Дисертації з теми "Theoreical and Computational Chemistry"
Оформте джерело за APA, MLA, Chicago, Harvard та іншими стилями
Ознайомтеся з топ-50 дисертацій для дослідження на тему "Theoreical and Computational Chemistry".
Біля кожної праці в переліку літератури доступна кнопка «Додати до бібліографії». Скористайтеся нею – і ми автоматично оформимо бібліографічне посилання на обрану працю в потрібному вам стилі цитування: APA, MLA, «Гарвард», «Чикаго», «Ванкувер» тощо.
Також ви можете завантажити повний текст наукової публікації у форматі «.pdf» та прочитати онлайн анотацію до роботи, якщо відповідні параметри наявні в метаданих.
Переглядайте дисертації для різних дисциплін та оформлюйте правильно вашу бібліографію.
Belding, Stephen Richard. "Computational electrochemistry." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:e997642f-fbaa-469c-98a3-f359b0996f03.
Повний текст джерелаDinescu, Adriana Cundari Thomas R. "Metals in chemistry and biology computational chemistry studies /." [Denton, Tex.] : University of North Texas, 2007. http://digital.library.unt.edu/permalink/meta-dc-3678.
Повний текст джерелаDinescu, Adriana. "Metals in Chemistry and Biology: Computational Chemistry Studies." Thesis, University of North Texas, 2007. https://digital.library.unt.edu/ark:/67531/metadc3678/.
Повний текст джерелаLathey, Daniel Craig. "Fluorescence prediction through computational chemistry." Huntington, WV : [Marshall University Libraries], 2005. http://www.marshall.edu/etd/descript.asp?ref=522.
Повний текст джерелаRajarathinam, Kayathri. "Nutraceuticals based computational medicinal chemistry." Licentiate thesis, KTH, Teoretisk kemi och biologi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-122681.
Повний текст джерелаQC 20130531
Brookes, Benjamin A. "Computational electrochemistry." Thesis, University of Oxford, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.270000.
Повний текст джерелаBertolani, Steve James. "Computational Methods for Modeling Enzymes." Thesis, University of California, Davis, 2019. http://pqdtopen.proquest.com/#viewpdf?dispub=10928544.
Повний текст джерелаEnzymes play a crucial role in modern biotechnology, industry, food processing and medical applications. Since their first discovered industrial use, man has attempted to discover new enzymes from Nature to catalyze different chemical reactions. In modern times, with the advent of computational methods, protein structure solutions, protein sequencing and DNA synthesis methods, we now have the tools to enable new approaches to rational enzyme engineering. With an enzyme structure in hand, a researcher may run an in silico experiment to sample different amino acids in the active site in order to identify new combinations which likely stabilize a transition-state-enzyme model. A suggested mutation can then be encoded into the desired enzyme gene, ordered, synthesized and tested. Although this truly astonishing feat of engineering and modern biotechnology allows the redesign of existing enzymes to acquire a new substrate specificity, it still requires a large amount of time, capital and technical capabilities.
Concurrently, while making strides in computational protein design, the cost of sequencing DNA plummeted after the turn of the century. With the reduced cost of sequencing, the number of sequences in public databases of naturally occurring proteins has grown exponentially. This new, large source of information can be utilized to enable rational enzyme design, as long as it can be coupled with accurate modeling of the protein sequences.
This work first describes a novel approach to reengineering enzymes (Genome Enzyme Orthologue Mining; GEO) that utilizes the vast amount of protein sequences in modern databases along with extensive computation modeling and achieves comparable results to the state-of-the-art rational enzyme design methods. Then, inspired by the success of this new method and aware of it's reliance on the accuracy of the protein models, we created a computational benchmark to both measure the accuracy of our models as well as improve it by encoding additional information about the structure, derived from mechanistic studies (Catalytic Geometry constraints; CG). Lastly, we use the improved accuracy method to automatically model hundreds of putative enzymes sequences and dock substrates into them to extract important features that are then used to inform experiments and design. This is used to reengineer a ribonucleotide reductase to catalyze a aldehyde deformylating oxygenase reaction.
These chapters advance the field of rational enzyme engineering, by providing a novel technique that may enable efficient routes to rationally design enzymes for reactions of interest. These chapters also advance the field of homology modeling, in the specific domain in which the researcher is modeling an enzyme with a known chemical reaction. Lastly, these chapters and techniques lead to an example which utilizes highly accurate computational models to create features which can help guide the rational design of enzyme catalysts.
Funes, Ardoiz Ignacio. "Computational Chemistry for Homogeneous Redox Catalysis." Doctoral thesis, Universitat Rovira i Virgili, 2017. http://hdl.handle.net/10803/456826.
Повний текст джерелаEsta Tesis Doctoral se ha centrado en el estudio computacional mediante metodología DFT (Teoría del funcional de la densidad) de reacciones redox catalizadas en fase homogénea. La primera parte versa sobre el estudio computacional de dos ciclos catalíticos de acoplamiento oxidativo. Este estudio dio con una de las claves en este tipo de reacciones, el efecto del oxidante externo. Demostramos en ambas reacciones como diferentes metales de transición podían colaborar para dar una reacción más eficiente y selectiva. Además descubrimos las claves para la regioselectividad en ambas reacciones. La segunda reacción fue estudiada en colaboración con el grupo experimental del profesor Frederic Patureau (University of Kaiserslautern). Por otro lado, la segunda parte de esta tesis se centra en el estudio teórico de la reacción de oxidación de agua catalizada por complejos de la primera serie de transición. Desarrollamos una nueva familia de catalizadores mononucleares de cobre con la colaboración experimental del grupo del profesor Antoni Llobet (ICIQ), descubriendo un nuevo mecanismo en la formación de enlace oxígeno-oxígeno, el ataque nucleófilo del agua mediante la transferencia de un electrón (SET-WNA). Tras esto extendimos este mecanismo a otros sistemas de cobre y de rutenio, redefiniendo el contexto mecanístico para esta reacción en catálisis homogénea. Esta tesis, por tanto, proporciona una profunda base mecanística sobre el estudio de importantes reacciones redox mediante química computacional a través de los métodos DFT.
This Doctoral Thesis is focused on the computational study by DFT methodology (Density Functional Theory) of homogeneous redox catalized reactions. The first part describes successfully the mechanism of two different catalytic cycles of oxidative coupling reactions. This study found out the explanation about one of the challenging questions on the field, the key role of the external oxidant. We demonstrated the cooperation between different transition metals is essential to catalyze the reaction efficiently and with good selectivities. Additionally, we explained also the regioselectivity of both reactions, in very good agreement with the experimental results. The second reaction was studied in collaboration with the experimental group of professor Frederic Patureau (University of Kaiserslautern). On the other hand, the second part of the thesis is focused on the theoretical study of water oxidation reaction catalyzed by first-row transition metal complexes. Firstly, we developed a new family of mononuclear copper complexes in collaboration with the experimental group of professor Antoni Llobet (ICIQ), discovering a new mechanism for the oxygen-oxygen bond formation step, the water nucleophilic attack. single electron transfer (SET-WNA). From this point, we extended the new mechanism to other catalytic systems based on copper and ruthenium, redefining the mechanistic scenario for the homogeneous catalytic version of this reaction. Therefore, this thesis provides a deep theoretical knowledge abour the homogeneous redox catalysis mechanisms by DFT calculations.
Sykes, Adam. "High-throughput computational chemistry of macromolecules." Thesis, University of Liverpool, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.507497.
Повний текст джерелаTassell, M. J. "Computational investigations of molecular actinide chemistry." Thesis, University College London (University of London), 2013. http://discovery.ucl.ac.uk/1386659/.
Повний текст джерелаVeloz, González Tomás Igor. "A Computational Study of Algebraic Chemistry." Tesis, Universidad de Chile, 2010. http://repositorio.uchile.cl/handle/2250/102300.
Повний текст джерелаBattersby, Paul. "Modelling supercritical fluid extraction using computational chemistry." Thesis, Northumbria University, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.245390.
Повний текст джерелаDavies, Richard Andrew. "Theoretical and computational aspects of organic chemistry." Thesis, Bangor University, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285502.
Повний текст джерелаDavin, Thomas J. "Computational chemistry of organometallic and inorganic species." Thesis, University of Glasgow, 2009. http://theses.gla.ac.uk/925/.
Повний текст джерелаWallace, Lynda Ann. "Computational aspects of ylide and dipole chemistry." Thesis, Queen's University Belfast, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.335620.
Повний текст джерелаAmini, Ata. "Computational chemistry as applied to electron transfer." Thesis, University of Newcastle Upon Tyne, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.397288.
Повний текст джерелаKervazo, Sophie. "Computational actinide chemistry : structure, bonding and thermodynamics." Thesis, Lille 1, 2018. http://www.theses.fr/2018LIL1R042/document.
Повний текст джерелаThe main question of this thesis is: do we have today the tools to efficiently describe the structure, the bonding and the thermodynamics of actinide systems? This broad question is answered thanks to three studies. The first two are directly applied to the plastic industry and the nuclear plant safety. The last one, more fundamental, concerns the benchmarking of newly developed theoretical approach on f-element systems.First, actinides and transition metal arene-coordinated alkyl cations have been recently proven to be efficient catalysts for ethylene polymerizations. Interestingly, thorium, uranium and zirconium alkyl cations’ catalytic activity depends on the solvent. To understand these behaviors and to confirm the tendency of these complexes to engage in unusual-arene coordination, relativistic DFT calculations combined with a characterization of the interaction thanks to the ETS-NOCV method are used. Second, in accident scenario along the reprocessing of spent nuclear fuel, plutonium can be released in various volatile forms (PuO2, PuO3 or PuO2(OH)2, …). The exploration of these scenarios by the use of simulations requires, among the various parameters, the knowledge of the thermodynamic properties of the possibly formed elements. Our in-silico study focusses on the determination of the enthalpies of formation of the former two species for which experimental uncertainties remain, using multi-configurational relativistic wavefunction method. The last part of the thesis focusses on the benchmark of the B2-PLYP functional for f-element systems, which turns out quite accurate with respect to the experimental data and the gold-standard CCSD(T) method
Skylaris, Chris-Kriton. "The computational modelling of heavy atom chemistry." Thesis, University of Cambridge, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.624478.
Повний текст джерелаSteiger, Don. "Numerical n-body methods in computational chemistry /." free to MU campus, to others for purchase, 1998. http://wwwlib.umi.com/cr/mo/fullcit?p9924930.
Повний текст джерелаFosso-Tande, Jacob. "A Computational Chemistry Study of Spin Traps." Digital Commons @ East Tennessee State University, 2007. https://dc.etsu.edu/etd/2127.
Повний текст джерелаGeremia, Kara L. "Computational Estimation of the pKa's of Purines and Related Compounds." Wright State University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=wright1449754930.
Повний текст джерелаMenshykau, Dzianis. "Computational electrochemistry." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:64e553c7-1bd2-429d-a5de-aeb4a29fc067.
Повний текст джерелаMartin, William R. "Computational Investigation of the Prothrombinase Complex." Cleveland State University / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=csu1544528008896018.
Повний текст джерелаSmith, Kevin J. "Computational approaches to fragment based screening." Thesis, University of Essex, 2016. http://repository.essex.ac.uk/17574/.
Повний текст джерелаCutress, Ian James. "Algorithm development in computational electrochemistry." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:a1cfb510-3656-4396-84b3-8e67b88d3d2f.
Повний текст джерелаMintz, Benjamin Wilson Angela K. "Reducing the computational cost of Ab Initio methods." [Denton, Tex.] : University of North Texas, 2008. http://digital.library.unt.edu/permalink/meta-dc-9061.
Повний текст джерелаRishard, Mohamed Zuhair Mohamed. "Spectroscopic and theoretical investigation of selected cyclic and bicyclic molecules in their ground and excited electronic states." [College Station, Tex. : Texas A&M University, 2007. http://hdl.handle.net/1969.1/ETD-TAMU-2030.
Повний текст джерелаSkone, Gwyn S. "Stratagems for effective function evaluation in computational chemistry." Thesis, University of Oxford, 2010. http://ora.ox.ac.uk/objects/uuid:8843465b-3e5f-45d9-a973-3b27949407ef.
Повний текст джерелаBosson, Maël. "Adaptive algorithms for computational chemistry and interactive modeling." Phd thesis, Université de Grenoble, 2012. http://tel.archives-ouvertes.fr/tel-00846458.
Повний текст джерелаBuendía-Atencio, Cristian, and Vaneza Lorett-Velásquez. "Climate change and computational chemistry: a molecular perspective." Revista de Química, 2017. http://repositorio.pucp.edu.pe/index/handle/123456789/123961.
Повний текст джерелаThe urgent need to understand the frequent negative changes that the planet Earth suffer on its soil, rivers and atmosphere and the need to mitigate climate change makes computational chemistry stand out as a branch of chemistry that allows thestudy and prediction of different physicochemical properties of several complex molecular systems of environmental significance which are sometimes impossible to study in a laboratory. The present article shows a molecular overview of the behavior and physicochemical characteristics of some atmospheric pollutants studied through computational chemistry.
Stenta, Marco <1979>. "Computational models in organic and bio-organic chemistry." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2008. http://amsdottorato.unibo.it/1069/1/Tesi_Stenta_Marco.pdf.
Повний текст джерелаStenta, Marco <1979>. "Computational models in organic and bio-organic chemistry." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2008. http://amsdottorato.unibo.it/1069/.
Повний текст джерелаBanerjee, S. "Computational insights into proton and hydride transfer chemistry." Thesis(Ph.D.), CSIR-National Chemical Laboratory, Pune, 2022. http://dspace.ncl.res.in:8080/xmlui/handle/20.500.12252/6090.
Повний текст джерелаCSIR
AcSIR
Oeffner, Robert Daniel. "A computational study of germanium dioxide." Thesis, University of Cambridge, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368372.
Повний текст джерелаHernandez, Eduardo Rafael Robert. "Computational studies of diffusion in zeolites." Thesis, University College London (University of London), 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.337925.
Повний текст джерелаChannon, Yvonne Mary. "Computational modelling of heulandite-type zeolites." Thesis, Keele University, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.389603.
Повний текст джерелаTang, Changguo. "Computational dynamics of classical nuclear spins in solids." Thesis, Massachusetts Institute of Technology, 1990. http://hdl.handle.net/1721.1/13597.
Повний текст джерелаBorin, Veniamin Aleksandrovich. "A Computational Study of Diiodomethane Photoisomerization." Bowling Green State University / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1477581227858711.
Повний текст джерелаCASALI, EMANUELE. "COMPUTATIONAL CHEMISTRY: a useful art to support asymmetric organic synthesis and organometallic chemistry." Doctoral thesis, Università degli studi di Pavia, 2022. http://hdl.handle.net/11571/1450083.
Повний текст джерелаThis thesis, as a conclusion of the three years of the Ph.D. course, reports the four topics that most significantly characterized the research. The first chapter concerns the computational study of the reasons behind the unexpected stereochemical output during the desymmetrization reaction of a meso-compound. Then, it continues with the research done at the University of Oxford, using Machine Learning to guide the design of new organic catalysts. The third chapter aims to understand the mechanism of ligand exchange on titanocene derivatives, which will then be suitably functionalized by bioorthogonal chemistry for imaging purposes and as possible anticancer agents. Finally, another mechanistic study on Fe-porphyrin catalysts has allowed to highlight the small details that regulate the cyclopropanation process and how the catalyst environment close to the metal center can further reduce the activation energies of the processes in a sort of enzyme-like behavior.
Turzo, SM Bargeen Alam. "Computational Investigation of Protein Assemblies." Cleveland State University / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=csu1532714714406789.
Повний текст джерелаSponseller, Daniel Ray. "Molecular Dynamics Study of Polymers and Atomic Clusters." Thesis, George Mason University, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10685723.
Повний текст джерелаThis dissertation contains investigations based on Molecular Dynamics (MD) of a variety of systems, from small atomic clusters to polymers in solution and in their condensed phases. The overall research is divided in three parts. First, I tested a new thermostat in the literature on the thermal equilibration of a small cluster of Lennard-Jones (LJ) atoms. The proposed thermostat is a Hamiltonian thermostat based on a logarithmic oscillator with the outstanding property that the mean value of its kinetic energy is constant independent of the mass and energy. I inspected several weak-coupling interaction models between the LJ cluster and the logarithmic oscillator in 3D. In all cases I show that this coupling gives rise to a kinetic motion of the cluster center of mass without transferring kinetic energy to the interatomic vibrations. This is a failure of the published thermostat because the temperature of the cluster is mainly due to vibrations in small atomic clusters This logarithmic oscillator cannot be used to thermostat any atomic or molecular system, small or large.
The second part of the dissertation is the investigation of the inherent structure of the polymer polyethylene glycol (PEG) solvated in three different solvents: water, water with 4% ethanol, and ethyl acetate. PEG with molecular weight of 2000 Da (PEG2000) is a polymer with many applications from industrial manufacturing to medicine that in bulk is a paste. However, its structure in very dilute solutions deserved a thorough study, important for the onset of aggregation with other polymer chains. I introduced a modification to the GROMOS 54A7 force field parameters for modeling PEG2000 and ethyl acetate. Both force fields are new and have now been incorporated into the database of known residues in the molecular dynamics package Gromacs. This research required numerous high performance computing MD simulations in the ARGO cluster of GMU for systems with about 100,000 solvent molecules. My findings show that PEG2000 in water acquires a ball-like structure without encapsulating solvent molecules. In addition, no hydrogen bonds were formed. In water with 4% ethanol, PEG2000 acquires also a ball-like structure but the polymer ends fluctuate folding outward and onward, although the general shape is still a compact ball-like structure.
In contrast, PEG2000 in ethyl acetate is quite elongated, as a very flexible spaghetti that forms kinks that unfold to give rise to folds and kinks in other positions along the polymer length. The behavior resembles an ideal polymer in a &thetas; solvent. A Principal Component Analysis (PCA) of the minima composing the inherent structure evidences the presence of two distinct groups of ball-like structures of PEG2000 in water and water with 4% ethanol. These groups give a definite signature to the solvated structure of PEG2000 in these two solvents. In contrast, PCA reveals several groups of avoided states for PEG2000 in ethyl acetate that disqualify the possibility of being an ideal polymer in a &thetas; solvent.
The third part of the dissertation is a work in progress, where I investigate the condensed phase of PEG2000 and study the interface between the condensed phase and the three different solvents under study. With a strategy of combining NPT MD simulations at different temperatures and pressures, PEG 2000 condensed phase displays the experimental density within a 1% discrepancy at 300 K and 1 atm. This is a very encouraging result on this ongoing project.
Tsai, Carol Leanne. "Heuristic Algorithms for Agnostically Identifying the Globally Stable and Competitive Metastable Morphologies of Block Copolymer Melts." Thesis, University of California, Santa Barbara, 2019. http://pqdtopen.proquest.com/#viewpdf?dispub=13423067.
Повний текст джерелаBlock copolymers are composed of chemically distinct polymer chains that can be covalently linked in a variety of sequences and architectures. They are ubiquitous as ingredients of consumer products and also have applications in advanced plastics, drug delivery, advanced membranes, and next generation nano-lithographic patterning. The wide spectrum of possible block copolymer applications is a consequence of block copolymer self-assembly into periodic, meso-scale morphologies as a function of varying block composition and architecture in both melt and solution states, and the broad spectrum of physical properties that such mesophases afford.
Materials exploration and discovery has traditionally been pursued through an iterative process between experimental and theoretical/computational collaborations. This process is often implemented in a trial-and-error fashion, and from the computational perspective of generating phase diagrams, usually requires some existing knowledge about the competitive phases for a given system. Self-Consistent Field Theory (SCFT) simulations have proven to be both qualitatively and quantitatively accurate in the determination, or forward mapping, of block copolymer phases of a given system. However, it is possible to miss candidates. This is because SCFT simulations are highly dependent on their initial configurations, and the ability to map phase diagrams requires a priori knowledge of what the competing candidate morphologies are. The unguided search for the stable phase of a block copolymer of a given composition and architecture is a problem of global optimization. SCFT by itself is a local optimization method, so we can combine it with population-based heuristic algorithms geared at global optimization to facilitate forward mapping. In this dissertation, we discuss the development of two such methods: Genetic Algorithm + SCFT (GA-SCFT) and Particle Swarm Optimization + SCFT (PSO-SCFT). Both methods allow a population of configurations to explore the space associated with the numerous states accessible to a block copolymer of a given composition and architecture.
GA-SCFT is a real-space method in which a population of SCFT field configurations “evolves” over time. This is achieved by initializing the population randomly, allowing the configurations to relax to local basins of attraction using SCFT simulations, then selecting fit members (lower free energy structures) to recombine their fields and undergo mutations to generate a new “generation” of structures that iterate through this process. We present results from benchmark testing of this GA-SCFT technique on the canonical AB diblock copolymer melt, for which the theoretical phase diagram has long been established. The GA-SCFT algorithm successfully predicts many of the conventional mesophases from random initial conditions in large, 3-dimensional simulation cells, including hexagonally-packed cylinders, BCC-packed spheres, and lamellae, over a broad composition range and weak to moderate segregation strength. However, the GA-SCFT method is currently not effective at discovery of network phases, such as the Double-Gyroid (GYR) structure.
PSO-SCFT is a reciprocal space approach in which Fourier components of SCFT fields near the principal shell are manipulated. Effectively, PSO-SCFT facilitates the search through a space of reciprocal-space SCFT seeds which yield a variety of morphologies. Using intensive free energy as a fitness metric by which to compare these morphologies, the PSO-SCFT methodology allows us to agnostically identify low-lying competitive and stable morphologies. We present results for applying PSO-SCFT to conformationally symmetric diblock copolymers and a miktoarm star polymer, AB4, which offers a rich variety of competing sphere structures. Unlike the GA-SCFT method we previously presented, PSO-SCFT successfully predicts the double gyroid morphology in the AB-diblock. Furthermore, PSO-SCFT successfully recovers the A 15 morphology at a composition where it is expected to be stable in the miktoarm system, as well as several competitive metastable candidates, and a new sphere morphology belonging to the hexagonal space group 191, which has not been seen before in polymer systems. Thus, we believe the PSO-SCFT method provides a promising platform for screening for competitive structures in a given block copolymer system.
Allis, Damian Gregory Spencer James T. Hudson Bruce S. "Computational quantum chemistry in initial designs and final analyses." Related electronic resource: Current Research at SU : database of SU dissertations, recent titles available full text, 2004. http://wwwlib.umi.com/cr/syr/main.
Повний текст джерелаSwett, Rebecca Jane. "Computational approaches to anti-toxin therapies and biomarker identification." Thesis, Wayne State University, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3601751.
Повний текст джерелаThis work describes the fundamental study of two bacterial toxins with computational methods, the rational design of a potent inhibitor using molecular dynamics, as well as the development of two bioinformatic methods for mining genomic data. Clostridium difficile is an opportunistic bacillus which produces two large glucosylating toxins. These toxins, TcdA and TcdB cause severe intestinal damage. As Clostridium difficile harbors considerable antibiotic resistance, one treatment strategy is to prevent the tissue damage that the toxins cause. The catalytic glucosyltransferase domain of TcdA and TcdB was studied using molecular dynamics in the presence of both a protein-protein binding partner and several substrates. These experiments were combined with lead optimization techniques to create a potent irreversible inhibitor which protects 95% of cells in vitro. Dynamics studies on a TcdB cysteine protease domain were performed to an allosteric communication pathway. Comparative analysis of the static and dynamic properties of the TcdA and TcdB glucosyltransferase domains were carried out to determine the basis for the differential lethality of these toxins. Large scale biological data is readily available in the post-genomic era, but it can be difficult to effectively use that data. Two bioinformatics methods were developed to process whole-genome data. Software was developed to return all genes containing a motif in single genome. This provides a list of genes which may be within the same regulatory network or targeted by a specific DNA binding factor. A second bioinformatic method was created to link the data from genome-wide association studies (GWAS) to specific genes. GWAS studies are frequently subjected to statistical analysis, but mutations are rarely investigated structurally. HyDn-SNP-S allows a researcher to find mutations in a gene that correlate to a GWAS studied phenotype. Across human DNA polymerases, this resulted in strongly predictive haplotypes for breast and prostate cancer. Molecular dynamics applied to DNA Polymerase Lambda suggested a structural explanation for the decrease in polymerase fidelity with that mutant. When applied to Histone Deacetylases, mutations were found that alter substrate binding, and post-translational modification.
Zhao, Hailiang. "Computational study of the boron-nitrogen dative bond." Thesis, Stellenbosch : Stellenbosch University, 2008. http://hdl.handle.net/10019.1/2846.
Повний текст джерелаIn this study, ten selected boron-nitrogen compounds and three borane carbonyl complexes were investigated by a number of computational methods. It is well known that the B-N dative bond is shorter in the solid state than in the gas phase. The B-CO distance, on the other hand, displays the opposite effect. Quantum mechanical techniques at the Hartree-Fock, Møller-Plesset second-order and Density Functional Theory level were used to calculate the geometries of the isolated molecules and to compare them with those found in molecular clusters built to model the solid state. It was found that calculated geometries were very sensitive to the choice of the basis set. The effects of dipole-dipole interactions were further investigated by applying an external electric field with varying strength to isolated molecules, and by replacing the central molecule in a cluster with a different compound. The B-N bond was found to respond much more to the applied field than the B-CO bond. An effort was made to correlate the lengthening or shortening of the dative bond to the strength of the crystal field, the latter being calculated classically from point charges. Unfortunately, large differences were noted between the charges calculated with common methods like Mulliken or Merz-Kollman-Singh. Furthermore, an analysis of 67 crystal structures taken from the Cambridge Structural Database did not reveal a correlation between the length of the B-N bond and the crystal field calculated with Charge Equilibration charges. Finally, a valence force field was developed for H3N-BH3. It was shown that a much better fit of the vibrational spectrum can be obtained if the B-N stretching mode is assigned to the 603 cm-1 band rather than the peak observed at 968 cm-1.
Maddox, Michael William. "Theoretical and computational studies of fluid mixtures." Thesis, University of Oxford, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.316880.
Повний текст джерелаValladares, Renela Maria. "Computational and experimental studies of organic systems." Thesis, University of Oxford, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.320651.
Повний текст джерелаSmith, Andrew. "The cationic Heck reaction : a computational study." Thesis, University of Warwick, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.369388.
Повний текст джерелаCherry, Michael. "Computational studies of perovskite-structured ion conductors." Thesis, University of Surrey, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.308631.
Повний текст джерелаWang, Nuo. "Computational Studies on Biomolecular Diffusion and Electrostatics." Thesis, University of California, San Diego, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=3731932.
Повний текст джерелаAs human understandings of physics, chemistry and biology converge and the development of computers proceeds, computational chemistry or computational biophysics has become a substantial field of research. It serves to explore the fundamentals of life and also has extended applications in the field of medicine. Among the many aspects of computational chemistry, this Ph. D. work focuses on the numerical methods for studying diffusion and electrostatics of biomolecules at the nanoscale. Diffusion and electrostatics are two independent subjects in terms of their physics, but closely related in applications. In living cells, the mechanism of diffusion powers a ligand to move towards its binding target. And electrostatic forces between the ligand and the target or the ligand and the environment guide the direction of the diffusion, the correct binding orientation and, together with other molecular forces, ensure the stability of the bound complex. More abstractly, diffusion describes the stochastic manner biomolecules move on their energy landscape and electrostatic forces are a major contributor to the shape of the energy landscape. This Ph. D. work aims to acquire a good understanding of both biomolecular diffusion and electrostatics and how the two are used together in numerical calculations. Three projects are presented. The first project is a proof of concept of the bead-model approach to calculate the diffusion tensor. The second project is the benchmark for a new electrostatics method, the size-modified Poisson-Boltzmann equation. The third project is an application that combines diffusion and electrostatics to calculate the substrate channeling efficiency between the human thymidylate synthase and dihydrofolate reductase.