Theoretical Studies of Proton-Coupled Electron Transfer: Models and Concepts Relevant to Bioenergetics

Theoretical studies of proton-coupled electron transfer (PCET) reactions for model systems provide insight into fundamental concepts relevant to bioenergetics. A dynamical theoretical formulation for vibronically nonadiabatic PCET reactions has been developed. This theory enables the calculation of rates and kinetic isotope effects, as well as the pH and temperature dependences, of PCET reactions. Methods for calculating the vibronic couplings for PCET systems have also been developed and implemented. These theoretical approaches have been applied to a wide range of PCET reactions, including tyrosyl radical generation in a tyrosine-bound rhenium polypyridyl complex, phenoxyl/phenol and benzyl/toluene self-exchange reactions, and hydrogen abstraction catalyzed by the enzyme lipoxygenase. These applications have elucidated some of the key underlying physical principles of PCET reactions. The tools and concepts derived from these theoretical studies provide the foundation for future theoretical studies of PCET in more complex bioenergetic systems such as Photosystem II.     

Fluidic assembly and packing of microspheres in confined channels

We study fluidic assembly and packing of spherical particles in rectilinear microchannels that are terminated by a flow constriction. First, we introduce a method for active assembly of particles in the confined microchannels by triggering a local constriction in the fluid channel using a partially closed membrane valve. This microfluidic valve allows active, on-demand particle assembly as opposed to previous passive assembly methods based on terminal channels and weirs. Second, we study the three-dimensional assembly and packing of particles against a weir in confined rectilinear microchannels. The packings result in achiral particle chains with alternating (zigzag) structure. This structure is characterized by a single, repeated bond angle whose components projected into the frame of the channel are quantified by confocal microscopy and image processing. Brownian dynamics simulation of the packing comprehensively delineates the range of bond angles possible in narrow, rectilinear microchannels as well as the complex dependence of these angles on the relative dimensions of the channel and particles. The simulations of the three-dimensional packings are accurately modeled by a compact theory based on trigonometric relationships. The experimentally measured bond angles show excellent agreement with the simulations, thereby validating the functional dependence of the achiral packing bond angles on channel dimensions. This functional relationship is immediately useful for the design of anisotropic particles by microfluidic synthesis.     

Structure and NMR assignment in calcined and as-synthesized forms of AlPO-14: a combined study by first-principles calculations and high-resolution 27Al-31P MAS NMR correlation

The high-resolution 27Al and 31P NMR spectra of two as-synthesized forms of the microporous aluminophosphate AlPO-14 and the corresponding calcined-dehydrated form were assigned using both "first-principles" calculations of NMR parameters (GIPAW, as implemented in NMR-CASTEP) and a 27Al-31P heteronuclear correlation NMR experiment (MQ-J-HETCOR) that exploits 27Al multiple-quantum coherences and J couplings to identify Al-O-P linkages. NMR parameters calculated from published AlPO-14 crystal structures, which are derived from powder X-ray diffraction (XRD) data, are in poor agreement with experiment and it was necessary to optimize the structure geometry using energy minimization before satisfactory agreement was obtained. Comparison of simulated powder XRD patterns from the experimental and the energy-minimized structures shows that the changes in relative atomic positions in the optimized structure are relatively small and yield only minor adjustments in the Bragg peak intensities. These results indicate that a combination of NMR spectroscopy and first-principles calculation of NMR parameters may soon be considered a generally useful step in the refinement of the structures of microporous materials derived from powder diffraction data.     

Modeling positrons in molecular electronic structure calculations with the nuclear-electronic orbital method

The nuclear-electronic orbital (NEO) method was modified and extended to positron systems for studying mixed positronic-electronic wavefunctions, replacing the mass of the proton with the mass of the positron. Within the modified NEO framework, the NEO-HF (Hartree-Fock) method provides the energy corresponding to the single-configuration mixed positronic-electronic wavefunction, minimized with respect to the molecular orbitals expressed as linear combinations of Gaussian basis functions. The electron-electron and electron-positron correlation can be treated in the NEO framework with second-order perturbation theory (NEO-MP2) or multiconfigurational methods such as the full configuration interaction (NEO-FCI) and complete active space self-consistent-field (NEO-CASSCF) methods. In addition to implementing these methods for positronic systems, strategies for calculating electron-positron annihilation rates using NEO-HF, NEO-MP2, and NEO-FCI wavefunctions were also developed. To apply the NEO method to the positronium hydride (PsH) system, positronic and electronic basis sets were optimized at the NEO-FCI level and used to compute NEO-MP2 and NEO-FCI energies and annihilation rates. The effects of basis set size on NEO-MP2 and NEO-FCI correlation energies and annihilation rates were compared. Even-tempered electronic and positronic basis sets were also optimized for the e+LiH molecule at the NEO-MP2 level and used to compute the equilibrium bond length and vibrational energy.     

Characterizing algebraic stacks

We extend the notion of algebraic stack to an arbitrary subcanonical site . If the topology on is local on the target and satisfies descent for morphisms, we show that algebraic stacks are precisely those which are weakly equivalent to representable presheaves of groupoids whose domain map is a cover. This leads naturally to a definition of algebraic -stacks. We also compare different sites naturally associated to a stack.

     

Nanostructure of complexes between cationic lipids and an oppositely charged polyelectrolyte

The morphology of aqueous solutions of polyelectrolytes and oppositely charged lipids is the subject of extensive colloid science research, because of their application in industry and medicine, the latter especially for gene therapy. In this work, we show that complexes of two different cationic lipids with the polyelectrolyte sodium poly(acrylic acid), PAA, share similar morphology with the complexes of those lipids with nucleic acids, implying a broader and universal packing phenomenon. We characterized by direct-imaging cryogenic-temperature transmission electron microscopy (cryo-TEM), dynamic light scattering (DLS), and zeta (ζ)-potential two cationic lipids, 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) and bis(11-ferrocenylundecyl) dimethylammonium bromide (BFDMA), which are used in gene transfection, at equivalent lipid/polyelectrolyte charge ratio. Our results revealed that, for both types of complexes, onion-like multilamellar nanostructures formed, which exhibited similar morphology as in complexes of DNA or oligonucleotides (lipoplexes), based on the same lipids. Our findings suggest that the onion-like packing may be energetically favorable for a wide range of polyelectrolyte-liposome systems, from oligonucleotides and DNA to PAA.     

Environmental Degradation of Microbial Polyhydroxyalkanoates and Oil Palm-Based Composites

This paper investigates the degradation of polyhydroxyalkanoates and its biofiber composites in both soil and lake environment. Time-dependent changes in the weight loss of films were monitored. The rate of degradation of poly(3-hydroxybutyrate) [P(3HB)], poly(3-hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-23?mol% 4HB)] and poly(3-hydroxybutyrate-co-3-hydroxyvalerate-co-4-hydroxybutyrate) [P(3HB-co-9?mol% 3HV-co-19?mol% 4HB)] were investigated. The rate of degradation in the lake is higher compared to that in the soil. The highest rate of degradation in lake environment (15.6?% w/w week^?1) was observed with P(3HB-co-3HV-co-4HB) terpolymer. Additionally, the rate of degradation of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-38?mol% 3HV)] was compared to PHBV biofiber composites containing compatibilizers and empty fruit bunch (EFB). Here, composites with 30?% EFB displayed the highest rate of degradation both in the lake (25.6?% w/w week^?1) and soil (15.6?% w/w week^?1) environment.     

Direct Infusion Electrospray Ionization – Ion Mobility – High Resolution Mass Spectrometry (DIESI-IM-HRMS) for Rapid Characterization of Potential Bioprocess Streams

Direct infusion electrospray ionization?-?ion mobility?-?high resolution mass spectrometry (DIESI-IM-HRMS) has been utilized as a rapid technique for the characterization of total molecular composition in "whole-sample" biomass hydrolysates and extracts. IM-HRMS data reveal a broad molecular weight distribution of sample components (up to 1100 m/z) and provide trendline isolation of feedstock components from those introduced "in process." Chemical formulas were obtained from HRMS exact mass measurements (with typical mass error less than 5 ppm) and were consistent with structural carbohydrates and other lignocellulosic degradation products. Analyte assignments are supported via IM-MS collision-cross-section measurements and trendline analysis (e.g., all carbohydrate oligomers identified in a corn stover hydrolysate were found to fall within 6% of an average trendline). These data represent the first report of collision cross sections for several negatively charged carbohydrates and other acidic species occurring natively in biomass hydrolysates.     

Bivariate interpolation based on univariate subdivision schemes

The paper presents a bivariate subdivision scheme interpolating data consisting of univariate functions along equidistant parallel lines by repeated refinements. This method can be applied to the construction of a surface passing through a given set of parametric curves. Following the methodology of polysplines and tension surfaces, we define a local interpolator of four consecutive univariate functions, from which we sample a univariate function at the mid-point. This refinement step is the basis to an extension of the 4-point subdivision scheme to our setting. The bivariate subdivision scheme can be reduced to a countable number of univariate, interpolatory, non-stationary subdivision schemes. Properties of the generated interpolant are derived, such as continuity, smoothness and approximation order.