1
|
Theoretical study of intramolecular hydrogen bond in selected symmetric "proton sponges" on the basis of DFT and CPMD methods. J Mol Model 2020; 26:37. [PMID: 31989276 DOI: 10.1007/s00894-020-4296-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/14/2020] [Indexed: 12/21/2022]
Abstract
"Proton sponges," derivatives of prototypic 1,8-bis(dimethylamino)naphthalene (DMAN), exhibit remarkable basicity, which made them interesting for various experimental and theoretical studies. The details of bridged proton dynamics in protonated DMAN and its derivative denoted as TMGN (1,8-bis(tetramethylguanidino)naphthalene) were investigated on the basis of density functional theory (DFT) and Car-Parrinello molecular dynamics (CPMD) methods. Special attention was paid to the effects of symmetry of the molecular skeleton and the type of substituent on the bridged proton neighborhood statistics and dynamics. The metric parameter analyses of hydrogen bridge provided us with a conclusion that proton migration events in TMGNH+ are less numerous than in DMANH+, which can be rationalized by noticing the slower dynamics of large substituents of TMGN with respect to the smaller -N(Me)2 groups of DMAN. The atomic velocity power spectra served as computational models of the vibrational signatures associated with the presence of the intramolecular hydrogen bond. A broad feature was registered for hydrogen bonds present in both compounds. The computations were verified by experimental data available.
Collapse
|
2
|
Mori Y, Masuda Y. Effect of solvent on proton location and dynamic behavior in short intramolecular hydrogen bonds studied by molecular dynamics simulations and NMR experiments. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
3
|
Jezierska A, Panek JJ. “Zwitterionic Proton Sponge” Hydrogen Bonding Investigations on the Basis of Car–Parrinello Molecular Dynamics. J Chem Inf Model 2015; 55:1148-57. [DOI: 10.1021/ci500560g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Aneta Jezierska
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Jarosław J. Panek
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
| |
Collapse
|
4
|
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
| |
Collapse
|
5
|
Ozeryanskii VA, Pozharskii AF. Simple and hydrolytically stable proton sponge based organic cation displaying hydrogen bonding and a number of related phenomena. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.01.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
6
|
‘Proton sponge’ amides: unusual chemistry and conversion into superbasic 6,7-bis(dimethylamino)perimidines. Tetrahedron 2013. [DOI: 10.1016/j.tet.2012.12.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
7
|
Bernatowicz P. Accurate determination of the ultrafast proton transfer rate in porphycene using nuclear spin relaxation. Phys Chem Chem Phys 2013; 15:8732-5. [DOI: 10.1039/c3cp50963j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
8
|
Nakano T, Masuda Y. Application of Nuclear Magnetic Relaxation To Elucidate Proton Location and Dynamics in N···H···O Hydrogen Bonds. J Phys Chem A 2012; 116:8409-18. [DOI: 10.1021/jp303297c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tomoko Nakano
- Department of Chemistry, Faculty
of Science, Ochanomizu University, Bunkyo-ku,
Tokyo 112-8610, Japan
| | - Yuichi Masuda
- Department of Chemistry, Faculty
of Science, Ochanomizu University, Bunkyo-ku,
Tokyo 112-8610, Japan
| |
Collapse
|
9
|
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]
|
10
|
Masuda Y, Nakano T, Sugiyama M. First observation of ultrafast intramolecular proton transfer rate between electronic ground states in solution. J Phys Chem A 2012; 116:4485-94. [PMID: 22510164 DOI: 10.1021/jp2110874] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Despite the importance of ultrafast (time scale exceeding 10(-11) s) intramolecular proton transfer (PT) events between electronic ground states in solution, experimental determination of the rates of such reactions has not yet been accomplished because of the limitations of the utilized methods. The objective of this study was to evaluate the PT rates of intramolecular O···H···O hydrogen-bonded systems in solution through the (1)H spin-lattice relaxation times of the hydroxyl protons, induced by the (1)H-(17)O dipolar interactions (T(1dd)(OH)), taking into account the contribution of the OH reorientational motion to T(1dd)(OH). Solutions of the benzoic acid dimer (BA dimer), 1-benzoyl-6-hydroxy-6-phenylfulvene (Fulvene), and dibenzoylmethane (DBM) were chosen as test systems. For Fulvene in CCl(4), the PT time, τ(PT), was deduced to be 7 × 10(-11) s. In the case of the BA dimer in CCl(4), the τ(PT) value was considerably greater than the OH reorientational correlation time, τ(R(OH)) = 4.3 × 10(-11) s. In contrast, the experimental results for DBM in CCl(4) indicated that the proton is located about midway between the two oxygen atoms, that is, the PT potential energy surface is a single well or a double well with a PT barrier near or below the zero-point energy.
Collapse
Affiliation(s)
- Yuichi Masuda
- Department of Chemistry, Faculty of Science, Ochanomizu University, Bunkyo-ku, Tokyo 112-8610, Japan.
| | | | | |
Collapse
|
11
|
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]
|
12
|
Bernatowicz P. Determination of the rotational diffusion tensor of porphycene by 13C and 1H spin relaxation methods. J Phys Chem A 2011; 115:8604-7. [PMID: 21721542 DOI: 10.1021/jp204950c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The longitudinal (13)C and (1)H relaxation rates were determined in porphycene in CD(2)Cl(2) solution. These data, augmented by (13)C{(1)H} NOE enhancements were numerically analyzed to evaluate the rotational diffusion tensor of the molecule and the vibrational correction for the one-bond (13)C-(1)H dipolar couplings. The (13)C and (1)H relaxation data seem to be consistent with each other, and the emerging picture of the rotational dynamics of porphycene compares well with the results that can be found in the literature.
Collapse
Affiliation(s)
- Piotr Bernatowicz
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| |
Collapse
|
13
|
Latanowicz L, Gdaniec Z. Nuclear spin–lattice relaxation and complex motion of macromolecules in solution. Mol Phys 2011. [DOI: 10.1080/00268976.2011.556578] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
14
|
Pietrzak M, Wehling J, Kong S, Tolstoy P, Shenderovich I, López C, Claramunt RM, Elguero J, Denisov G, Limbach HH. Symmetrization of Cationic Hydrogen Bridges of Protonated Sponges Induced by Solvent and Counteranion Interactions as Revealed by NMR Spectroscopy. Chemistry 2010; 16:1679-90. [DOI: 10.1002/chem.200902259] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
15
|
Bernatowicz P, Ruszczyńska-Bartnik K, Ejchart A, Dodziuk H, Kaczorowska E, Ueda H. Carbon-13 NMR Relaxation Study of the Internal Dynamics in Cyclodextrins in Isotropic Solution. J Phys Chem B 2009; 114:59-65. [DOI: 10.1021/jp9084734] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Piotr Bernatowicz
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland, and Department of Physical Chemistry, Hoshi University, 4-41 Ebara 2-chome, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Katarzyna Ruszczyńska-Bartnik
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland, and Department of Physical Chemistry, Hoshi University, 4-41 Ebara 2-chome, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Andrzej Ejchart
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland, and Department of Physical Chemistry, Hoshi University, 4-41 Ebara 2-chome, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Helena Dodziuk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland, and Department of Physical Chemistry, Hoshi University, 4-41 Ebara 2-chome, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Ewa Kaczorowska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland, and Department of Physical Chemistry, Hoshi University, 4-41 Ebara 2-chome, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Haruhisa Ueda
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland, and Department of Physical Chemistry, Hoshi University, 4-41 Ebara 2-chome, Shinagawa-ku, Tokyo 142-8501, Japan
| |
Collapse
|
16
|
Latanowicz L, Gdaniec Z. Effect of the frequency of intramolecular motions on the NMR relaxation in liquid state temperature regime. Mol Phys 2009. [DOI: 10.1080/00268970902980045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
17
|
2,7-Disubstituted proton sponges as borderline systems for investigating barrier-free intramolecular hydrogen bonds. Protonated 2,7-bis(trimethylsilyl)- and 2,7-di(hydroxymethyl)-1,8-bis(dimethylamino)naphthalenes. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.05.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
18
|
Bernatowicz P, Kowalewski J. Carbon-13 NMR Relaxation Study of 1,8-Bis(dimethylamino)naphthalene in Isotropic Solution. J Phys Chem A 2008; 112:4711-4. [DOI: 10.1021/jp802319g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Piotr Bernatowicz
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, and Department of Physical, Inorganic and Structural Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Jozef Kowalewski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, and Department of Physical, Inorganic and Structural Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| |
Collapse
|
19
|
Bernatowicz P, Kowalewski J, Szymanski S. Nuclear-spin relaxation in nonrigid molecules: discrete multisite local dynamics combined with anisotropic molecular reorientation. J Chem Phys 2007; 124:024108. [PMID: 16422572 DOI: 10.1063/1.2149858] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Nuclear-spin relaxation is considered in a molecular system undergoing two types of dynamic processes: asymmetric-top small-step rotational diffusion and discrete multisite local jumps. The two processes are assumed to be uncorrelated. Time correlation functions for relevant rank-two interactions and corresponding spectral density functions are derived for a general relation between the characteristic rate constants. In addition, limiting cases of fast and slow local motions and of some specific jump conditions are also investigated.
Collapse
Affiliation(s)
- Piotr Bernatowicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland.
| | | | | |
Collapse
|
20
|
Ozeryanskii VA, Pozharskii AF, Schilf W, Kamieński B, Sawka-Dobrowolska W, Sobczyk L, Grech E. Novel Polyfunctional Tautomeric Systems Containing Salicylideneamino and Proton Sponge Moieties. European J Org Chem 2006. [DOI: 10.1002/ejoc.200500574] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
21
|
Ozeryanskii VA, Pozharskii AF. A method for determination of the structure of the intramolecular hydrogen bond in the cations of unsymmetrically substituted 1,8-bis(dimethylamino)naphthalenes in solution. Russ Chem Bull 2006. [DOI: 10.1007/s11172-006-0231-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|