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In der vorliegenden Arbeit wird die Aufklärung der Konformation von Peptiden mit speziell modifizierten Aminosäuren beschrieben. Die Methoden der theoretischen Chemie (Quantenchemie, Molekülmechanik, Moleküldynamik) bilden dabei die Grundlage der Konformationsanalysen. Durch systematische Anwendung dieser Methoden werden im ersten Teil der Arbeit die konformativen Eigenschaften verschiedener [beta]-Aminosäuren und ihrer Oligomere ([beta]-Peptide) untersucht. Aus diesen Ergebnissen werden anschließend Regeln für das Sekundärstrukturdesign von ß-Peptiden abgeleitet. Der zweite Teil beschäftigt sich mit der theoretischen Konformationsanalyse von [alpha]- Hydrazinosäuren und ihrer Oligomere (Hydrazinopeptide). Aus den gewonnenen Erkenntnissen über die Ausbildung charakteristischer Sekundärstrukturelemente in diesen Verbindungen wird ebenfalls ein Regelwerk für das Design von Sekundärstrukturen aufgestellt. / The present work describes the conformational characteristics of pepttides with specifically modified amino acid constituents. For this purpose, the methods of theoretical chemistry (quantum chemistry, molecular mechanics, molecular dynamics) are utilisied for the conformational analyses. The conformation of various [beta]-amino acids and their oligomers ([beta]-peptides) are inverstigated in the first part of this work applying these methods. Rules for the design of definite secondary structures in [beta]-peptides are then derived from the obtained results. In the second part, systematic theoretical conformational analyses on [alpha]-hydrazino acids and their oligomers (hydrazino peptides) are described. The results are then used to compile a set of rules for the formation of characteriasitc secondary structures in this class of compounds.

<p>Bridging the accuracy of ab initio (AI) QM/MM with the efficiency of semi-empirical<br> (SE) QM/MM methods has long been a goal in computational chemistry. This dissertation<br> presents four ∆-Machine learning schemes aimed at achieving this objective. Firstly, the in-<br> corporation of negative force observations into the Gaussian process regression (GPR) model,<br> resulting in GPR with derivative observations, demonstrates the remarkable capability to<br> attain high-quality potential energy surfaces, accurate Cartesian force descriptions, and reli-<br> able free energy profiles using a training set of just 80 points. Secondly, the adaptation of the<br> sparse streaming GPR algorithm showcases the potential of memory retention from previous<br> phasespace, enabling energy-only models to converge using simple descriptors while faith-<br> fully reproducing high-quality potential energy surfaces and accurate free energy profiles.<br> Thirdly, the utilization of GPR with atomic environmental vectors as input features proves<br> effective in enhancing both potential energy surface and free energy description. Further-<br> more, incorporating derivative information on solute atoms further improves the accuracy<br> of force predictions on molecular mechanical (MM) atoms, addressing discrepancies arising<br> from QM/MM interaction energies between the target and base levels of theory. Finally, a<br> comprehensive comparison of three distinct GPR schemes, namely GAP, GPR with an aver-<br> age kernel, and GPR with a system-specific sum kernel, is conducted to evaluate the impact<br> of permutational invariance and atomistic learning on the model’s quality. Additionally, this<br> dissertation introduces the adaptation of the GAP method to be compatible with the sparse<br> variational Gaussian processes scheme and the streaming sparse GPR scheme, enhancing<br> their efficiency and applicability. Through these four ∆-Machine learning schemes, this dis-<br> sertation makes significant contributions to the field of computational chemistry, advancing<br> the quest for accurate potential energy surfaces, reliable force descriptions, and informative<br> free energy profiles in QM/MM simulations.<br> </p>

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Disertacijoje nagrinėjamas galimas aplinkos poveikis organinių molekulių elektroninių būsenų savybėms. Tam tikslui yra naudojami kompiuterizuotieji kvantinės mechanikos metodai, kuriais remiantis nagrinėjamos įvairių molekulių savybės. Ištirtos 2-(N-metil-α-iminoethyl)-fenol ir N-triphenylmethylsalicylidene imine molekelulių, esančių poliniame tirpiklyje, struktūros pagrindinėje ir sužadintose elektroninėse būsenose. Pirmą kartą parodyta, kad, norint gauti teisingą kokybinį ir artimą kiekybiniam vidujmolekulinės protono pernašos potencinės energijos paviršių, būtina atsižvelgti į polinių tirpiklio molekulių kuriamą vandenilinių ryšių tinklą bei į nulinių svyravimų energijas. Pastarieji ir nulemia protono pernašos vyksmo kryptį bei efektyvumą. Parodyta, kad anilų klasės molekulių konformerų susiformavimas priklauso nuo tirpiklio poliškumo, o jų susidarymas savo ruožtu konkuruoja su klasterių iš tirpiklio molekulių susiformavimo galimybėmis. Pirmą kartą parodyta, kad dipolinio momento vertė bakteriorodopsine yra nulemta membranos paviršiuose esančių radikalų. Pademonstruota, kad stilbazolio molekulė deformuojasi ir sudaro naujus konformerus (pademonstruota dviejų formų atsiradimo galimybė) tik esant molekulėms tirpalo apsuptyje. Šis rezultatas paaiškino eksperimente stebimus skirtuminių spektrinių pokyčių evoliucijos prigimtį. Apskaičiuotos ir išanalizuotos karotinoidų - luteino, violaksantino ir zeaksantino molekulių - žemiausios sužadintos elektroninės būsenos. Parodyta... [toliau žr. visą tekstą] / To explore changes caused by the environment on the internal characteristics of an organic molecule is the objective of the thesis. For this purpose we investigate a variety of organic molecules. Using various methods of quantum mechanics calculations possible influence of a polar solvent on the ground and excited states of 2-(N-metil-α-iminoethyl)-fenol and N-triphenylmethylsalicylidene imine is considered. It is shown for the first time that in order to obtain the correct qualitative and quantitative interpretation of possible pathways of the intermolecular proton transfer the hydrogen network of the polar solvent molecules together with the zero point energy have to be taken into consideration. It is also shown that conformational variability of anil-type molecules in polar solvents is competing with clusters formation of solvent molecules. It is shown for the first time that the dipole moment of bacteriorhodopsin is mainly defined by cytoplasmic and extracellular coils on the surfaces of the membrane. It is also demonstrated that the stilbazole molecule experiences the deformation resulting in formation of new conformers (at least two forms are present) in the solvent surrounding. The experimental data of the transient spectroscopy were explained in the basis of these model calculations. The lowest excited states of carotinoids, such as lutein, zeaxanthin and violoxantin are calculated and analyzed. Sensitivity of the excited electronic state on the polar environment is... [to full text]

As vias de sinalização celular por meio de moléculas são um dos principais meios de controle funcional de um organismo. O entendimento das funções de moléculas sinalizadoras facilita a compreensão das vias metabólicas de um organismo, assim possibilitando uma melhor compreensão de vários eventos biológicos e também de várias doenças. A sinalização pelo ácido retinóico (AR), e seus derivados, é responsável pelo controle de várias funções, por exemplo: crescimento celular, diferenciação celular, formação da retina, desenvolvimento cardíaco e também relacionado a várias patologias como diabetes, obesidades, cânceres, e doenças cardiovasculares. A ação do ácido retinóico é controlada em dois níveis: no metabolismo de síntese/degradação e na sua utilização na sinalização para a expressão gênica. A maquinaria que controla o metabolismo inclui as enzimas de síntese do AR (aldeído desidrogenase ALDH) e as enzimas de degradação do AR (Cyp26), que controlam a distribuição espaço-temporal do AR durante a embriogênese. As ALDHs são enzimas NAD(P)+ dependentes, que oxidam uma ampla gama de aldeídos para os seus correspondentes ácidos carboxílicos, sendo ALDH1A2 a principal enzima na transformação de retinal em ácido retinóico. A maquinaria da sinalização celular por AR contém os receptores nucleares controlados por AR (RARs) que estão envolvidos com o controle da transcrição gênica. Os mecanismos de controle de expressão mais comuns são os que ocorrem na fase transcricional. Um desses mecanismos envolve proteínas que se ligam às regiões promotoras de transcrição, representadas por trechos de DNA que geralmente estão localizados próximo à região de início da transcrição, mas que também podem estar a centenas ou até milhares de pares de bases desse início. Essas proteínas modulam a maquinaria transcricional, podendo ativá-la ou inibi-la. A associação de várias técnicas como a biologia molecular, bioinformática, filogenia, análises estruturais de biomoléculas, mecânica molecular e métodos termodinâmicos tem se mostrado uma poderosa abordagem para compreensão de sistemas biológicos simplificando e agilizando o desenvolvimento do conhecimento científico. Nessa direção, esse estudo desenvolveu duas análises: a primeira estudando a evolução das funções das enzimas ALDH, utilizando-se de técnicas de genômica combinatória, filogenia, bioinformática, estrutura de biomoléculas e de biologia do desenvolvimento, tentando compreender o modo como as ALDHs, que apresentam as seqüências de aminoácidos bastante similares, puderam divergir para gerar funções diversas como a destoxificação e a sinalização. Para este estudo foram analisados os genomas de 487 organismos em busca de seqüências de ALDHs e também o genoma do organismo modelo Branchiostoma floridae. Foram obtidas 190 seqüências que foram utilizadas em uma análise filogenética para tentar compreender a função primordial e também para definir grupos de aminoácidos candidatos a marcadores das diferentes famílias de ALDHs. Essas 190 seqüências também foram modeladas estruturalmente e analisada a forma e o volume do canal onde se aloja o aldeído a ser oxidado. A partir dessas informações foi possível prever que as ALDHs passaram das funções ancestrais de controle do padrão corporal para algo mais abrangente como funções protetoras. A segunda análise, utilizando-se das estruturas tridimensionais dos fatores de transcrição ligados ao DNA em diferentes posições e submetendo esses complexos a processos de mecânica molecular, cálculos termodinâmicos e análises das ligações de hidrogênio para tentar prever os mais prováveis sítios de interação entre os receptores e o DNA. O modelo escolhido para essa análise foram os fatores de transcrição regulados por ácido retinóico o RAR e RXR utilizando a região promotora do gene RARE-2 para avaliar as mais prováveis regiões de ligação desses fatores. Para esse estudo foram construídos 71 complexos proteína-DNA que foram submetidos a processos de mecânica molecular e cálculos termodinâmicos. A partir dessas informações foi possível prever uma região de maior afinidade entre o fator de transcrição e o DNA. As análises de ligações de hidrogênio possibilitaram definir exatamente a região de interação entre os fatores de transcrição e o DNA, e também descrever as interações moleculares responsáveis pela especificidade da interação. / Cellular signaling paths through molecules are one of the main processes of functional control of an organism. The comprehension of signaling molecules functions enables one to understand the metabolic pathways of an organism, along with related biological events and several diseases. The signaling through retinoic acid (RA) and its secondary products is responsible for controlling several functions, such as cellular growth and differentiation, retinas formation and cardio development, and is also related to several pathologies such as diabetes, obesity, cancers and cardiovascular disorders. There are two levels of control of retinoic acid activity: synthesis/degradation metabolism and its use in gene expression signaling. The machinery that controls the metabolism includes RAs synthesis (aldehyde dehydrogenase ALDH) and degradation (Cyp26) enzymes, which control the space-temporal distribution of RA during the embryogenesis. The ALDHs are NAD(P)+ dependent enzymes that oxidize many types of aldehydes into the related carboxylic acids, being the ALDH1A2 the main enzyme involved in the process of transformation of retinal into retinoic acid. The machinery of cellular signaling through RA contains the nuclear receptors controlled by RA (RARs) that are involved in the control of gene transcription. The most common mechanisms of expression control are the ones that occur during the transcriptional phase. One of these mechanisms involves proteins that bind to the transcription promoter regions, represented by DNA sequences that are usually located close to the region where the transcription starts, but can also be hundreds or thousands of base pairs apart from the starting point. These proteins modulate the transcriptional machinery, being responsible for both its activation and inhibition. The association of several techniques as molecular biology, bioinformatics, phylogeny, structural analysis of biomolecules, molecular mechanics and thermodynamic methods has been shown as a powerful tool for the understanding of biological systems, simplifying and speeding up the production of related scientific knowledge. Facing this direction, the present study developed two analyses. The first one studied the evolution of ALDH enzymes functions, using the techniques of combinatory genomic, phylogeny, bioinformatics, structure of biomolecules and developmental biology, in the attempt of understanding how the ALDHs could diverge and acquire different functions as detoxification and signaling, despite the fact that they have very similar aminoacid sequences. For this study, ALDHs sequences were searched for in the genome of 487 organisms plus the model organisms, Branchiostoma floridae. All 190 sequences obtained were used in a phylogenetic analysis, in the attempt of understanding the primordial function of the enzyme and defining possible groups of conserved aminoacids in the different families of ADLHs. These 190 sequences were also structurally modeled and the shape and volume of the channel where the aldehyde is placed to be oxidized were analyzed. Based on this information, it became possible to predict that the ALDHs moved from ancestral functions of corporal pattern control to a wider spectrum of protection functions. For the second analysis we submitted the complex formed by tridimensional structures of the transcriptional factors bond to DNA in different positions to processes of molecular mechanics, thermodynamic calculi and analysis of the hydrogen bonds, in order to predict the most probable sites of interaction between the receptors and the DNA. The model chosen for this analysis were the transcription factors regulated by retinoic acid, RAR and RXR, using the promoter region of the gene RARE-2 to assay the most probable binding regions of these factors. For this study, 71 protein-DNA complexes were built and submitted to processes of molecular mechanics and thermodynamic calculi. Based on the resulting data, it became possible to predict a region of greater affinity between the transcription factor and the DNA. The analyses of hydrogen bonds enabled us to define the exact region where the interaction between the transcription factor and the DNA takes place and also enabled us to describe the molecular interactions responsible for the specificity of this interaction.

Submitted by Rosivalda Pereira (mrs.pereira@ufma.br) on 2017-06-07T18:40:06Z No. of bitstreams: 1 ArivaldoCarvalho.pdf: 4594687 bytes, checksum: c5792781a97f8174ae6dcd9a0bfbd359 (MD5) / Made available in DSpace on 2017-06-07T18:40:06Z (GMT). No. of bitstreams: 1 ArivaldoCarvalho.pdf: 4594687 bytes, checksum: c5792781a97f8174ae6dcd9a0bfbd359 (MD5) Previous issue date: 2010-01-21 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / With the aim of the development of new nanodevices, there is great interest in understand the electronic properties of nanostructured materials. Above all, how to modify the electronic properties of nanostructures already well known in a controlled manner. With this goal, many methodologies and experiments has been developed. We studied the an entirely through computer simulation atomistic interaction of amino glycine with the surface of graphene using two methods, classical and quantum, for both modules use Materials Studio (Accelrys), and the Forcit Dmol3 states that are Art in atomistic simulations. From the classical point of view, we used force fields universal to describe the interactions, and the quantum point of view, the method of density functional. The methodology consisted basically realize a scan with glycine in different orientations on the surface of the graphene sheet grid in a considerable build a 3D map of potential interaction that enables us to accurately define where are enough sites and orientations of the amino acid glycine to more energetically favorable for adsorption. From the selection of the best candidates obtained from calculations in classical mechanics, we performed electronic structure calculations using the method DFT (Density Functional Theory) to estimate the binding energy and in that regime adsorption occurs. In addition, we obtained the electron density of the system and did Mulliken population analysis as well. / Com a finalidade do desenvolvimentos de novos nanodispositivos, há um grande interesse em conhecer as propriedades eletrônicas de materias nanoestruturados. Sobretudo, como modificar as propriedades eletrônicas de nanoestruturas já bem conhecidas de forma controlada. Com este objetivo, muitas metodologias e experimentos tem sido desenvolvidos. Estudou-se de forma inteiramente atomística através de simulação computacional a interação do aminoácido glicina com a superfície do grafeno utilizando dois métodos , clássico e quântico, para tanto utilizamos os módulos do Materials Studio (Accelrys), o Forcite e o Dmol3 que são estados de arte em simulações atomísticas. Do ponto de vista clássico, utilizou-se campos de força universal para descrever as interações; e do ponto de vista quântico, utilizamos o método do funcional da densidade. A metodologia consistiu basicamente em realizarmos um "scan"com a glicina em diversas orientações sobre a superfície da folha de grafeno num grid considerável, construímos uma mapa 3D do potencial de interação que nos possibilita conhecer com precisão suficiente onde são os sítios e as orientações do aminoácido glicina que mais favoráveis energeticamente para a adsorção. A partir da seleção dos melhores candidatos obtidos através dos cálculos de mecânica clássica, realizamos cálculos de estrutura eletrônica utilizando o método DFT (Density Functional Theory) a fim de estimar a energia de ligação e em que regime ocorre a adsorção. Além disso, nós obtivemos a densidade eletrônica do sistema e fizemos uma análise populacional de Mulliken também.

Nanotubos de carbono e polímeros condutores são fortes candidatos à miniaturização dos componentes eletrônicos disponíveis atualmente. Estudos teóricos afirmaram que 1/3 dos nanotubos seriam metálicos, enquanto que os outros seriam semicondutores, mas alguns grupos reportaram medidas experimentais evidenciando um pequeno gap eletrônico em tubos considerados metálicos. Protótipos de transístores compostos de nanotubos e moléculas orgânicas conjugadas foram propostos e foi observado que o recobrimento dos tubos por moléculas de pentaceno tornava os dispositivos menos suscetíveis à deposição de impurezas, o que diminuía a histerese na curva característica i x V, ao mesmo tempo que a formação de cristais de pentaceno era favorecida. Neste trabalho estudamos a estrutura eletrônica dos nanotubos (5,5) e (9,0) través de DFT e observamos presença de um gap nesses sistemas, assim como uma deformação de suas estruturas de ligações químicas, evidenciando a distorção de Peierls. O efeito do termo de troca de Hartree-Fock introduzido no funcional B3LYP foi avaliado variando-se seu peso e observando as propriedades destes sistemas. Em uma segunda etapa, utilizamos mecânica molecular e dinâmica molecular clássica com o campo de forças CVFF 950 e observamos a formação de estruturas de pentaceno em volta dos tubos, evidenciando o favorecimento da formação de cristais do mesmo quando depositado sobre os nanotubos. / Carbon Nanotubes and conducting polymers are strong candidates for use in nanoscale electronic devices. Theoretical studies claimed that 1/3 of the nanotubes are metallic, while the others are semiconductors, but some groups have reported experimental measurements of a small electronic gap in tubes considered metallic. Prototype transistors made of nanotubes and organic conjugated molecules were proposed and it has been noticed that the coverage of the tubes by pentacene molecules made those trasistors less susceptible to impurity deposition, reducing the hysteresis in the characteristic I x V curve, while the formation of pentacene cristals was favored. In this work, we studied the electronic structure of the nanotubes (5,5) and (9,0) using DFT and noticed an electronic gap in those systems, as well as a deformation of their structures, similar to a Peierls distortion. The effect of the Hartree-Fock exchange included in the B3LYP functional was studied, as we varied its weight to obtain some properties of those systems. Later, we used molecular mechanics and classical molecular dynamics with the CVFF 950 force field and obtained structures compatible with pentacene crystals around the tubes, showing that the tubes in fact favor the formation of of these structures around them.

La protéase du VIH-1 est une cible de choix dans le traitement du SIDA, car l’inhibition de son activité protéolytique contrecarre la réplication virale. Dans ce contexte, une approche de conception de novo d’inhibiteurs non peptidiques de cet enzyme, réalisée au sein de notre laboratoire, avait permis d’épingler une famille originale de complexes métallo-organiques au cuivre (II). Au cours de cette thèse, nous avons entrepris la caractérisation physico-chimique et structurale de ces composés afin d’élucider leur mode d’interaction avec la protéase, en nous appuyant sur diverses techniques expérimentales (DRX, RPE, ESI-MS) et théoriques(mécanique moléculaire, SIBFA). En particulier, nous avons montré que la stabilité thermodynamique de ces complexes en solution était indispensable à toute activité biologique. L’adaptation de la méthode SIBFA aux complexes au cuivre (II) nous a permis d’étudier les phénomènes énergétiques intervenant dans leur stabilité. Enfin, nous avons réuni les critères structuraux responsables de l’activité anti-protéolytique de ces complexes au sein d’un modèle pharmacophorique optimalisé./HIV-1 protease is a main target for the AIDS treatment, because its inhibition blocks the viral replication. De novo drug design, previously conducted in our laboratory, had pointed out several copper (II) chelates as a new family of non peptidic protease inhibitors. In order to provide a better understanding of their structure-activity relationships, we performed the physico-chemical characterization of these compounds using experimental (XRD, EPR, ESIMS)and theoretical (molecular mechanics, SIBFA method) techniques. We demonstrated that the thermodynamic stability of the complexes is an essential property to provide inhibitory activity. The SIBFA procedure adapted to copper (II) complexes helped us to study the energetics involved in the stability process. From our results, we derived a pharmacophore model describing the structural properties needed to achieve a good inhibition of the enzyme.

A technology for optimization of potential parameters from condensed phase simulations (POP) is discussed and illustrated. It is based on direct calculations of the derivatives of macroscopic observables with respect to the potential parameters. The derivatives are used in a local minimization scheme, comparing simulated and experimental data. In particular, we show that the Newton Trust-Region protocol allows for accurate and robust optimization. POP is illustrated for a toy problem of alanine dipeptide and is applied to folding of the peptide WAAAH. The helix fraction is highly sensitive to the potential parameters while the slope of the melting curve is not. The sensitivity variations make it difficult to satisfy both observations simultaneously. We conjecture that there is no set of parameters that reproduces experimental melting curves of short peptides that are modeled with the usual functional form of a force field. We then apply the newly developed technology to study the liquid mixture of tert-butanol and water. We are able to obtain, after 4 iterations, the correct phase behavior and accurately predict the value of the Kirkwood Buff (KB) integrals. We further illustrate that a potential that is determined solely by KB information, or the pair correlation function, is not necessarily unique. / text