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Theoretische Chemie - Aktuelle Forschungsartikel


 
Aktuelle Artikel (Abstracts) zur Forschung auf dem Gebiet der Theoretischen Chemie - veröffentlicht in wissenschaftlichen Fachzeitschriften.

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Auf dieser Seite beruecksichtige naturwissenschaftliche Journale:


Journal of Mathematical Chemistry - published by Springer -
JOMC publishes original, chemically important mathematical results which use non-routine mathematical methodologies often unfamiliar to the usual audience of mainstream experimental and theoretical chemistry journals.

Theoretical Chemistry Accounts - published by Springer -
TCA publishes papers in all fields of theoretical chemistry, computational chemistry, and modeling. Fundamental studies as well as applications are included in the scope.



Aktuelle wissenschaftliche Fachartikel der genannten Journale:


Theoretical studies on electronic structures and spectroscopic properties of a series of novel ÎČ-diketonate Os(II) complexes

Abstract  The geometries, electronic structures, and spectroscopic properties of a series of [Os(II)(CO)3(tfa)(acac(X)2)] (tfa = trifluoroacetate; acac = acetoylacetonate; X = H (1), CF3 (2), C6H5 (3), and C10H7 (4)) complexes have been investigated theoretically. The ground and excited state geometries were optimized at the B3LYP/LANL2DZ and CIS/LANL2DZ levels, respectively. The optimized geometry structural parameters agreed well with the corresponding experimental results. As indicated in this paper, the highest occupied molecular orbitals were dominantly localized on the Os atom, ctfa (abbv. of CO and tfa), and acac ligand for 1 and 2, acac ligand and X substituent for 3 and 4, while the lowest unoccupied molecular orbitals were mainly composed of acac ligand and X substituent. Under the time-dependent density functional theory (TDDFT) level with the polarized continuum model (PCM), the absorption and phosphorescence in CH2Cl2 media were calculated based on the optimized ground- and excited-state geometries, respectively. The calculated results show that the lowest energy absorptions at 317 (1), 342 (2), 377 (3), and 420 nm (4) are attributed to a change of ππ*/MLCT mixing transition to pure ππ* transition for 1–4, while their phosphorescence emission have similar transition properties. This indicates that the absorption and emission transition characters could be altered by adjusting the π electron-donating ability.

  • Content Type Journal Article
  • Category Regular Article
  • DOI 10.1007/s00214-008-0482-z
  • Authors
    • Jian-Po Zhang, Jilin University State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry Changchun 130023 People’s Republic of China
    • Xin Zhou, Jilin University State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry Changchun 130023 People’s Republic of China
    • Fu-Quan Bai, Jilin University State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry Changchun 130023 People’s Republic of China
    • Hong-Xing Zhang, Jilin University State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry Changchun 130023 People’s Republic of China
    • Au-Chin Tang, Jilin University State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry Changchun 130023 People’s Republic of China

Quelle: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 4 Oct 2008 | 11:25 am CEST

Analysis of a chemostat model with variable yield coefficient: Tessier kinetics

Abstract  We investigate a chemostat model in which the growth rate is given by a Tessier expression with a variable yield coefficient. We combine analytical results with path-following methods. The washout conditions are found. When washout does not occur we establish the conditions under which the reactor performance and reactor productivity are maximised. We also determine the parameter region in which oscillations may be generated in the reactor. We briefly discuss the implications of our results for comparing the performance of a single bioreactor against a cascade of two bioreactors.

  • Content Type Journal Article
  • Category Original Paper
  • DOI 10.1007/s10910-008-9463-7
  • Authors
    • M. I. Nelson, The University of Wollongong School of Mathematics and Applied Statistics Wollongong NSW 2522 Australia
    • H. S. Sidhu, UNSW at ADFA School of Physical, Environmental and Mathematical Science Canberra ACT 2600 Australia

Quelle: Journal of Mathematical Chemistry | 26 Sep 2008 | 8:14 am CEST

Zhang–Zhang polynomials of cyclo-polyphenacenes

Abstract  The Zhang–Zhang polynomial (i.e., Clar covering polynomial) of hexagonal systems is introduced by H. Zhang and F. Zhang, which can be used to calculate many important invariants such as the Clar number, the number of KekulĂ© structures and the first Herndon number, etc. In this paper, we give out an explicit recurrence expression for the Zhang–Zhang polynomials of the cyclo-polyphenacenes, and determine their Clar numbers, numbers of KekulĂ© structures and their first Herndon numbers.

  • Content Type Journal Article
  • Category Original Paper
  • DOI 10.1007/s10910-008-9466-4
  • Authors
    • Qiuzhi Guo, Hunan Normal University College of Mathematics and Computer Science Changsha Hunan 410081 People’s Republic of China
    • Hanyuan Deng, Hunan Normal University College of Mathematics and Computer Science Changsha Hunan 410081 People’s Republic of China
    • Dandan Chen, Hunan Normal University College of Mathematics and Computer Science Changsha Hunan 410081 People’s Republic of China

Quelle: Journal of Mathematical Chemistry | 25 Sep 2008 | 9:43 am CEST

Universality behaviour for polarity formation in channel-type inclusion compounds

Universality behaviour for polarity formation in channel-type inclusion compounds

  • Content Type Journal Article
  • Category Erratum
  • DOI 10.1007/s10910-008-9469-1
  • Authors
    • Athanasios Batagiannis, University of Berne Department of Chemistry and Biochemistry Freiestrasse 3 3012 Berne Switzerland
    • Thomas WĂŒst, University of Berne Department of Chemistry and Biochemistry Freiestrasse 3 3012 Berne Switzerland
    • JĂŒrg Hulliger, University of Berne Department of Chemistry and Biochemistry Freiestrasse 3 3012 Berne Switzerland

Quelle: Journal of Mathematical Chemistry | 25 Sep 2008 | 9:43 am CEST

A novel approach to measure all rate constants in the simplest enzyme kinetics model

Abstract  Enzymes play vital roles in life processes. Almost all biochemical reactions are mediated by enzymes. The rate constants of enzyme kinetics are the most important parameters for the reactions catalyzed by enzymes. In 1902, Adrian Brown proposed a simple single-substrate-single-product model which contains only three rate constants k 1, k −1 and k 2. So far, biologists can measure the Michaelis constant K M and the catalytic constant k cat , which actually is equal to k 2, according to Michaelis–Menten equation. Using temperature jump method or transient state kinetics, k 1, k −1 and k 2 can be determined. However, these methods are complicated. In this article, we design a novel simple method that could determine the rate constants k 1 and k −1 based on knowing k cat and K M . Our numerical experiments show that the three rate constants can be calculated rather precisely. Hence, we believe that biochemists could design experiments to measure the rate constants based on our method.

  • Content Type Journal Article
  • Category Original Paper
  • DOI 10.1007/s10910-008-9460-x
  • Authors
    • Banghe Li, Chinese Academy of Sciences Center of Bioinformatics and Key Laboratory of Mathematics Mechanization, Academy of Mathematics and Systems Science Beijing 100190 China
    • Bo Li, Chinese Academy of Sciences Center of Bioinformatics and Key Laboratory of Mathematics Mechanization, Academy of Mathematics and Systems Science Beijing 100190 China
    • Yuefeng Shen, Chinese Academy of Sciences Center of Bioinformatics and Key Laboratory of Mathematics Mechanization, Academy of Mathematics and Systems Science Beijing 100190 China

Quelle: Journal of Mathematical Chemistry | 25 Sep 2008 | 9:43 am CEST

Multiscale modeling of polymer materials using field-theoretic methodologies: a survey about recent developments

Abstract  Understanding the chemistry and physics of polymer systems challenges scientists from a wide spectrum of research areas, ranging from polymer science to molecular electronic structure theory. One of the characteristic features of polymer systems is that their physics involve a multitude of different length and time scales, which generally render the determination of their structure and physical properties on a detailed level computationally exhaustive. To overcome this difficulty, novel field-theoretic methodologies based on the mean field approximation have emerged recently and have proven to deliver useful results in the calculation of mesoscopic polymer models in the regime of high monomer concentrations. In this review we demonstrate that the field-theoretic approach is not only an useful formalism for treating highly concentrated polymer systems on the mesoscopic level of description, but that it is also a promising theoretical tool, to solve the multiscale problems arising in the calculation of physical properties of a wide variety of neutral and charged polymer materials. To this end, we show that the field-theoretic approach possesses the advantageous property to enable the treatment of all levels of description, spanning from the quantum to the continuum scale, within an unified theoretical framework. On the example of the coupling of the mesoscopic and continuum scale, we show that this specific feature constitutes a crucial advantage of field-theoretic approaches with regard to current state-of-the-art particle-based simulation methodologies for connecting different levels of description. Another major benefit relates to their favorable approximation characteristics, which permit to devise efficient approximation strategies for evaluating sophisticated polymer solution models in the low to moderate regime of monomer concentrations in a reliable way. To show this, we present novel low-cost approximation strategies beyond the mean field level of approximation using effective renormalization concepts, originating from the domain of quantum field theory, and demonstrate their usefulness in the calculation of structure and physical properties of several polymer models, described at various levels of description.

  • Content Type Journal Article
  • Category Original Paper
  • DOI 10.1007/s10910-008-9467-3
  • Authors
    • S. A. Baeurle, University of Regensburg Department of Chemistry & Pharmacy, Institute of Physical & Theoretical Chemistry 93053 Regensburg Germany

Quelle: Journal of Mathematical Chemistry | 25 Sep 2008 | 9:43 am CEST

Quasirelativistic energy-consistent 4f-in-core pseudopotentials for tetravalent lanthanide elements

Abstract  Quasirelativistic energy-consistent 4f-in-core pseudopotentials modeling tetravalent lanthanides (4f n−1 occupation with n = 1, 2, 3, 8, 9 for Ce, Pr, Nd, Tb, Dy) have been adjusted. Energy-optimized (6s5p4d) and (7s6p5d) valence basis sets contracted to polarized double- to quadruple-zeta quality as well as 2f1g correlation functions have been derived. Corresponding smaller (4s4p3d) and (5s5p4d) basis sets suitable for calculations on lanthanide(IV) ions in crystalline solids form subsets of these basis sets designed for calculations on neutral molecules. Calculations for lanthanide tetrafluorides using the 4f-in-core pseudopotentials at the Hartree–Fock level show satisfactory agreement with calculations using 4f-in-valence pseudopotentials. For cerium tetrafluoride the experimental bond length is well reproduced using the 4f-in-core pseudopotential at the coupled-cluster level with single and double excitation operators and a perturbative estimate of triple excitations. For cerium dioxide 4f-in-core and 4f-in-valence pseudopotential calculations agree quite well, if a proper f basis set instead of f polarization functions is applied.

  • Content Type Journal Article
  • Category Regular Article
  • DOI 10.1007/s00214-008-0481-0
  • Authors
    • Michael HĂŒlsen, UniversitĂ€t zu Köln Institut fĂŒr Theoretische Chemie Greinstr. 4 50939 Cologne Germany
    • Anna Weigand, UniversitĂ€t zu Köln Institut fĂŒr Theoretische Chemie Greinstr. 4 50939 Cologne Germany
    • Michael Dolg, UniversitĂ€t zu Köln Institut fĂŒr Theoretische Chemie Greinstr. 4 50939 Cologne Germany

Quelle: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 25 Sep 2008 | 9:23 am CEST

Thermodynamics of the gas-phase reactions in chemical vapor deposition of silicon carbide with methyltrichlorosilane precursor

Abstract  The gas-phase reaction thermodynamics in the chemical vapor deposition system of preparing silicon carbide via methyltrichlorosilane pyrolysis is investigated with a relatively complete set of 226 species, in which the thermodynamic data of 163 species are evaluated in this work with accurate model chemistry G3(MP2) and G3//B3LYP calculations combined with standard statistical thermodynamics. The data include heat capacity (C p,mΞ), entropy (S mΞ), enthalpy of formation (Δf H mΞ) and Gibbs free energy of formation (Δf G mΞ). All the results are consistent with the available reliable experiments. Based on these thermodynamic data, the equilibrium concentration distribution of the 226 possible species in 300–2,000 K is evaluated with the chemical equilibrium principle under a typical experimental condition. It is shown that the theoretical results are in very good agreement with the experiments. We conclude that the present work is instructive for experiments with different conditions.

  • Content Type Journal Article
  • Category Regular Article
  • DOI 10.1007/s00214-008-0478-8
  • Authors
    • Juanli Deng, Northwestern Polytechnical University School of Natural and Applied Sciences Xi’an Shaanxi 710072 People’s Republic of China
    • Kehe Su, Northwestern Polytechnical University School of Natural and Applied Sciences Xi’an Shaanxi 710072 People’s Republic of China
    • Xin Wang, Northwestern Polytechnical University School of Natural and Applied Sciences Xi’an Shaanxi 710072 People’s Republic of China
    • Qingfeng Zeng, Northwestern Polytechnical University National Key Laboratory of Thermostructure Composite Materials Xi’an Shaanxi 710072 People’s Republic of China
    • Laifei Cheng, Northwestern Polytechnical University National Key Laboratory of Thermostructure Composite Materials Xi’an Shaanxi 710072 People’s Republic of China
    • Yongdong Xu, Northwestern Polytechnical University National Key Laboratory of Thermostructure Composite Materials Xi’an Shaanxi 710072 People’s Republic of China
    • Litong Zhang, Northwestern Polytechnical University National Key Laboratory of Thermostructure Composite Materials Xi’an Shaanxi 710072 People’s Republic of China

Quelle: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 23 Sep 2008 | 12:13 pm CEST

Stability in generic mitochondrial models

Abstract  In this paper, we use a variety of mathematical techniques to explore existence, local stability, and global stability of equilibria in abstract models of mitochondrial metabolism. The class of models constructed is defined by the biochemical description of the system—an electron transport chain coupled to a process of charge translocation across a membrane. The conclusions are based on the reaction network structure, and we make minimal assumptions on the kinetics of the reactions involved. In the absence of charge translocation these models have previously been shown to behave in a very simple manner with a single, globally stable equilibrium. We show that with charge translocation the conclusion about a unique equilibrium remains true, but local and global stability do not necessarily follow. The length of the chains proves to be important: For short electron transport chains it is possible to make claims about local and global stability of the equilibrium which are no longer valid for longer chains. Some particular conditions which ensure stability of the equilibrium for chains of arbitrary length are presented.

  • Content Type Journal Article
  • Category Original Paper
  • DOI 10.1007/s10910-008-9464-6
  • Authors
    • Pete Donnell, University College London Department of Medical Physics and Bioengineering Gower Street London WC1E 6BT UK
    • Murad Banaji, University College London Department of Mathematics Gower Street London WC1E 6BT UK
    • Stephen Baigent, University College London Department of Mathematics Gower Street London WC1E 6BT UK

Quelle: Journal of Mathematical Chemistry | 23 Sep 2008 | 12:06 pm CEST

On the spectral radius of graphs with connectivity at most k

Abstract  In this paper, we study the spectral radius of graphs of order n with Îș(G) â‰€ k. We show that among those graphs, the maximal spectral radius is obtained uniquely at
Knk
, which is the graph obtained by joining k edges from k vertices of K n-1 to an isolated vertex. We also show that the spectral radius of
Knk
will be very close to n âˆ’ 2 for a fixed k and a sufficiently large n.

  • Content Type Journal Article
  • Category Original Paper
  • DOI 10.1007/s10910-008-9465-5
  • Authors
    • J. Li, Hong Kong Baptist University Department of Mathematics Kowloon Tong Hong Kong, People’s Republic of China
    • W. C. Shiu, Hong Kong Baptist University Department of Mathematics Kowloon Tong Hong Kong, People’s Republic of China
    • W. H. Chan, Hong Kong Baptist University Department of Mathematics Kowloon Tong Hong Kong, People’s Republic of China
    • A. Chang, Fuzhou University Software College/Center of Discrete Mathematics Fuzhou Fujian 350002 People’s Republic of China

Quelle: Journal of Mathematical Chemistry | 23 Sep 2008 | 12:06 pm CEST

Exact quantification of time signals from magnetic resonance spectroscopy by the fast Padé transform with applications to breast cancer diagnostics

Abstract  Mathematical modeling via the fast PadĂ© transform (FPT) is applied according to experimental NMR data encoded from (a) normal, non-infiltrated breast tissue, (b) benign pathology (fibroadenoma) and (c) malignant breast tissue. At a partial signal length N P  = 1500, the FPT provided exact reconstruction of all the input spectral parameters for the time signals corresponding to the normal, benign as well as to the malignant lesions. The converged parametric results remained stable at longer signal lengths. The PadĂ© absorption spectra yielded unequivocal resolution of all the extracted physical metabolites, even of those that were nearly completely overlapping (phosphocholine and phosphoethanolamine at 3.22 ppm). The capacity of the FPT to resolve and precisely quantify the physical resonances as encountered in normal versus benign versus malignant breast is demonstrated. In particular, the FPT unambiguously delineated and quantified diagnostically important metabolites such as lactate, as well as choline, phosphocholine and glycerophosphocholine that are very closely overlapping and may represent MR-retrievable molecular markers of breast cancer. This was achieved by the FPT without any fitting or numerical integration of peak areas. We conclude that these advantages of the FPT could be of definite benefit for breast cancer diagnostics via NMR and that this line of investigation should continue with encoded data from benign and malignant breast tissue, in vitro and in vivo. We anticipate that PadĂ©-optimized MRS will reduce the false positive rates of MR-based modalities and further improve their sensitivity. Once this is achieved, and given that MR entails no ionizing radiation, new possibilities for screening/early detection open up, especially for risk groups, e.g. PadĂ©-optimized MRS could be used with greater surveillance frequency among younger women with high breast cancer risk.

  • Content Type Journal Article
  • Category Original Paper
  • DOI 10.1007/s10910-008-9462-8
  • Authors
    • DĆŸevad Belkić, Karolinska Institute Department of Oncology-Pathology P.O. Box 260 Stockholm 17176 Sweden
    • Karen Belkić, Karolinska Institute Department of Oncology-Pathology P.O. Box 260 Stockholm 17176 Sweden

Quelle: Journal of Mathematical Chemistry | 23 Sep 2008 | 12:06 pm CEST

On resistance-distance and Kirchhoff index

Abstract  We provide some properties of the resistance-distance and the Kirchhoff index of a connected (molecular) graph, especially those related to its normalized Laplacian eigenvalues.

  • Content Type Journal Article
  • Category Original Paper
  • DOI 10.1007/s10910-008-9459-3
  • Authors
    • Bo Zhou, South China Normal University Department of Mathematics Guangzhou 510631 China
    • Nenad Trinajstić, The Rugjer BoĆĄković Institute P.O. Box 180 Zagreb 10002 Croatia

Quelle: Journal of Mathematical Chemistry | 20 Sep 2008 | 12:20 pm CEST

The kinetic energy operator in the subspaces of wavelet analysis

Abstract  At any resolution level of wavelet expansions the physical observable of the kinetic energy is represented by an infinite matrix which is “canonically” chosen as the projection of the operator  âˆ’ Î”/2 onto the subspace of the given resolution. It is shown, that this canonical choice is not optimal, as the regular grid of the basis set introduces an artificial consequence of its periodicity, and it is only a particular member of possible operator representations. We present an explicit method of preparing a near optimal kinetic energy matrix which leads to more appropriate results in numerical wavelet based calculations. This construction works even in those cases, where the usual definition is unusable (i.e., the derivative of the basis functions does not exist). It is also shown, that building an effective kinetic energy matrix is equivalent to the renormalization of the kinetic energy by a momentum dependent effective mass compensating for artificial periodicity effects.

  • Content Type Journal Article
  • Category Original Paper
  • DOI 10.1007/s10910-008-9458-4
  • Authors
    • JĂĄnos Pipek, Budapest University of Technology and Economics Department of Theoretical Physics, Institute of Physics 1521 Budapest Hungary
    • Szilvia Nagy, SzĂ©chenyi IstvĂĄn University Department of Telecommunication, Jedlik Ányos Institute of Informatics, Electrical and Mechanical Engineering Egyetem tĂ©r 1 9026 Gyor Hungary

Quelle: Journal of Mathematical Chemistry | 20 Sep 2008 | 12:20 pm CEST

Protochirons and protohelices

Abstract  A simple “protochiron” is used to systematically develop and describe molecular helices, especially on the cubic and diamond lattices.

  • Content Type Journal Article
  • Category Original Paper
  • DOI 10.1007/s10910-008-9382-7
  • Authors
    • Alexandru T. Balaban, Texas A&M University at Galveston 5007 Avenue U Galveston TX 77553-1675 USA
    • Kiran B. Chilakamarri, Texas Southern University Department of Mathematics Science Building 111G, 3100 Cleburne Street Houston TX 77004 USA
    • Douglas J. Klein, Texas A&M University at Galveston 5007 Avenue U Galveston TX 77553-1675 USA

Quelle: Journal of Mathematical Chemistry | 20 Sep 2008 | 12:20 pm CEST

Quasirelativistic energy-consistent 5f-in-core pseudopotentials for pentavalent and hexavalent actinide elements

Abstract  Quasirelativistic energy-consistent 5f-in-core pseudopotentials modeling pentavalent (5f n−2 occupation with n = 2–6 for Pa–Am) and hexavalent (5f n−3 occupation with n = 3–6 for U–Am) actinides have been adjusted. Energy-optimized (6s5p4d) and (7s6p5d) valence basis sets contracted to polarized double- to quadruple-zeta quality as well as 2f1g correlation functions have been derived. Corresponding smaller basis sets (4s4p3d) and (5s5p4d) suitable for calculations on actinide(V) and actinide(VI) ions in crystalline solids form subsets of these basis sets designed for calculations on neutral molecules. Calculations using the Hartree–Fock and the coupled-cluster method with single and double excitation operators and a perturbative estimate of triple excitations for actinide pentafluorides show satisfactory agreement with calculations using 5f-in-valence pseudopotentials and experimental data, respectively. However, in the hexavalent case the 5f-in-core approximation seems to reach its limitations except for hexavalent uranium (5f0), where results for both uranium hexafluoride and the uranyl ion deviate only slightly from the 5f-in-valence reference data.

  • Content Type Journal Article
  • Category Regular Article
  • DOI 10.1007/s00214-008-0477-9
  • Authors
    • Anna Moritz, UniversitĂ€t zu Köln Institut fĂŒr Theoretische Chemie Greinstr. 4 50939 Cologne Germany
    • Michael Dolg, UniversitĂ€t zu Köln Institut fĂŒr Theoretische Chemie Greinstr. 4 50939 Cologne Germany

Quelle: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 18 Sep 2008 | 8:31 am CEST

Metal induced molecular nano-extraction

Abstract  We have previously devised a “scorpion” like system which is composed of a zigzag (8,0) single walled carbon nanotube attached to a 20 ringed graphene sheet by a glycine dimer species. Theoretical density functional theory calculations on a potential mechanism driven by a metal induced charge transfer process has been proposed for the extraction of molecules from nanotubes.

  • Content Type Journal Article
  • Category Regular Article
  • DOI 10.1007/s00214-008-0470-3
  • Authors
    • Aned de Leon, Universidad Nacional AutĂłnoma de MĂ©xico Instituto de Ciencias Nucleares Circuito Exterior, Ciudad Universitaria 04510 Mexico D.F. Mexico
    • Abraham F. Jalbout, Universidad Nacional AutĂłnoma de MĂ©xico Instituto de Ciencias Nucleares Circuito Exterior, Ciudad Universitaria 04510 Mexico D.F. Mexico

Quelle: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 18 Sep 2008 | 8:31 am CEST

Regioselectivity preference of testosterone hydroxylation by cytochrome P450 3A4

Abstract  Theoretical studies are presented into the experimentally observed regioselectivity difference of testosterone hydroxylation by cytochrome P450 3A4 at the 1ÎČ, 2ÎČ, 6ÎČ, and 15ÎČ positions. Such regioselectivity is investigated by density functional theory calculations on a model system. The barrier heights of hydrogen abstraction, which are corrected by zero-point vibrational energies, are computed to be about 10.1, 13.6, 14.4, and 16.2 kcal/mol for the 6ÎČ-, 2ÎČ-, 15ÎČ-, and 1ÎČ-positions, respectively. The calculated barriers suggest the regioselectivity preference of 6ÎȠ≫ 2ÎČ > 15ÎČ > 1ÎČ, which is in good agreement with experimental findings.

  • Content Type Journal Article
  • Category Regular Article
  • DOI 10.1007/s00214-008-0480-1
  • Authors
    • Yan Zhang, University of Colorado Denver Chemistry Department PO Box 173364 Denver CO 80217 USA
    • Phani Morisetti, University of Colorado Denver Chemistry Department PO Box 173364 Denver CO 80217 USA
    • Jeffery Kim, University of Colorado Denver Chemistry Department PO Box 173364 Denver CO 80217 USA
    • Lynelle Smith, University of Colorado Denver Chemistry Department PO Box 173364 Denver CO 80217 USA
    • Hai Lin, University of Colorado Denver Chemistry Department PO Box 173364 Denver CO 80217 USA

Quelle: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 18 Sep 2008 | 8:31 am CEST

Omega polynomial and its use in nanostructure description

Abstract  A new counting polynomial, called “Omega” Ω (G, x), was recently proposed by Diudea. It is defined on the ground of quasi-orthogonal cut “qoc” edge strips. Three topological descriptors: (1) CI (Cluj-Ilmenau), eventually equal to the well-known PI index, in planar, bipartite graphs; (2) I Ω-defined on all the normalized derivatives of the above polynomial and (3) the coefficient of the first power term, called n p are exemplified and used in nanostructures (e.g., fullerenes, nanotubes and tori) description. Good ability of these descriptors in predicting the heat of formation and strain energy in small fullerenes or the resonance energy in planar benzenoids was found. Omega polynomial is useful in describing the topology of tubular nanostructures.

  • Content Type Journal Article
  • Category Original Paper
  • DOI 10.1007/s10910-008-9408-1
  • Authors
    • M. V. Diudea, Babes-Bolyai University Faculty of Chemistry and Chemical Engineering 400028 Cluj Romania
    • S. Cigher, Babes-Bolyai University Faculty of Chemistry and Chemical Engineering 400028 Cluj Romania
    • A. E. Vizitiu, Babes-Bolyai University Faculty of Chemistry and Chemical Engineering 400028 Cluj Romania
    • M. S. Florescu, Academy of Economic Sciences Bucharest Romania
    • P. E. John, Technical University of Ilmenau Institute of Mathematics 10 05 65 Ilmenau Germany

Quelle: Journal of Mathematical Chemistry | 18 Sep 2008 | 8:19 am CEST

Assessment of time-dependent density functional theory for predicting excitation energies of bichromophoric peptides: case of tryptophan-phenylalanine

Abstract  The ability of applied time-dependent density functional theory to predict the near-ultraviolet absorption spectrum of bichomophoric peptides in the gas phase has been tested by calculating the vertical excitation energies of the Tryptophan-Phenylalanine (Trp-Phe) dipeptide. We show that the contamination of the low-frequency part of the spectrum by spurious charge-transfer excitations depends both on the conformation of the peptide chain and the exchange-correlation approximation. For the most stable structure investigated, a hybrid density functional appears to eliminate a large proportion of the spurious states.

  • Content Type Journal Article
  • Category Regular Paper
  • DOI 10.1007/s00214-008-0479-7
  • Authors
    • Rodolphe Pollet, Laboratoire Francis Perrin, DSM/IRAMIS/SPAM-LFP (CEA-CNRS URA2453) Commissariat Ă  l’Énergie Atomique 91191 Gif-sur-Yvette France
    • ValĂ©rie Brenner, Laboratoire Francis Perrin, DSM/IRAMIS/SPAM-LFP (CEA-CNRS URA2453) Commissariat Ă  l’Énergie Atomique 91191 Gif-sur-Yvette France

Quelle: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 11 Sep 2008 | 10:53 am CEST

Diagonal coefficient representation of density functions and quantum similarity measures

Abstract  Quantum similarity measures within a new theoretical point of view are described for arbitrary order density functions, with the aid of attached pseudo-wave functions, in a vector semispace structure associated with a Minkowski metric.

  • Content Type Journal Article
  • Category Original Paper
  • DOI 10.1007/s10910-008-9441-0
  • Authors
    • Ramon CarbĂł-Dorca, Universitat de Girona Institut de QuĂ­mica Computacional Girona 17071 Catalonia Spain

Quelle: Journal of Mathematical Chemistry | 9 Sep 2008 | 1:17 pm CEST

Narcissistic reaction pathways: an example of Maxwell’s theorem of geometrical optics applied to the intrinsic reaction coordinate model

Abstract  Maxwell’s theorem and the concept of stigmatic transformations that appear in the theory of geometrical optics are extended to the intrinsic reaction coordinate model when it is applied to the specific case of narcissistic reactions. MediaObjects/214_2008_475_Figa_HTML.gif

  • Content Type Journal Article
  • Category Regular Article
  • DOI 10.1007/s00214-008-0475-y
  • Authors
    • Miquel Llunell, Universitat de Barcelona Departament de QuĂ­mica FĂ­sica, Institut de QuĂ­mica TeĂČrica i Computacional (IQTC) MartĂ­ i FranquĂšs, 1-11 08028 Barcelona Catalonia Spain
    • Pere Alemany, Universitat de Barcelona Departament de QuĂ­mica FĂ­sica, Institut de QuĂ­mica TeĂČrica i Computacional (IQTC) MartĂ­ i FranquĂšs, 1-11 08028 Barcelona Catalonia Spain
    • Josep Maria Bofill, Universitat de Barcelona Departament de QuĂ­mica OrgĂ nica, Institut de QuĂ­mica TeĂČrica i Computacional (IQTC) MartĂ­ i FranquĂšs, 1-11 08028 Barcelona Catalonia Spain

Quelle: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 9 Sep 2008 | 10:58 am CEST

On the derivative of the associated Legendre function of the first kind of integer degree with respect to its order (with applications to the construction of the associated Legendre function of the second kind of integer degree and order)

Abstract  The derivative of the associated Legendre function of the first kind of integer degree with respect to its order,
¶Pnm(z)/¶m
, is studied. After deriving and investigating general formulas for ÎŒ arbitrary complex, a detailed discussion of
[¶Pnm(z)/¶m]m = ±m
, where m is a non-negative integer, is carried out. The results are applied to obtain several explicit expressions for the associated Legendre function of the second kind of integer degree and order,
Qn±m(z)
. In particular, we arrive at formulas which generalize to the case of
Qn±m(z)
(0 ≀ m ≀ n) the well-known Christoffel’s representation of the Legendre function of the second kind, Q n (z). The derivatives
[¶2 Pnm(z)/¶m2]m = m,[¶Qnm(z)/¶m]m = m
and
[¶Q-n-1m(z)/¶m]m = m
, all with m > n, are also evaluated.

  • Content Type Journal Article
  • Category Original Paper
  • DOI 10.1007/s10910-008-9457-5
  • Authors
    • RadosƂaw Szmytkowski, GdaƄsk University of Technology Atomic Physics Division, Department of Atomic Physics and Luminescence, Faculty of Applied Physics and Mathematics Narutowicza 11/12 PL 80–952 Gdansk Poland

Quelle: Journal of Mathematical Chemistry | 9 Sep 2008 | 2:37 am CEST

Chemical trees minimizing energy and Hosoya index

Abstract  The energy of a molecular graph is a popular parameter that is defined as the sum of the absolute values of a graph’s eigenvalues. It is well known that the energy is related to the matching polynomial and thus also to the Hosoya index via a certain Coulson integral. It is quite a natural problem to minimize the energy of trees with bounded maximum degree—clearly, the case of maximum degree 4 (so-called chemical trees) is the most important one. We will show that the trees with given maximum degree that minimize the energy are the same that have been shown previously to minimize the Hosoya index and maximize the Merrifield-Simmons index, thus also proving a conjecture due to Fischermann et al. Finally, we show that the minimum energy grows linearly with the size of the trees, with explicitly computable growth constants that only depend on the maximum degree.

  • Content Type Journal Article
  • Category Original Paper
  • DOI 10.1007/s10910-008-9456-6
  • Authors
    • Clemens Heuberger, Technische UniversitĂ€t Graz Institut fĂŒr Mathematik B Graz Austria
    • Stephan G. Wagner, University of Stellenbosch Department of Mathematical Sciences Stellenbosch South Africa

Quelle: Journal of Mathematical Chemistry | 5 Sep 2008 | 7:46 pm CEST

Bifurcation in the stable manifold of the bioreactor with n th and m th order polynomial yields

Abstract  The three dimensional chemostat with nth and mth order polynomial yields, instead of the particular one such as A + BS, A + BS 2, A + BS 3, A + BS 4, A + BS 2 + CS 3 and A + BS n , is proposed. The existence of limit cycles in the two-dimensional stable manifold, the Hopf bifurcation and the stability of the periodic solution created by the bifurcation are proved.

  • Content Type Journal Article
  • Category Original Paper
  • DOI 10.1007/s10910-008-9455-7
  • Authors
    • Xuncheng Huang, Yangzhou Polytechnic University Yangzhou 225009 China
    • Lemin Zhu, Yangzhou Polytechnic University Yangzhou 225009 China

Quelle: Journal of Mathematical Chemistry | 5 Sep 2008 | 7:46 pm CEST

Calculation of two-center overlap integral in molecular coordinate system over Slater type orbital using Löwdin α -radial and Guseinov rotation–angular functions

Calculation of two-center overlap integral in molecular coordinate system over Slater type orbital using Löwdin α -radial and Guseinov rotation–angular functions

  • Content Type Journal Article
  • Category Erratum
  • DOI 10.1007/s10910-008-9449-5
  • Authors
    • B. A. Mamedov, Gaziosmanpaßa University Department of Physics, Faculty of Arts and Sciences Tokat Turkey
    • H. Koç, Gaziosmanpaßa University Department of Physics, Faculty of Arts and Sciences Tokat Turkey

Quelle: Journal of Mathematical Chemistry | 5 Sep 2008 | 7:46 pm CEST

Molecular quantum similarity measures in Minkowski metric vector semispaces

Abstract  Minkowski metric vector semispaces can be chosen as the natural mathematical framework, where quantum similarity measures are described and evaluated. The obtained results in this study show that the Minkowski metric option is easily feasible, providing a new set of computationally simpler expressions, computationally faster when compared with Euclidian based quantum similarity measures.

  • Content Type Journal Article
  • Category Original Paper
  • DOI 10.1007/s10910-008-9442-z
  • Authors
    • Ramon CarbĂł-Dorca, Universitat de Girona Institut de QuĂ­mica Computacional Girona 17071 Catalonia Spain

Quelle: Journal of Mathematical Chemistry | 4 Sep 2008 | 10:15 am CEST

Vibrational isotope effect by the low rank perturbation method

Abstract  Mathematical formalism of the Low Rank Perturbation method (LRP) is applied to the vibrational isotope effect in the harmonic approximation with a standard assumption that force field does not change under isotopic substitutions. A pair of two n-atom isotopic molecules A and B which are identical except for isotopic substitutions at ρ atomic sites is considered. In the LRP approach vibrational frequencies ω k and normal modes
|Yk ñ
of the isotopomer B are expressed in terms of the vibrational frequencies Μ i and normal modes
|Fi ñ
of the parent molecule A. In those relations complete specification of the normal modes
|Fi ñ
is not required. Only amplitudes
áts|Fi ñ
at sites τ affected by the isotopic substitutions and in the coordinate direction s (s = x, y, z) are needed. Out-of-plane vibrations of the (H,D)-benzene isotopomers are considered. Standard error of the LRP frequencies with respect to the DFT frequencies is on average
D » 0.48 cm-1
. This error is due to the uncertainty of the input data (± 0.5 cm−1) and in the absence of those uncertainties and in the harmonic approximation it should disappear. In comparing with experiment, one finds that LRP frequencies reproduces experimental frequencies of (H,D)-benzene isotopomers better (
DLRP » 4.74 cm-1
) than scaled DFT frequencies (
DDFT » 6.79 cm-1
) which are designed to minimize (by frequency scaling technique) this error. In addition, LRP is conceptually and numerically simple and it also provides a new insight in the vibrational isotope effect in the harmonic approximation.

  • Content Type Journal Article
  • Category Original Paper
  • DOI 10.1007/s10910-008-9445-9
  • Authors
    • Tomislav P. Ćœivković, Ruđer BoĆĄković Institute P.O.B. 180 10002 Zagreb Croatia

Quelle: Journal of Mathematical Chemistry | 4 Sep 2008 | 10:15 am CEST

Short- and long-range behavior of the inner and outer densities

Abstract  We report the short- and long-range behavior of the inner
r < (r)
and outer $$ \rho_>(r) $$ densities, which result from a rigorous partitioning of the spherically averaged one-electron density
r(r)
in many-electron atoms. It is found that for a small r,
r < (r)
has one-electron nature but $$ \rho_>(r) $$ has two-electron nature. For a large r, however, the opposite is true.

  • Content Type Journal Article
  • Category Regular Article
  • DOI 10.1007/s00214-008-0473-0
  • Authors
    • Toshikatsu Koga, Muroran Institute of Technology Department of Applied Chemistry Muroran Hokkaido 050-8585 Japan
    • Hisashi Matsuyama, Muroran Institute of Technology Department of Applied Chemistry Muroran Hokkaido 050-8585 Japan

Quelle: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 3 Sep 2008 | 12:48 pm CEST

The interconversion mechanism between TcO3+ and TcO2+ core of 99mTc labeled amine-oxime (AO) complexes

Abstract  Density functional theory, employing B3LYP/DZVP and B3LYP/6-31G*(LANL2DZ for Tc), has been used to investigate the interconversion mechanism between formal TcO3+ and TcO2 + core of 99mTc labeled amine-oxime (AO) complex, in which two water molecules have been used to simulate the possible interconversion process. The obtained results indicate that the length of amine-amine hydrocarbon backbone of AO ligand has a significant influence on the stabilities of formal TcO3+ and TcO2 + complex. The interconversion process between TcO–BnAO and TcO2–BnAO has been amply discussed, which releases the useful information for the further investigation of the structure and hypoxic mechanism of 99mTc-HL91.

  • Content Type Journal Article
  • Category Regular Article
  • DOI 10.1007/s00214-008-0474-z
  • Authors
    • Hong-Mei Jia, Beijing Normal University Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry 100875 Beijing People’s Republic of China
    • De-Cai Fang, Beijing Normal University Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry 100875 Beijing People’s Republic of China
    • Yan Feng, Beijing Normal University Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry 100875 Beijing People’s Republic of China
    • Jian-Ying Zhang, Beijing Normal University Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry 100875 Beijing People’s Republic of China
    • Wen-Bo Fan, Beijing Normal University Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry 100875 Beijing People’s Republic of China
    • Lin Zhu, Beijing Normal University Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry 100875 Beijing People’s Republic of China

Quelle: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 2 Sep 2008 | 8:01 am CEST

A perspective on the link between the exchange(-correlation) hole and dispersion forces

Abstract  In a recent series of papers, Becke and Johnson have proposed an elegant model for London dispersion (van der Waals’) forces in terms of the exchange hole. A perspective on this work is presented here, showing how the exchange-correlation hole is naturally related to “conventional” perturbative approaches to dispersion. The key to establishing this link is the fluctuation-dissipation theorem, which allows the exchange-correlation hole to be related to the frequency-dependent linear response.

  • Content Type Journal Article
  • Category Original Paper
  • DOI 10.1007/s10910-008-9451-y
  • Authors
    • Paul W. Ayers, McMaster University Department of Chemistry Hamilton ON Canada L8S 4M1

Quelle: Journal of Mathematical Chemistry | 30 Aug 2008 | 12:22 pm CEST

Rotational symmetry of the molecular potential energy in the Cartesian coordinates

Abstract  We consider the molecular Born-Oppenheimer potential energy as a function of atomic Cartesian coordinates and discuss the non-stationary Hessian properties arising due to rotational symmetry. A connection with the extended Hessian theory is included. New applications of Cartesian representation for examining and correcting raw numerical Hessian data and a simple formulation of harmonic vibrational analysis of partially optimized systems are proposed. Exemplary calculations for the porphyrin molecule with an internal proton transfer are reported. We also develop the normal transformation method to incorporate the rotational symmetry into the approximate analytical potentials, which are parametrized in the Cartesian coordinates. The transformation converts the coordinates from the space fixed frame to the frame which translates and rotates with the molecule and is determined by the Eckart conditions. New simple analytical formulas for the first and second derivatives of the transformed potential are derived. This fast method can be used to calculate the potential and its derivatives in the simulations of chemical reaction dynamics in the space fixed Cartesian frame without the need to constrain the molecular rotation or to define the local non-redundant internal coordinates.

  • Content Type Journal Article
  • Category Regular Article
  • DOI 10.1007/s00214-008-0472-1
  • Authors
    • PaweƂ Grochowski, University of Warsaw Interdisciplinary Centre for Mathematical and Computational Modelling 02-106 Warsaw Poland

Quelle: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 27 Aug 2008 | 5:31 pm CEST

Core-valence correlating basis sets for alkali and alkaline earth metal atoms

Abstract  For 12 alkali and alkaline earth metal atoms from Li to Ra, contracted Gaussian-type function sets are developed for the description of correlations among the (n−1)s, (n−1)p, and ns electrons, where n is the principal quantum number of the outermost shell. A segmented contraction scheme is employed for the compactness and efficiency. Contraction coefficients and exponents are determined so that the deviation from accurate natural orbitals of the ground states is minimized. For heavy atoms from Cs to Ra, the spin-free relativistic effects are considered through the third-order Douglas–Kroll approximation. To test the present correlating sets, all-electron calculations are performed for the ground state of 12 diatomic hydrides, 6 alkali metal dimers, 4 alkaline earth metal oxides, and 12 diatomic fluorides. The calculated spectroscopic constants are in excellent agreement with the experimental values.

  • Content Type Journal Article
  • Category Regular Article
  • DOI 10.1007/s00214-008-0476-x
  • Authors
    • Takeshi Noro, Hokkaido University Division of Chemistry, Graduate School of Science Sapporo Hokkaido 060-0810 Japan
    • Masahiro Sekiya, Tomakomai Komazawa University Department of Intercultural Studies Tomakomai Hokkaido 059-1292 Japan
    • Toshikatsu Koga, Muroran Institute of Technology Department of Applied Chemistry Muroran Hokkaido 050-8585 Japan

Quelle: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 27 Aug 2008 | 5:31 pm CEST

Combined ab initio and classical molecular dynamics simulations of alkyl-lithium aggregates in ethereal solutions

Abstract  Molecular dynamics simulations of organolithium aggregates in solution are reported for the first time. We use a combined quantum/classical force field (the so-called QM/MM approach) and study ethyl-lithium aggregates in dimethyl ether (DME) solvent. The solutes are described at the Density Functional Theory level while solvent molecules are described using molecular mechanics. NVT Molecular Dynamics simulations at 200 K are carried out in the Born–Oppenheimer approximation. After equilibration, the production phase was run for 80 ps (monomer), 40 ps (dimer) and 26 ps (tetramer). The analysis of the results focuses on Li coordination as a function of aggregate size and we show that the total Li coordination number is always 4. No decoordination has been observed along the simulations. Fluctuations of the structures are predicted to be large in some cases and possible implications on reactivity are discussed.

  • Content Type Journal Article
  • Category Letter
  • DOI 10.1007/s00214-008-0471-2
  • Authors
    • Hassan K. Khartabil, Nancy-University, CNRS Equipe de Chimie et Biochimie ThĂ©oriques, SRSMC Boulevard des Aiguillettes BP 239 54506 Vandoeuvre-lĂšs-Nancy France
    • Marilia T. C. Martins-Costa, Nancy-University, CNRS Equipe de Chimie et Biochimie ThĂ©oriques, SRSMC Boulevard des Aiguillettes BP 239 54506 Vandoeuvre-lĂšs-Nancy France
    • Philippe C. Gros, Nancy-University, CNRS Equipe de SynthĂšse OrganomĂ©tallique et RĂ©activitĂ©, SRSMC Boulevard des Aiguillettes BP 239 54506 Vandoeuvre-lĂšs-Nancy France
    • Yves Fort, Nancy-University, CNRS Equipe de SynthĂšse OrganomĂ©tallique et RĂ©activitĂ©, SRSMC Boulevard des Aiguillettes BP 239 54506 Vandoeuvre-lĂšs-Nancy France
    • Manuel F. Ruiz-LĂłpez, Nancy-University, CNRS Equipe de Chimie et Biochimie ThĂ©oriques, SRSMC Boulevard des Aiguillettes BP 239 54506 Vandoeuvre-lĂšs-Nancy France

Quelle: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 15 Aug 2008 | 8:15 am CEST

Excited electronic and ionized states of the nitramide molecule, H2NNO2, studied by the symmetry-adapted-cluster configuration interaction method

Abstract  Symmetry-adapted-cluster configuration interaction (SAC-CI) wave functions were employed to compute 16 singlet and 13 triplet vertical transitions, and 14 ionized states including relative intensities of the nitramide molecule, H2NNO2. This molecule is the simplest neutral closed-shell molecule which has an N–NO2 bond and is a member of the nitramine family, R,Râ€ČN(NO2), an important class of energetic materials with practical applications. The present nitramide results showed strong similarities with the ones of the N, N-dimethylnitramine molecule, which has also an N–NO2 bond and was previously studied using the SAC-CI method. Experimental ultraviolet and photoelectron band spectra of the nitramide molecule could be successfully assigned. All the singlet transitions have valence character. The computed singlet and triplet transitions, excepting a singlet one, result from excitation originating in the four highest occupied molecular orbitals, which have close energies. Most of the singlet and triplet transitions involved mixing of singly excited configurations. The strongest computed transition, at 6.8 eV, is a mixture of two nπNO2 → π* configurations corresponding to excitations from the highest occupied molecular orbital (HOMO) to the first two virtual orbitals and has an optical oscillator strength value of 0.2665. The computed ionized states described the whole measured spectrum, have excellent agreement when compared with the measured ionization potentials and revealed an inversion of the ordering of the first states not expected according to Koopmanns’ theorem, thereby showing the limitations of the latter.

  • Content Type Journal Article
  • Category Regular Article
  • DOI 10.1007/s00214-008-0469-9
  • Authors
    • Itamar Borges, Instituto Militar de Engenharia Departamento de QuĂ­mica Praça General TibĂșrcio, 80 22290-270 Rio de Janeiro Brazil

Quelle: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 5 Aug 2008 | 9:09 am CEST

DFT and ab initio study on the reaction mechanism of CH2SH + O2

Abstract  The mechanism for the CH2SH + O2 reaction was investigated by DFT and ab initio chemistry methods. The geometries of all possible stationary points were optimized at the B3LYP/6-311+G(d,p) level, and the single point energy was calculated at the CCSD(T)/cc-pVXZ(X = D and T), G3MP2 and BMC-CCSD levels. The results indicate that the oxidation of CH2SH by O2 to form HSCH2OO is a barrierless process. The most favorable channel is the rearrangement of the initial adduct HSCH2OO (IM1) to form another intermediate H2C(S)OOH (IM3) via a five-center transition state, and then the C–O bond fission in IM3 leads to a complex CH2S. . .HO2 (MC1), which finally gives out to the major product CH2S + HO2. Due to high barriers, other products including cis- and trans-HC(O)SH + HO could be negligible. The direct abstraction channel was also determined to yield CH2S + HO2, with the barrier height of 22.3, 18.1 and 15.0 kcal/mol at G3MP2, CCSD(T)/cc-pVTZ and BMC-CCSD levels, respectively, it is not competitive with the addition channel, in which all stationary points are lower than reactant energetically. The other channels to produce cis- and trans-CHSH + HO2 are also of no importance.

  • Content Type Journal Article
  • Category Regular Article
  • DOI 10.1007/s00214-008-0466-z
  • Authors
    • Yi-Zhen Tang, Northeast Normal University Institute of Functional Material Chemistry, Faculty of Chemistry Renmin Road 5268 Changchun Jilin 130024 People’s Republic of China
    • Ya-Ru Pan, Northeast Normal University Institute of Functional Material Chemistry, Faculty of Chemistry Renmin Road 5268 Changchun Jilin 130024 People’s Republic of China
    • Jing-Yu Sun, Northeast Normal University Institute of Functional Material Chemistry, Faculty of Chemistry Renmin Road 5268 Changchun Jilin 130024 People’s Republic of China
    • Hao Sun, Northeast Normal University Institute of Functional Material Chemistry, Faculty of Chemistry Renmin Road 5268 Changchun Jilin 130024 People’s Republic of China
    • Rong-Shun Wang, Northeast Normal University Institute of Functional Material Chemistry, Faculty of Chemistry Renmin Road 5268 Changchun Jilin 130024 People’s Republic of China

Quelle: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 5 Aug 2008 | 9:09 am CEST

Prediction of NMR order parameters in proteins using weighted protein contact-number model

Abstract  In the NMR experiment, the protein backbone motion can be described by the N–H order parameters. Though protein dynamics is determined by a complex network of atomic interactions, we show that the order parameter of residues can be determined using a very simple method, the weighted protein contact number model. We computed for each Cα atom the number of neighboring Cα atoms weighted by the inverse distance squared between them. We show that the weighted contact number of each residue is directly related to its order parameter. Despite the simplicity of this model, it performs better than the other method. Since we can compute the order parameters directly from the topological properties (such as protein contact number) of protein structures, our study underscores a very direct link between protein topological structure and its dynamics.

  • Content Type Journal Article
  • Category Regular Article
  • DOI 10.1007/s00214-008-0465-0
  • Authors
    • Shao-Wei Huang, National Chiao Tung University Institute of Bioinformatics HsinChu 30050 Taiwan, ROC
    • Chien-Hua Shih, National Chiao Tung University Institute of Bioinformatics HsinChu 30050 Taiwan, ROC
    • Chih-Peng Lin, National Chiao Tung University Institute of Bioinformatics HsinChu 30050 Taiwan, ROC
    • Jenn-Kang Hwang, National Chiao Tung University Institute of Bioinformatics HsinChu 30050 Taiwan, ROC

Quelle: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 1 Aug 2008 | 8:09 am CEST

An exponential multi-reference wavefunction ansatz: connectivity analysis and application to N2

Abstract  A connectivity analysis for the exponential multi-reference wavefunction ansatz (MRexpT) (J Chem Phys 123:84102, 2005) is carried out. Assuming a complete model space and separating interactions carrying active labels the cluster operator carrying no active labels is fully connected. The valence (active) part of the MRexpT cluster operator, however remains disconnected. Consequently, the MRexpT correlation energy scales linearly with the number of non-active electrons as single reference coupled cluster does while MRexpT additionally can treat multi reference cases. Therefore, MRexpT should be well suited to be applied to a large number of molecular applications. Its applicability to periodic systems with multi-reference unit cells however seems to be limited. An application to the triple bond breaking of the N2 molecule is presented.

  • Content Type Journal Article
  • Category Regular Article
  • DOI 10.1007/s00214-008-0464-1
  • Authors
    • Michael Hanrath, University of Cologne Institute for Theoretical Chemistry Greinstraße 4 50939 Cologne Germany

Quelle: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 30 Jul 2008 | 10:11 am CEST

On the mechanism of the OH initiated oxidation of acetylene in the presence of O2 and NO x

Abstract  The mechanism of the oxidation of acetylene, in the presence of O2 and NO x , has been studied. Different levels of theory have been tested for the first step of the mechanism: the acetylene + OH radical reaction. Based on these results the meta-hybrid functional MPWB1K has been chosen for modeling all the other steps involved in the oxidation of acetylene. Different reaction paths have been considered and the one leading to glyoxal formation and OH regeneration is predicted to be the main channel, independently of the presence of NO x . Two different mechanisms were modeled to account for formic acid formation, both of them involving cyclic intermediates. According to the computed activation free energies, the three-membered intermediate seems to be more likely to occur than the four-membered one. However, reaction barriers are very high and only a very small proportion of formic acid is expected to be formed through such intermediates. In the presence of NO x , considered in this work for the first time, the main product of the tropospheric oxidation of acetylene is also expected to be glyoxal.

  • Content Type Journal Article
  • Category Regular Article
  • DOI 10.1007/s00214-008-0467-y
  • Authors
    • Annia Galano, Universidad AutĂłnoma Metropolitana-Iztapalapa Departamento de QuĂ­mica San Rafael Atlixco 186, Col. Vicentina, Iztapalapa C.P. 09340 Mexico D.F. Mexico
    • Luis Gerardo Ruiz-SuĂĄrez, Universidad Nacional AutĂłnoma de MĂ©xico Centro de Ciencias de la AtmĂłsfera 04510 Mexico D.F. Mexico
    • Annik Vivier-Bunge, Universidad AutĂłnoma Metropolitana-Iztapalapa Departamento de QuĂ­mica San Rafael Atlixco 186, Col. Vicentina, Iztapalapa C.P. 09340 Mexico D.F. Mexico

Quelle: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 29 Jul 2008 | 8:49 am CEST

Chemical reaction paths and calculus of variations

Abstract  The reaction path is an important concept of theoretical chemistry. We analyze different forms of reaction pathways in the light of the abstract theory of calculus of variations such as steepest descent from saddle point, the intrinsic reaction coordinate (IRC), Newton trajectory, variationally optimized reaction paths and others. The paper is both a mathematical review and a pointer to future research. Besides the theoretical definitions, we shortly discuss hints at the numerical effect of the definitions.

  • Content Type Journal Article
  • Category Regular Article
  • DOI 10.1007/s00214-008-0468-x
  • Authors
    • Wolfgang Quapp, University of Leipzig Mathematical Institute Johannis-Gasse 26 PF 10 09 20 04009 Leipzig Germany

Quelle: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 29 Jul 2008 | 8:49 am CEST

Inverse hydrogen bonds between XeH2 and hydride and fluoride derivatives of Li, Be, Na and Mg

Abstract  A theoretical study of the inverse hydrogen bonds complexes formed by the XeH2 molecule and hydride and fluoride derivatives of Li, Be, Na and Mg has been carried out by means of DFT (B3LYP/DGDZVP) and ab initio [MP2/DGDZVP and MP2/LJ18/6-311++G(2d,2p)] calculations. The complexes obtained present interaction energies up to −81 kJ/mol. The analysis of the electron density shows electron transfer from the XeH2 to the electron acceptor molecules. The calculated absolute chemical shieldings show the high sensitivity of the xenon atom upon complexation.

  • Content Type Journal Article
  • Category Regular Article
  • DOI 10.1007/s00214-008-0462-3
  • Authors
    • Fernando Blanco, Instituto de QuĂ­mica MĂ©dica (CSIC) Juan de la Cierva, 3 28006 Madrid Spain
    • Mohammad Solimannejad, Arak University Quantum Chemistry Group, Department of Chemistry 38156-879 Arak Iran
    • Ibon Alkorta, Instituto de QuĂ­mica MĂ©dica (CSIC) Juan de la Cierva, 3 28006 Madrid Spain
    • Jose Elguero, Instituto de QuĂ­mica MĂ©dica (CSIC) Juan de la Cierva, 3 28006 Madrid Spain

Quelle: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 22 Jul 2008 | 8:11 pm CEST


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