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Harismah K, Hajali N, Zandi H. 6-Thioguanine bimolecular formation for dual chelation of iron: DFT study. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113308] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Harismah K, Dhumad AM, Ibraheem HS, Zandi H, Majeed HJ. A DFT approach on tioguanine: Exploring tio-tiol tautomers, frontier molecular orbitals, IR and UV spectra, and quadrupole coupling constants. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116018] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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3
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Tiam ER, Bikobo DSN, Ndassa IM, Nyemeck Ii NM, A Zintchem AA, Ayong L, Diboué PHB, Ndjakou BL, Mbing JN, Pegnyemb DE. Experimental and computational studies of an antiplasmodial derivative of allantoin; antimycobacterial essential oil from Cordia batesii WERNHAM (Boraginaceae). BMC Chem 2021; 15:15. [PMID: 33673871 PMCID: PMC7934435 DOI: 10.1186/s13065-021-00742-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Background Chemical and pharmacological investigations were performed on the stems of Cordia batesii (Boraginaeae); chemical studies included quantum calculations applied on a newly described compound. Results A new derivative of allantoin (1) named batesiin (2) was characterized. Thirteen other known compounds involving allantoin (1) were either isolated or identified. GC–MS enabled the identification of six compounds from a fraction containing essential oil. MeOH extract and some isolated compounds were tested in vitro against Pf7G8 CQS and Pf Dd2 CQR strains of Plasmodium falciparum; extract disclosed a moderate antiplasmodial activity (IC50 = 50 μg mL−1). Meantime, the CH2Cl2 extract and essential oil fraction were tested on a resistant mycobacterial strain of Mycobacterium tuberculosis; a potent antimycobacterial activity with a MIC = 9.52 μg mL−1 was deduced from essential oil. Density functional theory (DFT) calculations were carried on batesiin (2). Calculated chemical shifts at B3LYP/6-31G(d,p) and MPW1PW91/6-31G+(d,p) showed much better correlations with the experimental data. Time dependent DFT at B3LYP/6-31G+(d,p) displayed a major absorption band 3.01 nm higher than the experimental value. Conclusion Cordia batesii can be considered as promising in search of compounds with antimalarial and antitubercular properties. DFT studies are very helpful when trying to learn more about the spectroscopic insights of a derivative of allantoin (1).
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Affiliation(s)
- Eric Robert Tiam
- Department of Organic Chemistry, Faculty of Science, University of Yaoundé I, P.O Box 812, Yaounde, Cameroon
| | | | - Ibrahim Mbouombouo Ndassa
- Department of Inorganic Chemistry, Faculty of Science, University of Yaoundé I, P.O Box 812, Yaounde, Cameroon.,Department of Chemistry, Higher Training College, University of Yaoundé I, P.O Box 47, Yaounde, Cameroon
| | - Norbert Mbabi Nyemeck Ii
- Department of Organic Chemistry, Faculty of Science, University of Yaoundé I, P.O Box 812, Yaounde, Cameroon
| | - Auguste Abouem A Zintchem
- Department of Organic Chemistry, Faculty of Science, University of Yaoundé I, P.O Box 812, Yaounde, Cameroon. .,Department of Chemistry, Higher Training College, University of Yaoundé I, P.O Box 47, Yaounde, Cameroon.
| | | | - Patrick Hervé Betote Diboué
- Centre for Research on Medicinal Plants and Traditional Medicine, Institute of Medical Research and Medicinal Plants Studies, Yaounde, Cameroon
| | - Bruno Lenta Ndjakou
- Department of Organic Chemistry, Faculty of Science, University of Yaoundé I, P.O Box 812, Yaounde, Cameroon.,Department of Chemistry, Higher Training College, University of Yaoundé I, P.O Box 47, Yaounde, Cameroon
| | - Joséphine Ngo Mbing
- Department of Organic Chemistry, Faculty of Science, University of Yaoundé I, P.O Box 812, Yaounde, Cameroon
| | - Dieudonné Emmanuel Pegnyemb
- Department of Organic Chemistry, Faculty of Science, University of Yaoundé I, P.O Box 812, Yaounde, Cameroon
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Stare J, Gradišek A, Seliger J. Nuclear quadrupole resonance supported by periodic quantum calculations: a sensitive tool for precise structural characterization of short hydrogen bonds. Phys Chem Chem Phys 2020; 22:27681-27689. [PMID: 33237040 DOI: 10.1039/d0cp04710d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Systems with short hydrogen bonds (H-bonds) are notoriously difficult to describe even using cutting edge experimental techniques supported by advanced computational protocols. One of the most challenging issues is the highly dislocated H-bonded proton, which is typically smeared over a large area, featuring complex dynamics governed by pronounced nuclear quantum effects. Thus, in combination with experimental results, these systems offer a rich platform for the benchmarking of various computational approaches and methods. Herein, we present a methodology combining experimental and computational assessment of H-bond observables probed by the nuclear quadrupole resonance technique. Focusing on the case of picolinic acid N-oxide featuring one of the shortest known hydrogen bonds (ROO ∼ 2.425 Å), we compare the predictions of nuclear quadrupole coupling constants (NQCCs) for a series of computational models differing in fine structural details of the H-bond. By comparing the computed 14N and 17O NQCCs with the measured ones and by analyzing the sensitivity of NQCCs to H-bond geometry variations, we demonstrate that NQCCs represent a very sensitive probe for H-bond geometry, particularly the proton location, thereby offering, in conjunction with computations, an accurate and reliable tool for the fine structural characterization of short H-bonds. Importantly, the present methodology is a good compromise between accuracy and computational cost.
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Affiliation(s)
- Jernej Stare
- Theory Department, National Institute of Chemistry, Ljubljana, Slovenia.
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Fallah N, Gholivand K, Yousefi M, Aberoomand azar P, Dusek M, Eigner V. Synthesis, X-ray Diffraction Studies, and Hydrogen Bonding Analysis of a New Phosphoramide Counterion in Solid State. RUSS J INORG CHEM+ 2019. [DOI: 10.1134/s0036023619050061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Harismah K, Mirzaei M, Moradi R. DFT Studies of Single Lithium Adsorption on Coronene. ACTA ACUST UNITED AC 2018. [DOI: 10.1515/zna-2017-0458] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Density functional theory (DFT) calculations were performed to study the adsorption of neutral and cationic forms of single lithium (Li) on representative original and each of oxygen/sulfur-terminated coronene monolayer surfaces. First, the monolayers of coronene structures were prepared. Next, Li/Li+ adsorptions were investigated on the surfaces of the already optimised coronene models. The results indicate that the singular coronene models can be considered as appropriate surfaces for Li/Li+ adsorption, with stronger Li+ adsorption. Localisations of LI/Li+ species were carefully examined at the central carbon zone of the monolayer surface; however, only one model showed discrepancy by getting localised at the monolayer edge. Energy levels and distribution patters for the molecular orbitals indicate the effects of atomic terminations and Li/Li+ adsorptions, in which the singular and Li+-adsorbed models reveal identical results. Atomic-scale nuclear quadrupole resonance (NQR) properties were also evaluated, with the results indicating that the atomic properties can determine the major electronic properties for applying the coronene structure for specific applications.
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Affiliation(s)
- Kun Harismah
- Department of Chemical Engineering, Faculty of Engineering , Universitas Muhammadiyah Surakarta , Surakarta , Indonesia
| | - Mahmoud Mirzaei
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences , Isfahan University of Medical Sciences , Isfahan , Iran , Fax: +98 31 36680011
| | - Reza Moradi
- Young Researchers and Elite Club, Arak Branch , Islamic Azad University , Arak , Iran
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Veinberg SL, Lindquist AW, Jaroszewicz MJ, Schurko RW. Practical considerations for the acquisition of ultra-wideline 14N NMR spectra. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 84:45-58. [PMID: 28130009 DOI: 10.1016/j.ssnmr.2016.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/20/2016] [Accepted: 12/20/2016] [Indexed: 06/06/2023]
Abstract
Several considerations for the acquisition, processing, and analysis of high quality ultra-wideline (UW) 14N solid-state NMR (SSNMR) powder patterns under static conditions are discussed. It is shown that the 14N quadrupolar parameters may be determined accurately using the frequencies of only two discontinuities in 14N NMR powder patterns that are dominated by the first-order quadrupolar interaction, thereby eliminating the need for the acquisition of the entire pattern and concomitantly reducing experimental time. A framework for utilizing the WURST-CPMG pulse sequence to improve the efficiency of UW 14N SSNMR experiments is explored in two parts: (i) a systematic investigation of the design and parameterization of the WURST pulse is presented, and (ii) the development of the practical aspects of CPMG refocusing for the acquisition of UW 14N SSNMR powder patterns is discussed, with a focus on maximizing both signal-to-noise and resolution, and minimizing spectral distortions. Finally, a strategy is demonstrated that allows for the measurement of the 14N quadrupolar parameters for any nitrogen moiety whose quadrupolar coupling constant falls within the range 0.8≤|CQ|≤1.5MHz, by acquiring only two 14N NMR sub-spectra at strategically located transmitter frequencies; these results are compared to full powder patterns which are acquired using frequency-stepped methods. The methodologies and practical considerations outlined herein are not only useful for the rapid acquisition of UW 14N NMR spectra, but may also be modified and applied for UW NMR of a plethora of quadrupolar and spin-1/2 nuclides.
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Affiliation(s)
- Stanislav L Veinberg
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada N9B 3P4
| | - Austin W Lindquist
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada N9B 3P4
| | - Michael J Jaroszewicz
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada N9B 3P4
| | - Robert W Schurko
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada N9B 3P4.
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Mirzaei M, Gülseren O, Hadipour N. DFT explorations of quadrupole coupling constants for planar 5-fluorouracil pairs. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.06.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Dorosti N, Delfan B, Gholivand K, Valmoozi AAE. Synthesis, crystal structure, biological evaluation, electronic aspects of hydrogen bonds, and QSAR studies of some new N-(substituted phenylurea) diazaphosphore derivatives as anticancer agents. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1527-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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Gholivand K, Ebrahimi Valmoozi AA, Bonsaii M. Synthesis and crystal structure of new temephos analogues as cholinesterase inhibitor: molecular docking, QSAR study, and hydrogen bonding analysis of solid state. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:5761-5771. [PMID: 24893121 DOI: 10.1021/jf5011726] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A series of temephos (Tem) derivatives were synthesized and characterized by 31P, 13C, and 1H NMR and FT-IR spectral techniques. Also, the crystal structure of compound 9 was investigated. The hydrogen bonding energies (E2) were calculated by NBO analysis of the crystal cluster. The activities and the mixed-type mechanism of Tem derivatives were evaluated using the modified Ellman's and Lineweaver-Burk's methods on cholinesterase (ChE) enzymes. The inhibitory activities of Tem derivatives with a P═S moiety were higher than those with a P═O moiety. Docking analysis disclosed that the hydrogen bonds occurred between the OR (R=CH3 and C2H5) oxygen and N-H nitrogen atoms of the selected compounds and the receptor site (GLN and GLU) of ChEs. PCA-QSAR indicated that the correlation coefficients of the electronic variables were dominant compared to the structural descriptors. MLR-QSAR models clarified that the net charges of nitrogen and phosphorus atoms contribute important electronic function in the inhibition of ChEs. The validity of the QSAR model was confirmed by a LOO cross-validation method with q2=0.965 between the training and testing sets.
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Affiliation(s)
- Khodayar Gholivand
- Department of Chemistry, Tarbiat Modares University , P.O. Box 14115-175, Tehran, Iran
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Nozad AG, Meftah S, Ghasemi MH, Aghazadeh M. DFT calculations of 14N, 17O, and 2H NQR parameters: Investigation of hydrogen bond interactions in sulfapyridine crystalline structure. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2009. [DOI: 10.1134/s0036024409130159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Nozad AG, Najafi H, Meftah S, Aghazadeh M. A systematic study on hydrogen bond interactions in sulfabenzamide: DFT calculations of the N-14, O-17, and H-2 NQR parameters. Biophys Chem 2009; 139:116-22. [DOI: 10.1016/j.bpc.2008.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Revised: 10/26/2008] [Accepted: 10/27/2008] [Indexed: 10/21/2022]
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Kelly REA, Lukas M, Kantorovich LN, Otero R, Xu W, Mura M, Lægsgaard E, Stensgaard I, Besenbacher F. Understanding the disorder of the DNA base cytosine on the Au(111) surface. J Chem Phys 2008; 129:184707. [DOI: 10.1063/1.3001585] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Density functional theory study of N–H⋯O, O–H⋯O and C–H⋯O hydrogen-bonding effects on the 14N and 2H nuclear quadrupole coupling tensors of N-acetyl-valine. Biophys Chem 2008; 133:11-8. [DOI: 10.1016/j.bpc.2007.11.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Revised: 11/11/2007] [Accepted: 11/12/2007] [Indexed: 11/24/2022]
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Mirzaei M, Hadipour NL. A computational NQR study on the hydrogen-bonded lattice of cytosine-5-acetic acid. J Comput Chem 2008; 29:832-8. [DOI: 10.1002/jcc.20845] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Esrafili MD, Elmi F, Hadipour NL. Density functional theory investigation of hydrogen bonding effects on the oxygen, nitrogen and hydrogen electric field gradient and chemical shielding tensors of anhydrous chitosan crystalline structure. J Phys Chem A 2007; 111:963-70. [PMID: 17266238 DOI: 10.1021/jp066761r] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A systematic computational investigation was carried out to characterize the 17O, 14N and 2H electric field gradient, EFG, as well as 17O, 15N, 13C and 1H chemical shielding tensors in the anhydrous chitosan crystalline structure. To include the hydrogen-bonding effects in the calculations, the most probable interacting molecules with the target molecule in the crystalline phase were considered through a hexameric cluster. The computations were performed with the B3LYP method and 6-311++G(d,p) and 6-31++G(d,p) standard basis sets using the Gaussian 98 suite of programs. Calculated EFG and chemical shielding tensors were used to evaluate the 17O, 14N and 2H nuclear quadrupole resonance, NQR, and 17O, 15N, 13C and 1H nuclear magnetic resonance, NMR, parameters in the hexameric cluster, which are in good agreement with the available experimental data. The difference between the calculated NQR and NMR parameters of the monomer and hexamer cluster shows how much hydrogen bonding interactions affect the EFG and chemical shielding tensors of each nucleus. These results indicate that both O(3)-H(33)...O(5-3) and N-H(22)...O(6-4) hydrogen bonding have a major influence on NQR and NMR parameters. Also, the quantum chemical calculations indicate that the intra- and intermolecular hydrogen bonding interactions play an essential role in determining the relative orientation of EFG and chemical shielding principal components in the molecular frame axes.
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Affiliation(s)
- Mehdi D Esrafili
- Department of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
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Behzadi H, Esrafili MD, Hadipour NL. A theoretical study of 17O, 14N and 2H nuclear quadrupole coupling tensors in the real crystalline structure of acetaminophen. Chem Phys 2007. [DOI: 10.1016/j.chemphys.2007.01.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Mirzaei M, Hadipour NL, Ahmadi K. Investigation of C–H…OC and N–H…OC hydrogen-bonding interactions in crystalline thymine by DFT calculations of O-17, N-14 and H-2 NQR parameters. Biophys Chem 2007; 125:411-5. [PMID: 17175092 DOI: 10.1016/j.bpc.2006.10.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2006] [Revised: 10/09/2006] [Accepted: 10/12/2006] [Indexed: 11/17/2022]
Abstract
A computational study at the level of density functional theory (DFT) was carried out to investigate C-H...O=C and N-H...O=C hydrogen-bonding interactions (HBs) in the real crystalline cluster of thymine by O-17, N-14 and H-2 calculated nuclear quadrupole resonance (NQR) parameters. To perform the calculations, a hydrogen-bonded pentameric cluster of thymine was created using X-ray coordinates where the hydrogen atoms positions are optimized and the electric field gradient (EFG) tensors were calculated for the target molecule. Additional EFG calculations were also performed for crystalline monomer and an optimized isolated gas-phase thymine. The calculated EFG tensors at the level of B3LYP and B3PW91 DFT methods and 6-311++G**and CC-pVTZ basis sets were converted to those experimentally measurable NQR parameters, quadrupole coupling constants and asymmetry parameters. The results reveal that because of strong contribution to N-H...O=C HBs, NQR parameters of O2, N1 and N3 undergo significant changes from monomer to the target molecule in cluster. Furthermore, the NQR parameters of O2 also undergo some changes because of non-classical C-H...O=C HBs.
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Affiliation(s)
- Mahmoud Mirzaei
- Department of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
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Behzadi H, Hadipour NL, Mirzaei M. A density functional study of 17O, 14N and 2H electric field gradient tensors in the real crystalline structure of α-glycine. Biophys Chem 2007; 125:179-83. [PMID: 16914262 DOI: 10.1016/j.bpc.2006.07.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2006] [Revised: 07/19/2006] [Accepted: 07/20/2006] [Indexed: 10/24/2022]
Abstract
A density functional theory (DFT) study was carried out to calculate (17)O, (14)N and (2)H electric field gradient (EFG) tensors in accurate neutron diffraction structures of alpha-glycine at 288 and 427 K. B3LYP is the used method and 6-311+G(*) and 6-311++G(**) are the basis sets in the calculations of EFG tensors at the sites of (17)O, (14)N and (2)H nuclei in the monomer and the octameric cluster of alpha-glycine at two temperatures. Quadrupole coupling constants and asymmetry parameters are the converted parameters of calculated EFG tensors to experimentally measurable ones. The calculated results of monomer and the target molecule in octameric cluster reveal that hydrogen-bonding interactions play an important role in the crystalline structure of alpha-glycine where the results of the target molecule in octameric cluster are in good agreement with the experiments.
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Affiliation(s)
- Hadi Behzadi
- Department of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
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