Multireference perturbation CI III. Fast evaluation of the one-particle density matrix

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     

Computation of stationary points via a homotopy method

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     

Efficient boundary basis functions for time-independent quantum scattering calculations

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     

Molecular modeling study of an abasic DNA undecamer duplex: d(GCGTGOGTGCG) · d(CGCACTCACGC)

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     

Global geometry optimization of small silicon clusters at the level of density functional theory

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     

Ab initio calculations find 2,2-disilylcyclopentane-1,3-diyl is a singlet diradical with a high barrier to ring closure

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     

The partial averaging Fourier path Integral approach based on the harmonic reference path

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     

Equation for the direct determination of the density matrix: Time-dependent density equation and perturbation theory

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     

Towards an order-N DFT method

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     

Möbius function and characteristic monomials for combinatorial enumeration

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     

Some thoughts about the stability and reliability of commonly used exchange–correlation functionals – coverage of dynamic and nondynamic correlation effects

 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     

Molecular fragment approach to the study of pyrrole oligomers and polypyrrole

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     

Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods

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     

Bis-periazulene: a simple Kekulé biradical with a triplet ground state

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     

Direct subduction of Q-conjugacy representations to give characteristic monomials for combinatorial enumeration

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     

The structure and energetics of cryolite melts

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     

Sequence classification of water channels and related proteins in view of functional predictions

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     

Study of flexible joints and permanent bends in DNA fragments by brownian dynamics simulations

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     

Dissociative recombination of HeH+. I. Rovibrational spectrum of HeH Rydberg states

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     

The spin-forbidden reaction CH(2∏) + N2→ HCN + N(4S) revisited I. Ab initio study of the potential energy surfaces

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