Relevant bibliographies by topics / QM/MM simulations

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers
  5. Reports

Academic literature on the topic 'QM/MM simulations'

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Published: 14 March 2023

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Journal articles on the topic "QM/MM simulations"

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Suh, Donghyuk, Kwangho Nam, and Wonpil Im. "CHARMM-GUI QM/MM interfacer for the hybrid QM/MM molecular dynamics simulations." Biophysical Journal 122, no. 3 (February 2023): 424a. http://dx.doi.org/10.1016/j.bpj.2022.11.2299.

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Kulkarni, Prajakta U., Harshil Shah, and Vivek K. Vyas. "Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-Based Drug Design and Discovery." Mini-Reviews in Medicinal Chemistry 22, no. 8 (May 2022): 1096–107. http://dx.doi.org/10.2174/1389557521666211007115250.

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Abstract: Quantum Mechanics (QM) is the physics-based theory that explains the physical properties of nature at the level of atoms and sub-atoms. Molecular mechanics (MM) construct molecular systems through the use of classical mechanics. So, when combined, hybrid quantum mechanics and molecular mechanics (QM/MM) can act as computer-based methods that can be used to calculate the structure and property data of molecular structures. Hybrid QM/MM combines the strengths of QM with accuracy and MM with speed. QM/MM simulation can also be applied for the study of chemical processes in solutions, as well as in the proteins, and has a great scope in structure-based drug design (SBDD) and discovery. Hybrid QM/MM can also be applied to HTS to derive QSAR models. Due to the availability of many protein crystal structures, it has a great role in computational chemistry, especially in structure- and fragment-based drug design. Fused QM/MM simulations have been developed as a widespread method to explore chemical reactions in condensed phases. In QM/MM simulations, the quantum chemistry theory is used to treat the space in which the chemical reactions occur; however, the rest is defined through the molecular mechanics force field (MMFF). In this review, we have extensively reviewed recent literature pertaining to the use and applications of hybrid QM/MM simulations for ligand and structure-based computational methods for the design and discovery of therapeutic agents.
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Watanabe, Hiroshi C., and Qiang Cui. "Quantitative Analysis of QM/MM Boundary Artifacts and Correction in Adaptive QM/MM Simulations." Journal of Chemical Theory and Computation 15, no. 7 (May 16, 2019): 3917–28. http://dx.doi.org/10.1021/acs.jctc.9b00180.

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de la Lande, Aurélien, Aurelio Alvarez-Ibarra, Karim Hasnaoui, Fabien Cailliez, Xiaojing Wu, Tzonka Mineva, Jérôme Cuny, et al. "Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review." Molecules 24, no. 9 (April 26, 2019): 1653. http://dx.doi.org/10.3390/molecules24091653.

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deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born–Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.
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König, Gerhard, Frank Pickard, Jing Huang, Walter Thiel, Alexander MacKerell, Bernard Brooks, and Darrin York. "A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes." Molecules 23, no. 10 (October 19, 2018): 2695. http://dx.doi.org/10.3390/molecules23102695.

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Maintaining a proper balance between specific intermolecular interactions and non-specific solvent interactions is of critical importance in molecular simulations, especially when predicting binding affinities or reaction rates in the condensed phase. The most rigorous metric for characterizing solvent affinity are solvation free energies, which correspond to a transfer from the gas phase into solution. Due to the drastic change of the electrostatic environment during this process, it is also a stringent test of polarization response in the model. Here, we employ both the CHARMM fixed charge and polarizable force fields to predict hydration free energies of twelve simple solutes. The resulting classical ensembles are then reweighted to obtain QM/MM hydration free energies using a variety of QM methods, including MP2, Hartree–Fock, density functional methods (BLYP, B3LYP, M06-2X) and semi-empirical methods (OM2 and AM1 ). Our simulations test the compatibility of quantum-mechanical methods with molecular-mechanical water models and solute Lennard–Jones parameters. In all cases, the resulting QM/MM hydration free energies were inferior to purely classical results, with the QM/MM Drude force field predictions being only marginally better than the QM/MM fixed charge results. In addition, the QM/MM results for different quantum methods are highly divergent, with almost inverted trends for polarizable and fixed charge water models. While this does not necessarily imply deficiencies in the QM models themselves, it underscores the need to develop consistent and balanced QM/MM interactions. Both the QM and the MM component of a QM/MM simulation have to match, in order to avoid artifacts due to biased solute–solvent interactions. Finally, we discuss strategies to improve the convergence and efficiency of multi-scale free energy simulations by automatically adapting the molecular-mechanics force field to the target quantum method.
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Liang, Dongyue, Jiewei Hong, Dong Fang, Joseph W. Bennett, Sara E. Mason, Robert J. Hamers, and Qiang Cui. "Analysis of the conformational properties of amine ligands at the gold/water interface with QM, MM and QM/MM simulations." Physical Chemistry Chemical Physics 20, no. 5 (2018): 3349–62. http://dx.doi.org/10.1039/c7cp06709g.

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Yang, Wei, Ryan Bitetti-Putzer, and Martin Karplus. "Chaperoned alchemical free energy simulations: A general method for QM, MM, and QM/MM potentials." Journal of Chemical Physics 120, no. 20 (May 22, 2004): 9450–53. http://dx.doi.org/10.1063/1.1738106.

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Chalmet, S., D. Rinaldi, and M. F. Ruiz-López. "A QM/MM/continuum model for computations in solution: Comparison with QM/MM molecular dynamics simulations." International Journal of Quantum Chemistry 84, no. 5 (2001): 559–64. http://dx.doi.org/10.1002/qua.1410.

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Shimada, J., T. Sakuma, K. Nakata, T. Wasiho, and T. Takada. "3K1015 BioMolecular Simulations : MD and QM/MM calculations." Seibutsu Butsuri 42, supplement2 (2002): S180. http://dx.doi.org/10.2142/biophys.42.s180_2.

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Solt, Iván, Petr Kulhánek, István Simon, Steven Winfield, Mike C. Payne, Gábor Csányi, and Monika Fuxreiter. "Evaluating Boundary Dependent Errors in QM/MM Simulations." Journal of Physical Chemistry B 113, no. 17 (April 30, 2009): 5728–35. http://dx.doi.org/10.1021/jp807277r.

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Dissertations / Theses on the topic "QM/MM simulations"

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Shaw, Katherine E. "Testing QM/MM Methods Using Free Energy Simulations." Thesis, University of Bristol, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.525442.

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Várnai, Csilla. "Adaptive QM/MM simulations for reactions in solution." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609933.

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Ranaghan, Kara Elizabeth. "Analysis of key effects in enzyme-catalysed reactions by QM/MM simulations." Thesis, University of Bristol, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.432942.

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Martins, Ernane de Freitas. "QM/MM simulations of electronic transport properties for DNA sensing devices based on graphene." Universidade Estadual Paulista (UNESP), 2018. http://hdl.handle.net/11449/154328.

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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.
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Welke, Kai [Verfasser], and M. [Akademischer Betreuer] Elstner. "QM/MM Simulations of Channelrhodopsins - Elucidating Structure and Spectroscopic Properties / Kai Welke. Betreuer: M. Elstner." Karlsruhe : KIT-Bibliothek, 2013. http://d-nb.info/1047383446/34.

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Patel, Chandan. "Hybrid molecular simulations of oxidative complex lesions." Thesis, Lyon, École normale supérieure, 2013. http://www.theses.fr/2013ENSL0835.

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L'ADN est en permanence exposé à un grand nombre d'événements dommageables déclenchées par des agents endogènes et exogènes. De nombreux travaux expérimentaux ont fourni des informations cruciales sur les propriétés structurelles et la réparation de certains des lésions de l'ADN. Cependant, il manque une vision mécanistique ou énergétique sur leur formation. La biochimie computationnelle a émergé comme un outil puissant pour comprendre les réactions biochimiques et les propriétés électroniques de systèmes complexes.Dans cette thèse, nous étudions la formation de lésions complexes intra-brin et inter-brin. Ces lésions tandem constituent une puissant menace à l'intégrité du génome, en raison de leur haute fréquence mutagenique. Tout d'abord, nous discutons l'attaque d'une liaison covalente entre un radical pyrimidinique. En comparant avec les bases isolees, nos simulations hybrides Car-Parrinello demontrent que la reactivité de la thymine et de la cytosine radicalaires sont inversees dans l'environnement B-helical. De plus, nos resultats montrent egalement une deformation plus importante pour la lesion G[8-5]C.Nous rationalisons également la plus grande réactivité des cytosines par rapport aux purines vers la formation multi-etapes de lésions complexes inter-brins par condensation avec un site C4' abasique. Ces résultats bases sur des simulations avec solvatation explicite et combines a la théorie de la fonctionnelle de la densité sont en accord avec les données expérimentales
DNA is continuously exposed to a vast number of damaging events triggered by endogenous and exogenous agents. Numerous experimental studies have provided key information regarding structural properties of some of the DNA lesions and their repair. However, they lack in mechanistic or energetic information pertaining to their formation. Computational Biochemistry has emerged as a powerful tool to understand biochemical reactions and electronic properties of large systems.In this thesis we study the formation of inter- and intra-strand cross-links. These tandem lesions pose a potent threat to genome integrity, because of their high mutagenic frequency. First, we discuss the formation of complex defects which arise from the attack of a pyrimidine radical onto guanine. In comparison with the reactivity of isolated nucleobases, our hybrid Car-Parrinello Molecular Dynamics simulations reveal that the reactivity of hydrogen-abstracted thymine and cytosine is reversed within a B-helix environment. Further, our data also suggest a more severe distortion of the B-helix for G[8-5]C.Second, we rationalize the higher reactivity of cytosine vs. purines toward the multistep formation of inter-strand crosslinks with a C4' oxidized a basic site, which is in qualitative agreement with experiments on isolated nucleobases, using explicit solvent simulations combined to density functional theory
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Gillet, Natacha. "Simulations Numériques de Transferts Interdépendants d’Electrons et de Protons dans les Protéines." Thesis, Paris 11, 2014. http://www.theses.fr/2014PA112159/document.

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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
Redox processes involving organic molecules are ubiquitous in proteins. They generally imply global reactions such as Proton Coupled Electron Transfers, hydrogen atom or hydride transfers which can be decomposed into both electrons and proton transfers. Kinetic and thermodynamic information leads to a better understanding of these mechanisms. However, experiments are often limited to a milli- or microsecond timescales. We present here numerical simulations allowing modeling at shorter timescales (femto, pico or nanosecond) to complete experimental data. Many numerical methods combine quantum description (QM) of the active center and classical description (MM) of the environment to describe redox transformations into biological media. Molecular dynamics (MD) simulations allowed a conformational sampling of the global system. Nevertheless, depending on their level of description of the QM part, the methods can cost more or less CPU time to get a good conformational sampling. In this thesis, we have studied different redox mechanisms involving both proton and electron transfers with a particular care paid to the balance between quality of the electronic description and of conformational sampling. For each mechanism, the coupled proton and electron transfers are investigated differently. This manuscript thus falls into three parts: i) the evaluation of the redox potentials quinone derivatives ; ii) the mechanistic description of the L-lactate oxidation into pyruvate in the flavocytochrome b2 enzyme; iii) decomposition of the formal hydride transfer occurring between two flavins in EmoB protein. A QM+MM scheme is chosen to evaluate redox potential of quinone cofactors: the electronic behavior is described at DFT level in gas phase while classical MDs provide a large conformational sampling of the molecule and its environment. Deprotonation and oxidation free energies are estimated by applying the linear response approximation (LRA). We finally get a theoretical value of the redox potential for different quinocofactors in water and a calibration curve of these theoretical results in function of experimental data. This curve allowed predictions of quinone redox potentials in water with a good accuracy (less than 0.1 eV). We also try our method on the MADH protein containing a Tryptophan Tryptophilquinone cofactor. However, because of great fluctuations of the environment, the LRA is not suitable for this system. This underlines the limits of our methodology. The oxidation of L-lactate to pyruvate is described by free energy surfaces obtained at AM1/MM level. Biased MDs provide the AM1/MM profile which is then corrected at DFT level. Several reactions pathways have been noticed. They consist in sequential or concerted transfers of a proton from L-lactate to a histidine and a hydride from L-lactate to a flavin cofactor. The coupling between the two transfers depends on the conformation of the active site or on the mutations. The obtained surfaces fit qualitatively the experimental data but the theoretical activation barriers are too high. Other simulations must be explored: different methods, other mechanism... Finally, a combination of long classical MDs and constrained DFT (cDFT)/MM are employed to decompose a hydride transfer between two flavins into one hydrogen atom and one electron transfer. cDFT methodology allow us to describe diabatic states associated to the electron transfer during the hydrogen atom transfer. Applying the LRA, we can build parabola of the diabatic and determine the sequence of the two transfers. The comparison of our results in the EmoB protein or in aqueous medium shows that the protein allows the electron transfer only if the hydrogen atom transfer is happening. By this way, no semi-reduced flavin is created
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Yang, Xuchun. "Probing the Photochemistry of Rhodopsin Through Population Dynamics Simulations." Bowling Green State University / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1563553836632515.

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Rossich, Molina Estefanía. "Addressing the reactivity of biomolecules in the gas phase : coupling tandem mass spectrometry with chemical dynamics simulations." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLE043.

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Durant cette thèse, nous avons abordé l'étude de la réactivité en phase gazeuse des biomolécules. L’avènement des techniques d’ionisation douces telle que l’ionisation par éléctronébulisation, a rendu possible ces dernières années, la formation d'ions en phase gazeuse sans dégrader la biomolécule étudiée.La Dissociation Induite par Collision (CID) est un cas particulier de spectrométrie de masse en tandem, que nous avons utilisée durant ce travail. Le principe du CID est d'activer les modes rovibrationnelles d’un système moléculaire ionique par collision avec un gaz inerte, ce qui augmente la probabilité de fragmentation de l'ion. Bien qu'étant une technique très utile d'un point de vue analytique, la spectrométrie de masse en tandem ne donne pas d'informations sur les mécanismes des réactions se produisant dans la cellule de collision; afin d’obtenir ces informations, les simulations de dynamique chimiques apparaissent comme un outil satisfaisant. En effet, en utilisant la dynamique directe, nous évitons ainsi d'explorer la totalité de la surface d'énergie potentielle, qui devient compliquée lors de l’étude d’édifices moléculaires de grande taille. Etant donné que les simulations de dynamique chimiques sont limitées à de courtes échelles, de l’ordre de la dizaine de picosecondes, nous avons également employé la théorie unimoléculaire RRKM (Rice-Ramsperger-Kassel-Marcus) pour étudier la réactivité à des temps plus longs, en vue de comprendre les processus réactionnels se produisant à l’issue du processus de relaxation vibrationnelle intramoléculaire (IVR). Durant ce travail de thèse, nous avons choisi d'étudier comme système modèle de base nucléique la molécule d'uracile. Par ailleurs,nous avons aussi étudié la réactivité en phase gazeuse de sucres (cellobiose, maltose et gentiobiose), qui ont été au préalable dérivatisés afin de localiser la charge sur la molécule et ainsi simplifier l’étude théorique associée
In the present thesis, we address the study of the reactivity of biomolecules in the gasphase.The advent of soft ionization techniques such as electrospray ionization, made possible, in the last years, the gentle formation of ions in the gas phase without breaking the molecule understudy.Collision Induced Dissociation (CID) is aparticular case of tandem mass spectrometrydynamics simulations are pointed like asatisfactory tool. Using direct dynamics weavoid exploring the whole potential energysurface, which becomes really complicatedwhen dealing with big molecules.Since chemical dynamics simulations arerestricted to the short time scale reactivity,typically ~10ps, we make use of the Rice–Ramsperger–Kassel–Marcus (RRKM)unimolecular theory to study the reactivity atUniversité Paris-SaclayEspace Technologique / Immeuble DiscoveryRoute de l’Orme aux Merisiers RD 128 / 91190 Saint-Aubin, Francethat we use in the present thesis. The aim of CIDis to activate the rovibrational modes of an ionicmolecular system by collisions with an inert gas,increasing the probability of the ion of beingfragmented.Despite being a really useful technique, tandemmass spectrometry does not give informationabout the mechanisms of the reactions takingplace in the collision cell; in order to obtain suchinformation, chemicallonger time scales to understand reaction pathsthat take place after intramolecular vibrationrelaxation (IVR).In the present thesis we have chosen to study asmodel system of nucleobase the uracil molecule.Furthermore, we also studied the gas-phase reactivity of carbohydrates (cellobiose, maltose and gentiobiose), which were preliminarily derivatized in order to simplify the charge localization, and consequently the theoretical study
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Tamura, Kouichi. "Atomistically Deciphering Functional Large Conformational Changes of Proteins with Molecular Simulations." 京都大学 (Kyoto University), 2016. http://hdl.handle.net/2433/215334.

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Book chapters on the topic "QM/MM simulations"

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Steinbrecher, Thomas, and Marcus Elstner. "QM and QM/MM Simulations of Proteins." In Methods in Molecular Biology, 91–124. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-017-5_5.

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Muslim, Abdul-Mueed, Jonathan P. McNamara, Hoda Abdel-Aal, Ian H. Hillier, and Richard A. Bryce. "QM/MM Simulations of Carbohydrates." In ACS Symposium Series, 186–202. Washington, DC: American Chemical Society, 2006. http://dx.doi.org/10.1021/bk-2006-0930.ch010.

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Groenhof, Gerrit. "Introduction to QM/MM Simulations." In Methods in Molecular Biology, 43–66. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-017-5_3.

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Levi, Gianluca. "Computational Details of the QM/MM BOMD Simulations." In Springer Theses, 125–41. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-28611-8_10.

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Bucher, Denis, Fanny Masson, J. Samuel Arey, and Ursula Röthlisberger. "Hybrid QM/MM Simulations of Enzyme-Catalyzed DNA Repair Reactions." In Quantum Biochemistry, 517–35. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2010. http://dx.doi.org/10.1002/9783527629213.ch17.

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Mehmood, Rimsha, and Heather J. Kulik. "Quantum-Mechanical/Molecular-Mechanical (QM/MM) Simulations for Understanding Enzyme Dynamics." In Methods in Molecular Biology, 227–48. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1826-4_12.

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Rothlisberger, U., and P. Carloni. "Drug-Target Binding Investigated by Quantum Mechanical/Molecular Mechanical (QM/MM) Methods." In Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 2, 449–79. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/3-540-35284-8_17.

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Liu, Haiyan. "QM/MM Energy Functions, Configuration Optimizations, and Free Energy Simulations of Enzyme Catalysis." In Challenges and Advances in Computational Chemistry and Physics, 331–53. Dordrecht: Springer Netherlands, 2010. http://dx.doi.org/10.1007/978-90-481-3034-4_12.

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Martins-Costa, Marilia T. C., and Manuel F. Ruiz-López. "Advances in QM/MM Molecular Dynamics Simulations of Chemical Processes at Aqueous Interfaces." In Challenges and Advances in Computational Chemistry and Physics, 303–24. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-21626-3_11.

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Lodola, Alessio, Donatella Callegari, Laura Scalvini, Silvia Rivara, and Marco Mor. "Design and SAR Analysis of Covalent Inhibitors Driven by Hybrid QM/MM Simulations." In Methods in Molecular Biology, 307–37. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0282-9_19.

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Conference papers on the topic "QM/MM simulations"

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Xenides, Demetrios, Bernhard R. Randolf, Theodore E. Simos, and George Maroulis. "Ab Initio QM∕MM Simulations of Water and Hydrated Cations." In COMPUTATIONAL METHODS IN SCIENCE AND ENGINEERING: Theory and Computation: Old Problems and New Challenges. Lectures Presented at the International Conference on Computational Methods in Science and Engineering 2007 (ICCMSE 2007): VOLUME 1. AIP, 2007. http://dx.doi.org/10.1063/1.2836243.

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Lin, Jung-Hsin. "Abstract 1660: Unraveling isoform selectivities of a broad class of HDAC inhibitors with QM/MM molecular dynamics simulations." In Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-1660.

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Silva Teixeira, Carla S., Sergio F. Sousa, and Nuno M. F. S. A. Cerqueira. "Molecular dynamic simulations and QM/MM studies addressed to build an active Tryptophan Synthase model. A critical enzyme to treat tuberculosis." In 2019 IEEE 6th Portuguese Meeting on Bioengineering (ENBENG). IEEE, 2019. http://dx.doi.org/10.1109/enbeng.2019.8692492.

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Asada, Toshio, Kanta Ando, and Shiro Koseki. "Efficient approach to obtain free energy gradient using QM/MM MD simulation." In INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2015 (ICCMSE 2015). AIP Publishing LLC, 2015. http://dx.doi.org/10.1063/1.4938813.

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Elstner, M., M. Hoffmann, M. Wanko, George Maroulis, and Theodore E. Simos. "Simulation of Proton Transfer Processes and Excited-State Properties in Proteins with QM∕MM Methods." In Computational Methods in Science and Engineering. AIP, 2007. http://dx.doi.org/10.1063/1.2827035.

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Tongraar, Anan, Bernd M. Rode, Theodore E. Simos, and George Maroulis. "Preferential Solvation and Dynamics of Ions Solvated in Mixed Solvents: Insights from QM∕MM MD Simulation Approach." In COMPUTATIONAL METHODS IN SCIENCE AND ENGINEERING: Theory and Computation: Old Problems and New Challenges. Lectures Presented at the International Conference on Computational Methods in Science and Engineering 2007 (ICCMSE 2007): VOLUME 1. AIP, 2007. http://dx.doi.org/10.1063/1.2836244.

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Reports on the topic "QM/MM simulations"

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Schutt, Timothy, and Manoj Shukla. Predicting the impact of aqueous ions on fate and transport of munition compounds. Engineer Research and Development Center (U.S.), August 2021. http://dx.doi.org/10.21079/11681/41481.

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A model framework for natural water has been developed using computational chemistry techniques to elucidate the interactions between solvated munition compounds and eight common ions in naturally occurring water sources. The interaction energies, residence times, coordination statistics, and surface preferences of nine munition related compounds with each ion were evaluated. The propensity of these interactions to increase degradation of the munition compound was predicted using accelerated replica QM/MM simulations. The degradation prediction data qualitatively align with previous quantum mechanical studies. The results suggest that primary ions of interest for fate and transport modeling of munition compounds in natural waters may follow the relative importance of SO₄²⁻, Cl⁻ ≫ HCO₃⁻, Na⁺, Mg²⁺ > Ca²⁺, K⁺, and NH₄⁺.
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