Application of Molecular Modeling in the Noncovalent Dispersion of Carbon Nanomaterials

Molecular modeling is a powerful tool to better understand the intermolecular interactions of carbon nanostructures. It provides structures and energies not easily obtainable from experiments and predicts properties that can be tested experimentally. Intermolecular interactions play an important role in the aggregation of various carbon nanomaterials. Three molecular modeling studies of carbon nanomaterial dispersions are presented in this dissertation, with an emphasis on illustrating how effective these theoretical techniques are in providing insight on the selection of dispersion additives. To achieve our goals, we employed molecular mechanics based methods, along with semi-empirical methods, and quantum mechanical methods, such as density functional theory. Of these techniques, molecular mechanics based methods were the more frequently applied. Chapter I serves as a brief review of computational methods with an emphasis on molecular mechanics. The first project (Chapter II) includes theoretical studies on the dispersion of single-walled carbon nanotubes (SWNTs) via non-covalent attachment of dispersing polymers. This effort involved the investigation of the binding affinities between specific polymers and SWNTs. Dispersion of SWNTs has been of great interest for many years due to numerous applications promised by their unique combination of electronic, mechanical, chemical, and thermal properties. SWNTs are incompatible with most solvents and polymers, which results in poor dispersion of these compounds in the polymer matrix. Van der Waals attraction among tubes over a large surface area leads to significant agglomeration, thus preventing efficient transfer of their superior properties to the matrix. Improving our fundamental understanding of the interactions of polymer- SWNT interactions at the molecular level is needed for the development of new materials based on SWNTs. Structures of SWNT-polymer complexes were optimized using molecular mechanics, employing COMPASS forcefield. The optimized complexes enabled a morphological analysis of the arrangement of polymer strands on the SWNT surface and calculations of the intermolecular interaction energies. Our calculations identified a strong binding affinity between SWNTs and conjugated polymers containing heteroatoms. The inclusion of solvent effects in the theoretical calculations produced results matching experimental observations from laboratory dispersion studies. The second project (Chapter III) consists of computational studies on the potential dispersion of metallic nitride fullerenes (MNFs), e.g. Sc3N@Cgo, using a solventcompatible complexing agent. MNFs have a unique hollow-ball shape built from 12 carbon pentagons and 30 hexagons, possessing truncated icosahedra symmetry and encapsulating a trimetallic-nitride cluster at the core of the cage. This unique structure results in its distinctive physical and chemical properties. The ability of MNFs to bring a functional metal to polymeric nano-composite systems opens up the possibility for extraordinary properties, e.g. magnetic, electroactive, and radioactive properties, which hold great promise for medical, optical, and electronic applications. Incorporation of MNF materials in a polymer support material involves the uniform dispersion of MNFs in the matrix. Due to the all-carbon cage, MNFs are very hydrophobic materials and possess minimal solubility in common organic solvents (mg/mL scale), monomers, and polymers, complicating the dispersion process. The ability to disperse MNFs in polymers is paramount to realizing the potential of these materials in future commercial applications. MNFs are difficult to chemically functionalize without altering the desirable intrinsic properties; therefore, an important aspect of this work is the focus on potential non-covalent dispersion techniques using co-additives, which is a versatile, nondamaging chemistry and preserves all of the intrinsic properties of MNF. Here we studied the interactions between dispersing additive molecules and MNFs using molecular mechanics and specifically calculating interaction energies between MNFs and a variety of additive molecules. A series of resorcinarene and calixarene compounds were surveyed, and characteristics of suitable candidates were identified. Select resorcinarene and calixarene compounds were used in experimental MNF dispersion studies, analyzing samples by particle size measurements and NMR chemical shifts. These experimental studies supported theoretical results, and the dispersion of MNFs in DMF was achieved. In a third project (Chapter IV), interactions of naphthenic acids with crude oil asphaltenes were examined; thereby contributing significantly to the volume of knowledge available describing the affinities of these acidic and basic components of crude oil. In this project a molecular mechanical analysis with an accepted structure of asphaltene was performed, and intermolecular interactions between asphaltene and naphthenic acids dispersants were calculated. The geometries of the asphaltene - naphthenic acid complexes were optimized and five resultant regioisomers of the asphaltene-naphthenic acid complex were analyzed. The molecular mechanical calculations suggest that the intermolecular interactions between asphaltene and naphthenic acids consist of vdW and electrostatic interactions

SOLUTION AND SOLID STATE INTERACTIONS BETWEEN IONIC π-SYSTEMS

Although attractive interactions between π systems (π-π interaction) have been known for many years, understanding of its origin is still incomplete. Quantitative measuring of π-stacking is challenging due to the weak nature of the π-π interaction. This dissertation aims at elucidating a quantitative conformational analysis by NMR ring current anisotropy of an organic compound capable of intramolecular π-stacking in solution and studying charge effects on the stacking of π-systems. This dissertation offers four contributions to the area. (1) A general approach to four-state, conformational analysis based on the magnetic anisotropy of molecules undergoing fast dynamic exchange is described. (2) Study unveiled the importance of charges in the conformation of a dication in the solution. (3) Novel aromatic salt pairs of triangulene derivatives with the delocalized cation-anion interaction were synthesized and studied. (4) Study unveiled ionic π-systems preferred face-to-face stacking due to strong cation-π and anion-cation attractions. A general protocol for the application of magnetic anisotropy to quantitative multi-state conformational analysis of molecules undergoing fast conformational exchange was suggested in the current study. The reliability of this method of conformational analysis was checked by the mass balance. VT-NMR was also conducted to study the enthalpic parameters. This technique can be further used to study canonical interactions such as ion pairing, hydrogen boning, and molecular recognition. In the current study, dependence of the probe conformations on the dispersive interactions at the aromatic edges between solvent and probes was tested by conformational distributions of the fluorinated derivatives (2b and 2c) of the probe molecule (1a). Solution and solid studies of these molecules put the previous conclusion drawn by the Cammers group in question. Current studies show that the dispersive interaction at the aromatic edge could not be the predominant force on the conformational changes in the probe molecule 1a during the fluoroalkanol perturbation. This study indicated that charges might be important in the formation of the folding conformations in the solution and solid state of 1a, 2b, and 2c. A contribution of this thesis was to prepare and study a conformational model that lacked charges. The previous molecules were charged. The solid-state structures of pyridinium-derived aromatic rings from the CSD (Cambridge Structural Database) were studied to investigate the π-π interaction between cationic π-systems in solid state. Novel aromatic salt pairs of triangulene derivatives with the delocalized cation-anion interaction were synthesized to study the π-π interaction between two aromatic rings that carried opposite charges. This study showed that the interaction between ionic π-systems can be enhanced by cation-π and anion-cation attractions. The stackings of these π-systems introduce more overlap, closer packing and stronger atomic contact than that of the solid states of comparable neutral species. Cation-π and anion-cation attractions are synergistic in aromatic salts

The molecular modelling of calixarene inclusion complexes

Chapter 1: This consists of a literature review and an introduction into the variety of computational techniques and methodologies available. Chapter 2: The molecular modelling of alkali metal complexes with calixarenes. We have published three papers in this area1. The HyperChem molecular modelling software package has been demonstrated to be a straightforward and computationally undemanding technique that is surprisingly good at reproducing the structures of a range of metallocalixarenes. Chapter 3: The molecular modelling of the enantioselective complexation of chiral amines by chiral calix[4]arenes. With reference to the enantioselective complexation studies we have shown that by using molecular modelling software, an insight can be gained into the interactions that occur on complexation of chiral amines by chiral calixarenes. By observing the hydrogen bonding patterns formed between the host and guest we can postulate why one enantiomer interacts more strongly than the other and, hence, provide a plausible explanation for the observed enantiomeric selectivity observed in the fluorescence quenching experiments. Chapter 4: The catalysis of the Diels Alder reaction by ionic liquids. The first example of the usage of dialkylimidazolium salts (R2 lm+X‘) as heterogeneous and homogeneous Lewis acids catalysts in the Diels-Alder reaction is detailed in a published paper

Molecular modelling aided design and synthesis of photochromic dyes containing a permanent chromophore

Photochromic dyes are a very important and relatively novel class of dyes. The usual, though not exclusive, behaviour of these dyes is to show a reversible colour change from colourless to coloured when exposed to UV light. Among the photochromic dye classes, spirooxazines and naphthopyrans were selected for investigation. An attempt was made to construct molecules with a permanent chromophore (azo) in spirooxazines as well as naphthopyrans separately, with a view to providing a colour change from one colour to another. Three different isomers of dihydroxynaphthalene were used as one group of starting materials for the synthesis of spirooxazines with the introduction of the azo (hydrazone) chromophore by coupling. Other starting materials used were anthraquinones, naphthoquinones and pyrazolones. A range of molecular modelling techniques (molecular mechanics, MM2 and quantum mechanics, AM1) using the CAChe system, were applied to predict optimized geometrical conformations and energies of the ring-closed form and ringopened merocyanine forms of all the dyes. PPP-MO calculations were also carried out to predict the potential colour of the dyes. The dyes were characterized using DSC, FTIR, NMR, UV-Visible spectroscopy and elemental analysis. The photochromic properties of one of the azospirooxazines was subjected to a detailed study under different experimental conditions, and showed a unique slow colour change from orange to grey.Worshipful Company of Dyers (London

Molecular Dynamics Simulations of Peptide-Mineral Interactions

We present molecular dynamics (MD) simulations providing information about the mechanisms of biomineralization. We focus on osteopontin-related peptides, which inhibit the growth of calcium oxalate monohydrate (COM) the primary constituent of kidney stones. First, we performed two ab initio MD simulations: aspartic acid (Asp) and the dimer of aspartic acid and phosphoserine (Asp-pSer) interacting with a fully hydrated COM crystal slab exposing the {100} face. For Asp we found that one of the carboxyl and the amine group both interact with the crystal surface but neither forms a stable contact during the simulation. Asp-pSer interacts preferably with its carboxyl groups with the calcium ions of COM. Once a contact is formed, it remains stable for the remainder of the simulation. Comparing the results of Asp and Asp-pSer shows that even though during our simulation the phosphate group did not directly interact with the COM surface its presence results in a stronger interaction of the carboxyl groups with the crystal slab. This fact and the agreement in the bond length between the carboxyl oxygen of the amino acids and the calcium ions of COM in these ab initio and previously performed classical MD simulations validate the model used in the classical MD simulations. Second, we performed classical MD simulations of the growth-inhibiting, acidic peptides pOPAR and poly-glu interacting with the {100} and {010} faces of COM containing {121} growth steps. For both peptides similar results were found. In the system with the {100} terraces and the {121} steps the peptides interact with the terrace ({100} face). In the system with the {010} terraces and the {121} steps on the other hand the peptides interact with the step ({121} face). The negatively charged peptides make their choice of adsorption based on the densities of calcium ions on the surface of the different COM faces, the order of adsorption strength is the same as the density of calcium ions: {100} \u3e {121} \u3e {010}. These results are in agreement with experiments measuring the inhibiting effect of the peptides on COM crystals grown in the peptide’s presence

Preparation of hydroxyapatite/silk protein thin film implant surfaces, investigation of their microstructural properties and model protein interactions

Thesis (Doctoral)--Izmir Institute of Technology, Chemical Engineering, Izmir, 2009Includes bibliographical references (leaves: 258-267)Text in English; Abstract: Turkish and Englishxx, 267 leavesBiocompatible hydroxyapatite (HAp) coatings of load bearing metallic in vivo hard tissue implants act as local scaffolds for enhanced osteoconduction, providing fast bone apposition and cementless fixation. In this study, in an attempt to exploit the potential of hydroxyapatite as a carrier of bone morphogenetic proteins for post operative accelerated healing, and implant durability, the tailored microstructural properties, and protein adsorption capabilities of thin film hydroxyapatite implant surfaces were investigated.A novel particulate sol method was used to fabricate HAp thin films on bioinert glass, and Ti6Al4V substrates by dip and spin coating. The microstructural characterization of the thin films was carried out by SEM/EDX, AFM, XRD, and FTIR, and their surface roughness, Vickers hardness and adhesion strength were determined. The effects of silk fibroin and sericin thin film layers on the HAp film microstructure, and model protein (bovine serum albumin, BSA) adsorption behavior (by the size exclusion HPLC method) were investigated. The minimum threshold solid content of the suspensions was determined as 15% by weight for a continuous HAp film structure. The silk sericin and fibroin intermediate layers drastically improved homogeneity of the HAp layer. The BSA adsorption of the glass/sericin/commercial-HAp film was 2.6 ug/cm2, more than twice of the glass/commercial-HAp, and glass/sericin/dry-milled-HAp films, evidencing the effectiveness of surface micro/nano topographical structure as well as chemical structure. The XRD patterns of spin coated commercial-HAp films on Ti6Al4V pointed out to a particular crystal orientation which increased the positive degree of cooperativity between HAp and proteins during adsorption or deposition