I. The 3.7 Å crystal structure of horse heart ferricytochrome C. II. The application of the Karle-Hauptman tangent formula to protein phasing

I. The 3.7 Å Crystal Structure of Horse Heart Ferricytochrome C.

The crystal structure of horse heart ferricytochrome c has been determined to a resolution of 3.7 Å using the multiple isomorphous replacement technique. Two isomorphous derivatives were used in the analysis, leading to a map with a mean figure of merit of 0.458. The quality of the resulting map was extremely high, even though the derivative data did not appear to be of high quality.

Although it was impossible to fit the known amino acid sequence to the calculated structure in an unambiguous way, many important features of the molecule could still be determined from the 3.7 Å electron density map. Among these was the fact that cytochrome c contains little or no α-helix. The polypeptide chain appears to be wound about the heme group in such a way as to form a loosely packed hydrophobic core in the molecule.

The heme group is located in a cleft on the molecule with one edge exposed to the solvent. The fifth coordinating ligand is His 18 and the sixth coordinating ligand is probably neither His 26 nor His 33.

The high resolution analysis of cytochrome c is now in progress and should be completed within the next year.

II. The Application of the Karle-Hauptman Tangent Formula to Protein Phasing.

The Karle-Hauptman tangent formula has been shown to be applicable to the refinement of previously determined protein phases. Tests were made with both the cytochrome c data from Part I and a theoretical structure based on the myoglobin molecule. The refinement process was found to be highly dependent upon the manner in which the tangent formula was applied. Iterative procedures did not work well, at least at low resolution.

The tangent formula worked very well in selecting the true phase from the two possible phase choices resulting from a single isomorphous replacement phase analysis. The only restriction on this application is that the heavy atoms form a non-centric cluster in the unit cell.

Pages 156 through 284 in this Thesis consist of previously published papers relating to the above two sections. References to these papers can be found on page 155.

2,4-dimethylene-1,3-cyclobutanediyl and 2,4-dimethylenebicyclobutane. Synthesis, spectroscopy, and reactivity of a triplet biradical and its covalent isomer

The preparation and direct observation of triplet 2,4-dimethylene-1,3- cyclobutanediyl (1), the non-Kekule isomer of benzene, is described. The biradical was generated by photolysis of 5,6-dimethylene-2,3- diazabicyclo[2.1.1]hex-2-ene (2) (which was synthesized in several steps from benzvalene) under cryogenic, matrix-isolation conditions. Biradical 1 was characterized by EPR spectroscopy (‌‌‌‌‌│D/hc│ =0.0204 cm^(-1), │E/hc│ =0.0028 cm^(-1)) and found to have a triplet ground state. The Δm_s= 2 transition displays hyperfine splitting attributed to a 7.3-G coupling to the ring methine and a 5.9-G coupling to the exocyclic methylene protons. Several experiments, including application of the magnetophotoselection (mps) technique in the generation of biradical 1, have allowed a determination of the zero-field triplet sublevels as x = -0.0040, y = +0.0136, and z = -0.0096 cm^(-1), where x and y are respectively the long and short in-plane axes and z the out-of-plane axis of 1.

Triplet 1 is yellow-orange and displays highly structured absorption (λ_(max)= 506 nm) and fluorescence (λ_(max) = 510 nm) spectra, with vibronic spacings of 1520 and 620 cm^(-1) for absorption and 1570 and 620 cm^(-1) for emission. The spectra were unequivocally assigned to triplet 1 by the use of a novel technique that takes advantage of the biradical's photolability. The absorption є = 7200 M^(-1) cm^(-1) and f = 0.022, establishing that the transition is spin-allowed. Further use of the mps technique has demonstrated that the transition is x-polarized, and the excited state 1s therefore of B_(1g) symmetry, in accord with theoretical predictions.

Thermolysis or direct photolysis of diazene 2 in fluid solution produces 2,4- dimethylenebicyclo[l.l.0]butane (3), whose ^(l)H NMR spectrum (-80°C, CD_(2)Cl_(2)) consists of singlets at δ 4.22 and 3.18 in a 2:1 ratio. Compound 3 is thermally unstable and dimerizes with second-order kinetics between -80 and -25°C (∆H^(‡) = 6.8 kcal mol^(-1), (∆s^(‡) = -28 eu) by a mechanism involving direct combination of two molecules of 3 in the rate-determining step. This singlet-manifold reaction ultimately produces a mixture of two dimers, 3,8,9- trimethylenetricyclo[5.1.1.0^(2,5)]non-4-ene (75) and trans-3,10-dimethylenetricyclo[6.2.0.0^(2,5)]deca-4,8-diene (76t), with the former predominating. In contrast, triplet-sensitized photolysis of 2, which leads to triplet 1, provides, in addition to 75 and 76t, a substantial amount of trans-5,10- dimethylenetricyclo[6.2.0.0^(3,6)]deca-3,8-diene (77t) and small amounts of two unidentified dimers.

In addition, triplet biradical 1 ring-closes to 3 in rigid media both thermally (77-140 K) and photochemically. In solution 3 forms triplet 1 upon energy transfer from sensitizers having relatively low triplet energies. The implications of the thermal chemistry for the energy surfaces of the system are discussed.

Synthesis of (±)-7,8-epoxy-4-basmen-6-one by a transannular cyclization strategy

The first synthesis of the cembranoid natural product (±)-7,8-epoxy-4-basmen-6- one (1) is described. Key steps of the synthetic route include the cationic cyclization of the acid chloride from 15 to provide the macrocycle 16, and the photochemical transannular radical cyclization of the ester 41 to form the tricyclic product 50. Product 50 was transformed into 1 in ten steps. Transition-state molecular modeling studies were found to provide accurate predictions of the structural and stereochemical outcomes of cyclization reactions explored experimentally in the development of the synthetic route to 1. These investigations should prove valuable in the development of transannular cyclization as a strategy for synthetic simplification.

Multiwavelength observations of the black hole candidate 1E 1740.7-2942

Observations of the Galactic center region black hole candidate 1E 1740.7-2942 have been carried out using the Caltech Gamma-Ray Imaging Payload (GRIP), the Röntgensatellit (ROSAT) and the Very Large Array (VLA). These multiwavelength observations have helped to establish the association between a bright emitter of hard X-rays and soft γ-rays, the compact core of a double radio jet source, and the X-ray source, 1E 1740.7-2942. They have also provided information on the X-ray and hard X-ray spectrum.

The Galactic center region was observed by GRIP during balloon flights from Alice Springs, NT, Australia on 1988 April 12 and 1989 April 3. These observations revealed that 1E 1740.7-2942 was the strongest source of hard X-rays within ~10° of the Galactic center. The source spectrum from each flight is well fit by a single power law in the energy range 35-200 keV. The best-fit photon indices and 100 keV normalizations are: γ = (2.05 ± 0.15) and K_(100) = (8.5 ± 0.5) x 10^(-5) cm^(-2) s^(-1) keV^(-1) and γ = (2.2 ± 0.3) and K_(100) = (7.0 ± 0.7) x 10^(-5) cm^(-2) s^(-1) keV^(-1) for the 1988 and 1989 observations respectively. No flux above 200 keV was detected during either observation. These values are consistent with a constant spectrum and indicate that 1E 1740.7-2942 was in its normal hard X-ray emission state. A search on one hour time scales showed no evidence for variability.

The ROSAT HRI observed 1E 1740.7-2942 during the period 1991 March 20-24. An improved source location has been derived from this observation. The best fit coordinates (J2000) are: Right Ascension = 17^h43^m54^s.9, Declination = -29°44'45".3, with a 90% confidence error circle of radius 8".5. The PSPC observation was split between periods from 1992 September 28- October 4 and 1993 March 23-28. A thermal bremsstrahlung model fit to the data yields a column density of N_H = 1.12^(+1.51)_(0.18) x cm^(-2) , consistent with earlier X- ray measurements.

We observed the region of the Einstein IPC error circle for 1E 1740.7-2942 with the VLA at 1.5 and 4.9 GHz on 1989 March 2. The 4.9 GHz observation revealed two sources. Source 'A', which is the core of a double aligned radio jet source (Mirabel et al. 1992), lies within our ROSAT error circle, further strengthening its identification with 1E 1740.7-2942.

Searches for new symmetries in pp collisions with the razor kinematic variables at √s = 7 TeV

The construction and LHC phenomenology of the razor variables M_R, an event-by-event indicator of the heavy particle mass scale, and R, a dimensionless variable related to the transverse momentum imbalance of events and missing transverse energy, are presented.  The variables are used  in the analysis of the first proton-proton collisions dataset at CMS  (35 pb^-1) in a search for superpartners of the quarks and gluons, targeting indirect hints of dark matter candidates in the context of supersymmetric theoretical frameworks. The analysis produced the highest sensitivity results for SUSY to date and extended the LHC reach far beyond the previous Tevatron results.  A generalized inclusive search is subsequently presented for new heavy particle pairs produced in √s = 7 TeV proton-proton collisions at the LHC using 4.7±0.1 fb^-1 of integrated luminosity from the second LHC run of 2011.  The selected events are analyzed in the 2D razor-space of M_R and R and the analysis is performed in 12 tiers of all-hadronic, single and double leptons final states in the presence and absence of b-quarks, probing the third generation sector using the event heavy-flavor content.   The search is sensitive to generic supersymmetry models with minimal assumptions about the superpartner decay chains. No excess is observed in the number or shape of event yields relative to Standard Model predictions. Exclusion limits are derived in the CMSSM framework with  gluino masses up to 800 GeV and squark masses up to 1.35 TeV excluded at 95% confidence level, depending on the model parameters. The results are also interpreted for a collection of simplified models, in which gluinos are excluded with masses as large as 1.1 TeV, for small neutralino masses, and the first-two generation squarks, stops and sbottoms are excluded for masses up to about 800, 425 and 400 GeV, respectively.

With the discovery of a new boson by the CMS and ATLAS experiments in the γ-γ and 4 lepton final states, the identity of the putative Higgs candidate must be established through the measurements of its properties. The spin and quantum numbers are of particular importance, and we describe a method for measuring the J^PC of this particle using the observed signal events in the H to ZZ^* to 4 lepton channel developed before the discovery. Adaptations of the razor kinematic variables are introduced for the H to WW^* to 2 lepton/2 neutrino channel, improving the resonance mass resolution and increasing the discovery significance. The prospects for incorporating this channel in an examination of the new boson J^PC is discussed, with indications that this it could provide complementary information to the H to ZZ^* to 4 lepton final state, particularly for measuring CP-violation in these decays.

Studies of Zγ production and constraints on anomalous triple gauge couplings in pp collisions at √s = 7 TeV

In this thesis, we test the electroweak sector of the Standard Model of particle physics through the measurements of the cross section of the simultaneous production of the neutral weak boson Z and photon γ, and the limits on the anomalous Zγγ and ZZγ triple gauge couplings h3 and h4 with the Z decaying to leptons (electrons and muons). We analyze events collected in proton-proton collisions at center of mass energy of sqrt(s) = 7 TeV corresponding to an integrated luminosity of 5.0 inverse femtobarn. The analyzed events were recorded by the Compact Muon Solenoid detector at the Large Hadron Collider in 2011.

The production cross section has been measured for hard photons with transverse momentum greater than 15 GeV that are separated from the the final state leptons in the eta-phi plane by Delta R greater than 0.7, whose sum of the transverse energy of hadrons over the transverse energy of the photon in a cone around the photon with Delta R less than 0.3 is less than 0.5, and with the invariant mass of the dilepton system greater than 50 GeV. The measured cross section value is 5.33 +/- 0.08 (stat.) +/- 0.25 (syst.) +/- 0.12 (lumi.) picobarn. This is compatible with the Standard Model prediction that includes next-to-leading-order QCD contributions: 5.45 +/- 0.27 picobarn.

The measured 95 % confidence-level upper limits on the absolute values of the anomalous couplings h3 and h4 are 0.01 and 8.8E-5 for the Zγγ interactions, and, 8.6E-3 and 8.0E-5 for the ZZγ interactions. These values are also compatible with the Standard Model where they vanish in the tree-level approximation. They extend the sensitivity of the 2012 results from the ATLAS collaboration based on 1.02 inverse femtobarn of data by a factor of 2.4 to 3.1.

The photochemistry of dioxorhenium(V)

The excited-state properties of trans-ReO₂(py)₄⁺ (ReO₂⁺) in acetonitrile solution have been investigated. The excited-state absorption spectrum of ReO₂⁺ is dominated by bleaching of the ground state MLCT and d-d systems. The reduction potential of ReO₂^2+/+* is estimated from emission and electrochemical data to be -0.7 V (SSCE). The ReO₂⁺ excited state efficiently reduces methylviologen and other pyridinium and olefin acceptors. The resulting Re(VI) species oxidizes secondary alcohols and silanes. Acetophenone is the product of sec-phenethyl alcohol oxidation.

The emission properties of ReO₂⁺ in aqueous solutions of anionic and nonionic surfactants have been investigated. The emission and absorption maxima of ReO₂⁺ are dependent on the water content of its environment. Emission lifetimes vary over four orders of magnitude upon shifting from aqueous to nonaqueous environments. The emission lifetime has a large (8.6) isotope effect (k(H₂O)/k(D₂O)) that reflects its sensitivity towards the environment. These properties have been used to develop a model for the interactions of ReO₂⁺ with sodium dodecyl sulfate (SDS). A hydrophobic ReO₂⁺ derivative, ReO₂(3-Ph-py)₄⁺, has been used to probe micelles of nonionic surfactants, and these results are consistent with those obtained with SDS.

The emission properties of ReO₂⁺ in Nafion perfluorosulfonated membranes have been investigated. Absorption and emission spectroscopy indicate that the interior of the membrane is quite polar, similar to ethylene glycol. Two well-resolved emission components show different lifetimes and different isotope effects, indicative of varying degrees of solvent accessibility. These components are taken as evidence for chemically distinct regions in the polymer film, assigned as the interfacial region and the ion cluster region.

The unsubstituted pyridine complex shows monophasic, τ = 1.7 µs, emission decay when bound to calf thymus DNA. Switching to the 3-Ph-py complex yields a biphasic emission decay (τ₁ = 2.4 µs, τ₂ = 10 µs) indicative of an additional, solvent-inaccessible binding mode. Photoinduced electron transfer to methylviologen leads to oxidative cleavage of the DNA as detected by gel electrophoresis. Electrochemical and spectrophotometric techniques used with organic substrates also can be used to monitor the oxidation of DNA. Abstraction of the ribose 4' hydrogen by ReO₂²⁺ is a possible mechanism.

Structurally engineered cytochromes c with novel ligand-binding properties

Semisynthesis of horse heart cytochrome c and site-directed mutagenesis of Saccharomyces cerevisiae (S. c.) iso-1-cytochrome c have been utilized to substitute Ala for the cytochrome c heme axial ligand Met80 to yield ligand-binding proteins (horse heart Ala80cyt c and S.c. Ala80cyt c) with spectroscopic properties remarkably similar to those of myoglobin. Both species of Fe(II)Ala80cyt c form exceptionally stable dioxygen complexes with autoxidation rates 10-30x smaller and O₂ binding constants ~ 3x greater than those of myoglobin. The resistance of O₂-Fe(II)Ala80cyt c to autoxidation is attributed in part to protection of the heme site from solvent as exhibited by the exceptionally slow rate of CO binding to the heme as well as the low quantum yield of CO photodissociation.

UV/vis, EPR, and paramagnetic NMR spectroscopy indicate that at pH 7 the Fe(III)Ala80cyt c heme is low-spin with axial His-OH^- coordination and that below pH ~6.5, Fe(III)Ala80cyt cis high-spin with His-H₂O heme ligation. Significant differences in the pH dependence of the ¹H NMR spectra of S.c. Fe(III)Ala80cyt c compared to wild-type demonstrate that the axial ligands influence the conformational energetics of cytochrome c.

¹H NMR spectroscopy has been utilized to determine the solution structure of the cyanide derivative of S.c. Fe(III)Ala80cyt c. 82% of the resonances in the ¹H NMR spectrum of S.c. CN-Fe(III)Ala80cyt c have been assigned through 1D and 2D experiments. The RMSD values after restrained energy minimization of the family of 17 structures obtained from distance geometry calculations are 0.68 ± 0.11 Å for the backbone and 1.32 ± 0.14 Å for all heavy atoms. The solution structure indicates that a tyrosine in the "distal" pocket of CN-Fe(III)Ala80cyt c forms a hydrogen bond with the Fe(III)-CN unit, suggesting that it may play a role analogous to that of the distal histidine in myoglobin in stabilizing the dioxygen adduct.

Magnetic alignment of high-aspect ratio microwires into vertical arrays

Fundamental studies of magnetic alignment of highly anisotropic mesostructures can enable the clean-room-free fabrication of flexible, array-based solar and electronic devices, in which preferential orientation of nano- or microwire-type objects is desired. In this study, ensembles of 100 micron long Si microwires with ferromagnetic Ni and Co coatings are oriented vertically in the presence of magnetic fields. The degree of vertical alignment and threshold field strength depend on geometric factors, such as microwire length and ferromagnetic coating thickness, as well as interfacial interactions, which are modulated by varying solvent and substrate surface chemistry. Microwire ensembles with vertical alignment over 97% within 10 degrees of normal, as measured by X-ray diffraction, are achieved over square cm scale areas and set into flexible polymer films. A force balance model has been developed as a predictive tool for magnetic alignment, incorporating magnetic torque and empirically derived surface adhesion parameters. As supported by these calculations, microwires are shown to detach from the surface and align vertically in the presence of magnetic fields on the order of 100 gauss. Microwires aligned in this manner are set into a polydimethylsiloxane film where they retain their vertical alignment after the field has been removed and can subsequently be used as a flexible solar absorber layer. Finally, these microwires arrays can be protected for use in electrochemical cells by the conformal deposition of a graphene layer.

Extraction of CP Properties of the H(125) Boson Discovered in Proton-Proton Collisions at sqrt(s) = 7 and 8 TeV with the CMS Detector at the LHC

In this thesis we build a novel analysis framework to perform the direct extraction of all possible effective Higgs boson couplings to the neutral electroweak gauge bosons in the H → ZZ^(*) → 4l channel also referred to as the golden channel. We use analytic expressions of the full decay differential cross sections for the H → VV' → 4l process, and the dominant irreducible standard model qq ̄ → 4l background where 4l = 2e2μ,4e,4μ. Detector effects are included through an explicit convolution of these analytic expressions with transfer functions that model the detector responses as well as acceptance and efficiency effects. Using the full set of decay observables, we construct an unbinned 8-dimensional detector level likelihood function which is con- tinuous in the effective couplings, and includes systematics. All potential anomalous couplings of HVV' where V = Z,γ are considered, allowing for general CP even/odd admixtures and any possible phases. We measure the CP-odd mixing between the tree-level HZZ coupling and higher order CP-odd couplings to be compatible with zero, and in the range [−0.40, 0.43], and the mixing between HZZ tree-level coupling and higher order CP -even coupling to be in the ranges [−0.66, −0.57] ∪ [−0.15, 1.00]; namely compatible with a standard model Higgs. We discuss the expected precision in determining the various HVV' couplings in future LHC runs. A powerful and at first glance surprising prediction of the analysis is that with 100-400 fb^-1, the golden channel will be able to start probing the couplings of the Higgs boson to diphotons in the 4l channel. We discuss the implications and further optimization of the methods for the next LHC runs.

Oxy anion-accelerated rearrangements

The alkali metal salts of 1,5-hexadien-3-ols undergo accelerated Cope rearrangements to the enolates of δ, ε-unsaturated carbonyl compounds. The generality of the rearrangement was investigated in numerous systems, particularly acyclic cases, and the effect of changes in substituents, counterions, solvents, and geometrical structures were noted and discussed. Applications of this methodology in synthesis included the synthesis of the insect pheromone frontalin, the preparation of selectively monoprotected 1,6-dicarbonyl compounds from 4-methoxy- and 4-phenylthio-1,5-hexadien-3-ols, and the construction of complex ring structures such as a D-homo-estratetraenone derivative.

Thermochemical estimates of the energetics of anionpromoted alkoxide fragmentations were made, and in all cases heterolytic cleavage was favored over hemolytic cleavage by 8.5-53 kcal/mol. The implication of these and other thermochemical estimates is that the anionic oxy-Cope rearrangement occurs via a concerted mechanism rather than a dissociation-recombination process. The concepts of anion-induced bond weakening were successfully applied to an accelerated [1,3]-shift of a dithiane fragment in a cyclohexenyl system. Trapping experiments demonstrated that > 85% of the [1,3]-shift occurred within a solvent cage. Attempts at promoting an intramolecular ene reaction using the potassium salts of 2,7-octadien-1-o1 and 2,8-nonadien-1-o1 were unsuccessful. A general review of anion-promoted bond reorganizations and anion substituent effects is also presented.

Quantum Mechanics Studies of Fuel Cell Catalysts and Proton Conducting Ceramics with Validation by Experiment

We carried out quantum mechanics (QM) studies aimed at improving the performance of hydrogen fuel cells. This led to predictions of improved materials, some of which were subsequently validated with experiments by our collaborators.

In part I, the challenge was to find a replacement for the Pt cathode that would lead to improved performance for the Oxygen Reduction Reaction (ORR) while remaining stable under operational conditions and decreasing cost. Our design strategy was to find an alloy with composition Pt3M that would lead to surface segregation such that the top layer would be pure Pt, with the second and subsequent layers richer in M. Under operating conditions we expect the surface to have significant O and/or OH chemisorbed on the surface, and hence we searched for M that would remain segregated under these conditions. Using QM we examined surface segregation for 28 Pt₃M alloys, where M is a transition metal. We found that only Pt₃Os and Pt₃Ir showed significant surface segregation when O and OH are chemisorbed on the catalyst surfaces. This result indicates that Pt₃Os and Pt3Ir favor formation of a Pt-skin surface layer structure that would resist the acidic electrolyte corrosion during fuel cell operation environments. We chose to focus on Os because the phase diagram for Pt-Ir indicated that Pt-Ir could not form a homogeneous alloy at lower temperature. To determine the performance for ORR, we used QM to examine all intermediates, reaction pathways, and reaction barriers involved in the processes for which protons from the anode reactions react with O₂ to form H₂O. These QM calculations used our Poisson-Boltzmann implicit solvation model include the effects of the solvent (water with dielectric constant 78 with pH 7 at 298K). We found that the rate determination step (RDS) was the O_ad hydration reaction (O_ad + H₂O_ad -> OH_ad + OH_ad) in both cases, but that the barrier for pure Pt of 0.50 eV is reduced to 0.48 eV for Pt₃Os, which at 80 degrees C would increase the rate by 218%. We collaborated with the Pu-Wei Wu’s group to carry out experiments, where we found that the dealloying process-treated Pt2Os catalyst showed two-fold higher activity at 25 degrees C than pure Pt and that the alloy had 272% improved stability, validating our theoretical predictions.

We also carried out similar QM studies followed by experimental validation for the Os/Pt core-shell catalyst fabricated by the underpotential deposition (UPD) method. The QM results indicated that the RDS for ORR is a compromise between the OOH formation step (0.37 eV for Pt, 0.23 eV for Pt_2ML/Os core-shell) and H₂O formation steps (0.32 eV for Pt, 0.22 eV for Pt_2ML/Os core-shell). We found that Pt_2ML/Os has the highest activity (compared to pure Pt and to the Pt₃Os alloy) because the 0.37 eV barrier decreases to 0.23 eV. To understand what aspects of the core shell structure lead to this improved performance, we considered the effect on ORR of compressing the alloy slab to the dimensions of pure Pt. However this had little effect, with the same RDS barrier 0.37 eV. This shows that the ligand effect (the electronic structure modification resulting from the Os substrate) plays a more important role than the strain effect, and is responsible for the improved activity of the core- shell catalyst. Experimental materials characterization proves the core-shell feature of our catalyst. The electrochemical experiment for Pt_2ML/Os/C showed 3.5 to 5 times better ORR activity at 0.9V (vs. NHE) in 0.1M HClO₄ solution at 25 degrees C as compared to those of commercially available Pt/C. The excellent correlation between experimental half potential and the OH binding energies and RDS barriers validate the feasibility of predicting catalyst activity using QM calculation and a simple Langmuir–Hinshelwood model.

In part II, we used QM calculations to study methane stream reforming on a Ni-alloy catalyst surfaces for solid oxide fuel cell (SOFC) application. SOFC has wide fuel adaptability but the coking and sulfur poisoning will reduce its stability. Experimental results suggested that the Ni4Fe alloy improves both its activity and stability compared to pure Ni. To understand the atomistic origin of this, we carried out QM calculations on surface segregation and found that the most stable configuration for Ni₄Fe has a Fe atom distribution of (0%, 50%, 25%, 25%, 0%) starting at the bottom layer. We calculated that the binding of C atoms on the Ni4Fe surface is 142.9 Kcal/mol, which is about 10 Kcal/mol weaker compared to the pure Ni surface. This weaker C binding energy is expected to make coke formation less favorable, explaining why Ni₄Fe has better coking resistance. This result confirms the experimental observation. The reaction energy barriers for CHx decomposition and C binding on various alloy surface, Ni₄X (X=Fe, Co, Mn, and Mo), showed Ni₄Fe, Ni₄Co, and Fe₄Mn all have better coking resistance than pure Ni, but that only Ni₄Fe and Fe₄Mn have (slightly) improved activity compared to pure Ni.

In part III, we used QM to examine the proton transport in doped perovskite-ceramics. Here we used a 2x2x2 supercell of perovskite with composition Ba₈X₇M₁(OH)₁O₂₃ where X=Ce or Zr and M=Y, Gd, or Dy. Thus in each case a 4⁺ X is replace by a 3⁺ M plus a proton on one O. Here we predicted the barriers for proton diffusion allowing both includes intra-octahedron and inter-octahedra proton transfer. Without any restriction, we only observed the inter-octahedra proton transfer with similar energy barrier as previous computational work but 0.2 eV higher than experimental result for Y doped zirconate. For one restriction in our calculations is that the O_donor-O_acceptor atoms were kept at fixed distances, we found that the barrier difference between cerates/zirconates with various dopants are only 0.02~0.03 eV. To fully address performance one would need to examine proton transfer at grain boundaries, which will require larger scale ReaxFF reactive dynamics for systems with millions of atoms. The QM calculations used here will be used to train the ReaxFF force field.

Electromagnetic decay of the 1.7- and 2.43-MeV levels in ^9Be

The 1.7- and 2.43-MeV levels in ⁹Be were populated with the reaction ¹¹B(d, α)⁹Be* by bombarding thin boron on carbon foils with 1.7-MeV deuterons. The alpha particles were analyzed in energy with a surface-barrier counter set at the unique kinematically determined angle and the recoiling ⁹Be nuclei at 90^o were analyzed in rigidity with a magnetic spectrometer, in energy by a surface-barrier counter at the spectrometer focus, and in velocity by the time delay between an alpha and a ⁹Be count. When a pulse from the spectrometer counter was in the appropriate delayed coincidence with a pulse from the alpha counter, the two pulses were recorded in a two-dimensional pulse height analyzer. Most of the ⁹Be* decay by particle breakup. Only those that gamma decay are detected by the spectrometer counter. Thus the experiment provides a direct measurement of Γ_rad/Γ. Analysis of 384 observed events gives Γ_rad/Γ = (1.16 ± 0.14) X 10^-4 for the 2.43-MeV level. Combining this ratio with the value of Γ_rad = 0.122 ± 0.015 eV found from inelastic electron scattering gives Γ = (1.05 ± 0.18) keV. For the 1.7-MeV level, an upper limit, Γ_rad/Γ ≤ 2.4 = 10^-5, was determined.

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).

I. The crystal structure of potassium bis(tricyanovinyl)amine. II. Nuclear magnetic resonance studies of alkali halide solutions. III. Elucidation of the intramolecular hydrogen bond in acetylacetone by the deuterium isotope effect on the chemical shift of the bridge hydrogen

Part I

Potassium bis-(tricyanovinyl) amine, K⁺N[C(CN)=C(CN)₂]₂^-, crystallizes in the monoclinic system with the space group Cc and lattice constants, a = 13.346 ± 0.003 Å, c = 8.992 ± 0.003 Å, B = 114.42 ± 0.02°, and Z = 4. Three dimensional intensity data were collected by layers perpendicular to b* and c* axes. The crystal structure was refined by the least squares method with anisotropic temperature factor to an R value of 0.064.

The average carbon-carbon and carbon-nitrogen bond distances in –C-CΞN are 1.441 ± 0.016 Å and 1.146 ± 0.014 Å respectively. The bis-(tricyanovinyl) amine anion is approximately planar. The coordination number of the potassium ion is eight with bond distances from 2.890 Å to 3.408 Å. The bond angle C-N-C of the amine nitrogen is 132.4 ± 1.9°. Among six cyano groups in the molecule, two of them are bent by what appear to be significant amounts (5.0° and 7.2°). The remaining four are linear within the experimental error. The bending can probably be explained by molecular packing forces in the crystals.

Part II

The nuclear magnetic resonance of ⁸¹Br and ¹²⁷I in aqueous solutions were studied. The cation-halide ion interactions were studied by studying the effect of the Li⁺, Na⁺, K⁺, Mg⁺⁺, Cs⁺ upon the line width of the halide ions. The solvent-halide ion interactions were studied by studying the effects of methanol, acetonitrile, and acetone upon the line width of ⁸¹Br and ¹²⁷I in the aqueous solutions. It was found that the viscosity plays a very important role upon the halide ions line width. There is no specific cation-halide ion interaction for those ions such as Mg⁺⁺, Di⁺, Na⁺, and K⁺, whereas the Cs⁺ - halide ion interaction is strong. The effect of organic solvents upon the halide ion line width in aqueous solutions is in the order acetone ˃ acetonitrile ˃ methanol. It is suggested that halide ions do form some stable complex with the solvent molecules and the reason Cs⁺ can replace one of the ligands in the solvent-halide ion complex.

Part III

An unusually large isotope effect on the bridge hydrogen chemical shift of the enol form of pentanedione-2, 4(acetylacetone) and 3-methylpentanedione-2, 4 has been observed. An attempt has been made to interpret this effect. It is suggested from the deuterium isotope effect studies, temperature dependence of the bridge hydrogen chemical shift studies, IR studies in the OH, OD, and C=O stretch regions, and the HMO calculations, that there may probably be two structures for the enol form of acetylacetone. The difference between these two structures arises mainly from the electronic structure of the π-system. The relative population of these two structures at various temperatures for normal acetylacetone and at room temperature for the deuterated acetylacetone were calculated.