1
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Sarac K. Synthesis, Spectroscopic Properties, Quantum Chemical Calculations, and Biological Activities of 2-{[5-(2-Fluorophenyl)-4-(4-methylphenyl)-4H-1,2,4-triazol-3-yl]sulfanyl}-1-[3-methyl-3-(2,4,6-trimethylphenyl)-cyclobutyl]ethan-1-one. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1070428020010194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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2
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Sert Y, Gökce H, Chandra, Mahendra M, Srikantamurthy N, Çırak Ç. Molecular docking and vibrational spectroscopy studies of (E)-N′-hydroxy-1,3-diphenyl-4,5-dihydro-1H-pyrazole-5-carboximidamide. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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3
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Wang F, Zhao D, Dong H, Jiang L, Huang L, Liu Y, Li S. THz spectra and corresponding vibrational modes of DNA base pair cocrystals and polynucleotides. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 200:195-201. [PMID: 29689511 DOI: 10.1016/j.saa.2018.04.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/26/2018] [Accepted: 04/12/2018] [Indexed: 05/22/2023]
Abstract
The generalized energy-based fragmentation (GEBF) approach has been applied to study the THz spectra and vibrational modes of base pair cocrystals under periodic boundary conditions (denoted as PBC-GEBF). Results of vibrational mode reveal that hydrogen bonds play a pivotal role in the pairing process of base crystals, where most NH and CH bonds stretch to some extent. We also found that hydrogen bonds of a self-made A:T cocrystal completely break in a transition from liquid to the solid state, while self-made C:G cocrystal is different and easier to form a cocrystal, as confirmed by X-ray diffraction (XRD) and terahertz (THz) spectra. Furthermore, we have studied DNA polynucleotides (in both A and B forms) found that the vibrational modes changed a lot during the process of their forming double strand. Despite the key role played by hydrogen bonds, the key contribution originates from collective motions of the main skeleton. A comparative study of the spectra of some stranded fragments suggests that different sequences or forms have similar spectra in THz band. They distinguish from each other mainly in the low-frequency regions, especially below 1 THz. This study would make great contributions to the molecular dynamics model based DNA long-chain structure simulation in the future study.
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Affiliation(s)
- Fang Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China; School of Electronic and Information Engineering, Sanjiang University, Nanjing 210012, People's Republic of China
| | - Dongbo Zhao
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, 210023, People's Republic of China
| | - Ling Jiang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Lin Huang
- Forestry College, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Yunfei Liu
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, People's Republic of China.
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
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4
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Koparir P, Sarac K, Orek C, Koparir M. Molecular structure, spectroscopic properties and quantum chemical calculations of 8-t-buthyl-4-methyl-2H-chromen-2-one. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.07.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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5
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Sert Y, Mahendra M, Keskinoğlu S, Srikantamurthy N, Umesha KB, Çırak Ç. FT-IR, Laser-Raman spectra and computational analysis of 5-Methyl-3-phenylisoxazole-4-carboxylic acid. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 139:145-155. [PMID: 25554964 DOI: 10.1016/j.saa.2014.12.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/16/2014] [Accepted: 12/09/2014] [Indexed: 06/04/2023]
Abstract
In this study the experimental and theoretical vibrational frequencies of a newly synthesized anti-tumor, antiviral, hypoglycemic, antifungal and anti-HIV agent namely, 5-Methyl-3-phenylisoxazole-4-carboxylic acid has been investigated. The experimental FT-IR (4000-400 cm(-1)) and Laser-Raman spectra (4000-100 cm(-1)) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths, bond angles and torsion angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr and DFT/M06-2X: highly parametrized, empirical exchange correlation function) with 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data and results in the literature. In addition, the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy and the other related molecular energy values of the compound have been investigated by using the same theoretical calculations.
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Affiliation(s)
- Yusuf Sert
- Department of Physics, Faculty of Art & Sciences, Bozok University, Yozgat 66100, Turkey; Sorgun Vocational School, Bozok University, Yozgat 66100, Turkey.
| | - M Mahendra
- Department of Studies in Physics, Manasagangotri, University of Mysore, Mysore 570006, India
| | - S Keskinoğlu
- Department of Physics, Faculty of Art & Sciences, Bozok University, Yozgat 66100, Turkey
| | - N Srikantamurthy
- Department of Chemistry, Yuvaraja's College, University of Mysore, Mysore 570005, India
| | - K B Umesha
- Department of Chemistry, Yuvaraja's College, University of Mysore, Mysore 570005, India
| | - Ç Çırak
- Department of Physics, Faculty of Art & Sciences, Erzincan University, Erzincan 24100, Turkey
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6
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Karakaya M, Kürekçi M, Eskiyurt B, Sert Y, Çırak Ç. Experimental and computational study on molecular structure and vibrational analysis of an antihyperglycemic biomolecule: gliclazide. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 135:137-146. [PMID: 25062059 DOI: 10.1016/j.saa.2014.06.152] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/20/2014] [Accepted: 06/29/2014] [Indexed: 06/03/2023]
Abstract
In present study, the experimental and theoretical harmonic vibrational frequencies of gliclazide molecule have been investigated. The experimental FT-IR (400-4000 cm(-1)) and Laser-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) have been calculated using ab initio Hartree Fock (HF), density functional theory (B3LYP hybrid function) methods with 6-311++G(d,p) and 6-31G(d,p) basis sets by Gaussian 09W program. The assignments of the vibrational frequencies were performed by potential energy distribution (PED) analysis by using VEDA 4 program. Theoretical optimized geometric parameters and vibrational frequencies have been compared with the corresponding experimental data, and they have been shown to be in a good agreement with each other. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies have been found.
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Affiliation(s)
- Mustafa Karakaya
- Department of Energy Systems, Faculty of Engineering & Architecture, Sinop University, Sinop 57000, Turkey.
| | - Mehmet Kürekçi
- Department of Physics, Faculty of Art & Sciences, Erzincan University, Erzincan 24100, Turkey
| | - Buse Eskiyurt
- Department of Physics, Faculty of Art & Sciences, Erzincan University, Erzincan 24100, Turkey
| | - Yusuf Sert
- Department of Physics, Faculty of Art & Sciences, Bozok University, Yozgat 66100, Turkey; Sorgun Vocational School, Bozok University, Yozgat 66100, Turkey
| | - Çağrı Çırak
- Department of Physics, Faculty of Art & Sciences, Erzincan University, Erzincan 24100, Turkey
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7
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Sert Y, Balakit AA, Öztürk N, Ucun F, El-Hiti GA. Experimental (FT-IR, NMR and UV) and theoretical (M06-2X and DFT) investigation, and frequency estimation analyses on (E)-3-(4-bromo-5-methylthiophen-2-yl)acrylonitrile. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 131:502-511. [PMID: 24840492 DOI: 10.1016/j.saa.2014.04.105] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 04/16/2014] [Accepted: 04/22/2014] [Indexed: 06/03/2023]
Abstract
The spectroscopic properties of (E)-3-(4-bromo-5-methylthiophen-2-yl)acrylonitrile have been investigated by FT-IR, UV, (1)H and (13)C NMR techniques. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and angles) have been calculated using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and DFT/M06-2X (the highly parameterized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set by Gaussian 03 software, for the first time. The assignments of the vibrational frequencies have been carried out by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies were in good agreement with the corresponding experimental data, and with the results in the literature. (1)H and (13)C NMR chemical shifts were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, oscillator strength wavelengths were performed by B3LYP methods. In addition, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies and the other related molecular energy values have been calculated and depicted.
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Affiliation(s)
- Yusuf Sert
- Department of Physics, Faculty of Art & Sciences, Bozok University, Yozgat 66100, Turkey; Sorgun Vocational School, Bozok University, Yozgat 66100, Turkey.
| | - Asim A Balakit
- Department of Chemistry, College of Science for Women, University of Babylon, Babylon, Iraq; College of Pharmacy, Babylon University, Iraq
| | - Nuri Öztürk
- Department of Physics, Faculty of Art & Sciences, Süleyman Demirel University, Isparta 32100, Turkey
| | - Fatih Ucun
- Department of Physics, Faculty of Art & Sciences, Süleyman Demirel University, Isparta 32100, Turkey
| | - Gamal A El-Hiti
- Department of Optometry, College of Applied Medical Sciences, King Saud University, P.O. Box 10219, Riyadh 11433, Saudi Arabia
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8
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Sert Y, Miroslaw B, Çırak Ç, Doğan H, Szulczyk D, Struga M. Vibrational spectroscopy (FT-IR and Laser-Raman) investigation, and computational (M06-2X and B3LYP) analysis on the structure of 4-(3-fluorophenyl)-1-(propan-2-ylidene)-thiosemicarbazone. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 128:91-99. [PMID: 24662757 DOI: 10.1016/j.saa.2014.02.134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Revised: 01/31/2014] [Accepted: 02/19/2014] [Indexed: 06/03/2023]
Abstract
In this study, the experimental and theoretical vibrational spectral analysis of 4-(3-fluorophenyl)-1-(propan-2-ylidene)-thiosemicarbazone have been carried out. The experimental FT-IR (4000-400 cm(-1)) and Laser-Raman spectra (4000-100 cm(-1)) have been recorded for the solid state samples. The theoretical vibrational frequencies and the optimized geometric parameters (bond lengths and angles) have been calculated for gas phase using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set. The diversity in molecular geometry of fluorophenyl substituted thiosemicarbazones has been discussed based on the X-ray crystal structure reports and theoretical calculation results from the literature. The assignments of the vibrational frequencies have been done on the basis of potential energy distribution (PED) analysis by using VEDA4 software. A good correlation was found between the computed and experimental geometric and vibrational data. In addition, the highest occupied (HOMO) and lowest unoccupied (LUMO) molecular orbital energy levels and other related molecular energy values of the compound have been determined using the same level of theoretical calculations.
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Affiliation(s)
- Yusuf Sert
- Department of Physics, Faculty of Art & Sciences, Bozok University, Yozgat 66100, Turkey; Sorgun Vocational School, Bozok University, Yozgat 66100, Turkey.
| | - Barbara Miroslaw
- Faculty of Chemistry, Maria Curie-Sklodowska University, pl. M. Curie-Sklodowskiej 3, 20-031 Lublin, Poland
| | - Çağrı Çırak
- Department of Physics, Faculty of Art & Sciences, Erzincan University, Erzincan 24100, Turkey
| | - Hatice Doğan
- Department of Physics, Faculty of Art & Sciences, Bozok University, Yozgat 66100, Turkey
| | - Daniel Szulczyk
- Department of Medical Chemistry, Medical University of Warsaw, 02-007 Warszawa, Poland
| | - Marta Struga
- Department of Pharmacogenomics, Medical University of Warsaw, 02-097 Warszawa, Poland
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9
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Sert Y, Mahendra M, Shivashankar K, Puttaraju KB, Doğan H, Çırak Ç, Ucun F. Vibrational spectroscopy investigation using M06-2X and B3LYP methods analysis on the structure of 2-Trifluoromethyl-10H-benzo[4,5]-imidazo[1,2-a]pyrimidin-4-one. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 128:109-118. [PMID: 24662759 DOI: 10.1016/j.saa.2014.02.125] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Revised: 02/01/2014] [Accepted: 02/19/2014] [Indexed: 06/03/2023]
Abstract
In this study, the experimental and theoretical vibrational frequencies of a newly synthesized bioactive agent namely, 2-Trifluoromethyl-10H-benzo[4,5]-imidazo[1,2-a]pyrimidin-4-one (TIP) have been investigated. The experimental FT-IR (4000-400 cm(-1)) and Laser-Raman spectra (4000-100 cm(-1)) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and the optimized geometric parameters (bond lengths and bond angles) have been calculated using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data and results in the literature. In addition, the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy and the other related molecular energy values of the compound have been investigated using the same theoretical calculations.
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Affiliation(s)
- Yusuf Sert
- Department of Physics, Faculty of Art & Sciences, Bozok University, Yozgat 66100, Turkey; Sorgun Vocational School, Bozok University, Yozgat 66100, Turkey.
| | - M Mahendra
- Department of Studies in Physics, Manasagangotri, University of Mysore, Mysore 570 006, India
| | - K Shivashankar
- P.G. Department of Chemistry, Central College Campus, Bangalore University, Bangalore 560 001, India
| | - K B Puttaraju
- P.G. Department of Chemistry, Central College Campus, Bangalore University, Bangalore 560 001, India
| | - H Doğan
- Department of Physics, Faculty of Art & Sciences, Bozok University, Yozgat 66100, Turkey
| | - Çagrı Çırak
- Department of Physics, Faculty of Art & Sciences, Erzincan University, Erzincan 24100, Turkey
| | - Fatih Ucun
- Department of Physics, Faculty of Art & Sciences, Süleyman Demirel University, Isparta 32100, Turkey
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10
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Sert Y, Doğan H, Navarrete A, Somanathan R, Aguirre G, Çırak Ç. Experimental FT-IR, Laser-Raman and DFT spectroscopic analysis of 2,3,4,5,6-Pentafluoro-trans-cinnamic acid. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 128:119-126. [PMID: 24662760 DOI: 10.1016/j.saa.2014.02.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 02/04/2014] [Accepted: 02/19/2014] [Indexed: 06/03/2023]
Abstract
In this study, the experimental and theoretical vibrational frequencies of a newly synthesized 2,3,4,5,6-Pentafluoro-trans-cinnamic acid have been investigated. The experimental FT-IR (4000-400 cm(-1)) and Laser-Raman spectra (4000-100 cm(-1)) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and bond angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and DFT/M06-2X (the highly parameterized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data, and with the results in the literature. In addition, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies and the other related molecular energy values have been calculated and depicted.
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Affiliation(s)
- Yusuf Sert
- Department of Physics, Faculty of Art & Sciences, Bozok University, Yozgat 66100, Turkey; Sorgun Vocational School, Bozok University, Yozgat 66100, Turkey.
| | - Hatice Doğan
- Department of Physics, Faculty of Art & Sciences, Bozok University, Yozgat 66100, Turkey
| | - Angélica Navarrete
- Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, 22500 Tijuana, B.C., Mexico
| | - Ratnasamy Somanathan
- Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, 22500 Tijuana, B.C., Mexico
| | - Gerardo Aguirre
- Centro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, 22500 Tijuana, B.C., Mexico
| | - Çağrı Çırak
- Department of Physics, Faculty of Art & Sciences, Erzincan University, Erzincan 24100, Turkey
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Çırak Ç, Sert Y, Ucun F. Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of a biomolecule: 5-Hydroxymethyluracil. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 127:41-46. [PMID: 24632154 DOI: 10.1016/j.saa.2014.02.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 01/26/2014] [Accepted: 02/09/2014] [Indexed: 06/03/2023]
Abstract
In the present work, the experimental and theoretical vibrational spectra of 5-hydroxymethyluracil were investigated. The FT-IR (4000-400cm(-1)) spectrum of the molecule in the solid phase was recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared intensities of the title molecule in the ground state were calculated using density functional B3LYP and M06-2X methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data, and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 5-hydroxymethyluracil molecule was also simulated to evaluate the effect of intermolecular hydrogen bonding on its vibrational frequencies. It was observed that the NH stretching modes shifted to lower frequencies, while its in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular NH⋯O hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.
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Affiliation(s)
- Çağrı Çırak
- Department of Physics, Faculty of Art & Sciences, Erzincan University, Erzincan, Turkey.
| | - Yusuf Sert
- Department of Physics, Faculty of Art & Sciences, Bozok University, Yozgat, Turkey; Sorgun Vocational School, Bozok University, Yozgat 66100, Turkey
| | - Fatih Ucun
- Department of Physics, Faculty of Art & Sciences, Süleyman Demirel University, Isparta, Turkey
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12
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Sert Y, El-Emam AA, Al-Abdullah ES, Al-Tamimi AMS, Çırak Ç, Ucun F. Use of vibrational spectroscopy to study 4-benzyl-3-(thiophen-2-yl)-4,5-dihydro-1H-1,2,4-triazole-5-thione: A combined theoretical and experimental approach. SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 126:280-90. [PMID: 24608012 DOI: 10.1016/j.saa.2014.01.142] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/21/2014] [Accepted: 01/27/2014] [Indexed: 10/25/2022]
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13
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Sert Y, El-Emam AA, Al-Deeb OA, Al-Turkistani AA, Ucun F, Cırak C. The biomolecule, 2-[(2-methoxyl)sulfanyl]-4-(2-methylpropyl)-6-oxo-1,6-dihydropyrimidine-5-carbonitrile: FT-IR, Laser-Raman spectra and DFT. SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 126:86-97. [PMID: 24589995 DOI: 10.1016/j.saa.2014.01.140] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 01/21/2014] [Accepted: 01/27/2014] [Indexed: 11/25/2022]
Abstract
In this study, the experimental and theoretical vibrational frequencies of a newly synthesized potential chemotherapeutic agent namely, 2-[(2-methoxyl)sulfanyl]-4-(2-methylpropyl)-6-oxo-1,6-dihydropyrimidine-5-carbonitrile have been investigated. The experimental FT-IR (4000-400cm(-1)) and Laser-Raman spectra (4000-100cm(-1)) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and bond angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set by Gaussian 09W software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data, and with the results in the literature. In addition, the highest occupied molecular orbital (HOMO) energy, the lowest unoccupied molecular orbital (LUMO) energy and the other related molecular energy values of the compound have been investigated using the same theoretical calculations.
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Affiliation(s)
- Yusuf Sert
- Department of Physics, Faculty of Art & Sciences, Bozok University, Yozgat 66100, Turkey.
| | - Ali A El-Emam
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Omar A Al-Deeb
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | | | - Fatih Ucun
- Department of Physics, Faculty of Art & Sciences, Süleyman Demirel University, Isparta 32100, Turkey
| | - Cağrı Cırak
- Department of Physics, Faculty of Art & Sciences, Erzincan University, Erzincan 24100, Turkey
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14
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Sert Y, Al-Turkistani AA, Al-Deeb OA, El-Emam AA, Ucun F, Çırak Ç. Experimental FT-IR, Laser-Raman and DFT spectroscopic analysis of a potential chemotherapeutic agent 6-(2-methylpropyl)-4-oxo-2-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5-carbonitrile. SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 120:97-105. [PMID: 24177876 DOI: 10.1016/j.saa.2013.09.138] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 09/07/2013] [Accepted: 09/29/2013] [Indexed: 11/27/2022]
Abstract
In this study, the experimental and theoretical vibrational frequencies of a newly synthesized potential chemotherapeutic agent namely, 6-(2-methylpropyl)-4-oxo-2-sulfanylidene-1,2,3,4-tetrahydropyrimidine-5-carbonitrile have been investigated. The experimental FT-IR (4000-400 cm(-1)) and Laser-Raman spectra (4000-100 cm(-1)) of the molecule in solid phase have been recorded. The theoretical vibrational frequencies and optimized geometric parameters (bond lengths and bond angles) have been calculated by using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set by Gaussian 09 W software, for the first time. The assignments of the vibrational frequencies have been done by potential energy distribution (PED) analysis by using VEDA 4 software. The theoretical optimized geometric parameters and vibrational frequencies have been found to be in good agreement with the corresponding experimental data, and with the results in the literature. In addition, the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies and the other related molecular energy values have been calculated and depicted.
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Affiliation(s)
- Yusuf Sert
- Department of Physics, Faculty of Art and Sciences, Bozok University, Yozgat 66100, Turkey.
| | | | - Omar A Al-Deeb
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ali A El-Emam
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Fatih Ucun
- Department of Physics, Faculty of Art and Sciences, Süleyman Demirel University, Isparta 32100, Turkey
| | - Çağrı Çırak
- Department of Physics, Faculty of Art and Sciences, Erzincan University, Yozgat 24100, Turkey
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Ten GN, Yakovleva AA, Nechaev VV, Baranov VI. Hydrogen bond effect on the structure and vibrational spectra of complementary pairs of nucleic acid bases. III. Guanine-cytosine. J STRUCT CHEM+ 2012. [DOI: 10.1134/s0022476612050034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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Cırak C, Sert Y, Ucun F. Experimental and computational study on molecular structure and vibrational analysis of a modified biomolecule: 5-bromo-2'-deoxyuridine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 92:406-414. [PMID: 22459894 DOI: 10.1016/j.saa.2012.02.053] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 01/24/2012] [Accepted: 02/02/2012] [Indexed: 05/31/2023]
Abstract
In the present study, the experimental and theoretical vibrational spectra of 5-bromo-2'-deoxyuridine 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) and density functional B3LYP method with 6-31G(d), 6-31G(d,p), 6-311++G(d) and 6-311++G(d,p) basis sets by Gaussian program, for the first time. The assignments of vibrational frequencies were performed by potential energy distribution by using VEDA 4 program. The optimized geometric parameters and theoretical vibrational frequencies are compared with the corresponding experimental data and they were seen to be in a good agreement with the each other. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies were found.
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Affiliation(s)
- Cağrı Cırak
- Department of Physics, Faculty of Art & Sciences, Erzincan University, Erzincan, Turkey.
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Molecular structure and effects of intermolecular hydrogen bonding on the vibrational spectrum of trifluorothymine, an antitumor and antiviral agent. J Mol Model 2012; 18:4453-64. [DOI: 10.1007/s00894-012-1449-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 04/25/2012] [Indexed: 01/26/2023]
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