to be a satisfactory compromise between accuracy and simplicity and is proposed for study via higher‐order perturbation theory.
Behavior of the electron density near an impurity
Authors: Adawi I.
Published: December 2004

The behavior of the electron density n(r) and potential energy V(r) near the origin, where an impurity of charge Z is located, is studied using the Lindhard dielectric theory of the free‐electron gas. The leading odd terms in the power‐series expansion of n(r) and V(r) are obtained. It is shown that the derivative n′(0) = −2Zn0/a0, where n0 is the free‐electron gas density and a0 is the Bohr radius.
New self‐consistent theory of atoms: Toward a unified theory of atoms and atomic aggregates
Authors: Ogawa Tohru
Published: December 2004

A variational theory is proposed where the distance dependence of two‐center integrals is semianalytically given and the outer‐shell orbitals are eigenfunctions of the one‐particle Schrödinger equations. It is useful in the attempt of unifying the theory of atoms and atomic aggregates such as molecules, microclusters, crystals, etc., especially in the problems of predicting their stable structures. The purpose of this theory is not to derive lower ground‐state energies but to obtain some useful wave functions for the explanation of some tendencies of the atomic aggregates in the periodic table.
Formulation of the LCAS MS SCF method within the Gaussian basis set
Authors: Roszak Szczepan , Chojnacki Henryk
Published: December 2004

Within the presented LCAS MS (linear combination of atomic spinors–molecular spinors) SCF formalism both large and small components of the spinor radial parts have been expanded within the Gaussian basis set. The respective expressions for matrix elements as well as for one‐ and two‐electron integrals are given.
Vertical ionization potential in hydrogen molecule with many‐body Green's function method
Authors: Uehara Hiroshi , Itagaki Takuma
Published: December 2004

The many‐body Green's function method is applied to the vertical ionization potential of the hydrogen molecule. The ionization potential is calculated iteratively by expanding the self‐energy part up to third order. The effects of higher‐order correlation corrections and nondiagonal self‐energy elements on the solutions of the Dyson equation are examined with some techniques and approximations, by means of which a Koopmans' defect of 97.7% of the accurate value is obtained.
Temperature effect on the vapor‐phase exciplexes of cyano‐substituted anthracenes
Authors: Hirayama Satoshi
Published: December 2004

The emission spectra and lifetimes of the vapor‐phase exciplexes of four cyano‐substituted anthracenes with N,N‐dimethylaniline (DMA) as a donor are examined over a wide temperature range. The activation energies associated with the exciplex dissociation are calculated to be of the order of 10 kcal/mol. The entropy change in forming the exciplexes is discussed in relation to the efficiency of the exciplex formation. For various donors other than DMA, preliminary results on how they interact with excited 9,10‐dicyanoanthracene are also given.
Vibrational spectra of molecules in the Hartree–Fock dielectric screening approach
Authors: Van Camp P. E. , Van Doren V. E. , Devreese J. T.
Published: December 2004

Traditionally, the calculation of the vibrational spectra of molecules involves at one point or another a numerical differentiation procedure. Such a method has some serious drawbacks both in efficiency and in accuracy. In this paper, an alternative method based on linear response theory is presented. The second derivative of the ground‐state energy is expressed in terms of the electron density response matrix by means of perturbation theory. The unperturbed wave functions are obtained from the Hartree–Fock equation. First‐order perturbation theory applied to this equation leads to the Hartree–Fock linear response. As an illustration of this method the vibrational frequency of a H2 molecule is calculated. The result is 1.348 × 1014 Hz as compared to the experimental value of 1.319 × 1014 Hz. This method is also applicable in the calculation of the phonon dispersion curves of solids.
Moment expansion method to calculate vibrational frequencies of molecules and solids
Authors: Devreese J. T. , Van Camp P. E. , Van Doren V. E.
Published: December 2004

The vibrational properties of a quantum system are determined by the density response matrix. In linear response theory this quantity is connected to the polarizability matrix, which can be expressed in terms of a double summation over one‐particle energies and wave functions. In has been shown that this expression is not useful in the calculation of vibrational frequencies because of the very slow convergence of the summation in terms of the unoccupied states. In this paper, a different but equivalent expression is presented using a continued fraction. The resulting expression contains only one summation over the occupied states, solving in this way all the problems connected with the sum‐over‐states expression of the polarizability matrix. The elimination of all the unoccupied states via the use of the moment formula turns out to be a crucial step in the solution of the problem of the first‐principles calculation of the vibrational spectra of molecules and solids.
Metal bridge effect: V. Quantum chemical studies of some metal chelates
Authors: Fischer‐Hjalmars I. , Henriksson‐Enflo A.
Published: December 2004

Metal chelates [(C2H2X2)2M]n with ligating atoms X = NH, O, S and central atoms M = Be2+, Mg2+, Ni2+, Zn2+ (n = 0, ± 2), and M = Li+, Cu+ (n = ± 1, −3), have been studied in our Laboratory for some years by ab initio calculations. In this article it is shown that certain features of the complexes are the same for all the different metals in our series. These features include a drastic reduction of the energy gap between unoccupied and occupied orbitals, when electrons are added to the positively charged complexes. This change of the energy gap is shown to be an effect of the ligand dimer [(C2H2X2)2]n. But this dimer can only exist when a positive ion, e.g., a metal ion, forms a bridge between the two monomers. The reduced energy gap implies a strong bathochromic shift of the electronic spectrum and low electrical resistivity.
Hydrophile–hydrophobe equilibrium of some prostaglandins—CNDO/SW study
Authors: Grigoras S. , Rusu I. , Pausescu E. , Medesan A. , Moldoveanu S.
Published: December 2004

The problem of the existence of a prostaglandin (PG) receptor is still controversial, but it seems to be clear that the main action of the PGs concerns the interface of the cellular membrane (which has a predominantly lipid character) and the extracellular liquid (which mainly consists of water). Also especially in the case of the exogenous PGs, the transport of these substances in the organism in influenced by the hydrophilic‐hydrophobic properties of the reactive molecules. These properties can be estimated by MO studies using a solvation model and a semiempirical method of calculation. This paper is concerned with the molecules of PGA1 and PGE1. MO studies were performed for these molecules with the CNDO/SW method in order to calculate ionization potentials, dipole moments, and molecular polarizabilities. With these computed molecular properties, the electrostatic and van der Waals interactions with water and octanol molecules are evaluated and compared within the framework of the original model. This study allows the differentiation of the hydrophilic–hydrophobic character of the PGs investigated and the comparison of the results with experimental data.
Solvent effects on CD and MCD spectra of phenylalanine and its related compounds
Authors: Komiyama Tomoko , Miwa Makoto
Published: December 2004

Solvent effects and pH effects on CD and MCD spectra of phenylalanine and its derivatives were observed. CD spectra of N‐acetyl‐L‐phenylalanine ethyl ester in various solvents were analyzed using the rotamer population determined by NMR. The magnitude of optical activity due to each rotamer was determined for two CD bands. The signs of Cotton effect of rotamers I and II are positive and that of rotamer II is negative. The optical activity is greater in polar than in nonpolar solvents. MCD spectra of phenylalanine reveal a remarkable pH effect. In the alkaline pH range it is of the toluene type, from which it turns to a weak spectrum in the acid pH range.
Infrared absorption of nonpolar molecules in rattling motion
Authors: Hirokawa Shoji
Published: December 2004

A theoretical study has been made on the translational or “rattling” motion of homonuclear diatomic molecules encaged in β‐quinol clathrates. By the use of an adjustable parameter for the van der Waals radius, experimental results have been explained fairly well.
Binding energies of ionized donor–exciton complexes in polar crystals
Authors: Petelenz Piotr , Smith Vedene H.
Published: December 2004

Binding energies of ionized donor–exciton complexes in crystals of CdSe, CdTe, and ZnSe are calculated using the most realistic effective potentials available for the electron–hole interaction.
Fluorescence spectra and their temperature dependence of amorphous anthracene films doped with naphthacene
Authors: Maruyama Yusei , Takamiya‐Ichikawa Keiko
Published: December 2004

Fluorescence spectra and their temperature dependence of amorphous anthracene films doped with naphthacene were observed. An amorphous film was prepared by vacuum evaporation technique on a quartz plate cooled down to 30–40°K. The obtained results were discussed in relation to the structural change in the amorphous film.
On the localization of defects
Authors: Calais Jean‐Louis
Published: December 2004

The range in ordinary space of a defect in a solid, polymer, or a large molecule is an important parameter in many physical and chemical situations like, e.g., substitutional and interstitial impurities in ionic crystals, deep and shallow energy levels in semiconductors, core holes in systems studied by photoelectron spectroscopy, and hydrogen in metals. Both the electronic structure and the lattice of the host molecule or solid are normally influenced by the defect, and it is desirable to treat, as far as possible, these two aspects together. An explicit procedure for investigating the degree of localization is proposed that is based on the direct calculation of Wannier functions and partitioning technique.
Exciton transfer in the two‐dimensional antiferromagnet (C2H5NH3)2MnCl4
Authors: Kojima N. , Ban T. , Tsujikawa I.
Published: December 2004

Exciton transfers in the two‐dimensional and spin‐canted antiferromagnet (C2H5NH3)2MnCl4 were studied by investigating the absorption spectra 6A1g → 4T2g(4D) of Mn2+. A magnon side band (exciton–magnon simultaneous excitation) which has an anomalous shape with the cutoffs at the low‐energy as well as the high‐energy sides was observed. This anomalous shape could be reproduced in calculation as magnon side band, considering both the intersublattice and intrasublattice exciton transfers. From the analysis of this band shape, the magnitudes of the intersublattice and intrasublattice exciton transfers are estimated to be 10.2 and 6.8 cm−1, respectively. In the case of simple antiferromagnets without spin canting, the intersublattice exciton transfer process is forbidden because of the spin angular momentum. However, in the case of (C2H5NH3)2MnCl4, the prohibition of the intersublattice exciton transfer is removed by the canted‐spin arrangement.
Single‐determinantal open‐ and closed‐shell FSGO calculations for some diatomic molecules
Authors: Pakiari A. H. , Linnett J. W.
Published: December 2004

Open‐shell single‐determinantal calculations are reported here for the molecular species H2, Li2+, N2, O2 (triplet), O22−;, O2−, O22+, O2+, and F2; corresponding closed‐shell calculations are reported for the species H2, N2, O2 (singlet), O22−, O22+, and F2. The floating spherical Gaussian orbital (FSGO) method was employed. The calculated trend in bond lengths of isonucleic diatomic molecules is in agreement with experiment. For heteronucleic diatomic molecules, however, the experimental trend in bond lengths is not obtained; in this connection, the effect of lone pairs on bond length is discussed. The dissociation energies of H2 and Li2+ are evaluated. The energy gap between the triplet and singlet states of the oxygen molecule is calculated to be 8.96 eV compared to the experimental value of 4.54 eV.
Computer‐generated formulas for overlap integrals of slater‐type orbitals
Authors: Jones Herbert W.
Published: December 2004

Using a modified form of Sharma's method for the expansion of a Slater‐type orbital in spherical harmonics about a displaced center, a general expression for the overlap integral between two orbitals is derived that is equivalent to that given by Sharma. By use of a simple kind of “computer algebra” this expression is developed here into a formula that is equivalent to earlier known ones and may have computational advantages when the generated formula coefficients are stored. This method is capable of extension to more complicated integrals.
Simple relationship between total molecular correlation energies and LMO sizes
Authors: Peterson M. R. , Poirier R. A. , Daudel R. , Csizmadia I. G.
Published: December 2004

As an alternative to the density functional approach to estimating total molecular correlation energies, the equation Ecorr=−0.06593 ∑ R, where Ri=〈r2〉 and i runs over the localized molecular orbitals was fitted to 25 STO‐3G data points with a root‐mean‐square error of 0.025 hartree. Other more general equations were tried but no significant improvement was observed in the fit.
The graph center concept for polycyclic graphs
Authors: Bonchev Danail , Balaban Alexandru T. , Randić Milan
Published: December 2004

While the concept of the graph center is unambiguous (and quite old) in the case of acyclic graphs, an attempt has been made recently to extend the concept to polycyclic structures using the distance matrix of a graph as the basis. In this work we continue exploring such generalizations considering in addition to the distance matrix, self‐avoiding walks or paths as graph invariants of potential interest for discriminating distinctive vertex environments in a graph of polycyclic structures. A hierachy of criteria is suggested that offers a systematic approach to the vertex discrimination and eventually establishes in most cases the graph center as a single vertex, a single bond (edge), or a single group of equivalent vertices. Some applications and the significance of the concept of the graph center are presented.
Thermal dissociation of 1,2‐dioxethane. I. Charge density distribution along the reaction path and in different HF solutions
Authors: Hilal Rifaat
Published: December 2004

A charge density distribution study, based on ab initio SCF–6‐31G wave functions, on the optimized geometry of 1,2‐dioxethane indicates its high instability which results from (i) the high ring strain, (ii) the large amount of charge contained on the nonbonded sides of the oxygen nuclei, and (iii) the weak binding character of the charge density in the OO bond region. The redistribution of the charge density when 1,2‐dioxethane undergoes change in its nuclear configuration has been discussed. This redistribution of charge along the reaction path (the dissociation of 1,2‐dioxethane to formaldehyde products) shows clearly the preceding nature of the electron cloud. The characteristic features of the charge density distribution of the two Hartree–Fock solutions to which the SCF procedure converges have been analyzed and discussed.
Thermal dissociation of 1,2‐dioxethane. II. Quantum topology of the charge distributions
Authors: Hilal Rifaat
Published: December 2004

The topological properties of the charge distribution of 1,2‐dioxethane along the dissociation path (to formaldehyde products) and in different Hartree–Fock solutions are presented. At the equilibrium geometry of 1,2‐dioxethane, all bond paths do not coincide with the corresponding internuclear axes. The outward curvature of the OO bond path elaborates upon the concept of strain in the dioxethane ring. This weak binding of the ring is further confirmed by the considerably low ρ(r) value at the ring (3, +1) saddle point. An extension of the theory to the dynamic case has been discussed in terms of the topological changes in ρ(r) along the reaction path. The catastrophe of the chemical change, i.e., rupture of the dioxethane ring, takes the form of gradual merging and annhilation of the OO (3, −1) and the ring (3, +1) critical points. The values of ρ(r) at the positions of the critical points along the reaction path provide a topological characterization and definition of “partial valence.” The difference between the topological behavior of ρ(r), as obtained by different HF solutions, along the reaction path is analyzed and discussed.
Protein–Nucleic acid interactions: Investigations on the peptide backbone interaction with polynucleotides
Authors: Hosur Ramakrishna V. , Kumar N. Vasanth , Govil Girjesh
Published: December 2004

Model building, difference spectroscopy, and 1H and 13C NMR experiments have been carried out to study the binding of poly(L‐Ser) with the polyribonucleotides poly(A) and poly(U) at pH 7.1. Studies have also been carried out with base paired duplexes poly(A)ṁpoly(U). Peak doubling of Cα and carbonyl resonances in the 13C NMR spectrum of poly(L‐Ser) in presence of polyribonucleotides is observed. From the chemical shifts and the linewidth, it is concluded that the interaction occurs through hydrogen bonding between the nucleic acid bases and the peptide backbone. In case of poly(A) and poly(U) the hydrogen bonding scheme with peptide backbone is different from that in the base paired poly(A)ṁpoly(U). The possible binding schemes of double stranded DNA and peptide backbone have been investigated using model building and potential energy calculations. The hydrogen bonding schemes discriminate between various base pairs and their sequence. It is concluded that protein backbone can play an important role in protein–nucleic acid recognition schemes.
Complex formation between tryptophan‐containing peptides and nucleic acids: Fluorescence decay studies using synchrotron radiation
Authors: Montenay‐Garestier T. , Brochon J. C. , Hélène C.
Published: December 2004

Synchrotron radiation has been used to determine the fluorescence decay parameters of a tryptophan‐containing oligopeptide, Lys‐Trp‐Lys, bound to nucleic acids. All fluorescence decay curves can be fitted by a sum of two exponentials. The two lifetimes very likely correspond to two conformational states of the oligopeptide. The mean fluorescence lifetime of the peptide is not markedly affected upon binding to nucleic acids even though the fluorescence quantum yield is strongly reduced. A model is presented that accounts for the existing fluorescence data: two consecutive complexes are formed both involving electrostatic interactions. In one of the complexes the tryptophyl ring is stacked with the nucleic acid bases and its fluorescence is completely quenched. The other complex emits a fluorescence having characteristics which are similar to those of the free peptide.
Steric accessibility of reactive centers in B‐DNA
Authors: Lavery Richard , Pullman Alberte , Pullman Bernard
Published: December 2004

A method for calculating the “static” steric accessibilities of atoms within macromolecules for various probes is presented and an application is made to the accessibility of atoms within B‐DNA. Changes in accessibility in passing from the individual subunits of the nucleic acid to a single helical strand and then to a double helix are discussed. The influence of various base sequences is also investigated. The present methodology and results are compared to earlier attempts at the calculation of steric accessibilities and their significance for the interpretation of chemical reactivity is substantiated by an illustrative example.
Studies in some important aspects of rna transcription on the basis of intermolecular energy calculations
Authors: Sanyal Nitish K. , Roychoudhury Mihir
Published: December 2004

The model developed by Sanyal, Kumar, and Roychoudhury has been applied to some very important aspects of transcription such as (i) a rapid elongation of the newly synthesized RNA chain; (ii) simultaneous release of the nascent RNA; (iii) base sequence directed (or p independent) termination of RNA transcription; and (iv) absence of thymine in RNA. It has been found that the model successfully explains most of the aspects mentioned above. Also, as a consequence of these studies, a new insight to the unwinding mechanism during replication has been developed using intermolecular association studies.
Interaction energy studies for the specificity of transcription
Authors: Sanyal Nitish K. , Kumar Upendra , Roychoudhury Mihir
Published: December 2004

Electrostatic interaction energy has been studied for the DNA base pair–RNA base complexes inside the deep groove of the DNA. The allowed region has been continuously scanned in order to find out a minimum energy configuration for each complex. A comparative study of the interactiion energy values and the site of association has been carried out. It has been found that the Watson–Crick GC base pair shows a definite specificity similar to the model proposed by Zubay or Riley, while for the AT pair, no specificity can be assigned on the basis of the interaction energy studies alone. Instead, an assumption for a hypothetical backbone directed by the GC pair specificity, has been adopted to assign a specificity to the AT pair. As a consequence of these studies, a model for transcription without unwinding of the DNA double helix has been developed.
Structure, refinement, and function of human carbonic anhydrase‐B
Authors: Kannan K. K. , Ramanadham M.
Published: December 2004

The three dimensional structure of human carbonic anhydrase‐B has been model fitted to electron density maps in an interactive graphics display and improved by real space refinement and restrained least‐squares refinement. The crystallographic R factor for the 5 to 3 Å data dropped from 41.5% to 36.5% after four cycles of least‐squares refinement. The important residues involved in the function of the enzyme showed improved positional parameters after the refinement. Thus GLU106 and THR199 oxygen atoms are within hydrogen bond distance of each other after the refinement. Whereas they were very close to each other before the refinement. The procedures involved in the refinement and the implication of the structure to the mechanism of action of the enzyme are brought out.
Investigation of intermolecular interactions based on the atomic statistical model
Authors: Radzio‐Andzelm Elżbieta
Published: December 2004

Possibilities of improving individual contributions to the statistical interaction energy (kinetic and exchange) are examined. A new method of calculating statistical interaction energies is proposed. The exchange term is calculated using a suitably modified second‐order gradient correction. For the kinetic contribution the accurate formula corresponding to the first‐order perturbation theory is applied. The calculations have been carried out for several pairs of noble gas atoms.
Chemistry of excited states. XI. Interpretation of photoelectron spectra by final state single CI method within semiempirical formalisms
Authors: Kluge G. , Scholz M.
Published: December 2004

The single excited doublet states of some small molecule cations calculated by CI method in the framework of semiempirical CNDO and INDO models are correlated with the photoelectron spectra of the parent molecules. The purity of the Koopmans transitions is used to discuss the one‐particle interpretation of photoelectron bands by comparison with nonempirical many‐body calculations. Furthermore, empirical relations are applied with respect to the evaluation of shake‐up energies.
Calculations concerning Kato's equations
Authors: Tatum J. Patrick
Published: December 2004

Calculations of Kato's equations have been carried out as a function of the coordinates of the system using a number of approximate wave functions in order to determine the effects of the energy, electron density, constraints, and the functional form of the wave functions on how well Kato's equations are obeyed. It is shown that by putting constraints on the functional form of some wave functions, the wave functions will give the exact value of Kato's equations.
Generalized Racah method for the evaluation of CFP for mixed electronic configurations
Authors: Marić Z. , Popović‐Božić M. , Nikolovski Z.
Published: December 2004

The Racah method, proposed for the evaluation of coefficients of fractional parentage (CFP) for single shell configurations, is generalized for the cases of two and more than two shells. On the basis of the generalized Racah method, we have evaluated one‐particle CFP for all states of svpμ electronic configurations. Two‐particle CFP are expressed through one‐particle CFP and Racah coefficients.
Charge transfer and induced polarization in model peptide–ion complexes
Authors: Mezey P. G. , Re G. Del , Otto P. , Suhai S. , Ladik J.
Published: December 2004

Ab initio supermolecule computations of systems consisting of a peptide model (N‐methyl‐acetamide or N‐methyl‐propionamide) and monoatomic ions (Li+, Na+, F−, Cl−) have been analyzed and discussed in an attempt to throw more light on the possible role of charge transfer and related effects in biopolymers containing peptide links. Juxtaposition of ions to a peptide model appears to involve considerable overall charge transfer especially in the case of anions. This supports the assignment to charge transfer of long range electronic effects (like conduction) in polypeptides. On the other hand, induced polarization of the peptide system, which accompanies charge transfer suggests that weakening of hydrogen bonds (especially by cations) may activate long range transmission of perturbations via the concerted weakening of hydrogen bonds. A detailed analysis of the individual molecular orbitals in terms of valence–orbital weight and of hybridization has also been carried out. It is shown in particular that only a limited number of molecular orbitals are involved in the ion–peptide interaction, and that the changes at individual atoms are of different types and affect differently different regions of the molecule. Comparisons between minimal basis and 4‐31G calculations as well as ad hoc auxiliary computations on water–ion complexes have been made to check that conclusions based on the supermolecule approach are at least qualitatively reliable.
Uniform quality gaussian basis sets for molecular calculations. V. Property optimization: A study on H2O
Authors: Daudel Raymond , Poirier Raymond A. , Csizmadia Imre G.
Published: December 2004

Energy optimization (Eo) and property optimization (PO) were performed on the H2O molecule. A definition of the “optimality” κ, a dimensionless quantity of the form

has been proposed where ωi is a weighting factor, 〈ǒ〉i is the computed observable, and Oi is the corresponding property measured experimentally. The minimization of κ leads to property optimization methods (POM) which is a useful alternative to energy optimization methods (EOM).
Periodic table of the elements and the Thomas–Fermi atom
Authors: Essén Hanno
Published: December 2004

How the monotonic trend on which the periodicity of the periodic system is superposed is well described by Thomas–Fermi theory is explained. The mathematical structure of the periodicity is elucidated and explained. Algebraic formulas for the key atomic numbers are derived, e.g., the atomic number at which l electrons first appear is given by Zf(𝓁) = 4 (∑ n2)+1.
Carcinogenicity of naphthylamines: A theoretical study of the stacking interaction of 1‐ and 2‐naphthylnitrenium ions with guanine, adenine, and the dinucleoside monophosphate cytidyl‐(3′‐5′)‐guanosine
Authors: Gresh Nohad
Published: December 2004

Theoretical computations are performed with the stacking interactions of the 2‐naphthylnitrenium ion, the ultimate metabolite of 2‐naphthylamine and N‐hydroxy‐2‐naphthylamine, with guanine and adenine. The most stable stacked complex of guanine with this compound is found to be distinctly more stable than that of adenine. The optimized stacking interaction of guanine with 1‐naphthylnitrenium ion yields an energy close to that with 2‐naphthylnitrenium. By contrast, the dinucleoside monophosphate cytidyl‐(3′‐5′)‐guanosine held in two preselected intercalated conformations is seen to favor 2‐naphthylnitrenium over 1‐naphthylnitrenium by a significant amount of energy. The possible relevance of this finding to explain the difference in adduct formation with guanine in DNA by the isomeric naphthylnitrenium ions is discussed.
Evaluation of positron annihilation in Beryllium
Authors: Oriade J. O.
Published: December 2004

A band theoretical calculation of angular distribution of annihilation photons (ADAP) and the positron lifetime, up to and including higher momentum components is reported. The results obtained using biquadratic quasianalytic integration schemes for all Brillouin zone integrals, compare favorably with existing experimental data. There are, however, significant structures in the ADAP curve obtained than in the experimental curves.
Molecular point group adaptation of spin–free configurations
Authors: Rettrup S. , Sarma C. R. , Dahl J. P.
Published: December 2004

Symmetry adaptation of spin–free multishell electron configurations in molecules to general non‐Abelian point groups has been carried out. Using the basis spanning the irreducible representation [2N/2−S, 12S, 0n−N/2−S] of the unitary group U(n) as primitives, the Wigner operators for point groups were applied to generate the required basis. In the process it was found that the segments of the Weyl tableaux could be handled individually. Using this and the matric algebra of permutation group a viable procedure has been developed for point groups adaptation. A program based on the procedure has been generated and implemented.
Towards a new interpretation of quantum mechanics?
Authors: Julg A. , Julg P.
Published: December 2004

Quantum mechanics is a remarkable formalism for studying problems in the microscopic domain, and nobody has reasonably contested its power. Nevertheless, in spite of the many interpretations which have been proposed, its true meaning is far from being clear. The aim of this preliminary paper is to show that it is possible to conceive within a classical framework an interpretation of quantum mechanics and to make its limits of validity precise.
Approach to N representability
Authors: Guo Hong , Tang Au‐Chin
Published: December 2004

In this paper, some operator endomorphisms which give rise to conditions for N representability of pth order density matrices are presented.
Short‐time description of chemical reaction by Stochastic methods
Authors: Fonseca Teresa , Gomes J. A. N. F. , Grigolini Paolo
Published: December 2004

For a double well potential, the Smoluchowski equation including a multiplicative noise is solved by a method that depends on a continued fraction expansion. The relation between the rate of escape over the barrier and a noise parameter is discussed. The method of solution used, being applicable to both short and long time scales, may be useful for the study of certain types of incubation times observed in chemical reactions.
Time‐dependent density operator in the random impulse approximation: I. Connections with the “generalized sudden approximation” for photoionization and electron impact ionization; and II. Relevance to reduced density operators, particle–hole matrices, and propagators for the initial state
Authors: Larson Everett G.
Published: December 2004

A density operator analysis is made of the particle‐ejection (e.g., photoionization) problem in the “generalized sudden approximation” for the case in which the ejected particle is detected but its dynamical properties are not observed. It is shown that the resultant statistical density operator may be derived from that obtained in a particle‐conserving Hamiltonian‐evolution linear‐response model with a random impulse perturbation, and that the physical applicability of the latter model embraces the range of applicability of the former. The initial value of the statistical density operator for the above particle‐ejection problem is shown to be the N – (1)‐particle reduced density operator of the initial state; and the initial value of the statistical density operator for the excitations in the random impulse model is shown to be the N‐particle Hermitian operator whose matrix representation is the G matrix of Garrod and Percus. The significance of the eigenvalue spectrum of these operators to the excitation properties of the system is discussed, especially for the random impulse model, where a large eigenvalue of the G matrix can signal strong preferential excitation to its corresponding particle‐hole collective state, even for a random perturbation. Extensions of these ideas to excitations from states with a large eigenvalue of the two‐particle reduced density operator (e.g., superconducting states) are mentioned. The The applicability of these density matrices to the description of the excitation spectrum due to a well‐defined perturbation is discussed. The relationship of these time‐dependent density operators to the one‐particle propagator and the particle–hole propagator (polarization propagator) is established.
Thermodynamic aspects on accuracy in the synthesis of biomolecules
Authors: Blomberg Clas
Published: December 2004

In the synthesis of, e.g., a protein in a living cell, specific monomers are to be selected for each unit of the macromolecule in competition with similar molecules. The selection is performed at an enzyme complex, where correct molecules are bound tighter and, therefore, have a greater probability for being incorporated into the product. For similar molecules, there is a strong limitation on the possibility of selection in simple steps, and the accuracy is enhanced by a so‐called proofreading mechanism. For the selection to work, it is necessary to drive it out from equilibrium by a free‐energy decrease. The main purpose of the paper is to describe the free‐energy loss needed for a certain accuracy level. The underlying process is assumed to be optimized to make best use of available free energy. A formalism for this is developed, and will be discussed together with results. Many points of the internal structure of such a process are still unclear, and an aim of the formalism has been to remain open for various possibilities. It is also described how the individual accuracy levels can be determined by a requirement that the free‐energy cost per error free or functionable product is minimized.