bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure–Activity relationships in auxins
Authors: Raghunathan S. , Pattabhi Vasantha 
Published: December 2004

AbstractOf the various theories proposed for auxin activity, the conformational change theory and the charge separation theory have received considerable attention. However, no conclusive theory collating molecular structure with hormonal activity has yet been established. We have studied the structural requirements for hormonal activity in plants through single crystal x‐ray studies, as well as through conformational and charge density calculations on a series of plant hormones. We find that the existing theories are inadequate in explaining the activity of several auxins. We propose that the size of the auxin molecule in conjunction with the charge separation serves as a possible mechanism of action in plant hormones.
Biological activity of the nucleoside analogs: A theoretical study
Authors: Sanyal Nitish K. , Roychoudhury Mihir , Ojha Rajendra P. 
Published: December 2004

AbstractIt has been observed through the conformational analysis of nucleoside analogues that in most of the cases these molecules possess similar conformations to their parent molecules. Therefore, it is, generally believed that these molecules are incorporated as such in the nucleic acids during various biological functions, viz., replication, transcription, etc. A theoretical study for such incorporation has been carried out. Charge distribution of the base parts of these molecules has been calculated by using CNDO/2 method wherever they were not available in literature. Electrostatic energies for various base pairs with these bases have been calculated. Also a possible incorporation during transcription has been studied in view of the model developed by Sanyal, Kumar, and Roychoudhury by taking formycin as an examples. The results of these studies are discussed.
Probing possible left‐ and right‐handed poly(dinucleotide) helical conformations from (n–h) plots. models for polysequential nucleotides
Authors: Jayaraman S. , Yathindra N. 
Published: December 2004

AbstractIntroducing the concept of the “dinucleotide” as the helical repeat, theoretical attempts have been made to determine possible single and double stranded helical structures by using helical parameter calculations and model building investigations. By virtue of its flexible framework, the dinucleotide repeat offers a much greater scope of finding new secondary structural forms for nucleic acids. Considering only those conformations which show tendency for at least partial base overlap as does the dinucleotide helical repeat, it has been possible to predict poly(dinucleotide) helical models in which successive phosphodiesters as well as nucleotide conformations alternate. More important, the recently found left‐handed Z‐type polynucleotide helix is characterized rather uniquely on the helical parameter plot. The results further suggest the possibility of other Z‐type helices obtainable by alternative conformations for the exocyclic C4'–C5' bond and sugar pucker. Near neighbor long range conformational correlations between the dinucleotide repeat and the phosphodiester linking them have been established similar to poly(mononucleotide) helices. Need for considering higher repeats such as trinucleotide has been suggested to obtain models for looped out helical conformations.
Virtual bond probe to study ordered and random coil conformations of nucleic acids
Authors: Malathi R. , Yathindra N. 
Published: December 2004

AbstractRecognition of the stereochemical features inherent to a nucleotide, viz., the preferred trans character of the two CO bonds and the approximate chemical and conformational symmetry, has facilitated the representation of a nucleotide in terms of two nearly equal blocks or two virtual bonds spanning the atoms P to C4' on the 5' side and C4' to P on the 3' side. The scheme, by virtue of its unique ability to account for the main sources of flexibility and to incorporate their interdependence, could be effectively applied to probe ordered, as well as random coil conformations of polynucleotide chains. Using this scheme, conformations of nucleotide, dinucleotides, helices, and yeast tRNAPhe have been characterized by virtual bond parameters. The two blocks of nucleotide have also been described in terms of two approximate planes similar to peptides. Unperturbed end‐to‐end dimensions and persistence lengths of random coil polynucleotides have been computed by considering short‐range as well as near‐neighbor bond long‐range correlations and are in excellent agreement with the experimentally determined values. A striking finding of these studies is the relevation that random coils comprise of a large proportion of stacked A‐type helical segments in sharp contrast to earlier interpretations which invoked a high fraction of unstacked extended conformations.
Molecular electrostatic potential on the surface envelopes of macromolecules: B‐DNA
Authors: Lavery Richard , Pullman Bernard 
Published: December 2004

AbstractA procedure for calculating the molecular electrostatic potentials on surface envelopes surrounding macromolecules is presented. This new representation of potential is employed in studying B‐DNA double helices and, from the results, deductions are drawn on the interaction specificities of B‐DNA with electrophiles.
Calculation of the density of states of tight‐binding d band for simple cubic lattice
Authors: Modrak P. 
Published: December 2004

AbstractThe electronic density of states for d bands was calculated accurately in the tight‐binding approximation for a simple cubic lattice. Numerical values of the density of states for five subbands as well as of the total density of states were tabulated for the set of values of two‐center integrals of the magnitudes corresponding to those estimated for real crystal.
Calculation of periodic molecular systems with perturbed periodicity within the PCILO framework. I. Method
Authors: Lochmann R. , Weller Th. 
Published: December 2004

AbstractA method within the PCILO framework for the study of periodic molecular systems involving impurities is described regarding a one‐dimensional chain. The calculation of the whole system is reduced to the calculation of subsystem pairs only. By use of the first‐neighbor approximation only one or two subsystem pairs must be considered for subsystems with identical or differing surroundings, respectively. The procedure described yields the ground state energies and charge distributions of the subsystems.
Analytic expression of the rotation harmonics in the vibration–rotation wave function of a diatomic molecule
Authors: Kobeissi Hafez , Korek Mahmoud 
Published: December 2004

AbstractBy using the vibration–rotation canonical functions, we show that the wave function for a vibration–rotation level (v, J) can be represented by ψvJ(r) = ψv (r)+Σ λlϕl(r) with λ = J(J + 1). The radial Schrödinger equation can be written (Hv + λHJ)ψvλ = (Ev + Σ λlεl)ψvλ, where ε1, ε2, ε3,… stand for the rotational constants Bv, Dv, Hv,…. The radial equation being satisfied for any value of λ, the rotation “harmonics” ϕ1, ϕ2,… are found to be the solutions of a set of inhomogenous differential equations of the form Hϕl = Evϕl + fl(r)ψv. An analytic expression of the harmonics ϕi is given for any potential. The numerical application shows that, for a given r, the harmonics decrease in absolute values like Bv, Dv, Hv,… and that the agreement between the values of ψvJ deduced from the computation of the harmonics on one hand, and the direct computation on the other hand, is very satisfactory.
Studies in Löwdin's partitioning technique in quantum theory. II. Operators T and Ω
Authors: Wilson R. G. , Sharma C. S. 
Published: December 2004

AbstractOperator Ω and reaction operator T of Löwdin are studied with a slightly different approach, which leads to a clearer understanding of their nature and brings out the relevance of the conditions for the invertibility of K studied in the preceding work in this series.
Direct calculation of lattice sums. A method to account for the crystal field effects
Authors: Stolarczyk Leszek Z. , Piela Lucjan 
Published: December 2004

AbstractA method of direct calculation of lattice sums in three‐dimensional crystals is reported. The method is based on annihilation of some lowest multipole moments of the unit cell by a redefinition of the unit cell content. As a result, properties of the infinite crystal can be calculated as usual by taking a finite cluster of unit cells, but surrounded by an additional surface layer of a charge density (e.g., a layer of point charges). This charge density distribution produces the electric field approximating that one of the rest of the infinite crystal. The method proposed is easily applicable in the SCFLCAO procedure as well as in any method using a cluster representation for an infinite crystal. The validity of the infinite crystal model for a finite crystal is also discussed.
Reorganization effects in the photoelectron spectra of transition metal compounds: A Green's function study in the framework of a variable INDO hamiltonian
Authors: Böhm Michael C. 
Published: December 2004

AbstractThe magnitude of reorganization energies in the photoelectron (PE) spectra of various transition metal compounds with Mn, Fe, and Ni as 3d center is studied by means of a variable INDO Hamiltonian. The Koopmans defects are analyzed as a function of the one‐electron resonance integral β and as function of the one‐ and two‐center electron–electron interaction integrals. β has the property of an inverse coupling constant; reorganization effects are enlarged with reduced β values. In the limit of very small resonance integrals a reduction of the calculated Koopmans defects due to modified localization properties of the orbital wave function is encountered. The two‐center electron‐electron interaction integrals γ have been calculated via an exponential formula with a variable range parameter. In the limit of long‐range potentials with flattened γ; gradients a significant reduction of relaxation and correlation is diagnozed; large defects are predicted in the short‐range limit with steep gradients in the repulsion potential. The one‐center Coulomb and exchange integrals (γ, K) have been modified by a multiplicative factor. With enlarged one‐center integrals enhanced Koopmans defects are encountered. The reorganization energies are determined by means of a Green's function approach with a renormalized approximation for the self‐energy part.
Study of an approximate relation between the energy of an atom and the electronic potential at the nucleus
Authors: Alonso J. A. , González D. J. , Balbás L. C. 
Published: December 2004

AbstractThis paper provides an analysis of the reasons for the approximate validity of the relation \documentclass{article}\pagestyle{empty}\begin{document}$ E = \frac{3}{7}NV(0) $\end{document}, between the total energy E of a neutral atom, the number N of electrons, and the electronic potential at the nucleus V(0). Using the density functional formalism we find that the right‐hand side of the above equation also appears (and is the leading term) in density functional approximations more sophisticated than the Thomas–Fermi (TF) approximation (the above equation is exact in the TF approximation). Systematic improvements to the equation appear to be difficult because the main corrections come from those terms which are more difficult to handle in the density functional formalism. After this analysis we propose a kinetic energy functional for neutral atoms in the Hartree–Fock approximation. The first term of this new functional is a rescaled Thomas–Fermi term

, where γ = −0.0063 for light atoms and γ = 0.0085 for the others. The second term is the first gradient correction due to Kirzhnits

.For lithium to krypton atoms, this new functional gives an average error of 0.22%.
Ab initio molecular orbital study of the tautomerism of 4‐hydroxy‐2‐pyridinone
Authors: Schlegel H. Bernhard 
Published: December 2004

AbstractAb initio calculations were performed on 2,4‐pyridinediol, 4‐hydroxy‐2‐pyridinone, and 2hydroxy‐4‐pyridinone at the HF/3‐21G level with full geometry optimization. Two conformations of the hydroxyl group were considered for each tautomer. Corrections for polarization functions, electron correlation, and zero point energy were made by comparison with previous calculations on 2‐ and 4‐pyridinone tautomerism which included these contributions. The most stable structure is 4‐hydroxy‐2‐pyridinone, in agreement with experiment. Relative to 4‐hydroxy‐2‐pyridinone, the energies of the other tautomers are estimated to be 1.9 kcal/mol for 2,4‐pyridinediol and 8.9 kcal/mol for 2‐hydroxy‐4‐pyridinone. These are in accord with the experimental values 0.3 ± 1.9 and 10.6 ± 1.9 kcal/mol, respectively, deduced from equilibration studies of the tautomeric methyl derivatives.
ESCA Peak intensities in the dipole and generalized sudden approximations using fourier transforms of GTO's
Authors: Morales J. , Palma A. , Poulain E. 
Published: December 2004

AbstractAnalytical expressions for the square of the spherical average of Fourier transforms of Gaussian type orbitals (GTO's) are given. A direct application of these expressions to the calculation of molecular photoionization cross sections is considered under the generalized sudden (GSA) and dipole (DA) Approximations. Numerical calculations were done on the CO molecule using bound orbitals obtained by ab initio LCAO–MO calculations with Gaussian basis sets. The results are in good agreement with experiments. Those obtained by the GSA method however, suggest a limitation in its use: the GSA method is only applicable when comparing photoionization intensities of neighboring ionization energy orbitals. Applications to other molecules are immediate.
Theoretical study of the effect of substituents on electrophilic addition to olefins: Ab initioMO approach with energy decomposition
Authors: Ruo‐Zhuang (R.Z.Liu) Liu , Jian‐Guo (J.G.Yu) Yu 
Published: December 2004

AbstractThe interaction energies of proton with ethylene and substituted ethylenes in a positive bridged ion have been calculated by ab initio MO method with STO‐3G basis set, and the energies were further decomposed according to decomposition scheme proposed by Kitaura and Morokuma [Int. J. Quantum Chem. 10, 325 (1976)].
Calculation of the coherent memory functions from the eigenvalues and eigenvectors of the corresponding stationary Schrödinger equation
Authors: Skála L. 
Published: December 2004

AbstractUsing some properties of the Bessel functions the algebraic representation of the Nakajima–Zwanzig generalized master equation was derived. This representation makes possible the calculation of the memory functions in terms of the probabilities. Using this approach, the formulas for the memory functions giving their dependence on the eigenvalues and eigenvectors of the corresponding stationary Schrödinger equation are given and discussed in detail.
The fragments‐in‐molecules method. II. Fim method for σ‐bonded systems
Authors: Klessinger Martin 
Published: December 2004

AbstractA semiempirical SCF MO method has been developed in which the wave function of a composite molecule is written as a linear combination of localized fragment orbitals and which is formulated such that strictly transferable empirical data for the fragments may be introduced into the calculation. Results of FIM calculations in the CNDO/2 approximation for a number of RX molecules with R = alkyl and X = F, OH, NH2, and CH3 are presented and used to illustrate the possibilities and limitations of the method.
Photoelectron spectroscopy of chemisorbed atoms
Authors: Nicolaides C. A. , Andriotis A. N. 
Published: December 2004

AbstractWe outline a theory of UV and higher‐energy photoemission spectroscopy of chemisorbed atoms, that aims at the accurate calculation of inner electron binding energies and photoabsorption cross sections by including solid state and localized relativistic and correlation effects. It is based on an “atom on (in) solids” approach where one first extracts a surface potential and then uses it in a coupled Hartree–Fock theory to obtain self‐consistently the shifts and splittings of atomic levels. A first application of this theoretical program has been carried out on Na on the Al(100) system, by calculating from first principles the binding energies of the Na 1s and 2s electrons. For a coverage of 1.23 × 1014 adatoms/cm2 we find BE(1s) = 1075.2 eV and BE(2s) = 66.2 eV. Also, the Na 2p orbitals are found to split in the cylindrical symmetry by about 0.2 eV.
Reactivity comparison of one‐electron and two‐electron processes
Authors: Lee Tieh‐Sheng , Chu San‐Yan 
Published: December 2004

AbstractThe reaction activity is analyzed in terms of an electronic factor and a Franck–Condon factor, in analogy to that in problems of spectroscopy. A scheme for codifying a number of physical and chemical processes based on magnitude of the two factors is proposed. The electronic factor not only determines the topological feature of the potential surfaces, but also is capable of revealing certain clues leading to the mechanistic understanding from the type of operator involved. Based on such an analysis, it is concluded that all processes involving a one‐electron operator, either concerted or stepwise, may compete favorably with processes involving two‐electron operators. A forbidden reaction with a two‐electron process may therefore become a more efficient one‐electron process by either choosing a nonleast motion pathway, by carrying out the overall transformation stepwise, or by changing the occupation number of certain orbitals in the ionic form. The mechanisms of energy transfer in the excited state is also briefly discussed in terms of one‐electron and two‐electron processes.
Some considerations on Ueff values entering the hubbard hamiltonian
Authors: Friedel J. , Noguera C. 
Published: December 2004

AbstractOne of the simplest ways to take into account correlations between electrons in solid state physics, beyond the usual one electron approximation, is to use the Hubbard Hamiltonian

Although it corresponds to very severe approximations, since intersite correlations are neglected, and since the whole problem is reduced to a single parameter U, it is already very difficult to solve, and exact solutions exist in only a few cases. It is thus not desired to introduce more complications in the Hamiltonian; but it could be interesting to understand, at least qualitatively, which processes influence the value taken by parameter U. The question arises in concrete cases, such as transition metals or organic molecules; comparing experiments and approximate solutions of the Hubbard Hamiltonian has shown that, in most cases, the value of U that yields the best fit is very different from what would be expected from atomic considerations. For instance, if one wants to study correlations on atoms of type M, a pure atomic point of view would affect to U the change in energy Uat in the redox‐type equation

. However it seems that solid state effects play an important role and we discuss, in this paper, three of them: (i) the finite time that one electron spends on a given atom due to the delocalization of the electrons in a band (effect of βij which increases U relatively to Uat); (ii) the mixing of bands of different orbital character which allow two electrons not to be on the same orbital of an atom (and thus decreases U); and (iii) the existence of Coulomb repulsion between electrons on neighboring sites which reduces their effective exclusion on the same site.
Cluster calculations of the H2O/Pt(111) system
Authors: Paul J. , Rosén A. 
Published: December 2004

AbstractThe electronic interaction between water and a Pt(111) surface as evaluated for different Ptx(H2O)y clusters is discussed. Hartree–Fock–Slater (HFS) one‐electron ground state energies, ionization potentials, partial densities of states, and Mulliken occupation numbers are related to bonding shifts, as well as initial and final state screening for different orientations of the molecule. The formation of PtH2O bonds are sensitive to the orientation since surface oriented H atoms bridge the spatial separation between O 2p and Pt 5d orbitals and thus increase the intermixing of metal and adsorbate orbitals. The dipole moment and the net charge of the H2O molecule is also discussed. Finally, approximations of the metal–H2O potential for use in statistical models of the liquid–metal interface are suggested.
Comparison of theoretical and thermodynamic values of interconstituent interactions in DNA
Authors: Shibata Masayuki , Kieber‐Emmons Thomas , Rein Robert 
Published: December 2004

AbstractExperimental base stacking and hydrogen bonding enthalpies, as determined from double stranded DNA melting studies, are compared with theoretical calculations of interactions between the respective DNA interconstituent components. Comparisons are made in relation to the differences in magnitudes, sequence dependent spreads, and trends. It is shown that the use of an effective dielectric constant reconciles the differences between the experimental and theoretical values. Suggestions are made for calibration of potential functions suitable for nucleic acid conformational analysis.
Symmetry determined orbital and group overlap
Authors: Qianer Zhang 
Published: December 2004

AbstractThe MO theory of structural polyhedrons is one of the basic subjects closely related to the bonding theory of complex compounds and clusters. A series of valuable papers on this subject have been contributed by Hoffman, Wade, King, and Lauher et al. A method called “group overlap method” for constructing the symmetry orbitals and for calculating the group overlap integrals is proposed. It is hoped that the group overlap method may be used for the qualitative and quantitative MO study of structural polyhedrons.