The structure of atomic and molecular clusters, optimised using classical potentials

The problem of the determination of the minimum energy configuration of an arrangement of N point particles under the interaction of their interatomic forces is discussed. The interatomic forces are described by classical many body potentials. Different optimisation methods are considered, multi level single link, topographical differential evolution and a genetic algorithm but it is shown that genetic algorithms combined with an efficient local optimisation method is especially quick and reliable for this task. In addition to comparing some different optimisation methods, the structures of clusters of atoms described by interatomic potential functions containing up to a few hundred atoms are calculated including some with some special symmetries. A number of applications are given including covalent carbon and silicon clusters, close-packed structures such as argon and silver and the two-component carbon-hydrogen system

Structure, solvation, thermodynamics and fragmentation of molecular clusters

Cette thèse vise à étudier en détail le comportement d'agrégats moléculaires complexes et se concentre sur deux aspects principaux. Tout d'abord, la description des isomères de faible énergie des clusters d'ammonium et ammoniac et (H2O)1-7,11,12UH+ à travers l'exploration des surfaces d'énergie potentielle (PES) en utilisant une combinaison d'approches d'optimisation globales et locales. Les propriétés structurelles, de solvatation et thermodynamiques des isomères de basse énergie nouvellement identifiés ont été caractérisées. Par la suite, des simulations dynamiques de la dissociation induite par collision des (H2O)1-7,11,12UH+ et Py2+ ont été réalisées et analysées en termes de : mécanisme de dissociation, répartition d'énergie, spectres de masse et sections efficaces de collision pour complémenter des mesures expérimentales récentes menées sur ces espèces. L'optimisation globale des clusters (H2O)1-10NH4+ et (H2O)1-10NH3 a été réalisée au niveau de théorie SCC-DFTB (pour self-consistent-charge density-functional based tight-binding), pour laquelle des paramètres N-H améliorés ont été proposés, en combinaison avec l'approche d'exploration PTMD (pour parallel-tempering molecular dynamics). Les isomères de basse énergie nouvellement déterminés ont été optimisés au niveau MP2 afin d'évaluer la fiabilité de nos paramètres N-H modifiés. Les structures et les énergies de liaison obtenues avec la méthode SCC-DFTB sont en très bon accord avec les résultats de niveau MP2/Def2TZVP, ce qui démontre la capacité de l'approche SCC-DFTB à décrire la PES de ces espèces moléculaires et représente ainsi une première étape vers la modélisation d'agrégats complexes d'intérêt atmosphérique. L'intérêt porté aux (H2O)1-7,11,12UH+ vise à fournir une description détaillée d'expériences récentes de dissociation induite par collision (CID). Premièrement, les isomères stables des (H2O)1-7,11,12UH+ sont calculés en utilisant la même méthodologie que celle décrite ci-dessus. Ensuite, des simulations dynamiques des collisions entre isomères (H2O)1-7,11,12UH+ et un atome d'argon sont réalisées à énergie de collision constante au niveau SCC-DFTB. La proportion simulée d'agrégats neutres contenant l'uracile par rapport à celle d'agrégats chargés contenant l'uracile, la section efficace de fragmentation ainsi que les spectres de masse sont cohérents avec les données expérimentales ce qui met en évidence la précision de nos simulations. Ces dernières permettent de sonder en details les fragments qui se forment aux temps courts et de rationaliser la localisation du proton en excès sur ces fragments. Cette dernière propriété est fortement influencée par la nature de l'agrégat soumis à la collision. L'analyse de la proportion des fragments en fonction du temps et des spectres de masse démontrent que, jusqu'à 7 molécules d'eau, un mécanisme de dissociation direct alors que pour 11,12 molécules, un mécanisme statistique est plus susceptible d'intervenir. Enfin, des simulations d'expériences CID du Py2+ à différentes énergies de collision, entre 2,5 et 30 eV, sont présentées. Les simulations permettent de comprendre les processus de dissociation mis en jeu. L'accord entre les spectres de masse simulés et mesurés suggère que les principaux processus sont bien pris en compte par cette approche. Il semble que la majeure partie de la dissociation se produise sur une courte échelle de temps (moins de 3 ps). L'analyse de la répartition d'énergie cinétique est utilisée pour obtenir des informations sur les processus de collision/dissociation à l'échelle atomique. Les spectres de masse simulés des clusters parents et dissociés sont obtenus à partir en combinant simulations de dynamique moléculaire et théorie de l'espace des phases pour traiter respectivement la dissociation aux courtes et longues échelles de temps.This thesis aims at studying in details the behavior of complex molecular clusters and focuses on two main aspects. First, the description of low-energy isomers of ammonium/ammonia water clusters and (H2O)1-7,11,12UH+ through an extensive exploration of potential energy surfaces (PES) using a combination of global and local optimization schemes. Structural, solvation and thermodynamics properties of the newly identified low-energy isomers were characterized. Second, the dynamical simulations of collision-induced dissociation of (H2O)1-7,11,12UH+ and Py2+ were carried out to explore collision trajectories, dissociation mechanism, energy partition, mass spectra, and collision cross sections to complement experimental measurements conducted on these species. Global optimization of (H2O)1-10NH4+ and (H2O)1-10NH3 clusters is conducted at the self-consistent-charge density-functional based tight-binding (SCC-DFTB) level of theory, for which improved N-H parameters are proposed, in combination with the parallel-tempering molecular dynamics (PTMD) approach. Low-energy isomers of (H2O)1-10NH4+ and (H2O)1-10NH3 are further optimized at MP2 level in order to evaluate the reliability of our modified N-H parameters. Both structures and binding energies obtained at SCC-DFTB agree with the results at MP2/Def2TZVP level, which demonstrates the ability of SCC-DFTB to describe the PES of molecular species and represents a first step towards the modeling of complex aggregates of atmospheric interest. Focus on (H2O)1-7,11,12UH+ aims at providing a detailed description of recent collision-induced dissociation (CID) experiments. First, stable isomers of (H2O)1-7,11,12UH+ are calculated using the same methodology as described above. Then, dynamical simulations of the collisions between various (H2O)1-7,11,12UH+ isomers and argon is conducted at a constant collision energy at the SCC-DFTB level. Simulated proportion of formed neutral vs. protonated uracil containing clusters, fragmentation cross-section as well as mass spectra are consistent with the experimental data which highlights the accuracy of our simulations. They allow to probe which fragments are formed on the short time scale and rationalize the location of the excess proton on these fragments. This latter property is highly influenced by the nature of the aggregate undergoing the collision. Analyses of proportion of time-dependent fragments and mass spectra demonstrate that, up to 7 water molecules, a shattering mechanism occurs after collision whereas for n=11,12 a statistical mechanism is more likely to participate. Dynamical simulation of CID experiments of Py2+ for different collision energies between 2.5 and 30 eV is also presented. The dynamical simulations allow to understand the dissociation processes. The agreement between the simulated and measured mass spectra suggests that the main processes are captured by this approach. It appears that most of the dissociation occurs on a short timescale (less than 3 ps). Analysis of the kinetic energy partition is used to get insights into the collision/dissociation processes at the atomic scale. The simulated mass spectra of the parent and dissociated products are obtained from the combination of molecular dynamics simulations and phase space theory to address the short and long timescales dissociation, respectively

Unconstrained Global Optimization of Molecules on Surfaces: From globally optimized structures to scanning-probe data

The adsorption of molecules on a surface plays a vital role in heterogeneous catalysis. For a proper unterstanding of the reaction mechanisms involved, the adsorption ge ometry of the molecules on the surface needs to be known. So far, experimental data from tunneling microscopes and spectroscopy, such as STM and IRAS are the main ways to obtain such knowledge. Due to the vast search space of adsorption geometries, especially for oligomers, optimizations using ab initio methods can be used to confirm the experimental data only if good initial guesses are available. Global optimization can serve two purposes in these situations. On the one hand it allows for a thorough investigation of the given search space, which can provide good initial guesses for subsequent high-level structural refinements. On the other hand, given a known reaction mechanism, it could also be used to find catalysts that influence e.g. the relevant bonds. With respect to this idea the topic of this thesis is to find a local optimization method cheap enough such that the total computational cost of global optimization does not exceed availability and yet good enough that the results are meaningful to the problem at hand. With this in mind multiple force field and semiempirical methods have been tested and evaluated mainly on benzene, acetophenone and ethyl pyruvate on Pt(111) surfaces. Some other adsorbates have also been tested shortly. In addition to these global optimization results, DFT geometry optimizations of ethyl pyruvate on Pt(111) have been performed and the structures of the best adsorption geometry from global optimization and from DFT are compared. Furthermore, from the DFT data STM images have been calculated that are compared to experimental results. The theoretical and experimental STM images agree well

Molekulardynamische Untersuchungen heterogener Keimbildung

Heterogeneous nucleation phenomena, in particular the condensation of vapors in presence of a substrate, are studied by molecular dynamics simulations. The simulations reported to this date have paid little attention to the description on the substrate. Here the dynamics of the vapor phase and the surface are simultaneously treated. Two cases are studied: the condensation of argon and the condensation of platinum on polyethylene films. The fundamental difference between both systems is the relative strength of the adsorbate-substrate interactions. The United Atom Method is used to represent the interactions of methyl groups within the polymer. The properties of polyethylene in the bulk phase such as the glass transition temperature, the density and the formation of gauche defects in the crystalline phase can be well described with this model. The interactions between argon atoms can be well represented by the Lennard Jones potential. The Embedded Atom Method is used to describe interactions between platinum atoms since many body effects, important in metals, can be incorporated with a computation requirement similar to pair potentials. Cross interactions between different types of atoms and groups are here approximated by the Lennard Jones potential with Lorentz-Berthelot combining parameters. The aim of this investigation is to describe the dynamics of heterogeneous nucleation and to establish the variables which control the growth and structure formation of clusters on the surface, the nucleation rates, and possible modifications of the substrate during condensation. For this purpose, different conditions of the saturation of the vapor phase and temperature of the substrate were simulated in each of the systems studied. Stationary nucleation rates in vapor phase and on the surface are obtained from cluster size statistics using the method of Yasuoka and Matsumoto. Different growth mechanisms were observed in for the simulated systems. Argon tends to condense on the surface as two-dimensional islands which finally coalesce as layers on the polymer surface. Consistent with this type of growth the condensation in the regime of low saturated and undersaturated vapors can be explained by a two- dimensional model within the frame of the classical nucleation theory. Platinum clusters condense as three-dimensional islands and partially wet the polymer surface. For the first time the embedding of metal atoms and metal clusters growth into a polymer substrate, as observed in experiments, is attained by large-scale molecular simulations. Depending on their sizes, the platinum clusters can diffuse into the polymer matrix even at temperatures lower than the glass transition of the polymer. The routines used for the simulation and analysis have been specially developed for the systems studied. Among them are NpT and NVT ensemble molecular dynamics simulations for the preparation and equilibration of thin polymer films, simulations of condensation of argon and platinum on polyethylene films. Furthermore routines developed for the analysis of simulation results include the calculation of a) radial distribution functions, torsion angle distributions and density profiles for the characterization of polymers, b) algorithms for the recognition of clusters in bulk and on a surface and c) routines for the visualization of the performed simulations

Molecular Dynamics Modeling Of Scalable Micro/Nano Manufacturing

In this research, „Droplet Based Direct Write‟ micro/nano manufacturing is investigated using a molecular dynamics modeling and simulation approach. The aim of this investigation is characterization of the direct write inkjet printing process to promote optimization for the enhancement of scalability. The study was completed in four phases; nanodroplet evaporation modeling, substrate-nanodroplet interaction modeling, nanodroplet impingement study and nanodroplet-patterned substrate interaction modeling

Polarizable Force Field Development, and Applications to Conformational Sampling and Free Energy Calculation

The parameters of monovalent ions for the AMOEBA force field were revised. High level quantum mechanics results, relative solvation free energies of monovalent ions, lattice energies and lattice constants of salt crystals were used to calibrate the parameters. The revised parameters were validated against the quantum optimized structures and energies of ion-water dimers and ion-water clusters, and against thermodynamic properties of salt solutions at different concentrations measured in experiments, e.g. mean ionic activity coefficients, self-diffusion coefficients of water. In the simulations the sodium ion is found to qualitatively differ from larger cations in aqueous solution. Direct ionic interactions are predominant for potassium and larger cations, while sodium salt solutions at similar concentrations are dominated by ion-water interactions. A novel stochastic isokinetic integrator proposed by Tuckerman, et al. was extended and generalized in three respects. First, the Nos-Hoover chain algorithm was implemented in the original integrator. Next, the functional form of the isokinetic constraint was generalized so that it was no longer restricted to multiples of kBT. Finally, the isokinetic constraint was extended to be able to constrain the kinetic energies of multi-dimensional velocities, instead of only one degree of freedom as in its original form. An application of conformational sampling with molecular dynamics method, predictions of the binding free energies of cucurbit[8]uril and ligands in the SAMPL6 challenge, is presented. A great improvement in the prediction accuracy was made by more accurate torsional parameters of cucurbit[8]uril and by revised protocols annihilating the intra-molecular van der Waals and key torsions in the ligands. Corresponding methods for all portions of this work have been implemented in the Tinker software package, some of which are also available in the Tinker-OpenMM library

High-throughput Exploration of Glass Formation via Laser Deposition and the Study of Heterogeneous Microstructure in a Bulk Metallic Glass Alloy

Bulk metallic glasses are a relatively novel class of engineering alloys characterized by a disordered atomic structure devoid of long-range translational symmetry. Compared to crystalline alloys, the confluence of metallic bonding and amorphous structure imbues bulk metallic glasses with a unique set of properties that makes them particularly attractive for a wide variety of structural applications. Such properties include exceptional yield strengths, high elastic resilience, resistance to corrosion, and in particular, the unparalleled ability among metals to be thermoplastically formed across a wide range of length scales when heated above the glass transition temperature. Formation of metallic glass from a molten liquid depends on whether cooling is sufficiently rapid to bypass crystallization and vitrify into an amorphous solid; for a given alloy composition, the ease with which full vitrification can occur upon cooling from the liquid state is termed the alloy\u27s glass forming ability. Unfortunately, relatively few excellent glass formers have been reported in the vast, multicomponent composition space in which they reside. The apparent slowness of progress may be attributed largely to the inefficiency of the one-at-a-time experimental approach to discovery and design. In this thesis work, a high-throughput combinatorial methodology was developed to expedite the discovery process of new bulk metallic glasses. Laser deposition was used to fabricate continuously-graded composition libraries of Cu-Zr and Cu-Zr-Ti alloys. By processing the libraries with a range of laser heat input, the best glass formers in each alloy system could be efficiently and systematically deduced. Furthermore, instrumented nanoindentation performed on the libraries enabled rapid evaluation of mechanical property trends. Despite boasting high strengths, monolithic bulk metallic glasses generally suffer from an intrinsic lack of damage tolerance compared to other high performance alloys. Recent studies indicate that the macroscopic deformation behavior of the material may be controlled by structural heterogeneities, although the exact nature and origin of the heterogeneities remain ambiguous. To further the present knowledge, the heterogeneous microstructure of a zirconium-based bulk metallic glass was investigated with instrumented nanoindentation and dynamic modulus mapping. Significant spatial variations in the mechanical properties measured by both techniques suggests a hierarchical arrangement of structural/mechanical heterogeneities in bulk metallic glasses. Moreover, a previously unobserved elastic microstructure, comprising an interconnected network of elastic features, was revealed by dynamic modulus mapping. Despite the absence of visible contrast when imaged with electron microscopy, the aligned morphology of the elastic features and their sensitivity to thermal processing conditions imply the occurrence of spinodal decomposition in the supercooled liquid prior to glass formation. Finally, based on analysis of load-displacement data from nanoindentation experiments performed throughout the thesis work, a new parameter, the plastic work ratio, was proposed as a figure of merit for quantifying the intrinsic plasticity of monolithic metallic glass alloys

Data-Driven Approaches to Complex Materials: Applications to Amorphous Solids

While conventional approaches to materials modeling made significant contributions and advanced our understanding of materials properties in the past decades, these approaches often cannot be applied to disordered materials (e.g., glasses) for which accurate total-energy functionals or forces are either not available or it is infeasible to employ due to computational complexities associated with modeling disordered solids in the absence of translational symmetry. In this dissertation, a number of information-driven probabilistic methods were developed for the structural determination of a range of materials including disordered solids to transition metal clusters. The ground-state structures of transition-metal clusters of iron, nickel, and copper were determined by a force-biased Monte Carlo method and their structural and electronic properties were studied comparatively via force-biased Monte Carlo and ab initio simulations. The force-biased Monte Carlo approach has shown unambiguously that it can effectively determine the putative ground-state structures of a number of small transition-metal clusters. For complex amorphous materials, an information-driven probabilistic viewpoint was adopted by posing structural determination of disordered solids as an inferential program and the problem of materials design was addressed as an optimization program, jointly supported by experimental data and information. The hallmark of this new approach is that it can produce atomistic configurations of amorphous solids, which are thermodynamically stable and close to a stable local minimum of a quantum-mechanical total-energy functional. The models have structural, topological, electronic, and vibrational properties comparable to experiments. The data-driven approach presented here for amorphous solids not only can produce overall structural and electronic properties but also the microstructural properties of realistic samples from experiments, such as voids and vacancy-type defects, which cannot be addressed directly using currently available computational methods. Ab initio hydrogen dynamics were simulated inside nanometer-size voids in a-Si within the framework of the density-functional theory and the study revealed that the microstructure of the hydrogen distribution and the morphology of the voids were characterized by the presence of a significant number of monohydride Si–H bonds, along with a few dihydride Si–H2 configurations but not any isolated hydrogen. The study also revealed that a considerable number of total H atoms inside voids can appear as H2 molecules. The densities of the bonded and nonbonded hydrogens are observed to be consistent with those from the infrared and Rutherford backscattering spectrometry measurements

Effect of composition and thermal history on deformation behavior and cluster connections in model bulk metallic glasses

The compositional dependence and influence of relaxation state on the deformation behavior of a Pt-Pd-based bulk metallic glasses model system was investigated, where platinum is systematically replaced by topologically equivalent palladium atoms. The hardness and modulus increased with rising Pd content as well as by annealing below the glass transition temperature. Decreasing strain-rate sensitivity and increasing serration length are observed in nano indentation with increase in Pd content as well as thermal relaxation. Micro-pillar compression for alloys with different Pt/Pd ratios validated the greater tendency for shear localization and brittle behavior of the Pd-rich alloys. Based on total scattering experiments with synchrotron X-ray radiation, a correlation between the increase in stiffer 3-atom cluster connections and reduction in strain-rate sensitivity, as a measure of ductility, with Pd content and thermal history is suggested