1
|
León I, Montero R, Longarte A, Fernández JA. Revisiting the Spectroscopy of Water Dimer in Jets. J Phys Chem Lett 2021; 12:1316-1320. [PMID: 33535759 PMCID: PMC9157493 DOI: 10.1021/acs.jpclett.0c03001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
Laser spectroscopy in jets is one of the main sources of structural data from molecular aggregates. Consequently, numerous and sophisticated experimental systems have been developed to extract precise information, which is usually interpreted in the light of quantum mechanical calculations. However, even with the most sophisticated experiments, it is sometimes difficult to interpret the experimental results. We present here the example of water dimer and how after almost 70 years, the assignment of its mass-resolved IR spectrum still generates controversy that extends toward the mechanism of ionization of water aggregates.
Collapse
Affiliation(s)
- Iker León
- Grupo
de Espectroscopía Molecular (GEM), Edificio Quifima, Unidad Asociada CSIC, Universidad de Valladolid, 47005 Valladolid, Spain
| | - Raúl Montero
- SGIKER
Laser Facility, University of the Basque
Country (UPV/EHU), Barrio Sarriena s/n, Leioa 48940, Spain
| | - Asier Longarte
- Department
of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa 48940, Spain
| | - José A. Fernández
- Department
of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa 48940, Spain
| |
Collapse
|
2
|
Yamada Y, Goto Y, Fukuda Y, Ohba H, Nibu Y. Excited-State Dynamics Affected by Switching of a Hydrogen-Bond Network in Hydrated Aminopyrazine Clusters. J Phys Chem A 2020; 124:9963-9972. [PMID: 33206526 DOI: 10.1021/acs.jpca.0c08808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cluster structures of hydrated aminopyrazines, APz-(H2O)n=2-4, in supersonic jets have been investigated measuring the size-selected electronic and vibrational spectra and determined with the aid of quantum chemical calculations. The APz-(H2O)2 structure is assigned as a cyclic N1 type where a homodromic hydrogen-bond chain starts from the amino group and ends at the 1-position nitrogen atom of the pyrazine moiety, corresponding to 2-aminopyridine-(H2O)2. On the other hand, APz-(H2O)n=3,4 has a linear hydrogen-bond network ending at the 4-position one (N4), which resembles 3-aminopyridine-(H2O)n=3,4. The hydrogen-bond network switching from the N1 type to the N4 one provides the accompanying red shifts of the S1-S0 electronic transition that are entirely consistent with those of the corresponding 2-aminopyridine and 3-aminopyridine clusters and also shows the drastically strengthened fluorescence intensity of origin bands in the electronic spectrum. The significant change in the excited-state dynamics is explored by the fluorescence lifetime measurement and the time-dependent density functional theory (TD-DFT) calculation. It is suggested that the drastic elongation of fluorescence lifetimes is due to the change in the electronic structure of the first excited state from nπ* to ππ*, resulting in the decreasing spin-orbit coupling to T1 (ππ*).
Collapse
Affiliation(s)
- Yuji Yamada
- Department of Chemistry, Faculty of Science, Fukuoka University, Jonan-ku, Fukuoka 814-0180, Japan
| | - Yuji Goto
- Department of Chemistry, Faculty of Science, Fukuoka University, Jonan-ku, Fukuoka 814-0180, Japan
| | - Yuki Fukuda
- Department of Chemistry, Faculty of Science, Fukuoka University, Jonan-ku, Fukuoka 814-0180, Japan
| | - Hiroumi Ohba
- Department of Chemistry, Faculty of Science, Fukuoka University, Jonan-ku, Fukuoka 814-0180, Japan
| | - Yoshinori Nibu
- Department of Chemistry, Faculty of Science, Fukuoka University, Jonan-ku, Fukuoka 814-0180, Japan
| |
Collapse
|
3
|
Usabiaga I, Camiruaga A, Calabrese C, Veloso A, D'mello VC, Wategaonkar S, Fernández JA. Exploration of the theobromine-water dimer: comparison with DNA microhydration. Phys Chem Chem Phys 2020; 22:15759-15768. [PMID: 32627788 DOI: 10.1039/d0cp02397c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Understanding the molecular basis of the appearance of life on Earth is an exciting research field. Many factors may have influenced the election of the molecules used by living beings and evolution may have modified those original compounds. In an attempt to understand the role played by intermolecular interactions in the election of CGAT as the alphabet of life, we present here a thorough experimental and computational study on the interaction of theobromine with water. Theobromine is a xanthine derivative, structurally related to the nucleobases, and also present in many living beings. The experimental results demonstrate that the most stable isomer of theobromine-water was formed and detected in supersonic expansions. This isomer very well resembles the structure of the dimers between nucleobases and water, offering similar values of binding energy. A comparison between the results obtained for theobromine-water with those reported in the literature for monohydrates of nucleobases is also offered.
Collapse
Affiliation(s)
- Imanol Usabiaga
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), 48940, Leioa, Spain.
| | | | | | | | | | | | | |
Collapse
|
4
|
Pysanenko A, Kočišek J, Nachtigallová D, Poterya V, Fárník M. Clustering of Uracil Molecules on Ice Nanoparticles. J Phys Chem A 2017; 121:1069-1077. [PMID: 28098464 DOI: 10.1021/acs.jpca.6b12594] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We generate a molecular beam of ice nanoparticles (H2O)N, N̅ ≈ 130-220, which picks up several individual gas phase uracil (U) or 5-bromouracil (BrU) molecules. The mass spectra of the doped nanoparticles prove that the uracil and bromouracil molecules coagulate to clusters on the ice nanoparticles. Calculations of U and BrU monomers and dimers on the ice nanoparticles provide theoretical support for the cluster formation. The (U)mH+ and (BrU)mH+ intensity dependencies on m extracted from the mass spectra suggest a smaller tendency of BrU to coagulate compared to U, which is substantiated by a lower mobility of bromouracil on the ice surface. The hydrated Um·(H2O)nH+ series are also reported and discussed. On the basis of comparison with the previous experiments, we suggest that the observed propensity for aggregation on ice nanoparticles is a more general trend for biomolecules forming strong hydrogen bonds. This, together with their mobility, leads to their coagulation on ice nanoparticles which is an important aspect for astrochemistry.
Collapse
Affiliation(s)
- Andriy Pysanenko
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences , Dolejškova 3, 182 23 Prague, Czech Republic
| | - Jaroslav Kočišek
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences , Dolejškova 3, 182 23 Prague, Czech Republic
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences , Flemingovo nám. 2, 160610 Prague 6, Czech Republic
| | - Viktoriya Poterya
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences , Dolejškova 3, 182 23 Prague, Czech Republic
| | - Michal Fárník
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences , Dolejškova 3, 182 23 Prague, Czech Republic
| |
Collapse
|
5
|
Jumbri K, Micaelo NM, Abdul Rahman MB. Solvation free energies of nucleic acid bases in ionic liquids. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1227075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Khairulazhar Jumbri
- Faculty of Science, Department of Chemistry, Enzyme and Microbial Technology Research Centre (EMTech), Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Centre of Research in Ionic Liquids (CORILs), Universiti Teknologi PETRONAS, Seri Iskandar, Perak, Malaysia
| | | | - Mohd Basyaruddin Abdul Rahman
- Faculty of Science, Department of Chemistry, Enzyme and Microbial Technology Research Centre (EMTech), Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| |
Collapse
|
6
|
Rubovič P, Pysanenko A, Lengyel J, Nachtigallová D, Fárník M. Biomolecule Analogues 2-Hydroxypyridine and 2-Pyridone Base Pairing on Ice Nanoparticles. J Phys Chem A 2016; 120:4720-30. [PMID: 26785038 DOI: 10.1021/acs.jpca.5b11359] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ice nanoparticles (H2O)N, N ≈ 450 generated in a molecular beam experiment pick up individual gas phase molecules of 2-hydroxypyridine and 2-pyridone (HP) evaporated in a pickup cell at temperatures between 298 and 343 K. The mass spectra of the doped nanoparticles show evidence for generation of clusters of adsorbed molecules (HP)n up to n = 8. The clusters are ionized either by 70 eV electrons or by two photons at 315 nm (3.94 eV). The two ionization methods yield different spectra, and their comparison provides an insight into the neutral cluster composition, ionization and intracluster ion-molecule reactions, and cluster fragmentation. Quite a few molecules were reported not to coagulate on ice nanoparticles previously. The (HP)n cluster generation on ice nanoparticles represents the first evidence for coagulating of molecules and cluster formation on free ice nanoparticles. For comparison, we investigate the coagulation of HP molecules picked up on large clusters ArN, N ≈ 205, and also (HP)n clusters generated in supersonic expansions with Ar buffer gas. This comparison points to a propensity for the (HP)2 dimer generation on ice nanoparticles. This shows the feasibility of base pairing for model of biological molecules on free ice nanoparticles. This result is important for hypotheses of the biomolecule synthesis on ice grains in the space. We support our findings by theoretical calculations that show, among others, the HP dimer structures on water clusters.
Collapse
Affiliation(s)
- Peter Rubovič
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Andriy Pysanenko
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Jozef Lengyel
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Michal Fárník
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, 182 23 Prague, Czech Republic
| |
Collapse
|
7
|
Wu X, Karsili TNV, Domcke W. Excited-State Deactivation of Adenine by Electron-Driven Proton-Transfer Reactions in Adenine-Water Clusters: A Computational Study. Chemphyschem 2016; 17:1298-304. [DOI: 10.1002/cphc.201501154] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Xiuxiu Wu
- Department of Chemistry; Technische Universität München; 85747 Garching Germany
| | - Tolga N. V. Karsili
- Department of Chemistry; Technische Universität München; 85747 Garching Germany
| | - Wolfgang Domcke
- Department of Chemistry; Technische Universität München; 85747 Garching Germany
| |
Collapse
|
8
|
Pysanenko A, Habartová A, Svrčková P, Lengyel J, Poterya V, Roeselová M, Fedor J, Fárník M. Lack of Aggregation of Molecules on Ice Nanoparticles. J Phys Chem A 2015. [PMID: 26214577 DOI: 10.1021/acs.jpca.5b05368] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multiple molecules adsorbed on the surface of nanosized ice particles can either remain isolated or form aggregates, depending on their mobility. Such (non)aggregation may subsequently drive the outcome of chemical reactions that play an important role in atmospheric chemistry or astrochemistry. We present a molecular beam experiment in which the controlled number of guest molecules is deposited on the water and argon nanoparticles in a pickup chamber and their aggregation is studied mass spectrometrically. The studied molecules (HCl, CH3Cl, CH3CH2CH2Cl, C6H5Cl, CH4, and C6H6) form large aggregates on argon nanoparticles. On the other hand, no aggregation is observed on ice nanoparticles. Molecular simulations confirm the experimental results; they reveal a high degree of aggregation on the argon nanoparticles and show that the molecules remain mostly isolated on the water ice surface. This finding will influence the efficiency of ice grain-mediated synthesis (e.g., in outer space) and is also important for the cluster science community because it shows some limitations of pickup experiments on water clusters.
Collapse
|
9
|
Chaiwongwattana S, Sapunar M, Ponzi A, Decleva P, Došlić N. Exploration of Excited State Deactivation Pathways of Adenine Monohydrates. J Phys Chem A 2015; 119:10637-44. [DOI: 10.1021/acs.jpca.5b07496] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - Marin Sapunar
- Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Aurora Ponzi
- Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Piero Decleva
- Dipartimento di
Scienze Chimiche, Università di Trieste, 34127 Trieste, Italy
| | - Nađa Došlić
- Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| |
Collapse
|
10
|
Abstract
This chapter examines the structural characterisation of isolated neutral amino-acids and peptides. After a presentation of the experimental and theoretical state-of-the-art in the field, a review of the major structures and shaping interactions is presented. Special focus is made on conformationally-resolved studies which enable one to go beyond simple structural characterisation; probing flexibility and excited-state photophysics are given as examples of promising future directions.
Collapse
|
11
|
Förstel M, Neustetter M, Denifl S, Lelievre F, Hergenhahn U. A source for microhydrated biomolecules. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2015; 86:073103. [PMID: 26233352 DOI: 10.1063/1.4923247] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We describe the construction of an apparatus for the production of a molecular jet of microhydrated biomolecules. Our design uses a water reservoir producing water vapour, which then passes through a separate reservoir containing a vapour of a sublimated biomolecule. The mixture coexpands into a molecular beam apparatus through a conical nozzle. Mass spectra showing water-adenin and water-uracil complexes are shown as typical examples. Suitable expansion conditions are reached without the use of an inert carrier gas.
Collapse
Affiliation(s)
- M Förstel
- Max-Planck-Institut für Plasmaphysik, Wendelsteinstraße 1, 17491 Greifswald, Germany
| | - M Neustetter
- Institut für Ionenphysik und Angewandte Physik, Technikerstraße 25, 6020 Innsbruck, Austria
| | - S Denifl
- Institut für Ionenphysik und Angewandte Physik, Technikerstraße 25, 6020 Innsbruck, Austria
| | - F Lelievre
- Max-Planck-Institut für Plasmaphysik, Wendelsteinstraße 1, 17491 Greifswald, Germany
| | - U Hergenhahn
- Max-Planck-Institut für Plasmaphysik, Wendelsteinstraße 1, 17491 Greifswald, Germany
| |
Collapse
|
12
|
Stamm A, Weiler M, Brächer A, Schwing K, Gerhards M. A combined IR/IR and IR/UV spectroscopy study on the proton transfer coordinate of isolated 3-hydroxychromone in the electronic ground and excited state. Phys Chem Chem Phys 2014; 16:21795-803. [DOI: 10.1039/c4cp02546f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
13
|
Alam MJ, Ahmad S. Quantum chemical and spectroscopic investigations of 3-methyladenine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 128:653-664. [PMID: 24704482 DOI: 10.1016/j.saa.2014.02.170] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 02/17/2014] [Accepted: 02/21/2014] [Indexed: 06/03/2023]
Abstract
FTIR, FT-Raman and UV-Vis spectra of 3-methyladenine have been recorded and investigated using quantum chemical calculations. The molecular geometry and vibrational spectra of 3-methyladenine in the ground state are computed by using HF and DFT methods with 6-311G(d,p) basis set. VSCF, CC-VSCF methods based on 2MR-QFF and PT2 (Barone method) have been utilized for computing anharmonic vibrational frequencies. These methods yield results that are in remarkable agreement with the experimental data. The magnitudes of coupling between pair of modes have been also computed. Vibrational modes are assigned with the help of visual inspection of atomic displacements. The electronic spectra, simulated at TD-B3LYP/6-311++G(d,p) level of theory, are compared to the experiment. The global quantities: electronic chemical potential, electrophilicity index, chemical hardness and softness based on HOMO and LUMO energy eigenvalues are also computed at B3LYP/6-311++G(d,p) level of theory.
Collapse
Affiliation(s)
| | - Shabbir Ahmad
- Department of Physics, Aligarh Muslim University, Aligarh 202002, India.
| |
Collapse
|
14
|
Photochemistry of Nucleic Acid Bases and Their Thio- and Aza-Analogues in Solution. Top Curr Chem (Cham) 2014; 355:245-327. [DOI: 10.1007/128_2014_554] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
15
|
Lobsiger S, Sinha RK, Leutwyler S. Building Up Water-Wire Clusters: Isomer-Selective Ultraviolet and Infrared Spectra of Jet-Cooled 2-Aminopurine (H2O)n, n = 2 and 3. J Phys Chem B 2013; 117:12410-21. [DOI: 10.1021/jp407127c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simon Lobsiger
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, CH-3012 Bern, Switzerland
- Department
of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904-4319, United States
| | - Rajeev K. Sinha
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, CH-3012 Bern, Switzerland
- Department
of Atomic and Molecular Physics, Manipal University, Manipal-576104, Karnataka, India
| | - Samuel Leutwyler
- Department
of Chemistry and Biochemistry, University of Bern, Freiestrasse
3, CH-3012 Bern, Switzerland
| |
Collapse
|
16
|
Nosenko Y, Kunitski M, Stark T, Göbel M, Tarakeshwar P, Brutschy B. Vibrational signatures of Watson–Crick base pairing in adenine–thymine mimics. Phys Chem Chem Phys 2013; 15:11520-30. [DOI: 10.1039/c3cp50337b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
17
|
Sinha RK, Lobsiger S, Leutwyler S. Isomer- and Species-Selective Infrared Spectroscopy of Jet-Cooled 7H- and 9H-2-Aminopurine and 2-Aminopurine·H2O Clusters. J Phys Chem A 2012; 116:1129-36. [DOI: 10.1021/jp2077177] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Rajeev K. Sinha
- Department of Chemistry
and Biochemistry, University of Bern, Freiestrasse 3,
CH-3012 Bern, Switzerland
| | - Simon Lobsiger
- Department of Chemistry
and Biochemistry, University of Bern, Freiestrasse 3,
CH-3012 Bern, Switzerland
| | - Samuel Leutwyler
- Department of Chemistry
and Biochemistry, University of Bern, Freiestrasse 3,
CH-3012 Bern, Switzerland
| |
Collapse
|
18
|
Nosenko Y, Kunitski M, Stark T, Göbel M, Tarakeshwar P, Brutschy B. 4-Aminobenzimidazole–1-Methylthymine: A Model for Investigating Hoogsteen Base-Pairing between Adenine and Thymine. J Phys Chem A 2011; 115:11403-11. [DOI: 10.1021/jp205575w] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | - Pilarisetty Tarakeshwar
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | | |
Collapse
|
19
|
Araújo JMM, Ferreira R, Marrucho IM, Rebelo LPN. Solvation of Nucleobases in 1,3-Dialkylimidazolium Acetate Ionic Liquids: NMR Spectroscopy Insights into the Dissolution Mechanism. J Phys Chem B 2011; 115:10739-49. [DOI: 10.1021/jp203282k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- João M. M. Araújo
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2780-157 Oeiras, Portugal
| | - Rui Ferreira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2780-157 Oeiras, Portugal
| | - Isabel M. Marrucho
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2780-157 Oeiras, Portugal
| | - Luís P. N. Rebelo
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2780-157 Oeiras, Portugal
| |
Collapse
|
20
|
Nosenko Y, Kunitski M, Brutschy B. Specific photodynamics in thymine clusters: the role of hydrogen bonding. J Phys Chem A 2011; 115:9429-39. [PMID: 21648386 DOI: 10.1021/jp111373t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A photoionization detected IR study of thymine and 1-methylthymine monohydrates and of their homodimers was carried out to shed some light on the structure of the thymine clusters whose complex photodynamics has recently been the subject of great interest. Under supersonic jet conditions, thymine forms doubly H-bonded cyclic clusters with water or another base preferentially via its N1-H group and the adjacent carbonyl group. This hydrate is of no biological relevance since the N1-H group is the sugar binding site in thymidine. On the other hand, 1-methylthymine forms the donor H-bonds only via the N3-H group. Hence, properties of the N1-H and the N3-H bound clusters of thymine can be studied using thymine and 1-methylthymine molecules, respectively. No biologically relevant conformations of the dimers and hydrates of thymine, contrary to those of 1-methylthymine, are observed under supersonic jet conditions. Thymine homodimer, which extensively fragments upon UV ionization by formation of a protonated monomer, exhibits two N1-H···O═C2 hydrogen bonds. The photodynamics of hydrated thymines is found to be extremely sensitive to the hydration site: ranging from an ultrafast relaxation in less than 100 fs up to formation of a dark state with the lifetime on the microsecond time scale.
Collapse
Affiliation(s)
- Yevgeniy Nosenko
- Institut für Physikalische und Theoretische Chemie, Goethe-Universität, Max-von-Laue-str. 7, 60438 Frankfurt/Main, Germany
| | | | | |
Collapse
|
21
|
Kunitski M, Nosenko Y, Brutschy B. On the Nature of the Long-Lived “Dark” State of Isolated 1-Methylthymine. Chemphyschem 2011; 12:2024-30. [DOI: 10.1002/cphc.201000985] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 02/16/2011] [Indexed: 11/10/2022]
|