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A theoretical study of methanol oxidation mechanisms by methanol dehydrogenase enzymes for fuel cell applications

Enzymes are considered for electrochemical generation of power in fuel cells. Methanol dehydrogenase MDH) is one such enzyme, which has been used as an anodic catalyst for a methanol-fed biofuel cell producing enough power for small electronic device applications. In practice, however, there are power output limitations associated with this MDH fuel cell, which may potentially be eliminated or reduced if the reactivity of this enzyme during the oxidation of methanol at the molecular level is clearly understood. Two mechanisms for the methanol oxidation process by MDH have been proposed in the literature, Addition-Elimination A-E) and Hydride Transfer H-T), but no agreement has been reached about what mechanism actually operates in reality. Also, it was suggested that ion-modified MDH, particularly Ba 2＋-MDH enzyme, is more active towards oxidation of methanol than Ca 2＋-MDH from experimental kinetic observations. In this dissertation, MDH active site models of varying sizes were tested for the A-E and H-T methanol oxidation in the presence of both Ca2＋ and Ba2＋. Potential energy surfaces for the reactions were calculated, and the feasibility of the suggested reaction mechanisms was judged by comparison with available experimental free energy barriers. By systematically increasing the size of the models, deeper insight into the details of the reactions was obtained, and the role of the various active site residues was also analyzed. Comparison of free energy barriers calculated for the rate-determining steps in this work for the A-E and H-T oxidation mechanisms with experimental Gibbs energy of activation by Ca2＋-MDH showed that these two mechanisms may not be correctly proposed in the literature. Also, the reduction of barriers for the rate-determining steps in the presence of Ba2＋ for A-E and H-T obtained with the best MDH active site model tested here is almost twice as much the experimental free energy reduction with Ba 2＋-MDH for methanol oxidation. A modified first step of original H-T resulted in a newly proposed two-step H-T oxidation mechanism, where the barrier for the formation of final product, formaldehyde, during the first step is very much comparable 11.4 kcal/mol) to the experimental Gibbs energy of activation 8.5 kcal/mol). In the case of Ba2＋ presence during this new mechanism, the free energy barrier is 6.2 kcal/mol, which is comparable to free energy of activation for oxidation of methanol by Ba2＋-MDH 3.5 kcal/mol). The second and final step involving proton transfer in this Two-step H-T was observed to be mediated by a water molecule in the presence of both ions. Moreover, DFT-MD investigations on the reactant complex and necessary intermediates associated with all mechanisms also lead us to the conclusion that oxidation of methanol by MDH has a greater probability of proceeding through the two-step hydride transfer mechanism compared to proposed A-E and H-T.

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A physical approach to boundary conditions for the characterization of one-dimensional nanomaterials

The production of sub-micron structures has created a need for techniques to characterize these structures. This is especially true since many of the materials composing these structures do not behave as would be predicted by traditional meso-scale equations. This paper considers both experimental and theoretical aspects of the three-point bending method for measuring the elastic modulus of 1-D nanostructures such as wires, tubes, and belts. Three-point bending tests were performed using an atomic force microscope (AFM) on silica nanowires suspended over micro-channels. Detailed consideration was given to AFM calibration, measurement uncertainty, and the importance of the boundary conditions existing where the wires are anchored to the test structure. Correct representation of the boundary conditions is critical for the use of models with the observed data to estimate the elastic modulus. The standard fixed and simple beam models have been used exclusively for estimating the elastic modulus, despite their unrealistic representation of boundary conditions. The Winkler model is applied here to represent an elastic bond between the nanowires and the polymer film anchoring them to the test structure. The application of this model requires measurement of the elastic modulus of the polymer, which was accomplished in this study via indentation testing with an AFM probe. The results clearly indicate that the silica nanowires in this study, with diameters between 50 and 130 nm, have an apparent elastic modulus greater than bulk. The results suggest that the apparent elastic modulus increases with smaller diameters in a way consistent with predictions made through the consideration of energy stored in the nanowires in the form of surface tension.

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Data fusion in scientific data mining

Data fusion involves multi-sources or multi-presentations of a single source to perform inferences which are more comprehensive and accurate than those of any single method. Thus, data fusion makes it possible to create a synergistic process in which the consolidation of individual data creates a combined resource with a productive value greater than the sum of its parts. While considerable research has been done on data fusion in the past, most of them performed in the field of multi-sensor fusion. There has been relatively less work conducted in a data mining context. The goal of this dissertation is to develop a data fusion framework for predictive modeling, especially to the Quantitative Structure-Activity Relationship QSAR) problems, which includes a function-oriented model, general architecture paradigms and corresponding learning algorithms. Furthermore, kernel methods, e.g. kernel partial least squares K-PLS) ensemble with bagging and boosting is introduced as one of important decision level fusion methods. This approach can be applied to applications with multiple data sources available to obtain information of greater quality. In addition to the predefined three fusion levels, the kernel fusion method is further developed based on the properties of kernel in the feature space to take advantages of multiple physically different feature sets in order to build more accurate and robust predictive models. With Hessian-free and self-correction properties, the BFGS quasi-Newton method is employed for parameter tuning of kernel fusion. In addition to the regression algorithm applied in data fusion scheme introduced above, we also are trying to extend K-PLS to the classification, especially when the class distribution is highly skewed or changes dramatically over time. In this case, a probabilistic classifier with the capability to deal with high dimensional discrimination is desirable. To achieve this goal, a new kernel orthonormalized PLS logistic regression KOPLS-LR) and the corresponding ROC based adaptive threshold ROC-BAT) approach are proposed. KOPLS-LR inherits the advantages of K-PLS and logistic regression, while ROC-BAT provides an effective solution to predict observations in which the distribution dramatically changes over time. During the research process, a web-based modeling system has been designed and realized which integrates various learning methods, e.g. PLS, K-PLS and support vector machines SVM). Model selection parameter tuning) and performance estimation functionalities are also integrated in this online predictive modeling system. This predictive tool is open to the public and can be accessed at: http://reccr.chem.rpi.edu/Software/modeling/index.html

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Nuclear resonant scattering on nitrogenase, hydrogenase and model systems

Nitrogenase and hydrogenase are two critical iron-containing enzymes found in nature. Nitrogenase catalyzes the reduction of dinitrogen N 2) to ammonia, and hydrogenase catalyzes the evolution or consumption) of dihydrogen H2). A better understanding of these enzymes may have an impact on our ability to transition to more sustainable energy economy. Although X-ray crystallography has provided baseline structures of nitrogenase and hydrognease, and numerous spectroscopic studies and theoretical calculations have outlined catalytic mechanisms of these enzymes, the detailed mechanisms remain elusive. New spectroscopic techniques are needed. In this dissertation, three novel synchrotron radiation based nuclear resonant scattering techniques have been used to probe the metal sites of nitrogenase and hydrogenase. They are nuclear resonance vibrational spectroscopy NRVS), synchrotron radiation based perturbed angular correlations SRPAC), and nuclear forward scattering NFS, or synchrotron Mossbauer). Because of its unique selection rule, NRVS provides more detailed vibrational information about the Fe sites in metalloproteins than infrared and Raman spectroscopy. FeCO vibrations revealed by NRVS on a series of iron carbonyl complexes have been used to confirm a cis-FeCO)2 geometry in the iron center of Hmd hydrogenase. A possible water ligand has also been identified for the first time. In CO inhibited nitrogenase, NRVS revealed the relationship between the intensity of the strongest spectral feature at 188 cm-1 and the structural distortion of FeMo-co introduced by CO binding. NRVS also revealed a possible 7 iron structure for the VK cluster — a key FeMo-co precursor in the nitrogenase biosynthetic pathway. Selectively probing iron site vibrations in metalloproteins has been achieved for the first time by applying NRVS onto protein crystals from rubredoxin and MoFe protein of nitrogenase. SRPAC and NFS have been used for the first time to reveal nuclear hyperfine interactions on the metal sites of iron-sulfur proteins and related model complexes. These synchrotron radiation spectroscopic techniques demonstrate a great promise to obtain more detailed structural and electronic properties of the metal centers iron and nickel) in nitrogenase and hydrogenase than the conventional Mossbauer spectroscopy.

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Surface and bulk modification of poly(lactic acid)

The major drawbacks of PLA are its poor toughness and lack of readily reactable groups. Unfortunately, typical methods of PLA toughening are associated with significant modulus and/or ultimate tensile strength UTS) loss. The main objective of this research was to toughen PLA, with minimal modulus and/or UTS loss, and introduce reactive groups into the PLA matrix in one step. Initially, this objective was divided into two separate parts: PLA surface modification followed by toughening. PLA film was solvent cast from chloroform solution and was surface modified using a sequential two-step photografting approach. Benzophenone was photografted onto the film surface in Step 1 followed by photopolymerization of hydrophilic monomers, acrylic acid and acrylamide, from the film surface. The resultant films were characterized using ATR-FTIR spectroscopy, water contact angle goniometry, transmission FTIR microspectroscopy, and tensile testing. The effect of the reaction solvent ethanol and water) in Step 2 on PLA film surface and bulk properties was also studied. There was significant penetration of monomers into the films when ethanol was used as the reaction solvent, resulting in significant toughness loss. This monomer penetration into the films was successfully reduced by using water instead of ethanol as the reaction solvent in Step 2 and resultant films showed higher toughness than films surface-modified using ethanol as the reaction solvent in Step 2. It was also observed that solvent cast PLA film retained approximately 13 wt% chloroform, as characterized using thermogravimetric analyses TGA). The presence of residual chloroform in the film specimens is undesirable from a biocompatibility standpoint. Therefore, further work was conducted on melt-processed films where residual solvent from the film-formation method would not be an issue. Addition of a small amount of poly[3-hydroxybutyrate)-co-3-hydroxyhexanoate)] PHBHHx) to PLA improved the toughness of the resultant melt-processed blend from 4 ＋/- 2 MPa for neat PLA to 175 ＋/- 35 MPa for PLA-PHBHHx blend 90 wt% PLA). PLA-PHBHHx blend films were melt-processed using a single screw extruder. These polyblend films appeared to be non-compatible as characterized using dynamic mechanical analyses DMA). PLA-PHBHHx blend films underwent rapid physical aging losing their toughness from 175 ＋/- 35 MPa right after extrusion) to 68 ＋/- 34 MPa day 3). The blend films were surface modified using the sequential two-step photografting protocol using water as the reaction solvent in Step 2. PLA-PHBHHx blend films lost approximately 95% of their toughness on surface modification due to UV-assisted solvent induced crystallization as characterized using wide angle X-ray diffraction WAXD) analyses. A novel reactive blending approach was developed to toughen PLA with minimal modulus and UTS loss and introduce reactive groups into the PLA matrix. PLA was reactive blended with a stiffening polymer, polyacrylic acid) PAA), followed by physical blending with a toughening polymer, polyethylene glycol) PEG), in solution. The modified PLA was extruded into films using a co-rotating twin-screw extruder and characterized using tensile testing, differential scanning calorimetry DSC), DMA, and toluidine-blue-surface-staining. This material exhibited, for the first time, approximately 10 fold increase in PLAs toughness without significant modulus and/or UTS loss and also introduced a controlled concentration of surface modifiable reactive acid groups into the PLA matrix in one step.

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Amorphous and nanocrystalline phase formation in highly-driven aluminum-based binary alloys

Remarkable advances have been made since rapid solidification was first introduced to the field of materials science and technology. New types of materials such as amorphous alloys and nanostructure materials have been developed as a result of rapid solidification techniques. While these advances are, in many respects, ground breaking, much remains to be discerned concerning the fundamental relationships that exist between a liquid and a rapidly solidified solid. The scope of the current dissertation involves an extensive set of experimental, analytical, and computational studies designed to increase the overall understanding of morphological selection, phase competition, and structural hierarchy that occurs under far-from equilibrium conditions. High pressure gas atomization and Cu-block melt-spinning are the two different rapid solidification techniques applied in this study. The research is mainly focused on Al-Si and Al-Sm alloy systems. Silicon and samarium produce different, yet favorable, systems for exploration when alloyed with aluminum under far-from equilibrium conditions. One of the main differences comes from the positions of their respective T0 curves, which makes Al-Si a good candidate for solubility extension while the plunging T0 line in Al-Sm promotes glass formation. The rapidly solidified gas-atomized Al-Si powders within a composition range of 15 to 50 wt% Si are examined using scanning and transmission electron microscopy. The non-equilibrium partitioning and morphological selection observed by examining powders at different size classes are described via a microstructure map. The interface velocities and the amount of undercooling present in the powders are estimated from measured eutectic spacings based on Jackson-Hunt JH) and Trivedi-Magnin-Kurz TMK) models, which permit a direct comparison of theoretical predictions. For an average particle size of 10 microm with a Peclet number of ~0.2, JH and TMK deviate from each other. This deviation indicates an adiabatic type solidification path where heat of fusion is reabsorbed. It is interesting that this particle size range is also consistent with the appearance of a microcellular growth. While no glass formation is observed within this system, the smallest size powders appear to consist of a mixture of nanocrystalline Si and Al. Al-Sm alloys have been investigated within a composition range of 34 to 42 wt% Sm. Gas atomized powders of Al-Sm are investigated to explore the morphological and structural hierarchy that correlates with different degrees of departure from full equilibrium conditions. The resultant powders show a variety of structural selection with respect to amount of undercooling, with an amorphous structure appearing at the highest cooling rates. Because of the chaotic nature of gas atomization, Cu-block melt-spinning is used to produce a homogeneous amorphous structure. The as-quenched structure within Al-34 to 42 wt% Sm consists of nanocrystalline fcc-Al on the order of 5 nm) embedded in an amorphous matrix. The nucleation density of fcc-Al after initial crystallization is on the order of 1022-1023 m-3, which is 105-106 orders of magnitude higher than what classical nucleation theory predicts. Detailed analysis of liquid and as-quenched structures using high energy synchrotron X-ray diffraction, high energy transmission electron microscopy, and atom probe tomography techniques revealed an Al-Sm network similar in appearance to a medium range order MRO) structure. A model whereby these MRO clusters promote the observed high nucleation density of fcc-Al nanocrystals is proposed. The devitrification path was identified using high temperature, in-situ, high energy synchrotron X-ray diffraction techniques and the crystallization kinetics were described using an analytical Johnson-Mehl-Avrami JMA) approach.

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Computational study of pristine and titanium-doped sodium alanates for hydrogen storage applications

The emphasis of this research is to study and elucidate the underlying mechanisms of reversible hydrogen storage in pristine and Ti-doped sodium aluminum hydrides using molecular modeling techniques. An early breakthrough in using complex metal hydrides as hydrogen storage materials is from the research on sodium alanates by Bogdanovic et al., in 1997 reporting reversible hydrogen storage is possible at moderate temperatures and pressures in transition metal doped sodium alanates. Anton reported titanium salts as the best catalysts compared to all other transition metal salts from his further research on transition metal doped sodium alanates. However, a few questions remained unanswered regarding the role of Ti in reversible hydrogen storage of sodium alanates with improved thermodynamics and kinetics of hydrogen desorption. The first question is about the position of transition metal dopants in the sodium aluminum hydride lattice. The position is investigated by identifying the possible sites for titanium dopants in NaAlH4 lattice and studying the structure and dynamics of possible compounds resulting from titanium doping in sodium alanates. The second question is the role of titanium dopants in improved thermodynamics of hydrogen desorption in Ti-doped NaAlH4. Though it is accepted in the literature that formation of TiAl alloys Ti-Al and TiAl3) is favorable, reaction pathways are not clearly established. Furthermore, the source of aluminum for Ti-Al alloy formation is not clearly understood. The third question in this area is the role of titanium dopants in improved kinetics of hydrogen absorption and desorption in Ti-doped sodium alanates. This study is directed towards addressing the three longstanding questions in this area. Thermodynamic and kinetic pathways for hydrogen desorption in pristine NaAlH4 and formation of Ti-Al alloys in Ti-doped NaAlH 4, are elucidated to understand the underlying mechanisms of hydrogen desorption. Density functional theory formalism as implemented in CASTEP Cambridge Serial Total Energy Package) is used to study the structure and energetics of pristine and Ti-doped sodium alanates. From investigations of various models of sodium alanates with Ti dopants, it is shown that the difference between the energy required for Ti&rarr；SNa Ti-substituted Na at the lattice site on the surface) and Ti&rarr；TI Ti placed on top of the surface interstitial SI site) is 0.003 eV atom-1, and is minimal compared to other models. Since less energy is required for Ti&rarr；S Na and Ti&rarr；TI, these two sites SNa and T I) would be preferred by the Ti dopants. In Ti&rarr；SNa model, Ti is coordinated to two aluminum and seven hydrogen atoms resulting in the possible formation of a TiAl2H7 complex. At elevated temperatures 423 and 448 K), the number of aluminum atoms coordinating with titanium in the complex increase from two at distances in the 2.6-2.7 A range) to five at distances in the 2.6-2.7 A range). Besides the formation of a Ti-Al-H complex, Al-Al association with a 2.97 A bond length) is also seen from the DFT-MD results. In the case of Ti&rarr；TI, Ti is coordinated to two aluminum and two hydrogen atoms resulting in the possible formation of a TiAl2H2 complex. TiAl2 H2 complex becomes TiAl3H6 and TiAl 3H7 at elevated temperatures of 423 and 448 K, respectively. The investigation of thermodynamics pathways in Ti-doped sodium alanates illustrates a three step reaction pathway to the formation of TiAl3 Ti and AlH3 after the first reaction, TiAl after the second and finally TiAl3). This investigation also suggests aluminum in its ＋3 oxidation state present in aluminum hydride species is responsible in the formation of Ti-Al alloys. From kinetics studies, the proposed mechanism is related to transition from AlH4- to AlH6 3-. The rate limiting step is determined to be associated with hydrogen evolution from association of AlH3 species nucleating aluminum phase. This step is 15 kJ/mol higher than the nearest highest barrier in the reaction path related to transition from AlH52- to AlH63-. From the DFT-MD simulations, it is observed that the titanium dopants are present on the surface during the entire simulation time and exhibit the role in catalytic splitting of hydrogen from surrounding AlH4 groups. Besides the catalytic role, Ti dopants also form bonds with Al, and we also see that the AlH4 groups on the surface and that are present in the sub-surface layers are drawn towards the Ti dopants. This association of Al around titanium indicates the initiation of Al nucleation site facilitated by Ti dopants residing on the surface.

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Experimental phase diagram studies on the magnesium -manganese -cerium ternary system at magnesium-rich corner

The ternary Mg-Mn-Ce phase diagram was experimentally studied and thermodynamically calculated at the Mg-rich corner. More than twenty binary and ternary alloys were synthesized and heat-treated at both ambient and elevated temperatures. The microstructures and lattice parameters of the samples were studied via XRD, SEM/EDS and EPMA to determine phase equilibria. The ternary phase diagram was also calculated via thermodynamic calculation software FactSage. The results from both experiment and the assessment were compared and discussed. The binary phase diagrams were re-examined, especially the Mg-Ce system. In order to investigate the composition range of the intermetallic compounds Mg12Ce and Mg41Ce5, and to clarify data in the existing phase diagram, both the solid-liquid diffusion couple method and alloys synthesized with target phases were analyzed. Pure Mg – Ce contact was vacuum-encapsulated in quartz tube and the Mg and Ce inter-diffused at 400&deg；C. Alloys prepared were cast and annealed at a temperature range of 300-550&deg；C. All the four single-phase zones corresponding to the Mg-Ce phase diagram were observed via the diffusion couple technique. However, the stoichiometry of Mg12Ce studied on the synthesized and annealed alloys showed that on the Mg rich side of the present phase diagram, the compositional range of Mg12Ce should be redesignated as Mg11.17-10.81) Ce at ambient temperature, and Mg11.31-10.75)Ce at 530&deg；C. Mg41Ce5, on the other hand, has been confirmed as a line compound, but with composition 11.3at% Ce, rather than 10.9at% Ce. The binary phase diagram study was also extended to the Ce-rich side of Mg-Ce system. A new phase, Mg4Ce, was found in the study of phase Mg3Ce. Based on the investigation of the intermetallics in the Mg-Ce binary system, a modified phase diagram was suggested to accommodate the stoichiometry of Mg11Ce, Mg39Ce5, and Mg3Ce. The experimental study on the ternary phase diagram was conducted on three isopleths: 0.6, 1.8 and 2.5wt% Mn, respectively, and Ce varied between 0 and 25wt%. All alloys were synthesized from high purity starting materials. Two types of thermal analyses, namely, cooling curve analysis CCA) and differential scanning calorimetry DSC), were used to determine the liquidus and solid phase transformation temperatures. The heating/quenching tests on selected samples were conducted for phase analysis. The results showed that only one invariant point for ternary eutectic reaction was observed in the three isopleths, and the composition is 1wt% Mn and 22wt% Ce at 592&deg；C. Furthermore, a solid-solution type of ternary intermetallic compound Mg, Mn)11Ce is formed, holding the same tetragonal structure as Mg12Ce. The solid solution of Mn in Mg12Ce varies between 0.3&sim；0.6 at%, depending on alloy composition and quenching temperature. Finally, the phase diagram calculation with FactSage program was conducted and the small disagreement between the modeling results and present experimental data were found, especially for the eutectic temperature for L &rarr； Mghcp) ＋ Mg12Ce. This is mainly because the present experimental data were not available when the thermodynamic modeling had been performed. The Gibbs energy of Mg12Ce phase was re-optimized and the revised data can accurately reproduce the experimental results within experimental error limits.

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Probing protein folding using hydrogen/deuterium exchange-mass spectrometry

A new method and a modified method were developed to calculate folding energies of proteins based on the hydrogen deuterium exchange of globally protected amide protons. The modified method was electro spray ionization mass spectrometry ESI-MS) based and resembles the SUPREX method. This method is called the kinetic method. A novel method was also developed which is called the protein equilibrium population snapshot PEPS) method. Both these methods assume that the protein of interest follows a two state folding mechanism. The HX ESI-MS based kinetic method, which is the modified SUPREX method, measures hydrogen deuterium exchange at different guanidine hydrochloride GdHCl) concentrations as a function of time. This method utilizes ESI-MS, contrary to the usual MALDI-MS approach adopted by the SUPREX method. It measures the folding energies of proteins, which follow an EX2 type of exchange mechanism. Accurate folding energies were obtained for Ubiquitin as expected as it follows an EX2 exchange mechanism. Wild type staph nuclease and various quadruple staph nuclease mutants showed consistently higher values with good correlation. This can be attributed to deviation from EX2 exchange. Like SUPREX, this method is expected to work best for proteins, which follow EX2 exchange kinetics. The protein equilibrium population snapshot PEPS) method has been successfully used to accurately determine the folding energies of wild type staph nuclease and two of its mutants, which follow the EX1 mechanism of hydrogen deuterium exchange. This method measures the population distribution of open and closed states of a protein with hydrogen deuterium exchange as a function of denaturant concentration, under equilibrium. This method. when applied to Ubiquitin, which follows EX kinetics, also generated accurate folding energies comparable with literature values from NMR and fluorescence studies. So it is determined that the novel PEPS method is capable of measuring folding energies of a protein, regardless of the exchange mechanism is EX1 or EX2. This method is also based on fewer assumptions than the kinetic method.

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X-ray Diffraction Microscopy: Computational methods and scanning-type experiments

X-ray Diffraction Microscopy XDM) has been gaining in popularity for nanoscale imaging of biological and material science samples. Its high penetration depth compared to electron microscopy) and its good dose efficiency compared to its lens-based X-ray alternative) make it uniquely suited for imaging whole biological specimens, where radiation damage is a concern. Despite these advantages, XDM is still far from being a routine imaging tool. This is due to the computational challenge of reconstructing an image from recorded diffraction intensities as well as difficult-to-satisfy experimental requirements. I address these challenges by improving on the computational methods and by implementing a more reliable experimental geometry for our existing diffraction microscope at the Advanced Light Source, Lawrence Berkeley Lab. First, a software library has been developed that streamlines the post-experiment processing of data and that improves on an important aspect of data analysis. Results will be shown that illustrate the collective improvement to the reconstruction process. A modified version of a tool commonly used to assess the consistency of reconstructions is proposed and criteria of its validity are derived. Results show that it has improved utility for judging reconstruction quality. Second, a scanning-type experimental setup has been implemented for our existing diffraction microscope. Several possible geometries are discussed and preliminary results from recent experimental data are shown.

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