A Density Functional Theory Study on the Active Center of Fe-Only Hydrogenase: Characterization and Electronic Structure of the Redox States

We have carried out extensive density functional theory (DFT) calculations for possible redox states of the active center in Fe-only hydrogenases. The active center is modeled by [(H(CH(3))S)(CO)(CN(-))Fe(p)(mu-DTN)(mu-CO)Fe(d)(CO)(CN(-))(L)](z) (z is the net charge in the complex; Fe(p)= the proximal Fe, Fe(d) = the distal Fe, DTN = (-SCH(2)NHCH(2)S-), L is the ligand that bonds with the Fed at the trans position to the bridging CO). Structures of possible redox states are optimized, and CO stretching frequencies are calculated. By a detailed comparison of all the calculated structures and the vibrational frequencies with the available experimental data, we find that (i) the fully oxidized, inactive state is an Fe(II)-Fe(II) state with a hydroxyl (OH(-)) group bonded at the Fe(d), (ii) the oxidized, active state is an Fe(II)-Fe(l) complex which is consistent with the assignment of Cao and Hall (J. Am. Chem. Soc. 2001, 123, 3734), and (iii) the fully reduced state is a mixture with the major component being a protonated Fe(l)-Fe(l) complex and the other component being its self-arranged form, Fe(II)-Fe(II) hydride, Our calculations also show that the exogenous CO can strongly bond with the Fe(II)-Fe(l) species, but cannot bond with the Fe(l)-Fe(l) complex. This result is consistent with experiments that CO tends to inhibit the oxidized, active state, but not the fully reduced state. The electronic structures of all the redox states have been analyzed. It is found that a frontier orbital which is a mixing state between the e(g) of Fe and the 2pi of the bridging CO plays a key role concerning the reactivity of Fe-only hydrogenases: (1) it is unoccupied in the fully oxidized, inactive state, half-occupied in the oxidized, active state, and fully occupied in the fully reduced state; (ii) the e(g)-2pi orbital is a bonding state, and this is the key reason for stability of the low oxidation states, such as Fe(l)-Fe(l) complexes; and (iii) in the e(g)-2pi orbital more charge accumulates between the bridging CO and the Fe(d) than between the bridging CO and the Fe(p), and the occupation increase in this orbital will enhance the bonding between the bridging CO and the Fe(d), leading to the bridging-CO shift toward the Fe(d).

Electronic structure of the nitrogen-vacancy center in diamond from first-principles theory

The nitrogen-vacancy (NV) center is a paramagnetic defect in diamond with applications as a qubit. Here, we investigate its electronic structure by using ab initio density functional theory for five different NV center models of two different cluster sizes. We describe the symmetry and energetics of the low-lying states and compare the optical frequencies obtained to experimental results. We compute the major transition of the negatively charged NV centers to within 25–100 meV accuracy and find that it is energetically favorable for substitutional nitrogens to donate an electron to NV0. The excited state of the major transition and the NV0 state with a neutral donor nitrogen are found to be close in energy.

Electronic Structure of an XUV Photogenerated Solid-Density Aluminum Plasma

By use of high intensity XUV radiation from the FLASH free-electron laser at DESY, we have created highly excited exotic states of matter in solid-density aluminum samples. The XUV intensity is sufficiently high to excite an inner-shell electron from a large fraction of the atoms in the focal region. We show that soft-x-ray emission spectroscopy measurements reveal the electronic temperature and density of this highly excited system immediately after the excitation pulse, with detailed calculations of the electronic structure, based on finite-temperature density functional theory, in good agreement with the experimental results.

The synthesis and electronic structure of a novel [NiS4Fe2(CO)(6)] radical cluster: Implications for the active site of the [NiFe] hydrogenases

A novel [Ni'S-4'Fe-2(CO)(6)] cluster (1: 'S-4'=(CH3C6H3S2)(2)(CH2)(3)) has been synthesised, structurally characterised and has been shown to undergo a chemically reversible reduction process at -1.31 V versus Fc(+)/Fc to generate the EPR-active monoanion 1(-). Multifrequency Q-, X- and S-band EPR spectra of Ni-61-enriched 1(-) show a well-resolved quartet hyperfine splitting in the low-field region due to the interaction with a single Ni-61 (I = 3/2) nucleus. Simulations of the EPR spectra require the introduction of a single angle of non-coincidence between g, and A(1), and g(3) and A(3) to reproduce all of the features in the S- and X-band spectra. This behaviour provides a rare example of the detection and measurement of non-coincidence effects from frozen-solution EPR spectra without the need for single-crystal measurements, and in which the S-band experiment is sensitive to the non-coincidence. An analysis of the EPR spectra of 1(-) reveals a 24% Ni contribution to the SOMO in 1(-), supporting a delocalisation of the spin-density across the NiFe2 cluster. This observation is supported by IR spectroscopic results which show that the CO stretching frequencies, v(CO), shift to lower frequency by about 70 cm(-1) when 1 is reduced to 1(-). Density functional calculations provide a framework for the interpretation of the spectroscopic properties of 1(-) and suggest that the SOMO is delocalised over the whole cluster, but with little S-centre participation. This electronic structure contrasts with that of the Ni-A, -B, -C and -L forms of [NiFe] hydrogenase in which there is considerable S participation in the SOMO.

A theoretical study of the effects of lithium intercalation on the electronic structure of TiS

The band structure of the intercalation complex of LiTiS has been computed using a semi-empirical tight-binding method and this is compared with the results of a revised TiS calculation. The results obtained confirm that changes in the basic electrical characteristics of TiS, which occur when it is intercalated with lithium, can be attributed to a rigid-band filling of its lowest unoccupied electron states as has previously been proposed. However, they also suggest that intercalation can act to alter the nature and the dispersion of some of the energy bands in the unintercalated crystal. The bands which are most affected by the process are those which derive from orbitals which have the same symmetry as the lithium 2s orbital, namely, the titanium 4s conduction level and the tightly bound sulphur 3s levels.

Magnetic and electronic structure of TICo2S2

An extensive investigation of the ferromagnetic compound TlCo2S2 has resulted in new information on the electronic and magnetic structure. Electronic structure calculations showed that magnetic ordering is energetically favorable with a clear driving force for ferromagnetic coupling within the cobalt layers. TlCo2S2 is metallic and the conductivity is due to holes in the valence band. XPS single crystal measurements did not show evidence of mixed oxidation states of cobalt. Neutron powder diffraction resulted in a ferromagnetic structure with the magnetic moment in the ab-plane. The derived magnetic moment of the cobalt atom is 0.65(2) mu(B) at 10 K and is in very good agreement with the value, mu(sat) = 0.65(1) mu(B) at 10 K, inferred from the magnetic hysteresis curve. (C) 2004 Elsevier Inc. All rights reserved.

Optimal basis set for electronic structure calculations in periodic systems

An efficient method for calculating the electronic structure of systems that need a very fine sampling of the Brillouin zone is presented. The method is based on the variational optimization of a single (i.e., common to all points in the Brillouin zone) basis set for the expansion of the electronic orbitals. Considerations from k.p-approximation theory help to understand the efficiency of the method. The accuracy and the convergence properties of the method as a function of the optimal basis set size are analyzed for a test calculation on a 16-atom Na supercell.

Determining the electronic structure and chemical potentials of molecules in solution

A simulation scheme is proposed for determining the excess chemical potential of a substance in solution. First, a Monte Carlo simulation is performed with classical models for solute and solvent molecules. A representative sample of these configurations is then used in a hybrid quantum/classical (QM/MM) calculation, where the solute is treated quantum-mechanically, and the average electronic structure is used to construct an improved classical model. This procedure is iterated to self-consistency in the classical model, which in practice is attained in one or two steps, depending on the quality of the initial guess. The excess free energy of the molecule within the QM/MM approach is determined relative to the classical model using thermodynamic perturbation theory with a cumulant expansion. The procedure provides a method of constructing classical point charge models appropriate for the solution and gives a measure of the importance of solvent fluctuations.

A simple model of atomic interactions in noble metals based explicitly on electronic structure

A total energy tight-binding model with a basis of just one s state per atom is introduced. It is argued that this simplest of all tight-binding models provides a surprisingly good description of the structural stability and elastic constants of noble metals. By assuming inverse power scaling laws for the hopping integrals and the repulsive pair potential, it is shown that the density matrix in a perfect primitive crystal is independent of volume, and structural energy differences and equations of state are then derived analytically. The model is most likely to be of use when one wishes to consider explicitly and self-consistently the electronic and atomic structures of a generic metallic system, with the minium of computation expense. The relationship to the free-electron jellium model is described. The applicability of the model to other metals is also considered briefly.