Includes bibliographical references. / The mechanism of the corrosive action of sulphate reducing bacteria of the genus Desulfovibrio towards ferrous metals has been investigated. This corrosive action is anomalous when considered in the light of established knowledge of corrosion processes, since it occurs in the absence of oxygen, at more or less neutral pH values and at ordinary ambient temperatures. The hypothesis of von Wolzogen Kuhr and van der Vlugt, published in 1934, proposing that enzymic catalysis of sulphate reduction by cathodic charge constituted a "cathodic depolarizing" process, which appears t o be widely accepted as the most likely mechanism for this corrosive effect, is evaluated critically here in the light of established electrochemical and biochemical knowledge. The theoret ical arguments presented in this thesis show that this process, if it does occur, is unlikely to affect corrosion rates. The experimental results presented here indicate that all cathodic depolarizing activity demonstrated in pure cultures of these organisms is attributable to the cathodic activity of dissolved hydrogen sulphide produced by the organisms. The conclusions of other workers, quoted in support of proposed enzymic catalysis of charge transfer from cathodes to redox dyes in laboratory systems, are considered, in view of experimental work performed during this investigation, to be a misinterpretation of experimental results.

Proteins are dynamic structural entities that are involved in many biophysical processes through molecular interactions with their ligands. Protein-ligand interactions are of fundamental importance for computer-aided drug discovery. Due to the fast development in computer technologies and theoretical methods, computational studies are by now able to provide atomistic-level description of structures, thermodynamic and dynamic properties of protein-ligand systems, and are becoming indispensable in understanding complicated biomolecular systems. In this dissertation, I have applied molecular dynamic (MD) simulations combined with several state of the art free-energy calculation methodologies, to understand structures and binding properties of several protein-ligand systems. The dissertation consists of six chapters. In the first chapter, I present a brief introduction to classical MD simulations, to recently developed methods for binding free energy calculations, and to enhanced sampling of configuration space of biological systems. The basic features, including the Hamiltonian equations, force fields, integrators, thermostats, and barostats, that contribute to a complete MD simulation are described in chapter 2. In chapter 3, two classes of commonly used algorithms for estimating binding free energies are presented. I highlight enhanced sampling approaches in chapter 4, with a special focus on replica exchange MD simulations and metadynamics, as both of them have been utilized in my work presented in the chapter thereafter. In chapter 5, I outlined the work in the 5 papers included in the thesis. In paper I and II, I applied, respectively, the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and alchemical free energy calculation methods to identify the molecular determinant of the affibody protein ZAb3 bound to an amyloid b peptide, and to investigate the binding profile of the positive allosteric modulator NS-1738 with the α7 acetylcholine-binding protein (α7-AChBP protein); in paper III and VI, unbiased MD simulations were integrated with the well-tempered metadynamics approach, with the aim to reveal the mechanism behind the higher selectivity of an antagonist towards corticotropin-releasing factor receptor-1 (CRF1R) than towards CRF2R, and to understand how the allosteric modulation induced by a sodium ion is propagated to the intracellular side of the d-opioid receptor; in the last paper, I proved the structural heterogeneity of the intrinsically disordered AICD peptide, and then employed the bias-exchange metadynamics and kinetic Monte Carlo techniques to understand the coupled folding and binding of AICD to its receptor Fe65-PTB2. I finally proposed that the interactions between AICD and Fe65-PTB2 take place through an induced-fit mechanism. In chapter 6, I made a short conclusion of the work, with an outlook of computational simulations of biomolecular systems. / <p>QC 20170516</p>

This thesis describes developments towards incorporating spiropyran functionality into metal-organic frameworks (MOFs). Chapter 1 outlines the reported literature concerning the study of photochemistry with respect to MOFs; such materials have demonstrated potential as both alternative environments for the study of photoactivated processes and platforms to integrate photosensitive moieties. Incorporation of photoactive groups into MOFs has enabled these supramolecular materials to be altered chemically and physically via photo-initiated processes. Existing studies into reversible photoswitching groups are largely focussed on azobenzene. The chronological development of azobenzene incorporation into MOFs reflects the evolving strategies of exploiting this functionality to achieve photocontrol over the properties of MOF materials. These advances in accommodating photoswitching azobenzene into MOFs have been applied in reported studies with other photochromic groups and taken into consideration with the work described herein concerning spiropyrans. Chapter 2 focusses on the preparation of a carboxylic acid functionalised salicylaldehyde 3-formyl-4-hydroxybenzoic acid (H2L1), a key precursor in the synthesis of carboxylic acid functionalised spiropyrans. The serendipitous outcome in solvothermal reaction of H2L1 and copper nitrate in dimethylformamide affords {Cu2L12·(DMF)2(H2O)}n (1-Cu-DMF) which has been crystallographically characterised and is further described in this chapter. Channels run through the direction of the crystallographic a-axis of 1-Cu; its connectivity and porosity is retained upon solvent exchange of the single crystals with ethanol and tetrahydrofuran. Gas sorption experiments show 1-Cu exhibits type I adsorption behaviour with a Brunauer-Emmett-Teller (BET) surface area of 948 ± 1 m2 g−1. Notably, 1-Cu adsorbs negligible quantities of methane compared to carbon dioxide and other C2Hn hydrocarbons; the selectivities are confirmed by analysis via the ideal adsorbed solution theory (IAST) and Henry’s law. Of particular importance, 1-Cu demonstrates exceptional selectivity for acetylene, which has applicability in separation technologies for the isolation of acetylene. Chapter 3 details the design and synthesis of a series of carboxylic acid functionalised spiropyrans and bisbenzospiropyrans. These compounds serve as ligand precursors for MOFs but also have interesting photophysical properties as organic compounds, which are studied in this chapter. Condensation of prefunctionalised fragments, H2L1 and carboxylic acid functionalised Fischer’s base 5, afforded a novel dicarboxylic acid functionalised spiropyran H2L2. A second synthetic route to extended ligand precursors, via Suzuki-Miyaura cross coupling of ethyl ester functionalised boronic acids to dibrominated photoactive cores and subsequent hydrolysis, is described. Crystallographic characterisation of the ethyl esters indicates flexibility of the core moieties around the spiro carbon. Comparison of the UV-visible absorption spectra shows the properties of related spiropyrans and bisbenzospiropyrans to be influenced by electronic effects arising from both the type and positioning of the functional groups. The fluorescence quantum yields of novel spiropyrans 13, 15 and H2L5 have been determined as 0.025, 0.032 and 0.068 respectively. Cyclic voltammetric experiments show the electrochemical behaviour of spiropyrans to be influenced primarily by electronic effects related to the type of functional group attached, whereas the electrochemical properties of bisbenzospiropyrans is dominated by electronic effects arising from the positioning of the functional groups. Density functional theory (DFT) calculations of the spectroscopic properties are described and are consistent with experimental observations. Chapter 4 describes investigations to incorporate the carboxylic acid compounds prepared in Chapter 3 into framework materials. To mitigate potential instability problems from using solely photoresponsive and highly flexible components, co-crystallisation with pillaring agents was considered. Reaction of H2L2 with zinc nitrate and a dipyridyl terephthalamide pillaring agent L7 affords coordination network 2 Zn. Two isomers, {Zn(L2)(syn-L7)·(DMF)3(H2O)}n (2-syn-Zn) and {Zn(L2)(anti-L7)·(DMF)3.5(H2O)1.5}n (2-anti-Zn), have been crystallographically characterised; their differences rest upon the conformations adopted by ligand L7. The structure of the 2 anti Zn isomer has higher potential porosity, appearing as rhomboid channels running down the direction of the crystallographic b-axis. The two dimensional sheets of both 2-syn-Zn and 2-anti-Zn are linked in a third dimension through hydrogen bonding interactions between the carboxylate of (L2)2− and amide moiety of L7 in adjacent layers. UV irradiation (325 nm) of single crystals of both forms of 2 Zn initiates a growth in fluorescence of the material observed in situ on a Raman microscope. In situ monitoring of the fluorescence using a 785 nm laser shows a decay over 23 hours to recover the original Raman spectrum of the material. The fluorescence decay can be fitted to a biexponential process; the faster process (13 270 s−1 and 1290 s−1, 2-syn-Zn and 2-anti-Zn respectively) is approximately an order of magnitude greater than the slower process (3980 s−1 and 350 s−1 respectively). DFT calculations suggest the theoretical spectroscopic and electrochemical properties of (L2)2− are not significantly changed by coordination to zinc in 2-Zn. The structures 2-syn-Zn and 2-anti-Zn are the first known examples of spiropyran functionality being incorporated into frameworks.

In this thesis, surface electrocatalysis of several energy-conversion-relevant redox reactions in ionic liquid electrolytes is described. The first oxidation process investigated is the formation of surface oxide films on Pt electrodes by trace water oxidation in protic ionic liquids (PILs). This is followed by investigation of the oxidation of hydrazine (N2H4), formic acid (HCOOH), ethanol (EtOH) and dimethyl ether (DME) in PILs and a description of the role played by surface oxides during each oxidation process. Finally, the electrocatalytic reduction of CO2 at a variety of electrode materials is explored in room temperature aprotic ionic liquids. The data reveal that the surfaces of Pt electrodes become covered with oxide layers due to oxidation of trace water, which is omnipresent in PILs, at positive potentials (E > 1.0 V vs. Pd-H). X-ray photoelectron spectroscopy (XPS) shows that the oxide layers grow to form thick films as the potential is made more positive and as the temperature and water concentration of the PILs are increased. The mechanism and kinetics of oxide film growth are also discussed. Voltammetric analysis shows that the presence of residual surface oxides activates Pt electrodes towards electrooxidation of N2H4. Furthermore, immersion of oxidized Pt electrodes in N2H4-containing PILs deactivates the electrode indicating that N2H4 reacts with the residual surface oxides. Oxidation of HCOOH at Pt catalyst in PILs occurs mainly by dehydration plus COads oxidation at a potential that coincides with the onset of the formation of Pt surface oxides. Compared to Pt electrocatalysts, the overpotential for electrooxidation of HCOOH is higher at Au catalyst but lower at Pd catalyst. Oxidation of trace water in PILs at Pt also plays a pivotal role during the electrocatalytic oxidation of EtOH and DME in the PILs. Oxidation of both EtOH and DME coincides with coverage of the Pt surface by the adsorbed oxide species that helps to activate both processes by oxidizing the adsorbed poisoning CO and CO-like intermediate species via a 'bifunctional' reaction mechanism. Generally, higher overpotentials are observed for each oxidation, and higher activation energies are measured for EtOH oxidation in PILs than in aqueous electrolytes. Finally, it is shown that CO2 electroreduction takes place at lower overpotentials at Au and Ag electrocatalysts than at Cu, Pt and boron doped diamond (BDD) electrodes in the presence of ionic liquid electrolytes. Ag electrocatalysts reduce CO2 at ~0.2 V lower potential when 1-ethyl-3-methylimidazolium ethylsulphate [emim][EtSO4] is used as supporting electrolyte in acetonitrile compared to when the conventional supporting electrolyte tetrabutylammonium hexaflourophosphate [TBA][PF6] is used. CO is a product of CO2 reduction at Ag catalyst and the results highlight that Ag and imidazolium-based ILs could be a promising system for reduction of CO2 to CO at low overpotentials.

HTML clipboardKinetics on molecular excited states is a challenging subject in the field of theoretical chemistry. This thesis pays attention to theoretical studies on kinetics of photo-induced processes, including photo-chemical reactions, radiative and non-radiative transitions (intersystem crossing and internal conversion) in molecular and bio-related systems. One- or multi- dimensional potential energy surfaces (PESs) not only provide qualitative mechanistic explanation for excited state decay, but also make it possible to perform kinetic simulations. We have constructed several types of PESs by using computational methods of high-accuracy for a variety of systems of interest. In particular, density functional theory (DFT) and couple cluster singles and doubles (CCSD) method are employed to build PESs of the ground and lowest triple states. For medium-sized molecules, the complete active space self-consistent (CASSCF) method is used for constructing the PESs of excited states. Various kinetic theories for the decay processes of excite states are briefly introduced, in particularly adiabatic and nonadiabatic Rice–Ramsperger–Kassel -Marcus (RRKM) approaches for the kinetics of nonradiative decay of excited 2-aminopridine molecule. Special attention has been devoted to Monte Carlo transition state theory which can provide an efficient way to predict the rate of nonradiative transitions of polyatomic molecules on multi-dimensional PESs. Examples of Monte Carlo simulations on the intersystem crossing of isocyanic acid and a model molecule of hexacoordinate heme, as well as internal conversion process for 2-amininopyridine dimer and the adenine-thymine base pair are presented. / QC20100720

Different theoretical approaches have been presented in this thesis to study the Raman scattering effect. The first one is response theory applied up to third order of polarization, where the determination of α, β and γ is used to calculate linear Raman scattering (resonance Raman scattering (RRS) and normal Raman scattering (NRS)), hyper Raman scattering (HRS) and coherent anti-Stokes Raman scattering (CARS), respectively. The response theory refers to adiabatic time-dependent density functional theory in the complex domain with applications on RRS and NRS, and to a recently developed methodology (Thorvaldsen et al. [105, 106]) for the analytic calculation of frequency-dependentpolarizability gradients of arbitrary order, here with applications on CARSand HRS. Various systems have been studied with the response theory, such as explosive substances (DNT, TNT, RDX and H2O2), optical power limiting materials (platinum(II) acetylide molecules), DNA bases (methylguanine-methylcytosine) and other systems (Trans-1,3,5-hexatriene and Pyridine). We have explored the dependency of the calculated spectra on parametrization in terms of exchange-correlation functionals and basis sets, and on geometrica loptimization. The second approach refers to time-dependent wave packet methodology for RRS and its time-independent counterpart in the Kramers-Heisenberg equation for the scattering cross section, which reduces the calculation of the RRS amplitude to computation of matrix elements of transition dipole moments between vibrational wave functions. The time-dependent theory has been used to examine RRS as a dynamical process where particular attention is paid to the notion of fast scattering in which the choice of photon frequency controls the scattering time and the nuclear dynamics. It is shown that a detuning from resonance causes a depletion of the RRS spectrum from overtones and combination bands, a situation which is verified in experimental spectra. The cross section of NRS has been predicted for the studied molecules to be in the order of 10−30 cm2/sr. A further increase in sensitivity with a signal enhancement up to 104 to 105 is predicted for the RRS technique, while CARS conditions imply an overall increase of the intensity by several orders of magnitude over NRS. In contrast to RRS and CARS, the HRS intensity is predicted to be considerably weaker than NRS, by about four orders of magnitude. However, silent modes in NRS can be detected by HRS which in turncan provide essential spectroscopic information and become complementary to NRS scattering. With the above mention methodological development for NRS, RRS, CARS and HRS, we have at our disposal a powerful set of modelling tools for the four different Raman techniques. They have complementary merits and limitations which facilitate the use of these spectroscopes in applications of Raman scattering for practical applications, for instance stand-off detection of foreign substances. / QC 20110112

This thesis focuses on the applications of molecular dynamics simulation techniques in the fields of solution chemistry and atmospheric chemistry. The work behind the thesis takes account of the fast development of computer hardware, which has made computationally intensive simulations become more and more popular in disciplines like pharmacy, biology and materials science. In molecular dynamics simulations using classical force fields, the atoms are represented by mass points with partial charges and the inter-atomic interactions are modeled by approximate potential functions that produce satisfactory results at an economical computational cost. The three-dimensional trajectory of a many-body system is generated by integrating Newton’s equations of motion, and subsequent statistical analysis on the trajectories provides microscopic insight into the physical properties of the system. The applications in this thesis of molecular dynamics simulations in solution chemistry comprise four aspects: the 113Cd nuclear magnetic resonance shielding constant of aqua Cd(II) ions, paramagnetic 19F nuclear magnetic resonance shift in fluorinated cysteine, solvation free energies and structures of metal ions, and protein adsorption onto TiO2. In the studies of nuclear magnetic resonance parameters, the relativistic effect of the 113Cd nucleus and the paramagnetic shift of 19F induced by triplet O2 are well reproduced by a combined molecular dynamics and density functional theory approach. The simulation of the aqua Cd(II) ion is also extended to several other monovalent, divalent and trivalent metal ions, where careful parameterization of the metal ions ensures the reproduction of experimental solvation structures and free energies. Molecular dynamics simulations also provided insight into the mechanism of protein adsorption onto the TiO2 surface by suggesting that the interfacial water molecules play an important role of mediating the adsorption and that the hydroxylated TiO2 surface has a large affinity to the proteins. The applications of molecular dynamics simulations in atmospheric chemistry are mainly focused on two types of organic components in aerosol droplets: humic-like compounds and amino acids. The humic-like substances, including cis-pinonic acid, pinic acid and pinonaldehyde, are surface-active organic compounds that are able to depress the surface tension of water droplets, as revealed by both experimental measurements and theoretical computations. These compounds either concentrate on the droplet surface or aggregate inside the droplet. Their effects on the surface tension can be modeled by the Langmuir-Szyszkowski equation. The amino acids are not strong surfactants and their influence on the surface tension is much smaller. Simulations show that the zwitterionic forms of serine, glycine and alanine have hydrophilic characteristics, while those of valine, methionine and phenylalanine are hydrophobic. The curvature dependence of the surface tension is also analyzed, and a slight improvement in the Köhler equation is obtained by introducing surface tension corrections for droplets containing glycine and serine. Through several examples it is shown that molecular dynamics simulations serve as a promising tool in the study of aqueous systems. Both solute-solvent interactions and interfaces can be treated properly by choosing suitable potential functions and parameters. Specifically, molecular dynamics simulations provide a microscopic picture that evolves with time, making it possible to follow the dynamic processes such as protein adsorption or atmospheric droplet formation. Moreover, molecular dynamics simulations treat a large number of molecules and give a statistical description of the system; therefore it is convenient to compare the simulated results with experimentally measured data. The simulations can provide hints for better design of experiments, while experimental data can be fed into the refinement of the simulation model. As an important complementary to experiments, molecular dynamics simulations will continue to play significant roles in the research fields of physics, chemistry, materials science, biology and medicine. / QC 20110511

his thesis has been devoted to the study of underlying mechanisms for electron transport in molecular electronic devices. Not only has focus been on describing the elastic and inelastic electron transport processes with a Green's function based scattering theory approach, but also on how to construct computational models that are relevant to experimental systems. The thesis is essentially divided into two parts. While the rst part covers basic assumptions and the elastic transport properties, the second part covers the inelastic transport properties and its applications. It is discussed how di erent experimental approaches may give rise to di erent junction widths and thereby di erences in coupling strength between the bridging molecules and the contacts. This di erence in coupling strength is then directly related to the magnitude of the current that passes through the molecule and may thus explain observed di erences between di erent experiments. Another focus is the role of intermolecular interactions on the current-voltage (I-V) characteristics, where water molecules interacting with functional groups in a set of conjugated molecules are considered. This is interesting from several aspects; many experiments are performed under ambient conditions, which means that water molecules will be present and may interfere with the experiment. Another point is that many measurement are done on self-assembled monolayers, which raises the question of how such a measurement relates to that of a single molecule. By looking at the perturbations caused by the water molecules, one may get an understanding of what impact a neighboring molecule may have. The theoretical predictions show that intermolecular e ects may play a crucial role and is related to the functional groups, which has to be taken into consideration when looking at experimental data. In the second part, the inelastic contribution to the total current is shown to be quite small and its real importance lies in probing the device geometry. Several molecules are studied for which experimental data is available for comparison. It is demonstrated that the IETS is very sensitive to the molecular conformation, contact geometry and junction width. It is also found that some of the spectral features that appear in experiment cannot be attributed to the molecular device, but to the background contributions, which shows how theory may be used to complement experiment. This part concludes with a study of the temperature dependence of the inelastic transport. This is very important not only from a theoretical point of view, but also for the experiments since it gives experimentalists a sense of which temperature ranges they can operate for measuring IETS. / QC 20100804. Ändrat titeln från: "Understanding Electron Transport Properties in Molecular Devices" 20100804.

The self-interaction error (SIE) in density functional theory (DFT) appears from the fact that the residual self-interaction in the Coulomb part and that in the exchange part do not cancel each other exactly. This error is responsible for the unphysical orbital energies of DFT and the failure to reproduce the potential energy curves of several physical processes. The present thesis addresses several methods to solve the problem of SIE in DFT. A new algorithm is presented which is based on the Perdew-Zunger (PZ) energy correction and which includes the self-interaction correction (SIC) self-consistently (SC SIC PZ). When applied to the study of hydrogen abstraction reactions, for which conventional DFT can not describe the processes properly, SC PZ SIC DFT produces reasonable potential energy curves along the reaction coordinate and reasonable transition barriers. A semi-empirical SIC method is designed to correct the orbital energies. It is found that a potential coupling term is generally nonzero for all available approximate functionals. This coupling term also contributes to the self-interaction error. In this scheme, the potential coupling term is multiplied by an empirical parameter , introduced to indicate the strength of the potential coupling, and used to correct the PZ SIC DFT. Through a fitting scheme, we find that a unique can be used for C, N, O core orbitals in different molecules. Therefore this method is now used to correct the core orbital energies and relevant properties. This method is both efficient and accurate in predicting core ionization energies. A new approach has been designed to solve the problem of SIE. A functional is constructed based on electron-electron interactions, Coulomb and exchange-correlation parts, which are free of SIE. A post-SCF procedure for this method has been implemented. The orbital energies thus obtained are of higher quality than in conventional DFT. For a molecular system, the orbital energy of the highest occupied molecular orbital (HOMO) is comparable to the experimental first ionization potential energy. / QC 20100915

This thesis presents a theoretical study of the role of nuclear degrees of freedom in the x-ray absorption, x-ray resonant scattering  and some aspects of the interaction of matter with strong laser fields. Most numerical simulations are performed with a time-dependent wave-packet program that have proved its robustness  in previous investigations. The relevant experimental results are also presented for comparison when available. The first problem considered in the thesis is the possibility of obtaining x-ray absorption spectra with resolution beyond the natural lifetime broadening of the core-excited electronic states. It is shown that the method of measuring x-ray absorptionin the resonant scattering mode suggested earlier for that purpose exhibits severe limitations originating from the lifetime vibrational interference between the intermediate core-excited vibrational levels. However, a broad class of molecules is found for which spectra with super-high resolution can indeed be obtained. These molecules have parallel potential energy surfaces of the core-excited and final states for the x-ray scattering process. The interpretations of two interesting cases of x-ray absorption and Auger scattering follow. The first one is related to scattering through a doubly excited Π state in the CO molecule. A Doppler split feature near 299.4 eV and strong scattering anisotropy are  observed. Both features are well explained and reproduced by the theory. Next, theelectron-vibrational fine structure of the <img src="http://www.diva-portal.org/cgi-bin/mimetex.cgi?O1s%5Crightarrow%5Csigma%5E%7B*%7D" /> excitation for O2 is investigated by means of different models. We are able to single out the electronic states and interpotential crossing points responsible for the peculiar absorption profile. Based on these findings we explain and reproduce the x-ray Auger scattering spectra through the same excitation. Here we encounter a rather unusual situation in which the Auger spectra are affected by three types of the interference: Apart from the lifetime vibrational interference, a strong interference between two intermediate electronic states and an interference with the direct-scattering amplitude is also present. The process of intramolecular vibrational redistribution (IVR) is investigated in the context of formation of amplified spontaneous emissions (ASE) inside laser-pumped gain media. IVR raises to a higher energy region the threshold pump intensity after which blue-shifted ASE is observed. Finally, we suggest a new scheme of x-ray pump-probe spectroscopy based on the core-hole hopping in N2 induced by an infrared laser field. We investigate the result from the core-hole hoping on the vibrational structure of the x-ray absorption profile. Furthermore, by populating core-excited states with opposite parities, the laser field opens up symmetry forbidden resonant inelastic scattering channels, which can give new insights about the electronic structure of matter. / QC 20100917