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Song J, Wang M, Xu X, Shao Q, Zhao Y, Zhang G, Sun N. Charge-Shift Bonding Propensity in Halogen-Bonded BXY (B Is a Small Lewis Base H 2O or NH 3; X and Y Are Halogen Atoms) Complexes: An NBO/NRT/AIM Investigation. Molecules 2023; 28:6212. [PMID: 37687041 PMCID: PMC10489069 DOI: 10.3390/molecules28176212] [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: 07/26/2023] [Revised: 08/21/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
Charge-shift (CS) bonding is a new bonding paradigm in the field of chemical bonds. Our recent study has revealed that certain Cu/Ag/Au-bonds display both CS bonding and ω-bonding characters. In this investigation, we extend our study to halogen bonding. Our focus is on scrutinizing the CS bonding in halogen-bonded BXY (B is a small Lewis base H2O or NH3; X and Y are halogen atoms) complexes by using natural bond orbital (NBO) analysis, natural resonance theory (NRT), and atoms in molecules (AIM) methods. The primary objective is to establish a connection between halogen bonding (B-X) in BXY and CS bonding in free XY (di-halogens). The calculations indicate that the studied BXY can be classified into two types. One type with a weak halogen bond shows closed-shell interaction. The other type with a stronger B-X interaction exhibits both CS bonding and ω-bonding characters (as seen in NH3ClF, NH3BrF, and NH3IF). Another interesting finding is a novel propensity that the CS bonding in free XY tends to carry over the halogen bonding in BXY, and the same propensity is found in Cu/Ag/Au ω-bonded species. The present study may offer an approach to probe CS bonding in many more 3c/4e ω-bonded molecules.
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Affiliation(s)
- Junjie Song
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Mengyang Wang
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Xiaocheng Xu
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Qinghao Shao
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Ying Zhao
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Guiqiu Zhang
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Nan Sun
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
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Song J, Fu L, Li H, Su Y, Wang Q, Zhang G, Wang J. Equivalent and Complement of the ω-Bonding Model and Charge-Shift Bonding Model: A Natural Bond Orbital/Natural Resonance Theory/Atoms in Molecules Investigation via Cu/Ag/Au Bonding in BMX (B = H 2O, H 2S, NH 3, and PH 3; M = Cu, Ag, and Au; and X = F, Cl, Br, and I). J Phys Chem Lett 2023:5226-5233. [PMID: 37261929 DOI: 10.1021/acs.jpclett.3c01217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Chemical bonding is the language of logic for chemists. Two new resonance bonding models, ω-bonding and charge-shift (CS) bonding, are gaining popularity among chemists. This study investigated the Cu/Ag/Au bonding in BMX (B = H2O, H2S, NH3, and PH3; M = Cu, Ag, and Au; and X = F, Cl, Br, and I) complexes using natural bond orbital (NBO) analysis, natural resonance theory (NRT), and atoms in molecules (AIM) method. The main aim is to reveal the relation between ω-bonding model and CS bonding model via Cu/Ag/Au bonding. Our studies demonstrate that the Cu/Ag/Au bonds exhibit the characteristics of both ω-bonding and CS bonding. Further studies found that ω-bonding and CS bonding models are equivalent and complement each other in understanding the studied Cu/Ag/Au bonding. Another interesting finding is the implication of the omega symbol in the ω-bonding model. These findings could help to promote the communication and CS bonding understanding of many more similar ω-bonded complexes.
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Affiliation(s)
- Junjie Song
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
- Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, People's Republic of China
| | - Lei Fu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Hong Li
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong 250355, People's Republic of China
| | - Yue Su
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
| | - Qiong Wang
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
| | - Guiqiu Zhang
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
| | - Jin Wang
- Key Laboratory of Molecular and Nano Probes, Ministry of Education, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, Shandong 250014, People's Republic of China
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Varadwaj A, Varadwaj PR, Marques HM, Yamashita K. The Pnictogen Bond: The Covalently Bound Arsenic Atom in Molecular Entities in Crystals as a Pnictogen Bond Donor. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27113421. [PMID: 35684359 PMCID: PMC9181914 DOI: 10.3390/molecules27113421] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/08/2022] [Accepted: 05/17/2022] [Indexed: 12/04/2022]
Abstract
In chemical systems, the arsenic-centered pnictogen bond, or simply the arsenic bond, occurs when there is evidence of a net attractive interaction between the electrophilic region associated with a covalently or coordinately bound arsenic atom in a molecular entity and a nucleophile in another or the same molecular entity. It is the third member of the family of pnictogen bonds formed by the third atom of the pnictogen family, Group 15 of the periodic table, and is an inter- or intramolecular noncovalent interaction. In this overview, we present several illustrative crystal structures deposited into the Cambridge Structure Database (CSD) and the Inorganic Chemistry Structural Database (ICSD) during the last and current centuries to demonstrate that the arsenic atom in molecular entities has a significant ability to act as an electrophilic agent to make an attractive engagement with nucleophiles when in close vicinity, thereby forming σ-hole or π-hole interactions, and hence driving (in part, at least) the overall stability of the system’s crystalline phase. This overview does not include results from theoretical simulations reported by others as none of them address the signatory details of As-centered pnictogen bonds. Rather, we aimed at highlighting the interaction modes of arsenic-centered σ- and π-holes in the rationale design of crystal lattices to demonstrate that such interactions are abundant in crystalline materials, but care has to be taken to identify them as is usually done with the much more widely known noncovalent interactions in chemical systems, halogen bonding and hydrogen bonding. We also demonstrate that As-centered pnictogen bonds are usually accompanied by other primary and secondary interactions, which reinforce their occurrence and strength in most of the crystal structures illustrated. A statistical analysis of structures deposited into the CSD was performed for each interaction type As···D (D = N, O, S, Se, Te, F, Cl, Br, I, arene’s π system), thus providing insight into the typical nature of As···D interaction distances and ∠R–As···D bond angles of these interactions in crystals, where R is the remainder of the molecular entity.
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Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Tokyo 113-8656, Japan;
- Correspondence: (A.V.); (P.R.V.)
| | - Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Tokyo 113-8656, Japan;
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa;
- Correspondence: (A.V.); (P.R.V.)
| | - Helder M. Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa;
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo 7-3-1, Tokyo 113-8656, Japan;
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