1
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Melli A, Barone V, Puzzarini C. Unveiling Bifunctional Hydrogen Bonding with the Help of Quantum Chemistry: The Imidazole-Water Adduct as Test Case. J Phys Chem A 2021; 125:2989-2998. [PMID: 33818109 PMCID: PMC8154618 DOI: 10.1021/acs.jpca.1c01679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/22/2021] [Indexed: 11/30/2022]
Abstract
The ubiquitous role of water and its amphiprotic nature call for a deeper insight into the physical-chemical properties of hydrogen-bonded complexes formed with building blocks of biomolecules. In this work, the semiexperimental (SE) approach combined with the template model (TM) protocol allowed the accurate determination of the equilibrium structure of two isomeric forms of the imidazole-water complex. In this procedure, the integration of experiment (thanks to a recent rotational spectroscopy investigation) and theory is exploited, also providing the means of assessing the reliability and accuracy of different quantum-chemical approaches. Overall, this study demonstrated the robustness of the combined SE-TM approach, which can provide accurate results using affordable quantum-chemical methods. Finally, the structural and energetic characteristics of these complexes have been examined in detail and compared with those of analogous heterocycle-water adducts, also exploiting energy decomposition analyses.
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Affiliation(s)
- Alessio Melli
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Vincenzo Barone
- Scuola
Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento
di Chimica “Giacomo Ciamician”, Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
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2
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Barone V, Puzzarini C. Looking for the bricks of the life in the interstellar medium: The fascinating world of astrochemistry. EPJ WEB OF CONFERENCES 2020. [DOI: 10.1051/epjconf/202024600021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The discovery in the interstellar medium of molecules showing a certain degree of complexity, and in particular those with a prebiotic character, has attracted great interest. A complex chemistry takes place in space, but the processes that lead to the production of molecular species are a matter of intense discussion, the knowledge still being at a rather primitive stage. Debate on the origins of interstellar molecules has been further stimulated by the identification of biomolecular building blocks, such as nucleobases and amino acids, in meteorites and comets. Since many of the molecules found in space play a role in the chemistry of life, the issue of their molecular genesis and evolution might be related to the profound question of the origin of life itself. Understanding the underlying chemical processes, including the production, reactions and destruction of compounds, requires the concomitant study of spectroscopy, gas-phase reactivity, and heterogeneous processes on dust-grains. The aim of this contribution is to provide a general view of a complex and multifaceted challenge, while focusing on the role played by molecular spectroscopy and quantum-chemical computations. In particular, the derivation of the molecular spectroscopic features and the investigation of gas-phase formation routes of prebiotic species in the interstellar medium are addressed from a computational point of view.
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3
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Ye H, Mendolicchio M, Kruse H, Puzzarini C, Biczysko M, Barone V. The challenging equilibrium structure of HSSH: Another success of the rotational spectroscopy / quantum chemistry synergism. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127933] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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4
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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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5
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A never-ending story in the sky: The secrets of chemical evolution. Phys Life Rev 2020; 32:59-94. [DOI: 10.1016/j.plrev.2019.07.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/26/2019] [Accepted: 07/02/2019] [Indexed: 01/13/2023]
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6
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Chen J, Zheng Y, Melli A, Spada L, Lu T, Feng G, Gou Q, Barone V, Puzzarini C. Theory meets experiment for elucidating the structure and stability of non-covalent complexes: water–amine interaction as a proof of concept. Phys Chem Chem Phys 2020; 22:5024-5032. [DOI: 10.1039/c9cp06768j] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A joint experimental-theoretical spectroscopic investigation has focused on a better understanding of the nature of weak, non-covalent interactions in amine-water model systems.
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Affiliation(s)
- Junhua Chen
- Department of Chemistry
- School of Chemistry and Chemical Engineering
- Chongqing University
- 401331 Chongqing
- China
| | - Yang Zheng
- Department of Chemistry
- School of Chemistry and Chemical Engineering
- Chongqing University
- 401331 Chongqing
- China
| | - Alessio Melli
- Department of Chemistry “Giacomo Ciamician”
- University of Bologna
- 40126 Bologna
- Italy
| | - Lorenzo Spada
- Department of Chemistry “Giacomo Ciamician”
- University of Bologna
- 40126 Bologna
- Italy
- Scuola Normale Superiore
| | - Tao Lu
- Department of Chemistry
- School of Chemistry and Chemical Engineering
- Chongqing University
- 401331 Chongqing
- China
| | - Gang Feng
- Department of Chemistry
- School of Chemistry and Chemical Engineering
- Chongqing University
- 401331 Chongqing
- China
| | - Qian Gou
- Department of Chemistry
- School of Chemistry and Chemical Engineering
- Chongqing University
- 401331 Chongqing
- China
| | | | - Cristina Puzzarini
- Department of Chemistry “Giacomo Ciamician”
- University of Bologna
- 40126 Bologna
- Italy
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7
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Alessandrini S, Barone V, Puzzarini C. Extension of the “Cheap” Composite Approach to Noncovalent Interactions: The jun-ChS Scheme. J Chem Theory Comput 2019; 16:988-1006. [DOI: 10.1021/acs.jctc.9b01037] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Silvia Alessandrini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
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8
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Puzzarini C, Bloino J, Tasinato N, Barone V. Accuracy and Interpretability: The Devil and the Holy Grail. New Routes across Old Boundaries in Computational Spectroscopy. Chem Rev 2019; 119:8131-8191. [DOI: 10.1021/acs.chemrev.9b00007] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”, Università di Bologna, Via F. Selmi 2, I-40126 Bologna, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- 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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9
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Li W, Spada L, Tasinato N, Rampino S, Evangelisti L, Gualandi A, Cozzi PG, Melandri S, Barone V, Puzzarini C. Theory Meets Experiment for Noncovalent Complexes: The Puzzling Case of Pnicogen Interactions. Angew Chem Int Ed Engl 2018; 57:13853-13857. [DOI: 10.1002/anie.201807751] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/20/2018] [Indexed: 01/29/2023]
Affiliation(s)
- Weixing Li
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Lorenzo Spada
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Nicola Tasinato
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Sergio Rampino
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Luca Evangelisti
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Andrea Gualandi
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Pier Giorgio Cozzi
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Sonia Melandri
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Vincenzo Barone
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
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10
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Li W, Spada L, Tasinato N, Rampino S, Evangelisti L, Gualandi A, Cozzi PG, Melandri S, Barone V, Puzzarini C. Theory Meets Experiment for Noncovalent Complexes: The Puzzling Case of Pnicogen Interactions. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807751] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Weixing Li
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Lorenzo Spada
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Nicola Tasinato
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Sergio Rampino
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Luca Evangelisti
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Andrea Gualandi
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Pier Giorgio Cozzi
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Sonia Melandri
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Vincenzo Barone
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
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11
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Gottschalk HC, Poblotzki A, Suhm MA, Al-Mogren MM, Antony J, Auer AA, Baptista L, Benoit DM, Bistoni G, Bohle F, Dahmani R, Firaha D, Grimme S, Hansen A, Harding ME, Hochlaf M, Holzer C, Jansen G, Klopper W, Kopp WA, Kröger LC, Leonhard K, Mouhib H, Neese F, Pereira MN, Ulusoy IS, Wuttke A, Mata RA. The furan microsolvation blind challenge for quantum chemical methods: First steps. J Chem Phys 2018; 148:014301. [DOI: 10.1063/1.5009011] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Hannes C. Gottschalk
- Institut für Physikalische Chemie, University of Göttingen, Tammannstrasse 6, D-37077 Göttingen, Germany
| | - Anja Poblotzki
- Institut für Physikalische Chemie, University of Göttingen, Tammannstrasse 6, D-37077 Göttingen, Germany
| | - Martin A. Suhm
- Institut für Physikalische Chemie, University of Göttingen, Tammannstrasse 6, D-37077 Göttingen, Germany
| | - Muneerah M. Al-Mogren
- Chemistry Department, Faculty of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Kingdom of Saudi Arabia
| | - Jens Antony
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstrasse 4, D-53115 Bonn, Germany
| | - Alexander A. Auer
- Department of Molecular Theory and Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Leonardo Baptista
- Departamento de Química e Ambiental, Universidade do Estado do Rio de Janeiro, Faculdade de Tecnologia, Resende, RJ, Brazil
| | - David M. Benoit
- E. A. Milne Centre for Astrophysics and G. W. Gray Centre for Advanced Materials Chemistry, School of Mathematical and Physical Sciences, University of Hull, Hull HU6 7RX, United Kingdom
| | - Giovanni Bistoni
- Department of Molecular Theory and Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Fabian Bohle
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstrasse 4, D-53115 Bonn, Germany
| | - Rahma Dahmani
- Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 Blvd. Descartes, 77454 Marne-La-Vallée, France
| | - Dzmitry Firaha
- Lehrstuhl für Technische Thermodynamik, RWTH Aachen University, D-52062 Aachen, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstrasse 4, D-53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstrasse 4, D-53115 Bonn, Germany
| | - Michael E. Harding
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Majdi Hochlaf
- Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 Blvd. Descartes, 77454 Marne-La-Vallée, France
| | - Christof Holzer
- Theoretical Chemistry Group, Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), P.O. Box 6980, D-76049 Karlsruhe, Germany
| | - Georg Jansen
- Fakultät für Chemie, Universität Duisburg-Essen, Universitätsstraße 5, D-45117 Essen, Germany
| | - Wim Klopper
- Theoretical Chemistry Group, Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), P.O. Box 6980, D-76049 Karlsruhe, Germany
| | - Wassja A. Kopp
- Lehrstuhl für Technische Thermodynamik, RWTH Aachen University, D-52062 Aachen, Germany
| | - Leif C. Kröger
- Lehrstuhl für Technische Thermodynamik, RWTH Aachen University, D-52062 Aachen, Germany
| | - Kai Leonhard
- Lehrstuhl für Technische Thermodynamik, RWTH Aachen University, D-52062 Aachen, Germany
| | - Halima Mouhib
- Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 Blvd. Descartes, 77454 Marne-La-Vallée, France
| | - Frank Neese
- Department of Molecular Theory and Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Max N. Pereira
- Departamento de Química e Ambiental, Universidade do Estado do Rio de Janeiro, Faculdade de Tecnologia, Resende, RJ, Brazil
| | - Inga S. Ulusoy
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824-1322, USA
| | - Axel Wuttke
- Institut für Physikalische Chemie, University of Göttingen, Tammannstrasse 6, D-37077 Göttingen, Germany
| | - Ricardo A. Mata
- Institut für Physikalische Chemie, University of Göttingen, Tammannstrasse 6, D-37077 Göttingen, Germany
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12
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Spada L, Tasinato N, Bosi G, Vazart F, Barone V, Puzzarini C. On the competition between weak O-H···F and C-H···F hydrogen bonds, in cooperation with C-H···O contacts, in the difluoromethane - tert-butyl alcohol cluster. JOURNAL OF MOLECULAR SPECTROSCOPY 2017; 337:90-95. [PMID: 28919646 PMCID: PMC5597040 DOI: 10.1016/j.jms.2017.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The 1:1 complex of tert-butyl alcohol with difluoromethane has been characterized by means of a joint experimental-computational investigation. Its rotational spectrum has been recorded by using a pulsed-jet Fourier-Transform microwave spectrometer. The experimental work has been guided and supported by accurate quantum-chemical calculations. In particular, the computed potential energy landscape pointed out the formation of three stable isomers. However, the very low interconversion barriers explain why only one isomer, showing one O-H···F and two C-H···O weak hydrogen bonds, has been experimentally characterized. The effect of the H → tert-butyl- group substitution has been analyzed from the comparison to the difluoromethane-water adduct.
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Affiliation(s)
- Lorenzo Spada
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa (Italy)
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa (Italy)
| | - Giulio Bosi
- Dipartimento di Chimica ″G. Ciamician″ dell'Università di Bologna, Via Selmi 2, I-40126 Bologna, Italy
| | - Fanny Vazart
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa (Italy)
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa (Italy)
| | - Cristina Puzzarini
- Dipartimento di Chimica ″G. Ciamician″ dell'Università di Bologna, Via Selmi 2, I-40126 Bologna, Italy
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13
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Alcolea Palafox M, Rastogi V, Singh S. Effect of the sulphur atom on geometry and spectra of the biomolecule 2-thiouracil and in the WC base pair 2-thiouridine-adenosine. Influence of water in the first hydration shell. J Biomol Struct Dyn 2017; 36:1225-1254. [DOI: 10.1080/07391102.2017.1318304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- M. Alcolea Palafox
- Facultad de Ciencias Químicas, Departamento de Química-Fisica1, Universidad Complutense, Madrid 28040, Spain
| | - V.K. Rastogi
- R.D. Foundation Group of Institutions, NH-58, Kadrabad, Modinagar, Ghaziabad, India
- Indian Spectroscopy Society, KC 68/1, Old Kavinagar, Ghaziabad 201 002, India
| | - S.P. Singh
- Department of Physics, Dr B R Ambedkar Govt Degree College, Mainpuri, India
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14
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Spada L, Tasinato N, Vazart F, Barone V, Caminati W, Puzzarini C. Noncovalent Interactions and Internal Dynamics in Pyridine-Ammonia: A Combined Quantum-Chemical and Microwave Spectroscopy Study. Chemistry 2017; 23:4876-4883. [DOI: 10.1002/chem.201606014] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Lorenzo Spada
- Scuola Normale Superiore; Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Nicola Tasinato
- Scuola Normale Superiore; Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Fanny Vazart
- Scuola Normale Superiore; Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Vincenzo Barone
- Scuola Normale Superiore; Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Walther Caminati
- Dipartimento di Chimica; “Giacomo Ciamician” dell'Università; Via Selmi 2 40126 Bologna Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica; “Giacomo Ciamician” dell'Università; Via Selmi 2 40126 Bologna Italy
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15
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Wincel H. Microhydration of Deprotonated Nucleobases. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1383-92. [PMID: 27178262 PMCID: PMC4942500 DOI: 10.1007/s13361-016-1411-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 04/17/2016] [Accepted: 04/19/2016] [Indexed: 06/05/2023]
Abstract
Hydration reactions of deprotonated nucleobases (uracil, thymine, 5-fluorouracil,2-thiouracil, cytosine, adenine, and hypoxanthine) produced by electrospray have been experimentally studied in the gas phase at 10 mbar using a pulsed ion-beam high-pressure mass spectrometer. The thermochemical data, ΔH (o) , ΔS (o) , and ΔG (o) , for the monohydrated systems were determined. The hydration enthalpies were found to be similar for all studied systems and varied between 39.4 and 44.8 kJ/mol. A linear correlation was found between water binding energies in the hydrated complexes and the corresponding acidities of the most acidic site of nucleobases. The structural and energetic aspects of the precursors for the hydrated complexes are discussed in conjunction with available literature data. Graphical Abstract ᅟ.
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Affiliation(s)
- Henryk Wincel
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224, Warsaw, Poland.
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16
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Fornaro T, Biczysko M, Bloino J, Barone V. Reliable vibrational wavenumbers for C=O and N-H stretchings of isolated and hydrogen-bonded nucleic acid bases. Phys Chem Chem Phys 2016; 18:8479-90. [PMID: 26940362 PMCID: PMC5612391 DOI: 10.1039/c5cp07386c] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The accurate prediction of vibrational wavenumbers for functional groups involved in hydrogen-bonded bridges remains an important challenge for computational spectroscopy. For the specific case of the C=O and N-H stretching modes of nucleobases and their oligomers, the paucity of experimental reference values needs to be compensated by reliable computational data, which require the use of approaches going beyond the standard harmonic oscillator model. Test computations performed for model systems (formamide, acetamide and their cyclic homodimers) in the framework of the second order vibrational perturbation theory (VPT2) confirmed that anharmonic corrections can be safely computed by global hybrid (GHF) or double hybrid (DHF) functionals, whereas the harmonic part is particularly challenging. As a matter of fact, GHFs perform quite poorly and even DHFs, while fully satisfactory for C=O stretchings, face unexpected difficulties when dealing with N-H stretchings. On these grounds, a linear regression for N-H stretchings has been obtained and validated for the heterodimers formed by 4-aminopyrimidine with 6-methyl-4-pyrimidinone (4APM-M4PMN) and by uracil with water. In view of the good performance of this computational model, we have built a training set of B2PLYP-D3/maug-cc-pVTZ harmonic wavenumbers (including linear regression scaling for N-H) for six-different uracil dimers and a validation set including 4APM-M4PMN, one of the most stable hydrogen-bonded adenine homodimers, as well as the adenine-uracil, adenine-thymine, guanine-cytosine and adenine-4-thiouracil heterodimers. Because of the unfavourable scaling of DHF harmonic wavenumbers with the dimensions of the investigated systems, we have optimized a linear regression of B3LYP-D3/N07D harmonic wavenumbers for the training set, which has been next checked against the validation set. This relatively cheap model, which shows very good agreement with experimental data (average errors of about 10 cm(-1)), paves the route toward a reliable analysis of spectroscopic signatures for larger polynucleotides.
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Affiliation(s)
- Teresa Fornaro
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
| | - Malgorzata Biczysko
- International Centre for Quantum and Molecular Structures, College of Sciences, Shanghai University, 99 Shangda Road, Shanghai, 200444, China.
| | - Julien Bloino
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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17
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Barone V, Biczysko M, Bloino J, Cimino P, Penocchio E, Puzzarini C. CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study. J Chem Theory Comput 2015; 11:4342-63. [PMID: 26575928 PMCID: PMC5905675 DOI: 10.1021/acs.jctc.5b00580] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC calculations.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore,
Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Malgorzata Biczysko
- Consiglio Nazionale delle
Ricerche, Istituto di Chimica dei Composti
OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area
della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa,
Italy
| | - Julien Bloino
- Consiglio Nazionale delle
Ricerche, Istituto di Chimica dei Composti
OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area
della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa,
Italy
| | - Paola Cimino
- Dipartimento di Scienze
Farmaceutiche, Università degli Studi di
Salerno, via Ponte don Melillo, I-84084 Fisciano
(SA), Italy
| | | | - Cristina Puzzarini
- Dipartimento di Chimica
“Giacomo Ciamician”,
Università di Bologna, Via Selmi 2, I-40126
Bologna, Italy
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18
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Fornaro T, Burini D, Biczysko M, Barone V. Hydrogen-Bonding Effects on Infrared Spectra from Anharmonic Computations: Uracil–Water Complexes and Uracil Dimers. J Phys Chem A 2015; 119:4224-36. [DOI: 10.1021/acs.jpca.5b01561] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Teresa Fornaro
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
| | - Diletta Burini
- Dipartimento
di Matematica e Informatica, Università di Perugia, INFN Sezione
Perugia Via Vanvitelli, I-106123 Perugia, Italy
| | - Malgorzata Biczysko
- Physics
Department, and International Centre for Quantum and Molecular Structures, Shanghai University, 99 Shangda Road, Shanghai, 200444 China
- Consiglio
Nazionale delle Ricerche, Istituto di Chimica dei Composti OrganoMetallici
(ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, I-56126 Pisa, Italy
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