No description available.

The overall efficiency of organic photovoltaics cells (OPVs) is influenced by the nature of the charge injection barrier at the transparent conducting oxide (TCO) bottom contact. Modification of the transparent conducting oxide (TCO)/organic interface with an electroactive molecular monolayer will potentially create a robust ohmic contact that will influence the efficiency of hole injection into the TCO. Asymmetric zinc Phthalocyanines (ZnPc) with a flexible phosphonic acid (PA) linker have been synthesized and used to modify indium tin oxide (ITO) surfaces. The adsorption of PA functionalized asymmetric ZnPcs on an ITO/waveguide was monitored using attenuated total reflectance (ATR) spectroscopy. Polarized dependent ATR spectroscopy was used to determine the orientation of these absorbed subpopulations species on ITO modified surfaces as a function of wavelength using transverse electric (TE) or transverse magnetic (TM) polarized light. The first oxidation potential on absorbed monolayers was found by cyclic voltammetry to be resolved into two peaks indicative of two electrochemically distinct subpopulations of molecules, atributed to aggregates and monomerics forms of PA functionalized ZnPcs. Potential modulated ATR (PM-ATR) spectroelechtrochemistry was employed to measure the charge transfer rates constants (k(s,app)) at ITO modified surfaces using TE and TM polarized light. Faster charge transfer rate constants were found for molecules with a smaller tunneling distance. A k(s,app) of 3.9 x 10⁴ s⁻¹ represents the fastest rate measured for PA functionalized ZnPc chromophore tethered to an ITO waveguide electrode by PM-ATR. We synthesized and characterized the first examples of PA functionalized RuPcs to investigate the effect of molecular orientation on charge transfer properties at an ITO/organic interface. PA functionalized RuPcs have the ability to coordinate axial ligand to suppress aggregation, providing the flexibility of connecting the anchoring group through the axial position of the metal and allowing chemisorption of the molecule in plane with ITO. Cyclic voltammetry and ATR UV/vis spectroscopy on the modified ITO surface demonstrated a surface composition of a closed-packed monolayer of monomeric species. Measurement of the charge transfer rates constants demonstrated that RuPc anchored to ITO exhibited slow rates compared to corresponding surface bound ZnPcs. Finally, we describe the synthesis and characterization of a new PA functionalized N-pyridinyl perylenediimide (PDI)-RuPc donor-acceptor dyad capable of chemisorption to ITO surfaces as a molecular-level heterojunction system to study photo induced charge separated states. The developed ensemble was proven to be stable on ITO for further study of charge injection events from the dyad to the oxide surface.

No description available.

Submitted in fulfilment of the requirements of Master's Degree in Chemistry, Durban University of Technology, 2017. / DNA damage plays a pivotal role in the pathogenesis of Alzheimer’s disease (AD) therefore, an innovative ss-DNA/dopamine/TiO2/FTO electrode strategy was developed to detect the genotoxicity upon photocatalytic reactions. This study involves a computational and electrochemical investigation towards the direct measurement of DNA damage. Computational chemistry was useful to resolve the intricate chemistry problems behind electrode constructions. The computational protocols were simultaneously carried out comprising of density functional theory (DFT) calculations, Metropolis Monte Carlo (MC) adsorption studies, and molecular dynamics (MD) simulations. The DFT calculations elucidated the structural, electronics, and vibrational properties of the electrode components resulting in a good agreement with the experimental parameters. The MC simulations carried out using simulated annealing predicted the adsorption process within layer-by-layer electrode as well generating reliable inputs prior to MD simulations. A 100 ns MD simulations were performed using a canonical ensemble provided information on the thermodynamics parameters such as total energy, temperature, and potential energy profiles, including radius of gyrations and atomic density profiles. Binding energies calculated from the MD trajectories revealed increasing interaction energies for the layer-by-layer electrode, in agreement with the electrochemical characterization studies (i.e. gradual decrease of cyclic voltammogram (CV) as well as increasing diameter of electrochemical impedance spectroscopy (EIS) semicircle upon electrode modification). The higher binding energies may lead to smaller changes in the electrochemical polarizability which directly affect to the decreasing of redox peak current and charge transfer resistance enhancement. Instead, HOMO-LUMO DFT levels are also taken into account to explain electron transfer phenomena within layer construction leading to the alteration of CV behaviours. Experimentally, the ss-DNA was electronically linked to TiO2/FTO surface through dopamine as a molecular anchor. Electrochemical measurements using cyclic voltammetry and EIS were employed to characterize the electrode modifications. The square wave voltammetry was subsequently used to measure the DNA damage and the potency of antioxidant treatment using ascorbic acid (AA) due to its ability in protecting the DNA from the damages. The presence of AA significantly protected the DNA from the damage, therefore was able to be used as a potential treatment in AD. Theoretically, guanine residues predicted by DFT as the most reactive sites of the ss-DNA involved in the genotoxic reactions. Overall, the theoretical studies successfully validated the experimental study as well as providing the molecular basis of interaction phenomena towards electrode constructions. Our results highlight the potential application of this methodology to screen the genotoxicity in Alzheimer’s, suggesting the important role of theoretical studies to predict the molecular interaction and validation of the DNA-based sensors and bioelectronics. / M

Although semi-empirical quantum codes have existed for several years now, the computational chemistry has, by and large, remained the subject of major interest for organic chemists and quantum chemists. In this thesis numerous exercises are designed in order to explore various areas of chemical engineering where these quantum chemical software might be successfully utilized. In this sense, the following attempt is a feasibility study to bring these semi-empirical quantum codes to the attention of the chemical engineering community. / M.S.

Submitted in fulfillment of the requirements of the Degree of Doctor of Technology: Chemistry, Durban University of Technology, 2011. / Understanding the dynamics and mechanism of protein folding continues to be one of the central problems in molecular biology. Peptide folding experiments characterize the dynamics and molecular mechanisms of the early events of protein folding. However, generally the highly flexible nature of peptides makes their bioactive conformation assessment reasonably difficult as peptides fold at very fast rates experimentally, requiring probing on the nanosecond time resolution. On the other hand, determining the bioactive conformation of biological peptides is a requirement for the design of peptidomimetics in computer-aided drug design. Peptides offer a unique opportunity to bridge the gap between theoretical and experimental understanding of protein folding. Therefore, the present work focuses on the exploration of the conformational space of biologically active neuropeptides with the aim of characterizing their conformational profile. Specifically, bombesin, neuromedin B (NMB) and neuromedin C (NMC), have been chosen for the current investigations. These peptides are widely distributed in the gastrointestinal tract, spinal cord and brain, and are known to elicit various physiological effects, including inhibition of feeding, smooth muscle contraction, exocrine and endocrine secretions, thermoregulation, blood pressure and sucrose regulations and cell growth. These peptides act as a growth factor in a wide range of tumours including carcinomas of the pancreas, stomach, breast, prostate, and colon. This work is intended to get some insight into the performance of different procedures used to explore the configurational space to provide an adequate atomic description of these systems. Different methodological studies involving utilization of molecular dynamics (MD), multicanonical replica exchange molecular dynamics (REMD) and simulate annealing (SA) are undertaken to explore the folding characteristics and thermodynamics of these neuropeptides. MD and REMD calculations on bombesin peptide have revealed its dual conformational behaviour never discovered before and is described in chapter 3. These results explain the known structure-activity studies and open the door to the understanding of the affinity of this peptide to two different receptors: BB1 and BB2. In the case of NMC, REMD calculations are carried out in explicit and implicit solvents, using the Generalized Born (GB) surface area, and are then complemented with two additional MD simulations performed using Langevin and Berendsen thermostats. The results obtained clearly reveal that REMD, performed under explicit solvent conditions, is more efficient and samples preferentially folded conformations with a higher content of  and γ turns. Moreover, these results show good agreement with the experimental results supporting the role of two -turns for its biological action, as reported in the literature. Finally, the results obtained from MD, REMD and SA calculations on NMB reveal that the peptide has a tendency to adopt both turns and helices suggesting its two different receptor recognizing and binding conformations during its biological action. Hence, the present work provides comprehensive information about the conformational preferences of neuropeptides which could lead to a better understanding of their native conformations for future investigations and point the way towards developing their new antagonists.

Lee Ho-Lam. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2003. / Includes bibliographical references (leaves 71-72). / Abstracts in English and Chinese. / Abstract --- p.i / Acknowledgements --- p.iii / Table of Contents --- p.iv / List of Tables --- p.vi / List of Figures --- p.vii / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- The Gaussian´ؤ3 Method --- p.1 / Chapter 1.2 --- "The G2++, a Modified Gaussian-2 Method" --- p.2 / Chapter 1.3 --- Density Functional Theory (DFT) --- p.2 / Chapter 1.4 --- Calculation of Thermodynamical Data --- p.3 / Chapter 1.5 --- Remark on the Location of Equilibrium and Transition Structures --- p.3 / Chapter 1.6 --- Natural Bond Orbital (NBO) Analysis --- p.3 / Chapter 1.7 --- Scope of the Thesis --- p.4 / Chapter 1.8 --- References --- p.4 / Chapter Chapter 2 --- Structures and Energetics of C3H6S+´Ø Isomers: A Gaussian-3 ab initio Study --- p.6 / Chapter 2.1 --- Introduction --- p.7 / Chapter 2.2 --- Methods of Calculation --- p.8 / Chapter 2.3 --- Results and Discussion --- p.8 / Chapter 2.4 --- Conclusion --- p.21 / Chapter 2.5 --- Publication Note --- p.21 / Chapter 2.6 --- References --- p.22 / Chapter Chapter 3 --- A Gaussian-3 Study of the C3H6S Isomers and the Dissociation Channels of Diradical ´ØCH2CH2SCH2´Ø and Its Radical Cation ´ØCH2CH2SCH2+ --- p.24 / Chapter 3.1 --- Introduction --- p.24 / Chapter 3.2 --- Methods of Calculation --- p.25 / Chapter 3.3 --- Results and Discussion --- p.26 / Chapter 3.3.1 --- Structures and Energetics of C3H6S Isomers --- p.26 / Chapter 3.3.2 --- Dissociation Channels of ´ØCH2CH2SCH2´Ø and ´ØCH2CH2SCH2+ --- p.34 / Chapter 3.4 --- Conclusion --- p.40 / Chapter 3.5 --- Publication Note --- p.41 / Chapter 3.6 --- References --- p.41 / Chapter Chapter 4 --- Computational Study on the Electrocyclic Reactions of [16]Annulene --- p.43 / Chapter 4.1 --- Introduction --- p.43 / Chapter 4.2 --- Methods of Calculation --- p.45 / Chapter 4.3 --- Results and Discussion --- p.45 / Chapter 4.3.1 --- Reaction (1) --- p.49 / Chapter 4.3.2 --- Reaction (2) --- p.50 / Chapter 4.3.3 --- Reaction (3) --- p.52 / Chapter 4.3.4 --- Overall Reaction --- p.53 / Chapter 4.4 --- Conclusion --- p.54 / Chapter 4.5 --- Publication Note --- p.55 / Chapter 4.6 --- References --- p.55 / Chapter Chapter 5 --- Computational Study on the Structures and Stabilities of Some Hypothetical Silicon Nanotubes --- p.57 / Chapter 5.1 --- Introduction --- p.57 / Chapter 5.2 --- Model Design and Methods of Calculation --- p.59 / Chapter 5.3 --- Results and Discussion --- p.59 / Chapter 5.3.1 --- "Armchair (n,n) SiNTs" --- p.60 / Chapter 5.3.2 --- "Zigzag (n,0) SiNTs" --- p.61 / Chapter 5.3.3 --- "Chiral (n,m) SiNTs" --- p.65 / Chapter 5.3.4 --- Stabilities of SiNTs at Elevated Temperature --- p.69 / Chapter 5.4 --- Conclusion --- p.70 / Chapter 5.5 --- References --- p.71 / Chapter Chapter 6 --- Conclusion --- p.73 / Appendix A --- p.74 / Appendix B --- p.76 / Appendix C --- p.77

A necessity of managing scientific data is the ability to maintain experimental legacy information without continually modifying the applications that create and use that information. By facilitating the management of scientific data we hope to give scientists the ability to effectively use additional modeling applications and experimental data. We have demonstrated that an extensible interpreter, using a series of stored directives, allows the loading of data from computational chemistry applications into a generic database. Extending the interpreter to support a new application involves supplying a list of directives for each piece of information to be loaded. This research confirms that an extensible interpreter can be used to load computational chemistry experimental data into a generic database. This procedure may be applicable to the loading and retrieving of other types of experimental data without requiring modifications of the loading and retrieving applications.

PhD (Chemistry) / Department of Chemistry

Helices in proteins have substantial permanent dipole moments arising from the nearly perfect alignment of the individual dipole moments of each peptide bond. Interaction with this helix "macrodipole" is thought to perturb the pKa values of basic or acidic residues at the helix termini. The goal of this project is to investigate the effect of the helix confonnation on the proton affinities ofbasic amino acids placed at theN- or Ctenninus of helical model peptides in the gas phase. Several series of model peptides having a basic residue, lysine (K) or 2,3- diaminopropionic acid (Dap ), located at either terminus were synthesized by solid phase peptide synthesis using conventional techniques or the amino acid fluoride approach. Proton affinities were determined for several basic amino acids and peptides using mass spectrometry by applying the extended Cooks' kinetic method. Favorable conformations and theoretical proton affinities were probed using computational chemistry. The proton affinities determined for Na-acetyl-(L)-lysine, Ac-AK, Ac-KA, and Ac-KAA are 236.8 ± 1.9 kcal mol-1 , 249.4 ± 2.0 kcal mol-1 , 241.5 ± 1.9 kcal mol-1 , and 244.4 ± 2.0 kcal mol-1 respectively. The large negative entropy changes for each of the peptides upon protonation ( -11.2 to - 21.7 cal mol-1 K- 1 ) are consistent with globular confmmations adopted by the protonated peptides due to extensive intramolecular hydrogen bonding. The measured proton affinities of the peptides increased with the size of the peptide as expected. However, the measured proton affinity of the peptide with C-terminal lysine, Ac-AK, is substantially higher than that of the con·esponding peptide with N-terrninal lysine, Ac-KA, contrary to expectations. Proton affinities determined for these compounds using computational chemistry are in reasonable agreement with experimental results. Additionally, proton affinities calculated for helical polyalanine and Aib (aaminoisobutytic acid) modified polyalanine peptides with C-terminal basic residues (Ac AnK and Ac-(AibA)n-Dap) are much larger than proton affinities calculated for the corresponding peptides with N-terminal basic residues. These results indicate that the helix dipole has a substantial effect on the basicity of residues at the helix termini.