1
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Barone V. Quantum chemistry meets high-resolution spectroscopy for characterizing the molecular bricks of life in the gas-phase. Phys Chem Chem Phys 2024; 26:5802-5821. [PMID: 38099409 DOI: 10.1039/d3cp05169b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Computation of accurate geometrical structures and spectroscopic properties of large flexible molecules in the gas-phase is tackled at an affordable cost using a general exploration/exploitation strategy. The most distinctive feature of the approach is the careful selection of different quantum chemical models for energies, geometries and vibrational frequencies with the aim of maximizing the accuracy of the overall description while retaining a reasonable cost for all the steps. In particular, a composite wave-function method is used for energies, whereas a double-hybrid functional (with the addition of core-valence correlation) is employed for geometries and harmonic frequencies and a cheaper hybrid functional for anharmonic contributions. A thorough benchmark based on a wide range of prototypical molecular bricks of life shows that the proposed strategy is close to the accuracy of state-of-the-art composite wave-function methods, and is applicable to much larger systems. A freely available web-utility post-processes the geometries optimized by standard electronic structure codes paving the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules by experimentally-oriented researchers.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy.
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2
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Maciejczyk M, Pyrka M. Tautomeric equilibrium and spectroscopic properties of 8-azaguanine revealed by quantum chemistry methods. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:545-557. [PMID: 37507591 PMCID: PMC10618388 DOI: 10.1007/s00249-023-01672-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
8-azaguanine is a triazolopyrimidine nucleobase analog possessing potent antibacterial and antitumor activities, and it has been implicated as a lead molecule in cancer and malaria therapy. Its intrinsic fluorescence properties can be utilized for monitoring its interactions with biological polymers like proteins or nucleic acids. In order to better understand these interactions, it is important to know the tautomeric equilibrium of this compound. In this work, the tautomeric equilibrium of all natural neutral and anionic compound forms (except highly improbable imino-enol tautomers) as well as their methyl derivatives and ribosides was revealed by quantum chemistry methods. It was shown that, as expected, tautomers protonated at positions 1 and 9 dominate neutral forms both in gas phase and in aqueous solution. 8-azaguanines methylated at any position of the triazole ring are protonated at position 1. The computed vertical absorption and emission energies are in very good agreement with the experimental data. They confirm the validity of the assumption that replacing the proton with the methyl group does not significantly change the positions of absorption and fluorescence peaks.
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Affiliation(s)
- Maciej Maciejczyk
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, Oczapowskiego 4, 10-719, Olsztyn, Poland.
| | - Maciej Pyrka
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, Oczapowskiego 4, 10-719, Olsztyn, Poland
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3
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Barone V, Di Grande S, Lazzari F, Mendolicchio M. Accurate Structures and Spectroscopic Parameters of Guanine Tautomers in the Gas Phase by the Pisa Conventional and Explicitly Correlated Composite Schemes (PCS and PCS-F12). J Phys Chem A 2023; 127:6771-6778. [PMID: 37535450 PMCID: PMC10440789 DOI: 10.1021/acs.jpca.3c03999] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/21/2023] [Indexed: 08/05/2023]
Abstract
A general strategy for the accurate computation of structural and spectroscopic properties of biomolecule building blocks in the gas phase is proposed and validated for tautomeric equilibria. The main features of the new model are the inclusion of core-valence correlation in geometry optimizations by a double hybrid functional and the systematic use of wave-function composite methods in conjunction with cc-pVnZ-F12 basis sets with separate extrapolation of MP2 and post-MP2 contributions. The resulting Pisa composite scheme employing conventional (PCS) or explicitly correlated (PCS-F12) approaches is applied to the challenging problem of guanine tautomers in the gas phase. The results are in remarkable agreement with the experimental structures, relative stabilities, and spectroscopic signatures of different tautomers. The accuracy of the results obtained at reasonable cost by means of black-box parameter-free approaches paves the way toward systematic investigations of other molecular bricks of life also by non-specialists.
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Affiliation(s)
- Vincenzo Barone
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
| | - Silvia Di Grande
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
- Scuola
Superiore Meridionale, Largo San Marcellino 10, Napoli 80138, Italy
| | - Federico Lazzari
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, Pisa 56126, Italy
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4
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Moscato D, Gabas F, Conte R, Ceotto M. Vibrational spectroscopy simulation of solvation effects on a G-quadruplex. J Biomol Struct Dyn 2023; 41:14248-14258. [PMID: 36856120 DOI: 10.1080/07391102.2023.2180435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/07/2023] [Indexed: 03/02/2023]
Abstract
It is commonly believed that solvation effects on the vibrational properties of a solute are easily accounted for by simple rules of thumbs, that is, solvating a polar molecule in a polar medium has the only effect of red shifting all its spectroscopical features and, similarly, solvating a polar molecule in a nonpolar medium has the opposite effect. In this work, we use theoretical vibrational spectroscopy at quasi-classical and quantum approximate semiclassical level to gain atomistic insights about solvent-solute interactions for 2'-deoxyguanosine and the G-quadruplex. We employ the quasi-classical trajectory method to include full anharmonicity into our calculated spectra, and then introduce quantum nuclear effects by means of divide-and-conquer semiclassical spectroscopy calculations. Solvation is treated explicitly leading to a good reproducibility of the available experimental data and reliable predictions when an experimental reference is missing.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Davide Moscato
- Dipartimento di Chimica, Università degli Studi di Milano, Milano, Italy
| | - Fabio Gabas
- Dipartimento di Chimica, Università degli Studi di Milano, Milano, Italy
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, Milano, Italy
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5
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Molina F, Dezalay J, Soorkia S, Broquier M, Hochlaf M, Pino GA, Grégoire G. Cryogenic IR and UV spectroscopy of isomer-selected cytosine radical cation. Phys Chem Chem Phys 2022; 24:25182-25190. [DOI: 10.1039/d2cp03953b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
The UV photodissociation of cryogenic-cooled isomer-selected cytosine–silver complex leads to the production of cytosine radical cation without isomerization.
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Affiliation(s)
- Franco Molina
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d’Orsay, F-91405 Orsay, France
- INFIQC (CONICET-UNC), Ciudad Universitaria, Pabellón Argentina, 5000 Córdoba, Argentina
- Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
- Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
| | - Jordan Dezalay
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d’Orsay, F-91405 Orsay, France
| | - Satchin Soorkia
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d’Orsay, F-91405 Orsay, France
| | - Michel Broquier
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d’Orsay, F-91405 Orsay, France
| | - Majdi Hochlaf
- Université Gustave Eiffel, COSYS/IMSE, 5 Bd Descartes 77454, Champs sur Marne, France
| | - Gustavo Ariel Pino
- INFIQC (CONICET-UNC), Ciudad Universitaria, Pabellón Argentina, 5000 Córdoba, Argentina
- Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
| | - Gilles Grégoire
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d’Orsay, F-91405 Orsay, France
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6
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Saigusa H, Oyama A, Kitamura S, Asami H. Structural Characterization of 6-Thioguanosine and Its Monohydrate in the Gas Phase. J Phys Chem A 2021; 125:7217-7225. [PMID: 34433270 DOI: 10.1021/acs.jpca.1c05219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Detailed structural analysis of 6-thioguanosine (6TGs) in relation to its tautomerization and sugar conformation is performed in the gas phase using UV and IR spectroscopy combined with ab initio calculations. We have observed a thiol tautomer of 6TGs with its sugar moiety in the syn conformation that is stabilized by a strong intramolecular H-bonding between O5'H of the sugar and N3 atom of the guanine moiety. This observation is consistent with previous results for guanosine (Gs) in which the corresponding enol form is solely detected. We have also identified a monohydrate of 6TGs consisting of a thiol tautomer with the water linking guanine moiety and sugar OH group. It is demonstrated that hydration behavior of 6TGs is significantly different from that of Gs as a result of a weaker H-bonding ability of the thiol group.
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Affiliation(s)
- Hiroyuki Saigusa
- Graduate School for Bio- and Nanosystem Sciences, Yokohama City University, Yokohama 236-0027, Japan
| | - Ayumi Oyama
- Graduate School for Bio- and Nanosystem Sciences, Yokohama City University, Yokohama 236-0027, Japan
| | - Saki Kitamura
- Graduate School for Bio- and Nanosystem Sciences, Yokohama City University, Yokohama 236-0027, Japan
| | - Hiroya Asami
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan
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7
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Szatylowicz H, Stasyuk OA, Solà M, Krygowski TM. Aromaticity of nucleic acid bases. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1509] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Halina Szatylowicz
- Faculty of Chemistry Warsaw University of Technology, Noakowskiego 3, 00‐664 Warsaw Poland
| | - Olga A. Stasyuk
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, C/ Maria Aurélia Capmany 69, 17003 Girona Spain
| | - Miquel Solà
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, C/ Maria Aurélia Capmany 69, 17003 Girona Spain
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8
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Cruz-Ortiz AF, Molina FL, Maitre P, Pino GA. Guanine Tautomerism in Ionic Complexes with Ag + Investigated by IRMPD Spectroscopy and Mass Spectrometry. J Phys Chem B 2021; 125:7137-7146. [PMID: 34165305 DOI: 10.1021/acs.jpcb.1c03796] [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
In this paper, we present the IRMPD spectra of three ionic complexes between guanine (G) and silver (Ag+): [GAg-H2O]+, [GAgG]+ produced in the electrospray ionization source of the mass spectrometer, and [GAg]+ produced by collision induced dissociation of the [GAgG]+ complex. On the basis of the comparison of theoretically calculated IR spectra, we show that there are two isomers of each complex containing two different keto-amino (KA) tautomers of G (GKA(1,9) and GKA(1,7)). The observed isomers are the most stable structures in aqueous solution, and their experimentally estimated relative populations are in better agreement with the calculated relative populations in solution than in the gas phase, both at 298 K. We concluded that these observations suggest that GKA(1,9) and GKA(1,7) coexist in solution according to previous theoretical reports (Colominas, C.; et al. J. Am. Chem. Soc. 1996, 118, 6811). We were unable to find any evidence of the presence of the GEA(9), GKA(3,7), GKA(3,9), or GKA(7,9), whose relative stabilities in solution are strongly dependent on the theoretical method used to account for the solvent effect (Hanus, M.; et al. J. Am. Chem. Soc. 2003, 125, 7678).
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Affiliation(s)
- Andrés F Cruz-Ortiz
- INFIQC (CONICET-UNC), Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina.,Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina.,Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
| | - Franco L Molina
- INFIQC (CONICET-UNC), Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina.,Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina.,Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
| | - Philippe Maitre
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405, Orsay, France
| | - Gustavo A Pino
- INFIQC (CONICET-UNC), Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina.,Departamento de Fisicoquímica, Fac. de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina.,Centro Láser de Ciencias Moleculares, Universidad Nacional de Córdoba, Ciudad Universitaria, Pabellón Argentina, X5000HUA Córdoba, Argentina
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9
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Bull GD, Thompson KC. The oxidation of guanine by photoionized 2-aminopurine. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2021. [DOI: 10.1016/j.jpap.2021.100025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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10
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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.
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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.
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11
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Parshotam S, Joy M, Rossano-Tapia M, Mora-Gomez VA, Brown A. The thermochemical, structural, and spectroscopic analyses of the tautomers of sulfur and selenium modified emissive nucleobases. CAN J CHEM 2021. [DOI: 10.1139/cjc-2020-0294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, density functional theory (DFT) and time dependent density functional theory (TD-DFT) are used to investigate the stabilities and spectral properties [IR, UV–vis, and two-photon absorption (2PA)] of two sets of modified RNA nucleobase tautomers. The modifications introduce either a sulfur or selenium atom to form an isothiazolo[4,3-d]pyrimidine or isoselenazolo[4,3-d]pyrimidine heterocyclic core, respectively. The relative stabilities of both sets of modified tautomers determined with B3LYP/6-31++G(d,p) reveal that in water (with a polarizable continuum model), the 6-keto-2-amino tautomer of guanine and the rare 4-imino-2-keto tautomer of cytosine may be present at significant populations, whereas the 6-enol-2-amino tautomer of guanine is more common in the gas phase. The identification of these modified tautomers is possible due to the natural differences in their vibrational modes and hence IR spectra. Furthermore, the photophysical properties of both these sets of modified tautomers indicate that excitation and emission energies are shifted relative to their more abundant form in both one photon absorption and emission and 2PA spectra, as determined at the B3LYP/6-31++G(d,p) and CAM-B3LYP/aug-cc-pVDZ levels of theory, respectively. Even though the 2PA cross sections in water for all of the species are small (0.3–2.3 GM), the modified cytosine tautomer shows promise, as its cross section is larger than the more dominant form. The spectral separation between the dominant form and the tautomers of isoselenazole and isothiazole modified cytosine and guanine are relatively similar, suggesting both modifications could be useful in elucidating the tautomers from their more abundant counterparts.
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Affiliation(s)
- Shyam Parshotam
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Megan Joy
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Maria Rossano-Tapia
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - V. A. Mora-Gomez
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Alex Brown
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
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12
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Park Y, Shin S, Kang H. Recent Progress in the Manipulation of Molecules with DC Electric Fields. Acc Chem Res 2021; 54:323-331. [PMID: 33377765 DOI: 10.1021/acs.accounts.0c00609] [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 structure and reactivity of a molecule in the condensed phase are governed by its intermolecular interactions with the surrounding environment. The multipole expansion of each molecule in the condensed phase indicates that the intermolecular interactions are essentially electrostatic (e.g., ion-dipole, dipole-dipole, dipole-quadrupole, dipole-induced dipole). The electrostatic field is a fundamental language of intermolecular communications. Therefore, understanding the influence of the electrostatic field on a molecule, that is, the mechanisms by which an electrostatic field manipulates a molecule, from the perspective of molecular structure, energy states, and dynamics is indispensable for illustrating and, by extension, controlling the chemistry in molecular systems.In this Account, we describe the recent progress made in manipulation of molecular processes using an external DC electrostatic field. An electrostatic field with unprecedentedly high strength (≤4 × 108 V/m) was applied in a controlled manner across a molecular film sample using the ice film nanocapacitor method. This field strength is comparable in magnitude to that of weak intermolecular interactions such as van der Waals interactions in the condensed phases. The samples were prepared using a thin film growing technique in vacuum to obtain the desired chemically tailored molecular systems. The examples of prepared systems included small molecules and molecular clusters isolated in cryogenic Ar matrices, frozen molecular films in amorphous or crystalline phase, and interfaces of multilayered molecular films. The response of the molecules to the external field was monitored by reflection-absorption infrared spectroscopy. This approach allowed us to investigate a variety of molecular systems with various intermolecular strength and environments under the influence of strong electrostatic fields. The range of observed molecular behaviors includes the manipulation of molecular orientation, intramolecular dynamics, and proton transfer reactions as an example of stereodynamic control of chemical reactivity. These observations improve our understanding of molecular behaviors in strong electric fields and broaden our perspective on electrostatic manipulation of molecules. This information is also relevant to a variety of research topics in physical and biological sciences where electric fields play a role in molecular and biological functions.
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Affiliation(s)
- Youngwook Park
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Seoul 08826, South Korea
| | - Sunghwan Shin
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Seoul 08826, South Korea
| | - Heon Kang
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Seoul 08826, South Korea
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13
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Aieta C, Bertaina G, Micciarelli M, Ceotto M. Representing molecular ground and excited vibrational eigenstates with nuclear densities obtained from semiclassical initial value representation molecular dynamics. J Chem Phys 2020; 153:214117. [PMID: 33291909 DOI: 10.1063/5.0031391] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present in detail and validate an effective Monte Carlo approach for the calculation of the nuclear vibrational densities via integration of molecular eigenfunctions that we have preliminary employed to calculate the densities of the ground and the excited OH stretch vibrational states in the protonated glycine molecule [Aieta et al., Nat Commun 11, 4348 (2020)]. Here, we first validate and discuss in detail the features of the method on a benchmark water molecule. Then, we apply it to calculate on-the-fly the ab initio anharmonic nuclear densities in the correspondence of the fundamental transitions of NH and CH stretches in protonated glycine. We show how we can gain both qualitative and quantitative physical insight by inspection of different one-nucleus densities and assign a character to spectroscopic absorption peaks using the expansion of vibrational states in terms of harmonic basis functions. The visualization of the nuclear vibrations in a purely quantum picture allows us to observe and quantify the effects of anharmonicity on the molecular structure, also to exploit the effect of IR excitations on specific bonds or functional groups, beyond the harmonic approximation. We also calculate the quantum probability distribution of bond lengths, angles, and dihedrals of the molecule. Notably, we observe how in the case of one type of fundamental NH stretching, the typical harmonic nodal pattern is absent in the anharmonic distribution.
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Affiliation(s)
- Chiara Aieta
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milano, Italy
| | - Gianluca Bertaina
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milano, Italy
| | - Marco Micciarelli
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi 19, 20133 Milano, Italy
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14
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Gloaguen E, Mons M, Schwing K, Gerhards M. Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues. Chem Rev 2020; 120:12490-12562. [PMID: 33152238 DOI: 10.1021/acs.chemrev.0c00168] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.
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Affiliation(s)
- Eric Gloaguen
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Kirsten Schwing
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - Markus Gerhards
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
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15
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Gabas F, Conte R, Ceotto M. Semiclassical Vibrational Spectroscopy of Biological Molecules Using Force Fields. J Chem Theory Comput 2020; 16:3476-3485. [PMID: 32374992 PMCID: PMC7901649 DOI: 10.1021/acs.jctc.0c00127] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Semiclassical spectroscopy is a practical way to get an accurately approximate quantum
description of spectral features starting from ab initio molecular
dynamics simulations. The computational bottleneck for the method is represented by the
cost of ab initio potential, gradient, and Hessian matrix estimates.
This drawback is particularly severe for biological systems due to their unique
complexity and large dimensionality. The main goal of this manuscript is to demonstrate
that quantum dynamics and spectroscopy, at the level of semiclassical approximation, are
doable even for sizable biological systems. To this end, we investigate the possibility
of performing semiclassical spectroscopy simulations when ab initio
calculations are replaced by computationally cheaper force field evaluations. Both
polarizable (AMOEBABIO18) and nonpolarizable (AMBER14SB) force fields are tested.
Calculations of some particular vibrational frequencies of four nucleosides, i.e.,
uridine, thymidine, deoxyguanosine, and adenosine, show that ab initio
simulations are accurate and widely applicable. Conversely, simulations based on
AMBER14SB are limited to harmonic approximations, but those relying on AMOEBABIO18 yield
acceptable semiclassical values if the investigated conformation has been included in
the force field parametrization. The main conclusion is that AMOEBABIO18 may provide a
viable route to assist semiclassical spectroscopy in the study of large biological
molecules for which an ab initio approach is not computationally
affordable.
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Affiliation(s)
- Fabio Gabas
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
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16
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Nowak MJ, Reva I, Lopes Jesus AJ, Lapinski L, Fausto R. UV-promoted radical formation, and near-IR-induced and spontaneous conformational isomerization in monomeric 9-methylguanine isolated in low-temperature Ar matrices. Phys Chem Chem Phys 2019; 21:22857-22868. [PMID: 31599896 DOI: 10.1039/c9cp04487f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three low-energy isomers of 9-methylguanine, the amino-oxo (AO) form and two amino-hydroxy (AH1 and AH2) conformers, were trapped from the gas phase into low-temperature argon matrices. The AH1 and AH2 isomers, differing in the orientation of the OH group, were found to transform into each other upon excitation with near-IR light. The population of the AO form of the compound was not changed upon any near-IR irradiation of the matrix samples. Using monochromatic near-IR light, generated by a frequency-tunable laser source, it was possible to selectively induce the AH1 → AH2 or AH2 → AH1 conversion. Photoreversibility of this conformational transformation was then demonstrated. Exposure of matrix-isolated monomers of 9-methylguanine to broadband near-IR light also led to conformational conversions within the amino-hydroxy tautomeric form; the final stage of this process was always the same photostationary state independent of the initial ratio of AH1 and AH2 populations. Spontaneous conformational conversion, transforming the higher-energy AH2 form into the lower-energy AH1 isomer, was observed for matrix-isolated monomers of 9-methylguanine kept in the dark. The mechanism of this process must rely on quantum tunneling of the light hydrogen atom. Irradiation of matrix-isolated 9-methylguanine with UV laser light at λ = 288 or 285 nm led to a substantial consumption of the two AH forms, while the amount of AO isomer remained unchanged. On the other hand, a decrease in the population of the AO isomer occurred upon excitations at shorter wavelengths, λ = 280 or 275 nm. The spectral changes observed after UV-irradiation suggest the generation (and stabilization in the matrix) of a radical species, resulting from the photocleavage of the O-H or N1-H bonds, in the AH or AO isomer, respectively.
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Affiliation(s)
- Maciej J Nowak
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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17
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Gabas F, Di Liberto G, Ceotto M. Vibrational investigation of nucleobases by means of divide and conquer semiclassical dynamics. J Chem Phys 2019; 150:224107. [PMID: 31202241 DOI: 10.1063/1.5100503] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we report a computational study of the vibrational features of four different nucleobases employing the divide-and-conquer semiclassical initial value representation molecular dynamics method. Calculations are performed on uracil, cytosine, thymine, and adenine. Results show that the overall accuracy with respect to experiments is within 20 wavenumbers, regardless of the dimensionality of the nucleobase. Vibrational estimates are accurate even in the complex case of cytosine, where two relevant conformers are taken into account. These results are promising in the perspective of future studies on more complex systems, such as nucleotides or nucleobase pairs.
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Affiliation(s)
- Fabio Gabas
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Giovanni Di Liberto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
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18
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Karton A. Thermochemistry of Guanine Tautomers Re-Examined by Means of High-Level CCSD(T) Composite Ab Initio Methods. Aust J Chem 2019. [DOI: 10.1071/ch19276] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We obtained accurate gas-phase tautomerization energies for a set of 14 guanine tautomers by means of high-level thermochemical procedures approximating the CCSD(T) energy at the complete basis set (CBS) limit. For the five low-lying tautomers, we use the computationally demanding W1-F12 composite method for obtaining the tautomerization energies. The relative W1-F12 tautomerization enthalpies at 298K are: 0.00 (1), 2.37 (2), 2.63 (3), 4.03 (3′), and 14.31 (4) kJmol−1. Thus, as many as four tautomers are found within a small energy window of less than 1.0kcalmol−1 (1kcalmol−1=4.184kJmol−1). We use these highly accurate W1-F12 tautomerization energies to evaluate the performance of a wide range of lower-level composite ab initio procedures. The Gn composite procedures (G4, G4(MP2), G4(MP2)-6X, G3, G3B3, G3(MP2), and G3(MP2)B3) predict that the enol tautomer (3) is more stable than the keto tautomer (2) by amounts ranging from 0.36 (G4) to 1.28 (G3(MP2)) kJmol−1. We also find that an approximated CCSD(T)/CBS energy calculated as HF/jul-cc-pV{D,T}Z+CCSD/jul-cc-pVTZ+(T)/jul-cc-pVDZ results in a root-mean-square deviation (RMSD) of merely 0.11kJmol−1 relative to the W1-F12 reference values. We use this approximated CCSD(T)/CBS method to obtain the tautomerization energies of 14 guanine tautomers. The relative tautomerization enthalpies at 298K are: 0.00 (1), 2.20 (2), 2.51 (3), 4.06 (3′), 14.30 (4), 25.65 (5), 43.78 (4′), 53.50 (6′), 61.58 (6), 77.37 (7), 82.52 (8′), 86.02 (9), 100.70 (10), and 121.01 (8) kJmol−1. Using these tautomerization enthalpies, we evaluate the performance of standard and composite methods for the entire set of 14 guanine tautomers. The best-performing procedures emerge as (RMSDs are given in parentheses): G4(MP2)-6X (0.51), CCSD(T)+ΔMP2/CBS (0.52), and G4(MP2) (0.64kJmol−1). The worst performers are CCSD(T)/AVDZ (1.05), CBS-QB3 (1.24), and CBS-APNO (1.38kJmol−1).
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19
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Gate G, Szabla R, Haggmark MR, Šponer J, Sobolewski AL, de Vries MS. Photodynamics of alternative DNA base isoguanine. Phys Chem Chem Phys 2019; 21:13474-13485. [DOI: 10.1039/c9cp01622h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Pump–probe experiments and quantum-chemical simulations of UV-excited isoguanine elucidate its tautomer dependent photochemical properties.
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Affiliation(s)
- Gregory Gate
- Department of Chemistry and Biochemistry
- University of California
- Santa Barbara
- USA
| | - Rafał Szabla
- Institute of Physics
- Polish Academy of Sciences
- 02-668 Warsaw
- Poland
- Institute of Biophysics of the Czech Academy of Sciences
| | - Michael R. Haggmark
- Department of Chemistry and Biochemistry
- University of California
- Santa Barbara
- USA
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences
- 61265 Brno
- Czech Republic
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20
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Teschmit N, Horke DA, Küpper J. Spatially Separating the Conformers of a Dipeptide. Angew Chem Int Ed Engl 2018; 57:13775-13779. [PMID: 30106497 DOI: 10.1002/anie.201807646] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Indexed: 12/28/2022]
Abstract
Atomic-resolution-imaging approaches for single molecules, such as coherent X-ray diffraction at free-electron lasers, require the delivery of high-density beams of identical molecules. However, even very cold beams of biomolecules typically have multiple conformational states populated. We demonstrate the production of very cold (Trot ≈2.3 K) molecular beams of intact dipeptide molecules, which were then spatially separated into the individual populated conformational states. This is achieved using the combination of supersonic expansion laser-desorption vaporization with electrostatic deflection in strong inhomogeneous fields. This represents the first demonstration of a conformer-separated and rotationally cold molecular beam of a peptide, which enables the investigation of conformer-specific chemistry using inherently non-conformer-specific techniques. It furthermore represents a milestone toward the direct structural imaging of individual biological molecules with atomic resolution by ultrafast diffractive-imaging methods.
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Affiliation(s)
- Nicole Teschmit
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.,The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Department of Chemistry, Universität Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Daniel A Horke
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.,The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Jochen Küpper
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.,The Hamburg Center for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Department of Chemistry, Universität Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
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21
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Teschmit N, Horke DA, Küpper J. Räumliche Trennung der Konformere eines Dipeptids. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Nicole Teschmit
- Center for Free-Electron Laser ScienceDeutsches Elektronen-Synchrotron DESY Notkestraße 85 22607 Hamburg Deutschland
- The Hamburg Center for Ultrafast ImagingUniversität Hamburg Luruper Chaussee 149 22761 Hamburg Deutschland
- Fachbereich ChemieUniversität Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Deutschland
| | - Daniel A. Horke
- Center for Free-Electron Laser ScienceDeutsches Elektronen-Synchrotron DESY Notkestraße 85 22607 Hamburg Deutschland
- The Hamburg Center for Ultrafast ImagingUniversität Hamburg Luruper Chaussee 149 22761 Hamburg Deutschland
| | - Jochen Küpper
- Center for Free-Electron Laser ScienceDeutsches Elektronen-Synchrotron DESY Notkestraße 85 22607 Hamburg Deutschland
- The Hamburg Center for Ultrafast ImagingUniversität Hamburg Luruper Chaussee 149 22761 Hamburg Deutschland
- Fachbereich ChemieUniversität Hamburg Martin-Luther-King-Platz 6 20146 Hamburg Deutschland
- Fachbereich PhysikUniversität Hamburg Luruper Chaussee 149 22761 Hamburg Deutschland
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22
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Kong H, Zhang C, Sun Q, Yu X, Xie L, Wang L, Li L, Hu S, Ju H, He Y, Zhu J, Xu W. Nickel Adatoms Induced Tautomeric Dehydrogenation of Thymine Molecules on Au(111). ACS NANO 2018; 12:9033-9039. [PMID: 30130397 DOI: 10.1021/acsnano.8b02821] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tautomerization of nucleobases may induce base mismatches resulting in the abnormal disturbance of gene replication and expression, which has therefore attracted widespread interests in many disciplines. Metal atoms participating in a variety of important biological processes are found to be able to affect the nucleobase tautomerization as evidenced by many theoretical and spectroscopic studies. To get the real-space evidence and to unravel the underlying mechanism for the metal-induced tautomerization, especially from the keto form to the enol one, the interplay of high-resolution scanning tunneling microscopy imaging/manipulation and density functional theory (DFT) calculations has been employed. We present a process showing the Ni adatom-induced keto-enol tautomeric dehydrogenation of thymine molecules on Au(111). The key to making such a process feasible is the Ni atoms which greatly lower the energy barrier for the tautomerization from keto to enol form, which is rationalized by extensive DFT-based transition-state search calculations.
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Affiliation(s)
- Huihui Kong
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
- Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering , Nanjing University of Science and Technology , Xiaolingwei 200 , Nanjing 210094 , Jiangsu , P. R. China
| | - Chi Zhang
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
| | - Qiang Sun
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
| | - Xin Yu
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
| | - Lei Xie
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
| | - Likun Wang
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
| | - Lei Li
- Ministry of Education Key Laboratory of Green Preparation and Application for Functional Materials, School of Materials Science and Engineering , Hubei University , Wuhan 430062 , P. R. China
| | - Shanwei Hu
- National Synchrotron Radiation Laboratory , University of Science and Technology of China , Hefei 230029 , P. R. China
| | - Huanxin Ju
- National Synchrotron Radiation Laboratory , University of Science and Technology of China , Hefei 230029 , P. R. China
| | - Yunbin He
- Ministry of Education Key Laboratory of Green Preparation and Application for Functional Materials, School of Materials Science and Engineering , Hubei University , Wuhan 430062 , P. R. China
| | - Junfa Zhu
- National Synchrotron Radiation Laboratory , University of Science and Technology of China , Hefei 230029 , P. R. China
| | - Wei Xu
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering , Tongji University , Shanghai 201804 , P. R. China
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23
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Castrovilli MC, Bolognesi P, Bodo E, Mattioli G, Cartoni A, Avaldi L. An experimental and theoretical investigation of XPS and NEXAFS of 5-halouracils. Phys Chem Chem Phys 2018; 20:6657-6667. [PMID: 29457179 DOI: 10.1039/c8cp00026c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The C, N and O 1s excitation and ionization processes of 5X-uracil (X = F, Cl, Br, and I) were investigated using near edge X-ray absorption fine structure (NEXAFS) and X-ray photoemission (XPS) spectroscopies. This study aims at the fine assessment of the effects of the functionalization of uracil molecules by halogen atoms having different electronegativity and bound to the same molecular site. Two DFT-based approaches, which rely on different paradigms, have been used to simulate the experimental spectra and to assign the corresponding features. The analysis of the screening of the core holes of the different atoms via electronic charge density plots has turned out to be a useful tool to illustrate the competition between the partially aromatic and partially conjugate properties of this class of molecules.
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Affiliation(s)
- M C Castrovilli
- Istituto di Struttura della Materia-CNR, ISM-CNR, Area della Ricerca di Roma 1, CP10, 00015 Monterotondo Scalo, Italy.
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24
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Abstract
The response of nucleobases to UV radiation depends on structure in subtle ways, as revealed by gas-phase experiments.
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Affiliation(s)
- Samuel Boldissar
- Department of Chemistry and Biochemistry University of California Santa Barbara
- USA
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25
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Jun J, Han SY. Theoretical exploration of gas-phase conformers of proton-bound non-covalent heterodimers of guanine and cytosine rare tautomers: structures and energies. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2165-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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26
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Berenbeim JA, Boldissar S, Siouri FM, Gate G, Haggmark MR, Aboulache B, Cohen T, de Vries MS. Excited-State Dynamics of Isocytosine: A Hybrid Case of Canonical Nucleobase Photodynamics. J Phys Chem Lett 2017; 8:5184-5189. [PMID: 28985073 DOI: 10.1021/acs.jpclett.7b02032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present resonant two-photon ionization (R2PI) spectra of isocytosine (isoC) and pump-probe results on two of its tautomers. IsoC is one of a handful of alternative bases that have been proposed in scenarios of prebiotic chemistry. It is structurally similar to both cytosine (C) and guanine (G). We compare the excited-state dynamics with the Watson-Crick (WC) C and G tautomeric forms. These results suggest that the excited-state dynamics of WC form of G may primarily depend on the heterocyclic substructure of the pyrimidine moiety, which is chemically identical to isoC. For WC isoC we find a single excited-state decay with a rate of ∼1010 s-1, while the enol form has multiple decay rates, the fastest of which is 7 times slower than for WC isoC. The excited-state dynamics of isoC exhibits striking similarities with that of G, more so than with the photodynamics of C.
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Affiliation(s)
- Jacob A Berenbeim
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
| | - Samuel Boldissar
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
| | - Faady M Siouri
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
| | - Gregory Gate
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
| | - Michael R Haggmark
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
| | - Briana Aboulache
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
| | - Trevor Cohen
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
| | - Mattanjah S de Vries
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106-9510, United States
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27
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Abstract
Here we present the excited state dynamics of jet-cooled 6-thioguanine (6-TG), using resonance-enhanced multiphoton ionization (REMPI), IR-UV double resonance spectroscopy, and pump-probe spectroscopy in the nanosecond and picosecond time domains. We report data on two thiol tautomers, which appear to have different excited state dynamics. These decay to a dark state, possibly a triplet state, with rates depending on tautomer form and on excitation wavelength, with the fastest rate on the order of 1010 s-1. We also compare 6-TG with 9-enolguanine, for which we observed decay to a dark state with a 2 orders of magnitude smaller rate. At increased excitation energy (∼+500 cm-1) an additional pathway appears for the predominant thiol tautomer. Moreover, the excited state dynamics for 6-TG thiols is different from that recently predicted for thiones.
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Affiliation(s)
- Faady M Siouri
- Department of Chemistry and Biochemistry, University of California, Santa Barbara , Santa Barbara, California 93016-9510, United States
| | - Samuel Boldissar
- Department of Chemistry and Biochemistry, University of California, Santa Barbara , Santa Barbara, California 93016-9510, United States
| | - Jacob A Berenbeim
- Department of Chemistry and Biochemistry, University of California, Santa Barbara , Santa Barbara, California 93016-9510, United States
| | - Mattanjah S de Vries
- Department of Chemistry and Biochemistry, University of California, Santa Barbara , Santa Barbara, California 93016-9510, United States
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28
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Tolosa S, Sánchez J, Sansón J, Hidalgo A. Steered molecular dynamic simulations of the tautomeric equilibria in solution of DNA bases. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.03.118] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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29
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Min A, Ahn A, Moon CJ, Lee JH, Seong YG, Kim SK, Choi MY. Conformational structures of jet-cooled acetaminophen-water clusters: a gas phase spectroscopic and computational study. Phys Chem Chem Phys 2017; 19:4840-4848. [PMID: 28134364 DOI: 10.1039/c6cp06863d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Jet-cooled acetaminophen (AAP)-water clusters, AAP-(H2O)1, were investigated by mass-selected resonant two-photon ionization (R2PI), ultraviolet-ultraviolet hole-burning (UV-UV HB), infrared-dip (IR-dip), and infrared-ultraviolet hole-burning (IR-UV HB) spectroscopy. Each syn- and anti-AAP rotamer has three distinctive binding sites (-OH, >CO, and >NH) for a water molecule, thus 6 different AAP-(H2O)1 conformers are expected to exist in the molecular beam. The origin bands of the AAP(OH)-(H2O)1 and AAP(CO)-(H2O)1 conformers (including their syn- and anti-conformers) in the R2PI spectrum are shifted to red and blue compared to those of the AAP monomer, respectively. These frequency shifts upon complexation between a water molecule and a specific binding site of AAP are also predicted by theoretical calculations. The spectral assignments of the origin bands in the R2PI spectra and the IR vibrational bands in the IR-dip spectra of the four lowest-energy conformers of AAP-(H2O)1, [syn- and anti-AAP(OH)-(H2O)1 and syn- and anti-AAP(CO)-(H2O)1], are aided by ab initio and time-dependent density functional theory (TDDFT) calculations. Further investigation of the IR-dip spectra has revealed a hydrogen-bonded NH stretching mode, supporting the presence of the syn-AAP(NH)-(H2O)1 conformer. Moreover, by employing IR-UV HB spectroscopy, we have reconfirmed the existence of the syn-AAP(NH)-(H2O)1 conformer, which happened to be buried underneath the broad background contributed by the AAP(OH)-(H2O)1 conformers. These observations have led us to conclude that all of the possible conformers of AAP-(H2O)1 have been found in this study.
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Affiliation(s)
- Ahreum Min
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Ahreum Ahn
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Cheol Joo Moon
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Ji Hoon Lee
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Yeon Guk Seong
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Myong Yong Choi
- Department of Chemistry (BK21+) and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Republic of Korea.
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30
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Wu RR, Chen Y, Rodgers MT. Mechanisms and energetics for N-glycosidic bond cleavage of protonated 2'-deoxyguanosine and guanosine. Phys Chem Chem Phys 2016; 18:2968-80. [PMID: 26740232 DOI: 10.1039/c5cp05738h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Experimental and theoretical investigations suggest that hydrolysis of N-glycosidic bonds generally involves a concerted SN2 or a stepwise SN1 mechanism. While theoretical investigations have provided estimates for the intrinsic activation energies associated with N-glycosidic bond cleavage reactions, experimental measurements to validate the theoretical studies remain elusive. Here we report experimental investigations for N-glycosidic bond cleavage of the protonated guanine nucleosides, [dGuo+H](+) and [Guo+H](+), using threshold collision-induced dissociation (TCID) techniques. Two major dissociation pathways involving N-glycosidic bond cleavage, resulting in production of protonated guanine or the elimination of neutral guanine are observed in competition for both [dGuo+H](+) and [Guo+H](+). The detailed mechanistic pathways for the N-glycosidic bond cleavage reactions observed are mapped via electronic structure calculations. Excellent agreement between the measured and B3LYP calculated activation energies and reaction enthalpies for N-glycosidic bond cleavage of [dGuo+H](+) and [Guo+H](+) in the gas phase is found indicating that these dissociation pathways involve stepwise E1 mechanisms in analogy to the SN1 mechanisms that occur in the condensed phase. In contrast, MP2 is found to significantly overestimate the activation energies and slightly overestimate the reaction enthalpies. The 2'-hydroxyl substituent is found to stabilize the N-glycosidic bond such that [Guo+H](+) requires ∼25 kJ mol(-1) more than [dGuo+H](+) to activate the glycosidic bond.
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Affiliation(s)
- R R Wu
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - Yu Chen
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.
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31
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Brice JT, Liang T, Raston PL, McCoy AB, Douberly GE. Infrared Stark and Zeeman spectroscopy of OH–CO: The entrance channel complex along the OH + CO → trans-HOCO reaction pathway. J Chem Phys 2016; 145:124310. [DOI: 10.1063/1.4963226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Joseph T. Brice
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Tao Liang
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Paul L. Raston
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia 22807, USA
| | - Anne B. McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Gary E. Douberly
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
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32
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Chen YL, Wu DY, Tian ZQ. Theoretical Investigation on the Substituent Effect of Halogen Atoms at the C8 Position of Adenine: Relative Stability, Vibrational Frequencies, and Raman Spectra of Tautomers. J Phys Chem A 2016; 120:4049-58. [PMID: 27243104 DOI: 10.1021/acs.jpca.6b03604] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have theoretically investigated the substituent effect of adenine at the C8 position with a substituent X = H, F, Cl, and Br by using the density functional theory (DFT) at the B3LYP/6-311+G(d, p) level. The aim is to study the substituent effect of halogen atoms on the relative stability, vibrational frequencies, and solvation effect of tautomers. Our calculated results show that for substituted adenine molecules the N9H8X tautomer to be the most stable structure in gas phase at the present theoretical level. Here N9H8X denotes the hydrogen atom binds to the N9 position of imidazole ring and X denotes H, F, Cl, and Br atoms. The influence of the induced attraction of the fluorine substituent is significantly larger than chlorine and bromine ones. The halogen substituent effect has a significant influence on changes of vibrational frequencies and Raman intensities.
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Affiliation(s)
- Yan-Li Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
| | - De-Yin Wu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
| | - Zhong-Qun Tian
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University , Xiamen 361005, China
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33
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Asami H, Tokugawa M, Masaki Y, Ishiuchi SI, Gloaguen E, Seio K, Saigusa H, Fujii M, Sekine M, Mons M. Effective Strategy for Conformer-Selective Detection of Short-Lived Excited State Species: Application to the IR Spectroscopy of the N1H Keto Tautomer of Guanine. J Phys Chem A 2016; 120:2179-84. [DOI: 10.1021/acs.jpca.6b01194] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hiroya Asami
- Department
of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-J2-12, Nagatsuta-cho Midori, Yokohama 226-8501, Japan
- LIDYL,
CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Munefumi Tokugawa
- Department
of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-J2-12, Nagatsuta-cho Midori, Yokohama 226-8501, Japan
| | - Yoshiaki Masaki
- Department
of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-J2-12, Nagatsuta-cho Midori, Yokohama 226-8501, Japan
| | - Shun-ichi Ishiuchi
- Laboratory
for Chemistry and Life Science, Tokyo Institute of Technology, 4259-R1-15,
Nagatsuta-cho Midori, Yokohama 226-8503, Japan
| | - Eric Gloaguen
- LIDYL,
CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Kohji Seio
- Department
of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-J2-12, Nagatsuta-cho Midori, Yokohama 226-8501, Japan
| | - Hiroyuki Saigusa
- Graduate
School of Bio- and Nanosystem Science, Yokohama City University, Yokohama 236-0027, Japan
| | - Masaaki Fujii
- Laboratory
for Chemistry and Life Science, Tokyo Institute of Technology, 4259-R1-15,
Nagatsuta-cho Midori, Yokohama 226-8503, Japan
| | - Mitsuo Sekine
- Department
of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-J2-12, Nagatsuta-cho Midori, Yokohama 226-8501, Japan
| | - Michel Mons
- LIDYL,
CEA, CNRS, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
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34
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Improta R, Santoro F, Blancafort L. Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases. Chem Rev 2016; 116:3540-93. [PMID: 26928320 DOI: 10.1021/acs.chemrev.5b00444] [Citation(s) in RCA: 332] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.
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Affiliation(s)
- Roberto Improta
- Istituto di Biostrutture Biommagini (IBB-CNR), CNR-Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134, Napoli, Italy
| | - Fabrizio Santoro
- Area della Ricerca di Pisa, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), CNR-Consiglio Nazionale delle Ricerche , Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi , 17071 Girona, Spain
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35
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Ciesielski A, El Garah M, Masiero S, Samorì P. Self-assembly of Natural and Unnatural Nucleobases at Surfaces and Interfaces. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:83-95. [PMID: 26488679 DOI: 10.1002/smll.201501017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/19/2015] [Indexed: 06/05/2023]
Abstract
The self-assembly of small organic molecules interacting via non-covalent forces is a viable approach towards the construction of highly ordered nanostructured materials. Among various molecular components, natural and unnatural nucleobases can undergo non-covalent self-association to form supramolecular architectures with ad hoc structural motifs. Such structures, when decorated with appropriate electrically/optically active units, can be used as scaffolds to locate such units in pre-determined positions in 2D on a surface, thereby paving the way towards a wide range of applications, e.g., in optoelectronics. This review discusses some of the basic concepts of the supramolecular engineering of natural and unnatural nucleobases and derivatives thereof as well as self-assembly processes on conductive solid substrates, as investigated by scanning tunnelling microscopy in ultra-high vacuum and at the solid/liquid interface. By unravelling the structure and dynamics of these self-assembled architectures with a sub-nanometer resolution, a greater control over the formation of increasingly sophisticated functional systems is achieved. The ability to understand and predict how nucleobases interact, both among themselves as well as with other molecules, is extremely important, since it provides access to ever more complex DNA- and RNA-based nanostructures and nanomaterials as key components in nanomechanical devices.
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Affiliation(s)
- Artur Ciesielski
- ISIS & icFRC, Université de Strasbourg & CNRS, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Mohamed El Garah
- ISIS & icFRC, Université de Strasbourg & CNRS, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Stefano Masiero
- Dipartimento di Chimica "G. Caimician", Alma Mater Studiorum - Università di Bologna, v. San Giacomo, 11 - 40126, Bologna, Italy
| | - Paolo Samorì
- ISIS & icFRC, Université de Strasbourg & CNRS, 8 allée Gaspard Monge, 67000, Strasbourg, France
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36
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Abstract
IR spectroscopy of nucleobases in the gas phase reflects simultaneous advances in both experimental and computational techniques. Important properties, such as excited state dynamics, depend in subtle ways on structure variations, which can be followed by their infrared signatures. Isomer specific spectroscopy is a particularly powerful tool for studying the effects of nucleobase tautomeric form and base pair hydrogen-bonding patterns.
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Affiliation(s)
- Mattanjah S de Vries
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA,
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37
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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.
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38
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Stasyuk OA, Szatylowicz H, Krygowski TM. Aromaticity of H-bonded and metal complexes of guanine tautomers. Struct Chem 2015. [DOI: 10.1007/s11224-015-0605-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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39
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Hanke K, Kaufmann M, Schwaab G, Havenith M, Wolke CT, Gorlova O, Johnson MA, Kar BP, Sander W, Sanchez-Garcia E. Understanding the ionic liquid [NC4111][NTf2] from individual building blocks: an IR-spectroscopic study. Phys Chem Chem Phys 2015; 17:8518-29. [PMID: 25749545 DOI: 10.1039/c5cp00116a] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study explores the interactions underlying the IR spectra of the ionic liquid [NC4111][NTf2] and its deuterated isotopomer [d9-NC4111][NTf2] by first isolating the spectra of charged ionic building blocks using mass-selective CIVP spectroscopy and then following the evolution of these bands upon sequential assembly of the ionic constituents. The spectra of the (1,1) and (2,2) neutral ion pairs are recorded using superfluid helium droplets as well as a solid neon matrix, while those of the larger charged aggregates are again obtained with CIVP. In general, the cluster spectra are similar to that of the bulk, with the (2,2) system displaying the closest resemblance. Analysis of the polarization-dependent band intensities of the neutral ion pairs in liquid droplets as a function of external electric field yields dipole moments of the neutral aggregates. This information allows a coarse assessment of the packing structure of the neutral pairs to be antiparallel at 0.37 K, in contrast to the parallel arrangement found for the assembly of small, high-dipole neutral molecules with large rotational constants (e.g., HCN). The role of an extra anion or cation attached to both the (1,1) and the (2,2) ion pairs to form the charged clusters is discussed in the context of an additional remote, more unfavorable binding site intrinsic to the nature of the charged IL clusters and as such not anticipated in the bulk phase. Whereas for the anion itself only the lowest energy trans conformer was observed, the higher clusters showed an additional population of the cis conformer. The interactions are found to be consistent with a minimal role of hydrogen bonding.
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Affiliation(s)
- Kenny Hanke
- Department of Physical Chemistry II, Ruhr-University Bochum, D-44801 Bochum, Germany.
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40
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Complexation of Allyl Radicals and Hydrochloric Acid in Helium Nanodroplets. J Phys Chem A 2015; 119:1007-12. [DOI: 10.1021/jp511708s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Grimme S, Bauer CA. Automated quantum chemistry based molecular dynamics simulations of electron ionization induced fragmentations of the nucleobases Uracil, Thymine, Cytosine, and Guanine. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:125-140. [PMID: 26307693 DOI: 10.1255/ejms.1313] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The gas-phase decomposition pathways of electron ionization (EI)-induced radical cations of the nucleobases uracil, thymine, cytosine, and guanine are investigated by means of mixed quantum-classical molecular dynamics. No preconceived fragmentation channels are used in the calculations. The results compare well to a plethora of experimental and theoretical data for these important biomolecules. With our combined stochastic and dynamic approach, one can access in an unbiased way the energetically available decomposition mechanisms. Additionally, we are able to separate the EI mass spectra of different tautomers of cytosine and guanine. Our method (previously termed quantum chemistry electron ionization mass spectra) reproduces free nucleobase experimental mass spectra well and provides detailed mechanistic in-sight into high-energy unimolecular decomposition processes.
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Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich- Wilhelms-Universität Bonn, Beringstr. 4, D-53115, Bonn, Germany. - bonn.de
| | - Christopher Alexander Bauer
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich-Wilhelms-Universität Bonn, Beringstr. 4, D-53115, Bonn, Germany.
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42
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Chandraboss VL, Karthikeyan B, Senthilvelan S. Experimental and first-principles investigation of the adsorption and entrapping of guanine with SiO2 clusters of sol–gel silicate material for understanding DNA photodamage. Phys Chem Chem Phys 2015; 17:12100-14. [DOI: 10.1039/c5cp00451a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A sol–gel silicate matrix containing entrapped guanine was prepared. The SiO2 matrix provides UVA protection by reducing the light penetration to the entrapped guanine molecules.
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43
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Leavitt CM, Moore KB, Raston PL, Agarwal J, Moody GH, Shirley CC, Schaefer HF, Douberly GE. Liquid Hot NAGMA Cooled to 0.4 K: Benchmark Thermochemistry of a Gas-Phase Peptide. J Phys Chem A 2014; 118:9692-700. [DOI: 10.1021/jp5092653] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Paul L. Raston
- Department
of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia
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44
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Zhang J, He Y, Freund WM, Kong W. Electron Diffraction of Superfluid Helium Droplets. J Phys Chem Lett 2014; 5:1801-1805. [PMID: 24920997 PMCID: PMC4048102 DOI: 10.1021/jz5006829] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 05/07/2014] [Indexed: 06/03/2023]
Abstract
We present experimental results of electron diffraction of superfluid helium droplets and droplets doped with phthalocyanine gallium chloride and discuss the possibility of performing the same experiment with a laser aligned sample. The diffraction profile of pure droplets demonstrates dependence on the nozzle temperature, that is, on the average size of the droplets. Larger clusters demonstrate faster decay with increasing momentum transfer, whereas smaller clusters converge to isolated gas phase molecules at source temperatures of 18 K and higher. Electron diffraction of doped droplets shows similar modified molecular scattering intensity as that of the corresponding gas phase molecules. On the basis of fittings of the scattering profile, the number of remaining helium atoms of the doped droplets is estimated to be on the order of hundreds. This result offers guidance in assessing the possibility of electron diffraction from laser aligned molecules doped in superfluid helium droplets.
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Affiliation(s)
| | | | | | - Wei Kong
- E-mail: . Phone: 541-737-6714. Fax: 541-737-2062
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45
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Leavitt CM, Moradi CP, Stanton JF, Douberly GE. Communication: Helium nanodroplet isolation and rovibrational spectroscopy of hydroxymethylene. J Chem Phys 2014; 140:171102. [DOI: 10.1063/1.4874850] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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46
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Krygowski TM, Szatylowicz H, Stasyuk OA, Dominikowska J, Palusiak M. Aromaticity from the viewpoint of molecular geometry: application to planar systems. Chem Rev 2014; 114:6383-422. [PMID: 24779633 DOI: 10.1021/cr400252h] [Citation(s) in RCA: 366] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Tadeusz M Krygowski
- Department of Chemistry, Warsaw University , Pasteura 1, 02-093 Warsaw, Poland
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47
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Kong H, Sun Q, Wang L, Tan Q, Zhang C, Sheng K, Xu W. Atomic-scale investigation on the facilitation and inhibition of guanine tautomerization at Au(111) surface. ACS NANO 2014; 8:1804-1808. [PMID: 24476199 DOI: 10.1021/nn4061918] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nucleobase tautomerization might induce mismatch of base pairing. Metals, involved in many important biophysical processes, have been theoretically proven to be capable of affecting tautomeric equilibria and stabilities of different nucleobase tautomers. However, direct real-space evidence on demonstrating different nucleobase tautomers and further revealing the effect of metals on their tautomerization at surfaces has not been reported to date. From the interplay of high-resolution STM imaging and DFT calculations, we show for the first time that tautomerization of guanine from G/9H to G/7H is facilitated on Au(111) by heating, whereas such tautomerization process is effectively inhibited by introducing Ni atoms due to its preferential coordination at the N7 site of G/9H. These findings may help to elucidate possible influence of metals on nucleobase tautomerization and provide from a molecular level some theoretical basis on metal-based drug design.
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Affiliation(s)
- Huihui Kong
- College of Materials Science and Engineering, Key Laboratory for Advanced Civil Engineering Materials (Ministry of Education), Tongji University , Caoan Road 4800, Shanghai 201804, People's Republic of China
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48
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Nieto P, Letzner M, Endres T, Schwaab G, Havenith M. IR spectroscopy of pyridine–water structures in helium nanodroplets. Phys Chem Chem Phys 2014; 16:8384-91. [DOI: 10.1039/c3cp55284e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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49
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Ovchinnikov VA, Sundholm D. Coupled-cluster and density functional theory studies of the electronic 0–0 transitions of the DNA bases. Phys Chem Chem Phys 2014; 16:6931-41. [DOI: 10.1039/c3cp55080j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The 0–0 transitions of the electronic excitation spectra of the lowest tautomers of the four nucleotide (DNA) bases have been studied using linear-response approximate coupled-cluster singles and doubles (CC2) calculations.
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Affiliation(s)
- Vasily A. Ovchinnikov
- University of Helsinki
- 00014 Helsinki, Finland
- Emanuel Institute of Biochemical Physics RAS
- 119334 Moscow, Russia
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50
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Chandraboss VL, Karthikeyan B, Senthilvelan S. Experimental and first-principles study of guanine adsorption on ZnO clusters. Phys Chem Chem Phys 2014; 16:23461-75. [DOI: 10.1039/c4cp03274h] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electronic structure for interaction of guanine with Zn2O2 cluster and the most preferred N1-site to form a stable G–Zn2O2 model.
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Affiliation(s)
- V. L. Chandraboss
- Department of Chemistry
- Annamalai University
- Annamalai Nagar 608 002, India
| | - B. Karthikeyan
- Department of Chemistry
- Annamalai University
- Annamalai Nagar 608 002, India
| | - S. Senthilvelan
- Department of Chemistry
- Annamalai University
- Annamalai Nagar 608 002, India
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