Raman spectroscopy: techniques and applications in the life sciences

Raman spectroscopy is an increasingly popular technique in many areas including biology and medicine. It is based on Raman scattering, a phenomenon in which incident photons lose or gain energy via interactions with vibrating molecules in a sample. These energy shifts can be used to obtain information regarding molecular composition of the sample with very high accuracy. Applications of Raman spectroscopy in the life sciences have included quantification of biomolecules, hyperspectral molecular imaging of cells and tissue, medical diagnosis, and others. This review briefly presents the physical origin of Raman scattering explaining the key classical and quantum mechanical concepts. Variations of the Raman effect will also be considered, including resonance, coherent, and enhanced Raman scattering. We discuss the molecular origins of prominent bands often found in the Raman spectra of biological samples. Finally, we examine several variations of Raman spectroscopy techniques in practice, looking at their applications, strengths, and challenges. This review is intended to be a starting resource for scientists new to Raman spectroscopy, providing theoretical background and practical examples as the foundation for further study and exploration

Theoretical description of electronic excitations in extended systems: beyond the static material model

The theoretical description of bistable materials requires dealing with the interplay of various phenomena, like temperature, environmental effects and electron correlation. We developed a procedure to combine the benefits of the molecular dynamics techniques with the accuracy of the ab initio wave function based methods including various models for the surroundings. The combination of these computational methods involved the making of specific software tools. The proposed procedure has been applied successfully, obtaining good agreements with experimental data, on organic molecules in solvent (cytosine tautomers in water), crystalline materials (NiO, LaMnO3 and TTTA) and inorganic spin-crossover compounds (FeII(bpy)3). We achieved a significant improvement in the description of their absorption spectra: including ligand-to-metal and metal-to-metal charge transfer processes, formally dipole forbidden transitions and the broadening of the spectral bands. Moreover, we observe dramatic changes on the electronic structure by incorporating the environmental effects on the theoretical model.La descripció teòrica de materials biestables requereix el tractament de diversos fenòmens interactuants, com la temperatura, els efectes del medi i la correlació electrònica. S'ha desenvolupat un procediment que combina els beneficis de la dinàmica molecular amb la precisió dels mètodes ab initio basats en la funció d'ona incloent diferents models de l'entorn. La combinació d'aquests mètodes computacionals ha involucrat la creació de programari específic. El procediment proposat ha estat aplicat amb èxit, obtenint bona concordança amb els experiments, a molècules orgàniques en solvent (citosina en aigua), materials cristal•lins (NiO, LaMnO3 i TTTA) i compostos spin-crossover inorgànics (FeII(bpy)3). S'ha assolit una millora significativa en la descripció del seus espectres d'absorció: incloent la transferència de càrrega lligand-metall i metall-metall, les transicions formalment prohibides per dipol i l'eixamplament de les bandes espectrals. A més, s'observen canvis importants en l'estructura electrònica al incorporar els efectes de l'entorn en el model teòric

The Role of Conglomerate Crystallization in Spontaneous Resolution and Chiral Amplification

The mystery of the origin of homochirality in Nature has been thoroughly investigated due to the essential role it plays in Chemistry, Biochemistry and Biology. For example, enantiopure compounds are often essential in the pharmaceutical and agrochemical industries. New aspects of chemistry and chirality can be explored by effectively utilizing the unique nature of conglomerate crystals. In some cases, conglomerate crystals can be easily resolved by carefully observing the features of the crystals. Resolution is possible through observation of hemihedrism, macromorphology, circular polarization or various surface features. Cytosine and 1,2-bis(N-benzoyl-N-methylamino)benzene are two examples of compounds that form centrosymmetric monohydrate racemic crystals but non-centrosymmetric anhydrous conglomerate crystals. Herein, a novel approach to asymmetric amplification by coupling conglomerate crystal formation via dehydration, with subsequent Viedma ripening (i.e. attrition-enchanced deracemization) is being explored. A systematic search of the Cambridge Crystallographic Database for other crystal systems which can undergo desolvation and subsequent chiral amplification is ongoing. Enantiomer-specific oriented attachment, an essential process in Viedma ripening, was also investigated in guanidine carbonate crystals. Simply boiling or shaking powdered racemic guanidine carbonate in saturated solution leads to the formation of large crystalline clusters. These clusters, characterized by solid-state circular dichroism and X-ray powdered diffraction, were found to be nearly homochiral. Enantiomer-specific oriented attachment can be thought of as a mesoscale analogue of conglomerate crystallization

Performance of point charge embedding schemes for excited states in molecular organic crystals

Modeling excited state processes in molecular crystals is relevant for several applications. A popular approach for studying excited state molecular crystals is to use cluster models embedded in point charges. In this paper, we compare the performance of several embedding models in predicting excited states and S1-S0 optical gaps for a set of crystals from the X23 molecular crystal database. The performance of atomic charges based on ground or excited states was examined for cluster models, Ewald embedding, and self-consistent approaches. We investigated the impact of various factors, such as the level of theory, basis sets, embedding models, and the level of localization of the excitation. We consider different levels of theory, including time-dependent density functional theory and Tamm-Dancoff approximation (TDA) (DFT functionals: ωB97X-D and PBE0), CC2, complete active space self-consistent field, and CASPT2. We also explore the impact of selection of the QM region, charge leakage, and level of theory for the description of different kinds of excited states. We implemented three schemes based on distance thresholds to overcome overpolarization and charge leakage in molecular crystals. Our findings are compared against experimental data, G0W0-BSE, periodic TDA, and optimally tuned screened range-separated functionals

Supramolecular hydrogels and discrete structures based on metal coordination and hydrogen bonding

PhD ThesisThe complexation of thiolated nucleosides and nucleobases with a range of group 11 metal ions (Au(I), Ag(I), Cu(I/II), was observed to lead to the formation of hydrogels by simple inversion tests. Atomic force and electron microscopy of the xerogels showed, in many cases, the presence of fibres with lengths in the micrometre range and above; this provided evidence for the formation of coordination polymers. This thesis is concerned with the preparation, characterisation and investigation of the physical properties, mainly photoluminescence and conductivity, of these coordination polymers. 2’-Deoxy-6-thioguanosine was successfully synthesised and characterized by UV, IR, Mass, 1H-NMR, and 13C-NMR spectroscopy. The formation of coordination polymers upon reaction of Au(I), Ag(I), and Cu(II) ions with 2’-deoxy-6-thioguanosine and 6-thioguanosine in aqueous media produced hydrogels with up to 97% water+methanol by mass. The Au-6-thioguanosine gel was studied in more detail because of the interest in gold thiolate polymers and the novel properties observed for Au(I)-6-thioguanosine. Fluorescence spectroscopy observed a strong yellow emission (λmax = 606 nm) which is not present in 6-thioguanosine nor in the Au(I) solutions. The optical absorption spectrum of the coordination polymer showed a band at (λmax = 360 nm) assigned to the HOMO-LUMO transition located mainly on the S-Au-S…chain of the polymer. An induced CD band associated with the Au-S chain and an enhancement of the CD signal at shorter wavelengths, for transitions associated with the ligand, suggested the polymer has a helical structure. Further evidence was provided by analysis of the X-ray scattering pattern of the xerogel and atomic force microscopy of single fibres deposited on silicon chips. The observation of long Au(I)-6-thioguanosine fibres and strong photoluminescence suggests some delocalisation of the states associated with the Au-S chains and the possibility of electronic conductivity. This was demonstrated upon oxidative doping of Au(I)-6-thioguanosine xerogels coated over platinum microband electrodes. Treatment with iodine vapour or ([Br(C6H4)3N]SbCl6) in anhydrous acetonitrile were found to result in linear current-voltage characteristics. The temperature dependence of the conductance showed Arrhenius behaviour (over range of temperature 223 to 323 K) with an activation energy of 94 kJ mol-1. V More complex structures based on Au(I)-6-thioguanosine polymers were observed upon synthesising the polymer in the presence of duplex DNA (from calf thymus). The templating of the polymer on DNA produces long, regular, and uniform fibres with a beads-on-a-string morphology. An unusual self-assembly of Au(I)-6-thioguanosine at flat Si surfaces upon simple drop-casting, with slow evaporation was also observed. AFM images of these films showed the formation of well-defined layers, but with each layer comprising long ribbons exceeding the maximum length of the AFM scan (~15 micrometres). Ag(I)-containing hydrogels formed by reactions with 6-thioguanine, 6-mercaptopurine, and 2-thiocytosine were prepared and characterised by AFM, TEM, XPS, X-Ray, FTIR, UV-Vis, and fluorescent spectroscopy. Au(I) 2-thiocytosine was also prepared, but this produced a discrete complex rather than a gel. AFM of the Ag(I) xerogels showed the formation of very long fibres and this was confirmed by TEM images. FTIR and X-ray diffraction studies suggested the metal coordination occurred via S atoms in all three gels. The Au(I) 2-thiocytosine was found to have strong luminescence (λmax 622 nm). A new Ag(I):6-thioethero nucleoside complex was prepared containing 6-methylmercaptopurine riboside (6-MMPR) which was shown by single crystal X-ray diffraction to unexpectedly feature coordination via N7 rather than the thioether sulfur atom. Cu(II) & Co(II):6-methylmercaptopurine(6-MMP) were also synthesised as new discrete complexes. The metals binding was studied by single crystal X-ray diffraction which showed that the binding sites were N3& N9 for Cu(II) ions, and N9 for Co(II) ion in the complexes.Iraqi Ministry of Higher Education and Scientific Researc

X-Irradiation of DNA Components in the Solid State: Experimental and Computational Studies of Stabilized Radicals in Guanine Derivatives

Single crystals of sodium salt of guanosine dihydrate and 9 Ethyl Guanine were X-irradiated with the objective of identifying the radical products. Study with K-band EPR, ENDOR, and ENDOR-Induced EPR techniques indicated at least four radical species to appear in both crystals in the temperature range of 6K to room temperature. Three of these radicals (Radicals R1, R2, and R3) were present immediately after irradiation at 6K. Computational chemistry and EPR spectrum simulation methods were also used to assist in radical identifications. Radical R1, the product of net hydrogen addition to N7, and Radical R2, the product of electron loss from the parent molecule, were observed in both systems. Radical R3, in Na+.Guanosine-.2H2O, is the product of net hydrogen abstraction from C1\u27 of ribose group and radical R3 in 9EtG was left unassigned due to insufficient experimental data. Radical R4, the C8-H addition radical, was also detected in both systems. For Na+.Guanosine-.2H2O, R4 was observed after warming the irradiated crystals to the room temperature. But for the 9EtG crystals the corresponding radical form was detected after irradiation at room temperature. Density functional theory (DFT) based computational studies was conducted to investigate the radical formation mechanisms and their stability. Here possibilities of proton transfers from the neighboring molecules were considered. The first approach was to consider the proton affinities of the acceptor sites and deprotonation enthalpies of the donor sites. This approach supported the formation of radicals observed in both systems. The second approach, applied only to the 9EtG system, was based on proton transfers between 9EtG base-pair anion and cation radicals. Even though the charge and spins were localized as expected, the computed thermodynamic data predicted that the proton transfer processes are unfavorable for both anionic and cationic base-pairs. This indicates the need for additional work to draw final conclusions. In addition, DFT methods were used to compute the geometries and hyperfine coupling constants of 9EtG derived radicals in both single molecule and cluster models. The calculated results agreed well with the experimental results

Characterization of water-solid interactions in crystalline ingredients and development of deliquescence measurement recommendations

There are five major mechanisms of water-solid interactions. The primary focus of this thesis was on two of these: deliquescence and hydrate formation. Many crystalline food ingredients are deliquescent compounds (e.g., NaCl, sucrose, and ascorbic acid) and some are both deliquescent and hydrate formers (e.g., glucose, thiamine HCl, citric acid). Deliquescence is the first order phase transformation of a crystalline solid to a solution above a critical relative humidity (RH) known as the deliquescence point (RH0). A crystalline hydrate is a pseudo-polymorph in which water is incorporated into the crystal structure, altering the molecular formula and the physical properties.^ To design stable formulations, it is important to know the deliquescence points of all ingredients present. Multiple approaches have been reported for determining the RH0; however, the discontinuity between methods may influence the reported values. The objective of this study was to provide a comprehensive comparison of methods used to measure the deliquescence points of single ingredients and blends. The effects of altering sample preparation and experimental parameters on the measured deliquescence points were determined using the following methods: water activity of saturated solutions, gravimetric moisture sorption isotherms, dynamic dewpoint sorption profiles, and static isopiestic methods. Significant differences (p\u3c0.05) in measured deliquescence RHs were found between different methods. Advantages, disadvantages, precision, accuracy, run times, and costs of the different methods were summarized.^ When two or more deliquescent ingredients are in contact, the deliquescence RH of the blend, RH0mix, is always lower than the individual ingredient RH0s. The RH0mix has been be estimated using the Ross Equation, which assumes the presence of an ideal solution. However, when the compounds in a blend share a common ion, a diminished deliquescence lowering effect (higher than the Ross Equation predicted RH0mix) occurs. This can be attributed to the common-ion effect. The diminished deliquescence lowering effect was found in blends of organic and/or inorganic ingredients that shared a common ion (both anion and cation), and higher deviations between the Ross Equation predicted RH0mix and measured RH0mix increased with increasing number of ingredients. A new modified Ross Equation was developed to compensate for the common-ion effect, and RH0mixpredictions using this equation correlate well with measured RH0mix values of blends with common ions.^ Deliquescence and hydrate formation are influenced by RH and temperature and the boundaries can be plotted on a RH-Temperature phase diagram. Each deliquescent hydrate forming ingredient has a minimum of three boundaries: the hydrate RH0, the anhydrous RH0, and the hydrate formation boundaries. As temperature increases, the hydrate formation RH boundary increases and the hydrate RH0 boundary decreases, eventually intersecting. The intersection is known as the peritectic temperature. Above the peritectic temperature the hydrate is no longer thermodynamically stable and an anhydrous RH0 boundary is found. It was also shown that the anhydrous RH 0 is a critical boundary below the peritectic temperature as this is the point at which hydrate formation rapidly increases. It was proven that the anhydrous form can deliquesce below the peritectic temperature and RH 0 of the hydrate. Upon deliquescence, rapid hydrate formation takes place slowing down sorption kinetics. This is the first study to report not only the use of water activity measurements to create RH-temperature phase diagrams, but also the RH-temperature phase diagrams of common food ingredients and the relationship of deliquescence to hydrate formation behavior