Biomedical subjects

Gregory J O Beran

Publications and source records attributed to Gregory J O Beran.

6 recordsLinked to original sources

PubMed2006

Advances in methods and algorithms in a modern quantum chemistry program package.

Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.

Algorithms↗

PubMed2006

Second-order correction to perfect pairing: an inexpensive electronic structure method for the treatment of strong electron-electron correlations.

We have formulated a second-order perturbative correction for perfect-pairing wave functions [PP2] based on similarity-transformed perturbation techniques in coupled cluster theory. The perfect-pairing approximation is used to obtain a simple reference wave function which can qualitatively describe bond breaking, diradicals, and other highly correlated systems, and the perturbative correction accounts for the dynamical correlation. An efficient implementation of this correction using the resolution of the identity approximation enables PP2 to be computed at a cost only a few times larger than that of canonical MP2 for systems with hundreds of active electrons and tens of heavy atoms. PP2 significantly improves on MP2 predictions in various systems with a challenging electronic structure.

Journal Article↗

PubMed2005

Unrestricted perfect pairing: the simplest wave-function-based model chemistry beyond mean field.

The perfect pairing (PP) approximation from generalized valence bond theory is formulated in an unrestricted fashion for both closed- and open-shell systems using a coupled cluster ansatz. In the model chemistry proposed here, active electron pairs are correlated, but the unpaired or radical electrons remain uncorrelated, leading to a linear number of decoupled cluster amplitudes which can be solved for analytically. The alpha and beta spatial orbitals are variationally optimized independently. This minimal treatment of electron-electron correlation noticeably improves upon symmetry-breaking problems and other pathologies in Hartree-Fock (HF) theory and may be computed using the resolution of the identity approximation at only a factor of several times more effort than HF itself. PP also generally predicts improved molecular structures over HF. This compact, correlated wave function potentially provides a useful starting point for dynamical correlation corrections.

Journal Article↗

PubMed2005

Search for stratospheric bromine reservoir species: theoretical study of the photostability of mono-, tri-, and pentacoordinated bromine compounds.

Previous work has shown that pentacoordinated bromine compounds have their lowest excited electronic states shifted to the blue relative to monocoordinated bromine molecules, and that this shift may be large enough to render them photostable in the lower stratosphere. Our earlier work has also shown that certain pentacoordinated bromine compounds are thermodynamically stable relative to their mono- or tricoordinated isomers, suggesting that if a bromine stratospheric reservoir species exists, it may be a pentacoordinated compound. In this study we have examined the singlet and triplet excited electronic states of several bromine compounds, using time dependent density functional theory, to assess their photostability under stratospheric conditions and in order to elucidate the nature of lowest excited states in mono-, tri-, and pentacoordinated bromine molecules. The triplet states have been included due to the strong spin-orbit mixing in bromine. We have found several pentacoordinated bromine/oxygen compounds that could be photostable in the lower stratosphere, but we have also found that monovalent bromine compounds where the bromine atom is bonded to an atom with no lone-pair p-electrons is far and away the most photostable. Attachment/detachment electron density plots have been useful in ascertaining the nature of the excited electronic states and their likely path to photodissociation.

Bromine↗

PubMed2005

Nitrogen activation via three-coordinate molybdenum complexes: comparison of density functional theory performance with wave function based methods.

Obtaining an accurate theoretical model for the activation of dinitrogen by three-coordinate molybdenum amide complexes (e.g. Mo(NH2)3) is difficult due to the interaction of various high- and low-spin open-shell complexes along the reaction coordinate which must be treated with comparable levels of accuracy in order to obtain reasonable potential energy surfaces. Density functional theory with present-day functionals is a popular choice in this situation; however, the dinitrogen activation reaction energetics vary substantially with the choice of functional. An assessment of the reaction using specialized wave function based methods indicates that although current density functionals in general agree qualitatively on the mechanistic details of the reaction, a variety of high-level electron correlation methods (including CCSD(T), OD(T), CCSD(2), KS-CCSD(T), and spin-flip CCSD) provide a consistent but slightly different representation of the system.

Journal Article↗

PubMed2004

Extracting dominant pair correlations from many-body wave functions.

The singular value decomposition of the n-particle excitation operator as determined by coupled cluster or perturbation theory is used to extract the dominant and interesting electron-electron correlations from complex molecular wave functions. As an example of the very general formalism, the decomposition of the T(2) operator obtained from coupled cluster doubles calculations is used to analyze the strength and character of pair correlations in a variety of molecules with interesting electronic structure. The magnitude of the largest singular value(s) determines the strength of the correlation(s), and the corresponding right- and left-hand singular vectors characterize the physical and spatial nature of the correlations. The primary advantage of this tool over natural orbital analysis is that it provides direct associations between the occupied and virtual geminals involved in the correlations.

Journal Article↗