Computational Sciences - Research Publications

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    CuO Nanoparticles as a Simple and Efficient Green Catalyst for the Aziridine Ring-Opening: Examination of a Broad Range of Nucleophiles
    (Wiley-Blackwell, 2020) Chatterjee, R; Santra, S; Chakraborty, Ghosal N; Giri, K; Zyryanov, G.V; Majee, A.
    It has been observed that CuO nanoparticles act as effective and reusable catalyst for the ring-opening reaction of aziridines with a wide range of nucleophiles such as alcohols, thiols, and indoles. The catalytic activity has been tested in large scale reactions. The methodology is applicable in very low catalyst loading. The reaction proceeds under solvent-free conditions. The catalyst has been used for six consecutive cycles with comparable efficiency. The present methodology could be considered as environmentally benign as indicated by the calculation of E-factors which are very low in the range of 0.37-1.31. - 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
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    Synthesis and photophysics of new unsymmetrically substituted 5,5′-diaryl-2,2′-bypiridine-based “push-pull” fluorophores
    (Elsevier, 2019) Starnovskaya, E.S; Kopchuk ,D.S; Khasanov, A.F; Tanya, O.S; Santra, S; Giri, Kousik; Rahman, M; Kovalev, I.S; Zyryanov, G.V; Majee, A; Charushin, V.N.,
    New unsymmetrically substituted 5,5′-diaryl-2,2′-bypiridine “push-pull” fluorophores were prepared in good yields via the “1,2,4-triazine method”/Suzuki coupling reaction sequence. The obtained fluorophores contain the “push-pull” system with donor and acceptor moieties arranged in a D-π-A-π-D fashion, and that provides both the prospective photophysical properties and unique solvatocromic effects for the most representative compounds. © 2018 Elsevier Ltd
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    A study of mechanistic mapping of novel SNPs to male breast cancer
    (Humana Press Inc., 2019) Kaur, R.P; Kumar, V; Shafi, G; Vashistha, R; Kulharia, Mahesh; Munshi, Aanjan
    Alterations in BRCA2, PALB2, CHEK2, and p53 genes have been identified for their association with male breast cancer in various studies. The incidence of male breast cancer in India is consistent with its global rate. The present study was carried out with an aim to evaluate the genetic alterations in male breast cancer patients from Malwa region of Punjab, India. Four male breast cancer patients belonging to different families were recruited from Guru Gobind Singh Medical College and Hospital, Faridkot, India. A total of 51 genes reported with implications in the pathogenesis of breast cancer were screened using next generation sequencing. Germline variations were found in BRCA1, BRCA2, PMS2, p53, and PALB2 genes, previously reported to be associated with MBC as well as FBC. In addition to these, 13 novel missense alterations were detected in eight genes including STK11, FZR1, PALB2, BRCA2, NF2, BAP1, BARD1, and CHEK2. Impact of these missense alterations on structure and function of protein was also analyzed through molecular dynamics simulation. Structural analysis of these single nucleotide polymorphisms (SNPs) revealed significant impact on the encoded protein functioning. © 2019, Springer Science+Business Media, LLC, part of Springer Nature.
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    Electronic spectroscopy of carbon chains (C2 n +1, n = 7-10) of astrophysical importance. I. Quantum chemistry
    (American Institute of Physics, 2019) Reddy, S.R; Ghosh, Arpita; Mahapatra, Susanta
    Carbon chains have been predicted to be potential carriers of diffuse interstellar band features in astrophysical observations. Motivated by numerous predictions, we set out to carry out extensive ab initio quantum chemistry calculations to establish the ground and excited electronic potential energy surfaces and their coupling surfaces for carbon chains containing an odd number of carbon atoms (C2n+1, n = 7-10). Vibronic coupling models are established with the aid of the calculated electronic energies to investigate nuclear dynamics from first principles. The latter are reported in Ghosh et al. [J. Chem. Phys. 151, 054304 (2019)]. The mentioned carbon chains possess a linear cumulenic structure at the equilibrium minimum of their electronic ground state, and an electronic excited state of the ςu+1 term appears to be extremely bright optically and absorbs in the visible region of the electromagnetic spectrum. Vertical excitation energy of this state decreases and transition dipole moment increases, and as a result, the oscillator strength of this state linearly increases with an increase of the chain length. There are states belonging to 1Πg, 1Πu, ςg+1, 1Δg, and 1Δu terms, in the immediate vicinity of the ςu+1 state, which are optically dark but can gain intensity through vibronic coupling with the optically bright ςu+1 state. Construction of a coupling scheme considering the Renner-Teller coupling within the degenerate Π states and pseudo-Renner-Teller coupling between the Renner-Teller split component states as well as with the nondegenerate ς states is another motivation of this work. The coupled-state Hamiltonian is constructed in a diabatic electronic basis in terms of the dimensionless normal coordinates of the vibrational modes of the carbon chains. Both Renner-Teller and pseudo-Renner-Teller types of couplings are included in the Hamiltonian. The theoretical results are discussed in relation to the experimental findings. © 2019 Author(s).
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    Evaluation of in silico designed inhibitors targeting MelF (Rv1936) against Mycobacterium marinum within macrophages
    (Nature Publishing Group, 2019) Dharra, R; Radhakrishnan,V.S; Prasad, T; Thakur, Z; Cirillo, J.D; Sheoran, A; Pandey, A.K; Kulharia, Mahesh; Mehta P.K.
    We recently identified inhibitors targeting Mycobacterium marinum MelF (Rv1936) by in silico analysis, which exhibited bacteriostatic/bactericidal activity against M. marinum and M. tuberculosis in vitro. Herein, we evaluated the effect of best four inhibitors (# 5175552, # 6513745, # 5255829, # 9125618) obtained from the ChemBridge compound libraries, on intracellular replication and persistence of bacteria within IFN-γ activated murine RAW264.7 and human THP-1 macrophages infected with M. marinum. Inhibitors # 5175552 and # 6513745 significantly reduced (p < 0.05) the intracellular replication of bacilli during day 7 post-infection (p.i.) within RAW264.7 and THP-1 macrophages infected at multiplicity of infection (MOI) of ~1.0. These observations were substantiated by electron microscopy, which revealed the protective effect of # 5175552 in clearing the bacilli inside murine macrophages. Strikingly, # 6513745 displayed synergism with isoniazid against M. marinum in murine macrophages, whereas # 5175552 significantly suppressed (p < 0.05) the persistent bacilli during day 10–14 p.i. in infected RAW264.7 and THP-1 macrophages (MOI of ~ 0.1). Moreover, # 5175552 and # 6513745 were non-cytotoxic to host macrophages at both 1X and 5X MIC. Further validation of these inhibitors against M. tuberculosis-infected macrophages and animal models has potential for development as novel anti-tubercular agents. © 2019, The Author(s).
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    Comparative Review Study of Security of ARAN and AODV Routing Protocols in MANETs
    (eSAT Publishing House Private Limited, 2014) Goel, Ruby; Mittal, Meenakshi
    Mobile Ad-hoc networks are proposed because there are some areas where it is not possible to set up a network having fixedinfrastructure, like in areas of emergency services, military operations, personal area networks, etc. Ad hoc network allowscommunication between wireless nodes with the help of their transmission ranges and routing protocols facilitate thiscommunication among the nodes. But on these routing protocols variety of attacks are possible like- Eavesdropping, IP-spoofing, Blackhole, Denial of service attack, etc. By attacking the routing protocol attackers can access network traffic, can drop it or canmodify it. To prevent these attacks many secure routing protocols like- SEAD, ARAN, SAODV, SRP, etc have been developed. Inthis paper security aspects of ARAN (Authenticated Routing for Adhoc Network routing protocol) has been analyzed with respectto a commonly used routing protocol AODV (Adhoc On-Demand Distance Vector) i.e. how much these two protocols are resistantto Blackhole and IP-Spoofing attack under GloMoSim-2.03 simulator.
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    Could mycobacterial MelF protein (Rv1936) be used as a potential drug target?
    (Future Medicine Ltd., 2018) Mehta P.K.; Dharra R.; Kulharia, Mahesh
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    Effect of arsenate substitution on phosphate repository of cell: A computational study
    (Royal Society Publishing, 2018) Singh A.; Giri K.
    The structural analogy with phosphate derives arsenate into various metabolic processes associated with phosphate inside the organisms. But it is difficult to evaluate the effect of arsenate substitution on the stability of individual biological phosphate species, which span from a simpler monoester form like pyrophosphate to a more complex phosphodiester variant like DNA. In this study, we have classified the physiological phosphate esters into three different classes on the basis of their structural differences. This classification has helped us to present a concise theoretical study on the kinetic stability of phosphate analogue species of arsenate against hydrolysis. All the calculations have been carried out using QM/MM methods of our Own N-layer Integrated molecular Orbital molecular Mechanics (ONIOM). For quantum mechanical region, we have used M06-2X density functional with 6-31+G(2d,2p) basis set and for molecular mechanics we have used the AMBER force field. The calculated rate constants for hydrolysis show that none of the phosphate analogue species of arsenate has a reasonable stability against hydrolysis.
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    Solvent-free synthesis of 5-(aryl/alkyl)amino-1,2,4-triazines and ?-arylamino-2,2?-bipyridines with greener prospects
    (Royal Society of Chemistry, 2017) Kopchuk D.S.; Chepchugov N.V.; Kovalev I.S.; Santra S.; Rahman M.; Giri K.; Zyryanov G.V.; Majee A.; Charushin V.N.; Chupakhin O.N.
    A green and highly efficient method has been developed for the synthesis of 5-(aryl/alkyl)amino-1,2,4-triazines and ?-arylamino-2,2?-bipyridines according to the principles of atom economy. It has been performed by two consecutive solvent-free reaction pathways: the ipso-substitution of a cyano-group in 5-cyano-1,2,4-triazines and the aza-Diels-Alder reaction of the resulting 5-arylamino-1,2,4-triazines with 1-morpholinocyclopentene used as a dienophile. Solvent and catalyst-free conditions, operational simplicity, the compatibility with various functional groups, nonchromatographic purification technique, and high yields are the notable advantages of this procedure. The present methodology possesses a low E-factor.
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    PPInS: a repository of protein-protein interaction sitesbase
    (Nature Publishing Group, 2018) Kumar V.; Mahato S.; Munshi, Anjana; Kulharia, Mahesh
    Protein-Protein Interaction Sitesbase (PPInS), a high-performance database of protein-protein interacting interfaces, is presented. The atomic level information of the molecular interaction happening amongst various protein chains in protein-protein complexes (as reported in the Protein Data Bank [PDB]) together with their evolutionary information in Structural Classification of Proteins (SCOPe release 2.06), is made available in PPInS. Total 32468 PDB files representing X-ray crystallized multimeric protein-protein complexes with structural resolution better than 2.5 Å had been shortlisted to demarcate the protein-protein interaction interfaces (PPIIs). A total of 111857 PPIIs with ~32.24 million atomic contact pairs (ACPs) were generated and made available on a web server for on-site analysis and downloading purpose. All these PPIIs and protein-protein interacting patches (PPIPs) involved in them, were also analyzed in terms of a number of residues contributing in patch formation, their hydrophobic nature, amount of surface area they contributed in binding, and their homo and heterodimeric nature, to describe the diversity of information covered in PPInS. It was observed that 42.37% of total PPIPs were made up of 6-20 interacting residues, 53.08% PPIPs had interface area ?1000 Å 2 in PPII formation, 82.64% PPIPs were reported with hydrophobicity score of ?10, and 73.26% PPIPs were homologous to each other with the sequence similarity score ranging from 75-100%. A subset ''Non-Redundant Database (NRDB)'' of the PPInS containing 2265 PPIIs, with over 1.8 million ACPs corresponding to the 1931 protein-protein complexes (PDBs), was also designed by removing structural redundancies at the level of SCOP superfamily (SCOP release 1.75). The web interface of the PPInS (http://www.cup.edu.in:99/ppins/home.php) offers an easy-to-navigate, intuitive and user-friendly environment, and can be accessed by providing PDB ID, SCOP superfamily ID, and protein sequence. - 2018, The Author(s).