En stor samling dimolekylära vätebindningar med formen A – H … B, där AH är en alkyn, alkohol eller tiol och B = [Br–, Cl–, NH3, HCN] beräknas och utvärderas med Kohn-Sham täthetsfunktionalteori tillsammans med bassetet m062x/6-311+g(2df.2p). Dessa komplex utvärderas även med en punktladdningsmodell (som använder samma metod och basset), där atomerna i vätebindningsmottagaren B byts ut mot laddningar som passats för att återskapa laddningsfördelningen runt molekylen, med målet att separera och isolera de elektrostatiska och polariserande energikomponenterna från de totala interaktionsenergierna. Med hjälp av detta tillvägagångssätt visade det sig att vätebindningars komplexeringsenergi (i.e. interaktionsenergin med energikostnaden för att deformera atomkärnornas rymdgeometri borttagen), oberoende av karaktären hos monomeren AH eller B, till stor del består av elektrostatik och polarisation, medan laddningsutbyte, dispersion, och andra resttermer endast utgör en liten del av den totala interaktionen. Fördelningen mellan elektrostatik och polarisation varierar beroende på typen av monomerer i vätebindningen, men deras summa, den resulterande punktladdningsenergin, korrelerar linjärt (ΔECompl = 0.85ΔEPC ) med R2 = 0.995 över energiomfånget 0 < ΔECompl < 50 kcal mol–1. Detta blir ännu mer anmärkningsvärt då inkluderingen av komplexeringsenergierna från halogenbindningar i samma korrelation inte förändrar korrelationskoefficienten avsevärt, vilket indikerar att båda bindningstyperna består av samma energikomponenter även då bindningarna i sig är väldigt olika. / A large set of dimeric hydrogen bonds of the type A – H … B, where AH is an alkyne, alcohol, or thiol and B = [Br–, Cl–, NH3, HCN]  are computed and evaluated using Kohn-Sham density functional theory together with the m062x/6-311+g(2df.2p) basis set. These complexes are also evaluated using a point charge (PC) approach (using the same method and basis set), where the atoms of the hydrogen bond acceptor B are substituted for charges that are optimized to reproduce the charge distribution of the molecule, with the purpose of separating and isolating the electrostatics- and polarization energy components of the interaction energies. Using this approach it was discovered that the complexation energy of hydrogen bonds (i.e.the interaction energy with the energy cost of nuclear deformation corrected for), independent on the nature of either monomer AH or B, are largely made up of electrostatics and polarization, while charge transfer, dispersion, and other rest terms only make up a small fraction of the total interaction. The composition of electrostatics and polarization vary depending on the type of monomers in the hydrogen bond, but their sum, the PC interaction energy, correlates linearly (ΔECompl = 0.85ΔEPC )  with R2 = 0.995 over an energy span of 0 < ΔECompl < 50 kcal mol–1. This is made even more remarkable by the inclusion of halogen bonded complexation energies in the same correlation without changing the correlation coefficient significantly, indicating that the two bond types are comprised of the same components even though they are remarkably different in origin.

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Styrene production by a (FlDAB)PdII(TFA)(η2-C2H4) complex was modeled using density functional theory (DFT). Benzene C-H activation by this complex was studied via five mechanisms: oxidative addition/reductive elimination, sigma-bond metathesis, concerted metalation deprotonation (CMD), CMD activation of ethylene, and benzene substitution of ethylene followed by CMD of the ligated benzene. Calculations provided evidence that conversion of benzene and ethylene to styrene was initiated by the fifth pathway, arylation via CMD of coordinated benzene, followed by ethylene insertion into the Ru-Ph bond, and then β-hydrogen elimination. Also, monomer (active species)/dimer equilibrium concentrations were analyzed. The results obtained from present study were compared with that of a recently reported RhI complex to help identify more suitable catalysts for the direct production of styrene from ethylene and benzene. Second, theoretical studies of heterobimetallic {Ag–Fe(CO)5}+ fragments were performed in conjunction with experiments. The computational models suggested that for this first example of a heterodinuclear, metal-only FeAg Lewis pair (MOLP) that Fe(CO)5 acts as a Lewis base and AgI as a Lewis acid. The ῡCO bands of the studied molecules showed a blue shift relative to those measured for free Fe(CO)5, which indicated a reduction in Fe→CO backbonding upon coordination to silver(I). Electrostatic interaction is predicted via DFT as the dominant mode of Fe—Ag bonding augmented by a modest amount of charge transfer between Ag+ and Fe(CO)5. Third, computational analyses of hypothetical transition metal-terminal boride [MB(PNPR)] complexes were reported. DFT, natural orbital analysis (NBO), and multiconfiguration self-consistent field (MCSCF) calculations were employed to investigate the structure and bonding of terminal boride complexes, in particular the extent of metal dπ - boron pπ bonding. Comparison of metal-boride, -borylene and –boryl bond lengths confirms the presence of metal-boron π bonds, albeit the modest shortening (~ 3%) of the metal-boron bond suggests that the π-bonding is weak. Their instabilities, as measured by free energies of H2 addition to make the corresponding boryl complexes, indicate terminal boride complexes to be thermodynamically weak. It is concluded that for the boride complexes studied, covering a range of 4d and 5d metals, that the metal-boride bond consisted of a reasonably covalent σ and two very polarized π metal-boron bonds. High polarization of the boron to metal π-bonds indicated that a terminal boride is an acceptor or Z type ligand. Finally, anti-Markovnikov addition of water to olefins has been a long-standing goal in catalysis. The [Rh(COD)(DPEphos)]+ complex was found as a general and regioselective group 9 catalyst for intermolecular hydroamination of alkenes. The reaction mechanism was adapted for intermolecular hydration of alkenes catalyzed by a [Rh(DPEphos)]+ catalyst and studied by DFT calculations. Olefin hydration pathways were analyzed for anti-Markovnikov and Markovnikov regioselectivity. On the basis of the DFT results, the operating mechanism can be summarized as follows: styrene activation through nucleophilic attack by OHδ− of water to alkene with simultaneous Hδ+ transfer to the Rh; this is then followed by formation of primary alcohol via reductive elimination. The competitive formation of phenylethane was studied via a β-elimination pathway followed by hydrogenation. The origin of the regioselectivity (Markovnikov vs anti-Markovnikov) was analyzed by means of studying the molecular orbitals, plus natural atomic charges, and shown to be primarily orbital-driven rather than charge-driven.

This work discusses applications of computational simulations to enzymatic systems with a particular focus on the effects of various small perturbations on cancer and disease-related systems. First, we cover the development of carbohydrate-based PET imaging ligands for Galectin-3, which is a protein overexpressed in pancreatic cancer tumors. We uncover several structural features for the ligands that can be used to improve their binding and efficacy. Second, we discuss the AlkB family of enzymes. AlkB is the E. coli DNA repair protein for alkylation damage, and has human homologues with slightly different functions and substrates. Each has a conserved active site with a catalytic iron and a coordinating His...His...Asp triad. We have applied molecular dynamics (MD) to investigate the effect of a novel single nucleotide polymorphism for AlkBH7, which is correlated with prostate cancer and has an unknown function. We show that the mutation leads to active site distortion, which has been confirmed by experiments. Thirdly, we investigate the unfolding of hen egg white lysozyme in 90% ethanol solution and low pH, to show the initial steps of unfolding from a native-like state to the disease-associated beta-sheet structure. We compare to mass spectrometry experiments and also show differing pathways based on protonation state. Finally, we discuss three different DNA polymerase systems. DNA polymerases are the primary proteins that replicate DNA during cell division, and have various extra or specific functions. We look at a proofreading-deficient DNA polymerase III mutant, the effects of solvent on DNA polymerase IV's ability to bypass bulky DNA adducts, and a variety of mutations on DNA polymerase kappa.

The self-assembly of structured particles into monodisperse clusters is a challenge on the nano-, micro- and even macro-scale. While biological systems are able to self-assemble with comparative ease, many aspects of this self-assembly are not fully understood. In this thesis, we look at the strategies and rules that can be applied to encourage the formation of monodisperse clusters. Though much of the inspiration is biological in nature, the simulations use a simple minimal patchy particle model and are thus applicable to a wide range of systems. The topics that this thesis addresses include: Encapsulation: We show how clusters can be used to encapsulate objects and demonstrate that such `templates' can be used to control the assembly mechanisms and enhance the formation of more complex objects. Hierarchical self-assembly: We investigate the use of hierarchical mechanisms in enhancing the formation of clusters. We find that, while we are able to extend the ranges where we see successful assembly by using a hierarchical assembly pathway, it does not straightforwardly provide a route to enhance the complexity of structures that can be formed. Pore formation: We use our simple model to investigate a particular biological example, namely the self-assembly and formation of heptameric alpha-haemolysin pores, and show that pore insertion is key to rationalising experimental results on this system. Phase re-entrance: We look at the computation of equilibrium phase diagrams for self-assembling systems, particularly focusing on the possible presence of an unusual liquid-vapour phase re-entrance that has been suggested by dynamical simulations, using a variety of techniques.

This thesis addresses simulation of electrochemical experiments, with an emphasis on processes of diffusional mass transport to electrode surface. Following system has been studied: • Applying theoretical modeling and experimentation is shown that even significant surface roughness produced by deliberate polishing or scratching is not sufficient to be distinguished in cyclic voltammetry experiments conducted under the usual conditions. In stripping voltammetry experiment the shape of the voltammograms strongly depends on the model of the electron transfer but is not always sensitive to the precise model of the electrode surface; the conditions under which this is the case are identified, and generic roughness effects on stripping voltammetry are quantified. Electrode roughness can have a significant effect on the stripping of the metals from the solid electrode especially in respect of the voltammetric waveshape. • We first consider two different models of electrodes covered with electroinactive layers: the electrode is covered with a uniform layer and the layer contains pinholes. Both models are simulated and then compared to identify conditions under which they can be distinguished. Next we propose generic model to predict the influence of electroactive layer on the cyclic voltammetric. The conditions under which deviation from the behavior of a planar electrode are predicted. • We first consider one electron, one proton and next two electron, two proton reduction of surface bound species. Two mechanisms of reaction are considered: stepwise and concerted. Voltammetry studied under the three regimes of protons mass transport: infinitely fast (fully buffered solution), infinitely slow (infinitely high surface coverage of electrode) and intermediate case of finite rate of diffusional mass transport to electrode surface. Types of voltammograms observed in each case are presented and discussed. • Theory of chronoamperometry on disc and ring-recessed microelectrodes and their arrays is reported. Three and four different regimes of transient current versus time can be observed at microelectrode arrays of disc and ring electrodes, accordingly. A generic, accurate and easy to use method of experimental chronoamperometric data analysis is proposed. It is shown that the method can be applied to the simultaneous measurement of D and nC in solution. • The fabrication, characterization, and use of arrays of ring-recessed disk generator-colector microelectrodes are reported. Experiments and simulations relating to time- of-flight experiments in which material electrogenerated at a disk is diffusionally transported to the ring are reported. We further study voltammetry of electrochemically active species which undergoes first and second order chemical reactions. Current transients are found to be sensitive to the diffusion coefficient of both the reduced and oxidised species as well as to the rate of the chemical reaction and its mechanism.

Magnetic fields influence the rate and/or yield of chemical reactions that proceed via spin correlated radical pair intermediates. The field of spin chemistry centres around the study of such magnetic field effects (MFEs). This thesis is particularly concerned with the effects of the weak magnetic fields B₀ ~ 1mT relevant in the ongoing debates on the mechanism by which animals sense the geomagnetic field and on the putative health effects of environmental electromagnetic fields. Relatively few previous studies have dealt with such weak magnetic fields. This thesis presents several new theoretical tools and applies them to interpret experimental measurements. Chapter 1 surveys the development and theory of spin chemistry. Chapter 2 introduces the use of Tikhonov and Maximum Entropy Regularisation methods as a new means of analysing MARY field effect data. These are applied to recover details of the diffusive motion of reacting pyrene and N,N-dimethylaniline radicals. Chapter 3 gives a fresh derivation and appraisal of an approximate, semiclassical approach to MFEs. Monte Carlo calculations allow the elucidation of several "rules of thumb" for interpreting MFE data. Chapter 4 discusses recent optically-detected zero-field EPR measurements, adapting the gamma-COMPUTE algorithm from solid state NMR for their interpretation. Chapter 5 explores the role of RF polarisation in producing MFEs. The breakdown in weak fields of the familiar rotating frame approximation is analysed. Chapter 6 reviews current knowledge and landmark experiments in the area of animal magnetoreception. The origins of the sensitivity of European robins Erithacus rubecula to the Earth’s magnetic field are given particular attention. In Chapter 7, Schulten and Ritz’s hypothesis that avian magnetoreception is founded on a radical pair mechanism (RPM) reaction is appraised through calculations in model systems. Chapter 8 introduces quantitative methods of analysing anisotropic magnetic field effects using spherical harmonics. Chapter 9 considers recent observations that European robins may sometimes be disoriented by minuscule RF fields. These are shown to be consistent with magnetoreception via a radical pair with no (effective) magnetic nuclei in one of the radicals.

Few experimental techniques have found such a diverse range of applications as has ion imaging. The field of chemical dynamics is constantly advancing, and new applications of ion imaging are being realised with increasing frequency. This thesis is concerned with the application of a fast pixelated imaging sensor, the Pixel Imaging Mass Spectrometry (PImMS) camera, to ion imaging applications. The experimental possibilities of such a marriage are exceptionally broad in scope, and this thesis is concerned with the development of a selection of velocity-map imaging applications within the field of photoinduced molecular dynamics. The capabilities of the PImMS camera in three-dimensional and slice imaging applications are investigated, in which the product fragment Newton-sphere is temporally stretched along the time-of-flight axis, and time-resolved slices through the product fragment distribution are acquired. Through experimental results following the photodissociation of ethyl iodide (CH₃CH₂I) at around 230 nm, the PImMS camera is demonstrated to be capable of recording well-resolved time slices through the product fragment Newton-sphere in a single experiment, without the requirement to time-gate the acquisition. The various multi-hit capabilities of the device represent a unique and significant advantage over alternative technologies. The details of a new experiment that allows the simultaneous imaging of both photoelectrons and photoions on a single detector for each experimental acquisition cycle using pulsed ion extraction are presented. It is demonstrated that it is possible to maintain a high velocity resolution using this approach through the simultaneous imaging of the photoelectrons and photoions that result from the (3 + 2) resonantly enhanced multi-photon ionisation of Br atoms produced following the photodissociation of Br₂ at 446.41 nm. Pulsed ion extraction represents a substantial simplification in experimental design over conventional photoelectron-photoion coincidence (PEPICO) imaging spectrometers and is an important step towards performing coincidence experiments using a conventional ion imaging apparatus coupled with a fast imaging detector. The performance of the PImMS camera in this application is investigated, and a new method for the determination of the photofragment detection efficiencies based on a statistical fitting of the coincident photoelectron and photoion data is presented. The PImMS camera is applied to laser-induced Coulomb explosion imaging (CEI) of an axially chiral substituted biphenyl molecule. The multi-hit capabilities of the device allow the concurrent detection of individual 2D momentum images of all ionic fragments resulting from the Coulomb explosion of multiple molecules in each acquisition cycle. Correlations between the recoil directions of the fragment ions are determined through a covariance analysis. In combination with the ability to align the molecules in space prior to the Coulomb explosion event, the experimental results demonstrate that it is possible to extract extensive information pertaining to the parent molecular structure and fragmentation dynamics following strong field ionisation. Preliminary simulations of the Coulomb explosion dynamics suggest that such an approach may hold promise for determining elements of molecular structure on a femtosecond timescale, bringing the concept of the `molecular movie' closer to realisation. Finally, the PImMS camera is applied to the imaging of laser-induced torsional motion of axially chiral biphenyl molecules through femtosecond Coulomb explosion imaging. The target molecules are initially aligned in space using a nanosecond laser pulse, and torsional motion induced using a femtosecond 'kick' pulse. Instantaneous measurements of the dihedral angle of the molecules are inferred from the correlated F+ and Br+ ion trajectories following photoinitiated Coulomb explosion at various time delays after the initial kick pulse. The technique is extended to include a second kick pulse, in order to achieve either an increase in the amplitude of the oscillations or to damp the motion, representing a substantial degree of control of the system. Measurements out to long kick-probe delays (200 ps) reveal that the initially prepared torsional wave packet periodically dephases and rephases, in accordance with the predictions of recent theoretical work.

The work presented in this thesis examines the electrochemical behaviour of a number of species, both surface-bound and in the solution phase, in various room-temperature ionic liquids (RTILs), in order to identify systems which show altered reactivities in room-temperature ionic liquids, compared to that in conventional, molecular, aprotic solvents. The fundamentals of electrochemistry are outlined and an introduction to room-temperature ionic liquids is given, after which the results of six original investigations are presented, as follows; The electrochemical response of surface-bound anthraquinonyl films was investigated as a function of RTIL cation size. The reduction of oxygen to superoxide in the [C₂mim][NTf₂] RTIL was studied at different carbon electrodes. The mechanisms of electrodeposition and stripping of Zn(II) onto bulk zinc deposits, on glassy carbon electrodes, in the [C₄mPyrr][NTf₂] RTIL were investigated. A novel and successful method for the fabrication of zinc microdisk electrodes was developed and the electrochemical behaviour of these electrodes was investigated. The mechanisms for the electrochemical reductions of some bromo- and nitrobenzenes at platinum microelectrodes were determined in the [C₄mPyrr][NTf₂] ionic liquid, in order to identify systems which displayed changed reactivities in RTILs compared to those in molecular aprotic solvents. The altered reactivity of 1-bromo-4-nitrobenzene in the [C₄mPyrr][NTf₂] ionic liquid was utilised via electrochemical reduction at zinc microelectrodes in order to form arylzinc compounds. The work presented in this thesis shows that the oft-taken view that the reactivity of a given species in an ionic liquid will mimic that in conventional aprotic solvents is not always the case. Reactivities can be markedly different between RTILs and aprotic solvents and can also be highly dependent on the specific ionic liquid employed.

Cavity ring-down spectroscopy (CRDS) and cavity enhanced absorption spectroscopy (CEAS) are two well-established absorption spectroscopic techniques originally developed for gas-phase samples. Condensed-phase applications of these techniques still remain rare, complicated as they are by additional background losses induced by condensed-phase samples as well as the intracavity components in which the sample is constrained. This thesis is concerned with the development and application of optical-cavity-based techniques in the condensed phase. Polarization-dependent evanescent wave CRDS (EW-CRDS) has been used to study the molecular orientation at the solid/air and solid/liquid interfaces. An increase in average orientation angle with respect to the surface normal has been observed for both methylene blue and coumarin molecules as a function of coverage at the fused silica/air interface. An orientation-angle-dependent photobleaching of pyridin molecules at the fused silica/methanol interface have also been observed. EW-CRDS has also been used to monitor slow in situ photobleaching of thin dye films deposited on the prism surface. The photobleaching dynamics is interpreted as a combination of first- and second-order processes. A significant fraction of this thesis has been devoted to studying magnetic field effects (MFEs) on the kinetics of the radical pair (RP) reactions in solution, in an effort to understand the ability of animals to sense the geomagnetic field. Two novel optical-cavity-based techniques – broadband CEAS (BBCEAS) and CRDS have been developed for this purpose. BBCEAS uses a supercontinuum (SC) source as the cavity light source and a CCD camera as photodetector, enabling simultaneous acquisition of absorption spectrum across the whole visible region (400 – 800 nm). In CRDS, a tunable optical parametric oscillator has been used as the cavity light source. Combined with the switching of external magnetic field (SEMF) method, this technique allows the decay kinetics of the geminate RPs to be monitored, with nanosecond resolution. Both BBCEAS and CRDS provide sensitivity superior to single-pass transient absorption (TA), a technique traditionally used in the MFE studies. A series of photochemical systems have been studied by BBCEAS and CRDS, respectively, among which, the MFEs of drosophila melanogaster cryptochrome has been observed. Importantly, this is the first time an MFE has been observed in an animal cryptochrome, and provides key supporting evidence for the cryptochrome hypothesis of magnetoreception in animals. Besides the optical-cavity-based techniques, a novel fluorescence detection method of MFEs has also been demonstrated. This technique proved ultrahigh sensitivity when applicable.