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Kakalejčíková S, Bazeľ Y, Le Thi VA, Fizer M. An Innovative Vortex-Assisted Liquid-Liquid Microextraction Approach Using Deep Eutectic Solvent: Application for the Spectrofluorometric Determination of Rhodamine B in Water, Food and Cosmetic Samples. Molecules 2024; 29:3397. [PMID: 39064976 PMCID: PMC11280433 DOI: 10.3390/molecules29143397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/12/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
A new green and highly sensitive method for the determination of rhodamine B (RhB) by deep eutectic solvent-based vortex-assisted liquid-liquid microextraction with fluorescence detection (DES-VALLME-FLD) was developed. The extraction efficiency of conventional solvents and different deep eutectic solvent (DES) systems composed of tetrabutylammonium bromide (TBAB) and an alcohol (hexanol, octanol, or decanol) in different ratios were compared. DFT calculations of intermolecular electrostatic and non-covalent interactions of the most stable RhB forms with DES and water explain the experimental DESs' extraction efficiency. Semiempirical PM7 computations were used to obtain Hansen solubility parameters, which supported the good solubility of the monocationic RhB form in selected DESs. The dependence of the linear calibration of microextraction into 100 µL DES was observed in the RhB calibration range from 0.2 to 10.0 µg L-1 with a correlation coefficient of R2 = 0.9991. The LOD value was calculated to be 0.023 µg L-1. The accuracy and precision of the proposed method were verified over two days with RSD values of 2.9 to 4.1% and recovery of 94.6 to 103.7%. The developed method was applied to the determination of RhB in real samples (tap water, energy drink, and lipstick).
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Affiliation(s)
- Sofia Kakalejčíková
- Department of Analytical Chemistry, Institute of Chemistry, Pavol Jozef Šafárik University in Košice, 040 01 Košice, Slovakia; (S.K.); (V.A.L.T.)
| | - Yaroslav Bazeľ
- Department of Analytical Chemistry, Institute of Chemistry, Pavol Jozef Šafárik University in Košice, 040 01 Košice, Slovakia; (S.K.); (V.A.L.T.)
| | - Van Anh Le Thi
- Department of Analytical Chemistry, Institute of Chemistry, Pavol Jozef Šafárik University in Košice, 040 01 Košice, Slovakia; (S.K.); (V.A.L.T.)
| | - Maksym Fizer
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV 89557-0216, USA;
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Cruz R, Ataka K, Heberle J, Kozuch J. Evaluating aliphatic CF, CF2, and CF3 groups as vibrational Stark effect reporters. J Chem Phys 2024; 160:204308. [PMID: 38814010 DOI: 10.1063/5.0198303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/09/2024] [Indexed: 05/31/2024] Open
Abstract
Given the extensive use of fluorination in molecular design, it is imperative to understand the solvation properties of fluorinated compounds and the impact of the C-F bond on electrostatic interactions. Vibrational spectroscopy can provide direct insights into these interactions by using the C-F bond stretching [v(C-F)] as an electric field probe through the vibrational Stark effect (VSE). In this work, we explore the VSE of the three basic patterns of aliphatic fluorination, i.e., mono-, di-, and trifluorination in CF, CF2, and CF3 groups, respectively, and compare their response to the well-studied aromatic v(C-F). Magnitudes (i.e., Stark tuning rates) and orientations of the difference dipole vectors of the v(C-F)-containing normal modes were determined using density functional theory and a molecular dynamics (MD)-assisted solvatochromic analysis of model compounds in solvents of varying polarity. We obtain Stark tuning rates of 0.2-0.8 cm-1/(MV/cm), with smallest and largest electric field sensitivities for CFaliphatic and CF3,aliphatic, respectively. While average electric fields of solvation were oriented along the main symmetry axis of the CFn, and thus along its static dipole, the Stark tuning rate vectors were tilted by up to 87° potentially enabling to map electrostatics in multiple dimensions. We discuss the influence of conformational heterogeneity on spectral shifts and point out the importance of multipolar and/or polarizable MD force fields to describe the electrostatics of fluorinated molecules. The implications of this work are of direct relevance for studies of fluorinated molecules as found in pharmaceuticals, fluorinated peptides, and proteins.
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Affiliation(s)
- R Cruz
- Fachbereich Physik, Freie Universität Berlin, Berlin 14195, Germany
| | - K Ataka
- Fachbereich Physik, Freie Universität Berlin, Berlin 14195, Germany
| | - J Heberle
- Fachbereich Physik, Freie Universität Berlin, Berlin 14195, Germany
- Forschungsbau SupraFAB, Freie Universität Berlin, Berlin 14195, Germany
| | - J Kozuch
- Fachbereich Physik, Freie Universität Berlin, Berlin 14195, Germany
- Forschungsbau SupraFAB, Freie Universität Berlin, Berlin 14195, Germany
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3
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de Araújo AVS, Rangel CJ, Ando RA. Multiconfigurational Calculations and Experimental Resonant Raman/SERRS of a Donor-Acceptor Thiadiazole Dye. J Phys Chem A 2023; 127:10789-10796. [PMID: 38109666 DOI: 10.1021/acs.jpca.3c04798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
The resonant Raman (RR) and resonant SERS spectra of the thiadiazole-based dye dibromobenzo[c]-1,2,5-thiadiazole (DBTD) were studied through multiconfigurational XMS-CASPT2/CASSCF and experimental methods in solution. The results indicate that the S1 excited state of DBTD is described by π → π* with internal CT from the benzene ring to the thiadizole. In resonance conditions at 364 nm, the RR spectrum shows intensifications in modes that describe extensive geometrical changes at both the benzene ring and the thiadiazole region, indicating an internal CT character to the S1. The SERS spectra observed on gold and silver nanoparticles indicate different adsorption geometries, which leads to distinct enhancement patterns on the spectra with varying excitation energy. It evidences the major contribution of the chemical enhancement mechanism on the spectra from a metal → DBTD CT state, as confirmed by the simulated spectra. This theoretical approach proved strong in the prediction of the main features of the observed experimental resonant Raman and SERS spectra indicating a potential for adequate description of the chemical mechanism of SERS.
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Affiliation(s)
- Adalberto V Sanches de Araújo
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, Butantã, 05508-000 São Paulo-SP, Brazil
| | - Clara J Rangel
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, Butantã, 05508-000 São Paulo-SP, Brazil
| | - Rômulo A Ando
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, Butantã, 05508-000 São Paulo-SP, Brazil
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Cardoso LMB, de Oliveira Neto JG, Saraiva GD, Leite FF, Ayala AP, Dos Santos AO, de Sousa FF. New polymorphic phase of arachidic acid crystal: structure, intermolecular interactions, low-temperature stability and Raman spectroscopy combined with DFT calculations. RSC Adv 2023; 13:34032-34044. [PMID: 38020030 PMCID: PMC10660439 DOI: 10.1039/d3ra05388a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/04/2023] [Indexed: 12/01/2023] Open
Abstract
Saturated monocarboxylic fatty acids with long carbon chains are organic compounds widely used in several applied fields, such as energy production, thermal energy storage, antibactericidal, antimicrobial, among others. In this research, a new polymorphic phase of arachidic acid (AA) crystal was synthesized and its structural and vibrational properties were studied by single-crystal X-ray diffraction (XRD) and polarized Raman scattering. The new structure of AA was solved at two different temperature conditions (100 and 300 K). XRD analysis indicated that this polymorph belongs to the monoclinic space group P21/c (C2h5), with four molecules per unit cell (Z = 4). All molecules in the crystal lattice adopt a gauche configuration, exhibiting a R22(8) hydrogen bond pattern. Consequently, this new polymorphic phase, labeled as B form, is a polytype belonging to the monoclinic symmetry, i.e., Bm form. Complementarily, Hirshfeld's surfaces were employed to analyze the intermolecular interactions within the crystal lattice of this polymorph at temperatures of 100 and 300 K. Additionally, density functional theory (DFT) calculations were performed to assign all intramolecular vibration modes related to experimental Raman-active bands, which were properly calculated using a dimer model, considering a pair of AA molecules in the gauche configuration, according to the solved-crystal structure.
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Affiliation(s)
- Luanny M B Cardoso
- Institute of Exact and Natural Sciences, Federal University of Para - UFPA Belém Pará CEP 66075-110 Brazil
| | - João G de Oliveira Neto
- Center for Social Sciences, Health, and Technology, Federal University of Maranhao - UFMA Imperatriz Maranhão CEP 65900-410 Brazil
| | - Gilberto D Saraiva
- Physics Course, State University of Ceara - UECE Campus FECLESC Quixadá Ceará CEP 63900-000 Brazil
| | - Fábio F Leite
- Department of Exact and Technological Sciences, Federal University of Amapá - UNIFAP Macapá Amapá CEP 68903-419 Brazil
| | - Alejandro P Ayala
- Department of Physics, Federal University of Ceara - UFC Fortaleza Ceará CEP 65455-900 Brazil
| | - Adenilson O Dos Santos
- Center for Social Sciences, Health, and Technology, Federal University of Maranhao - UFMA Imperatriz Maranhão CEP 65900-410 Brazil
| | - Francisco F de Sousa
- Institute of Exact and Natural Sciences, Federal University of Para - UFPA Belém Pará CEP 66075-110 Brazil
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Marques LR, Ando RA. Infrared Spectroscopy Evidence of Weak Interactions in Frustrated Lewis Pairs Formed by Tris(pentafluorophenyl)borane. Chemphyschem 2023; 24:e202200715. [PMID: 36450662 DOI: 10.1002/cphc.202200715] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/26/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022]
Abstract
Frustrated Lewis pairs (FLPs) have been widely investigated as promising catalysts due to their metal-free feature and ability to activate small molecules. Since their discovery, many works have been investigating how these Lewis pairs (intermolecular pairs) are held together in an encounter complex. This prompted several studies based on theoretical investigations, but experimental ones are limited yet. In this communication we show evidence of weak intermolecular interactions between Lewis acids and Lewis bases, distinguishing the Lewis adduct from FLPs, by probing fluorine-carbon vibrational modes using infrared spectroscopy. The main evidence is based on the band shifts occurring in FLPs due to weak hydrogen bonds between the hydrogen atoms of the Lewis base and the fluorine atoms of Lewis acid.
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Affiliation(s)
- Leandro Ramos Marques
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, Butantã, 05508-000, São Paulo-SP, Brazil
| | - Rômulo Augusto Ando
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, Butantã, 05508-000, São Paulo-SP, Brazil
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Cedillo–Cruz A, Villalobos–López DC, Aguilar MI, Trejo–Soto PJ, Hernández–Campos A, Jung–Cook H. Praziquanamine enantiomers: crystal structure, Hirshfeld surface analysis, and quantum chemical studies. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
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7
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Nisini G, Scroccarello A, Ripanti F, Fasolato C, Cappelluti F, Capocefalo A, Della Pelle F, Compagnone D, Postorino P. Nanoscale Surface-Enhanced Raman Spectroscopy Investigation of a Polyphenol-Based Plasmonic Nanovector. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:377. [PMID: 36770338 PMCID: PMC9921702 DOI: 10.3390/nano13030377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/05/2023] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
The demand for next-generation multifunctional nanovectors, combining therapeutic effects with specific cellular targeting, has significantly grown during the last few years, pursuing less invasive therapy strategies. Polyphenol-conjugated silver nanoparticles (AgNPs) appear as potential multifunctional nanovectors, integrating the biorecognition capability and the antioxidant power of polyphenols, the antimicrobial activity of silver, and the drug delivery capability of NPs. We present a spectroscopic and microscopic investigation on polyphenol-synthesized AgNPs, selecting caffeic acid (CA) and catechol (CT) as model polyphenols and using them as reducing agents for the AgNP green synthesis, both in the presence and in the absence of a capping agent. We exploit the plasmonic properties of AgNPs to collect Surface-Enhanced Raman Scattering (SERS) spectra from the nanosized region next to the Ag surface and to characterize the molecular environment in the proximity of the NP, assessing the orientation and tunable deprotonation level of CA, depending on the synthesis conditions. Our results suggest that the SERS investigation of such nanovectors can provide crucial information for their perspective biomedical application.
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Affiliation(s)
- Giacomo Nisini
- Physics Department, Sapienza University, P.le A. Moro 5, 00185 Rome, Italy
| | - Annalisa Scroccarello
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, via R. Balzarini 1, 64100 Teramo, Italy
| | - Francesca Ripanti
- Physics Department, Sapienza University, P.le A. Moro 5, 00185 Rome, Italy
- Physics and Geology Department, University of Perugia, via A. Pascoli, 06123 Perugia, Italy
| | - Claudia Fasolato
- Institute for Complex Systems, National Research Council, P.le A. Moro 5, 00185 Rome, Italy
| | | | - Angela Capocefalo
- Institute for Complex Systems, National Research Council, P.le A. Moro 5, 00185 Rome, Italy
| | - Flavio Della Pelle
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, via R. Balzarini 1, 64100 Teramo, Italy
| | - Dario Compagnone
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, via R. Balzarini 1, 64100 Teramo, Italy
| | - Paolo Postorino
- Physics Department, Sapienza University, P.le A. Moro 5, 00185 Rome, Italy
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8
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Stocka J, Platakyte R, Hickman D, Carrigan-Broda T, Ceponkus J, Sablinskas V, Rodziewicz P, Guirgis G. Experimental (Raman and IR) and computational (DFT, MP2) studies of the conformational diversity of 1-chloromethyl-1-fluorosilacyclopentane molecule. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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9
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Fizer O, Fizer M, Filep M, Sidey V, Mariychuk R. On the structure of cetylpyridinium perchlorate: A combined XRD, NMR, IR and DFT study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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10
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Carvalho JO, Oliveira Neto JG, Silva Filho JG, de Sousa FF, Freire PTC, Santos AO, Façanha Filho PF. Physicochemical properties calculated using DFT method and changes of 5-methyluridine hemihydrate crystals at high temperatures. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 281:121594. [PMID: 35841856 DOI: 10.1016/j.saa.2022.121594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/13/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
5-methyluridine hemihydrate (5 mU) single crystals were synthesized by the slow solvent evaporation method. The physicochemical properties, such as frontier molecular orbitals, global reactivity indices and vibrational were computationally studied through density functional theory (DFT). In addition, structural, vibrational, and thermal properties were obtained by powder X-ray diffraction (PXRD), Raman spectroscopy, thermogravimetric (TG) analysis and differential scanning calorimetry (DSC). PXRD evaluated the structural behavior of 5 mU crystal in the temperature range of 300-460 K. The high-temperature PXRD results suggested that the crystal undergoes two dehydration processes, being a first occurring from the orthorhombic structure (P21212) to triclinic (P1), in which the water losses occurred around 380 K. A second dehydration triggers the change from the triclinic structure to monoclinic (P21) within the 420-435 K temperature range. Furthermore, after this temperature, the anhydrous 5 mU suffers a melting process near 460 K, which is remarkably characterized as an irreversible process. Raman spectroscopy was carried out to identify the vibrational modes linked to the water molecule and the noticeable changes in these bands due to high-temperature effects around 380 K and 410 K. Indeed, changes on Raman bands, such as intensity inversion, the disappearance of bands associated with the hydrogen bonds formed from the water molecules and uracil group, and the ribose group were observed. Finally, this study provided details on the structural and vibrational changes caused by the dehydration of 5 mU crystals and the importance of hydrogen bonds for understanding the intermolecular interactions of the 5 mU, a methylated nucleoside with important biological functions.
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Affiliation(s)
- Jhonatam O Carvalho
- Centro de Ciências Sociais, Saúde e Tecnologia, CCSST, Universidade Federal do Maranhão, Imperatriz, MA 65900-410, Brazil; Instituto Federal do Maranhão, Campus Açailândia, MA 65930-000, Brazil
| | - João G Oliveira Neto
- Centro de Ciências Sociais, Saúde e Tecnologia, CCSST, Universidade Federal do Maranhão, Imperatriz, MA 65900-410, Brazil
| | - José G Silva Filho
- Centro de Ciências Sociais, Saúde e Tecnologia, CCSST, Universidade Federal do Maranhão, Imperatriz, MA 65900-410, Brazil
| | - Francisco F de Sousa
- Centro de Ciências Sociais, Saúde e Tecnologia, CCSST, Universidade Federal do Maranhão, Imperatriz, MA 65900-410, Brazil; Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, PA 66075-110, Brazil
| | - Paulo T C Freire
- Departamento de Física, Universidade Federal do Ceará, Campus do Pici, Fortaleza, CE 60455-760, Brazil
| | - Adenilson O Santos
- Centro de Ciências Sociais, Saúde e Tecnologia, CCSST, Universidade Federal do Maranhão, Imperatriz, MA 65900-410, Brazil
| | - Pedro F Façanha Filho
- Centro de Ciências Sociais, Saúde e Tecnologia, CCSST, Universidade Federal do Maranhão, Imperatriz, MA 65900-410, Brazil.
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Chen T, Tang Z, Hu C. The combination of terahertz spectroscopy and density functional theory for vibrational modes and weak interactions analysis of vanillin derivatives. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Morais EM, Abdurrokhman I, Martinelli A. Solvent-free synthesis of protic ionic liquids. Synthesis, characterization and computational studies of triazolium based ionic liquids. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119358] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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13
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Rodrigues JAO, Oliveira Neto JG, Santos CC, Nogueira CES, de Sousa FF, de Menezes AS, Dos Santos AO. Phase changes of tris(glycinato)chromium(III) monohydrate crystal systematically studied by thermal analyses, XRPD, FTIR, and Raman combined with ab initio calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 271:120883. [PMID: 35042044 DOI: 10.1016/j.saa.2022.120883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Tris(glycinato)chromium(III) monohydrate [Cr(C2H4NO2)3·H2O] crystals were grown through the slow solvent evaporation method. The crystals were studied by Fourier transform infrared (FTIR) and Raman spectroscopy at room temperature. The assignments of vibration modes were performed using the Density Functional Theory (DFT). Thermal analyses (TGA, DTA, and DSC), X-ray diffraction (XRD), and Raman were used to study the phase changes on the crystals under high- and low-temperature conditions. Temperature-dependent XRPD measurements were carried out in the interval of 473-12 K. Several changes were observed in the patterns, like the appearance of new peaks and the disappearance of peaks occurring within 373-393 K due to water loss. In addition, the Raman measurements were performed in the 423-10 K interval. Several changes on the inter and intramolecular vibration bands during the cooling, such as decreasing bands' intensities, the appearance of vibration modes, and discontinuities on the modes' behavior, were observed. These spectral modifications occurred at about 370 K and within 120-220 K, thus, confirming that the crystals undergo two phase changes, one being structural and the other one conformational, respectively, at high- temperature and low-temperature conditions. Finally, thermal investigations corroborated the structural and vibrational results under high temperatures.
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Affiliation(s)
- J A O Rodrigues
- Programa de Pós-Graduação em Ciência dos Materiais, Universidade Federal do Maranhão, CCSST, Imperatriz, MA 65900-410, Brazil
| | - J G Oliveira Neto
- Programa de Pós-Graduação em Ciência dos Materiais, Universidade Federal do Maranhão, CCSST, Imperatriz, MA 65900-410, Brazil
| | - C C Santos
- Departamento de Física, Universidade Federal do Maranhão, CCET, São Luís, MA 65080-805, Brazil
| | - C E S Nogueira
- Universidade Regional da Cariri, Crato, CE 63010-970, Brazil
| | - F F de Sousa
- Programa de Pós-Graduação em Ciência dos Materiais, Universidade Federal do Maranhão, CCSST, Imperatriz, MA 65900-410, Brazil; Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, 66075-110 Belém, PA, Brazil.
| | - A S de Menezes
- Programa de Pós-Graduação em Ciência dos Materiais, Universidade Federal do Maranhão, CCSST, Imperatriz, MA 65900-410, Brazil; Departamento de Física, Universidade Federal do Maranhão, CCET, São Luís, MA 65080-805, Brazil
| | - A O Dos Santos
- Programa de Pós-Graduação em Ciência dos Materiais, Universidade Federal do Maranhão, CCSST, Imperatriz, MA 65900-410, Brazil
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Stocka J, Platakyte R, McFadden T, Ceponkus J, Aleksa V, Hanna A, Sablinskas V, Rodziewicz P, Guirgis G. Conformational diversity of 1‑chloro-1-chloromethylsilacyclohexane with experimental (Raman and IR) and computational (DFT, MP2) methods. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Direct orange 26 dye environmental degradation: experimental studies (UV, mass, and thermal) in comparison with computational exploration hydrogen bonding analysis of TD-DFT calculations. J Mol Model 2021; 27:325. [PMID: 34671847 DOI: 10.1007/s00894-021-04945-4] [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: 08/03/2021] [Accepted: 10/07/2021] [Indexed: 10/20/2022]
Abstract
The importance of this study stems from, it concentrates on new approach applying both practical and theoretical aspects to study structure stability of direct orange dye 26 (DO26) as an important dye widely used for dyeing of cotton or viscose for red orange direct printing. The stable dyes are so difficult to remove, decolorized and/or degrade, in pure solution or in wastewater samples, without using powerful removal environmental techniques electrochemical oxidations suggest and efficiently used in our Lab. Therefore, it is very important to compare between practical thermal and mass results as efficient techniques in studying dye stability, in comparison with theoretical results using Gaussian program for structural stability identification of DO26 dye, via careful inspection of various phenomena detected in its two symmetrical arms around urea center. Direct orange dye 26 (DO26) structure has been studied applying both practical spectroscopic and theoretical investigations. DFT-B3LYP/6-311 + + G(d,p) calculations and the electronic vibrational properties are performed to investigate its structure stability and consequently its degradation and removal from its environmental media. Correlation is found between experimental and calculated data. An intra-molecular hydrogen bonding interaction had been detected and characterized in dye skeleton. The hydrogen bonding present in the dye structure affecting its vibrational properties had been discussed. Natural population analysis like HOMO and LUMO and high-quality molecular electrostatic potential plots along with various electronics had been presented at the same level of theory. Chemical reactivity descriptors from conceptual density functional theory point of view and structure activity relationship descriptor were obtained. The experimental UV/visible, FT-IR, mass and GC-mass spectral data of the dye DO26 (D1) had been presented. These data had been supported by TD-DFT calculations to simulate the experimental spectra with computing the natural transition orbitals (NTO) and the orbital composition. Actually there is a problem that the degradation of this dye in wastewater by different techniques leads to various unknown fragments, but on using theoretical possibilities, it can be expected what happened in practical work.
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Lopes Jesus AJ, Fausto R, Reva I. Conformational Space, IR-Induced, and UV-Induced Chemistry of Carvacrol Isolated in a Low-Temperature Argon Matrix. J Phys Chem A 2021; 125:8215-8229. [PMID: 34506137 DOI: 10.1021/acs.jpca.1c05907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In this work, monomers of carvacrol (5-isopropyl-2-methylphenol), a natural monoterpene exhibiting wide range bioactivity, were trapped in a cryogenic argon matrix and characterized by infrared spectroscopy, while quantum chemical calculations at the B3LYP and MP2 levels were employed to characterize the conformational landscape of the isolated molecule. Four conformers have been localized on the potential energy surface, and the factors accounting for their relative stability were analyzed. The two most stable conformers of carvacrol, differing in the relative orientation of the isopropyl group and both having the OH group pointing away from the vicinal methyl fragment, were identified in the cryomatrix for the first time. The individual spectral signatures of the two conformers were distinguished based on the change in their relative abundance induced by exposing the matrix to broadband infrared light. Matrix-isolated carvacrol was also irradiated with broadband UV light (λ > 200 nm), which resulted in the cleavage of the OH group. Recombination of the released H atom at the ortho- or para-position of the ring resulted in the formation of alkyl-substituted cyclohexadienones. These were found to undergo subsequent valence and open-ring isomerizations, leading, respectively, to the formation of a Dewar isomer and open-chain conjugated ketenes. Decarbonylation of the photoproducts was also observed for longer irradiation times. A mechanistic analysis of the observed photochemical transformations is presented.
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Affiliation(s)
- A J Lopes Jesus
- University of Coimbra, CQC, Faculty of Pharmacy, 3004-295 Coimbra, Portugal
| | - Rui Fausto
- University of Coimbra, CQC, Department of Chemistry, 3004-535 Coimbra, Portugal
| | - Igor Reva
- University of Coimbra, CQC, Department of Chemistry, 3004-535 Coimbra, Portugal.,University of Coimbra, CIEPQPF, Department of Chemical Engineering, 3030-790 Coimbra, Portugal
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17
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Pereira NAM, Nunes CM, Reva I, Fausto R. Evidence of IR-Induced Chemistry in a Neat Solid: Tautomerization of Thiotropolone by Thermal, Electronic, and Vibrational Excitations. J Phys Chem A 2021; 125:6394-6403. [PMID: 34275275 DOI: 10.1021/acs.jpca.1c04081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thiotropolone isolated in argon and xenon matrices (as monomers) or in a neat solid (as the crystalline or amorphous state) at low temperature was found to exist only in the thione-enol form. Visible light irradiation (λ ≥ 400 nm) leads to thione-enol → thiol-keto tautomerization in matrices and under neat solid conditions at 15 K. The assignment of the IR spectra of the two thiotropolone tautomers (thione-enol and thiol-keto) was carried out with the support of B3LYP/6-311+G(2d,p) computations. The thiol-keto form generated in situ in a neat solid was found to tautomerize back to the thione-enol upon annealing up to 100 K. Gaussian-4 (G4) computations estimate that such a tautomerization process has an energy barrier of ∼25 kJ mol-1, which is consistent with the observations. Moreover, it was found that narrowband IR irradiation of the thiol-keto form in a neat solid, at the frequency of its CH stretching overtones/combination modes, also induces tautomerization to the thione-enol form. Such a result constitutes an important demonstration of vibrationally induced chemistry under neat solid conditions.
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Affiliation(s)
- Nelson A M Pereira
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Cláudio M Nunes
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Igor Reva
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal.,CIEPQPF, Department of Chemical Engineering, University of Coimbra, 3030-790 Coimbra, Portugal
| | - Rui Fausto
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
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18
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Bonegardt D, Klyamer D, Krasnov P, Sukhikh A, Basova T. Effect of the position of fluorine substituents in tetrasubstituted metal phthalocyanines on their vibrational spectra. J Fluor Chem 2021. [DOI: 10.1016/j.jfluchem.2021.109780] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Aieta C, Bertaina G, Micciarelli M, Ceotto M. Representing molecular ground and excited vibrational eigenstates with nuclear densities obtained from semiclassical initial value representation molecular dynamics. J Chem Phys 2020; 153:214117. [PMID: 33291909 DOI: 10.1063/5.0031391] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present in detail and validate an effective Monte Carlo approach for the calculation of the nuclear vibrational densities via integration of molecular eigenfunctions that we have preliminary employed to calculate the densities of the ground and the excited OH stretch vibrational states in the protonated glycine molecule [Aieta et al., Nat Commun 11, 4348 (2020)]. Here, we first validate and discuss in detail the features of the method on a benchmark water molecule. Then, we apply it to calculate on-the-fly the ab initio anharmonic nuclear densities in the correspondence of the fundamental transitions of NH and CH stretches in protonated glycine. We show how we can gain both qualitative and quantitative physical insight by inspection of different one-nucleus densities and assign a character to spectroscopic absorption peaks using the expansion of vibrational states in terms of harmonic basis functions. The visualization of the nuclear vibrations in a purely quantum picture allows us to observe and quantify the effects of anharmonicity on the molecular structure, also to exploit the effect of IR excitations on specific bonds or functional groups, beyond the harmonic approximation. We also calculate the quantum probability distribution of bond lengths, angles, and dihedrals of the molecule. Notably, we observe how in the case of one type of fundamental NH stretching, the typical harmonic nodal pattern is absent in the anharmonic distribution.
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Affiliation(s)
- Chiara Aieta
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milano, Italy
| | - Gianluca Bertaina
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milano, Italy
| | - Marco Micciarelli
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milano, Italy
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20
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Góbi S, Reva I, Tarczay G, Fausto R. Amorphous and crystalline thioacetamide ice: Infrared spectra as a probe for temperature and structure. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128719] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Lopes Jesus AJ, Rosado MTS, Fausto R, Reva I. UV-induced radical formation and isomerization of 4-methoxyindole and 5-methoxyindole. Phys Chem Chem Phys 2020; 22:22943-22955. [PMID: 33026378 DOI: 10.1039/d0cp04354k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Monomers of 4-methoxyindole and 5-methoxyindole trapped in low-temperature xenon matrices (15-16 K) were characterized by IR spectroscopy, in separate experiments. Each compound was shown to adopt the most stable 1H-tautomeric form. The photochemistry of the matrix-isolated compounds was then investigated by exciting the matrices with narrowband UV light with λ ≤ 305 nm. Two main photoproducts, similar for each compound, have been detected: (1) 4-methoxy- or 5-methoxy-indolyl radical, resulting from cleavage of the N-H bond; (2) 3H-tautomers (4-methoxy- or 5-methoxy-) with the released hydrogen atom reconnected at the C3 ring carbon atom. The presence of the two types of photoproducts in the UV-irradiated matrices was confirmed by comparison of their B3LYP/6-311++G(d,p) calculated IR spectra with the experimental spectra emerging upon the irradiations. The mechanism of the observed phototransformations was elucidated by Natural Bond Orbital and Natural Resonance Theory computations on the methoxy-substituted indolyl radicals resulting from the N-H bond cleavage. The highest natural atomic spin densities were predicted at the C3 and N1 positions of the indolyl ring, corresponding to a predominance of the resonance structures with the radical centres located at these two atoms. As a whole, the obtained experimental and theoretical data allowed establishing a general pattern for the photochemistry of methoxyindoles under matrix-isolation conditions.
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Affiliation(s)
- A J Lopes Jesus
- University of Coimbra, CQC, Department of Chemistry, 3004-535, Coimbra, Portugal.
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22
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Aieta C, Micciarelli M, Bertaina G, Ceotto M. Anharmonic quantum nuclear densities from full dimensional vibrational eigenfunctions with application to protonated glycine. Nat Commun 2020; 11:4348. [PMID: 32859910 PMCID: PMC7455743 DOI: 10.1038/s41467-020-18211-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 07/29/2020] [Indexed: 11/24/2022] Open
Abstract
The interpretation of molecular vibrational spectroscopic signals in terms of atomic motion is essential to understand molecular mechanisms and for chemical characterization. The signals are usually assigned after harmonic normal mode analysis, even if molecular vibrations are known to be anharmonic. Here we obtain the quantum anharmonic vibrational eigenfunctions of the 11-atom protonated glycine molecule and we calculate the density distribution of its nuclei and its geometry parameters, for both the ground and the O-H stretch excited states, using our semiclassical method based on ab initio molecular dynamics trajectories. Our quantum mechanical results describe a molecule elongated and more flexible with respect to what previously thought. More importantly, our method is able to assign each spectral peak in vibrational spectroscopy by showing quantitatively how normal modes involving different functional groups cooperate to originate that spectroscopic signal. The method will possibly allow for a better rationalization of experimental spectroscopy.
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Affiliation(s)
- Chiara Aieta
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133, Milano, Italy
| | - Marco Micciarelli
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133, Milano, Italy
| | - Gianluca Bertaina
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133, Milano, Italy
- Istituto Nazionale di Ricerca Metrologica, Strada delle Cacce 91, 10135, Torino, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133, Milano, Italy.
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Cappelluti F, Bencivenni L, Guidoni L. Spin-symmetrised structures and vibrational frequencies of iron-sulfur clusters. Phys Chem Chem Phys 2020; 22:16655-16664. [PMID: 32667376 DOI: 10.1039/d0cp01591a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Calculations of relaxed geometries of multi-centre transition metal compounds are routinely carried out using Broken Symmetry Density Functional Theory. The resulting low-spin open shell electronic state is described by one single Slater determinant and is affected by spin contamination. To alleviate this symmetry breaking, the Extended Broken Symmetry (EBS) approach can be applied to complexes with an arbitrary number of local high-spin metal ions. The actual symmetry is therefore reconstructed through minimization of an effective Hamiltonian leading to a relaxed geometry consistent with the magnetic couplings. In the present work we extend the approach already introduced by [Chu et al., J. Chem. Theory Comput., 2017, 13, 4675] to the calculation of vibrational frequencies. As prototypes we have considered the iron-sulfur clusters Fe2S2Cl42- and Fe4S4Cl4. We have compared the results obtained for different spin states (high spin, broken symmetry and extended broken symmetry) and by using different DFT functionals (B3LYP, OPBE, BP, M06 and B2PLYP) and a post-HF method (SCS-MP2). The data have shown that for specific vibrational modes the EBS technique produces shifts up to 40 cm-1 with respect to the routinely used Broken Symmetry approach, indicating that the use of a consistent spin-symmetrised state is a crucial ingredient for an accurate description of vibrational properties, as certified by the comparison with the experimental data for the Fe2S2Cl42- cluster.
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Affiliation(s)
- Francesco Cappelluti
- University of L'Aquila - Department of Engineering, Information Science and Mathematics, via Vetoio (Coppito), L'Aquila, Italy
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Nowak MJ, Reva I, Lopes Jesus AJ, Lapinski L, Fausto R. UV-promoted radical formation, and near-IR-induced and spontaneous conformational isomerization in monomeric 9-methylguanine isolated in low-temperature Ar matrices. Phys Chem Chem Phys 2019; 21:22857-22868. [PMID: 31599896 DOI: 10.1039/c9cp04487f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three low-energy isomers of 9-methylguanine, the amino-oxo (AO) form and two amino-hydroxy (AH1 and AH2) conformers, were trapped from the gas phase into low-temperature argon matrices. The AH1 and AH2 isomers, differing in the orientation of the OH group, were found to transform into each other upon excitation with near-IR light. The population of the AO form of the compound was not changed upon any near-IR irradiation of the matrix samples. Using monochromatic near-IR light, generated by a frequency-tunable laser source, it was possible to selectively induce the AH1 → AH2 or AH2 → AH1 conversion. Photoreversibility of this conformational transformation was then demonstrated. Exposure of matrix-isolated monomers of 9-methylguanine to broadband near-IR light also led to conformational conversions within the amino-hydroxy tautomeric form; the final stage of this process was always the same photostationary state independent of the initial ratio of AH1 and AH2 populations. Spontaneous conformational conversion, transforming the higher-energy AH2 form into the lower-energy AH1 isomer, was observed for matrix-isolated monomers of 9-methylguanine kept in the dark. The mechanism of this process must rely on quantum tunneling of the light hydrogen atom. Irradiation of matrix-isolated 9-methylguanine with UV laser light at λ = 288 or 285 nm led to a substantial consumption of the two AH forms, while the amount of AO isomer remained unchanged. On the other hand, a decrease in the population of the AO isomer occurred upon excitations at shorter wavelengths, λ = 280 or 275 nm. The spectral changes observed after UV-irradiation suggest the generation (and stabilization in the matrix) of a radical species, resulting from the photocleavage of the O-H or N1-H bonds, in the AH or AO isomer, respectively.
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Affiliation(s)
- Maciej J Nowak
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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