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Markovi, Z., JP Engelbrecht, and S. Markovi. "Theoretical Study of the Kolbe-Schmitt Reaction Mechanism." A Journal of Chemical Sciences, 2002. http://encore.tut.ac.za/iii/cpro/DigitalItemViewPage.external?sp=1002008.
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Abstract
A theoretical study of the Kolbe-Schmitt reaction mechanism, performed using a DFT method,
reveals that the reaction between sodium phenoxide and carbon dioxide proceedswith the formation
of three transition states and three intermediates. In the first step of the reaction, a polarized ONa
bond of sodium phenoxide is attacked by the carbon dioxide molecule, and the intermediate
NaPh-CO2 complex is formed. In the next step of the reaction the electrophilic carbon atom attacks
the ring primarily at the ortho position, thus forming two new intermediates. The final product,
sodium salicylate, is formed by a 1,3-proton shift from C to O atom. The mechanism agrees with
the experimental data related to the Kolbe-Schmitt reaction.
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Inagaki, Taichi. "Theoretical Study on Mechanism and Dynamics of Hydrogen Transfer Reaction." 京都大学 (Kyoto University), 2014. http://hdl.handle.net/2433/189341.
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Pérez, Gallegos Ayax. "Theoretical study on the mechanism of the reaction catalyzed by protein kinase." Doctoral thesis, Universitat Autònoma de Barcelona, 2016. http://hdl.handle.net/10803/386487.
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Malgrat el gran nombre d’estudis experimentals i computacionals sobre l’estructura i funció de les proteïnes quinases, els detalls exactes dels canvis estructurals i mecanístics dels passos individuals de la reacció catalítica de transferència del grup fosforil romanen incerts. En principi, els estudis computacionals poden subministrar informació minuciosa i una coneixença complementària al treball experimental, però aquest objectiu només es pot assolir si es fan servir els mètodes computacionals adequats i si el model teòric que s’utilitza representa correctament el sistema biològic.
En aquesta Tesi, el mètode QM/MM a nivell DFT/MM s’ha utilitzat per a descriure els diferents mecanismes de reacció sobre la hipersuperfície d’energia potencial de la reacció global de transferència del grup fosforil catalitzada per la Proteïna Quinasa A (PKA). Cal destacar, que a més d’utilitzar models complets i solvatats del sistema biomolecular i nivells de teoria més alts que en treballs anteriors, s’han fet servir també diferents tècniques i algoritmes inclosos en el codi ChemShell, a fi de millorar els càlculs dels camins de reacció i les optimitzacions d’estats estacionaris. En particular, coordenades de reacció més flexibles i el mètode microiteratiu per a localitzar estructures d’estats de transició ens han permès aplicar una metodologia multiescala consistent i fiable per a analitzar minuciosament tant el mecanisme associatiu (que implica la transferència de fosforil simultàniament amb la protonació del grup fosfat transferit) com el dissociatiu (que implica dues etapes: la transferència de fosforil i la protonació del substrat fosforilat) de la reacció de transferència de fosforil catalitzada per la PKA. S’ha prestat especial atenció a les funcions específiques dels residus Asp166, Lys168 i Thr201, al Gly-rich loop, als ions metàl·lics, i a la conformació i l’estat de protonació al llarg de la reacció química de la cadena lateral del substrat i del fosfat que es transfereix.
Els resultats d’aquesta Tesi han demostrat que la reacció catalitzada per la PKA no depèn del substrat i que el mecanisme dissociatiu és clarament favorable respecte el mecanisme associatiu. No obstant, els càlculs presentats també mostren que el mecanisme associatiu seria viable quan el dissociatiu està impedit, com amb el mutant D166A. Aquest punt reobre un debat sobre la viabilitat del mecanisme associatiu que semblava superat donat els darrers estudis teòrics. A més a més, els camins de reacció per a la retro-protonació del substrat fosforilat per part del residu Asp166 s’han localitzat, demostrant que Asp166 es comporta com un catalitzador àcid/base general al llarg del mecanisme dissociatiu. Per altra banda, els perfils d’energia potencial QM/MM calculats també demostren, per primera vegada, que la reacció catalítica de transferència de fosforil és viable amb ions metàl·lics alcalinoterris diferents del Mg2+, confirmant resultats experimentals recents que proposen el paper fisiològic del Ca2+ a l’activitat de les quinases. Tant pel mecanisme associatiu com pel dissociatiu, la localització precisa i l’orientació de la triada Asp166-Lys168-Thr201 i de la xarxa de ponts d’hidrogen que aquests residus estableixen al centre actiu, s’ha vist que són essencials per a la catàlisi i especialment per a l’estabilització de les estructures dels estats de transició involucrats.
Finalment, els resultats d’aquesta Tesi han proveït amb una seqüència completa de l’evolució geomètrica de l’estructura del complex ternari al llarg de la reacció catalítica. Això permet una comparació acurada amb les estructures de raigs-X cristal·logràfiques que han estat proposades experimentalment com a imatges moleculars del procés catalític de fosforilació. En particular, el bon acord entre les estructures teòriques i els estudis experimentals validen la visió atòmica de la reacció presentada en aquesta Tesi, revelant canvis conformacionals, de coordinació i dels ponts d’hidrogen que tenen lloc durant la recció química i la seva relació amb la dinàmica de l’enzim.<br>Despite extensive experimental and computational studies about the structure and function of kinases, exact details regarding the complex structural changes and the mechanistic details of individual stages involved in the catalyzed phosphoryl-transfer reaction remain uncertain. In principle, computational studies can provide detailed information and insights to complement experimental studies, but this goal can only be attained when the appropriate computational approaches are employed and the theoretical model used is a good mimic of the biological system.
In this Thesis, the QM/MM approach at the DFT/MM level of theory was used to describe the different reaction mechanisms on the potential energy hypersurface of the global phosphoryl-transfer reaction catalyzed by the Protein Kinase A (PKA). Remarkably, besides making use of more complete solvated models of the biomolecular system and higher levels of theory than the ones employed in previous works, several techniques and algorithms within the computational chemistry suite ChemShell were used to improve the accuracy of the reaction path calculations and stationary points optimizations. In particular, more flexible reaction coordinates, the location of the stationary points with the hybrid delocalized internal coordinates, and the microiterative method to locate transition structures allowed us to apply a consistent and reliable multiscale methodology to examine minutely both the associative (involving a concomitant phosphoryl-transfer and protonation of transferred phosphate) and dissociative (involving two steps: phosphoryl-transfer and back protonation of the phosphorylated substrate) mechanisms of the phosphoryl-transfer reaction catalyzed by PKA. Special attention was paid in the specific roles of the invariant residues Asp166, Lys168, and Thr201, the conserved Gly-rich loop, the metal ions, and the conformation and protonation state of the substrate residue side chain and transferred phosphate along the chemical reaction.
The results in this Thesis demonstrate that the catalytic reaction catalyzed by PKA is not substrate-dependent and that the dissociative mechanism is clearly more favorable than the associative one. Nevertheless, the presented calculations also show the plausibility of the associative reaction pathway when the dissociative counterpart is impeded as it is in the D166A mutant. This reopens the debate about the plausibility of the associative reaction pathway that in view of the last theoretical works in the field seemed to be overcame. Moreover, the reaction paths for the back protonation of the phosphorylated substrate by Asp166 have been located, so demonstrating that Asp166 behaves as a general acid/base catalyst along the dissociative mechanism. In addition, QM/MM potential energy profiles determined in this Thesis also demonstrate, for the first time, that the catalyzed phosphoryl-transfer is plausible with alkali earth metal ions other than Mg2+ ions, what confirms recent experimental results where the physiological role of Ca2+ in kinase activity has been proposed. For both the associative and the dissociative mechanisms, the precise location and orientation of the triad Asp166-Lys168-Thr201 and the hydrogen bond network these residues establish within the active site are shown to be essential for catalysis, particularly in the stabilization of the transition state structures involved.
Lastly, the results in this Thesis provide a complete sequence of the geometrical evolution of the structure of the ternary complex along the catalytic reaction. This permits an accurate comparison with new X-ray crystallographic structures that have been suggested as experimental snapshots of the catalyzed-phosphorylation process In particular, the good agreement between the theoretically determined structures and the crystallographic studies validate the atomic view of the reaction presented in this Thesis, thus revealing conformational, coordination, and hydrogen bond changes that occur during the chemical step and its relation with the enzyme dynamics.
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Moagi, Kgotso Herbet. "Reaction Mechanism of 2-monosubstituted Quinoxalines with Organolithium Compounds : a Theoretical Study." Diss., University of Pretoria, 2020. http://hdl.handle.net/2263/75182.
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This dissertation describes the density functional theory (DFT) computational modelling of reactions between organolithium nucleophiles and various substituted quinoxalines. These reactions result in the functionalisation of the C (sp2)–H bond, thus substituting the sigma-hydrogen. The reactions are known as nucleophilic substitution of hydrogen (SNH) and are used by experimental chemists to form new C–C bonds. The SNH reactions are very important in various industries, e.g. in designing and manufacturing of pharmaceuticals. Quinoxaline is widely used in medicinal chemistry due to its various biological activities; these reactions play a crucial role in the synthesis of new classes of compounds.
The reactions of 2-phenyl- (A), 2-butyl- (B), and 6-nitro-2-phenyl- (C) quinoxaline with lithiofuran (a) and lithiothiophene (b) involves a direct (1) nucleophilic attack on an activated electron-deficient system, leading to the intermediate sigma^H-complex. This is followed by hydrolysis (2), where an sp2-type nitrogen is changed to an sp3 while forming Li---OH as a by-product. The presence of Li---OH then allows the departure of an sigma-proton via oxidation reaction, concomitantly forming H2O2 as the second by-product. All approaches to functionalise the C(sp2)–H bond involve elimination of a proton, and an oxidant is needed for the departure of the sigma-hydrogen. Although the sequence of steps and mechanisms of these C–H transformations are the same, various factors have shown to affect the reactions differently.
The theoretical study of this catalytic-free transformation, shows that the formation of sigma^H-adducts is not easily reversible, and that their formation is spontaneous. The reaction does not just require an oxidant to eliminate the sigma-hydrogen with the pair of electrons, but rather requires the presence of water for hydrolysis prior to oxidation. We must stress the crucial role of the oxidant since the key problem of the SNH reactions is associated with the elimination of sigma-hydrogen. However, the main objective of this study is to present a correct and complete mechanistic picture of oxidative nucleophilic substitution of hydrogen (ONSH).
Previous reports indicated that the presence of an electron donating/withdrawing group on the quinoxaline ring had a significant influence on the yield and selectivity. This is between reactions A+a, A+b, and B+a. These experimental observations correlated well with the modelling results when the potential energy surfaces (PES) of the reactions were compared.<br>Dissertation (MSc)--University of Pretoria, 2020.<br>National Research Foundation (NRF)<br>Chemistry<br>MSc<br>Unrestricted
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Nowroozi-Isfahani, Taraneh. "Theoretical study on the mechanism of removing nitrogen oxides using isocyanic acid." [Johnson City, Tenn. : East Tennessee State University], 2001. http://etd-submit.etsu.edu/etd/theses/available/etd-0528101-112444/unrestricted/nowroozi0621.pdf.
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Jiménez, Halla José Óscar Carlos. "Theoretical study of catalytic reactions of carbenes: haptotropic rearrangements and the Dötz reaction." Doctoral thesis, Universitat de Girona, 2009. http://hdl.handle.net/10803/7942.
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En aquesta tesi s'han estudiat mecanismes de reaccions de cicloanulació en carbens de Fischer a través de mètodes teòrics, concretament fent servir el nivell de teoria B3LYP/(Wachters' basis / 6-31G**). Els alcoxi- i amino carbens de pentacarbonil crom, ja siguin vinílics o aromàtics, reaccionen amb acetilè per produir fenols, naftols o derivats ciclopentadiè o indè substituïts amb el Cr(CO)3 coordinat, d'una manera regioselectiva. L'objectiu d'aquest treball és discutir ambudes reaccions competitives particularment a la reacció de Dötz, la qual durant els darrers anys ha estat explorada experimentalment per W.D. Wulff, C.P. Casey, R. Aumann i J. Barluenga entre altres diferents propostes mecanístiques. A més K.H. Dötz va demostrar que la coordinació del Cr(CO)3, un cop l'anell ja està format, pot patir canvis haptotròpics, és a dir, la caminada del complex metàl·lic d'un anell a un altre -generalment almenys substituït- canviant la seva hapticitat (coordinació pi amb els membres de l'anell). Llavors, s'han estudiat les migracions haptotròpiques intramoleculars en petits hidrocarbons aromàtics policíclics amb l'objectiu d'analitzar les rutes de reacció per les quals aquestes reaccions es porten a terme
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Zhang, Tianhou. "Theoretical Studies of Fuel Cell Reaction Mechanisms: Water and Oxygen on Platinum Electrodes." Case Western Reserve University School of Graduate Studies / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=case1215456813.
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Tussupbayev, Samat. "Theoretical study of reactivity and dynamics of hybride-bridged diruthenium complexes and silylium." Doctoral thesis, Universitat de Girona, 2009. http://hdl.handle.net/10803/8052.
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Esta tesis presenta un estudio computacional de los sistemas con hidruros puente. En la primera parte se estudia la química de complejos de dirutenio con cuatro hidruros puente. Esto incluye las siguientes reacciones: el intercambio del hidruro con hidrógeno molecular; la activación del enlace C-H del etileno para formar el complejo de bis(vinilo)-etileno; el acoplamiento C-C entre el etileno coordinado y dos ligandos vinilo para producir el complejo rutenaciclopentadieno. Al final de esta parte, se discuten a detalle los mecanismos de estas reacciones. Además, se demostró la importancia de la flexibilidad de los ligandos hidruro y la cooperación entre los dos centros metálicos. <br/>En la segunda parte, se estudió el comportamiento fluxional de dos complejos μ-silileno y de un catión sililio. Con esto, se estableció la ruta más favorable en donde se realiza el intercambio de los ligandos hidruro y de los grupos metilo en los complejos μ-silileno. Finalmente, se encontró que hay dos posibles rutas relativas al cambio en la posición del puente Si-H-Si en el cation sililio poliagóstico, asociadas con la rotación interna de los grupos sililo.<br>The thesis presents a computational study of hydride bridged systems. The chemistry of diruthenium tetrahydride-bridged complex was studied in the first part. It includes the next reactions: the hydride exchange with dihydrogen; the C-H bond activation in ethylene to yield bis(vinyl) ethylene complex; the C-C coupling between coordinated ethy¬lene and two vinyl ligands to yield ruthenacyclopentadiene complex. The detailed mechanism of these reactions has been determined. The importance of flexibility of hydride ligands and cooperation between two metal centers has been demonstrated. <br/>The fluxional behavior of two μ-silylene complexes and a silylium cation was studied in the second part. The pathway responsible for the site-exchange of hydride ligands and methyl groups in the μ-silylene complexes has been established. Two possible mecha¬nisms of the shift of Si-H-Si bridge position in the polyagostic silylium cation, associated with internal rota¬tion of si¬lyl groups have been found.
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Fernández, Villanueva Estefanía. "Theoretical Study of the Geometrical, Electronic and Catalytic properties of Metal Clusters and Nanoparticles." Doctoral thesis, Universitat Politècnica de València, 2020. http://hdl.handle.net/10251/135277.
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[ES] Dado su tamaño subnanométrico, los clusters metálicos están regidos por el confinamiento cuántico, lo que les hace más "moleculares" y menos "metálicos". En consecuencia, manifiestan propiedades que difieren con respecto a las de partículas más grandes del mismo elemento, y que a menudo son ventajosas para la catálisis de reacciones específicas. Además, su menor tamaño los hace más económicos, con una mayor superficie expuesta. Todo ello hace que los clusters sean opciones muy interesantes en catálisis, y su estudio, síntesis y aplicación ha crecido continuamente desde su descubrimiento en los años 90.
Esta tesis se ha centrado principalmente en el cobre, del que se presenta, en primer lugar, un estudio fundamental sobre la disociación de oxígeno por clusters de diferentes tamaños. Después, se explora computacionalmente la catálisis de las oxidaciones de CO y propeno, confirmando que los clusters de Cu5 (o inferior) son prometedores para reacciones de oxidación. Las dos reacciones utilizadas son buenos ejemplos de la aplicación potencial en industria, sea para reducir emisiones de CO o para producir epóxido de propeno, que es un intermedio importante en la producción de plásticos y adhesivos, entre otros. Además, también se estudió la influencia de dos soportes en los clusters de cobre y su capacidad de oxidación: N-grafeno como un sistema más inerte y ceria como uno que puede participar activamente en reacciones de oxidación.
Finalmente, se incluyen otros dos estudios más específicos, sobre la capacidad de los clusters de Pt3 y Pd3 para catalizar reaciones de acoplamiento C-C como la reacción de Heck, importante para la síntesis de productos de la química fina, y sobre la reacción CO + NO en clusters de Pt, motivado por su uso potencial como catalizadores para la conversión de esas especies en los menos perjudiciales CO2 y N2 en motores de combustión interna.<br>[CAT] Atès que són de grandària subnanomètrica, els clusters metàl·lics estan regits pel confinament quàntic, el qual els fa més "moleculars" i menys "metàl·lics". En conseqüència, manifesten propietats que són diferents a les de partícules més grans del mateix element, i que sovint són avantatjoses per a la catàlisi de reaccions específiques. A més a més, la seua menor grandària fa que siguen més econòmics, amb una major superfície exposada. Així, els clusters són una opció molt interesant en catàlisi, i el seu estudi, síntesi i aplicació ha cres-cut contínuament des del seu descobriment als anys 90.
Aquesta tesi s'ha centrat principalment en el coure, del qual es presenta, en primer lloc, un estudi fonamental sobre la dissociació de l'oxígen per clusters de diferents grandàries. Després, s'explora computacionalment la catàlisi de les oxidacions de CO i de propè, confirmant que els clusters de Cu5 (o inferior) són prometedors per a reaccions d'oxidació. Les dues reaccions utilitzades són bons exemples de l'aplicació potencial en indústria, siga per reduir emissions de CO o per produir epòxid de propè, que és un intermedi important en la producció de plàstics i adhesius, entre altres. A més, també es va estudiar la influència de dos suports en els clusters de coure i la seua capacitat d'oxidació: N-grafè com a un sistema més inert i cèria com a un que pot participar activament en reaccions d'oxidació.
Finalment, s'inclouen altres dos estudis més específics, sobre la capacitat dels clusters de Pt3 y Pd3 per catalitzar reaccions d'acoblament C-C com la reacció de Heck, important per a la síntesi de productes de la química fina, i sobre la reacció CO + NO als clusters de Pt, motivat pel seu ús potencial com a catalitzadors per a la conversió d'eixes espècies en els menys perjudicials CO2 i N2 als motors de combustió interna.<br>[EN] Due to their subnanometric size, metal clusters belong to the regime affected by quantum confinement, which makes them more "molecular" and less "metallic". As a result, they exhibit properties that differ with respect to those of larger particles of the same element, and which are often advantageous in the catalysis of specific reactions. Besides, their smaller size makes them more economic and with a higher surface exposed. All of this renders metal clusters very interesting options for catalysis, and their study, synthesis and application has steadily increased since their discovery in the 90s.
In this work we have largely focused on copper, of which a fundamental study on the oxygen dissociation by clusters of different sizes is first presented. Then, the catalysis of the CO and propene oxidation reactions is theoretically explored, confirming that Cu5 (or smaller) clusters are promising systems for oxidation reactions. The two reactions used are good examples of the potential application in industry, either to reduce CO emissions or to produce propene epoxide, an important intermediate in the production of plastics and adhesives, among others. In addition, the influence of two supports in the copper clusters and their oxidation capability is explored: on N-graphene as a more inert system and on ceria as one that can actively participate in oxidation reactions.
Finally, two other more specific studies are included, regarding the capability of Pt3 and Pd3 clusters to undergo C-C coupling reactions such as the Heck reaction, important for the synthesis of many products of fine chemistry, and regarding the CO + NO reaction on Pt clusters, motivated by their potential use as catalysts for the conversion of those species in less harmful CO2 and N2 in internal combustion engines.<br>En primer lugar me gustaría agradecer al Ministerio de Economía y Competitividad
de España (MINECO) por la financiación de esta tesis mediante el programa Severo
Ochoa (SVP-2013-068146), incluyendo los costes adicionales de mi estancia de investigación (EEBB-I-17-12057).<br>Fernández Villanueva, E. (2019). Theoretical Study of the Geometrical, Electronic and Catalytic properties of Metal Clusters and Nanoparticles [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/135277<br>TESIS
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Acuña-Parés, Ferran. "Theoretical study of water oxidation and reduction mechanisms by aminopyridine first row transition metal catalysts." Doctoral thesis, Universitat de Girona, 2016. http://hdl.handle.net/10803/398411.
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One of the major current scientific goals is the development of renewable energy sources. An effective alternative to fossil fuels consists in the conversion of the sunlight energy into chemical fuels. The molecular hydrogen from water is considered the most promising energy carrier. In the natural photosynthesis the solar energy is stored into the carbohydrate chemical bonds derived from water and CO2. The key step of this process is the photo-oxidation of H2O molecules into O2, which provides the protons and electrons needed to produce H2. A detailed knowledge of the reaction mechanisms results essential to enhance the catalytic performance and to ensure the compatibility of the water oxidation and proton reduction catalysts. In this thesis, the key steps of the water oxidation and proton reduction reactions catalyzed by a group of metal complexes and the catalysts structural features that benefit both processes are studied using computational tools<br>Un dels grans reptes actuals consisteix en el desenvolupament de fonts d'energia renovables. Una alternativa eficaç als combustibles fòssils consisteix en la conversió de l'energia solar en combustibles químics. L’hidrogen molecular provinent de l’aigua és considerat el portador d’energia més prometador. En la fotosíntesi natural l’energia solar és emmagatzemada en els enllaços químics dels carbohidrats obtinguts a partir d’aigua i CO2. L’etapa clau del procés és la foto-oxidació de l'aigua en O2, que aporta els protons i electrons necessaris per produir H2. El coneixement detallat del mecanisme de reacció resulta essencial per millorar el rendiment catalític i assegurar la compatibilitat dels catalitzadors d’oxidació de l’aigua i reducció de protons. En aquesta tesi, les etapes fonamentals del mecanisme de les reaccions d’oxidació de l’aigua o la reducció de protons catalitzades per un grup de complexos metàl·lics i les característiques estructurals dels catalitzadors que beneficien ambdues reaccions són estudiades utilitzant eines computacionals
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Ishida, Toyokazu. "Theoretical Perspectives on the Reaction Mechanism of Serine Proteases." 京都大学 (Kyoto University), 2003. http://hdl.handle.net/2433/148355.
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Boumaraf, Latra. "Etude des réactions chimiques dans les ammoniacates solides : application du système BaCl2/NH3 à la réfrigération solaire." Grenoble INPG, 1989. http://www.theses.fr/1989INPG0026.
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Conception d'un dispositif experimental dans le but d'etudier les proprietes physiques et cinetiques des systemes bacl::(2)/nh::(3) et cacl::(2)/nh::(3). Mesures de vitesses de desorption et d'absorption. Modele d'optimisation des processus et experimentation d'un prototype de refrigeration a capteur solaire plan
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Markmann, Andreas. "Theoretical study of photoinduced reactions in ionic crystals mechanisms, energy dissipation and coherence effects." Thesis, University College London (University of London), 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.415331.
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Takahashi, Toshifumi. "Experimental and Theoretical Studies on Unique Reactivities of Nickel Catalysts." Doctoral thesis, Kyoto University, 2021. http://hdl.handle.net/2433/263674.
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Ha, Heon Phil. "An experimental and theoretical study of the peritectic reaction." Thesis, University of Oxford, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.298262.
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Morita, Akihiro. "Theoretical Study on Reaction Dynamics in Gas and Solution." 京都大学 (Kyoto University), 1995. http://hdl.handle.net/2433/160897.
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本文データは平成22年度国立国会図書館の学位論文(博士)のデジタル化実施により作成された画像ファイルを基にpdf変換したものである<br>Kyoto University (京都大学)<br>0048<br>新制・論文博士<br>博士(理学)<br>乙第8838号<br>論理博第1270号<br>新制||理||916(附属図書館)<br>UT51-95-D431<br>(主査)教授 加藤 重樹, 教授 廣田 襄, 教授 梶本 興亜<br>学位規則第4条第2項該当
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Georgieva, Polina. "Quantum Chemical Modeling of Enzymatic Methyl Transfer Reactions." Doctoral thesis, Stockholm : Bioteknologi, Kungliga Tekniska högskolan, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-9695.
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Gadea, Florent Xavier. "Theorie des hamiltoniens effectifs : applications aux problemes de diabatisation et de collision reactive." Toulouse 3, 1987. http://www.theses.fr/1987TOU30276.
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Etude approfondie sur la theorie des hamiltoniens effectifs et analyse de leurs applications aux methodes de diabatisation et au traitement des collisions reactives. Propositions pour le calcul des valeurs propres de l'hamiltonien par des methodes de perturbation ou iteratives, pour l'emploi d'hamiltoniens effectifs dans le calcul des surfaces quasi diabatiques et le traitement general des collisions reactives. Application a la reaction cs+h::(2) etudiee par les methodes ab initio pour la geometrie colineaire : surfaces de potentiel, sections efficaces et mecanismes predominants
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Xidos, James Dimitrios. "A theoretical study of stereoselectivity in the Diels-Alder reaction." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0015/NQ47505.pdf.
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Loewenberg, Michael Gavalas George R. "A theoretical study of reaction and diffusion in microstructured materials /." Diss., Pasadena, Calif. : California Institute of Technology, 1988. http://resolver.caltech.edu/CaltechETD:etd-06142006-135258.
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Loutchko, Dimitri. "A Theoretical Study of the Tryptophan Synthase Enzyme Reaction Network." Doctoral thesis, Humboldt-Universität zu Berlin, 2018. http://dx.doi.org/10.18452/19384.
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Das Enzym Tryptophan Synthase ist ein ausgezeichnetes Beispiel einer molekularen Fabrik auf der Nanoskala mit zwei katalytischen Zentren. Der katalytische Zyklus des Moleküls beruht zudem auf zahlreichen allosterischen Wechselwirkungen sowie der Übertragung des Intermediats Indol durch einen intramolekularen Tunnel. In dieser Arbeit wird das erste kinetische Modell eines einzelnen Tryptophan Synthase Moleküls konstruiert und analysiert. Simulationen zeigen starke Korrelationen zwischen den Zuständen der Katalysezentren sowie die Ausbildung von Synchronisation. Mit stochastischer Thermodynamik wird die experimentell unzugängliche Reaktionskonstante für die Rückübertragung des Indols aus Messdaten rekonstuiert. Methoden, die den Informationsaustausch in bipartiten Markovnetzwerken charakterisieren, werden auf beliebige Markovnetzwerke verallgemeinert und auf das Modell angewendet. Der abschließende Teil befasst sich mit chemischen Reaktionsnetzwerken von Metaboliten und Enzymen. Es werden algebraische Modelle (Halbgruppen) konstruiert, welche aufeinanderfolgende und simultane katalytische Funktionen von Enzymen und von Unternetzwerken erfassen. Diese Funktionen werden genutzt, um eine natürliche Dynamikum sowie hinreichende und notwendige Bedingungen für seine Selbsterhaltung zu formulieren.
Anschließend werden die algebraischen Modelle dazu genutzt, um eine Korrespondenz zwischen Halbgruppenkongruenzen und Skalenübergängen auf den Reaktionsnetzwerken herzustellen.
Insbesondere wird eine Art von Kongruenzen erörtert, welche dem Ausspuren der globalen Struktur des Netzwerkes unter vollständiger Beibehaltung seiner lokalen Komponenten entspicht. Während klassische Techniken eine bestimmte lokale Komponente fixieren und sämtliche Informationen über ihre Umgebung ausspuren, sind bei dem algebraischen Verfahren alle lokalen Komponenten zugleich sichtbar und eine Verknüpfung von Funktionen aus verschiedenen Komponenten ist problemlos möglich.<br>The channeling enzyme tryptophan synthase provides a paradigmatic example of a chemical nanomachine with two distinct catalytic subunits. It catalyzes the biosynthesis of tryptophan, whereby the catalytic activity in a subunit is enhanced or inhibited depending on the state of the other subunit, gates control the accessibility of the reactive sites and the intermediate product indole is directly channeled within the protein. The first single-molecule kinetic model of the enzyme is constructed. Simulations reveal strong correlations in the states of the active centers and the emergent synchronization. Thermodynamic data is used to calculate the rate constant for the reverse indole channeling. Using the fully reversible single-molecule model, the stochastic thermodynamics of the enzyme is closely examined. The current methods describing information exchange in bipartite systems are extended to arbitrary Markov networks and applied to the kinetic model. They allow the characterization of the information exchange between the subunits resulting from allosteric cross-regulations and channeling. The final part of this work is focused on chemical reaction networks of metabolites and enzymes. Algebraic semigroup models are constructed based on a formalism that emphasizes the catalytic function of reactants within the network. A correspondence between coarse-graining procedures and semigroup congruences respecting the functional structure is established. A family of congruences that leads to a rather unusual coarse-graining is analyzed: The network is covered with local patches in a way that the local information on the network is fully retained, but the environment of each patch is not resolved. Whereas classical coarse-graining procedures would fix a particular patch and delete information about the environment, the algebraic approach keeps the structure of all local patches and allows the interaction of functions within distinct patches.
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Gómez, Martínez Hansel. "Theoretical Study of the Catalytic Mechanism of Retaining Glycosyltransferases." Doctoral thesis, Universitat Autònoma de Barcelona, 2013. http://hdl.handle.net/10803/133280.
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Las Glicosiltransferasas (GTs) son las enzimas responsables de la síntesis de
glicanos, las moléculas orgánicas más abundantes en la naturaleza. Su relevancia
biológica hace necesario el conocimiento de su mecanismo catalítico, que es todavía
cuestión de debate en el caso de las GTs con retención de configuración.
La presente tesis doctoral se centra en el mecanismo catalítico de estas enzimas
desde un punto de vista computacional. Más específicamente, se realizó un estudio
utilizando aproximaciones de la Mecánica Cuántica y la Mecánica Molecular
(QM/MM) para tres GTs con retención de configuración: Lipopolisacaril-α-1,4-
galactosiltransferasa C de Neisseria meningitides (LgtC), α-1,3-galactosiltransferasa
bovina (α1,3-GalT) y UDP-N-acetilgalactosamina:polipeptido N-acetil-α-
galactosaminiltransferasa 2 humana (ppGalNAcT-2). Los diferentes mecanismos
catalíticos propuestos en la literatura son considerados y los factores responsables de
la eficiencia catalítica de las GTs con retención de configuración son analizados.<br>Glycosyltransferases (GTs) are responsible for glycans’ biosynthesis, the most
abundant organic molecules in nature. Their biological relevance makes necessary the
knowledge of their catalytic mechanism, which in the case of retaining GTs is still a
matter of debate.
The present thesis is focused on the catalytic mechanism of these enzymes
from the computational point of view. More specifically, a full-enzyme hybrid
quantum mechanics/molecular mechanics (QM/MM) study is performed for three
retaining GTs: Lipopolysaccharyl-α-1,4-galactosyltransferase C from Neisseria
meningitides (LgtC), bovine α-1,3-galactosyltransferase (α1,3-GalT) and human
UDP-N-acetylgalactosamine:polypeptide N-acetyl-α-galactosaminyltransferase 2
(ppGalNAcT-2). The different proposed mechanisms are considered and the factors
responsible for the catalytic efficiency of ret-GTs are analyzed.
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Gérard, Thomas. "Theoretical study of spatiotemporal dynamics resulting from reaction-diffusion-convection processes." Doctoral thesis, Universite Libre de Bruxelles, 2011. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/209861.
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Dans les réacteurs industriels ou dans la nature, l'écoulement de fluides peut être couplé à des réactions chimiques. Dans de nombreux cas, il en résulte l'apparition de structures complexes dont les propriétés dépendent entre autres de la géométrie du système.<p><p>Dans ce contexte, le but de notre thèse a été d'étudier de manière théorique et sur des modèles réaction-diffusion-convection simples les propriétés de dynamiques spatio-temporelles résultant du couplage chimie-hydrodynamique. <p>Nous nous sommes focalisés sur les instabilités hydrodynamiques de digitation visqueuse et de densité qui apparaissent respectivement lorsqu'un fluide dense est placé au-dessus d'un fluide moins dense dans le champ de gravité et lorsqu'un fluide visqueux est déplacé par un fluide moins visqueux dans un milieu poreux.<p><p>En particulier, nous avons étudié les problèmes suivants:<p>- L'influence d'une réaction chimique de type A + B → C sur la digitation visqueuse. Nous avons montré que les structures formées lors de cette instabilité varient selon que le réactif A est injecté dans le réactif B ou vice-versa si ces réactifs n'ont pas un coefficient de diffusion ou une concentration initiale identiques.<p>- Le rôle de pertes de chaleur par les parois du réacteur dans le cadre de la digitation de densité de fronts autocatalytiques exothermiques. Nous avons caractérisé les conditions de stabilité de fronts en fonction des pertes de chaleur et expliqué l'apparition de zones anormalement chaudes lors de cette instabilité.<p>- L'influence de l'inhomogénéité du milieu sur la digitation de densité de solutions réactives ou non. Nous avons montré que les variations spatiales de perméabilité d'un milieu poreux peuvent figer ou faire osciller la structure de digitation dans certaines conditions.<p>- L'influence d'un champ électrique transverse sur l'instabilité diffusive et la digitation de densité de fronts autocatalytiques. Il a été montré que cette interaction peut donner lieu à des nouvelles structures et changer les propriétés du front.<p><p>En conclusion, nous avons montré que le couplage entre réactions chimiques et mouvements hydrodynamiques est capable de générer de nouvelles structures spatio-temporelles dont les propriétés dépendent entre autres des conditions imposées au système.<p>/<p>In industrial reactors or in nature, fluid flows can be coupled to chemical reactions. In many cases, the result is the emergence of complex structures whose properties depend among others on the geometry of the system.<p>In this context, the purpose of our thesis was to study theoretically using simple models of reaction-diffusion-convection, the properties of dynamics resulting from the coupling between chemistry and hydrodynamics.<p><p>We focused on the hydrodynamic instabilities of viscous and density fingering that occur respectively when a dense fluid is placed above a less dense one in the gravity field and when a viscous fluid is displaced by a less viscous fluid in a porous medium.<p><p>In particular, we studied the following issues:<p>- The influence of a chemical reaction type A + B → C on viscous fingering. We have shown that the fingering patterns observed during this instability depends on whether the reactant A is injected into the reactant B or vice versa if they do not have identical diffusion coefficients or initial concentrations.<p>- The role of heat losses through the reactor walls on the density fingering of exothermic autocatalytic fronts. We have characterized the conditions of stability of fronts depending on heat losses and explained the appearance of unusually hot areas during this instability.<p>- The influence of the inhomogeneity of the medium on the density fingering of reactive solutions or not. We have shown that spatial variations of permeability of a porous medium may freeze or generate oscillating fingering pattern under certain conditions.<p>- The influence of a transverse electric field on the Rayleigh-Taylor and diffusive instabilities of autocatalytic fronts. It was shown that this interaction may lead to new structures and may change the properties of the front.<p><p>In conclusion, we showed that the coupling between chemical reactions and hydrodynamic motions can generate new space-time structures whose properties depend among others, on the conditions imposed on the system.<br>Doctorat en Sciences<br>info:eu-repo/semantics/nonPublished
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Asai, Yoshihiro. "A Theoretical Study on the Mechanism of the Vibronic Coupling." Kyoto University, 1986. http://hdl.handle.net/2433/74691.
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Crowley, J. N. "A study of reaction mechanism by matrix isolation / FTIR spectroscopy." Thesis, University of East Anglia, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.378892.
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Prat, Resina Xavier. "Study of the reaction mechanism in Mandelate racemase enzyme: reaction path and dynamical sampling approaches." Doctoral thesis, Universitat Autònoma de Barcelona, 2004. http://hdl.handle.net/10803/3175.
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En aquesta tesi s'ha dissenyat i aplicat diferents eines teòriques i computacionals per a l'estudi de la reactivitat de l'enzim Mandelat Racemasa.<br/>L'enzim Mandelat Racemasa catalitza la interconversió dels dos enantiòmers (S) i (R) de l'àcid mandèlic a una velocitat semblant. El mecanisme de reacció que es postula experimentalment passa per l'abstracció d'un protó molt poc àcid. Aquesta reacció molt poc favorable en medi aquós l'enzim la catalitza a una velocitat sorprenentment alta.<br/>Fent un estudi Mecànica Quàntica / Mecànica Molecular (QM/MM) de la reactivitat de l'enzim s'han trobat els intermedis i les barreres de reacció que permeten deduir tres mecanismes a través dels quals el substracte natural mandelat i altres dos substractes anàlegs poden racemitzar. Expliquem de quina manera l'enzim pot fer la catàlisi tant efectiva i equivalent per als dos enantiòmers.<br/>Partint de la necessitat de millorar l'estudi QM/MM anterior, sobretot pel què fa a l'acurada localització dels estats de transició (barreres reacció), s'ha dissenyat un mètode d'optimització d'estructures per ser aplicat a sistemes de milers d'àtoms com ho és el nostre enzim. <br/>El mètode anomenat micro-iteratiu es basa en una cerca segons les equacions Rational Function Optimization (RFO) en una zona reduida mentre es minimitza l'entorn amb un mètode computacionalment barat com el LBFGS. Aquest mètode micro-iteratiu ha estat formulat, implementat i testejat en sistemes moleculars grans i petits. Se n'ha estudiat les diferents opcions donant una recepta pràctica per al seu ús en altres reaccions. També se n'ha justificat el seu desenvolupament posant de relleu les millores obtingudes amb aquest nou mètode quan es comparen els nous resultats amb els obtinguts en l'estudi QM/MM inicial.<br/>Finalment, l'energia lliure de la reacció enzimàtica s'ha calculat amb tècniques de la dinàmica molecular i de l'Umbrella Sampling. Per aquest tipus de càlcul és imprescindible escollir a priori una coordenada de reacció que permeti anar de reactius a productes, en altres paraules, és necessari saber com té lloc la reacció. Gràcies a la prèvia localització d'estats de transició amb el mètode micro-iteratiu podem conèixer el mecanisme de reacció. I per tant podem emprar una coordenada de reacció adequada que ens permet calcular l'energia lliure de reacció de forma efectiva.<br>In this thesis several theoretical techniques to study the Mandelate Racemase enzyme reactivity are designed and used.<br/>The Mandelate Racemase enzyme catalyses the interconversion of both enantiomers (S) and (R) of mandelic acid at apparently the same rate. Experimental results suggest that the reaction mechanism takes place through the abstraction of a non-acid hydrogen. This reaction is very low in aqueous media but the enzyme catalyzes it at an extremely fast rate.<br/>We carry out a QM/MM study of the enzyme reativity. We have found the intermediate structures and the energy barriers corresponding to three proposed mechanisms that the natural substrate mandelate and two other substrate analogues may undergo. We are able to explain how the the efficient catalysis is performed for the two enantiomers.<br/>Due to the lack in the previous QM/MM study of an efficient method to locate transition state structures (energy barriers) we have designed an structure optimization method to be applied to systems constituted by thousands of atoms such as our enzyme.<br/>The so-called micro-iterative method consists in a search based on the Rational Function Optimization (RFO) equations applied in a core zone while the environment is minimized through a computationally affordable method such as LBFGS. The micro-iterative method has been formulated, implemented and tested for small and big molecular systems. We have studied several possible options giving as a result a practical guide for its usage in other reactions. Comparing the results coming from the initial QM/MM study with the ones found by this micro-iterative method we show an improvement that justifies the development.<br/>Finally, the free energy corresponding to the enzymatic reaction is calculated by means of Molecular Dynamics and Umbrella Sampling techniques. The free energy computation requires the a priori election of a reaction coordinate that allows the system to go from reactants to products. In other words, it is essential to know how the reaction takes place. Thanks to the accurate search of transition states performed previously by the micro-iterative we can find the reaction mechanism. In this sense we can use an adequate reaction coordinate that permits us an efficient calculation of the reaction free energy.
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Patterson, Nicky Paul. "Study of 28,27,26,25Ne and 29,28,27 Na isotpes via the single neutron knockout reaction reaction mechanism." Thesis, University of Surrey, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.529443.
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Miedzinska, K. M. E. (Katarzyna Malgorzata Ewa) Carleton University Dissertation Chemistry. "A study of the redox mechanism of exchanged zeolites." Ottawa, 1985.
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Ina, Toshiaki. "Study on Cathodic Reaction Mechanism of All Solid State Electrochemical Devices." Kyoto University, 2012. http://hdl.handle.net/2433/157658.
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Kyoto University (京都大学)<br>0048<br>新制・課程博士<br>博士(人間・環境学)<br>甲第16947号<br>人博第590号<br>新制||人||141(附属図書館)<br>23||人博||590(吉田南総合図書館)<br>29622<br>京都大学大学院人間・環境学研究科相関環境学専攻<br>(主査)教授 内本 喜晴, 教授 杉山 雅人, 教授 田部 勢津久, 准教授 藤原 直樹, 准教授 雨澤 浩史<br>学位規則第4条第1項該当
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Eyles, Chris J. "An experimental and theoretical study of the dynamics of atom-molecule scattering." Thesis, University of Oxford, 2010. http://ora.ox.ac.uk/objects/uuid:d887db09-915e-4b3b-80e0-e9f1684518db.
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In this thesis, a joint experimental and theoretical study of the dynamics of atom- molecule collisions will be presented. The focus of this study will be conducted towards the precise, quantitative theoretical description of the collision dynamics in terms of the vectors <strong>k</strong>, <strong>k'</strong>, <strong>j</strong>, and <strong>j'</strong> (the incoming and outgoing relative momenta associated with the collision, and the initial and final rotational angular momentum of the target diatom respectively) that define the collision, and on the experimental measurement of these vector correlations. Chapter 1 is introductory, providing an overview of the field of reaction dynamics, and the experimental and theoretical methods that exist to treat the collisions of atoms and molecules. This work focusses on the collisions of the spherically symmetric rare gas atoms Ar and He with the open-shell heteronuclear diatomic radicals NO and OH. In particular, the fully quantum state-to-state resolved differential cross-sections for the collisions of NO(X) with Ar (reflecting the <strong>k</strong> - <strong>k'</strong> vector correlation), and the collisional cross-sections for the depolarisation of the rotational angular momenta of the NO(A) and OH(A) radicals (reflecting the <strong>j</strong> - <strong>j'</strong> vector correlation) have been determined experimentally and theoretically, and the results have been discussed and interpreted in terms of the mechanistic aspects of the collision dynamics, and the features of the potential energy surface that give rise to these. In Chapter 2, the atom-molecule systems that constitute the subject of this work will be introduced in detail. The close-coupled quantum mechanical and quasi-classical trajectory scattering calculations performed as part of this work will be discussed in greater detail, providing a greater insight into molecular scattering theory. The explicit calculation of the quantities of interest (most significantly the differential cross-section, and the tensor/depolarisation cross-sections) will be presented for the quasi-classical and quantum cases, offering the most transparent definitions of these quantities. Finally the mathematical description of the spatial probability distribution of a single vector, a pair of correlated vectors, and three correlated vectors is described in detail, including a discussion of the quantum mechanical nature of the vectors in question. Chapter 3 describes the experimental measurement of the differential cross-sections for the collisions of NO(X) with Ar. A hexapole was used to select uniquely those NO molecules in the |Ω = 0.5; j = 0.5, f> quantum state, allowing full experimental quantum state-to-state selection for the first time. A crossed molecular beam apparatus with (1+1') resonantly enhanced multi-photon ionisation detection coupled with velocity mapped ion- imaging was employed to measure the differential cross-section, and the details of the experimental set-up are provided. The accurate extraction of the true, centre of mass frame differential cross-section from the laboratory frame information yielded by the experiment is something of an involved process, and much of this Chapter will be concerned with the development of a Monte Carlo method to achieve this end. In Chapter 4, the experimental and theoretical fully quantum state-to-state resolved differential cross-sections for the collisions of NO(X) with Ar are presented, having been measured for the first time. Full resolution of the initial parity of the rotational wave- function of the NO molecule has enabled the observation of parity dependent structures within the differential cross-section, and the origin of these structures has been investi- gated, employing quasi-classical, quantum mechanical and semi-classical methods in order to elucidate the mechanism by which they arise. Chapter 5 introduces the measurement of the collisional depolarisation of the rotational angular momentum of the diatom. Rate constants for the collisional depolarisation of <strong>j</strong> were measured by monitoring the time dependence of the amplitude of Zeeman and hyperfine quantum beats in the (1+1) laser induced fluorescence decays of an ensemble of NO(A) or OH(A) radicals in the presence of a series of background pressures of a collision partner. The creation and subsequent evolution of the polarisation of <strong>j</strong> induced by the absorption of polarised laser light is described, and the magnitude of this polarisation is linked to the amplitude of the quantum beat in the laser induced fluorescence decay. The extraction of the depolarisation cross-sections from the raw experimental data is discussed, and a Monte Carlo simulation of the experiment is described to account for any additional unwanted experimental factors that may contribute to the loss of polarisation of <strong>j</strong>. A formalism is also introduced that makes use of the tensor opacities to recover spin- rotation conserving and spin-rotation changing open-shell rotational energy transfer and depolarisation cross-sections from the intrinsically closed shell quasi-classical trajectory scattering calculations. In Chapter 6, the experimentally determined collisional depolarisation cross-sections for the collisions of NO(A) with He/Ar, and of OH(A) with Ar at collision energies of 39 meV/757meV are presented along with their theoretical counterparts. The relative magnitudes of the cross-sections are rationalised in terms of the potential energy surface over which the collision takes place, and the importance of spin-rotation conserving and spin-rotation changing transitions in the depolarisation process is assessed. A detailed study of the ensemble of quasi-classical trajectories is performed to determine the character of the various atom-molecule collisions, and to identify which conditions lead to the most efficient depolarisation of <strong>j</strong>. The relative importance of the potential energy surface and the collision kinematics is also assessed at this point. The results presented in this thesis thus investigate two complementary expressions of the collision dynamics, the <strong>k</strong> - <strong>k'</strong> and <strong>j</strong> - <strong>j'</strong> vector correlations, and encompass a variety of collision partners exhibiting vastly differing collision characteristics. As such, this work serves as an illustrative overview of atom-molecule scattering dynamics, containing both experimental and theoretical reflections of the collision dynamics, and relating this information back to the fundamentals of scattering theory.
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Buyens, Dominique. "Alkylation of adenine : a synthetic and computational study of the reaction mechanism." Diss., University of Pretoria, 2015. http://hdl.handle.net/2263/64255.
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This dissertation describes the benzylation of adenine under basic conditions, the unequivocal determination of the identity of the products of this reaction, an exploration of the effect of solvent on the reaction, a thorough computational study of the reaction mechanism and an investigation into the hydrogen-deuterium exchange reaction of the N-benzyladenine products and related compounds.
The preferential sites of alkylation of adenine under basic conditions in DMSO were proven to be the N9 and N3 positions. X-ray crystal structures were obtained for both compounds. Formation of the N9-benzyladenine product is the most favoured in polar aprotic solvents, such as DMSO, and as the proportion of polar protic solvents, such as water, increases, so does the formation of the N3-benzyladenine product. Characteristic 1H NMR chemical shifts of the purine ring protons and HMBC 1H-13C correlation NMR spectroscopy were useful tools to assign the 1H and 13C NMR spectra chemical shifts and confirm that the solution structures were the same as the isolated crystals.
Simulating the SN2 mechanism for the N1-, N3-, N7- and N9-pathways computationally, employing DMSO as the simulated solvent, resulted in ambiguous results when considering the electronic energies of initial, TS and final products alone. However, a novel approach was developed (employing IQA-defined energy terms) to study fragment interactions along the reaction paths. It provided a full explanation of the reaction mechanism and yielded results which supported the N3/N9 positions of alkylation over the N1/N7 sites. The preference for the sites of alkylation occurs after the transition state, in which the N1/N7 reaction paths fail to proceed favourably to the end product, N1- and N7-benzyladenine, respectively. The N9-pathway dominates the N3-pathway at the product formation step, which corresponds to the N9-
benzyladenine being the major product, as shown in Figure 1, and the N3-benzyladenine being
the minor product from the benzylation of adenine. The faster rate of deuteration at the C8 position of N9-benzyladenine as compared to the
deuteration rates at the C2 and the C8 of N3-benzyladenine, have shown support for a sp3
mediated mechanism and a carbene mediated mechanism of deuteration based on the “push” and
“pull” mechanisms proposed for the C8 proton transfer of ATP in kinase enzymes. The
deuteration of the C8 proton of 2,6-dichloropurine derivatives supports the existence of the
carbene mediated mechanism since these compounds lack the amine moiety necessary for the
sp3 mediated mechanism.
These results demonstrate how experimentation and computation have led to greater insights
into the reactivity of adenine and its derivatives. This strategy provides a useful platform for
future research into adenine reaction mechanisms and the role adenine plays in kinase catalysis.<br>Dissertation (MSc)--University of Pretoria, 2015.<br>National Research Foundation (NRF)<br>Chemistry<br>MSc<br>Unrestricted
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Dunn, Cameron R. "A crystallographic study of structural changes in L-lactate dehydrogenase induced by the binding substrate." Thesis, University of Bristol, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.330195.
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Zhang, Lipeng. "Theoretical study of oxygen reduction reaction catalytic properties of defective graphene in fuel cells." Thesis, The University of Akron, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=3718274.
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<p> In this dissertation density functional theory (DFT) was applied to study the electronic structure and catalytic properties of graphene containing different types of defects. These defects includes hetero-atoms such as nitrogen, sulfur doped graphene, point defects such as Stone-Wales defects, single vacancy, double vacancies and substituting pentagon ring at zigzag edge, line defects such as pentagon-heptagon carbon ring chains, pentagon-pentagon-octagon carbon ring chains locating at the middle of graphene. The mechanisms of oxygen reduction reaction (ORR) were studied on these defective graphene, and electron transfer processes were simulated. Using DFT methods, we also explored the effect of strains to ORR electronic catalytic properties on pure and nitrogen doped graphene. </p><p> Our simulaltion results show that nitrogen, sulfur doped graphene, graphene containing point defects, substituting pentagon ring at zigzag edge, graphene containing line defects, pentagon-heptagon chain or pentagon-pentagon-octagon chains which have odd number of heptagon or octagon carbon ring perform high catalytic properties for ORR. Four electron transfer reactions could occur, and there are also two electrons transfer occuring on these defective graphene. The Stone-Wales defect itself cannot generate the catalytic activity on the graphene, but can facilitate the formation of hetero atom doping on graphene, which could show high catalytic activities to ORR. The catalytic active sites on defective graphene are atoms possessing high spin or charge density, where the spin density plays more important effect on the catalytic properties. For the N-doped graphene, the identified active sites are closely related to doping cluster size and dopant-defect interactions. Generally speaking, a large doping cluster size (number of N atoms >2) reduces the number of catalytic active sites per N atom. In combination with N clustering, Stone-Wales defects can strongly promote ORR. For four-electron transfer, the effective reversible potential ranges from 1.04 to 1.15 V/SHE, depending on the defects and cluster size. The catalytic properties of graphene could be optimized by introducing small N clusters in combination with material defects. For S-doped graphene, sulfur atoms could be adsorbed on the graphene surface, substitute carbon atoms at the graphene edges in the form of sulfur/sulfur oxide, or connect two graphene sheets by forming a sulfur cluster ring. Catalytic active sites distribute at the zigzag edge or the neighboring carbon atoms of doped sulfur oxide atoms, which possess large spin or charge density. For those being the active catalytic sites, sulfur atoms with the highest charge density take two-electron transfer pathway while the carbon atoms with high spin or charge density follow four-electron transfer pathway. Stone-Wales defects not only promote the formation of sulfur-doped graphenes, but also facilitate the catalytic activity of these graphenes. The ORR catalytic capabilities of the graphene containing point or line defects denpend on whether the defects could introduce spin density into the system or not. The axial strain field applied on the graphene could change its electronic properties. Neither the compressive nor the tensile strain along the zigzag or armchair direction could facinitate the catalytic activities of perfect graphene without any defects. Tensile strain along zigzag direction could change the electronic properties of nitrogen doped graphene, which are favorable to its ORR catalytic property. </p><p> Our simulation results explored the ORR on defective graphene in essence and provide the theoretical base for searching and fabricating new high efficient catalysts using the carbon based materials for fuel cells.</p>
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Neave, Greg William. "A theoretical study of the reaction chemistry of group 10 metal-alkoxides and -amides." Thesis, Heriot-Watt University, 2004. http://hdl.handle.net/10399/329.
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Hasegawa, Jun-ya. "Theoretical Study on the Excited States and Electron Transfer Reactions in Photosynthetic Reaction Center." Kyoto University, 1998. http://hdl.handle.net/2433/77871.
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Zhang, Lipeng. "Theoretical Study of Oxygen Reduction Reaction Catalytic Properties of Defective Graphene in Fuel Cells." University of Akron / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=akron1374245184.
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Benitez, Diego Goddard William A. "Theoretical study of the mechanism of olefin metathesis and synthesis of cyclic polymers /." Diss., Pasadena, Calif. : California Institute of Technology, 2005. http://resolver.caltech.edu/CaltechETD:etd-08132004-132724.
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Aono, Shinji. "Theoretical Study of Electrostatic Solvent Effects within Free Energy Expression and Application to Solvated Reaction." 京都大学 (Kyoto University), 2010. http://hdl.handle.net/2433/126827.
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Yamamoto, Takeshi. "Theoretical study on the mode-specific unimolecular dissociation reaction HFCO→HF+CO by quantum dynamics calculations." 京都大学 (Kyoto University), 2000. http://hdl.handle.net/2433/181139.
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Hyman, Matthew P. "A theoretical study of the electrocatalytic oxygen reduction reaction and related reactions on platinum group metals." Connect to online resource, 2007. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3273680.
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Lai, Chun-Liang, and 賴俊良. "Theoretical Study on the Mechanism of N-Heterocyclic Carbene Catalyzed Transesterification Reaction." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/71096271416200896005.
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陳皆宏. "A Theoretical Study on the Mechanism of Reaction of Type-2 Alkene with Amino acid." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/6n3997.
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碩士<br>國立彰化師範大學<br>化學系<br>106<br>The post-translational modification of protein refers that amino acid, such as thiol groups of cysteine, imidazole moiety of histidine and the ε-amino group of
lysine residues, form adducts with electrophiles, and modify protein’s structures and functions. Nitro-fatty acids (NO2-FA) exert protective and anti-inflammatory via
Michael addition to thiol groups in post-translational modifications, they have been shown to be beneficial in treating diseases such as diabetes, renal injury, and
endotoxemia. Similar to NO2-FA, 15-deoxy-Δ12,14-prostaglandin J2 (15d-PGJ2) is also Type-2 alkene . 15d-PGJ2 is PPARγ agonist that has anti-inflammatory and
significant anti-cancer effect. The adduct formations of these reactions of these biologyical electro-philes with the residues mentioned above are investigated using
density functional theory. In addition to biological thiols, the adduct formations of biological amines with the electrophiles via Schiff base formation is also investigated.
Furthermore, we investigated several Type-2 alkenes, i.e., α,β-unsaturated carbonyl compounds, which have been identified to be neurotoxicity via forming adducts with sulfhydrl groups of Cysteine residue. We have compared the reactivity of Type-2 alkenes with the electrophiles, our computations reveal that the toxicity of Type-2 al-kenes are attributed to their more exergonic, i.e., less reversible adduct formations.
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楊仲瑜. "theoretical study of reaction mechanisms of some simple organic molecules." Thesis, 2004. http://ndltd.ncl.edu.tw/handle/01740225680548232350.
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碩士<br>國立臺灣師範大學<br>化學研究所<br>92<br>We carried out theoretical studies for two important reactions involving HNCO peptide bond: 1. the methylation of Hydroxamic Acid (RC(=X)NHOH, X=O、R=H) and its derivatives (X=S、R=CH3,Cl,CHCH2) with diazomethane , and 2. the thermal deamination and denitrosation of N-Nitrosoamides . The descriptions are following:
Part 1： There are seven possible pathways of methylation of (Z)HAs to generate O-alkylation and N-alkylation products. Path Z7 generating (Z)O,O-dimethylhydroxamates 9 has the lowest energy barrier 17.24 kcal/mol. The reaction between HAs and CH2N2 results in predominant formation of product 9 strictly high-site selective. When the substitutents of CH3, Cl and CHCH2 are added, the energy barrier of pathways and the site selection of product will be affected. The probability for the formation of (Z)N,O-dimethylhydroxamates 6 will be increase.
There are six possible pathways in the E-form Has methylation. Path E5、E6 generate (E)O,O-dimethylhydroxamate 24 , with the energy barriers, 22.85 kcal/mol, and 23.06 kcal/mol respectively. The substituents CH3, Cl and CHCH2 have little effect to the site-selectivity of the products except the Cl-substituent changes the rate-determine step. The production of (E)N,O-dimethylhydroxamates 27 has higher energy barrier.
Part 2： The similar methylation reaction of thiohydroxamic acid is investigated and the result compared with that of hydroxamic counterparts. We found that the relative energies、structures of transition state and the pathways of reaction were affected by two major factors: the size and the electronegativity of O and S atom. However products of Z and E isomers of SHAs also have high site-selectivity , with N-methyl product obtained at higher barrier, similar to Has counterparts.
Part 3： We studied theoretical the thermal decomposition of N-Nitrosoamides and designed two isodesmic reaction to understand the substitutions effects on the stability of the reactant and transition state . We found that the substitution at the different sites (N and C) of N-Nitrosoamides led to very different results. The silyl substituent at C-site even followed different pathway of decomposition.
The thermal decomposition of N-Nitrosoamides in acidic condition may undergo deaminative (loss of N2) and denitrosative (loss of NO+) two competitive pathways. According to our result, we may understand how the acidity, temperature and added nucleophilicity affect reaction barriers.
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Wang, Shu Hua, and 王樹華. "Theoretical Study on Droplet Ignition with Various Chemical Reaction Mechanisms." Thesis, 1994. http://ndltd.ncl.edu.tw/handle/38801886341469446582.
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Lin, Ta-Sheng, and 林達昇. "Theoretical Study on the Reaction Mechanisms of Rh with CO2 and N2O." Thesis, 2014. http://ndltd.ncl.edu.tw/handle/56457709761793519493.
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碩士<br>中原大學<br>化學研究所<br>102<br>In this thesis, theoretical calculations and the use of electronic density functional theory (Density Functional Theory), two major gas and carbon dioxide and nitrous oxide catalytic reaction do the calculation and study the reaction mechanism for the transition metals are rhodium (Rhodium, Rh).
Here we first electrically neutral rhodium, with a positively charged rhodium, carbon dioxide, nitrous oxide, the first structural optimization, process reaction, rhodium metal structural optimization using B3LYP/SDD first, then CCSD (T) / SDD single point calculations; portion of the carbon dioxide and nitrous oxide using B3LYP/6-31G (d) to optimize the structure first, then CCSD (T) / 6-311G (d) a higher level for more accurate calculations, and then the energy of the resulting structure to predict the structure of the transition state of the reaction and complete the whole path. From the results we can find a positive after giving metal can more easily cross the barrier, making it easier for us to find the transition state and discuss a reasonable reaction path.
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Yang, Chung-Yu, and 楊崇佑. "A theoretical study about substituent effect of 3,4-dimethylenethiophene and reaction mechanism of its derivatives (sultine and sulfolene)." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/40496661365632106519.
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碩士<br>國立清華大學<br>化學系<br>93<br>Sultine is also regarded as the precursor for producing diradical molecule, o-xylene(4). Recently W.-S. Chung synthesize a series of sultine(14) which may be the derivative of 3,4-dimethylenethiophene(8), and then discuss the thermo-reaction related to them. According the result, the isomeric reaction between sultine and sulfolene(15) is discovered accompanied with thermo-reaction of sultine and Nucleophile. This thesis first focuses on the molecular properties and substituent effect of 3,4-dimethylenethiophene(8) by using of the Density Fuctinoal Theory(DFT) . Then the study for the process of isomeric reaction described above is followed. From the calculation(B3LYP/6-31++G**) results, we found that molecule 8 is a little more stable within its triplet than singlet configuration. About the substituent effect, the more powerful electron-withdrawing group is, the more possibility is to appear energy inversion among electronic configurations. As for the reaction, we can acquire three sketches involving interaction paths for photolysis reaction of 14 and 15, including triplet potential surface only(via intersystem crossing(ISC) to exchange different configurations, this path support the Prof. Chung’s idea), singlet potential surface only, and mixing different configuration potential surface. Finally it’ll be elucidated that the tautomerism of sultne(because of S=O position, see 14-axi and 14-equ).
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Ma, Ching-kit, and 馬正杰. "Theoretical Study of Surface Reaction of SiH4,Si2H6,GeH4 and Ge2H6 on Si(100)-2x1 surface : Mechanism and Kinetics." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/46732039796341889671.
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碩士<br>國立臺灣科技大學<br>化學工程系<br>93<br>Modeling of chemical vapor deposition (CVD) processes requires knowledge of the gas-flow dynamics and chemical reaction occurring in the reactor. In order to go beyond simple growth rate predictions based on the lumped kinetics from incomplete experimental kinetic data , quantum chemistry techniques are used to investigate kinetics of chemical reaction involved in the adsorption of SiH4, GeH4 Si2H6, Ge2H6 on the Si (100) surface. Ab initio calculations have been used to determine the structures, energetics and vibration frequency of initial, final and transition states. All the geometries were optimized at B3LYP/6-31G(d) level and the energies were determined at B3LYP/aug-cc-pVTZ level. In addition, transition state theory with the correction of tunneling effect is used to do the kinetic evaluation. The results demonstrate the disilane molecule which adsorbs on the surface, because of a relatively high sticking coefficient, and a low activation energy for breaking the Si-Si bond to produce two SiH3, maybe the favorably pathway, which is in good agreement with the experimental prediction.
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Chin, Chih-Hao, and 金之豪. "1. Theoretical study of the Reaction Mechanism of B + CO2; BO, BS, B2O2 + H2 2. Synthesis and Superconductivity of Ca-doped NdBa2Cu3Oy." Thesis, 2004. http://ndltd.ncl.edu.tw/handle/24909796359156612089.
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博士<br>淡江大學<br>化學學系<br>92<br>Part I
This thesis deals with the calculation of reaction mechanism of B + CO2; BO, BS, B2O2 + H2; AlO +2 NO by density functional theory at B3LYP/6-311+G(d) and B3LYP/6-311+G(d,p) level. To find the potential energy diagram of above molecules in the reaction and analyzed their relationships. There are three reactions we studied and they are rendered here.
Ab initio and density functional G2M(MP2)//B3LYP/6-311+G(d) calculations have been carried out to investigate the potential energy surface for the B + CO2 BO + CO reaction. The most favorable reaction pathway has been shown to be B + CO2 (0.0 kcal/mol) TS1 (19.2 kcal/mol) trans-BOCO (-25.1 kcal/mol) TS2 (-22.0 kcal/mol) BO + CO (-64.0 kcal/mol) OBCO (-75.6 kcal/mol). The results explain observation of OBCO as the major reaction product in the earlier matrix isolation experiments, where this molecule was likely been produced through secondary recombination of the primary BO and CO products.
Potential energy surfaces of various reactions in the BO/H2, B2O2/H2, and BS/H2 systems have been studied at the G2M(MP2)//B3LYP/6-311+G(d,p) level of theory. The BO + H2 reaction is shown to proceed by abstraction of a hydrogen atom by B to produce OBH + H with the barrier and exothermicity of 8.3 and 6.8 kcal/mol, respectively. The reaction can also occur by 1, 2-insertion of BO into the H-H bond or by H abstraction by the O atom; however, the barriers for these channels are much higher, 36.4 and 42.7 kcal/mol, respectively. Via a low ~ 0.3 kcal/mol barrier, the OBH + H reaction produces the OBH2 radical, which is the most stable compound in the BO/H2 system and lies 15.9, 2.5, and 4.2 kcal/mol below BO + H2, trans-HBOH, and cis-HBOH, respectively. OBH2 can isomerize to trans-HBOH overcoming a barrier of 27.7 kcal/mol and the latter can rearrange to the cis conformer with a barrier of 10.8 kcal/mol. BOH and H can recombine and form cis- or trans-HBOH without barriers. In the B + H2O reaction, the reactants can first form a weakly bound B-H2O complex, which then can eliminate an H atom producing BOH + H or undergo insertion of B into an O-H bond giving trans-HBOH with barriers of 4.7 and 6.2 kcal/mol relative to the initial reactants, respectively, and trans-HBOH can eventually decompose to OBH + H and a minor amount of BO + H2. Singlet OBBO is shown to be much less reactive with respect to H2 than the BO monomer. Alternatively, after two BO recombine to form a triplet OBBO molecule over a moderate 8.3 kcal/mol barrier, t-OBBO can easily react with H2 producing either BO + OBH2 (via a t-OBBH2O intermediate) or OBBOH + H with barriers of 4.4 and 7.4 kcal/mol, respectively. The reactions in the BS/H2 system are shown to be similar to those for BO/H2, except that BS cannot insert into H2, SBH2 resides in a much deeper potential well (37.3 kcal/mol below BS + H2) and can rearrange both to trans- and cis-HBSH, the B-H2S complex is more strongly bound than B-H2O, and the B + H2S reaction is expected to be significantly faster than the reaction of B + H2O.
Part II
Two series of single phase triple-perovskite superconducting samples with nominal compositions of Nd1-xCaxBa2Cu3Oy and NdBa2-zCazCu3Oy are prepared by the solid state reaction method. For all the samples, both the Tc and the orthorhombicity of the unit cell decrease with increasing Ca content. The results of Rietveld analysis indicate that the Ca ions in the Nd1-xCaxBa2Cu3Oy series occupy R site causing a hole doping effect, whereas part of Ca ions in the NdBa2-zCazCu3Oy series occupy R site and push the same amount of Nd3+ ions into Ba site, causing a hole filling effect. It is also found that Tc decreases linearly with decreasing the distance of Cu(2)-Cu(2) along the c-axis. The O-1s and Cu-2p3/2 X-ray absorption near edge structure (XANES) show that both the holes in the CuO2 planes and on the apical oxygen sites have a significant effect on the superconductivity of Nd1-xCaxBa2Cu3Oy series in the overdoped region. In the NdBa2-xCaxCu3Oy series, the oxygen contents and orthorhombicity are decreased with increasing Ca content. The evening distribution of O(4) and O(5) in the basal plane leads to a reduction in the number of holes in the CuO2 planes and a decrease in Tc.
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Chi, Ziang Chaung, and 莊季臻. "Theoretical Study of the Oxidation –reduction reaction mechanisms of Cr(VI)O42-、As(III)O33- 、S(IV)O32- and P(III)O33-with Fe(VI)O42-." Thesis, 2015. http://ndltd.ncl.edu.tw/handle/nad8cv.
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碩士<br>東海大學<br>化學系<br>103<br>In this thesis, we study the oxidation - reduction reaction mechanisms
of Cr(VI)O42-, As(III)O33-, S(IV)O32-and P(III)O33-with Fe(VI)O42-of
oxidation - reduction reaction by DFT(Density Functional Theory )
methodB3LYP/6-311++G**in Gaussian 09 for gaseous state and aqueous
state by PCM method. Our results have shown that it would be thermodynamically more favorable for the oxidation- reduction reaction in the form of electron transfer when Fe(VI)O42-react with Cr(VI)O42-, As(III)O33-, S(IV)O32-and P(III)O33-in gas state and in aqueous state.
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Chang, I.-Ya, and 張怡雅. "Theoretical Studies of Potential Energy Surface and Reaction Mechanism of Photochemical Reactions." Thesis, 2009. http://ndltd.ncl.edu.tw/handle/47465997626933934701.
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