Analytic Energy Gradients for Multiconfigurational Self-Consistent Field Second-Order Quasidegenerate Perturbation Theory (MC-QDPT)

An analytic energy gradient method for second-order quasidegenerate perturbation theory with multiconfigurational self-consistent field reference functions (MC-QDPT) is derived along the lines of the response function formalism (RFF). According to the RFF, the gradients are calculated without solving coupled perturbed equations. Instead, it is necessary to solve seven sets of linear equations in order to determine Lagrangian multipliers, corresponding to four sets of parameter constraining conditions and three sets of additional parameter defining conditions in the Lagrangian. Just one of these linear equations is a large scale linear equation; the others are reducible to just partial differentiations or simple equations solvable by straightforward subroutines

Interaction and Localization of One-electron Orbitals in an Organic Molecule: Fictitious Parameter Analysis for Multi-physics Simulations

We present a new methodology to analyze complicated multi-physics simulations by introducing a fictitious parameter. Using the method, we study quantum mechanical aspects of an organic molecule in water. The simulation is variationally constructed from the ab initio molecular orbital method and the classical statistical mechanics with the fictitious parameter representing the coupling strength between solute and solvent. We obtain a number of one-electron orbital energies of the solute molecule derived from the Hartree-Fock approximation, and eigenvalue-statistical analysis developed in the study of nonintegrable systems is applied to them. Based on the results, we analyze localization properties of the electronic wavefunctions under the influence of the solvent.Comment: 4 pages, 5 figures, the revised version will appear in J. Phys. Soc. Jpn. Vol.76 (No.1

Quantum mechanical ab-initio simulation of the electron screening effect in metal deuteride crystals

In antecedent experiments the electron screening energies of the d+d reactions in metallic environments have been determined to be enhanced by an order of magnitude in comparison to the case of gaseous deuterium targets. The analytical models describing averaged material properties have not been able to explain the experimental results so far. Therefore, a first effort has been undertaken to simulate the dynamics of reacting deuterons in a metallic lattice by means of an ab-initio Hartree-Fock calculation of the total electrostatic force between the lattice and the successively approaching deuterons via path integration. The calculations have been performed for Li and Ta, clearly showing a migration of electrons from host metallic to the deuterium atoms. However, in order to avoid more of the necessary simplifications in the model the utilization of a massive parallel supercomputer would be required.Comment: 11 pages, 12 figures, svjour class. To be published in Eur. Phys. J.

Designing all-graphene nanojunctions by covalent functionalization

We investigated theoretically the effect of covalent edge functionalization, with organic functional groups, on the electronic properties of graphene nanostructures and nano-junctions. Our analysis shows that functionalization can be designed to tune electron affinities and ionization potentials of graphene flakes, and to control the energy alignment of frontier orbitals in nanometer-wide graphene junctions. The stability of the proposed mechanism is discussed with respect to the functional groups, their number as well as the width of graphene nanostructures. The results of our work indicate that different level alignments can be obtained and engineered in order to realize stable all-graphene nanodevices

Cyclic Density Functional Theory : A route to the first principles simulation of bending in nanostructures

We formulate and implement Cyclic Density Functional Theory (Cyclic DFT) -- a self-consistent first principles simulation method for nanostructures with cyclic symmetries. Using arguments based on Group Representation Theory, we rigorously demonstrate that the Kohn-Sham eigenvalue problem for such systems can be reduced to a fundamental domain (or cyclic unit cell) augmented with cyclic-Bloch boundary conditions. Analogously, the equations of electrostatics appearing in Kohn-Sham theory can be reduced to the fundamental domain augmented with cyclic boundary conditions. By making use of this symmetry cell reduction, we show that the electronic ground-state energy and the Hellmann-Feynman forces on the atoms can be calculated using quantities defined over the fundamental domain. We develop a symmetry-adapted finite-difference discretization scheme to obtain a fully functional numerical realization of the proposed approach. We verify that our formulation and implementation of Cyclic DFT is both accurate and efficient through selected examples. The connection of cyclic symmetries with uniform bending deformations provides an elegant route to the ab-initio study of bending in nanostructures using Cyclic DFT. As a demonstration of this capability, we simulate the uniform bending of a silicene nanoribbon and obtain its energy-curvature relationship from first principles. A self-consistent ab-initio simulation of this nature is unprecedented and well outside the scope of any other systematic first principles method in existence. Our simulations reveal that the bending stiffness of the silicene nanoribbon is intermediate between that of graphene and molybdenum disulphide. We describe several future avenues and applications of Cyclic DFT, including its extension to the study of non-uniform bending deformations and its possible use in the study of the nanoscale flexoelectric effect.Comment: Version 3 of the manuscript, Accepted for publication in Journal of the Mechanics and Physics of Solids, http://www.sciencedirect.com/science/article/pii/S002250961630368

A mathematical and computational review of Hartree-Fock SCF methods in Quantum Chemistry

We present here a review of the fundamental topics of Hartree-Fock theory in Quantum Chemistry. From the molecular Hamiltonian, using and discussing the Born-Oppenheimer approximation, we arrive to the Hartree and Hartree-Fock equations for the electronic problem. Special emphasis is placed in the most relevant mathematical aspects of the theoretical derivation of the final equations, as well as in the results regarding the existence and uniqueness of their solutions. All Hartree-Fock versions with different spin restrictions are systematically extracted from the general case, thus providing a unifying framework. Then, the discretization of the one-electron orbitals space is reviewed and the Roothaan-Hall formalism introduced. This leads to a exposition of the basic underlying concepts related to the construction and selection of Gaussian basis sets, focusing in algorithmic efficiency issues. Finally, we close the review with a section in which the most relevant modern developments (specially those related to the design of linear-scaling methods) are commented and linked to the issues discussed. The whole work is intentionally introductory and rather self-contained, so that it may be useful for non experts that aim to use quantum chemical methods in interdisciplinary applications. Moreover, much material that is found scattered in the literature has been put together here to facilitate comprehension and to serve as a handy reference.Comment: 64 pages, 3 figures, tMPH2e.cls style file, doublesp, mathbbol and subeqn package

Unprocessed Viral DNA Could Be the Primary Target of the HIV-1 Integrase Inhibitor Raltegravir

Integration of HIV DNA into host chromosome requires a 3′-processing (3′-P) and a strand transfer (ST) reactions catalyzed by virus integrase (IN). Raltegravir (RAL), commonly used in AIDS therapy, belongs to the family of IN ST inhibitors (INSTIs) acting on IN-viral DNA complexes (intasomes). However, studies show that RAL fails to bind IN alone, but nothing has been reported on the behaviour of RAL toward free viral DNA. Here, we assessed whether free viral DNA could be a primary target for RAL, assuming that the DNA molecule is a receptor for a huge number of pharmacological agents. Optical spectroscopy, molecular dynamics and free energy calculations, showed that RAL is a tight binder of both processed and unprocessed LTR (long terminal repeat) ends. Complex formation involved mainly van der Waals forces and was enthalpy driven. Dissociation constants (Kds) revealed that RAL affinity for unbound LTRs was stronger than for bound LTRs. Moreover, Kd value for binding of RAL to LTRs and IC50 value (half concentration for inhibition) were in same range, suggesting that RAL binding to DNA and ST inhibition are correlated events. Accommodation of RAL into terminal base-pairs of unprocessed LTR is facilitated by an extensive end fraying that lowers the RAL binding energy barrier. The RAL binding entails a weak damping of fraying and correlatively of 3′-P inhibition. Noteworthy, present calculated RAL structures bound to free viral DNA resemble those found in RAL-intasome crystals, especially concerning the contacts between the fluorobenzyl group and the conserved 5′C4pA33′ step. We propose that RAL inhibits IN, in binding first unprocessed DNA. Similarly to anticancer drug poisons acting on topoisomerases, its interaction with DNA does not alter the cut, but blocks the subsequent joining reaction. We also speculate that INSTIs having viral DNA rather IN as main target could induce less resistance