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Gary Tresadern Paul F. Faulder M. Paul Gleeson Zubeir Tai Grant MacKenzie Neil A. Burton Ian H. Hillier 《Theoretical chemistry accounts》2003,109(3):108-117
Hybrid quantum mechanical (QM)/molecular mechanical (MM) calculations are used to study two aspects of enzyme catalysis,
Kinetic isotope effects associated with the hydride ion transfer step in the reduction of benzyl alcohol by liver alcohol
dehydrogenase are studied by employing variational transition-state theory and optimised multidimensional tunnelling. With
the smaller QM region, described at the Hartree–Fock ab initio level, together with a parameterised zinc atom charge, good
agreement with experiment is obtained. A comparison is made with the proton transfer in methylamine dehydrogenase. The origin
of the large range in pharmacological activity shown by a series of α-ketoheterocycle inhibitors of the serine protease, elastase,
is investigated by both force field and QM/MM calculations. Both models point to two different inhibition mechanisms being
operative. Initial QM/MM calculations suggest that these are binding, and reaction to form a tetrahedral intermediate, the
latter process occurring for only the more potent set of inhibitors.
Recieved 3 October 2001 / Accepted: 6 September 2002 / Published online: 31 January 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: I. H. Hillier
Acknowledgements. We thank EPSRC and BBSRC for support of the research and D.G. Truhlar for the use of the POLYRATE code. 相似文献
3.
Davor Margetić Ronlad N. Warrener Mirjana Eckert-Maksić Ivana Antol Zoran Glasovac 《Theoretical chemistry accounts》2003,109(4):182-189
DFT calculations of 7′–oxasesquinorbornenes and 7,7′-dioxasesquinorbornenes using the B3LYP/6–31G* method are reported.
All the investigated structures (syn- and anti- derivatives) showed significant non-planarity of the central double bond, with the exception of those anti-derivatives possessing symmetrical structures. The influence of the replacement of the methylene groups at position 7- of
the norbornene fragment with oxygen and the introduction of second and third (peripheral) double bonds and benzene rings on
the molecular and electronic structures of these molecules have also been investigated.
Received: 11 November 2002 / Accepted: 6 June 2002 /
Published online: 29 April 2003 相似文献
4.
Ab initio calculations have been performed to study the molecular structures and vibrational levels of the four low-lying
ionic states (1, 22Π, and 1, 22Σ+) of carbonyl sulfide. The global regions of the potential-energy surfaces have been obtained by multireference single and
double excitation configuration interaction calculations. Vibrational calculations using explicit vibrational Hamiltonians
have been used for vibrational analysis. The equilibrium molecular structures and a vibrational analysis of the four ionic
states are presented. The theoretical ionization intensity curves including the vibrational structures of the ionic states
are also presented and are compared with the photoelectron spectrum.
Received: 20 January 2001 / Accepted: 22 August 2001 / Published online: 30 October 2001 相似文献
5.
Pablo A. Molina R. Steven Sikorski Jan H. Jensen 《Theoretical chemistry accounts》2003,109(3):100-107
The relationship between hydrogen bonding and NMR chemical shifts in the catalytic triad of low-pH α-chymotrypsin is investigated
by combined use of the effective fragment potential [(2001) J Phys Chem A 105:293] and ONIOM–NMR [(2000) Chem Phys Lett 317:589] methods. Our study shows that while the His57 Nδ1−H bond is stretched by a relatively modest amount (to about 1.060 ?) this lengthening, combined with the polarization due
to the molecular environment, is sufficient to explain the experimentally observed chemical shifts of 18.2 ppm. Furthermore,
the unusual down-field shift of Hɛ1 (9.2 ppm) observed experimentally is reproduced and shown to be induced by interactions with the C=O group of Ser214 as previously
postulated. The free-energy cost of moving Hδ1 from His57 to Asp102 is predicted to be 5.5 kcal/mol.
Received: 26 September 2001 / Accepted: 6 September 2002 / Published online: 21 January 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: J. H. Jensen e-mail: jan-jensen@uiowa.edu
Acknowledgements. This work was supported by a Research Innovation Award from the Research Corporation and a type G starter grant from the
Petroleum Research Fund. The calculations were performed on IBM RS/6000 workstations obtained through a CRIF grant from the
NSF (CHE-9974502) and on supercomputers at the National Center for Supercomputer Applications at Urbana-Champaign. The authors
are indebted to Visvaldas Kairys for help with the CHARMM program, and to Daniel Quinn for many helpful discussions. 相似文献
6.
The recent “chemical energy component analysis” permits the total energy of a molecule to be presented approximately but
to good accuracy as a sum of atomic and diatomic energy contributions. Here the diatomic energy components are further decomposed
into terms of different physical origin: electrostatics (in point-charge approximation and the distributed charge corrections),
exchange effects, diatomic overlap and atomic basis extension terms. This analysis may provide us with a deeper insight into
the factors influencing both the chemical bonds and the nonbonded interatomic interactions.
Received: 6 May 2002 / Accepted: 13 November 2002 / Published online: 19 March 2003
Acknowledgements. The authors are indebted to the Hungarian Scientific Research Fund for partial financial support (grant no. OTKA T29716).
Correspondence to: I. Mayer e-mail: mayer@chemres.hu 相似文献
7.
The ground state and several low-lying excited states of the Mg2 dimer have been studied by means of a combination of the complete-active-space multiconfiguration self-consistent-field (CASSCF)/CAS
multireference second-order perturbation theory (CASPT2) method and coupled-cluster with single and double excitations and
perturbative contribution of connected triple excitations [CCSD(T)] scheme. Reasonably good agreement with experiment has
been obtained for the CCSD(T) ground-state potential curve but the dissociation energy of the only experimentally known A1Σ
u
+ excited state of Mg2 is somewhat overestimated at the CASSCF/CASPT2 level. The spectroscopic constants D
e, R
e and ωe deduced from the calculated potential curves for other states are also reported. In addition, some spin–orbit matrix elements
between the excited singlet and triplet states of Mg2 have been evaluated as a function of internuclear separation.
Received: 10 May 2001 / Accepted: 15 August 2001 / Published online: 30 October 2001 相似文献
8.
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
9.
The complexation of p-tert-butylphenyl p-tert-butylbenzoate and N-(p-tert-butylphenyl)-p-tert-butylbenzamide with a β-cyclodextrin derivative formed by two cyclodextrin units linked by a disulfide bridge on one of the
C6 atoms has been studied by computational methods. The better amide solubility and the better internal interactions of the
ester complex explain the experimentally observed better association constant for the ester. The free-energy perturbation
methodology and molecular mechanics/Poisson–Boltzmann surface area analysis have been used to explain the problem and to compare
the results.
Received: 14 April 2002 / Accepted: 11 August 2002 / Published online: 4 November 2002
Acknowledgements. The Kollman group at the University of California San Francisco is gratefully acknowledged for support and encouragement
throughout all this study. The authors thank UAB for inland and outland fellowships to I.B.. Financial support was obtained
from grant no. PPQ2000-0369 from the “Ministerio de Ciencia y Tecnologia” (Spain). Intensive computations were performed either
with the computers of the Kollman group or with those of CESCA-C4 (Catalonia, Spain).
Correspondence to: C. Jaime e-mail: carlos.jaime@uab.es 相似文献
10.
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
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W. A. de Jong R. J. Harrison J. A. Nichols D. A. Dixon 《Theoretical chemistry accounts》2001,107(1):22-26
A complete set of fully-relativistic benchmark results for the bond lengths and vibrational frequencies of uranyl at various
levels of correlation treatment are presented. It is shown that the relativistic and correlation effects are of the same magnitude
and should be treated on an equal footing. Results of uranyl calculations using various relativistic effective core potentials
(RECP) are presented. Appropriate choices for RECPs for use in density functional theory (DFT) calculations in the local density
approximation (LDA) and with the gradient-corrected B3LYP exchange-correlation functional are discussed. The conclusion is
reached that small-core RECPs need to be used and that the best results as compared to the benchmark values are obtained by
using a DFT functional that includes some fraction of Hartree-Fock Exchange.
Received: 18 May 2001 / Accepted: 25 July 2001 / Published online: 30 October 2001 相似文献
13.
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
14.
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
15.
Victor Polo Jürgen Gräfenstein Elfi Kraka Dieter Cremer 《Theoretical chemistry accounts》2003,109(1):22-35
Exchange functionals used in density functional theory (DFT) are generally considered to simulate long-range electron correlation
effects. It is shown that these effects can be traced back to the self-interaction error (SIE) of approximate exchange functionals.
An analysis of the SIE with the help of the exchange hole reveals that both short-range (dynamic) and long-range (nondynamic)
electron correlation effects are simulated by DFT exchange where the local density approximation (LDA) accounts for stronger
effects than the generalized gradient expansion (GGA). This is a result of the fact that the GGA exchange hole describes the
exact exchange hole close to the reference electron more accurately than the LDA hole does. The LDA hole is more diffuse,
thus leading to an underestimation of exchange and stronger SIE effects, where the magnitude of the SIE energy is primarily
due to the contribution of the core orbitals. The GGA exchange hole is more compact, which leads to an exaggeration of exchange
in the bond and the nonbonding region and negative SIE contributions. Partitioning of the SIE into intra-/interelectronic
and individual orbital contributions makes it possible to test the performance of a given exchange functional in different
regions of the molecule. It is shown that Hartree–Fock exchange always covers some long-range effects via interelectronic
exchange while self-interaction-corrected DFT is lacking these effects.
Received: 25 May 2002 / Accepted: 7 October 2002 / Published online: 21 January 2003
Correspondence to: E. Kraka e-mail: kraka@theoc.gn.se
Acknowledgements. This work was supported financially by the Swedish Natural Science Research Council (NFR). Calculations were done on the
supercomputers of Nationellt Superdatorcentrum (NSC), Link?ping, Sweden. The authors thank the NSC for a generous allotment
of computer time. 相似文献
16.
Friedrich Grein 《Theoretical chemistry accounts》2003,109(5):274-277
Using 6-31G and 6-311G basis sets to which diffuse and polarization functions were added in a stepwise fashion (a total of
16 basis sets), Hartree–Fock (HF), MP2 and B3LYP geometry optimizations were performed on biphenyl. With the MP2 method, diffuse
functions raise the dihedral angle φ, for example, from 46.3° for 6-31G to 54.1° for 6-311++G, while polarization functions
lower it, for example, from 54.1° for 6-311++G to 42.1° for 6-311++G(2d,2p). For a single set of polarization functions, φ(MP2)
lies close to or above φ(HF) (44–47°), but for a double set it is below φ(HF) and is close to B3LYP values (38–42°) which
show little basis set dependence. The most reliable value for φ, 42.1° [MP2/6-311++G(2d,2p)], is expected to increase slightly
by adding more diffuse functions. The corresponding best calculated energy barrier at 0° (coplanar conformation) is 2.83 kcal/mol,
much higher than the experimental estimate (1.4 ± 0.5 kcal/mol). The barrier at 90° is 1.82 kcal/mol, in line with the experimental
estimate (1.6 ± 0.5 kcal/mol) and with previous theoretical results.
Received: 9 September 2002 / Accepted: 15 November 2002 /
Published online: 1 April 2003
Correspondence to: Friedrich Grein e-mail: fritz@unb.ca
Acknowledgement. The author would like to thank NSERC (Canada) for financial support. 相似文献
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Daniel M. Chipman 《Theoretical chemistry accounts》2002,107(2):80-89
Alternative ways are examined for representing a reaction field to treat the important effects of long-range electrostatic
interaction with a solvent in electronic structure calculations on the properties of a solute. Several extant boundary element
methods for approximate representation of the solvent reaction field in terms of surface charge distributions are considered,
and analogous new methods for approximate representation in terms of surface dipole distributions are introduced. Illustrative
computational results are presented on representative small neutral and ionic solutes to evaluate the relative accuracy of
various methods.
Received: 2 July 2001 / Accepted: 10 September 2001 / Published online: 19 December 2001 相似文献
19.
Methods are described to incorporate solvent reaction field effects into solute electronic structure calculations. Included
are several old and new approaches based on approximate solutions of Poisson's equation through boundary element methods,
wherein the solutions are represented in terms of certain apparent surface charge or apparent surface dipole distributions.
Practical algorithms to set up and solve the requisite equations are described and implemented in a new general reaction field
computer program. Illustrative computational results are presented to show the performance of the program.
Received: 2 July 2001 / Accepted: 11 September 2001 / Published online: 19 December 2001 相似文献
20.
The self-interaction error (SIE) of commonly used density functional theory (DFT) exchange functionals mimics long-range
(nondynamic) pair correlation effects in an unspecified way. Slater exchange suffers from a larger SIE and, therefore, covers
more nondynamic correlation effects than Becke exchange, which is the reason why exchange–correlation (XC) functionals based
on Slater exchange lead to stabler restricted DFT solutions than those based on Becke exchange. However, the stability of
an XC functional does not guarantee higher accuracy. On the contrary, if system-specific nondynamic correlation effects have
to be introduced via the form of the wave function, these will be suppressed by nondynamic correlation effects already covered
by the exchange functional. Hybrid functionals suffer less from the SIE and, therefore, cover a smaller number of nondynamic
electron correlation effects. Accordingly, they are better suited when nondynamic electron correlation has to be introduced
by the form of the wave function. It is shown that, for example, broken-symmetry unrestricted DFT calculations are more accurate
when carried out with B3LYP than BLYP contrary to claims made in the literature.
Received: 8 November 2001 / Accepted: 30 January 2002 / Published online: 8 April 2002 相似文献