PhD Theses (Chemistry)

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    (A) Computational Study of human Islet Amyloid Polypeptide Aggregation and its Inhibition
    (2023) Roy, Rituparna
    The aggregation of human islet amyloid polypeptide (hIAPP) stands at the nexus of Type II Diabetes (T2D) pathogenesis. In order to counteract the advancement of this disease, a possible therapeutic avenue is to curb the misfolding and aggregation of hIAPP. Within this thesis, we embark on the intricate journey of hIAPP aggregation, coupled with the myriad classes of compounds harboring the potential to impede this process. In Chapter I, a foundation is laid through the introduction of hIAPP and an array of different categories of inhibitors, each contributing to the modulation of hIAPP aggregation. A brief discussion of the molecular dynamics simulation methodology, which is a vital framework underpinning our study is followed. Thereafter, Chapter II takes the helm into venturing the different conformational states of an amyloid prone fragment of hIAPP, hIAPP20-29, via Markov State Modelling. Here, the transition pathway between the metastable states is analysed, which are crucial for the misfolding of hIAPP. Chapter III explores the influence of two small biological molecules on hIAPP aggregation. In Part (a), we have explored the effect of norepinephrine, which is a common neurotransmitter, on the amyloidogenesis of hIAPP. In Part (b), a new aspect of adenosine triphosphate (ATP), other than being the energy source for biochemical processes, is inquired. This chapter, thus, enlighten us about the diversity of the molecular structures that can modulate the aggregation of hIAPP and the effect of these structures on the activity of the inhibitors. Chapter IV turns the discourse towards peptides and peptidomimetics, probing their roles in shaping the aggregation narrative. Two such inhibitors are investigated, both of which are extracted from the amyloid core region of hIAPP, i.e., N22FGAIL27. In Part (a), this hIAPP fragment is replaced with all D-amino acids, and is used to prohibit the self-assembly of full-length hIAPP. In Part (b), a conformationally restricted element, aminobenzoic acid is incorporated into NFGAIL, by replacing Ile26 and/or Gly24 residues. Here, three different isomers of aminobenzoic acid is used, i.e., (β, γ, δ). β- and γ- containing peptidomimetics successfully prevent the aggregation of hIAPP, but δ- peptidomimetics promote it, highlighting the contrasting behaviour of the isomers. Hence, in this chapter, we have conveyed the effect of stereochemistry of the amino acid residues or modified organic moieties on the inhibitory potential of peptides or peptidomimetics. A novel dimension unfurls in Chapter V, where the alliance between boron nitride nanomaterials and hIAPP aggregation is explored. The curvature of the nanomaterials is observed to have an impact on their interaction site with hIAPP. Finally, Chapter VI unfurls a tapestry of conclusions, weaving together the diverse threads from our journey. In unity, this thesis stands as an ardent exploration, deciphering the aggregation pathway of hIAPP and unveiling a constellation of agents poised to intervene. The information regarding the structure and activity of the various inhibitors provides a holistic comprehension of the crucial molecular scaffolds and properties required to design drugs for combatting T2D's relentless advance.
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    (A) Progressive Endeavor to Develop Efficient Organic Chromogenic and Fluorogenic Sensing Probes for Ionic and Neutral Guest
    (2016) Samanta, Soham
    The overall thesis elucidates some important results in the field of developing chemosensors for some important ionic and neutral guests. Some new aggregation induced emission (AIE) active probes (Schiff base) have been developed here and the role of AIE in sensing outcome to overcome aggregation caused quenching (ACQ) effect has been discussed. Majority of the probes, reported in this thesis have naked eye sensing ability. In general, the research works describe a clear insight of the design principle involved in developing simple optical sensing probes which can detect various ionic and neutral guests in fully or partially aqueous solution and/or inside living cells. AIE-active probe L1 exhibited a selective TURN-ON fluorescence response towards Al3+ in solution and in live HeLa cells. Subsequently the highly emissive L1-Al3+ ensemble were used to track the ct-DNA by a dose dependant fluorescence quenching. L1 can also selectively sense Cu2+ through sharp colorimetric response. So, basically L1 is a metal ion responsive colorimetric and fluorescent probe which additionally can track DNA. On the other hand, a versatile fluorescent probe (L2) has demonstrated highly sensitive dual yet discerning sensing of SO32- and SO42–/HSO4– over competing analytes with beneficial attributes such as sensing in completely aqueous medium and an extremely fast response time. Moreover, L2 holds considerable potential as an analytical tool to investigate the physiological implications of sulfate/sulfite derivatives in cell by demonstrating differential intracellular sensing of SO32– and SO42-. Another AIE active probe L3 can sense multiple targets at a time. It can sense cations Al3+ and Zn2+ through individual Turn-On fluorescence responses and Cu2+ through colorimetric changes. Interestingly, L3 can also selectively sense anion fluoride by specific colorimetric response. Lastly, sensing probe L4 can discriminate geometrical isomers (Maleic Acid vs Fumaric Acid) by colorimetric as well as fluorescent changes as it can detect Maleic Acid over various other carboxylic acids in solution and food additives.
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    (A) Study on Aromatic Carboxylic Acids as Ligands and Receptors
    (2009) Karmakar, Anirban
    Coordination chemistry of metal carboxylates are of great interest due to its potential applications in material and biological chemistry. Supramolecular architecture of metal carboxylates can be directly constructed with metal ions in various coordination geometries in combination with multifunctional ligands. The directional and molecular recognition properties of carboxylic acids and its derivatives are controlled by supramolecular interaction like hydrogen bonding, D-D stacking, weak electrostatic interactions and van der Waals forces. The thesis deals with the synthesis, characterization and structural aspects of some first row transition metal carboxylates along with the study of molecular/anion recognition properties of carboxylic acid derivatives. Thus, the research work carried out is basically focused on the synthesis, characterization, and structural elucidation along with understanding of physical properties such as fluorescence emission. The structural features are investigated with an objective to understand the factors, which control the formation of basic carboxylate frameworks or secondary building block units. The content of the thesis is divided into six chapters which are described below....
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    Activity studies of indoleamine 2,3-dioxygenase 1 enzyme
    (2018) Roy, Ashalata
    Immunosuppressive enzyme, indoleamine 2,3-dioxygenase 1 (IDO1) plays a pivotal role in regulating the metabolism of L-tryptophan (L-Trp) through kynurenine pathway, which is a well-established therapeutic target for the treatment of diseases associated with immunosuppression. Under pathophysiological conditions the expression of IDO1 enzyme from its mRNA gets highly up-regulated in response to inflammatory signals (like interferon-γ) within the immune system. Up-regulation of the IDO1 enzyme is directly related with several diseases including cancer, neurodegenerative disorders (Alzheimer’s disease), Huntington’s disease, schizophrenia, depression, age-related cataract, and HIV-1 encephalitis. Hence, proper understanding of the IDO1 activity will be helpful for the development of novel IDO1 inhibitors as emerging immuno-oncology agents.On the basis of the experimental works performed during the research period, the content of the thesis entitled “Activity Studies of Indoleamine 2,3-Dioxygenase 1 Enzyme” have been divided into five chapters. Chapter 1 of the thesis provides an overview of IDO1 enzyme and demonstrates the activity and regulation of this immunosuppressive enzyme in medicine, life science and other related research fields. These enzymes are responsible for the degradation of an essential amino acid L-Trp, which is required for the protein synthesis and other important metabolic functions. IDO1 mediated depletion of the local L-Trp concentration and accumulation of the kynurenine metabolites regulate the local immunosuppression.
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    Aggregation Aptitude in Rigid and Flexible Molecular Systems: Comparative Photophysical and Analytical Studies
    (2023) De, Sagnik
    This thesis elucidates the important consequences in comprehension of aggregation outlook of flexible and rigid frameworks and their response towards environmentally and biologically relevant analytes. L1-L3 is designed which shows a comparative aggregation aptitude with chain length variation in amphiphiles. The entire photophysical study on aggregation process is dealt with. Then, these synthesized amphiphiles are used in creating hydrophobic surfaces due to their inherent property of hydrophobicity. Additionally, the concept of Photoinduced Electron Transfer or PET is applied in the detection of nitro antibiotics via fluorescence quenching. This chemo sensing is probed in biofluids viz; simulated gastric and body fluid. Next, a layout is provided where a comparative study between an amphiphile and a non-amphiphile is presented. The compounds designed and synthesized were substituted urea and amide (L4 & L5). Studies on aggregation-induced emission are shown by a binary solvent system DMF-Water. Morphological change is depicted on solvent switching by electronic microscopy imaging. Both solid and solution state emissive property is described. A unique photophysical prospect is shown in this piece of work i.e., light harvesting. Förster resonance energy transfer or FRET mechanism delivers the basis for this light-harvesting phenomenon between the amphiphile and a commercial dye; Rhodamine. Again, PET is applied to detect nitro explosives in water is demonstrated. This detection proceeds via disaggregation of the aggregated state. In the allied chapter, functionalization of amphiphile was done: a comparative outline on substituted urea and thiourea (L4 & L6). Apart from describing aggregational features through spectroscopy and microscopy, an edge on the chemo-sensing property is done. The thiourea selectively recognizes Hg (II) ions in an aqueous solution due to the soft-soft interaction between the sulfur atom and the heavy metal. Turn-On or fluorescence emission enhancement is achieved even in the presence of heavy metal during the chemosensing process. The toxic metal ion interaction causes disaggregation of the aggregated amphiphile confirmed through DLS and FESEM experiments. The chemo-sensing experiments are done in various real samples. Moreover, The Hg(II)-amphiphile ensemble detects sulfide ions in the water among all other sulfur-containing anions and amino acids.
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    Aldehyde deformylation by nonheme metal complexes – a mechanistic study
    (2021) Nag, Sayanta Sekhar
    The emission of greenhouse gases and particulate matter has profoundly impacted climate change by unsettling the earth's radiation balance. Fossil fuel burning is the primary reason for increasing the concentration of greenhouse gases and aerosol particles. Many of the so-called first-world countries are reducing their fossil fuel consumption substantially. In economically progressing countries like India, there is a lot of complexity depending on those alternatives. The crude oil refinery industry also produced a wide variety of commodity products for everyday uses. Biomass has particular interest among scientists because it can reduce the dependencies on fossil feedstock by generating both fuels and the necessary chemicals in a net carbon neutral biosynthetic pathway. In a petroleum refinery industry, apart from the extensive use of fuels, hydrocarbons are the primary raw material for producing various commodity products. The prospect of using the biosynthesis of hydrocarbon as an alternative to the crude oil refinery systems accelerated the fascination towards mechanistic enzymology.
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    (An) Endeavor in Receptor Design for Solid State Recognition of Anions/Hydrated Anions
    (2015) Hoque, Md. Najbul
    The contents of this thesis entitled “An Endeavor in Receptor Design for Solid State Recognition of Anions/Hydrated Anions” have been divided into seven chapters based on the results of experimental work carried out during the research period. Chapter 1: Introduction This chapter provides a brief introduction on ‘supramolecular host-guest chemistry’ of ionic species with special reference to recognition of anions or hydrated anions. Supramolecular chemistry offer many possible avenues like recognition, catalysis and transport. Anions are ubiquitous in nature. Hence, molecular recognition of anionic species has attracted great interest during the last decades because of the imperative role in various biological and environmental processes. Extensive research effort has been expended toward understanding how host structure influences anion binding with the goal of discovering more effective and more selective anion receptors. A very large number of artificial systems for recognition and sensing of anions have been designed and synthesized by properly exploiting supramolecular concepts. One successful approach for preparing anion hosts has been to synthesize molecules that offer an array of H-bonding sites to the guest. Because H-bonds exhibit directionality, it should be possible to achieve a structure-based recognition for anions of particular shape and size. The binding of anion guests within preorganized macrocyclic systems is relatively more predicated easy to understand supramolecular association but the binding processes of acyclic receptors is unpredictable and very tough to control due to freedom of many conformation. Hence it is great challenge to study receptor-anion assembly of flexible acyclic receptor. Sometimes specially design acyclic receptor forms capsular assemblies which have shown a number of interesting properties e.g. encapsulation of anion/anion–water clusters, capturing aerial CO2 as carbonate, selective salt extraction and anion transportation. On the other hand, Understanding the hydration of anions at the molecular level is thus important as the surface speciation and reactivity of aerosols, which play a key role in atmospheric and oceanic chemical cycles. The characterization of an isolated solvated ion serves to add to information about the solvation properties. As the properties of hydrated ions are quite different from those of isolated ions (in the gas phase) or ions in nonpolar media and are governed by the nature of the surrounding hydration network.
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    Anion and Ion-Pair Directed Self-Assembly of Urea Functionalized Molecules
    (2015) Chutia, Romen
    The thesis consists of five chapters including introduction and experimental sections. The first experimental work viz Chapter 3 describes the evidence of fluoride induced uptake of atmospheric CO2 and its stabilization as HCO3ˉ anion by a structurally simple acyclic 1,3-bis(4-iodophenyl)urea receptor, L1. The in situ formed HCO3ˉ complex (1a) is stabilized by a concert act of hydrogen and halogen bonding donated by the receptors. To the best of our knowledge, 1,3-bis(4-iodophenyl)urea is the simplest of anion receptors that displays a concert act of hydrogen and halogen bonding to stabilize aerial CO2 as HCO3ˉ. While 1,3-bis(4-bromophenyl)urea, L2 has shown completely lacking if halogen-bonding donor ability throughout its entire results. The second experimental work viz Chapter 4 is in two parts. Part 1 deals with a set of three nitrophenyl functionalized tripodal urea scaffolds, L3, L4 and L5 and demonstrate the effect of positional isomerism in anion coordination. The para-isomer (L3) self-assembles into dimeric (pseudo)molecular capsules as observed in carbonate and terephthalate complexes (3a and 3b). On the other hand, the meta-isomer (L4) self-assembles into dimeric capsules only in the presence of inorganic oxyanions (complex 4a), and assembles into a 2D sheet-like structure in the presence of terephthalate dianion (4b). In contrast to L3 and L4, structural authentication of the ortho-isomer (L5) in the presence of different oxyanions was not fruitful presumably due to the steric effect provided by the −NO2 group at the ortho-position, which hinders the facile inclusion and coordination of an anion due to electrostatic factor, as confirmed by 2D-NOESY NMR analysis of the free receptor. Part 2 of the Chapter 4 deals with the para-isomer (L3), which in association with 18-crown-6-ether self-assembles into an integrated 1D coordination polymer in the presence of K2CO3 (complex 3d). The last Chapter is about the recognition of tetrameric mixed phosphate clusters by L3 in its neutral and charged state. Receptor L3 self-assembles, in the presence of excess n-TBA(H2PO4), into a tetrahedral molecular cage by encapsulation of a tetrameric tetrahedral mixed phosphate cluster (3e). Further in the presence of H3PO4, L3 self-assembled with side-cleft bonded cyclic planar tetrameric anion-acid cluster (3f).
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    Anomalous Modulation of Photoinduced Electron Transfer of Coumarin Acceptors in Solvent Mixtures: Effect of Excited-State Hydrogen Bonding
    (2015) Barman, Nabajeet
    The thesis describes our results on anomalous fluorescence modulation to illustrate the much debated role of hydrogen bonding on photoinduced electron transfer (PET). We first experimentally confirmed the theoretical prediction that PET becomes facilitated through donoracceptor H-bonding between coumarin 102 (C102, acceptor) and phenol (donor). Thereafter we showed that PET depends unusually on the mole fraction of H-bond donor (aniline) in a mixture where an additional inert component is present along with the donor. The results may be attributed to possible modulation of polarity or H-bonding environment around the acceptor in the mixture. The anomalous PET behaviour retains even in similar polarity mixture of aniline (AN) and N,N-dimethylaniline (DMA) which demonstrates that the effect is primarily due to H-bonding and is discussed in the light of competitive H-bonding concept. Later we also showed that the competitive H-bonding concept can account for the anomalous behaviour of PET for a different H-bonding donor- phenol as well. We have utilized fluorescence up-conversion measurements to detect much more ultrafast H-bond assisted PET of a better electron acceptor coumarin 153 (C153) in AN-cyclohexane mixture.
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    Application of Modified Smooth Exterior Scaling Method to Study Auger and Shape Resonances in Different Atomic and Molecular Systems
    (2024) Banuary, Mwdansar
    This thesis focuses on the application of modified smooth exterior scaling (MSES) as an efficient method to impose outgoing boundary conditions in e-atom and e-molecule scattering resonances. This is the first time that the MSES method has been applied to calculate energies and widths of Auger and shape resonances in three-dimensional many-body electron systems. MSES converts the divergent resonance wave functions into square integrable ones thereby making the study of temporary bound states (resonance states) amenable to bound state electronic structure methods. The main objective of this thesis is to formulate the MSES method in bivariational SCF and electron propagator methods.
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    Application of Oxyma Based Reagents in Relevant Organic Transformations
    (2022) Kalita, Tapasi
    The work presented in this thesis is mainly focused on the different applications of the coupling reagent ortho-NosylOXY (I) to synthesize acetals, thioacetals, ureas, carbamates, and thiocarbamates. A newer methodology is also described to convert carboxylic acids into amides, dipeptides, esters, and hydroxamates. In chapter 1, the importance of the compounds mentioned above, their existing methodologies, and their drawbacks are discussed. Chapter 2 describes the synthesis of acetals and thioacetals from aldehydes using ortho-NosylOXY . In chapter 3, the racemization-free synthesis of ureas, carbamates, and thiocarbamates from carboxylic acids via Curtius rearrangement using o-NosylOXY is demonstrated. The mechanism study of the Beckmann rearrangement from ketoxime to amide using o-NosylOXY is extended in chapter 4. Finally, in chapter 5, a one-pot protocol to synthesize amides, peptides, esters, and hydroxamates using Oxyma and thionyl chloride with minimal racemization is proposed.
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    Application of Reconstructed Layered Materials for Environmental Energy Harvesting
    (2021) Deka, Jumi
    The present thesis, entitled as “Application of Reconstructed Layered Materials for Environmental Energy harvesting” is divided into six chapters. Chapter 1 contains a general overview of 2D materials, exfoliation techniques and their application in energy harvesting systems. Chapter 2 elaborates the fabrication of multifunctional soil membranes by tuning the structure of ubiquitous soil components, viz. clay and humic acids. Crosslinking of exfoliated clay layers with purified humic acids not only conferred mechanical strength but also enhanced chemical robustness of the membranes. The percolated network of molecularly sized channels of the soil membranes exhibits characteristic nanofluidic phenomena which is exploited to harvest energy from salinity gradient. Electrical conductivity is induced to otherwise insulating soil membranes by heating in an inert atmosphere, without affecting their nanofluidic ionic conductivity. Strips of heated membranes shown to exhibit excellent sensitivity towards NH3 gas under atmospheric conditions. In chapter 3, the complementary charge transfer activities of boron (B-r-GO) and nitrogen (N-r-GO) doped reduced graphene oxide (r-GO) flakes are exploited to extract energy from serene water resources. B-r-GO and N-r-GO samples prepared by annealing graphene oxide sheets with boric acid and urea were individually coated on cellulose membranes to fabricate B-r-GO/N-r-GO devices. DFT calculations were carried out to study charge transfer activities with water molecules. In chapter 4, we demonstrate the fabrication of a highly robust, inflammable, and pressure-responsive energy device. The energy device was prepared by pressing a polydiallyldimethylammonium chloride (PDDA) doped nanofluidic membrane of natural vermiculite clay (PDDA-VM) on kitchen-grade aluminium foil (PDDA-VM/Al) consumes atmospheric water molecules as the cathode reagent and aluminium atoms at the anodic reaction. Remarkably, the clay-based energy devices exhibit excellent resistance to fire. Moreover, multiple devices can be assembled to add up the output current and voltage generated by the individual devices to power electronic equipment. In Chapter 5, the principles of metal-water batteries were applied to develop a sustainable pressure responsive energy delivery system. Application of a humble pressure of 56 kPa on agar and glycerol-based hydrogel membrane sandwiched between aluminum foil and nanofluidic V2O5 membrane (Al-gel-VO device) generate opencircuit voltage up to 1.3 V accompanied by an output current of 85 μA (power density = 0.45 Wm-2). Unlike typical humidity powered energy systems, the energy output of the current device is resistant towards the diurnal variations in environmental conditions. Remarkably, both gel and V2O5 membrane can be completely regenerated after damage caused by prolong use or accidents without any deterioration in the energy-efficiencies. Chapter 6 consist of an overall conclusion of the work done during my PhD tenure and the future perspective of the work.
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    Applications of phosphonium- and sulfonium bromide & silica supported perchloric acid for developing new synthetic methodologies
    (2006) Choudhury, Md Lokman Hakim
    This dissertation describes the successful efforts on the development of new synthetic methodologies in protection-deprotection chemistry as well as α- bromination of β-ketoesters and 1,3-diketones employing mainly three versatile reagents acetonyltriphenylphosphonium bromide (ATPB), bromodimethylsulfonium bromide (BDMS) and silica supported perchloric acid. The thesis mainly contains three chapters. Each chapter is divided into two parts viz. Part I and Part II. Part I describes a general review on the usefulness of that particular reagent in various organic transformations and a brief literature survey from the year 1990 to till to date for dealing with that particular transformation investigated. Part II of the each chapter is subdivided into two sections : Section A and Section B which will describe an account of work carried out by the candidate. Chapter I, Part I describes a brief literature review on the application of acetonyltriphenylphosphonium bromide (ATPB) in various organic transformations and a brief survey on desilylation and acetylation.
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    Auxiliary-Assisted C-H Functionalization: Exploring the Realm of C-C and C-Heteroatom Bond Formation
    (2024) Talukdar, Kangkan
    The thesis is segmented into four chapters. The initial chapter delineates a Rh-Catalyzed Tandem C-C/C-N bond formation of quinoxalines with alkynes leading to heterocyclic ammonium salts. The second chapter explores the Pd-Catalyzed sp3 C-H alkoxycarbonylation of 8-methylquinolines using Mo(CO)6 as a CO surrogate. The third chapter showcases the Rh-catalyzed alkenylation of aryl 2-pyridyl ethers with vinyl acetate via sp2 C-H activation. Lastly, the fourth chapter delves into on Ru-catalyzed site selective acetoxylation of aryl 2-pyridyl ethers exploiting vinyl acetate as acetoxylating agent
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    Benzimidazole and Benzothiazole Based Chemosensors For Biologically Important Analytes
    (2015) Gogoi, Abhijit
    This thesis reports the efforts made in the improvisations of certain benzothiazole/benzimidazle functionalized receptors towards colorimetric and/or fluorescent cation and anion sensing in biologically relevant medium. Ninhydrin functionalized benzothiazole probe L1 is an excellent Zn2+ sensor and emits in the NIR (near infrared) region without no interference from the other metal ions. A visual distinction of H2PO4- from other phosphate related anion was also achieved with the probe-Zn2+ ensemble. Such long wavelength emissive chemosensors are very important for fluorescent imaging as they can penetrate much deeper into the sample. Next benzothiazole functionalized schiff base probe L2 senses Zn2+ and Cd2+ ion in physiological medium. The metal ensembles are further found to sensitive to both H2PO4- and PPi anion. Dipodal benzothiazole Schiff base L3 also selectively sense Zn2+ ion in nanomolar level. Furthermore, PPi anion could be separated from H2PO4- with this ‘L3-Zn2+’ ensemble even in the presence of other interfering anions.Direct anion sensing is always superior to that of metal assisted anion sensing but an intriguing task in pure aqueous medium. Aggregation induced emission (AIE) phenomenon could boost the emission intensity in aqueous medium. Benzimidazole functionalized probe L4 demonstrate AIE induced PPi sensing in physiological medium with any assistance from the metal ion. In addition, apart from metal based selectivity study, such benzimidazole functionalized AIE probes could also be applied to study sensing behavior of certain H-donor molecules, such as inorganic acids, organic acids like picric acid, amino acids etc.
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    Beyond Retrosynthetic Analysis:Copper Catalyzed Synthesis of Esters via C--H Functionalization
    (2014) Rout, Saroj Kumar
    Abstract Not Available
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