bluuebunny/crossref_metadata_2025_split huggingface dataset:
Particle‐hole symmetry and complementary quantum systems
Authors: Živković T. P. 
Published: January 2005

AbstractIt is well known that positive and negative ions derived from the same alternant hydrocarbon have almost indistinguishable electron spectra. Effective charges, bond orders, and many other properties also correlate between the two systems. These «alternancy» properties are due to the particle‐hole symmetry, and they can be generalized far beyond alternant hydrocarbons. In general, with each quantum system one can associate a «complementary» system. The eigenstates of the complementary system are related to the eigenstates of the original system in the same way as the anionic eigenstates of an alternant hydrocarbon are related to the cationic eigenstates of this hydrocarbon. In particular, the (N + k)‐electron spectrum of the complementary system is the same, up to the uniform shift, as the (N − k)‐electron spectrum of the original system; the effective charges in the complementary system are opposite to the corresponding effetive charges in the original system; bond orders in the two systems between vertices of the same and of the opposite parity are, respectively, opposite and the same, etc. Each particle‐hole symmetry operator associates with the original system one such complementary system. There is hence a large number of the systems complementary to the same original system. In the PPP model and in various generalizations of this model, systems complementary to conjugated hydrocarbons are Möbius‐type alterations of original hydrocarbons. In the case of conjugated heterocompounds, there is a formal replacement of all heteroatoms with some other heteroatoms, with or without an additional Möbius‐type change. Such complementary systems may correspond to entirely different molecules, and they also may describe some transition states of these molecules.
Total π‐electron energy in the “variable β” Hückel method
Authors: Cioslowski J. 
Published: January 2005

AbstractIt is demonstrated that the total π‐electron energy calculated within the “variable β” Hückel method is almost entirely determined by the total π‐electron energy computed within the ordinary (topological) Hückel method and the number of the carbon‐carbon bonds. This explains the fact that the topological Hückel method is capable of predicting relative stabilities of various molecules, even if they possess different bond lengths.
Supercomputing and supercomputers for science and engineering in general and for chemistry and biosciences in particular
Authors: Clementi E. , Chin S. , Corongiu G. , Detrich J. H. , Dupuis M. , Folsom D. , Lie G. C. , Logan D. , Sonnad V. 
Published: January 2005

AbstractWe start by pointing out relationships between production of information, global simulation, and supercomputing, thus placing our research activities in today's society context. Then we detail the evolution in hardware and software for 1CAP, our experimental supercomputer, which we claim to be especially well suited for supercomputing in science and engineering. A preliminary discussion of 1CAP/3090 (our latest experimental effort) is included. Many examples from different disciplines are provided to verify our assertions. We “prove” our point by presenting an example of global supercomputing. Starting with 3 nuclei and 10 electrons, building up to a single water molecule, then to a few hundred, we learn, for example, about Raman, infrared, and neutron scattering; we then move up to a few hundred thousand molecules to analyze particle flow and obstructions; finally we experiment, but only preliminarily, with a few million particles to learn more on nonequilibrium dynamics as in the Rayleigh‐Benard systems. In this way, quantum mechanics is overlapped with statistical mechanics and expanded into microdynamics. The entire paper is finally reanalyzed from a different perspective, presenting rather systematically, even if most briefly, our ideas on “modern” computational chemistry, where quantum mechanics is as much needed as fluid dynamics and graphics. In this section the main computational techniques are analyzed in terms of computer programs and their associated flow diagrams to solve the basic equations using parallel supercomputers.
Conformational implications of some nucleotide sequences
Authors: Poltev V. I. , Teplukhin A. V. 
Published: January 2005

AbstractThe conformational properties of some nucleotide sequences result in their ability to bind specifically some ligands or tobe recognized by specific proteins. In order to investigate the dependence of conformational behavior of the DNA duplex on nucleotide sequence, we analyzed the interaction energy of nucleic acid bases as a function of conformational parameters and base sequence. Extended regions of minimum energy values were found for different sequences. Although these regions (valleys) largely overlap, each one shows specificity for a particular sequence. This suggests that a specific pathway of changes in conformational parameters exists for each sequence. the changes may be accompanied by considerable shifts (2–3 Å) of the atom positions and an only slight variation (1–2 kcal/mol) of energy. Even small shifts in other directions can cause a drastic energy increase. For some nucleotide sequences, the energetically preferable conformations are the B‐like ones (e.g., ApA, TpA), whereas for others the A‐like ones are preferable (e.g., GpG, ApT). IN general, Pyr‐Pur sequences have a tendency to a larger τ and smaller H and D than Pur‐Pyr sequences. A large body of experimental data on nucleic acid structure in fibers and in solutions can be explained by results obtained.
Molecular interactions in aqueous solutions: The role of random fluctuations of external parameters and of thermodynamic instabilities
Authors: Palma‐Vittorelli M. B. 
Published: January 2005

AbstractA biological system usually operates under nonstable values of relevant parameters, such as pH, temperature, and ionic strength. The question therefore poses whether such fluctations do affect its relevant processes. Experimental studies on the role of random temperature fluctuations on functional encounters of biostructural polymer molecules, and consequent self‐assembly of supramolecular structures, have evidenced an additional, noise‐induced order of these structures. This type of effect is the result of nonlinearity in physical systems, and the case of a biosystem is especially interesting. As recent experiments have shown, spinodal decomposition resulting from thermodynamic instability may favor the onset of the supramolecular ordering process. If the random fluctuations of temperature are imposed in such conditions of thermodynamic instability, their ordering effect is further enhanced.
A comparative analysis of the active site properties of the resting states of cytochrome c peroxidase, metmyoglobin, and catalase
Authors: Axe Frank U. , Waleh Ahmad , Chantranupong Lek , Loew Gilda H. 
Published: January 2005

AbstractQuantum chemical studies (INDO‐RHF‐SCF) have been made for the resting state active sites of three closely related heme proteins, cytochrome c peroxidase (CCP), metmyoglobin (MMB), and catalase (CAT). The relative energies of the germane sextet, quartet, and doublet spin‐states of each active site were calculated. Both CCP and MMB have similar heme units, consisting of an Fe(III)‐protoporphyrin‐IX with an imidazole and water as axial ligands. Our calculations show that the larger doming of the porphyrin, greater out‐of‐planarity of the iron, and the shorter iron‐water distance in MMB leads to a sextet ground state with a low‐lying quartet state. By contrast, the order of these two states is reversed in CCP, when a neutral imidazole is used as the endogenous axial ligand. An imidazolate ligand, on the other hand, which is an extreme representation of the H‐bonding believed to occur in CCP with a nearby aspartate residue, leads to a sextet ground state with a low‐lying quartet state. Assuming at least a partially anionic ligand in the intact protein, it follows that the quartet contribution to the ground state properties will be larger in CCP than in MMB. These predictions are consistent with the observed differences in the temperature‐dependent magnetic susceptibility for these two proteins. The present results suggest that the experimentally observed Mössbauer resonance spectra of CCP should be reinterpreted in terms of sextet and quartet state contributions to the electric field gradient. Calculations for catalase, which has a single phenolate ligand, result in a sextet ground state with a low‐lying quartet state consistent with available Mössbauer and magnetic susceptibility data. Our calculations of the Im− form of CCP show that it more closely resembles CAT. Thus, the effect of proton transfer in CCP can account at least in part for the similarities between CCP and CAT function. Minor differences in ground spin‐state and electronic properties calculated for CCP and MMB, however, cannot explain why MMB does not have significant peroxidase activity. The different functions of MMB and CCP must then be due in part to other known differences in their protein environment such as polar residues around the distal ligand binding pocket of CCP, which are absent in MMB, and could help its transformation to an active oxidizing state.
Noncovalent interactions of medium strength. A revised interpretation and examples of its applications
Authors: Alagona G. , Cammi R. , Ghio C. , Tomasi J. 
Published: January 2005

AbstractRecent studies performed in our group on a classical problem of quantum chemistry, with strong implications for theoretical biochemistry and pharmacology, are here summarized. Ab initio descriptions of noncovalent interactions, and in particular H bonds and acid‐base couples, have been reexamined using as novel tools the decomposition of ΔE with the inclusion of CP corrections and a further decomposition of the ΔE components into group contributions. Some results of systematic analyses performed over H‐bonded dimers are reported, supplemented by a successful application of this approach to a problem of noticeable economic importance (the identification of catalysts for the industrial synthesis of tensioactives). A new feature, presented here for the first time, is the extension of the CP‐corrected decomposition of ΔE to bimolecular interactions in solution.
A many‐body diagrammatic theory of rotation–vibration spectra
Authors: Biskupič Stanislav , Kvasnička Vladimír 
Published: January 2005

AbstractA many‐body diagrammatic perturbation theory of rotation–vibration spectra is elaborated. The present approach is based on two many‐body techniques, namely on the second quantization formalism (a rotating–vibrating molecule is formally treated here as a system of interacting vibrons, obeying the Bose–Einstein statistics) and the many‐body diagrammatic theory of a model Hamiltonian, initially suggested in the microscopic theory of nuclei and in the last decade very frequently exploited in the accounting for the correlation effects in many electron systems. In the framework of this theory, the rotation–vibration energies are determined as the eigenvalues of a finite‐dimensional model eigenproblem.
A configuration‐averaged Hartree–Fock procedure
Authors: Zerner Michael C. 
Published: January 2005

AbstractA configuration‐averaged Fock (CAHF) operator is developed within the restricted open‐shell formulation (ROHF) for the case of any number of open‐shell orbitals containing any number of electrons. The resulting orbitals and energies should be useful for those cases where there is a great degeneracy of states, either preventing self‐consistent field convergence, or negating the value of a pure state description itself. This procedure is compared with the hyper‐Hartree–Fock method of Slater and the grand canonical Hartree–Fock ansatz of Abdulnar, Linderberg, Öhrn, and Thulstrup.
Improved treatment for matrix elements of spin‐dependent operators
Authors: Qianer Zhang , Xiangzhu Li 
Published: January 2005

AbstractIn this paper a general method for the evaluation of the matrix elements of spin‐dependent operators is proposed to improve the treatment primitively suggesteed by Cooper and Musher. This approach is largely based on the recent results which the present authors have achieved in the representation theory for the inner‐ and outer‐product reduction of the symmetric group. It is shown that the so‐called outer‐product coupling coefficients (OPCC) can be used to generalize the method for constructing the irreducible tensor operators of group Sn. Together with the use of inner‐product coupling coefficients (IPCC), an expression for the matrix elements of spin‐dependent operators is presented as the product of a Racah coefficient for Sn and a reduced matrix element which can be expressed in terms of IPCC, OPCC, and the related integrals. The treatment for one‐ and two‐electron spin‐dependent operators is discussed in detail.
The local orbital energy and density functional theory
Authors: Pearson Ralph G. , Palke William E. 
Published: January 2005

AbstractFrom the viewpoint of density functional theory, an expression is derived which improves the average energy of a trial density. Applications to atoms and molecules are made using wave function methods and are based on properties of the variance, which is defined as \documentclass{article}\pagestyle{empty}\begin{document}$ (\overline {\varepsilon ^2 } - (\overline \varepsilon)^2)^{1/2} $\end{document}, where ϵ is the local orbital energy. Calculated results for both Hartree‐Fock and correlated wave functions are quite encouraging.
Approximate density matrices and wigner distribution functions from density, kinetic energy density, and idempotency constraints
Authors: Morrison Robert C. , Yang Weitao , Parr Robert G. , Lee Chengteh 
Published: January 2005

AbstractThe Wigner distribution function and the corresponding density matrix are calculated using a form for the distribution function suggested by maximization of the entropy. Wigner functions and density matrices are determined by imposing conditions of idempotency on the density matrix. Exchange energies and Compton profiles calculated from density matrices obtained by imposing the idempotency constraints are compared with the results of calculations using the Hartree–Fock density matrix and a Gaussian approximation for the density matrix for H and the noble gases He through Xe. Compton profiles from Wigner functions with idempotency constraints show improvements over the Gaussian approximation for the lighter atoms, but do not show significant changes for the heavier atoms. Exchange energies from density matrices with idempotency constraints show improvements over the Gaussian approximation except for the heavier atoms Kr and Xe.
Second‐order polarization propagator calculations of dynamic dipole polarizabilities and C6 coefficients
Authors: Sauer Stephan P. A. , Diercksen Geerd H. F. , Oddershede Jens 
Published: January 2005

AbstractThe frequency‐dependent dipole polarizability, α(E), is calculated using the second‐order polarization propagator approximation (SOPPA). We have shown how to express α(E) as a function of E2 and thus obtained a form of α(E) that can be used to compute C6‐coefficients without invoking complex arithmetic. For He we find that SOPPA recovers a large fraction of the correlation contribution for all frequencies, whereas for H2 where the correlation contributions are much smaller and also basis set‐dependent, we find a less definite trend of SOPPA relative to RPA.
Energy deposition mechanisms and biochemical aspects of DNA strand breaks by ionizing radiation
Authors: Chatterjee Aloke , Holley William R. 
Published: January 2005

AbstractA theoretical model based on physical, chemical, and biochemical mechanisms has been presented to evaluate the yields of DNA strand breaks (single and double) as a function of linear energy transfer (LET) or −dE/dx. Energetic heavy charged particles are considered explicitly to provide a general theory for low‐ as well as for high‐LET radiation. There are three main features of the calculation: (a) track structure considerations for the energy deposition pattern, (b) three‐dimensional structure of DNA molecules to provide information on the exact location of damage, and (c) a Monte‐Carlo scheme to simulate the diffusion processes of water radicals. To avoid the complexities of a cellular medium, an aqueous solution of DNA is considered in the calculation. When the results of the calculations are compared with experimental measurements of the yields of strand breaks in mammalian DNA (exposed in a cellular complex), reasonable agreement is obtained. However, only those experimental data have been compared where there were no enzyme repair processes. The method of calculation has also been extended to study breaks in higher‐order structures of DNA molecules such as chromatin. Specific limitations of the present model have been pointed out for making further improvements.
An ab initio study of the unimolecular decomposition mechanism of formamidine. 4‐31G Characterization of potential energy hypersurface
Authors: Andrés Juan , Krechl Jiría , Carda Miguel , Silla Estanislao 
Published: January 2005

AbstractAb initio MO calculations have been carried out for the unimolecular decomposition of formamidine. The Hartree–Fock method in LCAO approximation with the 4‐31G basis set was used. The 4‐31G potential hypersurface has been further studied. The stationary points (R, TS, and P) were localized. A reaction analysis by correlation of bond‐order indices and localized molecular orbitals demonstrated that the decomposition is an asynchronous process. The TS can be described as four‐membered ring.
The elements of Flatland: Hartree‐Fock atomic ground states in two dimensions for Z = 1–24
Authors: Pyykkö Pekka , Zhao Yongfang 
Published: January 2005

AbstractThe Hartree–Fock problem in two dimensions (2D) has been solved for 1 ≤ Z ≤ 24 using a Gaussian basis and assuming r−1 Coulomb interactions. The order of occupation of the one‐electron states is

like in the 3D case. The 1s shell is found to be particularly small and strongly bound, making the 2D hydrogen a “superhalogen” and the 2D He a “superinert gas.” In contrast to 3D, 4s13d2 and 4s23d3 configurations are preferred for the 2D “Sc” and “Cu,” respectively. The six first 2D atoms have stronger and the later ones weaker valence‐bonding energies than do their 3D analogs. It is noted that the 2D Dirac energy expression for a hydrogenlike atom for mj = l + 1/2 agrees with the 3D Klein–Gordon one.
Linear depedence of total π‐electron energy of benzenoid hydrocarbons on Kekulé structure count
Authors: Gutman Ivan , Hall George G. 
Published: January 2005

AbstractIt is an empirically established fact that the total π‐electron energy (E) of benzenoid hydrocarbons is a linear function of the number of Kekulé structures (K). A general class of approximate formulas for E is shown to exhibit the required linear dependency on K. The condition for this is that the highest occupied molecular orbitals (MOS) are nondegenerate and well separated from the second highest occupied MOS.
A Dirac–Fock self‐consistent field method for closed‐shell molecules including Breit interaction
Authors: Mohanty Ajaya K. 
Published: January 2005

AbstractWe present a method for including the Breit interaction in relativistic self‐consistent field calculations for closed‐shell molecular systems using atomic basis spinors of kinetically balanced Gaussian‐type functions. The method extends the formalism described in a previous paper [A. Mohanty and E. Clementi, Int. J. Quantum Chem. 39, 487–517 (1991)] that dealt with the two‐electron effect due to Coulomb interaction only. It is shown that both frequency‐dependent and frequency‐independent Breit interactions can be treated on equal footing, and the corresponding matrix elements are evaluated following the well‐known Fourier transform technique applied to electron repulsion integral evaluation in nonrelativistic molecular calculations.
Advances in automatic speech recognition by combining information theory and neural network algorithms
Authors: Rigoll Gerhard 
Published: January 2005

AbstractThis paper presents some of the newest developments in the field of automatic speech recognition. It concentrates on describing the efforts of combining the two so‐far most successful approaches in automatic speech recognition, namely, information theory and neural network techniques, in order to obtain more improved speech recognition algorithms. An overview of the various approaches to the combination of these two basic technologies is given and the arising problems, such as the choice of the appropriate neural network paradigms, the best possible combination strategies and possibilities for an integrated training of the neural network, and the Markov model parameters, are discussed.
A theoretical study of the ground‐state potential surface of guanine and its binding with oxygen and water
Authors: Santhosh C. , Mishra P. C. 
Published: January 2005

AbstractA molecular orbital geometry optimization study of the potential surface of guanine, guanineO2, and guanineO2water reaction products in the ground state has been carried out. The origin of the asymmetric double‐well potential surface of guanine suggested earlier on the basis of experimental observations has been explained. The most stable binding of O2 with guanine (G) is found to occur at the C4C5 double bond of the latter molecule. In the case of GO2water reaction product (HOOGOH), the groups OOH and OH bind at C4 and C8, respectively. The possiblity of a polymeric reaction product of the type R1(GOOG)nR2 (R1, R2 = H, OH) has also been suggested. These results are broadly supported by experimental observations. The mechanism of spectral oscillations observed in UV‐irradiated guanine solutions has been discussed.
Matrix elements of the U(2n) generators in the spin‐orbit basis
Authors: Titov A. V. 
Published: January 2005

AbstractAn algorithm for the evaluation of the matrix elements of the U(2n) generators in the spin‐orbit basis [induced by the U(n) ⊗ U(2) subgroup] is proposed. This algorithm can be used for calculations with spin‐dependent Hamiltonians for many‐electron problems.
A gauge symmetric band model of the Woodward–Hoffmann rules
Authors: Squire A. E. , Squire R. H. 
Published: January 2005

AbstractThe Woodward–Hoffmann (WH) Rules for the prediction of relative rates and stereochemistry of concerted reactions are based on considerations of the orbital symmetry of the reactants and products. Literally hundreds of reactions have been successfully categorized by these remarkably simple‐appearing Rules. This paper develops a one‐dimensional band model of these Rules. By explicit inclusion of the effects of an electromagnetic field in a standard gauge‐invariant fashion, it can be shown that at certain levels of field strength the model suggests that the Rules may be reversed. This is because the Rules appear in the model as a consequence of a centrifugal angular momentum barrier that can be shifted by an electromagnetic field. This barrier could account for “aromatic” stabilization. As an additional effect, the model predicts flux‐dependent oscillations and persistent currents for “aromatic” molecules due to the Aharonov–Bohm effect. The possible health effects of electromagnetic fields are speculated. The likelihood of experimental observations to verify the applicability of the model is discussed.