Academic literature on the topic 'Quantum mechanics/molecular'

A theoretical study of the hydrolysis of a β-lactam antibiotic was carried out in gas phase at different levels of theory. Later, the reaction was studied in solution, describing the sub-set of atoms of the QM region with semiempirical and density functional theory methods while classical force fields were used to describe the explicit solvent water molecules. QM/MM Molecular Dynamics simulations were used to generate the potential of mean force for the reaction in solution. The mechanism of hydrolysis of two antibiotics were explored in the active site of a mononuclear β lactamase. QM/MM methods have been applied to the study of an enzyme belonging to the family of copper monooxygenases. In particular the mechanism of hydroxylation by peptidylglycine α-hydroxylating monooxygenase was the subject of the study. Due to the electronic complexity of the system, ab initio MD simulations were required in order to get a proper description of the reaction.<br>Se realizó un estudio teórico de la hidrólisis de un antibiótico β-lactámico en vacio a diferentes niveles de cálculo. A continuación la reacción se estudió en disolución acuosa utilizando métodos semiempíricos y métodos basados en la teoría del funcional de la densidad para describir el subconjunto de átomos de la región QM, las moléculas de agua se describieron de forma discreta con campos de fuerza clásicos. Se utilizaron simulaciones de dinámica molecular con potenciales híbridos QM/MM para generar el potencial de fuerza media para la reacción en disolución. Se exploró el mecanismo de hidrólisis de dos antibióticos en el centro activo de una enzima β lactamasa. Y se estudió una enzima de la familia de las monooxigenasas de cobre. El objeto de estudio fue el mecanismo de hidroxilación por la peptidilglicina α-monooxigenasa hidroxilante. Fue necesario simulaciones de MD ab initio con el fin de obtener una descripción adecuada de la reacción.

Le père même de la mécanique quantique relativiste P. A. M. Dirac a prédit que la version plus réaliste de la mécanique quant ique qu'il a misen place n'offrirait pas beaucoup plus par rapport à la formulation non relativiste de la mécanique quantique lorsqu'il est appliqué à des systèmes atomiques et moléculaires ordinaires. Lorsque la théorie quantique relativiste avait environ 40 années, les gens avaient commencé à recogenize à quel point les effets relativistes peuvent être même pour l'étude des systèmes atomiques et moléculaires. Les effets relativistes se manifestent par la contraction dess atomiques et orbitales p, l'expansion des orbitales d et 1 atomiques, et le couplage spin-orbite. Un exemple classique de l'importance des effets relativistes est la structure de bande d'or métallique pour lequel les calculs non-relativistes vont conduire à une surestimation de l'écart 5d - 6p et prédire une bande d'absorption UV qui est compatible avec un métal qui ressemble à l'argent. La thèse porte sur les calculs atomiques et moléculaires dans le cadre relativiste à 4-composantes. En particulier, l'utilisation de la théorie des perturbations variationnelle dans un cadre relativiste. La théorie des perturbations dans la mécanique quantique, est basée sur le partitionnement du Hamiltonien il en l'Hamiltonien Ho a l'ordre zéro et \Î qui forme la perturbation par le biais d'un paramètre lambda. Dans la théorie des perturbations à N-corps {Rayleigh-Schrodinger), nous disposons d 'une solution exacte de l'Hamiltonien Ho. Alors que dans la théorie des perturbations variationnelle, nous supposons d'avoir une énergie optimisée pour toute valeur du paramètre À. La thèse contient deux projets principaux. Le premier projet concerne la discription de la corrélation électronique dans le cadre relativiste. Dans ce projet, nous nous sommes concentrés sur l'approche perturbative pour dériver des formules necessiry relativiste de l'énergie dans les atomes à deux électrons. L'énergie de corrélation est la différence entre la valeur propre exacte de l'hamiltonien et sa valeur d'attente dans l'approximationHartree-Fock. La valeur propre exacte ne sont pas disponibles, mais dans le domaine non-relativiste la meilleure solution est un Cl complet pour une base donnée. Notre objectif principal, dans ce projet, est de montrer que la meilleure solution de l'équation d'onde pour l' Hamiltonien DiracCoulomb, n'est pas un Cl complète, comme dans le cas non-relativis te, mais un MCSCF q ui utilise un développement Cl en orbitales énergiepositive seulement, mais qui permet la rotation entre les o rbitales d 'énerg ie positive et négative afin d 'optimiser l'opérateur de project ion. Le second projet concerne une étude sur les effets du volume nucléaire dans les spectres de vibration des molécules d iatomiques. Au début desannées 80, le groupe du professeur Eberhardt T iemann à Hanovre a util isé la spectroscopie de rotation avec une haute résolution pour étudier unesérie de molécules diatomiques contenant des atomes lo urds comme le plomb, afin d'établir des constantes spectroscopiques (Re longueur de laliaison, la fréquence vibratoire w. Etc. ) avec une grande précision. Une molécule AB a plusieurs isotopomères selon les isotopes des atomes A etB, et il était bien connu à cette époque que le spectre de chaque isotopomère est légèrement différente en raison des d ifférences de masse entrechaque isotope de l'atomes A et B. Prof. Tiemann et ses collaborateurs découvert que nous devons également ten ir compte de la différence devolume nucléa ire de chaque isotope. Nous fournissons un contrôle indépendant sur les études expérimentales et t héoriques précédentes d'effetsde volume nucléaires en spectroscopie de rotation, notamment re-calcul de la t héorie et des calculs antérieurs de référence par l'état relativiste4-composantes de l'art corrélée calculs<br>The father of relativistic quantum mechan ics P. A. M. Dirac predicted that, the more realistic version of quantum mechanics that he established wouId not offer much more when compared to the non-relativistic formulation of quantum mechanics when applied to ordinary atomic and molecular systems. When the relativistic quantum theory was around forty years old, people had started to recognize how important relativistic effects can beeven for the study of atomic and molecular systems. Relativistic effects are manifested via the contraction of atomics and p orbitais, the expansion of atomic d and 1 orbitais, and spin-orbit coupling. A classical example on t he importance of relativistic effects is the band struct ure of metallic gold for which non-relativistic caleulations will lead to an overestimation of the 5d-6p gap predicting a UV absorption band which is compatible with a metal that looks like silver. The thesis focuses on the atomic and molecular calculations within the 4-component relativistic framework. Ln particular, the use of the variational perturbation theory in relativistic framework. The perturbation theory in quantum mechanics is based on partitioning the Hamiltonian H into zeroth-order Hamiltonian Ho and V that forms the perturbation through a para meter lambda. Ln many-body (Rayleigh-Sch rodinger) perturbation theory, we have an exact solution of t he Hamiltonian l/0 , whereas in the variational perturbation theory, we assume to have anoptimized energy for any value of the parameter À. The thesis contains two principal projects, the first project concerns the description of the electron correlation in the relativistic framework. Ln this project , we focused on the perturbative approach to derive t he relativistic formulas nece~sary for the energy in two-electron atoms. T hecorrelation energy is the difference between the exact eigenvalue of the Ha mi ltonian and its expectation value in the Hartree-Fock approximation. The exact eigenvalue is not avail able, but in the non- relativistic domain t he best solution is a full Cl for a given basis. Our main goal, in this project , will be to show that the best solution of the wave equation for the embedded Dirac-Coulomb Hamil tonian, is not a Full Cl, as in thenon- relativistic case, but a MCSCF which uses a Cl development in positive-energy orbitais only, but which keeps rotations between the positive and negative energy orbitais to optimize the projection operator. The second project concerns a study of the effects of t he nuclear volume in the vibrational spectra of diatomic molecules. Ln the early 80s, Theg roup of Professor Eberhardt Tiemann in Hanover used the rotational spectroscopy with high resolution to study a series of diatomic molecules containing heavy a toms like lead in order to establish spectroscopie constants (R. Bond length, vibrational frequency W c etc. ) with a great precision. A molecule AB has several isotopomers according to isotopes atoms A and B and it was weil known at that t ime only the spectrum of eachisotopomer is slightly d iffe rent because of the mass differences between each isotope of the atoms A and B. Prof. Tiemann and his collaborators discovered that we must also take into account the difference in nuclear volume of each isotope. We provide an independent check on previous experimental and t heoretical studies of nuclear volume effects in rotational spectroscopy, notably re-derivation of theory and benchmark previous calculations by 4-component relativistic state of the art correlated calculations

Thesis (Ph.D.)--Physics, Georgia Institute of Technology, 2008.<br>Committee Chair: Alexei Marchenkov; Committee Member: Bruno Frazier; Committee Member: Dragomir Davidovic; Committee Member: Markus Kindermann; Committee Member: Phillip First

Glycosaminoglycans (GAGs) play an important role in many biological processes in the extracellular matrix. In a theoretical approach, structures of monosaccharide building blocks of natural GAGs and their sulfated derivatives were optimized by a B3LYP6311ppdd//B3LYP/ 6-31+G(d) method. The dependence of the observed conformational properties on the applied methodology is described. NMR chemical shifts and proton-proton spin-spin coupling constants were calculated using the GIAO approach and analyzed in terms of the method's accuracy and sensitivity towards the influence of sulfation, O1-methylation, conformations of sugar ring, and ω dihedral angle. The net sulfation of the monosaccharides was found to be correlated with the 1H chemical shifts in the methyl group of the N-acetylated saccharides both theoretically and experimentally. The ω dihedral angle conformation populations of free monosaccharides and monosaccharide blocks within polymeric GAG molecules were calculated by a molecular dynamics approach using the GLYCAM06 force field and compared with the available NMR and quantum mechanical data. Qualitative trends for the impact of sulfation and ring conformation on the chemical shifts and proton-proton spin-spin coupling constants were obtained and discussed in terms of the potential and limitations of the computational methodology used to be complementary to NMR experiments and to assist in experimental data assignment.

The past several decades have witnessed tremendous strides in the capabilities of computational chemistry simulations, driven in large part by the extensive parallelism offered by powerful computer clusters and scalable programming methods in high performance computing (HPC). However, such massively parallel simulations increasingly require more complicated software to achieve good performance across the vastly diverse ecosystem of modern heterogeneous computer systems. Furthermore, advanced “multi-resolution” methods for modeling atoms and molecules continue to evolve, and scientific software developers struggle to keep up with the hardships involved with building, scaling, and maintaining these coupled code systems. This dissertation describes these challenges facing the computational chemistry community in detail, along with recent solutions and techniques that circumvent some primary obstacles. In particular, I describe several projects and classify them by the 3 primary models used to simulate atoms and molecules: quantum mechanics (QM), molecular mechanics (MM), and coarse-grained (CG) models. Initially, the projects investigate methods for scaling simulations to larger and more relevant chemical applications within the same resolution model of either QM, MM, or CG. However, the grand challenge lies in effectively bridging these scales, both spatially and temporally, to study richer chemical models that go beyond single-scale physics and toward hybrid QM/MM/CG models. This dissertation concludes with an analysis of the state of the art in multiscale computational chemistry, with an eye toward improving developer productivity on upcoming computer architectures, in which we require productive software environments, enhanced support for coupled scientific workflows, useful abstractions to aid with data transfer, adaptive runtime systems, and extreme scalability. This dissertation includes previously published and co-authored material, as well as unpublished co-authored material.