A priori Wannier functions from modified Hartree-Fock and Kohn-Sham equations

The Hartree-Fock equations are modified to directly yield Wannier functions following a proposal of Shukla et al. [Chem. Phys. Lett. 262, 213-218 (1996)]. This approach circumvents the a posteriori application of the Wannier transformation to Bloch functions. I give a novel and rigorous derivation of the relevant equations by introducing an orthogonalizing potential to ensure the orthogonality among the resulting functions. The properties of these, so-called a priori Wannier functions, are analyzed and the relation of the modified Hartree-Fock equations to the conventional, Bloch-function-based equations is elucidated. It is pointed out that the modified equations offer a different route to maximally localized Wannier functions. Their computational solution is found to involve an effort that is comparable to the effort for the solution of the conventional equations. Above all, I show how a priori Wannier functions can be obtained by a modification of the Kohn-Sham equations of density-functional theory.Comment: 7 pages, RevTeX4, revise

Second bound state of the positronium molecule and biexcitons

A new, hitherto unknown bound state of the positronium molecule, with orbital angular momentum L=1 and negative parity is reported. This state is stable against autodissociation even if the masses of the positive and negative charges are not equal. The existence of a similar state in two-dimension has also been investigated. The fact that the biexcitons have a second bound state may help the better understanding of their binding mechanism.Comment: Latex, 8 pages, 2 Postscript figure

New representation of orbital motion with arbitrary angular momenta

A new formulation is presented for a variational calculation of $N$-body systems on a correlated Gaussian basis with arbitrary angular momenta. The rotational motion of the system is described with a single spherical harmonic of the total angular momentum $L$, and thereby needs no explicit coupling of partial waves between particles. A simple generating function for the correlated Gaussian is exploited to derive the matrix elements. The formulation is applied to various Coulomb three-body systems such as $e^-e^-e^+, tt\mu, td\mu$, and $\alpha e^-e^-$ up to $L=4$ in order to show its usefulness and versatility. A stochastic selection of the basis functions gives good results for various angular momentum states.Comment: Revte

Direct generation of local orbitals for multireference treatment and subsequent uses for the calculation of the correlation energy

We present a method that uses the one-particle density matrix to generate directly localized orbitals dedicated to multireference wave functions. On one hand, it is shown that the definition of local orbitals making possible physically justified truncations of the CAS ~complete active space! is particularly adequate for the treatment of multireference problems. On the other hand, as it will be shown in the case of bond breaking, the control of the spatial location of the active orbitals may permit description of the desired physics with a smaller number of active orbitals than when starting from canonical molecular orbitals. The subsequent calculation of the dynamical correlation energy can be achieved with a lower computational effort either due to this reduction of the active space, or by truncation of the CAS to a shorter set of references. The ground- and excited-state energies are very close to the current complete active space self-consistent field ones and several examples of multireference singles and doubles calculations illustrate the interest of the procedur

Molecular-orbital theory for the stopping power of atoms in the low velocity regime:the case of helium in alkali metals

A free-parameter linear-combination-of-atomic-orbitals approach is presented for analyzing the stopping power of slow ions moving in a metal. The method is applied to the case of He moving in alkali metals. Mean stopping powers for He present a good agreement with local-density-approximation calculations. Our results show important variations in the stopping power of channeled atoms with respect to their mean values.Comment: LATEX, 3 PostScript Figures attached. Total size 0.54

Deciphering the Curly Arrow Representation and Electron Flow for the 1,3-Dipolar Rearrangement between Acetonitrile Oxide and (1S,2R,4S)‑2-Cyano-7-oxabicyclo[2.2.1]hept-5-en-2-yl Acetate Derivatives

This study is focused on describing the molecular mechanism beyond the molecular picture provided by the evolution of molecular orbitals, valence bond structures along the reaction progress, or conceptual density functional theory. Using bonding evolution theory (BET) analysis, we have deciphered the mechanism of the 1,3-dipolar rearrangement between acetonitrile oxide and (1S,2R,4S)-2-cyano-7-oxabicyclo[2.2.1]hept-5-en-2-yl acetate derivatives. The BET study revealed that the formation of the C−C bond takes place via a usual sharing model before the O−C one that is also formed in the halogenated species through a not very usual sharing model. The mechanism includes depopulation of the electron density at the N−C triple bond and creation of the V(N) and V(C) monosynaptic basins, depopulation of the former C−C double bond with the creation of V(C,C) basins, and final formation of the V(O,C) basin associated with the O−C bond. The topological changes along the reaction pathway take place in a highly synchronous way. BET provides a convenient quantitative method for deriving curly arrows and electron flow representation to unravel molecular mechanisms

Environments of the Four Tryptophans in the Extracellular Domain of Human Tissue Factor: Comparison of Results from Absorption and Fluorescence Difference Spectra of Tryptophan Replacement Mutants with the Crystal Structure of the Wild-Type Protein

The local environments of the four tryptophan residues of the extracellular domain of human tissue factor (sTF) were assessed from difference absorption and fluorescence spectra. The difference spectra were derived by subtracting spectra from single Trp-to-Phe or Trp-to-Tyr replacement mutants from the corresponding spectrum of the wild-type protein. Each of the mutants was capable of enhancing the proteolytic activity of factor Vila showing that the mutations did not introduce major structural changes, although the mutants were more susceptible to denaturation by guanidinium chloride. The difference spectra indicate that the Trp residues are buried to different extents within the protein matrix. This evaluation was compared with the x-ray crystal structure of sTF. There is excellent agreement between predictions from the difference spectra and the environments of the Trp residues observed in the x-ray crystal structure, demonstrating that difference absorption and particularly fluorescence spectra derived from functional single-Trp replacement mutants can be used to obtain information about the local environments of individual Trp residues in multi-tryptophan proteins

A population Monte Carlo scheme with transformed weights and its application to stochastic kinetic models

This paper addresses the problem of Monte Carlo approximation of posterior probability distributions. In particular, we have considered a recently proposed technique known as population Monte Carlo (PMC), which is based on an iterative importance sampling approach. An important drawback of this methodology is the degeneracy of the importance weights when the dimension of either the observations or the variables of interest is high. To alleviate this difficulty, we propose a novel method that performs a nonlinear transformation on the importance weights. This operation reduces the weight variation, hence it avoids their degeneracy and increases the efficiency of the importance sampling scheme, specially when drawing from a proposal functions which are poorly adapted to the true posterior. For the sake of illustration, we have applied the proposed algorithm to the estimation of the parameters of a Gaussian mixture model. This is a very simple problem that enables us to clearly show and discuss the main features of the proposed technique. As a practical application, we have also considered the popular (and challenging) problem of estimating the rate parameters of stochastic kinetic models (SKM). SKMs are highly multivariate systems that model molecular interactions in biological and chemical problems. We introduce a particularization of the proposed algorithm to SKMs and present numerical results.Comment: 35 pages, 8 figure

Maximally-localized generalized Wannier functions for composite energy bands

We discuss a method for determining the optimally-localized set of generalized Wannier functions associated with a set of Bloch bands in a crystalline solid. By ``generalized Wannier functions'' we mean a set of localized orthonormal orbitals spanning the same space as the specified set of Bloch bands. Although we minimize a functional that represents the total spread sum_n [ _n - _n^2 ] of the Wannier functions in real space, our method proceeds directly from the Bloch functions as represented on a mesh of k-points, and carries out the minimization in a space of unitary matrices U_mn^k describing the rotation among the Bloch bands at each k-point. The method is thus suitable for use in connection with conventional electronic-structure codes. The procedure also returns the total electric polarization as well as the location of each Wannier center. Sample results for Si, GaAs, molecular C2H4, and LiCl will be presented.Comment: 22 pages, two-column style with 4 postscript figures embedded. Uses REVTEX and epsf macros. Also available at http://www.physics.rutgers.edu/~dhv/preprints/index.html#nm_wan