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1.
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
2.
Strategies for computing chemical reactivity indices 总被引:3,自引:0,他引:3
Paul W. Ayers 《Theoretical chemistry accounts》2001,106(4):271-279
Two recent articles [(2000) J Am Chem Soc 122: 2010, (2001) J Am Chem Soc 123: 2007] have explored electron-density-based and external-potential-based chemical reactivity indices. In this article,
methods are presented for computing these indices from the output of a Kohn–Sham density functional theory calculation.
Received: 18 October 2000 / Accepted: 4 April 2001 / Published online: 9 August 2001 相似文献
3.
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
4.
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
5.
The partial Hessian vibrational analysis (PHVA), in which only a subblock of the Hesssian matrix is diagonalized to yield
vibrational frequencies for partially optimized systems, is extended to the calculation of vibrational enthalpy and entropy
changes for chemical reactions. The utility of this method is demonstrated for various deprotonation reactions by reproducing
full HVA values to within 0.1–0.4 kcal/mol, depending on the number atoms included in the PHVA. When combined with the hybrid
effective fragment potential method [Gordon MS, et al. (2001) J Phys Chem A 105:293–307], the PHVA method can provide (harmonic) free-energy changes for localized chemical reactions in very large systems.
Received: 21 September 2001 / Accepted: 30 October 2001 / Published online: 22 March 2002 相似文献
6.
José R. Mohallem 《Theoretical chemistry accounts》2002,107(6):372-374
It is shown that a supposed catastrophe of Bader's theory of atoms in molecules, suggested by Cassam-chena? and Jayatilaka
[Theor Chem Acc (2001) 105: 213] is merely a consequence of the approximate character of the adiabatic Born–Oppenheimer theory of molecular
structure, and that nonadiabatic approaches could be in accordance with Bader's ideas.
Received: 4 April 2001 / Accepted: 5 September 2001 / Published online: 3 June 2002 相似文献
7.
8.
Ramon Crehuet Josep Maria Bofill Josep Maria Anglada 《Theoretical chemistry accounts》2002,107(3):130-139
The mathematical structure of the reduced-gradient-following (RGF) path introduced by Quapp et al. (1988 J. Comput. Chem. 19:1087) is reviewed and analyzed. We report two new algorithms to evaluate the RGF path. The RGF path is also compared mathematically
and computationally with the gradient extremals path. An example of the evaluation of the RGF path is also reported.
Received: 21 May 2001 / Accepted: 27 September 2001 / Published online: 9 January 2002 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.
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
11.
Eugene S. Kryachko 《Theoretical chemistry accounts》2002,107(6):375-377
The article by P. Cassam-Chena? and D. Jayatilaka (Theor Chem Acc (2001) 105: 213) is critically analyzed.
Received: 18 April 2001 / Accepted: 9 September 2001 / Published online: 3 June 2002 相似文献
12.
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
13.
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
14.
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
15.
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
16.
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
17.
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
18.
Soluble polymers have been prepared that are designed to undergo enhanced rates of hydrolysis at pH values less than that
observed in blood circulation. The degradable element in the polymer mainchain is derived from cis-aconityl acid and is defined by a carboxylic acid pendent functionality (C-4) that is cis across a double bond to an amide
at C-1 in the polymer mainchain. While degradation studies in vitro have confirmed these polymers do undergo enhanced rates
of degradation at acidic pH values, there is also increasing evidence that during the degradation process the double bond
isomerises to the trans configuration and thus prevents the full degradation of a polymer. From a molecular modelling perspective
we are seeking to understand the propensity for this cis–trans isomerisation and the mechanism of this cis–trans isomerisation
is discussed.
Received: 29 April 2002 / Accepted: 6 September 2002 /
Published online: 14 February 2003 相似文献
19.
Contracted Gaussian-type function sets are developed for correlating p, d, and f functions for a valence electron of the
hydrogen atom and alkali-metal atoms from Li to Rb. A segmented contraction scheme is used for its compactness and efficiency.
Contraction coefficients and exponents are determined by minimizing the deviation from the K orbitals of the atoms. The present basis sets yield an accuracy comparable to the correlation-consistent basis set for the
hydrogen atom and also give a similar high accuracy for the alkali-metal atoms. In the calculations of spectroscopic constants
of alkali hydrides, the decontraction of the p function plays an important role, especially for LiH. The contributions of
d and f functions are nontrivial for KH and RbH.
Received: 6 September 2002 / Accepted: 13 November 2002 / Published online: 19 March 2003
Acknowledgements. This work was supported in part by a Grant-in-Aid for Scientific Research from the Ministry of Education of Japan.
Correspondence to: T. Noro e-mail: tashi@sci.hokudai.ac.jp 相似文献
20.
Variational calculations are reported for the ground states of the helium atom and its isoelectronic ions H−, Li+, …, Ne8+. The calculations use generalized Kinoshita expansions with freely optimized, noninteger powers of the Hylleraas coordinates
s and u. One hundred-term expansions of this type lead to better energies than any other expansions in the literature with comparable
numbers of terms.
Received: 4 September 2002 / Accepted: 14 October 2002 / Published online: 21 January 2003
Correspondence to: T. Koga e-mail: koga@mmm.muroran−it.ac.jp
Acknowledgements. This work was supported in part by the Natural Sciences and Engineering Research Council of Canada, and in part by a Grant-in-Aid
for Scientific Research from the Ministry of Education of Japan. The final 100-term computations with real powers were performed
at the Advanced Computational Research Laboratory of the University of New Brunswick. 相似文献