In this work pentacene adsorption on both flat and stepped Ag(111) surfaces were investigated by using Density Functional Theory within Projected Augmented Wave method. On the flat Ag(111) surface favorable adsorption site for a single pentacene molecule was determined to be the bridge site with an angle of 60&amp / #9702 / between pentacene molecular long axis and [011] lattice direction. Potential energy surface was found to be flat, especially along lattice directions. Diffusion and rotation barriers for pentacene on this surface were found to be smaller than 40 meV indicating the possibility of a two dimensional gas phase. Calculated adsorption energies for the flat surface indicate a weak interaction between molecule and the surface indicating physisorption. On the flat surface monolayer case is found to have lower adsorption energy than the isolated case due to pentacene&amp / #8722 / pentacene interactions. On the stepped Ag(233) surface, close to the step edge, adsorption energy increased significantly due to the stronger interaction between pentacene molecule and low coordinated silver step atoms. On the terraces of this surface, far from step edges, however a flat potential energy surface was observed similar to the case of flat Ag(111) surface. On the stepped surface pentacene found its favorable configuration as parallel to the step with a tilt angle similar to the observed thin film phase of pentacene on Ag(111) surface. Pentacene molecule showed small distortions on stepped surface and are closer to the silver step atoms 1 &Aring / more than the case of flat surface, hinting a chemical interaction as well as van der Waals interactions. However on Ag(799) surface, the perpendicular orientation of the pentacene molecule to the step direction showed no strong interaction due to less matching of carbon atoms with silver step atoms.

Ethylene adsorption was studied by use of DFT/B3LYP with basis set 6-31G(d,p) in Gaussian&lsquo / 03 software. It was found that ethylene adsorbs molecularly on the Ni13 nanocluster with &amp / #960 / adsorption mode. &amp / #960 / adsorption mode is studied for the Ni10 (1 1 1), Ni13 (1 0 0) and Ni10 (1 1 0) surface cluster as well. Relative energy values were calculated as &amp / #8722 / 50.86 kcal/mol, &amp / #8722 / 20.48 kcal/mol, &amp / #8722 / 32.44 kcal/mol and &amp / #8722 / 39.27 kcal/mol for Ni13 nanocluster, Ni10 (1 1 1), Ni13 (1 0 0) and Ni10 (1 1 0) surface cluster models, respectively. Ethylene adsorption energy was found inversely proportional to Ni coordination number when Ni10 (1 1 1), Ni13 (1 0 0) and Ni10 (1 1 0) cluster models and Ni13 nanocluster were compared with each other. DFT/B3LYP and basis set of 86-411(41d)G in Gaussian&lsquo / 03 was used to investigate Ni55 nanocluster. Ethylene adsorption on Ni55 nanocluster was studied by means of equilibrium geometry calculations with &amp / #960 / adsorption modes for two different coordination numbers as 6 and 8. The related adsorption energies were approximately found as -22.07 and -14.82 kcal/mol for these coordination numbers of surfaces, respectively. In addition, the binding energies stated in literature that are for Ni2 dimer and Ni13 nanoclusters were considered together with our binding energy results for Ni55 nanocluster. Accordingly, when a correlation line was drawn and the intercept of binding energies was obtained against the value of &amp / #8213 / n&amp / #8722 / 1/3&amp / #8214 / where n is the number of atoms in the cluster / the result of interception gives a good estimation for bulk nickel binding energy at infinite &amp / #8213 / n&amp / #8214 / . This interception result was found as 4.58 eV/atom where the experimental value is reported as 4.45 eV/atom for bulk in the literature. Ehtylene hydrogenation mechanisms were also investigated in terms of the resultant geometries and total energy required for the related mechanism steps.

This work computationally investigates the partial oxidation of ethylene (i.e. ethylene epoxidation) using periodic Density Functional Theory (DFT) on slab models that represent the catalyst surfaces. The mechanical aspects of the reaction were investigated on silver surfaces, which are industrially applied catalysts, for a wide range of surface models varying from metallic surfaces with low oxygen coverage to oxide surfaces. For comparison, the metallic and oxide phases of copper and gold were also studied. On these surfaces, the reaction paths and the transition states along these paths for the selective and non-selective reaction channels were obtained using the climbing image nudged elastic band (CI-NEB) method. In order to answer the question &ldquo / what is the relation between the surface state and the ethylene oxide selectivity?&rdquo / metallic (100), (110) and (111) surfaces of Cu, Ag and Au / and, (001) surfaces of Cu2O, Ag2O and Au2O oxides were studied and compared. For the studied metallic surfaces, it was found that the selective and non-selective reaction channels proceed through the oxametallacycle (OMC) intermediate, and the product selectivity depends on the relative barriers of the these channels, in agreement with the previous reports. However for the studied metallic surfaces and oxygen coverages, a surface state that favors the ethylene oxide (EO) formation was not identified. The studied Au surfaces did not favor the oxygen adsorption and dissociation, and the Cu surfaces favored the non-selective product (acetaldehyde, AA) formation. Nevertheless, the results of Ag surfaces are in agreement with the ~50% EO selectivity of the un-promoted silver catalyst. The catalyst surface in the oxide state was modeled by the (001) surfaces of the well defined Cu2O, Ag2O and Au2O oxide phases. Among these three oxides, the Cu2O is found not to favor EO formation whereas Au2O is known to be unstable, however selective for epoxidation. The major finding of this work is the identification of a direct epoxidation path that is enabled by the reaction of the surface oxygen atoms, which are in two-fold (i.e. bridge) positions and naturally exist on (001) oxide surfaces of the studied metals. Among the three oxides studied, only Ag2O(001) surface does not show a barrier for the formation of adsorbed epoxide along the direct epoxidation path. Moreover, the overall heat of reaction that is around 105 kJ/mol agrees well with the previous reports. The single step, direct epoxidation path is a key step in explaining the high EO selectivities observed. Also for the oxide surfaces, the un-selective reaction that ends up in combustion products is found to proceed through the OMC mechanism where aldehyde formation is favored. Another major finding of this study is that, for the studied oxide surfaces two different types of OMC intermediates are possible. The first possibility is the formation of the OMC intermediate on oxygen vacant sites, where the ethylene can interact with the surface metal atoms directly. The second possibility is the formation of a direct OMC intermediate, through the interaction of the gas phase ethylene with the non-vacant oxide surface. This occurs through the local surface reconstruction induced by the ethylene. The effect of Cl promotion was also studied. Coadsorption of Cl is found to suppress the oxygen vacant sites and also the reconstruction effects that are induced by ethylene adsorption. Thus, by preventing the interaction of the ethylene directly with the surface metal atoms, Cl prevents the OMC formation, therefore the non-selective channel. At the same time Cl increases the electrophilicity of reacting surface oxygen. The direct epoxidation path appears to be stabilized by coadsorbed oxygen atoms. Thus, we carry the discussions on the silver catalyzed ethylene epoxidation one step further. Herein we present that the EO selectivity will be limited in the case of metallic catalyst, whereas, the oxide surfaces enable a direct mechanism where EO is produced selectively. The role of the Cl promoter is found to be mainly steric where it blocks the sites of non-selective channel.

Noncovalent interactions play a vital role throughout much of chemistry. The understanding and characterization of these interactions is an area where theoretical chemistry can provide unique insight. While many methods have been developed to study noncovalent interactions, symmetry-adapted perturbation theory (SAPT) stands out as one of the most robust. In addition to providing energetic information about an interaction, it provides insight into the underlying physics of the interaction by decomposing the energy into electrostatics, exchange, induction and dispersion. Therefore, SAPT is capable of not only answering questions about how strongly a complex is bound, but also why it is bound. This proves to be an invaluable tool for the understanding of noncovalent interactions in complex systems. The wavefunction-based formulation of SAPT can provide qualitative results for large systems as well as quantitative results for smaller systems. In order to extend the applicability of this method, approximations to the two-electron integrals must be introduced. At low-order, the introduction of density fitting approximations allows SAPT computations to be performed on systems with up to 220 atoms and 2850 basis functions. Higher-orders of SAPT, which boasts accuracy rivaling the best theoretical methods, can be applied to systems with over 40 atoms. Higher-order SAPT also benefits from approximations that attempt to truncate unneccesary unoccupied orbitals.

This thesis focuses on the construction and role of benchmark quality computations in the area of non-covalent interactions. We have provided a detailed error analysis of focal-point schemes commonly used in benchmark quality computations, as well as provide error and speedup analysis of commonly used approximations to these methods. An analysis of basis set effects on higher-order corrections to MP2/CBS has been carried out, providing the community error bounds on future benchmarks. We demonstrate how these high-level computations can elucidate a better understanding of non-bonded interactions in chemistry as well as provide high-quality reference data to refit existing methods against to increase the overall accuracy of the method.

Thesis (Ph. D.)--University of Missouri-Columbia, 2000. / Typescript. Vita. Includes bibliographical references (leaves 161-175). Also available on the Internet.

Thesis (Ph. D.)--University of Missouri-Columbia, 2000. / Typescript. Vita. Includes bibliographical references (leaves 161-175). Also available on the Internet.

Molecular simulation is an indispensable tool in many different disciplines such as physics, biology, chemical engineering, materials science, drug design, and others. Performing large-scale molecular simulation is of great interest to biologists and chemists, because many important biological and pharmaceutical phenomena can only be observed in very large molecule systems and after sufficiently long time dynamics. On the other hand, molecular simulation methods usually have very steep computational costs, which limits current molecular simulation studies to relatively small systems. The gap between the scale of molecular simulation that existing techniques can handle and the scale of interest has become a major barrier for applying molecular simulation to study real-world problems. In order to study large-scale molecular systems using molecular simulation, it requires developing highly parallel simulation algorithms and constantly adapting the algorithms to rapidly changing high performance computing architectures. However, many existing algorithms and codes for molecular simulation are from more than a decade ago, which were designed for sequential computers or early parallel architectures. They may not scale efficiently and do not fully exploit features of today's hardware. Given the rapid evolution in computer architectures, the time has come to revisit these molecular simulation algorithms and codes. In this thesis, we demonstrate our approach to addressing the computational challenges of large-scale molecular simulation by presenting both the high-performance algorithms and software for two important molecular simulation applications: Hartree-Fock (HF) calculations and hydrodynamics simulations, on highly parallel computer architectures. The algorithms and software presented in this thesis have been used by biologists and chemists to study some problems that were unable to solve using existing codes. The parallel techniques and methods developed in this work can be also applied to other molecular simulation applications.

Στην παρούσα εργασία μελετώνται οι μη γραμμικές ιδιότητες παραγώγων φουλλερενίων καθώς και η επίδραση της μεταφοράς φορτίου στην ενίσχυση της μη γραμμικότητας. Για τις πειραματικές μετρήσεις χρησιμοποιήθηκε η τεχνική ΟΚΕ ενώ έγιναν και θεωρητικοί υπολογισμοί , κβαντικής χημείας, προκειμένου να γίνει η απαραίτητη σύγκριση μεταξύ πειράματος και θεωρίας. / Ιn this project the nonlinear properties of some fullerene derivatives is studied. Particularly we examine the role of charge transfer in the nonlinear enhancement. The method that it was used for the experimental part was OKE technique. Moreover in the second part of this study theoretical calculations were held, in order to do a satisfying comparison between theory and experiment.

Density-functional theory has become an indispensible tool for studying matter on the atomic level, being routinely applied across diverse disciplines from solid-state physics to chemistry and molecular biology. Its failure to account for dispersion interactions has spurred intensive research over the past decade. In this thesis, a semilocal density-functional approximation including dispersion is developed by combining standard functionals for exchange and correlation with the nonempirical “exchange-hole dipole moment“ (XDM) dispersion model of Becke and Johnson. With a minimum of empiricism, the method accurately describes all types of noncovalent interactions, from the extremely weak dispersion forces in rare-gas systems to the hydrogen bonding and stacking interactions responsible for the structure and function of biological macromolecules such as DNA and proteins. The method is compatible with a wide variety of standard Gaussian basis sets, and is easily applied to any system that can be modeled with density-functional theory.