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1.
Patricia Amara Martin J. Field Cristobal Alhambra Jiali Gao 《Theoretical chemistry accounts》2000,104(5):336-343
Hybrid quantum mechanical (QM) and molecular mechanical (MM) potentials are becoming increasingly important for studying
condensed-phase systems but one of the outstanding problems in the field has been how to treat covalent bonds between atoms
of the QM and MM regions. Recently, we presented a generalized hybrid orbital (GHO) method that was designed to tackle this
problem for hybrid potentials using semiempirical QM methods [Gao et al. (1998) J Phys Chem A 102: 4714–4721]. We tested the method on some small molecules and showed that it performed well when compared to the purely
QM or MM potentials. In this article, we describe the formalism for the determination of the GHO energy derivatives and then
present the results of more tests aimed at validating the model. These tests, involving the calculation of the proton affinities
of some model compounds and a molecular dynamics simulation of a protein, indicate that the GHO method will prove useful for
the application of hybrid potentials to solution-phase macromolecular systems.
Received: 4 October 1999 / Accepted: 18 December 1999 / Published online: 5 June 2000 相似文献
2.
A technique for implementing the integrated molecular orbital and molecular mechanics (IMOMM) methodology developed by Maseras
and Morokuma that is used to perform combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations,
frequency calculations and simulations of macromolecules including explicit solvent is presented. Although the IMOMM methodology
is generalized to any coordinate system, the implementation first described by Maseras and Morokuma requires that the QM and
MM gradients be transformed into internal coordinates before they are added together. This coordinate transformation can be
cumbersome for macromolecular systems and can become ill-defined during the course of a molecular dynamics simulation. We
describe an implementation of the IMOMM method in which the QM and MM gradients are combined in the cartesian coordinate system,
thereby avoiding potential problems associated with using the internal coordinate system. The implementation can be used to
perform combined QM/MM molecular dynamics simulations and frequency calculations within the IMOMM framework. Finally, we have
examined the applicability of thermochemical data derived from IMOMM framework. Finally, we have examined the applicability
of thermochemical data derived from IMOMM frequency calculations.
Received: 11 May 1998 / Accepted: 14 August 1998 / Published online: 16 November 1998 相似文献
3.
The second-order correlation energy of M?ller–Plesset perturbation theory is computed for the neon atom using a wave function
that depends explicitly on the interelectronic coordinates (MP2-R12). The resolution-of-identity (RI) approximation, which
is invoked in the standard formulation of MP2-R12 theory, is largely avoided by rigorously computing the necessary three-electron
integrals. The basis-set limit for the second-order correlation energy is reached to within 0.1 mE
h. A comparison with the conventional RI-based MP2-R12 method shows that only three-electron integrals over s and p orbitals need to be computed exactly, indicating that the RI approximation can be safely used for integrals involving orbitals
of higher angular momentum.
Received: 9 May 2001 / Accepted: 31 October 2001 / Published online: 9 January 2002 相似文献
4.
Molecular mechanics minimizations based on the CVFF force field and molecular dynamics simulation for a time of 2.5 ns were
performed to examine the conformational behaviour and the molecular motion of acetylcholine in vacuo and in aqueous solution.
Five low-lying conformations, namely the TT, TG, GG, G*G and GT, were obtained from molecular mechanics computations with
the GT structure as the absolute minimum. Molecular dynamics trajectories in vacuo and in water show that only four (GT, GG,
G*G and TG) and three (TG, TT and GT) conformations are present in the simulation time, respectively. Density functional B3LYP
and second-order M?ller–Plesset (MP2) methods were then used to study all the five lowest-lying conformers of acetylcholine
neurotransmitter in vacuo and in water by the polarizable continuum model approach. The B3LYP and MP2 computations show that
in the gas phase all minima lie in a narrow range of energy with the G*G conformer as the most stable one. The relative minima
GG, GT, TG and TT are located at 1.1 (3.3), 1.8 (4.2), 2.1 (4.5) and 4.3 (7.3) kcal/mol above the absolute one at the B3LYP
(MP2) level. The preferred conformation in water is the TG. Solvation reduces the relative energy differences between the
five minima in both computations.
Received: 4 April 2001 / Accepted: 5 July 2001 / Published online: 30 October 2001 相似文献
5.
Jacqueline Langlet Jacqueline Bergès Jacqueline Caillet Jiri Kozelka 《Theoretical chemistry accounts》2000,104(3-4):247-251
This work is related to the interaction of water with two platinum(II) complexes, [Pt(NH3)4]2+ (denoted 1) and trans-[Pt(OH)2(NH3)2] (denoted 2). We have considered two approaches of a water molecule to complexes 1 and 2 along the z-axis normal to the platinum(II) coordination plane: approach I, with the water oxygen oriented towards Pt, and approach II,
with one water hydrogen directed towards Pt. Calculations have been performed within a molecular mechanics method based upon
the interaction potentials proposed earlier by Claverie et al. and subsequently adjusted to results obtained with symmetry
– adapted perturbational theory as well as with supermolecule (up to second-order M?ller–Plesset, MP2) methods. We discuss
some possible simplifications of the potentials mentioned. The results relative to the hydration of Pt complexes 1 and 2 following
approach I or II are discussed and compared to recent (MP2) ab initio energy–distance curves that we have recently determined.
The MP2 calculations have shown that besides exchange–repulsion contributions, which are very similar in all hydrated complexes,
approach I is mainly governed by electrostatics, whereas for approach II both electrostatic and dispersion contributions are
important.
Received: 16 September 1999 / Accepted: 3 February 2000 / Published online: 5 June 2000 相似文献
6.
Xianyang Chen Chongde Li Tao Wu Tianyang Yao Guanzhi Ju 《Theoretical chemistry accounts》1998,99(4):272-276
Ab initio molecular electronic structure methods have been used to study the relative stability of the planar inorganic ring
(HAlNH)n (n = 2–4) during homodesmotic and monomer polymerization reactions. Optimized geometries, frequencies and energies through
restricted Hartree-Fock/6-31G* are reported, and energies at the self-consistent field optimized geometries including M?ller-Plesset
fourth perturbation theory with single, double and quadruple excitation (MP4SDQ) corrections are also reported for both reactions.
Homodesmotic reactions with MP4SDQ −28.5 kcal/mol for (AlN)2, 1.9 kcal/mol for (AlN)3 and −0.97 kcal/mol for (AlN)4. On analysing a π-molecular orbitals diagram, only one, three and three strongly bonding π-molecular orbitals exist for the
planar four-, six- and eight-membered AlN rings, respectively.
Received: 9 March 1998 / Accepted: 19 March 1998 / Published online: 23 June 1998 相似文献
7.
The B3LYP/6-311G(d) and CCSD(T)/6-311G(2df) (single-point) methods have been used to investigate the singlet potential energy
surface of C2NP, in which seven stationary isomers and seventeen interconversion transition states are involved. At the final CCSD(T)/6-311G(2df)//B3LYP6-311G(d)
level with zero-point vibrational energy correction the lowest-lying isomer is a linear NCCP followed by two linear CNCP isomers
at 23.9 and CCNP at 65.8 kcal mol−1, respectively. The three isomers are kinetically very stable towards both isomerization and dissociation, and CCNP is even
more kinetically stable than CNCP – by 14.3 kcal mol−1 despite its high energy. Further comparative calculations were performed at the QCISD and QCISD(T) levels with the 6-311G(d)
and 6-311G(2d) basis sets to obtain more reliable structures and spectroscopy for the three isomers. The calculated bond lengths,
rotational constant, and dipole moment for NCCP were in close agreement with the experimentally determined values. Finally,
similarities and discrepancies between the potential energy surface of C2NP and those of the analogous species C2N2 and C2P2 were compared. The results presented in this paper might be helpful for future identification of the two still unknown yet
kinetically very stable isomers CNCP and CCNP, both in the laboratory and in interstellar space.
Received: 3 January 2001 / Accepted: 6 June 2001 / Published online: 30 October 2001 相似文献
8.
Kinetic isotope effects, KIEs, for hydrogen abstraction from C2H6 and C2D6 by chlorine atom have been studied by the dual-level direct dynamics approach. A low-level potential energy surface is obtained
with the MNDO-SRP method. High-level structural properties of the reactants, transition state, and products were obtained
at the MP2 level with the cc-pVDZ, aug-cc-pVDZ, and the cc-pVTZ basis sets. Using the variational transition state theory
with microcanonical optimized multidimensional tunneling, the values of deuterium KIE, at 300 K, range from 2.28 to 3.27,
in good agreement with the experimental values (2.69–5.88).
Received: 6 June 2001 / Accepted: 12 July 2001 / Published online: 19 November 2001 相似文献
9.
H. Strømsnes S. Jusuf A. Bagatur'yants O. Gropen U. Wahlgren 《Theoretical chemistry accounts》2001,106(5):329-338
The convergence of chemisorption energy for hydrogen and oxygen on gold clusters is studied. Two theoretical approaches have
been employed; wavefunction methods at the self-consistent-field second–order M?ller–Plesset level and density functional
theory and the two methods are compared. Relativistic effective core potentials exploited in the former approach were developed
in this work.
Received: 25 October 1999 / Accepted: 21 February 2001 / Published online: 11 October 2001 相似文献
10.
Low-spin/high-spin energy splittings for Fe(II) transition-metal complexes – particularly in weak ligand fields – cannot
be well described by density functional methods. Different density functionals yield results which differ by up to 1 eV in
transition-metal complexes with sulfur-rich first coordination spheres. We attribute this failure to the fact that the high-spin
state is systematically favoured in Hartree–Fock-type theories, because Fermi correlation is included in the exact exchange,
while Coulomb correlation is not. We thus expect that the admixture of exact exchange to a given density functional will heavily
influence the energy splitting between states of different multiplicity. We demonstrate that the energy splitting depends
linearly on the coefficient of exact exchange admixture. This remarkable result is found for all the Fe(II)–S complexes studied.
From this observation we conclude in connection with experimental results that Becke's 20% admixture should be reduced to
about 15% if meaningful energetics are sought for transition-metal compounds. We rationalize that this reduction by 5% will
not affect the quality of the hybrid functional since we arrive at a slightly modified functional, which lies between the
pure density functional and the hybrid density functional, which both give good results for “standard” systems.
Received: 13 July 2001 / Accepted: 31 August 2001 / Published online: 16 November 2001 相似文献
11.
Paul A. Rejto Djamal Bouzida Gennady M. Verkhivker 《Theoretical chemistry accounts》1999,101(1-3):138-142
Binding-energy landscapes are used to investigate the thermodynamics of molecular recognition for the pteridine ring, a recognition
anchor in binding with dihydrofolate reductase, and two molecules with the same shape but different heteroatom substitutions.
The relative importance of hydrogen bonding and hydrophobic interactions in this system is analyzed by comparing these three
different decorations of the pteridine scaffold.
Received: 5 May 1998 / Accepted: 3 September 1998 / Published online: 17 December 1998 相似文献
12.
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
13.
Molecular mechanics calculations were performed with the JUMNA program on d(GCGTGOGTGCG) · d(CGCACTCACGC) where “O” is a
modified abasic site: 3-hydroxy-2-(hydroxymethyl)tetrahydrofuran. From energy minimizations, for intrahelical or extrahelical
positions of the unpaired thymine, various structures with different curvatures were obtained. Dynamical properties of this
abasic sequence were also investigated through the controlled studies of DNA bending. Poisson-Boltzmann calculations were
used to mimic the electrostatic effect of solvent on this sequence. The lowest energy structures show an acceptable agreement
with experimental data.
Received: 1 June 1998 / Accepted: 17 September 1998 / Published online: 10 December 1998 相似文献
14.
Geometries and stabilization energies of various simple H-bonded complexes (water dimer, hydrogen fluoride dimer, formamide
dimer, formic acid dimer) have been determined by a gradient optimization that eliminates the basis set superposition error
(BSSE) by the counterpoise (CP) method in each gradient cycle as well as by the standard gradient optimization. Both optimization
methods lead to different potential energy surfaces (PES). The difference depends on the theoretical level used and is larger
if correlation energy is considered. Intermolecular distances from the CP-corrected PES are consistently longer, and this
difference might be significant (∼0.1 ?); also angular characteristics determined from both surfaces differ significantly.
Different geometries were obtained even when passing to larger basis sets (aug-cc-pVDZ). The standard optimization procedure
can result in a completely wrong structure. For example, the “quasi-linear” structure of the (HF)2 (global minimum) does not exist at the standard MP2/ 6-31G** PES (where only cyclic structure was detected) and is found
only at the CP-corrected PES. Stabilization energies obtained from the CP-corrected PES are always larger than these from
the standard PES where the BSSE is added only a posteriori for the final optimized structure; both energies converge only
when passing to a larger basis set (aug-cc-pVDZ).
Received: 11 March 1998 / Accepted: 19 June 1998 / Published online: 4 September 1998
RID="
ID=" <E6>Acknowledgements.</E6> The project was supported by the Grant Agency of the Czech Republic (Grant No. 203/98/1166).
RID="
ID=" <E5>Correspondence to</E5>: P. Hobza 相似文献
15.
Jean-Pierre Duneau Serge Crouzy Yves Chapron Monique Genest 《Theoretical chemistry accounts》1999,101(1-3):87-91
The structure and dynamics of the ErbB-2 transmembrane domain have been examined using molecular dynamics techniques both
in vacuum and within an explicit hydrated L-α-dilauroyl-phosphatidyl-ethanolamine environment. In-vacuum simulations show that a highly cooperative structural transition
occurs frequently within the α-helical transmembrane domain which converts to local π-helices. We show that the α-helix alteration
does not depend upon the force field or initial side-chain conformations but is intimately related to the sequence. The membrane-like
environment does not prevent the structural transition in the helix but slows down the peptide dynamics indicating that the
appearance of a π-bulge is not an artifact of the vacuum approximation. The consequences of π-helix formation could be very
huge for the ErbB-2 receptor which is involved in numerous human cancers and also for other membrane proteins wherein similar
local structures are also observed experimentally.
Received: 9 May 1998 / Accepted: 3 September 1998 / Published online: 17 December 1998 相似文献
16.
H. O. Bertrand A. Pullman K. Zakrzewska B. Hartmann S. Fermandjian 《Theoretical chemistry accounts》1999,101(4):269-273
Phosphorothioate DNAs, have emerged as a new class of potent drugs. They are obtained by the replacement of the anionic oxygens
of the phophodiester backbone by sulphur. A set of parameters has been developed for the FLEX force field implemented in JUMNA
10.0 to take into account the influence of sulphur on the structure of the DNA double helix. The consistency of our parameters
was tested by modelling a phosphorothioate oligomer namely d(GC)8. d(GC)8. Results, obtained on both R-pS and S-pS diastereoisomers, were compared to the phosphodiester counterpart and are in agreement with available experimental data.
Thus, our set of parameters seems suitable for further molecular modelling of other phosphorothioate oligomers.
Received: 15 July 1998 / Accepted: 8 September 1998 / Published online: 10 December 1998 相似文献
17.
18.
The full configuration interaction method in the space of fractionally occupied unrestricted natural orbitals (UNO-CAS method)
is extended to excited states as well as to strongly correlated and reactive systems with large active spaces. This is accomplished
by␣using restricted active space (RAS) wave functions introduced by Olsen et al. [(1988) J Chem Phys 89: 2185] and using the
UNOs without the expensive orbital optimization step. In RAS, the space of active orbitals is subdivided into three groups:
a group with essentially doubly occupied orbitals (RAS1), the usual CAS space (RAS2), and a space with weakly occupied active
orbitals (RAS3). We select these spaces on the basis of the occupation numbers of the UNOs. All possible electron distributions
are allowed in the usual CAS space, but the number of vacancies is limited in RAS1 and the number of electrons is limited
in RAS3. We discuss an efficient algorithm for generating a RAS wave function. This is based on the Handy-Knowles determinantal
expansion with an addressing scheme adopted for the restricted expansion. Results for both ground and excited states of azulene
and free base porphyrin are presented.
Received: 16 July 1998 / Accepted: 7 August 1998 / Published online: 19 October 1998 相似文献
19.
A computer program for the calculation of the MP2 energy correction for a Kramers-restricted Dirac-Hartree-Fock four component
wave-function is presented. In the spirit of the integral-driven direct SCF scheme the algorithm has been developed as direct
MP2, calculating integrals as they are needed and avoiding the integral storage bottle-neck of conventional MP2. Relativistic
MP2 is applied to ground state (1Σ+) CuF, AgF and AuF.
Received: 15 December 1996 / Accepted: 2 April 1997 相似文献
20.
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