Rozprawy doktorskie na temat „Complex systems- Molecular dynamics study”

In this work we focused our attention on the lithium amide/imide, LiNH2/Li2NH, a very important system for hydrogen storage. By means of ab initio simulations we have resolved the structure of the two crystalline phases of Li2NH stable below and above 356 K and provide a comprehensive description of the elementary steps in the dehydrogenation and rehydrogenation processes. We performed molecular dynamics simulations based on density-functional theory and optimizations of the reaction pathways of elementary steps to provide estimates of reaction rates within the harmonic transition state theory.

La polyarthrite rhumatoïde (PR) est unemaladie auto-immune complexe qui entraîne uneinflammation synoviale et une hyperplasie pouvantprovoquer une érosion osseuse et une destruction ducartilage dans les articulations. L'étiologie de la PR restepartiellement inconnue, mais elle implique de multiplescascades de signalisation croisées et l'expression demédiateurs pro-inflammatoires. Dans la première partie demon projet de doctorat, nous présentons un effortsystématique pour construire une base de connaissancessur la PR, entièrement annotée et validée par des experts.Cette carte de la PR illustre les voies moléculaires et designalisation importantes impliquées dans la maladie. Latransduction du signal est systématiquement représentéedes récepteurs au noyau en utilisant la représentationstandard de notation graphique en biologie des systèmes(SBGN). La curation manuelle est basée sur des critèresstricts et spécifique aux études sur l'homme, limitantl'apparition de faux positifs sur la carte. Cette carte peutservir de base de connaissances interactive pour la maladiemais aussi de tableau pour la visualisation des donnéesomiques. De plus, c’est une excellente base pour ledéveloppement d'un modèle informatique. La naturestatique de la carte PR pourrait fournir une compréhensionrelativement limitée du comportement émergeant dusystème dans différentes conditions. La modélisationinformatique pourra révéler les propriétés dynamiques duréseau par le biais de perturbations in silico et peut êtreutilisée pour tester et prédire des hypothèses.Dans la deuxième partie du projet, nous présentons unpipeline permettant la construction automatisée d'un grandmodèle booléen, à partir d'une carte d'interactionsmoléculaires. Pour cela, nous avons développé l'outilCaSQ (CellDesigner as SBML-qual), qui automatise laconversion des cartes moléculaires en modèles booléensexécutables basés sur la topologie et la sémantique descartes. Le modèle booléen résultant pourrait être utilisépour des simulations in silico afin de reproduire lecomportement biologique connu du système et de prédirede nouvelles cibles thérapeutiques. Pour l'analyse deperformance de l’outil, nous avons utilisé différentescartes et modèles de maladies en mettant l'accent sur lagrande carte moléculaire de la PR.Dans la troisième partie du projet, nous présentons nosefforts pour créer un modèle dynamique (booléen) àgrande échelle pour les synoviocytes de type fibroblastede polyarthrite rhumatoïde (RA-FLS). Parmi denombreuses cellules de l'articulation et du systèmeimmunitaire impliquées dans la pathogenèse de la PR, lesRA-FLS joue un rôle important dans l'initiation et laperpétuation de l'inflammation articulaire destructrice.Les RA-FLS expriment des cytokinesimmunomodulatrices, des molécules d'adhésion et desenzymes de modélisation matricielle. De plus, les RAFLSprésentent des taux de prolifération élevés et unphénotype résistant à l'apoptose. Les RA-FLS peuventégalement se comporter comme les principaux moteurs del'inflammation, et les thérapies dirigées contre les RA FLSpourraient devenir une approche complémentaire auximmunothérapies. Le défi est de prédire les conditionsoptimales qui favoriseraient l'apoptose des RA FLS,limiteraient l'inflammation, ralentiraient le taux deprolifération et minimiseraient l'érosion osseuse et ladestruction du cartilage
Rheumatoid arthritis (RA) is a complexautoimmune disease that results in synovial inflammationand hyperplasia leading to bone erosion and cartilagedestruction in the joints. The aetiology of RA remainspartially unknown, yet, it involves a variety of intertwinedsignalling cascades and the expression of pro-inflammatorymediators. In the first part of my PhD project, we present asystematic effort to construct a fully annotated, expertvalidated, state of the art knowledge-base for RA. The RAmap illustrates significant molecular and signallingpathways implicated in the disease. Signal transduction isdepicted from receptors to the nucleus systematically usingthe systems biology graphical notation (SBGN) standardrepresentation. Manual curation based on strict criteria andrestricted to only human-specific studies limits theoccurrence of false positives in the map. The RA map canserve as an interactive knowledge base for the disease butalso as a template for omic data visualization and as anexcellent base for the development of a computationalmodel. The static nature of the RA map could provide arelatively limited understanding of the emerging behaviorof the system under different conditions. Computationalmodeling can reveal dynamic network properties throughin silico perturbations and can be used to test and predictassumptions.In the second part of the project, we present a pipelineallowing the automated construction of a large Booleanmodel, starting from a molecular interaction map. For thispurpose, we developed the tool CaSQ (CellDesigner asSBML-qual), which automates the conversion ofmolecular maps to executable Boolean models based ontopology and map semantics. The resulting Booleanmodel could be used for in silico simulations to reproduceknown biological behavior of the system and to furtherpredict novel therapeutic targets. For benchmarking, weused different disease maps and models with a focus onthe large molecular map for RA.In the third part of the project we present our efforts tocreate a large scale dynamical (Boolean) model forrheumatoid arthritis fibroblast-like synoviocytes (RAFLS).Among many cells of the joint and of the immunesystem involved in the pathogenesis of RA, RA FLS playa significant role in the initiation and perpetuation ofdestructive joint inflammation. RA-FLS are shown toexpress immuno-modulating cytokines, adhesionmolecules, and matrix-modelling enzymes. Moreover,RA-FLS display high proliferative rates and an apoptosisresistantphenotype. RA-FLS can also behave as primarydrivers of inflammation, and RA FLS-directed therapiescould become a complementary approach to immunedirectedtherapies. The challenge is to predict the optimalconditions that would favour RA FLS apoptosis, limitinflammation, slow down the proliferation rate andminimize bone erosion and cartilage destruction

Advances in supercomputer architectures have resulted in a situation where many scientific codes are used on systems whose performance characteristics differ considerably from the platform they were developed and optimised for. This is particularly apparent in the realm of Grid computing, where new technologies such as MPIg allow researchers to connect geographically disparate resources together into virtual parallel machines. Finding ways to exploit these new resources efficiently is necessary both to extract the maximum benefit from them, and to provide the enticing possibility of enabling new science. In this thesis, an existing general purpose molecular dynamics code (LAMMPS) is extended to allow it to perform more efficiently in a geographically distributed Grid environment showing considerable performance gains as a result. The technique of replica exchange molecular dynamics is discussed along with its applicability to the Grid model and its benefits with respect to increasing sampling of configurational space. The dynamics of two sub-structures of the HIV-1 protease (known as the flaps) are investigated using replica exchange molecular dynamics in LAMMPS showing considerable movement that would have been difficult to investigate by traditional methods. To complement this, a study was carried out investigating the use of computational tools to calculate binding affinity between HIV-1 protease mutants and the drug lopinavir in comparison with results derived experimentally by other research groups. The results demonstrate some promise for computational methods in helping to determine the most effective course of treatment for patients in the future.

With more atoms in a system, coupling between quantum states complicates the system dynamics. We shine intense laser pulses on three systems with increasing complexity: a molecule, a dimer, and a solid. For single molecules, a 400 nm photon excites NO_2 and initiates a dissociation process. We probe the dynamics using a strong laser pulse to ionize the molecule, and detect the resulting electrons and ions. The evolution of the NO-O molecular bond was directly measured in our experiment. For dimers, a laser pulse removes three electrons from (CO)_2. The dimer breaks up into C^+, O^+ and CO^+. Compared to a monomer, CO^{2+} in the dimer has a new prompt dissociation pathway that produces fragments with higher kinetic energy. Calculation shows that the Coulomb field of the neighboring CO^+ modifies the electronic state of the dimer, giving rise to a prompt channel. Coupling between different charge state configurations results in a new dimer electronic state, which leads to dissociation with higher kinetic energy. For solids, coupling among many atoms creates bands and a bandgap that plays the role of the ionization potential and reduces the threshold for electron-hole pair generation. Thus, solids are a good medium for high-order harmonic generation at the high repetition rates needed for frequency combs. We generate up to the 7th harmonic in silicon and zinc oxide with femtosecond pulses from a thulium fiber laser.

In the first part of this dissertation, recent efforts to understand quantum mechanical effects in biological systems are discussed. Especially, long-lived quantum coherences observed during the electronic energy transfer process in the Fenna-Matthews-Olson complex at physiological condition are studied extensively using theories of open quantum systems. In addition to the usual master equation based approaches, the effect of the protein structure is investigated in atomistic detail through the combined application of quantum chemistry and molecular dynamics simulations. To evaluate the thermalized reduced density matrix, a path-integral Monte Carlo method with a novel importance sampling approach is developed for excitons coupled to an arbitrary phonon bath at a finite temperature. In the second part of the thesis, simulations of molecular systems and applications to vibrational spectra are discussed. First, the quantum dynamics of a molecule is simulated by combining semiclassical initial value representation and density funcitonal theory with analytic derivatives. A computationally-tractable approximation to the sum-of-states formalism of Raman spectra is subsequently discussed.

Proteins and DNA are large, complex molecules that carry out biological functions essential to all life. Their successful operation relies on adopting specific structures, stabilized by intra-molecular interactions between atoms. The spatial and temporal resolution required to study the mechanics of these molecules in full detail can only be obtained using computer simulations of molecular models. In a molecular dynamics simulation, a trajectory of the system is generated, which allows mapping out the states and dynamics of the molecule. However, the time and length scales characteristic of biological events are many orders of magnitude larger than the resolution needed to accurately describe the microscopic processes of the atoms. To overcome this problem, sampling methods have been developed that enhance the occurrence of rare but important events, which improves the statistics of simulation data. This thesis summarizes my work on developing the AWH method, an algorithm that adaptively optimizes sampling toward a target function and simultaneously finds and assigns probabilities to states of the simulated system. I have adapted AWH for use in molecular dynamics simulations. In doing so, I investigated the convergence of the method as a function of its input parameters and improved the robustness of the method. I have also worked on a generally applicable approach for calculating the target function in an automatic and non-arbitrary way. Traditionally, the target is set in an ad hoc way, while now sampling can be improved by 50% or more without extra effort. I have also used AWH to improve sampling in two biologically relevant applications. In one paper, we study the opening of a DNA base pair, which due to the stability of the DNA double helix only very rarely occurs spontaneously. We show that the probability of opening depends on both nearest-neighbor and longer-range sequence effect and furthermore structurally characterize the open states. In the second application the permeability and ammonia selectivity of the membrane protein aquaporin is investigated and we show that these functions are sensitive to specific mutations.

QC 20171117

La aplicación de métodos de dinámica molecular (MD) para el estudio de sistemas biológicos. Esta tesis se centra en la aplicación tanto de dinámica molecular clásica como perturbación de energía libre (FEP) para estudiar sistemas biológicos tales como los receptores acoplados a proteínas G y los inhibidores de BACE1. La tesis se divide en 5 secciones, en primer lugar, una introducción donde se explica la evolución de la metodología de MD, en segundo lugar, una sección sobre métodos utilizados en esta tesis, la tercera sección se centra en el uso de simulaciones de MD para estudiar dos aspectos diferentes de los GPCR, oligomerización del tetrámero formado por receptores de adenosina y el mecanismo de activación por ligandos alostéricos dirigidos al receptor metabotrópico de glutamato 2. La cuarta sección se centra en la aplicación de FEP con el objetivo de diseñar nuevos inhibidores de BACE1 y poner en práctica esta metodología en un proyecto de desarrollo de fármacos realizado en colaboración con Janssen Pharmaceutica. La última sección resume las conclusiones alcanzadas. En general, se demuestra que los métodos de Dinámica Molecular, puede ser de gran valor para comprender los escenarios descritos a nivel molecular, y, en particular, las interacciones y los procesos dinámicos que se producen. Esto a su vez ayudará a la comprensión más detallada de la biología básica y el diseño de fármacos. El trabajo justifica aplicaciones futuras en estas áreas y continua la exploración de forma detallada de la influencia que los métodos MD y FEP pueden alcanzar.
Application of Molecular Dynamics (MD) methods to the study of biological systems. This thesis is focused on the application of both classical MD and free energy perturbation (FEP) to study biological systems such as G protein-coupled receptors and BACE1 inhibitors. The thesis is divided into 5 sections, firstly an introduction where a timeline and evolution of MD methodology is explained, secondly a second section on Methods, the third section focuses on the use of MD simulation to study two different aspects of GPCRs, oligomerization of the tetramer formed by Adenosine receptors and the mechanism of activation by allosteric ligands targeting the metabotropic glutamate 2 receptor. The fourth section is focused on the application of FEP with the aim of designing new BACE1 inhibitors and to implement this methodology into a real drug discovery project performed in collaboration with Janssen Pharmaceutica. The final section summarizes the conclusions reached. Overall, it is shown that state of the art MD simulations, and hence modern computational methodology, can be of value to understand the described scenarios at the molecular level, and in particular the interactions and dynamic processes which occur. This in turn will help with more detailed understanding of basic biology and drug design. The work justifies future applications in these areas and continued deeper exploration of the limits of the impact which MD and FEP methods can reach.

The classical molecular dynamics model is used for a study of the possible nuclear phase transition in heavy ion collisions at intermediate energies. We implemented this model through Monte Carlo techniques. Different kinds of initial configurations are considered, as well as different methods of particles propagation. In order to simulate the canonical ensemble dynamic evolution we investigate two methods of keeping the temperature constant.
We consider a system of 85 nucleons interacting through two-body nucleon-nucleon potential. The calculations are first carried out ignoring Coulomb interaction and then including it. Data on various thermodynamic quantities are obtained and the question of the existence of the phase transition is investigated.
To estimate the effect of a finite particle number on critical parameters we go to a system of 200 nucleons.

Monodrama is a work for a sole protagonist, utilising both sung and spoken vocalism over a cathartic narrative. Developed as a subgenre of opera relatively recently, monodrama emerged in the era of Freudian psychology. Monodrama aims to convince the audience of the authority and infallibility of the protagonist’s point of view. An operatic monodrama rehearsal is a unique sociological dynamic, one that functions as a complex adaptive process with director, conductor and performer as principal agents. The effective functioning of this dynamic causes beneficial coherence, measurable by successful performance outcomes (Snowden, 2012). An interesting phenomenon is observed in monodrama rehearsals, divergent from traditionally hierarchical rehearsal dynamics found in opera. The singer has increased agency in rehearsal, effectively transforming the dynamic from a negotiation between stage director and conductor, as occurs in opera, into a collaboration of equal yet distinct roles. Director, conductor and performer form a triumvirate of mutual respect, exhibiting porous boundaries of roles and responsibilities (or linkages). Monodrama rehearsals comprise a series of “safe to fail” experiments, repeating acceptable patterns with mutual agreement of three principal participants (or nodes), and creating unique norms leading to successful performance. The relative agency of each participant in a rehearsal, changing notions of authorship, and the success of this complex collaboration are discussed in detail, showing the possibilities for adaptive rehearsal structures in a traditionally conservative art-form. Primary research is conducted through participation as director and singer in three monodrama production rehearsal periods: “Pierrot Lunaire” by Arnold Schoenberg, “The Seven Deadly Sins” by Kurt Weill, and “The Pomegranate Cycle” by Eve Klein. Industry professionals’ perceptions of the dynamics in monodrama and opera rehearsals are also studied through semi-structured interviews and surveys with thirteen subjects (N=13), four directors (D=4), four conductors (C=4) and five singers (P=5), considering self-reported “successful” performance in opera and monodrama. Both the performance practice research and qualitative research herein supports the hypothesis that a monodrama rehearsal is a collaborative triumvirate functioning as a complex adaptive system, contrasting with the power structures and dynamics commonly observed in opera rehearsals.

Complex systems offer broad, unique research challenges due to their inability to be understood through a classic reductionist perspective, as they exhibit emergent phenomena that arise through the interactions of their components. In this thesis, we briefly review some characteristics of complex systems and the interplay of mathematical and computational methods to study them. We then discuss these approaches, how they are implemented, and how they support one another in three settings. First, we present a study that connects weather data to seasonal population-abundance of mosquitoes, using a microscopic model. Secondly, we consider the collective motions that arise in ensembles of disks interacting through non-elastic collisions and investigate how such behaviors affect macroscopic transport properties. Finally, we consider a 'self-sorting' one-dimensional collection of point-particles. In all of these cases, agent-based models and simulations are used to guide analysis, and in the final example, we explain how the simulations led to new theorems. Articles and molecular dynamics computer codes are provided as appendices.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2007.
Includes bibliographical references (p. 112-123).
It is now well established that cells can sense mechanical force, but the mechanisms by which force is transduced into a biochemical signal remain poorly understood. One example is the recruitment of vinculin to reinforce initial contacts between a cell and the extracellular matrix due to tensile force. Talin, an essential structural protein in the adhesion, contains the N-terminal five-helix bundle in the rod domain with a known cryptic vinculin binding site 1 (VBS1). The perturbation of this stable structure through elevated temperature or destabilizing mutation activates vinculin binding. Here, molecular dynamics (MD) is employed to demonstrate a force-induced conformational change that exposes the cryptic vinculin-binding-residues of VBS1 to solvent under applied forces along a realistic pulling direction. VBS 1 undergoes a rigid body rotation by an applied torque transmitted through hydrogen-bonds and salt bridges. Activation was observed with mean force of 13.2±8.0pN during constant velocity simulation and with steady force greater than 18.0pN. The crystal structure of vinculin head subdomain (Vhl) bound to the talin VBS1 implies that vinculin undergoes a large conformational change upon binding to talin, but the molecular basis for this, or the precise nature of the binding pathway remain elusive. In the second part of the thesis, MD is employed to investigate the binding mechanism of Vhl and VBS1 with minimal constraints to facilitate the binding. One simulation demonstrates binding of the two molecules in the complete absence of external force. VBS1 makes early hydrophobic contact with Vhl through an initial hydrophobic insertion. Then, other solvent-exposed hydrophobic residues of VBS1 gradually embed into the hydrophobic core of Vhl further displacing helix 1 from helix 2.
(cont.) These highly conserved critical residues are experimentally shown to be essential in Vhl-VBS1 binding, and are also the same residues that are shown to become exposed by applied tension to talin in the first part of the thesis. Similar mechanisms are demonstrated in separate MD simulations of Vhl binding to other VBSs both in talin and a-actinin. Together, these results provide molecular insights, for the first time, into the early force-induced recruitment of vinculin to the mechanosensitive mechanisms of cell-matrix adhesion complex, and establish the basis for further numerical and experimental studies to fully understand the force response of focal adhesions.
by Seung Eun Lee.
Ph.D.

Molecular dynamics (MD) simulations are a powerful tool to study biochemical processes at the atomic level and to complement experiments by providing otherwise unattainable structural and dynamic information. In this thesis, different simulative approaches were applied to two classes of problems. The first regards the mechanism of lipid bilayer perturbation by antimicrobial peptides (AMPs), which kill bacteria by disrupting their membranes. Our computational results on peptides temporin L, LAH4, trichogin GAIV and PMAP-23 clarified several aspects of the mechanism of action of AMPs, illustrating how peptide sequence modulates aggregation and insertion in the lipid bilayer, and showing several facets of membrane disruption by AMPs, such as formation of bilayer defects, membrane thinning and perturbation of lipid dynamics. Overall, these data indicate that AMPs activity is regulated by several complex equilibria that should be taken into account in the rational design of new antibiotic drugs. Other studies focused on RRAS and SHP-2, two proteins involved in the MAPK pathway and in a family of disorders called RASopathies. We analyzed an RRAS mutation, isolated in a patient affected by Noonan syndrome, causing an enhancement in the rate of GDP dissociation. MD simulations revealed that this effect is related to the perturbation of the conformational transitions of the RRAS molecular switch. Similarly, simulations showed that the motions of an α-helix resulted to be essential in the function of SHP-2, thus providing new indications on the possible molecular effects of several pathogenic mutations. These studies underline once more the importance of conformational fluctuations in the physiological and aberrant function of proteins. All MD simulations reported in this thesis were consistent with the available experimental data, thus confirming the reliability of in silico approaches in obtaining novel insights in the characterization of complex biomolecular systems.

Diffusion is the fundamental process behind many molecular phenomena such as the mixing of substances. Its physical basis is the random motion of particles in a fluid. In complex porous media, diffusion is restricted by interactions with internal structures. In this work, we present studies of restricted diffusion that aim to efficiently produce quantitative models for obtaining detailed information about the morphology of biological porous media from diffusion tensor imaging experiments. We achieved this by developing a Langevin dynamics algorithm to provide physically realistic modelling of water/barrier interactions and the Lattice-Path Count algorithm to enumerate all available particle trajectories to evaluate molecular transport properties. We also performed diffusion tensor imaging experiments of the fibre networks of tissue engineering scaffolds. The findings of this thesis provide further insight into the physics underlying restricted diffusion.

Complex systems abound on this planet, in the composition of the human body, in ecosystems, in social interaction, in political decision-making, and more. Analytical methods allowing us to better understand how these systems operate and, consequently, to have a chance to intervene and change the undesirable behavior of some of the more pernicious systems have developed and continue to be enhanced via quickly changing technology. Some of these analytical methods are accessible by pre-college students, but have not been widely used at that level of education. Jay Forrester, the founder of one of the methodologies, System Dynamics (SD), used to study complex system behavior involving feedback, laments the lack of understanding of complex systems evident in short-sited decisions made by legislators -- global climate change and fiscal policies being cases in point. In order to better prepare future decision makers with tools that could allow them to make more informed decisions about issues involving complex systems efforts have been underway to increase pre-college teacher understanding of the SD method. The research described in this dissertation introduces the mathematics education community to the value of System Dynamics modeling in pre-college algebra classes, indicates a path by which a traditional mathematics curriculum could be enhanced to include small SD models as a new representation for elementary functions studied in algebra classes, and provides an empirical study regarding conceptual understanding of functions by students. Chapter 2 indicates the numerous beneficial learning outcomes that empirical studies have shown accompany model-building activities. Chapter 3 indicates the need for students to become familiar with complex systems analysis, how SD modeling (one method of complex systems analysis) aligns with the Common Core State Standards in Mathematics, and the work that has transpired over the past two decades using SD in K-12. Chapter 4 focuses on the importance of the concept of function in high school mathematics, some limitations of exclusive reliance on the closed form equation representation for mathematizing problems and the SD stock/flow representations of some of the elementary functions that are studied in algebra classes. Chapter 5 looks at the issues affecting two traditional teachers and the challenges they faced when trying to reintroduce SD modeling into their algebra classes. Chapter 6 explains the student component of the classroom experiment that was conducted by the teachers who are highlighted in Chapter 5. The analysis of the results of student model-building activities in the two classroom studies that are part of the third paper did not indicate a statistical difference between the two experimental groups and the two control groups. Many environmental and scheduling issues conspired to adversely affect the experiment. However, positive outcomes were evident from the two pairs of students who were videotaped while they built the final multi-function drug model, the final student lesson in the experiment. Research focused on student outcomes is needed to further assess the strengths and weakness of the SD approach for student learning in mathematics.

Investigations presented here are (a) the study of reorientational dynamics and internal rotation in transition metal complexes by NMR relaxation experiments, and (b) the study of ligand exchange dynamics in transition metal complexes by exchange NMR experiments. The phenyl ring rotation in Ru3(CO)9(μ3-CO)(μ3-NPh) and Re(Co)2(CO)10(μ3- CPh) was monitored by 13C NMR relaxation experiments to probe intramolecular electronic and/or steric interactions. It was found that the rotation is relatively free in the first complex, but is restrained in the second one. The steric interactions in the complexes were ascertained by the measurement of the closest approach intramolecular distances. The rotational energy barriers in the two complexes were also calculated by using both the Extended Hiickel and Fenske-Hall methods. The study suggests that the barrier is due mainly to the steric interactions. The exchange NMR study revealed two carbonyl exchange processes in both Ru3(CO)9(μ3-CO)(μ3-NPh) and Ru3(CO)8(PPh3)(μ3-CO)(μ3-NPh). The lower energy process is a tripodal rotation of the terminal carbonyls. The higher energy process, resulting in the exchange between the equatorial and bridging carbonyls, but not between the axial and bridging carbonyls, involves the concerted formation of edge-bridging μ2-CO moieties. The effect of the PPh3 ligand on the carbonyl exchange rates has been discussed. A combination of relaxation and exchange NMR found that PPh3 ligand rotation about the Ru-P bond is slow on the exchange NMR time scale and the phenyl rotation about the P-Cipso bond is fast on the exchange NMR time scale but is slow on the NMR relaxation time scale.

Electronic energy transfer has been investigated in pure donor systems by means of computer simulations. Calculated properties were the probability that the initially excited donor is excited at a time t after the excitation, Gs(t), the mean square displacement of the excitation and different fluorescence observables. For three dimensional systems the results obtained by Monte Carlo simulations were compared to the so-called GAF-theory {Gouchanour,C. R., Andersen, H. C. and Fayer, M. D., J. Chem. Phys. 81, 4380 (1984)}, and the agreement was found to be good. Anisotropic systems, i.e. mono-, bi- and multilayer systems, were compared to the two-particle model {Baumann,J. and Fayer, M. D., J. Chem. Phys. 85, 4087 (1986)}. The agreement between the Gs(t) calculated from the tp- model and the Monte Carlo simulations were good for all systems investigated. However, the agreement between the fluorescence observables obtained by MC and the tp-model were in general poor. A much better agreement was found when a phenomenological approach was used for calculating the fluorescence depolarization ratios. Three dimensional systems where the donors are rotating on the same time scale as the energy transfer takes place have also been studied and compared to analytical theories. The Molecular Dynamics simulations of decapeptide H142 shows that simulations in a continuum with a relative permeability do not provide a reliable alternative to simulations with explicit solvent molecules.

Diss. (sammanfattning) Umeå : Umeå universitet, 1991, härtill 5 uppsatser

digitalisering@umu

En nous concentrant sur les valeurs du module de cisaillement l’équilibre Geq pour le modèle bien connu des polymères vitrifiables (echantillionné par le biais de la MD), nous avons adressé la question générale de en quoi les propriétées méchaniques des couches mince diffères de la phase volumique. Il a été démontrè que dans les deux cas Geq de manière non ambigus sèpare l’état fluide (Geq = 0) de l’état vitreux (Geq > 0). Nous avons aussi insisté sur le fait que Geq pour la couche mince dépend de lépaisseur du film h mais aussi de de la pression tangentielle qui est un résultante de la procédure de préparation de la couche mince
Focusing on the equilibrium shear modulus Geq of well-known glass-forming polymer model system (sampled by means of MD), we have addressed the general question of how the mechanical properties of the thin polymer films differs from the bulk. Using ”stress fluctuation” formalism we obtained Geq(T) for the bulk and films. It has been demonstrated that in both cases Geq unambiguously separates the fluid state (Geq = 0) from the glass (Geq > 0). We also stressed that Geq for the film does not only depend on film thickness h, but also on tangential pressure that is a consequence of the film preparation procedure

The Doctoral dissertation titled “Theoretical Study of Phospholipid Membranes: the Complex Role of Cholesterol and Lipid Unsaturation” covers biological membrane modeling by means of molecular dynamics. The main focus of the dissertation is to study the role of phospholipid unsaturation and cholesterol in animal cell membrane properties. In general, it aims to find the molecular mechanisms underlying naturally occurring phenomena, such as the preference displayed by nature for phospholipids with an unsaturated sn-2 chain where the double bond is placed in its middle. Significant results were obtained regarding the importance of the double bond position in phospholipidic membranes. We report that lipids with a double bond in the middle of their acyl chain present the largest capacity to induce disorder in the membrane. We also found that this effect is enhanced when the unsaturated acyl chain is attached to the sn-2 lipid. Another important result obtained in this work is the explanation of the role of cholesterol as promoter of in-plane ordering due to its collective action over surrounding phospholipids. We report the natural preference of cholesterol to be placed in the second coordination shell in the membrane plane in respect to other cholesterols. In other words cholesterols do not like to be in direct contact with each other. This result strongly supports the umbrella theory. Additionally we found that cholesterols place themselves in respect to the others in a well-defined 3 fold symmetry pattern. The combination of these two features is likely responsible for the condensation effect, as the ordering of the lipid tails could be explained by their sandwiching between cholesterols. These results, never reported before, shed light on the reasons behind the natural lipid selection and the mechanism underlying the well-known ordering effects of cholesterol which are largely controversial. Final part of this Doctoral dissertation focuses on membranes that contain cardiolipins instead of cholesterol like the one present in the mitochondria.
L'objectiu principal d'aquesta tesi és estudiar el paper dels fosfolípids insaturats i del colesterol en les propietats de les membranes cel·lulars animals mitjançant dinàmica molecular clàssica. En general, s'han estudiat els mecanismes moleculars subjacents responsables de la preferència, dictada genèticament, per composicions lipídiques determinades en aquestes membranes. Per exemple, la preferència general pels fosfolípids insaturats amb un doble enllaç al mig de la cadena sn-2. Entre els resultats obtinguts destaquen les evidències trobades que justifiquen la importància de la posició del doble enllaç en els fosfolípids que constitueixen les membranes. S'ha observat que els fosfolípids insaturats amb un doble enllaç al mig de la cua presenten una major capacitat d'induir desordre en la membrana. Aquesta capacitat d'induir desordre es maximitza quan la cadena insaturada és la sn-2, posició genèticament afavorida. Un altre resultat important obtingut en aquest treball és l'explicació del paper del colesterol com a promotor d'ordre en el pla de la membrana a causa de la seva acció col·lectiva sobre els fosfolípids circumdants. Hem constatat la preferència natural del colesterol per col·locar-se en la segona esfera de coordinació en relació amb els altres colesterols adjacents. En altres paraules, al colesterol no li agrada estar en contacte directe amb altres colesterols. Aquest resultat dóna suport a la teoria del paraigües. A més, s'ha trobat que els colesterols s'emplacen entre ells formant un patró dinàmic amb simetria trigonal. Aquest resultat no és gens intuïtiu tenint en compte la naturalesa fluïda del medi i que els colesterols no es troben en contacte directe. La combinació d'aquestes dues característiques justifica el conegut efecte de condensació dels colesterols: colesterols adjacents ordenen les cues fosfolipídiques aixafant-les entre ells. Aquests resultats, fins ara desconeguts, aclareixen algunes de les raons existents darrere de la selecció natural dels lípids i els mecanismes responsables dels coneguts efectes de condensació que indueix el colesterol, que fins ara eren en gran mesura controvertits. Per acabar, aquesta tesi doctoral dedica el seu darrer capítol a l'estudi de membranes que contenen cardiolípids en comptes de colesterol, com és el cas de la membrana mitocondrial.

Adult second language acquisition takes time over an extended period of time during which the L2 motivation of learners goes through periods of ups and downs. Dörnyei, MacIntyre and Henry (2015) recognized the inherently dynamic nature of L2 motivation and called for adopting the Complex Dynamic System Theory (CDST) when studying this phenomenon. While using a CDST perspective, this mixed method study drew on Dörnyei’s (2009b) model of the Motivational Self System to examine the L2 motivation of 86 Saudi study-abroad students. Also, the construct of the Anti-ought to Self (Thompson, 2015) and aspects of the Appraisal Theory (Schumann, 2001) were adopted to guide this examination. The results of the study showed that the L2 motivation of the participants fell into four main motivational patterns. Also, some of the participants shifted into new attractor states over the course of their academic semester. Another important finding was that the Anti-ought to Self appeared as an important construct. The results of the standard multiple regressions showed that the amount of the variance in the Intended Learning Effort that was accounted for by the Anti-ought to Self alone exceeded the amount of the variance accounted for by the other explanatory variables put together. Also, the analysis of the quantitative and qualitative data showed that the use of the Appraisal Theory improved the construct validity of the Learning Experiences. The implications of these findings and future directions of the L2 motivational research were also discussed in the study.

Projects and programmes are inherently complex; the interaction of people, systems, processes and data within a dynamic environment creates an intricate network of agents whose behaviour can be unpredictable and unexpected. The management of this complexity is ordinarily concerned with the implementation of tools and techniques to ensure that projects are completed within the desired cost and time, at the agreed level of performance and quality – this is often referred to as the †̃iron triangleâ€TM. However, the impact of a dynamic external environment on the †̃softâ€TM boundaries of the project domain can lead to extreme difficulty in attempting to forecast or predict outcomes and system behaviours. This thesis contends that there is a clear desideratum for a new paradigm in project management practice and research that moves beyond the traditionalist (reductionist) approach to one that embraces, rather than attempts to simplify complexity. The research described in this thesis seeks to uncover the characteristics of complexity, in the context of projects and programmes, in an attempt to uncover if complexity is a factor in the determination of †̃valuableâ€TM outcomes. Subsequently, and through the theoretical lens of complexity theory, this research seeks to highlight the importance of our understanding and treatment of complexity in the execution and management of projects and programmes. The research further seeks to demonstrate how complexity thinking may inform a more sophisticated understanding of how projects, programmes and portfolios delivered successfully (Ziadat, 2017). The context of the research is the oil and gas (O & G) engineering sector in the Middle East and North Africa (MENA) region. A two stage qualitative and quantitative methodology is applied, based on deductive reasoning. The first stage involves the development of a questionnaire and a series of unstructured interviews to gain an understanding of the practical consideration that emerges from the literature review. The second stage of the research involves the application of meta-analysis to study the correlation between the complexity factors identified in the first stage, aiming for heterogeneity, identification of patterns and directing to achieve robust conclusions by using sensitivity analysis. The thesis proposes a new model of complexity factors for oil & gas engineering projects in the MENA region. The model is designed to facilitate the analysis of the project complexity landscape and to define requirements for oil & gas organisations involved with the delivery of projects and programmes to cope with different complexity factors within and across the MENA region. The outcomes include substantial relationship between technical and health, safety & environment complexity factors and project performance despite the mediation of project management complexity factors, yet the organizational complexity factors can be observed at a significant level when project management in complexity factors are considered as a mediator in the model (Ziadat, 2016).

[ES] En este trabajo estudiamos dos reacciones catalíticas relevantes para la industria y la localización del anión fluoruro en la zeolita RTH, sintetizada en medio fluoruro. El capítulo 3 es el primer capítulo de resultados, donde se estudia la reducción quimioselectiva del nitroestireno en las superficies Ni(111), Co(111), Cu(111) y Pd(111). El mecanismo generalmente aceptado de esta reacción está basado en el esquema propuesto por Haber en 1898, en el que la reacción puede transcurrir por dos rutas, la directa y la de condensación. En este capítulo exploramos ambas rutas, y observamos que la ruptura de los enlaces N-O y la consecuente formación de enlaces metal-O está más favorecida que la formación de enlaces N-H en las superficies Ni(111) y Co(111), debido al carácter oxofílico de ambos metales. Las etapas más lentas involucran la formación de enlaces N-H. En las superficies de metales nobles como Pt(111) y Pd(111) se observa el comportamiento contrario. La superficie Cu(111) es un caso intermedio comparado con los metales nobles y no nobles. Además, el nitroestireno interactúa con los átomos de Cu de la superficie solo a través de grupo nitro, con lo cual es un candidato ideal para alcanzar selectividades cerca del 100%. Sin embargo, la superficie Cu(111) no es capaz de activar la molécula de H2. En este sentido, proponemos un catalizador bimetálico basado en Cu, dopado con otro metal capaz de activar al H2, tales como el Pd o el Ni. En los capítulos 4 y 5 se ha estudiado la reducción catalítica selectiva de los óxidos de nitrógeno (SCR, en inglés) con amoníaco. Usando métodos de DFT, hemos encontrado rutas para la oxidación de NO a NO2, nitritos y nitratos con energías de activación relativamente bajas. También, hemos encontrado que la reducción de Cu2+ a Cu+ requiere la participación simultánea de NO y NH3. Posteriormente, hemos estudiado la influencia del NH3 en este sistema con métodos de dinámica molecular. El NH3 interacciona fuertemente con el Cu+ de forma que dos moléculas de este gas son suficientes para romper la coordinación del catión Cu+ con los oxígenos del anillo 6r, y formar el complejo lineal [Cu(NH3)2]+. Además, los cationes Cu2+ pueden ser estabilizados fuera de la red mediante la formación del complejo tetraamincobre(II). Debido a la presencia de los cationes Cu+ y Cu2+ coordinados a la red de la zeolita, aparecen bandas en la región entre 800-1000 cm-1 del espectro infrarrojo. El análisis de las frecuencias IR de varios modelos con Cu+ y Cu2+ coordinados al anillo 6r, o formando complejos con amoniaco indica que cuando los cationes Cu+ y Cu2+ están coordinados a los oxígenos del anillo 6r aparecen vibraciones entre 830 y 960 cm-1. Frecuencias en esta zona también se obtienen en los casos en que NO, NO2, O2 y combinaciones de dos de ellos están adsorbidos en Cu+ y Cu2+. Sin embargo, cuando los cationes Cu+ y Cu2+ están fuera del anillo (no hay enlaces entre los cationes de cobre y los oxígenos del anillo 6r) no se obtienen vibraciones de IR en esta región del espectro. Estos resultados indican que con el seguimiento del espectro IR durante la reacción SCR es posible determinar si los cationes Cu+ y Cu2+ están coordinados o no al anillo de 6r en las etapas de oxidación y reducción. Por último, hemos simulado el desplazamiento químico de 19F, δiso,, en la zeolita sintetizada RTH. El análisis del δiso de los distintos modelos utilizados nos ha permitido reconocer la simetría del material sintetizado, el cual pertenece al grupo espacial P1 y la nueva celda unidad ha sido confirmada experimentalmente por difracción de rayos X. Finalmente, hemos asignado la señal experimental que aparece en el espectro de 19F a -67.2_ppm, al F- localizado en un sitio T2, el cual es a su vez la posición más estable. Además, la señal a -71.8 ppm se ha asignado al anión F- localizado en un sitio T4.
[CA] En aquest treball estudiem dues reaccions catalítiques rellevants per a la indústria i la localització de l'anió fluorur en la zeolita RTH, sintetitzada al mig fluorur. El capítol 3 és el primer capítol de resultats, on s'estudia la reducció quimioselectiva del nitroestireno en les superfícies Ni(111), Co(111), Cu(111) i Pd(111). El mecanisme generalment acceptat d'aquesta reacció està basat en l'esquema proposat per Haver-hi en 1898, en el qual la reacció pot transcórrer per dues rutes, la directa i la de condensació. En aquest capítol explorem totes dues rutes, i observem que la ruptura dels enllaços N-O i la conseqüent formació d'enllaços metall-O està més afavorida que la formació d'enllaços N-H en les superfícies Ni(111) i Co(111), a causa del caràcter oxofílico de tots dos metalls. Les etapes més lentes involucren la formació d'enllaços N-H. En les superfícies de metalls nobles com Pt(111) i Pd(111) s'observa el comportament contrari. La superfície Cu(111) és un cas intermedi comparat amb els metalls nobles i no nobles. A més, el nitroestireno interactua amb els àtoms de Cu de la superfície sol a través de grup nitre, amb la qual cosa és un candidat ideal per a aconseguir selectivitats prop del 100%. No obstant això, la superfície Cu(111) no és capaç d'activar la molècula d'H2. En aquest sentit, proposem un catalitzador bimetàl·lic basat en Cu, dopat amb un altre metall capaç d'activar a l'H2, com ara el Pd o el Ni. En els capítols 4 i 5 hem estudiat la reducció catalítica selectiva dels òxids de nitrogen (SCR, en anglés) amb amoníac. Usant mètodes de DFT, hem trobat rutes per a l'oxidació de NO a NO2, nitrits i nitrats amb energies d'activació relativament baixes. També, hem trobat que la reducció de Cu2+ a Cu+ requereix la participació simultània de NO i NH3. Posteriorment, hem estudiat la influència del NH3 en aquest sistema amb mètodes de dinàmica molecular. El NH3 interacciona fortament amb el Cu+ de manera que dues molècules d'aquest gas són suficients per a trencar la coordinació del catió Cu+ amb els oxígens de l'anell 6r, i formar el complex lineal [Cu(NH3)2]+. A més, els cations Cu2+ poden ser estabilitzats fora de la xarxa mitjançant la formació del complex tetraamincobre(II). A causa de la presència dels cations Cu+ i Cu2+ coordinats a la xarxa de la zeolita, apareixen bandes a la regió entre 800-1000 cm-1 de l'espectre infraroig. L'anàlisi de les freqüències IR de diversos models amb Cu+ i Cu2+ coordinats a l'anell 6r, o formant complexos amb amoníac indica que quan els cations Cu+ i Cu2+ estan coordinats als oxígens de l'anell 6r apareixen vibracions entre 830 i 960 cm-1. Freqüències en aquesta zona també s'obtenen en els casos en què NO, NO2, O2 i combinacions de dues d'ells estan adsorbidos en Cu+ i Cu2+. No obstant això, quan els cations Cu+ i Cu2+ estan fora de l'anell (no hi ha enllaços entre els cations de coure i els oxígens de l'anell 6r) no s'obtenen vibracions d'IR en aquesta regió de l'espectre. Aquests resultats indiquen que amb el seguiment de l'espectre IR durant la reacció SCR és possible determinar si els cations Cu+ i Cu2+ estan coordinats o no a l'anell de 6r en les etapes d'oxidació i reducció. Finalment, hem simulat el desplaçament químic de 19F, δiso, en la zeolita sintetitzada RTH. L'anàlisi del δiso dels diferents models utilitzats ens ha permés reconéixer la simetria del material sintetitzat, el qual pertany al grup espacial P1 i la nova cel·la unitat ha sigut confirmada experimentalment per difracció de raigs X. Finalment, hem assignat el senyal experimental que apareix en l'espectre de 19F a -67.2 ppm, al F- localitzat en un lloc T2, el qual és al seu torn la posició més estable. A més, el senyal a -71.8 ppm s'ha assignat a l'anió F- localitzat en un lloc T4.
[EN] In this work, we have studied two heterogeneous catalytic reactions and the localization of the fluoride anion in the as-made RTH framework, synthesized in fluoride medium. The first results, included in chapter 3, correspond to the chemoselective reduction of nitrostyrene on different metal surfaces, i.e, Ni(111), Co(111), Cu(111) and Pd(111). Until very recently, the reduction of the nitro group was explained on the basis of the general mechanism proposed by Haber in 1898 where the reaction can follow two routes, the direct and condensation route. We have explored the relevant elementary steps of both routes and found that because of the oxophilic nature of Ni and Co, the steps involving the dissociation of N-O bonds and formation of metal-O bonds are significantly favored compared with the other steps on both metal surfaces. In addition, the most demanding steps in terms of energy involve the formation of N-H bonds. These findings are in contrast to those of noble metals such as Pt and Pd, where the opposite behavior is observed. The behavior of Cu(111) lies in between the aforementioned cases, and also no chemical bonds between the carbon atoms of the aromatic ring of nitrostyrene and the Cu(111) surface is formed. For this reason, it might be an ideal candidate to achieve nearly 100 % selectivity. However, the Cu(111) surface does not seem to activate the H2 molecule. In this regard, we propose a bimetallic Cu-based catalyst whose surface is doped with atoms of a H2-activating metal, such as Ni or Pd. On another matter, we have also investigated the selective catalytic reduction of nitrogen oxides (SCR-NOx) and the main results are presented in the following two chapters, 4 and 5. By using static DFT methods, we found pathways for the oxidation of NO to NO2, nitrites and nitrates with relatively low activation energies. We also found, in agreement with experimental reports, that the reduction of Cu2+ to Cu+ requires the simultaneous participation of NO and NH3. Later, molecular dynamics simulations allowed us to assess the influence of NH3. The strong interaction of NH3 with the Cu+ cation is evidenced by its ability to detach Cu+ from the zeolite framework and form the mobile linear complex [Cu(NH3)2]+. Cu+ is no longer coordinated to the zeolite framework in the presence of two NH3 molecules. This observation and the fact that the T-O-T vibrations of the framework produce bands in the 800-1000 cm-1 region of the IR spectrum when perturbed by the coordination of Cu+ and Cu2+ cations, indicate that bands in the 800-1000 cm-1 regions should be observed when both copper cations are bonded to the framework oxygens. Finally, we have also studied NMR properties of the as-made pure silica RTH framework, aiming at locating the compensating fluoride anion. The calculation of the 19F chemical shift in different T sites and comparison with the experimental NMR spectra shows that the as-made RTH belongs to the P-1 space group with 16 Si, 32 O atoms, one fluoride anion and one OSDA cation. These results have been confirmed experimentally by XRD. In addition, we have assigned the experimental signal of 19F at -67.2 ppm to the fluoride anion in a T2 site, which in turn is the most stable location found, and the signal of -71.8 ppm to a fluoride anion sitting in a T4 site.
My acknowledgements to “La Caixa foundation” for the financial support through “La Caixa−Severo Ochoa” International PhD Fellowships (call 2015), to the Spanish Supercomputing Network (RES), to the Centre de Càlcul de la Universitat de València, to the Flemish Supercomputer Center (VSC) of Ghent University for the computational resources and technical support, and to the Spanish Government through the MAT2017-82288-C2-1-P programme
Millan Cabrera, R. (2021). Computational study of heterogeneous catalytic systems. Kinetic and structural insights from Density Functional Theory [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/161934
TESIS

Thesis (M.S.)--University of Tennessee, Knoxville, 2006.
Title from title page screen (viewed June 12, 2006). Thesis advisors: David J. Keffer, William V. Steele. Vita. Includes bibliographical references.

Thesis (M.S.)--University of Wisconsin--Madison, 1999.
Typescript. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves 41-42).

This thesis presents an implementation of path integral molecular dynamics (PIMD) for sampling equilibrium and dynamical properties within the molecular modelling toolkit (MMTK) [J. Comp. Chem. 21, 79 (2000)], an open source Python package. Rigorous simulation using this code serves to benchmark this implementation as well as the robust- ness of the path integral Langevin equation as a thermostat [J. Chem. Phys. 133, 124104 (2010)]. PIMD is used to calculate equilibrium properties for clusters of HeN-CO2 at low- temperatures, with comparison to experimental and exact results. We characterize the convergence of structural and energetic properties as a function of path-integral discretiza- tion error. The radial and angular distribution of these clusters is studied as a function of size in the absence of rotation and bosonic exchange. These distributions are subsequently used to calculate vibrational shifts of CO2. This result is compared to high-accuracy path integral Monte Carlo simulations which include rotational and exchange effects. These sim- ulations indicate that the neglect of rotational degrees of freedom leads to an unphysical localization of helium atoms and incorrect vibrational shifts when compared to experiment. Approximate real-time quantum dynamics is presented for doped helium clusters using the ring-polymer molecular dynamics (RPMD) method. The accuracy of RPMD is tested iii for low-temperature simulations and compared to exact results. Preliminary calculation of the dynamics of the helium solvated CO2 dopant with respect to the center of mass of the cluster is presented. The effect of a cartesian integrator versus a normal-mode integrator for quantum dynamics is addressed. The path integral ground-state method is applied in order to calculate T = 0 properties. A convergence study of the ground-state energy of the quantum harmonic oscillator with respect to sampling time and path discretization is shown. As a final application of this implementation, a sugar in a periodic water box is simulated at T = 300K. The calculation of rotamer populations and a dipole autocorrelation indicate negligible change with the inclusion of quantum effects. This work offers a comprehensive foundation from which to base future PIMD centered research.

Proteins and DNA are essential to life as we know it and understanding their function is understanding their structure and dynamics. The importance of the latter is being appreciated more in recent years and has led to the development of novel interdisciplinary techniques and approaches to studying protein function. Three techniques to study protein structure and dynamics have been used and combined in different ways in the context of this thesis and have led to a better understanding of the three systems described herein. X-ray crystallography is the oldest and still arguably most popular technique to study macromolecular structures. Nuclear magnetic resonance (NMR) spectroscopy is a not much younger technique that is a powerful tool not only to probe molecular structure but also dynamics. The last technique described herein are molecular dynamics (MD) simulations, which are only just growing out of their infancy. MD simulations are computer simulations of macromolecules based on structures solved by X-ray crystallography or NMR spectroscopy, that can give mechanistic insight into dynamic processes of macromolecules whose amplitudes can be estimated by the former two techniques. MD simulations of the model protein GB3 (B3 immunoglobulin-binding domain of streptococcal protein G) were conducted to identify origins of discrepancies between order parameters derived from different sets of MD simulations and NMR relaxation experiments.The results highlight the importance of time scales as well as sampling when comparing MD simulations to NMR experiments. Discrepancies are seen for unstructured regions like loops and termini and often correspond to nanosecond time scale transitions between conformational substates that are either over- or undersampled in simulation. Sampling biases can be somewhat remedied by running longer (microsecond time scale) simulations. However, some discrepancies persist over even very long trajectories. We show that these discrepancies can be due to the choice of the starting structure and more specifically even differences in protonation procedures. A test for convergence on the nanosecond time scale is shown to be able to correct for many of the observed discrepancies. Next, MD simulations were used to predict in vitro thermostability of members of the bacterial Ribonuclease HI (RNase H) family of endonucleases. Thermodynamic stability is a central requirement for protein function and a goal of protein engineering is improvement of stability, particularly for applications in biotechnology. The temperature dependence of the generalized order parameter, S, for four RNase H homologs, from psychrotrophic, mesophilic and thermophilic organisms, is highly correlated with experimentally determined melting temperatures and with calculated free energies of folding at the midpoint temperature of the simulations. This study provides an approach for in silico mutational screens to improve thermostability of biologically and industrially relevant enzymes. Lastly, we used a combination of X-ray crystallography, NMR spectroscopy and MD simulations to study specificity of the interaction between Drosophila Hox proteins and their DNA target sites. Hox proteins are transcription factors specifying segment identity during embryogenesis of bilaterian animals. The DNA binding homeodomains have been shown to confer specificity to the different Hox paralogs, while being very similar in sequence and structure. Our results underline earlier findings about the importance of the N-terminal arm and linker region of Hox homeodomains, the cofactor Exd, as well as DNA shape, for specificity. A comparison of predicted DNA shapes based on sequence alone with the shapes observed for different DNA target sequences in four crystal structures when in complex with the Drosophila Hox protein AbdB and the cofactor Exd, shows that a combined ”induced fit”/”conformational selection” mechanism is the most likely mechanism by which Hox homeodomains recognize DNA shape and achieve specificity. The minor groove widths for all sequences is close to identical for all ternary complexes found in the different crystal structures, whereas predicted shapes vary between the different DNA sequences. The sequences that have shown higher affinity to AbdB in vitro have a predicted DNA shape that matches the observed DNA shape in the ternary complexes more closely than the sequences that show low in vitro affinity to AbdB. This strongly suggests that the AbdB-Exd complex selects DNA sequences with a higher propensity to adopt the final shape in their unbound form, leading to higher affinity. An additional AbdB monomer binding site with a strongly preformed binding competent shape is observed for one of the oligomers in the reverse complement strand of one of the canonical (weak) Hox-Exd complex binding site. The shape preference seems strong enough for AbdB monomer binding to compete with AbdB-Exd dimer binding to that same oligomer, suggested by the presence of both binding modes in the same crystal. The monomer binding site is essentially able to compete with the dimer binding site, even though binding with the cofactor is not possible, because its shape is very close to the ideal shape. A comparison of different crystal structures solved herein and in the literature as well as a set of molecular dynamics simulations was performed and led to insights about the importance of residues in the Hox N-terminal arm for the preference of certain Hox paralogs to certain DNA shapes. Taken together all these insights contribute to our understanding of Hox specificity in particular as well as protein-DNA interactions in general.

This thesis is dedicated to studies of the excited-state dynamics in organic molecular systems for solar energy conversion by employing time-resolved experimental techniques. Organic photovoltaic (OPV) devices have received significant attention in the past decade and reaching record high power conversion efficiencies (PCE) above 17%. An essential step towards reaching the predicted PCE limit of 25.5% is to develop a comprehensive picture of the photophysical processes, specifically the loss processes, in OPV devices. It is the aim of this thesis to investigate and understand the fate of excited-states in organic electron donor/acceptor systems by ultrafast spectroscopic techniques, specifically, to reveal the interplay between energy and charge transfer processes. The first part deals with the identification of different polymorphs in a diketopyrrolopyrrole-based (DPP) polymer. Applying time-resolved photoluminescence (TRPL) measurements to the polymer dissolved in different solvent mixtures and using multivariate curve resolution (MCR) to deconvolute the ground-state absorption spectra reveals the co-existence of an amorphous (α) and two semi-crystalline (β1 and β2) polymer phases. The OPV device performance is shown to increase by the additional absorption of the β2 phase. The second part compares the efficiency of direct and energy transfer-mediated charge generation in prototypical donor-acceptor dyads that use as the electron donor triangulene derivatives chemically linked to the electron acceptor perylenediimide (PDI) block via oligophenylene spacers of different lengths. Charge generation efficiencies are found to be similar and increase with the donor-acceptor spatial separation. A combination of transient absorption (TA) measurements and computation of the dyad’s excited-state landscape revealed the presence of “optically-dark” excited-states that are populated by ultrafast donor-acceptor energy transfer prior to hole (back) transfer. The last part of the dissertation uses TRPL, TA, and time-delayed collection field (TDCF) measurements alongside MCR analysis to provide a comprehensive analysis of the yield of individual photophysical processes in OPV devices. A systematic methodology is proposed and tested on two all-polymer BHJ devices used as model systems. The experimental findings are supported by successful simulation of the solar cells’ JV characteristics using the spectroscopically-determined kinetic parameters. More generally, this approach can be used to quantify efficiency-limiting processes in other donor-acceptor BHJs.

This thesis collects the results of a series of experiments aimed at the characterization of energy and charge transfer processes in organic systems, carried out during my PhD course. The complexity of the subject is connected to the identification of the micro-scale phenomena that occur after visible excitation of the systems. The goal is to control these processes in order to maximize the energy migration throughout the systems, aiming to their potential application in OPV devices. Stationary and time-resolved spectroscopic techniques are excellent experimental methods to investigate ET in organic molecular complexes, because the electronic properties are revealed in the absorption and emission spectra. The characterization of the spectral features and their time-evolution, on femtosecond timescale, gives important pieces of information about the nature and dynamics of the excited state, and its interaction with the surrounding. The first experimental work I carried out in the Ultrafast group of Prof. Paolo Foggi at LENS was focused on the spectroscopic investigation of a substituted Zn-Phtalocyanine (ZnPc) dye, that has a potential application as sensitizer in Dye Sensitized Solar Cells (DSSCs). Transient Absorption Spectroscopy (TAS), an ultrafast pump-probe technique with sub-picosecond time resolution, was employed to investigate the excited state dynamics of the dye in ethanol (EtOH) solution and adsorbed on nanocrystalline films of Titania (TiO2) and Zirconia (ZrO2). TAS results allowed us to identify the timescales of the different relaxation processes occurring after visible excitation, and to propose a scheme of the energetic levels involved in the excited state dynamics. Furthermore, we had evidence electron injection in the Titania conduction band, which makes the molecule suitable for DSSCs applications. Many research group are focused toward the realization of artificial light-harvesting antennae for energy capture, based on organic molecules. The optimal electronic properties of such systems are still object of scientific debates, because different ET mechanisms take part in the overall exciton migration, which interplay is not trivial. During a one-year period spent in the M. G. Bawendi group at MIT, I studied the exciton transport properties in self-assembled light-harvesting nanotubes (LHNs), quasi one-dimensional aggregates consisting of ordered amphiphillic cyanine dyes. These systems present interesting excitonic properties, which derive from the unusual electronic coupling between the monomers. Because of the low static disorder, large exciton delocalization and the negligible reorganization energy (low coupling with the environment), LHNs represent an ideal model system to explore the quantum contribution and the influence of energetic disorder on the ET. The experimental investigation of LHNs was carried out by stationary and time resolved spectroscopy, at room temperature and as a function of temperature, from room temperature to 5K: the change in the spectral lineshape was interpreted in terms of homogeneous broadening. Intensity dependent fluorescence measurements gave evidence of exciton-exciton nnihilation (EEA). In order to get insight the effect of energetic disorder, a ballistic model for exciton diffusion was developed: two regimes of exciton migration were identified, depending on the relative value of the 2homogeneous and inhomogeneous timescales. Stationary fluorescence was measured as a function of the visible light irradiation, over several minutes, showing Photobrightening (PB) phenomena followed by Photodarkening (PD) on longer timescales. This results, confirmed also by 2D electronic spectroscopy (2DES), have been interpreted in terms of exciton migration mediated by super-radiance, a collective emission process arising from the coherent exciton delocalization. In order to deeply investigate the view on the molecular aggregate and their influence on exciton dynamics, I performed 2DES measurements on mixed monomer / H-aggregate systems made of ZnPc molecules. When dissolved in particular solvents, such as Cloroform (CHCl 3 ), the ZnPc molecules forms aggregates. Aggregation is one of the main issues that prevents a high efficiency of electron injection in the semiconductor conduction band. In the aggregation process, radiative channels of deactivation from the dye excited state are introduced. 2DES is a powerful multidimensional coherent spectroscopic technique that allows to: investigate the exciton dynamics and the lineshape time-evolution on femtosecond timescale, identifying the homogeneous and inhomogeneous timescales; highlight the coupling between electronic states and the possible coherent contribution. Broadband excitation of the sample allowed to discriminate between the monomer and aggregate kinetic traces. We had evidence of electronic coupling between the aggregate and the isolated molecules in close proximity. Furthermore, electronic coupling mediated by an internal vibrational mode was observed between two non-degenerate Q-states of the monomer.

Thesis (Ph. D.)--University of Notre Dame, 2006.
Thesis directed by J. Daniel Gezelter for the Department of Chemistry and Biochemistry. "October 2006." Includes bibliographical references (leaves 163-173).

This thesis deals with the understanding of the structure, dynamics and thermodynamics in complex systems (proteins, hydration layers, DNA, ice polymorphs) by employing computer simulations, theoretical analysis, and in some cases, collaborative experimental efforts. There are mainly 5 parts with 13 chapters. In Part I, we study the effects of solvent on the structure and stabilization of insulin hexamer. In Chapter 1 we discuss the structural features of the different oligomers of insulin. Chapter 2 deals with insulin hexamer in neat water. We find that a group of ~10 water molecules present in the cavity of insulin hexamer is crucial in stabilizing the structure of the biomolecular assembly. In Chapter 3, we study the effect of ethanol on the structure of insulin hexamer. Ethanol, by virtue of its amphiphilic nature, interacts with both hydrophilic and hydrophobic residues, thereby destroying the native state structure of insulin hexamer. In Part II, we study the interactions between several proteins and water. We start with a brief introduction of the different techniques used to study protein hydration layer (PHL) in Chapter 4. In Chapter 5, we find that the protein self-interaction energy fluctuations are strongly anti-correlated to the protein-water cross interaction energy fluctuations. The total energy spectrum of protein shows bimodal 1/f noise characteristics. We posit that water exerts control over protein dynamics via an exchange of energy between these two domains. In Chapter 6, from distributions of dynamical timescales, we find that PHL contains both fast and slow water molecules. Shell-wise decomposition of the PHL demonstrates a gradual increase of dielectric constant and decrease of specific heat from the protein surface to the bulk. In chapter 7 we study the heterogeneous solvation dynamics of protein. We find that the slow component in the solvation relaxation originates from side chain and hydration layer fluctuations. Charged neighbourhood of the probe results in slower dynamics. Cross-correlations between water and side-chains are anti-correlated, making the solvation faster. In Part III, we study the solvation dynamics of DNA. In Chapter 8 we briefly review the literature in this field. In Chapter 9 we employ multiple theoretical and simulation analyses to understand the origin of the long time power law behaviour in the solvation dynamics of DNA. We find that electrolytic friction and movement of ions along the DNA backbone could be responsible for this mysterious behaviour. Part IV deals with the different phases of water and their transitions. In Chapter 10, we discuss the phase diagram of water and its multiple regions. In Chapter 11 we compare the solid-liquid interfaces in TIP4P/ice and mW water models with Lennard-Jones argon. We find that ice-water interface is much sharper than its LJ counterpart, mainly due to sharp change in rotational entropy. We also study the growth rate of ice at different temperatures and compare it with experimental observations. We find that Wilson-Frenkel equation of crystal growth breaks down at higher temperatures. In Chapter 12, we observe the pressure induced crystal to glass transition in low density ice. High density crystalline ice show no transition. We find that hydrogen bond defects can be used as effective order parameters to study these phase transitions. At very high pressure (150 kbar), we observe the emergence of crystalline order from the disordered glassy phase. In Part V, we study of a small medicinally important molecule metformin. In Chapter 13, we develop a force field of this molecule and validate it with multiple experimental observations. We study the structural and dynamical features of metformin and develop a free energy landscape of DNA-metformin interactions. The last part of the thesis (Part VI) contains a single chapter (Chapter 14) which includes the concluding remarks and the future plans and research prospects derived from this thesis.
INSPIRE Fellowship, DST, India

Proton exchange membrane (PEM) fuel cells are an eco-friendly power source that has great potential to reduce our oil dependence for our stationary and transportation applications. In order to make PEM fuel cells an economically viable option, further effort is needed to improve proton conduction under wide operating conditions and reduce the cost of production. Design and synthesis of novel membranes that have superior characteristics require a fundamental molecular-level understanding of the relationship between the polymer chemistry, water content and proton conduction. The performance of a fuel cell is influenced by the electrochemical and molecular/proton transport processes that occur at the catalytic sites in the electrode/electrolyte interface. Therefore, understanding the molecular-level details of proton transport and structure of the multi-phase interfaces is critical. This work is subdivided into two main tasks. The first task is to model membrane/water vapor interfaces and to study their morphology and the transport properties of water and hydronium ions. Classical molecular dynamics simulation is used as the modeling tool for the characterization of the interface. The second task is to model proton transport through the aqueous domains of PEM. Such a model is inherently challenging since proton transport occurs through a combination of structural and vehicular diffusions that are associated with disparate time scales. Toward this end, we have developed and implemented a new reactive molecular dynamics algorithm to model the structural diffusion of proton that involves breaking and forming of covalent bonds. The proton transport through aqueous channels in PEM is governed by acidity and confinement. Therefore, systems in which the acidity and confinement can be independently varied, including bulk water, aqueous hydrochloric acid solutions and water confined in carbon nanotubes are also examined in addition to the application in PEM. We have developed an understanding of how acidity and confinement independently impact proton transport. The correlation between the two components of charge diffusion and their contribution to the total charge diffusion has also been explored for a basic understanding of the proton transport mechanisms. These studies will eventually help us establish the correlation between the morphology of the membrane and proton conduction.

The development of novel polymer electrolyte membrane (PEM) materials which operate at high temperature (i.e. > 100˚C) and low humidity conditions and efficiently transport protons has been a major focus for PEM fuel cell technology. The motivation behind a high temperature PEM fuel cell is based on the fact that, at high temperature, the catalysts used in the fuel cell are more active and less susceptible to poisoning due to impurities in the feed stream. The challenge lies in the fact that as the temperature is increased, the membrane loses water and its ability to transport protons. The successful design and synthesis of high-performance PEMs would benefit from a fundamental, molecular-scale understanding of how polymer chemistry, hydration levels, and morphology affect proton mobility within the membrane. Additionally, substantially less work has concentrated on the molecular-level details of proton transport at the multi-phase interfaces among the PEM, vapor, water, electrodes, and catalyst surface. The electrochemical processes occurred at such interfaces dictate the performance of the PEM fuel cells. Understanding the structural and dynamic properties at these interfaces is, therefore, crucial for the optimization of current energy devices. All such information cannot come from experimental investigations alone, but requires knowledge of multiscale simulations which are successful in bridging distinct time and length scales, providing insights into the morphology and structure through analysis of the molecular processes. The first objective of this work is to use molecular dynamic (MD) simulations to investigate the nanophase-segregated structure in the PEM as a function of polymer chemistry and hydration levels. The variables probed to define polymer chemistry include (1) side chain length, (2) equivalent weight, and (3) molecular weight. We examine the structure in attempts to establish a relationship between the polymer chemical composition and the hydrated morphology and transport properties. The second objective is to use MD simulations to generate the structure of the interfaces involving the PEM within the Membrane-Electrode Assemblies (MEAs). These interfaces include (1) the PEM/vapor interface, (2) the PEM/vapor/catalyst interface, and (3) the PEM/vapor/carbon electrode interface. We examine these interfaces in order to establish an understanding of the structure of these interfaces as a function of water content.

Food systems physical properties and stability are critical for delivering safe and healthy food to the consumers, and thus this is a theme that attracts food scientists for a long time. Recently, literature suggests that stability can only be fully grasped if food molecular dynamics and structure are taken into consideration, i.e. an appropriate understanding of the behaviour of food products requires knowledge of its composition, structure and molecular dynamics, through the three-dimensional arrangement of the various structural elements and their interactions. Food systems behaviour is strongly dependent on the water molecular dynamics. Understanding changes in water location and mobility represents a significant step in food stability knowledge, once that water “availability” profoundly affects the chemical, physical and microbiological quality of foods. Nuclear magnetic resonance (NMR), through the analysis of nuclear magnetisation relaxation times, has been presented as a powerful technique to investigate water dynamics and physical structures of foods. It provides information on molecular dynamics of different components in complex systems. The application of this technique may be very useful in predicting food systems physicochemical changes, namely texture, viscosity or water migration. The research leading to this thesis focused on two main food systems: i) films from biological sources, for their interest as model matrices and potential for food industry; and ii) fresh-cut fruit, due to its complexity and significance in food markets. Films from biological sources, particularly chitosan, present several applications including biodegradable packaging and edible coatings for shelf-life extension. As model food systems, films from biological sources are partially crystalline, partially amorphous, and easily reproducible materials. From a fundamental perspective, foods are mainly edible and digestible biopolymers that are also partially crystalline/partially amorphous. Despite of the wealth of information on literature, a systematic approach to understand the contribution of film forming solutions (FFS) on chitosan films physical properties, as well as the knowledge on its molecular dynamics to such properties, are still uncommon. In this thesis, the relevance of FFS composition on films properties is highlighted through the monitoring of solutions with different polymer/plasticiser ratios. Also the molecular dynamics, evaluated through NMR methodology, was analysed and compared with the films physical properties. Results demonstrated the influence of solutions polymer/plasticiser concentrations on both thermomechanical and water related properties. Chitosan concentration in solutions affected consistency coefficient, and this was related with differences in films water retention and structure. Plasticiser quantities used in FFS are responsible for films compositions, while polymer/plasticiser ratio determined the thickness and thus the structure of the films. NMR allows understanding the films molecular rearrangement, demonstrating that water is also an important component in these matrices and performs differently when compared with the plasticiser. A relationship between water and plasticiser dynamics and films macroscopic properties was also observed. Fruits are high water content products with a complex cellular structure, where water can be present in both intra and extra cellular spaces. Fresh-cut fruit, due to processing, has high metabolic rates with faster physiological and biochemical changes and microbial degradation, which results in product’s colour and texture alterations. The second part of this thesis focused on fresh-cut fruits, pear and melon, which were chosen for their significantly different composition and structure. Fresh-cut fruit was monitored during 7 days of refrigerated storage conditions. Relevant quality parameters, such as colour and firmness, were analysed. Water activity (aw) and water molecular dynamics (T2), measured by a NMR technique, were also assessed throughout storage. Results demonstrated that processing and storage affected quality parameters, as was expected, but also system’s water molecular dynamics. Throughout storage, it was possible to find relationships between the molecular dynamics and the quality parameters. These relationships were different for the two studied fruits, and the role of microstructure on food stability could be observed. These studies highlight the significance and impact of molecular dynamics on physical properties and stability of foods, and also the usefulness of NMR methodology as a tool to evaluate food physical properties and stability. Therefore, NMR could provide a novel instrument to improve the knowledge of food systems, even when complex.
O controlo das propriedades físicas e da estabilidade dos alimentos é requisito essencial para o fornecimento de produtos seguros e saudáveis aos consumidores. Por este motivo, desde há muito tempo que o tema tem despertado a atenção e a curiosidade dos cientistas que trabalham na área alimentar. A literatura tem vindo a sugerir que as propriedades físicas e a estabilidade só podem ser plenamente compreendidas se a dinâmica molecular e a estrutura dos alimentos for tida em consideração; ou seja, é necessário um conhecimento da composição, da estrutura e da dinâmica molecular dos sistemas alimentares, entendendo o arranjo tridimensional dos vários elementos estruturais e das suas interacções. No caso particular dos alimentos, a dinâmica molecular da água desempenha um papel fundamental no seu comportamento. A “disponibilidade” da água influencia profundamente a qualidade química, física e microbiológica dos sistemas alimentares. A compreensão das alterações na localização e mobilidade da água do sistema representa um passo significativo no conhecimento dos mecanismos que estão associados às reacções de degradação dos alimentos. A ressonância magnética nuclear (RMN), através da análise dos tempos de relaxação da magnetização nuclear, tem sido considerada uma poderosa técnica para investigar a dinâmica da água e avaliar estruturas físicas em sistemas complexos como os alimentos. A aplicação desta técnica pode ser muito útil na previsão de alterações físico-químicas como a textura, a viscosidade ou a migração da água na matriz. Esta tese considerou dois sistemas alimentares distintos: (i) filmes de origem biológica, pelo seu interesse como matrizes modelo e potencial para a indústria alimentar; e (ii) fruta minimamente processada, pela sua complexidade e reconhecida importância económica nos mercados de alimentos. Os filmes com origem biológica, neste caso específico provenientes do quitosano, possuem várias aplicações industriais como é o caso das embalagens ou revestimentos comestíveis, que têm como objectivo prolongar a vida útil dos produtos. Como modelo para sistemas alimentares mais complexos têm as vantagens de: serem facilmente reprodutíveis; e tal como os alimentos, de um ponto de vista fundamental podem ser considerados biopolímeros comestíveis parcialmente cristalinos, e parcialmente amorfos. Apesar da vasta informação que existe na literatura sobre as propriedades físicas dos filmes de quitosano, uma abordagem sistemática para a identificação da contribuição das soluções formadoras do filme, assim como a influência da dinâmica molecular nessas propriedades, revela-se ainda necessária. Nesta tese, a importância da composição das soluções formadoras nas propriedades dos filmes é realçada através da monitorização de soluções formadoras com diferentes proporções polímero/plasticizante. A importância destas soluções foi avaliada também nas alterações das propriedades termomecânicas dos filmes assim como a sua influência na dinâmica molecular dos mesmos (através de técnicas de RMN). Os resultados demonstram que a composição das soluções formadoras influenciou as propriedades mecânicas e térmicas dos filmes, bem como as propriedades relacionadas com a água (atividade, solubilidade, permeabilidade e a dinâmica molecular). A concentração de quitosano afetou o coeficiente de consistência das soluções formadoras, o que pode ser relacionado com diferenças na estrutura e na retenção de água dos filmes. Por outro lado, a quantidade de plasticizante usado na preparação das soluções formadoras é responsável pela composição dos filmes, enquanto a razão polímero/plasticizante determinou a espessura, logo a estrutura dos filmes. Através dos estudos de RMN foi possível compreender o rearranjo molecular dos filmes, demonstrando o papel importante que a água, como componente, desempenha neste tipo de matrizes, revelando diferenças de comportamento entre esta e o plasticizante. Estes resultados revelaram ainda que existe uma relação entre a dinâmica molecular quer da água quer do plasticizante nos filmes com as propriedades macroscópicas dos mesmos. As frutas são alimentos com uma estrutura celular muito complexa, ricos em água que pode estar presente quer nos espaços intracelulares, quer nos extracelulares. As frutas, minimamente processadas, devido ao ferimento a que são sujeitas, tem altas taxas metabólicas que provocam rápidas alterações fisiológicas, bioquímicas e de degradação microbianas, resultando, por exemplo, em perda de cor e textura. A segunda parte desta tese dedica-se ao estudo de pêra e melão minimamente processados. Estas frutas são muito diferentes no que diz respeito à estrutura. As amostras foram estudadas durante 7 dias de armazenamento em condições de refrigeração. Foram avaliados alguns dos parâmetros de qualidade mais relevantes, como é o caso da cor e da textura. A atividade da água (aw) e a dinâmica molecular da água (T2), analisada através de uma técnica de RMN, foram também monitorizadas durante o tempo de armazenamento. Os resultados mostram que quer o processamento quer o tempo de armazenamento afetaram os parâmetros de qualidade, bem como a dinâmica da água nos sistemas. Observou-se ainda uma relação entre os parâmetros de qualidade e os valores da dinâmica da água. Esta relação foi diferente para os dois frutos estudados, realçando o papel da estrutura na estabilidade dos alimentos. Nesta tese evidencia-se o interesse e a utilidade dos estudos de dinâmica molecular, utilizando a técnica de RMN como ferramenta na avaliação das propriedades físicas e da estabilidade de sistemas alimentares e complexos.

This thesis presents a study of applications and techniques for molecular dynamics simulations. Three studies are presented that are intended to improve our ability to simulate larger systems more realistically. A comparison study of two- and three-body potential models for liquid and amorphous Si0��� is presented. The structural, vibrational, and dynamic properties of the substance are compared using two- and three-body potential energy models against experimental results. The three-body interaction does poorly at reproducing the experimental phonon density of states, but better at reproducing the Si-O-Si bond angle distribution. The three-body interaction also produces much higher diffusivities than the two-body interactions. A study of tabulated functions in molecular dynamics is presented. Results show that the use of tabulated functions as a method for accelerating the force and potential energy calculation can be advantageous for interactions above a certain complexity level. The decrease in precision due to the use of tabulated functions is negligible when the tables are sufficiently large. Finally, an investigation into the benefits of multi-threaded programming for molecular dynamics is presented.
Graduation date: 1999

碩士
淡江大學
化學學系碩士班
97
Abstract: In part 1 , total energy calculation based on Density Function Theory (DFT) with Ultrasoft-pseudopotenital and generalized gradient spin-polarized approximation (GGSA) was used to investigate (1) O-H cleavage of ethanol and (2)C-H hydrogen elimination via four-membered ring and five-membered ring on Pt(111)-3x3 surface. By means of Partial Structure Constrain Path Minimization(PSCPM) method , our calculated energy barrier for O-H cleavage is 0.849eV and C-H hydrogen elimination via four-membered ring and five-membered ring are 0.319eV and 0.966eV , respectively. These results are in good agreement with TPD experimental result. Furthermore , we found that (1) less change in Pt-Pt dimmer bond length and (2) more H-Pt bond formation , less change in carbon hybrid orbital and π bonding in C=O by means of the partial density of state (PDOS) for the four-membered-ring hydrogen elimination to explain reaction selectivity. In part 2 , we performed first principle molecular dynamics based on Density Function Theory with norm-conversing pseudopotential and accurate LCAO basis set in SIESTA package on CN-CH=CH-NH2 , NO2-CH=CH-NH2 and BH2-CH=CH-NH2¬ push-pull molecule system and we collected dipole moment ,structure and charge trajectory in 3ps molecular dynamics. We used Fourier Transformed dipole moment AutoCorrelation Function to simulate IR spectra and analyzed characteristic vibration mode in molecule by using PaDAF and SCAF method. By comparison of Fourier Transformed charge AutoCorrelation Function (FT[charge-ACF]) and IR spectra , we found that main-chain vibration mode induced charge transfer. Furthermore , we calculated charge transfer rate by utilizing charge dynamics and explain charge transfer effect of these push-pull molecules.Finally , we also investigated temperature effect on charge transfer and calculated activation barrier of charge transfer.