Theoretical Chemistry: Current Research Articles

 
Current Articles in the field of Theoretical Chemistry published online in scientific journals.

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On this page considered biochemistry journals:

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.

Current research articles of the mentioned journals:

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 Hülsen, Universität zu Köln Institut für Theoretische Chemie Greinstr. 4 50939 Cologne Germany Anna Weigand, Universität zu Köln Institut für Theoretische Chemie Greinstr. 4 50939 Cologne Germany Michael Dolg, Universität zu Köln Institut für Theoretische Chemie Greinstr. 4 50939 Cologne Germany Journal Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) Online ISSN 1432-2234 Print ISSN 1432-881X Source: 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,mθ), entropy (S mθ), enthalpy of formation (Δf H mθ) and Gibbs free energy of formation (Δf G mθ). 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 Journal Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) Online ISSN 1432-2234 Print ISSN 1432-881X Source: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 23 Sep 2008 | 12:13 pm 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 Autónoma de México Instituto de Ciencias Nucleares Circuito Exterior, Ciudad Universitaria 04510 Mexico D.F. Mexico Abraham F. Jalbout, Universidad Nacional Autónoma de México Instituto de Ciencias Nucleares Circuito Exterior, Ciudad Universitaria 04510 Mexico D.F. Mexico Journal Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) Online ISSN 1432-2234 Print ISSN 1432-881X Source: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 18 Sep 2008 | 8:31 am 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, Universität zu Köln Institut für Theoretische Chemie Greinstr. 4 50939 Cologne Germany Michael Dolg, Universität zu Köln Institut für Theoretische Chemie Greinstr. 4 50939 Cologne Germany Journal Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) Online ISSN 1432-2234 Print ISSN 1432-881X Source: 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 1β, 2β, 6β, and 15β 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 6β-, 2β-, 15β-, and 1β-positions, respectively. The calculated barriers suggest the regioselectivity preference of 6β ≫ 2β > 15β > 1β, 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 Journal Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) Online ISSN 1432-2234 Print ISSN 1432-881X Source: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 18 Sep 2008 | 8:31 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 à l’Énergie Atomique 91191 Gif-sur-Yvette France Valérie Brenner, Laboratoire Francis Perrin, DSM/IRAMIS/SPAM-LFP (CEA-CNRS URA2453) Commissariat à l’Énergie Atomique 91191 Gif-sur-Yvette France Journal Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) Online ISSN 1432-2234 Print ISSN 1432-881X Source: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 11 Sep 2008 | 10:53 am 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. Content Type Journal Article Category Regular Article DOI 10.1007/s00214-008-0475-y Authors Miquel Llunell, Universitat de Barcelona Departament de Química Física, Institut de Química Teòrica i Computacional (IQTC) Martí i Franquès, 1-11 08028 Barcelona Catalonia Spain Pere Alemany, Universitat de Barcelona Departament de Química Física, Institut de Química Teòrica i Computacional (IQTC) Martí i Franquès, 1-11 08028 Barcelona Catalonia Spain Josep Maria Bofill, Universitat de Barcelona Departament de Química Orgànica, Institut de Química Teòrica i Computacional (IQTC) Martí i Franquès, 1-11 08028 Barcelona Catalonia Spain Journal Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) Online ISSN 1432-2234 Print ISSN 1432-881X Source: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 9 Sep 2008 | 10:58 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 Journal Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) Online ISSN 1432-2234 Print ISSN 1432-881X Source: 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 Journal Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) Online ISSN 1432-2234 Print ISSN 1432-881X Source: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 2 Sep 2008 | 8:01 am 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 Paweł Grochowski, University of Warsaw Interdisciplinary Centre for Mathematical and Computational Modelling 02-106 Warsaw Poland Journal Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) Online ISSN 1432-2234 Print ISSN 1432-881X Source: 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 Journal Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) Online ISSN 1432-2234 Print ISSN 1432-881X Source: 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 Théoriques, SRSMC Boulevard des Aiguillettes BP 239 54506 Vandoeuvre-lès-Nancy France Marilia T. C. Martins-Costa, Nancy-University, CNRS Equipe de Chimie et Biochimie Théoriques, SRSMC Boulevard des Aiguillettes BP 239 54506 Vandoeuvre-lès-Nancy France Philippe C. Gros, Nancy-University, CNRS Equipe de Synthèse Organométallique et Réactivité, SRSMC Boulevard des Aiguillettes BP 239 54506 Vandoeuvre-lès-Nancy France Yves Fort, Nancy-University, CNRS Equipe de Synthèse Organométallique et Réactivité, SRSMC Boulevard des Aiguillettes BP 239 54506 Vandoeuvre-lès-Nancy France Manuel F. Ruiz-López, Nancy-University, CNRS Equipe de Chimie et Biochimie Théoriques, SRSMC Boulevard des Aiguillettes BP 239 54506 Vandoeuvre-lès-Nancy France Journal Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) Online ISSN 1432-2234 Print ISSN 1432-881X Source: 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,R′N(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 Química Praça General Tibúrcio, 80 22290-270 Rio de Janeiro Brazil Journal Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) Online ISSN 1432-2234 Print ISSN 1432-881X Source: 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 Journal Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) Online ISSN 1432-2234 Print ISSN 1432-881X Source: 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 Journal Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) Online ISSN 1432-2234 Print ISSN 1432-881X Source: 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 Journal Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) Online ISSN 1432-2234 Print ISSN 1432-881X Source: 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 Autónoma Metropolitana-Iztapalapa Departamento de Química San Rafael Atlixco 186, Col. Vicentina, Iztapalapa C.P. 09340 Mexico D.F. Mexico Luis Gerardo Ruiz-Suárez, Universidad Nacional Autónoma de México Centro de Ciencias de la Atmósfera 04510 Mexico D.F. Mexico Annik Vivier-Bunge, Universidad Autónoma Metropolitana-Iztapalapa Departamento de Química San Rafael Atlixco 186, Col. Vicentina, Iztapalapa C.P. 09340 Mexico D.F. Mexico Journal Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) Online ISSN 1432-2234 Print ISSN 1432-881X Source: 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 Journal Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) Online ISSN 1432-2234 Print ISSN 1432-881X Source: 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 Química Médica (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 Química Médica (CSIC) Juan de la Cierva, 3 28006 Madrid Spain Jose Elguero, Instituto de Química Médica (CSIC) Juan de la Cierva, 3 28006 Madrid Spain Journal Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) Online ISSN 1432-2234 Print ISSN 1432-881X Source: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 22 Jul 2008 | 8:11 pm CEST

Evolution of class C β-lactamases: factors influencing their hydrolysis and recognition mechanisms Abstract  The most common bacterial resistance mechanism to β-lactam antibiotics is the production of β-lactamases. So far, β-lactamases have been classified into four different classes, three of them (A, C and D) have a serine in the active site as the nucleophilic group, which attacks to lactam antibiotic. Despite the large number of kinetic and theoretical studies and many native and complexed β-lactamases crystal structures, the mechanism by which they act is not well understood. The aim of this review is to show the different hypotheses which have been proposed to explain the hydrolysis mechanisms for class A and C lactamases and to cast light onto the interactions between the antibiotic and the Enterobacter cloacae P99 (a class C β-lactamase) in the Henry-Michaelis complex formed previous to the serine attack. Knowledge of these crucial points is essential for obtaining new β-lactam antibiotics not vulnerable to β-lactamases in order to minimize bacterial resistance. Content Type Journal Article Category Overview DOI 10.1007/s00214-008-0463-2 Authors Cristina Fenollar-Ferrer, Scuola Internazionale Superiore di Studi Avanzati (SISSA) Trieste Italy Juan Frau, Universitat Illes Balears Chemistry Department Edifici Mateu Orfila i Rotger 07122 Palma de Mallorca Islas Baleares Spain Josefa Donoso, Universitat Illes Balears Chemistry Department Edifici Mateu Orfila i Rotger 07122 Palma de Mallorca Islas Baleares Spain Francisco Muñoz, Universitat Illes Balears Chemistry Department Edifici Mateu Orfila i Rotger 07122 Palma de Mallorca Islas Baleares Spain Journal Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) Online ISSN 1432-2234 Print ISSN 1432-881X Source: Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) | 22 Jul 2008 | 8:11 pm CEST

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