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Lopes S, Nikitin T, Fausto R. Structural, spectroscopic, and photochemical study of ethyl propiolate isolated in cryogenic argon and nitrogen matrices. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 241:118670. [PMID: 32679483 DOI: 10.1016/j.saa.2020.118670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/25/2020] [Accepted: 06/27/2020] [Indexed: 06/11/2023]
Abstract
Ethyl propiolate (HC ≡ CCOOCH2CH3, EP) was studied experimentally by infrared spectroscopy in argon and nitrogen cryomatrices (15 K) and by quantum chemical calculations (at the DFT(B3LYP) and MP2 levels of theory). Calculations predict the existence of four conformers: two low-energy conformers (I and II) possessing the carboxylic moiety in the cis configuration (O=C-O-C dihedral equal to ~0°) and two higher-energy trans forms (O=C-O-C dihedral equal to ~180°; III and IV). The conformation of the ethyl ester group within each pair of conformers is either anti (C-O-C-C equal to 180°; in conformers I and III) or gauche (C-O-C-C equal to ±86.6° in II, and ± 92.5° in IV). The two low-energy cis conformers (I and II) were predicted to differ in energy by less than 2.5 kJ mol-1 and were shown to be present in the studied cryogenic matrices. Characteristic bands for each one of these conformers were identified in the infrared spectra of the matrix-isolated compound and assigned taking into account the results of normal coordinate analysis, which used the geometries and harmonic force constants obtained in the DFT calculations. The two trans conformers (III and IV) were estimated to be 17.5 kJ mol-1 higher in energy than the conformational ground state (form I) and were not observed experimentally. The unimolecular photochemistry of matrix-isolated EP (in N2 matrix) was also investigated. In situ irradiation with UV light (λ > 235 nm) leads mainly to decarbonylation of the compound, with generation of ethoxyethyne, which in a subsequent photoreaction generates ketene (plus ethene).
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Affiliation(s)
- S Lopes
- University of Coimbra, CQC, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - T Nikitin
- University of Coimbra, CQC, Department of Chemistry, 3004-535 Coimbra, Portugal; University of Coimbra, CFisUC, Department of Physics, 3004-516 Coimbra, Portugal
| | - Rui Fausto
- University of Coimbra, CQC, Department of Chemistry, 3004-535 Coimbra, Portugal.
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Maté B, Tanarro I, Escribano R, Moreno MA, Herrero VJ. STABILITY OF EXTRATERRESTRIAL GLYCINE UNDER ENERGETIC PARTICLE RADIATION ESTIMATED FROM 2 keV ELECTRON BOMBARDMENT EXPERIMENTS. ACTA ACUST UNITED AC 2015. [DOI: 10.1088/0004-637x/806/2/151] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Maté B, Tanarro I, Moreno MA, Jiménez-Redondo M, Escribano R, Herrero VJ. Stability of carbonaceous dust analogues and glycine under UV irradiation and electron bombardment. Faraday Discuss 2014; 168:267-85. [PMID: 25302385 DOI: 10.1039/c3fd00132f] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The effect of UV photon (120–200 nm) and electron (2 keV) irradiation of analogues of interstellar carbonaceous dust and of glycine were investigated by means of IR spectroscopy. Films of hydrogenated amorphous carbon (HAC), taken as dust analogues, were found to be stable under UV photon and electron bombardment. High fluences of photons and electrons, of the order of 1019cm−2, were needed for a film depletion of a few percent. UV photons were energetically more effective than electrons for depletion and led to a certain dehydrogenation of the HAC samples, whereas electrons led seemingly to a gradual erosion with no appreciable changes in the hydrocarbon structure. The rates of change observed may be relevant over the lifetime of a diffuse cloud, but cannot account for the rapid changes in hydrocarbon IR bands during the evolution of some proto-planetary nebulae. Glycine samples under the same photon and electron fluxes decay at a much faster rate, but tend usually to an equilibrium value different from zero, especially at low temperatures. Reversible reactions re-forming glycine, or the build-up of less transparent products, could explain this behavior. CO2and methylamine were identified as UV photoproducts. Electron irradiation led to a gradual disappearance of the glycine layers, also with formation of CO2. No other reaction products were clearly identified. The thicker glycine layers (a few hundred nm) were not wholly depleted, but a film of the order of the electron penetration depth (80 nm), was totally destroyed with an electron fluence of ∼1 × 1018cm−2. A 60 nm ice layer on top of glycine provided only partial shielding from the 2 keV electrons. From an energetic point of view, 2 keV electrons are less efficient than UV photons and, according to literature data, much less efficient than MeV protons for the destruction of glycine. The use of keV electrons to simulate effects of cosmic rays on analogues of interstellar grains should be taken with care, due to the low penetration depths of electrons in many samples of interest.
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Affiliation(s)
- Belén Maté
- Instituto de Estructura de la Materia
- IEM-CSIC
- 28006 Madrid, Spain
| | - Isabel Tanarro
- Instituto de Estructura de la Materia
- IEM-CSIC
- 28006 Madrid, Spain
| | - Miguel A. Moreno
- Instituto de Estructura de la Materia
- IEM-CSIC
- 28006 Madrid, Spain
| | | | - Rafael Escribano
- Instituto de Estructura de la Materia
- IEM-CSIC
- 28006 Madrid, Spain
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Cormanich RA, Ducati LC, Tormena CF, Rittner R. A theoretical investigation of the dictating forces in small amino acid conformational preferences: The case of glycine, sarcosine and N,N-dimethylglycine. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Kuş N, Sharma A, Reva I, Lapinski L, Fausto R. Using heavy atom rare gas matrix to control the reactivity of 4-methoxybenzaldehyde: A comparison with benzaldehyde. J Chem Phys 2012; 136:144509. [DOI: 10.1063/1.3701734] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Lopes S, Nunes CM, Gómez-Zavaglia A, Pinho e Melo TMVD, Fausto R. Conformational Space and Vibrational Spectra of Methyl 4-Chloro-5-phenyl-1,3-oxazole-2-carboxylate. J Phys Chem A 2010; 114:9074-82. [DOI: 10.1021/jp103665b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Susy Lopes
- Department of Chemistry, University of Coimbra, P-3004-535 Coimbra, Portugal, and Centro de Investigación y Desarrollo en Criotecnología de Alimentos (Conicet La Plata, UNLP), RA-1900 La Plata, Argentina
| | - Cláudio M. Nunes
- Department of Chemistry, University of Coimbra, P-3004-535 Coimbra, Portugal, and Centro de Investigación y Desarrollo en Criotecnología de Alimentos (Conicet La Plata, UNLP), RA-1900 La Plata, Argentina
| | - Andrea Gómez-Zavaglia
- Department of Chemistry, University of Coimbra, P-3004-535 Coimbra, Portugal, and Centro de Investigación y Desarrollo en Criotecnología de Alimentos (Conicet La Plata, UNLP), RA-1900 La Plata, Argentina
| | - Teresa M. V. D. Pinho e Melo
- Department of Chemistry, University of Coimbra, P-3004-535 Coimbra, Portugal, and Centro de Investigación y Desarrollo en Criotecnología de Alimentos (Conicet La Plata, UNLP), RA-1900 La Plata, Argentina
| | - Rui Fausto
- Department of Chemistry, University of Coimbra, P-3004-535 Coimbra, Portugal, and Centro de Investigación y Desarrollo en Criotecnología de Alimentos (Conicet La Plata, UNLP), RA-1900 La Plata, Argentina
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Pagacz-Kostrzewa M, Białońska A, Bronisz R, Wierzejewska M. Structural, spectroscopic and conformational properties of 2-methyl-2-(1H-tetrazol-1-yl)propan-1-ol experimental and theoretical approach. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.03.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Sałdyka M. Isomerical and structural determination of N-hydroxyurea: a matrix isolation and theoretical study. Phys Chem Chem Phys 2010; 12:15111-8. [DOI: 10.1039/c0cp00709a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Nunes CM, Lopes S, Pinho e Melo TM, Fausto R. Spectroscopic and theoretical investigation of the conformational space of a pyrazolo-thiazole precursor of extended dipole diazafulvenium methide intermediates. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2008.12.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Gómez-Zavaglia A, Kaczor A, Coelho D, Cristiano MLS, Fausto R. Conformational and structural analysis of 2-allyl-1,2-benzisothiazol-3(2H)-one 1,1-dioxide as probed by matrix-isolation spectroscopy and quantum chemical calculations. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2008.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Olbert-Majkut A, Wierzejewska M. Conformational Study of Eugenol by Density Functional Theory Method and Matrix-Isolation Infrared Spectroscopy. J Phys Chem A 2008; 112:5691-9. [DOI: 10.1021/jp801430d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Maria Wierzejewska
- Faculty of Chemistry, Wrocław University, F.Joliot-Curie 14, 50-383 Wrocław, POLAND
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Gómez-Zavaglia A, Kaczor A, Almeida R, Cristiano MDLS, Fausto R. Conformational Space of the Pseudosaccharin Allyl Ether 3-(Allyloxy)-1,2-benzisothiazole 1,1-Dioxide in Gas Phase and in Rare Gas Matrices. J Phys Chem A 2008; 112:1762-72. [DOI: 10.1021/jp0770918] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Andrea Gómez-Zavaglia
- Department of Chemistry, University of Coimbra, Coimbra, P-3004-535, Portugal, Faculty of Pharmacy and Biochemistry, University of Buenos Aires, C.P. 1113 Buenos Aires, Argentina, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland, and Department of Chemistry and Biochemistry, F.C.T., and CCMAR, University of Algarve, Campus de Gambelas, 8005-039 Faro, Portugal
| | - Agnieszka Kaczor
- Department of Chemistry, University of Coimbra, Coimbra, P-3004-535, Portugal, Faculty of Pharmacy and Biochemistry, University of Buenos Aires, C.P. 1113 Buenos Aires, Argentina, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland, and Department of Chemistry and Biochemistry, F.C.T., and CCMAR, University of Algarve, Campus de Gambelas, 8005-039 Faro, Portugal
| | - Rui Almeida
- Department of Chemistry, University of Coimbra, Coimbra, P-3004-535, Portugal, Faculty of Pharmacy and Biochemistry, University of Buenos Aires, C.P. 1113 Buenos Aires, Argentina, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland, and Department of Chemistry and Biochemistry, F.C.T., and CCMAR, University of Algarve, Campus de Gambelas, 8005-039 Faro, Portugal
| | - Maria de Lurdes S. Cristiano
- Department of Chemistry, University of Coimbra, Coimbra, P-3004-535, Portugal, Faculty of Pharmacy and Biochemistry, University of Buenos Aires, C.P. 1113 Buenos Aires, Argentina, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland, and Department of Chemistry and Biochemistry, F.C.T., and CCMAR, University of Algarve, Campus de Gambelas, 8005-039 Faro, Portugal
| | - Rui Fausto
- Department of Chemistry, University of Coimbra, Coimbra, P-3004-535, Portugal, Faculty of Pharmacy and Biochemistry, University of Buenos Aires, C.P. 1113 Buenos Aires, Argentina, Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland, and Department of Chemistry and Biochemistry, F.C.T., and CCMAR, University of Algarve, Campus de Gambelas, 8005-039 Faro, Portugal
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Borba A, Gómez-Zavaglia A, Fausto R. Conformational cooling and conformation selective aggregation in dimethyl sulfite isolated in solid rare gases. J Mol Struct 2006. [DOI: 10.1016/j.molstruc.2006.02.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Gómez-Zavaglia A, Kaczor A, Cardoso AL, Pinho e Melo TMVD, Fausto R. Unusual Photochemical C−N Bond Cleavage in the Novel Methyl 2-Chloro-3-methyl-2H-azirine-2-carboxylate. J Phys Chem A 2006; 110:8081-92. [PMID: 16805494 DOI: 10.1021/jp062094q] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The structure, preferred conformers, vibrational spectrum, and photochemical behavior of the novel azirine, methyl 2-chloro-3-methyl-2H-azirine-2-carboxylate (MCMAC) were investigated in low-temperature matrixes and in the neat solid amorphous state by infrared spectroscopy and quantum-chemical calculations. Two conformers of the compound were observed in argon, krypton, and xenon matrixes, in agreement with the DFT(B3LYP)/6-311++G(d,p) and MP2/6-311++G(d,p) theoretical calculations. Both conformers were found to exhibit the carboxylic ester group in the cis conformation, differing in the arrangement defined by the O=C-C-Cl dihedral angle (cis and trans, for Ct and Cc forms, respectively). The Ct conformer was found to be the most stable conformer in the gaseous phase as well as in both argon and krypton matrixes, whereas the more polar Cc conformer became the most stable form in the xenon matrix and in the neat solid amorphous phase. In situ broadband UV (lambda > 235 nm) excitation of matrix-isolated MCMAC led to azirine ring C-C and C-N bond cleavages, the latter process corresponding to the most efficient reaction channel. The photochemical cleavage of the C-N bond had never been previously observed in the case of aliphatic 2H-azirines. Two electron withdrawing substituents (methoxycarbonyl group and chlorine atom) are connected to the azirine ring in the novel MCMAC azirine. The simultaneous presence of these two groups accelerates intersystem crossing toward the triplet state where cleavage of the C-N bond takes place. The primary photoproducts resulting from the C-N and C-C ring-opening reactions were also found to undergo further photochemical decarbonylation or decarboxylation reactions.
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Kaczor A, Pinho e Melo TMVD, Soares MIL, Fausto R. Conformational Behavior of Dimethyl 5-Methyl-1H,3H-pyrrolo[1,2-c][1,3]thiazole-6,7-dicarboxylate 2,2-Dioxide Isolated in Low-Temperature Matrixes. J Phys Chem A 2006; 110:6531-9. [PMID: 16706411 DOI: 10.1021/jp0607667] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The structure of dimethyl 5-methyl-1H,3H-pyrrolo[1,2-c][1,3]thiazole-6,7-dicarboxylate 2,2-dioxide (PTD) was investigated in low-temperature noble gas matrixes (Ar, Kr, Xe), amorphous solid, and the crystalline state by infrared spectroscopy and computational methods. The geometry of PTD conformers is defined by the orientation of two methyl ester groups, which may adopt pseudo-trans or pseudo-cis positions in relation to the pyrrolo-thiazole system. For both methyl ester groups, the latter arrangement was predicted by the calculations to be energetically the most favorable in the isolated molecule. The envelope form of the thiazolidine ring is present in all conformers, with the sulfur atom placed in the apex position, while the pyrrole ring is almost planar. Three types of conformers differing in the orientation of the methyl ester groups relative to the pyrrolo-thiazole system (cis/cis, trans/cis, cis/trans) were identified in the matrixes. The cis/cis forms were found to be the most stable ones in both gaseous state and argon matrixes. On the other hand, the more polar trans/cis forms were found to be stabilized in the more polarizable krypton and xenon matrixes as well as in the neat amorphous and crystalline phases. On the basis of annealing experiments, performed in argon and xenon matrixes up to 35 and 68 K, respectively, conformational changes preceding the aggregation of the compound are suggested.
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Affiliation(s)
- A Kaczor
- Department of Chemistry, University of Coimbra, P-3004-535 Coimbra, Portugal
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Borba A, Gómez-Zavaglia A, Simões PNNL, Fausto R. Matrix Isolation FTIR Spectroscopic and Theoretical Study of Dimethyl Sulfite. J Phys Chem A 2005; 109:3578-86. [PMID: 16839024 DOI: 10.1021/jp050020t] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The preferred conformations of dimethyl sulfite and their vibrational spectra were studied by matrix-isolation Fourier transform infrared spectroscopy and theoretical methods (density functional theory (DFT) and Moller-Plesset (MP2), with basis sets of different sizes, including the quadruple-zeta, aug-cc-pVQZ basis). Five minima were found at these levels of theory. At the MP2/6-31++G(d,p) and DFT/B3LYP/aug-cc-pVQPZ levels, the GG conformer (where the O-S-O-C dihedral angles are 73.2 and 70.8 degrees ) resulted in the conformational ground state. At the highest level of theory used, the GT conformer (O-S-O-C = +68.5 and -173.2 degrees ) is 0.83 kJ mol(-1) higher in energy than the GG form, while conformer GG' (O-S-O-C = +85.7 and -85.7 degrees ) has a relative energy of 1.18 kJ mol(-1). The remaining two conformers (G'T and TT) are high-energy forms and not experimentally relevant. In consonance with the theoretical predictions, conformer GG was found to be the most stable conformer in the gaseous phase as well as in the low-temperature matrices. Annealing of the argon matrices first promotes the GG'-->GT isomerization, which is followed by conversion of GT into the most stable conformer. There is no evidence of occurrence of GG'-->GG direct conversion in the low-temperature matrices. On the other hand, during deposition of the xenon matrices conformer GG' totally converts to conformer GT. Two observations demonstrated this fact: no evidence of bands corresponding to GG' were observed in xenon matrices and the GG/GT intensity ratio became similar to the GG/(GT + GG') intensity ratio observed in argon matrices. All these results could be explained by taking into account the relative values of the theoretically predicted energy barriers for the different isomerization processes: GG'-->GT, 1.90 kJ mol(-1); GT-->GG, 9.64 kJ mol(-1); and GG'-->GG, 19.46 kJ mol(-1).
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Affiliation(s)
- Ana Borba
- Department of Chemistry, University of Coimbra, P-3004-535 Coimbra, Portugal
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Jarmelo S, Maiti N, Anderson V, Carey PR, Fausto R. Cα−H Bond-Stretching Frequency in Alcohols as a Probe of Hydrogen-Bonding Strength: A Combined Vibrational Spectroscopic and Theoretical Study of n-[1-D]Propanol. J Phys Chem A 2005; 109:2069-77. [PMID: 16838977 DOI: 10.1021/jp046683c] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The sensitivity of the nu(C)()alpha(-)(H/D) vibrational stretching frequency to hydrogen bonding in alcohols is examined by infrared and Raman spectroscopy, supported by DFT(B3LYP)/6-311++G(d,p) calculations. The model compound studied is (R,S)-n-[1-D]propanol. It is shown that the nu(C)()alpha(-)(H/D) mode can be successfully correlated with the hydrogen-bond strength in a given solvent, provided the O-H group involved in the hydrogen bond is not acting simultaneously as a hydrogen-bond donor and acceptor. In addition, a detailed analysis of the spectroscopic features observed in both the nu(O)(-)(H) and nu(C)()alpha(-)(H/D) spectral regions of the spectra of n-propanol and (R,S)-n-[1-D]propanol, in a series of different experimental conditions, which include the matrix-isolated compound (in argon matrix), pure liquid and low-temperature glassy states, and solution in different solvents, is undertaken. This permits the contribution of the different conformers of the studied compounds to be assigned to the bands observed in the nu(O)(-)(H) and nu(C)(-)(H) spectral regions.
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Affiliation(s)
- S Jarmelo
- Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
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Gómez-Zavaglia A, Fausto R. Matrix isolation FT-IR spectroscopy and molecular orbital study of sarcosine methyl ester. J Mol Struct 2004. [DOI: 10.1016/j.molstruc.2003.10.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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