bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermal dissociation of 1,2‐dioxethane. II. Quantum topology of the charge distributions
Authors: Hilal Rifaat 
Published: December 2004

AbstractThe 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

AbstractModel 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

AbstractSynchrotron 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

AbstractA 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

AbstractThe 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

AbstractElectrostatic 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

AbstractThe 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

AbstractPossibilities 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

AbstractThe 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

AbstractCalculations 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

AbstractThe 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

AbstractAb 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

AbstractEnergy 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

AbstractHow 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

AbstractTheoretical 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

AbstractA 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

AbstractSymmetry 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

AbstractQuantum 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.
Short‐time description of chemical reaction by Stochastic methods
Authors: Fonseca Teresa , Gomes J. A. N. F. , Grigolini Paolo 
Published: December 2004

AbstractFor 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

AbstractA 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

AbstractIn 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.
Computer generation and identification of carcinogenic bay regions in benzenoid hydrocarbons
Authors: Knop J. V. , Szymanski K. , Jeričević Ž. , Trinajstić N. 
Published: December 2004

AbstractA computer‐oriented algorithm is developed for identification and enumeration of carcinogenic bay regions in benzenoid hydrocarbons. The results are reported for geometrically planar benzenoid systems up to ten fused rings. They fully agree with those obtained in a different way by Balasubramanian et al. The advantage of the proposed method is that we can display all planar benzenoid structures and identify the carcinogenic bays in each of them.
Interaction of p‐benzoquinone and mitomycin C with complementary base pairs
Authors: Chojnacki H. , Sawaryn A. 
Published: December 2004

AbstractQuantum chemical studies on interaction of p‐benzoquinone and mitomycin C with complementary base pairs have been performed. The empirical potential function and semitheoretical algorithm were applied for estimation of intermolecular interaction energy. Non‐negligible intercalation of the quinone ring into fragments of nucleic acid seems to be justified. Extensive calculations on the specificity of mitomycin C intercalation were performed using AGNAS/IMNAS algorithm based on an empirical potential function. No clear preference for intercalation into any kind of base pairs was found.
CNDO/S parameters of C, O, and Si for solid state calculations
Authors: Deák P. 
Published: December 2004

AbstractSemiempirical methods used in cluster‐type calculations must be applicable for calculating ionization potentials (“valence band”) and electronic transitions (“gap”). CNDO/S seems to be an appropriate choice for this purpose. However, the solids of main interest (as, e.g., diamond and silica) contain saturated bonds for which the original parametrization does not work well. A new set of parameters was determined for C, O, and Si by fitting them to vertical ionization potentials and to singlet electronic transitions of their saturated molecules. The transferability of the parameters were also checked. By these parameters a successful description of the electronic structures of diamond and silica became possible.
Recent investigations on the electronic structure of the fourth and fifth group transition metal monocarbides, mononitrides, and monoxides
Authors: Neckel A. 
Published: December 2004

AbstractAn overview is given here of band structure calculations on the fourth and fifth group transition metal monocarbides, mononitrides, and monoxides, published since the review article by Calais [J.‐L. Calais, Adv. Phys. 26, 847 (1977)]. Furthermore, the relations of three categories of experimental properties, which allow insight into the electronic structure of the above mentioned compounds, and the results of band structure calculations are discussed. Theoretical predictions are compared with experimental findings. The considered experimental properties are valence band photoemission spectra, valence band x‐ray emission spectra, and optical properties.
Conformational studies of the β(1→3) linked disaccharide component of the immunologically active pentasaccharide of the Forssman antigen
Authors: Yadav Janardan Singh , Luger Peter 
Published: December 2004

AbstractConformational energy calculations at the PCILO level of approximation were performed on β(1 → 3) linked disaccharide consisting of N‐acetylgalactosamine and galactose of the Forssman antigen to examine the side group conformations and their influence on the mutual orientations of the two pyranosyl rings. Two low energy regions for the glycosidic bond conformation have been located in the grid search using classical potential functions. The PCILO energy minimizations were then carried out in each of these regions. The preferred orientations of the nonreducing pyranosyl ring relative to the reducing ring were found to be in agreement with the available x‐ray results. Moreover, the orientations of groups attached to the anomeric carbons were in good accordance with the requirements of the exo‐anomeric effect.