Locked Nucleic Acid (LNA): An Improved Alternative to DNA for Nanoscale ‘On-Surface’ Nucleic Acid Detection

The research work embodied in the present thesis entitled “Locked Nucleic Acid (LNA): An Improved Alternative to DNA for Nanoscale ‘On-Surface’ Nucleic Acid Detection” deals with the effectiveness of the locked nucleic acid (LNA) probe, which is conformationally more rigid than DNA, is nuclease resistant, and is less susceptible to molecule-surface non-specific interactions, as a better alternative to DNA probe towards development of sensitive, target-specific and robust nucleic acid sensorResearch was carried out under the supervision of Prof. Rupa Mukhopadhyay of Biological Chemistry division under SBS [School of Biological Sciences]Research was conducted under CSIR grant & fellowshi

Fabrication, Characterization and Reactivity of Bio-electrodes

This thesis focuses on understanding of the electrocatalytic reactivity of the bioelectrodes for the O2 reduction reaction or nitric oxide reduction reaction. A number of synthetic methods were attempted to synthesize a modified heme cofactor. The heme cofactors were modified in a way so that they can be covalently attached to the electrode followed by the site specific attachment of the apoprotein onto the electrodes. A variety of spectroscopic tools have been used to probe the spectroscopic features of the active site structure as well as the protein conformations and the reactivity of the heme based bioelectrocatalysts involved in the reduction of O2 or that of nitric oxide.The research was conducted under Dr. Avishek Dey of Inorganic Chemistry division under SCS [School of Chemical Sciences

Gold Electrode Functionalized with Amide SAM: Electron Transfer Properties and Fabrication of Bio-inspired Electrodes

Amide bonds provide primary linkage between amino acids which are basic functional groups in biology. They support complex structures of protein backbones, form scaffolds that transport ions and they mediate electron transfer as well. The entire thesis work had two major objectives. First objective was to study the electron transfer properties through self assembled monolayers (SAMs) containing alkyl and amide linkages. This has been achieved by performing conventional cyclic voltametry and chronoamperometry on alkyl and amide functionalized SAMs terminated with a redox active group like ferrocene (Fc) and hemin. These SAM modified surfaces have been characterized using attenuated total reflection mode FTIR (ATR-FTIR) spectroscopy, X-ray photoelectron spectroscopy (XPS) and surface enhanced Raman spectroscopy (SERS). The goal was to understand how the presence of amide linkages in the electron transfer pathway alters its rate. These rates have been compared with those obtained using straight chain alkane thiols where no amide linkage exists. Individual residues are mutated on SAMs to understand their role in tuning the electron transfer rate. Specifically we are interested in understanding how cysteine and tryptophan residues tune the rate of electron transfer. For this reason alkylthiol SAMs are functionalized with terminal thiol and imidazole groups, which provide coordination sites of transition metal catalysts. In particular heme based catalysts are used which bind to these terminal thiol and imidazole to create bioinspired electrodes (modified electrodes with biological structure or activity can be used for electrochemical investigations). Thiol and imidazole bound bioinspired electrodes can be used for mimicking the active sites of cytochrome P450 and myoglobin, respectively. The electron transfer rate constant as well as the reorganization energies has been determined for these catalysts bound modified surfaces using conventional “Laviron” procedure. Second objective was to study the nature of S-H bond of alkylthiols at the interfaces, forming SAMs on metal (Au/Ag) surfaces. Initially the normal Raman spectra of alkylthiols and deuterated alkylthiols were collected to determine any shift in C-S stretching mode (nCS) and C-S-H bending mode (bCSH) after deuteration. This observation was extended to the detection of SH/SD on surfaces. H/D sensitive SER spectra of a series of thiols forming SAMs on Ag and Au surfaces and NPs have been recorded. The presence of characteristic H/D shifts or the lack of any shift was then used to elucidate the protonation state of thiols in a series of SAMs.Research was carried out under the supervision of Dr. Avishek Dey of the Inorganic Chemistry division of SCS [School of Chemical Sciences

COMPUTATIONAL STUDY OF MECHANISM AND ENERGETICS OF CHEMICAL PROCESSES INVOLVED IN MATERIAL INDUSTRY

The thesis provides insight into electronic structure, complex reaction mechanism, kinetics, and thermochemistry of molecules and processes having industrial interest employing high-level theoretical methods.An introduction to the thesis, containing five chapters, is given in the first chapter to provide an idea about the industrial chemistry. The second chapter briefly describes the computational chemistry and provides a review of theoretical methods. The remaining chapters of the thesis are based on the research papers published in reputed international journals. The original papers have been properly formatted to match the style of the thesis. Each chapter reviews the material presented in two papers.The research was conducted under the supervision of Prof. Abhijit Kumar Das of the Spectroscopy division under SPS [School of Physical Sciences]The research was carried out under CSIR fellowship and research gran

Multifunctional Composite Nanomaterials for Biomedical Applications

Research was conducted under the supervision of Prof. N R Jana of SMS [School of Materials Sciences]Research was carried out under CSIR fellowshi

Population transfer and dissociation control in diatomic molecules in intense pulse lasers

The study of laser molecular interactions continues to be a highly exciting and significant field of research both for probing the intricacies of molecular dynamics as well as to control the different field induced molecular processes. The control aspects of laser molecular interactions have gained prominence in recent times and with the availability of intense ultrashort laser pulses it has become easier to manipulate the desired outcome of the different field induced molecular processes. The study of multiphoton dissociation and population transfer, in presence of a pulsed laser field within the theoretical framework of wavepacket propagation have been discussed in this thesis. The thesis also includes discussions of results related to generation of wavepackets for molecular ions under intense field and the subsequent probing and control of such wavepackets. Small diatomic molecules have been chosen as the model quantum system for this work and this helps in a simple physical interpretation of the complicated dynamical processes involved. The thesis starts with a brief introduction of the current scenario of the laser molecular interaction studies. It also gives an account of the basic objectives of the works undertaken. The rest of the thesis is divided into two parts. The first part deals with the time dependent studies of laser induced molecular dissociation and wavepacket dynamics- their generation, probing and control. The second part includes studies related to laser induced population transfer to particular quantum states in diatomic molecules.The research was carried out under the supervision of Prof. S S Bhattacharya of the Materials Science division under the SMS [School of Materials Science]The research was conducted under the CSIR research grant and fellowshi

Electronic Structure and Magnetic Behaviour of Ultrathin Epitaxial Films and Nanostructures on Surfaces

Controlled fabrication of nanostructures and thin films on well defined substrate surfaces, their stability and exploration of new physical phenomena are important aspects not only for the development of future nanoscale devices but also for the advancement of basic physics research. Self-organized growth at surfaces is one of the most efficient and versatile methods for producing these structures as it offers control over size, shape and organization on the nanometer length scale. Atomic-scale thin films and nanostructures of materials show interesting and unusual behaviour in various physical properties. Molecular beam epitaxy (MBE) is the one of the most sophisticated single crystal thin film growth techniques. MBE provides contamination-free epitaxial nanostructure growth on substrate surfaces with extreme control under ultrahigh vacuum (UHV) environment. This thesis deals with epitaxial growth of nanostructures, mainly by molecular beam epitaxy (MBE), and associated diffusion phenomena, electronic structure, electronic transport and magnetic behaviour. Keeping the potential applications in mind and possible integration with silicon technology, all our investigations involve growth of nanostructures on silicon substrates. Various aspects of MBE-grown Ag and Co thin films and nanostructures on atomically clean silicon substrates have been investigated in the present thesis using in-situ surface science techniques involving microscopy and spectroscopy. This thesis also includes investigation of the diffusion phenomena in parallel nanostripes in n-type Si substrates which have been fabricated by implanting energetic ions from a focused ion beam (FIB) source.Research was carried out under the supervision of Prof. B N Dev of the Materials Science division under SMS [School of Materials Science]Research was conducted under DST grant and IACS fellowshi

Studies of Protein Confirmation in Water and Air/Water Interface by Langmuir Blodgett Technique

Extensive studies on the protein structure and conformation is needed due to variety of reasons. Proteins are suitable for preparing bioactive thin film. The formation of protein monomolecular thin film with lesser aggregation is a current scientific interest for its biological activity for the application of biomedical device fabrication. Apart from these, it is important for biosensor, preparation of biocompatible substrate, preparation of protein based monolayer/multilayer template for the growth of inorganic crystal (biomineralization) etc. The protein aggregation/dissociation has enormous relevance in the study of protein based molecular diseases such Thalasamia, Alzheimer disease, etc. Moreover, the fundamental studies of protein folding/unfolding in biophysics or biochemistry has also relevance in the work. The study of protein aggregation could be studied in Langmuir-Blodgett (LB) trough at the molecular level. This dissertation entitled as “Studies on Protein Conformation in Water and Air/Water Interface by Langmuir Blodgett (LB) Technique” deals with some multi disciplinary work involving the combination of different techniques on the basic study of development and characterization of protein and protein based bioactive thin film at air/water interface and subsequent transfer onto solid substrate. To understand the basic principles behind the these thin film formation, influence of surface treatment, the role of net charge of the system, the study of different aspects of protein-based film on air/water interface and subsequent transfer on a solid substrate is essential. Thus the protein conformation in water and air/water interface as well as in LB films are the focal theme of the proposed research that aims towards the understanding the science behind the various interactions involved in protein conformation. This dissertation comprises of nine chapters and two appendices.The research was carried out under the supervision of Prof. G B Talapatra of the Spectroscopy division under SPS [School of Physical Sciences]The research was conducted under the CSIR grant and CSIR -NET fellowshi

Self Assembling Peptides and Amino Acids based Soft Materials: Functional Gels and Charge Transfer Complexes

This thesis describes the formation of supramolecular hydrogels and organogels from different synthetic amino acid based amphiphiles and semiconducting organic moiety named naphthalenediimide appended peptide based derivatives. Amino acid and peptide derivatives have been synthesized, purified, characterized and studied in details. Their gelation ability in different aqueous and organic (aromatic/aliphatic) solvents has been studied extensively. These gelator molecules self-associated using various non-covalent interactions including intermolecular hydrogen bonds, electrostatic interactions, - staking etc. to form fibrillar assembly that can encapsulate solvent molecules into their interstitial pores to form self-supported gels. These gel materials have been characterized morphologically, structurally and rheologically. Furthermore, different kinds of applications of these gel materials have been explored.Research was carried out under the supervision of Prof. Arindam Banerjee of the Biological Chemistry division under SBS [School of Biological Sciences]Research was conducted under CSIR fellowshi

Theoretical study of structure, dissociation, reaction and thermochemistry of molecules of environmental and industrial interest

The present dissertation entitled “Theoretical study of structure, dissociation, reaction and thermochemistry of molecules of environmental and industrial interest” is submitted to fulfill the requirements for the degree of Doctor of Philosophy (Science) of Jadavpur University. The study has been done for the investigation of electronic structure, metal ligand coordination, potential energy surface of reaction and thermochemistry of molecules having environmental and industrial interest using high-level theoretical methods. This thesis contains five chapters. An introduction of the thesis is given in first chapter for understanding the environment and industrial chemistry. The second chapter describes briefly the computational science, computational chemistry and a review of the theoretical methods. Third chapter deals with the electronic structure and metal ligand coordination observed in some chelates. The fourth chapter gives a theoretical account of the study of the reaction mechanism of an interesting atmospheric reaction. The dissociation channels, thermochemistry and spectroscopy of some molecules of industrial and atmospheric interest are studied in detail in last chapter five.The research was carried out under supervision of Prof. Abhijit Kr. Das of the Spectroscopy division of the SPS [School of Physical Sciences