Depolarizing Effects in Hydrogen Bond Energy in 3<sub>10</sub>-Helices Revealed by Quantum Chemical Analysis
Hydrogen-bond (H-bond) energies in 3<sub>10</sub>-helices of short alanine peptides were systematically examined by precise DFT calculations with the negative fragmentation approach (NFA), a modified method based on the molecular tailoring approach. The contribution of each H-bond was ev...
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MDPI AG
2022-08-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/16/9032 |
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| author | Hiroko X. Kondo Haruki Nakamura Yu Takano |
| author_facet | Hiroko X. Kondo Haruki Nakamura Yu Takano |
| author_sort | Hiroko X. Kondo |
| collection | DOAJ |
| description | Hydrogen-bond (H-bond) energies in 3<sub>10</sub>-helices of short alanine peptides were systematically examined by precise DFT calculations with the negative fragmentation approach (NFA), a modified method based on the molecular tailoring approach. The contribution of each H-bond was evaluated in detail from the 3<sub>10</sub>-helical conformation of total energies (whole helical model, WH<sub>3-10</sub> model), and the results were compared with the property of H-bond in α-helix from our previous study. The H-bond energies of the WH<sub>3-10</sub> model exhibited tendencies different from those exhibited by the α-helix in that they depended on the helical position of the relevant H-bond pair. H-bond pairs adjacent to the terminal H-bond pairs were observed to be strongly destabilized. The analysis of electronic structures indicated that structural characteristics cause the destabilization of the H-bond in 3<sub>10</sub>-helices. We also found that the longer the helix length, the more stable the H-bond in the terminal pairs of the WH<sub>3-10</sub> model, suggesting the action of H-bond cooperativity. |
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| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T04:20:40Z |
| publishDate | 2022-08-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-27345896aa754ae890bf730e100869d32023-12-03T13:48:07ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-08-012316903210.3390/ijms23169032Depolarizing Effects in Hydrogen Bond Energy in 3<sub>10</sub>-Helices Revealed by Quantum Chemical AnalysisHiroko X. Kondo0Haruki Nakamura1Yu Takano2School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, Kitami 090-8507, JapanInstitute for Protein Research, Osaka University, Suita 565-0871, JapanDepartment of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, Hiroshima 731-3194, JapanHydrogen-bond (H-bond) energies in 3<sub>10</sub>-helices of short alanine peptides were systematically examined by precise DFT calculations with the negative fragmentation approach (NFA), a modified method based on the molecular tailoring approach. The contribution of each H-bond was evaluated in detail from the 3<sub>10</sub>-helical conformation of total energies (whole helical model, WH<sub>3-10</sub> model), and the results were compared with the property of H-bond in α-helix from our previous study. The H-bond energies of the WH<sub>3-10</sub> model exhibited tendencies different from those exhibited by the α-helix in that they depended on the helical position of the relevant H-bond pair. H-bond pairs adjacent to the terminal H-bond pairs were observed to be strongly destabilized. The analysis of electronic structures indicated that structural characteristics cause the destabilization of the H-bond in 3<sub>10</sub>-helices. We also found that the longer the helix length, the more stable the H-bond in the terminal pairs of the WH<sub>3-10</sub> model, suggesting the action of H-bond cooperativity.https://www.mdpi.com/1422-0067/23/16/90323<sub>10</sub>-helixhydrogen bond energydensity functional theorynegative fragmentation analysis |
| spellingShingle | Hiroko X. Kondo Haruki Nakamura Yu Takano Depolarizing Effects in Hydrogen Bond Energy in 3<sub>10</sub>-Helices Revealed by Quantum Chemical Analysis International Journal of Molecular Sciences 3<sub>10</sub>-helix hydrogen bond energy density functional theory negative fragmentation analysis |
| title | Depolarizing Effects in Hydrogen Bond Energy in 3<sub>10</sub>-Helices Revealed by Quantum Chemical Analysis |
| title_full | Depolarizing Effects in Hydrogen Bond Energy in 3<sub>10</sub>-Helices Revealed by Quantum Chemical Analysis |
| title_fullStr | Depolarizing Effects in Hydrogen Bond Energy in 3<sub>10</sub>-Helices Revealed by Quantum Chemical Analysis |
| title_full_unstemmed | Depolarizing Effects in Hydrogen Bond Energy in 3<sub>10</sub>-Helices Revealed by Quantum Chemical Analysis |
| title_short | Depolarizing Effects in Hydrogen Bond Energy in 3<sub>10</sub>-Helices Revealed by Quantum Chemical Analysis |
| title_sort | depolarizing effects in hydrogen bond energy in 3 sub 10 sub helices revealed by quantum chemical analysis |
| topic | 3<sub>10</sub>-helix hydrogen bond energy density functional theory negative fragmentation analysis |
| url | https://www.mdpi.com/1422-0067/23/16/9032 |
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