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Palafox MA, Kattan D, de Pedraza Velasco ML, Isasi J, Posada-Moreno P, Rani K, Singh SP, Rastogi VK. Base pairs with 4-amino-3-nitrobenzonitrile: comparison with the natural WC pairs. Dimer and tetramer forms, Infrared and Raman spectra, and several proposed antiviral modified nucleosides. J Biomol Struct Dyn 2022:1-23. [PMID: 35583120 DOI: 10.1080/07391102.2022.2069864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Base pairs of 4-amino-3-nitrobenzonitrile (4A-3NBN) molecule with uracil, thymine and cytosine nucleobases were optimized and compared to natural Watson-Crick (WC) pairs. The slightly greater flexibility of the -NO2 group of 4A-3NBN than the N3-H group of the natural nucleobases together with a noticeable higher dipole moment of its pairs can facilitate disruption of the DNA/RNA helix formation. Several new mutagenic modified nucleosides with 4A-3NBN and 3-amino-2-nitrobenzonitrile (3A-2NBN) were proposed as antiviral prodrugs and their base pairs optimized. The special characteristics of these prodrugs appear appropriated for their clinical use. The counterpoise (CP) corrected interaction energies of the base pairs were calculated and compared to the natural ones. The M06-2X DFT method was used for this purpose. The molecular structure of 4A-3NBN was analyzed in detail and the crystal unit cell was simulated by a tetramer form and eight dimer forms. The performance of the B3LYP, X3LYP and M06-2X methods was tested on the vibrational wavenumbers in the monomer, dimer and tetramer forms of 4A-3NBN. The observed IR and Raman bands were assigned according to the optimum dimer II form determined by B3LYP and by the tetramer form calculated by M06-2X, which is the expected unit cell that forms the crystal net. The two best scaling procedures were used.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- M Alcolea Palafox
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
| | - D Kattan
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense, Madrid, Spain
| | - M L de Pedraza Velasco
- Dpto. de Enfermería, Facultad de Enfermería, Fisioterapia y Podología, UCM, Madrid, Spain
| | - J Isasi
- Dpto. de Química Inorgánica, Facultad de Ciencias Químicas, UCM, Madrid, Spain
| | - P Posada-Moreno
- Dpto. de Enfermería, Facultad de Enfermería, Fisioterapia y Podología, UCM, Madrid, Spain.,Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
| | - Kaushal Rani
- Department of Physics, Meerut College, Meerut, India
| | - S P Singh
- Department of Physics, Dr B R Ambedkar College, Mainpuri, India
| | - V K Rastogi
- Indian Spectroscopy Society, Ghaziabad, India
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Alcolea Palafox M, Bena Jothy V, Singhal S, Hubert Joe I, Kumar S, Rastogi VK. FT-IR, FT-Raman spectra and other molecular properties of 3,5-dichlorobenzonitrile: a DFT study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 116:509-517. [PMID: 23978738 DOI: 10.1016/j.saa.2013.07.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 07/12/2013] [Accepted: 07/21/2013] [Indexed: 06/02/2023]
Abstract
The IR and Raman spectra of 3,5-dichlorobenzonitrile (3,5-DCBN) molecule were recorded at room temperature and then the assignment of the observed fundamental bands were achieved by the aid of the theoretical vibrational spectral data obtained from a quantum chemical study carried out for the free molecule case. In the calculations performed to determine the molecular geometry, vibrational spectral data and thermodynamic parameters, Møller-Plesset second order perturbation theory (MP2) and hybrid Density Functional Theory (DFT) types of electronic structure methods, B3LYP and B3PW91, were used. The overestimations of the calculated harmonic wavenumbers were efficiently corrected by the aid of a specific scaling procedure. This empirical scaling process significantly increased the reliability of our assignments and analyses on the observed bands due to different vibrational normal modes of the molecule. For the majority of the normal modes, the deviations between the corresponding experimental and scaled theoretical wavenumbers have located in the expected range. A correct characterization of the normal modes is of vital importance in the assignment of the observed bands, and this was successfully done by the aid of the Potential Energy Distributions (PEDs) separately calculated for each normal mode of 3,5-DCBN.
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Affiliation(s)
- M Alcolea Palafox
- Departamento de Química-Física I, Facultad de Ciencias Químicas, Universidad Complutense, Madrid 28040, Spain
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Rastogi VK, Alcolea Palafox M, Tomar R, Singh U. 2-Amino-3,5-dichlorobenzonitrile: DFT calculations in the monomer and dimer forms, FT-IR and FT-Raman spectra, molecular geometry, atomic charges and thermodynamical parameters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 110:458-470. [PMID: 23591076 DOI: 10.1016/j.saa.2013.03.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 02/21/2013] [Accepted: 03/03/2013] [Indexed: 06/02/2023]
Abstract
The experimental IR and Raman spectra of 2-amino-3,5-dichlorobenzonitrile molecule were recorded, and the results compared with theoretical values. Molecular geometry, vibrational wavenumbers and thermodynamic parameters were calculated using MP2 and DFT quantum chemical methods. With the help of specific scaling procedures for the computed wavenumbers, the experimentally observed FTIR and FT-Raman bands were analyzed and assigned to different normal modes of vibrations of the molecule. Simulations in the dimer form were carried out to improve the assignment of the bands in the solid state experimental spectra. The error obtained was in general very low. Using PED's were determined the contributions of the different modes to each wavenumber. Several general conclusions were also deduced.
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Affiliation(s)
- V K Rastogi
- Physics Department, CCS University Campus, Meerut 250 004, India.
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Sert Y, Çırak Ç, Ucun F. Vibrational analysis of 4-chloro-3-nitrobenzonitrile by quantum chemical calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 107:248-255. [PMID: 23434551 DOI: 10.1016/j.saa.2013.01.046] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 01/11/2013] [Accepted: 01/17/2013] [Indexed: 06/01/2023]
Abstract
In the present study, the experimental and theoretical harmonic and anharmonic vibrational frequencies of 4-chloro-3-nitrobenzonitrile were investigated. The experimental FT-IR (400-4000 cm(-1)) and μ-Raman spectra (100-4000 cm(-1)) of the molecule in the solid phase were recorded. Theoretical vibrational frequencies and geometric parameters (bond lengths and bond angles) were calculated using ab initio Hartree Fock (HF), density functional B3LYP and M06-2X methods with 6-311++G(d,p) basis set by Gaussian 09 W program, for the first time. The assignments of the vibrational frequencies were performed by potential energy distribution (PED) analysis by using VEDA 4 program. The theoretical optimized geometric parameters and vibrational frequencies were compared with the corresponding experimental data, and they were seen to be in a good agreement with each other. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies were found.
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Affiliation(s)
- Yusuf Sert
- Department of Physics, Faculty of Art & Sciences, Bozok University, Yozgat, Turkey.
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Ma C, Kwok WM, Matousek P, Parker AW, Phillips D, Toner WT, Towrie M. Excited States of 4-Aminobenzonitrile (ABN) and 4-Dimethylaminobenzonitrile (DMABN): Time-resolved Resonance Raman, Transient Absorption, Fluorescence, and ab Initio Calculations. J Phys Chem A 2002. [DOI: 10.1021/jp012765e] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- C. Ma
- Department of Chemistry, Imperial College, Exhibition Road, London SW7 2AY, UK, Central Laser Facility, CLRC Rutherford Appleton Laboratory, Didcot, Oxfordshire, OX11 0QX, UK, and Department of Physics, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
| | - W. M. Kwok
- Department of Chemistry, Imperial College, Exhibition Road, London SW7 2AY, UK, Central Laser Facility, CLRC Rutherford Appleton Laboratory, Didcot, Oxfordshire, OX11 0QX, UK, and Department of Physics, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
| | - P. Matousek
- Department of Chemistry, Imperial College, Exhibition Road, London SW7 2AY, UK, Central Laser Facility, CLRC Rutherford Appleton Laboratory, Didcot, Oxfordshire, OX11 0QX, UK, and Department of Physics, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
| | - A. W. Parker
- Department of Chemistry, Imperial College, Exhibition Road, London SW7 2AY, UK, Central Laser Facility, CLRC Rutherford Appleton Laboratory, Didcot, Oxfordshire, OX11 0QX, UK, and Department of Physics, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
| | - D. Phillips
- Department of Chemistry, Imperial College, Exhibition Road, London SW7 2AY, UK, Central Laser Facility, CLRC Rutherford Appleton Laboratory, Didcot, Oxfordshire, OX11 0QX, UK, and Department of Physics, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
| | - W. T. Toner
- Department of Chemistry, Imperial College, Exhibition Road, London SW7 2AY, UK, Central Laser Facility, CLRC Rutherford Appleton Laboratory, Didcot, Oxfordshire, OX11 0QX, UK, and Department of Physics, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
| | - M. Towrie
- Department of Chemistry, Imperial College, Exhibition Road, London SW7 2AY, UK, Central Laser Facility, CLRC Rutherford Appleton Laboratory, Didcot, Oxfordshire, OX11 0QX, UK, and Department of Physics, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU, UK
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