Spin densities from subsystem density-functional theory: Assessment and application to a photosynthetic reaction center complex model

2012 ◽  
Vol 136 (19) ◽  
pp. 194104 ◽  
Author(s):  
Alisa Solovyeva ◽  
Michele Pavanello ◽  
Johannes Neugebauer
Keyword(s):  
Density Functional Theory ◽  
Reaction Center ◽  
Density Functional ◽  
Photosynthetic Reaction Center ◽  
Complex Model ◽  
Functional Theory ◽  
Reaction Center Complex ◽  
Spin Densities

Subsystem density-functional theory for interacting open-shell systems: spin densities and magnetic exchange couplings

2020 ◽  
Vol 224 ◽  
pp. 201-226
Author(s):  
Anja Massolle ◽  
Johannes Neugebauer
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Open Shell ◽  
Broken Symmetry ◽  
Easy Access ◽  
Magnetic Exchange ◽  
Functional Theory ◽  
Spin Densities

Subsystem DFT allows easy access to spin densities for arbitrary broken-symmetry states of radical aggregates.

SPIN DENSITIES AND CURRENTS IN THE ROUTHIAN APPROXIMATION

2006 ◽  
Vol 15 (02) ◽  
pp. 553-559
Author(s):  
JOHANN BARTEL ◽  
KAMEL BENCHEIKH ◽  
PHILIPPE QUENTIN
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Degrees Of Freedom ◽  
Vector Fields ◽  
Semiclassical Approximation ◽  
Spin Current ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Current Densities ◽  
Spin Densities

The structure of spin densities and the associated spin-current densities, induced by the coupling of external vector fields to the orbital and spin degrees of freedom, is studied within the framework of the Extended Thomas-Fermi method, a semiclassical version of the density-functional theory. A special emphasis is put on the rotational case where our approach amounts to perform a semiclassical approximation of the so-called generalized Routhian approach.

A density functional theory study of the free radicals NH2, NF2, NCl2, PH2, PF2, and PCl2

1994 ◽  
Vol 72 (3) ◽  
pp. 695-704 ◽  
Author(s):  
Maggie A. Austen ◽  
Leif A. Eriksson ◽  
Russell J. Boyd
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Local Density ◽  
Basis Set ◽  
Basis Sets ◽  
Functional Theory ◽  
Unpaired Spin ◽  
Non Local ◽  
Local Potentials ◽  
Spin Densities

The linear combination of Gaussian-type orbitals–density functional theory (LCGTO–DFT) approach is used to study geometries and hyperfine structures of a set of neutral radicals. Each of the title molecules is investigated by means of local density approximation calculations, and using the Becke–Perdew and Perdew–Wang–Perdew corrections to the exchange and correlation functionals. The effects of local vs. non-local potentials and of various basis sets are investigated. Total densities and unpaired spin densities are compared. The isotropic couplings are found to be very dependent on the type of exchange functional used, whereas the anisotropic couplings are relatively insensitive to the choice of basis set and functional. In most cases, the Perdew–Wang exchange corrections provide isotropic couplings in satisfactory agreement with experiment.

Multiple mutations in RNA polymerase β-Subunit gene (rpoB) in Streptomyces incarnatus NRRL8089 enhance production of antiviral antibiotic sinefungin: modeling rif cluster region by density functional theory

2021 ◽  
Author(s):  
Saori Ogawa ◽  
Hitomi Shimidzu ◽  
Koji Fukuda ◽  
Naoki Tsunekawa ◽  
Toshiyuki Hirano ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Rna Polymerase ◽  
Density Functional ◽  
Rpob Gene ◽  
Complex Model ◽  
Dynamics Simulation ◽  
Β Subunit ◽  
Negative Effects ◽  
Gene Encoding ◽  
Functional Theory

Abstract Streptomyces incarnatus NRRL8089 produces the antiviral, antifungal, anti-protozoal nucleoside antibiotic sinefungin. To enhance sinefungin production, multiple mutations were introduced to the rpoB gene encoding RNA polymerase (RNAP) β-subunit at the target residues, D447, S453, H457, and R460. Sparse regression analysis using elastic net lasso-ridge penalties on previously reported H457X mutations identified a numeric parameter set, which suggested that H457R/Y/F may cause production enhancement. H457R/R460C mutation successfully enhanced the sinefungin production by 3-fold, while other groups of mutations, such as D447G/R460C or D447G/H457Y made moderate or even negative effects. To identify why the rif-cluster residues have diverse effects on sinefungin production, an RNAP/DNA/mRNA complex model was constructed by homology modeling and molecular dynamics simulation. The four residues were located near the mRNA strand. Density functional theory-based calculation suggested that D447, H457, and R460 are in direct contact with ribonucleotide, and partially positive charges are induced by negatively charged chain of mRNA.

scholarly journals Multiconfiguration Pair-Density Functional Theory

2021 ◽  
Vol 72 (1) ◽  
pp. 541-564
Author(s):  
Prachi Sharma ◽  
Jie J. Bao ◽  
Donald G. Truhlar ◽  
Laura Gagliardi
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Strongly Correlated Systems ◽  
Background Information ◽  
Total Density ◽  
Strongly Correlated ◽  
Functional Theory ◽  
Correlated Systems ◽  
Pair Density ◽  
Spin Densities

Kohn-Sham density functional theory with the available exchange–correlation functionals is less accurate for strongly correlated systems, which require a multiconfigurational description as a zero-order function, than for weakly correlated systems, and available functionals of the spin densities do not accurately predict energies for many strongly correlated systems when one uses multiconfigurational wave functions with spin symmetry. Furthermore, adding a correlation functional to a multiconfigurational reference energy can lead to double counting of electron correlation. Multiconfiguration pair-density functional theory (MC-PDFT) overcomes both obstacles, the second by calculating the quantum mechanical part of the electronic energy entirely by a functional, and the first by using a functional of the total density and the on-top pair density rather than the spin densities. This allows one to calculate the energy of strongly correlated systems efficiently with a pair-density functional and a suitable multiconfigurational reference function. This article reviews MC-PDFT and related background information.

Density functional theory analyses of bis(bipyridine)ruthenium noninnocent quinonoid and thiolosulfinato complexes containing ligands formally in the semiquinone oxidation state

2009 ◽  
Vol 87 (10) ◽  
pp. 1451-1459 ◽  
Author(s):  
A. B.P. Lever
Keyword(s):  
Density Functional Theory ◽  
Oxidation State ◽  
Electronic Structures ◽  
Continuum Model ◽  
Density Functional ◽  
Open Shell ◽  
Functional Theory ◽  
Polarized Continuum Model ◽  
Spin Densities ◽  
Sulfur Donor

Density functional theory and the polarized continuum model are used to derive the electronic structures of some open-shell, bis(bipyridine)ruthenium complexes bound to noninnocent quinonoid or thiolosulfinato ligands formally in the semiquinone oxidation state. The noninnocent properties of the o-thiolosulfinato ligand are explored and compared with those of the more conventional o-semiquinones with nitrogen, oxygen, and sulfur donor atoms. Spin densities are shown to be fairly localized in the metallocycle ring. It is demonstrated that oxidation of the parent [RuII(bpy)2 (1,2-(S,SO2)–C6H4] species occurs primarily in the metallocycle ring and is localized in the Ru–S0 bond.

Sign in / Sign up

Export Citation Format

Share Document