BITS Faculty Publications
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Item Mechanistic insights into the C-myc G-quadruplex and berberine binding inside an aqueous two-phase system mimicking biomolecular condensates(ACS, 2024-08) Patra, SatyajitWe investigated the binding between the c-MYC G-quadruplex (GQ) and berberine chloride (BCl) in an aqueous two-phase system (ATPS) with 12.3 wt % polyethylene glycol and 5.6 wt % dextran, mimicking the highly crowded intracellular biomolecular condensates formed via liquid–liquid phase separation. We found that in the ATPS, complex formation is significantly altered, leading to an increase in affinity and a change in the stoichiometry of the complex with respect to neat buffer conditions. Thermodynamic studies reveal that binding becomes more thermodynamically favorable in the ATPS due to entropic effects, as the strong excluded volume effect inside ATPS droplets reduces the entropic penalty associated with binding. Finally, the binding affinity of BCl for the c-MYC GQ is higher than those for other DNA structures, indicating potential specific interactions. Overall, these findings will be helpful in the design of potential drugs targeting the c-MYC GQ structures in cancer-related biocondensates.Item Density Functional Investigation of Structure and Stability of Gen and GenNi (n = 1−20) Clusters: Validity of the Electron Counting Rule(ACS, 2010-01) Bandyopadhyay, DebashisStructure and electronic properties of neutral and cationic pure and Ni-doped Ge clusters containing 1−20 Ge atoms are calculated within the framework of linear combination of atomic orbitals density functional theory. It is found that in clusters containing more than 8 Ge atoms the Ni atom is absorbed endohedrally in the Ge cage. Relative stability of Ni-doped clusters at different sizes is studied by calculating their binding energy, embedding energy of a Ni atom in a Ge cluster, highest-occupied molecular orbital to lowest-unoccupied molecular orbital gap, and the second-order energy difference. Clusters having 20 valence electrons turn out to be relatively more stable in both the neutral and the cationic series. There is, infact, a sharp drop in IP as the valence electron count increases from 20 to 21, in agreement with predictions of shell models. Relevance of these results to the designing of Ge-based superatoms is discussed.Item Coordination Chemistry Based Approach to Lipophilic Inhibitors of 1-Deoxy-d-xylulose-5-phosphate Reductoisomerase(ACS, 2009-10) Sundriyal, Sandeep1-Deoxy-d-xylulose-5-phosphate reductoisomerase (DXR) in the non-mevalonate pathway found in most bacteria is a validated anti-infective drug target. Fosmidomycin, a potent DXR inhibitor, is active against Gram-negative bacteria. A coordination chemistry and structure based approach was used to discover a novel, lipophilic DXR inhibitor with an IC50 of 1.4 μM. It exhibited a broad spectrum of activity against Gram-negative and -positive bacteria with minimal inhibition concentrations of 20−100 μM (or 3.7−19 μg/mL).Item Gas Phase Spectroscopic Studies of Hydroquinone Dimer(ACS, 2004-09-23) Chakraborty, ShamikHydroquinone is one of the molecules that forms organic inclusion compounds, which have a wide range of commercial and technological applications. A lot of work has been done on this important molecule in the solid phase, but so far no work has been reported on its homoclusters in the gas phase. We report here the spectroscopic study of the hydroquinone dimer carried out under the jet-cooled conditions using the resonantly enhanced multiphoton ionization (REMPI) technique. The REMPI spectrum was quite rich in terms of the low-frequency transitions indicative of substantial geometry change upon excitation. The number of possible conformers formed in the jet was identified using the hole-burning spectroscopy. Ab initio calculations at the Hartree−Fock, density functional theory level using B3LYP functional and MP2 level for the ground state and the CIS level for the first excited state were carried out to understand the Franck−Condon activity in the spectrum as well as the number of possible stable conformers.Item Fine Mesh Computational Fluid Dynamics Study on Gas-Fluidization of Geldart A Particles: Homogeneous to Bubbling Bed(ACS, 2016-02-29) Ray, SaumiGas-fluidization of Geldart A particles was simulated for a domain of lab-scale dimensions. Hydrodynamics of homogeneous regime and transition to bubbling were studied. In this context a detailed fine mesh simulation study is presented for the first time, using the state-of-the-art two-fluid model (TFM). The effect of particle density was investigated. The fine mesh simulations were analyzed for insights into bed transition from homogeneous to bubbling regime and the effect of interparticle forces (IPFs). Simulations reveal that transition to bubbling occurs over a velocity range rather than at a discrete velocity. We propose an index to quantify the effect of IPFs on bed expansion. During homogeneous expansion this IPF index was found to drop exponentially with velocity. It became negligible as bubbling ensued which is in line with the literature. The simulated average bed voidage was found comparable to the corresponding Eulerian−Lagrangian and experimental data.Item Structure-Based Drug Design of Novel Aurora Kinase A Inhibitors: Structural Basis for Potency and Specificity(ACS, 2009-01-13) Shukla, ParitoshAurora kinases have emerged as attractive targets for the design of anticancer drugs. Through structure-based virtual screening, novel pyrazole hit 8a was identified as Aurora kinase A inhibitor (IC50 = 15.1 μM). X-ray cocrystal structure of 8a in complex with Aurora A protein revealed the C-4 position ethyl carboxylate side chain as a possible modification site for improving the potency. On the basis of this insight, bioisosteric replacement of the ester with amide linkage and changing the ethyl substituent to hydrophobic 3-acetamidophenyl ring led to the identification of 12w with a ∼450-fold improved Aurora kinase A inhibition potency (IC50 = 33 nM), compared to 8a. Compound 12w showed selective inhibition of Aurora A kinase over Aurora B/C, which might be due to the presence of a unique H-bond interaction between the 3-acetamido group and the Aurora A nonconserved Thr217 residue, which in Aurora B/C is Glu and found to sterically clash with the 3-acetamido group in modeling studies.Item Photoelectrochemical Water Splitting by In2S3/In2O3 Composite Nanopyramids(ACS, 2020) Basu, MrinmoyeePhotoelectrochemical (PEC) water-splitting reaction becomes an important path for the requirement of the fulfillment of global energy demand. For PEC water-splitting reactions, here In2O3 is grown in situ in the nanopyramidal structure of In2S3 via a simple hydrothermal technique. The limited supply of S2– in the reaction medium plays an important role in the development of In2O3 along with In2S3, leading to the In2S3/In2O3 nanocomposite. The In2S3/In2O3 nanocomposite shows an enriched carrier density compared to bare In2S3. The optimum amount of In2O3 in the composite helps to achieve efficient photoactivity. In addition, the observed negative shift of the flat band potential of the nanocomposite demonstrates the assistance of the early onset potential. Moreover, the In2S3/In2O3 nanocomposite shows improved visible light absorbance due to its pyramidal nanostructure. It can generate a high photoconversion efficiency of ∼0.55% at 0.77 V versus the reversible hydrogen electrode (RHE) in 0.5 M Na2SO4. The stability of the In2S3/In2O3 nanopyramid is determined under chopped illumination condition for 1000 s, which shows decay in the stability in the Na2SO4 medium. Importantly, to widen the applicability of the In2S3/In2O3 composite, the PEC water-splitting performance is determined in 3.5% saline water. Under such a corrosive environment, In2S3/In2O3 can show efficient photoactivity as well as outstanding stability. It can generate a photocurrent density of 0.83 mA/cm2 under an applied potential of 1.18 V versus the RHE. The present research suggests the development of the In2S3/In2O3 nanopyramid composite as a chloride environment-withstanding and high corrosion-resistant photoanode. The advantage of the faceted nanopyramidal structure and the composite is focused here. It paves an avenue for the development and engineering of highly persistent seawater-splitting photoelectrodes, which provides an opportunity to use the vast seawater on the Earth as an energy carrier.Item Amide-to-Amide Hydrogen Bonds in the Presence of a Pyridine Functionality: Crystal Structures of Bis(pyridinecarboxamido)alkanes(ACS, 2005-09-09) Sarkar, MadhushreeCrystal structures of bis(4-pyridinecarboxamido)alkane and bis(3-pyridinecarboxamido)alkane derivatives were determined and analyzed in terms of hydrogen bond networks. Seven crystal structures out of the eight structures studied exhibited amide-to-amide hydrogen bonds. Out of these seven, five form the anticipated β-sheet network whereas two structures form a doubly interpenetrated (4,4)-network. In only one structure does the pyridyl group interfere in the amide-to-amide hydrogen bond, leading to the formation of an N−H···N hydrogen bond network. The analyses and rationalization of these structures and also related derivatives in the Cambridge Structural Database suggested that amide-to-amide hydrogen bond formation depends on the interplanar angle between amide and pyridine groups.Item Highly Selective Detection of H+ and OH– with a Single-Emissive Iridium(III) Complex: A Mild Approach to Conversion of Non-AIEE to AIEE Complex(ACS, 2015) Roy, Ram Kinkar; Laskar, Inamur RahamanA greenish-blue emissive bis-cyclometalated iridium(III) complex with octahedral geometry was synthesized in a convenient route where a bulky substituted ligand, N1-tritylethane-1,2-diamine ligand (trityl-based rotating unit) (L1), was coordinated to iridium(III) in nonchelating mode, [Ir(F2ppy)2(L1)(Cl)], [F2ppy = 2-(2′,4′-difluoro)phenylpyridine; L1 = N1-tritylethane-1,2-diamine], 1. The purpose of introducing a rotor in 1 was anticipated to initiate aggregation-induced emission (AIE) activity in it. The presence of a secondary amine in L1 has attributed to 1 the ability to sense acids. The mechanism of this change in 1 under acidic medium was explored. A bright yellow emissive complex was formed on exposing 1 to hydroxide ion, which was isolated, characterized, and identified as a new aggregation-induced enhanced emission (AIEE) active complex. The detection limit of hydroxide ion was determined to 126 nM. Ground- and excited-state properties of 1 were investigated using DFT- and TD-DFT-based calculations, and several important aspects of the experimental facts were validated.Item Fine Mesh Computational Fluid Dynamics Study on Gas-Fluidization of Geldart A Particles: Homogeneous to Bubbling Bed(ACS, 2016) Sande, Priya CGas-fluidization of Geldart A particles was simulated for a domain of lab-scale dimensions. Hydrodynamics of homogeneous regime and transition to bubbling were studied. In this context a detailed fine mesh simulation study is presented for the first time, using the state-of-the-art two-fluid model (TFM). The effect of particle density was investigated. The fine mesh simulations were analyzed for insights into bed transition from homogeneous to bubbling regime and the effect of interparticle forces (IPFs). Simulations reveal that transition to bubbling occurs over a velocity range rather than at a discrete velocity. We propose an index to quantify the effect of IPFs on bed expansion. During homogeneous expansion this IPF index was found to drop exponentially with velocity. It became negligible as bubbling ensued which is in line with the literature. The simulated average bed voidage was found comparable to the corresponding Eulerian−Lagrangian and experimental data.