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Celik S, Yilmaz G, Akyuz S, Ozel AE. Shedding light into the biological activity of aminopterin, via molecular structural, docking, and molecular dynamics analyses. J Biomol Struct Dyn 2024; 42:7773-7794. [PMID: 37565332 DOI: 10.1080/07391102.2023.2245493] [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: 05/19/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
In this study, the structural and anticancer properties of aminopterin, as well as its antiviral characteristics, were elucidated. The preferred conformations of the title molecule were investigated with semiempirical AM1 method, and the obtained the lowest energy conformer was then optimized by using density functional (DFT/B3LYP) method with 6-311++G(d,p) as basis set. The vibrational frequencies of the optimized structure were calculated by the same level of theory and were compared with the experimental values. The vibrational assignments were performed based on the computed potential energy distribution (PED) of the vibrational modes. The molecular electrostatic potential (MEP) and frontier molecular orbitals (HOMO, LUMO) analyses were carried out for the optimized structure and the chemical reactivity has been scrutinized. To enlighten the biological activity of aminopterin as anticancer and anti-COVID-19 agents, aminopterin was docked into DNA, αIIBβ3 and α5β1integrins, human dihydrofolate reductase, main protease (Mpro) of SARS-CoV-2 and SARS-CoV-2/ACE2 complex receptor. The binding mechanisms of aminopterin with the receptors were clarified. The molecular docking results revealed the strong interaction of the aminopterin with DNA (-8.2 kcal/mol), αIIBβ3 and α5β1 integrins (-9.0 and -10.8 kcal/mol, respectively), human dihydrofolate reductase (-9.7 kcal/mol), Mpro of SARS-CoV-2 (-6.7 kcal/mol), and SARS-CoV-2/ACE2 complex receptor (-8.1 kcal/mol). Moreover, after molecular docking calculations, top-scoring ligand-receptor complexes of the aminopterin with SARS-CoV-2 enzymes (6M03 and 6M0J) were subjected to 50 ns all-atom MD simulations to investigate the ligand-receptor interactions in more detail, and to determine the binding free energies accurately. The predicted results indicate that the aminopterin may significantly inhibit SARS-CoV-2 infection. Thus, in this study, as both anticancer and anti-COVID-19 agents, the versatility of the biological activity of aminopterin was shown.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sefa Celik
- Physics Department, Science Faculty, Istanbul University, Istanbul, Turkey
| | - Gozde Yilmaz
- Opticianry Program, Vocational School, Istanbul Kultur University, Istanbul, Turkey
| | - Sevim Akyuz
- Physics Department, Science and Letters Faculty, Istanbul Kultur University, Istanbul, Turkey
| | - Aysen E Ozel
- Physics Department, Science Faculty, Istanbul University, Istanbul, Turkey
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2
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Samreen HS, Hussain A, Yar M, Alshammari MB, Ayub K, Adeel M, Tariq M, Lateef M, Bakht MA, Rasool F. Photophysical and biological aspects of α, β-unsaturated ketones: Experimental and in silico approach. J Biochem Mol Toxicol 2023; 37:e23433. [PMID: 37394811 DOI: 10.1002/jbt.23433] [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: 11/27/2022] [Revised: 04/04/2023] [Accepted: 06/12/2023] [Indexed: 07/04/2023]
Abstract
In this work, four fluorinated α, β-unsaturated ketones named as 3-(3-bromophenyl)-1-(3-(trifluoromethyl)phenyl)prop-2-en-1-one (1), 3-(4-methoxyphenyl)-1-(3-(trifluoromethyl)phenyl) prop-2-en-1-one (2), 3-(3-bromo-5-chloro-2-hydroxyphenyl)-1-(3-(trifluoromethyl)phenyl) prop-2-en-1-one (3) and 3-(2-hydroxy-5-methylphenyl)-1-(3-(trifluoromethyl)phenyl)prop-2-en-1-one (4) were synthesized by Claisen-Schmidt reaction. The synthesized molecules were then characterized through ultraviolet-visible spectroscopy (UV-Vis), Fourier transform infrared (FTIR), 1 H-NMR, 13 C-NMR, and mass spectrometry. The antioxidant potential, Urease inhibition, and interaction of compounds 1-4 with Salmon sperm DNA were experimentally explored and supported by molecular docking studies. The synthesized compounds strongly interact with SS-DNA through intercalative mode. It was noticed that compound 1 served as potent Urease inhibitor while compound 4 as better antioxidant among synthesized compounds. Moreover, frontier molecular orbitals, nonlinear optical (NLO) properties, natural bond orbitals, molecular electrostatic potential, natural population analysis, and photophysical properties of synthesized compounds were accomplished through density functional theory and time-dependent density functional theory. The band gap of all the compounds have been worked out using Taucs method. In addition to that, a precise comparative account of UV and IR data obtained from theoretical and experimental findings showed good agreement between theoretical and experimental data. The findings of our studies reflected that compounds 1-4 possess better NLO properties than Urea standard and the band gap data also reflected their prospective use towards optoelectronic materials. The better NLO behavior of compounds was attributed to the noncentrosymmetric structure of synthesized compounds.
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Affiliation(s)
- Hafiza Saba Samreen
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, Pakistan
| | - Ajaz Hussain
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Yar
- Department of Chemistry, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Mohammed Battah Alshammari
- Department of Chemistry, College of Science and Humanities, Prince Sattam bin Abdul Aziz university, Al-Kharj, Saudi Arabia
| | - Khurshid Ayub
- Department of Chemistry, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Muhammad Adeel
- Institute of Chemical Sciences, Gomal University, Dera Ismaeel Khan, Pakistan
| | - Muhammad Tariq
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, Pakistan
| | - Mehreen Lateef
- Multidisciplinary Research Laboratories, Bahria University Medical and Dental College, Karachi, Pakistan
| | - Mohammed Afroz Bakht
- Department of Chemistry, College of Science and Humanities, Prince Sattam bin Abdul Aziz university, Al-Kharj, Saudi Arabia
| | - Faiz Rasool
- Institute of Chemical Sciences, Bahauddin Zakariya University, Multan, Pakistan
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Ravindranath L, Srishailam K, Venkatram Reddy B. Experimental and DFT Quantum Chemical Studies on Structural, Vibrational and Molecular Properties of Some Substituted 4-Phenylphenols. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2161584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- L. Ravindranath
- Department of Physics, Malla Reddy Engineering College(a), Hyderabad, India
- Department of Physics, Kakatiya University, Warangal, India
| | - K. Srishailam
- Department of Physics, SR University, Warangal, India
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4
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Spectral characteristics of 3, 5-diaminobenzoic acid in pure and mixed solvents: Experimental and theoretical study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120783] [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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Suryachandram J, Prashanth J, Bhargavi D, Behera JN, Rao KP. Investigations of Donor–Acceptor Interactions in 1,3,5-Tris-(3-Methoxy & 3-Methyl Carboxy) Phenyl Ethynyl Benzene Derivatives Using Experimental and DFT Study. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2021.1924802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Jettiboina Suryachandram
- New Generation Materials Lab (NGML), Department of Science and Humanities, Vignan’s Foundation for Science Technology and Research (VFSTR) (Deemed to be University), Guntur, Andhra Pradesh, India
| | - Jyothi Prashanth
- Department of Physics, Kakatiya University, Warangal, Telangana, India
| | - Dodda Bhargavi
- New Generation Materials Lab (NGML), Department of Science and Humanities, Vignan’s Foundation for Science Technology and Research (VFSTR) (Deemed to be University), Guntur, Andhra Pradesh, India
| | - J. N. Behera
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar, Odisha, India
- HomiBhabha National Institute, Mumbai, Maharashtra, India
| | - Koya Prabhakara Rao
- New Generation Materials Lab (NGML), Department of Science and Humanities, Vignan’s Foundation for Science Technology and Research (VFSTR) (Deemed to be University), Guntur, Andhra Pradesh, India
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Bravanjalin Subi E, Arul Dhas D, Balachandran S, Hubert Joe I. Crystal Growth, Structural, Vibrational, Effects of Hydrogen Bonding(C-H…O and C-H…N), Chemical Reactivity, Antimicrobial Activity, Inhibitory Effects and Molecular Dynamic Simulation of 4-Methoxy-N-(Nitrobenzylidene)-Aniline. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2052116] [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)
- E. Bravanjalin Subi
- Manonmaniam Sundaranar University, Abishekapatti, Tirunelveli, Tamil Nadu, India
- Department of Physics, Research Centre, Nesamony Memorial Christian College, Marthandam, Tamil Nadu, India
| | - D. Arul Dhas
- Department of Physics, Research Centre, Nesamony Memorial Christian College, Marthandam, Tamil Nadu, India
| | - S. Balachandran
- Department of Chemistry, NSS College Ottapalam, Palakad, Kerala, India
| | - I. Hubert Joe
- Centre for Molecular and Biophysics Research, Department of Physics, Mar Ivanios College, Thiruvanathapuram, Kerala, India
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Kavitha N, Alivelu M. The Computational Study, 3D-QSAR, and Molecular Docking Study of 2-Amino 5-Methyl Pyridine. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2028871] [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)
- Natte Kavitha
- Department of Chemistry, Pingle Govt. College for Women, Warangal, Telangana, India
| | - Munagala Alivelu
- Department of Chemistry, Pingle Govt. College for Women, Warangal, Telangana, India
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8
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Radhika B, Prashanth J, Basavoju S, Jyothi S, Venkatram Reddy B. Synthesis, single-crystal X-ray diffraction, NLO and DFT studies of centrosymmetric 4-amino-3,5-dimethyl-1H-pyrazolium citrate monohydrate salt. Mol Phys 2022. [DOI: 10.1080/00268976.2021.2022797] [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)
- B. Radhika
- Department of Chemistry, Kakatiya University, Warangal, India
| | - J. Prashanth
- Department of Physics, Kakatiya University, Warangal, India
| | - Srinivas Basavoju
- Department of Chemistry, National Institute of Technology, Warangal, India
| | - S. Jyothi
- Department of Chemistry, Kakatiya University, Warangal, India
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9
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Synthesis, spectral characterization and biological evaluations with DFT analysis on molecular geometry and NLO of 1,4,7,10-tetraazacyclotetradecane-11,14-dione. J INDIAN CHEM SOC 2021. [DOI: 10.1016/j.jics.2021.100132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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10
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Structural, Electronic and NLO Properties of 6-aminoquinoline: A DFT/TD-DFT Study. J Fluoresc 2021; 31:1719-1729. [PMID: 34427839 DOI: 10.1007/s10895-021-02788-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/13/2021] [Indexed: 10/20/2022]
Abstract
A computational study based on the DFT/TD-DFT approach was performed to explore various properties of 6-aminoquinoline (6AQ). The geometrical parameters, molecular orbitals (MOs), electronic spectra, electrostatic potential, molecular surface, reactivity parameters and thermodynamic properties of 6AQ were explored. The absorption and emission spectra of 6AQ in solvents have been estimated by TD-DFT coupled with the PCM model and correlated with the available experimental results. Depending on the solvents, the computed absorption maxima of 6AQ were noticed between 327 nm - 340 nm and ascribed to [Formula: see text] transition. The simulated emission maxima were obtained between 389 to 407 nm and ascribed to [Formula: see text] transition. On increasing the solvent polarity, both the emission and absorption maxima showed a bathochromic shift. The LUMO and HOMO were localized on the entire molecule. It was observed that the lowest excited state is possibly the [Formula: see text] charge-transfer (CT) state. The natural bonding orbital (NBO) study points out that ICT plays a significant role in stabilizing the molecular system. Moreover, the NLO (nonlinear optical) properties (polarizability, first-order hyperpolarizability and dipole moment) were computed using different hybrid functionals. The estimated values indicate that 6AQ can be considered a desirable molecule for further studies of the NLO applications.
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11
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Synthesis and evaluation of molecular structure from torsional scans, study of molecular characteristics using spectroscopic and DFT methods of some thiosemicarbazones, and investigation of their anticancer activity. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01595-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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12
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Konakanchi R, Pamidimalla GS, Prashanth J, Naveen T, Kotha LR. Structural elucidation, theoretical investigation, biological screening and molecular docking studies of metal(II) complexes of NN donor ligand derived from 4-(2-aminopyridin-3-methylene)aminobenzoic acid. Biometals 2021; 34:529-556. [PMID: 33651218 DOI: 10.1007/s10534-021-00293-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/12/2021] [Indexed: 01/02/2023]
Abstract
Complexes of 4-(((2-aminopyridin-3-yl)methylene)amino)benzoic acid ligand with cobalt(II) (1), nickel(II) (2), copper(II) (3), zinc(II) (4) and palladium(II) (5) are synthesized and characterized by using different spectroscopic methods like, UV-Visible, infrared, 1H, 13C NMR, molar conductance, ESR and elemental analysis. Quantum chemical computations were made using DFT (density functional theory), B3LYP functional and 6-31+ +G(d,p)/SDD basis set in order to determine optimized structure parameters, frontier molecular orbital parameters and NLO properties. Based on DFT and experimental evidence, the complexes ensured that the octahedral geometry have been proposed for complexes 1, 2 and 4, square planar for complexes 3 and 5. All the complexes showed only residual molar conductance values and hence they were considered as non-electrolytes in DMF. In addition, the anti-proliferative activity of the compounds was evaluated against different human cancer cell lines (IMR-32, MCF-7, COLO205, A549, HeLa and HEK 293) and cisplatin is used as a reference drug. Compounds 1 and 4 showed remarkable cytotoxicity in five cancer cell lines tested except MCF-7. Also, the compounds were examined for their in vitro antimicrobial and scavenging activities. The molecular docking results are well corroborated with the experimental anticancer activity results.
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Affiliation(s)
- Ramaiah Konakanchi
- Chemistry Division, H&S Department, Malla Reddy Engineering College for Women (Autonomous Institution), Hyderabad, 500100, India.,Department of Chemistry, National Institute of Technology, Warangal, 506004, India
| | - Geetha Swarupa Pamidimalla
- Chemistry Division, H&S Department, Malla Reddy College of Engineering for Women, Hyderabad, 500014, India
| | - Jyothi Prashanth
- Department of Physics, Kakatiya University, Warangal, 506009, India
| | - Togati Naveen
- Applied Chemistry Department, S. V. National Institute of Technology, Surat, 395007, India
| | - Laxma Reddy Kotha
- Department of Chemistry, National Institute of Technology, Warangal, 506004, India.
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13
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Konakanchi R, Jyothi P, Kotha LR. Investigation of Structures, FTIR, FT-Raman, In Vivo Anti-Inflammatory, Molecular Docking and Molecular Characteristics of 2-Amino-3-Pyridine Carboxaldehyde and Its Copper(II) Complex Using Experimental and Theoretical Approach. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1725899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Ramaiah Konakanchi
- H&S Department, Chemistry Division, Vignan Institute of Technology and Science, Hyderabad, India
- Department of Chemistry, National Institute of Technology, Warangal, India
| | | | - Laxma Reddy Kotha
- Department of Chemistry, National Institute of Technology, Warangal, India
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14
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Prashanth J, Konakanchi R, Venkatram Reddy B. Barrier potentials, molecular structure, force filed calculations and quantum chemical studies of some bipyridine di-carboxylic acids using the experimental and theoretical using (DFT, IVP) approach. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1634807] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
| | - Ramaiah Konakanchi
- Department of Chemistry, National Institute of Technology, Warangal, India
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15
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Ramaiah K, Srishailam K, Laxma Reddy K, Reddy BV, Ramana Rao G. Synthesis, crystal and molecular structure, and characterization of 2-((2-aminopyridin-3-yl)methylene)-N-ethylhydrazinecarbothioamide using spectroscopic (1H and 13C NMR, FT-IR, FT-Raman, UV–Vis) and DFT methods and evaluation of its anticancer activity. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.02.060] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Gandhaveeti R, Konakanchi R, Jyothi P, Bhuvanesh NSP, Anandaram S. Unusual coordination mode of aroyl/acyl thiourea ligands and their π‐arene ruthenium (II) piano‐stool complexes: Synthesis, molecular geometry, theoretical studies and biological applications. Appl Organomet Chem 2019. [DOI: 10.1002/aoc.4899] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Rohini Gandhaveeti
- Department of ChemistryNational Institute of Technology Tiruchirappalli 620015 India
| | - Ramaiah Konakanchi
- Department of ChemistryNational Institute of Technology Warangal 506004 India
| | | | | | - Sreekanth Anandaram
- Department of ChemistryNational Institute of Technology Tiruchirappalli 620015 India
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18
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Vibrational spectroscopic (FT-IR, FT-Raman), anti-inflammatory, docking and molecular characteristic studies of Ni(II) complex of 2-aminonicotinaldehyde using theoretical and experimental methods. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.08.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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19
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Ramesh G, Prashanth J, Laxman Naik J, Venkatram Reddy B. Molecular Structure, Vibrational Analysis, Hyperpolarizability and NBO Analysis of 3-Methyl-Picolinic Acid Using SQM Calculations. J STRUCT CHEM+ 2018. [DOI: 10.1134/s0022476618050037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Ramesh G, Reddy BV. Spectroscopic investigation on structure (monomer and dimer), molecular characteristics and comparative study on vibrational analysis of picolinic and isonicotinic acids using experimental and theoretical (DFT & IVP) methods. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.01.083] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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21
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Highly efficient organic indolocarbazole dye in different acceptor units for optoelectronic applications—a first principle study. Struct Chem 2018. [DOI: 10.1007/s11224-018-1073-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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22
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Synthesis, characterization, cytotoxicity, DNA binding and computational studies of an anionic palladium(II) complex derived from 8-hydroxyquinoline and 1,1-cyclobutanedicarboxylate. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2017. [DOI: 10.1007/s13738-017-1269-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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23
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Pavitha P, Prashanth J, Ramu G, Ramesh G, Mamatha K, Venkatram Reddy B. Synthesis, structural, spectroscopic, anti-cancer and molecular docking studies on novel 2-[(Anthracene-9-ylmethylene)amino]-2-methylpropane-1,3-diol using XRD, FTIR, NMR, UV–Vis spectra and DFT. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.06.095] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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24
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Spectroscopic (FT-IR,1H and 13C NMR) characterization and density functional theory calculations for (Z)-5-(4-nitrobenzyliden)-3-N(2-ethoxyphenyl)-2-thioxo-thiazolidin-4-one (ARNO). J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.06.102] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Shahraki S, Heydari A. Binding forces between a novel Schiff base palladium(II) complex and two carrier proteins: human serum albumi and β-lactoglobulin. J Biomol Struct Dyn 2017; 36:2807-2821. [PMID: 28812944 DOI: 10.1080/07391102.2017.1367723] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ligand binding studies on carrier proteins are crucial in determining the pharmacological properties of drug candidates. Here, a new palladium(II) complex was synthesized and characterized. The in vitro binding studies of this complex with two carrier proteins, human serum albumin (HSA), and β-lactoglobulin (βLG) were investigated by employing biophysical techniques as well as computational modeling. The experimental results showed that the Pd(II) complex interacted with two carrier proteins with moderate binding affinity (Kb ≈ .5 × 104 M-1 for HSA and .2 × 103 M-1 for βLG). Binding of Pd(II) complex to HSA and βLG caused strong fluorescence quenching of both proteins through static quenching mechanism. In two studied systems hydrogen bonds and van der Waals forces were the major stabilizing forces in the drug-protein complex formation. UV-Visible and FT-IR measurements indicated that the binding of above complex to HSA and βLG may induce conformational and micro-environmental changes of two proteins. Protein-ligand docking analysis confirmed that the Pd(II) complex binds to residues located in the subdomain IIA of HSA and site A of βLG. All these experimental and computational results suggest that βLG and HSA might act as carrier protein for Pd(II) complex to deliver it to the target molecules.
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Key Words
- Ala, Alanine
- Cys, Cysteine
- DFT, Density Functional Theory
- DMSO, Dimethyl sulfoxide
- HOMO, highest occupied molecular orbital
- HSA, Human Serum Albumin
- LUMO, lowest unoccupied molecular orbital
- Leu, Leucine
- Lys, Lysine
- NMR, Nuclear Magnetic Resonance
- Pd(II) complex
- Pro, Proline
- Schiff base
- TMS, Tetramethylsilane
- Trp, Tryptophan
- Tyr, Tyrosine
- Val, Valine
- human serum albumin
- protein interactions
- β-lactoglobulin
- βLG, β-lactoglobulin
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Affiliation(s)
- Somaye Shahraki
- a Department of Chemistry , University of Zabol , Zabol , Iran
| | - Ali Heydari
- b Department of Chemistry , University of Sistan and Baluchestan , Zahedan , Iran
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Nawaz F, Cao H, Xie Y, Xiao J, Chen Y, Ghazi ZA. Selection of active phase of MnO 2 for catalytic ozonation of 4-nitrophenol. CHEMOSPHERE 2017; 168:1457-1466. [PMID: 27923503 DOI: 10.1016/j.chemosphere.2016.11.138] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 11/08/2016] [Accepted: 11/27/2016] [Indexed: 06/06/2023]
Abstract
Catalytic ozonation is a highly effective method in wastewater treatment, and MnO2 materials are widely recognized as active heterogeneous catalysts in this process. Many works reported the progress in active MnO2 synthesis, but the active phase is rarely systematically studied. In this paper, all six phases of MnO2 (α-, β-, δ-, γ-, λ- and ε-) were synthesized by facile methods. Their catalytic activities in ozonation of 4-nitrophenol (4-NP) were evaluated and correlated with the physicochemical properties obtained from X-ray Diffraction (XRD), transmission electron microscopy (TEM), physical adsorption and cyclic voltammetry (CV) analysis. α- MnO2 was found to be the most active catalyst in 4-NP degradation at neutral pH. MnO2 with low average oxidation state (AOS) showed stronger oxidation/reduction peaks in CV characterization, which benefited catalytic decomposition of ozone to generate active species. Superoxide radical was confirmed as the main oxidizing species, along with singlet oxygen and ozone molecule oxidation in bulk solution and little contribution of oxidation on the MnO2 surface. Mn2+ leaching happened during catalytic ozonation, but its catalytic role is negligible. This result may give rise to the preparation of new active MnO2 catalysts.
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Affiliation(s)
- Faheem Nawaz
- Beijing Engineering Research Center of Process Pollution Control, Division of Environmental Engineering and Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongbin Cao
- Beijing Engineering Research Center of Process Pollution Control, Division of Environmental Engineering and Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Yongbing Xie
- Beijing Engineering Research Center of Process Pollution Control, Division of Environmental Engineering and Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China.
| | - Jiadong Xiao
- Beijing Engineering Research Center of Process Pollution Control, Division of Environmental Engineering and Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Chen
- Beijing Engineering Research Center of Process Pollution Control, Division of Environmental Engineering and Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Zahid Ali Ghazi
- University of Chinese Academy of Sciences, Beijing 100049, China
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27
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Srivastava AK, Kumar A, Pandey SK, Misra N. Spectroscopic analyses, intra-molecular interaction, chemical reactivity and molecular docking of imerubrine into bradykinin receptor. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1710-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Joy M, Alex N, Malayan JJ, Sudarsanakumar C, Mathews A. In SilicoQuantum Chemical and Crystallographic Treatment of α-Formylketene Dithioacetal towards the Elucidation of Its Structural and Optical Nature. ChemistrySelect 2016. [DOI: 10.1002/slct.201600988] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Monu Joy
- School of Pure & Applied Physics; MG University; Kottayam Kerala- 686560 India
- Department of Chemistry; Baselius College; Kottayam Kerala- 686001 India
| | - Neethu Alex
- Department of Chemistry; Baselius College; Kottayam Kerala- 686001 India
| | - Jalaja J Malayan
- Department of Chemistry; Baselius College; Kottayam Kerala- 686001 India
| | - C. Sudarsanakumar
- School of Pure & Applied Physics; MG University; Kottayam Kerala- 686560 India
| | - Annie Mathews
- Department of Chemistry; Baselius College; Kottayam Kerala- 686001 India
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29
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Prashanth J, Reddy BV, Rao GR. Investigation of torsional potentials, molecular structure, vibrational properties, molecular characteristics and NBO analysis of some bipyridines using experimental and theoretical tools. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.03.062] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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30
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Demir S, Sarioğlu AO, Güler S, Dege N, Sönmez M. Synthesis, crystal structure analysis, spectral IR, NMR UV–Vis investigations, NBO and NLO of 2-benzoyl-N-(4-chlorophenyl)-3-oxo-3-phenylpropanamide with use of X-ray diffractions studies along with DFT calculations. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.04.042] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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31
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Heydari A, Mansouri-Torshizi H. Design, synthesis, characterization, cytotoxicity, molecular docking and analysis of binding interactions of novel acetylacetonatopalladium(ii) alanine and valine complexes with CT-DNA and BSA. RSC Adv 2016. [DOI: 10.1039/c6ra18803f] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The neutral, water soluble palladium(ii) amino acid complexes, interact with CT-DNA (groove binding) and BSA (H-binding in main pocket). Molecular docking supports the interactions.
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Affiliation(s)
- Ali Heydari
- Department of Chemistry
- University of Sistan and Baluchestan
- Zahedan
- Iran
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32
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Cao J, Xiong Z, Yuan Y, Lai B, Yang P. Treatment of wastewater derived from dinitrodiazophenol (DDNP) manufacturing by the Fe/Cu/O3 process. RSC Adv 2016. [DOI: 10.1039/c6ra19095b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this paper, the Fe/Cu bimetallic particles and ozone were combined to decompose or transform the toxic and refractory pollutants in dinitrodiazophenol (DDNP) wastewater.
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Affiliation(s)
- Jinyan Cao
- Department of Environmental Science and Engineering
- School of Architecture and Environment
- Sichuan University
- Chengdu 610065
- China
| | - Zhaokun Xiong
- Department of Environmental Science and Engineering
- School of Architecture and Environment
- Sichuan University
- Chengdu 610065
- China
| | - Yue Yuan
- Department of Environmental Science and Engineering
- School of Architecture and Environment
- Sichuan University
- Chengdu 610065
- China
| | - Bo Lai
- Department of Environmental Science and Engineering
- School of Architecture and Environment
- Sichuan University
- Chengdu 610065
- China
| | - Ping Yang
- Department of Environmental Science and Engineering
- School of Architecture and Environment
- Sichuan University
- Chengdu 610065
- China
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33
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Meenakshi R. Spectral investigations, inhibition efficiency analysis and a TD-DFT study on tuning the light harvesting efficiency (LHE) of heterocyclic 5-nitro-1,3-benzodioxole as a photosensitizer for dye sensitized solar cells (DSSCs). RSC Adv 2016. [DOI: 10.1039/c6ra07550a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The vibrational wavenumber of 5-nitro-1,3-benzodioxole (NBD) are obtained and the complete assignments are performed on the basis of the total energy distribution (TED) of the vibrational modes.
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Affiliation(s)
- R. Meenakshi
- Department of Physics
- Cauvery College for Women
- Tiruchirappalli – 620 018
- India
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34
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Molecular geometry, NBO analysis, Hyperpolarizability and HOMO-LUMO energies of 2-azido-1-phenylethanone using Quantum chemical calculations. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.matpr.2016.11.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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35
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Laxman Naik J, Venkatram Reddy B, Prabavathi N. Experimental (FTIR and FT-Raman) and theoretical investigation of some pyridine-dicarboxylic acids. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.06.064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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36
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Prabavathi N, Senthil Nayaki N, Venkatram Reddy B. Molecular structure, vibrational spectra, natural bond orbital and thermodynamic analysis of 3,6-dichloro-4-methylpyridazine and 3,6-dichloropyridazine-4-carboxylic acid by dft approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt B:1134-1148. [PMID: 25459510 DOI: 10.1016/j.saa.2014.09.137] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 09/26/2014] [Accepted: 09/30/2014] [Indexed: 06/04/2023]
Abstract
Vibrational spectral analysis of the molecules 3,6-dichloro-4-methylpyridazine (DMP) and 3,6-dichloropyridazine-4-carboxylic acid (DPC) was carried out using FT-IR and FT-Raman spectroscopic techniques. The molecular structure and vibrational spectra of DMP and DPC were obtained by the density functional theory (DFT) method, using B3LYP functional, with 6-311++G(d,p) basis set. A detailed interpretation of the Infrared and Raman spectra of the two molecules were reported based on potential energy distribution (PED). The theoretically predicted FTIR and FT-Raman spectra of the titled molecules have been simulated and were compared with the experimental spectra. Determination of electric dipole moment (μ) and hyperpolarizability β0 helps to study the non-linear optical (NLO) behavior of DMP and DPC. Stability of the molecules arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. (13)C and (1)H NMR spectra were recorded and (13)C and (1)H NMR chemical shifts of the molecules were calculated using the gauge independent atomic orbital (GIAO) method. UV-visible spectrum of the compounds was also recorded in the region 200-1100 nm and electronic properties, HOMO (Highest Occupied Molecular Orbitals) and LUMO (Lowest Unoccupied Molecular Orbitals) energies were measured by time-dependent TD-DFT approach. Charge density distribution and site of chemical reactivity of the molecule have been studied by mapping electron density isosurface with molecular electrostatic potential (MESP).
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Affiliation(s)
- N Prabavathi
- Department of Physics, Sri Sarada College for Women (Autonomous), Salem 636 016, India.
| | - N Senthil Nayaki
- Department of Physics, Sri Sarada College for Women (Autonomous), Salem 636 016, India
| | - B Venkatram Reddy
- Department of Physics, Kakatiya University, Warangal, Telangana 506009, India
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37
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Senthil kumar J, Jeyavijayan S, Arivazhagan M. Spectroscopic (FT-IR and FT-Raman) investigation, first order hyperpolarizability, NBO, HOMO-LUMO and MEP analysis of 6-nitrochromone by ab initio and density functional theory calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt B:771-781. [PMID: 25448928 DOI: 10.1016/j.saa.2014.09.094] [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: 06/08/2014] [Revised: 09/17/2014] [Accepted: 09/22/2014] [Indexed: 06/04/2023]
Abstract
The vibrational spectral analysis is carried out using FT-Raman and FT-IR spectroscopy in the range 3500-50 cm(-1) and 4000-400 cm(-1), respectively, for 6-nitrochromone (6NC). The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimization and normal coordinates force field calculation based on ab initio HF and DFT gradient calculations employing the HF/6-311++G(d,p) and B3LYP/6-311++G(d,p) basis set. Stability of the molecule has been analyzed using NBO analysis. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. Thermodynamic properties like entropy, heat capacity, zero-point energy and Mulliken's charge analysis have been calculated for the 6NC. The complete assignments were performed on the basis of total energy distribution (TED) of the vibrational modes with scaled quantum mechanical (SQM) method. The MEP map shows the negative potential sites are on oxygen atoms as well as the positive potential sites are around the hydrogen atoms.
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Affiliation(s)
- J Senthil kumar
- PG & Research Department of Physics, Periyar EVR College, Tiruchirappalli 620 023, India.
| | - S Jeyavijayan
- Department of Physics, JJ College of Engineering and Technology, Tiruchirappalli 620 009, India
| | - M Arivazhagan
- Department of Physics, Government Arts College, Tiruchirappalli 620 022, India
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38
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Govindasamy P, Gunasekaran S, Srinivasan S. Molecular geometry, conformational, vibrational spectroscopic, molecular orbital and Mulliken charge analysis of 2-acetoxybenzoic acid. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 130:329-36. [PMID: 24793483 DOI: 10.1016/j.saa.2014.03.056] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 03/01/2014] [Accepted: 03/20/2014] [Indexed: 05/24/2023]
Abstract
The Fourier transform infrared (FT-IR) and FT-Raman spectra of 2-acetoxybenzoic acid (2ABA), a painkiller agent were recorded in the region 4000-450 cm(-1) and 5000-50 cm(-1) respectively. Hartree Fock (HF) and Density functional theory (DFT) methods have been used to determine its optimized geometrical parameter, atomic charges, and vibrational wavenumbers and intensity of the vibrational bands of the title molecule. The computed vibrational wave numbers were compared with the FT-IR and FT-Raman experimental data. The computational calculations were done at HF and DFT/B3LYP level with 6-311++G(d,p) basis set. The complete vibrational assignments were performed on the basis of the potential energy distribution (PED) analysis. The Mulliken charges, UV-Visible spectral analysis and HOMO-LUMO energy gap have been calculated and reported. The B3LYP method of calculated parameters is a good complement with the experimental findings. The thermodynamic properties like entropy, heat capacity and zero vibrational energy have been calculated and discussed. The electrostatic potential (ESP) contour surface and molecular electrostatic potential (MESP) of the molecule were constructed.
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Affiliation(s)
- P Govindasamy
- Department of Physics, Karpagam University, Eachanari, Coimbatore 641021, TN, India.
| | - S Gunasekaran
- Research and Development St. Peter's Institute of Higher Education and Research, St. Peter's University, Avadi, Chennai 600054, TN, India
| | - S Srinivasan
- Department of Physics, Presidency College, Chennai 600005, India
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39
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Govindasamy P, Gunasekaran S, Ramkumaar GR. Natural bond orbital analysis, electronic structure and vibrational spectral analysis of N-(4-hydroxyl phenyl) acetamide: a density functional theory. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 130:621-633. [PMID: 24813292 DOI: 10.1016/j.saa.2014.03.065] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 03/14/2014] [Accepted: 03/21/2014] [Indexed: 06/03/2023]
Abstract
The Fourier transform infrared (FT-IR) and FT-Raman spectra of N-(4-hydroxy phenyl) acetamide (N4HPA) of painkiller agent were recorded in the region 4000-450 cm(-1) and 4000-50 cm(-1) respectively. Density functional theory (DFT) has been used to calculate the optimized geometrical parameter, atomic charges, and vibrational wavenumbers and intensity of the vibrational bands. The computed vibrational wave numbers were compared with the FT-IR and FT-Raman experimental data. The computational calculations at DFT/B3LYP level with 6-31G(d,p), 6-31++G(d,p), 6-311G(d,p) and 6-311++G(d,p) basis sets. The complete vibrational assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes calculated using Vibrational energy distribution analysis (VEDA 4) program. The oscillator's strength calculated by TD-DFT and N4HPA is approach complement with the experimental findings. The NMR chemical shifts 13C and 1H were recorded and calculated using the gauge independent atomic orbital (GIAO) method. The molecular electrostatic potential (MESP) and electron density surfaces of the molecule were constructed. The Natural charges and intermolecular contacts have been interpreted using Natural Bond orbital (NBO) analysis the HOMO-LUMO energy gap has been calculated. The thermodynamic properties like entropy, heat capacity and zero vibrational energy have been calculated.
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Affiliation(s)
- P Govindasamy
- Department of Physics, Karpagam University, Eachanari, Coimbatore 641021, TN, India
| | - S Gunasekaran
- Research and Development St. Peter's Institute of Higher Education and Research, St. Peter's University, Avadi, Chennai 600054, TN, India.
| | - G R Ramkumaar
- PG and Research Department of Physics, Pachaiyappa's College, Chennai 600030, TN, India
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40
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Baykara H, Ilhan S, Levent A, Salih Seyitoglu M, Özdemir S, Okumuş V, Öztomsuk A, Cornejo M. Synthesis, characterization and experimental, theoretical, electrochemical, antioxidant and antibacterial study of a new Schiff base and its complexes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 130:270-279. [PMID: 24792202 DOI: 10.1016/j.saa.2014.03.094] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 03/02/2014] [Accepted: 03/18/2014] [Indexed: 06/03/2023]
Abstract
A new Schiff base ligand was synthesized by reaction of salicylaldehyde with 1,6-bis(4-chloro-2-aminophenoxy)hexane. Then the Schiff base complexes were synthesized by metal salts and the Schiff base. The metal to ligand ratio of metal complexes was found to be 1:1. The Cu(II) complex is proposed to be square planar and the Co(II), Ni(II), Mn(II) and Zn(II) complexes are proposed to be tetrahedral geometry. The Ti(III) and V(III) complexes are proposed to be a capped octahedron in which a seventh ligand has been added to triangular face. The complexes are non-electrolytes as shown by their molar conductivities (ΛM). The structure of metal complexes is proposed from elemental analysis, FT-IR, UV-vis, magnetic susceptibility measurements, molar conductivity measurements, Mass Spectra and thermal gravimetric analysis. In addition antimicrobial and antioxidant studies, cyclic voltammetry of the complexes, theoretical 1H NMR and HOMO-LUMO energy calculations of the new di-functional ligand were done.
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Affiliation(s)
- Haci Baykara
- Faculty of Art and Science, Chemistry Department, Siirt University, Siirt, Turkey; Escuela Superior Politécnica del Litoral, ESPOL, CIDNA, Km 30.5 Via Perimetral, Guayaquil, Ecuador
| | - Salih Ilhan
- Faculty of Art and Science, Chemistry Department, Siirt University, Siirt, Turkey.
| | - Abdulkadir Levent
- Batman University, Health Services Vocational College, 72100 Batman, Turkey
| | - M Salih Seyitoglu
- Faculty of Art and Science, Chemistry Department, Siirt University, Siirt, Turkey
| | - Sadin Özdemir
- Faculty of Art and Science, Biology Department, Siirt University, Siirt, Turkey
| | - Veysi Okumuş
- Faculty of Art and Science, Biology Department, Siirt University, Siirt, Turkey
| | - Abdussamet Öztomsuk
- Faculty of Art and Science, Chemistry Department, Siirt University, Siirt, Turkey
| | - Mauricio Cornejo
- Escuela Superior Politécnica del Litoral, ESPOL, CIDNA, Km 30.5 Via Perimetral, Guayaquil, Ecuador
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41
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Baykara H, Ilhan S, Levent A, Salih Seyitoglu M, Özdemir S, Okumuş V, Öztomsuk A, Cornejo M. Synthesis, characterization and experimental, theoretical, electrochemical, antioxidant and antibacterial study of a new Schiff base and its complexes. SPECTROCHIMICA ACTA PART A: MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 130:270-279. [DOI: https:/doi.org/10.1016/j.saa.2014.03.094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/01/2024]
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42
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Prabavathi N, Senthil Nayaki N. The spectroscopic (FT-IR, FT-Raman and NMR), first order hyperpolarizability and HOMO-LUMO analysis of 2-mercapto-4(3H)-quinazolinone. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 129:572-583. [PMID: 24815813 DOI: 10.1016/j.saa.2014.04.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 03/06/2014] [Accepted: 04/07/2014] [Indexed: 06/03/2023]
Abstract
The FTIR and FT-Raman spectra of 2-mercapto-4(3H) quinazolinone have been recorded in the region 4000-450 and 4000-100 cm(-1), respectively. The optimized geometry, frequency and intensity of the vibrational bands of 2-mercapto-4(3H) quinazolinone (2MQ) were obtained by the density functional theory (DFT) using 6-311++G(d,p) basis set. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FTIR and FT-Raman spectra. The (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecule were also calculated using the gauge independent atomic orbital (GIAO) method. The theoretical UV-VIS spectrum of the compound and the electronic properties, such as HOMO (highest occupied molecular orbital) and LUMO (lowest occupied molecular orbital) energies were performed by time-dependent DFT (TD-DFT) approach. The change in electron density (ED) in the σ(*) antibonding orbitals and stabilization energies E((2)) have been calculated by natural bond (NBO) analysis, to give clear evidence of stabilization originating in the hyper conjugation of hydrogen-bonded interactions. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecule has been obtained by mapping electron density isosurface with molecular electrostatic potential (MESP).
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Affiliation(s)
- N Prabavathi
- Department of Physics, Sri Sarada College for Women (Autonomous), Salem 636 016, India.
| | - N Senthil Nayaki
- Department of Physics, Sri Sarada College for Women (Autonomous), Salem 636 016, India
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43
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Aydın L, Şahan E, Önal Z, Özpozan T. Synthesis, experimental spectra (IR & Raman and NMR), vibrational analysis and theoretical DFT investigations of N-(5-(4-methylbenzoyl)-2-oxo-4-(4-methylphenyl)pyrimidine-1(2H)-yl)-4-methylbenzamide. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 129:22-34. [PMID: 24835751 DOI: 10.1016/j.saa.2014.02.176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 02/20/2014] [Accepted: 02/23/2014] [Indexed: 06/03/2023]
Abstract
The title molecule, N-(5-(4-methylbenzoyl)-2-oxo-4-(4-methylphenyl)pyrimidine-1(2H)-yl)-4-methylbenzamide (C27H23N3O3), was synthesized and characterized by elemental analysis, IR, Raman, (1)H and (13)C NMR spectral data. To determine conformational flexibility, potential energy surfaces of the title compound were obtained by DFT regarding the selected degree of torsional freedom, which was varied from 0° to 360° in 6° and 20° steps. The ten conformers of the title compound were determined and it was found that the conformer 1 basis the most stable one. All conformers were also optimized by using the density functional theory (DFT/B3LYP) method with the 6-31G(d,p), 6-311G(d,p) and cc-pVDZ basis sets in the ground state. Potential energy distribution was calculated with the 6-31G(d,p) basis set. The vibrational spectra were recorded in solid phase IR and Raman spectra were compared based on the results of the theoretical calculations. The formation of hydrogen bonds was explained using natural bond orbital (NBO) analysis and spectroscopic analysis. NMR analysis and frontier molecular orbitals (FMOs) were also investigated by DFT.
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Affiliation(s)
- Lütfiye Aydın
- Erciyes University, Faculty of Science, Department of Chemistry, Kayseri, Turkey.
| | - Emine Şahan
- Erciyes University, Faculty of Science, Department of Chemistry, Kayseri, Turkey
| | - Zülbiye Önal
- Erciyes University, Faculty of Science, Department of Chemistry, Kayseri, Turkey
| | - Talat Özpozan
- Erciyes University, Faculty of Science, Department of Chemistry, Kayseri, Turkey
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44
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Sakthivel S, Alagesan T, Al-Saadi AA, Renuga S, Muthu S. Vibrational spectra of 3,5-diamino-6-chloro-N-(diaminomethylene) pyrazine-2-carboxamide: combined experimental and theoretical studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 127:157-167. [PMID: 24632230 DOI: 10.1016/j.saa.2014.02.066] [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: 11/30/2013] [Revised: 01/25/2014] [Accepted: 02/11/2014] [Indexed: 06/03/2023]
Abstract
In this work, the vibrational spectral analysis of 3,5-diamino-6-chloro-N-(diaminomethylene)pyrazine-2-carboxamide(3DCNDPC) was carried out using FT-Raman and FT-IR spectroscopy in the range 4000-50cm(-1) and 4000-500cm(-1) respectively. The experimental spectra were recorded in the solid phase. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT) B3LYP with the standard basis set 6-311++G(d,p). The optimized geometric parameters (bond lengths and bond angles) were compared with experimental values. Normal co-ordinate calculations were performed with the DFT force field corrected by a recommended set of scaling factors yielding fairly good agreement between observed and calculated frequencies. Simulation of infrared and Raman spectra utilizing the results of these calculations led to excellent overall agreement with the observed spectral patterns. The complete assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The stability of the molecule arising from hyper conjugative interactions and the charge delocalization has been analyzed by using Natural Bond Orbital (NBO) analysis. UV-Vis spectrum of the compound was recorded. The calculated HOMO and LUMO energies show that chemical activity of the molecule.
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Affiliation(s)
- S Sakthivel
- Department of Physics, Panimalar Engineering College, Chennai, Tamil Nadu, India
| | - T Alagesan
- Department of Physics, Presidency College, Chennai, India
| | - Abdulaziz A Al-Saadi
- Department of Chemistry, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia
| | - S Renuga
- Department of Physics, Indira Institute of Engineering and Technology, Thiruvallur, Tamil Nadu, India
| | - S Muthu
- Department of Physics, Sri Venkateswara College of Engineering, Sriperumbudur, India.
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45
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Alam MJ, Ahmad S. Molecular structure, anharmonic vibrational analysis and electronic spectra of o-, m-, p-iodonitrobenzene using DFT calculations. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2013.12.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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46
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Krishna Kumar V, Sangeetha R, Barathi D, Mathammal R, Jayamani N. Vibrational assignment of the spectral data, molecular dipole moment, polarizability, first hyperpolarizability, HOMO-LUMO and thermodynamic properties of 5-nitoindan using DFT quantum chemical calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 118:663-671. [PMID: 24096062 DOI: 10.1016/j.saa.2013.08.089] [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: 05/23/2013] [Revised: 08/15/2013] [Accepted: 08/23/2013] [Indexed: 06/02/2023]
Abstract
The vibrational spectra of 5-nitroindan (NI) was computed using B3LYP methodology with 6-31G(*) and 6-31G(**) basis sets. The FTIR and FT-Raman spectra were recorded in the region 4000-400 cm(-1) and 4000-50 cm(-1) respectively. A similarity was achieved between the observed and calculated frequencies by refinement of the scale factors. The (1)H and (13)CNMR chemical shifts results were also compared with the experimental values. The Mulliken charges, the values of electric dipole moment (μ) of the molecule were computed using DFT calculations. The first order hyperpolarizability (β0) and related properties (β, α0, and Δα) of both are calculated using B3LYP method on the finite-field approach. The electronic properties HOMO and LUMO energies are calculated. Thermodynamic properties (heat capacity, entropy and enthalpy) of the title compound were calculated.
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Affiliation(s)
- V Krishna Kumar
- Department of Physics, Periyar University, Salem 636011, India.
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Muthu S, Elamurugu Porchelvi E. FTIR, FT-RAMAN, NMR, spectra, normal co-ordinate analysis, NBO, NLO and DFT calculation of N,N-diethyl-4-methylpiperazine-1-carboxamide molecule. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 115:275-286. [PMID: 23845985 DOI: 10.1016/j.saa.2013.06.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/24/2013] [Accepted: 06/04/2013] [Indexed: 06/02/2023]
Abstract
The Fourier Transform Infrared (FT-IR) and FT-Raman of N,N-diethyl-4-methylpiperazine-1-carboxamide (NND4MC) have been recorded and analyzed. The structure of the compound was optimized and the structural characteristics were determined by density functional theory (DFT) using B3LYP method with 6-31G(d,p) and 6-311G(d,p) basis sets. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. The theoretically predicted FT-IR and FT-Raman spectra of the title molecule have been constructed. The detailed interpretation of the vibrational spectra has been carried out with aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The results show that electron density (ED) in the σ(*) and π(*) antibonding orbitals and second order delocalization energies (E2) confirm the occurrence of intramolecular charge transfer (ICT) within the molecule. The electronic dipole moment (μD) and the first hyperpolarizability (βtot) values of the investigated molecule were computed using Density Functional Theory (DFT/B3LYP) with 6-31G(d,p) and 6-311G(d,p) basis sets. The calculated results also show that the NND4MC molecule may have microscopy nonlinear optical (NLO) behavior with non zero values. Mulliken atomic charges of NND4MC were calculated. The (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. The UV-Vis spectrum of the compound was recorded. The theoretical electronic absorption spectra have been calculated by using CIS, TD-DFT methods. A study on the electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MEP) were also performed.
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Affiliation(s)
- S Muthu
- Department of Physics, Sri Venkateswara College of Engineering, Sriperumbudur 602 105, Tamil Nadu, India.
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Prabavathi N, Nilufer A, Krishnakumar V. Vibrational spectroscopic (FT-IR and FT-Raman) studies, natural bond orbital analysis and molecular electrostatic potential surface of Isoxanthopterin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 114:101-113. [PMID: 23751224 DOI: 10.1016/j.saa.2013.05.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 06/02/2023]
Abstract
The FTIR and FT-Raman spectra of Isoxanthopterin have been recorded in the region 4000-450 and 4000-100 cm(-1), respectively. The optimized geometry, frequency and intensity of the vibrational bands of Isoxanthopterin were obtained by the density functional theory (DFT) using 6-311++G(d,p) basis set. The harmonic vibrational frequencies were scaled and compared with experimental values. The observed and the calculated frequencies are found to be in good agreement. The (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecule were also calculated using the gauge independent atomic orbital (GIAO) method. The UV-visible spectrum was also recorded and compared with the theoretical values. The calculated HOMO and LUMO energies show that charge transfer occurs within molecule. The first order hyperpolarizability (β0), related properties (β, α0 and Δα) and the Mulliken charges of the molecule were also computed using DFT calculations. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The results show that charge in electron density (ED) in the σ* and π* antibonding orbitals and second order delocalization energies (E2) confirms the occurrence of intramolecular charge transfer (ICT) within the molecule. Information about the charge density distribution of the molecule and its chemical reactivity has been obtained by mapping molecular electrostatic potential surface. In addition, the non-linear optical properties were discussed from the dipole moment values and excitation wavelength in the UV-visible region.
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Affiliation(s)
- N Prabavathi
- Department of Physics, Sri Sarada College for Women (Autonomous), Salem, India.
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Xavier RJ, Dinesh P. Conformational stability, vibrational spectra, HOMO-LUMO and NBO analysis of 1,3,4-thiadiazolidine-2,5-dithione with experimental (FT-IR and FT-Raman) techniques and scaled quantum mechanical calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 113:171-181. [PMID: 23727670 DOI: 10.1016/j.saa.2013.04.108] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 04/19/2013] [Accepted: 04/24/2013] [Indexed: 06/02/2023]
Abstract
The experimental and theoretical study on the structure and vibrations of 1,3,4-thiadiazolidine-2,5-dithione (TDZD) is presented. The FT-IR spectra (4000-400 cm(-1)) and the FT-Raman spectra (4000-50 cm(-1)) of the title molecule have been recorded. The energies of TDZD were obtained for all the possible four conformers from HF and DFT with 6-311G(d,p) and 6-311++G(d,p) basis set calculations. From the computational results, conformer C4 is identified as the most stable conformers of TDZD. The spectroscopic and theoretical results are compared with the corresponding properties for TDZD of C4 conformer. The temperature dependence of thermodynamic properties has been analyzed. Molecular stability and bond strength were investigated by applying the natural bond orbital analysis (NBO). The calculated HOMO and LUMO energies show that charge transfer occurs in the molecules. Information about the size, shape, charge density distribution, and site of chemical reactivity of the molecules has been obtained by mapping electron density isosurface with electrostatic potential (ESP). The dipole moment (λ) and polarizability (α), anisotropy polarizability (Δα) and first hyperpolarizability (βtotal) of the molecule have been reported.
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Affiliation(s)
- R John Xavier
- Department of Physics, Periyar EVR College (Autonomous), Tiruchirappalli 620 023, India.
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Sriram S, Chandiramouli R. DFT studies on the stability of linear, ring, and 3D structures in CdTe nanoclusters. RESEARCH ON CHEMICAL INTERMEDIATES 2013. [DOI: 10.1007/s11164-013-1334-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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