No description available.

In this thesis, we have employed two computational methods, molecular dynamics (MD) and hybrid quantum mechanics/molecular mechanics (QM/MM) MD simulations with umbrella sampling (US), to gain insights into the molecular mechanism governing the molecular recognition and reactivity in several protein-ligand complexes. Three systems involving protein-ligand interactions are examined in this dissertation utilizing well-established computational methodologies and mathematical modeling. The three proteins studied here are acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1). These enzymes are known to interact with a variety of ligands. AChE dysfunction caused by organophosphorus (OP) chemicals is a severe hazard since AChE is a critical enzyme in neurotransmission. Oximes are chemical compounds that can reactivate inhibited AChE; hence in the development of better oximes, it is critical to understand the mechanism through which OPs block AChE. We have described the covalent inhibition mechanism between AChE and the OP insecticide phorate oxon and its more potent metabolites and established their free energy profiles using QM/MM MD-US for the first time. Our results suggest a concerted mechanism and provide insights into the challenges in reactivating phorate oxon inhibited AChE. Reactivating BChE is another therapeutic approach to detoxifying circulating OP molecules before reaching the target AChE. We explored the covalent modification of BChE with phorate oxon and its metabolites using hybrid quantum mechanics/molecular mechanics (QM/MM) umbrella sampling simulations (PM6/ff14SB) for the inhibition process. Our results reveal that the mechanism is distinct between the inhibitors. The PM6 methodology is a good predictor of these compounds' potency, which may efficiently help study OPs like phorate oxon with larger leaving groups. Finally, we investigated the interactions between Peptidyl-prolyl isomerase (PPIase), which consists of a peptidyl isomerase (PPIase) domain flexibly tethered to a smaller Trp-Trp (WW) protein-binding domain, and chimeric peptides based on the human histone H1.4 sequence (KATGAApTPKKSAKW), as well as the effects on inter-domain dynamics. Using explicit solvent MD simulations, simulated annealing, and native contact analysis, our modeling sugget that the residues in the N-terminal immediate to the pSer/Thr Pro site connect the PPIase and WW domains via a series of hydrogen bonds and native contacts.

<p>In this thesis, we present novel computational methods and frameworks to address the challenges associated with the determination of free energy profiles for condensed-phase chemical reactions using combined quantum mechanical and molecular mechanical (QM/MM) approaches. We focus on overcoming issues related to force matching, molecular polarizability, and convergence of free energy profiles. First, we introduce a method called Reaction Path-Force Matching in Collective Variables (RP-FM-CV) that efficiently carries out ab initio QM/MM free energy simulations through mean force fitting. This method provides accurate and robust simulations of solution-phase chemical reactions by significantly reducing deviations on the collective variables forces, thereby bringing simulated free energy profiles closer to experimental and benchmark AI/MM results. Second, we explore the role of pairwise repulsive correcting potentials in generating converged free energy profiles for chemical reactions using QM/MM simulations. We develop a free energy correcting model that sheds light on the behavior of repulsive pairwise potentials with large force deviations in collective variables. Our findings contribute to a deeper understanding of force matching models, paving the way for more accurate predictions of free energy profiles in chemical reactions. Next, we address the underpolarization problem in semiempirical (SE) molecular orbital methods by introducing a hybrid framework called doubly polarized QM/MM (dp-QM/MM). This framework improves the response property of SE/MM methods through high-level molecular polarizability fitting using machine learning (ML)-derived corrective polarizabilities, referred to as chaperone polarizabilities. We demonstrate the effectiveness of the dp-QM/MM method in simulating the Menshutkin reaction in water, showing that ML chaperones significantly reduce the error in solute molecular polarizability, bringing simulated free energy profiles closer to experimental results. In summary, this thesis presents a series of novel methods and frameworks that improve the accuracy and reliability of free energy profile estimations in condensed-phase chemical reactions using QM/MM simulations. By addressing the challenges of force matching, molecular polarizability, and convergence, these advancements have the potential to impact various fields, including computational chemistry, materials science, and drug design.</p>

Indiana University-Purdue University Indianapolis (IUPUI) / In this thesis, we present novel computational methods and frameworks to address the challenges associated with the determination of free energy profiles for condensed-phase chemical reactions using combined quantum mechanical and molecular mechanical (QM/MM) approaches. We focus on overcoming issues related to force matching, molecular polarizability, and convergence of free energy profiles. First, we introduce a method called Reaction Path-Force Matching in Collective Variables (RP-FM-CV) that efficiently carries out ab initio QM/MM free energy simulations through mean force fitting. This method provides accurate and robust simulations of solution-phase chemical reactions by significantly reducing deviations on the collective variables forces, thereby bringing simulated free energy profiles closer to experimental and benchmark AI/MM results. Second, we explore the role of pairwise repulsive correcting potentials in generating converged free energy profiles for chemical reactions using QM/MM simulations. We develop a free energy correcting model that sheds light on the behavior of repulsive pairwise potentials with large force deviations in collective variables. Our findings contribute to a deeper understanding of force matching models, paving the way for more accurate predictions of free energy profiles in chemical reactions. Next, we address the underpolarization problem in semiempirical (SE) molecular orbital methods by introducing a hybrid framework called doubly polarized QM/MM (dp-QM/MM). This framework improves the response property of SE/MM methods through high-level molecular polarizability fitting using machine learning (ML)-derived corrective polarizabilities, referred to as chaperone polarizabilities. We demonstrate the effectiveness of the dp-QM/MM method in simulating the Menshutkin reaction in water, showing that ML chaperones significantly reduce the error in solute molecular polarizability, bringing simulated free energy profiles closer to experimental results. In summary, this thesis presents a series of novel methods and frameworks that improve the accuracy and reliability of free energy profile estimations in condensed-phase chemical reactions using QM/MM simulations. By addressing the challenges of force matching, molecular polarizability, and convergence, these advancements have the potential to impact various fields, including computational chemistry, materials science, and drug design.

No description available.

Nous étudions l'hydratation des ions fluorures et iodures, paradigmes des ions structurants et déstructurants, grâce ` a une étude structurale et dynamique. Concernant la structure, nous observons l'opposé de ce que la définition classique des structurants/déstructurants suggère (F- déforme le réseau de liaisons hydrogènes et I- l'améliore). Ensuite, nous calculons les temps de vie des liaisons hydrogènes halogénures-eau ainsi que les temps de résidence et de réorientation des molécules d'eau de la première couche des anions. Ces mesures confirment la grande stabilité, induite par la force de la liaison H, de la couche d'hydratation de F - et la grande mobilité de l'eau dans la couche d'hydratation de I -. Puis, nous appliquons le modèle étendu de saut (GJM) pour une molécule d'eau dans la couche d'hydratation des ions. Pour F -, la situation inhabituelle, où les deux mécanismes de réorientation (de saut et diffusif) ont la même contribution, est due à la force de la liaison H qui inhibe les sauts de la liaison OH. Dans un second temps, nous appliquons les méthodes précédentes sur l'hydratation du nitrate en utilisant des simulations QM/MM. Les résultats sont similaires pour la structure et la dynamique à ceux de l'iodure et le GJM révèle deux mécanismes de saut pour l'eau initialement liée à Ono3- : un saut vers une autre molécule d'eau ou un saut vers un autre Ono3- . Enfin, grâce aux ordres de liaison et aux charges, nous mettons en évidence la rupture de symétrie du nitrate induite par l'eau, ainsi que la dynamique rapide d'interconversion entre les états du nitrate.

Les processus d'oxydo-réduction impliquant des molécules organiques se retrouvent très fréquemment dans les protéines. Ces réactions comprennent généralement des transferts d'électrons et de protons qui se traduisent dans le bilan réactionnel par des transferts couplés proton-électron, des transferts simples d'hydrogène, d'hydrure... Une des principales méthodes pour élucider ces mécanismes est fournie par l'évaluation de grandeurs thermodynamiques et cinétiques. Expérimentalement, ces informations sont cependant obtenues avec une résolution temporelle souvent limitée à la milli/microseconde. Les simulations numériques présentées ici complètent, à des échelles de temps plus courtes (femto, pico, nanosecondes), ces données expérimentales. Il existe de nombreuses méthodes de simulations dédiées à l'étude de mécanismes redox dans les protéines combinant la description quantique des réactifs (QM) nécessaire à l'étude des changements d'états électroniques et la description classique de l'environnement (MM), l'échantillonnage de conformations se faisant grâce à des simulations de dynamique moléculaire (MD). Ces méthodes diffèrent par la qualité de la description du mécanisme réactionnel et le coût en temps de calcul. L'objectif de cette thèse est d'étudier les mécanismes de différents processus impliquant des transferts de protons et d'électrons en recherchant à chaque fois les outils adaptés. Elle comporte trois parties : i) l'évaluation de potentiels redox de cofacteurs quinones ; ii) la description du mécanisme d'oxydation du L-lactate dans l'enzyme flavocytochrome b2 ; iii) la décomposition d'un transfert formel d'hydrure entre deux flavines au sein de la protéine EmoB. Dans le cas du calcul des potentiels redox, nous utilisons une méthode notée QM+MM où la description électronique se fait en phase gaz au niveau DFT tandis que les simulations de MD s'effectuent classiquement. Nous appliquons l'approximation de réponse linéaire (ARL) pour décrire la réponse du système aux étapes de changement d'état de protonation ou d'oxydation de la fonction quinone ce qui aboutit au calcul du potentiel redox théorique. Nous avons ainsi pu établir une courbe de calibration des résultats théoriques en fonction des données expérimentales, confirmant la validité de l'ARL pour les cofacteurs quinones dans l'eau. La méthode a été étendue à la protéine MADH mais les limites de l'ARL ont été atteintes du fait des fluctuations importantes de l'environnement. L'étude de l'oxydation du L-lactate en pyruvate repose sur le calcul de surfaces d'énergie libre au niveau AM1/MM. Ces surfaces sont obtenues à l'aide de simulations de MD biaisées puis corrigées à l'aide de calculs d'énergies DFT. Différents chemins de réactions impliquant les transferts d'un proton et d'un hydrure du substrat vers une histidine et une flavine respectivement ont pu être identifiés. Ces transferts peuvent être séquentiels ou concertés suivant la conformation du site actif ou les mutations effectuées. Les surfaces concordent avec les effets observés expérimentalement. Les barrières obtenues restent cependant supérieures à celles attendues ouvrant la voie à d'autres simulations. La décomposition du mécanisme de transfert d'hydrure en transfert d'électron et d'atome d'hydrogène s'appuie sur de longues simulations classiques et des calculs d'énergies au niveau DFT contrainte (cDFT)/MM. La DFT contrainte permet de décrire les états diabatiques associés au transfert d'électron à différents stades du transfert d'hydrogène. En appliquant l'ARL, nous pouvons construire des paraboles correspondant aux états diabatiques et déterminer la séquence des évènements de transfert d'électron et d'hydrogène. La comparaison entre milieux protéique et aqueux nous a permis d'établir que le rôle de la protéine dans le transfert d'hydrure global est de bloquer le transfert d'électron en l'absence du transfert d'hydrogène empêchant ainsi la formation de flavines semi-réduites.

Fourier transform infrared difference spectroscopy (FTIR DS) is widely used to study the structural details of electron transfer cofactors in photosynthetic protein complexes. In photosynthetic proteins quinones play an important role, functioning as a cofactor in light-driven electron transfer. In photosystem I (PS I) phylloquinone (PhQ) functions as an intermediary in electron transfer. To investigate the properties of PhQ that occupies the, so called, A1 binding site in PS I, time-resolved step-scan FTIR DS, with 5µs time resolution at 77K has been used. By replacing PhQ in the A1 binding site with specifically isotope labeled version, information on the vibrational frequencies associated specifically with the quinone in the binding site were obtained, which could be compared to the vibrational properties of quinone in solution or quinones in other protein binding sites. To further aid in assessing the origin of bands in the spectra, quantum mechanics /molecular mechanics (QM/MM) ONIOM type calculations were undertaken. ONIOM is an acronym for Our own N-layered Integrated molecular Orbital and molecular Mechanics. We find that the phytyl tail of PhQ does not play an important role in the orientation of PhQ in the A1 binding site. We also find that PhQ, in both neutral and reduced states, is strongly hydrogen bonded. To test and verify the applicability of our QM/MM approach, ONIOM calculations were also undertaken for ubiquinone and a variety of other quinones incorporated into the, so called, QA binding site in purple bacteria photosynthetic reaction centers. The calculated and experimental spectra agree well, demonstrating the utility and applicability of our ONIOM approach. Hydrogen bonding to the carbonyl groups of quinones in the QA binding site was shown to be relatively weak, and it was found that hydrogen bonding to neutral ubiquinone in purple bacterial reaction centers can be considered in purely electrostatic terms, contrary to the widely held belief that the hydrogen bonding amino acids should be treated quantum mechanically.

Submitted by ERNANE DE FREITAS MARTINS (ernanefmg@hotmail.com) on 2018-06-21T18:31:22Z No. of bitstreams: 1 Tese_Ernane_FINAL.pdf: 73762259 bytes, checksum: 783c569159077630257fc1df333452da (MD5) / Approved for entry into archive by Hellen Sayuri Sato null (hellen@ift.unesp.br) on 2018-06-22T17:57:30Z (GMT) No. of bitstreams: 1 martins_ef_dr_ift.pdf: 73762259 bytes, checksum: 783c569159077630257fc1df333452da (MD5) / Made available in DSpace on 2018-06-22T17:57:30Z (GMT). No. of bitstreams: 1 martins_ef_dr_ift.pdf: 73762259 bytes, checksum: 783c569159077630257fc1df333452da (MD5) Previous issue date: 2018-06-04 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Nanotechnology is an important and very active area of research contributing to many different fields. The development of new devices applied to personalized medicine is one of its applications. When we desire to develop new devices many effort are done, including experimental and theoretical investigations. The theoretical/computational physics can enormously contribute to this area, since the simulations can reveal the working mechanism in these systems being possible to understand and propose new devices with improved performance. We present an extensive theoretical investigation of the electronic transport properties of graphene-based devices for DNA sensing. We have used a hybrid methodology which combines quantum mechanics and molecular mechanics, the so called QM/MM method, coupled to electronic transport calculations using non-equilibrium Green’s functions. First, we studied graphene in solution in order to understand the effects of polarization on the electronic and transport properties under different salt concentrations. We also stud- ied graphene with Stone-Wales defect in pure water. For these systems we tested a simple polarization model based on rigid rods. Our analysis were also done over different QM/MM partitions including explicit water molecules in the quantum part. Our results showed that the inclusion of the solvent in the electronic transport calculations for graphene decreases the total transmission, showing the important role played by the water. Our results also showed that the electronic transport properties of graphene do not suffer significant changes as we increase the salt concentration in the solution. The inclusion of polarization effects in graphene, despite changing the structuring of water molecules that make up the first solvation shell of graphene, do not significantly affect the electronic transport through graphene. We then studied DNA sequencing devices. First we focused on sequencing using a nanopore between topological line defects in graphene. Our results showed that sequencing DNA with high selectivity and sensitivity using these devices appears possible. We also address nanogap in graphene. For this we looked at the effects of water on electronic transport by using different setups for the QM/MM partition. We showed that the inclusion of water molecules in the quantum part increases the electronic transmission in several orders of magnitude, also showing the fundamental role played by water in tunneling devices. The electronic transport simulations showed that the proposed device has the potential to be used in DNA sequencing, presenting high selectivity and sensitivity. We propose an graphene-based biochip for sequence-specific detection of DNA strands. The main idea of this sort of device is to detect hybridization of single-stranded DNA, forming double-stranded DNA. We showed that the vertical DNA adsorption, either through an anchor molecule (pyrene) or using the nucleotide itself as anchor, do not present good results for detection, since the signals for the single and double strands are quite similar. For the case of horizontal DNA adsorption on graphene our results indicated that the two signals can be distinguishable, showing promising potential for sensitivity and selectivity. / Nanotecnologia é uma importante e muito ativa área de pesquisa contribuindo para muitos campos diferentes. O desenvolvimento de novos dispositivos aplicados à medicina personalizada é uma de suas aplicações. Quando desejamos desenvolver novos dispositivos muitos esforços são feitos, incluindo investigações experimentais e teóricas. A Física teórica/computacional pode contribuir enormemente com esta área, já que simulações podem revelar o mecanismo de funcionamento nesses sistemas tornando possível entender e propor novos dispositivos com desempenho melhorado. Nós apresentamos uma extensa investigação teórica das propriedades de transporte eletrônico de dispositivos baseados em grafeno para sensoriamento de DNA. Utilizamos uma metodologia híbrida que combina mecânica quântica e mecânica molecular, o chamado método QM/MM, acoplado a cálculos de transporte eletrônico utilizando funções de Green fora do equilíbrio. Primeiramente nós estudamos grafeno em solução de modo a entender os efeitos de polarização nas propriedades eletrônica e de transporte em diferentes concentrações de sal. Também estudamos grafeno com defeito Stone-Wales em água pura. Para esses sistemas, testamos um modelo de polarização simples baseado em bastões rígidos. Nossas análises também foram feitas em diferentes partições QM/MM incluindo moléculas de água explícitas na parte quântica. Nossos resultados mostraram que a inclusão do solvente nos cálculos de transporte eletrônico para o grafeno diminui a transmissão total, mostrando o papel fundamento desempenhado pelo água. Nossos resultados também mostraram que as propriedades de transporte eletrônico do grafeno não sofrem mudanças significativas na medida em que aumentamos a concentração de sal na solução. A inclusão de efeitos de polarização em grafeno, apesar de mudar a estruturação das moléculas de água que compõem a primeira camada de solvatação do grafeno, não afeta significativamente o transporte eletrônico através do grafeno. Nós, então, estudamos dispositivos para sequenciamento de DNA. Focamos primeira- mente no sequenciamento usando nanoporo entre defeitos de linha topológicos no grafeno. Nossos resultados mostraram que o sequenciamento de DNA com alta seletividade e sensitividade usando esses dispositivos se mostra possível. Nós também abordamos nanogap em grafeno. Para tal, avaliamos os efeitos da água no transporte eletrônico utilizando diferentes configurações para a partição QM/MM. Mostramos que a inclusão de moléculas de água na parte quântica aumenta a transmissão eletrônica em várias ordens de grandeza, também mostrando o papel fundamental desempenhado pela água em dispositivos de tunelamento. As simulações de transporte eletrônico mostraram que o dispositivo proposto tem o potencial de ser usado em sequenciamento de DNA, apresentando alta seletividade e sensitividade. Propusemos um biochip baseado em grafeno para detecção de sequências específicas de fitas de DNA. A ideia principal desta classe de dispositivos é detectar a hibridização da fita simples de DNA, formando a fita dupla de DNA. Mostramos que a adsorção vertical de DNA, seja utilizando uma molécula âncora (pireno) ou utilizando o próprio nucleotídio como âncora, não apresenta bons resultados para detecção, já que os sinais para as fitas simples e dupla são bem próximos. Para o caso da adsorção horizontal de DNA em grafeno nossos resultados indicaram que os dois sinais podem ser distinguíveis, mostrando potencial promissor para sensitividade e seletividade.

This thesis contains three main sections. In the first section, we examine methodologies to discriminate Type II protein kinase inhibitors from the Type I inhibitors. We have studied the structure of 55 Type II kinase inhibitors and have notice specific descriptive geometric features. Using this information we have developed a pharmacophore and a shape based screening approach. We have found that these methods did not effectively discriminate between the two inhibitor types used independently, but when combined in a consecutive way – pharmacophore search first, then shape based screening, we have found a method that successfully filtered out all Type I molecules. The effect of protonation states and using different conformer generators were studied as well. This method was then tested on a freely available database of decoy molecules and again shown to be discriminative. In the second section of the thesis, we implement and assess swarm-based docking methods. We implement a repulsive particle swarm optimization (RPSO) based conformational search approach into Autodock 3.05. The performance of this approach with different parameters was then tested on a set of 51 protein ligand complexes. The effect of using different factoring for the cognitive, social and repulsive terms and the importance of the inertia weight were explored. We found that the RPSO method gives similar performance to the particle swarm optimization method. Compared to the genetic algorithm approach used in Autodock 3.05, our RPSO method gives better results in terms of finding lower energy conformations. In the final, third section we have implemented a Monte Carlo (MC) based conformer searching approach into Gaussian03. This enables high level quantum mechanics/molecular mechanics (QM/MM) potentials to be used in docking molecules in a protein active site. This program was tested on two Zn2+ ion-containing complexes, carbonic anhydrase II and cytidine deaminase. The effects of different QM region definitions were explored in both systems. A consecutive and a parallel docking approach were used to study the volume of the active site explored by the MC search algorithm. In case of the carbonic anhydrase II complex, we have used 1,2-difluorobenzene as a ligand to explore the favourable interactions within the binding site. With the cytidine deaminase complex, we have evaluated the ability of the approach to discriminate the native pose from other higher energy conformations during the exploration of the active site of the protein. We find from our initial calculations, that our program is able to perform a conformational search in both cases, and the effect of QM region definition is noticeable, especially in the description of the hydrophobic interactions within the carbonic anhydrase II system. Our approach is also able to find poses of the cytidine deaminase ligand within 1 Å of the native pose.