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1.
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
2.
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
3.
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
4.
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
5.
Jon Applequist 《Theoretical chemistry accounts》2002,107(2):103-115
The nature of the Maxwell–Cartesian spherical harmonics S
(n)
K
and their relation to tesseral harmonics Y
nm
is examined with the help of “tricorn arrays” that display the components of a totally symmetric Cartesian tensor of any
rank in a systematic way. The arrays show the symmetries of the Maxwell–Cartesian harmonic tensors with respect to permutation
of axes, the traceless properties of the tensors, the linearly independent subsets, the nonorthogonal subsets, and the subsets
whose linear combinations produce the tesseral harmonics. The two families of harmonics are related by their connection with
the gradients of 1/r, and explicit formulas for the transformation coefficients are derived. The rotational transformation of S
(n)
K
functions is described by a relatively simple Cartesian tensor method. The utility of the Maxwell–Cartesian harmonics in
the theory of multipole potentials, where these functions originated in the work of Maxwell, is illustrated with some newer
applications which employ a detracer exchange theorem and make use of the partial linear independence of the functions. The
properties of atomic orbitals whose angular part is described by Maxwell–Cartesian harmonics are explored, including their
angular momenta, adherence to an Uns?ld-type spherical symmetry relation, and potential for eliminating an angular momentum
“contamination” problem in Cartesian Gaussian basis sets.
Received: 9 July 2001 / Accepted: 7 September 2001 / Published online: 19 December 2001 相似文献
6.
A series of correlation-consistent basis sets are developed for Fe. Our best computed 5F–5D separation in the Fe atom is in excellent agreement with experiment. Our best estimate for the FeCO D
0 value is in good agreement with experiment. The 5Σ−–3Σ− separation in FeCO has an error of 3.6 kcal/mol; while the origin of this error is not clear, it is probably not due to the
basis set.
Received: 5 March 2001 / Accepted: 2 May 2001 / Published online: 9 August 2001 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.
Rois Benassi 《Theoretical chemistry accounts》2001,106(4):259-263
In order to calculate more accurately the enthalpies of formation, ΔH
f°(298 K), for large molecules using the CBS-4M method, a new formulation of the empirical higher-level correction to the energy
is proposed: ΔE=a|S|2
i
i
I
i
i
+b(n
α+n
β)+cΔ<S
2>+Σn
i
d
i
. The new methodology (CBS-4MB) applied to a set of 114 molecules of different size significantly decreases the mean absolute
deviation from 3.78 to 2.06 kcal/mol.
Received: 7 February 2001 / Accepted: 5 April 2001 / Published online: 13 June 2001 相似文献
9.
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
10.
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
11.
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
12.
Masao Masamura 《Theoretical chemistry accounts》2001,106(4):301-313
For the intermolecular interaction energies of ion-water clusters [OH−(H2O)
n
(n=1,2), F−(H2O), Cl−(H2O), H3O+(H2O)
n
(n=1,2), and NH4
+(H2O)
n
(n=1,2)] calculated with correlation-consistent basis sets at MP2, MP4, QCISD(T), and CCSD(T) levels, the basis set superposition
error is nearly zero in the complete basis set (CBS) limit. That is, the counterpoise-uncorrected intermolecular interaction
energies are nearly equal to the counterpoise-corrected intermolecular interaction energies in the CBS limit. When the basis
set is smaller, the counterpoise-uncorrected intermolecular interaction energies are more reliable than the counterpoise-corrected
intermolecular interaction energies. The counterpoise-uncorrected intermolecular interaction energies evaluated using the
MP2/aug-cc-pVDZ level is reliable.
Received: 14 March 2001 / Accepted: 25 April 2001 / Published online: 9 August 2001 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.
L. Delle Site 《Theoretical chemistry accounts》2002,107(6):378-380
In this work we comment on the statement about the nonuniqueness of the solution of Bader's equation for defining atoms in
molecules reported in the article of P. Cassam-Chena? and D. Jayatilaka in Theoretical Chemistry Accounts (2001) 105: 213–218
Received: 10 May 2001 / Accepted: 7 September 2001 / Published online: 3 June 2002 相似文献
15.
Steven M. Bachrach Joseph M. Hayes Trang Dao Justin L. Mynar 《Theoretical chemistry accounts》2002,107(5):266-271
Density functional calculations indicate that nucleophilic substitution in the thiolate–disulfide and thiolate–trisulfide
exchange reactions proceeds by an addition–elimination pathway. Solution calculations were performed using B3LYP/6-31+G* and
the polarized continuum method. These solution-phase calculations indicate that for the reactions where the sulfur under attack
bears a hydrogen atom, the substitution proceeds via an addition–elimination mechanism; however, when a methyl group is attached
to the sulfur under attack, the SN2 mechanism is predicted.
Received: 12 October 2001 / Accepted: 28 November 2001 / Published online: 8 April 2002 相似文献
16.
We have investigated the S0 and S1 electronic states in bacteriorhodopsin using a variety of QM/MM levels. The decomposition of the calculated excitation energies
into electronic and electrostatic components shows that the interaction of the chromophore with the protein electric field
increases the excitation energy, while polarization effects are negligible. Therefore, the experimentally observed reduction
in excitation energy from solution phase to protein environment (the Opsin shift) does not come from the electrostatic interaction
with the protein environment, but from either the interaction ofthe chromophore with the solvent or counter ion, or structural
effects. Our high-level ONIOM(TD– B3LYP:Amber) calculation predicts the excitation energy within 8 kcal/mol from experiment,
the discrepancy probably being caused by the neglect of polarization of the protein environment. In addition, we have shown
that the level of optimization is extremely critical for the calculation of accurate excitation energies in bacteriorhodopsin.
Received: 13 October 2001 / Accepted: 6 September 2002 / Published online: 3 February 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: K. Morokuma e-mail: morokuma@emory.edu 相似文献
17.
18.
Shigeyoshi Yamamoto Hiroshi Tatewaki Osamu Kitao Geerd H.F. Diercksen 《Theoretical chemistry accounts》2001,106(4):287-296
The Rydberg character of the excited states of free-base porphin (FBP) has been investigated by the ab initio configuration
interaction singles (CIS) method and the state-averaged complete-active-space self-consistent-field method. Double-zeta basis
sets augmented with s, p, and d Rydberg functions and d polarization functions have been employed. Two types of molecular
orbitals sets, the restricted Hartree–Fock molecular orbitals obtained for the ground state (1A
g
) and for the cation state (2A
u
), have been used in the CIS calculations. All the calculations show that Rydberg-type excitations play important roles especially
in the N bands. In this article we propose applying the model of a perturbed Rydberg series to interpret the excited states
of FBP. By using this model, we have succeeded in analyzing the characteristics of the excited states as well as the experimental
oscillator strengths, which have considerable magnitude even in the higher excited states.
Received: 27 November 2000 / Accepted: 11 April 2001 / Published online: 27 June 2001 相似文献
19.
The radial electron-pair intracule (relative motion) H(u) and extracule (center-of-mass motion) D(R) densities in position space were known to reveal four types of maxima which are related to the four inner electron shells,
K, L, M, and N, of atoms. The corresponding radial electron-pair intracule Hˉ(v) and extracule Dˉ(P) densities in momentum space are studied for the 102 atoms from He (atomic number Z=2) to Lr (Z=103). The densities Hˉ(v) and Dˉ(P) are found to have either one maximum or two maxima, and the numbers of maxima in Hˉ(v) and Dˉ(P) are the same for 98 atoms. For these atoms, the locations υ
max and P
max and the heights Hˉ
max
and Dˉ
max
of the corresponding maxima satisfy the approximate relations υ
max ≅ 2P
max and Hˉ
max
≅Dˉ
max
/2. On the basis of their Z-dependence, the maxima in Hˉ(v) and Dˉ(P) of the 102 atoms are classified into five types. Shell-pair decompositions of the radial densities show that these maxima
reflect five outer electron shells of atoms.
Received: 24 January 2001 / Accepted: 12 March 2001 / Published online: 13 June 2001 相似文献
20.
An algorithm is presented for the efficient evaluation of two types of one-center three-electron Gaussian integrals. These
integrals are required to avoid the resolution-of-identity (RI) approximation in explicitly correlated linear R12 methods.
Without the RI approximation, it is possible to enforce rigorously the strong orthogonality of the second-order M?ller–Plesset
R12 ansatz. A test calculation is performed using atomic Gaussian-type orbitals of the neon atom.
Received: 21 November 2000 / Accepted: 6 April 2001 / Published online: 9 August 2001 相似文献