1
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Buczek A, Rzepiela K, Kupka T, Broda MA, Kar T. Uracil-water interaction revisited - in search of single H-bonded secondary minima. Phys Chem Chem Phys 2024; 26:5169-5182. [PMID: 38261334 DOI: 10.1039/d3cp04057g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Monohydrated uracil (UW) complexes are stabilized by both O⋯HO and NH⋯O hydrogen bonds (H-bonds), simultaneously participating in forming three stable cyclic structures. The role and contribution of these individual H-bonds (O⋯HO and NH⋯O) to the stability of the three UW complexes are still not understood, because of the technical problems in obtaining their optimized structures by standard geometry optimization. The present study explores a non-standard approach to identify three single H-bonded local minima structures without imaginary frequency using DFT (M06-2X, B3LYP and B3LYP-D3), MP2 and CCSD(T) theories and Dunning's correlation-consistent aug-cc-pVTZ basis set, in both vacuum and aqueous media (CPCM method). The results reveal that these new structures are very shallow secondary minima between two deep wells or next to a deep well of primary minima (double H-bonded structures) in the potential energy surface. The H-bond energy of these single H-bonded complexes is found to be less sensitive to a wide range (about 15-20 degrees) of O⋯HO and NH⋯O angles, and the linearity is preferred in the stable three single H-bonded structures. The technical method used to locate such a shallow minimum is described in detail and may be useful for identifying local minima in other cases where consecutive multiple H-bonded structures are global minima. Energy decomposition (using symmetry adapted perturbation theory (SAPT)) of interaction energy, electron redistribution, and relevant vibrational modes are discussed.
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Affiliation(s)
- Aneta Buczek
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland.
| | - Kacper Rzepiela
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland.
| | - Teobald Kupka
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland.
| | - Małgorzata A Broda
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland.
| | - Tapas Kar
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA.
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2
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Shin HK. Influence of a Methyl Group on the Unidirectional Flow of Vibrational Energy in an Adenine-Thymine Base Pair. J Phys Chem B 2023; 127:163-171. [PMID: 36594729 DOI: 10.1021/acs.jpcb.2c07416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The role of a methyl group in intramolecular vibrational energy redistribution (IVR) of the hydrogen-bonded adenine-thymine base pair has been studied using classical dynamics procedures. Energy transferred to the doorway bond thymine-NH from the vibrationally excited H2O(v) efficiently redistributes among various bonds of the base pair through vibration-to-vibration coupling, depositing a large fraction of the available energy in the terminal bond adenine-NH. On the other hand, the extent of energy flow in the reverse direction from the excited adenine-NH to thymine-NH is insignificant, indicating IVR in adenine-thymine resulting from the intermolecular interaction with a vibrationally excited H2O molecule, is direction-specific. The unidirectional flow is due to the coupling of stretch-torsion vibrations of a methyl group with conjugated bonds on the thymine ring, when the methyl rotor is present and is adjacent to the vibrationally excited thymine-NH. The insignificance of energy flow from the terminal-to-terminal bond in the reverse direction is attributed to the absence of a methyl group on the adenine moiety, even though the molecule has many CC and CN bonds coupled to their neighbors.
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Affiliation(s)
- H K Shin
- Department of Chemistry, University of Nevada, Reno, Nevada89557, United States
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3
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Intermolecular interactions in microhydrated ribonucleoside and deoxyribonucleoside: A computational study. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113422] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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4
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Cabezas C, Peña I, Caminati W. Rotational spectrum and internal dynamics of the hydrogen-bonded pyrrole-pyridine aromatic pair. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 249:119320. [PMID: 33360563 PMCID: PMC7610520 DOI: 10.1016/j.saa.2020.119320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/29/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
Non-covalent interactions determine the three-dimensional structure and activity of biological molecules. In this work, the pyrrole-pyridine complex considered as a model of the NH⋯N hydrogen-bonded Watson-Crick base pairs has been generated in a supersonic expansion and characterized by chirped pulse Fourier transform microwave spectroscopy. The analysis of the unconventional spectral pattern of the 1:1 pyrrole-pyridine adduct and its 13C and 15N isotopologues reveal a non-planar complex, with a bent NH⋯N hydrogen bond and large amplitude motion of the pyrrole subunit. The bent structure is likely to arise from the stablishment of the secondary CH⋯N interaction between pyridine and pyrrole moieties.
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Affiliation(s)
- Carlos Cabezas
- Instituto de Física Fundamental (IFF-CSIC), Group of Molecular Astrophysics, C/Serrano 121, 28006 Madrid, Spain.
| | - Isabel Peña
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, 47011 Valladolid, Spain.
| | - Walther Caminati
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, Bologna 40126, Italy
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5
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Ree J, Ko KC, Kim YH, Shin HK. Vibrational Energy Flow in the Uracil-H 2O Complexes. J Phys Chem B 2021; 125:874-882. [PMID: 33444503 DOI: 10.1021/acs.jpcb.0c10733] [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 the uracil-H2O complex, the vibrational energy initially stored in the OH(v = 1) stretch efficiently transfers to the first overtone-bending mode under a near-resonant condition. The relaxation of the overtone vibration redistributes its energy to uracil and the two hydrogen bonds in the intermolecular zone, which consists of the OH bond and the bonds between nearby C, N, O, and H atoms of uracil. The uracil NH bond and the hydrogen bond it formed with the H2O molecule, N-H···O, store the major portion of the energy released by the relaxing bending mode, thus forming a localized hot band in the intermolecular zone. Energy transfer to the bonds beyond the zone is found to be not significant. The excited uracil NH is found to transfer its energy to the bending mode, thus indicating that the hydrogen bond of N-H···O is the principal energy pathway in both directions. In the presence of efficient near-resonant energy transfer pathways, the time evolution of the centers of mass distance shows the phenomenon of beats. One global and two different local minima energy structures are considered. The results of energy transfer do not differ significantly, suggesting that the two hydrogen bonds in all three structures have similar contributions to the energy transfer.
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Affiliation(s)
- Jongbaik Ree
- Department of Chemistry Education, Chonnam National University, Gwangju 61186, Korea
| | - Kyoung Chul Ko
- Department of Chemistry Education, Chonnam National University, Gwangju 61186, Korea
| | - Yoo Hang Kim
- Department of Chemistry, Inha University, Incheon 22212, Korea
| | - Hyung K Shin
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, United States
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6
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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.
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Affiliation(s)
- Imanol Usabiaga
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), 48940, Leioa, Spain.
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7
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Puzzarini C, Spada L, Alessandrini S, Barone V. The challenge of non-covalent interactions: theory meets experiment for reconciling accuracy and interpretation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:343002. [PMID: 32203942 DOI: 10.1088/1361-648x/ab8253] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 03/23/2020] [Indexed: 06/10/2023]
Abstract
In the past decade, many gas-phase spectroscopic investigations have focused on the understanding of the nature of weak interactions in model systems. Despite the fact that non-covalent interactions play a key role in several biological and technological processes, their characterization and interpretation are still far from being satisfactory. In this connection, integrated experimental and computational investigations can play an invaluable role. Indeed, a number of different issues relevant to unraveling the properties of bulk or solvated systems can be addressed from experimental investigations on molecular complexes. Focusing on the interaction of biological model systems with solvent molecules (e.g., water), since the hydration of the biomolecules controls their structure and mechanism of action, the study of the molecular properties of hydrated systems containing a limited number of water molecules (microsolvation) is the basis for understanding the solvation process and how structure and reactivity vary from gas phase to solution. Although hydrogen bonding is probably the most widespread interaction in nature, other emerging classes, such as halogen, chalcogen and pnicogen interactions, have attracted much attention because of the role they play in different fields. Their understanding requires, first of all, the characterization of the directionality, strength, and nature of such interactions as well as a comprehensive analysis of their competition with other non-covalent bonds. In this review, it is shown how state-of-the-art quantum-chemical computations combined with rotational spectroscopy allow for fully characterizing intermolecular interactions taking place in molecular complexes from both structural and energetic points of view. The transition from bi-molecular complex to microsolvation and then to condensed phase is shortly addressed.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi 2, I-40126 Bologna, Italy
| | - Lorenzo Spada
- Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi 2, I-40126 Bologna, Italy
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Silvia Alessandrini
- Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi 2, I-40126 Bologna, Italy
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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8
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Gruet S, Pérez C, Steber AL, Schnell M. Where's water? The many binding sites of hydantoin. Phys Chem Chem Phys 2018; 20:5545-5552. [DOI: 10.1039/c7cp06518c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Investigation of an astrobiologically relevant prebiotic molecule, hydantoin, by broadband rotational spectroscopy and its plethora of water complexes.
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Affiliation(s)
- Sébastien Gruet
- Deutsches Elektronensychrotron
- D-22607 Hamburg
- Germany
- Institut für Physikalische Chemie
- Christian-Albrechts-Universität zu Kiel
| | - Cristóbal Pérez
- Deutsches Elektronensychrotron
- D-22607 Hamburg
- Germany
- Institut für Physikalische Chemie
- Christian-Albrechts-Universität zu Kiel
| | - Amanda L. Steber
- Deutsches Elektronensychrotron
- D-22607 Hamburg
- Germany
- Institut für Physikalische Chemie
- Christian-Albrechts-Universität zu Kiel
| | - Melanie Schnell
- Deutsches Elektronensychrotron
- D-22607 Hamburg
- Germany
- Institut für Physikalische Chemie
- Christian-Albrechts-Universität zu Kiel
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9
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Molchanov S, Gryff-Keller A. Solvation of Amides in DMSO and CDCl3: An Attempt at Quantitative DFT-Based Interpretation of 1H and 13C NMR Chemical Shifts. J Phys Chem A 2017; 121:9645-9653. [DOI: 10.1021/acs.jpca.7b10110] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sergey Molchanov
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Adam Gryff-Keller
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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10
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Intermolecular interaction in nucleobases and dimethyl sulfoxide/water molecules: A DFT, NBO, AIM and NCI analysis. J Mol Graph Model 2017; 78:48-60. [DOI: 10.1016/j.jmgm.2017.09.022] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 01/05/2023]
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11
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Kubica D, Molchanov S, Gryff-Keller A. Solvation of Uracil and Its Derivatives by DMSO: A DFT-Supported 1H NMR and 13C NMR Study. J Phys Chem A 2017; 121:1841-1848. [PMID: 28195476 DOI: 10.1021/acs.jpca.7b00144] [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
1H NMR and 13C NMR spectra of uracil, thymine, 5-hydroxymethyluracil, 5,6-dihydrouracil, and 5,6-dihydrothymine in DMSO-d6 solutions have been measured. Additionally, molecular structures as well as NMR parameters of these compounds and their various solvates have been calculated using DFT B3LYP/6-311++G(2d,p) PCM(DMSO) method. The analysis of the chemical shift data for these compounds has shown that, indeed, in DMSO solutions they occur as equilibrium mixtures of free molecules and solvates in which solute and solvent molecules are joined by NH···O or OH···O hydrogen bonds. The populations of particular species present in the solutions have been estimated. Moreover, it has been found that 5,6-dihydrothymine exists in DMSO solution preferentially in conformation with the methyl group occupying the pseudoequatorial position. This finding is based on the molecular energy calculations and remains in full agreement with the interpretation of NMR data and theoretical calculations of NMR parameters.
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Affiliation(s)
- Dominika Kubica
- COBRO - Packaging Research Institute , Konstancińska 11, 02-942 Warsaw, Poland
| | - Sergey Molchanov
- Faculty of Chemistry, Warsaw University of Technology , Noakowskiego 3, 00-664 Warsaw, Poland
| | - Adam Gryff-Keller
- Faculty of Chemistry, Warsaw University of Technology , Noakowskiego 3, 00-664 Warsaw, Poland
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12
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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.
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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
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13
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Effects of hydrogen bonding with H2O on the resonance Raman spectra of uracil and thymine. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2016.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Gou Q, Spada L, Vallejo-Lopez M, Melandri S, Lesarri A, Cocinero EJ, Caminati W. Intermolecular Hydrogen Bonding in 2-Fluoropyridine-Water. ChemistrySelect 2016. [DOI: 10.1002/slct.201600370] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Qian Gou
- College of Chemistry and Chemical Engineering; Chongqing University, No.55 Daxuecheng South Rd., Shapingba; Chongqing 401331 China
- Dipartimento di Chimica “G. Ciamician”; Università di Bologna; Via Selmi 2 I-40126 Bologna Italy
| | - Lorenzo Spada
- Dipartimento di Chimica “G. Ciamician”; Università di Bologna; Via Selmi 2 I-40126 Bologna Italy
| | - Montserrat Vallejo-Lopez
- Dipartimento di Chimica “G. Ciamician”; Università di Bologna; Via Selmi 2 I-40126 Bologna Italy
- Departamento de Química Física y Química Inorgánica; Facultad de Ciencias; Universidad de Valladolid; Paseo de Belén, 7 E-47011 Valladolid Spain
- Departamento de Química Física; Facultad de Ciencia y Tecnología; Universidad del País Vasco (UPV/EHU); Apartado 644 48080 Bilbao Spain
| | - Sonia Melandri
- Dipartimento di Chimica “G. Ciamician”; Università di Bologna; Via Selmi 2 I-40126 Bologna Italy
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica; Facultad de Ciencias; Universidad de Valladolid; Paseo de Belén, 7 E-47011 Valladolid Spain
| | - Emilio J. Cocinero
- Departamento de Química Física; Facultad de Ciencia y Tecnología; Universidad del País Vasco (UPV/EHU); Apartado 644 48080 Bilbao Spain
| | - Walther Caminati
- Dipartimento di Chimica “G. Ciamician”; Università di Bologna; Via Selmi 2 I-40126 Bologna Italy
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15
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Becucci M, Melandri S. High-Resolution Spectroscopic Studies of Complexes Formed by Medium-Size Organic Molecules. Chem Rev 2016; 116:5014-37. [DOI: 10.1021/acs.chemrev.5b00512] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maurizio Becucci
- Department
of Chemistry “Ugo Schiff” and European Laboratory for
Nonlinear Spectroscopy, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Firenze, Italy
| | - Sonia Melandri
- Department
of Chemistry “Giacomo Ciamician”, University of Bologna, Via Francesco Selmi 2, 40126 Bologna, Italy
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16
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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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17
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Ligare M, Siouri F, Bludsky O, Nachtigallová D, de Vries MS. Characterizing the dark state in thymine and uracil by double resonant spectroscopy and quantum computation. Phys Chem Chem Phys 2015; 17:24336-41. [DOI: 10.1039/c5cp03516c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Double resonant spectroscopy characterizes both grounds state and dark excited state of uracil and thymine.
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Affiliation(s)
- M. Ligare
- Department of Chemistry and Biochemistry
- University of California
- Santa Barbara
- USA
| | - F. Siouri
- Department of Chemistry and Biochemistry
- University of California
- Santa Barbara
- USA
| | - O. Bludsky
- Institute of Organic Chemistry and Biochemistry v.v.i
- AS CR
- 16610 Prague
- Czech Republic
| | - D. Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i
- AS CR
- 16610 Prague
- Czech Republic
| | - M. S. de Vries
- Department of Chemistry and Biochemistry
- University of California
- Santa Barbara
- USA
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18
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López JC, Sánchez R, Blanco S, Alonso JL. Microsolvation of 2-azetidinone: a model for the peptide group–water interactions. Phys Chem Chem Phys 2015; 17:2054-66. [DOI: 10.1039/c4cp04577g] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The geometries of the 2-azetidinone–(H2O)n clusters, determined by rotational spectroscopy, show the preference of water to interact with the CO group and the effects of cooperative hydrogen bonding.
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Affiliation(s)
- Juan C. López
- Grupo de Espectroscopía Molecular (GEM)
- Universidad de Valladolid
- Laboratorios de Espectroscopía y Bioespectroscopía
- Edificio Quifima
- 47011 Valladolid
| | - Raquel Sánchez
- Grupo de Espectroscopía Molecular (GEM)
- Universidad de Valladolid
- Laboratorios de Espectroscopía y Bioespectroscopía
- Edificio Quifima
- 47011 Valladolid
| | - Susana Blanco
- Grupo de Espectroscopía Molecular (GEM)
- Universidad de Valladolid
- Laboratorios de Espectroscopía y Bioespectroscopía
- Edificio Quifima
- 47011 Valladolid
| | - José L. Alonso
- Grupo de Espectroscopía Molecular (GEM)
- Universidad de Valladolid
- Laboratorios de Espectroscopía y Bioespectroscopía
- Edificio Quifima
- 47011 Valladolid
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19
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Puzzarini C, Biczysko M. Microsolvation of 2-thiouracil: molecular structure and spectroscopic parameters of the thiouracil-water complex. J Phys Chem A 2014; 119:5386-95. [PMID: 25474644 DOI: 10.1021/jp510511d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
State-of-the-art quantum-chemical computations have been employed to accurately determine the equilibrium structure and interaction energy of the 2-thiouracil-water complex, thus extending available reference data for biomolecule solvation patterns. The coupled-cluster level of theory in conjunction with a triple-ζ basis set has been considered together with extrapolation to the basis set limit, performed by employing second-order Møller-Plesset perturbation theory, and inclusion of core-correlation and diffuse-function corrections. On the basis of the comparison of experiment and theory for 2-thiouracil [ Puzzarini et al. Phys. Chem. Chem. Phys. 2013 , 15 , 16965 - 16975 ], structural changes due to water complexation have been pointed out. Molecular and spectroscopic properties of the 2-thiouracil-water complex have then been studied by means of the composite computational approach introduced for the molecular structure evaluation. Among the results achieved, we mention the accurate determination of the molecular dipole moment and of the spectroscopic parameters required for predicting the rotational spectrum.
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Affiliation(s)
- Cristina Puzzarini
- †Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via Selmi 2, I-40126 Bologna, Italy
| | - Malgorzata Biczysko
- ‡Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,§Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Consiglio Nazionale delle Ricerche, Via G. Moruzzi 1, I-56124 Pisa, Italy
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21
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Galvão TLP, Rocha IM, Ribeiro da Silva MDMC, Ribeiro da Silva MAV. Is Uracil Aromatic? The Enthalpies of Hydrogenation in the Gaseous and Crystalline Phases, and in Aqueous Solution, as Tools to Obtain an Answer. J Phys Chem A 2013; 117:5826-36. [DOI: 10.1021/jp404938u] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tiago L. P. Galvão
- Centro de Investigação
em Química,
Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007,
Portugal
| | - Inês M. Rocha
- Centro de Investigação
em Química,
Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007,
Portugal
| | - Maria D. M. C. Ribeiro da Silva
- Centro de Investigação
em Química,
Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007,
Portugal
| | - Manuel A. V. Ribeiro da Silva
- Centro de Investigação
em Química,
Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Rua do Campo Alegre, 687, P-4169-007,
Portugal
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22
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Abstract
Rotational spectroscopy is known to be a technique that is widely used to infer information on molecular structure and dynamics. In the last few decades, its role in the field of atmospheric and astrophysical investigations has rapidly grown. However, several are the challenging aspects in rotational spectroscopy, since the detection and analysis of spectra as well as interpretation of obtained results are not at all straightforward. Quantum chemistry has reached such an accuracy that can be used to disentangle these challenging situations by guiding the experimental investigation, assisting in the determination of the spectroscopic parameters, and extracting information of chemical interest. This perspective provides an overview of the theoretical background and computational requirements needed for the accurate evaluation of the spectroscopic parameters of relevance to rotational spectroscopy. The role of theory in guiding and supporting experiment is detailed through a few examples, and the interplay of experiment and theory is discussed in terms of the information of physical and chemical interest that can be derived.
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Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica Giacomo Ciamician, Università di Bologna, Via Selmi 2, I-40126 Bologna, Italy.
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23
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Hutchison C, Ganeev RA, Castillejo M, Lopez-Quintas I, Zaïr A, Weber SJ, McGrath F, Abdelrahman Z, Oppermann M, Martin M, Lei DY, Maier SA, Tisch JWG, Marangos JP. Comparison of high-order harmonic generation in uracil and thymine ablation plumes. Phys Chem Chem Phys 2013; 15:12308-13. [DOI: 10.1039/c3cp00004d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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24
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Écija P, Basterretxea FJ, Lesarri A, Millán J, Castaño F, Cocinero EJ. Single Hydration of the Peptide Bond: The Case of the Vince Lactam. J Phys Chem A 2012; 116:10099-106. [DOI: 10.1021/jp3072734] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Patricia Écija
- Departamento de Química
Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Campus
de Leioa, Ap. 644, E-48080 Bilbao, Spain
| | - Francisco J. Basterretxea
- Departamento de Química
Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Campus
de Leioa, Ap. 644, E-48080 Bilbao, Spain
| | - Alberto Lesarri
- Departamento de Química
Física y Química Inorgánica, Facultad de Ciencias, Universidad de Valladolid, E-47011 Valladolid, Spain
| | - Judith Millán
- Departamento de Química,
Facultad de Ciencias, Estudios Agroalimentarios e Informática, Universidad de La Rioja, E-26006 Logroño, Spain
| | - Fernando Castaño
- Departamento de Química
Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Campus
de Leioa, Ap. 644, E-48080 Bilbao, Spain
| | - Emilio J. Cocinero
- Departamento de Química
Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Campus
de Leioa, Ap. 644, E-48080 Bilbao, Spain
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25
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Chen J, Ai H, Zhao Y, Liu J. A theoretical prediction on the ground-state complexes bound by metal ions to thymine base isomers. J PHYS ORG CHEM 2011. [DOI: 10.1002/poc.1881] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Jinpeng Chen
- Shandong Provincial Key Laboratory of Fluorine Chemistry and Chemical Materials, School of Chemistry and Chemical Engineering; University of Jinan; Jinan City 250022 China
| | - Hongqi Ai
- Shandong Provincial Key Laboratory of Fluorine Chemistry and Chemical Materials, School of Chemistry and Chemical Engineering; University of Jinan; Jinan City 250022 China
| | - Yongping Zhao
- Shandong Provincial Key Laboratory of Fluorine Chemistry and Chemical Materials, School of Chemistry and Chemical Engineering; University of Jinan; Jinan City 250022 China
| | - Jingjing Liu
- Shandong Provincial Key Laboratory of Fluorine Chemistry and Chemical Materials, School of Chemistry and Chemical Engineering; University of Jinan; Jinan City 250022 China
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26
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Abstract
The term “hydrogen bond” has been used in the literature for nearly a century now. While its importance has been realized by physicists, chemists, biologists, and material scientists, there has been a continual debate about what this term means. This debate has intensified following some important experimental results, especially in the last decade, which questioned the basis of the traditional view on hydrogen bonding. Most important among them are the direct experimental evidence for a partial covalent nature and the observation of a blue-shift in stretching frequency following X–H···Y hydrogen bond formation (XH being the hydrogen bond donor and Y being the hydrogen bond acceptor). Considering the recent experimental and theoretical advances, we have proposed a new definition of the hydrogen bond, which emphasizes the need for evidence. A list of criteria has been provided, and these can be used as evidence for the hydrogen bond formation. This list is followed by some characteristics that are observed in typical hydrogen-bonding environments.
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