1
|
Kumaran M, Sivaranjani T, Suresh S, Periandy S, Soundhariya S, Alibrahim KA, Alodhayb AN. Investigation of the molecular structure of CHBP, biological activities and SARS-CoV-2 protein binding interaction by molecular and biomolecular spectroscopy approaches. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 322:124853. [PMID: 39053114 DOI: 10.1016/j.saa.2024.124853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 07/10/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
The objective of this investigation is to learn more about the structural, electrical, spectroscopic, and physiochemical characteristics of biologically active cyano-4'-hydroxybiphenyl (CHBP). The title molecule's optimized conformational analysis was computed using the DFT/B3LYP/6-311++G (d, p) level of theory. The observed wavenumbers were compared with theoretical FT-IR and FT-Raman spectra. 1H and 13C NMR experimental spectra in CDCl3 solution (solvent phase) were recorded and the chemical shift was calculated. NBO analysis was used to examine the transfer of charge as well as the intermolecular and intramolecular bonding of orbitals. The TD-DFT (time-dependent DFT) approach was used to estimate theoretical values for both the gas and solvent (ethanol) in the corresponding transitional research, which was conducted using UV-Vis's spectra. Energy gap (Eg = 0.26764 eV) implies that the strong potential for charge transfer, and the stability of the CHBP compound. CHBP compound's has bioactive nature, its drug-likeness and biological properties were evaluated. The predicted topological polar surface area of 44.02 \AA2 for the molecule falls within the permissible range of < 140 \AA2. Based on the docking results, the most stable docking score value is -6.84 kcal/mol. In that interaction, MET 165 affects both phenyl rings in a pi-sulphur fashion and a single bond hydrogen with protein moieties GLN 192. This suggests that the pi-alkyl in PRO 168 is a hydroxyl substitutional ring. Our findings demonstrate the CHBP compound is a good inhibitor against the SAR COVID-19 viral protein.
Collapse
Affiliation(s)
- M Kumaran
- Department of Physics, Sri ManakulaVinayagar Engineering College, Pondicherry 605107, India
| | - T Sivaranjani
- Department of Physics, Sri ManakulaVinayagar Engineering College, Pondicherry 605107, India.
| | - S Suresh
- Department of Physics, Saveetha Engineering College (Autonomous), Thandalam, Chennai 602105, Tamil Nadu, India.
| | - S Periandy
- Department of Physics, Kanchi Mamunivar Centre for Post Graduate Studies and Research, Pondicherry, India
| | - S Soundhariya
- Department of Physics, Kanchi Mamunivar Centre for Post Graduate Studies and Research, Pondicherry, India
| | - Khuloud A Alibrahim
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Abdullah N Alodhayb
- Department of Physics and Astronomy, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| |
Collapse
|
2
|
Pandimeena G, Mathavan T, James Jebaseelan Samuel E, Milton Franklin Benial A. Quantum chemical, spectroscopic and molecular docking studies on methyl 2-chloro-6-methyl pyridine-4-carboxylate: A potential inhibitor for irritable bowel syndrome. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 294:122544. [PMID: 36868022 DOI: 10.1016/j.saa.2023.122544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 02/07/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
The methyl 2-chloro-6-methyl pyridine-4-carboxylate (MCMP) was studied using quantum chemical density functional theory (DFT) approach. The DFT/B3LYP method with cc-pVTZ basis set was employed to obtain the optimized stable structure and vibrational frequencies. The potential energy distribution (PED) calculations were used to assign the vibrational bands. The 13C NMR spectrum of MCMP molecule was simulated by the Gauge-Invariant-atomic orbital (GIAO) method using DMSO solution and the corresponding chemical shift values were calculated and observed. The maximum absorption wavelength was obtained using TD-DFT method and were compared with the experimental values. The bioactive nature of the MCMP compound was identified using the FMO analysis. The possible sites of electrophilic and nucleophilic attack were predicted using the MEP analysis and local descriptor analysis. The pharmaceutical activity of the MCMP molecule is validated through the NBO analysis. The molecular docking analysis confirms that the MCMP molecule can be used in the drug designing for the treatment of irritable bowel syndrome (IBS).
Collapse
Affiliation(s)
- G Pandimeena
- P.G., Research Department of Physics, N.M.S.S.V.N. College, Madurai 625019, Tamil Nadu, India
| | - T Mathavan
- P.G., Research Department of Physics, N.M.S.S.V.N. College, Madurai 625019, Tamil Nadu, India
| | - E James Jebaseelan Samuel
- Department of Physics, School of Advanced Sciences, Vellore Institute of Technology (VIT) university, Vellore, Tamilnadu, India
| | | |
Collapse
|
3
|
Oburn SM, Huss S, Cox J, Gerthoffer MC, Wu S, Biswas A, Murphy M, Crespi VH, Badding JV, Lopez SA, Elacqua E. Photochemically Mediated Polymerization of Molecular Furan and Pyridine: Synthesis of Nanothreads at Reduced Pressures. J Am Chem Soc 2022; 144:22026-22034. [PMID: 36417898 DOI: 10.1021/jacs.2c09204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Nanothreads are emerging one-dimensional sp3-hybridized materials with high predicted tensile strength and a tunable band gap. They can be synthesized by compressing aromatic or nonaromatic small molecules to pressures ranging from 15-30 GPa. Recently, new avenues are being sought that reduce the pressure required to afford nanothreads; the focus has been placed on the polymerization of molecules with reduced aromaticity, favorable stacking, and/or the use of higher reaction temperatures. Herein, we report the photochemically mediated polymerization of pyridine and furan aromatic precursors, which achieves nanothread formation at reduced pressures. In the case of pyridine, it was found that a combination of slow compression/decompression with broadband UV light exposure yielded a crystalline product featuring a six-fold diffraction pattern with similar interplanar spacings to previously synthesized pyridine-derived nanothreads at a reduced pressure. When furan is compressed to 8 GPa and exposed to broadband UV light, a crystalline solid is recovered that similarly demonstrates X-ray diffraction with an interplanar spacing akin to that of the high-pressure synthesized furan-derived nanothreads. Our method realizes a 1.9-fold reduction in the maximum pressure required to afford furan-derived nanothreads and a 1.4-fold reduction in pressure required for pyridine-derived nanothreads. Density functional theory and multiconfigurational wavefunction-based computations were used to understand the photochemical activation of furan and subsequent cascade thermal cycloadditions. The reduction of the onset pressure is caused by an initial [4+4] cycloaddition followed by increasingly facile thermal [4+2]-cycloadditions during polymerization.
Collapse
Affiliation(s)
- Shalisa M Oburn
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Steven Huss
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Jordan Cox
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Margaret C Gerthoffer
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sikai Wu
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Arani Biswas
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Morgan Murphy
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Vincent H Crespi
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Materials Research Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - John V Badding
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Physics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Materials Research Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, United States.,Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Steven A Lopez
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Elizabeth Elacqua
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| |
Collapse
|
4
|
Pandimeena G, Mathavan T, Samuel EJJ, Benial AMF. Conformational, spectroscopic, electronic and Molecular docking Studies on 2-methoxy-4-methyl-5-nitropyridine: A potential bioactive agent. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
5
|
Aina AA, Misquitta AJ, Price SL. A non-empirical intermolecular force-field for trinitrobenzene and its application in crystal structure prediction. J Chem Phys 2021; 154:094123. [PMID: 33685142 DOI: 10.1063/5.0043746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An anisotropic atom-atom distributed intermolecular force-field (DIFF) for rigid trinitrobenzene (TNB) is developed using distributed multipole moments, dipolar polarizabilities, and dispersion coefficients derived from the charge density of the isolated molecule. The short-range parameters of the force-field are fitted to first- and second-order symmetry-adapted perturbation theory dimer interaction energy calculations using the distributed density-overlap model to guide the parameterization of the short-range anisotropy. The second-order calculations are used for fitting the damping coefficients of the long-range dispersion and polarization and also for relaxing the isotropic short-range coefficients in the final model, DIFF-srL2(rel). We assess the accuracy of the unrelaxed model, DIFF-srL2(norel), and its equivalent without short-range anisotropy, DIFF-srL0(norel), as these models are easier to derive. The model potentials are contrasted with empirical models for the repulsion-dispersion fitted to organic crystal structures with multipoles of iterated stockholder atoms (ISAs), FIT(ISA,L4), and with Gaussian Distributed Analysis (GDMA) multipoles, FIT(GDMA,L4), commonly used in modeling organic crystals. The potentials are tested for their ability to model the solid state of TNB. The non-empirical models provide more reasonable relative lattice energies of the three polymorphs of TNB and propose more sensible hypothetical structures than the empirical force-field (FIT). The DIFF-srL2(rel) model successfully has the most stable structure as one of the many structures that match the coordination sphere of form III. The neglect of the conformational flexibility of the nitro-groups is a significant approximation. This methodology provides a step toward force-fields capable of representing all phases of a molecule in molecular dynamics simulations.
Collapse
Affiliation(s)
- Alex A Aina
- Department of Chemistry, University College London, 20 Gordon St., London WC1H 0AJ, United Kingdom
| | - Alston J Misquitta
- School of Physics and Astronomy and The Thomas Young Centre for Theory and Simulation of Materials at Queen Mary, University of London, London E1 4NS, United Kingdom
| | - Sarah L Price
- Department of Chemistry, University College London, 20 Gordon St., London WC1H 0AJ, United Kingdom
| |
Collapse
|
6
|
Abe H, Koyama Y, Kishimura H, Matsuishi K. High-pressure crystal polymorph of the protic ionic liquid: Ethylammonium nitrate. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
7
|
Funnell NP, Bull CL, Ridley CJ, Parsons S, Tellam JP. Alloxan under pressure-squeezing an extremely dense molecular crystal structure. Chem Commun (Camb) 2020; 56:6428-6431. [PMID: 32391830 DOI: 10.1039/d0cc02418j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The crystal structure of the small organic molecule, alloxan, has been explored using high-pressure neutron diffraction; its already efficiently-packed structure provides a 'chemical head-start' on the pressure experiment. At the highest pressure measured, alloxan reaches a density of 2.36 g cm-3-unprecedented for a C, H(D), N, O-containing organic material of appreciable molecular weight. Its crystal structure is stable until ca. 6.5 GPa above which the sample starts to undergo amorphisation.
Collapse
Affiliation(s)
- Nicholas P Funnell
- ISIS Neutron and Muon Facility, Rutherford Appleton Laboratory, Chilton, UK.
| | - Craig L Bull
- ISIS Neutron and Muon Facility, Rutherford Appleton Laboratory, Chilton, UK.
| | | | - Simon Parsons
- EaStCHEM School of Chemistry and Centre for Science at Extreme Conditions, University of Edinburgh, The King's Buildings, West Mains Road, Edinburgh, UK
| | - James P Tellam
- ISIS Neutron and Muon Facility, Rutherford Appleton Laboratory, Chilton, UK.
| |
Collapse
|
8
|
Fanetti S, Santoro M, Alabarse F, Enrico B, Bini R. Modulating the H-bond strength by varying the temperature for the high pressure synthesis of nitrogen rich carbon nanothreads. NANOSCALE 2020; 12:5233-5242. [PMID: 32073094 DOI: 10.1039/c9nr10716a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Carbon nanothreads are among the most attractive new materials produced under high pressure conditions. Their synthesis can be achieved by compressing the crystals of aromatic molecules exploiting both the anisotropic stress produced by the unidirectional applied force and that intrinsic to the crystal arrangement. We explored here the transformation of pyridine into a nitrogen rich carbon nanothread crystal by varying the pressure and temperature conditions with the twofold purpose of disclosing the microscopic mechanism of transformation and optimizing the yield and quality of the produced crystalline nanothreads. The best conditions for the synthesis were identified in the 14-18 GPa range at temperatures between 400 and 500 K with a product yield greater than 30%. The comparison of experiments performed under different P-T conditions allowed us to understand the role of high temperature, which is necessary to weaken or even destroy the complex H-bond network characterizing the pyridine crystal and preventing the correct approach of the aromatic rings for nanothread formation. X-ray diffraction data confirm the excellent 2D hexagonal packing of the nanothreads over several tens of microns, whereas the sharp absorption lines observed in the IR spectrum strongly support a substantial order along the threads. Diffraction results suggest a polytwistane structure of the threads derived from a Diels-Alder [4 + 2] polymerization involving molecules arranged in a slipped parallel configuration along the pyridine crystal a and b axes. Electron microscopy evidences an arrangement of the nanothreads in bundles of tens of nanometers.
Collapse
Affiliation(s)
- Samuele Fanetti
- LENS, European Laboratory for Non-linear Spectroscopy, Via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy. and ICCOM, Istituto di Chimica dei Composti OrganoMetallici, Via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Mario Santoro
- CNR-INO, Istituto Nazionale di Ottica, via Nello Carrara 1, 50019 Sesto Fiorentino, FI, Italy and LENS, European Laboratory for Non-linear Spectroscopy, Via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy.
| | - Frederico Alabarse
- ELETTRA, Elettra Sincrotrone Trieste S.C.p.A, in AREA Science Park 34149 Basovizza, Trieste, Italy
| | - Berretti Enrico
- ICCOM, Istituto di Chimica dei Composti OrganoMetallici, Via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Roberto Bini
- LENS, European Laboratory for Non-linear Spectroscopy, Via N. Carrara 1, I-50019 Sesto Fiorentino, Firenze, Italy. and ICCOM, Istituto di Chimica dei Composti OrganoMetallici, Via Madonna del Piano 10, I-50019 Sesto Fiorentino, Firenze, Italy and Dipartimento di Chimica "Ugo Schiff", Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| |
Collapse
|
9
|
A Short Review of Current Computational Concepts for High-Pressure Phase Transition Studies in Molecular Crystals. CRYSTALS 2020. [DOI: 10.3390/cryst10020081] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
High-pressure chemistry of organic compounds is a hot topic of modern chemistry. In this work, basic computational concepts for high-pressure phase transition studies in molecular crystals are described, showing their advantages and disadvantages. The interconnection of experimental and computational methods is highlighted, showing the importance of energy calculations in this field. Based on our deep understanding of methods’ limitations, we suggested the most convenient scheme for the computational study of high-pressure crystal structure changes. Finally, challenges and possible ways for progress in high-pressure phase transitions research of organic compounds are briefly discussed.
Collapse
|