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Clara TH, Prasana JC, Prabhu N, Rizwana BF. Spectroscopic profiling and molecular docking of novel chalcone derivative (2E)-1-(3,4-dimethoxyphenyl)-3-(4-n-propyloxyphenyl)-2-propen-1-one- A prospective respiratory drug. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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2
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George Thomas M, Ebenezer C, Solomon RV. Tuning the structure of disulfonated phenanthroline based ligands for effective separation of Am(III)/Eu(III) ions : A DFT investigation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117151] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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3
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Likhitha U, Narayana B, Sarojini B, Madan Kumar S, Karthick T. Crystallographic and theoretical interpretation of supramolecular architecture in a new salt hydrate of DL-Tartaric acid and Dimethylamine (DLTA-DA). J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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4
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Understanding the potency of malarial ligand (D44) in plasmodium FKBP35 and modelled halogen atom (Br, Cl, F) functional groups. J Mol Graph Model 2020; 97:107553. [PMID: 32035313 DOI: 10.1016/j.jmgm.2020.107553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/10/2020] [Accepted: 01/27/2020] [Indexed: 11/21/2022]
Abstract
The present study clearly depicts the understanding of the D44 in Plasmodium FKBP35 around the hinge region. To analyse the binding stability of D44 ligand and to understand the role of halogen bond, hydrogen bond interaction formed between the hinge region amino acids: Isoleucine (Ile74), Phenylalanine (Phe54), Aspartic acid (Asp55) Phenylalanine (Phe64),Tyrosine (Tyr100), Tryptophan (TRP 77) and ligand D44 was portrayed specifically through interaction energy calculations at HF, M062X, MP2 level of theories for different basis set (6-311G**, 6-31+G*, LANL2DZ). The investigation will provide an apparent picture regarding the non-covalent interaction that hold the contact of ligand and amino acids in the hinge region and the implication of modelled functional groups (Br, Cl, F, OSO and NH2) on ligand, which will help chemist in synthesizing new novel ligands. HOMO, LUMO chart calculated for D44 ligands reveals graphic illustration of orbital's that stimulate for contact. The aim and natural bond orbital analysis identified key contribution of individual hydrogen/halogen bonds that contribute for the binding strength through stabilization energy, ρ and ∇2ρ values. Overall this study finds out that the Stability of D44 in Plasmodium FKBP35 was enhanced by the Halogen atom (Br, Cl, F) functional groups; which provide an innovative pathway for the selection of functional groups that opt for the hinge region side chains on the ligand.
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Gutiérrez EL, Godoy AA, Narda GE, Ellena J. Rational design, supramolecular synthesis and solid state characterization of two bicomponent solid forms of mebendazole. CrystEngComm 2020. [DOI: 10.1039/d0ce00924e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
MBZ methyl sulfate and perchlorate were designed based on the statistical probability of the formation of an R22(8) supramolecular heterosynthon.
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Affiliation(s)
- Eduardo L. Gutiérrez
- INQUISAL–CONICET
- Área de Química Física
- Facultad de Química
- Bioquímica y Farmacia
- Universidad Nacional de San Luis
| | - Agustín A. Godoy
- Instituto de Investigaciones en Tecnología Química (INTEQUI)
- Área de Química General e Inorgánica “Dr. G. F. Puelles”
- Facultad de Química, Bioquímica y Farmacia
- Universidad Nacional de San Luis
- San Luis
| | - Griselda E. Narda
- Instituto de Investigaciones en Tecnología Química (INTEQUI)
- Área de Química General e Inorgánica “Dr. G. F. Puelles”
- Facultad de Química, Bioquímica y Farmacia
- Universidad Nacional de San Luis
- San Luis
| | - Javier Ellena
- Instituto de Física de São Carlos
- Universidade de São Paulo
- São Carlos
- Brazil
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6
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Palanisamy D. A quantum chemical perspective on the potency of electron donors and acceptors in pnicogen bonds (AS...N, P...N, N...N). J Mol Model 2019; 26:11. [PMID: 31834505 DOI: 10.1007/s00894-019-4263-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/17/2019] [Indexed: 11/28/2022]
Abstract
A quantum chemical perspective of 31 structures contains electron acceptors: ASCl3 (arsenic trichloride), PCl3 (phosphorous trichloride) and NCl3 (nitrogen trichloride); forming non-covalent bond with various nitrogen-based electron donors that resulted in pnicogen bonds, AS...N, P...N and N...N were calculated at M062X/def2-QZVP level of theory. Besides the above method, MP2/def2-QZVP and CCSD(T)/def2-QZVP level of theories have also been analysed to have in depth knowledge about the bonds formed. The nature of the bonds was assumed from the electrostatic potential evaluated for all the monomers, where σ hole is positive for all the monomers. The strongest pnicogen bonds are ASCl3-NF2H, PCl3-NCH3CH3CH3 and NCl3-NCH3CH3CH3 having interaction energies as -4.15, -11.58 and -3.25 kcal/mol, respectively, at MP2/def2-QZVP level of theory. Further at CCSD(T)/def2-QZVP level of theory, ASCl3-NF2H and NCl3-NCH3CH3CH3 are found to be the most stable with interaction energies as -3.53 and -2.45 kcal/mol, respectively. The potential energy surface scan was performed for all the stable complexes in order to confirm the existences of energies are true minima. Moreover to confirm the halogen and pnicogen bonds, AIM analysis was carried out. The results from the above factors of pnicogen bond will help crystal growth, material science and engineering community to explore novel materials, which abide for modernization. Graphical abstract PCl3-NCH3CH3CH3 complex with 2.61 Å and pnicogen angle of 178.54° is strong, and interaction energy is -11.58 kcal/mol. Electron donors - ASCl3, PCl3 and NCl3 and electron acceptors -NCH3CH3CH3, NH3C2 and NHCO have strong electrostatic contribution. High and low values of (ρ) ∇2(ρ) reveal the strong and weak pnicogen bond. Schematic representation of acceptors surrounded by its donors and Electrostatic Potential map.
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Affiliation(s)
- Deepa Palanisamy
- Young Scientist (DST-SERB), Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, 627012, India.
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7
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Adilakshmi A, Deepan Kumar M, Jaccob M, Tamilmani V. Theoretical Investigation of Steric Effect Influence on Reactivity of Substituted Butadienes with Bromocyclobutenone. J Chem Inf Model 2019; 59:2231-2241. [DOI: 10.1021/acs.jcim.9b00177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Arumugam Adilakshmi
- Department of Chemistry, University College of Engineering, Ariyalur (A Constituent College of Anna University−Chennai), Ariyalur−621704, Tamil Nadu, India
| | - Madhu Deepan Kumar
- Computational Chemistry Laboratory, Loyola Institute of Frontier Energy (LIFE) and Department of Chemistry, Loyola College (Autonomous), Chennai−600 034, Tamil Nadu, India
| | - Madhavan Jaccob
- Computational Chemistry Laboratory, Loyola Institute of Frontier Energy (LIFE) and Department of Chemistry, Loyola College (Autonomous), Chennai−600 034, Tamil Nadu, India
| | - Venkatachalam Tamilmani
- Department of Chemistry, Bharathidasan Institute of Technology (A Constituent College of Anna University−Chennai), Tiruchirappalli−620 024, Tamil Nadu, India
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8
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Deepa P, Thirumeignanam D, Kolandaivel P. An overview about the impact of hinge region towards the anticancer binding affinity of the Ck2 ligands: a quantum chemical analysis. J Biomol Struct Dyn 2018; 37:3859-3876. [DOI: 10.1080/07391102.2018.1533498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- P. Deepa
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, Tamil Nadu, India
| | - D. Thirumeignanam
- Department of Animal Nutrition, Veterinary College and Research Institute, Tirunelveli, Tamil Nadu, India
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9
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Gutiérrez EL, Souza MS, Diniz LF, Ellena J. Synthesis, characterization and solubility of a new anthelmintic salt: Mebendazole nitrate. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.02.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Panneerselvam M, Kumar MD, Jaccob M, Solomon RV. Computational Unravelling of the Role of Alkyl Groups on the Host-Guest Complexation of Pillar[5]arenes with Neutral Dihalobutanes. ChemistrySelect 2018. [DOI: 10.1002/slct.201702541] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Murugesan Panneerselvam
- Department of Chemistry; Loyola College (Autonomous); Chennai - 600 034, Tamil Nadu India
- Computational Chemistry Laboratory; Loyola Institute of Frontier Energy (LIFE); Loyola College (Autonomous); Chennai - 600 034, Tamil Nadu India
| | - Madhu Deepan Kumar
- Department of Chemistry; Loyola College (Autonomous); Chennai - 600 034, Tamil Nadu India
- Computational Chemistry Laboratory; Loyola Institute of Frontier Energy (LIFE); Loyola College (Autonomous); Chennai - 600 034, Tamil Nadu India
| | - Madhavan Jaccob
- Department of Chemistry; Loyola College (Autonomous); Chennai - 600 034, Tamil Nadu India
- Computational Chemistry Laboratory; Loyola Institute of Frontier Energy (LIFE); Loyola College (Autonomous); Chennai - 600 034, Tamil Nadu India
| | - Rajadurai Vijay Solomon
- Department of Chemistry; Madras Christian College (Autonomous), Tambaram East; Chennai - 600 059, Tamil Nadu India
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11
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Martínez-Rugerio G, Arbe A, Colmenero J, Alegría A. Supramolecular Self-Assembly of Monocarboxydecyl-Terminated Dimethylsiloxane Oligomer. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b01910] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gerardo Martínez-Rugerio
- Centro de Física
de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
| | - Arantxa Arbe
- Centro de Física
de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
| | - Juan Colmenero
- Centro de Física
de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
- Departamento
de Física de Materiales, UPV/EHU, Apartado 1072, E-20080 San Sebastián, Spain
- Donostia International
Physics Center (DIPC), Paseo Manuel
de Lardizabal 4, E-20018 San Sebastián, Spain
| | - Angel Alegría
- Centro de Física
de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
- Departamento
de Física de Materiales, UPV/EHU, Apartado 1072, E-20080 San Sebastián, Spain
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Sugimura N, Igarashi Y, Aoyama R, Shibue T. Energy-decomposition analysis of ion-neutral complexes along reaction coordinates of unimolecular proton-transfer reaction in gas phase: Comparison between 2-butanol radical ion and protonated 2-ethoxypropane ion. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.08.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Sugimura N, Igarashi Y, Aoyama R, Shibue T. Energy decomposition analysis of the interactions in adduct ions of acetophenone and Na+, NH4+ and H+ in the gas phase. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.06.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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14
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Pandiyan BV, Deepa P, Kolandaivel P. Does the occurrence of resonance (by the delocalization of radical/cationic/anionic charges) induce the existence of intramolecular halogen–halogen contacts? RSC Adv 2016. [DOI: 10.1039/c6ra14270b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Exotic intramolecular homo/hetero dihalogen bonding (C–X⋯X–C: X = Br, Cl and F) in radical, cationic and anionic five-membered ring systems was analyzed using wave functional theory (MP2/aug-cc-pVTZ) analysis.
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Affiliation(s)
| | - P. Deepa
- Department of Computational Chemistry
- Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic
- Flemingovo nám. 2
- Czech Republic
| | - P. Kolandaivel
- Department of Physics
- Bharathiar University
- Coimbatore
- India
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