Elementary steps in aqueous proton transfer reactions : a first principles molecular dynamics study

La nature des acides dans un environnement aqueux est primordiale dans de nombreux aspects de la chimie et de la biologie. La caractéristique principale d'un acide est sa capacité à transférer un proton vers une molécule d'eau ou vers n'importe quelle base, mais ce procédé n'est pas aussi simple qu'il y paraît. Il peut au contraire être extrêmement complexe et dépendre de manière cruciale de la solvatation des différents intermédiaires de réaction impliqués. Cette thèse décrit les études computationnelles basées sur des simulations de dynamique moléculaire ab initio qui ont pour but d'obtenir une description à l'échelle moléculaire des divers procédés de transferts de proton entre acide et bases dans un milieu aqueux. Pour cela, nous avons étudié une serie de système, dont l'acide hydrofluorique aqueux, l'acide trifluoroacétique aqueux, et un système modèle constitué d'un phénol et d'une entité carboxylate reliés entre eux par une molécule d'eau en solution aqueuse. Deux états intermédiaires ont été identifiés pour le transfert d'un proton depuis un acide. Ces intermédiaires apparaissent stabilisés par un motif local de solvatation via des ponts H. Leurs signatures spectroscopiques ont été caractérisées au moyen de la spectroscopie infrarouge, en utilisant le formalisme de la dynamique moléculaire ab initio, qui inclut l'effet quantique nucléaire de manière explicite. Cette étude a aussi identifié trois chemins de réaction élémentaire, qui sont responsable pour le transfert d'un proton d'un acide à une base, ainsi que leurs échelles de temps caractéristiques. Les conclusions tirées de ces études sont discutées dans les détails, au niveau moléculaire, avec une emphase sur les comparaisons entre les résultats théoriques et les mesures expérimentales obtenues dans a littérature ou via des collaborateurs.

In situ infrared (FTIR) study of the mechanism of the borohydride oxidation reaction

Early reports stated that Au was a catalyst of choice for the BOR because it would yield a near complete faradaic efficiency. However, it has recently been suggested that gold could yield to some extent the heterogeneous hydrolysis of BH(4)(-),therefore lowering the electron count per BH(4)(-), especially at low potential. Actually, the blur will exist regarding the BOR mechanism on Au as long as no physical proof regarding the reaction intermediates is not put forward. In that frame, in situ physical techniques like FTIR exhibit some interest to study the BOR. Consequently, in situ infrared reflectance spectroscopy measurements (SPAIRS technique) have been performed in 1 M NaOH/1 M NaBH(4) on a gold electrode with the aim to detect the intermediate species. We monitored several bands in B-H ((nu) over bar similar to 1180,1080 and 972 cm(-1)) and B-O bond regions ((nu) over bar =1325 and similar to 1425cm(-1)), which appear sequentially as a function of the electrode polarization. These absorption bands are assigned to BH(3), BH(2) and BO(2)(-) species. At the light of the experimental results, possible initial elementary steps of the BOR on gold electrode have been proposed and discussed according to the relevant literature data.

T cell receptor-ligand interactions: a conformational preequilibrium or an induced fit.

Kinetic parameters of T cell receptor (TCR) interactions with its ligand have been proposed to control T cell activation. Analysis of kinetic data obtained has so far produced conflicting insights; here, we offer a consideration of this problem. As a model system, association and dissociation of a soluble TCR (sT1) and its specific ligand, an azidobenzoic acid derivative of the peptide SYIPSAEK-(ABA)I (residues 252-260 from Plasmodium berghei circumsporozoite protein), bound to class I MHC H-2K(d)-encoded molecule (MHCp) were studied by surface plasmon resonance. The association time courses exhibited biphasic patterns. The fast and dominant phase was assigned to ligand association with the major fraction of TCR molecules, whereas the slow component was attributed to the presence of traces of TCR dimers. The association rate constant derived for the fast phase, assuming a reversible, single-step reaction mechanism, was relatively slow and markedly temperature-dependent, decreasing from 7.0 x 10(3) at 25 degrees C to 1.8 x 10(2) M(-1).s(-1) at 4 degrees C. Hence, it is suggested that these observed slow rate constants are the result of unresolved elementary steps of the process. Indeed, our analysis of the kinetic data shows that the time courses of TCR-MHCp interaction fit well to two different, yet closely related mechanisms, where an induced fit or a preequilibrium of two unbound TCR conformers are operational. These mechanisms may provide a rationale for the reported conformational flexibility of the TCR and its unusual ligand recognition properties, which combine high specificity with considerable crossreactivity.

Operador dipolo-dipolo na base de momento angular: um complemento ao estudo de ressonância magnética nuclear

The relationship between the magnetic dipole-dipole potential energy function and its quantum analogue is presented in this work. It is assumed the reader is familiar with the classical expression of the dipolar interaction and has basic knowledge of the quantum mechanics of angular momentum. Except for these two points only elementary steps are involved.

Picosecond Dynamics of the Prototropic Reactions of 7-Hydroxyflavylium Photoacids Anchored at an Anionic Micellar Surface

Three water-insoluble, micelle-anchored flavylium salts, 7-hydroxy-3-octyl-flavylium chloride, 4`-hexyl-7-hydroxyflavylium chloride, and 6-hexyl-7-hydroxy-4-methyl-flavylium chloride, have been employed to probe excited-state prototropic reactions in micellar sodium dodecyl sulfate (SDS). In SDS micelles, the fluorescence decays of these three flavylium salts are tetraexponential functions in the pH range from 1.0 to 4.6 at temperatures from 293 to 318 K. The four components of the decays are assigned to Four kinetically coupled excited species in the micelle: specifically, promptly deprotonable (AH(+)*) and nonpromptly deprotonable (AH(h)(+)*) orientations of the acid in the micelle. the base-proton geminate pair (A*center dot center dot center dot H(+)), and the free conjugate base (A*). The initial prompt deprotonation to form the germinate pair occurs at essentially the same rate (k(d) similar to 6-7 x 10(10) s(-1)) for all three photoacids. Recombination of the germinate pair is similar to 3-fold faster than the rate of proton escape from the pair (k(rec) similar to 3 x 10(10) s(-1) and k(diss) similar to 1 x 10(10) s(-1)), corresponding to an intrinsic recombination efficiency of the pair of similar to 75%. Finally, the reprotonation of the short-lived free A* (200-350 ps, depending oil the photoacid) has two components, only one of which depends oil the proton concentration in the intermicellar aqueous phase. Ultrafast transfer of the proton to water and substantial compartmentalization of the photogenerated proton at the micelle surface Oil the picosecond time scale strongly suggest preferential transfer of the proton to preformed hydrogen-bonded water bridges between the photoacid and the anionic headgroups. This localizes the proton in the vicinity of the excited base much more efficiently than ill bulk water, resulting ill the predominance of geminate re reprotonation at the micelle surface.

In Situ Infrared (FTIR) Study of the Mechanism of the Borohydride Oxidation Reaction on Smooth Pt Electrode

Although Pt has been thoroughly studied regarding its activity for the borohydride oxidation reaction (BOR), the BOR mechanism at Pt remains unclear: Depending on the applied potential, spontaneous BH(4)(-) hydrolysis can compete with the direct BOR. The goal of the present work is to provide more insight into the behavior of smooth Pt electrodes toward the BOR, by coupling in situ infrared reflectance spectroscopy with electrochemistry. The measurements were performed on a Pt electrode in 1 M NaOH/1 M NaBH(4), so as to detect the reaction intermediate species generated as a function of the applied potential. Several bands were monitored in the B-H ((v) over bar approximate to 1180, 1080, and 972 cm(-1)) and B-O ((v) over bar = 1325 and similar to 1425 cm(-1)) bond regions upon increased electrode polarization. These absorption bands, which appear sequentially and were already detected for similar measurements on Au electrodes, are assigned to BH(3), BH(2), and BO(2)(-) species. In light of these experimental data and previous results obtained in our group for Pt- or Au-based electrodes, possible initial elementary steps of the BOR on platinum electrodes are proposed and discussed according to the relevant literature data.

José Feliciano de Castilho e a tradição clássica no século XIX: a tradução da Farsália

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

A macroscopic kinetic model for DNA polymerase elongation and high-fidelity nucleotide election

The enzymatically catalyzed template-directed extension of ssDNA/primer complex is an impor-tant reaction of extraordinary complexity. The DNA polymerase does not merely facilitate the insertion of dNMP, but it also performs rapid screening of substrates to ensure a high degree of fidelity. Several kinetic studies have determined rate constants and equilibrium constants for the elementary steps that make up the overall pathway. The information is used to develop a macro-scopic kinetic model, using an approach described by Ninio [Ninio J., 1987. Alternative to the steady-state method: derivation of reaction rates from first-passage times and pathway probabili-ties. Proc. Natl. Acad. Sci. U.S.A. 84, 663–667]. The principle idea of the Ninio approach is to track a single template/primer complex over time and to identify the expected behavior. The average time to insert a single nucleotide is a weighted sum of several terms, in-cluding the actual time to insert a nucleotide plus delays due to polymerase detachment from ei-ther the ternary (template-primer-polymerase) or quaternary (+nucleotide) complexes and time delays associated with the identification and ultimate rejection of an incorrect nucleotide from the binding site. The passage times of all events and their probability of occurrence are ex-pressed in terms of the rate constants of the elementary steps of the reaction pathway. The model accounts for variations in the average insertion time with different nucleotides as well as the in-fluence of G+C content of the sequence in the vicinity of the insertion site. Furthermore the model provides estimates of error frequencies. If nucleotide extension is recognized as a compe-tition between successful insertions and time delaying events, it can be described as a binomial process with a probability distribution. The distribution gives the probability to extend a primer/template complex with a certain number of base pairs and in general it maps annealed complexes into extension products.

Computational investigations of ion conduction mechanisms using enhanced sampling methods

Proper ion channels’ functioning is a prerequisite for a normal cell and disorders involving ion channels, or channelopathies, underlie many human diseases. Long QT syndromes (LQTS) for example may arise from the malfunctioning of hERG channel, caused either by the binding of drugs or mutations in HERG gene. In the first part of this thesis I present a framework to investigate the mechanism of ion conduction through hERG channel. The free energy profile governing the elementary steps of ion translocation in the pore was computed by means of umbrella sampling simulations. Compared to previous studies, we detected a different dynamic behavior: according to our data hERG is more likely to mediate a conduction mechanism which has been referred to as “single-vacancy-like” by Roux and coworkers (2001), rather then a “knock-on” mechanism. The same protocol was applied to a model of hERG presenting the Gly628Ser mutation, found to be cause of congenital LQTS. The results provided interesting insights about the reason of the malfunctioning of the mutant channel. Since they have critical functions in viruses’ life cycle, viral ion channels, such as M2 proton channel, are considered attractive targets for antiviral therapy. A deep knowledge of the mechanisms that the virus employs to survive in the host cell is of primary importance in the identification of new antiviral strategies. In the second part of this thesis I shed light on the role that M2 plays in the control of electrical potential inside the virus, being the charge equilibration a condition required to allow proton influx. The ion conduction through M2 was simulated using metadynamics technique. Based on our results we suggest that a potential anion-mediated cation-proton exchange, as well as a direct anion-proton exchange could both contribute to explain the activity of the M2 channel.

Nucleotide binding-promoted conformational changes release a nonnative polypeptide from the Escherichia coli chaperonin GroEL.

The Escherichia coli chaperonins GroEL and GroES facilitate the refolding of polypeptide chains in an ATP hydrolysis-dependent reaction. The elementary steps in the binding and release of polypeptide substrates to GroEL were investigated in surface plasmon resonance studies to measure the rates of binding and dissociation of a normative variant of subtilisin. The rate constants determined for GroEL association with and dissociation from this variant yielded a micromolar dissociation constant, in agreement with independent calorimetric estimates. The rate of GroEL dissociation from the nonnative chain was increased significantly in the presence of 5'-adenylylimidodiphosphate (AMP-PNP), ADP, and ATP, yielding maximal values between 0.04 and 0.22 s(-1). The sigmoidal dependence of the dissociation rate on the concentration of AMP-PNP and ADP indicated that polypeptide dissociation is limited by a concerted conformational change that occurs after nucleotide binding. The dependence of the rate of release on ATP exhibited two sigmoidal transitions attributable to nucleotide binding to the distal and proximal toroid of a GroEL-polypeptide chain complex. The addition of GroES resulted in a marked increase in the rate of nonnative polypeptide release from GroEL, indicating that the cochaperonin binds more rapidly than the dissociation of polypeptides. These data demonstrate the importance of nucleotide binding-promoted concerted conformational changes for the release of chains from GroEL, which correlate with the sigmoidal hydrolysis of ATP by the chaperonin. The implications of these findings are discussed in terms of a working hypothesis for a single cycle of chaperonin action.

Investigação do mecanismo cinético da reação de redução de oxigênio em solventes não aquosos

O aumento no consumo energético e a crescente preocupação ambiental frente à emissão de gases poluentes criam um apelo mundial favorável para pesquisas de novas tecnologias não poluentes de fontes de energia. Baterias recarregáveis de lítio-ar em solventes não aquosos possuem uma alta densidade de energia teórica (5200 Wh kg-1), o que as tornam promissoras para aplicação em dispositivos estacionários e em veículos elétricos. Entretanto, muitos problemas relacionados ao cátodo necessitam ser contornados para permitir a aplicação desta tecnologia, por exemplo, a baixa reversibilidade das reações, baixa potência e instabilidades dos materiais empregados nos eletrodos e dos solventes eletrolíticos. Assim, neste trabalho um modelo cinético foi empregado para os dados experimentais de espectroscopia de impedância eletroquímica, para a obtenção das constantes cinéticas das etapas elementares do mecanismo da reação de redução de oxigênio (RRO), o que permitiu investigar a influência de parâmetros como o tipo e tamanho de partícula do eletrocatalisador, o papel do solvente utilizado na RRO e compreender melhor as reações ocorridas no cátodo dessa bateria. A investigação inicial se deu com a utilização de sistemas menos complexos como uma folha de platina ou eletrodo de carbono vítreo como eletrodos de trabalho em 1,2-dimetoxietano (DME)/perclorato de lítio (LiClO4). A seguir, sistemas complexos com a presença de nanopartículas de carbono favoreceu o processo de adsorção das moléculas de oxigênio e aumentou ligeiramente (uma ordem de magnitude) a etapa de formação de superóxido de lítio (etapa determinante de reação) quando comparada com os eletrodos de platina e carbono vítreo, atribuída à presença dos grupos laterais mediando à transferência eletrônica para as moléculas de oxigênio. No entanto, foi observada uma rápida passivação da superfície eletrocatalítica através da formação de filmes finos de Li2O2 e Li2CO3 aumentando o sobrepotencial da bateria durante a carga (diferença de potencial entre a carga e descarga > 1 V). Adicionalmente, a incorporação das nanopartículas de platina (Ptnp), ao invés da folha de platina, resultou no aumento da constante cinética da etapa determinante da reação em duas ordens de magnitude, o qual pode ser atribuído a uma mudança das propriedades eletrônicas na banda d metálica em função do tamanho nanométrico das partículas, e estas modificações contribuíram para uma melhor eficiência energética quando comparado ao sistema sem a presença de eletrocatalisador. Entretanto, as Ptnp se mostraram não específicas para a RRO, catalisando as reações de degradação do solvente eletrolítico e diminuindo rapidamente a eficiência energética do dispositivo prático, devido ao acúmulo de material no eletrodo. O emprego de líquido iônico como solvente eletrolítico, ao invés de DME, promoveu uma maior estabilização do intermediário superóxido formado na primeira etapa de transferência eletrônica, devido à interação com os cátions do líquido iônico em solução, o qual resultou em um valor de constante cinética da formação do superóxido de três ordens de magnitude maior que o obtido com o mesmo eletrodo de carbono vítreo em DME, além de diminuir as reações de degradação do solvente. Estes fatores podem contribuir para uma maior potência e ciclabilidade da bateria de lítio-ar operando com líquidos iônicos.

Competitive processes in controlled cationic ring-opening polymerization of oxetane:a Lotka-Volterra predator-prey model of two growing species competing for the same resources

The activation-deactivation pseudo-equilibrium coefficient Qt and constant K0 (=Qt x PaT1,t = ([A1]x[Ox])/([T1]x[T])) as well as the factor of activation (PaT1,t) and rate constants of elementary steps reactions that govern the increase of Mn with conversion in controlled cationic ring-opening polymerization of oxetane (Ox) in 1,4-dioxane (1,4-D) and in tetrahydropyran (THP) (i.e. cyclic ethers which have no homopolymerizability (T)) were determined using terminal-model kinetics. We show analytically that the dynamic behavior of the two growing species (A1 and T1) competing for the same resources (Ox and T) follows a Lotka-Volterra model of predator-prey interactions. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Adsorption Calorimetry for Energy Conversion Technologies: Applications in Organic Photovoltaics, Catalysis, and Atomic Layer Deposition

Thesis (Ph.D.)--University of Washington, 2016-07

First steps in Zulu; being an elementary grammar of the Zulu language,

Spine title: First steps in Zulu-Kafir.

Proactive and Preventive Student Welfare Activities in Finnish Preschool and Elementary School: Handling of Transition to Formal Schooling and a National Anti-Bullying Program as Examples

Prerequisites and effects of proactive and preventive psycho-social student welfare activities in Finnish preschool and elementary school were of interest in the present thesis. So far, Finnish student welfare work has mainly focused on interventions and individuals, and the voluminous possibilities to enhance well-being of all students as a part of everyday school work have not been fully exploited. Consequently, in this thesis three goals were set: (1) To present concrete examples of proactive and preventive psycho-social student welfare activities in Finnish basic education; (2) To investigate measurable positive effects of proactive and preventive activities; and (3) To investigate implementation of proactive and preventive activities in ecological contexts. Two prominent phenomena in preschool and elementary school years—transition to formal schooling and school bullying—were chosen as examples of critical situations that are appropriate targets for proactive and preventive psycho-social student welfare activities. Until lately, the procedures concerning both school transitions and school bullying have been rather problem-focused and reactive in nature. Theoretically, we lean on the bioecological model of development by Bronfenbrenner and Morris with concentric micro-, meso-, exo- and macrosystems. Data were drawn from two large-scale research projects, the longitudinal First Steps Study: Interactive Learning in the Child–Parent– Teacher Triangle, and the Evaluation Study of the National Antibullying Program KiVa. In Study I, we found that the academic skills of children from preschool–elementary school pairs that implemented several supportive activities during the preschool year developed more quickly from preschool to Grade 1 compared with the skills of children from pairs that used fewer practices. In Study II, we focused on possible effects of proactive and preventive actions on teachers and found that participation in the KiVa antibullying program influenced teachers‘ self-evaluated competence to tackle bullying. In Studies III and IV, we investigated factors that affect implementation rate of these proactive and preventive actions. In Study III, we found that principal‘s commitment and support for antibullying work has a clear-cut positive effect on implementation adherence of student lessons of the KiVa antibullying program. The more teachers experience support for and commitment to anti-bullying work from their principal, the more they report having covered KiVa student lessons and topics. In Study IV, we wanted to find out why some schools implement several useful and inexpensive transition practices, whereas other schools use only a few of them. We were interested in broadening the scope and looking at local-level (exosystem) qualities, and, in fact, the local-level activities and guidelines, along with teacherreported importance of the transition practices, were the only factors significantly associated with the implementation rate of transition practices between elementary schools and partner preschools. Teacher- and school-level factors available in this study turned out to be mostly not significant. To summarize, the results confirm that school-based promotion and prevention activities may have beneficial effects not only on students but also on teachers. Second, various top-down processes, such as engagement at the level of elementary school principals or local administration may enhance implementation of these beneficial activities. The main message is that when aiming to support the lives of children the primary focus should be on adults. In future, promotion of psychosocial well-being and the intrinsic value of inter- and intrapersonal skills need to be strengthened in the Finnish educational systems. Future research efforts in student welfare and school psychology, as well as focused training for psychologists in educational contexts, should be encouraged in the departments of psychology and education in Finnish universities. Moreover, a specific research centre for school health and well-being should be established.