Elastic constants of single-walled carbon nanotubes (SWCNTs) and single-layer graphene sheets (SLGSs) are determined by studying their free vibration characteristics using molecular mechanics (MM) simulations with the MM3 potential and finding their equivalent continuum structures (ECSs). The computational framework has been validated by comparing the presently computed basal plane stiffness and frequencies of radial breathing modes (RBMs) with those available in the literature. We have considered armchair, zigzag and chiral SWCNTs of aspect ratios (length/ diameter in the unloaded relaxed configuration) ranging from 2 to 15. The wall thickness of ECSs of SWCNTs is determined by applying continuum theories, viz., beam, shell and 3D-linear elasticity to ECSs and equating their frequencies with those of SWCNTs obtained from the MM simulations. An expression for the wall thickness of an ECS of a SWCNT in terms of its chiral indices is deduced. The wall thickness of an ECS of a SWCNT is found to increase with an increase in its radius and to saturate at 1.37 Ã for the radius exceeding 15 Ã . Poisson's ratio for zigzag SWCNTs decreses with an increase in the tube radius, but that for armchair SWCNTs exhibits the opposite trend. For the same radius, Poisson's ratio of a chiral SWCNT is slightly more than that for an armchair tube but a little less than that for a zigzag tube. For zigzag SWCNTs, frequencies of inextensional modes of vibration saturate with an increase in the circumferential wave number but those of their ECSs do not. The MM simulations of uniaxial tensile deformations of SLGSs of aspect ratios (length/width) ~ 10 give the basal plane stiffness of ~ 340 N/m. The MM simulations of free vibrations of clamped SLGSs and the analysis of vibrations of their ECSs with a continuum theory gives a wall thickness of ~ 1 Ã for a SLGS. / Ph. D.

Thesis (MSc)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: 2,7-dimethylocta-3,5-diyne-2,7-diol forms inclusion complexes with various guests molecules, where the guest molecules are polar-ordered. A Cambridge Structural Database (CSD) search revealed ten inclusion complexes where the guest molecules were polar-ordered. Using Density Functional Theory (DFT) computational methods (in the absence of the host), we evaluated the intra-channel and lateral guest-guest interactions between the guest molecules. Two polar-ordered inclusion complexes ((1,4,7-cyclohexane-1,2,4,5,7,8-hexaoxonane)·CHCl3 and (2,4,6-(endolongifolyl)-1,3,5-trioxane)·CDCl3) were singled out in the CSD search for further studies along with 2,7-dimethylocta-3,5-diyne-2,7-diol. Synthesis of any 1,2,4,5,7,8-hexaoxonane and 1,3,5-trioxane derivatives was attempted to establish whether the polar-ordering ability extends into the family of compounds. We managed to produce three new polar-ordered inclusion complexes with 2,7-dimethylocta-3,5-diyne-2,7-diol (ClC(CH3)3, BrC(CH3)3 and IC(CH3)3), thus extending the series to six guest polar-ordered systems. We were only able to synthesise 1,4,7-cyclohexane-1,2,4,5,7,8-hexaoxonane and produce the CHCl3 inclusion complex and one new polar-ordered inclusion complex (CHBr3). Three 1,3,5-trioxanes was synthesised (the cyclohexyl, cyclohex-3-en-1-yl and cyclopentyl derivatives), which did not include any solvents. However, these 1,3,5-trioxanes also form polar-ordered crystals. These compounds and inclusion complexes were analysed by means of single crystal X-ray diffraction to determine their crystal structures. All the crystal structures could be solved and refined to adequate accuracy (except for 2,4,6-tri(cyclopentyl)-1,3,5-trioxane) with no disorder of the guest molecules (where applicable) and their polar-ordering property investigated. Due to their vast molecular differences, these compounds were studied separately by means of visual crystal structure analysis and computational modelling techniques (Density functional theory, molecular mechanics, molecular dynamics and molecular quench dynamics). / AFRIKAANSE OPSOMMING: 2,7-dimetielokta-3,5-diyn-2,7-diol vorm insluitingskomplekse met verskeie molekules as gaste, waar die gas-molekules polêr georden is. 'n Cambridge Struktuur Databasis (CSD) soektog lewer tien insluitings komplekse waarvan die gas-molekules polêr georden is. Deur gebruik te maak van Digtheidsfunksionele teorie (DFT) berekeninge (in die afwesigheid van die gasheer) het ons die inter-kanaal en wedersydse gas-gas interaksies tussen die gas molekules geëvalueer. Twee polêr geordende insluitingskomplekse ((1,4,7-sikloheksaan-1,2,4,5,7,8-heksaoksonaan)·CHCl3 en (2,4,6-(endolongifolyl)-1,3,5-trioksaan)·CDCl3) is uitgesonder uit die CSD soektog vir verdere studies saam met 2,7-dimetielokta-3,5-diyn-2,7-diol. Aanslag was gemaak om enige 1,2,4,5,7,8-heksaoksonaan en 1,3,5-trioksaan derivate te sintetiseer en vas te stel of die polêre ordensvermoë oor die familie van verbindings strek. Ons het daarin geslaag om drie nuwe polêr geordende insluitingskomplekse op te lewer met 2,7-dimetielokta-3,5-diyn-2,7-diol (Cl(CH3)3, BrC(CH3)3 en I(CH3)3), en sodoende die reeks uitgebrei na ses gaste wat polêr geordende insluitingskomplekse vorm. Net 1,4,7-sikloheksaan-1,2,4,5,7,8-heksaoksonaan kon gesintetiseer word en dit lewer twee polêr geordende insluitingskomplekse (CHCl3 en CHBr3 (nuut)). Drie 1,3,5-trioksane is gesintetiseer (die sikloheksiel, sikloheks-3-een-1-iel en siklopentiel derivate) en het nie enige oplosmiddels (gaste) ingesluit nie. Nietemin vorm hiedie 1,3,5-trioksane ook polêr geordende kristalle. Hierdie verbindings en insluitingskomplekse is geanaliseer deur middel van enkelkristal X-straal diffraksie om hul kristalstrukture te bepaal. Alle kristalstrukture was opgelos en verwerk tot voldoende akkuraatheid (behalwe vir 2,4,6-tri(siklopentiel)-1,3,5-trioxane) met geen wanorde in die gas molekuul posisies nie (waar van toepassing) en hul polêre ordensvermoë is ondersoek. As gevolg van groot verskille in hul molekulêre strukture, is hierdie verbindings afsonderlik bestudeer deur middel van molekulêre modellerings metodes (Digtheidsfunksionele teorie, molekulêre meganika, molekulêre dinamika en molekulêre stakings dinamika).

xv Abstract The aim of this thesis is to investigate the accurate stabilization energy and binding free energy in various non-covalent complexes spanned from small organic molecules to biomolecules. Non-covalent interactions such as H-bonds, π...π stacking and halogen bonds are mainly responsible for understanding of most biological processes, such as small molecule interactions with surface, protein-ligand binding in the cell machinery, etc. In the thesis, different non-covalent complexes such as graphene…electron donor- acceptor complexes, DNA base pair interaction with silica surface, etc, were investigated. The reference stabilization energies were calculated at ab initio level, e.g., CCSD(T)/CBS method wherever possible. On the other hand, more approximated scaled MP2 method (MP2.5/CBS/6-31G*(0.25)) is taken as reference instead of CCSD(T)/CBS due to the size of the complexes. Further, the DFT and MM energies were also tested towards the reference one. The knowledge of non- covalent interaction is required for rationalizing of any association processes in nature which requires accurate description of the free energy change. The state-of- the-art molecular dynamics simulation in full atomic scale and biased metadynamics free energy method is used for binding free energy calculations. The well tempered...

In dieser Arbeit wurden die Molekülstrukturen und die elektronischen Eigenschaften von Vanadium(IV)- und Oxo-Rhenium(V)-Chelaten mit einem kombinierten molekülmechanisch-quantenchemischen Ansatz untersucht, um sterische und elektronische Effekte der Komplexierung mit einem theoretischen Modell zu quantifizieren. Es konnte gezeigt werden, daß auf diese Weise detaillierte Aussagen zu den Bindungsverhältnissen der Metallchelate getroffen werden können. Die Berechnung der Molekülstrukturen gelingt mit exzellenter Übereinstimmung mit den Kristallstrukturen der Komplexe. Die molekülmechanischen Berechnungen erfolgen auf der Grundlage des Extensible Systematic Force Field ESFF und des Consistent Force Field 91 (CFF91). Dabei konnte die hohe Flexibilität und Zuverlässigkeit des regelbasierten ESFF für eine Vielzahl verschiedenster Metallchelate nachgewiesen werden. Aufgrund der mangelhaften Ergebnisse für trigonal-prismatische Komplexgeometrien mit dem ESFF wurden eine Anpassung des CFF91 für derartige Vanadiumkomplexe vorgenommen. Auf Grundlage von theoretischen Ergebnissen wurden die alternativen Strukturen von isoelektronischen Vanadiumkomplexen berechnet und in Übereinstimmung mit experimentellen Daten, theoretischen Modellen der Komplexchemie und empirischen Fakten eine Hypothese für die Ursache der strukturellen Differenzen erarbeitet.<br> Der hier vorgestellte, kombinierte Algorithmus aus kraftfeldbasierter Geometrieoptimierung und single-point-Rechnung an diesen Strukturen ist ein zuverlässiger und relativ schneller Weg Molekülgeometrien von Metallkomplexen zu berechnen. Er kann somit zur Voraussagen von Komplexstrukturen und zur gezielten Modellierung definierter Koordinationsgeometrien verwendet werden. / In this work the molecular structures and the electronic properties of Vanadium(IV)- and Oxo-Rhenium(V)-chelates have been investigated to quantify steric and electronic effects of complexation. It has been shown, that in this way detailed insight can be gained into the bonding conditions of that metal complexes. Molecular mechanic calculations based on the Extensible Systematic Force Field (ESFF) and the Consistent Force Field 91 (CFF91) have been carried out. High flexibility and reliability of the rule based ESFF has been proven for a large variety of different metal chelates. Due to the poor ESFF-results for trigonal-prismatic complex geometries, a fit of the CFF91 for that species was done. Based on the theoretical results the alternative structure of isoelectronical vanadium(IV)- complexes have been calculated and a hypothesis on the reason for the structural differnces have been stated in accordance with experimental results, theoretical models of complex chemistry, and empirical facts. This combined approach of force field based geometry optimization and single point calculation at these structures has been proven to be a reliable and fast way to get molecular structures of metal complexes. It can be used to predict complex structures for modelling destinct coordination geometries.

Polymer nanocomposites refer to a broad range of composite materials with polymer acting as the matrix and any material which has at least one dimension in the order of 1 ~ 100 nanometer acting as the filler. Due to unprecedented improvement observed in properties of the nanocomposites, research interest in this area has grown exponentially in recent years. In designing better nano-composites for advanced technological applications some of the major challenges are: understanding the structure-property relationships, interaction and integrity of the two components at the interface, the role of nanofillers in enhancing the properties of the resulting material. In our work, we have utilized first principle calculations, atomistic simulations, coarse-grained modeling and constitutive equations to develop structureproperty relationships for an amorphous aromatic piezoelectric polyimide substituted with nitrile dipole, carbon nanotubes and resulting nanocomposites. We have studied in detail structure-property relationships for carbon nanotubes and (? ?CN)APB/ODPA polyimide. We have developed chemically sound coarse-grained model based on atomic level simulations of the piezoelectric polyimide to address the larger length and time scale phenomena. The challenge of coarse grain model for these polymers is to reproduce electrical properties in addition to the structure and energetics; our model is the first to successfully achieve this goal. We have compared and analyzed atomistic scale simulation results on the nanocomposite with those predicted from micromechanics analysis. Notably, we have investigated the time dependent response of these highly complex polymers, to our best knowledge this is the first of its kind. In particular we have studied the thermal, mechanical and dielectric properties of the polyimide, nanotube and their nanocomposites through multi-scale modeling technique. We expect the results obtained and understanding gained through modeling and simulations may be used in guiding development of new nanocomposites for various advanced future applications. In conclusion we have developed a computational paradigm to rationally develop next generation nano-materials.

While there have been many recently developed Elastic Network Models (ENM) to calculate the fluctuation dynamics of proteins, e.g., Gaussian Network Model (GNM), Anisotropic Network Model (ANM), Distance Network Model (DNM), the concept of loading these models to study the molecular mechanics and constitutive behavior of structural proteins has remained relatively untouched, until very recently. This work entails using the ANM as the framework for developing a finite element model of a 9–monomer strand of actin. Critical input parameters to the model, such as the cutoff radius, r[subscript c], and spring constant, k, are generated by matching the all-atom steered molecular dynamics (SMD) residue displacements to that of the ANM. The parameters yielding the best match between the SMD and structural ENM (SENM) simulations will then be input into the finite element model (FEM) for a more in depth analysis. The finite element model incorporates a 9–monomer strand of actin. The F–actin strand is subjected axial and torsional loads comparable to those seen in vivo. Key areas of interest in the protein are examined, such as the nucleotide binding pocket (NBP) and the DNase I binding loop, to demonstrate how loading affects the protein’s conformation. Local residue displacements are tracked in an effort to garner a better understanding of how various loads are transmitted through F–actin during key events. Insights and conclusions are discussed along with the implications of this work. / text

In der vorliegenden Arbeit wird die Aufklärung der Konformation von Peptiden mit speziell modifizierten Aminosäuren beschrieben. Die Methoden der theoretischen Chemie (Quantenchemie, Molekülmechanik, Moleküldynamik) bilden dabei die Grundlage der Konformationsanalysen. Durch systematische Anwendung dieser Methoden werden im ersten Teil der Arbeit die konformativen Eigenschaften verschiedener [beta]-Aminosäuren und ihrer Oligomere ([beta]-Peptide) untersucht. Aus diesen Ergebnissen werden anschließend Regeln für das Sekundärstrukturdesign von ß-Peptiden abgeleitet. Der zweite Teil beschäftigt sich mit der theoretischen Konformationsanalyse von [alpha]- Hydrazinosäuren und ihrer Oligomere (Hydrazinopeptide). Aus den gewonnenen Erkenntnissen über die Ausbildung charakteristischer Sekundärstrukturelemente in diesen Verbindungen wird ebenfalls ein Regelwerk für das Design von Sekundärstrukturen aufgestellt. / The present work describes the conformational characteristics of pepttides with specifically modified amino acid constituents. For this purpose, the methods of theoretical chemistry (quantum chemistry, molecular mechanics, molecular dynamics) are utilisied for the conformational analyses. The conformation of various [beta]-amino acids and their oligomers ([beta]-peptides) are inverstigated in the first part of this work applying these methods. Rules for the design of definite secondary structures in [beta]-peptides are then derived from the obtained results. In the second part, systematic theoretical conformational analyses on [alpha]-hydrazino acids and their oligomers (hydrazino peptides) are described. The results are then used to compile a set of rules for the formation of characteriasitc secondary structures in this class of compounds.

In the search for a sustainable and environmentally friendly energy source, artificial photosynthesis has been proposed  as a promising solution. Using water as a substrate, solar energy can be utilised to store energy in the chemical form of hydrogen fuel. In part of this global scientific effort, this thesis work focuses on enabling molecular dynamics simulations of a particular set of ruthenium centred  water oxidation catalysts. The new catalysts show great success because of a binuclear  reaction  pathway in aqueous solution which makes it very interesting to model and investigate. Utilising quantum  mechanical tools, a set of molecular mechanics force field parameters for Ru-involved bonds, angles, torsions, and partial charges was successfully obtained and examined. The work allows future large scale simulation of water  oxidation and oxygen evolution in order to gain understanding and improve artificial photosynthesis.

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

The typical form for a molecular mechanics force field consists of a foundation of pair-wise terms to describe bonded and non-bonded atomic interactions, with multi-body correction terms to deal with the limitations of pair-wise terms. I present here the first attempts of a molecular mechanics model that is founded on multi-body terms, which are based on the Bond Valence Model (Brown, 2002) and recent developments in the Vectorial Bond Valence Model (Bickmore et al., 2013a; Harvey et al., 2006). I calibrated these models on pressure vs. energy curves for a set of SiO2 polymorphs. The average deviation for the best-fit iteration, with only six adjustable parameters was ±1.98 kcal/mol.