Kwiseon Kim

Molecular dynamics and experimental investigation of H2 and O2 diffusion in [Fe]-hydrogenase

The [Fe]-hydrogenase enzymes are highly efficient H(2) catalysts found in ecologically and phylogenetically diverse microorganisms, including the photosynthetic green alga, Chlamydomonas reinhardtii. Although these enzymes can occur in several forms, H(2) catalysis takes place at a unique [FeS] prosthetic group or H-cluster, located at the active site. Significant to the function of hydrogenases is how the surrounding protein structure facilitates substrate-product transfer, and protects the active site H-cluster from inactivation. To elucidate the role of protein structure in O(2) inactivation of [Fe]-hydrogenases, experimental and theoretical investigations have been performed. Molecular dynamics was used to comparatively investigate O(2) and H(2) diffusion in CpI ([Fe]-hydrogenase I from Clostridium pasteurianum). Our preliminary results suggest that H(2) diffuses more easily and freely than O(2), which is restricted to a small number of allowed pathways to and from the active site. These O(2) pathways are located in the conserved active site domain, shown experimentally to have an essential role in active site protection.

Approaches to developing biological H 2 -photoproducing organisms and processes

The development of efficient biological systems for the direct photoproduction of H(2) gas from water faces several challenges, the more serious of which is the sensitivity of the H(2)-evolving enzymes (hydrogenases) to O(2), an obligatory by-product of photosynthesis. This high sensitivity is common to both FeFe and NiFe hydrogenases, and is caused by O(2) binding to their respective metallocatalytic sites. This overview describes approaches to (i) molecular engineering of algal FeFe-hydrogenase to prevent O(2) access to its catalytic site; (ii) transform a cyanobacterium with an O(2)-tolerant bacterial NiFe hydrogenase or (c) partially inactivate algal O(2)-evolution activity to create physiologically anaerobiosis and induce hydrogenase expression.

Charge transport simulations in conjugated dendrimers.

We present here a theoretical methodology that exploits quantum mechanical calculations, molecular mechanics calculations, and Monte Carlo simulations to predict the time-of-flight measurement mobilities in films of phenyl-cored conjugated thiophene dendrimers. Our aim is to reveal structure-property relationships in amorphous films of organic pi-conjugated materials. The simulations show that both hole and electron mobilities increase with the size of dendrimer, and that the former is larger than latter in all dendrimers. Internal reorganization energies are inversely correlated with the mobilities. Our simulations also indicate that dendrimers have small density of states for energetic disorder (<60 meV), and both hole and electron mobilities possess weak electric field dependence. We examine the influence of external reorganization energy as well as the possible trap sites on charge transport in these materials.

Density Functional Theory Calculation of Bonding and Charge Parameters for Molecular Dynamics Studies on [FeFe] Hydrogenases.

We have developed and tested molecular mechanics parameters for [FeS] clusters found in known [FeFe] hydrogenases. Bond stretching, angle bending, dihedral and improper torsion parameters for models of the oxidized and reduced catalytic H-cluster, [4Fe4S](+,2+)Cys4, [4Fe4S](+,2+)Cys3His, and [2Fe2S](+,2+)Cys4, were calculated solely from Kohn-Sham density functional theory and Natural Population Analysis. Circumsphere analysis of the cubane clusters in the energy-minimized structure of the full Clostridium pasteurianum hydrogenase I showed the resulting metallocluster structures to be similar to known cubane structures. All clusters were additionally stable in molecular dynamics simulations over the course of 1.0 ns in the fully oxidized and fully reduced enzyme models. Normal modes calculated by quasiharmonic analysis from the dynamics data show unexpected couplings among internal coordinate motions, which may reflect the effects of the protein structure on metallocluster dynamics.

Brownian Dynamics and Molecular Dynamics Study of the Association between Hydrogenase and Ferredoxin from Chlamydomonas reinhardtii

The [FeFe] hydrogenase from the green alga Chlamydomonas reinhardtii can catalyze the reduction of protons to hydrogen gas using electrons supplied from photosystem I and transferred via ferredoxin. To better understand the association of the hydrogenase and the ferredoxin, we have simulated the process over multiple timescales. A Brownian dynamics simulation method gave an initial thorough sampling of the rigid-body translational and rotational phase spaces, and the resulting trajectories were used to compute the occupancy and free-energy landscapes. Several important hydrogenase-ferredoxin encounter complexes were identified from this analysis, which were then individually simulated using atomistic molecular dynamics to provide more details of the hydrogenase and ferredoxin interaction. The ferredoxin appeared to form reasonable complexes with the hydrogenase in multiple orientations, some of which were good candidates for inclusion in a transition state ensemble of configurations for electron transfer.

Hydrogenase/ferredoxin charge-transfer complexes: effect of hydrogenase mutations on the complex association.

The [FeFe]-hydrogenases in the green alga Chlamydomonas reinhardtii utilize photogenerated electrons to reduce protons into hydrogen gas. The electrons are supplied from photosystem I and transferred to the [FeFe]-hydrogenase through specific hydrogenase-ferredoxin association. To understand how structural and kinetic factors control the association better, we used Brownian dynamics simulation methods to simulate the charge-transfer complex formation between both native and in silico mutants of the [FeFe]-hydrogenase HYDA2 and the [2Fe2S]-ferredoxin FDX1 from C. reinhardtii . The changes in binding free energy between different HYDA2 mutants and the native FDX1 were calculated by the free-energy perturbation method. Within the limits of our current models, we found that two HYDA2 mutations, T99K(H) and D102K(H), led to lower binding free energies and higher association rate with FDX1 and are thus promising targets for improving hydrogen production rates in engineered organisms.

Exciton migration in conjugated dendrimers: a joint experimental and theoretical study.

We report a joint experimental and theoretical investigation of exciton diffusion in phenyl-cored thiophene dendrimers. Experimental exciton diffusion lengths of the dendrimers vary between 8 and 17 nm, increasing with the size of the dendrimer. A theoretical methodology is developed to estimate exciton diffusion lengths for conjugated small molecules in a simulated amorphous film. The theoretical approach exploits Fermis Golden Rule to estimate the energy transfer rates for a large ensemble of bimolecular complexes in random relative orientations. Utilization of Poissons equation in the evaluation of the Coulomb integral leads to very efficient calculation of excitonic couplings between the donor and the acceptor chromophores. Electronic coupling calculations with delocalized transition densities revealed efficient coupling pathways in the bulk of the material, but do not result in strong couplings between the chromophores which are calculated for more localized transition densities. The molecular structures of dendrimers seem to be playing a significant role in the magnitude of electronic coupling between chromophores. Simulated diffusion lengths correlate well with the experimental data. The chemical structure of the chromophore, the shape of the transition densities and the exciton lifetime are found to be the most important factors in determining the size of the exciton diffusion length in amorphous films of conjugated materials.

[FeFe]-hydrogenases and photobiological hydrogen production

The promise of efficient, economic and renewable H2 photoproduction from water can potentially be met by green algae. These organisms are able to functionally link photosynthetic water oxidation to the catalytic recombination of protons and electrons to generate H2 gas through the activity of the hydrogenase enzyme. Green algal hydrogenases contain a unique metallo-catalytic H-cluster that performs the reversible H2 oxidation /evolution reactions. The H-cluster, located in the interior of the protein structure is irreversibly inactivated by O2, the by-product of water oxidation. We developed an Escherichi coli expression system to produce [FeFe]-hydrogenases from different biological sources and demonstrated that clostridial [FeFe]-hydrogenases have higher tolerance to O2 inactivation compared to their algal counterparts. We have been using computational simulations of gas diffusion within the Clostridium pasteurianum CpI hydrogenase to identify the pathways through which O2 can reach its catalytic site. Subsequently, we modify the protein structure at specific sites along the O2 pathways (identified by the computational simulations) by site-directed mutagenesis with the goal of generating recombinant enzymes with higher O2 tolerance. In this paper, we review the computational simulation work and report on preliminary results obtained through this strategy.

Electronic and optical properties of the group-III nitrides, their heterostructures and alloys

Various aspects of the electronic structure of the group III nitrides are discussed. The relation between band structures and optical response in the vacuum ultraviolet is analyzed for zincblende and wurtzite GaN and for wurtzite AlN and compared with available experimental data obtained from reflectivity and spectroscopic ellipsometry. The spin-orbit and crystal field splittings of the valence band edges and their relations to exciton fine structure are discussed including substrate induced biaxial strain effects. The band-offsets between the III-nitrides and some relevant semiconductor substrates obtained within the dielectric midgap energy model are presented and strain effects which may alter these values are discussed. The importance of lattice mismatch in bandgap bowing is exemplified by comparing Al{sub x}Ga{sub 1{minus}x}N and In{sub x}Ga{sub 1{minus}x}N.

Negative band gap bowing in epitaxial InAs/GaAs alloys and predicted band offsets of the strained binaries and alloys on various substrates

We use pseudopotential theory to provide (1) the band offsets of strained GaAs and InAs on various substrates and (2) the energies Ev(x) and Ec(x) of the valence and conduction bands of InxGa1−xAs alloy, as a function of composition. Results are presented for both the bulk alloy and for the alloy strained on InP or GaAs. We predict that while Ec(x) bows downward for relaxed bulk alloys, it bows upward for strained epitaxial alloys. The calculated alloy offsets are used to discuss electron and hole localization in this system.