1
|
Rostkowska H, Lapinski L, Nowak MJ. Intramolecular hydrogen-atom tunneling in matrix-isolated heterocyclic compounds: 2-thiouracil and its analogues. Phys Chem Chem Phys 2024. [PMID: 39235301 DOI: 10.1039/d4cp02799j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Hydrogen-atom tunneling leading to spontaneous tautomeric conversion in monomeric heterocyclic molecules without intramolecular hydrogen bonds has been experimentally detected for the first time. For monomers of 2-thiouracil, 6-aza-2-thiouracil and 1-methyl-2-thiouracil isolated in low-temperature matrices, higher-energy thiol forms were generated upon UV (λ = 305 nm) excitation of the most stable thione tautomers. When the matrices were subsequently kept in the dark and at low temperature, hydrogen-atom tunneling occurred, leading to the thiol → thione conversion. During this process, the photoproduced thiol form spontaneously converted into the lowest energy thione tautomer.
Collapse
Affiliation(s)
- Hanna Rostkowska
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, Warsaw 02-668, Poland.
| | - Leszek Lapinski
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, Warsaw 02-668, Poland.
| | - Maciej J Nowak
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, Warsaw 02-668, Poland.
| |
Collapse
|
2
|
Rostkowska H, Lapinski L, Nowak MJ. Hydrogen-atom tunneling in small thioamides: N-methylthiourea, thiobenzamide and 2-cyanothioacetamide. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124139. [PMID: 38503255 DOI: 10.1016/j.saa.2024.124139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/26/2024] [Accepted: 03/06/2024] [Indexed: 03/21/2024]
Abstract
The most stable thione tautomeric forms of N-methylthiourea, thiobenzamide and 2-cyanothioacetamide were isolated in low-temperature argon matrices. The higher-energy thiol tautomers of these compounds were generated upon irradiation of matrix-isolated monomers with UV (λ > 270 nm) light. For N-methylthiourea and thiobenzamide, kept in the dark at 3.5 K for a long period of time, a spontaneous thiol → thione hydrogen atom tunneling transformation occurred. Only the thiol isomers with the favorably oriented hydrogen atom of the imino group underwent these hydrogen-atom tunneling processes. The other thiol isomers, with the hydrogen atom of the imino group oriented towards the sulfur atom, did not undergo the thiol → thione conversion. For the photogenerated thiol forms of 2-cyanothioacetamide, no spontaneous thiol → thione tautomeric transformation was detected. Instead, only the spontaneous conformational change of one S-H rotamer of the thiol 2-cyanothioacetamide tautomer into the other S-H rotamer was observed.
Collapse
Affiliation(s)
- Hanna Rostkowska
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Leszek Lapinski
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Maciej J Nowak
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| |
Collapse
|
3
|
Pagacz-Kostrzewa M, Szaniawska W, Wierzejewska M. NIR and UV induced transformations of indazole-3-carboxylic acid isolated in low temperature matrices. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 290:122283. [PMID: 36586171 DOI: 10.1016/j.saa.2022.122283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
The molecular structure and NIR and UV induced phototransformations of indazole-3-carboxylic acid were studied in low temperature argon and nitrogen matrices by FTIR spectroscopy and B3LYP/6-311++G(2d,2p) calculations. Eleven minima of IC were located on the S0 potential energy surface. The three most stable structures were detected experimentally in both matrices after deposition. Upon NIR irradiation a dominant process was rotamerization within the carboxylic group leading to changes in the population of the trans 1HIC1 and cis 1HIC2 forms. In turn, at UV irradiation at λ = 260 nm two new tautomers (2HIC2 and 2HIC3) were generated indicating that the hydrogen atom transfer in pyrazole ring took place. Based on the obtained kinetic curves, differences in the phototransformation rates in different matrices were indicated.
Collapse
Affiliation(s)
- M Pagacz-Kostrzewa
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland.
| | - W Szaniawska
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - M Wierzejewska
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| |
Collapse
|
4
|
Roque JPL, Nunes CM, Fausto R. Matrix Isolation in Heterocyclic Chemistry. HETEROCYCLES 2022. [DOI: 10.1002/9783527832002.ch12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
5
|
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
|
6
|
M Nunes C, Pereira NAM, Viegas LP, Pinho E Melo TMVD, Fausto R. Inducing molecular reactions by selective vibrational excitation of a remote antenna with near-infrared light. Chem Commun (Camb) 2021; 57:9570-9573. [PMID: 34546241 DOI: 10.1039/d1cc03574f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate here that selective vibrational excitation of a moiety, remotely attached in relation to the molecular reaction site, might offer a generalized strategy for inducing bond-breaking/bond-forming reactions with exquisite precision. As a proof-of-principle, the electrocyclic ring-expansion of a benzazirine to a ketenimine was induced, in a cryogenic matrix, by near-IR light tuned at the overtone stretching frequency of its OH remote antenna. This accomplishment paves the way for harnessing IR vibrational excitation as a tool to guide a variety of molecular structure manipulations in an exceptional highly-selective manner.
Collapse
Affiliation(s)
- Cláudio M Nunes
- University of Coimbra, CQC, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - Nelson A M Pereira
- University of Coimbra, CQC, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - Luís P Viegas
- University of Coimbra, CQC, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | | | - Rui Fausto
- University of Coimbra, CQC, Department of Chemistry, 3004-535 Coimbra, Portugal.
| |
Collapse
|
7
|
Rozenberg M, Fausto R, Reva I. Variable temperature FTIR spectra of polycrystalline purine nucleobases and estimating strengths of individual hydrogen bonds. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 251:119323. [PMID: 33508682 DOI: 10.1016/j.saa.2020.119323] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/19/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
In the first part of this work, we report the FTIR spectra of pure NH and isotopically substituted ND (10-15% D and 80-90% D) polycrystalline hypoxanthine, xanthine, adenine and guanine recorded in the 400-4000 cm-1 range, as a function of temperature (10-300 K). We provide assignments of the stretching and out-of-plane bending amine (NH2) and imine (NH) bands to the distinct H-bonds present in the crystal, based on the temperature sensitivity and isotopic exchange behavior. Empirical correlations between spectral and thermodynamic or structural parameters enabled us to estimate the energies and lengths of H-bonds in the studied nucleobase crystals and to correlate them with literature data. The empirical H-bonding energies are compared with H-bonding and stacking energies computed for hypoxanthine. In the second part, strategies for using the empirical correlations together with information extracted from quantum mechanical data (in particular from the Bader's quantum theory of atoms in molecules, QTAIM) for the evaluation of hydrogen bonding properties are discussed, and their advantages and drawbacks pointed out. The justification for a cooperative use of quantum-mechanical calculations with empirical spectra-energy correlations is discussed.
Collapse
Affiliation(s)
- M Rozenberg
- The Hebrew University of Jerusalem, Department of Inorganic and Analytical Chemistry, Jerusalem, Givat Ram 91904, Israel.
| | - R Fausto
- University of Coimbra, CQC, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - I Reva
- University of Coimbra, CQC, Department of Chemistry, 3004-535 Coimbra, Portugal; University of Coimbra, CIEPQPF, Department of Chemical Engineering, 3030-790 Coimbra, Portugal.
| |
Collapse
|
8
|
Roque JPL, Sharma A, Rosado MTS, Fausto R, Reva I. Vibrationally Induced Conformational Isomerization and Tunneling in Pyrrole-2-Carboxylic Acid. J Phys Chem A 2020; 124:10277-10287. [PMID: 33245233 DOI: 10.1021/acs.jpca.0c09141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conformational behavior of carboxylic acids has attracted considerable attention, as it can be used as a gateway for the study of more complex phenomena. Here, we present an experimental and computational study of pyrrole-2-carboxylic acid (PCA) conformational space and the vibrational characterization of the compound by infrared spectroscopy. The possibility of promoting conformational transformations using selective vibrational excitation of the 2ν(OH) and 2ν(NH) stretching overtones is explored. Two conformers, exhibiting the cis configuration of the COOH group (O═C-O-H dihedral angle near 0°) and differing by the orientation of the carboxylic group with respect to the pyrrole ring (i.e., showing either a cis or a trans NCC═O arrangement), were found to coexist initially for the compound isolated in a cryogenic nitrogen matrix, in an 86:14 ratio, and were characterized by infrared spectroscopy. A third conformer, with the COOH group in the trans configuration, was produced, in situ, by narrowband near-infrared (NIR) excitation of the most stable PCA form (with a cis NCC═O moiety). The photogenerated PCA conformer was found to decay back to the most stable PCA form, by H-atom quantum mechanical tunneling, with a characteristic half-life time of ∼10 min in the nitrogen matrix at 10 K. Tunneling rates were theoretically estimated and compared for the observed isomerization of pyrrole-2-carboxylic acid and for the structurally similar furan-2-carboxylic acid. This comparison showcases the effect of small modifications in the potential energy surface and the implications of quantum tunneling for the stability of short-living species.
Collapse
Affiliation(s)
- José P L Roque
- CQC, Department of Chemistry, University of Coimbra, Coimbra 3004-535, Portugal
| | - Archna Sharma
- CQC, Department of Chemistry, University of Coimbra, Coimbra 3004-535, Portugal.,Department of Physics, University of Jammu, Jammu 180001, India
| | - Mário T S Rosado
- CQC, Department of Chemistry, University of Coimbra, Coimbra 3004-535, Portugal
| | - Rui Fausto
- CQC, Department of Chemistry, University of Coimbra, Coimbra 3004-535, Portugal
| | - Igor Reva
- CQC, Department of Chemistry, University of Coimbra, Coimbra 3004-535, Portugal
| |
Collapse
|
9
|
Mosquera-Lois I, Ferro-Costas D, Fernández-Ramos A. Chemical reactivity from the vibrational ground-state level. The role of the tunneling path in the tautomerization of urea and derivatives. Phys Chem Chem Phys 2020; 22:24951-24963. [PMID: 33140774 DOI: 10.1039/d0cp04857g] [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
Recent developments of low-temperature techniques are providing valuable knowledge about chemical processes that manifest in the quantum regimen. The tunneling effect from the vibrational ground-state is the main mechanism of these reactions, which usually involves the motion or transfer of hydrogen atoms. Theoretical methods can enrich the information supplied by these experimental methods through an insightful analysis of the tunneling process. In this context, canonical variational transition state theory with multidimensional tunneling corrections (CVT/MT) can handle this type of reaction, and it has been applied to several systems within the small-curvature approximation for tunneling (SCT). This method is of proven reliability for polyatomic reactions occurring at room temperature and above, but no tests have been performed to check its performance when only the lowest energy level is populated. In this work, we compare SCT against the least-action tunneling (LAT) method to study the tautomerization and cis-trans interconversion reactions in the enol forms of urea, thiourea, and selenourea. To the best of our knowledge, this is the first time that the LAT method is applied to a polyatomic reaction occurring in the deep-tunneling region. The theoretical results indicate that the reaction mechanisms are controlled by tunneling. The SCT and LAT tautomerization reaction times are in good agreement with the experimental values; however, LAT seems superior to SCT for reactions (tautomerizations) that involve moderate reaction path curvature, whereas the opposite is true for reactions with small curvature (interconversions). These results led us to introduce and recommend the microcanonically optimized tunneling path that selects the tunneling probability as the maximum between the SCT and LAT tunneling probabilities.
Collapse
Affiliation(s)
- Irea Mosquera-Lois
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | | | | |
Collapse
|
10
|
Lopes Jesus A, Reva I, Nunes CM, Roque JP, Pinto SM, Fausto R. Kinetically unstable 2–isocyanophenol isolated in cryogenic matrices: Vibrational excitation, conformational changes and spontaneous tunneling. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2019.137069] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
11
|
Beć KB, Grabska J, Ozaki Y, Czarnecki MA, Huck CW. Simulated NIR spectra as sensitive markers of the structure and interactions in nucleobases. Sci Rep 2019; 9:17398. [PMID: 31758033 PMCID: PMC6874539 DOI: 10.1038/s41598-019-53827-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 10/11/2019] [Indexed: 11/16/2022] Open
Abstract
Near-infrared (near-IR; NIR) spectroscopy is continuously advancing in biophysical and biochemical fields of investigation. For instance, recent progresses in NIR hyperspectral imaging of biological systems may be noted. However, interpretation of NIR bands for biological samples is difficult and creates a considerable barrier in exploring the full potential of NIR spectroscopy in bioscience. For this reason, we carried out a systematic study of NIR spectra of adenine, cytosine, guanine, and thymine in polycrystalline state. Interpretation of NIR spectra of these nucleobases was supported by anharmonic vibrational analysis using Deperturbed Vibrational Second-Order Perturbation Theory (DVPT2). A number of molecular models of nucleobases was applied to study the effect of the inter-molecular interactions on the NIR spectra. The accuracy of simulated NIR spectra appears to depend on the intra-layer interactions; in contrast, the inter-layer interactions are less influential. The best results were achieved by combining the simulated spectra of monomers and dimers. It is of particular note that in-plane deformation bands are far more populated than out-of-plane ones and the importance of ring modes is relatively small. This trend is in contrast to that observed in mid-IR region. As shown, the local, short-range chemical neighborhood of nucleobase molecules influence their NIR spectra more considerably. This suggests that NIR spectra are more sensitive probe of the nucleobase pairing than mid-IR ones. The obtained results allow, for the first time, to construct a frequency correlation table for NIR spectra of purines and pyrimidines.
Collapse
Affiliation(s)
- Krzysztof B Beć
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, CCB-Center for Chemistry and Biomedicine, 6020, Innsbruck, Austria.
| | - Justyna Grabska
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, CCB-Center for Chemistry and Biomedicine, 6020, Innsbruck, Austria
| | - Yukihiro Ozaki
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo, 669-1337, Japan
| | - Mirosław A Czarnecki
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383, Wrocław, Poland
| | - Christan W Huck
- Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80/82, CCB-Center for Chemistry and Biomedicine, 6020, Innsbruck, Austria
| |
Collapse
|
12
|
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.
Collapse
Affiliation(s)
- Maciej J Nowak
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | | | | | | | | |
Collapse
|
13
|
Zhu G, Qian C, Wang L. Tautomer‐Specific Resonant Photoelectron Imaging of Deprotonated Cytosine Anions. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Guo‐Zhu Zhu
- Department of Chemistry Brown University Providence RI 02912 USA
| | - Chen‐Hui Qian
- Department of Chemistry Brown University Providence RI 02912 USA
| | - Lai‐Sheng Wang
- Department of Chemistry Brown University Providence RI 02912 USA
| |
Collapse
|
14
|
Zhu G, Qian C, Wang L. Tautomer‐Specific Resonant Photoelectron Imaging of Deprotonated Cytosine Anions. Angew Chem Int Ed Engl 2019; 58:7856-7860. [DOI: 10.1002/anie.201903444] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Guo‐Zhu Zhu
- Department of ChemistryBrown University Providence RI 02912 USA
| | - Chen‐Hui Qian
- Department of ChemistryBrown University Providence RI 02912 USA
| | - Lai‐Sheng Wang
- Department of ChemistryBrown University Providence RI 02912 USA
| |
Collapse
|
15
|
Lopes Jesus AJ, Nunes CM, Reva I, Pinto SMV, Fausto R. Effects of Entangled IR Radiation and Tunneling on the Conformational Interconversion of 2-Cyanophenol. J Phys Chem A 2019; 123:4396-4405. [DOI: 10.1021/acs.jpca.9b01382] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- A. J. Lopes Jesus
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- CQC, Faculty of Pharmacy, University of Coimbra, 3004-295 Coimbra, Portugal
| | - Cláudio M. Nunes
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - I. Reva
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Sandra M. V. Pinto
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- Scuola Normale Superiore, Piazza dei Cavalieri, 7, I-56124 Pisa, Italy
| | - R. Fausto
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| |
Collapse
|
16
|
Góbi S, Nunes CM, Reva I, Tarczay G, Fausto R. S–H rotamerizationviatunneling in a thiol form of thioacetamide. Phys Chem Chem Phys 2019; 21:17063-17071. [DOI: 10.1039/c9cp03417j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rotamerization of the S–H groupviahydrogen tunneling is reported for the first time.
Collapse
Affiliation(s)
- Sándor Góbi
- CQC
- Department of Chemistry
- University of Coimbra
- Coimbra
- Portugal
| | | | - Igor Reva
- CQC
- Department of Chemistry
- University of Coimbra
- Coimbra
- Portugal
| | - György Tarczay
- Laboratory of Molecular Spectroscopy
- Institute of Chemistry
- ELTE Eötvös Loránd University
- H-1518 Budapest
- Hungary
| | - Rui Fausto
- CQC
- Department of Chemistry
- University of Coimbra
- Coimbra
- Portugal
| |
Collapse
|
17
|
Góbi S, Reva I, Csonka IP, M. Nunes C, Tarczay G, Fausto R. Selective conformational control by excitation of NH imino vibrational antennas. Phys Chem Chem Phys 2019; 21:24935-24949. [DOI: 10.1039/c9cp05370k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We provide experimental evidence for the occurrence of selective and reversible conformational control over the SH group by vibrational excitation of remote NH groups. Using an imino group that acts as a molecular antenna has no precedents.
Collapse
Affiliation(s)
- Sándor Góbi
- CQC
- Department of Chemistry
- University of Coimbra
- Coimbra
- Portugal
| | - Igor Reva
- CQC
- Department of Chemistry
- University of Coimbra
- Coimbra
- Portugal
| | - István Pál Csonka
- MTA-ELTE Lendület Laboratory Astrochemistry Research Group
- Institute of Chemistry
- ELTE Eötvös Loránd University
- H–1518 Budapest
- Hungary
| | | | - György Tarczay
- MTA-ELTE Lendület Laboratory Astrochemistry Research Group
- Institute of Chemistry
- ELTE Eötvös Loránd University
- H–1518 Budapest
- Hungary
| | - Rui Fausto
- CQC
- Department of Chemistry
- University of Coimbra
- Coimbra
- Portugal
| |
Collapse
|
18
|
Lapinski L, Reva I, Gerega A, Nowak MJ, Fausto R. UV-induced transformations of matrix-isolated 6-azacytosine. J Chem Phys 2018; 149:104301. [DOI: 10.1063/1.5045735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Leszek Lapinski
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Igor Reva
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Anna Gerega
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
- Nalecz Institute of Biocybernetics and Biomedical Engineering, Polish Academy of Sciences, Trojdena 4, 02-109 Warsaw, Poland
| | - Maciej J. Nowak
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Rui Fausto
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| |
Collapse
|
19
|
Lopes Jesus AJ, M. Nunes C, Fausto R, Reva I. Conformational control over an aldehyde fragment by selective vibrational excitation of interchangeable remote antennas. Chem Commun (Camb) 2018; 54:4778-4781. [DOI: 10.1039/c8cc01052h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We apply vibrational antennas (OH or NH2 group) to achieve unprecedented conformational control over the heavy aldehyde fragment in 2-formyl-2H-azirine, using selective vibrational excitations of the OH or NH2 stretching overtones and combination modes.
Collapse
Affiliation(s)
| | | | - Rui Fausto
- CQC
- Department of Chemistry
- University of Coimbra
- Coimbra
- Portugal
| | - Igor Reva
- CQC
- Department of Chemistry
- University of Coimbra
- Coimbra
- Portugal
| |
Collapse
|
20
|
Rostkowska H, Lapinski L, Nowak MJ. Hydrogen-atom tunneling through a very high barrier; spontaneous thiol → thione conversion in thiourea isolated in low-temperature Ar, Ne, H2and D2matrices. Phys Chem Chem Phys 2018; 20:13994-14002. [DOI: 10.1039/c8cp01703d] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen-atom tunneling in thiourea involves breaking of the S–H chemical bond and the formation of a new N–H bond.
Collapse
Affiliation(s)
- Hanna Rostkowska
- Institute of Physics
- Polish Academy of Sciences
- 02-668 Warsaw
- Poland
| | - Leszek Lapinski
- Institute of Physics
- Polish Academy of Sciences
- 02-668 Warsaw
- Poland
| | - Maciej J. Nowak
- Institute of Physics
- Polish Academy of Sciences
- 02-668 Warsaw
- Poland
| |
Collapse
|
21
|
Nunes CM, Reva I, Kozuch S, McMahon RJ, Fausto R. Photochemistry of 2-Formylphenylnitrene: A Doorway to Heavy-Atom Tunneling of a Benzazirine to a Cyclic Ketenimine. J Am Chem Soc 2017; 139:17649-17659. [DOI: 10.1021/jacs.7b10495] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- 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
| | - Sebastian Kozuch
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel
| | - Robert J. McMahon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1322, United States
| | - Rui Fausto
- CQC, Department
of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| |
Collapse
|
22
|
Rostkowska H, Lapinski L, Nowak MJ. UV-Induced Hydrogen-Atom-Transfer Processes in 3-Thio-1,2,4-triazole Isolated in Ar and H2 Low-Temperature Matrixes. J Phys Chem A 2017; 121:6932-6941. [DOI: 10.1021/acs.jpca.7b05621] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hanna Rostkowska
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Leszek Lapinski
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Maciej J. Nowak
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| |
Collapse
|
23
|
Lopes Jesus AJ, Fausto R, Reva I. Conformational Changes in 5-Methoxyindole: Effects of Thermal, Vibrational, and Electronic Excitations. J Phys Chem A 2017; 121:3372-3382. [DOI: 10.1021/acs.jpca.7b01713] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A. J. Lopes Jesus
- CQC,
Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
- CQC,
Faculty of Pharmacy, University of Coimbra, 3004-295 Coimbra, Portugal
| | - R. Fausto
- CQC,
Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - I. Reva
- CQC,
Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| |
Collapse
|
24
|
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
|
25
|
Justino LLG, Reva I, Fausto R. Thermally and vibrationally induced conformational isomerizations, infrared spectra, and photochemistry of gallic acid in low-temperature matrices. J Chem Phys 2017; 145:014304. [PMID: 27394105 DOI: 10.1063/1.4954894] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Near-infrared (near-IR) narrowband selective vibrational excitation and annealing of gallic acid (3,4,5-trihydroxybenzoic acid) isolated in cryogenic matrices were used to induce interconversions between its most stable conformers. The isomerizations were probed by infrared spectroscopy. An extensive set of quantum chemical calculations, carried out at the DFT(B3LYP)/6-311++G(d,p) level of approximation, was used to undertake a detailed analysis of the ground state potential energy surface of the molecule. This investigation of the molecule conformational space allowed extracting mechanistic insights into the observed annealing- or near-IR-induced isomerization processes. The infrared spectra of the two most stable conformers of gallic acid in N2, Xe, and Ar matrices were fully assigned. Finally, the UV-induced photochemistry of the matrix isolated compound was investigated.
Collapse
Affiliation(s)
- Licínia L G Justino
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Igor Reva
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Rui Fausto
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| |
Collapse
|
26
|
Halasa A, Reva I, Lapinski L, Nowak MJ, Fausto R. Conformational Changes in Thiazole-2-carboxylic Acid Selectively Induced by Excitation with Narrowband Near-IR and UV Light. J Phys Chem A 2016; 120:2078-88. [DOI: 10.1021/acs.jpca.5b11615] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anna Halasa
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Igor Reva
- CQC,
Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Leszek Lapinski
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Maciej J. Nowak
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Rui Fausto
- CQC,
Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| |
Collapse
|
27
|
Lopes Jesus AJ, Reva I, Araujo-Andrade C, Fausto R. Conformational changes in matrix-isolated 6-methoxyindole: Effects of the thermal and infrared light excitations. J Chem Phys 2016; 144:124306. [PMID: 27036447 DOI: 10.1063/1.4944528] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Conformational changes induced thermally or upon infrared excitation of matrix-isolated 6-methoxyindole were investigated. Narrowband near-infrared excitation of the first overtone of the N-H stretching vibration of each one of the two identified conformers is found to induce a selective large-scale conversion of the pumped conformer into the other one. This easily controllable bidirectional process consists in the intramolecular reorientation of the methoxy group and allowed a full assignment of the infrared spectra of the two conformers. Matrices with different conformational compositions prepared by narrow-band irradiations were subsequently used to investigate the effects of both thermal and broadband infrared excitations on the conformational mixtures. Particular attention is given to the influence of the matrix medium (Ar vs. Xe) and conformational effects of exposition of the sample to the spectrometer light source during the measurements.
Collapse
Affiliation(s)
- A J Lopes Jesus
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - I Reva
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - C Araujo-Andrade
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - R Fausto
- CQC, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| |
Collapse
|
28
|
Meisner J, Kästner J. Atom Tunneling in Chemistry. Angew Chem Int Ed Engl 2016; 55:5400-13. [DOI: 10.1002/anie.201511028] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/08/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Jan Meisner
- Institut für Theoretische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Johannes Kästner
- Institut für Theoretische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| |
Collapse
|
29
|
Affiliation(s)
- Jan Meisner
- Institut für Theoretische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Deutschland
| | - Johannes Kästner
- Institut für Theoretische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Deutschland
| |
Collapse
|
30
|
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
|
31
|
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
|
32
|
Halasa A, Lapinski L, Rostkowska H, Nowak MJ. Intramolecular Vibrational Energy Redistribution in 2-Thiocytosine: SH Rotamerization Induced by Near-IR Selective Excitation of NH2 Stretching Overtone. J Phys Chem A 2015; 119:9262-71. [DOI: 10.1021/acs.jpca.5b06221] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anna Halasa
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Leszek Lapinski
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Hanna Rostkowska
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Maciej J. Nowak
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| |
Collapse
|
33
|
Kuş N, Sharma A, Peña I, Bermúdez MC, Cabezas C, Alonso JL, Fausto R. Conformers of β-aminoisobutyric acid probed by jet-cooled microwave and matrix isolation infrared spectroscopic techniques. J Chem Phys 2015; 138:144305. [PMID: 24981533 DOI: 10.1063/1.4799456] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
β-aminoisobutyric acid (BAIBA) has been studied in isolation conditions: in the gas phase and trapped into a cryogenic N2 matrix. A solid sample of the compound was vaporized by laser ablation and investigated through their rotational spectra in a supersonic expansion using two different spectroscopic techniques: broadband chirped pulse Fourier transform microwave spectroscopy and conventional molecular beam Fourier transform microwave spectroscopy. Four conformers with structures of two types could be successfully identified by comparison of the experimental rotational and (14)N nuclear quadruple coupling constants with those predicted theoretically: type A, bearing an OH⋯N intramolecular hydrogen bond and its carboxylic group in the trans geometry (H-O-C=O dihedral ∼180°), and type B, having an NH⋯O bond and the cis arrangement of the carboxylic group. These two types of conformers could also be trapped from the gas phase into a cryogenic N2 matrix and probed by Fourier transform infrared (IR) spectroscopy. In situ irradiation of BAIBA isolated in N2 matrix of type B conformers using near-IR radiation tuned at the frequency of the O-H stretching 1st overtone (∼6930 cm(-1)) of these forms allowed to selectively convert them into type A conformers and into a new type of conformers of higher energy (type D) bearing an NH⋯O=C bond and a O-H "free" trans carboxylic group.
Collapse
Affiliation(s)
- N Kuş
- Department of Chemistry, University of Coimbra, P-3004-535 Coimbra, Portugal
| | - A Sharma
- Department of Chemistry, University of Coimbra, P-3004-535 Coimbra, Portugal
| | - I Peña
- Grupo de Espectroscopia Molecular (GEM), Unidad Asociada CSIC, Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Universidad de Valladolid, 47005 Valladolid, Spain
| | - M C Bermúdez
- Grupo de Espectroscopia Molecular (GEM), Unidad Asociada CSIC, Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Universidad de Valladolid, 47005 Valladolid, Spain
| | - C Cabezas
- Grupo de Espectroscopia Molecular (GEM), Unidad Asociada CSIC, Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Universidad de Valladolid, 47005 Valladolid, Spain
| | - J L Alonso
- Grupo de Espectroscopia Molecular (GEM), Unidad Asociada CSIC, Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Universidad de Valladolid, 47005 Valladolid, Spain
| | - R Fausto
- Department of Chemistry, University of Coimbra, P-3004-535 Coimbra, Portugal
| |
Collapse
|
34
|
Lopes Jesus AJ, Jarmelo S, Fausto R, Reva I. Conformational preferences of 3,4-dihydroxyphenylacetic acid (DOPAC). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 140:54-64. [PMID: 25589387 DOI: 10.1016/j.saa.2014.12.078] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 11/22/2014] [Accepted: 12/17/2014] [Indexed: 06/04/2023]
Abstract
The conformational space of 3,4-dihydroxyphenylacetic acid (DOPAC), an important dopamine metabolite, has been investigated by quantum chemical methods (B3LYP and MP2, with the 6-311++G(d,p) basis set) and matrix-isolation infrared spectroscopy. Detailed analysis of the calculated potential energy surfaces of the molecule led to identification of thirteen unique conformers, all of them showing the acetic acid side chain out of the aromatic ring plane by 60-95°. According to the calculated Gibbs energies, the five lowest energy conformers make up 99.7% of the conformational mixture at 298.15K, exhibiting individual populations falling between 16% and 24%. The main conformational trends of this molecule were interpreted on the grounds of a thorough analysis of the structural parameters and by the application of the Natural Bond Orbital theory. The role of the intramolecular interactions on the relative stability and structure of the conformers was also investigated. The infrared spectrum of DOPAC was registered after isolation of its monomers in argon and xenon matrices. Only one of DOPAC forms populated in the gas phase could be trapped in both matrix gases. This result is in agreement with the predicted low energy barriers for conformational isomerization and is also supported by annealing experiments. The spectra of matrix-isolated model compounds, phenylacetic acid and catechol, were studied under the same experimental conditions. These data were used as references and assisted in the interpretation of the results obtained for DOPAC.
Collapse
Affiliation(s)
- A J Lopes Jesus
- Centre of Chemistry - Coimbra, Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal.
| | - S Jarmelo
- Centre of Chemistry - Coimbra, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - R Fausto
- Centre of Chemistry - Coimbra, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - I Reva
- Centre of Chemistry - Coimbra, Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| |
Collapse
|
35
|
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
|
36
|
Kócs L, Najbauer EE, Bazsó G, Magyarfalvi G, Tarczay G. Near-Infrared Laser-Induced Structural Changes of Glycine·Water Complexes in an Ar Matrix. J Phys Chem A 2014; 119:2429-37. [DOI: 10.1021/jp508493c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lenke Kócs
- Laboratory
of Molecular Spectroscopy, Institute of Chemistry, Eötvös University, P.O.
Box 32, H-1518 Budapest 112, Hungary
| | - Eszter E. Najbauer
- Laboratory
of Molecular Spectroscopy, Institute of Chemistry, Eötvös University, P.O.
Box 32, H-1518 Budapest 112, Hungary
| | - Gábor Bazsó
- Laboratory
of Molecular Spectroscopy, Institute of Chemistry, Eötvös University, P.O.
Box 32, H-1518 Budapest 112, Hungary
| | - Gábor Magyarfalvi
- Laboratory
of Molecular Spectroscopy, Institute of Chemistry, Eötvös University, P.O.
Box 32, H-1518 Budapest 112, Hungary
| | - György Tarczay
- Laboratory
of Molecular Spectroscopy, Institute of Chemistry, Eötvös University, P.O.
Box 32, H-1518 Budapest 112, Hungary
| |
Collapse
|
37
|
Halasa A, Lapinski L, Rostkowska H, Reva I, Nowak MJ. Tunable Diode Lasers as a Tool for Conformational Control: The Case of Matrix-Isolated Oxamic Acid. J Phys Chem A 2014; 119:2203-10. [DOI: 10.1021/jp501448m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anna Halasa
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Leszek Lapinski
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Hanna Rostkowska
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Igor Reva
- Department
of Chemistry, University of Coimbra, 3004−535 Coimbra, Portugal
| | - Maciej J. Nowak
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| |
Collapse
|
38
|
Ertelt M, Hrovat DA, Borden WT, Sander W. Heavy-Atom Tunneling in the Ring Opening of a Strained Cyclopropene at Very Low Temperatures. Chemistry 2014; 20:4713-20. [DOI: 10.1002/chem.201303792] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Indexed: 11/09/2022]
|
39
|
Lapinski L, Reva I, Rostkowska H, Fausto R, Nowak MJ. Near-IR-Induced, UV-Induced, and Spontaneous Isomerizations in 5-Methylcytosine and 5-Fluorocytosine. J Phys Chem B 2014; 118:2831-41. [DOI: 10.1021/jp411423c] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Leszek Lapinski
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Igor Reva
- Department
of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Hanna Rostkowska
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Rui Fausto
- Department
of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Maciej J. Nowak
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| |
Collapse
|
40
|
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
|
41
|
Najbauer EE, Bazsó G, Góbi S, Magyarfalvi G, Tarczay G. Exploring the Conformational Space of Cysteine by Matrix Isolation Spectroscopy Combined with Near-Infrared Laser Induced Conformational Change. J Phys Chem B 2014; 118:2093-103. [DOI: 10.1021/jp412550q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eszter E. Najbauer
- Laboratory of Molecular Spectroscopy,
Institute of Chemistry, Eötvös University, P.O. Box 32 H-1518, Budapest 112, Hungary
| | - Gábor Bazsó
- Laboratory of Molecular Spectroscopy,
Institute of Chemistry, Eötvös University, P.O. Box 32 H-1518, Budapest 112, Hungary
| | - Sándor Góbi
- Laboratory of Molecular Spectroscopy,
Institute of Chemistry, Eötvös University, P.O. Box 32 H-1518, Budapest 112, Hungary
| | - Gábor Magyarfalvi
- Laboratory of Molecular Spectroscopy,
Institute of Chemistry, Eötvös University, P.O. Box 32 H-1518, Budapest 112, Hungary
| | - György Tarczay
- Laboratory of Molecular Spectroscopy,
Institute of Chemistry, Eötvös University, P.O. Box 32 H-1518, Budapest 112, Hungary
| |
Collapse
|
42
|
Kuş N, Bayarı SH, Fausto R. Methylparaben Isolated in Solid Argon: Structural Characterization and UV-Induced Conversion into Methylparaben Radical and Isomeric Ketenes. J Phys Chem B 2013; 117:13543-55. [DOI: 10.1021/jp408366x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nihal Kuş
- Department
of Chemistry, University of Coimbra, P-3004-535 Coimbra, Portugal
- Department
of Physics, Anadolu University, 26470 Eskişehir, Turkey
| | - Sevgi H. Bayarı
- Department
of Physics, Hacettepe University, 06800 Ankara, Turkey
| | - Rui Fausto
- Department
of Chemistry, University of Coimbra, P-3004-535 Coimbra, Portugal
| |
Collapse
|
43
|
Giuliano BM, Melandri S, Reva I, Fausto R. Conformational space and photochemistry of tyramine isolated in argon and xenon cryomatrixes. J Phys Chem A 2013; 117:10248-59. [PMID: 24011365 DOI: 10.1021/jp404707e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The infrared spectra of tyramine monomers trapped in low-temperature argon and xenon matrixes were recorded. The presence of the flexible ethylamino side chain gives rise to a complex conformational surface that contains several minima of relatively low energies, some of them stabilized by a weak N-H···π hydrogen bond interaction between the amino group and the phenyl ring. The experimental infrared spectra confirm the presence of at least two stable conformers isolated in the matrixes. Annealing experiments performed on the xenon matrix revealed a change in the relative population of the experimentally relevant conformers upon isolation in this polarizable matrix, compared to the gas phase. The general interpretation of the spectra was based on harmonic and anharmonic quantum chemical calculations, undertaken at the DFT/B3LYP and MP2 levels of theory with the 6-311++G(d,p) basis set. The photochemical behavior of the matrix-isolated compound upon narrow-band UV irradiation was also investigated. Identification of ketene species in the spectra of the irradiated matrixes suggests the occurrence of a ring-opening reaction, which in the xenon matrix occurs concomitantly with the conformational isomerization of tyramine.
Collapse
Affiliation(s)
- Barbara M Giuliano
- Department of Chemistry, University of Coimbra , P-3004-535 Coimbra, Portugal
| | | | | | | |
Collapse
|
44
|
Triandafillou CG, Matsika S. Excited-state tautomerization of gas-phase cytosine. J Phys Chem A 2013; 117:12165-74. [PMID: 24094271 DOI: 10.1021/jp407758w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In order to investigate experimentally observed phototautomerization of gas-phase cytosine, several excited-state tautomerization mechanisms were characterized at the EOM-CCSD and TDDFT levels. All pathways that took place exclusively on the S1 surface were found to have significant barriers that were much higher than the barriers involved in radiationless decay of cytosine tautomers through conical intersections back to the ground state; tautomerization in this fashion cannot compete with radiationless relaxation. However, an alternative possibility is that the conical intersections that facilitate radiationless decay could also facilitate tautomerization. Barrierless pathways indicate that it is energetically possible that bifurcation at the conical intersections can lead to a subset of the population reaching different tautomers. This could be an explanation for the observed tautomerization of keto cytosine after exposure to low-energy UV light.
Collapse
|
45
|
Lapinski L, Reva I, Rostkowska H, Halasa A, Fausto R, Nowak MJ. Conformational Transformation in Squaric Acid Induced by Near-IR Laser Light. J Phys Chem A 2013; 117:5251-9. [DOI: 10.1021/jp402128g] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Leszek Lapinski
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668
Warsaw, Poland
| | - Igor Reva
- Department
of Chemistry, University of Coimbra, 3004−535
Coimbra, Portugal
| | - Hanna Rostkowska
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668
Warsaw, Poland
| | - Anna Halasa
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668
Warsaw, Poland
| | - Rui Fausto
- Department
of Chemistry, University of Coimbra, 3004−535
Coimbra, Portugal
| | - Maciej J. Nowak
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668
Warsaw, Poland
| |
Collapse
|
46
|
Nunes CM, Lapinski L, Fausto R, Reva I. Near-IR laser generation of a high-energy conformer of L-alanine and the mechanism of its decay in a low-temperature nitrogen matrix. J Chem Phys 2013; 138:125101. [DOI: 10.1063/1.4795823] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
|
47
|
Bazsó G, Najbauer EE, Magyarfalvi G, Tarczay G. Near-Infrared Laser Induced Conformational Change of Alanine in Low-Temperature Matrixes and the Tunneling Lifetime of Its Conformer VI. J Phys Chem A 2013; 117:1952-62. [DOI: 10.1021/jp400196b] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gábor Bazsó
- Laboratory of Molecular
Spectroscopy, Institute of Chemistry, Eötvös University, P.O. Box 32, H-1518, Budapest 112, Hungary
| | - Eszter E. Najbauer
- Laboratory of Molecular
Spectroscopy, Institute of Chemistry, Eötvös University, P.O. Box 32, H-1518, Budapest 112, Hungary
| | - Gábor Magyarfalvi
- Laboratory of Molecular
Spectroscopy, Institute of Chemistry, Eötvös University, P.O. Box 32, H-1518, Budapest 112, Hungary
| | - György Tarczay
- Laboratory of Molecular
Spectroscopy, Institute of Chemistry, Eötvös University, P.O. Box 32, H-1518, Budapest 112, Hungary
| |
Collapse
|
48
|
Bazsó G, Magyarfalvi G, Tarczay G. Tunneling Lifetime of the ttc/VIp Conformer of Glycine in Low-Temperature Matrices. J Phys Chem A 2012; 116:10539-47. [DOI: 10.1021/jp3076436] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gábor Bazsó
- Laboratory of Molecular
Spectroscopy, Institute of
Chemistry, Eötvös University, P.O. Box 32, H-1518, Budapest 112, Hungary
| | - Gábor Magyarfalvi
- Laboratory of Molecular
Spectroscopy, Institute of
Chemistry, Eötvös University, P.O. Box 32, H-1518, Budapest 112, Hungary
| | - György Tarczay
- Laboratory of Molecular
Spectroscopy, Institute of
Chemistry, Eötvös University, P.O. Box 32, H-1518, Budapest 112, Hungary
| |
Collapse
|
49
|
Bazsó G, Magyarfalvi G, Tarczay G. Near-infrared laser induced conformational change and UV laser photolysis of glycine in low-temperature matrices: Observation of a short-lived conformer. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.04.066] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
50
|
Bazsó G, Góbi S, Tarczay G. Near-Infrared Radiation Induced Conformational Change and Hydrogen Atom Tunneling of 2-Chloropropionic Acid in Low-Temperature Ar Matrix. J Phys Chem A 2012; 116:4823-32. [DOI: 10.1021/jp212597y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gábor Bazsó
- Laboratory of Molecular
Spectroscopy, Institute of
Chemistry, Eötvös University, PO Box 32, H-1518, Budapest 112, Hungary
| | - Sándor Góbi
- Laboratory of Molecular
Spectroscopy, Institute of
Chemistry, Eötvös University, PO Box 32, H-1518, Budapest 112, Hungary
| | - György Tarczay
- Laboratory of Molecular
Spectroscopy, Institute of
Chemistry, Eötvös University, PO Box 32, H-1518, Budapest 112, Hungary
| |
Collapse
|