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1.
Celestino Angeli Renzo Cimiraglia Maurizio Persico 《Theoretical chemistry accounts》1998,100(5-6):324-328
Within the frame of multireference perturbation configuration interaction we have developed a fast algorithm, based on diagrammatic
techniques, for the calculation of the first-order correction to the one-particle density matrix. As an example of an application
we have chosen the evaluation of the dipole moment of the CO molecule, where utilization of the first-order density is shown
to corroborate the variational calculation.
Received: 4 August 1998 / Accepted: 21 September 1998 / Published online: 16 November 1998 相似文献
2.
A homotopy method is presented that locates both minimizers and saddle points of energy functions in an efficient manner.
In contrast to other methods, it makes possible the exploration of large parts of potential energy surfaces. Along a homotopy
path stationary points of odd and even order occur alternately. A path tracing procedure requiring only gradients and at most
one evaluation of the Hessian matrix is given. Test results on a model potential and three MINDO/3 potentials are reported.
Received: 6 May 1996 / Accepted: 2 April 1998 / Published online: 23 June 1998 相似文献
3.
Hyo Weon Jang 《Theoretical chemistry accounts》1998,99(6):420-425
Novel parametrically energy-dependent boundary functions, F, combined with a finite L
2 basis set, permit accurate and efficient calculation of scattering wavefunctions for many energies. Both accuracy and efficiency
are achieved simultaneously because all the necessary integrals are energy-independent and also certain functionals, (H−E)|F>, in the Schr?dinger equation are allowed to satisfy desirable boundary conditions. In addition, slight modification of the
Schr?dinger equation in the boundary region is shown to be useful for improving the numerical accuracy when a cutoff-radius-truncated
basis set is used. The advantages of the present approaches are demonstrated for the one-dimensional Eckart barrier problem.
Received: 17 June 1998 / Accepted: 13 July 1998 / Published online: 18 September 1998 相似文献
4.
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
5.
Bernd Hartke 《Theoretical chemistry accounts》1998,99(4):241-247
By an application to small silicon clusters Si
N
(with N = 4,5,7,10) it is shown that truly global geometry optimization on an ab initio or density functional theory level can be achieved, at a computational cost of approximately
1–5 traditional local optimization runs (depending on cluster size). This extends global optimization from the limited area
of empirical potentials into the realm of ab initio quantum chemistry.
Received: 24 February 1998 / Accepted: 6 March 1998 / Published online: 17 June 1998 相似文献
6.
William T. G. Johnson David A. Hrovat Anne Skancke Weston Thatcher Borden 《Theoretical chemistry accounts》1999,102(1-6):207-225
Ab initio calculations on the lowest singlet and triplet states of 2,2-disilylcyclopentane-1,3-diyl find that the singlet
lies well below the triplet. The C
2 singlet diradical is calculated to be a minimum on the potential energy surface with an enthalpic barrier to ring closure
of ΔH
‡
298 = 13.5 kcal/mol at the CASPT2/6-31G* level of theory. The energy of the 1,3-divinyl-substituted singlet diradical is calculated
to be only 0.8 kcal/mol higher than that of 5,5-disilyl-1,3-divinylbicyclo[2.1.0]pentane at this level of theory, but the
transition state for their equilibration is computed to be 12.8 kcal/mol above the diradical in energy.
Received: 2 July 1998 / Accepted: 4 August 1998 / Published online: 16 November 1998 相似文献
7.
Jenn-Kang Hwang 《Theoretical chemistry accounts》1999,101(5):359-363
The Monte Carlo Fourier path integral approach has proved to be quite useful in calculating equilibrium thermodynamic properties.
One of its advantages is that it can be formulated in such a way as to include higher order terms using the partial averaging
technique, which includes the contribution from higher terms usually neglected by the discretized path integral approach.
In the original approach, the Feynman path integral is evaluated via a free-particle reference state. Here, using a new expression
for the Feynman paths expanded around a harmonic reference path, we derive an alternative formulation for the density matrix
element and its corresponding partial averaging expression.
Received: 16 September 1998 / Accepted: 30 October 1998 / Published online: 1 February 1999 相似文献
8.
Towards an order-N DFT method 总被引:5,自引:0,他引:5
C. Fonseca Guerra J. G. Snijders G. te Velde E. J. Baerends 《Theoretical chemistry accounts》1998,99(6):391-403
One of the most important steps in a Kohn-Sham (KS) type density functional theory calculation is the construction of the
matrix of the KS operator (the “Fock” matrix). It is desirable to develop an algorithm for this step that scales linearly
with system size. We discuss attempts to achieve linear scaling for the calculation of the matrix elements of the exchange-correlation
and Coulomb potentials within a particular implementation (the Amsterdam density functional, ADF, code) of the KS method.
In the ADF scheme the matrix elements are completely determined by 3D numerical integration, the value of the potentials in
each grid point being determined with the help of an auxiliary function representation of the electronic density. Nearly linear
scaling for building the total Fock matrix is demonstrated for systems of intermediate size (in the order of 1000 atoms).
For larger systems further development is desirable for the treatment of the Coulomb potential.
Received: 30 March 1998 / Accepted: 6 July 1998 / Published online: 15 September 1998 相似文献
9.
Hiroshi Nakatsuji 《Theoretical chemistry accounts》1999,102(1-6):97-104
The density equation proposed previously for the direct determination of the density matrix, i.e. for the wave mechanics
without wave, is extended to a time-dependent case. The time-dependent density equation has been shown to be equivalent to
the time-dependent Schr?dinger equation so long as the density matrix, included as a self-contained variable, is N-representable. Formally, it is obtainable from the previous time-independent equation by replacing the energy E with . The perturbation theory formulas for the density equation have also been given for both the time-dependent and time-independent
cases.
Received: 16 June 1998 / Accepted: 2 September 1998 / Published online: 8 February 1999 相似文献
10.
Shinsaku Fujita 《Theoretical chemistry accounts》1999,101(6):409-420
After the definitions of amplified representations and number-theoretical vectors, the markaracter table of a cyclic subgroup
is converted into the corresponding Q-conjugacy character table. The conversion is shown to necessitate an interconversion matrix that contains M?bius functions
as elements. Since the interconversion matrix gives characteristic monomials for cyclic groups, all the powers appearing in
each of the characteristic monomials are shown to be integers. Characteristic monomials for finite groups are then built up
by starting from those of cyclic groups. This procedure clarifies the fact that all the powers appearing in each characteristic
monomial for finite groups are integers. The relationship between characteristic monomial tables and unit-subduced-cycle-index
tables is discussed with respect to their application to isomer enumeration.
Received: 15 July 1998 / Accepted: 16 December 1998 / Published online: 16 March 1999 相似文献
11.
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
12.
Renato Colle Raffaele Montagnani Oriano Salvetti 《Theoretical chemistry accounts》1999,101(4):262-268
A molecular fragment approach is used to compute ionization potentials, transition energies and electron affinities of pyrrole
oligomers. The calculations of these quantities include correlation energy contributions evaluated by integrating a functional
of the two-particle Hartree-Fock density matrix. Pyrrole oligomers with chains of up to 16 rings are explicitly treated and
the calculated quantities extrapolated to the limit of an infinitely long chain, to predict polymer properties. The theoretical
results compare favorably with data on gas-phase ionization potentials deduced from experimental oxidation potentials, and
with optical absorption peaks recorded in solution or on solid films. The large discrepancy between electron affinities obtained
from the eigenvalues of an independent-particle frozen-orbital calculation and those obtained from separate, correlated calculations
on the neutral system and the negative ion in shown.
Received: 24 March 1998 / Accepted: 2 September 1998 / Published online: 7 December 1998 相似文献
13.
Adam Liwo Jarosław Pillardy Rajmund Kaźmierkiewicz Ryszard J. Wawak Małgorzata Groth Cezary Czaplewski Stanisaw Ołdziej Harold A. Scheraga 《Theoretical chemistry accounts》1999,101(1-3):16-20
A united-residue model of polypeptide chains developed in our laboratories with united side-chains and united peptide groups
as interaction sites is presented. The model is designed to work in continuous space; hence efficient global-optimization
methods can be applied. In this work, we adopted the distance-scaling method that is based on continuous deformation of the original
rugged energy hypersurface to obtain a smoothed surface. The method has been applied successfully to predict the structures
of simple motifs, such as the three-helix bundle structure of the 10-58 fragment of staphylococcal protein A in de novo folding
simulations and more complicated motifs in inverse-folding simulations.
Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998 相似文献
14.
Shinsaku Fujita 《Theoretical chemistry accounts》1998,99(6):404-410
Characteristic monomials for a finite group are obtained by direct subductions of Q-conjugate representations. They are shown to give a generating function that is capable of solving enumeration problems.
Received: 1 May 1998 / Accepted: 16 July 1998 / Published online: 18 September 1998 相似文献
15.
Maja Nendel Bernd Goldfuss K. N. Houk Klaus Hafner Udo Grieser 《Theoretical chemistry accounts》1999,102(1-6):397-400
B3LYP/6-31G* calculations on bis-periazulene (cyclohepta[def]-fluorene) predict a triplet ground state for this molecule. The singlet has an aromatic 14π-electron periphery but is 2 kcal/mol
higher in energy. The results agree with earlier predictions by Heilbronner.
Received: 19 August 1998 / Accepted: 6 October 1998 / Published online: 23 February 1999 相似文献
16.
M. Micov L. Turi Nagy D. Tunega M. Liška P. Perichta 《Theoretical chemistry accounts》1998,99(6):378-383
A method of solvation energy computation is proposed for ions and molecules in the environment of an ionic melt, based on
the approximation of the ionic melt as an ideal conductor. The method is used to compute equilibrium constants of some equilibria
in cryolite melt. Theoretically obtained results predict that aluminium is bound in tetrafluorocomplexes AlF4
−.
Received: 16 March 1998 / Accepted: 19 June 1998 / Published online: 7 October 1998 相似文献
17.
B. Tallur J. Nicolas A. Froger D. Thomas C. Delamarche 《Theoretical chemistry accounts》1999,101(1-3):77-81
We have worked with a classification method based upon a notion of probabilistic similarity or “likelihood of similarity”
between aligned sequences. One important parameter, among others, affecting the sequence similarities and hence the classification
results is the amino acid similarity matrix. We present a method for choosing the most adapted matrix to classify protein
sequences. This method has been applied to the transmembrane channels of the major intrinsic protein (MIP) family. At present,
two functional subgroups have been well characterized in this family: (1) specific water transport by the aquaporins and (2)
small neutral solutes transport. The aim of the present study is to show the usefulness of the classification method in the
prediction of sequence segments important for substrate selectivity. Moreover, we show that this method can also be used to
predict the function of undetermined MIP proteins. The method could be applied to other protein families as well.
Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998 相似文献
18.
The use of Brownian dynamics simulations to investigate the presence of structural (kinks) and dynamic (bulges) anomalies
in short DNA stretches is analyzed in connection with a string-of-beads model. A scaling method to choose the hydrodynamic
translational and rotational parameters of the beads is proposed and tested on straight, kinked and bulged DNA fragments 17 nm
long. The model reproduces the rigid-body rotational diffusion for the straight DNA and for the fluorescence polarization
anisotropy decay of the kinked and bulged DNAs the model predicts a different behavior which is found experimentally.
Received: 24 March 1998 / Accepted: 3 September 1998 / Published online: 23 November 1998 相似文献
19.
The repulsive ground electronic state X2Σ+ of HeH is strongly coupled to the Rydberg states at small interatomic distances. Such large couplings also occur between
some of the Rydberg states. HeH+ ions that capture an electron in a Rydberg state end up in separated He and H atoms by indirect predissociation. This paper
presents a study of potential functions and pertinent matrix elements involving the lowest electronic states: the 2Σ+ states, X, A, C, and D, and the 2Π states B and E. Individual transition rates as well as total radiative and non-radiative lifetimes have been computed for
the lowest vibrational and rotational levels.
Received: 22 June 1998 / Accepted: 21 August 1998 / Published online: 12 October 1998 相似文献
20.
High-level ab initio electronic structure theories have been applied to investigate the detailed reaction mechanism of the
spin-forbidden reaction CH(2∏) + N2 → HCN + N(4S). The G2M(RCC) calculations provide accurate energies for the intermediates and transition states involved in the reaction,
whereas the B3LYP/6-311G(d,p) method overestimates the stability of some intermediates by as much as about 10 kcal/mol. A few new structures have been
found for both the doublet and quartet electronic states, which are mainly involved in the dative pathways. However, due to
the higher energies of these structures, the dominant mechanism remains the one involving the C
2 intersystem-crossing step. The C
2 minima on the seam of crossing (MSX) structures and the spin-orbit coupling between the doublet and quartet electronic states
are rather close to those found in previous studies. Vibrational frequencies orthogonal to the normal of the seam which have
been applied in a separate publication to calculate the rate of the CH(2∏) + N2 → HCN + N(4S) reaction with a newly proposed nonadiabatic transition-state theory for spin-forbidden reactions have been calculated at
the MSX from first principles.
Received: 23 June 1998 / Accepted: 21 September 1998 / Published online: 8 February 1999 相似文献