The unique physical properties of nanomaterials, attributed to the combined effects of their size, shape, and composition, have sparked significant interest in the field of nanotechnology. Fabrication of nanodevices using nanomaterials as building-blocks are underway to enable novel technological applications. A fundamental understanding on the structure-property relationships and the mechanism of synthesizing nanomaterials with tailored physical properties is critical for a rationale design of functional nanodevices. In this thesis, molecular simulations that employ a detailed atomistic description of the nanoscopic structures were used to understand the structure-transport property relationships in two novel classes of porous nanomaterials, namely, polymer/porous inorganic layered nanocomposite materials and single-walled metal oxide nanotubes, and provide predictions for the design of nanodevices using these nanomaterials. We employed molecular dynamics to study transport of gas molecules (in particular He, H2, N2 and O2) through a polydimethylsiloxane/porous layered silicate (AMH-3) nanocomposite membrane material as a function of its composition. Gas separation performance of the nanocomposite was found to be substantially enhanced for H2/N2 and H2/O2 compared to pure polymeric material due to the molecular sieving effect of AMH-3, suggesting the possibility of developing a new class of superior separation devices. We also developed force field parameters for layered aluminophosphates that are emerging as potential inorganic layers for construction of nanocomposite materials. We presented preliminary work on developing Transition State Approach-Monte Carlo simulation method for calculating gas transport properties of nanocomposite materials. We investigated in detail the diameter control phenomenon in single-walled metal oxide nanotubes using molecular dynamics simulations and demonstrated the existence of a thermodynamic 'handle' for tuning the nanotube diameters and derived a unique correlation between nanotube energy, composition, and diameter to precisely predict nanotube diameters. Finally, using a combination of molecular dynamics, monte carlo and sorption experiments, we investigated adsorption and diffusion properties of water in single-walled aluminosilicate nanotubes. We predicted high water fluxes in these nanotubes, due to short lengths, hydrophilic interior and near-bulk-water diffusivities. Overall, my research represents two examples of the progress in developing a predictive basis for the design and analysis of nanostructures for applications in separations, nanofluidics, and fuel cell technology.

Utilitzant temperatura i pressió com a agents desnaturalitzants s'ha explorat la contribució a l'estabilitat de diferents residus del principal nucli hidrofòbic de la RNasa A. Aquests resutats suggereixen que el principal nucli hidrofòbic d'aquest enzim, està fortament empaquetat i ha revelat l'existència de reordenacions en l'interior de la proteïna.El mètode dels valors , han permès estudiar el paper de les interaccions hidrofòbiques establertes pels residus del principal nucli hidrofòbic de la RNasa A en el seu estat de transició induït per pressió. En conjunt, aquests resultats suggereixen que l'estat de transició de la RNasa A, s'assemblaria a un glòbul col·lapsat amb una cadena estructurada però amb un debilitat nucli hidrofòbic.S'ha explorat també, el paisatge energètic del plegament/desplegament proteic de la variant Y115W de la RNasa A. L'estat de transició sembla interaccionar fortament amb la capa d'hidratació d'aquest estat, tal i com indiquen els resultats en presència de glicerol. / Using temperature and pressure as denaturants we have explored the contributions to stability of the hydrophobic core residues of RNase A. These results are consistent with an exquisite tight core packing and the existence of rearrangements in the protein interior.The role of hydrophobic interactions established by the residues of the main hydrophobic core of RNase A in its pressure-folding transition state, was investigated using the -value method. Altogether the results suggest that the pressure-folding transition state of RNase A, looks like a collapsed globule with some secondary structure and a weakened hydrophobic core. Pressure-jump induced relaxation kinetics was used to explore the energy landscape of protein folding/unfolding of Y115W variant of RNase A. The transition state appears to interact strongly with the hydration shell, as indicated by results in the presence of glycerol.

Cálculos usando métodos de estrutura eletrônica (Hartree-Fock, Mõller-Plesset de segunda ordem e DFT, B3LYP) foram efetuados pelo programa Gaussian98 em microcomputadores e estações de trabalho, com o objetivo de elucidar os canais de decomposição unimolecular de éter dietílico em fase gasosa e foram comparados com valores obtidos através de aproximações baseadas na mecânica estatística pela metodologia de Benson. O éter dietílico vem sendo usado como um aditivo para o óleo diesel e combustível alternativo e o conhecimento de suas vias vias de decomposição é fundamental nestas investigações. Dezesseis modos primários, do qual, quatro ocorrem através de cisão de ligações simples C-O, C-C,C(1)-H e C(2)-H e doze ocorrendo através de estados de transição cíclicos, os quais eliminam produtos como hidrogênio etano, acetaldeído, etano, álcool etílico, metil etil éter, metano, alguns carbenos e também di-radicais, foram considerados para a determinação das barreiras de ativação, entalpias de reação, entropias de reação e energia livre de Gibbs de reação. Vias primárias ocorrendo através de cisão de ligação, não reproduziram os valores experimentais para as barreiras de ativação, mas reproduziram de modo significante, valores da entalpia da reação. Eliminação de eteno e álcool etílico, ocorrendo através de um estado de transição de quatro centros, apresentou a barreira de ativação mais baixa. Acetaldeído e eliminação de etano, ocorrendo através de quatro centros, apresentou barreira significativamente alta, mas por outro lado, a menor entalpia, ligeiramente exotérmica por -0,8 kcal.mol-1. Eliminações 1,2 de metano e carbeno ocorrendo através de três centros, junto com a eliminação 1, 1 de hidrogênio e carbeno por três centros, eliminação 2,2 hidrogênio e carbeno por três centros e eliminação 1,4 de hidrogênio, acetaldeído e eteno por seis centros, apresentaram barreiras de ativação relativamente próximas mostrando que elas são competitivas entre si. Os valores computados dos canais que ocorrem por estados de transição cíclicos foram comparados com os resultados experimentais disponíveis e discutida a validade desta abordagem computacional para o estudo de reações unimoleculares de multi-canais. Determinação de parâmetros termoquímicos, como calor de formação para espécies radicalares dos canais de decomposição primário e alguns radicais alcóxidos, junto com a estimativa de afinidade eletrônica e protônica (com a abordagem ab initio Gaussian 2 a qual estima energias eletrônicas muito precisas) foram efetuados e seus resultados foram comparados com os valores experimentais disponíveis e valores obtidos através de energias de ligação e da regra de aditividade de Benson. / Calculations using methods of electronic structure(Hartree-Fock, second order Moller-Plesset and DFT: B3LYP) had been effected through the Gaussian98 program in microcomputers and workstations, with the objective to elucidate the unimolecular decomposition channels of diethyl ether in gaseous phase. These results also had been compared to those obtained by the methodology based in statistical mechanics through Benson\'s approach. Sixteen primary ways, which, four occur through the break of simple bonds C-O, C-C,C(1)-H, C(2)-H, and twelve occur through cyclical transistion states, which eliminate products as hydrogen, ethene, acetaldehyde, ethane, ethyl alcohol, methyl ethyl ether, methane, some carbenes and also diradicals. These products had been considered to the determination of the activation barriers, enthalpies of reaction, entropies of reaction and free energy of Gibbs of reaction. Primary ways occurring through the break of bonds, had not reproduced experimental values for the activation barriers, however they had reproduced in a significant way, values of the enthalpy of the reaction. Elimination of ethene and ethyl alcohol, occurring by a transition state of four centers, presented the lowest activation barrier. Acetaldehyde and ethane elimination occurring through four centers, presented a high significantly barrier, but on the other hand it presented the smallest enthalpy, lightly exothermic above -0,8 kcal.mol-1. Eliminations 1,2 of methane and carbene occurring through three centers, together with the elimination 1,1 of hydrogen and carbene through three centers, elimination 2,2 of hydrogen and carbene through three centers and elimination 1,4 of hydrogen, acetaldehyde and ethene through six centers, had presented relatively next activation barriers, showing that they are competitive among themselves. The computed values of the channels that occur through cyclical transition states had been compared with the available experimental results and the trustworthiness of this computational boarding for the study of unimolecular reactions in multi-channel had been dicussed. Determination of thermochemical parameters, as heat of formation for radicalar species of the primary channel of decomposition and some alcoxyde radicais, together with the estimative of the electronic and protonic affinities,( with the ab initio Gaussian 2 boarding which estimate very precise eletronic energies ) and their results had been compared with the available experimental values and with values gotten through energies of bond and Benson\'s additivity rule.

Abstract The aim of this PhD-study was to better understand the structure-function relationship of triosephosphate isomerase (TIM) and to use this expertise to change its substrate specificity. TIM is an important enzyme of the glycolytic pathway which catalyzes the interconversion of D-glyceraldehyde phosphate (D-GAP) and dihydroxyacetone phosphate (DHAP). Two main subjects are discussed: the engineering of monomeric TIM to create new substrate specificity and the structure-function relationship studies of the catalytically important mobile loop6. The starting point for the protein engineering project was the monomeric ml8bTIM, with an extended binding pocket between loop7 and loop8. Rational protein engineering efforts have resulted in a new variant called A-TIM that can competently bind wild type transition state analogues. A-TIM was also able to bind citrate, a compound that the wild type TIM does not bind. This A-TIM citrate complex structure is a good starting point for future protein engineering efforts. Based on the assumption that it would be beneficial for the monomeric forms of TIM to have loop6 closed permanently to increase the population of competent active sites, two point mutation variants, A178L and P168A were generated and characterized. The A178L-mutation was made to favor the closed conformation of loop6 through steric clashes in the open conformation. The P168A variant was made to stabilize the closed conformation of loop6 by removing strain. The A178L mutation induced some features of the closed conformation, but did not result in a closed conformation in the absence of ligands. Our structural studies also show that the P168A mutation does not favor the closed conformation either. However, the structures of the unliganded and liganded P168A variant, together with other known TIM structures show that the substrate binding first induces closure of loop7. This conformational switch subsequently forces loop6 to adopt its closed conformation. The protein engineering project was successful, but the efforts to find variants with a permanently closed loop6 did not fully succeed. In the context of this thesis a monomeric variant of TIM, with new binding properties, was created. Nevertheless, A-TIM still competently binds the inhibitors and transition state analogues of wild type TIM. Also, when combined, results discussed in the context of this thesis indicate that in wild type TIM the closure of loop7 after ligand binding is the initial step in the series of conformational changes that lead to the formation of the competent active site. / Tiivistelmä Tämän väitöskirjatyön tarkoituksena oli oppia paremmin ymmärtämään trioosifosfaatti-isomeraasin (TIM) toimintamekanismeja sen rakenteen perusteella ja käyttää tätä tietämystä samaisen proteiinin muokkaamiseen uusiin tarkoituksiin. TIM on keskeinen entsyymi solun energian tuotannossa ja sen toiminta on välttämätöntä kaikille eliöille. Tämän vuoksi on tärkeää oppia ymmärtämään miten se saavuttaa tehokkaan reaktionopeutensa ja miksi se katalysoi vain D-glyseraldehydi-3-fosfaattia (D-GAP) ja dihydroksiasetonifosfaattia (DHAP). TIM:n toiminta mekanismien ymmärtämiseksi sen aminohapposekvenssiä muokattiin kahdesta kohtaa (P168A ja A178L) ja seuraukset todettiin mittaamalla tuotettujen proteiinien stabiilisuutta optisesti eri lämpötiloissa ja selvittämällä niiden kolmiulotteinen rakenne käyttäen röntgensädekristallografiaa. Mutaatioita tehtiin dimeeriseen villityypin TIM:in (wtTIM) ja jo aikaisemmin muokattuun monomeeriseen TIM:in (ml1TIM). Näiden mutaatioiden tarkoituksena oli suosia entsyymin aktiivista konformaatiota, jossa reaktion kannalta välttämätön vapaasti liikkuva peptidisilmukka numero 6 on suljetussa konformaatiossa. Monomeerisissä TIM:ssa peptidisilmukka numero 6:n ei ole välttämätöntä aueta. Tulokset mutaatiokokeista olivat osittain lupaavia. P168A-mutaatio lisäsi D-GAP:in sitoutumista, mutta rikkoi tärkeän mekanismin suljetussa, ligandia sitovassa, konformaatiossa. A178L-mutaatio aiheutti muutoksia avoimeen konformaatioon ja teki siitä suljettua konformaatiota muistuttavan jopa ilman ligandia, mutta samalla koko proteiini muuttui epävakaammaksi. Näistä kahdesta mutaatiosta A178L voisi olla hyödyllinen muokattujen TIM-versioiden ominaisuuksien parantamiseksi. Lisäksi yhdessä jo aikaisemmin julkaistujen yksityiskohtien kanssa nämä tulokset tekevät mahdolliseksi esittää tarkennusta siihen miten TIM toimii kun ligandi saapuu sen lähettyville. Tämän väitöskirjatyön yksi tavoite oli myös muokata edelleen monomeeristä TIM versiota (ml8bTIM), joka on suunniteltu siten, että se voi mahdollisesti sitoa uudenlaisia ligandeja. Tämä projekti vaati onnistuakseen 20 eri versiota ml8bTIM:n sekvenssistä ja noin 30 rakennetta. Uusia ligandeja sitova muoto (A-TIM) sitoi onnistuneesti sitraattia ja villityypin TIM:n inhibiittoreita. Erityisen lupaavaa oli, että A-TIM sitoi myös bromohydroksiasetonifosfaattia (BHAP), joka sitoutuu ainoastaan toimivaan aktiiviseen kohtaan. Nämä tulokset osoittavat, että A-TIM kykenee tarvittaessa katalysoimaan isomerisaatio reaktion uudenlaisille molekyyleille. Esimerkiksi katalysoimaan isomerisointireaktiota sokerianalogien tuotannossa.

Les alliages à haute entropie forment une nouvelle classe de matériaux découverts récemment et démontrant des propriétés physiques et mécaniques très prometteuses. Ces solutions solides à phase unique présentent une grande dureté, une haute résistance à la corrosion, une bonne résistance aux dommages causés par l’irradiation ionique et une phase stable même à température élevée. Pour ces raisons, ils ont attiré l’attention pour plusieurs utilisations potentielles, notamment dans la prochaine génération de réacteurs nucléaires. Dans ce mémoire, nous étudierons la diffusion de défauts ponctuels dans l’alliage de 55Fe-28Ni-17Cr. Ces défauts sont très fréquemment créés par l’irradiation par ion ayant lieu dans les cuves des réacteurs nucléaires. Nous profiterons de l’occasion d’étudier un alliage ayant une microstructure complexe afin d’introduire et de tester une méthode du calcul du taux de transition global et local se basant sur le calcul du facteur pré-exponentiel de la théorie de l’état de transition harmonique (hTST). Ces méthodes sont implantées dans la technique d’activation-relaxation cinétique, une méthode de Monte Carlo cinétique, que nous utiliserons pour réaliser la diffusion de défauts ponctuels dans l’alliage. Nous démontrons une différence importante entre le taux de transition calculé avec et sans hTST qui peut mener à une erreur dans les propriétés calculées de diffusion des défauts. Nous démontrons également que le facteur pré-exponentiel obéit à une anti-loi de compensation de Meyer-Neldel. Le calcul local du facteur pré-exponentiel est étudié et nous démontrons qu’il est capable de reproduire le taux global pour plusieurs événements. / High-entropy alloys are a novel class of materials discovered recently and demonstrating promising physical and mechanical properties. These single-phase solid solutions present a high hardness, a great resistance to corrosion, a good resistance to ion radiation damages and a stable phase even at high temperature. For these reasons they have attracted the attention for numerous potential uses, notably in the next generation of nuclear reactors. In this thesis, we study the diffusion of point defects in the 55Fe-28Ni-17Cr alloy. This kind of defect being very frequently created by irradiation in nuclear reactors. We will also use the occasion of having an alloy with a complex microstructure to add and test a method of computing the transition rate globally and locally based on the computation of the prefactor of the harmonic Transition State Theory (hTST). These additions will be made in the kinetic Activation-Relaxation Technique, a kinetic Monte Carlo method that will be used to study the diffusion of point defects in the alloy. We demonstrate that there is an important discrepancy between the rate computed with and without the hTST that can lead to an error in the computed diffusion properties of defects. We also show that the prefactor obeys an anti Meyer-Neldel compensation law. The local method to compute the prefactor is then studied and proven to be able to reproduce the global rate for a large number of events.

Au cours de cette thèse, nous avons étudié deux protéines par RMN : la créatine kinase musculaire (CK-MM) et le domaine UIM-SH3 de la protéine STAM2, seuls ou en interaction avec leurs partenaires. La CK-MM est une enzyme active sous forme dimérique. Elle appartient à la famille des guanidino-kinases et intervient dans le processus énergétique de la cellule. Le but de l’étude était d’élucider le mode de fonctionnement de la CK-MM. Pour cela, nous avons enregistré des expériences de relaxation R1, R2 et des expériences de perturbation de déplacement chimique sur la CK-MM libre et complexée avec MgADP et sous forme TSAC. Ces expériences montrent que la boucle 320s, spécifique à la reconnaissance des substrats, possède une dynamique rapide en absence de substrats et une dynamique ralentie en présence de substrats. La fixation des substrats dans les sites actifs de la CK-MM induit des modifications conformationelles importantes. La protéine STAM2 est composée de deux UBDs : VHS, et UIM et d’un domaine SH3 connu pour interagir avec des déubiquitinases UBPY et AMSH. Cette protéine est impliquée dans la voie de dégradation lysosomale. L’objectif de cette étude est la caractérisation du complexe SH3/ubiquitine. Pour cela, nous avons enregistré des expériences de perturbation de déplacement chimique et de relaxation R1, R2 et nOes sur le complexe UIM-SH3/ubiquitine. Ces expériences mettent en évidence que les domaines UIM et SH3 sont capables d’interagir chacun avec une ubiquitine, avec une affinité de l’ordre de la centaine de micromolaire. L’interface entre les UBDs et l’ubiquitine implique majoritairement des résidus hydrophobes et conservés / In this thesis, we study two proteins by NMR: the muscular creatine kinase (CK-MM) and the SH3 domain of STAM2 protein, in the free and complexed forms. CK-MM is an active homodimeric enzyme which belongs to the guanidino-phosphagen-kinase family. This enzyme is involved in energetic process in the cell. The aim of this study is to elucidate the functional mode of the CK-MM. For this purpose, we measured R1 and R2 relaxation rates and chemical shit perturbation experiments on the substrate-free CK-MM, the CK-MM/MgADP complex, and the inhibitory ternary complex CK-MM/MgADP-creatine-nitrate. The experiments show that the loop 320s, specific recognition of the substrates, possesses a fast dynamic in absence of substrates (in the order of nano-picosecond) and a slower dynamic in presence of creatine-MgADP-nitrate ion. The binding of the substrate in the two active sites induces of significant conformational modification of the CK-MM. STAM2 protein consists in two ubiquitin binding domains (VHS and UIM) and a SH3 domain which interacts with deubiquinating enzymes AMSH and UBPY. This protein is involved in the lysosomal degradation pathway. The aim of this study is the characterization of the interaction between SH3 domain of STAM2 and ubiquitin. For this, we recorded the R1, R2, nOes relaxation experiments and chemical shift perturbation experiments on the UIM-SH3/ubiquitin complex. These experiments show that SH3 and UIM domains interact each with a single ubiquitin, with affinity of the order of hundred micromolars. The interface between these UBDs and ubiquitin, involves mainly hydrophobic and conserved amino-acids

Explosive materials have always been attracting the attention of scientists. Various explosives either in pure bulk form or as admixtures are synthesized and investigated from different points of view. However, because of dangerous character of these materials, their syntheses and properties have to be forecasted by theoretical studies. The new research trends of explosive materials generally include the designs of novel derivatives of well&ndash / known explosives to improve their detonation performances (heats of explosion, detonation velocities and detonation pressures) and thermal stabilities and decrease their sensitivities towards friction, electric spark, shock and impact either experimentally or theoretically. NTO (5&ndash / nitro&ndash / 2,4&ndash / dihydro&ndash / 3H&ndash / 1,2,4&ndash / triazol&ndash / 3&ndash / one) and PATO (3&ndash / picrylamino&ndash / 1,2,4&ndash / triazole) are very important secondary explosives that take place in the literature for many years in terms of their explosive properties. In this thesis study, new species of these explosives have been designed to enhance their detonation performances (ballistic properties) and to lower their sensitivities and reactivities computationally. Additionally, aromatic nitration reactions and their mechanisms for unprotonated and protonated PATO species have been analyzed. The ab initio quantum chemistry methods, Hartree&ndash / Fock (HF) and Density Functional Theory (DFT), have been used in the calculations with Pople basis sets. Novel NTO and PATO tautomeric species have been designed and investigated to enlighten the effects of tautomerism on their quantum chemical properties and detonation performances in the gas phase. Various aromatic nitration mechanisms (carbon and nitrogen mono&ndash / nitration mechanisms) of unprotonated tautomeric PATO species as well as PATO have been designed in gas phase and the reaction states (pre&ndash / transition states, transition states, intermediates and nitration products) have been detected belonging to these mechanisms. Nitrations in solution phase have also been analyzed. The reaction states have been detected for carbon and nitrogen mono&ndash / nitrations of protonated PATO species in the gas phase. The detonation performances of unnitrated and nitrated PATO products have been presented.

<p> Radical species are essential in modern chemistry. In addition to fundamental chemistry, their unique chemical bonding and distinct physicochemical features serve critical functions in materials science in the form of organic electronics. Due to their high reactivity, radicals of the main group element are often transient. In recent years, remarkably stable radicals are often stabilized by π-delocalization, sterically demanding side groups, carbenes, and weakly coordinating anions. The impacts of modifications such as electron-donating, electron-withdrawing, and end-capping on the spin density distribution and thermodynamic and kinetic stability of archetypal radical-driven processes such as dimerization are not well understood. This dissertation aims to track the perturbation of spin density from EDG and EWG modifications, provide mechanistic insight into the radical-initiated reactions of conjugated radical cations, and establish correlations between molecular design and thermochemical properties and their resulting kinetic stability by computationally evaluating these characteristics against experimental data. The disclosed connections give useful new recommendations for the rational design of thermodynamically and kinetically stable novel materials.</p>

Background: Subtilin is a peptide antibiotic (lantibiotic) natively produced by Bacillus subtilis ATCC6633. It is encoded in a gene cluster spaBTCSIFEGRK (spa-locus) consisting of four transcriptional units: spaS (subtilin pre-peptide), spaBTC (modification and export), spaIFEG (immunity) and spaRK (regulation). Despite the pioneer understanding on subtilin biosynthesis, a robust platform to facilitate subtilin research and improve subtilin production is still a poorly explored spot. Results: In this work, the intact spa-locus was successfully integrated into the chromosome of Bacillus subtilis W168, which is the by far best-characterized Gram-positive model organism with powerful genetics and many advantages in industrial use. Through systematic analysis of spa-promoter activities in B. subtilis W168 wild type and mutant strains, our work demonstrates that subtilin is basally expressed in B. subtilis W168, and the transition state regulator AbrB strongly represses subtilin biosynthesis in a growth phase-dependent manner. The deletion of AbrB remarkably enhanced subtilin gene expression, resulting in comparable yield of bioactive subtilin production as for B. subtilis ATCC6633. However, while in B. subtilis ATCC6633 AbrB regulates subtilin gene expression via SigH, which in turn activates spaRK, AbrB of B. subtilis W168 controls subtilin gene expression in SigH-independent manner, except for the regulation of spaBTC. Furthermore, the work shows that subtilin biosynthesis in B. subtilis W168 is regulated by the two-component regulatory system SpaRK and strictly relies on subtilin itself as inducer to fulfill the autoregulatory circuit. In addition, by incorporating the subtilin-producing system (spa-locus) and subtilin-reporting system (PpsdA-lux) together, we developed “online” reporter strains to efficiently monitor the dynamics of subtilin biosynthesis. Conclusions: Within this study, the model organism B. subtilis W168 was successfully established as a novel platform for subtilin biosynthesis and the underlying regulatory mechanism was comprehensively characterized. This work will not only facilitate genetic (engineering) studies on subtilin, but also pave the way for its industrial production. More broadly, this work will shed new light on the heterologous production of other lantibiotics.