Structural and mechanistic motifs in membrane proteins: the three-dimensional modelling of rhodopsin, band 3, and the nicotinic acetylcholine receptor

Because so little is known about the structure of membrane proteins, an attempt has been made in this work to develop techniques by which to model them in three dimensions. The procedures devised rely heavily upon the availability of several sequences of a given protein. The modelling procedure is composed of two parts. The first identifies transmembrane regions within the protein sequence on the basis of hydrophobicity, β-turn potential, and the presence of certain amino acid types, specifically, proline and basic residues. The second part of the procedure arranges these transmembrane helices within the bilayer based upon the evolutionary conservation of their residues. Conserved residues are oriented toward other helices and variable residues are positioned to face the surrounding lipids. Available structural information concerning the protein's helical arrangement, including the lengths of interhelical loops, is also taken into account. Rhodopsin, band 3, and the nicotinic acetylcholine receptor have all been modelled using this methodology, and mechanisms of action could be proposed based upon the resulting structures.

Specific residues in the rhodopsin and iodopsin sequences were identified, which may regulate the proteins' wavelength selectivities. A hinge-like motion of helices M3, M4, and M5 with respect to the rest of the protein was proposed to result in the activation of transducin, the G-protein associated with rhodopsin. A similar mechanism is also proposed for signal transduction by the muscarinic acetylcholine and β-adrenergic receptors.

The nicotinic acetylcholine receptor was modelled with four trans-membrane helices per subunit and with the five homologous M2 helices forming the cation channel. Putative channel-lining residues were identified and a mechanism of channel-opening based upon the concerted, tangential rotation of the M2 helices was proposed.

Band 3, the anion exchange protein found in the erythrocyte membrane, was modelled with 14 transmembrane helices. In general the pathway of anion transport can be viewed as a channel composed of six helices that contains a single hydrophobic restriction. This hydrophobic region will not allow the passage of charged species, unless they are part of an ion-pair. An arginine residue located near this restriction is proposed to be responsible for anion transport. When ion-paired with a transportable anion it rotates across the barrier and releases the anion on the other side of the membrane. A similar process returns it to its original position. This proposed mechanism, based on the three-dimensional model, can account for the passive, electroneutral, anion exchange observed for band 3. Dianions can be transported through a similar mechanism with the additional participation of a histidine residue. Both residues are located on M10.

Measurement of the band bending and surface dipole at chemically functionalized Si(111)/vacuum interfaces

The core-level energy shifts observed using X-ray photoelectron spectroscopy (XPS) have been used to determine the band bending at Si(111) surfaces terminated with Si-Br, Si-H, and Si-CH₃ groups, respectively. The surface termination influenced the band bending, with the Si 2p_3/2 binding energy affected more by the surface chemistry than by the dopant type. The highest binding energies were measured on Si(111)-Br (whose Fermi level was positioned near the conduction band at the surface), followed by Si(111)-H, followed by Si(111)-CH₃ (whose Fermi level was positioned near mid-gap at the surface). Si(111)-CH₃ surfaces exposed to Br₂(g) yielded the lowest binding energies, with the Fermi level positioned between mid-gap and the valence band. The Fermi level position of Br₂(g)-exposed Si(111)-CH₃ was consistent with the presence of negatively charged bromine-containing ions on such surfaces. The binding energies of all of the species detected on the surface (C, O, Br) shifted with the band bending, illustrating the importance of isolating the effects of band bending when measuring chemical shifts on semiconductor surfaces. The influence of band bending was confirmed by surface photovoltage (SPV) measurements, which showed that the core levels shifted toward their flat-band values upon illumination. Where applicable, the contribution from the X-ray source to the SPV was isolated and quantified. Work functions were measured by ultraviolet photoelectron spectroscopy (UPS), allowing for calculation of the sign and magnitude of the surface dipole in such systems. The values of the surface dipoles were in good agreement with previous measurements as well as with electronegativity considerations. The binding energies of the adventitious carbon signals were affected by band bending as well as by the surface dipole. A model of band bending in which charged surface states are located exterior to the surface dipole is consistent with the XPS and UPS behavior of the chemically functionalized Si(111) surfaces investigated herein.

Variable-angle electron spectroscopic studies of various polyatomic molecular systems

The complementary techniques of low-energy, variable-angle electron-impact spectroscopy and ultraviolet variable-angle photoelectron spectroscopy have been used to study the electronic spectroscopy and structure of several series of molecules. Electron-impact studies were performed at incident beam energies between 25 eV and 100 eV and at scattering angles ranging from 0° to 90°. The energy-loss regions from 0 eV to greater than 15 eV were studied. Photoelectron spectroscopic studies were conducted using a HeI radiation source and spectra were measured at scattering angles from 45° to 90°. The molecules studied were chosen because of their spectroscopic, chemical, and structural interest. The operation of a new electron-impact spectrometer with multiple-mode target source capability is described. This spectrometer has been used to investigate the spin-forbidden transitions in a number of molecular systems.

The electron-impact spectroscopy of the six chloro-substituted ethylenes has been studied over the energy-loss region from 0-15 eV. Spin-forbidden excitations corresponding to the π → π*, N → T transition have been observed at excitation energies ranging from 4.13 eV in vinyl chloride to 3.54 eV in tetrachloroethylene. Symmetry-forbidden transitions of the type π → np have been oberved in trans-dichloroethyene and tetrachlor oethylene. In addition, transitions to many states lying above the first ionization potential were observed for the first time. Many of these bands have been assigned to Rydberg series converging to higher ionization potentials. The trends observed in the measured transition energies for the π → π*, N → T, and N → V as well as the π → 3s excitation are discussed and compared to those observed in the methyl- and fluoro- substituted ethylenes.

The electron energy-loss spectra of the group VIb transition metal hexacarbonyls have been studied in the 0 eV to 15 eV region. The differential cross sections were obtained for several features in the 3-7 eV energy-loss region. The symmetry-forbidden nature of the ¹A_1g → ¹A_1g, 2t_2g(π) → 3t_2g(π*) transition in these compounds was confirmed by the high-energy, low-angle behavior of their relative intensities. Several low lying transitions have been assigned to ligand field transitions on the basis of the energy and angular behavior of the differential cross sections for these transitions. No transitions which could clearly be assigned to singlet → triplet excitations involving metal orbitals were located. A number of states lying above the first ionization potential have been observed for the first time. A number of features in the 6-14 eV energy-loss region of the spectra of these compounds correspond quite well to those observed in free CO.

A number of exploratory studies have been performed. The π → π*, N → T, singlet → triplet excitation has been located in vinyl bromide at 4.05 eV. We have also observed this transition at approximately 3.8 eV in a cis-/trans- mixture of the 1,2-dibromoethylenes. The low-angle spectrum of iron pentacarbonyl was measured over the energy-loss region extending from 2-12 eV. A number of transitions of 8 eV or greater excitation energy were observed for the first time. Cyclopropane was also studied at both high and low angles but no clear evidence for any spin- forbidden transitions was found. The electron-impact spectrum of the methyl radical resulting from the pyrolysis of tetramethyl tin was obtained at 100 eV incident energy and at 0° scattering angle. Transitions observed at 5.70 eV and 8.30 eV agree well with the previous optical results. In addition, a number of bands were observed in the 8-14 eV region which are most likely due to Rydberg transitions converging to the higher ionization potentials of this molecule. This is the first reported electron-impact spectrum of a polyatomic free radical.

Variable-angle photoelectron spectroscopic studies were performed on a series of three-membered-ring heterocyclic compounds. These compounds are of great interest due to their highly unusual structure. Photoelectron angular distributions using HeI radiation have been measured for the first time for ethylene oxide and ethyleneimine. The measured anisotropy parameters, β, along with those measured for cyclopropane were used to confirm the orbital correlations and photoelectron band assignments. No high values of β similar to those expected for alkene π orbitals were observed for the Walsh or Forster-Coulson-Moffit type orbitals.

Metasomatism and magmatic assimilation at a gabbro-limestone contact, Christmas Mountains, Big Bend region, Texas

A composite stock of alkaline gabbro and syenite is intrusive into limestone of the Del Carmen, Sue Peake and Santa Elena Formations at the northwest end of the Christmas Mountains. There is abundant evidence of solution of wallrock by magma but nowhere are gabbro and limestone in direct contact. The sequence of lithologies developed across the intrusive contact and across xenoliths is gabbro, pyroxenite, calc-silicate skarn, marble. Pyroxenite is made up of euhedral crystals of titanaugite and sphene in a leucocratic matrix of nepheline, Wollastonite and alkali feldspar. The uneven modal distribution of phases in pyroxenite and the occurrence' of nepheline syenite dikes, intrusive into pyroxenite and skarn, suggest that pyroxenite represents an accumulation of clinopyroxene "cemented" together by late-solidifying residual magma of nepheline syenite composition. Assimilation of limestone by gabbroic magma involves reactions between calcite and magma and/or crystals in equilibrium with magma and crystallization of phases in which the magma is saturated, to supply energy for the solution reaction. Gabbroic magma was saturated with plagioclase and clinopyroxene at the time of emplacement. The textural and mineralogic features of pyroxenite can be produced by the reaction 2( 1-X) CALCITE + AN_XAB_l-X = (1-X) NEPHELINE+ 2(1-X) WOLLASTONITE+ X ANORTHITE+ 2(1-X) CO₂. Plagioclase in pyroxenite has corroded margins and is rimmed by nepheline, suggestive of resorption by magma. Anorthite and wollastonite enter solid solution in titanaugite. For each mole of calcite dissolved, approximately one mole of clinopyroxene was crystallized. Thus the amount of limestone that may be assimilated is limited by the concentration of potential clinopyroxene in the magma. Wollastonite appears as a phase when magma has been depleted in iron and magnesium by crystallization of titanaugite. The predominance of mafic and ultramafic compositions among contaminated rocks and their restriction to a narrow zone along the intrusive contact provides little evidence for the generation of a significant volume of desilicated magma as a result of limestone assimilation.

Within 60 m of the intrusive contact with the gabbro, nodular chert in the Santa Elena Limestone reacted with the enveloping marble to form spherical nodules of high-temperature calc-silicate minerals. The phases wollastonite, rankinite, spurrite, tilleyite and calcite, form a series of sharply-bounded, concentric monomineralic and two-phase shells which record a step-wise decrease in silica content from the core of a nodule to its rim. Mineral zones in the nodules vary 'with distance from the gabbro as follows:

0-5 m CALCITE + SPURRITE + RANKINITE + WOLLASTONITE
5-16 m CALCITE + TILLEYITE ± SPURRITE + RANKINITE + WOLLASTONITE
16-31 m CALCITE + TILLEYITE + WOLLASTONITE
31-60 m CALCITE + WOLLASTONITE
60-plus CALCITE + QUARTZ

The mineral of a one-phase zone is compatible with the phases bounding it on either side but these phases are incompatible in the same volume of P-T-X_CO2.

Growth of a monomineralio zone is initiated by reaction between minerals of adjacent one-phase zones which become unstable with rising temperature to form a thin layer of a new single phase that separates the reactants and is compatible with both of them. Because the mineral of the new zone is in equilibrium with the phases at both of its contacts, gradients in the chemical potentials of the exchangeable components are established across it. Although zone boundaries mark discontinuities in the gradients of bulk composition, two-phase equilibria at the contacts demonstrate that the chemical potentials are continuous. Hence, Ca, Si and CO₂ were redistributed in the growing nodule by diffusion. A monomineralic zone grows at the expense of an adjacent zone by reaction between diffusing components and the mineral of the adjacent zone. Equilibria between two phases at zone boundaries buffers the chemical potentials of the diffusing species. Thus, within a monomineralic zone, the chemical potentials of the diffusing components are controlled external to the local assemblage by the two-phase equilibria at the zone boundaries.

Mineralogically zoned calc-silicate skarn occurs as a narrow band that separates pyroxenite and marble along the intrusive contact and forms a rim on marble xenoliths in gabbro. Skarn consists of melilite or idocrase pseudomorphs of melili te, one or two . stoichiometric calcsilicate phases and accessory Ti-Zr garnet, perovskite and magnetite. The sequence of mineral zones from pyroxenite to marble, defined by a characteristic calc-silicate, is wollastonite, rankinite, spurrite, calcite. Mineral assemblages of adjacent skarn zones are compatible and the set of zones in a skarn band defines a facies type, indicating that the different mineral assemblages represent different bulk compositions recrystallized under identical conditions. The number of phases in each zone is less than the number that might be expected to result from metamorphism of a general bulk composition under conditions of equilibrium, trivariant in P, T and u_CO2. The "special" bulk composition of each zone is controlled by reaction between phases of the zones bounding it on either side. The continuity of the gradients of composition of melilite and garnet solid solutions across the skarn is consistent with the local equilibrium hypothesis and verifies that diffusion was the mechanism of mass transport. The formula proportions of Ti and Zr in garnet from skarn vary antithetically with that of Si Which systematically decreases from pyroxenite to marble. The chemical potential of Si in each skarn zone was controlled by the coexisting stoichiometric calc-silicate phases in the assemblage. Thus the formula proportion of Si in garnet is a direct measure of the chemical potential of Si from point to point in skarn. Reaction between gabbroic magma saturated with plagioclase and clinopyroxene produced nepheline pyroxenite and melilite-wollastonite skarn. The calcsilicate zones result from reaction between calcite and wollastonite to form spurrite and rankinite.

Biophysical and network mechanisms of high frequency extracellular potentials in the rat hippocampus

A fundamental question in neuroscience is how distributed networks of neurons communicate and coordinate dynamically and specifically. Several models propose that oscillating local networks can transiently couple to each other through phase-locked firing. Coherent local field potentials (LFP) between synaptically connected regions is often presented as evidence for such coupling. The physiological correlates of LFP signals depend on many anatomical and physiological factors, however, and how the underlying neural processes collectively generate features of different spatiotemporal scales is poorly understood. High frequency oscillations in the hippocampus, including gamma rhythms (30-100 Hz) that are organized by the theta oscillations (5-10 Hz) during active exploration and REM sleep, as well as sharp wave-ripples (SWRs, 140-200 Hz) during immobility or slow wave sleep, have each been associated with various aspects of learning and memory. Deciphering their physiology and functional consequences is crucial to understanding the operation of the hippocampal network.

We investigated the origins and coordination of high frequency LFPs in the hippocampo-entorhinal network using both biophysical models and analyses of large-scale recordings in behaving and sleeping rats. We found that the synchronization of pyramidal cell spikes substantially shapes, or even dominates, the electrical signature of SWRs in area CA1 of the hippocampus. The precise mechanisms coordinating this synchrony are still unresolved, but they appear to also affect CA1 activity during theta oscillations. The input to CA1, which often arrives in the form of gamma-frequency waves of activity from area CA3 and layer 3 of entorhinal cortex (EC3), did not strongly influence the timing of CA1 pyramidal cells. Rather, our data are more consistent with local network interactions governing pyramidal cells' spike timing during the integration of their inputs. Furthermore, the relative timing of input from EC3 and CA3 during the theta cycle matched that found in previous work to engage mechanisms for synapse modification and active dendritic processes. Our work demonstrates how local networks interact with upstream inputs to generate a coordinated hippocampal output during behavior and sleep, in the form of theta-gamma coupling and SWRs.

Band structure and transport properties of simple cubic tellurium-base alloys

The electrical transport properties and lattice spacings of simple cubic Te-Au, Te-Au-Fe, and Te-Au-Mn alloys, prepared by rapid quenching from the liquid state, hove been measured and correlated with a proposed bond structure. The variations of superconducting transition temperature, absolute thermoelectric power, and lattice spacing with Te concentration all showed related anomalies in the binary Te-Au alloys. The unusual behavior of these properties has been interpreted by using nearly free electron theory to predict the effect of the second Brillouin zone boundary on the area of the Fermi surface, and the electronic density of states. The behavior of the superconducting transition temperature and the lattice parameter as Fe and Mn ore added further supports the proposed interpretation as well as providing information on the existence of localized magnetic states in the ternary alloys. In addition, it was found that a very distinct bond structure effect on the transition temperatures of the Te-Au-Fe alloys could be identified.

First principles based multiparadigm modeling of electronic structures and dynamics

Electronic structures and dynamics are the key to linking the material composition and structure to functionality and performance.

An essential issue in developing semiconductor devices for photovoltaics is to design materials with optimal band gaps and relative positioning of band levels. Approximate DFT methods have been justified to predict band gaps from KS/GKS eigenvalues, but the accuracy is decisively dependent on the choice of XC functionals. We show here for CuInSe₂ and CuGaSe₂, the parent compounds of the promising CIGS solar cells, conventional LDA and GGA obtain gaps of 0.0-0.01 and 0.02-0.24 eV (versus experimental values of 1.04 and 1.67 eV), while the historically first global hybrid functional, B3PW91, is surprisingly the best, with band gaps of 1.07 and 1.58 eV. Furthermore, we show that for 27 related binary and ternary semiconductors, B3PW91 predicts gaps with a MAD of only 0.09 eV, which is substantially better than all modern hybrid functionals, including B3LYP (MAD of 0.19 eV) and screened hybrid functional HSE06 (MAD of 0.18 eV).

The laboratory performance of CIGS solar cells (> 20% efficiency) makes them promising candidate photovoltaic devices. However, there remains little understanding of how defects at the CIGS/CdS interface affect the band offsets and interfacial energies, and hence the performance of manufactured devices. To determine these relationships, we use the B3PW91 hybrid functional of DFT with the AEP method that we validate to provide very accurate descriptions of both band gaps and band offsets. This confirms the weak dependence of band offsets on surface orientation observed experimentally. We predict that the CBO of perfect CuInSe₂/CdS interface is large, 0.79 eV, which would dramatically degrade performance. Moreover we show that band gap widening induced by Ga adjusts only the VBO, and we find that Cd impurities do not significantly affect the CBO. Thus we show that Cu vacancies at the interface play the key role in enabling the tunability of CBO. We predict that Na further improves the CBO through electrostatically elevating the valence levels to decrease the CBO, explaining the observed essential role of Na for high performance. Moreover we find that K leads to a dramatic decrease in the CBO to 0.05 eV, much better than Na. We suggest that the efficiency of CIGS devices might be improved substantially by tuning the ratio of Na to K, with the improved phase stability of Na balancing phase instability from K. All these defects reduce interfacial stability slightly, but not significantly.

A number of exotic structures have been formed through high pressure chemistry, but applications have been hindered by difficulties in recovering the high pressure phase to ambient conditions (i.e., one atmosphere and room temperature). Here we use dispersion-corrected DFT (PBE-ulg flavor) to predict that above 60 GPa the most stable form of N₂O (the laughing gas in its molecular form) is a 1D polymer with an all-nitrogen backbone analogous to cis-polyacetylene in which alternate N are bonded (ionic covalent) to O. The analogous trans-polymer is only 0.03-0.10 eV/molecular unit less stable. Upon relaxation to ambient conditions both polymers relax below 14 GPa to the same stable non-planar trans-polymer, accompanied by possible electronic structure transitions. The predicted phonon spectrum and dissociation kinetics validate the stability of this trans-poly-NNO at ambient conditions, which has potential applications as a new type of conducting polymer with all-nitrogen chains and as a high-energy oxidizer for rocket propulsion. This work illustrates in silico materials discovery particularly in the realm of extreme conditions.

Modeling non-adiabatic electron dynamics has been a long-standing challenge for computational chemistry and materials science, and the eFF method presents a cost-efficient alternative. However, due to the deficiency of FSG representation, eFF is limited to low-Z elements with electrons of predominant s-character. To overcome this, we introduce a formal set of ECP extensions that enable accurate description of p-block elements. The extensions consist of a model representing the core electrons with the nucleus as a single pseudo particle represented by FSG, interacting with valence electrons through ECPs. We demonstrate and validate the ECP extensions for complex bonding structures, geometries, and energetics of systems with p-block character (C, O, Al, Si) and apply them to study materials under extreme mechanical loading conditions.

Despite its success, the eFF framework has some limitations, originated from both the design of Pauli potentials and the FSG representation. To overcome these, we develop a new framework of two-level hierarchy that is a more rigorous and accurate successor to the eFF method. The fundamental level, GHA-QM, is based on a new set of Pauli potentials that renders exact QM level of accuracy for any FSG represented electron systems. To achieve this, we start with using exactly derived energy expressions for the same spin electron pair, and fitting a simple functional form, inspired by DFT, against open singlet electron pair curves (H₂ systems). Symmetric and asymmetric scaling factors are then introduced at this level to recover the QM total energies of multiple electron pair systems from the sum of local interactions. To complement the imperfect FSG representation, the AMPERE extension is implemented, and aims at embedding the interactions associated with both the cusp condition and explicit nodal structures. The whole GHA-QM+AMPERE framework is tested on H element, and the preliminary results are promising.

Band Engineering in Thermoelectric Materials Using Optical, Electronic, and Ab-Initio Computed Properties

Thermoelectric materials have demanded a significant amount of attention for their ability to convert waste heat directly to electricity with no moving parts. A resurgence in thermoelectrics research has led to significant enhancements in the thermoelectric figure of merit, zT, even for materials that were already well studied. This thesis approaches thermoelectric zT optimization by developing a detailed understanding of the electronic structure using a combination of electronic/thermoelectric properties, optical properties, and ab-initio computed electronic band structures. This is accomplished by applying these techniques to three important classes of thermoelectric materials: IV-VI materials (the lead chalcogenides), Half-Heusler’s (XNiSn where X=Zr, Ti, Hf), and CoSb₃ skutterudites.

In the IV-VI materials (PbTe, PbSe, PbS) I present a shifting temperature-dependent optical absorption edge which correlates well to the computed ab-initio molecular dynamics result. Contrary to prior literature that suggests convergence of the primary and secondary bands at 400 K, I suggest a higher convergence temperature of 700, 900, and 1000 K for PbTe, PbSe, and PbS, respectively. This finding can help guide electronic properties modelling by providing a concrete value for the band gap and valence band offset as a function of temperature.

Another important thermoelectric material, ZrNiSn (half-Heusler), is analyzed for both its optical and electronic properties; transport properties indicate a largely different band gap depending on whether the material is doped n-type or p-type. By measuring and reporting the optical band gap value of 0.13 eV, I resolve the discrepancy in the gap calculated from electronic properties (maximum Seebeck and resistivity) by correlating these estimates to the electron-to-hole weighted mobility ratio, A, in narrow gap materials (A is found to be approximately 5.0 in ZrNiSn).

I also show that CoSb₃ contains multiple conduction bands that contribute to the thermoelectric properties. These bands are also observed to shift towards each other with temperature, eventually reaching effective convergence for T>500 K. This implies that the electronic structure in CoSb₃ is critically important (and possibly engineerable) with regards to its high thermoelectric figure of merit.

Design of antenna-coupled lumped-element titanium nitride KIDs for long-wavelength multi-band continuum imaging

Many applications in cosmology and astrophysics at millimeter wavelengths including CMB polarization, studies of galaxy clusters using the Sunyaev-Zeldovich effect (SZE), and studies of star formation at high redshift and in our local universe and our galaxy, require large-format arrays of millimeter-wave detectors. Feedhorn and phased-array antenna architectures for receiving mm-wave light present numerous advantages for control of systematics, for simultaneous coverage of both polarizations and/or multiple spectral bands, and for preserving the coherent nature of the incoming light. This enables the application of many traditional "RF" structures such as hybrids, switches, and lumped-element or microstrip band-defining filters.

Simultaneously, kinetic inductance detectors (KIDs) using high-resistivity materials like titanium nitride are an attractive sensor option for large-format arrays because they are highly multiplexable and because they can have sensitivities reaching the condition of background-limited detection. A KID is a LC resonator. Its inductance includes the geometric inductance and kinetic inductance of the inductor in the superconducting phase. A photon absorbed by the superconductor breaks a Cooper pair into normal-state electrons and perturbs its kinetic inductance, rendering it a detector of light. The responsivity of KID is given by the fractional frequency shift of the LC resonator per unit optical power.

However, coupling these types of optical reception elements to KIDs is a challenge because of the impedance mismatch between the microstrip transmission line exiting these architectures and the high resistivity of titanium nitride. Mitigating direct absorption of light through free space coupling to the inductor of KID is another challenge. We present a detailed titanium nitride KID design that addresses these challenges. The KID inductor is capacitively coupled to the microstrip in such a way as to form a lossy termination without creating an impedance mismatch. A parallel plate capacitor design mitigates direct absorption, uses hydrogenated amorphous silicon, and yields acceptable noise. We show that the optimized design can yield expected sensitivities very close to the fundamental limit for a long wavelength imager (LWCam) that covers six spectral bands from 90 to 400 GHz for SZE studies.

Excess phase (frequency) noise has been observed in KID and is very likely caused by two-level systems (TLS) in dielectric materials. The TLS hypothesis is supported by the measured dependence of the noise on resonator internal power and temperature. However, there is still a lack of a unified microscopic theory which can quantitatively model the properties of the TLS noise. In this thesis we derive the noise power spectral density due to the coupling of TLS with phonon bath based on an existing model and compare the theoretical predictions about power and temperature dependences with experimental data. We discuss the limitation of such a model and propose the direction for future study.

Investigations of DNA-mediated protein oxidation

DNA charge transport (CT) involves the efficient transfer of electrons or electron holes through the DNA π-stack over long molecular distances of at least 100 base-pairs. Despite this shallow distance dependence, DNA CT is sensitive to mismatches or lesions that disrupt π-stacking and is critically dependent on proper electronic coupling of the donor and acceptor moieties into the base stack. Favorable DNA CT is very rapid, occurring on the picosecond timescale. Because of this speed, electron holes equilibrate along the DNA π-stack, forming a characteristic pattern of DNA damage at low oxidation potential guanine multiplets. Furthermore, DNA CT may be used in a biological context. DNA processing enzymes with 4Fe4S clusters can perform DNA-mediated electron transfer (ET) self-exchange reactions with other 4Fe4S cluster proteins, even if the proteins are quite dissimilar, as long as the DNA-bound [4Fe4S]^3+/2+ redox potentials are conserved. This mechanism would allow low copy number DNA repair proteins to find their lesions efficiently within the cell. DNA CT may also be used biologically for the long-range, selective activation of redox-active transcription factors. Within this work, we pursue other proteins that may utilize DNA CT within the cell and further elucidate aspects of the DNA-mediated ET self-exchange reaction of 4Fe4S cluster proteins.

Dps proteins, bacterial mini-ferritins that protect DNA from oxidative stress, are implicated in the survival and virulence of pathogenic bacteria. One aspect of their protection involves ferroxidase activity, whereby ferrous iron is bound and oxidized selectively by hydrogen peroxide, thereby preventing formation of damaging hydroxyl radicals via Fenton chemistry. Understanding the specific mechanism by which Dps proteins protect the bacterial genome could inform the development of new antibiotics. We investigate whether DNA-binding E. coli Dps can utilize DNA CT to protect the genome from a distance. An intercalating ruthenium photooxidant was employed to generate oxidative DNA damage via the flash-quench technique, which localizes to a low potential guanine triplet. We find that Dps loaded with ferrous iron, in contrast to Apo-Dps and ferric iron-loaded Dps which lack available reducing equivalents, significantly attenuates the yield of oxidative DNA damage at the guanine triplet. These data demonstrate that ferrous iron-loaded Dps is selectively oxidized to fill guanine radical holes, thereby restoring the integrity of the DNA. Luminescence studies indicate no direct interaction between the ruthenium photooxidant and Dps, supporting the DNA-mediated oxidation of ferrous iron-loaded Dps. Thus DNA CT may be a mechanism by which Dps efficiently protects the genome of pathogenic bacteria from a distance.

Further work focused on spectroscopic characterization of the DNA-mediated oxidation of ferrous iron-loaded Dps. X-band EPR was used to monitor the oxidation of DNA-bound Dps after DNA photooxidation via the flash-quench technique. Upon irradiation with poly(dGdC)₂, a signal arises with g = 4.3, consistent with the formation of mononuclear high-spin Fe(III) sites of low symmetry, the expected oxidation product of Dps with one iron bound at each ferroxidase site. When poly(dGdC)₂ is substituted with poly(dAdT)₂, the yield of Dps oxidation is decreased significantly, indicating that guanine radicals facilitate Dps oxidation. The more favorable oxidation of Dps by guanine radicals supports the feasibility of a long-distance protection mechanism via DNA CT where Dps is oxidized to fill guanine radical holes in the bacterial genome produced by reactive oxygen species.

We have also explored possible electron transfer intermediates in the DNA-mediated oxidation of ferrous iron-loaded Dps. Dps proteins contain a conserved tryptophan residue in close proximity to the ferroxidase site (W52 in E. coli Dps). In comparison to WT Dps, in EPR studies of the oxidation of ferrous iron-loaded Dps following DNA photooxidation, W52Y and W52A mutants were deficient in forming the characteristic EPR signal at g = 4.3, with a larger deficiency for W52A compared to W52Y. In addition to EPR, we also probed the role of W52 Dps in cells using a hydrogen peroxide survival assay. Bacteria containing W52Y Dps survived the hydrogen peroxide challenge more similarly to those containing WT Dps, whereas cells with W52A Dps died off as quickly as cells without Dps. Overall, these results suggest the possibility of W52 as a CT hopping intermediate.

DNA-modified electrodes have become an essential tool for the study of the redox chemistry of DNA processing enzymes with 4Fe4S clusters. In many cases, it is necessary to investigate different complex samples and substrates in parallel in order to elucidate this chemistry. Therefore, we optimized and characterized a multiplexed electrochemical platform with the 4Fe4S cluster base excision repair glycosylase Endonuclease III (EndoIII). Closely packed DNA films, where the protein has limited surface accessibility, produce EndoIII electrochemical signals sensitive to an intervening mismatch, indicating a DNA-mediated process. Multiplexed analysis allowed more robust characterization of the CT-deficient Y82A EndoIII mutant, as well as comparison of a new family of mutations altering the electrostatics surrounding the 4Fe4S cluster in an effort to shift the reduction potential of the cluster. While little change in the DNA-bound midpoint potential was found for this family of mutants, likely indicating the dominant effect of DNA-binding on establishing the protein redox potential, significant variations in the efficiency of DNA-mediated electron transfer were apparent. On the basis of the stability of these proteins, examined by circular dichroism, we proposed that the electron transfer pathway in EndoIII can be perturbed not only by the removal of aromatic residues but also through changes in solvation near the cluster.

While the 4Fe4S cluster of EndoIII is relatively insensitive to oxidation and reduction in solution, we have found that upon DNA binding, the reduction potential of the [4Fe4S]^3+/2+ couple shifts negatively by approximately 200 mV, bringing this couple into a physiologically relevant range. Demonstrated using electrochemistry experiments in the presence and absence of DNA, these studies do not provide direct molecular evidence for the species being observed. Sulfur K-edge X-ray absorbance spectroscopy (XAS) can be used to probe directly the covalency of iron-sulfur clusters, which is correlated to their reduction potential. We have shown that the Fe-S covalency of the 4Fe4S cluster of EndoIII increases upon DNA binding, stabilizing the oxidized [4Fe4S]³⁺ cluster, consistent with a negative shift in reduction potential. The 7% increase in Fe-S covalency corresponds to an approximately 150 mV shift, remarkably similar to DNA electrochemistry results. Therefore we have obtained direct molecular evidence for the shift in 4Fe4S reduction potential of EndoIII upon DNA binding, supporting the feasibility of our model whereby these proteins can utilize DNA CT to cooperate in order to efficiently find DNA lesions inside cells.

In conclusion, in this work we have explored the biological applications of DNA CT. We discovered that the DNA-binding bacterial ferritin Dps can protect the bacterial genome from a distance via DNA CT, perhaps contributing to pathogen survival and virulence. Furthermore, we optimized a multiplexed electrochemical platform for the study of the redox chemistry of DNA-bound 4Fe4S cluster proteins. Finally, we have used sulfur K-edge XAS to obtain direct molecular evidence for the negative shift in 4Fe4S cluster reduction potential of EndoIII upon DNA binding. These studies contribute to the understanding of DNA-mediated protein oxidation within cells.

Spectroscopic investigations of inter- and intramolecular processes in crystalline benzene

I. Introductory Remarks

A brief discussion of the overall organization of the thesis is presented along with a discussion of the relationship between this thesis and previous work on the spectroscopic properties of benzene.

II. Radiationless Transitions and Line broadening

Radiationless rates have been calculated for the ³B_1u→¹A_1g transitions of benzene and perdeuterobenzene as well as for the ¹B_2u→¹A_1g transition of benzene. The rates were calculated using a model that considers the radiationless transition as a tunneling process between two multi-demensional potential surfaces and assuming both harmonic and anharmonic vibrational potentials. Whenever possible experimental parameters were used in the calculation. To this end we have obtained experimental values for the anharmonicities of the carbon-carbon and carbon-hydrogen vibrations and the size of the lowest triplet state of benzene. The use of the breakdown of the Born-Oppenheimer approximation in describing radiationless transitions is critically examined and it is concluded that Herzberg-Teller vibronic coupling is 100 times more efficient at inducing radiationless transitions.

The results of the radiationless transition rate calculation are used to calculate line broadening in several of the excited electronic states of benzene. The calculated line broadening in all cases is in qualitative agreement with experimental line widths.

III. ³B_1u←¹A_1g Absorption Spectra

The ³B_1u←¹A_1g absorption spectra of C₆H₆ and C₆D₆ at 4.2˚K have been obtained at high resolution using the phosphorescence photoexcitation method. The spectrum exhibits very clear evidence of a pseudo-Jahn-Teller distortion of the normally hexagonal benzene molecule upon excitation to the triplet state. Factor group splitting of the 0 – 0 and 0 – 0 + v exciton bands have also been observed. The position of the mean of the 0 – 0 exciton band of C₆H₆ when compared to the phosphorescence origin of a C₆H₆ guest in a C₆D₆ host crystal indicates that the “static” intermolecular interactions between guest and hose are different for C₆H₆ and C₆D₆. Further investigation of this difference using the currently accepted theory of isotopic mixed crystals indicates that there is a 2cm^-1 shift of the ideal mixed crystal level per hot deuterium atom. This shift is observed for both the singlet and triplet states of benzene.

IV. ³E_1u←¹A_1g, Absorption Spectra

The ³E_1u←¹A_1g absorption spectra of C₆H₆ and C₆D₆ at 4.2˚K have been obtained using the phosphorescence photoexcitation technique. In both cases the spectrum is broad and structureless as would be expected from the line broadening calculations.

Electronic structure in five-coordinate complexes of nickel(II) with heavy-donor ligands

I.

Various studies designed to elucidate the electronic structure of the arsenic donor ligand, o-phenylenebisdimethylarsine (diarsine), have been carried out. The electronic spectrum of diarsine has been measured at 300 and 77˚K. Electronic spectra of the molecular complexes of various substituted organoarsines and phosphines with tetracyanoethylene have been measured and used to estimate the relative ionization potentials of these molecules.

Uv photolysis of arsines in frozen solution (96˚K) has yielded thermally labile, paramagnetic products. These include the molecular cations of the photolyzed compounds. The species (diars)⁺ exhibits hyper-fine splitting due to two equivalent ⁷⁵As(I=3/2) nuclei. Resonances due to secondary products are reported and assignments discussed.

Evidence is presented for the involvement of d-orbitals in the bonding of arsines. In (diars)⁺ there is mixing of arsenic “lone-pair” orbitals with benzene ring π-orbitals.

II.

Detailed electronic spectral measurements at 300 and 77˚K have been carried out on five-coordinate complexes of low-spin nickel(II), including complexes of both trigonal bipyramidal (TBP) and square pyramidal (SPY) geometry. TBP complexes are of the form NiLX⁺ (X=halide or cyanide,

L = Qƭ(CH₂)₃As(CH₃)₂]₃ or

P [hexagon - Q'CH₃] , Q = P, As,

Q’=S, Se).

The electronic spectra of these compounds exhibit a novel feature at low temperature. The first ligand field band, which is asymmetric in the room temperature solution spectrum, is considerably more symmetrical at 77˚K. This effect is interpreted in terms of changes in the structure of the complex.

The SPY complexes are of the form Ni(diars)₂X^z (X=CL, Br, CNS, CN, thiourea, NO₂, As). On the basis of the spectral results, the d-level ordering is concluded to be xy ˂ xz, yz ˂ z² ˂˂ x² - y². Central to this interpretation is identification of the symmetry-allowed ¹A₁ → ¹E (xz, yz → x² - y²) transition. This assignment was facilitated by the low temperature measurements.

An assignment of the charge-transfer spectra of the five-coordinate complexes is reported, and electronic spectral criteria for distinguishing the two limiting geometries are discussed.

I. Electronic processes in α-sulfur. II. Polaron motion in a D.C. electric field

Part I: The mobilities of photo-generated electrons and holes in orthorhombic sulfur are determined by drift mobility techniques. At room temperature electron mobilities between 0.4 cm²/V-sec and 4.8 cm²/V-sec and hole mobilities of about 5.0 cm²/V-sec are reported. The temperature dependence of the electron mobility is attributed to a level of traps whose effective depth is about 0.12 eV. This value is further supported by both the voltage dependence of the space-charge-limited, D.C. photocurrents and the photocurrent versus photon energy measurements.

As the field is increased from 10 kV/cm to 30 kV/cm a second mechanism for electron transport becomes appreciable and eventually dominates. Evidence that this is due to impurity band conduction at an appreciably lower mobility (4.10^-4 cm²/V-sec) is presented. No low mobility hole current could be detected. When fields exceeding 30 kV/cm for electron transport and 35 kV/cm for hole transport are applied, avalanche phenomena are observed. The results obtained are consistent with recent energy gap studies in sulfur.

The theory of the transport of photo-generated carriers is modified to include the case of appreciable thermos-regeneration from the traps in one transit time.

Part II: An explicit formula for the electric field E necessary to accelerate an electron to a steady-state velocity v in a polarizable crystal at arbitrary temperature is determined via two methods utilizing Feynman Path Integrals. No approximation is made regarding the magnitude of the velocity or the strength of the field. However, the actual electron-lattice Coulombic interaction is approximated by a distribution of harmonic oscillator potentials. One may be able to find the “best possible” distribution of oscillators using a variational principle, but we have not been able to find the expected criterion. However, our result is relatively insensitive to the actual distribution of oscillators used, and our E-v relationship exhibits the physical behavior expected for the polaron. Threshold fields for ejecting the electron for the polaron state are calculated for several substances using numerical results for a simple oscillator distribution.

I. Site effects and exciton structure in molecular crystals - Benzene. II. The first and second triplet states of solid benzene

The effect of intermolecular coupling in molecular energy levels (electronic and vibrational) has been investigated in neat and isotopic mixed crystals of benzene. In the isotopic mixed crystals of C₆H₆, C₆H₅D, m-C₆H₄D₂, p-C₆H₄D₂, sym-C₆H₃D₃, C₆D₅H, and C₆D₆ in either a C₆H₆ or C₆D₆ host, the following phenomena have been observed and interpreted in terms of a refined Frenkel exciton theory: a) Site shifts; b) site group splittings of the degenerate ground state vibrations of C₆H₆, C₆D₆, and sym-C₆H₃D₃; c) the orientational effect for the isotopes without a trigonal axis in both the ¹B_2u electronic state and the ground state vibrations; d) intrasite Fermi resonance between molecular fundamentals due to the reduced symmetry of the crystal site; and e) intermolecular or intersite Fermi resonance between nearly degenerate states of the host and guest molecules. In the neat crystal experiments on the ground state vibrations it was possible to observe many of these phenomena in conjunction with and in addition to the exciton structure.

To theoretically interpret these diverse experimental data, the concepts of interchange symmetry, the ideal mixed crystal, and site wave functions have been developed and are presented in detail. In the interpretation of the exciton data the relative signs of the intermolecular coupling constants have been emphasized, and in the limit of the ideal mixed crystal a technique is discussed for locating the exciton band center or unobserved exciton components. A differentiation between static and dynamic interactions is made in the Frenkel limit which enables the concepts of site effects and exciton coupling to be sharpened. It is thus possible to treat the crystal induced effects in such a fashion as to make their similarities and differences quite apparent.

A calculation of the ground state vibrational phenomena (site shifts and splittings, orientational effects, and exciton structure) and of the crystal lattice modes has been carried out for these systems. This calculation serves as a test of the approximations of first order Frenkel theory and the atom-atom, pair wise interaction model for the intermolecular potentials. The general form of the potential employed was V(r) = Be^-Cr - A/r⁶ ; the force constants were obtained from the potential by assuming the atoms were undergoing simple harmonic motion.

In part II the location and identification of the benzene first and second triplet states (³B_1u and ³E_1u) is given.

Rydberg states of diatomic and polyatomic molecules using model potentials

A simple model potential is used to calculate Rydberg series for the molecules: nitrogen, oxygen, nitric oxide, carbon monoxide, carbon dioxide, nitrogen dioxide, nitrous oxide, acetylene, formaldehyde, formic acid, diazomethane, ketene, ethylene, allene, acetaldehyde, propyne, acrolein, dimethyl ether, 1, 3-butadiene, 2-butene, and benzene. The model potential for a molecule is taken as the sum of atomic potentials, which are calibrated to atomic data and contain no further parameters. Our results agree with experimentally measured values to within 5-10% in all cases. The results of these calculations are applied to many unresolved problems connected with the above molecules. Some of the more notable of these problems are the reassignment of states in carbon monoxide, the first ionization potential of nitrogen dioxide, the interpretation of the V state in ethylene, and the mystery bands in substituted ethylenes, the identification of the R and R’ series in benzene and the determination of the orbital scheme in benzene from electron impact data.