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Sankar Ganesan T, Elangovan N, Thirumavalavan M, Seenan S, Sowrirajan S, Chandrasekar S, Arumugam N, Almansour AI, Mahalingam SM, V M DD, Kanchi S, Sivaramakrishnan V. Synthesis, topology, molecular docking and dynamics studies of o-phenylenediamine derivative. J Biomol Struct Dyn 2024:1-20. [PMID: 38577881 DOI: 10.1080/07391102.2024.2317981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/07/2024] [Indexed: 04/06/2024]
Abstract
The N, N'-(1,2-phenylene) bis (1- (4- chlorophenyl) methanimine) (CS4) was synthesized and characterized by infrared (IR), absorption (UV-vis) and NMR (1H and 13C) spectral analyses. The structural parameters, vibrational frequencies, potential energy and the distribution analysis (PED) were calculated by using DFT with the basis set of B3LYP/cc-pVDZ and these spectral values were compared to the experimental values. HOMO and LUMO studied were performed in order to understand the stability and biological activity of the compound. The most reactive sites on the compound were investigated by utilizing MEP energy surface and Fukui function descriptor with the natural population analysis (NPA) of the charges. The study of the natural bond orbitals (NBO) reveals the delocalization of the intramolecular interaction of the charges in the compound. Additionally, topological investigations (ELF, LOL), determination of thermodynamic parameters and noncovalent interaction (NCI) study by using topology (RDG) analysis were also carried out. Finally, the molecular docking and molecular dynamics simulations was carried out by examining against glycosylphosphatidylinositol phospholipase D inhibitor receptor for distinct protein targets (3MZG).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- T Sankar Ganesan
- Department of Chemistry, Arignar Anna Government Arts College, Affiliated to Bharathidasan University, Tiruchirappalli, Tamilnadu, India
| | - N Elangovan
- Research Centre for Computational and Theoretical Chemistry, Tiruchirappalli, Tamilnadu, India
| | | | - Shanthi Seenan
- Department of Chemistry, Saveetha Engineering College, Chennai, Tamil Nadu, India
| | - S Sowrirajan
- Research Centre for Computational and Theoretical Chemistry, Tiruchirappalli, Tamilnadu, India
| | - S Chandrasekar
- Department of Chemistry, Arignar Anna Government Arts College, Affiliated to Bharathidasan University, Tiruchirappalli, Tamilnadu, India
| | - Natarajan Arumugam
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | | | - Datta Darshan V M
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, Andhra Pradesh, India
| | - Subbarao Kanchi
- Department of Physics, Sri Sathya Sai Institute of Higher Learning, Puttaparthi, Andhra Pradesh, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Anantapur, Andhra Pradesh, India
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Iyasamy S, Varadharajan K, Sivagnanam S. Density Functional Theory Calculations, Spectroscopic (FT-IR, FT-RAMAN), Frontier Molecular Orbital, Molecular Electrostatic Potential Analysis of 5-Fluoro-2-Methylbenzaldehyde. Z PHYS CHEM 2016. [DOI: 10.1515/zpch-2016-0839] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The FT-IR and FT-Raman spectra of 5-fluoro-2-methylbenzaldehyde (5F2MB) have been recorded in the regions 4000–400 cm−1 and 4000–100 cm−1, respectively. Using the observed FT-IR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of vibrations of the compound were carried out. The optimum molecular geometry, vibrational frequencies and Raman scattering activities were calculated by density functional theory with B3LYP/6-311+G** basis sets. A close agreement was achieved between the calculated and observed frequencies by refinement of scale factors. Unambiguously normal modes of vibrational assignments have been made with the help of the GUASSVIEW 5.0 program and the potential energy distribution (PED) calculated by the density functional theory calculations. Natural bonding orbital (NBO) analyses were carried out to discuss the stability of the molecule. The molecular electrostatic potential (MEP) map and electron density map were drawn and analyzed. Using nuclear magnetic resonance (NMR) analysis, the chemical shifts of hydrogen atoms and carbon atoms were calculated. The charge distribution, Mullikan atomic charge values and HOMO–LUMO energy have been calculated to explore the reasons for the change in biological activity. Furthermore, the first hyperpolarizability and the dipole moment of the molecule have also been calculated.
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Affiliation(s)
- Sehar Iyasamy
- Department of Physics, Aditanar College of Arts and Science, Tiruchendur, Tamilnadu – 628215, India
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Morzyk-Ociepa B, Dysz K, Turowska-Tyrk I, Michalska D. X-ray crystal structure, vibrational spectra and DFT calculations of 3-chloro-7-azaindole: a case of dual N-H⋯N hydrogen bonds in dimers. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt B:405-415. [PMID: 25315872 DOI: 10.1016/j.saa.2014.09.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/05/2014] [Accepted: 09/18/2014] [Indexed: 06/04/2023]
Abstract
3-Chloro-7-azaindole (3Cl7AI) is the carrier ligand in a new anticancer platinum(II) agent cis-[PtCl2(3Cl7AI)2]. In this work 3Cl7AI has been studied by a single crystal X-ray diffraction, infrared and Raman spectroscopy and density functional calculations. The compound crystallizes in the monoclinic system, space group P21/n, with a=12.3438(3), b=3.85964(11), c=14.4698(4)Å, β=100.739(2)°, V=677.31(3)Å(3) and Z=4. In the crystal, a pair of 3Cl7AI molecules forms a centrosymmetric dimer linked by the moderately strong dual N-H⋯N hydrogen bonds. The nitrogen atom in the pyrrole ring acts as the proton donor, while the nitrogen atom in the pyridine ring is the proton acceptor. The FT-IR and FT-Raman spectra (3500-60 cm(-1)) have been recorded. The theoretical studies on the molecular structures and vibrational spectra of the monomeric and dimeric forms of 3Cl7AI and its N-deuterated derivative were performed using the B3LYP method with 6-311++G(d,p) basis set. The theoretically predicted Raman spectrum for the dimer shows very good agreement with experiment. Detailed vibrational assignments for the two isotopomers have been made on the basis of the calculated potential energy distributions (PEDs). The dual N-H⋯N hydrogen bonds in 3Cl7AI dimer are characterized by a very broad and complicated structure of the absorption band between 3300 and 2500 cm(-1), which is caused by multiple Fermi resonances between the N-H stretching vibration and various combinations bands.
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Affiliation(s)
- Barbara Morzyk-Ociepa
- Institute of Chemistry, Environmental Protection and Biotechnology, Jan Długosz University, Armii Krajowej 13/15 Ave., 42-200 Częstochowa, Poland.
| | - Karolina Dysz
- Institute of Chemistry, Environmental Protection and Biotechnology, Jan Długosz University, Armii Krajowej 13/15 Ave., 42-200 Częstochowa, Poland
| | - Ilona Turowska-Tyrk
- Faculty of Chemistry, Wrocław University of Technology, Smoluchowskiego 23, 50-370 Wrocław, Poland
| | - Danuta Michalska
- Faculty of Chemistry, Wrocław University of Technology, Smoluchowskiego 23, 50-370 Wrocław, Poland
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