First-principles calculation of thermodynamic stability of acids and bases under pH environment: a microscopic pH theory.

Despite being one of the most important thermodynamic variables, pH has yet to be incorporated into first-principles thermodynamics to calculate stability of acidic and basic solutes in aqueous solutions. By treating the solutes as defects in homogeneous liquids, we formulate a first-principles approach to calculate their formation energies under proton chemical potential, or pH, based on explicit molecular dynamics. The method draws analogy to first-principle calculations of defect formation energies under electron chemical potential, or Fermi energy, in semiconductors. From this, we propose a simple pictorial representation of the general theory of acid-base chemistry. By performing first-principles molecular dynamics of liquid water models with solutes, we apply the formulation to calculate formation energies of various neutral and charged solutes such as H(+), OH(-), NH(3), NH(4)(+), HCOOH, and HCOO(-) in water. The deduced auto-dissociation constant of water and the difference in the pKa values of NH(3) and HCOOH show good agreement with known experimental values. Our first-principles approach can be further extended and applied to other bio- and electro-chemical molecules such as amino acids and redox reaction couples that could exist in aqueous environments to understand their thermodynamic stability.

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.

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 Fermi's Golden Rule to estimate the energy transfer rates for a large ensemble of bimolecular complexes in random relative orientations. Utilization of Poisson's 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.

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.

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.

Finding gas diffusion pathways in proteins: application to O2 and H2 transport in CpI [FeFe]-hydrogenase and the role of packing defects.

We report on a computational investigation of the passive transport of H2 and O2 between the external solution and the hydrogen-producing active site of CpI [FeFe]-hydrogenase from Clostridium pasteurianum. Two distinct methodologies for studying gas access are discussed and applied: (1) temperature-controlled locally enhanced sampling, and (2) volumetric solvent accessibility maps, providing consistent results. Both methodologies confirm the existence and function of a previously hypothesized pathway and reveal a second major pathway that had not been detected by previous analyses of CpI's static crystal structure. Our results suggest that small hydrophobic molecules, such as H2 and O2, diffusing inside CpI, take advantage of well-defined preexisting packing defects that are not always apparent from the protein's static structure, but that can be predicted from the protein's dynamical motion. Finally, we describe two contrasting modes of intraprotein transport for H2 and O2, which in our model are differentiated only by their size.

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.

Atomic resolution modeling of the ferredoxin:[FeFe] hydrogenase complex from Chlamydomonas reinhardtii.

The [FeFe] hydrogenases HydA1 and HydA2 in the green alga Chlamydomonas reinhardtii catalyze the final reaction in a remarkable metabolic pathway allowing this photosynthetic organism to produce H(2) from water in the chloroplast. A [2Fe-2S] ferredoxin is a critical branch point in electron flow from Photosystem I toward a variety of metabolic fates, including proton reduction by hydrogenases. To better understand the binding determinants involved in ferredoxin:hydrogenase interactions, we have modeled Chlamydomonas PetF1 and HydA2 based on amino-acid sequence homology, and produced two promising electron-transfer model complexes by computational docking. To characterize these models, quantitative free energy calculations at atomic resolution were carried out, and detailed analysis of the interprotein interactions undertaken. The protein complex model we propose for ferredoxin:HydA2 interaction is energetically favored over the alternative candidate by 20 kcal/mol. This proposed model of the electron-transfer complex between PetF1 and HydA2 permits a more detailed view of the molecular events leading up to H(2) evolution, and suggests potential mutagenic strategies to modulate electron flow to HydA2.

Shape dependence of band-edge exciton fine structure in CdSe nanocrystals.

The band-edge exciton fine structure of wurtzite CdSe nanocrystals is investigated by a plane-wave pseudopotential method that includes spin-orbit coupling, screened electron-hole Coulomb interactions, and exchange interactions. Large-scale, systematic simulations have been carried out on quantum dots, nanorods, nanowires, and nanodisks. The size and shape dependence of the exciton fine structure is explored over the whole diameter-length configuration space and is explained by the interplay of quantum confinement, intrinsic crystal-field splitting, and electron-hole exchange interactions. Our results show that the band-edge exciton fine structure of CdSe nanocrystals is determined by the origin of their valence-band single-particle wave functions. Nanocrystals where the valence-band maximum originates from the bulk A band have a "dark" ground-state exciton. Nanocrystals where the valence-band maximum is derived from the bulk B band have a "quasi-bright" ground-state exciton. Thus, the diameter-length configuration map can be divided into two regions, corresponding to dark and quasi-bright ground-state excitons. We find that the dark/quasi-bright ground-state exciton crossover is not only diameter-dependent but also length-dependent, and it is characterized by a curve in the two-parameter space of diameter and length.

Theoretical studies on conjugated phenyl-cored thiophene dendrimers for photovoltaic applications.

Pi-conjugated dendrimers are an important class of materials for optoelectronic devices, especially for light-harvesting systems. We report here a theoretical investigation of the optical response and of the excited-state properties of three-arm and four-arm phenyl-cored dendrimers for photovoltaic applications. A variety of theoretical methods are used and evaluated against each other to calculate vertical transition energies, absorption and excitation spectra with vibronic structure, charge transport, and excitonic behavior upon photoexcitation and photoemission processes. Photophysical phenomena in these dendrimers are, in general, better explained with ab initio methods rather than with semiempirical techniques. Calculated reorganization energies were found to correlate well with the device photocurrent data where available. The excitons formed during photoexcitation are calculated to be more delocalized than the ones formed after vibrational relaxation in the excited states for fluorescence emission. The localization of excitons in emission processes is a result of geometrical changes in the excited state coupled with vibronic modes. Correlated electron-hole pair diagrams illustrate breaking of pi-conjugation in three-arm dendrimers due to meta linkage of arms with the core, whereas four-arm dendrimers are not affected by such breaking due to presence of ortho and para branching. Yet, ortho branching causes large twist angles between the core and the arms that are detrimental to pi-electron system delocalization over the structure.