Aktuelle Artikel (Abstracts) zur Forschung auf dem Gebiet der Theoretischen Chemie - veröffentlicht in wissenschaftlichen Fachzeitschriften.
Die Urheberrechte und
Veroeffentlichungsrechte der in der nachfolgenden Liste aufgefuehrten
Fachartikel liegen bei den jeweiligen Verlagen, die am Ende des
jeweiligen Artikels
als Quelle genannt werden. Diese sind auch fuer die Inhalte
verantwortlich.
Hinweise zur Veroeffentlichung Ihrer
Pressmitteilung unter Internetchemie.Info entnehmen Sie bitte der
entsprechenden Info-Seite.
Diese Seite koennen Sie mit folgender Tastenkombination nach Stichwoertern
durchsuchen: <STRG> und <F>.
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:
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 ÏÏ*/MLCT mixing transition to pure ÏÏ* transition for 1â4, while their phosphorescence emission have similar transition properties. This indicates that the absorption and emission
transition characters could be altered by adjusting the Ï 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 Peopleâs Republic of China
Xin Zhou, Jilin University State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry Changchun 130023 Peopleâs Republic of China
Fu-Quan Bai, Jilin University State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry Changchun 130023 Peopleâs Republic of China
Hong-Xing Zhang, Jilin University State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry Changchun 130023 Peopleâs Republic of China
Au-Chin Tang, Jilin University State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry Changchun 130023 Peopleâs Republic of China
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
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 k1, kâ1 and k2. So far, biologists can measure the Michaelis constant KM and the catalytic constant kcat, which actually is equal to k2, according to MichaelisâMenten equation. Using temperature jump method or transient state kinetics, k1, kâ1 and k2 can be determined. However, these methods are complicated. In this article, we design a novel simple method that could determine
the rate constants k1 and kâ1 based on knowing kcat and KM. 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
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
Abstract Quasirelativistic energy-consistent 4f-in-core pseudopotentials modeling tetravalent lanthanides (4fnâ1 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 HartreeâFock 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
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 (Cp,mΞ), entropy (SmΞ), enthalpy of formation (ÎfHmΞ) and Gibbs free energy of formation (ÎfGmΞ). 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 300â2,000 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 Xiâan Shaanxi 710072 Peopleâs Republic of China
Kehe Su, Northwestern Polytechnical University School of Natural and Applied Sciences Xiâan Shaanxi 710072 Peopleâs Republic of China
Xin Wang, Northwestern Polytechnical University School of Natural and Applied Sciences Xiâan Shaanxi 710072 Peopleâs Republic of China
Qingfeng Zeng, Northwestern Polytechnical University National Key Laboratory of Thermostructure Composite Materials Xiâan Shaanxi 710072 Peopleâs Republic of China
Laifei Cheng, Northwestern Polytechnical University National Key Laboratory of Thermostructure Composite Materials Xiâan Shaanxi 710072 Peopleâs Republic of China
Yongdong Xu, Northwestern Polytechnical University National Key Laboratory of Thermostructure Composite Materials Xiâan Shaanxi 710072 Peopleâs Republic of China
Litong Zhang, Northwestern Polytechnical University National Key Laboratory of Thermostructure Composite Materials Xiâan Shaanxi 710072 Peopleâs Republic of China
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 systemâan 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
Abstract In this paper, we study the spectral radius of graphs of order n with Îș(G) †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 Kn-1 to an isolated vertex. We also show that the spectral radius of
Knk
will be very close to n â 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, Peopleâs Republic of China
W. C. Shiu, Hong Kong Baptist University Department of Mathematics Kowloon Tong Hong Kong, Peopleâs Republic of China
W. H. Chan, Hong Kong Baptist University Department of Mathematics Kowloon Tong Hong Kong, Peopleâs Republic of China
A. Chang, Fuzhou University Software College/Center of Discrete Mathematics Fuzhou Fujian 350002 Peopleâs Republic of China
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 TrinajstiÄ, The Rugjer BoĆĄkoviÄ Institute P.O. Box 180 Zagreb 10002 Croatia
Abstract At any resolution level of wavelet expansions the physical observable of the kinetic energy is represented by an infinite
matrix which is âcanonicallyâ chosen as the projection of the operator â 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
Abstract Quasirelativistic energy-consistent 5f-in-core pseudopotentials modeling pentavalent (5fnâ2 occupation with n = 2â6 for PaâAm) and hexavalent (5fnâ3 occupation with n = 3â6 for UâAm) 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 HartreeâFock 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
Abstract We have previously devised a âscorpionâ 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.
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 6ÎČ â« 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
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 lâĂnergie Atomique 91191 Gif-sur-Yvette France
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
Abstract Maxwellâs 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 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
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 Ό 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 Christoffelâs representation of the Legendre function of the second kind, Qn(z). The derivatives
[¶2Pnm(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
RadosĆaw Szmytkowski, GdaĆsk University of Technology Atomic Physics Division, Department of Atomic Physics and Luminescence, Faculty of Applied Physics and Mathematics Narutowicza 11/12 PL 80â952 Gdansk Poland
Abstract The energy of a molecular graph is a popular parameter that is defined as the sum of the absolute values of a graphâs 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 degreeâclearly, 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
Abstract The three dimensional chemostat with nth and mth order polynomial yields, instead of the particular one such as A + BS, A + BS2, A + BS3, A + BS4, A + BS2 + CS3 and A + BSn, 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
Calculation of two-center overlap integral in molecular coordinate system over Slater type orbital using Löwdin
α
-radial and Guseinov rotationâangular functions
Content Type Journal Article
Category Erratum
DOI 10.1007/s10910-008-9449-5
Authors
B. A. Mamedov, GaziosmanpaĆa University Department of Physics, Faculty of Arts and Sciences Tokat Turkey
H. Koç, GaziosmanpaĆa University Department of Physics, Faculty of Arts and Sciences Tokat Turkey
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
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 Ï atomic sites is considered. In the LRP approach vibrational frequencies Ïk and normal modes
|Yk
ñ
of the isotopomer B are expressed in terms of the vibrational frequencies Îœi 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 Ï 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 cmâ1) 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. ĆœivkoviÄ, RuÄer BoĆĄkoviÄ Institute P.O.B. 180 10002 Zagreb Croatia
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 TcOâBnAO and TcO2âBnAO 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 Peopleâs Republic of China
De-Cai Fang, Beijing Normal University Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry 100875 Beijing Peopleâs Republic of China
Yan Feng, Beijing Normal University Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry 100875 Beijing Peopleâs Republic of China
Jian-Ying Zhang, Beijing Normal University Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry 100875 Beijing Peopleâs Republic of China
Wen-Bo Fan, Beijing Normal University Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry 100875 Beijing Peopleâs Republic of China
Lin Zhu, Beijing Normal University Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry 100875 Beijing Peopleâs Republic of China
Abstract In a recent series of papers, Becke and Johnson have proposed an elegant model for London dispersion (van der Waalsâ) 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 âconventionalâ 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
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
PaweĆ Grochowski, University of Warsaw Interdisciplinary Centre for Mathematical and Computational Modelling 02-106 Warsaw Poland
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 (nâ1)s, (nâ1)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 DouglasâKroll 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
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 BornâOppenheimer 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.
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 NâNO2 bond and is a member of the nitramine family, R,RâČN(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 NâNO2 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 nÏNO2 â Ï* 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 Koopmannsâ 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
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 CâO 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 Peopleâs Republic of China
Ya-Ru Pan, Northeast Normal University Institute of Functional Material Chemistry, Faculty of Chemistry Renmin Road 5268 Changchun Jilin 130024 Peopleâs Republic of China
Jing-Yu Sun, Northeast Normal University Institute of Functional Material Chemistry, Faculty of Chemistry Renmin Road 5268 Changchun Jilin 130024 Peopleâs Republic of China
Hao Sun, Northeast Normal University Institute of Functional Material Chemistry, Faculty of Chemistry Renmin Road 5268 Changchun Jilin 130024 Peopleâs Republic of China
Rong-Shun Wang, Northeast Normal University Institute of Functional Material Chemistry, Faculty of Chemistry Renmin Road 5268 Changchun Jilin 130024 Peopleâs Republic of China
Abstract In the NMR experiment, the protein backbone motion can be described by the NâH 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
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 GreinstraĂe 4 50939 Cologne Germany
Abstract The mechanism of the oxidation of acetylene, in the presence of O2 and NOx, 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 NOx. 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 NOx, 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
Annik Vivier-Bunge, Universidad AutĂłnoma Metropolitana-Iztapalapa Departamento de QuĂmica San Rafael Atlixco 186, Col. Vicentina, Iztapalapa C.P. 09340 Mexico D.F. Mexico
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
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
â81 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.
