Electron tunneling in proteins and water

The subject of this thesis is electronic coupling in donor-bridge-acceptor systems. In Chapter 2, ET properties of cyanide-bridged dinuclear ruthenium complexes were investigated. The strong interaction between the mixed-valent ruthenium centers leads to intense metal-to-metal charge transfer bands (MMCT). Hush analysis of the MMCT absorption bands yields the electronic-coupling strength between the metal centers (H_(AB)) and the total reorganization energy (λ). Comparison of ET kinetics to calculated rates shows that classical ET models fail to account for the observed kinetics and nuclear tunneling must be considered.

In Chapter 3, ET rates were measured in four ruthenium-modified highpotential iron-sulfur proteins (HiPIP), which were modified at position His50, His81, His42 and His18, respectively. ET kinetics for the His50 and His81 mutants are a factor of 300 different, while the donor-acceptor separation is nearly identical. PATHWAY calculations corroborate these measurements and highlight the importance of structural detail of the intervening protein matrix.

In Chapter 4, the distance dependence of ET through water bridges was measured. Photoinduced ET measurements in aqueous glasses at 77 K show that water is a poor medium for ET. Luminescence decay and quantum yield data were analyzed in the context of a quenching model that accounts for the exponential distance dependence of ET, the distance distribution of donors and acceptors embedded in the glass and the excluded volumes generated by the finite sizes of the donors and acceptors.

In Chapter 5, the pH-dependent excited state dynamics of ruthenium-modified amino acids were measured. The [Ru(bpy)_(3)] ^(2+) chromophore was linked to amino acids via an amide linkage. Protonation of the amide oxygen effectively quenches the excited state. In addition. time-resolved and steady-state luminescence data reveal that nonradiative rates are very sensitive to the protonation state and the structure of the amino acid moiety.

Oxidation of Volatile Organic Compounds in Aqueous Solution and at the Air-water Interface of Aqueous Microdroplets

Isoprene (ISO),the most abundant non-methane VOC, is the major contributor to secondary organic aerosols (SOA) formation. The mechanisms involved in such transformation, however, are not fully understood. Current mechanisms, which are based on the oxidation of ISO in the gas-phase, underestimate SOA yields. The heightened awareness that ISO is only partially processed in the gas-phase has turned attention to heterogeneous processes as alternative pathways toward SOA.

During my research project, I investigated the photochemical oxidation of isoprene in bulk water. Below, I will report on the λ > 305 nm photolysis of H₂O₂ in dilute ISO solutions. This process yields C₁₀H₁₅OH species as primary products, whose formation both requires and is inhibited by O₂. Several isomers of C₁₀H₁₅OH were resolved by reverse-phase high-performance liquid chromatography and detected as MH⁺ (m/z = 153) and MH⁺-18 (m/z = 135) signals by electrospray ionization mass spectrometry. This finding is consistent with the addition of ·OH to ISO, followed by HO-ISO· reactions with ISO (in competition with O₂) leading to second generation HO(ISO)₂· radicals that terminate as C₁₀H₁₅OH via β-H abstraction by O₂.

It is not generally realized that chemistry on the surface of water cannot be deduced, extrapolated or translated to those in bulk gas and liquid phases. The water density drops a thousand-fold within a few Angstroms through the gas-liquid interfacial region and therefore hydrophobic VOCs such as ISO will likely remain in these relatively 'dry' interfacial water layers rather than proceed into bulk water. In previous experiments from our laboratory, it was found that gas-phase olefins can be protonated on the surface of pH < 4 water. This phenomenon increases the residence time of gases at the interface, an event that makes them increasingly susceptible to interaction with gaseous atmospheric oxidants such as ozone and hydroxyl radicals.

In order to test this hypothesis, I carried out experiments in which ISO(g) collides with the surface of aqueous microdroplets of various compositions. Herein I report that ISO(g) is oxidized into soluble species via Fenton chemistry on the surface of aqueous Fe(II)Cl₂ solutions simultaneously exposed to H₂O₂(g). Monomer and oligomeric species (ISO)1-8H⁺ were detected via online electrospray ionization mass spectrometry (ESI-MS) on the surface of pH ~ 2 water, and were then oxidized into a suite of products whose combined yields exceed ~ 5% of (ISO)1-8H⁺. MS/MS analysis revealed that products mainly consisted of alcohols, ketones, epoxides and acids. Our experiments demonstrated that olefins in ambient air may be oxidized upon impact on the surface of Fe-containing aqueous acidic media, such as those of typical to tropospheric aerosols.

Related experiments involving the reaction of ISO(g) with ·OH radicals from the photolysis of dissolved H₂O₂ were also carried out to test the surface oxidation of ISO(g) by photolyzing H₂O₂(aq) at 266 nm at various pH. The products were analyzed via online electrospray ionization mass spectrometry. Similar to our Fenton experiments, we detected (ISO)1-7H⁺ at pH < 4, and new m/z⁺ = 271 and m/z^- = 76 products at pH > 5.

The Equation of State and Petrogenesis of Komatiite

(1) Equation of State of Komatiite

The equation of state (EOS) of a molten komatiite (27 wt% MgO) was detennined in the 5 to 36 GPa pressure range via shock wave compression from 1550°C and 0 bar. Shock wave velocity, U_S, and particle velocity, U_P, in km/s follow the linear relationship U_S = 3.13(±0.03) + 1.47(±0.03) U_P. Based on a calculated density at 1550°C, 0 bar of 2.745±0.005 glee, this U_S-U_P relationship gives the isentropic bulk modulus K_S = 27.0 ± 0.6 GPa, and its first and second isentropic pressure derivatives, K'_S = 4.9 ± 0.1 and K"_S = -0.109 ± 0.003 GPa^-1.

The calculated liquidus compression curve agrees within error with the static compression results of Agee and Walker [1988a] to 6 GPa. We detennine that olivine (FO₉₄) will be neutrally buoyant in komatiitic melt of the composition we studied near 8.2 GPa. Clinopyroxene would also be neutrally buoyant near this pressure. Liquidus garnet-majorite may be less dense than this komatiitic liquid in the 20-24 GPa interval, however pyropic-garnet and perovskite phases are denser than this komatiitic liquid in their respective liquidus pressure intervals to 36 GPa. Liquidus perovskite may be neutrally buoyant near 70 GPa.

At 40 GPa, the density of shock-compressed molten komatiite would be approximately equal to the calculated density of an equivalent mixture of dense solid oxide components. This observation supports the model of Rigden et al. [1989] for compressibilities of liquid oxide components. Using their theoretical EOS for liquid forsterite and fayalite, we calculate the densities of a spectrum of melts from basaltic through peridotitic that are related to the experimentally studied komatiitic liquid by addition or subtraction of olivine. At low pressure, olivine fractionation lowers the density of basic magmas, but above 14 GPa this trend is reversed. All of these basic to ultrabasic liquids are predicted to have similar densities at 14 GPa, and this density is approximately equal to the bulk (PREM) mantle. This suggests that melts derived from a peridotitic mantle may be inhibited from ascending from depths greater than 400 km.

The EOS of ultrabasic magmas was used to model adiabatic melting in a peridotitic mantle. If komatiites are formed by >15% partial melting of a peridotitic mantle, then komatiites generated by adiabatic melting come from source regions in the lower transition zone (≈500-670 km) or the lower mantle (>670 km). The great depth of incipient melting implied by this model, and the melt density constraint mentioned above, suggest that komatiitic volcanism may be gravitationally hindered. Although komatiitic magmas are thought to separate from their coexisting crystals at a temperature =200°C greater than that for modern MORBs, their ultimate sources are predicted to be diapirs that, if adiabatically decompressed from initially solid mantle, were more than 700°C hotter than the sources of MORBs and derived from great depth.

We considered the evolution of an initially molten mantle, i.e., a magma ocean. Our model considers the thermal structure of the magma ocean, density constraints on crystal segregation, and approximate phase relationships for a nominally chondritic mantle. Crystallization will begin at the core-mantle boundary. Perovskite buoyancy at > 70 GPa may lead to a compositionally stratified lower mantle with iron-enriched mangesiowiistite content increasing with depth. The upper mantle may be depleted in perovskite components. Olivine neutral buoyancy may lead to the formation of a dunite septum in the upper mantle, partitioning the ocean into upper and lower reservoirs, but this septum must be permeable.

(2) Viscosity Measurement with Shock Waves

We have examined in detail the analytical method for measuring shear viscosity from the decay of perturbations on a corrugated shock front The relevance of initial conditions, finite shock amplitude, bulk viscosity, and the sensitivity of the measurements to the shock boundary conditions are discussed. The validity of the viscous perturbation approach is examined by numerically solving the second-order Navier-Stokes equations. These numerical experiments indicate that shock instabilities may occur even when the Kontorovich-D'yakov stability criteria are satisfied. The experimental results for water at 15 GPa are discussed, and it is suggested that the large effective viscosity determined by this method may reflect the existence of ice VII on the Rayleigh path of the Hugoniot This interpretation reconciles the experimental results with estimates and measurements obtained by other means, and is consistent with the relationship of the Hugoniot with the phase diagram for water. Sound waves are generated at 4.8 MHz at in the water experiments at 15 GPa. The existence of anelastic absorption modes near this frequency would also lead to large effective viscosity estimates.

(3) Equation of State of Molybdenum at 1400°C

Shock compression data to 96 GPa for pure molybdenum, initially heated to 1400°C, are presented. Finite strain analysis of the data gives a bulk modulus at 1400°C, K'_S. of 244±2 GPa and its pressure derivative, K'_OS of 4. A fit of shock velocity to particle velocity gives the coefficients of U_S = C_O+S U_P to be C_O = 4.77±0.06 km/s and S = 1.43±0.05. From the zero pressure sound speed, C_O, a bulk modulus of 232±6 GPa is calculated that is consistent with extrapolation of ultrasonic elasticity measurements. The temperature derivative of the bulk modulus at zero pressure, θK_OSθT|_P, is approximately -0.012 GPa/K. A thermodynamic model is used to show that the thermodynamic Grüneisen parameter is proportional to the density and independent of temperature. The Mie-Grüneisen equation of state adequately describes the high temperature behavior of molybdenum under the present range of shock loading conditions.

Part I. Approximate Hartree-Fock wavefunctions one-electron properties and electronic structure of the water molecule. Part II. Perturbation-variational calculation of the nuclear spin-spin isotope coupling constant in HD

Part I

Several approximate Hartree-Fock SCF wavefunctions for the ground electronic state of the water molecule have been obtained using an increasing number of multicenter s, p, and d Slater-type atomic orbitals as basis sets. The predicted charge distribution has been extensively tested at each stage by calculating the electric dipole moment, molecular quadrupole moment, diamagnetic shielding, Hellmann-Feynman forces, and electric field gradients at both the hydrogen and the oxygen nuclei. It was found that a carefully optimized minimal basis set suffices to describe the electronic charge distribution adequately except in the vicinity of the oxygen nucleus. Our calculations indicate, for example, that the correct prediction of the field gradient at this nucleus requires a more flexible linear combination of p-orbitals centered on this nucleus than that in the minimal basis set. Theoretical values for the molecular octopole moment components are also reported.

Part II

The perturbation-variational theory of R. M. Pitzer for nuclear spin-spin coupling constants is applied to the HD molecule. The zero-order molecular orbital is described in terms of a single 1s Slater-type basis function centered on each nucleus. The first-order molecular orbital is expressed in terms of these two functions plus one singular basis function each of the types e^-r/r and e^-r ln r centered on one of the nuclei. The new kinds of molecular integrals were evaluated to high accuracy using numerical and analytical means. The value of the HD spin-spin coupling constant calculated with this near-minimal set of basis functions is J_HD = +96.6 cps. This represents an improvement over the previous calculated value of +120 cps obtained without using the logarithmic basis function but is still considerably off in magnitude compared with the experimental measurement of J_HD = +43 0 ± 0.5 cps.

1. Ultrasonic studies of binary liquid structure in the critical region. Theory and experiment for the 2,6-lutidine/water system. 2. Hartree-Fock calculations of electric polarizabilities of some simple atoms and molecules, and their practicality. 3. Calculation of vibrational transition probabilities in collinear atom-diatom and diatom-diatom collisions with Lennard-Jones interaction

Part 1. Many interesting visual and mechanical phenomena occur in the critical region of fluids, both for the gas-liquid and liquid-liquid transitions. The precise thermodynamic and transport behavior here has some broad consequences for the molecular theory of liquids. Previous studies in this laboratory on a liquid-liquid critical mixture via ultrasonics supported a basically classical analysis of fluid behavior by M. Fixman (e. g., the free energy is assumed analytic in intensive variables in the thermodynamics)--at least when the fluid is not too close to critical. A breakdown in classical concepts is evidenced close to critical, in some well-defined ways. We have studied herein a liquid-liquid critical system of complementary nature (possessing a lower critical mixing or consolute temperature) to all previous mixtures, to look for new qualitative critical behavior. We did not find such new behavior in the ultrasonic absorption ascribable to the critical fluctuations, but we did find extra absorption due to chemical processes (yet these are related to the mixing behavior generating the lower consolute point). We rederived, corrected, and extended Fixman's analysis to interpret our experimental results in these more complex circumstances. The entire account of theory and experiment is prefaced by an extensive introduction recounting the general status of liquid state theory. The introduction provides a context for our present work, and also points out problems deserving attention. Interest in these problems was stimulated by this work but also by work in Part 3.

Part 2. Among variational theories of electronic structure, the Hartree-Fock theory has proved particularly valuable for a practical understanding of such properties as chemical binding, electric multipole moments, and X-ray scattering intensity. It also provides the most tractable method of calculating first-order properties under external or internal one-electron perturbations, either developed explicitly in orders of perturbation theory or in the fully self-consistent method. The accuracy and consistency of first-order properties are poorer than those of zero-order properties, but this is most often due to the use of explicit approximations in solving the perturbed equations, or to inadequacy of the variational basis in size or composition. We have calculated the electric polarizabilities of H₂, He, Li, Be, LiH, and N₂ by Hartree-Fock theory, using exact perturbation theory or the fully self-consistent method, as dictated by convenience. By careful studies on total basis set composition, we obtained good approximations to limiting Hartree-Fock values of polarizabilities with bases of reasonable size. The values for all species, and for each direction in the molecular cases, are within 8% of experiment, or of best theoretical values in the absence of the former. Our results support the use of unadorned Hartree-Pock theory for static polarizabilities needed in interpreting electron-molecule scattering data, collision-induced light scattering experiments, and other phenomena involving experimentally inaccessible polarizabilities.

Part 3. Numerical integration of the close-coupled scattering equations has been carried out to obtain vibrational transition probabilities for some models of the electronically adiabatic H₂-H₂ collision. All the models use a Lennard-Jones interaction potential between nearest atoms in the collision partners. We have analyzed the results for some insight into the vibrational excitation process in its dependence on the energy of collision, the nature of the vibrational binding potential, and other factors. We conclude also that replacement of earlier, simpler models of the interaction potential by the Lennard-Jones form adds very little realism for all the complication it introduces. A brief introduction precedes the presentation of our work and places it in the context of attempts to understand the collisional activation process in chemical reactions as well as some other chemical dynamics.