Faculty Publications
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Item Efficient shape descriptors for feature extraction in 3D protein structures(2007) Ranganath, A.; Shet, K.C.; Vidyavathi, N.Structural Genomics initiatives are generating an increasing number of protein structures with very limited biochemical characterization. Characterization of a protein's function and understanding the specific nature of a protein's binding is a critical part of both protein engineering and structure-based drug discovery. The accurate detection of binding site in these protein structures can be valuable in determining its function. As shape plays a crucial role in bimolecular recognition and function, the development of shape analysis techniques is important for understanding protein structure-function relationships. This paper describes the use of the continuous wavelet transforms (CWT) for characterizing shape features of 3D protein structures. The goal is to explore the CWT as a multiscale tool to generate rotation- and translation-invariant shape features. © 2007 IOS Press. All rights reserved.Item Nickel(II) complex of p-[N,N-bis(2-chloroethyl)amino]benzaldehyde-4-methyl thiosemicarbazone: Synthesis, structural characterization and biological application(Elsevier Ltd, 2013) Sankaraperumal, A.; Karthikeyan, J.; Nityananda Shetty, A.N.; Lakshmisundaram, R.New complex of Ni(II) with p-[N,N-bis(2-chloroethyl)amino]benzaldehyde-4- methyl thiosemicarbazone (CEAB-4-MTSC) have been synthesized and characterized by elemental analysis, IR, electronic, 1H NMR spectroscopy. The crystal structure of the free ligand and complex has been determined by single crystal X-ray diffraction technique. In the complex, thiosemicarbazone ligand is coordinated to nickel through (1:2 complex) SNNS mode. The complex crystallizes in the triclinic with space group P1?. The complex has been tested for their antibacterial activity against various pathogenic bacteria. From this study, it was found out that the activity of complex reaches the effectiveness of the conventional bacteriocide Streptomycin compared to simple ligand. © 2012 Elsevier Ltd. All rights reserved.Item Cobalt pincer complex catalyzed Suzuki-Miyaura cross coupling – A green approach(Elsevier B.V., 2017) Kumar, L.M.; Badekai Ramachandra, B.A series of cobalt complexes with tridentate pincer ligands were synthesized to study their catalytic activity in Suzuki-Miyaura coupling reactions. Cobalt complexes, C-1, C-2, C-3 bearing asymmetrical PNCOP pincer ligand [C6H4-1-(NHPPh2)-3-(OPPh2)] (L-1) and symmetrical PNCNP, PNNNP pincer ligands [C6H4-2,6-(NHPPh2)2] (L-2) and [C5H3N-2,6-(NHPPh2)2] (L-3) were synthesized by the reaction of diphenylchlorophosphine with m-aminophenol, m-phenylenediamine and 2,6-diaminopyridine respectively in a 1:2 ratio in the presence of triethylamine as a base and tetrahydrofuran as solvent media. The synthesized complexes were examined for their C-C coupling efficiency in cross-coupling between phenyl boronic acid and para substituted bromobenzenes. Effect of variation of the ligand on the catalytic activity of cobalt pincer complex was explored based on the coupling yields. It is observed that as the number of ‘N’ atoms increases in the side arm of the ligand, the donating ability of the ligand increases which leads to the increased catalytic activity of the complex. The symmetrical PNNNP pincer complex (C-3) was found to be more effective as a catalyst among the complexes synthesized and reported in the present study. © 2016 Elsevier B.V.Item Air-Stable Cobalt(II) and Nickel(II) Complexes with Schiff Base Ligand for Catalyzing Suzuki–Miyaura Cross-Coupling Reaction(Pleiades journals, 2018) Ansari, R.M.; Kumar, L.M.; Badekai Ramachandra, B.R.The Co(II) complex [Co{C6H4–1,2-(N=CH–C6H4O)2}] (I) and Ni(II) complex [Ni{C6H4–1,2-(N=CH–C6H4O)2}] (II) with Schiff base of o-phenylenediamine and salicylaldehyde have been synthesized. The structure of the ligand and its complexes were derived on the basis of various techniques such as elemental analysis, mass, FT-IR, electronic spectra and magnetic susceptibility. From the Singal crystal X-ray diffraction (SCXRD) analysis techniques (CIF file CCDC no. 1498772 (II)), it has been confirmed that the Schiff base ligand (L), coordinates to the metal ion in a tetradentate fashion through the nitrogen and oxygen atom. In addition, the square planar geometry of Ni(II) complex also has been confirmed from SCXRD. Electronic spectra, mass spectra, and magnetic susceptibility measurements reveal square planar geometry for the Co(II) complex. Synthesized complexes were used in cross-coupling of arylhalides with phenylboronic acid. The transformation offers products in good yields using 0.02 mmol catalysts loading, thereby proving the efficiency of the complexes as catalysts for Suzuki–Miyaura reaction. © 2018, Pleiades Publishing, Ltd.Item Phase analysis, FTIR/Raman, and optical properties of Fe3BO6 nanocrystallites prepared by glass route at moderate temperature in ambient air(Elsevier B.V., 2018) Kumari, K.In this paper, a facile synthesis method is explored from a supercooled liquid Fe2O3–B2O3 precursor using microwave furnace in order to obtain a single phase Fe3BO6 compound. Study includes X-ray diffraction (XRD), Field emission scanning electron microscope (FESEM), high resolution transmission electron microscopy (HRTEM) images, FTIR/Raman and optical property of sample. The crystal structure and size of the Fe3BO6 crystallites have been characterized in terms of XRD pattern in correlation to the FESEM/HRTEM images. A single phase compound Fe3BO6 of an orthorhombic crystal structure with Pnma space group and average crystallites size D = 49 nm is analyzed from the XRD pattern. IR and Raman bands in the oxygen polygons confer the results of forming Fe3BO6 with a bonded surface layer. UV–visible absorption spectrum over a spectral range 200–800 nm of wavelengths reveals two high-energy bands 222 and 277 nm possibly represent a ligand to metal charge transfer transition while one broad and relatively weak band appears in the visible region at 400 nm ascribed to a ligand field transition 6A1 ? 4T1 of the 3 d5 electrons in the Fe3+ ions occupied. This compound also endures good optical properties in the visible and ultraviolet regions that can be combined to magnetic and other properties useful for developing multifunctional features for possible applications. © 2018Item Computational insights into factor affecting the potency of diaryl sulfone analogs as Escherichia coli dihydropteroate synthase inhibitors(Elsevier Ltd, 2019) Das, B.K.; PV, P.; Chakraborty, D.Dihydropteroate synthase (DHPS) is an alluring target for designing novel drug candidates to prevent infections caused by pathogenic Escherichia coli strains. Diaryl Sulfone (SO) compounds are found to inhibit DHPS competitively with respect to the substrate pABA (p-aminobenzoate). The extra aromatic ring of diaryl sulfone compounds found to stabilize them in highly flexible pABA binding loops. In this present study, a statistically significant 3D-QSAR model was developed using a data set of diaryl sulfone compounds. The favourable and unfavourable contributions of substitutions in sulfone compounds were illustrated by contour plot obtained from the developed 3D-QSAR model. Molecular docking calculations were performed to investigate the putative binding mode of diaryl sulfone compounds at the catalytic pocket. DFT calculations were carried out using SCF approach, B3LYP- 6-31 G (d) basis set to compute the HOMO, LUMO energies and their respective location at pABA binding pocket. Further, the developed model was validated by FEP (Free Energy Perturbation) calculations. The calculated relative free energy of binding between the highly potent and less potent sulfone compound was found to be ?3.78 kcal/ mol which is comparable to the experimental value of ?5.85 kcal/mol. A 10 ns molecular dynamics simulation of inhibitor and DHPS confirmed its stability at pABA catalytic site. Outcomes of the present work provide deeper insight in designing novel drug candidates for pathogenic Escherichia coli strains. © 2018 Elsevier LtdItem Enhanced photostability and optical nonlinearity of nickel and cobalt organometallic complexes(Elsevier B.V., 2019) Manjunatha, K.B.; Rajarao, R.; Poornesh, P.; Rudresha, B.J.; Umesh, G.; Badekai Ramachandra, B.R.Nonlinear optical and limiting properties of nickel, cobalt metal-organic complexes and ligand (L) {L = N,N?-o-phenylenebis (4-hyrdoxy-salicylideneimine)} were studied using Z-scan technique using Q-switched Nd: YAG laser with nanosecond pulses at 532 nm. The results reveal that metal complexes exhibit large negative nonlinear refractive index (n2) of the order of 10?11 esu. The metal complexes displays large nonlinearity than the ligand due to effective charge delocalization between metal ion and ligand. The magnitude of ground state absorption cross section is small compared to the effective excited-state absorption cross section implying the observed nonlinearity is due to reverse saturable absorption. Further, metal-organic complexes exhibit enhanced optical limiting behaviour at nanosecond laser pulses. © 2019 Elsevier B.V.Item SnO2 nanoparticles functionalized MoS2 nanosheets as the electrode material for supercapacitor applications(Institute of Physics Publishing helen.craven@iop.org, 2019) Prabukumar, C.; Mohamed, M.; Krishna Bhat, D.; Udaya Bhat, K.Tin oxide (SnO2) nanoparticles undergo the volume expansion during an electrochemical cycle. This volume expansion leads to discontinuities in the form of microcracks in the electrode material. The problem of charge transportation associated with this microcracking limits the application of SnO2 in the energy storage application such as supercapacitors. The present work approached to solve this problem by incorporating the MoS2 nanosheets along with the SnO2 nanoparticles. The SnO2 nanoparticles are functionalized onto the surface of the MoS2 nanosheets by the ligand exchange process. The MoS2 nanosheets act as the support material for the SnO2 nanoparticles. The electrode material prepared using SnO2 nanoparticles and nanocomposite of SnO2 functionalized MoS2 nanosheets are tested by cyclic voltammetry and galvanostatic charge-discharge measurements. The specific capacity of the MoS2-SnO2 nanocomposite is calculated to be 61.6 F g-1 which is 4.4 fold higher than that of bare SnO2 nanoparticles. The improvement in the electrochemical performance of SnO2 is attributed to the high surface area and the charge transportation provided by the MoS2 nanosheets. © 2019 IOP Publishing Ltd.Item Effect of hydrophobic and hydrogen bonding interactions on the potency of ß-alanine analogs of G-protein coupled glucagon receptor inhibitors(John Wiley and Sons Inc. P.O.Box 18667 Newark NJ 07191-8667, 2020) Venugopal, P.P.; Das, B.K.; Soorya, E.; Chakraborty, D.G-protein coupled glucagon receptors (GCGRs) play an important role in glucose homeostasis and pathophysiology of Type-II Diabetes Mellitus (T2DM). The allosteric pocket located at the trans-membrane domain of GCGR consists of hydrophobic (TM5) and hydrophilic (TM7) units. Hydrophobic interactions with the amino acid residues present at TM5, found to facilitate the favorable orientation of antagonist at GCGR allosteric pocket. A statistically robust and highly predictive 3D-QSAR model was developed using 58 ?-alanine based GCGR antagonists with significant variation in structure and potency profile. The correlation coefficient (R2) and cross-validation coefficient (Q2) of the developed model were found to be 0.9981 and 0.8253, respectively at the PLS factor of 8. The analysis of the favorable and unfavorable contribution of different structural features on the glucagon receptor antagonists was done by 3D-QSAR contour plots. Hydrophobic and hydrogen bonding interactions are found to be main dominating non-bonding interactions in docking studies. Presence of highest occupied molecular orbital (HOMO) in the polar part and lowest unoccupied molecular orbital (LUMO) in the hydrophobic part of antagonists leads to favorable protein-ligand interactions. Molecular mechanics/generalized born surface area (MM/GBSA) calculations showed that van der Waals and nonpolar solvation energy terms are crucial components for thermodynamically stable binding of the inhibitors. The binding free energy of highly potent compound was found to be ?63.475 kcal/mol; whereas the least active compound exhibited binding energy of ?41.097 kcal/mol. Further, five 100 ns molecular dynamics simulation (MD) simulations were done to confirm the stability of the inhibitor-receptor complex. Outcomes of the present study can serve as the basis for designing improved GCGR antagonists. © 2019 Wiley Periodicals, Inc.Item Understanding and tuning of spinterface for chemisorbed Ni-dinuclear quinonoid on Co(001) substrate(IOP Publishing Ltd, 2021) Reddy, I.R.; Tarafder, K.Planar magnetic molecules are of great research interest in the past few years because of their possible application in molecular spintronics. Microscopic understanding of the adsorption and magnetic exchange interaction of these molecules to the metallic/magnetic surfaces may pave the way in developing efficient molecular spin switching devices. Herein, using density functional theory + U calculations, we have studied the structural, electronic, and magnetic properties of a Ni-dinuclear molecule chemically adsorbed on a Co(001) substrate. Switching of the spin and oxidation state of the Ni atom present in the molecule was observed due to the adsorption. We report a strong antiferromagnetic coupling between the spins of the Ni-dinuclear molecule to the ferromagnetic Co(001) substrate. The study reveals an indirect exchange interaction between the magnetic center of the molecule and the substrate Co atoms. The exchange interaction is mediated through the ligands of the molecule that stabilizes the spin moment of the molecule in an antiferromagnetic alignment to the substrate magnetization. Our study also shows that the spin state and strength of MAE of the adsorbed molecule can be tailored through the magneto-chemical method by adding the Cl atom as an axial ligand to the magnetic center of the molecule. © 2021 IOP Publishing Ltd.