Direct simulation of proton-coupled electron transfer reaction dynamics and mechanisms

Proton-coupled electron transfer (PCET) reactions are ubiquitous throughout chemistry and biology. However, challenges arise in both the the experimental and theoretical investigation of PCET reactions; the rare-event nature of the reactions and the coupling between quantum mechanical electron- and proton-transfer with the slower classical dynamics of the surrounding environment necessitates the development of robust simulation methodology. In the following dissertation, novel path-integral based methods are developed and employed for the direct simulation of the reaction dynamics and mechanisms of condensed-phase PCET.

Engineering and Characterization of Cytochrome P450 Enzymes for Nitrogen-Atom Transfer Reactions

The creation of novel enzyme activity is a great challenge to protein engineers, but nature has done so repeatedly throughout the process of natural selection. I begin by outlining the multitude of distinct reactions catalyzed by a single enzyme class, cytochrome P450 monooxygenases. I discuss the ability of cytochrome P450 to generate reactive intermediates capable of diverse reactivity, suggesting this enzyme can also be used to generate novel reactive intermediates in the form of metal-carbenoid and nitrenoid species. I then show that cytochrome P450 from Bacillus megaterium (P450_BM3) and its isolated cofactor can catalyze metal-nitrenoid transfer in the form of intramolecular C–H bond amination. Mutations to the protein sequence can enhance the reactivity and selectivity of this transformation significantly beyond that of the free cofactor. Next, I demonstrate an intermolecular nitrene transfer reaction catalyzed by P450_BM3 in the form of sulfide imidation. Understanding that sulfur heteroatoms are strong nucleophiles, I show that increasing the sulfide nucleophilicity through substituents on the aryl sulfide ring can dramatically increase reaction productivity. To explore engineering nitrenoid transfer in P450BM3, active site mutagenesis is employed to tune the regioselectivity intramolecular C–H amination catalysts. The solution of the crystal structure of a highly selective variant demonstrates that hydrophobic residues in the active site strongly modulate reactivity and regioselectivity. Finally, I use a similar strategy to develop P450-based catalysts for intermolecular olefin aziridination, demonstrating that active site mutagenesis can greatly enhance this nitrene transfer reaction. The resulting variant can catalyze intermolecular aziridination with more than 1000 total turnovers and enantioselectivity of up to 99% ee.

Electron transfer in chemically and genetically modified myoglobins

The temperature dependences of the reduction potentials (E^o') of wildtype human myoglobin (Mb) and three site-directed mutants have been measured by using thin-layer spectroelectrochemistry. Residue Val68, which is in van der Waals contact with the heme in Mb, has been replaced by Glu, Asp, and Asn. At pH 7.0, reduction of the heme iron (III) in the former two proteins is accompanied by uptake of a proton by the protein. The changes in E^o', and the standard entropy (ΔS^o') and enthalpy (ΔH^o') of reduction in the mutant proteins were determined relative to values for wild-type; the change in E^o' at 25°C was about -200 millivolts for the Glu and Asp mutants, and about -80 millivolts for the Asn mutant. Reduction of Fe(III) to Fe(II) in the Glu and Asp mutants is accompanied by uptake of a proton. These studies demonstrate that Mb can tolerate substitution of a buried hydrophobic group by potentially charged and polar residues, and that such amino acid replacements can lead to substantial changes in the redox thermodynamics of the protein.

Through analysis of the temperature dependence and shapes of NMR dispersion signals, it is determined that a water molecule is bound to the sixth coordination site of the ferric heme in the Val68Asp and in the Val68Asn recombinant proteins while the carboxyl group of the sidechain of Glu68 occupies this position in Val68Glu. The relative rhombic distortions in the ESR spectra of these mutant proteins combined with H₂¹⁷O and spin interconversion experiments performed on them confirm the conclusions of the NMRD study.

The rates of intramolecular electron transfer (ET) of (NH₃)₅Ru-His48 (Val68Asp, His81GIn, Cys110AIa)Mb and (NH₃)₅Ru-His48 (Val68GIu,His81GIn,Cys110Ala)Mb were measured to be .85(3)s^-1 and .30(2)s^-1, respectively. This data supports the hypothesis that entropy of 111 reduction and reorganization energy of ET are inversely related. The rates of forward and reverse ET for (NH₃)₅ Ru-His48 (Val68GIu, His81 GIn, Cys110AIa)ZnMb -7.2(5)•10⁴s^-1and 1.4(2)•10⁵s^-1, respectively- demonstrate that the placement of a highly polar residue nearby does not significantly change the reorganization energy of the photoactive Zn porphyrin.

The distal histidine imidazoles of (NH₃)₄isnRu-His48 SWMb and (NH₃)₅Ru-His48 SWMb were cyanated with BrCN. The intramolecular ET rates of these BrCN-modified Mb derivatives are 5.5(6)s^-1 and 3.2(5)s^-1, respectively. These respective rates are 20 and 10 times faster than those of their noncyanated counterparts after the differences in ET rate from driving force are scaled according to the Marcus equation. This increase in ET rate of the cyanated Mb derivatives is attributed to lower reorganization energy since the cyanated Mb heme is pentacoordinate in both oxidation states; whereas, the native Mb heme loses a water molecule upon reduction so that it changes from six to five coordinate. The reorganization energy from Fe-OH₂ dissociation is estimated to be .2eV. This conclusion is used to reconcile data from previous experiments in our lab. ET in photoactive porphyrin-substituted myoglobins proceed faster than predicted by Marcus Theory when it is assumed that the only difference in ET parameters between photoactive porphyrins and native heme systems is driving force. However, the data can be consistently fit to Marcus Theory if one corrects for the smaller reorganization in the photoactive porphyrin systems since they do not undergo a coordination change upon ET.

Finally, the intramolecular ET rate of (NH₃)₄isnRu-His48 SWMb was measured to be 3.0(4)s^-1. This rate is within experimental error of that for (NH₃)₄pyrRu-His48 SWMb even though the former has 80mV more driving force. One likely possibility for this observation is that the tetraamminepyridineruthenium group undergoes less reorganization upon ET than the tetraammineisonicotinamideruthenium group. Moreover, analysis of the (NH₃)₄isnRu-His48 SWMb experimental system gives a likely explanation of why ET was not observed previously in (NH₃)₄isnRu-Cytochrome C.

Gestión y negociación intercultural

El objetivo principal de este trabajo de fin de grado es analizar la cultura de la región del País Vasco y Francia, a través de encuestas y entrevistas a un colectivo homogéneo, con el fin de obtener información sobre ellas y de este modo poder analizar sus efectos en las técnicas de gestión, liderazgo y negociación de cada sociedad.

Intercultural leadership and negotiation

This project will examine cultural differences and dimensions and how they affect negotiations and intercultural management. It is necessary to consider that the cultural characteristics of each society, which in turn is made of different individuals, make intercultural relations complex and with many subtleties. We will apply these proposals to draw a comparison between Spain and two Southeast Asian countries: India and Sri Lanka using Hofstede’s cultural dimensions.This project will examine cultural differences and dimensions and how they affect negotiations and intercultural management. It is necessary to consider that the cultural characteristics of each society, which in turn is made of different individuals, make intercultural relations complex and with many subtleties. We will apply these proposals to draw a comparison between Spain and two Southeast Asian countries: India and Sri Lanka using Hofstede’s cultural dimensions.

Mechanism of mass transfer in the formation of hydrothermal deposits of sulphides [Translation from: Trudy Inst.Geol.rudn.Mesterozh. 16, 80 [pages 44-46 ”Solubility of sulphides of iron” only], 1958]

This partial translation of the original paper provides the summary of this study of the mechanism of mass transfer in the formation of hydrothermal deposits of sulphides. For determining the solubility of sulphides of iron, the radioactive isotope Fe59 was used. The solubility of two sulphides was determined.

Mass transfer from a cylinder to an air stream in axisymmetrical flow (an experimental study)

Mass transfer from wetted surfaces on one-inch cylinders with unwetted approach sections was studied experimentally by means of the evaporation of n-octane and n-heptane into an air stream in axisymmetrical flow, for Reynolds numbers from 5,000 to 310,000. A transition from the laminar to the turbulent boundary layer was observed to occur at Reynolds numbers from 10,000 to 15,000. The results were expressed in terms of the Sherwood number as a function of the Reynolds number, the Schmidt number, and the ratio of the unwetted approach length to the total length. Empirical formulas were obtained for both laminar and turbulent regimes. The rates of mass transfer obtained were higher than theoretical and experimental results obtained by previous investigators for mass and heat transfer from flat plates.

Part I: Latent heat of vaporization of n-decane. Part II: Heat and mass transfer from a cylinder placed in a turbulent air stream - Sherwood and Frössling numbers as a function of free stream turbulence level and Reynolds number

Part I

The latent heat of vaporization of n-decane is measured calorimetrically at temperatures between 160° and 340°F. The internal energy change upon vaporization, and the specific volume of the vapor at its dew point are calculated from these data and are included in this work. The measurements are in excellent agreement with available data at 77° and also at 345°F, and are presented in graphical and tabular form.

Part II

Simultaneous material and energy transport from a one-inch adiabatic porous cylinder is studied as a function of free stream Reynolds Number and turbulence level. Experimental data is presented for Reynolds Numbers between 1600 and 15,000 based on the cylinder diameter, and for apparent turbulence levels between 1.3 and 25.0 per cent. n-heptane and n-octane are the evaporating fluids used in this investigation.

Gross Sherwood Numbers are calculated from the data and are in substantial agreement with existing correlations of the results of other workers. The Sherwood Numbers, characterizing mass transfer rates, increase approximately as the 0.55 power of the Reynolds Number. At a free stream Reynolds Number of 3700 the Sherwood Number showed a 40% increase as the apparent turbulence level of the free stream was raised from 1.3 to 25 per cent.

Within the uncertainties involved in the diffusion coefficients used for n-heptane and n-octane, the Sherwood Numbers are comparable for both materials. A dimensionless Frössling Number is computed which characterizes either heat or mass transfer rates for cylinders on a comparable basis. The calculated Frössling Numbers based on mass transfer measurements are in substantial agreement with Frössling Numbers calculated from the data of other workers in heat transfer.

Photochemical electron transfer at fixed distance : a synthetic model of the photosynthetic primary process

A series of meso-phenyloctamethylporphyrins covalently bonded at the 4'phenyl position to quinones via rigid bicyclo[2.2.2]octane spacers were synthesized for the study of the dependence of electron transfer reaction rate on solvent, distance, temperature, and energy gap. A general and convergent synthesis was developed based on the condensation of ac-biladienes with masked quinonespacer-benzaldehydes. From picosecond fluorescence spectroscopy emission lifetimes were measured in seven solvents of varying polarity. Rate constants were determined to vary from 5.0x10⁹sec^-1 in N,N-dimethylformamide to 1.15x10¹⁰ Sec^-1 in benzene, and were observed to rise at most by about a factor of three with decreasing solvent polarity. Experiments at low temperature in 2-MTHF glass (77K) revealed fast, nearly temperature-independent electron transfer characterized by non-exponential fluorescence decays, in contrast to monophasic behavior in fluid solution at 298K. This example evidently represents the first photosynthetic model system not based on proteins to display nearly temperature-independent electron transfer at high temperatures (nuclear tunneling). Low temperatures appear to freeze out the rotational motion of the chromophores, and the observed nonexponential fluorescence decays may be explained as a result of electron transfer from an ensemble of rotational conformations. The nonexponentiality demonstrates the sensitivity of the electron transfer rate to the precise magnitude of the electronic matrix element, which supports the expectation that electron transfer is nonadiabatic in this system. The addition of a second bicyclooctane moiety (15 Å vs. 18 Å edge-to-edge between porphyrin and quinone) reduces the transfer rate by at least a factor of 500-1500. Porphyrinquinones with variously substituted quinones allowed an examination of the dependence of the electron transfer rate constant κ_ET on reaction driving force. The classical trend of increasing rate versus increasing exothermicity occurs from 0.7 eV≤ |ΔG^0'(R)| ≤ 1.0 eV until a maximum is reached (κ_ET = 3 x 10⁸ sec^-1 rising to 1.15 x 10¹⁰ sec^-1 in acetonitrile). The rate remains insensitive to ΔG⁰ for ~ 300 mV from 1.0 eV≤ |ΔG^0’(R)| ≤ 1.3 eV, and then slightly decreases in the most exothermic case studied (cyanoquinone, κ_ET = 5 x 10⁹ sec^-1).

Optical spectroscopy and energy transfer of Er3+/Ce3+ in B2O3-doped bismuth-silicate glasses

Ce3+ and B2O3 are introduced into erbium-doped Bi2O3-SiO2 glass to enhance the luminescence emission and optic spectra characters of Er3+. The energy transfer from Er3+ to Ce3+ will obviously be improved with the phonon energy increasing by the addition of B2O3. Here, the nonradiative rate, the lifetime of the I-4(11/2) -> I-4(3/2) transition, and the emission intensity and bandwidth of the 1.5 mu m luminescence with the I-4(13/2) -> I-4(5/2) transition of Er3+ are discussed in detail. The results show that the optical parameters of Er3+ in this bismuth-borate-silicate glass are nearly as good as that in tellurite glass, and the physical properties are similar to those in silicate glass. With the Judd-Ofelt and nonradiative theory analyses, the multiphonon decay and phonon-assisted energy-transfer (PAT) rates are calculated for the Er3+/Ce3+ codoped glasses. For the PAT process, an optimum value of the glass phonon energy is obtained after B2O3 is introduced into the Er3+/Ce3+ codoped bismuth-silicate glasses, and it much improves the energy-transfer rate between Er3+ I-4(11/2)-I-4(13/2) and Ce3+ F-2(5/2) -> F-2(7/2), although there is an energy mismatch. (c) 2007 Optical Society of America.

Part I. Coenzyme B12 as a hydroformylation-type catalyst. Part II. Mechanisms of hydrogen transfer in the methylmalonyl coenzyme a mutase reaction

Part I

The mechanism of the hydroformylation reaction was studied. Using cobalt deuterotetracarbonyl and 1-pentene as substrates, the first step in the reaction, addition of cobalt tetracarbonyl to an olefin, was shown to be reversible.

Part II

The role of coenzyme B₁₂ in the isomerization of methylmalonyl coenzyme A to succinyl coenzyme A by methylmalonyl coenzyme A mutase was studied. The reaction was allowed to proceed to partial completion using a mixture of methylmalonyl coenzyme A and 4, 4, 4-tri-²H-methylmalonyl coenzyme A as substrate. The deuterium distribution in the product, succinyl coenzyme A, was shown to best fit a model in which hydrogen is transferred from C-4 of methylmalonyl coenzyme A to C-5’ of the adenosyl moiety of coenzyme B₁₂ in the rate determining step. The three hydrogens at the 5’-adenosyl position of the coenzyme B₁₂ intermediate are then able to become enzymatically equivalent before hydrogen is transferred from the coenzyme B₁₂ intermediate to form succinyl coenzyme A.

Energy transfer in molecular collisions

Two general, numerically exact, quantum mechanical methods have been developed for the calculation of energy transfer in molecular collisions. The methods do not treat electronic transitions because of the exchange symmetry of the electrons. All interactions between the atoms in the system are written as potential energies.

The first method is a matrix generalization of the invariant imbedding procedure, ^{17, 20} adapted for multi-channel collision processes. The second method is based on a direct integration of the matrix Schrödinger equation, with a re-orthogonalization transform applied during the integration.

Both methods have been applied to a collinear collision model for two diatoms, interacting via a repulsive exponential potential. Two major studies were performed. The first was to determine the energy dependence of the transition probabilities for an H₂ on the H₂ model system. Transitions are possible between translational energy and vibrational energy, and from vibrational modes of one H₂ to the other H₂. The second study was to determine the variation of vibrational energy transfer probability with differences in natural frequency of two diatoms similar to N₂.

Comparisons were made to previous approximate analytical solutions of this same problem. For translational to vibrational energy transfer, the previous approximations were not adequate. For vibrational to vibrational energy transfer of one vibrational quantum, the approximations were quite good.