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Shukla R, Sen A. Hydrogen- and halogen-bonding-directed trimeric supramolecular motifs in dihalogenated 1,2,4-triazoles. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2024; 80:163-170. [PMID: 38682692 DOI: 10.1107/s2052520624002427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/13/2024] [Indexed: 05/01/2024]
Abstract
Hydrogen-bonding and halogen-bonding interactions are important noncovalent interactions that play a significant role in the crystal structure of organic molecules. An in-depth analysis is given of the crystal packing of two previously reported crystal structures of dihalogenated 1,2,4-triazole derivatives, namely 3,5-dichloro-1H-1,2,4-triazole and 3,5-dibromo-1H-1,2,4-triazole. This work provides insights into the complex interplay of hydrogen-bonding and halogen-bonding interactions resulting in the formation of multiple trimeric motifs in the crystal structure of 1,2,4-triazole derivatives. Analysis of the crystal packing of these isostructural crystal structures revealed that the molecular arrangement in these molecules is primarily stabilized by the formation of different trimeric motifs stabilized by N-H...N hydrogen bonds, N-H...X (X = Cl/Br) halogen bonds and C-X...X halogen-bonding interactions. Computational studies further revealed that all these trimers are energetically stable. A crystallographic database search further reveals that while the cyclic trimers reported in this study are present in other molecules, structures analyzed in this study are the sole instances where all are present simultaneously.
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Affiliation(s)
- Rahul Shukla
- Department of Chemistry (NCI Laboratory), School of Science, GITAM (Deemed to be University), Rushikonda, Visakhapatnam, Andhra Pradesh 530045, India
| | - Anik Sen
- Department of Chemistry (CMDD Laboratory), School of Science, GITAM (Deemed to be University), Visakhapatnam, Andhra Pradesh 530045, India
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Fatima A, Khanum G, Srivastava SK, Bhattacharya P, Ali A, Arora H, Siddiqui N, Javed S. Exploring quantum computational, molecular docking, and molecular dynamics simulation with MMGBSA studies of ethyl-2-amino-4-methyl thiophene-3-carboxylate. J Biomol Struct Dyn 2023; 41:10411-10429. [PMID: 37942665 DOI: 10.1080/07391102.2023.2180667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/10/2022] [Indexed: 02/24/2023]
Abstract
2-aminothiophenes derivative, Ethyl-2-amino-4-methyl thiophene-3-carboxylate (EAMC) has been synthesized, characterized, and investigated quantum chemically. It was experimentally investigated by different spectroscopic methods like- NMR (1H-NMR and 13C-NMR), FT-IR, and UV-Visible. B3LYP method and 6-311++G(d,p) basis set were employed for optimization of molecular structure and calculation of wave numbers of normal modes of vibrations and various other important parameters. Calculated bond lengths and angles were compared with the experimental bond lengths and Bond Angle Parameters. Optimized bond parameters and experimental bond parameters were found in good agreement. Complete potential energy distribution assignments were done successfully by VEDA. The HOMO/LUMO energy gap emphasizes adequate charge transfer happening within the molecule. A study of donor-acceptor interconnections was done via NBO analysis. MEP surface analysis was done to demonstrate charge distribution and reactive areas qualitatively in the molecule. The degree of relative localization of electrons was analyzed via ELF Diagram. The Fukui function analysis showed possible sites for attacks by different substituents. By using the TD-DFT method and PCM solvent model, the UV-Vis spectrum (gas, methanol, DMSO) and the maximum absorption wavelength was computed and compared with experimental data. 3D and 2D intermolecular interactions in the crystal were analyzed via Hirshfeld surface analysis and fingerprint plots reveal that the EAMC crystal was stabilized by H--H/H--H/C--H bond formation. The molecular docking was done with 7 different protein receptors on the molecule to find the best ligand-protein interactions. Molecular dynamic simulations and MMGBSA calculations were also carried out to find out the best binding of the ligand with the protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aysha Fatima
- S.O.S in Chemistry, Jiwaji University, Gwalior, India
- Department of Chemistry, CMP College, University of Allahabad, Prayagraj, India
| | | | | | | | - Akram Ali
- Department of Chemistry, CMP College, University of Allahabad, Prayagraj, India
| | - Himanshu Arora
- Department of Chemistry, University of Allahabad, Prayagraj, India
| | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute, Agra, India
| | - Saleem Javed
- Department of Chemistry, University of Allahabad, Prayagraj, India
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Agarwal P, Kumar A, Verma I, Khanum G, Siddiqui N, Choquesillo-Lazarte D, Mota AJ, Javed S, Arora H. Dinuclear Phenoxo-Bridged Nickel(II) and Copper(II) Complexes of Phenolate-Based Tripodal Ligand: Theoretical and Experimental Insights. Polycycl Aromat Compd 2023. [DOI: 10.1080/10406638.2023.2173619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Affiliation(s)
- Pratibha Agarwal
- School of Engineering and Sciences, G. D. Goenka University, Gurugram, Haryana, India
| | - Akhilesh Kumar
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
| | - Indresh Verma
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh, India
| | - Ghazala Khanum
- S.O. S in Chemistry, Jiwaji University, Gwalior, Madhya Pradesh, India
| | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute, Agra, Uttar Pradesh, India
| | | | - Antonio J. Mota
- Department of Inorganic Chemistry, Faculty of Science, University of Granada, Granada, Spain
| | - Saleem Javed
- Department of Chemistry, University of Allahabad, Prayagraj, Uttar Pradesh, India
| | - Himanshu Arora
- School of Engineering and Sciences, G. D. Goenka University, Gurugram, Haryana, India
- Department of Chemistry, University of Allahabad, Prayagraj, Uttar Pradesh, India
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Yankova R, Tankov I, Tsaneva T. Crystal structure, intermolecular interactions and NLO properties for imidazolium hydrogen sulfate ionic liquid. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Patkar D, Deshmukh MM, Chopra D. Characterization of non-covalent contacts in mono- and di-halo substituted acetaldehydes: probing the substitution effects of electron donating and withdrawing groups. Phys Chem Chem Phys 2023; 25:2946-2962. [PMID: 36606453 DOI: 10.1039/d2cp05269e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the current work, a systematic evaluation of the different types of non-covalent interactions (NCIs) in acetaldehyde dimers, including dimers of mono-halo (XCH2CHO)2, di-halo (X2CHCHO)2 and tri-halo substituted (X3CCHO)2 acetaldehydes via the associated stabilization energy of these dimers has been performed. Furthermore, a topological analysis of the electron density based on the quantum theory of atoms in molecules (QTAIM) and non-covalent interaction reduced density gradient (NCI-RDG) isosurfaces has also been performed to evaluate the nature of these NCIs. The geometrical and electronic characteristics have been evaluated via the presence of different electron-donating groups (EDGs) and electron-withdrawing groups (EWGs) or substituents in dimers of these molecules, namely, XCH(Y)CHO and X2C(Y)CHO (wherein X = -F, -Cl, and -Br and Y = -SO3H, -CN, -NO2, -NH2, -CH3, -OCH3, and -SMe3). The C-H⋯O, C-H⋯X, X⋯X, X⋯O and C⋯O tetrel bonded contacts have been recognized to play an important role in the stabilization of the formed dimers. This study also establishes the fact that the overall stability of the dimeric assemblies is governed by the contributions from the mutual and complex interplay of a variety of interactions in the investigated dimers. Hence considerations based on strong H-bond donor-acceptor characteristics hold relevance for simple systems only, but slight alteration in the electronic environment can affect the overall stabilization energies of the system being investigated and the nature of the interactions that contribute towards the same.
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Affiliation(s)
- Deepak Patkar
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya, (A Central University), Sagar, 470003, India.
| | - Milind M Deshmukh
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya, (A Central University), Sagar, 470003, India.
| | - Deepak Chopra
- Crystallography and Crystal Chemistry Laboratory, Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal By-Pass Road, Bhauri, Bhopal-462066, Madhya Pradesh, India.
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Synthesis and spectral studies of Ni(Ⅱ) complexes involving functionalized dithiocarbamates and triphenylphosphine: X-ray crystal structure, thermal stability, Hirshfeld surface analysis, DFT and biological evaluation. Inorganica Chim Acta 2023. [DOI: 10.1016/j.ica.2022.121271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Selective N-allylation via SN2ꞌ reaction: Synthesis, characterization, crystal structure, theoretical and biological studies of Ethyl (E)-2-(4-aminobenzene-1-sulphonylimino-thiazol-3-yl-methyl)-3-phenyl acrylate. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Fatima A, Ali A, Rajan R, Verma I, Muthu S, Siddiqui N, Garg P, Javed S. Experimental Spectroscopic, DFT, Molecular Docking, and Molecular Dynamics Simulation Investigations on m-Phenylenediamine (Monomer and Trimer). Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2150655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Aysha Fatima
- S.O.S in Chemistry, Jiwaji University, Gwalior, India
| | - Akram Ali
- Department of Chemistry, CMP College, Allahabad, India
| | - Ramya Rajan
- Department of Chemistry, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Indresh Verma
- Department of Chemistry, Indian Institute of Technology, Kanpur, India
| | - S. Muthu
- Department of Physics, Aringnar Anna Govt. Arts College, Cheyyar, India
| | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute Agra, Agra, India
| | - Pankaj Garg
- Department of Chemistry, GLA University, Mathura, India
| | - Saleem Javed
- Department of Chemistry, University of Allahabad, Prayagraj, India
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Khanum G, Fatima A, Siddiqui N, Butcher RJ, Alsaiari NS, Srivastava SK, Javed S. Experimental Spectroscopic (FT-IR, 1H and 13C NMR, ESI-MS, UV) Analysis, Single Crystal X-Ray, Computational, Hirshfeld Analysis, and Molecular Docking of 2-Amino- N-Cyclopropyl-5-Heptylthiophene-3-Carboxamide and Its Derivatives. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2130372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Ghazala Khanum
- The School of Studies in Chemistry, Jiwaji University, Gwalior, India
| | - Aysha Fatima
- The School of Studies in Chemistry, Jiwaji University, Gwalior, India
| | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute Agra, Agra, India
| | - R. J. Butcher
- Department of Chemistry, Howard University, Washington, DC, USA
| | - Norah Salem Alsaiari
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | - Saleem Javed
- Department of Chemistry, Institute of Home Science, Dr. Bhimrao Ambedkar University, Agra, India
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Manhas FM, Fatima A, Verma I, Siddiqui N, Muthu S, AlSalem HS, Savita S, Singh M, Javed S. Quantum computational, spectroscopic (FT-IR, NMR and UV–Vis) profiling, Hirshfeld surface, molecular docking and dynamics simulation studies on pyridine-2,6-dicarbonyl dichloride. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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11
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Synthesis, crystal structure, characterization, Hirshfeld analysis, molecular docking and DFT calculations of 5-Phenylamino-isophthalic acid: A good NLO material. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132791] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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12
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Baykov SV, Tarasenko MV, Semenov AV, Katlenok EA, Shetnev AA, Boyarskiy VP. Dualism of 1,2,4-oxadiazole ring in noncovalent interactions with carboxylic group. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Sharma A, Khanum G, Kumar A, Fatima A, Singh M, Abualnaja KM, Althubeiti K, Muthu S, Siddiqui N, Javed S. Conformational stability, quantum computational, spectroscopic, molecular docking and molecular dynamic simulation study of 2-hydroxy-1-naphthaldehyde. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132755] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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14
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Fatima A, Khanum G, Agrawal DD, Srivastava SK, Butcher RJ, Muthu S, Ahmad M, Althubeiti K, Siddiqui N, Javed S. Synthesis, Spectroscopic, Crystal Structure, DFT, Hirshfeld Surface and Molecular Docking Analysis of Hexahydroquinoline Derivative (HQ). Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2089174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Aysha Fatima
- S.O.S in Chemistry, Jiwaji University, Gwalior, Madhaya Pradesh, India
| | - Ghazala Khanum
- S.O.S in Chemistry, Jiwaji University, Gwalior, Madhaya Pradesh, India
| | - Dau D. Agrawal
- S.O.S in Chemistry, Jiwaji University, Gwalior, Madhaya Pradesh, India
| | | | - Ray J. Butcher
- Department of Chemistry, Howard University, Washington, District of Columbia, USA
| | - S. Muthu
- Department of Physics, Aringnar Anna Govt. Arts College, Cheyyar, India
| | - Musheer Ahmad
- Department of Applied Chemistry, Faculty of Engineering and Technology, ZHCET, Aligarh Muslim University, Aligarh, India
| | - Khaled Althubeiti
- Department of Chemistry, College of Science, Taif University, Taif, Saudi Arabia
| | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute Agra, Agra, Uttar Pradesh, India
| | - Saleem Javed
- Department of Chemistry, Institute of H. Science, Dr. Bhimrao Ambedkar University, Agra, Uttar Pradesh, India
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Çakmak Ş, Demircioğlu Z, Uzun S, Veyisoğlu A, Yakan H, Ersanli CC. Synthesis, X-ray structure, antimicrobial activity, DFT and molecular docking studies of N-(thiophen-2-ylmethyl)thiophene-2-carboxamide. ACTA CRYSTALLOGRAPHICA SECTION C STRUCTURAL CHEMISTRY 2022; 78:390-397. [DOI: 10.1107/s2053229622006283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/14/2022] [Indexed: 11/10/2022]
Abstract
In the present study, N-(thiophen-2-ylmethyl)thiophene-2-carboxamide, C10H9NOS2, (I), was obtained by the reaction of thiophene-2-carbonyl chloride and thiophen-2-ylmethanamine. Characterization of (I) was carried out using X-ray diffraction, spectroscopic techniques and elemental analyses. The DFT/B3LYP/6-311++G(d,p) theoretical level was successfully applied to calculate the optimized geometry and the local and global chemical activity parameters. The results obtained show good agreement between the experimental and theoretical geometrical parameters. The local and global chemical activity parameters were examined to determine the electrophilic and nucleophilic sites in (I). The natural bond orbital (NBO) analysis of (I) gives an efficient methodology for investigating the inter- and intramolecular bonding, as well as giving a convenient basis for investigating charge transfer or conjugative interactions in molecular systems. Also, the antimicrobial activity of (I) was investigated against eight microorganisms using the microdilution method and it is found to have an effective antibacterial activity. In addition, molecular docking studies were calculated in order to understand the nature of the binding of (I) with a lung cancer protein (PDB entry 1x2j).
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Fatima A, Singh M, Abualnaja KM, Althubeiti K, Muthu S, Siddiqui N, Javed S. Experimental Spectroscopic, Structural (Monomer and Dimer), Molecular Docking, Molecular Dynamics Simulation and Hirshfeld Surface Analysis of 2-Amino-6-Methylpyridine. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2080726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Aysha Fatima
- School of Studies in Chemistry, Jiwaji University, Gwalior, India
- Department of Chemistry, Institute of H. Science, Dr. Bhimrao Ambedkar University, Agra, India
| | - Meenakshi Singh
- Department of Chemistry, Institute of H. Science, Dr. Bhimrao Ambedkar University, Agra, India
| | - Khamael M. Abualnaja
- Department of Chemistry, College of Science, Taif University, Taif, Saudi Arabia
| | - Khaled Althubeiti
- Department of Chemistry, College of Science, Taif University, Taif, Saudi Arabia
| | - S. Muthu
- Department of Physics, Arignar Anna Government Arts College, Cheyyar, India
| | - Nazia Siddiqui
- Department of Chemistry, Dayalbagh Educational Institute, Agra, India
| | - Saleem Javed
- Department of Chemistry, Institute of H. Science, Dr. Bhimrao Ambedkar University, Agra, India
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Palaniyasan E, Radhakrishnan A, Maidur SR, Patil PS, Jeyaperumal KS. Evolution of physicochemical properties of 2-(2-(4-(4-chloro) phenyl) vinyl)-1, 1, 3-trimethyl-1H-benzo[e] Indolium iodide via experimental and quantum chemical calculation for third-harmonic generation applications. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Fatima A, Khanum G, Verma I, Butcher RJ, Siddiqui N, Srivastava SK, Javed S. Synthesis, Characterization, Crystal Structure, Hirshfeld Surface, Electronic Excitation, Molecular Docking, and DFT Studies on 2-Amino Thiophene Derivative. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2032769] [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]
Affiliation(s)
- Aysha Fatima
- S.O.S in Chemistry, Jiwaji University, Gwalior, MP, India
- Department of Chemistry, Institute of H. Science, Khandari, Dr. Bhimrao Ambedkar University, Agra, UP, India
| | - Ghazala Khanum
- S.O.S in Chemistry, Jiwaji University, Gwalior, MP, India
| | - Indresh Verma
- Department of Chemistry, Indian Institute of Technology, Kanpur, UP, India
| | - Ray J. Butcher
- Department of Chemistry, Howard University, Washington, DC, USA
| | | | | | - Saleem Javed
- Department of Chemistry, Institute of H. Science, Khandari, Dr. Bhimrao Ambedkar University, Agra, UP, India
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Fatima A, Khanum G, Sharma A, Garima K, Savita S, Verma I, Siddiqui N, Javed S. Computational, spectroscopic, Hirshfeld surface, electronic state and molecular docking studies on phthalic anhydride. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131571] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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20
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Khanum G, Fatima A, Siddiqui N, Agarwal D, Butcher R, Srivastava SK, Javed S. Synthesis, single crystal, characterization and computational study of 2-amino-N-cyclopropyl-5-ethyl-thiophene-3-carboxamide. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131890] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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21
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Fatima A, Khanum G, Sharma A, Verma I, Arora H, Siddiqui N, Javed S. Experimental Spectroscopic, Computational, Hirshfeld Surface, Molecular Docking Investigations on 1H-Indole-3-Carbaldehyde. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2026989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Aysha Fatima
- S.O.S in chemistry, Jiwaji University, Gwalior, M. P., India
- Department of Chemistry, Dr. Bhimrao Ambedkar University, Agra, U.P., India
| | - Ghazala Khanum
- S.O.S in chemistry, Jiwaji University, Gwalior, M. P., India
| | - Arun Sharma
- S.O.S in chemistry, Jiwaji University, Gwalior, M. P., India
| | - Indresh Verma
- Department of Chemistry, Indian Institute of Technology, Kanpur, U.P., India
| | - Himanshu Arora
- Department of Basic and Applied Sciences, School of Engineering and Sciences, G D Goenka University, Gurugram, Haryana, India
| | | | - Saleem Javed
- Department of Chemistry, Dr. Bhimrao Ambedkar University, Agra, U.P., India
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Fatima A, Khanum G, Savita S, Pooja K, Verma I, Siddiqui N, Javed S. Quantum computational, spectroscopic, Hirshfeld surface, electronic state and molecular docking studies on sulfanilic acid: An anti-bacterial drug. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117150] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Jagan R, Sathya D, Sivakumar K. Interplay of Hydrogen and Halogen Bonds in Supramolecular Framework of Oxy-Acid Based 3-Chloroanilinium Hydrogen Sulfate, Bis(2,5-dichloroanilinium) Sulfate and 2,5-Dichloroanilinium Perchlorate Hydrate Salts. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s106377452106016x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Fatima A, Singh M, Agarwal N, Verma I, Butcher RJ, Siddiqui N, Javed S. Spectroscopic, molecular structure, electronic, Hirshfeld surface, molecular docking, and thermodynamic investigations of trans-4-hydroxy-L-proline by DFT method. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117549] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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25
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Quantum Chemical, experimental spectroscopic, Hirshfeld surface and molecular docking studies of the anti-microbial drug Sulfathiazole. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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Synthesis, computational, spectroscopic, hirshfeld surface, electronic state and molecular docking studies on diethyl-5-amino-3-methylthiophene-2,4-dicarboxylate. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.139103] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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Savita S, Fatima A, Garima K, Pooja K, Verma I, Siddiqui N, Javed S. Experimental spectroscopic, Quantum computational, Hirshfeld surface and molecular docking studies on 3-Pyridinepropionic acid. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Medetalibeyoglu H. Synthesis, Antioxidant Activity, Spectroscopic, Electronic, Nonlinear Optical (NLO) and Thermodynamic Properties of 2-Ethoxy-4-[(5-oxo-3-phenyl-1,5-dihydro-1,2,4-triazol-4-ylimino)-methyl]-phenyl-4-methoxybenzoate: A Theoretical and Experimental Study. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2021. [DOI: 10.1007/s13738-021-02401-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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29
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Tankov I, Yankova R. Nature of the chemical interactions in the multifunctional ionic liquid tris(2-aminothiazolium) hydrogen sulfate sulfate monohydrate. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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The Influence of Solvent on the Crystal Packing of Ethacridinium Phthalate Solvates. MATERIALS 2020; 13:ma13225073. [PMID: 33182832 PMCID: PMC7697871 DOI: 10.3390/ma13225073] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/29/2020] [Accepted: 11/05/2020] [Indexed: 11/16/2022]
Abstract
The synthesis, structural characterization and influence of solvents on the crystal packing of solvated complexes of ethacridine with phthalic acid: 6,9-diamino-2-ethoxyacridinium phthalate methanol solvate (1), 6,9-diamino-2-ethoxyacridinium phthalate ethanol solvate (2), 6,9-diamino-2-ethoxyacridinium phthalate isobutanol solvate (3), and 6,9-diamino-2-ethoxyacridinium phthalate tert-butanol solvate monohydrate (4) are described in this article. Single-crystal XRD measurements revealed that the compounds 1–4 crystallized in the triclinic P-1 space group, and the 6,9-diamino-2-ethoxyacridinium cations, phthalic acid anions and solvent molecules interact via strong N–H···O, O–H···O, C–H···O hydrogen bonds, and C–H···π and π–π interactions to form different types of basic structural motifs, such as: heterotetramer bis[···cation···anion···] in compound 1 and 2, heterohexamer bis[···cation···alcohol···anion···] in compound 3, and heterohexamer bis[···cation···water···anion···] in compound 4. Presence of solvents molecule(s) in the crystals causes different supramolecular synthons to be obtained and thus has an influence on the crystal packing of the compounds analyzed.
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Anti-Tubercular Properties of 4-Amino-5-(4-Fluoro-3- Phenoxyphenyl)-4 H-1,2,4-Triazole-3-Thiol and Its Schiff Bases: Computational Input and Molecular Dynamics. Antibiotics (Basel) 2020; 9:antibiotics9090559. [PMID: 32878018 PMCID: PMC7560126 DOI: 10.3390/antibiotics9090559] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/26/2020] [Accepted: 08/29/2020] [Indexed: 12/26/2022] Open
Abstract
In the present investigation, the parent compound 4-amino-5-(4-fluoro-3-phenoxyphenyl)-4H-1,2,4-triazole-3-thiol (1) and its Schiff bases 2, 3, and 4 were subjected to whole-cell anti-TB against H37Rv and multi-drug-resistant (MDR) strains of Mycobacterium tuberculosis (MTB) by resazurin microtiter assay (REMA) plate method. Test compound 1 exhibited promising anti-TB activity against H37Rv and MDR strains of MTB at 5.5 µg/mL and 11 µg/mL, respectively. An attempt to identify the suitable molecular target for compound 1 was performed using a set of triazole thiol cellular targets, including β-ketoacyl carrier protein synthase III (FABH), β-ketoacyl ACP synthase I (KasA), CYP121, dihydrofolate reductase, enoyl-acyl carrier protein reductase, and N-acetylglucosamine-1-phosphate uridyltransferase. MTB β-ketoacyl ACP synthase I (KasA) was identified as the cellular target for the promising anti-TB parent compound 1 via docking and molecular dynamics simulation. MM(GB/PB)SA binding free energy calculation revealed stronger binding of compound 1 compared with KasA standard inhibitor thiolactomycin (TLM). The inhibitory mechanism of test compound 1 involves the formation of hydrogen bonding with the catalytic histidine residues, and it also impedes access of fatty-acid substrates to the active site through interference with α5–α6 helix movement. Test compound 1-specific structural changes at the ALA274–ALA281 loop might be the contributing factor underlying the stronger anti-TB effect of compound 1 when compared with TLM, as it tends to adopt a closed conformation for the access of malonyl substrate to its binding site.
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Influence of Halogen Substituent on the Self-Assembly and Crystal Packing of Multicomponent Crystals Formed from Ethacridine and Meta-Halobenzoic Acids. CRYSTALS 2020. [DOI: 10.3390/cryst10020079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In order to determine the influence of halogen substituent on the self-assembly of the 6,9-diamino-2-ethoxyacridinium cations and 3-halobenzoate anions in the crystals formed from ethacridine and halobenzoic acids, the series of ethacridinium meta-halobenzoates dihydrates: ethacridinium 3-chlorobenzoate dihydrate (1), ethacridinium 3-bromobenzoate dihydrate (2), and ethacridinium 3-iodobenzoate dihydrate (3), were synthesized and structurally characterized. Single-crystal X-ray diffraction measurements showed that the title compounds crystallized in the monoclinic P21/c space group and are isostructural. In the crystals of title compounds, the ions and water molecules interact via N–H⋯O, O–H⋯O and C–H⋯O hydrogen bonds and π–π stacking interactions to produce blocks. The relationship between the distance X⋯O between the halogen atom (X=Cl, Br, I) of meta-halobenzoate anion and the O-atom from the ethoxy group of cation from neighbouring blocks and crystal packing is observed in the crystals of the title compounds.
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Role of lone pair- π interaction and halogen bonding in the crystal packing of 1,2,4-oxadiazole derivatives. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.07.107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Tankov I, Yankova R. Mechanistic investigation of molecular geometry, intermolecular interactions and spectroscopic properties of pyridinium nitrate. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 219:53-67. [PMID: 31030047 DOI: 10.1016/j.saa.2019.04.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/10/2019] [Accepted: 04/14/2019] [Indexed: 06/09/2023]
Abstract
The molecular structure, vibrational frequencies of the fundamental modes and electronic transitions of the ionic liquid pyridinium nitrate ([H-Pyr]+[NO3]-) have been determined by means of density functional theory (DFT) at B3LYP/6-311++G (2d,2p) level. The chemical bonds nature and the intermolecular interactions in the title compound were investigated using the Quantum theory of atoms in molecules and Hirshfeld surface analysis. Natural bond orbital analysis has been performed in order to elucidate the hybridization and delocalization of electron density within the ion pair [H-Pyr]+[NO3]-. A detailed vibrational spectral analysis was carried out and the assignments of the observed bands have been proposed on the basis of potential energy distribution. A good correlation between experimental and theoretical IR frequencies was observed. To study the charge transfers occurred in the title molecule, UV-vis analysis was conducted.
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Affiliation(s)
- Ivaylo Tankov
- University "Prof. Dr. Assen Zlatarov" Burgas, 8010, Bulgaria.
| | - Rumyana Yankova
- University "Prof. Dr. Assen Zlatarov" Burgas, 8010, Bulgaria
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Yankova R, Dimov M, Dobreva K, Stoyanova A. Electronic structure, reactivity, and Hirshfeld surface analysis of carvone. JOURNAL OF CHEMICAL RESEARCH 2019. [DOI: 10.1177/1747519819863957] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The density functional theory (at the B3LYP level using 6-311++G(2d,2p) basis set) was used for the investigation of the geometry and electronic properties of the carvone. The electronic properties and chemical activity of the titled compound were investigated by means of several theoretical approaches, molecular electrostatic potential surface, natural bond orbital, and frontier molecular orbital analyses. It was established that the oxygen atom in the structure characterized the electrophilic reactivity; the positive regions are localized on the hydrogen atoms, which can be considered as possible sites for nucleophilic attack. A detailed analysis of the intermolecular interactions via Hirshfeld surface analysis and fingerprint plots revealed that the carvone structure is stabilized mainly by the formation of O. . .H/H. . .O hydrogen bonds. However, close contacts were established between C. . .H/H. . .C and H. . .H contacts.
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Affiliation(s)
| | - Milen Dimov
- University “Prof. Dr. Assen Zlatarov,” Burgas, Bulgaria
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Bhowal R, Biswas S, Thumbarathil A, Koner AL, Chopra D. Exploring the Relationship between Intermolecular Interactions and Solid-State Photophysical Properties of Organic Co-Crystals. THE JOURNAL OF PHYSICAL CHEMISTRY C 2019; 123:9311-9322. [DOI: 10.1021/acs.jpcc.8b10643] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Affiliation(s)
- Rohit Bhowal
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, India
| | - Suprakash Biswas
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, India
| | - Athulbabu Thumbarathil
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, India
| | - Apurba L. Koner
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, India
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462066, India
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Tankov I, Yankova R. Hirshfeld surface, DFT vibrational (FT-IR) and electronic (UV–vis) studies on 4-amino-1H-1,2,4-triazolium nitrate. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.11.050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Shukla R, Nayak SK, Chopra D, Reddy MK, Guru Row T. Observation of 3D isostructurality in halogen substituted N -benzoyl- N -phenylbenzamides. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.03.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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39
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Shukla R, Nayak SK, Chopra D, Reddy MK, Guru Row TN. Quantitative investigation of intermolecular interactions in dimorphs of 3-Chloro-N-(2-fluorophenyl)benzamide and 2-Iodo-N-(4- bromophenyl)benzamide. J CHEM SCI 2018. [DOI: 10.1007/s12039-018-1444-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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40
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Shukla R, Chopra D. Characterization of the short OC⋯OC π-hole tetrel bond in the solid state. CrystEngComm 2018. [DOI: 10.1039/c8ce00697k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An in-depth structure database investigation and experimental charge density analysis of the OC⋯OC π-hole tetrel bonds.
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Affiliation(s)
- Rahul Shukla
- Crystallography and Crystal Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal
- 462066 India
| | - Deepak Chopra
- Crystallography and Crystal Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal
- 462066 India
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Mandal A, Patel BK. Rationalization of weak interactions in two fluorescence active imidazo-[1,5-a]-pyridine derivatives: A combined experimental and computational study. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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42
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Tedesco C, Macedi E, Meli A, Pierri G, Della Sala G, Drathen C, Fitch AN, Vaughan GBM, Izzo I, De Riccardis F. Synthesis, crystallization, X-ray structural characterization and solid-state assembly of a cyclic hexapeptoid with propargyl and methoxyethyl side chains. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2017; 73:399-412. [DOI: 10.1107/s2052520617002505] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 02/13/2017] [Indexed: 05/29/2023]
Abstract
The synthesis and the structural characterization of a cyclic hexapeptoid with four methoxyethyl and two propargyl side chains have disclosed the presence of a hydrate crystal form [form (I)] and an anhydrous crystal form [form (II)]. The relative amounts of form (I) and form (II) in the as-purified product were determined by Rietveld refinement and depend on the purification procedures. In crystal form (I), peptoid molecules assemble in a columnar arrangement by means of side-chain-to-backbone C=CH...OC hydrogen bonds. In the anhydrous crystal form (II), cyclopeptoid molecules form ribbons by means of backbone-to-backbone CH2...OC hydrogen bonds, thus mimicking β-sheet secondary structures in proteins. In both crystal forms side chains act as joints among the columns or the ribbons and contribute to the stability of the whole solid-state assembly. Water molecules in the hydrate crystal form (I) bridge columns of cyclic peptoid molecules, providing a more efficient packing.
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Shukla R, Mohan T, Vishalakshi B, Chopra D. Synthesis, crystal structure and theoretical analysis of intermolecular interactions in two biologically active derivatives of 1,2,4-triazoles. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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44
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Shukla R, Khan I, Ibrar A, Simpson J, Chopra D. Complex electronic interplay of σ-hole and π-hole interactions in crystals of halogen substituted 1,3,4-oxadiazol-2(3H)-thiones. CrystEngComm 2017. [DOI: 10.1039/c7ce00678k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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45
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SHUKLA RAHUL, CHOPRA DEEPAK. Understanding the effect of substitution on the formation of S. . .F chalcogen bond. J CHEM SCI 2016. [DOI: 10.1007/s12039-016-1176-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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46
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Panini P, Gonnade RG, Chopra D. Experimental and computational analysis of supramolecular motifs involving Csp2(aromatic)–F and CF3groups in organic solids. NEW J CHEM 2016. [DOI: 10.1039/c5nj03211c] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural motif by Csp2–F and CF3group have been identified and investigated by the PIXEL method and QTAIM approach.
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Affiliation(s)
- Piyush Panini
- Crystallography and Crystal Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India-462066
| | - Rajesh G. Gonnade
- Center for Materials Characterization (CMC)
- CSIR-National Chemical Laboratory
- Pune-411008
- India
| | - Deepak Chopra
- Crystallography and Crystal Chemistry Laboratory
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- India-462066
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Dey D, Chopra D. Solvatomorphism in (Z)-4-fluoro-N′-(3-fluorophenyl)benzimidamide: the role of intermolecular O–H⋯F interaction. CrystEngComm 2016. [DOI: 10.1039/c6ce01668e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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48
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Verma SK, Singh VK. Synthesis and characterization of ferrocene functionalized transition metal dithiocarbamate complexes: Investigations of antimicrobial, electrochemical properties and a new polymorphic form of [Cu{κ2S,S–S2CN(CH2C4H3O)CH2Fc}2]. J Organomet Chem 2015. [DOI: 10.1016/j.jorganchem.2015.05.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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49
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The Bright Future of Unconventional σ/π-Hole Interactions. Chemphyschem 2015; 16:2496-517. [DOI: 10.1002/cphc.201500314] [Citation(s) in RCA: 475] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Indexed: 01/25/2023]
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50
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The role of hydrogen bonding on supramolecular assembly of the mercury coordination compounds and final structure influenced by solvent effect. Inorganica Chim Acta 2015. [DOI: 10.1016/j.ica.2014.12.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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