In this thesis the structural relationships of a family of fifty crystal structures of 4,4’-disubstitituted chalcones, X-C6H5-CO-C2H2-C6H5-Y, where X = CF3, Br, Cl, F, H, Me, Et, OMe and Y = Br, Cl, F, H, Me, Et, OMe are investigated by comparative study of the molecular packing in each of the structures. The members of this family contain no strong hydrogen bond donor functionalities and thus directionally more diffuse intermolecular interactions dominate in the crystal structures. The concept of supramolecular constructs (CrystEngComm., 2005, 7, 324) is used to compare this family and common zero- to three-dimensional structure fragments are identified and discussed. It is shown that five fragments of closely-packed chalcone molecules form the basic motifs for 94% of the crystal structures and that these structures can be divided into three groups based on the presence of one or more of these basic motifs. The largest group comprises 68% of the crystal structures which contain a one-dimensional close-packed row of molecules. The majority of these structures are approximately close-packed and may be characterised by combinations of four basic two-dimensional sheet fragments based on the one-dimensional motif. The remaining two groups comprise 26% of the crystal structures and are each based on a combination of two of the five fragments. There is evidence of weak hydrogen bonding in many of the structures of these groups. Only the structures of Y = F, H, OMe substituted chalcones are found in these groups. The results of this thesis highlight the great importance that the molecular shape plays in the assembly of molecules in the solid state especially in such cases where only weak hydrogen bonds are present.

This thesis reports the synthesis and study of the anion recognition properties of a variety of synthetic organic and inorganic receptors. A series of known anion receptors containing a common urea and varying alkyl and aryl substituents have been investigated for their ability to bind the alkylcarbamate portion of two alkylammonium-alkylcarbamate salts and the CO2 adduct of a cyclic amidine, in an investigation into novel CO2 fixation strategies. Chemical shift changes were used to observe relative binding strengths for interactions between the alkylcarbamate and the receptors in DMSO-d6. The results show that it is possible to bind the alkylcarbamate anion in the presence of the primary alkylammonium cation, when a receptor of sufficient strength is employed. The strength of this interaction was increased when 18-crown-6 was added, which acts as a receptor for the alkylammonium cation. The CO2 adduct of the cyclic amidine, (1,4,5,6, tetrahydropyrimidine) was shown to have the strongest interactions with the receptor series. Several Schiff-base and urea containing receptors have been synthesised and assessed for anion complexation properties in solution using 1H NMR in DMSO-d6 : water mixtures. These are selective for acetate, benzoate and dihydrogen phosphate over chloride and hydrogen sulfate, and exhibit a mixture of 1:1 and 2:1, (guest:host), binding stoichiometries in several cases. Zinc(II) and cobalt(II) chloride complexes of one of this series were synthesised. The cobalt(II)chloride complex was observed to be a stark colorimetric indicator for chloride and dihydrogen phosphate. A number of isophthalamide derivatives containing activated NH and / or CH protons have been synthesised and assessed for anion complexation solution using 1H NMR in DMSOd6. Their interactions with fluoride, chloride and bromide were investigated, which demonstrate a significant contribution from the activated CH protons

Modelling of the charge transport in different types of organic semiconductors (molecular crystals and semicrystalline polymers) is undertaken using a number of different methods. Using a polarisable force field we have determined the extent of the external reorganisation energy for hole transport in molecular crystals. We have found that this key parameter is very small for naphthalene, anthracene, tetracene, pentacene and rubrene and discussed the implications of this finding in the context of charge transport modelling. Charge trapping in organic crystals due to defect states is studied by computation of the rate of escape of a trapped charge carrier using non-adiabatic rate theory. Two cases are considered, the first is hopping between separate identical defect states and the second is hopping from a defect state into the bulk (delocalised) states. This latter process is determined as the more likely to occur for a realistic defect concentration. The necessity of the inclusion of an effective quantum mode of vibration for the accurate computation of the rate is also demonstrated. A linear scaling method based on the definition of a localised molecular orbital set is devised for the computation of the electronic structure of a conjugated polymer (poly(3-hexylthiophene) (P3HT)). Utilising a combined classical and quantum chemical approach we show that charge carriers are localised in correspondence with long-lived traps which are also present in the crystalline phase of the polymer. The regio-regularity of P3HT is shown to have little impact on the shape and tail of the density of states; we compute the 2D localised trap density as ~3.1×1013 cm-2, a value which is not found to significantly change with the regioregularity. The states in the tail of the density of states are found to be predominantly localised but energetically close to delocalised "quasi-band" states which are accessible under device operation.

In this work monolayers of alkyl amides adsorbed on a graphite surface have been successfully identified and investigated using a combination of synchrotron X-ray and neutron diffraction and Differential Scanning Calorimetry (DSC). Exceptionally stable solid layers have been observed at temperatures well above the bulk melting point, at both high multilayer coverages and, very unusually, at sub-monolayer coverages. The molecular structure of the two-dimensional crystals of these alkyl amides has been obtained from diffraction and interpreted in terms of the subtle intermolecular interactions, particularly the contribution of hydrogen bonding in monolayer assembly. Thermodynamic information provides insight on the mixing behaviour in adsorbed amide layers. A systematic study on the variation in monolayer crystal structures with alkyl chain length (between five and sixteen carbon atoms) of saturated alkyl amides using diffraction identifies that all the amide molecules investigated lie flat on the graphite surface. An odd-even variation isobserved in the monolayer crystal structures and this is supported by the melting enthalpies of the amides determined by DSC. The structure of the even members is found to support the qualitative monolayer arrangement proposed by an STM report of one member of the series, but with more quantitative insight here. Significantly, a new monolayer symmetry group for odd members of the homologous series has been identified. Characteristics of the hydrogen bond geometrybetween the molecules in the solid monolayers are reported exploiting the high level of detail available from the diffraction techniques. Secondly, the formation of solid monolayers of unsaturated alkyl amides has been reported and their crystal structures determined. This is believed to be the first report of these monolayer structures. The position and nature of the double bond have an important effect in the stability of the monolayer. Unusually, certain unsaturated amides that have a double bond conjugated with the amide group are found to form considerably more stable layers than their saturated homologues. The abnormally high melting points and enhanced stability of amide monolayers have been attributed to the existence of a network of hydrogen bonds in the layer. Phase diagrams obtained by DSC for binary mixtures of alkyl amides on graphite have been quantitatively analysed using a combination of thermodynamic models (ideal, eutectic and the regular solution models). The determined mixing behaviour is supported by conclusions based on the monolayer crystal structures of the individual components calculated using diffraction. Saturated amide mixtures that have the same plane group symmetry are found to mix non-ideally in the solid layer and phase separate if the symmetry is different, whereas the mixing behaviour of saturated/unsaturated amides considered here was found to depend on the nature of the double bond (cis/trans). Results from an initial investigation into the adsorption of alkyl amides at the polymer/air interface are also presented. This complements the study above and provides an alternative situation where amide monolayers have a central role. A reduction in the coefficient of friction is seen with increasing bulk concentration of the amide and with increasing time indicating migration of the amide to the surface. A powerful combination of surface reflection techniquesincluding neutron and X-ray reflection and ellipsometry have been used to gain uniquelyquantitative insight into this system. Initial estimates of the concentration of amides at the polystyrene surface are presented for the first time.

The effect of temperature on the crystal structure of deuterated piperidine has been studied using neutron powder diffraction. Differential scanning calorimetry indicates that there are multiple phases accessible via changes in temperature however there is no evidence of this in the neutron powder diffraction study with only one phase observed in the range 2 – 250 K and under various crystallisation conditions. The effect of pressure up to 2.79 GPa has also been determined. The compression of the structure is facilitated through the closing up of voids in the structure and no phase transition is observed. Differential scanning calorimetry has shown N-methyl and N,N-dimethylformamide both exhibit a thermal event prior to melting. Low temperature neutron powder diffraction has shown these transitions are associated with the onset of methyl group rotation. Neutron powder diffraction studies show formamide exhibits remarkable polymorphism at ambient temperature and pressures between 0.1 GPa and 3.6 GPa, forming four new polymorphs. All the structures consist of N-H…O hydrogen bonded chains. The formation of the various polymorphs can be rationalised in terms of the orientation of the molecules within the hydrogen bonded chains and the resultant structures formed by further hydrogen bonds between the chains. This is in stark contrast to the effect of varying conditions of temperature where only one structure exists from 2 K right up to the melting point. The effect of temperature on the crystal structure of pyrazine in the range 8 – 315 K is described. At temperatures below 90 K the structure undergoes a phase transition to a previously uncharacterised phase, designated phase IV, which is closely related to the previously known phase I. The crystal structure of phase III has been determined at 315 K. The crystal structure of pyrazine has been determined at room temperature at pressures between 0.11 GPa and 9.36 GPa. At 0.94 GPa a transition from phase I to phase IV is observed. This is the same phase as observed at low temperatures. Crystal growth at 215 K results in the formation of two different phases of mesitylene; phase II and a new previously unknown phase designated phase IV. The structure of phase IV has been determined and found to be stable in the range 90 – 221 K. On cooling a crystal of deuterated mesitylene in phase II to 90 K a transition to phase III was observed and the resultant crystal structure is closely related to that of phase II.

This thesis focuses on two of the major challenges of carbon nanotube (CNT) research: understanding the growth mechanism of nanotubes by chemical vapour deposition (CVD) and the positioning of nanotubes on surfaces. The mechanism of growth of single–walled nanotubes (SWNTs) has been studied in two ways. Firstly, a novel iron nanoparticle catalyst for the production of single–walled nanotubes was developed. CVD conditions were established that produced high quality tubes. These optimised CVD conditions were then used as the basis of several comparative CVD experiments showing that the quality of nanotubes and the yield of carbon depended on the availability of carbon to react. The availability could be controlled by the varying concentration of methane in the gas phase or the residence time of the methane over the catalyst. Evidence is presented that the diameters of the tubes produced were affected by the availability of methane. A second mechanistic investigation was carried out to study the validity of the previously proposed ring addition mechanism for the growth of carbon nanotubes from camphor. In this mechanism, the formation of tubes is thought to occur through the addition of preformed carbon rings: so it would be expected that there would be a relationship between the molecular structure of the precursor and the resulting SWNTs. To explore this relationship, comparative CVDs were carried out to produce SWNTs with several different cyclic and acyclic compounds similar in structure to camphor. The vapour pressure and the chemical stability of the precursor were found to be important to the formation of nanotubes, while the compound’s structure was not related to the quality of tubes produced. The lack of a relationship between the structure of the precursor and the production of SWNTs suggests that preformed rings are not vital to the production of SWNTs. Differences in the growth of SWNT from benzene and methane were related to the stability of each compound. In particular, differences in the distributions of the diameters of the tubes formed from methane and benzene have been observed. These differences have been explained in terms of the relative kinetic stabilities of these molecules, and in terms of a competition between end–cap and sidewall growth. Positioning of nanotubes on surfaces has been explored using two approaches. In the first approach, commercially obtained SWNTs were functionalized by a sulfur plasma so that the products would form bonds with gold surfaces. The nanotubes were found to selectively deposit themselves onto gold surfaces from ethanolic dispersions of the functionalized samples. This selective deposition of the nanotubes allowed the production of prototype carbon nanotube field–effect transistors with higher device yields than were obtained with unfunctionalized tubes. In a second approach to positioning of carbon nanotubes, the growth of tubes on surfaces by CVD was explored. Iron nitrate and different magnesium compounds were dip–coated onto SiO2 surfaces so that MgO supported–Fe catalysts would be formed by calcination. SWNTs were grown on the surfaces by CVD. Surface area measurements of the equivalent powdered catalysts showed that a high surface area was vital to produce dense growth of high quality SWNTs. The morphology of the surface was also found to play a key role in the growth of the tubes. Patterned growth of carbon nanotubes was accomplished using soft lithography techniques to control the localization of catalyst deposition onto a surface. A long calcination step (10 h, 950 °C) before CVD, was found to improve the quality of nanotubes grown. Catalysts that had been calcined for 10 hours were also found to produce smaller diameter nanotubes than uncalcined samples. The formation of smaller diameter tubes was explained in terms of the formation of MgFe2O4 alloys, consistent with results reported previously in the literature. In addition, Raman spectroscopy of the calcined catalysts with 3% w/w loadings of Fe was used to confirm directly the presence of MgFe2O4.

The majority of research in this thesis uses X-ray crystallography to investigate the structural features of peri-substituted naphthalene compounds. X-ray crystallography is introduced in chapter one, followed by a discussion on modes of distortion peri-substituted naphthalene derivatives can undergo, in chapter two. In chapter three, compounds having non-bonded -SPh and -EPh (E = S, Se, or Te) peri-substituents are compared. These similar compounds react differently when oxidized with bromine. The oxidation products are used to discuss a recently proposed mechanism and a more specific mechanism is suggested. In chapter four, a one-pot synthesis for naphtho[1,8-c,d]-1,2-diselenole (Se₂naph) is reported. Substituents were added to Se₂naph to form two new naphthalene compounds. The substituents are found to distort the Se-Se bond and influence packing. In chapter five, several diselenium-containing compounds are used as ligands in platinum(II)-bisdiphosphine complexes. The preference for platinum(II) to stay square planar dictates the geometry around the metal center, not the rigidity of the naphthalene backbone. Chapter six introduces (8-phenylsulfanylnaphth-1-yl)diphenylphosphine, a peri-substituted naphthalene containing -SPh and -PPh₂ substituents, and several derivatives. This ligand is used in a variety of complexes containing platinum(II), ruthenium(II), and copper(I) metal halides, whose coordination geometries are discussed in chapter 7. The naphthalene-based ligands in Cu(I) and Ru(II) seem to determine the geometry around the metal, whereas the metal center d-orbitals dominate in the Pt(II) examples. Chapters eight and nine deviate from the naphthalene theme. In chapter eight, X-ray analysis of sulfoxide compounds is used to discuss the structural environment around the sulfur. Various intra- and inter-molecular interactions were discovered in crystal packing. Finally, chapter 9 uses STANDARD (St ANDrews Automated Robotic Diffractometer) to statistically analyze numerous E₂Ph₂ (E = S, Se, or Te) crystals to determine chirality. It is intriguing that Te₂Ph₂ shows a preference for one enantiomer over the other.

Over the past ten years, the development of High Throughput (HT) synthetic chemistry techniques has allowed the rapid preparation of libraries of hundreds to thousands of compounds. These tools are now extensively used for drug and material discovery programmes. The subsequent development of analytical capabilities to carry out qualitative and quantitative assessment of the compounds generated by HT synthesis as well as their HT screening has led to a dramatic broadening of the scope of HT techniques, ranging from image based analysis techniques to mass spectrometry (MS). Based on the latter, a range of solid phase and solution phase analytical constructs was developed to enable the qualitative and quantitative assessment of mixtures of small compounds, using positive electrospray MS as the sole analytical tool. A version of the construct allowed HT reactivity profiling to be carried out on a range of ten carboxylic acids, ten aldehydes and ten isonitriles in the Ugi 4-component condensation reaction. The effect of various parameters such as the concentration of the monomers on the reactivity was investigated. The elaboration of a HT Hammett parameter assessment method was made possible by the development of an electrophilic version of the construct. The value of the Hammett value was afforded by means of combinatorial Hammett plots and values were successfully evaluated in a HT mode for around thirty anilines with substituents in the meta and para position of the aromatic ring. Finally, analytical constructs were used in an attempt to evaluate enzyme reaction kinetics via the labelling of peptides and small drug fragment with coded constructs, to afford affinity determinations between the enzyme (protease) and peptidic or fragment based substrates.

The work in this thesis mainly focuses on the assessment of density functional methods for computing structures and energies of organic and bioorganic molecules. Previous studies found dramatic conformational and stability changes from B3LYP to MP2 geometry optimization for some Tyr-Gly conformers. Possible reasons could be large intramolecular basis set superposition errors (BSSEs) in the MP2 calculations and the lack of dispersion in the B3LYP calculations. The fragmentation method and three kinds of rotation methods were used to investigate intramolecular BSSE. It is concluded that the rotation method cannot be used to correct intramolecular BSSE along a rotation profile. Another methodology is to employ modern density functionals. We focused on M06-L with the Tyr-Gly conformer ‘book6’. Potential energy profiles were determined by computing the energy for geometries optimized at various fixed values of a distance that controls the degree of foldedness of the structure. M06-L manifested itself as a very promising method to investigate the potential energy surface of small peptides containing aromatic residues. To predict Tyr-Gly structures, 108 potential conformers were created with a Fortran program. The geometry optimizations were done using M06-L/6-31G(d) and M05-2X/6-31+G(d). Two schemes were employed and the most stable conformers were compared to the 20 stable conformers found by B3LYP. Both schemes found 10 conformers similar to one of the B3LYP stable conformers, as well as several newly found conformers. The study of a missing B3LYP stable conformer showed that the possible reason of missing conformers may be the lack in dispersion in B3LYP theory. To study the hydration effect, we studied the conformations of neutral and zwitterionic 3-fluoro-γ-aminobutyric acid (3F-GABA) in solution using different solvation models, mainly the explicit water molecule models. Zwitterionic forms of 3F-GABA are preferred in solution. M06-2X performs better in calculating transition energy profiles than MP2.

The knowledge of the packing behaviour of small organic compounds in crystal lattices is of great importance for industries dealing with solid state materials. The properties of materials depend on how the molecules arrange themselves in a crystalline environment. Crystal structure prediction provides a theoretical approach through the application of computational strategies to seek possible crystal packing arrangements (or polymorphs) a compound may adopt. Based on the chemical diagrams, this thesis investigates polymorphism of several small organic compounds. Plausible crystal packings of those compounds are generated, and their lattice energies are minimised using molecular mechanics and/or quantum mechanics methods. Most of the work presented here is conducted using two software packages commercially available in this field, Polymorph Predictor of Materials Studio 4.0 and GRACE 1.0. In general, the computational techniques implemented in GRACE are very good at reproducing the geometries of the crystal structures corresponding to the experimental observations of the compounds, in addition to describing their solid state energetics correctly. Complementing the CSP results obtained using GRACE with isostructurality offers a route by which new potential polymorphs of the targeted compounds might be crystallised using the existing experimental data. Based on all calculations in this thesis, four new potential polymorphs for four different compounds, which have not yet been determined experimentally, are predicted to exist and may be obtained under the right crystallisation conditions. One polymorph is expected to crystallise under pressure. The remaining three polymorphs might be obtained by using a seeding technique or the utilisation of suitable tailor made additives.