This thesis presents a joint experimental and theoretical study of a bimolecular collision between OH(A) and H₂ diatoms. The study focuses on the relationship between the initial, <b><i>j</i></b>, and final rotational angular momentum, <b><i>j'</i></b>. This relationship is explored from both a scalar point of view by measuring rotational energy transfer (RET), and a vectorial viewpoint by considering the collisional depolarisation. The experimental technique used in this investigation, Zeeman quantum beat spectroscopy, is first demonstrated by applying it to the determination of the lab-frame orientation of OH(X) photofragments following the photolysis of H₂O₂. The H₂O₂ is photolysed by circularly-polarised light at 248 nm, and Zeeman quantum beat spectroscopy probes the angular momentum orientation as a function of the photofragment spin-rotation level. The results of this experiment are compared with orientation parameters predicted by a simulation that couples the rotation of the parent molecule to the torsional motion during bond cleavage. The calculations from the model agree qualitatively with those from the experiment. The Zeeman quantum beat spectroscopy technique is then used to monitor the evolution of angular momentum polarisation of OH(A) radicals during collisions with H₂. The technique allows for the determination of depolarisation cross sections for oriented and aligned distributions, as a result of collisions with H₂. Alongside this, cross sections for collisional quenching to non-reactive OH(X)+H₂ and reactive H₂O+H products are determined. By resolving the fuorescence with a monochromator the contributions to depolarisation from elastic collisions (the elastic depolarisation cross sections) are measured alongside cross sections for RET. Cross sections for total depolarisation and rotational energy transfer demonstrate only weak dependence on the rotational quantum number of the OH(A) radical, <i>N</i>_OH. Competing quenching processes that fall with <i>N</i>_OH are likely a considerable cause of this weak dependence. Furthermore, the polarisation of the angular momentum of OH(A) is randomised following RET. The elastic depolarisation cross sections make only a small contribution to the depolarisation and fall with increasing <i>N</i>_OH. Collectively these trends have not been seen previously in similar studies on OH(A) collisions with atomic colliders. For the theoretical calculations, a four-atom quasi-classical trajectory (QCT) method has been developed, utilising Lagrangian multipliers to fix the OH(A) and H₂ bonds. The calculations demonstrate that collisions involving the formation of complexes that survive for several rotational periods are prevalent in this collision system, and that these lead to large amounts of depolarisation. The calculations also demonstrate that RET in the H₂ diatom supports higher levels of RET in OH(A) than seen in previous triatomic systems. Additionally, when one diatom is depolarised the accompanying diatom is typically also depolarised. These trends, at least in part, are owed to the highly attractive and anisotropic potential energy surface (PES) describing the interaction. The QCT calculations overestimate the experimentally-measured cross sections by more than a factor of 2. The calculations are adiabatic and do not account for the non-adiabatic activity associated with this collision system, and this is likely one cause of the discrepancies. In an attempt to further account for this overestimation, alternative angular momentum binning approaches for the QCT calculations are developed, but with limited success. Further exploration of the topology of the PES used in the calculations suggests that inadequacies in this surface are a major contributor to the discrepancies.

Dans le contexte du développement durable, l’'utilisation des ressources renouvelables, biodégradable et peu toxique, est particulièrement recherchée. En particulier, la littérature montre que les molécules amphiphiles biosourcées avec une tête sucre, type glycolipides, sont d'excellents candidats pour substituer les tensioactifs pétrochimiques actuellement utilisés massivement en formulation. Pour limiter le criblage expérimental et orienter le choix des synthèses de telles molécules, une démarche prédictive à partir de l'analyse de la structure moléculaire permettrait d'anticiper les propriétés des molécules amphiphiles et d'identifier celles répondant à des propriétés spécifiques recherchées. L'objectif des travaux de thèse est de développer une méthodologie via la synthèse à façon avec modification graduelle de la structure, la caractérisation et l'analyse systématique de glycolipides, dans le but d'identifier des liens pertinents entre leurs propriétés amphiphiles et leurs caractéristiques structurales. Les données expérimentales générées doivent permettent d'établir une base de données comparables et fiables, nécessaire pour le développement de modèles 1 prédictifs. Les résultats ont mis en évidence l'influence significative de certains paramètres de structure sur j les propriétés physico-chimiques, avec des tendances claires, autrement difficiles à observer à partir des données globales non-comparables de la littérature. Ce travail a également démontré l'importance de prendre en considération le comportement des molécules amphiphiles dans l'eau, via la connaissance de leur diagramme de phase, afin de définir sans ambiguïté certaines propriétés telles que la CMC. / In the context of sustainable development, the use of biodegradable and low toxic renewable resources is particularly important. ln particular, the literature shows that the bio-based amphiphilic molecules with a sugar head, or the glycolipids, are excellent substitutes of the petrochemical surfactants used massively in current formulations. To limit the experimental screening and to orient the choice of the syntheses of such molecules, a predictive approach based on the analysis of the molecular structure would make it possible to anticipate the properties of the amphiphilic molecules and to identify those with specific properties. The objective of this work is to develop a methodology through systematic syntheses, characterizations and analyses of glycolipids with gradual structural modifications, with the aim of identifying relevant links between heir amphiphilic properties and their structural characteristics. The obtained experimental data should make it possible to establish a comparable and reliable database, necessary for the development of predictive models. The results showed the significant influence of some structural parameters on the physico-chemical properties with clear trends, which are otherwise difficult to observe by using the non-comparable data collected from the literature. This work also demonstrated the importance of considering the behavior of amphiphilic molecules in water, through knowledge of their phase diagram, which allows for the unambiguous definition of certain properties like the CMC.

The synthesis of materials with molecular recognition properties has become a topic of great technological and scientific interest. Molecular imprinting is one of the most effective strategies in preparing highly selective synthetic receptors. The technique of molecular imprinting involves the copolymerization of functional and cross-linking monomers in the presence of a molecular template. Following polymerization and subsequent removal of the template, the molecularly imprinted polymer (MIP) retains a “molecular memory” of the template. During rebinding, the resultant polymer shows higher affinity and selectivity towards the molecular template when compared to other structural analogs. Ease of preparation and high thermal and chemical stability of this class of materials offers a broad range of potential applications. Promising areas of application include separation, chromatography, catalysis, sensors, antibody mimics, and drug delivery etc. The thesis entitled “Molecularly Imprinted Polymers based on Fluorescent and Template binding Cross-linker” deals with the design and synthesis of several molecularly imprinted polymers (MIPs) using different functional and cross-linking monomers, the main focus being use of preformed template-monomer complex, use of fluorescent cross-linker and development of functional group containing cross-linker. Chapter 1: An Introduction to Molecularly Imprinted Polymers. The first chapter provides an introduction to the field of molecularly imprinted polymers. It presents an overview of molecular imprinting process including a brief history of its discovery and its evolution to the present form. This chapter further elaborates on the principle of molecular imprinting with an emphasis on different parameters that directly affect their performance. It also provides a brief review of the applications of molecularly imprinted polymers. Chapter 2: Highly Cross-linked Metal Ion Imprinted Polymers. The second chapter deals with the synthesis of series of highly cross-linked metal-ion imprinted polymers. The process of metal ion-imprinting usually involves carrying out the polymerization and cross-linking directly in presence of the appropriate metal ion. In the present study, chemical-immobilization method was adopted which involves the use of preformed metal complexes with polymerizable group for the imprinting. Acrylate complexes of various metal-ions, such as Cu2+, Zn2+, Co2+, Ni2+, Pb2+ and Cr3+, were synthesized prior to polymerization. These pre-assembled complexes were then used to prepare MIPs, in the anticipation that this would lead to enhanced selectivity. Ethyleneglycol dimethacrylate (EGDMA) was used as the cross-linking monomer. As a control, the respective non-imprinted polymers (NIPs) were also made in absence of the template metal ion. Following polymerization, the template metal ion was extracted from the resultant metal ion-imprinted polymer. The selectivity of the metal ion-imprinted polymers was examined by a batch process using analytical tools, such as, Atomic Absorption Spectroscopy (AAS) and Inductively Coupled Plasma Spectroscopy (ICP). The spectroscopic studies revealed significant selectivity of all the MIPs towards the template metal ion. Among all six metal ion-imprinted polymers, Pb2+ and Cr3+ ion-imprinted polymer showed remarkable selectivity, followed by Cu2+ and Zn2+ ion-imprinted polymers. The Co2+ and Ni2+ ion-imprinted polymers exhibited comparatively poor selectivity. Representative plots depicting the selectivity exhibited by Pb2+ and Cr3+ ion-imprinted polymers are shown in Figure 1. These observations were rationalized based on the size and geometric preferences imposed by the imprinted site on the ion that binds to it. Figure 1. Selectivity study for (a) Pb2+ ion-imprinted polymer, (b) Cr3+ ion-imprinted polymer. Chapter 3. Molecularly Imprinted Fluorescent Chemosensor for Copper (II). Cu(II) is a source of important pollutant and therefore, the development of sensors that can detect Cu(II) selectively as well as remove Cu(II) from contaminated samples is an important objective. The use of molecular imprinting technique is an appealing approach in this regard. For this, a fluorophore containing cross-linker, namely 9,10-bis-(acryloyloxymethyl)anthracene (BAMA) was synthesized. This fluorescent cross-linker was used along with the standard cross-linker, EGDMA, for preparing Cu2+ ion-imprinted polymer. The complex of copper methacrylate (Cu-MAA) was prepared prior to polymerization used for the preparation of MIP. The resultant imprinted polymer exhibited quenching of the fluorescence in presence of Cu2+ ion, both in organic and aqueous medium. The efficiency of quenching of NIP (prepared in absence of Cu2+ ion) was significantly lower than that of MIP. A typical stack spectra showing the quenching process, along with a comparison of the quenching efficiency of MIP and NIP is shown in Figure 2. The imprinted polymers showed significant selectivity over other non-template metal ions, thereby reaffirming the importance of the imprinting process. The sensitivity of the fluorescence detection could be enhanced by increasing the level of the fluorophore incorporation. The increased sensitivity in detecting Cu2+ ion, demonstrated by the MIP suggests that a statistically random incorporation of the fluorophore into MIP matrices could be a useful approach for imparting a sensing element to MIPs. Figure 2. Fluorescence spectra of the (a) imprinted (MIP-1) and (b) non-imprinted (NIP-1) polymers in the presence of various concentration of Cu(OAc)2 in methanol. (c) Comparison of quenching efficiency of MIP-1 and NIP-1. Data were collected 3 h after addition of copper solution. I0 and I are the fluorescence intensities at 399 nm of the polymers in the absence presence of copper respectively. Two individual runs are presented in (c). Chapter 4. Molecularly Imprinted Turn-Off-On Sensor. This chapter describes the design and synthesis of molecularly imprinted fluorescent turn-off-on sensor utilizing the same fluorescent cross-linker, BAMA. Combining the process of fluorescence resonance energy transfer (FRET) with molecular imprinting technique, a novel turn-off-on sensor was developed. A molecularly imprinted polymer was prepared using a fluorescent template Coumarin-30 (C-30). C-30 was chosen as the template to ensure a significant overlap of the emission spectra of BAMA and the absorption spectra of C-30, thereby optimizing for FRET. Figure 3. Structures of relevant molecules. The C-30 imprinted polymer exhibited simultaneous quenching in fluorescence (turn-off) of BAMA and enhancement in fluorescence (turn-on) of C-30 (Figure 4). The imprinted polymer showed significantly better performance over the non-imprinted polymer (NIP). Figure 4. Fluorescence spectra of the (a) imprinted (MIP) and (b) non-imprinted (NIP) polymers with increasing concentration of the template Coumarine-30 in methanol. The UV-vis studies revealed that the more effective quenching is indeed due to the affinity for C-30 exhibited by the higher binding imprinted polymer. The imprinted polymer also showed significant selectivity over structurally analogous molecules. Therefore, both high sensitivity and selectivity were realized in such novel off-on sensor. Extension of this concept to other biologically relevant fluorescent templates could lead to potentially useful applications. Chapter 5. Design of New Template Binding Cross-linker. In molecularly imprinted polymers (MIP), high cross-linking density (~80 to 90 mole percent) is essential to ensure high selectivity, which limits the functional (binding) monomer to about 10-20 mole percent. Methacrylic acid (MAA) and ethyleneglycol dimethacrylate (EGDMA) are the most common combination of functional monomer and cross-linker, respectively, used in molecular imprinting. Generally a molecularly imprinted polymer made with this combination, contains only 10-20% binding sites. This limitation of binding site density is an aspect that has largely been overlooked. In order to improve the efficiency of MIP materials by enhancing the number of binding sites, a new cross-linking monomer (CYDI, 1) with two carboxylic acid groups was designed and synthesized by coupling itaconic anhydride with cyclohexane dimethanol (Figure 5). Figure 5. Structures of relevant molecules. The new functional group bearing cross-linking monomer (1) Itaconate ester of cyclohexanedimethanol (CYDI), the template (2) theophylline (Theop) and the structural analogue of template (3) caffeine (Caff). This new cross-linking monomer was then employed for preparing molecularly imprinted polymer using a drug molecule, theophylline (Theop 2, a bronchodilator) as the template. Seven molecularly imprinted polymers were synthesized with different ratios of CYDI and EGDMA, keeping the cross-linking density constant. The binding efficiency and the selectivity of these imprinted polymers were thoroughly investigated. It was seen that while saturation binding values for theophylline increased continuously with functional cross-linker (CYDI) content, the optimum selectivity with respect to analogous substrate, caffeine, was attained at 40 mol% CYDI. These studies suggest that the approach of using functional group containing cross-linkers could lead to improved MIP performance.

The diethyl ester of o-phenylenebis(oxamic acid) (opbaH2Et2) was treated with an excess of RNH2 in MeOH to cause the exclusive formation of the respective o-phenylenebis(N(R)-oxamides) (opboH4R2, R = Me 1, Et 2, nPr 3) in good yields. Treatment of 1–3 with half an equivalent of [Cu2(AcO)4(H2O)2] or one equivalent of [Ni(AcO)2(H2O)4] followed by the addition of four equivalents of [nBu4N]OH resulted in the formation of mononuclear bis(oxamidato) type complexes [nBu4N]2[M(opboR2)] (M = Ni, R = Me 4, Et 5, nPr 6; M = Cu, R = Me 7, Et 8, nPr 9). By addition of two equivalents of [Cu(pmdta)(NO3)2] to MeCN solutions of 7–9, novel trinuclear complexes [Cu3(opboR2)(L)2](NO3)2 (L = pmdta, R = Me 10, Et 11, nPr 12) could be obtained. Compounds 4–12 have been characterized by elemental analysis and NMR/IR spectroscopy. Furthermore, the solid state structures of 4–10 and 12 have been determined by single-crystal X-ray diffraction studies. By controlled cocrystallization, diamagnetically diluted 8 and 9 (1%) in the host lattice of 5 and 6 (99%) (8@5 and 9@6), respectively, in the form of single crystals have been made available, allowing single crystal ESR studies to extract all components of the g-factor and the tensors of onsite CuA and transferred NA hyperfine (HF) interaction. From these studies, the spin density distribution of the [Cu(opboEt2)]2− and [Cu(opbonPr2)]2− complex fragments of 8 and 9, respectively, could be determined. Additionally, as a single crystal ENDOR measurement of 8@5 revealed the individual HF tensors of the N donor atoms to be unequal, individual estimates of the spin densities on each N donor atom were made. The magnetic properties of 10–12 were studied by susceptibility measurements versus temperature to give J values varying from −96 cm−1 (10) over −104 cm−1 (11) to −132 cm−1 (12). These three trinuclear CuII-containing bis(oxamidato) type complexes exhibit J values which are comparable to and slightly larger in magnitude than those of related bis(oxamato) type complexes. In a summarizing discussion involving experimentally obtained ESR results (spin density distribution) of 8 and 9, the geometries of the terminal [Cu(pmdta)]2+ fragments of 12 determined by crystallographic studies, together with accompanying quantum chemical calculations, an approach is derived to explain these phenomena and to conclude if the spin density distribution of mononuclear bis(oxamato)/bis(oxamidato) type complexes could be a measure of the J couplings of corresponding trinuclear complexes. / Dieser Beitrag ist aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

No description available.

Fibronectin is an extracellular multidomain glycoprotein that directs and regulates a variety of cell processes such as proliferation, development, haemostasis, embryogenesis, and wound healing. As a major component of blood, fibronectin exists as a soluble disulphide linked dimer, but it can also be incorporated into an insoluble cross-linked fibrillar network to form a major component of the extracellular matrix. Fibronectin is composed of an extended chain of module repeats termed Fn1, Fn2, and Fn3 that bind to a wide range of transmembrane receptors and extracellular matrix components, including collagen. The gelatin binding domain of fibronectin was first isolated as a 45kDa proteolytic fragment and has since been found to be composed of six modules: 6Fn1-1Fn2-2Fn2-7Fn1-8Fn1-9Fn1 (in this notation nFX represents the nth type X module in the native protein). This domain has been reported to bind to both collagen and denatured collagen (gelatin), but with 10-100 times higher affinity to the latter; it can be purified to homogeneity on a gelatin affinity column. In the work presented here, fragments of the gelatin binding domain are expressed in P. pastoris, purified to homogeneity, and investigated at the molecular level. Through a dissection approach, surface plasmon resonance (SPR) is used to characterise the recombinantly produced protein, to accumulate more information about the function of the full domain. NMR is used to assess the folding of the protein fragments at atomic resolution. In particular, the secondary structure of 8Fn1-9Fn1 is mapped using inter-strand NOEs, which suggests that the construct takes the fold of a pair of typical Fn1 modules. Gelatin affinity chromatography is used to confirm that both Fn1 and Fn2 modules contribute to gelatin binding, possibly in two clusters (1Fn2-2Fn2 and 8Fn1-9Fn1). The 7Fn1 module may perform a structural role in linking together these two interaction sites, in the same way as suggested for 6Fn1, which is thought to act in a structural manner to enhance the binding of 1Fn2-2Fn2 to gelatin. Three carbohydrate moieties are found on this domain, one on 2Fn2 and two on 8Fn1. Here, by means of expressing different protein length fragments, and by site directed mutagenesis, the role of each sugar chain is investigated independently. The sugar chain on 2Fn2 does not appear to promote binding to collagen, nor does the first sugar chain on 8Fn1 (N-linked to N497), implying another role for these sugars such as protection from proteolysis. However, the presence of at least a single GlcNAc sugar residue on the second sugar chain site on 8Fn1 (N- linked to N511) is essential for full affinity binding to collagen. Direct binding of the 8Fn1-9Fn1 module pair to collagen is assessed with a short collagen peptide and the binding is monitored by NMR. The peptide appears to bind, predominantly to the final strand of 8Fn1, the first β- strand of 9Fn1, and the linker between the two modules, with μM affinity. A model for bound peptide is proposed. The highly conserved amino acid motif Ile-Gly-Asp (IGD) is found on four of the nine N-terminal Fn1 modules of fibronectin. Tetrapeptides containing the IGD were demonstrated to promote the migration of fibroblast cells into a native collagen matrix. Two of these “bioactive” IGD motifs are found within the gelatin binding domain, one on 7Fn1 and one on 9Fn1. In this study, the motif in the 8Fn1-9Fn1 module pair is shown to be located in a tightly constrained loop within 9Fn1. By site directed mutagenesis, the IGD motifs of 7Fn1 and 9Fn1 are subjected to single amino acid substitutions, and their ability to stimulate cell migration assessed in our assay. By NMR, the fold of the IGD mutant proteins is found to be unaffected by the mutation with respect to the wild type, with the exception of small perturbations around the substitution site. While the wild type module is able to stimulate fibroblast migration, the mutant proteins show reduced or negligible bioactivity. The larger fragments show far more potency in stimulating fibroblast migration, with 8Fn1-9Fn1 (one IGD motif) 104 times more potent than the IGD peptide, and the full gelatin binding domain (two IGD motifs) 106 times more potent than the 8Fn1-9Fn1. Potential mechanisms for this enormous enhancement of the IGD potency in different contexts are discussed.

Diode lasers are a convenient and economical source of near-infrared radiation, which may usefully be applied to a host of different sensitive detection methods; this thesis presents novel extensions of these methods, making use of the favourable characteristics of this type of light source. The first part of this thesis details the development of an optical feedback cavity-enhanced absorption spectroscopy (OF-CEAS) apparatus, including the development of the optical system, the sample handling, and the electronics for feedback phase control. A preliminary demonstration of the system is reported, presenting the detection of atmospheric water absorptions close to 1596 nm. Optimisation and application of the OF-CEAS spectrometer are then demonstrated, after which the spectrometer is applied to the sensitive detection of carbon dioxide absorptions suitable as a diagnostic aid in identifying Heliobacter pylori infection. A time-normalised α-min value of 5.8 × 10⁻⁹ cm⁻¹s^1/2 was measured for these spectra. Further optimisation of the system leads to an ultimate detection sensitivity of 1.42 × 10⁻⁹ cm⁻¹s^1/2, measured on absorption transitions in acetylene close to 1532 nm. In order further to characterise the performance of the OF-CEAS system, analogous experiments are presented using the OF-CEAS setup and a standard diode-laser cavity-enhanced absorption spectroscopy (CEAS) apparatus. Detection is carried out on the P(6) line of the ν₁ + ν₃ vibrational band of the mixed isotopologue of acetylene, ¹²-C¹³-CH₂. Direct comparison is made between the sensitivities of the two methods, and in light of this the suitability of each technique for detection in different environments is considered. The well-characterised and consistent frequency scale which is inherent to the OF-CEAS technique is then applied to a line shape analysis for the presented absorption spectra. Pressure-broadening coefficients are determined for selected absorptions in the ν₁ + ν₃ band of acetylene. In spite of the low resolution associated with this technique, this accurate frequency scaling allows observation of subtle line shape effects such as Dicke collisional narrowing using the data presented in Chapter 3 for the R(60) line in the 3ν₁ + ν₃ vibrational band of CO₂. These effects are quantified through use of a Galatry fit to each absorption spectrum. The statistical significance associated with the use of such a model, and the physical meaning of the results, are examined and discussed. An alternative strategy for increasing the sensitivity of a diode-laser-based gas monitoring technique lies in moving detection to the mid-infrared region, where the absorption cross-sections are generally larger. With this motivation, difference frequency generation is presented, to produce radiation close to 3.5 µm which is then applied to a series of different enhanced spectroscopy techniques. The optimal sensitivity, of 32 ppb NO2 at 45 Torr total sample pressure, was achieved using wavelength modulation spectroscopy. The different techniques are compared and possible improvements to them are put forward. Finally, proof-of-principle work is presented seeking to combine the enhanced circulating power associated with the optical-feedback-locked techniques and non-linear optical techniques to move detection to a more favourable spectral region. Light close to 429 nm is generated by second harmonic generation in a crystal of potassium niobate, with resonance-enhancement afforded by a feedback V-cavity of the sort employed in OF-CEAS. The potential of such a system for diode-laser-based generation of blue and ultraviolet light is demonstrated and discussed, along with improvements that might be implemented to increase the efficiency of the system.

Conventional computing faces a huge technical challenge as traditional transistors will soon reach their size limitations. This will halt progress in reaching faster processing speeds and to overcome this problem, require an entirely new approach. Quantum computing (QC) is a natural solution offering a route to miniaturisation by, for example, storing information in electron or nuclear spin states, whilst harnessing the power of quantum physics to perform certain calculations exponentially faster than its classical counterpart. However, QCs face many difficulties, such as, protecting the quantum-bit (qubit) from the environment and its irreversible loss through the process of decoherence. Hybrid systems provide a route to harnessing the benefits of multiple degrees of freedom through the coherent transfer of quantum information between them. In this thesis I show coherent qubit transfer between electron and nuclear spin states in a ¹⁵N@C₆₀ molecular system (comprising a nitrogen atom encapsulated in a carbon cage) and a solid state system, using phosphorous donors in silicon (Si:P). The propagation uses a series of resonant mi- crowave and radiofrequency pulses and is shown with a two-way fidelity of around 90% for an arbitrary qubit state. The transfer allows quantum information to be held in the nuclear spin for up to 3 orders of magnitude longer than in the electron spin, producing a ¹⁵N@C₆₀ and Si:P ‘quantum memory’ of up to 130 ms and 1.75 s, respectively. I show electron and nuclear spin relaxation (T₁), in both systems, is dominated by a two-phonon process resonant with an excited state, with a constant electron/nuclear T₁ ratio. The thesis further investigates the decoherence and relaxation properties of metal atoms encapsulated in a carbon cage, termed metallofullerenes, discovering that exceptionally long electron spin decoherence times are possible, such that these can be considered a viable QC candidate.

This thesis presents work examining the characteristics and applicability of quantum cascade lasers. An introduction is given explaining both the desire for a widely tunable, narrow bandwidth device working in the midinfrared, as well as detailing the ways in which quantum cascade lasers (QCLs) fulfill these requirements. The development and manufacture of QCLs are then discussed. The experimental section of this thesis is then split into three parts. Chapter 2 concerns the characterisation and application of several pulsed QCLs. The intrapulse mode of operation is employed and the effect of the resulting rapid frequency chirp upon molecular spectra is investigated in the form of rapid passage signals. The evolution of said rapid passage signals is then investigated as a function of chromophore pressure and identity, with different QCLs, chirp rates, and optical path lengths. The prospect of producing population transfer with chirped lasers is discussed. Chapters 3, 4, and 5 are then concerned with the application and characterisation of continuous wave QCLs. In these chapters a widely tunable commercially produced EC-QCL is utilised as well as two DFB QCLs, one of which is used in tandem with a home-made mount and temperature controller. In Chapter 3 a number of sensitive detection techniques are compared with the employment of wavelength modulation spectroscopy, long path cells and optical cavities, and the narrow bandwidth of QCLs utilised to determine a previously unknown spectral constant of DBr. Chapters 4 and 5 then utilise the high power of an external cavity quantum cascade laser in sub-Doppler Lamb-dip and polarisation spectroscopy measurements and then a pump-probe experiment. The laser linewidth is investigated on a millisecond timescale returning a current noise limited value of c.a. 2 MHz and the fundamental linewidth of the device investigated by altering the injection current. Chapter 5 is concerned with the pump-probe experiment, directly measuring the hot band absorption in a ladder like transition (R(6.5)$_\frac{1}{2}$ $v=1\leftarrow0$ and P(7.5)$_\frac{1}{2}$ $v=1\leftarrow0$). The Bennett peak in the hot band is observed with a DFB-QCL swept at $\sim 0.15$ MHz ns$^{-1}$ and is seen not just as a pump bandwidth limited lineshape, but as a highly velocity selected rapid passage signal. The effect of pressure, pump and probe scan rate and power upon this rapid passage signal is also studied. It is further noted that rapid thermalisation occurs within $v=1$ such that at pressures above c.a. 30 mTorr a broad NO doublet absorption is observed beneath the Bennett peak from which a total population transfer of c.a. $16 \%$ can be estimated. Finally an experiment is discussed in which this population transfer could be increased for use in secondary applications. Chapter 6 then presents initial measurements with two prototype pulsed 3.3 \si{\micro\metre} QCLs considering the prospects of such devices. A Fabry-P\'rot device is first studied using a Fourier transform spectrometer and temperature tuning used to produce a spectrum of the Q-branch of CH$_4$ around 3025 cm$^$. Experiments are then performed using a DFB QCL investigating the chirp rate of the system as an indicator of the rate of heat accumulation within the system. Heat management is of particular consideration when the sea-change is made from pulsed to continuous devices. For this device absorption spectra of two CH$_4$ transitions at 2971 cm$^$ are used to determine the chirp rate, which is found to be c.a. 1.8 GHz ns$^$, at least an order of magnitude higher than that of the longer wavelength pulsed devices considered in Chapter 2.

In recent years, the potential benefits of high-throughput virtual screening to the drug discovery community have been recognized, bringing an increase in the number of tools developed for this purpose. These programs have to process large quantities of data, searching for an optimal solution in a vast combinatorial range. This is particularly the case for protein-ligand docking, since proteins are sophisticated structures with complicated interactions for which either molecule might reshape itself. Even the very limited flexibility model to be considered here, using ligand conformation ensembles, requires six dimensions of exploration - three translations and three rotations - per rigid conformation. The functions for evaluating pose suitability can also be complex to calculate. Consequently, the programs being written for these biochemical simulations are extremely resource-intensive. This work introduces a pure computer science approach to the field, developing techniques to improve the effectiveness of such tools. Their architecture is generalized to an abstract pattern of nested layers for discussion, covering scoring functions, search methods, and screening overall. Based on this, new stratagems for molecular docking software design are described, including lazy or partial evaluation, geometric analysis, and parallel processing implementation. In addition, a range of novel algorithms are presented for applications such as active site detection with linear complexity (PIES) and small molecule shape description (PASTRY) for pre-alignment of ligands. The various stratagems are assessed individually and in combination, using several modified versions of an existing docking program, to demonstrate their benefit to virtual screening in practical contexts. In particular, the importance of appropriate precision in calculations is highlighted.