Substituted trimethylammonium cations serve as small molecule analogues for tetherable cations in anion exchange membranes. In turn, these membranes serve as the basis for alkaline membrane fuel ...cells by allowing facile conduction of hydroxide. As these cations are susceptible to hydroxide attack, they degrade over time and greatly limit the lifetime of the fuel cell. In this research, we performed density functional theory calculations to investigate the degradation pathways of substituted trimethylammonium cations to probe the relative durability of cation tethering strategies in alkyl and aromatic tethers. Our results show that significant changes in calculated energy barriers occur when substitution groups change. Specifically, we have found that, when available, the Hofmann elimination pathway is the most vulnerable pathway for degradation; however, this barrier is also found to depend on the carbon chain length and number of hydrogens susceptible to Hofmann elimination. SN2 barriers were also investigated for both methyl groups and substitution groups. The reported findings give important insight into potential tethering strategies for trimethylammonium cations in anion exchange membranes.
Proton transfer and local structures in 3M (EW 825) and Nafion (EW 890) membranes are investigated in this study by both standard nonreactive molecular dynamics and the self-consistent iterative ...multistate empirical valence bond method, which is capable of simulating multiple reactive protons and accounting for the Grotthuss mechanism of proton transport. The Nafion and 3M systems have the same backbone, so we can isolate and compare the effect of the different side chains by calculating the radial distribution functions (RDFs), self-diffusion constants, and other properties for three hydration levels at 5, 9, and 14 at 300 and 353 K. The conformations of the 3M and Nafion side chains are also compared. We found that even though many results are similar for both F3C and SPC/Fw water models, certain trends such as the sulfonate clustering can depend on the water model selected. The relationship between the different RDFs for the sulfonate, water, and hydronium is discussed. The self-diffusion constants of water for both membranes are found to be close with respect to each water model selected, even though the experimental values for 3M at 300 K are higher. The calculated self-diffusion constants of the excess protons are found to be higher for 3M than Nafion for hydration levels 9 and 14 at 300 K but statistically the same at 353 K.
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.
π-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 π-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 π-electron system delocalization over the structure.
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.
Surface passivation optimization using DIRECT Graf, Peter A.; Kim, Kwiseon; Jones, Wesley B. ...
Journal of computational physics,
06/2007, Letnik:
224, Številka:
2
Journal Article
Recenzirano
We describe a systematic and efficient method of determining pseudo-atom positions and potentials for use in nanostructure calculations based on bulk empirical pseudopotentials (EPMs). Given a bulk ...EPM for binary semiconductor X, we produce parameters for pseudo-atoms necessary to passivate a nanostructure of X in preparation for quantum mechanical electronic structure calculations. These passivants are based on the quality of the wave functions of a set of small test structures that include the passivants. Our method is based on the global optimization method DIRECT. It enables and/or streamlines surface passivation for empirical pseudopotential calculations.
In contrast to pseudobinary alloys, the relative number of bonds in quaternary alloys cannot be determined uniquely from the composition. Indeed, we do not know if the Ga0.5In0.5As0.5N0.5 alloy ...should be thought of as InAs+GaN or as InN+GaAs. We study the distribution of bonds using Monte Carlo simulation and find that the number of In-N and Ga-As bonds increases relative to random alloys. This quaternary-unique short range order affects the band structure: we calculate a blueshift of the band gap and predict the emergence of a broadband tail of localized states around the conduction band minimum.
Charge Transport Simulations in Conjugated Dendrimers Köse, Muhammet E; Long, Hai; Kim, Kwiseon ...
The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory,
04/2010, Letnik:
114, Številka:
12
Journal Article
Recenzirano
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 π-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.
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