No / The first Raman spectrometers to be used for in situ analysis of planetary material will be launched as part of powerful, rover-based analytical laboratories within the next 6 years. There are a number of significant challenges associated with building spectrometers for space applications, including limited volume, power and mass budgets, the need to operate in harsh environments and the need to operate independently and intelligently for long periods of time (due to communication limitations). Here, we give an overview of the technical capabilities of the Raman instruments planned for future planetary missions and give a review of the preparatory work being pursued to ensure that such instruments are operated successfully and optimally. This includes analysis of extremophile samples containing pigments associated with biological processes, synthetic materials which incorporate biological material within a mineral matrix, planetary analogues containing low levels of reduced carbon and samples coated with desert varnish that incorporate both geo-markers and biomarkers. We discuss the scientific importance of each sample type and the challenges using portable/flight-prototype instrumentation. We also report on technical development work undertaken to enable the next generation of Raman instruments to reach higher levels of sensitivity and operational efficiency.

No / In this paper, it is demonstrated how Raman spectroscopy can be used to detect different carotenoids as possible biomarkers in various groups of microorganisms. The question which arose from previous studies concerns the level of unambiguity of discriminating carotenoids using common Raman microspectrometers. A series of laboratory-grown microorganisms of different taxonomic affiliation was investigated, such as halophilic heterotrophic bacteria, cyanobacteria, the anoxygenic phototrophs, the non-halophilic heterotrophs as well as eukaryotes (Ochrophyta, Rhodophyta and Chlorophyta). The data presented show that Raman spectroscopy is a suitable tool to assess the presence of carotenoids of these organisms in cultures. Comparison is made with the high-performance liquid chromatography approach of analysing pigments in extracts. Direct measurements on cultures provide fast and reliable identification of the pigments. Some of the carotenoids studied are proposed as tracers for halophiles, in contrast with others which can be considered as biomarkers of other genera. The limits of application of Raman spectroscopy are discussed for a few cases where the current Raman spectroscopic approach does not allow discriminating structurally very similar carotenoids. The database reported can be used for applications in geobiology and exobiology for the detection of pigment signals in natural settings.

No / Scytonemin-imine, a novel derivative of scytonemin, has been isolated and identified very recently and proposed to serve as a photoprotective biomarker for certain bacteria growing under intense photon flux density. This study predicts theoretically the Raman spectrum of scytonemin-imine by density functional theory calculations and provides comparison of major bands to those of scytonemin, the parent compound for which both the experimentally characterized and theoretically predicted spectra exist in the literature. It is proposed to be an addendum to the collection of our previous work on scytonamin and its derivatives to facilitate recognition of the diagnostic Raman spectral signatures for scytonemin-imine.

No / Raman spectroscopy has been identified as an important first-pass analytical technique for deployment on planetary surfaces as part of a suite of instrumentation in projected remote space exploration missions to detect extant or extinct extraterrestrial life signatures. Aside from the demonstrable advantages of a non-destructive sampling procedure and an ability to record simultaneously the molecular signatures of biological, geobiological and geological components in admixture in the geological record, the interrogation and subsequent interpretation of spectroscopic data from these experiments will be critically dependent upon the recognition of key biomolecular markers indicative of life existing or having once existed in extreme habitats. A comparison made with the characteristic Raman spectral wavenumbers obtained from standards is not acceptable because of shifts that can occur in the presence of other biomolecules and their host mineral matrices. In this paper, we identify the major sources of difficulty experienced in the interpretation of spectroscopic data centring on a key family of biomarker molecules, namely scytonemin and its derivatives; the parent scytonemin has been characterized spectroscopically in cyanobacterial colonies inhabiting some of the most extreme terrestrial environments and, with the support of theoretical calculations, spectra have been predicted for the characterization of several of its derivatives which could occur in novel extraterrestrial environments. This work will form the foundation for the identification of novel biomarkers and for their Raman spectroscopic discrimination, an essential step in the interpretation of potentially complex and hitherto unknown biological radiation protectants based on the scytoneman and scytonin molecular skeletons which may exist in niche geological scenarios in the surface and subsurface of planets and their satellites in our Solar System.

No / In 1834 in a tumulus at Gristhorpe, North Yorkshire, UK, an intact coffin fashioned from the hollowed-out trunk of an oak tree was found to contain a well-preserved skeleton stained black from the oak tannins, wrapped in an animal skin and buried with a range of grave artefacts, including a bronze dagger, flints and a bark vessel. The remains were deposited in the Rotunda Museum at Scarborough, where closure due to refurbishment in 2005–2008 provided an opportunity for the scientific investigation of the skeletal remains and artefacts using a wide range of techniques. Dendrochronological and radiocarbon dating has established the age of the skeleton as 2140–1940 BC at 95% confidence, in the Early Bronze Age. As part of this project, Raman spectra of several mysterious small spherical objects discovered in the coffin underneath the skeleton and initially believed to be ‘mistletoe berries’ associated with ancient burial customs have been recorded non-destructively. The interpretation of the Raman spectral data, microscopic analysis and comparison with modern specimens has led to the conclusion that the small spheres are phosphatic urinary stones, which reflect the archaeological dietary evidence and stable isotope analysis of bone collagen of Gristhorpe Man.

No / Specimens from human remains exhibiting unusual preservation excavated from a seventh century stone cist burial at Towyn y Capel in Anglesey, UK, have been analysed using Raman spectroscopy with near-infrared laser excitation at 1,064 and 785 nm. Specimens of hair and bone provided evidence for severe degradation and microbial colonisation. The deposits within the stone cist showed that some microbially mediated compounds had been formed. Analysis of crystals found at the interface between the hair and the skeletal neck vertebrae revealed a mixture of newberyite and haematite, associated with decomposition products of the hair and bone. An interesting differential degradation was noted in the specimens analysed which could be related to the air-void and the presence of plant root inclusions into the stone cist. This is the first time that Raman spectroscopy has been used in the forensic archaeological evaluation of burial remains in complex and dynamic environments.

No / Knowledge and control of the polymorphic phases of chemical compounds are important aspects of drug development in the pharmaceutical industry. Salmeterol xinafoate, a long acting β-adrenergic receptor agonist, exists in two polymorphic Forms, I and II. Raman and near infrared spectra were obtained of these polymorphs at selected wavelengths in the range of 488–1064 nm; significant differences in the Raman and near-infrared spectra were apparent and key spectral marker bands have been identified for the vibrational spectro-scopic characterisation of the individual polymorphs which were also characterised with X ray diffractometry. The solid-state transition of salmeterol xinafoate polymorphs was studied using simultaneous in situ portable Raman spectroscopy and differential scanning calorimetry isothermally between transitions. This method assisted in the unambiguous characterisation of the two polymorphic forms by providing a simultaneous probe of both the thermal and vibrational data. The study demonstrates the value of a rapid in situ analysis of a drug polymorph which can be of potential value for at-line in-process control.

In electrocatalysis, two-dimensional conjugated metal-organic frameworks (2D c-MOFs) are increasingly recognized as potential candidates for sustainable energy conversion, offering customizable active sites and electronic properties. This thesis presents a comprehensive investigation into the (photo)electrocatalytic active sites and mechanisms of 2D c-MOFs, with a particular focus on the interplay between their metal and organic components. Employing in situ Raman spectroscopy and electrochemical analyses, it was determined that within the copper-phthalocyanine-based MOF (CuPc-CuO4), the CuO4 nodes serve as the primary active sites for the Oxygen Reduction Reaction (ORR) below -0.2 V. Distinct redox potentials of -0.04 V for CuPc and +0.33 V for CuO4 versus Ag|AgCl were observed, further enhanced by Nickel-Nitrilotriacetic Acid (Ni-NTA) functionalization on the electrodes. Rotating Disk Electrode (RDE) testing revealed that CuPc-CuO4 MOFs exhibit an electron transfer number of 3.6 for ORR. The electrocatalytic activity was most favorable when both the phthalocyanine copper and the copper in the CuO4 linkage were in the +1 oxidation state (CuI/CuI), with the Cu in CuO4 primarily responsible for oxygen reduction. This state's effectiveness is attributed to a decrease in bandgap and an increase in π-conjugation, supported by Density Function Theory (DFT) calculations, which suggest that electron transfer rates in the mixed-valence state are critical for catalysis. Substitution of Cu with other metals (Zinc, Cobalt, Manganese, and Nickel) in CuPc-MO4 MOFs shifted the onset potentials and electron transfer number for ORR, as tested with RDE, underscoring the significant role of metal-oxygen linkages in the process. Remarkably, CuPc-CoO4 substitution exhibited lowest overpotential and highest electron transfer number for ORR, highlighting its potential for enhancing electrocatalytic processes. Additionally, this study explores a novel sp-carbon incorporated MOF with CuO4 linkages, Cu3HHAE2, demonstrating photocatalytic activity for Hydrogen Evolution Reaction (HER). This activity is primarily attributed to the acetylene units within the framework, evidenced by a shift in the C≡C band from 2116 to 2044 cm-1. However, the presence of CuO4 linkages is essential, indicating a synergistic effect crucial for enhanced catalytic performance. This research highlights the dependence of electrocatalytic activity on the structural configuration of the MOF, revealing that while certain components may act as primary active sites, other elements of the MOF structure play an indispensable role in facilitating overall catalysis.

Process Analytical Technology (PAT) is framed with the objective of the design and development of processes to ensure predefined quality of the product at the end of manufacturing. PAT implementation includes better understanding of process, reduction in production time with use of in-line, at-line and on-line measurements, yield improvement and energy and cost reductions. Hot Melt Extrusion process (HME) used in the present work is proving increasingly popular in industry for its continuous and green processing which is beneficial over traditional batch processing. The present work was focused on applications of Raman spectroscopy as off - line and in - line monitoring techniques as a PAT for production of pharmaceutical solid dispersions and co-crystals. Solid dispersions (SDs) of the anti-convulsant Carbamazepine (CBZ) with two pharmaceutical grade polymers have been produced using HME at a range of drug loadings and their amorphous nature confirmed using a variety of analytical techniques. Off-line and in-line Raman spectroscopy has been shown to be suitable techniques for proving preparation of these SDs. Through calibration curves generated from chemometric analysis in-line Raman spectroscopy was shown to be more accurate than off-line measurements proving the quantification ability of Raman spectroscopy as well as a PAT tool. Pure co-crystals of Ibuprofen-Nicotinamide and Carbamazepine-Nicotinamide have been produced using solvent evaporation and microwave radiation techniques. Raman spectroscopy proved its superiority over off-line analytical techniques such as DSC, FTIR and XRD for co-crystal purity determination adding to its key advantage in its ability to be used as an in-line, non-destructive technique.

Pathogenic microbial contamination of the environment poses a significant threat to human health. Accordingly, microbial surveillance is needed to ensure safe drinking water and air quality. Current analytical methods for microbes are generally either culture-based, gene amplification-based, or sequencing-based. However, these approaches require centralized facilities, well-trained personnel, and specialized instruments that result in high costs and long turnaround times. Surface-enhanced Raman spectroscopy (SERS)-based techniques have been proposed to overcome these limitations. In this dissertation, we discuss work conducted to develop novel SERS-based methods to enable both sensitive microbial quantification and analysis of the interactions of pathogens, their hosts, and the surrounding environment. We first developed a labeled SERS-based lateral flow test for virus quantification. Optimization of the lateral flow design and digital signal analysis enabled high sensitivity towards SARS-CoV-2. To elicit a comprehensive understanding of pathogen infection, label-free living-cell SERS sensors were engineered by incubating host cells with nanoparticles. SERS spectral changes in host cellular components and metabolites during infection were used for viral quantification and offered inherent insights into the temporal and spatial molecular-level mechanisms of infection. These biosensors were validated using bacteriophage Phi6 and then developed for infectious H1N1 influenza. To understand microbial survival in the environment, living-cell SERS methods were applied under various conditions. Results showed cell inactivation and antibiotic treatment induced significant cellular and metabolic responses in the living whole-cell sensors, implying their potential applicability to various environmental conditions. Our research achieves rapid and on-site pathogen quantification and infection mechanism identification. / Doctor of Philosophy / Pathogenic microbes, such as the SARS-CoV-2 virus, can spread through air and water and are potentially harmful to human health. Monitoring the concentrations of these microbes in the environment is crucial to track their presence and provide an early warning of their spread. Unfortunately, current microbial detection methods are often expensive and take a long time since they typically require professional facilities and expert elicitation. Our research relies on a technique called surface-enhanced Raman spectroscopy (SERS) to address these challenges. SERS enables identification and quantification of microbes by analyzing specific features (i.e., peak position, peak intensity) in the spectra. We first applied this technique by modifying a commercial SARS-CoV-2 antigen test kit with a label molecule that provides SERS signals. We achieve accurate and sensitive quantification, even in the presence of high levels of environmental interference. To better understand how these harmful microbes interact with our bodies, we developed sensors that can measure SERS signal changes in host cells before and after infection. These sensors were tested using the bacteriophage virus Phi6 that infects bacteria and infectious H1N1 influenza virus. Furthermore, we applied these sensors to study how bacteria respond to different environmental conditions, providing valuable insights into their survival and behavior under various conditions. In summary, our research introduces methods that are more accessible to identify and quantify harmful microbes that can be potentially used by the general public. The methods provide us with molecular level understanding of pathogen interactions with humans and the environment.