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Symmetry/Asymmetry of the NHN Hydrogen Bond in Protonated 1,8-Bis(dimethylamino)naphthalene. Symmetry (Basel) 2020. [DOI: 10.3390/sym12111924] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Experimental and theoretical results are presented based on vibrational spectra and motional dynamics of 1,8-bis(dimethylamino)naphthalene (DMAN) and its protonated forms (DMANH+ and the DMANH+ HSO4− complex). The studies of these compounds have been performed in the gas phase and solid-state. Spectroscopic investigations were carried out by infrared spectroscopy (IR), Raman, and incoherent inelastic neutron scattering (IINS) experimental methods. Density functional theory (DFT) and Car–Parrinello molecular dynamics (CPMD) methods were applied to support our experimental findings. The fundamental investigations of hydrogen bridge vibrations were accomplished on the basis of isotopic substitutions (NH → ND). Special attention was paid to the bridged proton dynamics in the DMANH+ complex, which was found to be affected by interactions with the HSO4− anion.
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Gregorovič A, Apih T, Žagar V, Seliger J. 14N NQR spectroscopy reveals the proton position in N–H⋯N bonds: a case study with proton sponges. Phys Chem Chem Phys 2019; 21:306-313. [DOI: 10.1039/c8cp05183f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The position of the proton in intramolecular N–H⋯N hydrogen bonds has been determined to a high accuracy with 14N Nuclear Quadrupole Resonance (NQR) spectroscopy.
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Affiliation(s)
| | - Tomaž Apih
- Institute “Jožef Stefan”
- 1000 Ljubljana
- Slovenia
| | | | - Janez Seliger
- Institute “Jožef Stefan”
- 1000 Ljubljana
- Slovenia
- Faculty of Mathematics and Physics
- University of Ljubljana
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3
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Athokpam B, Ramesh SG, McKenzie RH. Effect of hydrogen bonding on the infrared absorption intensity of OH stretch vibrations. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2017.03.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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4
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Reimers JR, McKemmish LK, McKenzie RH, Hush NS. A unified diabatic description for electron transfer reactions, isomerization reactions, proton transfer reactions, and aromaticity. Phys Chem Chem Phys 2015; 17:24598-617. [DOI: 10.1039/c5cp02236c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A way is found for describing general chemical reactions using diabatic multi-state and “twin-state” models. (Image adapted with permission from https://www.flickr.com/photos/cybaea/64638988/).
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Affiliation(s)
- Jeffrey R. Reimers
- International Centre for Quantum and Molecular Structure
- College of Sciences
- Shanghai University
- Shanghai 200444
- China
| | - Laura K. McKemmish
- Department of Physics and Astronomy
- University College London
- London WC1E 6BT
- UK
- School of Chemistry
| | - Ross H. McKenzie
- School of Mathematics and Physics
- The University of Queensland
- Australia
| | - Noel S. Hush
- School of Chemistry
- The University of Sydney
- Sydney
- Australia
- School of Molecular Biosciences
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5
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Deshlahra P, Carr RT, Chai SH, Iglesia E. Mechanistic Details and Reactivity Descriptors in Oxidation and Acid Catalysis of Methanol. ACS Catal 2014. [DOI: 10.1021/cs501599y] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Prashant Deshlahra
- Department of Chemical Engineering, University of California at Berkeley and ‡Chemical Sciences Division, E.O. Lawrence
Berkeley National Laboratory Berkeley, Berkeley, California 94720, United States
| | - Robert T. Carr
- Department of Chemical Engineering, University of California at Berkeley and ‡Chemical Sciences Division, E.O. Lawrence
Berkeley National Laboratory Berkeley, Berkeley, California 94720, United States
| | - Song-Hai Chai
- Department of Chemical Engineering, University of California at Berkeley and ‡Chemical Sciences Division, E.O. Lawrence
Berkeley National Laboratory Berkeley, Berkeley, California 94720, United States
| | - Enrique Iglesia
- Department of Chemical Engineering, University of California at Berkeley and ‡Chemical Sciences Division, E.O. Lawrence
Berkeley National Laboratory Berkeley, Berkeley, California 94720, United States
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6
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Madsen AØ, Hoser AA. SHADE3server: a streamlined approach to estimate H-atom anisotropic displacement parameters using periodicab initiocalculations or experimental information. J Appl Crystallogr 2014. [DOI: 10.1107/s1600576714022973] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A major update of theSHADEserver (http://shade.ki.ku.dk) is presented. In addition to all of the previous options for estimating H-atom anisotropic displacement parameters (ADPs) that were offered bySHADE2, the newest version offers two new methods. The first method combines the original translation–libration–screw analysis with input from periodicab initiocalculations. The second method allows the user to input experimental information from spectroscopic measurements or from neutron diffraction experiments on related structures and utilize this information to evaluate ADPs of H atoms. Tools are provided to set up theab initiocalculations and to derive the internal motion from the calculations. The new server was tested on a range of compounds where neutron diffraction data were available. In most cases, the results are significantly better than previous estimates, and for strong hydrogen bonds in proton sponges, theab initiocalculations become crucial.
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Smedarchina Z, Siebrand W, Fernández-Ramos A. Tunneling splitting in double-proton transfer: Direct diagonalization results for porphycene. J Chem Phys 2014; 141:174312. [DOI: 10.1063/1.4900717] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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8
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McKenzie RH, Bekker C, Athokpam B, Ramesh SG. Effect of quantum nuclear motion on hydrogen bonding. J Chem Phys 2014; 140:174508. [DOI: 10.1063/1.4873352] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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Kögel JF, Oelkers B, Kovačević B, Sundermeyer J. A New Synthetic Pathway to the Second and Third Generation of Superbasic Bisphosphazene Proton Sponges: The Run for the Best Chelating Ligand for a Proton. J Am Chem Soc 2013; 135:17768-74. [DOI: 10.1021/ja409760z] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Julius F. Kögel
- Fachbereich Chemie, Philipps-Universität Marburg Hans-Meerwein-Straße, 35032 Marburg, Germany
| | - Benjamin Oelkers
- Fachbereich Chemie, Philipps-Universität Marburg Hans-Meerwein-Straße, 35032 Marburg, Germany
| | - Borislav Kovačević
- Quantum Chemistry
Group, Rudjer Bošković Institute, Bijenička c. 54, 10000 Zagreb-HR, Croatia
| | - Jörg Sundermeyer
- Fachbereich Chemie, Philipps-Universität Marburg Hans-Meerwein-Straße, 35032 Marburg, Germany
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Yang B, Wu RR, Berden G, Oomens J, Rodgers MT. Infrared multiple photon dissociation action spectroscopy of proton-bound dimers of cytosine and modified cytosines: effects of modifications on gas-phase conformations. J Phys Chem B 2013; 117:14191-201. [PMID: 24151932 DOI: 10.1021/jp405105w] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gas-phase structures of proton-bound dimers of cytosine and modified cytosines and their d6-analogues generated by electrospray ionization are probed via infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical electronic structure calculations. The modified cytosines examined include the 5-methyl-, 5-fluoro-, and 5-bromo-substituted species. IRMPD action spectra of seven proton-bound dimers exhibit both similar and distinctive spectral features over the range of ∼2600-3700 cm(-1). The IRMPD spectra of all of these proton-bound dimers are relatively simple, but exhibit obvious shifts in the positions of several bands that correlate with the properties of the substituent. The measured IRMPD spectra are compared to linear IR spectra calculated for the stable low-energy tautomeric conformations, determined at the B3LYP/6-31G* level of theory, to identify the conformations accessed in the experiments. Comparison of the measured IRMPD and calculated IR spectra indicates that only a single conformation, the ground-state structure, is accessed for all proton-bound homodimers, whereas the ground-state and a small population of the first-excited tautomeric conformations are accessed for all proton-bound heterodimers. In all cases, three hydrogen-bonding interactions in which the nucleobases are aligned in an antiparallel fashion analogous to that of the DNA i-motif are responsible for stabilizing the base pairing. Thus, base modifications such as 5-methyl- and 5-halo-substitution of cytosine should not alter the structure of the DNA i-motif.
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Affiliation(s)
- Bo Yang
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
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11
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Ding XH, Li YH, Wang S, Li XA, Huang W. Proton-transfer supramolecular salts based on proton sponge 2,2′-dipyridylamine. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.07.056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Masuda Y, Mori Y, Sakurai K. Effects of Counterion and Solvent on Proton Location and Proton Transfer Dynamics of N–H···N Hydrogen Bond of Monoprotonated 1,8-Bis(dimethylamino)naphthalene. J Phys Chem A 2013; 117:10576-87. [DOI: 10.1021/jp4061297] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuichi Masuda
- Department of Chemistry,
Faculty of Science, Ochanomizu University, Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Yukie Mori
- Department of Chemistry,
Faculty of Science, Ochanomizu University, Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Kazumi Sakurai
- Department of Chemistry,
Faculty of Science, Ochanomizu University, Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
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13
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Horbatenko Y, Vyboishchikov SF. Dynamic Behavior of Hydrogen in Transition Metal Bis(silyl) Hydride Complexes. Organometallics 2013. [DOI: 10.1021/om300981y] [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)
- Yevhen Horbatenko
- Institut de Química
Computacional i Catàlisi
and Departament de Química, Campus de Montilivi, Universitat de Girona, 17071, Girona, Spain
| | - Sergei F. Vyboishchikov
- Institut de Química
Computacional i Catàlisi
and Departament de Química, Campus de Montilivi, Universitat de Girona, 17071, Girona, Spain
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14
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Pozharskii AF, Ozeryanskii VA. Proton Sponges and Hydrogen Transfer Phenomena. MENDELEEV COMMUNICATIONS 2012. [DOI: 10.1016/j.mencom.2012.05.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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15
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16
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Mori Y, Takano K. Location of protons in N–H⋯N hydrogen-bonded systems: a theoretical study on intramolecular pyridine–dihydropyridine and pyridine–pyridinium pairs. Phys Chem Chem Phys 2012; 14:11090-8. [DOI: 10.1039/c2cp41425b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Beran GJO, Chronister EL, Daemen LL, Moehlig AR, Mueller LJ, Oomens J, Rice A, Santiago-Dieppa DR, Tham FS, Theel K, Yaghmaei S, Morton TH. Vibrations of a chelated proton in a protonated tertiary diamine. Phys Chem Chem Phys 2011; 13:20380-92. [DOI: 10.1039/c1cp22065a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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