<p>This licentiate thesis deals with quantum chemistry methods for large systems. In particular, the thesis focuses on the efficient construction of the Coulomb and exchange matrices which are important parts of the Fock matrix in Hartree--Fock calculations.The methods described are also applicable in Kohn--Sham Density FunctionalTheory calculations, where the Coulomb and exchange matrices areparts of the Kohn--Sham matrix. Screening techniques for reducing the computational complexity of bot Coulomb and exchange computations are discussed, as well as the fast multipole method, used for efficient computation of the Coulomb matrix.</p><p>The thesis also discusses how sparsity in the matrices occurring in Hartree--Fock and Kohn--Sham Density Functional Theory calculations can be used to achieve more efficient storage of matrices as well as more efficient operations on them.</p><p>As an example of a possible type of application, the thesis includes a theoretical study of Heisenberg exchange constants, using unrestricted Kohn--Sham Density Functional Theory calculations.</p>

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Thesis (Ph. D.)--Princeton University, 1932.

Thesis (Ph. D.)--University of Chicago, 1929. / Lithoprinted.

Thesis (Ph. D.)--Princeton University, 1932.

The work presented in this thesis describes the development and applications of hollow carbon nanostructures both as the catalytically active, magnetically separable carbon nanoreactors, and electrodes for electrocatalytic reactions. The work is separated into three distinct parts, the formation of carbon nanoreactors of different diameters and shapes in which the effect of confinement imposed by the nanotube is probed in exploratory hydrogenation reactions, the functionalisation of carbon nanoreactors with magnetic nanoparticles for magnetically separable catalyst supports, and the development of new hybrid metal-carbon nanoreactors as efficient electrocatalysts for hydrogen fuel cell applications. In the first part of the thesis, a Ru3(CO)12 precursor was successfully inserted into carbon nanoreactors of different diameters – very narrow single walled carbon nanotubes (SWNTs, DSWNT ~1.5 nm) and much wider hollow graphitised carbon nanofibers (GNFs, internal dGNF ~50 nm) using sublimation followed by the formation of uncoated metallic Ru nanoparticles via thermal decomposition. The resultant RuNPs@SWNT and RuNPs@GNF nanoreactors were then tested in hydrogenation reactions using a high pressure scCO2 batch reactor, where the excellent diffusivity and mass transfer properties of scCO2 as solvent enabled the efficient delivery of the reagents to the catalyst surface within the narrow nanoreactors. RuNPs confined in the narrowest channels of SWNT was observed to be highly active and selective in competitive hydrogenation reaction of alkenes, but concurrently reduce the accessible volume of the SWNTs by 30-40 % resulting in lower overall turnover numbers (TONs). In contrast, RuNPs confined in wider GNFs were entirely accessible and indicated outstanding activity in comparison to unconfined RuNPs on the outer surface of SWNTs or carbon black. In the second part of the work, GNFs sidewalls were functionalised by non-covalent attachment of commercial graphene-like carbon coated magnetic Co nanomagnets (Co@Cn) exploiting van der Waals forces via dispersion in an organic solvent using ultrasonic treatment, and by the in situ formation of carbon coated iron nanomagnets (Fe@Cn). A number of experiments were carried out to find the minimum amount of nanomagnets required to enable complete separation of the nanotubes from the solution with an external magnetic field. Characterisation of this composite material by high resolution transmission electron microscopy (HRTEM) showed that Co@Cn and Fe@Cn successfully attached to the GNFs. Magnetic functionalisation steps were then combined with uncoated, palladium and platinum nanoparticle catalyst formation and the resultant catalytically active and magnetically separable hybrid materials were investigated in the reduction of nitrobenzene. The recyclability and stability of these magnetic and catalytic nanoreactors were studied in the reduction of nitrobenzene using magnetic recovery, and only negligible catalyst loss (< 0.5% by wt.) was observed over 5 cycles in comparison to that of filtration based catalyst recovery (>10% catalyst loss by wt.). In the third part, GNFs were shortened by ball milling and combined with palladium catalyst to form (PdNPs/-PdNPs@)s-GNF using a novel procedure and the resultant activity and stability towards hydrogen evolution and hydrogen oxidation reactions (HER/HOR) in acid media was studied. (PdNPs/-PdNPs@)s-GNF exhibited enhanced activity and excellent durability during 30000 electro-catalytic cycles in HER compared to that of state-art commercial Pt/C which exhibited decreasing activity and poor durability during the cycling in acid. Moreover, s-GNF demonstrated an enhanced HER activity and stability during 5000 cycles. HRTEM revealed some chemical transformations at the step edges within GNF during the electrochemical cycling contributing to durability of the electrocatalyst. Overall, the superior HER/HOR activity and durability was attributed to the corrugated morphology of s-GNF, and therefore the ability to stabilise the Pd nanoparticles at the graphitic step-edges effectively through strong bonding and synergetic effects between the Pd and s-GNF support. These results clearly indicate that carbon nanoreactors as catalyst supports and electrocatalystd show significant promise for a variety of chemical reactions.

Chapter 1: Introduction This Chapter provides an introduction to the study of reactive intermediates and the specialised techniques which have been developed in order to study these extremely short lived species. In particular, it provides an overview of ultrafast Time Resolved Infrared Spectroscopy (TRIR). This key technique underpins a large amount of the work presented in this Thesis as well as a description of the apparatus and methods used across the other Chapters of this Thesis. Chapter 2: Ultrafast TRIR studies of rhenium complexes of thioether substituted hexaazatrinapthylene ligands The excited states and photophysical properties of mono, bi and trinuclear (Re(CO)3Cl) complexes of the 2,3,8,9,1314-hexa (octyl-thioether)-1,6,7,12,13,18-hexaazatrinapthylene ligand (HATN-S(C8H17)6) have been investigated using ultrafast TRIR spectroscopy. These measurements are supported by theoretical calculations and resonance Raman spectroscopic investigations of these compounds. The position and the intensity of the (CO) bands of the photoexcited species directly report on the electron transfer/distribution in the excited state. In all cases the observed product bands were blue shifted compared to the parent, this is consistent with electron transfer away from the metal centre. The observed shift for the thioether substituted HATN complexes studied here was smaller than that reported for the analogous HATN-Me6 complexes, indicating reduced electron transfer upon excitation. Red shifted product bands corresponding to “spectator” metal centres were also observed for the bi and trinuclear species, these bands were shifted by approximately the same amount as for the HATN-Me6 species, indicating a similar reduction of the HATN core upon excitation. These results are consistent with the formation of a dual charge transfer ILCT/MLCT excited state involving electron donation from both a metal centre and the thioether moieties upon excitation. Chapter 3: Ultrafast TRIR studies of rhenium and platinum complexes of Pyridyl-1,2,3-Triazole and related ligands The excited states and photophysics of a series of substituted rhenium and platinum complexes that contain a 2-pyridyl-1,2-3-triazole ligand, an easily modified analogue of the common 2,2’-bipyridine (bpy)ligand, have been studied by TRIR spectroscopy. The compounds are found to be analogous of similar complexes with bpy, exhibiting MLCT or MLLCT exicted states (in the case of the (Re(CO)3X) and (Pt(CCHPh)2) complexes respectively). Changing the substitution of the triazole ring has little effect on the excited state band positions, this is attributed to the insulating effect of the triazole moiety. Complexes substituted with conjugated phenyl groups on the triazole ring exhibit greatly increased excited state lifetimes than those substituted with non-conjugated benzyl groups. This is attributed to the rigid rotor effect. The addition of an electron donating triphenylamine group to the pyridyl moiety results in the observation of ILCT states. Chapter 4: Towards long lived alkane and noble gas complexes from cationic piano stool complexes in the fluorous phase The synthesis and characterisation of a series of cationic transition metal tricarbonyl half sandwich complexes solubilised in perfluoroalkane solvents by means of the weakly coordinating, fluorous solubilising anion tetrakis(3,5-bis(perfluorohexyl)phenyl)borate (BArF64) is described. These complexes were photolysed in perfluoroalkane solutions doped with methane, heptane and xenon and followed by ultrafast TRIR spectroscopy with the aim of generating long-lived organometallic alkane and noble gas complexes suitable for study by NMR at room temperature. While no organometallic alkane or noble gas complexes were observed, several novel transition metal-BArF64 zwitterionic species are generated upon photolysis. These species are the result of -2 binding of one of the aryl moieties of the BArF64 anion to the vacant coordination sites generated following photoejection of a carbonyl ligand. While highly reactive they are long lived and appear to be permanent photoproducts. In the case of the rhenium complex an additional product band assigned as a dimeric species is also observed. Chapter 5: Towards the synthesis of fluorous phase soluble cationic piano stool complexes. The synthesis of fluorous tagged cationic transition metal tricarbonyl complexes is explored with the eventual aim of performing fluorous phase TRIR experiments utilising the more weakly coordinating (but less solubilising) anion tetrakis(perfluoro-tert-butoxy)aluminate in place of the previously studied BArF64 anion. Several routes to perfluoroalkyl arene ligands are explored and evaluated, as is the use of different lengths of alkyl spacer to insulate the ligand binding site from the strong electron withdrawing effects of the perfluoroalkyl moiety. This process lead to the synthesis of the new complexes [(m-(3-(perfluorooctyl)-propyl)n-benzene)manganesetricarbonyl] hexafluorophosphate for n =1-3. These compounds are soluble in the fluorous phase despite their charge. The use of the m-(3-(perfluorooctyl)-propyl)n-benzene ligand to solubilise complexes of rhenium and rhodium was also attempted. The addition of methyl groups to the ring was explored as a route to additional steric bulk and a more electron rich, strongly binding ligand. In addition to arenes, the fluorous tagging of other ligand systems was also investigated, including cyclopentadienyl and tris(1-pyrazolyl)methane.

The standard preparation of valuable chemical compounds often exploits reactions that are plagued by suboptimal yields and a considerable amount of toxic waste, especially when it comes to asymmetric synthesis and metal catalysts. In the quest to achieve cleaner processes, enzymes are compelling alternatives; these natural devices offer "green" and efficient reactions. Furthermore, they are generally very enantioselective yielding optically pure products. Enzymes however have also many drawbacks: they especially suffer when forced to work under non-physiological conditions. A solution could be to exploit extremophile organisms, which are naturally adapted to work in “extreme” environments, as sources of new biocatalysts. Among the various classes of enzymes, aminotransferases (EC 2.6.1) are particularly interesting, since these biocatalysts are able to catalyze the amino transfer between two molecules, a reaction particularly difficult to perform with traditional synthetic approaches. An aminotransferase from Halomonas elongata (HEWT), a halotolerant organism, was isolated and characterized to verify its ability to work in the presence of organic solvents. Despite a broad substrate scope, HEWT was poorly active against ketones under standard condition. The investigation of the stereoelectronic effects of the reactions through a series of rationally engineered variants, led to a better understanding of the residues in the active pocket but produced only minimal improvement in activity. HEWT was therfore evolved towards the desired substrates applying iterative cycles of mutagenesis and screening to select the ameliorated protein. The development of an efficient high-throughput screening allowed isolation novel mutants with enhanced activity towards substituted acetophenones and small aliphatic ketones, with up to 60-fold improvement in the enzyme reactivity against para-CN-acetophenone. Furthermore, HEWT stability and tolerance were improved through protein immobilization, which showed excellent results especially in the presence of solvents. The methodology adopted was further developed by installing a protein spacer to preserve the integrity of the enzyme and prevent the significant loss of activity upon non-specific covalent linking. Immobilised HEWT was then applied in continuous flow biotransformations for the efficient production and isolation of amines. This cutting-edge approach showed about one order of magnitude higher synthetic efficiency with respect to batch processes and opened new avenues for the efficient application of enzymes in biotechnology.

This thesis primarily concerns the development of new tools and reactions through the activation of chemical moieties to generate either function, as protein labels or the synthetically valuable sulfonyl azides, or unusual chemical reactivity. Chapter 1 contains a brief introduction to the concept of Click Chemistry, with an overview of the nature of Click Chemistry reactions and their corresponding applications. Chapter 2 focusses on the use of diazirines, high energy but remarkably stable functionality as tools to probe protein structure. A protein footprinting technique has been developed employing aromatic based diazirine photoactive labels to decorate the protein surface. Following analysis by mass spectrometry, information could be inferred regarding the binding site of an Ub-IsoT ZnF protein complex. In addition, a range of diazirine probes of varying steric and electronic demands have been synthesised and their labelling properties characterised. The recently developed SuFEx activation has been applied in Chapter 3, with the development of a protocol for formation of sulfonyl azides from the robust sulfonyl fluorides. The methodology was extended to an in situ diazo transfer reaction, which circumvents the requirement to handle the potentially unstable diazo transfer reagent. Additionally, it was the pursuit of a novel mode of activation for the azide-alkyne cycloaddition, which generated a serendipitous result that led to the results in Chapter 4. Radical cation activation led to a selection of reactive intermediates that engaged in unusual chemistry.

Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(工学) / 甲第16875号 / 工博第3596号 / 新制||工||1543(附属図書館) / 29550 / 京都大学大学院工学研究科分子工学専攻 / (主査)教授 佐藤 啓文, 教授 田中 一義, 教授 梶 弘典 / 学位規則第4条第1項該当