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1.
Georg Schreckenbach 《Theoretical chemistry accounts》2002,108(4):246-253
In this article the formal equivalence between the “gauge including atomic orbitals” (GIAO) and the simpler common gauge
(cg) formulations of the nuclear magnetic resonance (NMR) shielding tensor is proven. To be able to give this proof, one has
to assume exactly solved zeroth order quantum mechanical equations and complete basis sets. The proof of the equivalence has
been known in the literature for some time (e.g. S.T. Epstein `The variation method in quantum chemistry', Academic Press,
1974). However, our approach has the advantage that, by comparing the GIAO and cg methods, it provides insight into the para-
and diamagnetic contributions of the shielding. Thus, it yields justification for qualitative analysis schemes that have been
used to explain trends in chemical shifts. Our formal proof is based on density functional theory. However, it is argued that
very similar arguments should apply to other levels of theory as well.
Received: 25 June 2002 / Accepted: 18 July 2002 / Published online: 15 October 2002
Acknowledgments. The author would like to acknowledge Tom Ziegler, Calgary, for numerous discussions on the subject. The reviewer is acknowledged
for the insightful and detailed comments.
Correspondence to: G. Schreckenbach e-mail: schrecke@alcor.concordia.ca 相似文献
2.
Martin Gruebele 《Theoretical chemistry accounts》2003,109(2):53-63
Vibrational energy flow in organic molecules occurs by a multiple-time-scale mechanism that can be modeled by a single exponential
only in its initial stages. The mechanism is a consequence of the hierarchical structure of the vibrational Hamiltonian, which
leads to diffusion of vibrational wavepackets on a manifold with far fewer than the 3N−6 dimensions of the full vibrational state space. The dynamics are controlled by a local density of states, which does not
keep increasing with molecular size. In addition, the number of vibrational coordinates severely perturbed during chemical
reaction is small, leading to preservation of the hierarchical structure at chemically interesting energies. This regularity
opens up the possibility of controlling chemical reactions by controlling the vibrational energy flow. Computationally, laser
control of intramolecular vibrational energy redistribution can be modeled by quantum-classical, or by purely quantum-mechanical
models of the molecule and control field.
Received: 26 July 2002 / Accepted: 30 September 2002 / Published online: 2 December 2002
Electronic Supplementary Material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00214-002-0394-2.
Acknowledgements. This work was supported by NSF grant CHE 9986670.
Correspondence to: M. Gruebele e-mail: gruebele@scs.uiuc.edu 相似文献
3.
Starting with the Levinthal paradox, a brief introduction to the protein folding problem is presented. The existing theories
of protein folding, including the folding funnel scenario, are discussed. After briefly discussing different simulation studies
of model proteins, we discuss our recent work on the dynamics of folding of the model HP-36 (the chicken villin headpiece)
protein by using a simplified hydropathy scale. Special attention has been paid to the statics and dynamics of contact formation
among the hydrophobic residues. The results obtained from this simple model appear to be surprisingly similar to several features
observed in the folding of real proteins. The account concludes with a discussion of future problems.
Received: 28 April 2002 / Accepted: 11 August 2002 / Published online: 13 November 2002
Correspondence to: B. Bagchi e-mail: bbagchi@sscu.iisc.ernet.in
Acknowledgements. We thank Samir Pal and Arnab Mukherjee for many discussions and Arun Yethiraj for helpful suggestions. The financial support
from DST, India, is gratefully acknowledged. G. S. thanks CSIR for a research fellowship. 相似文献
4.
Molecular dynamics thermodynamic integration (MDTI) method and quantum chemical calculations at the density functional theory
B3LYP 6-31+(d,p) level, which included the Tomasi model of the solvent reaction field, were applied to study the tautomeric
equilibrium of Mannich base in methanol solution. The values obtained for the free-energy difference are in good agreement
with experimental data. However, the results from quantum mechanical calculations were not as good as the results of MDTI
simulations owing to inappropriate treatment of intermolecular hydrogen bonds between the solute molecule and the first shell
of solvent molecules in the Tomasi model of the solvent reaction field. The radial distribution functions between solute atoms
and solvent atoms confirmed the formation of hydrogen bonds between the solute molecule and surrounding methanol molecules
and indicated that the zwitterionic form is associated more with an organized solvent structure at the level of the first
solvation shell than is the molecular form.
Received: 26 April 2002 / Accepted: 9 September 2002 /
Published online: 31 March 2003 相似文献
5.
Michael A. Collins 《Theoretical chemistry accounts》2002,108(6):313-324
This paper reviews the construction of molecular potential-energy surfaces by an interpolation method which has been developed
over the last several years. The method uses ab initio quantum chemistry calculations of the molecular electronic energy in
an automated procedure to construct global potential- energy surfaces which can be used to simulate chemical reactions with
either classical or quantum dynamics. The methodology is explained and several applications are presented to illustrate the
approach.
Received: 22 February 2002 / Accepted: 2 May 2002 / Published online: 6 November 2002
Correspondence to: M. A. Collins e-mail: collins@rsc.anu.edu.au
Acknowledgements. The methods described in this overview are the result of collaborations with former members of my group, in particular with
Josef Ischtwan, Meredith Jordon, Keiran Thompson and Ryan Bettens. I am also indebted for inspiration gained from many discussions
with my colleagues Leo Radom and Donghui Zhang (National University of Singapore). This work has been supported by the Supercomputer
Facility of the Australian National University and the Australian Partnership for Advanced Computing. 相似文献
6.
Transition structures associated with the C-C bond-formation step of the proline-catalyzed intermolecular aldol reaction
between acetone and isobutyraldehyde have been studies using density functional theory methods at the B3LYP/6-31G** computational
level. A continuum model has been selected to represent solvent effects. For this step, which is the stereocontrolling and
rate-determining step, four reactive channels corresponding to the syn and anti arrangement of the active methylene of the
enamine relative to the carboxylic acid group of l-proline and the re and si attack modes to both faces of the aldehyde carbonyl group have been analyzed. The B3LYP/6-31G**
energies are in good agreement with experiment, allowing us to explain the origin of the catalysis and stereoselectivity for
these proline-catalyzed aldol reactions.
Received: 2 April 2002 / Accepted: 18 July 2002 / Published online: 11 October 2002
Acknowledgements. This work was supported by research funds provided by the Ministerio de Educación y Cultura of the Spanish Government by
DGICYT (project PB98–1429). All the calculations were performed on a Cray–Silicon Graphics Origin 2000 of the Servicio de
Informática de la Universidad de Valencia. We are most indebted to this center for providing us with computer capabilities.
Correspondence to: L. R. Domingo e-mail: domingo@utopia.uv.es 相似文献
7.
Recent advances in the study of short-lived reactive resonances are reviewed. Special emphasis is given to addressing the
question of how reactive resonances might be observed in molecular beam scattering experiments. Three case studies are presented
for simple triatomic systems that are believed to exhibit resonance phenomena: F + HD → D + HF, F + H2 → H + HF, and H + HD → D + H2. It is seen that reactive resonances do strongly influence collision observables, but in a different way for each case. At
this stage, there does not appear to be a unique resonance signature that can be applied to all reactions.
Received: 2 March 2002 / Accepted: 2 June 2002 / Published online: 17 October 2002
Acknowledgements. For their valuable input into the research discussed here, we are grateful to our collaborators, K. Liu, S.H. nk;Lee, F.
Dong, D.E. Manolopoulos, D, Skouteris, X. Yang, S. Harich, D. Dai, and C.C. Wang. This work was supported by the National
Science Foundation.
Correspondence to: R. T. Skodje e-mail: skokje@spot.colorado.edu 相似文献
8.
Joel M. Bowman 《Theoretical chemistry accounts》2002,108(3):125-133
In this overview I discuss recent advances as well as outstanding issues in reduced dimensionality quantum approaches to
reactive scattering. “Reduced dimensionality” in the present context signifies treating a subset of all degrees of freedom
(the most strongly coupled ones) by rigorous quantum methods and treating the remaining (weakly coupled) degrees of freedom
by a variety of approximate methods, ranging from simple, so-called energy shifts to more elaborate adiabatic treatments.
The most widely used example of this approach is termed “J-shifting”, and this overview will concentrate on this method and discuss its application and generalization to both “direct”
and “complex” reactions, exemplified by O(3P) + HCl and O(1D) + HCl, respectively. In addition, for O(3P) + HCl, resonances in the tunneling region, due to van der Waals wells, are discussed and their challenge to reduced dimensionality
methods is stressed. Another new aspect of the reduced dimensionality treatment of polyatomic reactions is the need to describe
anharmonicity in a consistent fashion. This is exemplified by the H + CH4 reaction.
Received: 3 February 2002 / Accepted: 8 April 2002 / Published online: 19 August 2002 相似文献
9.
A large succinic acid (HOOC(CH2)2COOH) matrix containing 7 × 7 × 7 unit cells with guest oligonucleotide AGCAGCT was modeled with molecular dynamics simulation
for infrared matrix-assisted laser desorption ionization. We simulated the laser heating of the succinic acid (this data is
still missing from the literature) with λ=2.94 μm infrared laser pulses and compared it to ultraviolet excitation. We did
this in order to elucidate the cluster formation of succinic acid in the gas phase in itself and around the analyte. At this
wavelength, the laser energy is coupled into the matrix through the OH vibrations of the carboxyl groups. The most pronounced
difference we observed at 1,500 K simulation is that infrared heating generates about 10–15 more succinic acid molecules bound
to the analyte in noncovalent complex form than the ultraviolet mode, which generates about 2 molecules thus bound. We report
energy redistribution within the matrix between the host and guest species as well as other dynamical properties. The parameter
and topology data for succinic acid that we used are reported and ready for use in CHARMM computer code environment for simulation.
Revised: 12 October 2001 / Accepted: 27 February 2002 / Published online: 13 June 2002 相似文献
10.
Xavier Fradera Jordi Poater Sílvia Simon Miquel Duran Miquel Solà 《Theoretical chemistry accounts》2002,108(4):214-224
This article presents an overview of recent advances in the study of electron pairing through the use of localization and
delocalization indices obtained from double integration over atomic basins of the exchange–correlation density in the framework
of the atoms-in-molecules theory. These localization and delocalization indices describe the intra- and interatomic distribution
of the electron pairs in a molecule. The main results of the application of these second-order indices to the analysis of
molecular structure and chemical reactivity are briefly reviewed. It is shown that localization and delocalization indices
represent a powerful tool to describe the electron-pair structure of molecules, which, in turn, provides deeper insight into
relevant chemical phenomena such as electron correlation effects and the formation of localized α, β electron pairs.
Received: 8 April 2002 / Accepted: 26 June 2002 / Published online: 6 September 2002
Acknowledgements. Financial help was furnished by the Spanish DGES projects no. PB98-0457-C02-01 and BQU2002-04112-C02-02. J.P. thanks the
Departament d'Universitats, Recerca i Societat de la Informació de la Generalitat de Catalunya for benefiting from a doctoral
fellowship, no. 2000FI-00582. M.S. is indebted to the Departament d'Universitats, Recerca i Societat de la Informació of the
Generalitat de Catalunya for financial support through the Distinguished University Research Promotion, 2001. We also thank
the Centre de Supercomputació de Catalunya for providing us with computing facilities.
Correspondence to: M. Solà e-mail: miquel.sola@udg.es 相似文献
11.
M.M. Hurley J.B. Wright G.H. Lushington W.E. White 《Theoretical chemistry accounts》2003,109(3):160-168
The accurate modeling of biological processes presents major computational difficulties owing to the inherent complexity
of the macromolecular systems of interest. Simulations of biochemical reactivity tend to require highly computationally intensive
quantum mechanical methods, but localized chemical effects tend to depend significantly on properties of the extended biological
environment – a regime far more readily examined with lower-level classical empirical models. Mixed quantum/classical techniques
are gaining in popularity as a means of bridging these competing requirements. Here we present results comparing two quantum
mechanics/molecular mechanics implementations (the SIMOMM technique of Gordon et al. as implemented in GAMESS, and the ONIOM
technique of Morokuma et al. found in Gaussian 98) as performed on the enzyme acetylcholinesterase and model nerve agents.
This work represents part of the initial phase of a DoD HPCMP Challenge project in which we are attempting to reliably characterize
the biochemical processes responsible for nerve agent activity and inhibition, thereby allowing predictions on compounds unrelated
to those already studied.
Received: 10 October 2001 / Accepted: 13 November 2002 / Published online: 1 April 2003
Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 222nd National Meeting of the American
Chemical Society, 2001
Correspondence to: M. M. Hurley e-mail: hurley@arl.army.mil 相似文献
12.
Evaluation of an ab initio quantum mechanical/molecular mechanical hybrid-potential link-atom method
Hybrid potentials have become a common tool in the study of many condensed-phase processes and are the subject of much active
research. An important aspect of the formulation of a hybrid potential concerns how to handle covalent bonds between atoms
that are described with different potentials and, most notably, those at the interface of the quantum mechanical (QM) and
molecular mechanical (MM) regions. Several methods have been proposed to deal with this problem, ranging from the simple link-atom
method to more sophisticated hybrid-orbital techniques. Although it has been heavily criticized, the link-atom method has
probably been the most widely used in applications, especially with hybrid potentials that use semiempirical QM methods. Our
aim in this paper has been to evaluate the link-atom method for ab initio QM/MM hybrid potentials and to compare the results
it gives with those of previously published studies. Given its simplicity and robustness, we find that the link-atom method
can produce results of comparable accuracy to other methods as long as the charge distribution on the MM atoms at the interface
is treated appropriately.
Received: 27 September 2002 / Accepted: 21 October 2002 / Published online: 8 January 2003
Correspondence to: M. J. Field e-mail: mjfield@ibs.fr
Acknowledgements. The authors thank the Institut de Biologie Structurale – Jean-Pierre Ebel, the Commissariat à l'Energie Atomique and the
Centre National de la Recherche Scientifique for support of this work. 相似文献
13.
Ab initio calculations with inclusion of correlation effects at the MP2/6-31G* level have been used to predict the interaction
energy of stacked cytosine dimer (C/C) as a function of twisting and sliding in the gas phase. Systematic calculations have
also been carried out on the solvation free energies of various rotated and translated C/C dimers using a polarized continuum
model approach at the HF/6-31G* level with a view to probe the role of various degrees of freedom on the free energy of solvation
of the C/C dimer. The interaction energy of the C/C dimer decreases upon changing from a parallel to an antiparallel conformation
in the gas phase. The 180°-rotated conformation has been found to be the most stable arrangement when compared to other rotated
positions. The rotated and translated dimers exhibit lower solvation free energy than the parallel conformation. The decrease
in the dipole moment upon rotation from the parallel to the antiparallel conformation indicates the cancellation of charge
distribution upon rotation in the z direction of one cytosine base with respect to the other. The calculation reveals that the present approach could not yield
association energy, ΔΔG
Asso, in a solvent medium. This may be due to the fact that in the case of floppy molecules the contribution from translational,
rotational and vibrational free energies plays a significant role in the calculation of ΔΔG
Asso.
Received: 13 December 2001 / Accepted: 25 March 2002 / Published online: 13 June 2002 相似文献
14.
Multicenter integrals appearing in the Hartree–Fock–Roothaan equations for molecules are calculated using different kinds
of series expansion formulas obtained from the expansions of integer and noninteger n Slater-type orbitals, in terms of Ψ
α
-exponential-type orbitals (where α=1, 0, –1, –2,...) at a displaced center, that form complete orthonormal sets and are represented by linear combinations of
integer n Slater-type orbitals. The convergence of these series is tested by calculating concrete cases. The accuracy of the results
is quite high for quantum numbers, screening constants, and location of orbitals.
Received: 13 February 2002 / Accepted: 11 March 2002 / Published online: 4 July 2002 相似文献
15.
Binding energies of helium, neon and atomic hydrogen encapsulated inside a C20 cage were calculated using an ab initio method at the B3LYP/6-31+G⋆ level of theory. The standard equilibrium constants for
the reactions of noble-gas atoms going into the C20 molecular cage have also been studied. The transition states for the reactions of C20 with hydrogen and helium were further obtained with an ab initio method at the B3LYP/6-31+G⋆ level and the rate constants
were estimated by using conventional transition-state theory. It was found that the hydrogen and helium atoms are extremely
difficult to put into the C20 cage. Once inside the cage, a helium atom can hardly get out, while a hydrogen atom can easily escape from the cage. The
results are expected to enrich fullerene science and be helpful for fullerene applications such as storage.
Received: 2 November 2002 / Accepted: 19 December 2002 /
Published online: 30 April 2003
Correspondence to: R. Q. Zhang, e-mail: aprqz@cityu.edu.hk
Acknowledgements. The work described in this paper was jointly supported by a grant from the City University of Hong Kong (project no. 7001222)
and a grant from the Research Grants Council of the Hong Kong Special Administrative Region, China (project no. 9040633/CityU,
1011/01P]. 相似文献
16.
Sequential Monte Carlo/quantum mechanical calculations are performed to study the solvent effects on the electronic absorption
spectrum of formamide (FMA) in aqueous solution, varying from hydrogen bonds to the outer solvation shells. Full quantum-mechanical
intermediate neglect of differential overlap/singly excited configuration interaction calculations are performed in the supermolecular
structures generated by the Monte Carlo simulation. The largest calculation involves the ensemble average of 75 statistically
uncorrelated quantum mechanical results obtained with the FMA solute surrounded by 150 water solvent molecules. We find that
the n → π* transition suffers a blueshift of 1,600 cm−1 upon solvation and the π → π* transition undergoes a redshift of 800 cm−1. On average, 1.5 hydrogen bonds are formed between FMA and water and these contribute with about 20% and about 30% of the
total solvation shifts of the n → π* and π → π* transitions, respectively. The autocorrelation function of the energy is used
to sample configurations from the Monte Carlo simulation, and the solvation shifts are shown to be converged values.
Received: 14 March 2002 / Accepted: 3 April 2002 / Published online: 24 June 2002 相似文献
17.
This paper reports a new AM1/d model for phosphorus that can be used to model nucleophilic attack of phosphates relevant
for biological phosphate hydrolysis reactions. The parameters were derived from a quantum dataset calculated with hybrid density-functional
theory [B3LYP/6-311++G(3df,2p)//B3LYP/6-31++G(d,p)] of phosphates and phosphoranes in various charge states, and on transitions
states for nucleophilic attacks. A suite of non-linear optimization methods is outlined for semiempirical parameter development
based on integrated evolutionary (genetic), Monte Carlo simulated annealing and direction set minimization algorithms. The
performance of the new AM1/d model and the standard AM1 and MNDO/d models are compared with the density-functional results.
The results demonstrate that the strategy of developing semiempirical parameters specific for biological reactions offers
considerable promise for application to large-scale biological problems.
Received: 15 January 2002 / Accepted: 6 September 2002 / Published online: 28 March 2003
Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 222nd National Meeting of the American
Chemical Society, 2001
Correspondence to: D.M. York e-mail: york@chem.umn.edu
Acknowledgements. D.M.Y. is grateful for financial support provided by the National Institutes of Health (grant 1R01-GM62248-01A1) and the
Donors of The Petroleum Research Fund, administered by the American Chemical Society, and the Minnesota Supercomputing Institute
through a 6-month research scholar award (X.L.). Computational resources were provided by the Minnesota Supercomputing Institute. 相似文献
18.
A method applying ab initio direct dynamics has been utilized in studying the hydrogen abstraction reaction HCN + OH → CN + H2O. The geometries of the reactants, products, and the transition state have been optimized at the QCISD/6-311G(d, p) level.
Single-point energies were further evaluated at the QCISD(T)/6-311+G(2df, 2p)//QCISD/6-311G(d, p) level. The barrier heights
for the forward and reverse reactions were predicted to be 15.95 and 7.51 kcal mol−1 at the QCISD(T)/6-311 + G(2df, 2p)//QCISD/6-311G(d, p) level, respectively. The reaction rate constants were calculated in
the temperature range from 298 to 4,000 K using the canonical variational transition-state theory with a small-curvature tunneling
correction. The results of the calculation show that the theoretical rate constants are in good agreement with experimental
data over the measured temperature range of 400–2,600 K.
Received: 18 August 2002 / Accepted: 30 August 2002 / Published online: 20 November 2002
Acknowledgements. Our thanks are due to D.G. Truhlar for providing the POLYRATE 8.2 program. This work was supported by the National Science
Foundation of China. We also thank D.C. Fang and Y. M. Xie for their valuable help, and P.R. Yan for reading our paper.
Correspondence to: Q. S. Li e-mail: qsli@mh.bit.edu.cn 相似文献
19.
Jordi Poater Miquel Solà Miquel Duran Xavier Fradera 《Theoretical chemistry accounts》2002,107(6):362-371
Localization, λ(A), and delocalization indices, δ(A,B), as defined in the atoms in molecules theory, are a convenient tool for the analysis of molecular electronic structure from
an electron-pair perspective. These indices can be calculated at any level of theory, provided that first- and second-order
electron densities are available. In particular, calculations at the Hartree–Fock (HF) and configuration interaction (CI)
levels have been previously reported for many molecules. However, λ(A) and δ(A,B) cannot be calculated exactly in the framework of Kohn–Sham (KS) density functional theory (DFT), where the electron-pair
density is not defined. As a practical workaround, one can derive a HF-like electron-pair density from the KS orbitals and
calculate approximate localization and delocalization indices at the DFT level. Recently, several calculations using this
approach have been reported. Here we present HF, CI and approximate DFT calculations of λ(A) and δ(A,B) values for a number of molecules. Furthermore, we also perform approximate CI calculations using the HF formalism to obtain
the electron-pair density. In general, the approximate DFT and CI results are closer to the HF results than to the CI ones.
Indeed, the approximate calculations take into account Coulomb electron correlation effects on the first-order electron density
but not on the electron-pair density. In summary, approximate DFT and CI localization and delocalization indices are easy
to calculate and can be useful in the analysis of molecular electronic structure; however, one should take into account that
this approximation increases systematically the delocalization between covalently bonded atoms, with respect to the exact
CI results.
Received: 13 February 2002 / Accepted: 24 April 2002 / Published online: 18 June 2002 相似文献
20.
Jing-yao Liu Ze-sheng Li Zhen-wen Dai Xu-ri Huang Chia-chung Sun 《Theoretical chemistry accounts》2002,108(3):179-186
The hydrogen-abstraction reaction C2H5F+O → C2H4F+OH has been studied by a dual-level direct dynamics method. For the reaction, three reaction channels, one for α-abstraction
and two for β-abstraction, have been identified. The potential-energy surface information is obtained at the MP2(full)/6-311G(d,p)
and PMP2(full)/6-311G(3df,3pd) (single-point) levels. By canonical variational transition-state theory, rate constants for
each reaction channel are calculated with a small-curvature tunneling correction. The total rate constant is calculated from
the sum of the individual rate constants and the temperature dependence of the branching ratios is obtained over a wide range
of temperatures from 300 to 5,000 K. The agreement of the rate constants with experiment is good in the experimental temperature
range from 1,000 to 1,250 K. The calculated results indicate that at low temperatures α-abstraction is most likely to be the
major reaction channel, while β-abstraction channels will significantly contribute to the whole reaction rate as the temperature
increases.
Received: 23 January 2002 / Accepted: 23 June 2002 / Published online: 20 September 2002 相似文献