1
|
Amado PSM, Lopes S, Brás EM, Paixão JA, Takano MA, Abe M, Fausto R, Cristiano MLS. Molecular and Crystal Structure, Spectroscopy, and Photochemistry of a Dispiro Compound Bearing the Tetraoxane Pharmacophore. Chemistry 2023; 29:e202301315. [PMID: 37343198 DOI: 10.1002/chem.202301315] [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: 04/26/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 06/23/2023]
Abstract
The molecular structure and photochemistry of dispiro[cyclohexane-1,3'-[1,2,4,5]tetraoxane-6',2''-tricyclo[3.3.1.13,7 ]decan]-4-one (TX), an antiparasitic 1,2,4,5-tetraoxane was investigated using matrix isolation IR and EPR spectroscopies, together with quantum chemical calculations undertaken at the DFT(B3LYP)/6-311++G(3df,3pd) level of theory, with and without Grimme's dispersion correction. Photolysis of the matrix-isolated TX, induced by in situ broadband (λ>235 nm) or narrowband (λ in the range 220-263 nm) irradiation, led to new bands in the infrared spectrum that could be ascribed to two distinct photoproducts, oxepane-2,5-dione, and 4-oxohomoadamantan-5-one. Our studies show that these photoproducts result from initial photoinduced cleavage of an O-O bond, with the formation of an oxygen-centered diradical that regioselectivity rearranges to a more stable (secondary carbon-centered)/(oxygen-centered) diradical, yielding the final products. Formation of the diradical species was confirmed by EPR measurements, upon photolysis of the compound at λ=266 nm, in acetonitrile ice (T=10-80 K). Single-crystal X-ray diffraction (XRD) studies demonstrated that the TX molecule adopts nearly the same conformation in the crystal and matrix-isolation conditions, revealing that the intermolecular interactions in the TX crystal are weak. This result is in keeping with observed similarities between the infrared spectrum of the crystalline material and that of matrix-isolated TX. The detailed structural, vibrational, and photochemical data reported here appear relevant to the practical uses of TX in medicinal chemistry, considering its efficient and broad parasiticidal properties.
Collapse
Affiliation(s)
- Patrícia S M Amado
- Center of Marine Sciences, CCMAR, Gambelas Campus, University of Algarve UAlg, 8005-139, Faro, Portugal
- Department of Chemistry and Pharmacy Faculty of Sciences and Technology, Gambelas Campus, University of Algarve UAlg, 8005-139, Faro, Portugal
| | - Susy Lopes
- CQC-IMS, Department of Chemistry, University of Coimbra, 3004-535, Coimbra, Portugal
| | - Elisa M Brás
- CQC-IMS, Department of Chemistry, University of Coimbra, 3004-535, Coimbra, Portugal
| | - José A Paixão
- CFisUC, Department of Physics, University of Coimbra, 3004-516, Coimbra, Portugal
| | - Ma-Aya Takano
- Department of Chemistry Graduate School of Advanced Science and Engineering, Hiroshima University Higashi-Hiroshima, Hiroshima, 739-8526, Japan
- International Institute for Sustainability with Knotted Chiral Meta Matter (SKCM2) Higashi-Hiroshima, Hiroshima, 739-0046, Japan
| | - Manabu Abe
- Department of Chemistry Graduate School of Advanced Science and Engineering, Hiroshima University Higashi-Hiroshima, Hiroshima, 739-8526, Japan
- International Institute for Sustainability with Knotted Chiral Meta Matter (SKCM2) Higashi-Hiroshima, Hiroshima, 739-0046, Japan
| | - Rui Fausto
- CQC-IMS, Department of Chemistry, University of Coimbra, 3004-535, Coimbra, Portugal
- Faculty of Sciences and Letters, Department of Physics, Istanbul Kultur University Ataköy Campus, Bakirköy, 34156, Istanbul, Turkey
| | - Maria L S Cristiano
- Center of Marine Sciences, CCMAR, Gambelas Campus, University of Algarve UAlg, 8005-139, Faro, Portugal
- Department of Chemistry and Pharmacy Faculty of Sciences and Technology, Gambelas Campus, University of Algarve UAlg, 8005-139, Faro, Portugal
| |
Collapse
|
2
|
Fausto R, Ildiz GO, Nunes CM. IR-induced and tunneling reactions in cryogenic matrices: the (incomplete) story of a successful endeavor. Chem Soc Rev 2022; 51:2853-2872. [PMID: 35302145 DOI: 10.1039/d1cs01026c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this article, IR-induced and tunneling-driven reactions observed in cryogenic matrices are described in a historical perspective, the entangling of the two types of processes being highlighted. The story of this still ongoing fascinating scientific endeavor is presented here following closely our own involvement in the field for more than 30 years, and thus focuses mostly on our work. It is, because of this reason, also an incomplete story. Nevertheless, it considers a large range of examples, from very selective IR-induced conformational isomerizations to IR-induced bond-breaking/bond-forming reactions and successful observations of rare heavy atom tunneling processes. As a whole, this article provides a rather general overview of the major progress achieved in the field.
Collapse
Affiliation(s)
- Rui Fausto
- CQC-IMS, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal.
| | - Gulce O Ildiz
- CQC-IMS, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal. .,Department of Physics, Faculty of Sciences and Letters, Istanbul Kultur University, 34158 Bakirkoy, Istanbul, Turkey
| | - Cláudio M Nunes
- CQC-IMS, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal.
| |
Collapse
|
3
|
Structure and IR Spectra of 3(5)-Aminopyrazoles and UV-Induced Tautomerization in Argon Matrix. Molecules 2021; 26:molecules26144299. [PMID: 34299574 PMCID: PMC8304260 DOI: 10.3390/molecules26144299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 01/20/2023] Open
Abstract
The prototropic tautomerism in 3(5)-aminopyrazoles was investigated by matrix isolation infrared (IR) spectroscopy, supported by DFT(B3LYP)/6-311++G(d,p) calculations. In consonance with the experimental data, the calculations predict tautomer 3-aminopyrazole (3AP) to be more stable than the 5-aminopyrazole (5AP) tautomer (calculated energy difference: 10.7 kJ mol-1; Gibbs free energy difference: 9.8 kJ mol-1). The obtained matrix isolation IR spectra (in both argon and xenon matrices) were interpreted, and the observed bands were assigned to the tautomeric forms with help of vibrational calculations carried out at both harmonic and anharmonic levels. The matrix-isolated compound (in argon matrix) was then subjected to in situ broadband UV irradiation (λ > 235 nm), and the UV-induced transformations were followed by IR spectroscopy. Phototautomerization of the 3AP tautomer into the 5AP form was observed as the strongly prevalent reaction.
Collapse
|
4
|
Structural Relevance of Intramolecular H-Bonding in Ortho-Hydroxyaryl Schiff Bases: The Case of 3-(5-bromo-2-hydroxybenzylideneamino) Phenol. Molecules 2021; 26:molecules26092814. [PMID: 34068634 PMCID: PMC8126046 DOI: 10.3390/molecules26092814] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 12/22/2022] Open
Abstract
A new Schiff base compound, 3-(5-bromo-2-hydroxybenzylideneamino)phenol (abbreviated as BHAP) was synthesized and characterized by 1H- and 13C- nuclear magnetic resonance and infrared spectroscopies. DFT/B3LYP/6-311++G(d,p) calculations were undertaken in order to explore the conformational space of both the E- and Z- geometrical isomers of the enol-imine and keto-amine tautomers of the compound. Optimized geometries and relative energies were obtained, and it was shown that the most stable species is the E-enol-imine form, which may exist in four low-energy intramolecularly hydrogen-bonded forms (I, II, V, and VI) that are almost isoenergetic. These conformers were concluded to exist in the gas phase equilibrium with nearly equal populations. On the other hand, the infrared spectra of the compound isolated in a cryogenic argon matrix (10 K) are compatible with the presence in the matrix of only two of these conformers (conformers II and V), while conformers I and VI convert to these ones by quantum mechanical tunneling through the barrier associated with the rotation of the OH phenolic group around the C–O bond. The matrix isolation infrared spectrum was then assigned and interpreted with help of the DFT(B3LYP)/6-311++G(d,p) calculated infrared spectra for conformers II and V. In addition, natural bond orbital (NBO) analysis was performed on the most stable conformer of the experimentally relevant isomeric form (E-enol-imino conformer V) to shed light on details of its electronic structure. This investigation stresses the fundamental structural relevance of the O–H···N intramolecular H-bond in o-hydroxyaryl Schiff base compounds.
Collapse
|
5
|
Zhang H, Krupa J, Wierzejewska M, Biczysko M. The role of dispersion and anharmonic corrections in conformational analysis of flexible molecules: the allyl group rotamerization of matrix isolated safrole. Phys Chem Chem Phys 2019; 21:8352-8364. [PMID: 30958495 DOI: 10.1039/c9cp00926d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Conformational changes of the monomeric safrole (5-(2-propenyl)-1,3-benzodioxole) isolated in low temperature xenon matrices were induced thermally or using narrow-band UV radiation. The rotation of the allyl group taking place in the studied matrices was followed by FTIR spectroscopy. Safrole represents a challenging example of a flexible molecule highlighting the importance of dispersion interactions and anharmonic effects in the structural, spectroscopic and energetic analysis. Structures of the safrole conformers, their energetics and infrared spectra have been calculated using various computational methods ranging from density functional theory (DFT) to coupled cluster (CC). The best theoretical results were obtained by integrating CCSD(T) energies including complete basis set extrapolation and core-valence corrections with B2PLYP-D3 equilibrium structures and hybrid B2PLYP-D3/B3LYP-D3 anharmonic computations for IR spectra and thermodynamics.
Collapse
Affiliation(s)
- Hongli Zhang
- International Centre for Quantum and Molecular Structures, Department of Physics, College of Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China.
| | | | | | | |
Collapse
|
6
|
Simão A, Cabezas C, León I, Alonso ER, Mata S, Alonso JL. Elucidating the multiple structures of pipecolic acid by rotational spectroscopy. Phys Chem Chem Phys 2019; 21:4155-4161. [PMID: 30520481 PMCID: PMC6478119 DOI: 10.1039/c8cp06120c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The complex conformational space of the non-proteinogenic cyclic amino acid pipecolic acid has been explored in the gas phase for the first time. Solid pipecolic acid samples were vaporized by laser ablation and expanded in a supersonic jet where the rotational spectral signatures owing to nine different conformers were observed by Fourier transform microwave spectroscopy. All species were identified by comparison of the experimental rotational and nuclear quadrupole coupling constants with those predicted theoretically. Observation of type-III conformers, leading to a difference when compared against the conformational behavior of the analog amino acid proline, has been interpreted by an increment in steric hindrance when increasing the number of carbons present in the ring.
Collapse
Affiliation(s)
- A Simão
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | | | | | | | | | | |
Collapse
|
7
|
Apóstolo RFG, Bazsó G, Ogruc-Ildiz G, Tarczay G, Fausto R. Near-infrared in situ generation of the higher-energy trans conformer of tribromoacetic acid: Observation of a large-scale matrix-site changing mediated by conformational conversion. J Chem Phys 2018; 148:044303. [PMID: 29390807 DOI: 10.1063/1.5010288] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Rui F. G. Apóstolo
- CQC, Department of Chemistry, University of Coimbra, P 3004−535 Coimbra, Portugal
| | - Gábor Bazsó
- Department of Inorganic Chemistry, Eötvös University, H-1117 Budapest, Hungary
| | - Gulce Ogruc-Ildiz
- CQC, Department of Chemistry, University of Coimbra, P 3004−535 Coimbra, Portugal
- Faculty of Sciences and Letters, Department of Physics, Istanbul Kultur University, Atakoy Campus, Bakirkoy, 34156 Istanbul, Turkey
| | - György Tarczay
- Department of Inorganic Chemistry, Eötvös University, H-1117 Budapest, Hungary
| | - Rui Fausto
- CQC, Department of Chemistry, University of Coimbra, P 3004−535 Coimbra, Portugal
| |
Collapse
|
8
|
Kuş N, Fausto R. Effects of the matrix and intramolecular interactions on the stability of the higher-energy conformers of 2-fluorobenzoic acid. J Chem Phys 2017; 146:124305. [DOI: 10.1063/1.4978794] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
9
|
Borba A, Gómez-Zavaglia A, Fausto R. Conformers, infrared spectrum, UV-induced photochemistry, and near-IR-induced generation of two rare conformers of matrix-isolated phenylglycine. J Chem Phys 2015; 141:154306. [PMID: 25338895 DOI: 10.1063/1.4897526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The conformational space of α-phenylglycine (PG) have been investigated theoretically at both the DFT/B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) levels of approximation. Seventeen different minima were found on the investigated potential energy surfaces, which are characterized by different dominant intramolecular interactions: type I conformers are stabilized by hydrogen bonds of the type N-H···O=C, type II by a strong O-H···N hydrogen bond, type III by weak N-H···O-H hydrogen bonds, and type IV by a C=O···H-C contact. The calculations indicate also that entropic effects are relevant in determining the equilibrium populations of the conformers of PG in the gas phase, in particular in the case of conformers of type II, where the strong intramolecular O-H···N hydrogen bond considerably diminishes entropy by reducing the conformational mobility of the molecule. In consonance with the relative energies of the conformers and barriers for conformational interconversion, only 3 conformers of PG were observed for the compound isolated in cryogenic Ar, Xe, and N2 matrices: the conformational ground state (ICa), and forms ICc and IITa. All other significantly populated conformers existing in the gas phase prior to deposition convert either to conformer ICa or to conformer ICc during matrix deposition. The experimental observation of ICc had never been achieved hitherto. Narrowband near-IR irradiation of the first overtone of νOH vibrational mode of ICa and ICc in nitrogen matrices (at 6910 and 6930 cm(-1), respectively) led to selective generation of two additional conformers of high-energy, ITc and ITa, respectively, which were also observed experimentally for the first time. In addition, these experiments also provided the key information for the detailed vibrational characterization of the 3 conformers initially present in the matrices. On the other hand, UV irradiation (λ = 255 nm) of PG isolated in a xenon matrix revealed that PG undergoes facile photofragmentation through two photochemical pathways that are favored for different initial conformations of the reactant: (a) decarboxylation, leading to CO2 plus benzylamine (the dominant photofragmentation channel in PG cis-COOH conformers ICa and ICc) and (b) decarbonylation, with generation of CO plus benzonitrile, H2O and H2 (prevalent in the case of the trans-COOH conformer, IITa).
Collapse
Affiliation(s)
- Ana Borba
- Department of Chemistry, University of Coimbra, Coimbra P-3004-535, Portugal
| | | | - Rui Fausto
- Department of Chemistry, University of Coimbra, Coimbra P-3004-535, Portugal
| |
Collapse
|
10
|
Lopes Jesus AJ, Reva I, Araujo-Andrade C, Fausto R. Conformational Switching by Vibrational Excitation of a Remote NH Bond. J Am Chem Soc 2015; 137:14240-3. [DOI: 10.1021/jacs.5b08588] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- António Jorge Lopes Jesus
- CQC,
Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- CQC,
Faculty of Pharmacy, University of Coimbra, 3004-295 Coimbra, Portugal
| | - Igor Reva
- CQC,
Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Cuauhtémoc Araujo-Andrade
- CQC,
Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- Unidad Académica de Física de la Universidad Autónoma de Zacatecas, 98068 Zacatecas, Mexico
| | - Rui Fausto
- CQC,
Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| |
Collapse
|
11
|
Barone V, Biczysko M, Bloino J, Cimino P, Penocchio E, Puzzarini C. CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study. J Chem Theory Comput 2015; 11:4342-63. [PMID: 26575928 PMCID: PMC5905675 DOI: 10.1021/acs.jctc.5b00580] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC calculations.
Collapse
Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore,
Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Malgorzata Biczysko
- Consiglio Nazionale delle
Ricerche, Istituto di Chimica dei Composti
OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area
della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa,
Italy
| | - Julien Bloino
- Consiglio Nazionale delle
Ricerche, Istituto di Chimica dei Composti
OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area
della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa,
Italy
| | - Paola Cimino
- Dipartimento di Scienze
Farmaceutiche, Università degli Studi di
Salerno, via Ponte don Melillo, I-84084 Fisciano
(SA), Italy
| | | | - Cristina Puzzarini
- Dipartimento di Chimica
“Giacomo Ciamician”,
Università di Bologna, Via Selmi 2, I-40126
Bologna, Italy
| |
Collapse
|
12
|
Avadanei M, Kuş N, Cozan V, Fausto R. Structure and Photochemistry of N-Salicylidene-p-carboxyaniline Isolated in Solid Argon. J Phys Chem A 2015; 119:9121-32. [PMID: 26273723 DOI: 10.1021/acs.jpca.5b06516] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Infrared matrix isolation spectroscopy and DFT/B3LYP/6-311++G(d,p) calculations have been used to characterize the conformational space of the enol-imine and keto-amine tautomers of N-salicylidene-p-carboxyaniline (SCA) in both their E and Z isomeric forms. Monomers of SCA were isolated in an argon matrix (15 K), which was shown to contain only the most stable conformer of the E-enol isomer of the compound. The matrix-isolated E-enol was then subjected to in situ UV irradiation (λ = 335; 345 nm, provided by a laser/MOPO system, or λ > 235 nm, provided by a Hg(Xe) broad-band source), and the photoinduced processes probed by infrared spectroscopy. Two photoreaction channels were observed, with a branching ratio of ∼1:1, corresponding to E-enol → Z-enol isomerization and E-enol → E-keto tautomerization. Both processes were found to be rather effective, with practically complete consumption of the reactant after broad-band irradiation by 1 min only. Identification among the photoproduced species of the Z-enol conformer that differs from the reactant only by E-to-Z isomerization suggests the initial photoproduction of this conformer, which subsequently decays into the lowest energy Z-enol conformer (also identified experimentally). The E-enol → E-keto tautomerization requires an excited state intramolecular proton transfer and twisting about the exocyclic CC bond of the molecule. These processes most probably take place sequentially. However, in the present study the Z-keto isomer, which should act as intermediate in this sequence of processes, could not be detected, most probably due to its short lifetime under the used experimental conditions. On the contrary, the detailed structural and vibrational characterization of the photoproduced E-keto form was successfully achieved.
Collapse
Affiliation(s)
- Mihaela Avadanei
- "P. Poni" Institute of Macromolecular Chemistry , 700487 Iasi, Romania
| | - Nihal Kuş
- Department of Chemistry, University of Coimbra , 3004-535 Coimbra, Portugal.,Department of Physics, Anadolu University , 26470 Eskişehir, Turkey
| | - Vasile Cozan
- "P. Poni" Institute of Macromolecular Chemistry , 700487 Iasi, Romania
| | - Rui Fausto
- Department of Chemistry, University of Coimbra , 3004-535 Coimbra, Portugal
| |
Collapse
|
13
|
Najbauer EE, Bazsó G, Apóstolo R, Fausto R, Biczysko M, Barone V, Tarczay G. Identification of Serine Conformers by Matrix-Isolation IR Spectroscopy Aided by Near-Infrared Laser-Induced Conformational Change, 2D Correlation Analysis, and Quantum Mechanical Anharmonic Computations. J Phys Chem B 2015. [PMID: 26201050 DOI: 10.1021/acs.jpcb.5b05768] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conformers of α-serine were investigated by matrix-isolation IR spectroscopy combined with NIR laser irradiation. This method, aided by 2D correlation analysis, enabled unambiguously grouping the spectral lines to individual conformers. On the basis of comparison of at least nine experimentally observed vibrational transitions of each conformer with empirically scaled (SQM) and anharmonic (GVPT2) computed IR spectra, six conformers were identified. In addition, the presence of at least one more conformer in Ar matrix was proved, and a short-lived conformer with a half-life of (3.7 ± 0.5) × 10(3) s in N2 matrix was generated by NIR irradiation. The analysis of the NIR laser-induced conversions revealed that the excitation of the stretching overtone of both the side chain and the carboxylic OH groups can effectively promote conformational changes, but remarkably different paths were observed for the two kinds of excitations.
Collapse
Affiliation(s)
- Eszter E Najbauer
- †Laboratory of Molecular Spectroscopy, Institute of Chemistry, Eötvös University, PO Box 32, H-1518, Budapest 112, Hungary
| | - Gábor Bazsó
- †Laboratory of Molecular Spectroscopy, Institute of Chemistry, Eötvös University, PO Box 32, H-1518, Budapest 112, Hungary
| | - Rui Apóstolo
- ‡Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Rui Fausto
- ‡Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Malgorzata Biczysko
- §Physics Department and International Centre for Quantum and Molecular Structure, Shanghai University, Shanghai, 200444 China
| | - Vincenzo Barone
- ∥Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - György Tarczay
- †Laboratory of Molecular Spectroscopy, Institute of Chemistry, Eötvös University, PO Box 32, H-1518, Budapest 112, Hungary
| |
Collapse
|
14
|
Kuş N, Fausto R. Near-infrared and ultraviolet induced isomerization of crotonic acid in N2 and Xe cryomatrices: First observation of two high-energy trans C–O conformers and mechanistic insights. J Chem Phys 2014; 141:234310. [DOI: 10.1063/1.4903841] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nihal Kuş
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- Department of Physics, Anadolu University, 26470 Eskişehir, Turkey
| | - Rui Fausto
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| |
Collapse
|
15
|
Reva I, M Nunes C, Biczysko M, Fausto R. Conformational switching in pyruvic acid isolated in Ar and N₂ matrixes: spectroscopic analysis, anharmonic simulation, and tunneling. J Phys Chem A 2014; 119:2614-27. [PMID: 25332047 DOI: 10.1021/jp509578c] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Monomers of pyruvic acid (PA) isolated in cryogenic argon and nitrogen matrixes were characterized by mid- and near-infrared spectroscopy. Interpretation of the experiments was aided by fully anharmonic calculations of the fundamental modes, overtones, and combinations up to two quanta, including their infrared intensities. The initially dominating PA conformer (Tc) has a cis CCOH arrangement and is stabilized by a strong intramolecular H-bond. Selective near-infrared excitation of Tc at the first OH overtone (6630 cm(-1) in Ar, 6643 cm(-1) in N2) induced a large scale conformational conversion to the higher-energy conformer (Tt) with trans CCOH arrangement. Tt was then converted back to Tc by selective NIR irradiation at the first Tt OH overtone (6940 cm(-1) in Ar, 6894 cm(-1) in N2). In N2 matrix, the Tt form was stabilized due to interaction between the OH group and the matrix molecules. This stabilization manifested itself in the absence of Tt → Tc relaxation and in a considerable change of the vibrational Tt signature upon going from argon to nitrogen matrix. In argon, the Tt form spontaneously decayed back to Tc in the dark (characteristic lifetime +16 h). In the presence of broad-band near-infrared light, the Tt → Tc relaxation speed considerably increased. The decay mechanisms are discussed.
Collapse
Affiliation(s)
- Igor Reva
- †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
| | - Malgorzata Biczysko
- ‡Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,§Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Rui Fausto
- †CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| |
Collapse
|
16
|
Araujo-Andrade C, Reva I, Fausto R. Tetrazole acetic acid: Tautomers, conformers, and isomerization. J Chem Phys 2014; 140:064306. [DOI: 10.1063/1.4864119] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|