arXiv subjects

R. G. Endres

Publications and source records attributed to R. G. Endres.

7 recordsLinked to original sources

arXiv2005

Optical conductivity of wet DNA

Motivated by recent experiments we have studied the optical conductivity of DNA in its natural environment containing water molecules and counter ions. Our density functional theory calculations (using SIESTA) for four base pair B-DNA with order 250 surrounding water molecules suggest a thermally activated doping of the DNA by water states which generically leads to an electronic contribution to low-frequency absorption. The main contributions to the doping result from water near DNA ends, breaks, or nicks and are thus potentially associated with temporal or structural defects in the DNA.

cond-mat.soft↗

arXiv2004

An Anderson Impurity Model for Efficient Sampling of Adiabatic Potential Energy Surfaces of Transition Metal Complexes

We present a model intended for rapid sampling of ground and excited state potential energy surfaces for first-row transition metal active sites. The method is computationally inexpensive and is suited for dynamics simulations where (1) adiabatic states are required "on-the-fly" and (2) the primary source of the electronic coupling between the diabatic states is the perturbative spin-orbit interaction among the 3d electrons. The model Hamiltonian we develop is a variant of the Anderson impurity model and achieves efficiency through a physically motivated basis set reduction based on the large value of the d-d Coulomb interaction U_{d} and a Lanczos matrix diagonalization routine to solve for eigenvalues. The model parameters are constrained by fits to the partial density of states (PDOS) obtained from ab initio density functional theory calculations. For a particular application of our model we focus on electron-transfer occuring between cobalt ions solvated by ammonium, incorporating configuration interaction between multiplet states for both metal ions. We demonstrate the capability of the method to efficiently calculate adiabatic potential energy surfaces and the electronic coupling factor we have calculated compares well to previous calculations and experiment.

physics.chem-ph↗

arXiv2002

Theory of adiabatic Hexaamminecobalt-Self-Exchange

We have reexamined the thermally induced Co(NH_3)_6^{2+/3+} [Co(II/III)] redox reaction using the first principles density-functional-theory method, semiclassical Marcus theory, and known charge transfer parameters. We confirm a previously suggested mechanism involving excited state (^2E_g) of Co(II) which becomes lower than the ground state (^4T_1g) in the transition state region. This lowers the transition state barrier considerably by about 6.9 kcal/mol and leads to a spin-allowed and adiabatic electron exchange process. Our calculations are consistent with previous experimental results regarding the spin-excitation energy (^3T_1g) of Co(III), and the fact that an optical absorption peak (^2E_g) of the Co(II) species could not be found experimentally. Our rate is of order 6 10^{-3} 1/Ms and hence 2 orders of magnitude faster than determined previously by experiments.

physics.chem-ph↗

arXiv2002

Structural and electronic properties of pentacene molecule and molecular pentacene solid

The structural and electronic properties of a single pentacene molecule and a pentacene molecular crystal, an organic semiconductor, are examined by a first-principles method based on the generalized gradient approximation of density functional theory. Calculations were carried out for a triclinic unit cell containing two pentacene molecules. The bandwidths of the valence and conduction bands which determine the charge migration mechanism are found to depend strongly on the crystallographic direction. Along the triclinic reciprocal lattice vectors A and B which are orientated approximately perpendicular to the molecular axes the maximal valence (conduction) band width amounts to only 75 (59) meV, even smaller values are obtained for the C direction parallel to molecular axes even less. Along the stacking directions A+B and A-B, however, the maximal valence (conduction) band width is found to reach 145 (260) meV. The value for the conduction band width is larger than estimates for the polaron binding energy but significantly smaller than recent results obtained by semiempirical methods. The single molecule has a HOMO-LUMO gap of about 1.1 eV as deduced from the Kohn-Sham eigenvalue differences. When using the self-consistent field method, which is expected to yield more reliable results, a value of 1.64 eV is obtained. The theoretical value for the band gap in the molecular solid amounts to 1.0 eV at the Gamma-point.

cond-mat.mtrl-sci↗

arXiv2002

Electronic properties of DNA: structural and chemical influence on the quest for high conductance and charge transfer

Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced electronic overlaps or from small activation energies. In particular, we examine A- vs B-DNA, the ribbon-like structures proposed to arise from molecular stretching, the potential role of counterions in hole doping the DNA orbitals, the possibility of backbone conduction, and the effects of water. We find that small activation gaps observed in conductivity experiments may arise in the presence of water and counter ions. We further discuss the role of harmonic vibration and twisting motion on electron tight binding matrix elements using ab initio density functional theory and model Koster-Slater theory calculations. We find that partial cancellation between pp-sigma and pp-pi interaction of Pz orbitals on adjacent base pairs, along with destructive interference of phase factors are needed to explain the weak conductance of A-DNA. Our results lead also to a physical interpretation of the angular dependence of inter-base pair tight binding matrix elements. Furthermore, we estimate Franck-Condon factors, reorganization energies and nuclear frequencies essential for charge transfer rates, and find our estimated hole transfer rates between base pairs to be in excellent agreement with recent picosecond dynamics data.

cond-mat.soft↗

arXiv2002

Mediation of Long Range Charge Transfer by Kondo Bound States

We present a theory of non-equilibrium long range charge transfer between donor and acceptor centers in a model polymer mediated by magnetic exciton (Kondo) bound states. Our model produces electron tunneling lengths easily exceeding 10$Å$, as observed recently in DNA and organic charge transfer systems. This long ranged tunneling is effective for weak to intermediate donor-bridge coupling, and is enhanced both by weak to intermediate strength Coulomb hole-electron attraction (through the orthogonality catastrophe) and by coupling to local vibrational modes.

cond-mat.str-el↗

arXiv2002

Strong electron correlations in cobalt valence tautomers

We have examined cobalt based valence tautomer molecules such as Co(SQ)$_2$(phen) using density functional theory (DFT) and variational configuration interaction (VCI) approaches based upon a model Hamiltonian. Our DFT results extend earlier work by finding a reduced total energy gap (order 0.6 eV) between high temperature and low temperature states when we fully relax the coordinates (relative to experimental ones). Futhermore we demonstrate that the charge transfer picture based upon formal valence arguments succeeds qualitatively while failing quantitatively due to strong covalency between the Co 3$d$ orbitals and ligand $p$ orbitals. With the VCI approach, we argue that the high temperature, high spin phase is strongly mixed valent, with about 30 % admixture of Co(III) into the predominantly Co(II) ground state. We confirm this mixed valence through a fit to the XANES spectra. Moreover, the strong electron correlations of the mixed valent phase provide an energy lowering of about 0.2-0.3 eV of the high temperature phase relative to the low temperature one. Finally, we use the domain model to account for the extraordinarily large entropy and enthalpy values associated with the transition.

cond-mat↗