Synthesis and anion photoelectron spectroscopy studies of oxyluciferins and oxyinfraluciferins

Firefly bioluminescence occurs by the enzyme catalysed oxidation of D-luciferin to oxyluciferin in its electronically excited by a luciferase in the presence of ATP, Mg2+ and O2 co-factors. Relaxation to its ground state results in the emission of a photon of light. The wavelength of light emission can be altered by mutating the luciferase and/or synthesising analogues of luciferin. In the Anderson group, a synthetic π-extended analogue of luciferin, infraluciferin, was synthesised and exhibited a significant red shifted emission, but was ~ 100 times dimmer than D-luciferin. An understanding of the excited state dynamics of the light emitter oxyluciferin in vacuo may help to design better bioluminescent systems for analytical applications. Part one describes the results of anion photoelectron spectroscopy measurements employed to determine the electronic structure of oxyluciferin in vacuo. These were interpreted with the aid of quantum chemistry calculations performed by another PhD student. Oxyluciferin can exist in three anionic resonance forms (keto, enol and enolate). To track the dynamics of these different species, the known protected derivatives, which trap the resonance forms, were synthesised from the literature and their photoelectron measurements were recorded between wavelengths 359 – 294 nm. The excited state dynamics of the analogues were unravelled by linking spectral features with the calculated excited state energies. Part two describes the synthesis of three protected π-extended resonance forms of oxyinfraluciferin and preliminary photoelectron measurements of the keto and enolate derivatives recorded at 346 nm. The synthesis features two unique cyclisation strategies to form the keto and acetyl-protected enolate derivatives. The acetyl-protected enolate derivative was successfully deacetylated in situ before running photoelectron measurements. Preliminary analysis of the 346 nm photoelectron spectra of keto and enolate derivatives provides a good starting point for future detailed spectroscopic investigations on understanding how increasing the conjugation affects the electronic structure and dynamics relative to their oxyluciferyl derivatives

Progress of Surface Science Studies on ABX(3)-Based Metal Halide Perovskite Solar Cells

ABX(3) type metal halide perovskite solar cells (PSCs) have shown efficiencies over 25%, rocketing toward their theoretical limit. To gain the full potential of PSCs relies on the understanding of the device working mechanisms and recombination, the material quality, and the match of energy levels in the device stacks. In this review, the importance of designing PSCs from the viewpoint of surface/interface science studies is presented. For this purpose, recent case studies are discussed to demonstrate how probing of local heterogeneities (e.g., grains, grain boundaries, atomic structure, etc.) in perovskites by surface science techniques can help correlate material properties and PSC device performance. At the solar cell device level with active areas larger than millimeter scale, the ensemble average measurement techniques can characterize the overall average properties of perovskite films as well as their adjacent layers and provide clues to understand better the solar cell parameters. How generation and healing of electronic defects in perovskite films limit the device efficiency, reproducibility, and stability, and induce the time-dependent transient behavior in the current-voltage curves are also the central focus of this review. On the basis of these studies, strategies to further improve efficiency and stability, as well as reducing hysteresis are presented

N,N-Diaryl Dihydrophenazine photoredox catalysis for organocatalyzed atom transfer radical polymerization

2019 Summer.Includes bibliographical references.The synthesis, application, and mechanistic investigation of the 5,10-diaryldihydrophenazine catalyst family as applied to organocatalyzed atom transfer radical polymerization is presented in this dissertation. The N,N-Diaryl Dihydrophenazine catalyst family, which will be referred to in this dissertation as the phenazines, are an appealing class of molecules due to their strongly reducing excited states, accessed through modular syntheses enabling a wide range of photophysical and electrochemical properties. This class of molecules represented the first example of organic catalysts capable of operating a controlled, visible light driven, organocatalyzed atom transfer radical polymerization for the precision syntheses of (meth)acrylic polymers. Phenazine catalysts were shown to polymerize (meth)acrylic monomers to polymers of very low dispersities (< 1.10) in a process with quantitative initiator efficiency; both features crucial to produce precision polymeric materials poised for myriad applications. Supported by computational efforts, mechanistic understanding and structure-property-catalyst activity relationships were identified and harnessed to design optimal polymerization conditions, which have laid the groundwork for new research efforts into highly reducing, visible light absorbing, organic photocatalysts

SPECTROSCOPY AND STRUCTURES OF Cu-ORGANONITROGEN COMPLEXES

Copper-organonitrogen complexes are studied by threshold photoionization and zero electron kinetic energy photoelectron spectroscopy. These complexes are prepared in pulsed laser vaporization supersonic molecular beams. Adiabatic ionization energies of the neutral species and vibrational frequencies of the neutral and ionic complexes were measured. Metal-ligand bond dissociation energies were obtained from the theoretical calculations or the experiments. More importantly, by combining the spectroscopic measurements, quantum chemical calculations, and spectral simulations, metal-ligand bonding structures are determined for copper complexes of diamines, pyridine, diazines, aminopyridines, polypyridines, and imidazole. The Cu-ethylenediamine, -(1,3-propanediamine), and -(1,4-butenediamine) complexes have been determined to be in a hydrogen-bond stabilized monodentate configuration. However, Cu atom binds to both two nitrogens in the methyl-substituted ethylenediamines. The change of the Cu binding from the monodentate to the bidentate mode arises from the competition between copper coordination and hydrogen bonding. Although pyridine, diazines, and imidazole molecules can function as a s-donor through the nitrogen atom, a p-acceptor or p-donor through six-membered or five-membered aromatic ring, only the s bonding mode is predicted by the theory and identified by the ZEKE spectroscopy. For aminopyridine molecules, s bonding through the sp2 or sp3 hybrid electron lone pair and p bonding through the pyridine ring are possible. Yet, the s bonding through the sp2 electron donation is calculated to be the strongest, and the Cuaminopyridine complexes formed by such bonding mechanism are identified by the experiments. Moreover, monodentate Cu-(4,4\u27-bipyridine), bidentate Cu-(2,2\u27-bipyridine) and Cu-(1,10-phenanthroline), and tridentate Cu-(2,2\u27:6\u27,2?-terpyridine) are established to be the most stable structure and are observed by experiments. It is surprising to find that the tridendate planar structure of Cu-(2,2\u27:6\u27,2?-terpyridine) changes to a twisted Cs structure upon ionization

The synthesis and characterisations of metallo-beta-amino alcohol complexes

The ligands N,N‟-bis(2-hydroxycyclohexyl)-1,3-propanediamine (Cy2-tn), and 2,2‟-[(hydroxypropane-1,3-diyl)diimino]dicyclohexanol, (Cy2-Otn) and were synthesised and their solid state structures determined by X-ray diffraction experiments. Complexes were formed with the metal ions Pb(II), Cd(II), Ni(II), Cu(II) and Zn(II). The solid state structures of the Ni(II), Zn(II) and Cd(II) complex of Cy2-tn were determined by X-ray diffraction studies. The solid state structures of both the ligands, and their polymorphs, as well as the Cy2-tn/metal complexes mentioned, indicated the presence of hydrogen-hydrogen bonds between hydrogens on the cyclohexenyl rings and hydrogens on the propyl bridge. DFT calculations (X3LYP/6-31G(d,p))were performed on the Cy2-tn free ligand, the Cy2-tn Ni(II), Cu(II) and Zn(II) complexes, and on the ligand N,N‟-bis(2-hydroxycyclohexyl)-trans-cyclohexane-1,2- diamine (TCA) with Cu(II). The wavefunction files generated were used to study topolygical properties of the electron density using Bader‟s Quantum Theory of Atoms in Molecules (QTAIM). The resulting molecular graphs showed there were bond paths between hydrogen atoms on the cyclohexenyl rings in the TCA/Cu complex, but not in the Cy2-tn free ligand or the Cy2-tn/metal complexes. The DFT calculation also indicated that the L-M bonds are ionic with some covalent character, while the M-N bonds are suggested to be stronger, and more covalent in character than the M-O bonds. The slightly shared electron density character in the M-L bonds is seen by the charge on the metal ions being less than the formal 2+ charge. Potentiometric studies were performed on the Cy2-Otn ligand, and the complexes with Cu(II), Ni(II), Zn(II), Cd(II) and Pb(II). The protonation constant determination of the Cy2-Otn ligand resulted in pKa1 = 8.73 and a pKa2 = 7.31, however an impurity was present that was not seen in the characterisations. The Cy2-Otn/Cd and Pb(II) systems showed precipitation and were not analysed, while the Cy2-Otn/Zn system gave poor data. The Cy2-Otn/Cu system showed M(LH), ML and ML(OH) species present, whilst the Cy2-Otn/Ni system showed the presence of M(LH), ML, ML(OH), and ML(OH)2 species. The stability constants of the Cy2-Otn/metal ML species were compared to those previously reported for the Cy2-tn and Cy2-en ligands and their complexes with the metals studied

Theoretical studies of nitrilotriacetic acid and nitrilotripropionic acid geometries for estimation of the stability of metal complexes by Density Functional Theory

Nitrilotriacetic Acid (NTA) is an organic ligand which has been extensively studied due to its biological significance and excellent chelating properties. Nitrilotripropionic Acid (NTPA) is a ligand that is believed to possess similar properties to NTA, but has not been as extensively studied. It has been experimentally determined that metal complexes of NTA are orders of magnitude stronger than those formed with NTPA. This is surprising, especially considering that the ligands do not differ that much from each other. NTPA contains an additional –CH2– group in each of the acid containing arms as compared to NTA. The aim of these studies were to explain, theoretically, why this is the case. Analyses were conducted with a number of software programs including, Gaussian 03, Schrödinger Maestro and AIM 2000. All Density Functional Theory (DFT) studies were conducted in solvent at the RB3LYP/6-311+G(d,p) level of theory in conjunction with a number of different solvation models. En route to explaining why the complexes differ in stability a new methodology was utilized (isodesmic reactions) in which the four stepwise protonation constants of both NTA and NTPA were successfully predicted; in fact these were the most accurate values predicted to date by DFT methods. The final step of these studies focused on predicting stability constants of metal (Zn2+ and Ni2+) complexes of NTA and NTPA. These predictions were not as accurate as those achieved for the prediction of protonation constants; however, success was achieved in predicting the trend – complexes with NTA are orders of magnitude stronger than complexes formed with NTPA. The most important observation revealed that H–clashes and C–H∙∙∙O hydrogen bonds present in M(NTPA) complexes, which are not present in M(NTA) complexes, result in the formation of additional rings which contributes to the formation of a cage. It was discovered that the H-clashes present in the M(NTPA) complexes were contributing to the overall stability of the molecule. This is completely contradictory to a previous explanation in which H-clashes, being a result of steric crowding, resulted in destabilization of a complex. If the H-clashes were not present in the M(NTPA) complexes there would not be enough stabilizing factors present in the molecule which will inevitably result in the non-existence of M(NTPA) complexes. CopyrightDissertation (MSc)--University of Pretoria, 2010.Chemistryunrestricte

Theoretical Studies of the Growth and Functionality of Layered Materials

In this thesis, we present several projects on the growth and functionality of layered materials, using density functional theory (DFT) method and phenomenological modeling approach. Beyond the understanding of growth mechanisms and exploration of properties, we propose novel avenues to realize controllable growth processes and layered materials with desirable properties. The contents have three major parts: (1) Graphene growth on Cu(111) and Ni(111) substrates. We first demonstrate that the inherent multi-orientational degeneracy of the graphene islands on Cu(111) in the early stages of nucleation could result in the prevalence of grain boundaries (GBs). Next, we propose a possible solution to tackle this standing obstacle, by invoking a functionalized Cu(111) surface to lift the orientational degeneracy and consequently suppress the GBs. Following this work, we explore the contrasting mechanisms of graphene bilayer growth on Cu(111) and Ni(111), develop a phenomenological model to predict the critical graphene size for the nucleation of the second layer underneath, and propose ways to substantially enhance the growth rate of the second-layer graphene on Cu. (2) Contrasting alignment of hexagonal boron nitride (h-BN) and graphene grown on Cu(100). Collaborating with the experimental group, we find that the three-fold symmetric BN exhibits definitive orientation alignments when grown on the four fold-symmetric Cu(100) surface. This is in stark contrast to graphene/Cu(100) epitaxy, despite the crystallographic similarity between graphene and h-BN. Our results reveal that the stronger C-Cu interaction lead to the misalignment, a conclusion runs counter to the conventional wisdom that stronger epilayer-substrate interactions enhance orientational order. (3) Electronic and chemical properties of monolayer molybdenum disulfide (MoS2) on metal substrates. We investigate the properties of a single-layer MoS2 adsorbed on Ir(111), Pd(111), or Ru(0001). We find the contact nature is Schottky type, and the dependence of the barrier height on the work function exhibits a partial Fermi-level pinning picture. Using hydrogen adsorption as a testing example, we further demonstrate that the introduction of a metal substrate can substantially alter the chemical reactivity on the MoS2 planar surface

NOVEL AROMATIC ION–PAIRS: SYNERGY BETWEEN ELECTROSTATICS AND Π-FACE AROMATIC INTERACTIONS

This dissertation focuses on the design and study of charged aromatic molecules where weak π-π interactions synergize with electrostatic interactions to enhance the overall interaction between aromatic moieties. Each chapter investigates some aspect of this hypothetical synergy between electrostatics and π-face aromatic cohesion. The first chapter unveiled the importance of electrostatics in the intramolecular stacking of flexible aromatic molecular templates 1-2Br and 2a. While our previous studies found dicationic molecular template 1-2Br to have intramolecular π-stacking between electron poor pyridinium and electron rich xylylene moieties, no such stacking interaction was observed in the neutral analog 2a. Chapter two systematically explored the stacking pattern of electron poor aromatics in the form of oxygen- and / or nitrogen- substituted triangulenium cations, [1(NR)3]+ and [1(O)3(OH)3]+. As indicated in the chemical literature, triazatriangulenium cations [1(NR)3]+ with N- ethyl (and longer alkyl chains) chains were found to pack as face-to-face dimers. This study found the formation of columnar, face-to-face, n-meric association between aromatic cations in the structures with decreased steric interactions of the side chains in the stacking planes ([1(NMe)3]+ and [1(O)3(OH)3]+). Similar iso-structural triangulene based aromatic anions, (2)- and (3)2- didn’t indicate any facial interactions in the solid states. The possible synergy between unit charge electrostatics and π-face aromatic interactions was explored in aromatic ion pairs 1•2 of triangulene based aromatic cations and aromatic anions. This charge-assisted π-π stacking seems to be the novel way of getting strong π-system interactions where the strongest non-covalent force and the weakest non-covalent force: ionic bonding and π-stacking respectively synergize together. The π-π interaction between ionic aromatics in the solid state was investigated by means of single crystal x-ray diffraction and powder x-ray diffraction (PXRD). The interaction in the solution state was examined by UV-Vis spectroscopy, electrospray ionization mass spectroscopy (ESI-MS) and electrochemical studies. Studies found that optimal synergy was possible only in the ion pairs with no steric interactions of alkyl (or aryl) side chains in the stacking planes (1(O)3•2 & 1(NMe)3•2) and the interaction was found to be comparable with the strongest radical-assisted π-stacking described in the chemical literature