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Arathi PK, Suresh CH. Direct Estimation of Aromatization Energy from 1H NMR and UV-Vis Absorption Data of Homodesmotic Molecules. J Org Chem 2024; 89:10485-10497. [PMID: 39042814 DOI: 10.1021/acs.joc.4c00668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
This study delves into the ring-opening reaction of two distinct diaryl-ring-pyran systems, referred to as drnp1 and drnp2, where the term 'ring' encompasses aromatic, nonaromatic, or antiaromatic motifs. These systems transform into the corresponding cis-ortho quinonoid systems, denoted as c-drnq1 and c-drnq2. Homodesmotic pairs (drnp1, drnp2) and (c-drnq1, c-drnq2) are categorized as (aromatic, nonaromatic), (aromatic, partially aromatic), (antiaromatic, nonaromatic), and (nonaromatic, nonaromatic), with their energy difference representing aromatization energy (Earoma). Using reliable density functional theory, Earoma is assessed for various aromatic and antiaromatic ring motifs, including borderline cases and nonaromatic structures. For example, benzene exhibits an Earoma of 23.4 kcal/mol, indicating 3.9 kcal/mol aromatic stabilization per CC bond, while cyclobutadiene shows -29.9 kcal/mol, indicating a 7.5 kcal/mol destabilization of the CC bond. This approach extends to evaluating global and local aromatic stabilization effects in polycyclic hydrocarbons, nonbenzenoid systems, and heterocyclic compounds. Additionally, variation in 1H NMR chemical shift (δavg) correlates with Earoma, suggesting that a -1.0 ppm shift corresponds to 24.2 kcal/mol aromatization energy. UV-vis absorption maxima difference (Δλavg) correlates linearly with Earoma, enabling direct assessment of aromatization energy from UV-vis spectra using suitable homodesmotic pairs. This comprehensive approach enhances our understanding of structural, energetic, and spectroscopic aspects of aromatic and antiaromatic systems.
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Affiliation(s)
- Puthiyavalappil K Arathi
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Cherumuttathu H Suresh
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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2
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Liu X, Gong J, Jiang Y, He X, Yang J. Optimizing cell voltage dependence on size of carbon nanotube-based electrodes in Na-ion and K-ion batteries. Phys Chem Chem Phys 2024; 26:12027-12034. [PMID: 38576389 DOI: 10.1039/d3cp04268e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Sodium-ion batteries (NIBs) and potassium-ion batteries (KIBs) are gaining extensive attention as promising alternatives to lithium-ion batteries owing to their superior energy density and cost-effectiveness. However, the larger ionic radius of Na+ and K+ ions in comparison to Li+ ions poses a challenge in designing anode materials characterized by enduring structures and elevated voltage to facilitate the efficacy of high-performance NIBs and KIBs. Carbon nanomaterials, particularly carbon nanotubes (CNTs), have emerged as a potential candidate in anode materials. Herein, we used density functional theory calculations to study the cell voltage of CNTs in relation to Na-ion and K-ion storage as a function of CNT size. The adsorption energy profiles of both Na+@CNT and K+@CNT systems exhibit a descending trend concomitant with the increase in the CNT diameter, where Na+/K+ ion primarily prefers to adsorb in the interior wall of CNT. Conversely, the cell voltage for the Na and K system gradually increases with the increasing diameter of CNT, which can be attributed to the stronger electrostatic interaction validated by energy decomposition calculation. The voltage of Na-ion adsorbed on the inter wall of (10,10) CNT attains 1.29 V, close to the previously theoretical voltage of Li-ion on the same CNT (1.35 V), while the much lower voltage pertaining to K-ion adsorption on the inter wall of (10,10) CNT just stands at 0.59 V, suggesting the viability of CNT-based electrode for NIBs but not for KIBs. These findings lay a solid foundation for delineating the interrelationship between the voltage properties of CNT as prospective anode material and their structural characteristics, thereby expanding the application of CNT-based optoelectronic devices.
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Affiliation(s)
- Xia Liu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.
| | - Jiacheng Gong
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.
| | - Yizhi Jiang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.
- New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai, 200062, China.
| | - Jinrong Yang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.
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3
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Sallum LO, Duarte VS, Custodio JMF, Faria ECM, da Silva AM, Lima RS, Camargo AJ, Napolitano HB. Cyclohexanone-Based Chalcones as Alternatives for Fuel Additives. ACS OMEGA 2022; 7:11871-11886. [PMID: 35449976 PMCID: PMC9016815 DOI: 10.1021/acsomega.1c07333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
The use of small molecules, such as chalcones and their derivatives, for more efficient fuels is in increasing demand due to environmental factors. Here, three crystal structures (BH I, II, and III) of cyclohexanone-based chalcones were synthesized and described by single-crystal X-ray diffraction and Hirshfeld surface analysis. The supramolecular modeling analysis on the hyperconjugative interaction energies and QTAIM analysis at the ωB97XD/6-311++G(d,p) level of theory were carried out to analyze the intermolecular interactions in the solid-state. The structure-property relationship, frontier molecular orbital, molecular electrostatic potential, and the experimental calorific value analysis show that the three compounds are a good alternative to be used as an additive for some fuels. Our findings represent a further step forward in the development of cheaper and more efficient fuel additives and pose an opportunity for further investigation on similar analogues.
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Affiliation(s)
- Lóide O. Sallum
- Grupo
de Química Teórica e Estrutural, Universidade Estadual de Goiás, Anápolis, Goiás 75132-903, Brazil
- Laboratório
de Novos Materiais, Universidade Evangélica
de Goiás, Anápolis, Goiás 75083-515, Brazil
| | - Vitor S. Duarte
- Grupo
de Química Teórica e Estrutural, Universidade Estadual de Goiás, Anápolis, Goiás 75132-903, Brazil
- Centro
de Pesquisa e Eficiência Energética, CAOA Montadora de Veículos LTDA, Anápolis, Goiás 75184-000, Brazil
| | - Jean M. F. Custodio
- Grupo
de Química Teórica e Estrutural, Universidade Estadual de Goiás, Anápolis, Goiás 75132-903, Brazil
| | - Eduardo C. M. Faria
- Grupo
de Química Teórica e Estrutural, Universidade Estadual de Goiás, Anápolis, Goiás 75132-903, Brazil
- Centro
de Pesquisa e Eficiência Energética, CAOA Montadora de Veículos LTDA, Anápolis, Goiás 75184-000, Brazil
| | - Aline M. da Silva
- Centro
de Pesquisa e Eficiência Energética, CAOA Montadora de Veículos LTDA, Anápolis, Goiás 75184-000, Brazil
| | - Rosa S. Lima
- Faculdade
do Instituto Brasil, Anápolis, Goiás 75133-050, Brazil
| | - Ademir J. Camargo
- Grupo
de Química Teórica e Estrutural, Universidade Estadual de Goiás, Anápolis, Goiás 75132-903, Brazil
| | - Hamilton B. Napolitano
- Grupo
de Química Teórica e Estrutural, Universidade Estadual de Goiás, Anápolis, Goiás 75132-903, Brazil
- Laboratório
de Novos Materiais, Universidade Evangélica
de Goiás, Anápolis, Goiás 75083-515, Brazil
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4
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Kaur M, Kaushal R. Synthesis and in-silico molecular modelling, DFT studies, antiradical and antihyperglycemic activity of novel vanadyl complexes based on chalcone derivatives. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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5
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Wang Y. Extension and Quantification of the Fries Rule and Its Connection to Aromaticity: Large-Scale Validation by Wave-Function-Based Resonance Analysis. J Chem Inf Model 2021; 62:5136-5148. [PMID: 34428367 DOI: 10.1021/acs.jcim.1c00735] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Fries rule is a simple, intuitive tool to predict the most dominant Kekulé structures of polycyclic aromatic hydrocarbons (PAHs), which is valuable for understanding the structure, stability, reactivity, and aromaticity of these conjugated compounds. However, it still remains an empirical hypothesis, with limited qualitative applications. Herein, we verify, generalize, and quantify the Fries rule based on the recently developed resonance analysis of the DFT wave functions of over 1500 PAH and fullerene molecules with over a billion Kekulé structures. The extended rules, counting the numbers of electrons within all rings (not just sextets), are able to rank the relative importance of all Kekulé structures for all considered systems. The statistically meaningful quantification also opens a way to evaluate ring aromaticity based on the resonance theory, which generally agrees well with conventional aromaticity descriptors. Furthermore, we propose a purely graph-based aromaticity indicator nicely applicable to PAHs and fullerenes, with no need of any quantum chemistry calculations, so that it can make valuable predictions for molecular properties that are related to local aromaticity.
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Affiliation(s)
- Yang Wang
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, Jiangsu 225002, China
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6
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Musawwir A, Farhat A, Khera RA, Ayub AR, Iqbal J. Theoretical and computational study on electronic effect caused by electron withdrawing/electron-donating groups upon the coumarin thiourea derivatives. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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7
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Karayel A. Molecular stabilities, conformational analyses and molecular docking studies of benzimidazole derivatives bearing 1,2,4-triazole as EGFR inhibitors. Struct Chem 2021. [DOI: 10.1007/s11224-021-01760-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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8
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Hassanpour A, Youseftabar-Miri L, Nezhad PDK, Ahmadi S, Ebrahimiasl S. Kinetic stability and NBO analysis of the C20-nAln nanocages (n = 1–5) using DFT investigation. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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9
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Silva MC, Duarte VS, Custodio JM, Queiroz JE, de Aquino GL, Oliver AG, Napolitano HB. Comparative Conformational Study of a New Terpenoid-like Chalcone. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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Chaudhary MK, Srivastava A, Singh KK, Tandon P, Joshi BD. Computational evaluation on molecular stability, reactivity, and drug potential of frovatriptan from DFT and molecular docking approach. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.113031] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Kinetic stability of imidazolium cations and ionic liquids: A frontier molecular orbital approach. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.12.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Prajapati P, Pandey J, Tandon P, Sinha K. Combined spectroscopic and quantum chemical approach to study the effect of hydrogen bonding interactions in ezetimibe. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 206:246-253. [PMID: 30121023 DOI: 10.1016/j.saa.2018.08.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 08/07/2018] [Accepted: 08/12/2018] [Indexed: 06/08/2023]
Abstract
Molecular structure, chemical and physical reactivity, spectroscopic behavior, intermolecular interactions play an important role in understanding the biological nature of pharmaceutical drugs. The objective of the study is to combine the spectroscopic and computational methodology for the investigation of structural behavior of ezetimibe (EZT). Computational study was done on monomeric, dimeric and trimeric models of EZT using B3LYP/6-311G(d,p). Hydrogen bond interactions were taken into consideration to validate the theoretical results with the experimental one. Results obtained for trimeric model were better than monomer and dimer. HOMO-LUMO energy band gap shows that the chemical reactivity calculated using dimeric and trimeric model is higher than that of monomeric model. Higher value of electrophilicity index (ω = 2.5654 eV) also confirms that trimer behaves as a strong electrophile in comparison with monomer and dimer. To examine the hyperconjugation interactions and the stability of the molecule, natural bond analysis (NBO) was done on dimer and trimer of EZT. Nature and the strength of hydrogen bonds were examined by quantum theory of atoms in molecules (QTAIM). Binding energy calculated from counterpoise method was -7.40 kcal/mol for dimer and -21.47 kcal/mol for trimer.
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Affiliation(s)
- Preeti Prajapati
- Department of Physics, University of Lucknow, Lucknow 226007, India
| | - Jaya Pandey
- Department of Physics, University of Lucknow, Lucknow 226007, India
| | - Poonam Tandon
- Department of Physics, University of Lucknow, Lucknow 226007, India.
| | - Kirti Sinha
- Department of Physics, University of Lucknow, Lucknow 226007, India
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13
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Abstract
The potential energy surfaces for the interior rotation of a series of pairs of noble gas atoms encapsulated in the C70 cavity have been explored.
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Affiliation(s)
- Sara Gómez
- Scuola Normale Superiore
- Classe di Scienze
- 56126 Pisa
- Italy
| | - Albeiro Restrepo
- Instituto de Química
- Universidad de Antioquia UdeA
- Medellín
- Colombia
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14
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Hakkar F, Zouchoune B. Predicted Structures and Electronic Properties of Gallium-Indium Clusters GamInn–m (n = 4, 6, 8 and m < n): A Density Functional Study. J STRUCT CHEM+ 2018. [DOI: 10.1134/s0022476618050013] [Citation(s) in RCA: 1] [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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15
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Koohi M, Soleimani Amiri S, Shariati M. Silicon impacts on structure, stability and aromaticity of C20-nSin heterofullerenes (n = 1–10): A density functional perspective. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.08.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Effect of Mono- and Poly-CH/P Exchange(s) on the Aromaticity of the Tropylium Ion. Molecules 2016; 21:molecules21081099. [PMID: 27556433 PMCID: PMC6274420 DOI: 10.3390/molecules21081099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/09/2016] [Accepted: 08/11/2016] [Indexed: 11/17/2022] Open
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17
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Naderi F. Structures and electronic properties of C12Si8X8 (X = H, F, and Cl). RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2016. [DOI: 10.1134/s0036024416070220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Kurt M, Sas EB, Can M, Okur S, Icli S, Demic S, Karabacak M, Jayavarthanan T, Sundaraganesan N. Synthesis and spectroscopic characterization on 4-(2,5-di-2-thienyl-1H-pyrrol-1-yl) benzoic acid: A DFT approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 152:8-17. [PMID: 26186392 DOI: 10.1016/j.saa.2015.07.058] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 07/08/2015] [Accepted: 07/09/2015] [Indexed: 06/04/2023]
Abstract
A complete structural and vibrational analysis of the 4-(2,5-di-2-thienyl-1H-pyrrol-1-yl) benzoic acid (TPBA), was carried out by ab initio calculations, at the density functional theory (DFT) method. Molecular geometry, vibrational wavenumbers and gauge including atomic orbital (GIAO) (13)C NMR and (1)H NMR chemical shift values of (TPBA), in the ground state have been calculated by using ab initio density functional theory (DFT/B3LYP) method with 6-311G(d,p) as basis set for the first time. Comparison of the observed fundamental vibrational modes of (TPBA) and calculated results by DFT/B3LYP method indicates that B3LYP level of theory giving yield good results for quantum chemical studies. Vibrational wavenumbers obtained by the DFT/B3LYP method are in good agreement with the experimental data. The study was complemented with a natural bond orbital (NBO) analysis, to evaluate the significance of hyperconjugative interactions and electrostatic effects on such molecular structure. By using TD-DFT method, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD-DFT method and the experimental one is determined. In addition, the molecular electrostatic potential (MEP), frontier molecular orbitals analysis and thermodynamic properties of TPBA were investigated using theoretical calculations.
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Affiliation(s)
- M Kurt
- Department of Physics, Ahi Evran University, Kırsehir, Turkey
| | - E Babur Sas
- Department of Physics, Ahi Evran University, Kırsehir, Turkey
| | - M Can
- Department of Engineering Sciences, Faculty of Engineering, Izmir Katip Celebi University, Cigli, 35620 Izmir, Turkey
| | - S Okur
- Izmir Katip Celebi University, Material Science and Engineering, Cigli, Izmir, Turkey
| | - S Icli
- Ege University, Solar Energy Institute, 35040 Bornova, Izmir, Turkey
| | - S Demic
- Izmir Katip Celebi University, Material Science and Engineering, Cigli, Izmir, Turkey
| | - M Karabacak
- Department of Mechatronics Engineering, H.F.T. Technology Faculty, Celal Bayar University, Turgutlu, Manisa, Turkey
| | - T Jayavarthanan
- Department of Physics (Science and Humanities), Sri Manakula Vinayagar Engg. College, Madagadipet, Puducherry 605107, India
| | - N Sundaraganesan
- Department of Physics (Engg.), Annamalai University, Annamalai Nagar 608 002, Tamil Nadu, India.
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19
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Theoretical study on monometallic cyanide cluster fullerenes MCN@C74 (M=Y, Tb). J Mol Model 2015; 21:295. [DOI: 10.1007/s00894-015-2844-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 10/19/2015] [Indexed: 11/26/2022]
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20
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Quantum mechanical and experimental analyses of TNT metabolite 2-hydroxylamino-4,6-dinitrotoluene. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2014.09.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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21
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Galano A, Pérez-González A, del Olmo L, Francisco-Marquez M, León-Carmona JR. On the chemical behavior of C60 hosting H2O and other isoelectronic neutral molecules. J Mol Model 2014; 20:2412. [DOI: 10.1007/s00894-014-2412-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 07/30/2014] [Indexed: 11/29/2022]
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22
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Choudhary N, Agarwal P, Gupta A, Tandon P. Quantum chemical calculations of conformation, vibrational spectroscopic, electronic, NBO and thermodynamic properties of 2,2-dichloro-N-(2,3-dichlorophenyl) acetamide and 2,2-dichloro-N-(2,3-dichlorophenyl) acetamide. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.01.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Hilder TA, Chung SH. Designing a C84 fullerene as a specific voltage-gated sodium channel blocker. NANOSCALE RESEARCH LETTERS 2013; 8:323. [PMID: 23855749 PMCID: PMC3726465 DOI: 10.1186/1556-276x-8-323] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 07/09/2013] [Indexed: 05/15/2023]
Abstract
Fullerene derivatives demonstrate considerable potential for numerous biological applications, such as the effective inhibition of HIV protease. Recently, they were identified for their ability to indiscriminately block biological ion channels. A fullerene derivative which specifically blocks a particular ion channel could lead to a new set of drug leads for the treatment of various ion channel-related diseases. Here, we demonstrate their extraordinary potential by designing a fullerene which mimics some of the functions of μ-conotoxin, a peptide derived from cone snail venom which potently binds to the bacterial voltage-gated sodium channel (NavAb). We show, using molecular dynamics simulations, that the C84 fullerene with six lysine derivatives uniformly attached to its surface is selective to NavAb over a voltage-gated potassium channel (Kv1.3). The side chain of one of the lysine residues protrudes into the selectivity filter of the channel, while the methionine residues located just outside of the channel form hydrophobic contacts with the carbon atoms of the fullerene. The modified C84 fullerene strongly binds to the NavAb channel with an affinity of 46 nM but binds weakly to Kv1.3 with an affinity of 3 mM. This potent blocker of NavAb may serve as a structural template from which potent compounds can be designed for the targeting of mammalian Nav channels. There is a genuine need to target mammalian Nav channels as a form of treatment of various diseases which have been linked to their malfunction, such as epilepsy and chronic pain.
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Affiliation(s)
- Tamsyn A Hilder
- Computational Biophysics Group, Research School of Biology, Australian National University, ACT 0200 Canberra, Australia
| | - Shin-Ho Chung
- Computational Biophysics Group, Research School of Biology, Australian National University, ACT 0200 Canberra, Australia
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24
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Gao Y, Zhang F, Meng Q, Sun X, Wang D. Comparative study of the D5h and Ih isomers of Sc3NC@C80 and Sc3N@C80. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.03.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Arivazhagan M, Anitha Rexalin D. Vibrational spectra, UV-vis spectral analysis and HOMO-LUMO studies of 2,4-dichloro-5-nitropyrimidine and 4-methyl-2-(methylthio)pyrimidine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 107:347-358. [PMID: 23434563 DOI: 10.1016/j.saa.2013.01.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 01/05/2013] [Accepted: 01/10/2013] [Indexed: 06/01/2023]
Abstract
The FT-IR and FT-Raman vibrational spectra of 2,4-dichloro-5-nitropyrimidine (DCNP) and 4-methyl-2-(methylthio)pyrimidine (MTP) have been recorded in the range 4000-400 and 3600-50 cm(-1), respectively. A detailed vibrational spectral analysis has been carried out and assignments of the observed fundamental bands have been proposed on the basis of peak positions and relative intensities. The optimized molecular geometry and vibrational frequencies in the ground state are calculated using density functional B3LYP method with 6-31+G(d,p) and 6-311++G(d,p) basis set combinations. With the help of specific scaling procedures, the observed vibrational wavenumbers in FT-IR and FT-Raman spectra are analyzed and assigned to different normal modes of the molecules. The predicted first hyperpolarizability reveals that the molecules are an attractive object for future studies of non-linear optical properties. And also HOMO-LUMO energy gap explains the eventual charge transfer interaction taking place within the molecules. UV-vis spectral analysis of the title compounds has been researched by theoretical calculations. The frontier orbital energies, absorption wavelengths (λ), oscillator strengths (f) and excitation energies (E) studied using TD-DFT (B3LYP) with 6-311++G(d,p) basis set are calculated in this work.
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Affiliation(s)
- M Arivazhagan
- Department of Physics, A.A. Government Arts College, Musiri 621 211, Tamil Nadu, India.
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Ravi P, Babu BK, Tewari SP. Theoretical investigations on the structure, density, thermodynamic and performance properties of amino-, methyl-, nitroso- and nitrotriazolones. J Mol Model 2012; 19:33-48. [PMID: 22777428 DOI: 10.1007/s00894-012-1515-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 06/20/2012] [Indexed: 11/30/2022]
Abstract
We have studied herein the effect of position and the number of -NO, -NO2, -NH2 and -CH3 groups on the structure, stability, impact sensitivity, density, thermodynamic and detonation properties of triazolones by performing density functional theory calculations at the B3LYP/aug-cc-pVDZ level. The optimized structures, vibrational frequencies and thermodynamic values for triazolones have been obtained in their ground state. Kamlet-Jacob equations were used to calculate the detonation velocity and detonation pressure of model compounds. The detonation properties of NNTO (D 8.75 to 9.10 km/s, P 34.0 to 37.57 GPa), DNTO (D 8.80 to 9.05 km/s, P 35.55 to 38.27 GPa), ADNTO (D 9.01 to 9.42 km/s and P 37.81 to 41.10 GPa) and ANNTO (D 8.58 to 9.0 km/s, P 30.81 to 36.25 GPa) are compared with those of 1,3,5-trinitro-1,3,5-triazine (RDX) (D 8.75 km/s, P 34.70 Gpa) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) (D 8.96 km/s, P 35.96 GPa). The designed compounds satisfy the criteria of high energy materials.
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Affiliation(s)
- P Ravi
- Advanced Centre of Research in High Energy Materials, University of Hyderabad, Hyderabad, 500 046, India.
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Sundaraganesan N, Mariappan G, Manoharan S. Molecular structure and vibrational spectroscopic studies of Chrysin using HF and Density Functional Theory. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 87:67-76. [PMID: 22153594 DOI: 10.1016/j.saa.2011.11.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Revised: 10/31/2011] [Accepted: 11/09/2011] [Indexed: 05/31/2023]
Abstract
In the present study, the molecular confirmation, vibrational and electronic transition analysis of 5,7-dihyroxyflavone (Chrysin) were investigated using experimental techniques (FT-IR, FT-Raman and UV) and quantum chemical calculations by HF and DFT/B3LYP method with 6-31G(d,p) as basis set. The FT-IR and FT-Raman spectra in solid phase were recorded in the region 4000-400cm(-1) and 3500-50cm(-1) respectively. The UV absorption spectra of the title compound dissolved in water, methanol and ethanol were recorded in the range of 200-400nm. The complete vibrational assignments were performed on the basis of total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanic (SQM) method. By using TD-DFT calculation, electronic absorption spectra of the title compound have been predicted and a good agreement with experimental one is established. In addition, the molecular electrostatic potential (MEP), natural bond orbital (NBO) analysis have been investigated using theoretical calculations. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule.
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Affiliation(s)
- N Sundaraganesan
- Department of Physics (Engg.), Annamalai University, Annamalainagar 608002, India.
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Density functional studies on the endohedral complex of fullerene C70 with tetrahedrane (C4H4): C4H4@C70. J Mol Model 2012; 18:3213-7. [DOI: 10.1007/s00894-011-1343-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 12/19/2011] [Indexed: 10/14/2022]
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Kalaichelvan S, Sundaraganesan N, Dereli O, Sayin U. Experimental, theoretical calculations of the vibrational spectra and conformational analysis of 2,4-di-tert-butylphenol. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 85:198-209. [PMID: 22020168 DOI: 10.1016/j.saa.2011.09.061] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 09/26/2011] [Accepted: 09/29/2011] [Indexed: 05/31/2023]
Abstract
In the present work, we reported a combined experimental and theoretical study on conformational stability, molecular structure and vibrational spectra of 2,4-di-tert-butylphenol (2,4-DTBP). The FT-IR (400-4000cm(-1)) and FT-Raman spectra (50-3500cm(-1)) of 2,4-DTBP were recorded. The molecular geometry, harmonic vibrational frequencies and bonding features of 2,4-DTBP in the ground-state have been calculated by using the density functional BLYP/B3LYP methods. The energy calculated by time-dependent density functional theory (TD-DFT) result complements with the experimental findings. The calculated highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) energies show that charge transfer occurs within the molecule. Finally the calculation results were compared with measured infrared and Raman spectra of the title compound which showed good agreement with observed spectra.
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Affiliation(s)
- S Kalaichelvan
- Department of Physics, A.A. Govt. Arts College, Namakkal 637001, Tamil Nadu, India
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31
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Wang DL, Xu HL, Su ZM, Hou DY. Ab initio and density functional study on fullerene C44 and its derivatives. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Flores-Cervantes DX, Bucheli TD. Testing the resistance of fullerenes to chemothermal oxidation used to isolate soots from environmental samples. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2011; 159:3793-3796. [PMID: 21872974 DOI: 10.1016/j.envpol.2011.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 07/12/2011] [Accepted: 08/01/2011] [Indexed: 05/31/2023]
Abstract
We tested the resistance of five different fullerenes (C(60), C(70), C(76/78) mix, and C(84)) to chemothermal oxidation at 375 °C (CTO-375), a method that has been used and tested for quantifying black carbon (BC) and CNTs in soils and sediments. C(60) survived CTO-375 the most (50%), while C(70) was the fullerene with the lowest survival rate (<1%). Standard additions of C(60) to soil and sediment reference materials yielded recoveries between 18 and 36%. Although lower than recoveries previously observed for soot and CNTs, these results demonstrate the capability of CTO-375 to partially isolate C(60) from solid environmental matrices. Standard additions of C(70), C(76/78), and C(84) yielded slightly higher survival rates when added to soil and sediment than in their pure form. These results indicate that the mineral matrices of these samples probably had a catalytic effect towards C(60) and a protective effect towards C(70), C(76/78), and C(84) during CTO-375.
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Affiliation(s)
- D Xanat Flores-Cervantes
- Agroscope Reckenholz-Tänikon Research Station ART, Reckenholzstrasse 191, 8046 Zürich, Switzerland.
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34
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Rodríguez-Fortea A, Irle S, Poblet JM. Fullerenes: formation, stability, and reactivity. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.21] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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TÜRKER LEMI, BAYAR ÇAĞLARÇELIK, BALABAN ALEXANDRUT. A DFT Study on Push-Pull (Amino-Nitro) Fulminenes and Hexahelicenes. Polycycl Aromat Compd 2010. [DOI: 10.1080/10406631003756005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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36
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He N, Gao T, Zhang Z, Tian X, Han H. Theoretical study of structure stability, vibrational frequencies, and electronic properties of hydrogen storage in titanium–ethylene complex. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.09.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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37
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Jin L, Ding YH. [N3MN5]q: A Type of Low-Lying Sandwich-like Isomer on [N8M]q Hypersurface with (M, q) = (Ni, 0), (Co, −1), and (Fe, −2). J Phys Chem A 2009; 113:13645-50. [DOI: 10.1021/jp906313b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Lin Jin
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Yi-hong Ding
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, People’s Republic of China
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Fu Q, He T, Guo W, Zhao L, Chai Y, Zhou T, Liu Y, Liu C. Theoretical study of substituent effect on acridine as one model molecule of asphaltene. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.03.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Endohedral complex of fullerene C60 with tetrahedrane, C4H4@C60. J Mol Graph Model 2008; 27:558-62. [DOI: 10.1016/j.jmgm.2008.09.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 09/19/2008] [Accepted: 09/22/2008] [Indexed: 11/20/2022]
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40
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Ren XY, Liu ZY. Structural and electron properties of the highest epoxygenated fullerene C60O30, a DFT study. J Mol Graph Model 2007; 26:336-41. [PMID: 17241802 DOI: 10.1016/j.jmgm.2006.12.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2006] [Revised: 12/19/2006] [Accepted: 12/19/2006] [Indexed: 10/23/2022]
Abstract
Ab initio Hartree-Fock (HF) and density functional theory (DFT) calculations were carried out to determine the structural and electronic properties of the highest epoxygenated fullerenes C(60)O(30). For comparison, other fullerene oxides C(60)O(29), C(60)O(3), C(60)O(2) and C(60)O were also studied. The highly symmetrical I(h) structure of the parent C(60) is reserved in C(60)O(30) and C(60)O(30) was calculated to be a nonpolar molecule. It was demonstrated that C(60)O(30) should be more stable than other C(60) oxides such as C(60)O(29), C(60)O(3), C(60)O(2) and C(60)O. Compared with C(60), it is less possible for C(60)O(30) to accept or donate electrons from the reduced EAs and enhanced IPs. The IR active modes and harmonic vibrational frequencies of C(60)O(30) were also discussed.
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Affiliation(s)
- Xiao-Yuan Ren
- College of Life Science, Zhejiang Sci-Tech University, Hangzhou 310018, China.
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41
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42
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Li WQ, Tian WQ, Feng JK, Liu ZZ, Ren AM, Sun CC, Aoki Y. Electronic properties of tricoordinated phosphorus in hexagonal phosphininium compounds and molecular aromaticity. J Comput Chem 2007; 28:1467-1475. [PMID: 17330883 DOI: 10.1002/jcc.20650] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Calculations with B3LYP within quantum chemical density functional theory have been carried out for 1-H-phosphininium cation and a series of 1-R-phosphininium molecules (R=cyclopentadiene, alpha and beta pyrroles, alpha and beta phosphole, C5BH5-- and CH2--). The negative nuclear-independent chemical shift values and the positive aromatic stabilization energies confirm that they are aromatic compounds. In particular, the 1-H-phosphininium cation even exhibits stronger aromatic character than the well-known aromatic phosphinine. The aromatic substituents have strong capability to attract electrons. It is the conjugation and aromaticity that keeps the stability and conformations of the molecules investigated. Owing to the perturbation of the aromatic substituted groups, the predicted large T values and the enlarged HOMO-LUMO gap of the phosphininium cation indicate that these compounds are expected in experiment.
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Affiliation(s)
- Wei-Qi Li
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Wei-Quan Tian
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasugakoen, Kasuga, Fukuoka 816-8580, Japan
| | - Ji-Kang Feng
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
- College of Chemistry, Jilin University, Changchun 130023, China
| | - Zi-Zhong Liu
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
- Chemistry and Environment Science College, Inner Mongolia Normal University, Huhehaote 010022, China
| | - Ai-Min Ren
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Chia-Chung Sun
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Yuriko Aoki
- Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasugakoen, Kasuga, Fukuoka 816-8580, Japan
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Affiliation(s)
- K. Balasubramanian
- a Department of Chemistry and Biochemistry , Arizona State University , Tempe , Arizona , 85287-1604 , USA
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45
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46
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Watanabe M, Ishimaru D, Mizorogi N, Kiuchi M, Aihara JI. Thermodynamically and kinetically stable isomers of the C88 and C90 fullerenes. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.theochem.2005.03.042] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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47
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Ren XY, Liu ZY. Structural and electronic properties of S-doped fullerene C58: Where is the S atom situated? J Chem Phys 2005; 122:34306. [PMID: 15740200 DOI: 10.1063/1.1830483] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Structural and electronic properties of S-doped fullerene C58 were calculated systematically via Hartree-Fock self-consistent field (SCF) and density functional B3LYP levels of theory with 6-31G(d) basis set. The most stable C58S represents an open cage structure with a nine-member ring orifice, which provides a large hole for large atoms or small molecules to pass through into the cage. The most stable endohedral S@C58 has the S atom seated near the center of the C58 cage. The calculated highest occupied molecular orbital-lowest unoccupied molecular orbital energy gaps of the isomers lie in the range of 1.42-2.50 eV. The electron affinity and the ionization potential were also presented as an indicator of the kinetic stability. Our results may aid in the design of experimental methods for controlling the nature of fullerene cages (for example, doping, opening, and reclosing them).
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Affiliation(s)
- Xiao Yuan Ren
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China
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48
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Kiuchi M, Aihara JI. Localization energies and kinetic stability of C86 fullerene isomers. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.theochem.2004.06.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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49
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Bettinger HF. Effects of finite carbon nanotube length on sidewall addition of fluorine atom and methylene. Org Lett 2004; 6:731-4. [PMID: 14986961 DOI: 10.1021/ol0363974] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Density functional computations (PBE and B3LYP) in conjunction with 3-21G and 6-31G basis sets are used to determine the energy of fluorine atom and CH(2) addition to the sidewall of (5,5) C(30+10)(n)()H(20) (n = 0, 1, 2.18) carbon nanotube slabs. A pronounced oscillation of the addition energy is found for fluorine atom addition, while oscillations are significantly damped for carbene addition due to the insertion into CC bonds. [structure: see text]
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Affiliation(s)
- Holger F Bettinger
- Lehrstuhl für Organische Chemie 2, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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50
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