bluuebunny/crossref_metadata_2025 huggingface dataset:
Corrections to coupled Hartree–Fock theory: the rearrangement effect
Authors: Bhattacharya A. K. , Moitra R. K. , Mukherji A.
Published: December 2004

In this communication we discuss a method of incorporating corrections to the coupled Hartree–Fock (CHF) formalism by introducing the so‐called “rearrangement effect.” In this we take account of the relaxation of the core orbitals when excitations from a starting Hartree–Fock wave function occur. The magnitude of this correction numerically is found to be quite significant for the polarizabilities of two‐electron atomic systems, results for which are reported.
Comparison between the point‐charge electrostatic model and the angular overlap model: The general case
Authors: Kibler Maurice R.
Published: December 2004

The aim of this paper is to explore in detail the mathematical connection between the point‐charge electrostatic model and the angular overlap model. More precisely, for any configuration nlx in any symmetry, the matrix elements, and therefore the energy levels, as given by the angular overlap model restricted to the antibonding effects λ (for any of the possible λ's), are deduced from an effective potential constructed according to the point‐charge electrostatic model. This allows us to give a mathematical proof of the equivalence between the point‐charge electrostatic model and the angular overlap model taking into account all the antibonding effects λ. Finally, the sum rules for the angular overlap model are examined in the light of the formulae connecting the two models considered. Numerical tables for obtaining the results as given by the angular overlap model restricted to any of the antibonding effects from those as given by the point‐charge electrostatic model are listed for the configurations nlx with l = p, d, f and g.
An alternative parametrization for the theory of complex spectra
Authors: Kibler Maurice R.
Published: December 2004

The aim of this paper is to investigate a new parametrization for the matrix, set up on the states of an open (nuclear or atomic) shell, of any two‐body interaction expandable in multipoles. Such a parametrization is particularly convenient for expressing the term energies in a simple form and for producing high degeneracies among the terms. Further, the parametrization considered allows the two‐body interaction to be decomposed into a Dirac interaction and a remaining part.
Spin densities in the Waller–Hartree spin‐free method
Authors: Lim T. K.
Published: December 2004

Spin densities in the Waller–Hartree spin‐free method were found to be the same as in the spin‐projected Slater determinant method. The reduced spin projector Q is introduced and its relation with the spin projector P is discussed. An equation is obtained to show that a Sanibel coefficient can be expressed as a linear combination of N! products of Sanibel coefficients.
Dynamical screening by Σ‐electrons in π‐electron transitions: Treatment in the equations‐of‐motion method
Authors: Shibuya Tai‐Ichi , I'haya Yasumasa J. , McKoy Vincent
Published: December 2004

Dynamical screening in π‐electron systems is studied by the equations of motion method. By using a partitioning technique on the equations of motion we can obtain simple expressions for the effect of dynamical screening directly on the transition energies and transition moments in π‐electron systems. These results are used to study the effect of such screening in the N → V transition in ethylene. This procedure can be used to extend the equations‐of‐motion method to larger π‐electron systems.
Density matrix in the open shell theory
Authors: Mestechkin M. M. , Whyman G. E.
Published: December 2004

All the second‐order density matrix spin components for the spin‐projected Slater determinant are presented as expansions in direct products of powers of unprojected spin‐ and residual electron density matrices. Spin components of the second‐order transition density matrices between spin‐projected Slater determinants built of orthogonal orbitals are also obtained.
Effect of orbiting resonance on the elastic differential cross sections
Authors: Sheen S. H. , Skofronick J. G. , Mueller C. R.
Published: December 2004

The effects of orbiting resonances on elastic differential cross sections are investigated for the Lennard‐Jones (12, 6) model potential. The elastic differential cross section consists of three terms: a resonance term, a potential scattering term and an interference term. The interference term has a significant effect only at small angles of the differential cross section. The importance of the potential scattering term depends proportionally upon the orbiting resonance energy. For the low‐lying orbiting resonance states, the resonance term is the dominant term, but at higher energy it appears only in the backward differential cross sections. Generally, by fitting the large angle differential cross sections, the resonance orbital angular momentum can be estimated.
Nonadiabatic core polarization and penetration correction in alkali‐like atoms: Model computations on excited states of helium
Authors: Young Ralph H. , Deal Walter J.
Published: December 2004

Correlation between the motion of a highly excited outer electron and that of the remaining ionic “core” of an atom is generally treated in an adiabatic approximation, in which it is assumed that the outer electron affects the core in the same way as a stationary point charge. An alternative approach to this correlation problem which avoids the adiabatic approximation is tested here on the 1s2p, 1s3d, and 1s4f states of helium. The results provide the first accurate test of the adiabatic approximation and of a simple correction for the nonzero velocity of the outer electron. The approach used here is based on neglect, in the “correlation” part of the wave function, of the possibility that the outer electron comes closer to the nucleus than any core electron (“penetration”). A correction for this neglect is derived and tested on a version of the adiabatic approximation that likewise neglects penetration.
A density functional representation of quantum chemistry. III. Rigorous realization of the program in lattice space
Authors: Schleicher M. , Primas H.
Published: December 2004

A mathematically rigorous reformulation of molecular quantum mechanics in terms of the particle density operator and a canonically conjugated phase field is given. Using a momentum cutoff, it is shown that the usual molecular Hamiltonian can be expressed in terms of the particle density operator and a rigorously defined phase operator. It is shown that this Hamiltonian converges strongly to the cutoff‐free Hamiltonian. In spite of the fact that this Hamiltonian is of second order in the phase operators, all hitherto published expressions are not correct. Unfortunately, the correct formulation destroys the intuitive appeal of using the particle density operator as a coordinate for the many‐body problems of quantum chemistry. Unless somebody provides an essential new and clever idea, we propose to resist the fascination of a local quantum field theory of molecular matter in terms of the particle density operator.
The electronic structure of molecules having arbitrary boundaries
Authors: Scheire L. , Phariseau P.
Published: December 2004

In this paper we discuss an extension of the standard multiple scattered wave method for molecular electronic structure calculations to the case of arbitrarily shaped molecules. A general theory is presented where the difficulties arising from the matching problem across an arbitrary boundary are avoided. The secular equation to determine the energy spectrum is obtained and the wave functions are calculated in all regions.
Semi‐quantitative and semi‐empirical versions in the quasi‐relativistic SCF‐MO‐LCAO methods: Numerical calculations for (PtCl6)2−
Authors: Bersuker I. B. , Budnikov S. S. , Leizerov B. A.
Published: December 2004

Quasi‐relativistic (QR) versions of the CNDO and Mulliken–Wolfsberg–Helmholz (MWH) semiempirical methods based on the SCF‐QR‐MO‐LCAO method given earlier are worked out. For the CNDO method only the basic formulas and matrix element expressions are given, while for the MWH one, the parametrization as well as the basis functions and group spinor overlap integral calculation were discussed. (PtCl6)2− complex was chosen for a test calculation. The energy level values and LCAO coefficients were obtained and compared with the nonrelativistic calculations. One of the results was the occurrence of a very strong reduction of the spin‐orbit interaction due to covalency. The calculation proves the semi‐empirical versions of the QR‐MO‐LCAO method to be quite realizable in practice.
Quantum theoretical calculations of van der Waals interactions between molecules. Anisotropic long range interactions
Authors: Wormer Paul E. S. , Mulder Fred , Van Der Avoird Ad
Published: December 2004

Presenting a relatively simple ab initio method to calculate full van der Waals interaction potentials between molecules, we give rules for the optimization of basis functions which permit the reliable evaluation of second order long range interactions. Closed expressions for the long range interaction energy are derived in which the orientational dependence is simplified to the utmost. Calculations show that even for molecules which have no dipole moment, such as ethylene, the strongly anisotropic electrostatic interactions are of the same magnitude as the dispersion interactions, but also that the anisotropic (“cross”) terms in the dispersion energy are about equal in size to the corresponding “quadratic” terms. Even though these anisotropic forces cancel to a large extent in the cohesion energy of the ethylene crystal, they can have important effects on some of the other crystal properties.
Variational localized‐site cluster expansions. VIII. Projection of spin symmetries
Authors: Klein D. J. , García‐Bach M. A.
Published: December 2004

We investigate the total spin structure of an approximate localized‐site wave function for a collection of paramagnetic sites interacting so as to favor a singlet ground state. As the number of sites becomes infinite we obtain the distribution of weights of the different symmetry components of the localized site wave function; further, although only a very small fraction of such nonsymmetric wave functions is actually singlet, we find that it generally yields the same bulk property expectation values as its singlet‐projected component.
Orthonormalization, polar decomposition, and transformation to an effective hamiltonian
Authors: Jørgensen Flemming
Published: December 2004

Klein has pointed out that des Cloizeaux's orthonormalization is just another formulation of Löwdin's symmetric orthonormalization. We demonstrate that des Cloizeaux's formulation is convenient for theoretical discussions and that it is intimately connected with polar decomposition–‐which is a generalization to operators of the fact that any complex number z can be written r exp (iθ) where r is positive and θ real. We generalize two other properties for z and find an interpretation of the Carlson‐Keller theorem. Recently Lathouwers found that Löwdin's canonical orthonormalization leads to the eigenvectors of a positive operator. This operator is des Cloizeaux's. We discuss some variational theorems on this background and find the Courant‐Hilbert‐Löwdin “measure of linear independence” from a simple least squares consideration, closely related to Lathouwers' results.

An orthonormalization due to Schweinler and Wigner (1970) is observed to be Löwdin's canonical. The Schweinler‐Wigner maximum characterization is referred to a simple general theorem, which also implies a new maximum characterization.

In Sections 6 and 7 we consider transformation to an effective Hamiltonian from the point of view of polar decomposition and symmetric orthonormalization. It turns out that the polar part of Bloch's transformation is des Cloizeaux's. The characterizations of this by both Klein and Jørgensen are visualized in a simple way.
Molecular orbital study of the electronic absorption spectra of dithienyls
Authors: Abu‐eittah R. , Al‐sageir F.
Published: December 2004

The localized orbital method has been used in an SCF study of the electronic absorption spectra of the three isomers of dithienyl. Transition energies are computed for planar, perpendicular, and polyconfigurational descriptions of the molecule. Band intensities are calculated for the planar conformers. The results show that: (1) the coplanarity of the two thiophene rings in dithienyl is not significantly distorted; (2) excited states of dithienyls arise from substantial configuration interaction; and (3) the charge transfer wave function contributes significantly to the excited state.
Spin‐Dependent operators in the spin‐free quantum chemistry
Authors: Mestechkin M. M. , Klimko G. T.
Published: December 2004

The two‐particle spatial density matrix components introduced by McWeeny are expressed in terms of the Fock coordinate wave function, which is constructed from an arbitrary function of N spatial coordinates. The integral relations for these components are verified. The necessary matrix elements of a standard representation of the SN group are calculated.
Absorption line shape of two coupled oscillators decaying in the same bath
Authors: Hardisson A. , Mauricio F. , Velasco S.
Published: December 2004

In this paper the linear response theory approximation is used to calculate the electromagnetic energy absorption coefficient of two coupled oscillators decaying in the same medium. The model seems to be suitable for the treatment of the infrared spectroscopy of certain isolated molecules trapped in a rare gas crystal.
Some potential‐energy relationships for isoelectronic atomic series
Authors: Politzer Peter , Daiker Kenneth C.
Published: December 2004

Relationships between the total energy E, the nuclear‐electronic attraction energy Vne, and the interelectronic repulsion energy Vee are derived for isoelectronic series of atoms and ions. Using these, it is possible to determine Vne and Vee for the members of such series from a knowledge of just their total energies. The method is applied to the ground and first excited states of the two‐electron series, and the ground states of the three‐ and four‐electron series, and the results are discussed.
Symmetry forcing and convergence properties of perturbation expansions for molecular interaction energies
Authors: Jeziorski Bogumił , Szalewicz Krzysztof , Chałasiński Grzegorz
Published: December 2004

The convergence properties of perturbation theories for molecular interaction energies are tested by performing high‐accuracy high‐order numerical calculations for a ground‐state hydrogen atom interacting with a proton. It is shown that a strong symmetry forcing used in the Eisenschitz‐London‐Hirschfelder‐van der Avoird (EL‐HAV) theory leads to rapidly convergent perturbation expansion whereas a weak symmetry forcing, peculiar to the Murrell‐Shaw‐Musher‐Amos (MSMA) theory, is not able to guarantee the convergence of the resulting perturbation series. The perturbation expansion introduced recently by Jeziorski and Kolos and corresponding to an intermediate symmetry forcing is shown to converge rapidly ensuring the correct asymptotic behavior of the interaction energy calculated through second order. Despite the divergence of the resulting perturbation series the MSMA theory is shown to give very useful results at the distances corresponding to the van der Waals minimum. In this region, however, virtually the same results can be obtained by using a simpler theory employing a properly symmetrized wave function of the usual Rayleigh‐Schrödinger (RS) polarization theory.
The BERKELEY system. III. General configuration‐interaction methods for open‐shell molecular electronic states
Authors: Brooks Bernard R. , Schaefer Henry F.
Published: December 2004

A system of general “open‐ended” configuration‐interaction (CI) programs, specifically designed for the Harris Corporation Slash Four minicomputer, is described. These methods are general in the sense that an arbitrary list of configurations (linear combinations of Slater determinants) may be used, and open ended in that peripheral (i.e., disk) storage capacity determines the maximum size problem that can be solved. The largest variational calculations carried out to date using BERKELEY involve 7064 open‐shell singlet configurations (31,898 Slater determinants). Detailed timing breakdowns are presented for four test cases, two of which involve the lowest ππ* singlet state of ethylene. The other two examples are the orthogonal or bisected singlet state of trimethylenemethane and the 8B1 state of the MnCH2 complex. In the latter case, it is found that the predicted MnCH2 dissociation energy is only slightly increased by electron correlation effects.
Classical dynamics of the O + ClO → Cl + O2 and Cl + O3 → ClO + O2 reactions
Authors: Farantos S. C. , Murrell J. N.
Published: December 2004

An explicit function has been derived for the potential‐energy surface of the ground state of ClO3 with the six interatomic distances as variables. This surface is valid over all configurations of the atoms. The surface has been used to calculate classical trajectories for the reactions R1: O(3P2)+ClO(2Π3/2)→ O2(3∑)+Cl(2)P3/2 and R2: Cl(2P3/2)+O3(1A1)→ClO(2Π3/2)+O2(3∑). An appreciable fraction (∼1/3) of the reactive trajectories for R1 go through a long‐lived complex ClOO(2A″). The cross section decreases with increasing rotational state of the ClO; and 37% of the energy release is vibrational. The calculated rate constant at 298°K is 2.6 × 10−11 cm3/molecule sec. For reaction R2 there is no evidence of long‐lived complexes. The product ClO is predominantly found in the backward‐scattering direction. Most of the internal energy is carries off by ClO but O2 carried off most translational energy. An Arrhenius expression has been deduced from calculations at 220 and 300°K to give an A factor of 2.488 × 10−11 cm3/molecule sec and an activation energy of 1.543 kJ/mol.
Complex‐coordinate studies of helium autoionizing resonances
Authors: Moiseyev N. , Certain P. R. , Weinhold F.
Published: December 2004

Several aspects of the numerical application of the complex‐coordinate method for calculating helium autoionizing resonances are discussed. A direct‐search algorithm is used to locate resonance eigensolutions that satisfy the virial theorem, and the influence of the basis set on the accuracy of the calculated positions and widths is investigated. The complex‐coordinate method is related to the stabilization method of Holøien and Midtdal.
Interpretation of electron spectra. III. Spectra of formamide, studied with HAM/3
Authors: Lindholm E. , Bieri G. , Åsbrink L. , Fridh C.
Published: December 2004

The molecular spectra of formamide (HCONH2) are interpreted by the use of the new semiempirical method HAM/3. Very good agreement with experiments can be obtained for the calculation of all valence ionization energies as well as for the (negative) electron affinity. In addition, the calculated excitation energies allow an unambiguous interpretation of the UV spectrum, for which previously different ordering of the triplet 3ππ* and 3nπ* transitions have been suggested.
Ab initio molecular orbital studies of sigmatropic rearrangements
Authors: Bouma Willem J. , Vincent Mark A. , Radom Leo
Published: December 2004

Ab initio molecular‐orbital theory with the STO‐3G and 4‐31 G basis sets has been used to study the 1,3‐sigmatropic hydrogen rearrangements: propene→propene, formic acid→formic acid, and vinyl alcohol→acetaldehyde, and the1,5‐shifts:1,3‐pentadiene→ 1,3‐pentadiene and β‐hydroxyacrolein→ β‐hydroxyacrolein. Transition states have been determined using gradient procedures. Improved descriptions of the energies of the reactions have been obtained using 3 × 3 configuration interaction. In accord with expectations based on orbital‐symmetry considerations, the calculated barriers are considerably greater for 1,3‐ than for 1,5‐shifts. The forbidden pathway for the degenerate 1,3‐shift in propene is predicted to require less activation energy than the allowed pathway, a result that can be rationalized in terms of interactions with subjacent and superjacent orbitals.
First‐order properties and the Hellmann–Feynman theorem in the case of a limited CI wave function
Authors: Nerbrant P.‐O. , Roos B. , Sadlej A. J.
Published: December 2004

Two distinct approaches to the calculation of first‐order properties with a limited CI wave function are discussed. One is based on the Hellmann–Feynman theorem and the other on the direct evaluation of the total energy derivative at zero perturbation. Corrections to the Hellmann–Feynman expectation value are given for the CI wave function consisting of a single determinant reference state and all single and double replacements of this. These corrections are the extended Brillouin matrix elements and involve interactions between the zeroth‐order wave function and triply substituted configurations. The usefulness of these matrix elements for the generation of MC SCF orbitals and for the calculation of cluster corrections to the wave function is briefly discussed. The formulas for the Brillouin matrix elements expressed in terms of one‐ and two‐electron integrals have been automatically generated using the syntax of the algebraic program SCHOONSCHIP.
Expansion and completeness theorems for operator manifolds
Authors: Dalgaard Esper
Published: December 2004

Some expansion and completeness theorems for operator manifolds, which are currently being employed in propagator theory, are derived. It is shown that excitation or ionization operators satisfying the conditions Q|0〉 = |Λ〉 and QΛ|0〉 = 0 for general excited states |Λ〉 and reference state |0〉 may be expanded uniquely in particular sets of basis operators. These results are then used to discuss rigorous expressions for fermion propagators.
Electron and nuclear density matrices and the separation of electronic and nuclear motion
Authors: Goscinski O. , Palma A.
Published: December 2004

The so‐called parametric dependency of the electronic wave function in the Born–Oppenheimer approximation is discussed. Considering a function beyond this approximation, a new set of equations is derived with parametric and nonparametric dependency. Nuclear and electron reduced density matrices are introduced in this derivation. They are used in a formulation of the problem of separation of nuclear and electronic motion.
Solitons, bioenergetics, and the mechanism of muscle contraction
Authors: Davydov A. S.
Published: December 2004

The properties of exciton and soliton excitations in one‐dimensional molecular systems and in α‐helical protein molecules are investigated. It is shown that collective excitations—solitons, corresponding to a combination of vibrational excitations in peptide groups and a local deformation of molecules—are possible in α‐helical protein molecules. These excitations move along the molecule without energy losses and are perfect energy carriers. A qualitative description of the shortening in the length of muscular fibers is given using the concept of solitons occurring under the hydrolysis of ATP molecules at the ends of thick fibers contained in the sarcomeres of muscular fibers.
Organization of phospholipids in biological membranes
Authors: Govil Girjesh , Hosur Ramakrishna V.
Published: December 2004

Preferred conformations of phospholipids have been predicted through quantum‐chemical techniques and classical potential functions. An essential condition for a conformation to exist in a biomembrane is that it should be possible for it to organize in the form of a bilayer. Taking into consideration the conformational flexibility of the polar head group, organization at the lipid–water interface has been considered. The biological implications of such an organization in terms of formation of “hydrophobic channels” is discussed. Quantum‐mechanical investigations on the transport phenomenon have shown that the “selectivity” of biological membranes is connected with the “organization.” Calculations of the quantum‐mechanical transmission coefficients for different model potential profiles indicate that minor differences in the height of potential barriers in certain regions can lead to significant changes in transmission coefficients. The “directional selectivity” of substrates (differences in transmission coefficients for flow in and out of the cell) can be explained on the basis of differences in membrane organization. These results have some important consequences in the evolutionary process in biological membranes.
Ab initio molecular fragment calculations with pseudopotentials
Authors: Gáspár R. , Gáspár R.
Published: December 2004

Pseudopotential theory is introduced into the ab initio FSGO molecular fragment method. Pseudopotential molecular fragments using pseudopotentials of double‐zeta quality are characterized, and a method of their assembly into larger molecules is presented. Core–valence electron separation is achieved at both levels of the molecular calculations. Heteroatom incorporation into the method is also considered. Applications of the pseudo‐FSGO molecular fragment method to hydrocarbons and simple molecular systems containing heteroatoms are discussed. Results are compared to those of the original FSGO method and experiment.
Role of electron correlation in the quantum‐mechanical calculations of the coulomb interaction energy in the DNA base pairs
Authors: Kuprievich V. A. , Kudritskaya Z. G. , Klymenko V. E.
Published: December 2004

The intermolecular electronic correlation contributions to the Coulomb component of the nucleic acid base interaction energy are estimated. The Coulomb energy is evaluated with the use of atomic monopoles, which are determined from the π‐electronic densities calculated by the SCF method and by employing partially or completely optimized APSG wave functions. When the correlation is thus taken into account, a systematic decrease in atomic charges occurs; this effect is considerable only if an optimized orbital set is used. As a result, the Coulomb interaction energy due to the π‐electronic atoms decreases from −1.13 to −0.85 kcal/mol for the AT pair and from −7.15 to −4.61 kcal/mol for the GC pair.
Multimolecular clusters: Their isomerism and effective characteristics evaluated by quantum chemistry
Authors: Slanina Z.
Published: December 2004

A method is described for processing the enthalpy, entropy, and Gibbs free energy terms of formation of the individual isomers of n‐particle clusters obtained by means of quantum‐chemical calculations, to enable a comparison of these partial theoretical characteristics with the overall experimental ones. The general scheme of weighting treatment is illustrated by examples based on recent quantum‐chemical results of studies of isomeric forms of (NO)2, (H2O)5 and (D2O)5, and CH3OH · 3H2O and CH3OH · 6H2O clusters.
Geometry of ammonia molecule in the lowest triplet state estimated theoretically
Authors: Jeziorek Danuta , Żurawski Bronislaw
Published: December 2004

The geometrical parameters of the ammonia molecule in the lowest‐lying triplet state have been estimated by means of the SCF method and by making an extrapolation to take into account electron correlation effects. The planar configuration has been obtained as the most probable geometrical arrangement (3 A2″).
Electrostatic isopotential maps for large biomolecules
Authors: Náray‐Szabó G.
Published: December 2004

A new method for the calculation of electrostatic isopotential maps, based on completely transferable bond orbitals, is proposed. According to the simple form of the potential term the amount of computational work is proportional to the first power of the number of valence electrons. Slater‐type atomic orbitals are used to construct the bond orbitals, thus all integrals can be calculated explicitly. The subtilisin charge‐relay system is studied as an example. It is found, in agreement with the results of Beppu and Yomosa, that the two protons transfer in a stepwise manner.
Theoretical studies on substrate binding to the active site of carbonic anhydrase
Authors: Sawaryn Andrzej , Andrzej Sokalski W.
Published: December 2004

The role of some amino acids and metal ions in the catalytic activity of carbonic anhydrase (carbonate dehydratase EC 4.2.1.1) has been investigated. The additional stabilization of the transition state complex was used as the qualitative measure of the effect of molecular surrounding on CO2 hydration reaction calculated within the approximate CNDO/2 approach. The effect of the molecular environment has been simulated by inclusion into the SCF LCAO MO Hamiltonian, a term representing the interaction with a set of point charges and atomic dipoles centered on experimentally determined position of Zn2+ ion and all atoms of histidine 94, 96, 119 and threonine 199, 200 (or histidine 200 in the case of carbonic anhydrase B). The possible molecular mechanism of CO2 hydration inside the active site has been also discussed.
Intermolecular charge transfer in model hydrogen‐bonded systems—biological implications
Authors: Chojnacki Henryk
Published: December 2004

The electronic structure of the model hydrogen‐bonded systems has been studied at the all‐valence level in relation to the charge transfer mechanism. It is concluded that together with the intermolecular proton transfer an electronic charge transport occurs for hydrogen bonds of 2.70–3.00 Å in length, i.e., when the proton motion within the bond is anticipated. For elucidation of transport properties of one‐dimensional hydrogen‐bonded systems the tunneling–hopping model is preferred instead of the band theory. The importance of the proposed mechanism of the charge transfer for biological processes has been emphasized.
Mechanism of protein folding
Authors: Ptitsyn O. B. , Finkelstein A. V.
Published: December 2004

The first stage of protein self‐organization—the formation of a fluctuating secondary structure in the unfolded protein chain—is considered. The stereochemical theory is presented enabling one to calculate helix‐coil and β‐structure‐coil equilibrium constants. It is shown that the most probable localization of fluctuating α‐ and β‐structure in the unfolded protein chain corresponds to the native localization of these structures. The formation of large α‐ and β‐structural blocks is observed, each of them including several native α‐helices or β‐strands.
Relationship between spatial structure and pharmacological activity of a series of β‐adrenomimetics
Authors: Zhorov B. S. , Govyrin V. A.
Published: December 2004

All equilibrium conformations of a series of N‐alkyl‐α‐alkyl derivatives of noradrenaline and their synthetic precursors—phenylaminoketones—have been calculated. It has been shown that spasmodic changes in bronchodilating activity of the catecholamines, observed with the increase in α‐alkyl substituent size, may arise from the difference in the ratio of diastereoisomers produced by reduction of aminoketones.
Regularities of the processes of radiationless conversion in polyatomic molecules
Authors: Plotnikov V. G.
Published: December 2004

The processes of radiationless conversion in aromatic and heteroaromatic molecules are investigated theoretically. The values of constant rates of internal conversion are calculated. The theoretical estimation of constant rates of S–T conversion aromatic hydrocarbon molecules and in their carbonyl‐, thiocarbonyl‐, and nitroderivatives and in azaheterocyclic molecules are given. The S‐T conversion probability between the states of different orbital nature (nπ* and ππ*) is equal to ca. 1010–1011 sec−1 that is two to four orders higher than the conversion probability between the states of the same orbital nature. It is shown that the process of T‐S conversion may be described in the second and in the highest orders of perturbation theory. The luminescent characteristics of molecules are connected with the relative position of electron states of different orbital nature and multiplicity and conversion characteristics.
Calculations of 1H NMR coupling constants for conformational studies of isomeric pentofuranosyl nucleosides
Authors: Jaworski Andrzej , Ekiel Irena
Published: December 2004

The SCF FPT method in the INDO approximation of molecular orbital theory is employed for calculations of 1H NMR cisoidal coupling constants in model compounds. Obtained results are used for finding conformational states of α‐xylo‐, β‐lyxo‐, and α‐2′‐deoxyribonucleosides in solution.
Excitons and Bose–Einstein condensation in living systems
Authors: Mishra R. K. , Bhaumik K. , Mathur S. C. , Mitra S.
Published: December 2004

The problems connected with the transformations of energy in the living systems are reviewed. Possibility of Bose–Einstein condensation by input of radiant energy over a critical level is considered as a route for overcoming the barriers of activation energy under the conditions of a pump and a thermalizing environment. Molecular force fields constitute the pump. Under our scheme excitons constitute the major fraction of bosons to so condense. Instantaneous dipoles of London theory are then examined as excitons. Lastly an energy packet from a quantized dipolar field is suggested rather than the concept of “conformons.” Questions of charge and of other modes of energy transfer are briefly discussed.
Photoinduced electron transport across protein‐containing membranes
Authors: Marinov B. S.
Published: December 2004

It is shown in the present work that a protein globule can mediate the donor‐to‐acceptor electron transport, when the protein is in the solution or incorporated into the membrane.
Quantum‐Chemical investigation of cation motion mechanism in modes of biological channels with phosphate groups
Authors: Strelko V. V. , Lavrinenko‐Ometzinskaja K. D. , Karaseva T. A. , Pisarzhevsky L. V.
Published: December 2004

Specimens of amorphous zirconium phosphates specifically formed by alkali metal cations were first studied as models of biological membranes. The mechanism of ion motion in zirconium phosphate ultrapores was investigated by the SCF MO LCAO method using a CNDO/2 approximation. Differently arranged dihydrophosphate groups were considered as models of the sorbent channel surface. Analysis of the form of potential surfaces resulting from the motion of lithium, sodium, and potassium ions near the charged centers showed that the value and position of energy barriers essentially depend on the nature of cation and the size of the pore that it penetrated into. Optimum conditions for the selectivity absorption of the ions and their further advance along the ultrapore channel are created if the cation size corresponds to the ultrapore diameter.
Influence of solvent structure on the conformation of the native DNA molecule
Authors: Frisman E. V. , Slonitsky S. V. , Veselkov A. N.
Published: December 2004

The investigation of the factors determining the formation and stability of the higher biopolymers structures is one of the most important trends of the development of molecular biophysics. A feature common to most macromolecular systems under physiological conditions is that they function in an aqueous environment. Thus, it is natural to assume that the peculiarities of biological macromolecules structures and their functional activity as well are closely related to the specific properties of such a unique solvent as water. The investigations of the conformational changes of biopolymer, induced by dehydration of the macromolecule, give information about the nature of the forces stabilizing its structure. The dehydration of the macromolecule in solution can be attained by addition of a nonaqueous cosolvent. Generally low‐molecular‐weight aliphatic alcohols, amides, and amines are used as a nonaqueous component. At present a vast number of experimental and theoretical data concerning the properties of water and aqueous systems are available. The specificity of water as a solvent arises primarily from the spatial hydrogen‐bonded structure. The addition of a nonaqueous component exerts changes in this structure, which evolve to the singularities of the physical characteristics of water‐nonelectrolyte mixtures. It is generally assumed that nonelectrolytes may be divided, according to their effect on the spatial water structure, largely into two basic classes: (1) the structure makers, i.e., the compounds of aliphatic alcohols type; (2) the structure breakers, i.e., the compounds of urea type. The agents belonging to the first class show a stabilizing effect in the range of low nonelectrolyte content. At a certain critical concentration, Ccrit, characteristic of each substance, the nonaqueous solute molecules leave the cavities of the spatial water structure which leads to a disruption of the latter. The agents belonging to the second class exert a structure‐breaking effect even in the range of extremely low concentrations, which arises from their high competitive ability for hydrogen bonding.
Conditions of formation of liquid crystals from biopolymer solutions
Authors: Khokhlov A. R.
Published: December 2004

Using the representation of a completely stiff macromolecule as a long rigid rod and the representation of a semiflexible macromolecule as a chain of freely rotating connected effective rigid rods, the conditions of formation of the liquid‐crystalline phase in the solutions of such macromolecules are obtained and the diagram of states for the corresponding phase transitions in the variables temperature‐volume fraction of polymer in the solution is constructed.
Quantum‐chemical investigation of spatial and electronic structure of verdazyl and its derivatives
Authors: Markovsky L. N. , Polumbrik O. M. , Nesterenko A. M.
Published: December 2004

The unrestricted HF method in the INDO approximation with optimized geometry was used to describe the electronic structure of the hetero‐ring of verdazyl and the derivatives of the latter. The results obtained are in good agreement with the experimental EPR spectra of triphenylverdazyl radical and its dipole moment. These data may be a basis for understanding and predicting the chemical properties and reactivity of verdazyl and its derivatives.
Metabolic activation of chemical carcinogens and binding of metabolites with nucleic acid bases
Authors: Nagata Chikayoshi , Kodama Masahiko , Kimura Teruyuki , Yamaguchi Tamié
Published: December 2004

A free radical was produced enzymatically by incubating benzo(a)pyrene with liver microsomes. This radical, identified as the 6‐oxybenzo(a) pyrene radical, was sufficiently reactive to bind covalently with nucleic acid bases. Similar reactive free radicals were produced enzymatically from anthanthrene and 10‐aza‐benzo(a)pyrene, which are carcinogenic in spite of lacking so‐called “bay regions.” Hepatocarcinogens such as 3′‐methyl‐4‐dimethylaminoazobenzene and related compounds, naphthylamines, and 2‐acetylaminofluorene yield free radicals after being incubated with liver microsomes. Thus, various kinds of chemical carcinogens are found to be converted to free radicals, suggesting causal significance for the formation of free radicals in chemical carcinogenesis.
Diagram approach to character formulas for finite and compact groups
Authors: Kibler M. , Elbaz E.
Published: December 2004

Some basic relations for the representation theory and the Wigner–Racah algebra of a finite or compact continuous group are discussed and transcribed in terms of diagrams. Special emphasis is placed on the case of a simply reducible group and all the diagrams are applicable to SU2 without any change.
Transferable integrals in a deformation‐density approach to crystal orbital calculations. I
Authors: Avery John
Published: December 2004

In the usual ab initio method of calculating molecular orbitals, the number of integrals to be evaluated increases as M4, where M is the number of basis functions. In this paper, an alternative method is discussed, where the computation time increases much less violently with the number of basis functions. Matrix elements of the deformation potential are evaluated by Fourier transform methods, while matrix elements of the neutral‐atom potential are evaluated by means of transferable integrals. The transferable integrals (moments of the neutral‐atom potentials) can be evaluated once and for all and incorporated as input data in computer programs. In an appendix to the paper, a general expansion theorem is discussed. This theorem allows an arbitrary spherically symmetric function to be expanded about another center.
Configuration interaction matrix elements. II. Graphical approach to the relationship between unitary group generators and permutations
Authors: Paldus J. , Wormer P. E. S.
Published: December 2004

The explicit expressions for the matrix elements of unitary group generators between geminally antisymmetric spin‐adapted N‐electron configurations in terms of the orbital occupancies and spin factors, given as spin function matrix elements of appropriate orbital permutations, are derived using the many‐body time‐independent diagrammatic techniques. It is also shown how this approach can be conveniently combined with graphical methods of spin algebras to obtain explicit expressions for the spin factors, once a definite coupling scheme is chosen. This method yields explicit expressions for the orbital permutations defining the spin factors. However, if desired, the explicit determination of line‐up permutations can be avoided in this approach, since they are implicitly contained in the orbital diagrams. It also clearly indicates why the geminally antisymmetric spin functions have to be used when a simple formalism is desired.
Free‐electron molecular‐orbital treatment of chalcone group of dyes
Authors: Basu Biswajit , Tiwari R. D. , Dey Arun K.
Published: December 2004

The position and intensity of the absorption bands of a number of chalcone dyes have been calculated on the basis of the free‐electron molecular‐orbital (FEMO) theory. The three to four absorption maxima of the chalcones are calculated by assuming the molecule to consist of two parts. The hypothetical cleavage is affected at the site of CO bond such that first and second part of the molecule contains six and eight π electrons, respectively. Each part is then treated as an independent entity and the absorption maxima obtained by the application of joint and continuity condition of Kuhn are in agreement with the experimental values. The perturbation energy correction due to the substituted functional groups with higher electronegativity than carbon have also been made in the absorption maxima. The oscillator strengths corresponding to the values of the absorption maxima have been obtained as well.
Equations‐of‐motion method: Calculation of the k lowest or highest solutions
Authors: Flament J. P. , Gervais H. P.
Published: December 2004

The method of optimal relaxation to determine the eigenvalues of symmetric matrices, as proposed by Shavitt, has been adapted to solve the equation‐of‐motion problem. Matrices Z and Y are obtained by one diagonalization, while matrices A and B remain unchanged. This procedure is particularly useful for high‐dimensional or nonorthogonal bases, if one needs only the lowest transition energies.
Time‐dependent variational principle in quantum field theory
Authors: Jackiw R.
Published: December 2004

This paper proposes a direct, quantum‐mechanical definition for Γ (effective action) using a two‐step procedure for applying the variational principle to time‐dependent quantum problems.
Notes on asymptotic series by H0‐strictly singular perturbations
Authors: Ingólfsson K.
Published: December 2004

Let two strongly continuous one‐parameter semigroups of contraction operators, {Z(t); t≧ 0} and {Z0(t); t ≧ 0}, determine physical evolutions realized in the Hilbert spaces ℋ and ℋ0, respectively. We consider the mappings under Z(t) and Z0(t), when the infinitesimal generators G and G0 belong to a product class, properly defined with respect to an H0‐norm. The inversed transform of each side in the identity R(λ, G) = R(λ, –iH0)–iR(λ, –iH0)VR(λ, G), which represents a simple algebraic decomposition of the resolvent of G, converges on Ψ if and only if Ψ ∈ 𝒟(G). By iteration an asymptotic series emerges, when t → 0. Numerical considerations of this approximation in its first order may support the form of a deviation from the pure exponential decay when the semigroup is compared with a integral transform corresponding to a certain self‐adjoint H0 in ℋ0. The deviation may hardly ever be observed and it is therefore most fruitful to discuss the results inside the framework of the enveloping algebra of the semigroups.
Interaction of methane molecules
Authors: Kołos W. , Ranghino G. , Clementi E. , Novaro O.
Published: December 2004

Potential‐energy curves for CH4·CH4 have been calculated using the SCF LCAO MO method. Six different mutual orientations of the molecules have been considered and several basis sets have been employed. An analytical potential has been fitted to the computed energy values and used in a Monte Carlo calculation to yield a spherically averaged CH4·CH4 potential. The potential, if corrected for dispersion interaction, agrees fairly well with that derived from thermophysical data. At short distances it disagrees with the potentials derived from scattering experiments which, however, are also incompatible with the experimental potential for large distances.
How good is good agreement: Evaluating the reliability of quantum‐mechanically calculated observables
Authors: Ransil Bernard J.
Published: December 2004

The practical value of a wave function derives from its ability to estimate or predict the chemical and physical properties of the electronic structure which it describes. Reliability is defined as a property to be evaluated on the basis of (i) the magnitude of the difference between the measured and calculated values of the observable together with (ii) the sign of the difference, (ii) the number and nature of observables correctly estimated, and (iv) the number and type of electronic structures that are correctly estimated. Systematic statistical comparison implies the existence of both internally consistent sets of wave functions for homologous series of molecules and their corresponding experimental values together with reliable error estimates. The most complete data base currently available for comparison is the spectroscopic constants for the first and second row diatomic hydrides. Utilizing appropriate statistical comparison techniques, four approximations (CEPA, PNO‐CI, GTO‐SCF, and STO‐SCF) are compared among themselves and against experimentally measured values. The CEPA approximation yields differences from experiment that approximate a normal error distribution, while the other approximations show systematic departures from experiment. Two values, ωe and ωeχe, for SH exhibit differences large enough to cast doubt upon the calculated value, the experimental value, or both.
Topological characterization of cyclic structures
Authors: Bonchev D. , Mekenyan Ov. , Trinajstić N.
Published: December 2004

The sum of the topological distances in the molecular graph (the Wiener number) is used for a topological characterization of the condensed polycyclic molecular systems. This topological index discriminates well the isomeric cyclic molecules. In addition, it also properly reflects their structural features. On this basis the principal points of molecular cyclicity are formulated in 15 rules.
High accuracy wave functions and eigenenergies for vibration–rotation states of diatomic molecules
Authors: Mohammad S. Noor
Published: December 2004

A solution of the wave equation for the rotational–vibrational motion in diatomic molecules with a new exponential potential function is carried out in detail. The solution gives simple expressions for the wave functions, eigenenergies, and other related spectroscopic constants. With these expressions Franck–Condon factors for the R branches of the A 1∑‐X 1∑ band system of Ca2, have been calculated which are in excellent agreement with experiment. Various strengths and weaknesses of the present method are also discussed.