1
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Pomogaeva AV, Lisovenko AS, Timoshkin AY. Structures and stability of I 2 and ICl complexes with pyridine: Ab initio and DFT study. J Comput Chem 2024; 45:903-914. [PMID: 38165152 DOI: 10.1002/jcc.27300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 01/03/2024]
Abstract
Theoretical investigation of thermodynamic stability and bonding features of possible isomers of the molecular and ionic complexes of pyridine with molecular iodine and iodine monochloride IX (X = I,Cl) is presented. M06-2X DFT functional is found to provide bond distances and dissociation energies which are close to those obtained at high-level ab initio CCSD(T)/aug-cc-pvtz//CCSD/aug-cc-pvtz benchmark computations for the most stable isomers, formed via donation of a lone pair of nitrogen atom of pyridine to the iodine atom. These isomers are by 23-33 kJ mol-1 (in case of I2) and by 39-56 kJ mol-1 (in case of ICl) more stable than other molecular complexes. T-shaped π-σ* bonded isomers turn out to be energetically comparable with van der Waals bound compounds. Among the ionic isomers, structures featuring [IPy2]+ cation with I3 - or ICl2 - counterions are more stable. Oligomerization favors ionic isomers starting from the tetrameric clusters of the composition (IX)4Py4.
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Affiliation(s)
- Anna V Pomogaeva
- Institute of Chemistry, Saint Petersburg State University, St. Petersburg, Russia
| | - Anna S Lisovenko
- Institute of Chemistry, Saint Petersburg State University, St. Petersburg, Russia
| | - Alexey Y Timoshkin
- Institute of Chemistry, Saint Petersburg State University, St. Petersburg, Russia
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2
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Sakai T, Torii H. Substituent Effect and Its Halogen-Atom Dependence of Halogen Bonding Viewed through Electron Density Changes. Chem Asian J 2023; 18:e202201196. [PMID: 36545823 DOI: 10.1002/asia.202201196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022]
Abstract
Elucidating how the halogen-bonding ability and strength are controlled by the substituent effect and how this control depends on halogen atom will be essential for finely-tuned design of functionally important molecules. Here, this problem is tackled by analyzing the electron density differences/changes for variously substituted halobenzenes. It is shown that the anisotropy of the electron distribution around the halogen atom, which is an important factor for halogen-bonding ability, is not much affected by the substituent effect and rather simply depends on the halogen atom, while the partial charge on the halogen atom, which is related to the bond dipole of the C-X bond, is significantly modulated by the substituent effect and gives rise to enhancement of the electrostatic potential on the line extended from the C-X bond. The properties related to the polarization effect are also discussed.
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Affiliation(s)
- Takanori Sakai
- Applied Chemistry and Biochemical Engineering Course Department of Engineering Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, 432-8561, Japan
| | - Hajime Torii
- Applied Chemistry and Biochemical Engineering Course Department of Engineering Graduate School of Integrated Science and Technology and Department of Optoelectronics and Nanostructure Science Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, 432-8561, Japan
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3
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Torii H, Kimura A, Sakai T. Nature of hydrogen-bond-enhanced halogen bonding viewed through electron density changes. Phys Chem Chem Phys 2022; 24:17951-17955. [PMID: 35861167 DOI: 10.1039/d2cp02845j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Elucidating the mechanism of how we can achieve fine tuning of intermolecular interaction strength will be helpful for designing functionally important molecules. In the present study, a theoretical analysis is conducted, by examining the electron density changes, for two halogen-bonding iodinated systems whose halogen-bond strengths have been considered to be enhanced by the presence of a hydrogen-bond donating group (termed hydrogen-bond-enhanced halogen bonding). It is shown that, contrary to the expectation obtained from the enhancement of electrostatic potential along the line extended from the C-I bond, the anisotropy of electron distribution on the iodine atom remains nearly the same. This means that the hydrogen bond and halogen bond contribute almost independently and additively to the enhancement of electrostatic potential, indicating the nature of this enhancement and, in a more general sense, the relationship between the strength and the extent of directionality of halogen bonding.
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Affiliation(s)
- Hajime Torii
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan. .,Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan
| | - Akari Kimura
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan.
| | - Takanori Sakai
- Applied Chemistry and Biochemical Engineering Course, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu 432-8561, Japan.
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4
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Kikkawa Y, Nagasaki M, Koyama E, Ito S, Tsuzuki S. Halogen bond-directed self-assembly in bicomponent blends at the solid/liquid interface: Effect of the alkyl chain substitution position. Phys Chem Chem Phys 2022; 24:17088-17097. [DOI: 10.1039/d2cp02206k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fabrication of well-organised molecular assemblies on surfaces is fundamental for the creation of functional molecular systems applicable to nanoelectronics and molecular devices. In this study, we investigated the effect...
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5
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Takaya D, Watanabe C, Nagase S, Kamisaka K, Okiyama Y, Moriwaki H, Yuki H, Sato T, Kurita N, Yagi Y, Takagi T, Kawashita N, Takaba K, Ozawa T, Takimoto-Kamimura M, Tanaka S, Fukuzawa K, Honma T. FMODB: The World's First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method. J Chem Inf Model 2021; 61:777-794. [PMID: 33511845 DOI: 10.1021/acs.jcim.0c01062] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We developed the world's first web-based public database for the storage, management, and sharing of fragment molecular orbital (FMO) calculation data sets describing the complex interactions between biomacromolecules, named FMO Database (https://drugdesign.riken.jp/FMODB/). Each entry in the database contains relevant background information on how the data was compiled as well as the total energy of each molecular system and interfragment interaction energy (IFIE) and pair interaction energy decomposition analysis (PIEDA) values. Currently, the database contains more than 13 600 FMO calculation data sets, and a comprehensive search function implemented at the front-end. The procedure for selecting target proteins, preprocessing the experimental structures, construction of the database, and details of the database front-end were described. Then, we demonstrated a use of the FMODB by comparing IFIE value distributions of hydrogen bond, ion-pair, and XH/π interactions obtained by FMO method to those by molecular mechanics approach. From the comparison, the statistical analysis of the data provided standard reference values for the three types of interactions that will be useful for determining whether each interaction in a given system is relatively strong or weak compared to the interactions contained within the data in the FMODB. In the final part, we demonstrate the use of the database to examine the contribution of halogen atoms to the binding affinity between human cathepsin L and its inhibitors. We found that the electrostatic term derived by PIEDA greatly correlated with the binding affinities of the halogen containing cathepsin L inhibitors, indicating the importance of QM calculation for quantitative analysis of halogen interactions. Thus, the FMO calculation data in FMODB will be useful for conducting statistical analyses to drug discovery, for conducting molecular recognition studies in structural biology, and for other studies involving quantum mechanics-based interactions.
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Affiliation(s)
- Daisuke Takaya
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Chiduru Watanabe
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,JST PRESTO, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Shunpei Nagase
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kikuko Kamisaka
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshio Okiyama
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
| | - Hirotomo Moriwaki
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hitomi Yuki
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tomohiro Sato
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
| | - Yoichiro Yagi
- Graduate School of Engineering, Okayama University of Science, Okayama, 1-1 Ridai-cho, Okayama 700-0005, Japan
| | - Tatsuya Takagi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Norihito Kawashita
- Faculty of Science and Engineering, Kindai University, 3-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan
| | - Kenichiro Takaba
- Pharmaceutical Research Center, Laboratory for Medicinal Chemistry, Asahi Kasei Pharma Corporation, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
| | - Tomonaga Ozawa
- Kissei Pharmaceutical Co., LTD., Frontier Technology Research Lab., Research Div. 4365-1 Hotaka Kashiwabara, Azumino, Nagano 399-8304, Japan
| | - Midori Takimoto-Kamimura
- Teijin Institute for Biomedical Research, Teijin Pharma Ltd., 4-3-2 Asahigaoka, Hino, Tokyo 191-8512, Japan
| | - Shigenori Tanaka
- Graduate School of System Informatics, Department of Computational Science, Kobe University, 1-1 Rokkodai, Kobe, Hyogo 657-8501, Japan
| | - Kaori Fukuzawa
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa, Tokyo 142-8501, Japan.,Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Sendai, Miyagi 980-8579, Japan
| | - Teruki Honma
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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6
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Halogen bonding interactions in the XC 5H 4N···YCF 3 (X = CH 3, H, Cl, CN, NO 2; Y = Cl, Br, I) complexes. J Mol Model 2020; 26:344. [PMID: 33205319 DOI: 10.1007/s00894-020-04606-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/08/2020] [Indexed: 10/23/2022]
Abstract
The noncovalent interactions between the σ-hole region outside the halogen atom and the nitrogen atom of pyridine and its para-substituted derivatives are the focus of this work. Based on the analyses of the electrostatic potentials, YCF3 (Y = Cl, Br, I) act as halogen bond donors, XC5H4N (X = CH3, H, Cl, CN, NO2) act as halogen bond acceptors, and the binary halogen-bonded complexes XC5H4N···YCF3 have been designed and investigated by B3LYP-D3/aug-cc-pVDZ calculations together with the aug-cc-pVDZ-PP basis set for iodine. When the halogen bond acceptor remains unchanged, the interactions between C5H5N and YCF3 (Y = Cl, Br, I) increase with the order of Y = Cl, Br, and I. When the halogen donor ICF3 is fixed, the halogen bonding interactions decrease along the sequence of X = CH3, H, Cl, CN, NO2. Therefore, the halogen bond of the CH3C5H4N···ICF3 complex is the strongest. The interactions between Lewis acid YCF3 (Y = Cl, Br, I) and pyridine and para-substituted pyridine are closed-shell and noncovalent interactions. On the one hand, when the halogen bond acceptor XC5H4N is fixed, with the increase of halogen atomic number, the strength of halogen bond increases; on the other hand, when the halogen bond donor ICF3 is fixed, as the electron-withdrawing ability of the electron-withdrawing group (X) increases, the halogen bond gradually weakens.
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7
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Kikkawa Y, Nagasaki M, Koyama E, Tsuzuki S, Fouquet T, Hiratani K. Dynamic host-guest behavior in halogen-bonded two-dimensional molecular networks investigated by scanning tunneling microscopy at the solid/liquid interface. NANOSCALE ADVANCES 2020; 2:4895-4901. [PMID: 36132910 PMCID: PMC9419264 DOI: 10.1039/d0na00616e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 08/20/2020] [Indexed: 06/14/2023]
Abstract
The fabrication of supramolecularly engineered two-dimensional (2D) networks using simple molecular building blocks is an effective means for studying host-guest chemistry at surfaces toward the potential application of such systems in nanoelectronics and molecular devices. In this study, halogen-bonded molecular networks were constructed by the combination of linear halogen-bond donor and acceptor ligands, and their 2D structures at the highly oriented pyrolytic graphite/1-phenyloctane interface were studied by scanning tunneling microscopy. The bi-component blend of the molecular building blocks possessing tetradecyloxy chains formed a lozenge structure via halogen bonding. Upon the introduction of an appropriate guest molecule (e.g., coronene) into the system, the 2D structure transformed into a hexagonal array, and the central pore of this array was occupied by the guest molecules. Remarkably, the halogen bonding of the original structure was maintained after the introduction of the guest molecule. Thus, the halogen-bonded molecular networks are applicable for assembling guest species on the substrate without the requirement of the conventional rigid molecular building blocks with C 3 symmetry.
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Affiliation(s)
- Yoshihiro Kikkawa
- National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Central 5, 1-1-1 Higashi Tsukuba Ibaraki 305-8565 Japan
| | - Mayumi Nagasaki
- National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Central 5, 1-1-1 Higashi Tsukuba Ibaraki 305-8565 Japan
| | - Emiko Koyama
- National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Central 5, 1-1-1 Higashi Tsukuba Ibaraki 305-8565 Japan
| | - Seiji Tsuzuki
- National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Central 5, 1-1-1 Higashi Tsukuba Ibaraki 305-8565 Japan
| | - Thierry Fouquet
- National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Central 5, 1-1-1 Higashi Tsukuba Ibaraki 305-8565 Japan
| | - Kazuhisa Hiratani
- National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Central 5, 1-1-1 Higashi Tsukuba Ibaraki 305-8565 Japan
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8
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Zhu Z, Xu Z, Zhu W. Interaction Nature and Computational Methods for Halogen Bonding: A Perspective. J Chem Inf Model 2020; 60:2683-2696. [DOI: 10.1021/acs.jcim.0c00032] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zhengdan Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China
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9
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Wang R, Cheng Z, Li Q, McDowell SA. Regular/abnormal variation in the strength and nature of the halogen bond between H
2
Te and the dihalogens: Prominent effect of methyl substituents. Appl Organomet Chem 2020. [DOI: 10.1002/aoc.5468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ruijing Wang
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical EngineeringYantai University Yantai 264005 China
| | - Ziyi Cheng
- Institute of Functional Materials and Molecular Imaging, Key Laboratory of Emergency and Trauma, Ministry of Education, College of Emergency and TraumaHainan Medical University Haikou 571199 China
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical EngineeringYantai University Yantai 264005 China
| | - Sean A.C. McDowell
- Department of Biological and Chemical SciencesThe University of the West Indies Cave Hill Campus Barbados
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10
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Kikkawa Y, Nagasaki M, Koyama E, Tsuzuki S, Hiratani K. Hexagonal array formation by intermolecular halogen bonding using a binary blend of linear building blocks: STM study. Chem Commun (Camb) 2019; 55:3955-3958. [PMID: 30874258 DOI: 10.1039/c9cc00532c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Hexagonal arrays were fabricated via intermolecular halogen bonding between two linear molecular building blocks in a bicomponent blend. The substitution position of the pyridine N atom involved in the halogen bond plays an important role in the formation of the hexagonal structures.
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Affiliation(s)
- Yoshihiro Kikkawa
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan.
| | - Mayumi Nagasaki
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan.
| | - Emiko Koyama
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan.
| | - Seiji Tsuzuki
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan.
| | - Kazuhisa Hiratani
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan.
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11
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Torii H. Correlation of the partial charge-transfer and covalent nature of halogen bonding with the THz and IR spectral changes. Phys Chem Chem Phys 2019; 21:17118-17125. [DOI: 10.1039/c9cp02747e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Changes in the spectral intensities in the THz region are good probes for the non-electrostatic aspect of halogen bonding.
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Affiliation(s)
- Hajime Torii
- Department of Applied Chemistry and Biochemical Engineering
- Faculty of Engineering, and Department of Optoelectronics and Nanostructure Science
- Graduate School of Science and Technology
- Shizuoka University
- Hamamatsu 432-8561
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12
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Comparative study on the interactions of sulfide and iodine mediators with a dye in p-type dye-sensitized solar cells. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2018.07.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Kusama H. Interaction between dyes and iodide mediators in p-type dye-sensitized solar cells. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2018.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Kusama H. Interaction between disulfide/thiolate mediators and ruthenium complex in dye-sensitized solar cells. J Photochem Photobiol A Chem 2017. [DOI: 10.1016/j.jphotochem.2017.09.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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15
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The σ and π Holes. The Halogen and Tetrel Bondings: Their Nature, Importance and Chemical, Biological and Medicinal Implications. ChemistrySelect 2017. [DOI: 10.1002/slct.201701676] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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16
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Adasme-Carreño F, Alzate-Morales J, Ireta J. Modeling cooperative effects in halogen-bonded infinite linear chains. Phys Chem Chem Phys 2017; 19:18529-18538. [PMID: 28682384 DOI: 10.1039/c7cp03078a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Non-additivity in noncovalent interactions is an important aspect of complex systems that can lead to stronger (cooperative) interactions when three or more molecular units influence each other. The halogen bond (XB) is a highly-directional noncovalent interaction that has been found to be cooperative. Here the strength and nature of cooperativity arising in X-bonded infinite linear chains of cyanogen halides and 4-halopyridines are investigated by means of density functional theory calculations. It is found that cyanogen halide chains are highly cooperative (up to 77%), whereas pyridines are only slightly cooperative (below 21%). It is demonstrated that XB and its non-additivity can be modeled as the sum of a local term, which depends on first nearest-neighbors only, and long-range effective dipole-dipole attractions. It is shown that the local term in cyanogen halides primarily accounts for repulsive short-range screened Coulomb interactions, whereas in 4-halopyridines such a term also includes attractive contributions, which are particularly sizeable in some elongated XB conformations. This outcome reveals differences in the nature of the XBs formed in these molecular systems. Nevertheless, it is shown that both systems behave as effective point dipoles regarding cooperative effects, at any point of the XB dissociation path. As such, these results are useful contributions for the understanding and modeling of non-additive effects of noncovalent interactions.
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Affiliation(s)
- Francisco Adasme-Carreño
- Centro de Bioinformática y Simulación Molecular (CBSM), Facultad de Ingeniería, Universidad de Talca, 1 Poniente 1141, Casilla 721, Talca, Chile.
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17
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Benchmarking DFT methods with small basis sets for the calculation of halogen-bond strengths. J Mol Model 2017; 23:50. [DOI: 10.1007/s00894-017-3212-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/09/2017] [Indexed: 01/14/2023]
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18
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Hakkert SB, Gräfenstein J, Erdelyi M. The15N NMR chemical shift in the characterization of weak halogen bonding in solution. Faraday Discuss 2017; 203:333-346. [DOI: 10.1039/c7fd00107j] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have studied the applicability of15N NMR spectroscopy in the characterization of the very weak halogen bonds of nonfluorinated halogen bond donors with a nitrogenous Lewis base in solution. The ability of the technique to detect the relative strength of iodine-, bromine- and chlorine-centered halogen bonds, as well as solvent and substituent effects was evaluated. Whereas computations on the DFT level indicate that15N NMR chemical shifts reflect the diamagnetic deshielding associated with the formation of a weak halogen bond, the experimentally observed chemical shift differences were on the edge of detectability due to the low molar fraction of halogen-bonded complexes in solution. The formation of the analogous yet stronger hydrogen bond of phenols have induced approximately ten times larger chemical shift changes, and could be detected and correlated to the electronic properties of substituents of the hydrogen bond donors. Overall,15N NMR is shown to be a suitable tool for the characterization of comparably strong secondary interactions in solution, but not sufficiently accurate for the detection of the formation of thermodynamically labile, weak halogen bonded complexes.
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Affiliation(s)
- Sebastiaan B. Hakkert
- Department of Chemistry and Molecular Biology
- University of Gothenburg
- SE-412 96 Gothenburg
- Sweden
| | - Jürgen Gräfenstein
- Department of Chemistry and Molecular Biology
- University of Gothenburg
- SE-412 96 Gothenburg
- Sweden
| | - Mate Erdelyi
- Department of Chemistry and Molecular Biology
- University of Gothenburg
- SE-412 96 Gothenburg
- Sweden
- The Swedish NMR Centre
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19
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Kusama H, Sayama K. Comparative study on the interactions of TEMPO and iodine with organic dyes in dye-sensitized solar cells. J Photochem Photobiol A Chem 2016. [DOI: 10.1016/j.jphotochem.2016.07.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Hęclik K, Dobrowolski JC. On the nonadditivity of the substituent effect in homo-disubstituted pyridines. J PHYS ORG CHEM 2016. [DOI: 10.1002/poc.3656] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Karol Hęclik
- Rzeszów University of Technology; 12 Powstańcow Warszawy-Street 35-959 Rzeszów Poland
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21
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Maugeri L, Asencio-Hernández J, Lébl T, Cordes DB, Slawin AMZ, Delsuc MA, Philp D. Neutral iodotriazoles as scaffolds for stable halogen-bonded assemblies in solution. Chem Sci 2016; 7:6422-6428. [PMID: 28451098 PMCID: PMC5355977 DOI: 10.1039/c6sc01974a] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 06/22/2016] [Indexed: 12/19/2022] Open
Abstract
The halogen bond (XB) donor properties of neutral 1,4-diaryl-5-iodo-1,2,3-triazoles are explored using a combination of computational and experimental results and are shown to be competitive in halogen bonding efficiency with the classic pentafluoroiodobenzene XB donor. The SNAr reactivity of these donors permits the facile assembly of an iodotriazole functionalised with a 3-oxypyridine XB acceptor, thus generating a molecular scaffold capable of undergoing dimerisation through the formation of two halogen bonds. The formation of this halogen-bonded dimer is demonstrated by 1H and DOSY NMR experiments and a plausible structure generated using DFT calculations.
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Affiliation(s)
- Leonardo Maugeri
- School of Chemistry and EaStCHEM , University of St Andrews , North Haugh St Andrews , Fife KY16 9ST , UK . ; ; Tel: +44 (0)1334 467264
| | - Julia Asencio-Hernández
- Institut de Génétique et de Biologie Moléculaire et Cellulaire , INSERM U596 , CNRS UMR 7104 , Université de Strasbourg , 1 rue Laurent Fries , 67404 Illkirch-Graffenstaden , France
| | - Tomáš Lébl
- School of Chemistry and EaStCHEM , University of St Andrews , North Haugh St Andrews , Fife KY16 9ST , UK . ; ; Tel: +44 (0)1334 467264
| | - David B Cordes
- School of Chemistry and EaStCHEM , University of St Andrews , North Haugh St Andrews , Fife KY16 9ST , UK . ; ; Tel: +44 (0)1334 467264
| | - Alexandra M Z Slawin
- School of Chemistry and EaStCHEM , University of St Andrews , North Haugh St Andrews , Fife KY16 9ST , UK . ; ; Tel: +44 (0)1334 467264
| | - Marc-André Delsuc
- Institut de Génétique et de Biologie Moléculaire et Cellulaire , INSERM U596 , CNRS UMR 7104 , Université de Strasbourg , 1 rue Laurent Fries , 67404 Illkirch-Graffenstaden , France
| | - Douglas Philp
- School of Chemistry and EaStCHEM , University of St Andrews , North Haugh St Andrews , Fife KY16 9ST , UK . ; ; Tel: +44 (0)1334 467264
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22
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Tsuzuki S, Uchimaru T, Wakisaka A, Ono T. Magnitude and Directionality of Halogen Bond of Benzene with C6F5X, C6H5X, and CF3X (X = I, Br, Cl, and F). J Phys Chem A 2016; 120:7020-9. [PMID: 27525985 DOI: 10.1021/acs.jpca.6b06295] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Geometries of benzene complexes with C6F5X, C6H5X, and CF3X (X is I, Br, Cl, and F) were optimized, and their interaction energies were evaluated. The CCSD(T) interaction energies at the basis set limit (Eint) of C6F5X (X is I, Br, Cl, and F) with benzene were -3.24, -2.88, -2.31, and -0.92 kcal mol(-1). Eint of C6H5X (X is I, Br, and Cl) with benzene were -2.31, -1.97, and -1.48 kcal mol(-1). The fluorination of halobenzenes slightly enhances the attraction. Eint of CF3X (X is I, Br, Cl, and F) with benzene (-3.11, -2.74, -2.22, and -0.71 kcal mol(-1)) were very close to Eint of corresponding C6F5X with benzene. In contrast to the halogen bond of iodine and bromine with pyridine (n-type halogen bond acceptor) where the main cause of the attraction is the electrostatic interactions, that of halogen bond with benzene (p-type acceptor) is dispersion interaction. In the halogen bonds with p-type acceptors (halogen-π interactions), the electrostatic interactions and induction interactions are small. The overall orbital-orbital interactions are repulsive. The directionality of halogen bonds with p-type acceptors is very weak, owing to the weak electrostatic interactions, in contrast to the strong directionality of the halogen bonds with n-type acceptors and hydrogen bonds.
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Affiliation(s)
- Seiji Tsuzuki
- Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology , 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Tadafumi Uchimaru
- Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology , 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Akihiro Wakisaka
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology , 16-1 Onogawa, Tsukuba, 305-8569, Japan
| | - Taizo Ono
- Structural Materials Research Institute, National Institute of Advanced Industrial Science and Technology , 2266-98, Anagahora, Shimoshidami, Moriyama-ku, Nagoya, Aichi 463-8560 Japan
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23
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Torii H, Noge S. Roles of the scalar and vector components of the solvation effects on the vibrational properties of hydrogen- or halogen-bond accepting stretching modes. Phys Chem Chem Phys 2016; 18:10081-96. [PMID: 27009802 DOI: 10.1039/c5cp08008h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solvation-induced vibrational frequency shifts and infrared (IR) intensity changes of the hydrogen- or halogen-bond accepting stretching modes, especially their dependence on the angular position of the hydrogen- or halogen-bond donating molecule, are examined theoretically. Calculations are carried out for some modes of hydrogen- or halogen-bonding molecular complexes, including the S[double bond, length as m-dash]O stretch of dimethyl sulfoxide-(13)C2H2O, the C[triple bond, length as m-dash]N stretch of acetonitrileH2O, and the amide I' mode of the N-methylacetamide-d1BrNC 1 : 1 complex. It is shown that, in all the example cases dealt with in this study, the frequency shift depends rather strongly on the hydrogen- or halogen-bond angle (e.g., S[double bond, length as m-dash]OH angle), with a larger low-frequency shift as the hydrogen or halogen bond becomes more bent, indicating the generality of the results obtained for the amide I' mode of the N-methylacetamide-d1(2)H2O 1 : 1 complex in a previous study. Contrary to our vague expectation, the frequency shift is not well correlated to the hydrogen- or halogen-bond distance or strength, but nevertheless, it is well reproduced by an electrostatic interaction model if it is carefully constructed by considering the scalar and vector components separately in a reasonable way. On the basis of this electrostatic interaction model, the reason why our vague expectation is not realized is clarified, and a unified understanding is achieved on the hydration-induced high-frequency shift of the C[triple bond, length as m-dash]N stretch and the low-frequency shifts of the S[double bond, length as m-dash]O stretch and amide I'. With regard to the IR intensity, it is shown that, in some of the example cases, it also has rather strong angular position dependence. The mechanism of the IR intensity changes is estimated by analyzing the dipole derivative vector, especially its angular relation with the hydrogen or halogen bond.
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Affiliation(s)
- Hajime Torii
- Department of Chemistry, Faculty of Education, Shizuoka University, 836 Ohya, Shizuoka 422-8529, Japan.
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24
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Vasylyeva V, Catalano L, Nervi C, Gobetto R, Metrangolo P, Resnati G. Characteristic redshift and intensity enhancement as far-IR fingerprints of the halogen bond involving aromatic donors. CrystEngComm 2016. [DOI: 10.1039/c5ce02385h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Characteristic redshift and intensity enhancement of the C–I stretching band have been proven to be distinct signatures of the halogen bond involving iodopentafluorobenzene.
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Affiliation(s)
- Vera Vasylyeva
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”
- Politecnico di Milano
- 20131 Milan, Italy
| | - Luca Catalano
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”
- Politecnico di Milano
- 20131 Milan, Italy
| | - Carlo Nervi
- Department of Chemistry and NIS
- University of Turin
- 10125 Turin, Italy
| | - Roberto Gobetto
- Department of Chemistry and NIS
- University of Turin
- 10125 Turin, Italy
| | - Pierangelo Metrangolo
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”
- Politecnico di Milano
- 20131 Milan, Italy
- VTT-Technical Research Centre of Finland
| | - Giuseppe Resnati
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)
- Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”
- Politecnico di Milano
- 20131 Milan, Italy
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25
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Adasme-Carreño F, Muñoz-Gutierrez C, Alzate-Morales JH. Halogen bonding in drug-like molecules: a computational and systematic study of the substituent effect. RSC Adv 2016. [DOI: 10.1039/c6ra14837a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Systematic study of the effect of fourteen chemical groups at the ortho, para and meta positions of NMA⋯halobenzene complexes showed a significant influence on halogen bonding, and also non-additive effects. A comprehensive description is reported.
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Affiliation(s)
- Francisco Adasme-Carreño
- Centro de Bioinformática y Simulación Molecular
- Facultad de Ingeniería
- Universidad de Talca
- Talca
- Chile
| | - Camila Muñoz-Gutierrez
- Centro de Bioinformática y Simulación Molecular
- Facultad de Ingeniería
- Universidad de Talca
- Talca
- Chile
| | - Jans H. Alzate-Morales
- Centro de Bioinformática y Simulación Molecular
- Facultad de Ingeniería
- Universidad de Talca
- Talca
- Chile
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26
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27
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28
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TSUZUKI S, UCHIMARU T. Origin of Attraction and Directionality of Halogen Bond. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2015. [DOI: 10.2477/jccj.2014-0062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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29
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Han N, Zeng Y, Sun C, Li X, Sun Z, Meng L. N···I Halogen Bonding Interactions: Influence of Lewis Bases on Their Strength and Characters. J Phys Chem A 2014; 118:7058-65. [DOI: 10.1021/jp502558p] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Na Han
- Institute
of Computational Quantum Chemistry, College of Chemistry and Material
Science, Hebei Normal University, Shijiazhuang 050024, PR China
| | - Yanli Zeng
- Institute
of Computational Quantum Chemistry, College of Chemistry and Material
Science, Hebei Normal University, Shijiazhuang 050024, PR China
| | - Cuihong Sun
- Institute
of Computational Quantum Chemistry, College of Chemistry and Material
Science, Hebei Normal University, Shijiazhuang 050024, PR China
- College
of Chemical Engineering, Shijiazhuang University, Shijiazhuang 050035, PR China
| | - Xiaoyan Li
- Institute
of Computational Quantum Chemistry, College of Chemistry and Material
Science, Hebei Normal University, Shijiazhuang 050024, PR China
| | - Zheng Sun
- Institute
of Computational Quantum Chemistry, College of Chemistry and Material
Science, Hebei Normal University, Shijiazhuang 050024, PR China
| | - Lingpeng Meng
- Institute
of Computational Quantum Chemistry, College of Chemistry and Material
Science, Hebei Normal University, Shijiazhuang 050024, PR China
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30
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Lv H, Zhuo HY, Li QZ, Yang X, Li WZ, Cheng JB. Halogen bonds with N-heterocyclic carbenes as halogen acceptors: a partially covalent character. Mol Phys 2014. [DOI: 10.1080/00268976.2014.926031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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31
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Berger G, Soubhye J, van der Lee A, Vande Velde C, Wintjens R, Dubois P, Clément S, Meyer F. Interplay between Halogen Bonding and Lone Pair-π Interactions: A Computational and Crystal Packing Study. Chempluschem 2014; 79:552-558. [DOI: 10.1002/cplu.201400005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Indexed: 11/10/2022]
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32
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Syzgantseva OA, Tognetti V, Joubert L. On the Physical Nature of Halogen Bonds: A QTAIM Study. J Phys Chem A 2013; 117:8969-80. [DOI: 10.1021/jp4059774] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Olga A. Syzgantseva
- Normandy Université, COBRA UMR 6014 and FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére, 76821
Mont Saint Aignan, Cedex, France
| | - Vincent Tognetti
- Normandy Université, COBRA UMR 6014 and FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére, 76821
Mont Saint Aignan, Cedex, France
| | - Laurent Joubert
- Normandy Université, COBRA UMR 6014 and FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesniére, 76821
Mont Saint Aignan, Cedex, France
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33
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A theoretical evidence for cooperativity effects in fluorine-centered halogen bonds: linear (FCN)2–7 and (FNC)2–7 clusters. Struct Chem 2013. [DOI: 10.1007/s11224-013-0303-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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