Studies in molecular spectroscopy

This thesis is divided into two parts. The first part deals with some studies in molecular mechanics Using spectroscopic data and has four chapters in it. Certain approximation methods for the evaluation of molecular force fields are herein developed The second part, which consists of the last two chaptcrs, deals with infrared spectral studies of ternary liquid systems and a polymer film prepared by glow discharge method.

Posta a punt, automatització i validació d’una tècnica analítica per a la determinació de crom (VI) en continu mitjançant espectroscòpia d’absorció molecular

La determinació de Cr(VI) en l’aigua per espectroscòpia d’absorció molecular a la regió visible es realitza mitjançant una tècnica colorimètrica per reacció amb un reactiu cromogènic. El Cr(VI) reacciona amb la 1,5-Difenilcarbacida formant un complex de color vermell-violeta que absorbeix radiació a la longitud d’ona de 540 nm. Tradicionalment, la determinació de Cr(VI) per colorimetria es realitza de forma manual i discontínua, essent un mètode repetitiu i laboriós que té implícit un cost de mà d’obra i de temps considerable, tant pel que es refereix a la preparació de les mostres i dels patrons, com al propi acte de la mesura a l’aparell. Aquest projecte s’ha realitzat sota la idea que les determinacions de Cr(VI) per colorimetria, poden complir els requisits bàsics operacionals dels mètodes d’anàlisi de flux en continu. Partint d’aquesta base, s’ha desenvolupat un nou equip de mesura per realitzar les determinacions de Cr(VI) amb una presa de mostres automatitzada, i un règim de treball en continu. L’objectiu d’aquest projecte és la posta a punt, automatització, i validació de la tècnica d’anàlisi instrumental de determinació de crom (VI) en continu per espectroscòpia molecular visible

Metal complexes of a tetraazacyclophane: solution and molecular modelling studies

An alternative synthetic approach to yield the compound 2,3,5,6,8,9,11,14-octahydrobenzo[1][ 1,4,7,10]tetraazacyclotetradecine (bz[14]N-4) is presented. The protonation constants of bz[14]N-4 and the stability constants of its complexes with Ni2+, Cu2+, Zn2+, Cd2+, Pb2+ were determined in H2O at 25degreesC with ionic strength 0.10 mol dm(-3) in KNO3 and they were compared with structurally related macrocycles cyclam (1,4,8,11-tetraazacyclotetradecane) and cyclen (1,4,7,10-tetraazacyclododecane). These studies indicate that only 1 : 1 ( M : L) species are formed in solution, and the ligand exhibits a high affinity for larger ions such as Cd2+ and Pb2+. The X-ray study of [bz[14]N4H3](3+) shows that an inclusion compound with a chloride counter-anion is formed through NH...Cl hydrogen bonds. Spectroscopic data in solution ( electronic and NMR spectra) showed that the macrocycle adopts a planar arrangement upon metal complexation. Molecular mechanics calculations reveal that in spite of the presence of the benzene ring in the macrocyclic framework this ligand can encapsulate metal ions with different stereo-electronic sizes in square planar arrangements. Our results indicate that the presence of the benzene ring in the backbone of the bz[14]N-4 confers a coordination behaviour intermediate between that of cyclam and cyclen.

Dinuclear copper and zinc complexes of a hexaazamacrocycle containing p-xylyl spacers and bridging anions: theoretical and spectroscopic studies

The hexaazamacrocycle 7,22-dimethyl-3,7,11,18,22,26-hexaazatricyclo[26.2.2.2(13,16)] tetratriaconta-1(30), 13,15,28,31,33- hexaene (Me-2[30] pbz(2)N(6)) was synthesized and characterised by single crystal X-ray diffraction. The macrocycle adopts a conformation with the two aromatic rings almost parallel at a distance of ca. 4.24 Angstrom, but displaced relative to each other by ca. 1.51 Angstrom. The protonation constants of this compound and the stability constants of its complexes with Cu2+ and Zn2+, were determined in water - methanol (9 : 1 v/v) at 25 degreesC with ionic strength 0.10 mol dm(-3) in KCl. The potentiometric and spectroscopic studies (NMR of zinc, cadmium and lead complexes, and EPR of the copper complexes) indicate the formation of only dinuclear complexes. The association constants of the dinuclear copper complex with anions ( thiocyanate, terephthalate and glyphosate) and neutral molecules (1,4-benzenedimethanol, p-xylylenediamine and terephthalic acid) were determined at 20 degreesC in methanol. The structural preferences of this ligand and of its dinuclear copper(II) complex with a variety of bridging ligands were evaluated theoretically by molecular mechanics calculations (MM) and molecular dynamics (MD) using quenching techniques.

Molecular modelling studies of binding of DACD derivatives into G-Quadruplex DNA: comparison of force field and quantum polarized ligand docking methods

The DNA G-qadruplexes are one of the targets being actively explored for anti-cancer therapy by inhibiting them through small molecules. This computational study was conducted to predict the binding strengths and orientations of a set of novel dimethyl-amino-ethyl-acridine (DACA) analogues that are designed and synthesized in our laboratory, but did not diffract in Synchrotron light.Thecrystal structure of DNA G-Quadruplex(TGGGGT)4(PDB: 1O0K) was used as target for their binding properties in our studies.We used both the force field (FF) and QM/MM derived atomic charge schemes simultaneously for comparing the predictions of drug binding modes and their energetics. This study evaluates the comparative performance of fixed point charge based Glide XP docking and the quantum polarized ligand docking schemes. These results will provide insights on the effects of including or ignoring the drug-receptor interfacial polarization events in molecular docking simulations, which in turn, will aid the rational selection of computational methods at different levels of theory in future drug design programs. Plenty of molecular modelling tools and methods currently exist for modelling drug-receptor or protein-protein, or DNA-protein interactionssat different levels of complexities.Yet, the capasity of such tools to describevarious physico-chemical propertiesmore accuratelyis the next step ahead in currentresearch.Especially, the usage of most accurate methods in quantum mechanics(QM) is severely restricted by theirtedious nature. Though the usage of massively parallel super computing environments resulted in a tremendous improvement in molecular mechanics (MM) calculations like molecular dynamics,they are still capable of dealing with only a couple of tens to hundreds of atoms for QM methods. One such efficient strategy that utilizes thepowers of both MM and QM are the QM/MM hybrid methods. Lately, attempts have been directed towards the goal of deploying several different QM methods for betterment of force field based simulations, but with practical restrictions in place. One of such methods utilizes the inclusion of charge polarization events at the drug-receptor interface, that is not explicitly present in the MM FF.

Use of grape polyphenols against carcinogenesis: Putative molecular mechanisms of action using in vitro and in vivo test systems

Polyphenols are present in foods and beverages and are related to sensorial qualities such as color, bitterness, and astringency, which are relevant in wine, tea, grape juice, and other products. These compounds occur naturally in forms varying from simple phenolic acids to complex polymerized tannins. Thus, it is reasonable to expect that grape-derived products elaborated in the presence of skins and seeds, such as wine and grape juice, are natural sources of flavonoids in the diet. Carcinogenesis is a multistep process that is characterized by genetic, epigenetic, and phenotypic changes. With increasing knowledge of these mechanisms, and the conclusion that most cases of cancer are preventable, efforts have focused on identifying the agents with potential anticancer properties. The use of grape polyphenols against the carcinogenesis process seems to be a suitable alternative for either prevention and/or therapeutic purposes. The aim of this article is to show the molecular data generated from the use of grape polyphenols against carcinogenesis using in vivo and in vitro test systems. © Mary Ann Liebert, Inc. and Korean Society of Food Science and Nutrition.

Water-in-Oil Micro-Emulsion Enhances the Secondary Structure of a Protein by Confinement

A scheme is presented in which an organic solvent environment in combination with surfactants is used to confine a natively unfolded protein inside an inverse microemulsion droplet. This type of confinement allows a study that provides unique insight into the dynamic structure of an unfolded, flexible protein which is still solvated and thus under near-physiological conditions. In a model system, the protein osteopontin (OPN) is used. It is a highly phosphorylated glycoprotein that is expressed in a wide range of cells and tissues for which limited structural analysis exists due to the high degree of flexibility and large number of post-translational modifications. OPN is implicated in tissue functions, such as inflammation and mineralisation. It also has a key function in tumour metastasis and progression. Circular dichroism measurements show that confinement enhances the secondary structural features of the protein. Small-angle X-ray scattering and dynamic light scattering show that OPN changes from being a flexible protein in aqueous solution to adopting a less flexible and more compact structure inside the microemulsion droplets. This novel approach for confining proteins while they are still hydrated may aid in studying the structure of a wide range of natively unfolded proteins.

Characterisation of soils with the use of instrumental techniques : a multivariate forensic study

The value of soil evidence in the forensic discipline is well known. However, it would be advantageous if an in-situ method was available that could record responses from tyre or shoe impressions in ground soil at the crime scene. The development of optical fibres and emerging portable NIR instruments has unveiled a potential methodology which could permit such a proposal. The NIR spectral region contains rich chemical information in the form of overtone and combination bands of the fundamental infrared absorptions and low-energy electronic transitions. This region has in the past, been perceived as being too complex for interpretation and consequently was scarcely utilized. The application of NIR in the forensic discipline is virtually non-existent creating a vacancy for research in this area. NIR spectroscopy has great potential in the forensic discipline as it is simple, nondestructive and capable of rapidly providing information relating to chemical composition. The objective of this study is to investigate the ability of NIR spectroscopy combined with Chemometrics to discriminate between individual soils. A further objective is to apply the NIR process to a simulated forensic scenario where soil transfer occurs. NIR spectra were recorded from twenty-seven soils sampled from the Logan region in South-East Queensland, Australia. A series of three high quartz soils were mixed with three different kaolinites in varying ratios and NIR spectra collected. Spectra were also collected from six soils as the temperature of the soils was ramped from room temperature up to 6000C. Finally, a forensic scenario was simulated where the transferral of ground soil to shoe soles was investigated. Chemometrics methods such as the commonly known Principal Component Analysis (PCA), the less well known fuzzy clustering (FC) and ranking by means of multicriteria decision making (MCDM) methodology were employed to interpret the spectral results. All soils were characterised using Inductively Coupled Plasma Optical Emission Spectroscopy and X-Ray Diffractometry. Results were promising revealing NIR combined with Chemometrics is capable of discriminating between the various soils. Peak assignments were established by comparing the spectra of known minerals with the spectra collected from the soil samples. The temperature dependent NIR analysis confirmed the assignments of the absorptions due to adsorbed and molecular bound water. The relative intensities of the identified NIR absorptions reflected the quantitative XRD and ICP characterisation results. PCA and FC analysis of the raw soils in the initial NIR investigation revealed that the soils were primarily distinguished on the basis of their relative quartz and kaolinte contents, and to a lesser extent on the horizon from which they originated. Furthermore, PCA could distinguish between the three kaolinites used in the study, suggesting that the NIR spectral region was sensitive enough to contain information describing variation within kaolinite itself. The forensic scenario simulation PCA successfully discriminated between the ‘Backyard Soil’ and ‘Melcann® Sand’, as well as the two sampling methods employed. Further PCA exploration revealed that it was possible to distinguish between the various shoes used in the simulation. In addition, it was possible to establish association between specific sampling sites on the shoe with the corresponding site remaining in the impression. The forensic application revealed some limitations of the process relating to moisture content and homogeneity of the soil. These limitations can both be overcome by simple sampling practices and maintaining the original integrity of the soil. The results from the forensic scenario simulation proved that the concept shows great promise in the forensic discipline.

Prediction of pull-out force of multi-walled carbon nanotube (MWCNT) in sword-in-sheath mode

The pull-out force of some outer walls against other inner walls in multi-walled carbon nanotubes (MWCNTs) was systematically studied by molecular mechanics simulations. The obtained results reveal that the pull-out force is proportional to the square of the diameter of the immediate outer wall on the sliding interface, which highlights the primary contribution of the capped section of MWCNT to the pull-out force. A simple empirical formula was proposed based on the numerical results to predict the pull-out force for an arbitrary pull-out in a given MWCNT directly from the diameter of the immediate outer wall on the sliding interface. Moreover, tensile tests for MWCNTs with and without acid-treatment were performed with a nanomanipulator inside a vacuum chamber of a scanning electron microscope (SEM) to validate the present empirical formula. It was found that the theoretical pull-out forces agree with the present and some previous experimental results very well.

A Mouse Model of Early-Onset Renal Failure Due to a Xanthine Dehydrogenase Nonsense Mutation

Chronic kidney disease (CKD) is characterized by renal fibrosis that can lead to end-stage renal failure, and studies have supported a strong genetic influence on the risk of developing CKD. However, investigations of the underlying molecular mechanisms are hampered by the lack of suitable hereditary models in animals. We therefore sought to establish hereditary mouse models for CKD and renal fibrosis by investigating mice treated with the chemical mutagen N-ethyl-N-nitrosourea, and identified a mouse with autosomal recessive renal failure, designated RENF. Three-week old RENF mice were smaller than their littermates, whereas at birth they had been of similar size. RENF mice, at 4-weeks of age, had elevated concentrations of plasma urea and creatinine, indicating renal failure, which was associated with small and irregularly shaped kidneys. Genetic studies using DNA from 10 affected mice and 91 single nucleotide polymorphisms mapped the Renf locus to a 5.8Mbp region on chromosome 17E1.3. DNA sequencing of the xanthine dehydrogenase (Xdh) gene revealed a nonsense mutation at codon 26 that co-segregated with affected RENF mice. The Xdh mutation resulted in loss of hepatic XDH and renal Cyclooxygenase-2 (COX-2) expression. XDH mutations in man cause xanthinuria with undetectable plasma uric acid levels and three RENF mice had plasma uric acid levels below the limit of detection. Histological analysis of RENF kidney sections revealed abnormal arrangement of glomeruli, intratubular casts, cellular infiltration in the interstitial space, and interstitial fibrosis. TUNEL analysis of RENF kidney sections showed extensive apoptosis predominantly affecting the tubules. Thus, we have established a mouse model for autosomal recessive early-onset renal failure due to a nonsense mutation in Xdh that is a model for xanthinuria in man. This mouse model could help to increase our understanding of the molecular mechanisms associated with renal fibrosis and the specific roles of XDH and uric acid. © 2012 Piret et al.

Immunogenetic characteristics of immunoglobulin E in allergic disease

Patients with allergic diseases produce an excess of allergen-specific IgE, the specific effector molecule that triggers allergic reactions. The provocation for this excess IgE production is still uncertain. Current ideas include oligoclonal expansion of allergen-specific B cells emanating from germinal centres, activation by superantigen of a subset of B cells, or polyclonal B cells class switching to IgE due to an IL-4 predominance. Additionally, genetic elements contribute to a propensity for increased allergen-specific IgE production. The procedure of RT-PCR allows for amplification of infrequent IgE mRNA transcripts from B cells of atopic individuals, and so facilitates examination of expressed Ig cDNA sequences. Better knowledge of the molecular characteristics of IgE produced by patients with allergic diseases would elucidate the immunogenetic basis for elevated allergen-specific IgE levels. The 'immunogenetic footprint' of IgE transcripts may elucidate the origin and activation of IgE-producing B cells in allergic disease. Here we review studies of the immunogenetic features of IgE in allergic diseases, highlighting the major advances and the experimental limitations.

Immunopathogenesis of ankylosing spondylitis

Ankylosing spondylitis is a model immunogenetic disease with major common and rare genetic risk factors, likely environmental contributors to its pathogenesis and, to date, no treatment that has been shown to induce disease remission in long-term studies. The discovery of the association of HLA-B27 with the disease in the early 1970s triggered extensive efforts to elucidate the mechanism of this association. However, the precise role of HLA-B27 in ankylosing spondylitis pathogenesis remains unclear. In recent years, rapid progress made in the discovery of non-MHC genes involved in susceptibility to ankylosing spondylitis has combined with increasing ability to investigate the immune system to make rapid progress in unraveling the etiopathogenesis of the condition. © 2013 Future Medicine Ltd.

Significant deterioration in nanomechanical quality occurs through incomplete extrafibrillar mineralization in rachitic bone: Evidence from in-situ synchrotron X-ray scattering and backscattered electron imaging

Bone diseases such as rickets and osteoporosis cause significant reduction in bone quantity and quality, which leads to mechanical abnormalities. However, the precise ultrastructural mechanism by which altered bone quality affects mechanical properties is not clearly understood. Here we demonstrate the functional link between altered bone quality (reduced mineralization) and abnormal fibrillar-level mechanics using a novel, real-time synchrotron X-ray nanomechanical imaging method to study a mouse model with rickets due to reduced extrafibrillar mineralization. A previously unreported N-ethyl-N-nitrosourea (ENU) mouse model for hypophosphatemic rickets (Hpr), as a result of missense Trp314Arg mutation of the phosphate regulating gene with homologies to endopeptidase on the X chromosome (Phex) and with features consistent with X-linked hypophosphatemic rickets (XLHR) in man, was investigated using in situ synchrotron small angle X-ray scattering to measure real-time changes in axial periodicity of the nanoscale mineralized fibrils in bone during tensile loading. These determine nanomechanical parameters including fibril elastic modulus and maximum fibril strain. Mineral content was estimated using backscattered electron imaging. A significant reduction of effective fibril modulus and enhancement of maximum fibril strain was found in Hpr mice. Effective fibril modulus and maximum fibril strain in the elastic region increased consistently with age in Hpr and wild-type mice. However, the mean mineral content was ∼21% lower in Hpr mice and was more heterogeneous in its distribution. Our results are consistent with a nanostructural mechanism in which incompletely mineralized fibrils show greater extensibility and lower stiffness, leading to macroscopic outcomes such as greater bone flexibility. Our study demonstrates the value of in situ X-ray nanomechanical imaging in linking the alterations in bone nanostructure to nanoscale mechanical deterioration in a metabolic bone disease. Copyright

Diamond-Graphite Hybrids And The Nature Of Amorphous-Carbon And Diamond-Like Carbon

The nature of amorphous carbon has been explored by molecular mechanics by examining the structures of species such as C84Hx and C150Hx, wherein the percentage of sp(3) carbons is progressively increased in a graphitic network. The nature of diamond-like carbon has been similarly investigated by examining the structures of C84Hx and C102Hx where the percentage of sp(2) carbons is varied in an sp(3) network. The dependence of the average coordination number as well as the sp(3)/sp(2) atom ratio on the atom fraction of hydrogen has been investigated in light of the random covalent network model.