Knowledge about the insertion and stabilization of membrane proteins is a key step towards understanding their function and enabling membrane protein design. Transmembrane helices are normally quite hydrophobic to insert efficiently, but there are many exceptions with unfavorable polar or titratable residues. Since evolutionary conserved these amino acids are likely of paramount functional importance, e.g. the four arginines in the S4 voltage sensor helix of voltage-gated ion channels. This has lead to vivid discussion about their conformation, protonation state and cost of insertion. To address such questions, the main focus of this thesis has been membrane protein solvation in lipid bilayers, evaluated using molecular dynamics simulations methods. A main result is that polar and charged amino acids tend to deform the bilayer by pulling water/head-groups into the hydrophobic core to keep their hydrogen bonds paired, thus demonstrating the adaptiveness of the membrane to allow specific and quite complex solvation. In addition, this retained hydration suggests that the solvation cost is mainly due to entropy, not enthalpy loss. To further quantify solvation properties, free energy profiles were calculated for all amino acids in pure bilayers, with shapes correlating well with experimental in vivo values but with higher magnitudes. Additional profiles were calculated for different protonation states of the titratable amino acids, varying lipid composition and with transmembrane helices present in the bilayer. While the two first both influence solvation properties, the latter seems to be a critical aspect. When the protein fraction in the models resemble biological membranes, the solvation cost drops significantly - even to values compatible with experiment. In conclusion, by using simulation based methods I have been able to provide atomic scale explanations to experimental results, and in particular present a hypothesis for how the solvation of charged groups occurs.

<p>This thesis is part of an effort to enable large-scale Hartree-Fock/Kohn-Sham (HF/KS) calculations. The objective is to model molecules and materials containing thousands of atoms at the quantum mechanical level. HF/KS calculations are usually performed with the Self-Consistent Field (SCF) method. This method involves two computationally intensive steps. These steps are the construction of the Fock/Kohn-Sham potential matrix from a given electron density and the subsequent update of the electron density usually represented by the so-called density matrix. In this thesis the focus lies on the representation of potentials and electron density and on the density matrix construction step in the SCF method. Traditionally a diagonalization has been used for the construction of the density matrix. This diagonalization method is, however, not appropriate for large systems since the time complexity for this operation is σ(n³). Three types of alternative methods are described in this thesis; energy minimization, Chebyshev expansion, and density matrix purification. The efficiency of these methods relies on fast matrix-matrix multiplication. Since the occurring matrices become sparse when the separation between atoms exceeds some value, the matrix-matrix multiplication can be performed with complexity σ(n).</p><p>A hierarchic sparse matrix data structure is proposed for the storage and manipulation of matrices. This data structure allows for easy development and implementation of algebraic matrix operations, particularly needed for the density matrix construction, but also for other parts of the SCF calculation. The thesis addresses also truncation of small elements to enforce sparsity, permutation and blocking of matrices, and furthermore calculation of the HOMO-LUMO gap and a few surrounding eigenpairs when density matrix purification is used instead of the traditional diagonalization method.</p>

<p>In this thesis I have theoretically studied electron recombination processes with small molecular ions.</p><p>In these kind of processes resonant states are involved. To calculate the potential energy for these states as a function of internuclear distance, structure calculations and scattering calculations have to be performed.</p><p>So far I have been studying the ion-pair formation with in electron recombination with H₃⁺. The cross section for this process has been calculated using different kind of models, both a time dependent quantum mechanical and a semiclassical.</p><p>I have also studied the direct process of dissociative recombination of HF⁺. To calculate the total cross section for this process, we have performed wave packet propagation on thirty resonant states and summed up the individual cross sections for these states.</p><p>The cross sections for both these processes have a similar appearance to those measured experimentally in the ion storage ring CRYRING in Stockholm.</p>

The understanding of molecular effects in nanoscale environments is becoming increasingly relevant for various emerging fields. These include spectroscopy for molecular identification as well as in finding molecules for energy harvesting. Theoretical quantum chemistry has been increasingly useful to address these phenomena to yield an understanding of these effects. In the first part of this dissertation, we study the chemical effect of surface-enhanced Raman scattering (SERS). We use quantum chemistry simulations to study the metal-molecule interactions present in these systems. We find that the excitations that provide a chemical enhancement contain a mixed contribution from the metal and the molecule. Moreover, using atomistic studies we propose an additional source of enhancement, where a transition metal dopant surface could provide an additional enhancement. We also develop methods to study the electrostatic effects of molecules in metallic environments. We study the importance of image-charge effects, as well as field-bias to molecules interacting with perfect conductors. The atomistic modeling and the electrostatic approximation enable us to study the effects of the metal interacting with the molecule in a complementary fashion, which provides a better understanding of the complex effects present in SERS. In the second part of this dissertation, we present the Harvard Clean Energy project, a high-throughput approach for a large-scale computational screening and design of organic photovoltaic materials. We create molecular libraries to search for candidates structures and use quantum chemistry, machine learning and cheminformatics methods to characterize these systems and find structure-property relations. The scale of this study requires an equally large computational resource. We rely on distributed volunteer computing to obtain these properties. In the third part of this dissertation we present our work related to the acceleration of electronic structure methods using graphics processing units. This hardware represents a change of paradigm with respect to the typical CPU device architectures. We accelerate the resolution-of-the-identity Moller-Plesset second-order perturbation theory algorithm using graphics cards. We also provide detailed tools to address memory and single-precision issues that these cards often present.

The C͂¹B₂ ←　X͂¹A₁ electronic transition of SeO₂ has been investigated under high resolution, at a rotational temperature of around 10 K, using the technique of Laser Excitation Spectroscopy. The vibrationally-resolved survey spectrum contained around 100 new bands in addition to the bands which had been reported in a previous study of the same region (G.W. King and P.R. McLean, J. Mol. Spec. 51, 1974). In the light of this new spectrum a number of bands have been reassigned, most significantly the O⁰₀ band, and a number of progressions have been extended. This led to a revised determination of the vibrational constants of the excited state, and a more acceptable estimate of v'₃ than was suggested in the previous work. These reassignments and extensions of existing assignments accounted for only a small fraction of the newly observed bands; those remaining are thought to be due to a different electronic transition which lies in the same region as the C͂¹B₂ ←　X͂¹A₁ transition. The 1³₀, 1²₀ and 1¹₀ bands of the C͂¹B₂ ←　X͂¹A₁ transition were also recorded at rotational resolution and analysed using the method of ground state combination differences. The 1³₀ band was found to be perturbed, which was one of the major factors which prompted the survey study described above. From the analysis of these bands the rotational constants of the excited state were determined and hence the geometry of the SeO₂ molecule in the given vibrational levels of the ¹B₂ excited state was calculated. This in turn enabled the rotational constants and the geometry of the (00) vibrational level of the excited state to be estimated. This work confirms that the symmetry of the excited state is ¹B₂ and the transition studied is C͂¹B₂ ←　X͂¹A₁. An additional band around 31957 cm⁻¹ was also recorded at rotational resolution, which was initially though to be the O⁰₀ band, on the basis of King and McLean's assignments. However in the light of the reassignments the nature of this band is not known, and attempts to assign it as vibrationally cold band of the C͂¹B₂ ←　X͂¹A₁ transition were unsuccessful, implying that it is probably either a hot band of the C͂¹B₂ ←　X͂¹A₁ transition or a band belonging to different electronic transition.

Thesis (Ph.D.)--McMaster University (Canada), 1991. / Source: Dissertation Abstracts International, Volume: 53-01, Section: B, page: 0503. Supervisor: I. D. Brown.

Zeeman deceleration is an experimental technique which allows for the manipulation of open-shell atoms and molecules in a supersonic beam thus producing mK-cold, velocity-tunable beams of particles in selected quantum states. The method relies on the Zeeman interaction between paramagnetic particles and time-varying, inhomogeneous magnetic fields generated by pulsing high currents through an array of solenoid coils. This thesis describes the construction and implementation of a supersonic beam setup including a 12-stage Zeeman decelerator. The Zeeman decelerator follows an original design that makes it possible to replace individual deceleration coils. Using ground-state hydrogen atoms as a test system, it is shown that the transverse acceptance in a Zeeman decelerator can be significantly increased by generating a rather low, temporally varying quadrupole field in one of the solenoid coils. An electron-impact source was constructed and optimised enabling, for the first time, the Zeeman deceleration of metastable helium atoms in the 23S1 state, with an up to 40 % decrease in the kinetic energy of the beam. It is shown that the pulse duration for electron-impact excitation needs to be matched to the acceptance of the decelerator in order to attain a good contrast between the decelerated and undecelerated parts of the beam. Experimental results are rigorously analysed and interpreted using three-dimensional numerical particle trajectory simulations. A phase-space model provides, for the first time, a means to estimate the six-dimensional phase-space acceptance in a Zeeman decelerator and to find optimum parameter sets for improved Zeeman deceleration schemes. The approach also reveals a hitherto unconsidered velocity dependence of the phase stability which is ascribed mainly to the rise and fall times of the current pulses that generate the magnetic fields inside the deceleration coils. In the future, it is planned to combine the Zeeman decelerator with a source of cold atomic and molecular ions to study chemical collisions at low temperatures. A hybrid magnetic guide consisting of permanent magnet assemblies (Halbach arrays) in hexapole configuration and a set of current-carrying wires is proposed and simulated as an interface between these setups. The design promises very efficient velocity selection, a high degree of quantum-state selection and a nearly complete removal of residual carrier gas. Prospects for using magnetic hexapole focusing in front of the Zeeman decelerator are discussed. The work represents a major step towards the study and control of chemical reactivity of paramagnetic species in the low-temperature regime and it will help in the testing of fundamental chemical reaction theories.

Dans ce travail, nous nous sommes principalement intéressé à la description et à la rationalisation de certaines propriétés des complexes de coordination, par des approches mixtes expérience/théorie. La première de ces études, purement théorique, revisite les propriétés de coordination des ligands par des méthodes de type DFT conceptuelle. Dans un premier temps, les ligands seuls sont étudiés, puis les résultats de cette première approche sont utilisés pour caractériser et rationaliser les effets trans dans les complexes octaédriques. La deuxième étude ci-présentée concerne la synthèse et la caractérisation de complexes polynucléaires de Cu(II) et de ligands de type base de Schiff dérivés d'acides aminés. Dans un premier temps, la réactivité de ces complexes en solution est rationalisée par des mesures spectroscopiques et des calculs de type DFT. Puis, les propriétés magnétiques de deux complexes trinucléaires sont présentées et analysées grâce au support de calculs ab initio de haut niveau. Enfin, dans la troisième étude nous nous intéressons à des complexes mononucléaires d'ion lanthanides présentant une dynamique lente de l'aimantation à basse température. Des mesures magnétiques, mais aussi de luminescence et de diffraction de neutrons polarisés, combinées à des calculs de type SA-CASSCF/RASSI-SO permettent de rationaliser les propriétés magnétiques ainsi observées / In this work, we focused on the description and rationalisation of certain properties of coordination complexes through the use of joint experiment/theory approaches. The first study is purely theoretical, and revisits the coordination properties of ligands using conceptual DFT methods. In a first time, ligands alone are studied, and the results of this study are then employed to characterise and rationaliser the trans effects in octahedral complexes. The second study deals with the syntheses and characterisation of polynuclear Cu(II) complexes deriving from amino-acid based Schiff base-like ligands. In a first time, the reactivity of these complexes in solution is rationalised through the use of spectroscopies and DFT calculations. Then, the magnetic properties of two trinuclear complexes are presented and analysed thanks to high level ab initio calculations. Finally, in the third study we focus on mononuclear lanthanide-based complexes presenting a slow dynamics of magnetisation at low temperature. Magnetic measurements, as well as luminescence and polarised neutron diffraction experiments, combined to SA-CASSCF/RASSI-SO calculation allow the rationalisation of the observed magnetic properties

Ceria based materials have attracted a great deal of interest particularly in area of UV shielding, oxide ion conductivity, solid state electrolyte for fuel cells, automotive exhaust catalysis, water gas shift (WGS) reaction catalysis and also in thermo-chemical water splitting cycles to generate hydrogen. Therefore great deal of efforts was devoted to synthesize nanocrystalline ceria and related materials with different shape and sizes. For example, hierarchically mesostructured doped CeO2 showed potential photvoltic response for solar cell applications. Substitution of lower valent metal ions (Ca2+, Gd3+, Tb3+, Sm3+) in CeO2 enhances oxide ion conductivity for solid oxide fuel cell applications. Eventhough ZrO2 is a nonreducible oxide, CeO2-ZrO2 solid solution has attracted a lot of attention in exhaust catalysis because it exhibited high oxygen storage capacity (OSC). Noble metal ion (M = Pt4+/2+, Au3+, Rh3+, Pd2+ and Ag+) substituted CeO2 (Ce1-xMxO2-δ and Ti1-xMxO2-δ, x = 0.01-0.03) prepared by solution combustion method have shown much higher three-way catalytic property compared same amount of noble metal impregnated to CeO2. Ionically substituted Pt and Au in CeO2 also showed high WGS activity. CeO2-MOx (M= Mn, Fe, Cu, Ni) mixed oxides have shown high activity for hydrogen generation by thermal splitting of water. In chapter 1, we have discussed recent developments on various synthesis strategies of ceria based materials for specific catalytic application. In this thesis, we have explored new route to synthesize Ce1-xMxO2-δ and Ti1-xMxO2-δ (M = transition metal, noble metal) nanocrystallites. Specifically we have addressed the effect of reducible metal ion substitution on the OSC of CeO2 for auto exhaust treatment, hydrogen generation and electro-chemical applications. Controlled synthesis of CeO2 and Ce1-xMxO2-δ (M = Zr, Ti, Y, Pr and Fe) nanocrystallites by hydrothermal method is presented in Chapter 2. The method is based on complexation of metal ion by diethylenetriamine (DETA) or melamine and the simultaneous hydrolysis of metal ion complexes in hydrothermal condition. Size of the crystallites can be controlled by varying the time and temperature of the reaction. 15% Fe3+ ion substituted CeO2 (Ce0.85Fe0.15O2-δ) nanocrystallites have shown higher oxygen storage capacity than Ce0.5Zr0.5O2 at lower temperature. A brief description of material characterization techniques such as powder X-ray diffraction (XRD) and Rietveld refinement of structure, high resolution transmission electron microscopy (HRTEM) and X-ray photoelectron spectroscopy (XPS) is presented. The home-built hydrogen uptake measurement system for OSC study and temperature programmed catalytic reaction system with a quadrupole mass spectrometer and an on-line gas-chromatograph for gas analysis is also described in this chapter. In chapter 3, hydrothermal synthesis of Ce1-xCrxO2+δ (0≤x≤1/3) nanocrystallites is presented. Up to 33% Cr ion substitution in CeO2 could be achieved only by the complexation of Ce(NH4)2(NO3)6 and CrO3 with DETA and simultaneous hydrolysis of the complexes in hydrothermal condition at 200 oC. Powder XRD, XPS and TEM studies confirm that the compound crystallizes in cubic fluorite structure where Ce exist in +4 oxidation state and Cr exist in 4+ and +6 (mixed valance) oxidation states in the ratio of 2: 1. Composition x = 0.33 (Ce2/3Cr1/3O2+δ) showed higher OSC (0.33 mol of [O]) than the maximum OSC observed for CeO2-ZrO2 solid solutions. Formation and higher OSC of Ce2/3Cr1/3O2+δ is attributed to interaction of Ce4+/3+ and Cr3+/4+/6+ redox couples in fluorite structure. The material shows oxygen evolution at ~400 oC in air and hence it is a true oxygen storage material. Oxygen evolution property of Ce0.67Cr0.33O2.11 and subsequent generation of hydrogen by thermal splitting of water is presented in chapter 4. Among the ceria based oxides, Ce0.67Cr0.33O2.11 being the only compound like UO2+δ to have excess oxygen possessing fluorite structure, it releases a large proportion of its lattice oxygen (0.167 M [O]/mole of compound) by heating the material under N2 flow at relatively low temperature (465 oC) directly and almost stoichiometric amount of H2 (0.152 M/Mol of compound) is generated at much lower temperature (65 oC) by thermosplitting of water. The reversible nature of oxygen release and intake of this material is attributed to its fluorite structure and internal coupling between the Ce4+/Ce3+ and Cr4+/6+/Cr3+ redox couples. In chapter 5, we present the hydrothermal synthesis and three-way catalytic activity of Ce1-xRuxO2-δ (0≤x≤0.1) nanocrystallites. Powder XRD, Rietveld refinement, TEM and XPS reveals that the compounds crystallized in fluorite structure where Ru exist in +4 state and Ce in mixed valent (+3, +4) state. Substitution of Ru4+ ion in CeO2 activated the lattice oxygen and Ce0.9Ru0.1O2-δ can reversibly releases 0.42[O]/mol of compound, which is higher than maximum OSC of 0.22 [O]/mol of compound observed for Ce0.50Zr0.50O2. Utilization of higher OSC of Ce1-xRuxO2-δ (x = 0.05 and 0.10) is also shown by low temperature CO oxidation with these catalysts, both in presence/absence of feed oxygen. Ru4+ ion act as active centre for reducing molecules (CO, hydrocarbon ‘HC’) and oxide ion vacancy acts as an active centre for O2 and NOx in this compound. Ce1-xRuxO2-δ not only act as a high oxygen storage material but it also shows high activity towards CO, hydrocarbon ‘HC’ oxidation and NO reduction by CO at low temperature with high N2 selectivity for 3-way catalysis. Study of water gas shift reaction over Ce0.95Ru0.05O2-δ catalyst is presented in chapter 6. The catalyst showed very high WGS activity in terms of high conversion rate (20.5 μmol.g-1.s-1 at 275 oC) and low activation energy (~50.6 kcal/mol). The reason for this seems to be high adsorption propensity of CO on Ru4+ ion and easy extraction of oxygen from lattice to form CO2. This step creates oxide ion vacancy in the catalyst lattice and H2O can adsorb on lattice sites oxygen vacancy and regenerate the lattice by releasing H2. Even in presence of externally fed CO2 and H2, complete conversion of CO to CO2 was observed with 100 % H2 selectivity with Ce0.95Ru0.05O2-δcatalyst in the temperature range of 305-385 oC and no trace of methane formation was observed in this temperature range. Catalyst does not deactivate in long duration on/off WGS reaction cycle because sintering of noble metal or active sites is avoided in this catalyst as Ru4+ ion is substituted in CeO2 lattice. Due to highly acidic nature of Ru4+ ion, surface carbonated formation is prohibited. In chapter 7, synthesis of Ce1-xFexO2-δ (0≤x≤0.45) and Ce0.65Fe0.33Pd0.02O2-δnanocrystallites is presented by sonochemical method. Powder XRD, XPS and TEM studies confirm that the compounds of ~4 nm sizes is crystallized in fluorite structure where Fe is in +3, Ce is in +4 and Pd is in +2 oxidation state. Due to substitution of smaller Fe3+ ion in CeO2, lattice oxygen is activated and Ce0.67Fe0.33O1.835 reversibly releases 0.31[O] up to 600 oC which is higher or comparable to the maximum OSC observed for CeO2-ZrO2 based solid solutions. Due to internal interaction of Pd2+/0(0.89 V), Fe3+/2+ (0.77 V) with Ce4+/3+ (1.61 V) redox couples, Pd ion accelerates the electron transfer from Fe2+ to Ce4+ in Ce0.65Fe0.33Pd0.02O1.815, making it a high oxygen storage material as well as highly active catalyst for CO oxidation and WGS reaction. Activation energy for CO oxidation with O2 over Ce0.65Fe0.33Pd0.02O1.815 is found as low as 38 kJ/mol. CO conversion to CO2 is 100% H2 specific in WGS reaction with these catalysts. Conversion rate was found as high 27.2 μmol.g-1.s-1 and activation energy was found 46.4 kJ/mol for Ce0.65Fe0.33Pd0.02O1.815. Only 1-3% Pt, Pd ion can be substituted in CeO2 is by the solution combustion method. We show that even up to 10% of Pt and Pd ion can be substituted in CeO2 by sonication method. In chapter 8, we present the sonochemical synthesis redox property and methanol electro-oxidation activity of hierarchical Ce1-xMxO2-δ (M = Pt and Pd, 0≤x≤0.1) nanocrystallites. Powder XRD, TEM, SEM and XPS study confirms that hierarchical structure compound crystallize in fluorite structure. Pt exists in +4 state and Ce in mixed valent (+3, +4) state in Ce1-xPtxO2-δ and Pd exist in +2 state and Ce in mixed valent (+3, +4) state in Ce1-xPdxO2-δ. Substitution of Pt and Pd ion in CeO2 activated the lattice oxygen. Hydrogen absorption study show higher H/Pt ratio ~8.1 and H/Pd ratio ~4.2 in respective oxides. Reversible nature of higher oxygen storage capacity or higher H/P, H/Pd ratio is due to interaction of redox couples of Pt4+/2+(0.91V), Pt2+/0(1.18V), Pd2+/0(0.92V) and Ce4+/3+(1.61V). Due to participation of lattice oxygen, Ce0.95Pt0.05O1.95 and Ce0.95Pd0.05O1.90 have shown higher electro-oxidation of methanol compared to same moles of Pt in 5%Pt/C. In chapter 9, we present sonochemical synthesis of Ti1-xPtxO2 (0≤x≤0.1) nanocrystallites: a new high capacity anode material for rechargeable Li ion battery. Continuing our interest in synthesis of nanomaterials, we thought if we can extend the same sonochemical method to synthesize metal ion doped TiO2. Doping of TiO2 with a suitable metal ion where dopant redox potential couples with that of titanium (Ti4+) and act as catalyst for additional reduction of Ti4+ to Ti2+ (Ti4+ →Ti3+→Ti2+) is envisaged here to enhance lithium storage even higher than one Li/TiO2. 10 atom % Pt ion substituted TiO2, Ti0.9Pt0.1O2 nanocrystallites of ~4 nm size was synthesized by sonochemical method using diethylenetriamine (DETA) as complexing agent. Powder XRD, Rietveld refinement, TEM and XPS studies reveal that Ti0.9Pt0.1O2 nanocrystallites crystallize in anatase structure and both Ti and Pt are in 4+ oxidation state. Due to Pt4+ ion substitution in TiO2, reducibility of TiO2 was enhanced and Ti4+ was reduced up to Ti2+ state via coupling of Pt states (Pt4+/Pt2+/Pt0) with Ti states (Ti4+/Ti3+/Ti2+). Galvanostatic cycling of Ti0.9Pt0.1O2 against lithium showed very high capacity of 430 mAhg-1 or exchange of ~1.5Li/Ti0.9Pt0.1O2 which is much higher than the highest capacity of 305 mAhg-1 or insertion of ~0.9Li/TiO2 achieved for TiO2(B) nanowires. In chapter 10, we present the conclusions and critical review on the study of transition metal and noble metal ion substituted CeO2 and TiO2.

The studies on cocrystals and salts presented in the the chapters clearly bring out the influence of intermolecular interactions as the main evaluators of the cocrystal-salt regime. The observations made in Chapter 2 indicate that in case if the cocrystal formation is through hydrogen bonds the location of the proton decides the nature of the complex in the energy landscape. The observation that the coformer controls the topology of intermolecular space as demonstrated in Chapter 3 provides insights into the importance of directionality rather than strength of intermolecular interactions. Indeed halogen bonding in cocrystals gain importance in this context.