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Jezierska A, Panek JJ, Błaziak K, Raczyński K, Koll A. Exploring Intra- and Intermolecular Interactions in Selected N-Oxides-The Role of Hydrogen Bonds. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030792. [PMID: 35164056 PMCID: PMC8846293 DOI: 10.3390/molecules27030792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 11/30/2022]
Abstract
Intra- and intermolecular interactions have been explored in selected N-oxide derivatives: 2-(N,N-dimethylamino-N-oxymethyl)-4,6-dimethylphenyl (1) and 5,5’-dibromo-3-diethylaminomethyl-2,2’-biphenol N-oxide (2). Both compounds possess intramolecular hydrogen bonding, which is classified as moderate in 1 and strong in 2, and resonance-assisted in both cases. Density Functional Theory (DFT) in its classical formulation as well as Time-Dependent extension (TD-DFT) were employed to study proton transfer phenomena. The simulations were performed in the gas phase and with implicit and explicit solvation models. The obtained structures of the studied N-oxides were compared with experimental data available. The proton reaction path was investigated using scan with an optimization method, and water molecule reorientation in the monohydrate of 1 was found upon the proton scan progress. It was found that spontaneous proton transfer phenomenon cannot occur in the electronic ground state of the compound 1. An opposite situation was noticed for the compound 2. The changes of nucleophilicity and electrophilicity upon the bridged proton migration were analyzed on the basis of Fukui functions in the case of 1. The interaction energy decomposition of dimers and microsolvation models was investigated using Symmetry-Adapted Perturbation Theory (SAPT). The simulations were performed in both phases to introduce polar environment influence on the interaction energies. The SAPT study showed rather minor role of induction in the formation of homodimers. However, it is worth noticing that the same induction term is responsible for the preference of water molecules’ interaction with N-oxide hydrogen bond acceptor atoms in the microsolvation study. The Natural Bond Orbital (NBO) analysis was performed for the complexes with water to investigate the charge flow upon the polar environment introduction. Finally, the TD-DFT was applied for isolated molecules as well as for microsolvation models showing that the presence of solvent affects excited states, especially when the N-oxide acceptor atom is microsolvated.
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Affiliation(s)
- Aneta Jezierska
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland; (J.J.P.); (K.R.)
- Correspondence: ; Tel.: +48-71-3757-224; Fax: +48-71-3282-348
| | - Jarosław J. Panek
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland; (J.J.P.); (K.R.)
| | - Kacper Błaziak
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 01-224 Warsaw, Poland;
- Biological and Chemical Research Center, University of Warsaw, Żwirki i Wigury 101, 01-224 Warsaw, Poland
| | - Kamil Raczyński
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland; (J.J.P.); (K.R.)
| | - Aleksander Koll
- Non-Public Medical School in Wrocław, ul. Nowowiejska 69, 50-340 Wrocław, Poland;
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Brela MZ, Klimas O, Boczar M, Nakajima T, Wójcik MJ. A comparison of the hydrogen bond interaction dynamics in the adenine and thymine crystals: BOMD and spectroscopic study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 237:118398. [PMID: 32361519 DOI: 10.1016/j.saa.2020.118398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/09/2020] [Accepted: 04/19/2020] [Indexed: 06/11/2023]
Abstract
In this work we present the comparison study of Adenine and Thymine crystals based on the hydrogen bond dynamics. The ab initio molecular dynamics have been used as the base for the further studied interactions observed inside crystals. The generated power spectra, as well as the fluctuation of the interaction energies, showed large differences between hydrogen bond networks in the considered crystals. The analysis of intermolecular interactions have been done base on the reactivity descriptors as well frontiers orbitals along trajectories. The main results showed that in adenine crystals the intermolecular interactions have three directions and fluctuate, while in the thymine crystal have only two directions and are weak but stable. These results explain also on the difference between adenine and thymine melting temperature.
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Affiliation(s)
- Mateusz Z Brela
- Faculty of Chemistry, Jagiellonian University, 30-387 Kraków, Gronostajowa 2, Poland.
| | - Oskar Klimas
- Faculty of Chemistry, Jagiellonian University, 30-387 Kraków, Gronostajowa 2, Poland
| | - Marek Boczar
- Faculty of Chemistry, Jagiellonian University, 30-387 Kraków, Gronostajowa 2, Poland
| | - Takahito Nakajima
- RIKEN, Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Marek J Wójcik
- Faculty of Chemistry, Jagiellonian University, 30-387 Kraków, Gronostajowa 2, Poland; RIKEN, Center for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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Brela MZ, Klimas O, Surmiak E, Boczar M, Nakajima T, Wójcik MJ. Comparison of the Hydrogen Bond Interaction Dynamics in the Guanine and Cytosine Crystals: Ab Initio Molecular Dynamics and Spectroscopic Study. J Phys Chem A 2019; 123:10757-10763. [DOI: 10.1021/acs.jpca.9b09655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Mateusz Z. Brela
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Oskar Klimas
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Ewa Surmiak
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Marek Boczar
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Takahito Nakajima
- RIKEN, Advanced Institute for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Marek J. Wójcik
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
- RIKEN, Advanced Institute for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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Brela MZ, Wójcik MJ, Boczar M, Witek ŁJ, Yonehara T, Nakajima T, Ozaki Y. Proton dynamics in crystalline tropolone studied by Born-Oppenheimer molecular simulations. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.07.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Brela MZ, Boczar M, Malec LM, Wójcik MJ, Nakajima T. Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 197:194-201. [PMID: 29395929 DOI: 10.1016/j.saa.2018.01.050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/11/2018] [Accepted: 01/16/2018] [Indexed: 06/07/2023]
Abstract
Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers.
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Affiliation(s)
- Mateusz Z Brela
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Marek Boczar
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Leszek M Malec
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Marek J Wójcik
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; Department of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan.
| | - Takahito Nakajima
- RIKEN, Advanced Institute for Computational Science, 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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Beć KB, Morisawa Y, Kobashi K, Grabska J, Tanabe I, Tanimura E, Sato H, Wójcik MJ, Ozaki Y. Rydberg transitions as a probe for structural changes and phase transition at polymer surfaces: an ATR-FUV-DUV and quantum chemical study of poly(3-hydroxybutyrate) and its nanocomposite with graphene. Phys Chem Chem Phys 2018. [DOI: 10.1039/c7cp07271f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
ATR-FUV-DUV (145–300 nm; 8.55–4.13 eV) and quantum mechanical calculations study of PHB and its nanocomposite with graphene.
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Affiliation(s)
- Krzysztof B. Beć
- Department of Chemistry
- School of Science and Technology
- Kwansei Gakuin University
- Sanda
- Japan
| | - Yusuke Morisawa
- Department of Chemistry
- School of Science and Engineering
- Kindai University
- Osaka 577-8502
- Japan
| | - Kenta Kobashi
- Department of Chemistry
- School of Science and Technology
- Kwansei Gakuin University
- Sanda
- Japan
| | - Justyna Grabska
- Department of Chemistry
- School of Science and Technology
- Kwansei Gakuin University
- Sanda
- Japan
| | - Ichiro Tanabe
- Graduate School of Engineering Science
- Osaka University
- Osaka 560-8531
- Japan
| | - Erika Tanimura
- Department of Chemistry
- School of Science and Technology
- Kwansei Gakuin University
- Sanda
- Japan
| | - Harumi Sato
- Graduate School of Human Development and Environment
- Kobe University
- Kobe 657-8501
- Japan
| | - Marek J. Wójcik
- Department of Chemistry
- School of Science and Technology
- Kwansei Gakuin University
- Sanda
- Japan
| | - Yukihiro Ozaki
- Department of Chemistry
- School of Science and Technology
- Kwansei Gakuin University
- Sanda
- Japan
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