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Bilkay M, Satana Kara HE. Synthesis of novel phenylalanine-coated copper nanoclusters for fluorescent probes to determine the interactions of cancer drugs with DNA. J Pharm Biomed Anal 2024; 249:116365. [PMID: 39024792 DOI: 10.1016/j.jpba.2024.116365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/20/2024]
Abstract
Abiraterone acetate (ATA) is an FDA-approved prodrug that exerts its effects by irreversibly inhibiting the enzymatic activities of 17α-hydroxylase and C17,20-lyase, which are responsible for testosterone production, particularly. Drug-DNA interaction studies are conducted using various methods. In this study, CuNCs were used as a fluorescent probe for the first time to investigate drug-DNA interactions. Additionally, a new synthesis was developed for copper nanoclusters coated with phenylalanine (Phe). Ascorbic acid served as the reducing agent, while Phe was used as a surface functionalizing and stabilizing agent. Phe/CuNCs were characterized using various techniques including TEM, DLS, XPS, UV-Vis spectroscopy, and fluorescence spectroscopy. Optimization studies were conducted for synthesis parameters such as ascorbic acid concentration, Phe concentration, incubation time, and incubation temperature. This new synthesis method offers various advantages such as easy synthesis procedure, short synthesis time, and compatibility with green chemistry principles. Phe/CuNCs were used as a fluorescent probe for ATA-DNA interactions. The binding constant (Ka) between ATA and DNA was calculated as 1.03 × 104. Furthermore, thermodynamic studies indicated that the effective forces involved in ATA-DNA interaction are Van der Waals and hydrogen bonding.
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Affiliation(s)
- Mehmetcan Bilkay
- Department of Analytical Chemistry, Faculty of Pharmacy, Gazi University, Ankara, Turkiye.
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2
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Hernández B, Coïc YM, Kruglik SG, Sanchez-Cortes S, Ghomi M. The relationship between the tyrosine residue 850-830 cm -1 Raman doublet intensity ratio and the aromatic side chain χ 1 torsion angle. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 308:123681. [PMID: 38039641 DOI: 10.1016/j.saa.2023.123681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 11/21/2023] [Indexed: 12/03/2023]
Abstract
Tyrosine (Tyr) residue in a peptide chain is characterized by the presence of seven Raman markers, referred to as Yi (i = 1, …, 7), distributed over the middle wavenumber spectral region. Particularly, the changes observed in the relative intensity of Y5 and Y6 markers, appearing as a side by side doublet at ca. 850-830 cm-1, has received a great attention. Primarily assigned to a Fermi-resonance effect between phenol ring planar and nonplanar modes, former density functional theory calculations led us to affiliate the Y5-Y6 doublet to two distinct fundamental modes. Furthermore, despite the previous assumptions, it was evidenced that the reversal of the doublet intensity ratio cannot be solely explained by hydrogen bonding on the phenol hydroxyl group involved in Tyr. Herein, upon analyzing the observed and theoretical data collected from the cationic species of the tripeptide Gly-Tyr-Gly, the crucial effect of the aromatic side chain orientation, especially that of the χ1 torsion angle defined around the CαCβ bond, on the Tyr doublet intensity ratio has been evidenced.
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Affiliation(s)
- Belén Hernández
- LVTS, INSERM U1148, 74 rue Marcel Cachin, 93017 Bobigny Cédex, France
| | - Yves-Marie Coïc
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Unité de Chimie des Biomolécules, F-75015 Paris, France
| | - Sergei G Kruglik
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean-Perrin, 4 Place Jussieu, 75005 Paris, France
| | | | - Mahmoud Ghomi
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 121, 28006 Madrid, Spain.
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3
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Kanemura Y, Kanazawa M, Hashimoto S, Hayashi Y, Fujiwara E, Suzuki A, Ishii T, Goto M, Nozaki H, Inoue T, Takanari H. Assessment of skin inflammation using near-infrared Raman spectroscopy combined with artificial intelligence analysis in an animal model. Analyst 2022; 147:2843-2850. [DOI: 10.1039/d2an00193d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Near-infrared (NIR) Raman spectroscopy was applied to detect skin inflammation in an animal model. Artificial intelligence (AI) analysis improved prediction accuracy for skin inflammation.
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Affiliation(s)
- Yohei Kanemura
- Department of Interdisciplinary Researches for Medicine and Photonics, Institute of Post-LED Photonics, Tokushima University, 3-18-15, Kuramoto, Tokushima 770-8503, Japan
- Tokushima University, Faculty of Science and Technology, 2-1, Minami-Josanjima, Tokushima 770-8506, Japan
| | - Meiko Kanazawa
- Department of Interdisciplinary Researches for Medicine and Photonics, Institute of Post-LED Photonics, Tokushima University, 3-18-15, Kuramoto, Tokushima 770-8503, Japan
- Tokushima University, Faculty of Medicine, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Satoru Hashimoto
- Division of Applied Chemistry, Faculty of Science and Technology, Oita University Graduate School of Engineering, 700, Dan-noharu, Oita 870-1124, Japan
| | - Yuri Hayashi
- Department of Interdisciplinary Researches for Medicine and Photonics, Institute of Post-LED Photonics, Tokushima University, 3-18-15, Kuramoto, Tokushima 770-8503, Japan
- Tokushima University, Faculty of Medicine, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Erina Fujiwara
- Division of Applied Chemistry, Faculty of Science and Technology, Oita University Graduate School of Engineering, 700, Dan-noharu, Oita 870-1124, Japan
| | - Ayako Suzuki
- Division of Applied Chemistry, Faculty of Science and Technology, Oita University Graduate School of Engineering, 700, Dan-noharu, Oita 870-1124, Japan
| | - Takashige Ishii
- Division of DX Promotion, OEC Co., Ltd., 17-57, Higashi-Kasuga, Oita 870-0037, Japan
| | - Masakazu Goto
- Division of DX Promotion, OEC Co., Ltd., 17-57, Higashi-Kasuga, Oita 870-0037, Japan
| | - Hiroshi Nozaki
- Division of DX Promotion, OEC Co., Ltd., 17-57, Higashi-Kasuga, Oita 870-0037, Japan
| | - Takanori Inoue
- Division of Applied Chemistry, Faculty of Science and Technology, Oita University Graduate School of Engineering, 700, Dan-noharu, Oita 870-1124, Japan
| | - Hiroki Takanari
- Department of Interdisciplinary Researches for Medicine and Photonics, Institute of Post-LED Photonics, Tokushima University, 3-18-15, Kuramoto, Tokushima 770-8503, Japan
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4
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Shardlow E, Exley C. The size of micro-crystalline tyrosine (MCT®) influences its recognition and uptake by THP-1 macrophages in vitro. RSC Adv 2019; 9:24505-24518. [PMID: 35527856 PMCID: PMC9069726 DOI: 10.1039/c9ra03831k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/26/2019] [Indexed: 11/21/2022] Open
Abstract
The physicochemical hallmarks of particulate immunopotentiators play a pivotal role with regards to their adjuvanticity in vivo. These properties have not been fully characterised in the case of MCT®, an amino acid-based adjuvant used as an alternative to aluminium salts in subcutaneous allergy immunotherapy (SCIT). This study presents a full characterisation of MCT® and in a preliminary capacity reveals how parameters, specifically particle size, might influence the recognition of MCT® by antigen presenting cells (APCs) in vitro. Light microscopic analysis demonstrated that MCT® was composed of highly crystalline needles, the majority of which exceeded 10 μm in length under physiological conditions (median size – 20.8 μm). While the substantial length of crystals presented a significant barrier to cellular recognition and uptake, isolated incidences of perpendicular recognition were observed owing to the smaller comparative width of crystallites (median size – 2.8 μm). This appeared to allow a small proportion of material to be ingested both fully and partially by THP-1 macrophages, although further studies are required to unequivocally confirm this observation. Preferential recognition of needle tips also favoured the direct presentation of antigen to immune cells as proteinaceous adsorption appeared to be isolated to these regions. Furthermore, the data herein provide valuable insights into the mechanisms surrounding how this adjuvant potentiates an immunological response following administration. The large size of MCT® crystallites partially stymies their recognition and uptake by THP-1 macrophages in vitro.![]()
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Affiliation(s)
- Emma Shardlow
- The Birchall Centre, Lennard-Jones Laboratories, Keele University Keele Staffordshire ST5 5BG UK
| | - Christopher Exley
- The Birchall Centre, Lennard-Jones Laboratories, Keele University Keele Staffordshire ST5 5BG UK
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5
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Braga CB, Rittner R. Combined Utilization of 1H NMR, IR, and Theoretical Calculations To Elucidate the Conformational Preferences of Some l-Histidine Derivatives. J Phys Chem A 2017; 121:729-740. [DOI: 10.1021/acs.jpca.6b12515] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carolyne B. Braga
- Chemistry Institute, University of Campinas, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
| | - Roberto Rittner
- Chemistry Institute, University of Campinas, P.O. Box 6154, 13083-970 Campinas, SP, Brazil
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6
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Yao G, Zhang J, Huang Q. Conformational and vibrational analyses of meta-tyrosine: An experimental and theoretical study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 151:111-123. [PMID: 26125991 DOI: 10.1016/j.saa.2015.06.073] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 06/18/2015] [Accepted: 06/22/2015] [Indexed: 06/04/2023]
Abstract
M-tyrosine is one kind of positional isomer of tyrosine which is widely applied in agrichemical, medicinal chemistry, and food science. However, the structural and vibrational features of m-tyrosine have not been reported or systematically investigated. In this work, potential energy surface (PES) calculations were used for searching and determining the stable zwitterionic conformers of m-tyrosine, and the Raman spectra of m-tyrosine and deuterated m-tyrosine were measured and interpreted based on theoretical computation. For the spectral simulation, several DFT-based quantum chemistry (QC) methods were employed, and the M06-2X functional with SMD solvent model was found to be best in reproducing the Raman spectra and geometrical property. As such, this study has not only presented a detailed study of m-tyrosine's vibrational property which is lack in the literature, but also may shed some light on the optimal choice of QC methods for calculation of conformations and vibrational properties of zwitterionic amino acids.
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Affiliation(s)
- Guohua Yao
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, PR China
| | - Jingjing Zhang
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, PR China
| | - Qing Huang
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, PR China; University of Science & Technology of China, Hefei, Anhui 230026, PR China.
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7
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Raja B, Balachandran V, Revathi B. Structural study, NCA, FT-IR, FT-Raman spectral investigations, NBO analysis, thermodynamic functions of N-acetyl-l-phenylalanine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 138:283-295. [PMID: 25498825 DOI: 10.1016/j.saa.2014.11.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 10/23/2014] [Accepted: 11/20/2014] [Indexed: 06/04/2023]
Abstract
The FT-IR and FT-Raman spectra of N-acetyl-l-phenylalanine were recorded and analyzed. Natural bond orbital analysis has been carried out for various intramolecular interactions that are responsible for the stabilization of the molecule. HOMO-LUMO energy gap has been computed with the help of density functional theory. The statistical thermodynamic functions (heat capacity, entropy, vibrational partition function and Gibbs energy) were obtained for the range of temperature 100-1000K. The polarizability, first hyperpolarizability, anisotropy polarizability invariant has been computed using quantum chemical calculations. The infrared and Raman spectra were also predicted from the calculated intensities. Comparison of the experimental and theoretical spectra values provides important information about the ability of the computational method to describe the vibrational modes.
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Affiliation(s)
- B Raja
- Department of Physics, Government Arts College, Kulithalai 639120, Karur, India
| | - V Balachandran
- Research Department of Physics, A.A. Government Arts College, Musiri 621211, India.
| | - B Revathi
- Research Department of Physics, A.A. Government Arts College, Musiri 621211, India
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Quesada-Moreno MM, Avilés-Moreno JR, Márquez-García AA, López-González JJ. Deducing the molecular properties of zwitterionic, protonated, deprotonated, and double-deprotonated forms of L-cysteine from vibrational spectroscopy (IR, Raman, VCD) and quantum chemical calculations. J Mol Model 2014; 20:2229. [PMID: 24916344 DOI: 10.1007/s00894-014-2229-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Accepted: 04/02/2014] [Indexed: 10/25/2022]
Abstract
The behavior of L-cysteine (C3H7NO2S, (2R)-2-amino-3-sulfanylpropanoic acid) in water at different pH values was analyzed both experimentally and theoretically. The behavior was studied at pH values of 5.21 (at this pH, L-cysteine is a zwitterionic species), 1.00 (protonated species), 8.84 (monodeprotonated species), and 13.00 (dideprotonated species). We carried out a vibrational study using nonchiroptical (IR-Raman) and chiroptical (VCD) techniques complemented by quantum chemical calculations. We adopted a dual strategy, as follows. (i) The hybrid density functionals B3LYP and M062X and the ab initio MP2 method were employed, with the same 6-311++G (d,p) basis set, in order to characterize the relative energies and structures of an extensive set of conformers of L-cysteine. The presence of water was included by utilizing the IEF-PCM implicit solvation model. (ii) The vibrational analysis was made using a chirality-sensitive using a chirality-sensitive technique (VCD) and chirality-insensitive techniques (IR, including MIR and FIR, and Raman), especially in aqueous solution. The results obtained theoretically and experimentally were compared in order to deduce the most stable structures at each pH. Moreover, for the first time, the monodeprotonated anion of L-cysteine was detected in aqueous solution by means of IR, Raman and vibrational circular dichroism (VCD). Finally, analysis of the low-frequency region using the IR and Raman techniques was shown to be a very important way to understanding the conformational preference of the zwitterionic species.
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Affiliation(s)
- María Mar Quesada-Moreno
- Department of Physical and Analytical Chemistry, University of Jaén, Campus Las Lagunillas, 23071, Jaén, Spain
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9
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Virgili A, Quesada-Moreno MM, Avilés-Moreno JR, López-González JJ, Ángeles García M, Claramunt RM, Torres MR, Jimeno ML, Reviriego F, Alkorta I, Elguero J. A Spectroscopic Study of Colchicine in the Solid State and in Solution by Multinuclear Magnetic Resonance and Vibrational Circular Dichroism. Helv Chim Acta 2014. [DOI: 10.1002/hlca.201300395] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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10
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Quesada-Moreno MM, Avilés-Moreno JR, López-González JJ, Claramunt RM, López C, Alkorta I, Elguero J. Chiral self-assembly of enantiomerically pure (4S,7R)-campho[2,3-c]pyrazole in the solid state: a vibrational circular dichroism (VCD) and computational study. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.tetasy.2014.02.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Azofra LM, Quesada-Moreno MM, Alkorta I, Avilés-Moreno JR, López-González JJ, Elguero J. Carbohydrates in the gas phase: conformational preference ofd-ribose and 2-deoxy-d-ribose. NEW J CHEM 2014. [DOI: 10.1039/c3nj01076g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Quesada-Moreno MM, Márquez-García AÁ, Avilés-Moreno JR, López-González JJ. Conformational landscape of l-threonine in neutral, acid and basic solutions from vibrational circular dichroism spectroscopy and quantum chemical calculations. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.tetasy.2013.09.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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13
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Duarte CJ, Cormanich RA, Ducati LC, Rittner R. 1H NMR and theoretical studies on the conformational equilibrium of tryptophan methyl ester. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.07.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Avilés-Moreno JR, Quesada-Moreno MM, López-González JJ, Martínez-Haya B. Chiral Recognition of Amino Acid Enantiomers by a Crown Ether: Chiroptical IR-VCD Response and Computational Study. J Phys Chem B 2013; 117:9362-70. [DOI: 10.1021/jp405027s] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juan Ramón Avilés-Moreno
- Department of Physical and Analytical
Chemistry, Campus Las Lagunillas, University of Jaén, E-23071 Jaén, Spain
| | - María Mar Quesada-Moreno
- Department of Physical and Analytical
Chemistry, Campus Las Lagunillas, University of Jaén, E-23071 Jaén, Spain
| | - Juan Jesús López-González
- Department of Physical and Analytical
Chemistry, Campus Las Lagunillas, University of Jaén, E-23071 Jaén, Spain
| | - Bruno Martínez-Haya
- Department of Physical, Chemical
and Natural Systems, Universidad Pablo de Olavide, E-41013 Seville, Spain
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15
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l-Serine in aqueous solutions at different pH: Conformational preferences and vibrational spectra of cationic, anionic and zwitterionic species. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.04.038] [Citation(s) in RCA: 22] [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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16
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Avilés Moreno JR, Quesada Moreno MM, López González JJ, Claramunt RM, López C, Alkorta I, Elguero J. Self-assembly structures of 1H-indazoles in the solution and solid phases: a vibrational (IR, FIR, Raman, and VCD) spectroscopy and computational study. Chemphyschem 2013; 14:3355-60. [PMID: 23853070 DOI: 10.1002/cphc.201300503] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Indexed: 11/12/2022]
Abstract
1H-indazoles are good candidates for studying the phenomena of molecular association and spontaneous resolution of chiral compounds. Thus, because the 1H-indazoles can crystallize as dimers, trimers, or catemers, depending on their structure and the phase that they are in, the difficulty in the experimental analysis of the structure of the family of 1H-indazoles becomes clear. This difficulty leads us to contemplate several questions: How can we determine the presence of different structures of a given molecular species if they change according to the phase? Could these different structures be present in the same phase simultaneously? How can they be determined? To shed light on these questions, we outline a very complete strategy by using various vibrational spectroscopic techniques that are sensitive (VCD) and insensitive (IR, FIR, and Raman) towards the chirality, together with quantum chemical calculations.
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Affiliation(s)
- J R Avilés Moreno
- Departamento de Química Física y Analítica, Universidad de Jaén, Campus Las Lagunillas, 23071 Jaén (Spain)
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17
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Goerigk L, Reimers JR. Efficient Methods for the Quantum Chemical Treatment of Protein Structures: The Effects of London-Dispersion and Basis-Set Incompleteness on Peptide and Water-Cluster Geometries. J Chem Theory Comput 2013; 9:3240-51. [DOI: 10.1021/ct400321m] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Lars Goerigk
- School of Chemistry, The University of Sydney, New South Wales 2006, Australia
| | - Jeffrey R. Reimers
- School of Chemistry, The University of Sydney, New South Wales 2006, Australia
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