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Zhu Z, Wang G, Xu Z, Chen Z, Wang J, Shi J, Zhu W. Halogen bonding in differently charged complexes: basic profile, essential interaction terms and intrinsic σ-hole. Phys Chem Chem Phys 2019; 21:15106-15119. [PMID: 31241121 DOI: 10.1039/c9cp01379b] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Studies on halogen bonds (XB) between organohalogens and their acceptors in crystal structures revealed that the XB donor and acceptor could be differently charged, making it difficult to understand the nature of the interaction, especially the negatively charged donor's electrophilicity and positively charged acceptor's nucleophilicity. In this paper, 9 XB systems mimicking all possibly charged halogen bonding interactions were designed and explored computationally. The results revealed that all XBs could be stable, with binding energies after removing background interaction as strong as -1.2, -3.4, and -8.3 kcal mol-1 for Cl, Br, and I involved XBs respectively. Orbital and dispersion interactions are found to be always attractive while unidirectional intermolecular electron transfer from a XB acceptor to a XB donor occurs in all XB complexes. These observations could be attributed to the intrinsic σ-hole of the XB donor and the intrinsic electronic properties of the XB acceptor regardless of their charge states. Intramolecular charge redistribution inside both the donor and the acceptor is found to be system-dependent but always leads to a more stable XB. Accordingly, this study demonstrates that the orbital-based origin of halogen bonds could successfully interpret the complicated behaviour of differently charged XB complexes, while electrostatic interaction may dramatically change the overall bonding strength. The results should further promote the application of halogens in all related areas.
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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. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guimin Wang
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. and 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. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaoqiang Chen
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinan Wang
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiye Shi
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, 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. and University of Chinese Academy of Sciences, Beijing 100049, China and 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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A theoretical study on the coordination behavior of some phosphoryl, carbonyl and sulfoxide derivatives in lanthanide complexation. J Mol Model 2018; 24:328. [PMID: 30374628 DOI: 10.1007/s00894-018-3865-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/08/2018] [Indexed: 10/28/2022]
Abstract
The selectivity of phosphoryl P(O)R3, sulfoxide S(O)R2, and carbonyl C(O)R2 (R = NH2, CH3, OH, and F) derivatives with lanthanide cations (La3+, Eu3+, Lu3+) was studied by density functional theory calculations. Theoretical approaches were also used to investigate energy and the nature of metal-ligand interaction in the model complexes. Atoms in molecules and natural bond orbital (NBO) analyses were accomplished to understand the electronic structure of ligands, L, and the related complexes, L-Ln3+. NBO analysis demonstrated that the negative charge on phosphoryl, carbonyl, and sulfoxide oxygen (OP, OC, and OS) has maximum and minimum values when the connected -R groups are -NH2 and -F. The metal-ligand distance declines as, -F > -OH > -CH3 > -NH2. Charge density at the bond critical point and on the lanthanide cation in the L-Ln3+ complexes varies in the order -F < -OH < -CH3 < -NH2, due to greater ligand to metal charge transfer, which is well explained by energy decomposition analysis. It was also illustrated that E(2) values of Lp(N) → σ*(Y-N) vary in the order P=O ˃ S=O ˃ C=O and the related values of Lp(N) → σ*(Y=O) change as C=O ˃ S=O ˃ P=O in (NH2)nYO ligands (Y = P, C, and S). Trends in the L-Ln3+ CP-corrected bond energies are in good accordance with the optimized OY⋯Ln distances. It seems that, comparing the three types of ligands studied, NH2-substituted are the better coordination ligands. Graphical Abstract Density functional theory (B3LYP) calculations were used to compare structural, electronic and energy aspects of lanthanide (La, Eu, Lu) complexes of phosphine derivatives with those of carbonyls and sulfoxides in which the R- groups connected to the P=O, C=O and S=O are -NH2, -CH3, -OH and -F.
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Quiñonero D. Sigma-hole carbon-bonding interactions in carbon-carbon double bonds: an unnoticed contact. Phys Chem Chem Phys 2018; 19:15530-15540. [PMID: 28581553 DOI: 10.1039/c7cp01780d] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this manuscript, we combine high-level ab initio calculations on some small complexes and a CSD survey to analyze the existence of unprecedented noncovalent carbon bonds in X2C[double bond, length as m-dash]CH2Y systems (Y = electron-rich atom or group). The methylene group is usually seen as a weak hydrogen bond donor when interacting with an electron-rich atom. However, we demonstrate that when the electron-rich atom is located equidistant from the two H atoms and along the C[double bond, length as m-dash]C bond a σ-hole noncovalent carbon-bonding interaction is established, instead of a bifurcated hydrogen bond, as derived from Atoms-in-Molecules (AIM) and Natural bond orbital (NBO) analyses. The physical nature of the interaction has been analyzed using the Symmetry Adapted Perturbation Theory (SAPT) method. The results indicate that electrostatics is very important followed by either the induction or dispersion terms in anionic and neutral complexes, respectively. In addition the CSD analysis reveals the existence of such interactions, giving reliability to our calculations, which are much more numerous for neutral than for anionic Y systems.
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Affiliation(s)
- D Quiñonero
- Department de Química, Universitat de les Illes Balears, Crta. Valldemossa km 7.5, 07122 Palma de Mallorca, Spain.
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Keefe CD, Istvankova Z. Computational study of proper and improper hydrogen bonding in methanol complexes. CAN J CHEM 2011. [DOI: 10.1139/v10-155] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The bulk properties of alcohols, like those of aqueous solutions, are governed mostly by hydrogen bonding; however, in contrast with water molecules, the chemical structure of a simple alcohol such as methanol offers an opportunity to explore the effects of both proper and improper hydrogen bonding on a single hydrogen donor. The presence of the hydroxyl group generally gives rise to a strong proper hydrogen bond, while the methyl group of methanol is likely involved in the weaker improper hydrogen bond, among other weak non-covalent interactions. The effects of the two types of hydrogen bonds on the stability, geometric parameters, and properties of electron density of methanol complexes are examined while considering different geometrical arrangements of the methanol dimer and the binary complexes of methanol with water, acetonitrile, and chloromethane. Subsequently, potential conclusions about the nature of improper hydrogen bonding and the origin of the C–H bond contraction that results upon complex formation are discussed. Quantum theory of atoms in molecules and natural bond orbital methods were used in the analysis; all calculations were performed at the MP2(full)/6-311++G(d,p) level of theory.
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Affiliation(s)
- C. Dale Keefe
- Department of Chemistry, Cape Breton University, Sydney, NS B1P 6L2, Canada
| | - Zuzana Istvankova
- Department of Chemistry, Cape Breton University, Sydney, NS B1P 6L2, Canada
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