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Lai Z, Shen M, Shen Y, Ye YX, Zhu F, Xu J, Ouyang G. Hydrogen bond networks in gas-phase complex anions. RSC Adv 2022; 12:29137-29142. [PMID: 36320744 PMCID: PMC9558071 DOI: 10.1039/d2ra05029c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/02/2022] [Indexed: 11/05/2022] Open
Abstract
Hydrogen bond networks (HBNs) have piqued the interest of the scientific community due to their crucial roles in nature. However, HBNs that are isolated from complicated backgrounds for unraveling their characteristics are still scarce. Herein, we propose that HBNs exist in complex anions formed between α-cyclodextrin (α-CD) and four benzoic acids (RBAs) in the gas phase. The complex anions are facilely extracted from solutions via the electrospray ionization technique, and subsequently activated through collision for the investigation of their transition dynamics. It is revealed that the generation of deprotonated α-CD and neutral RBAs is the unexpected dominant dissociation pathway for all the four complex anions, and the complex anions formed from more acidic RBAs exhibit higher stabilities. These dissociation results are successfully explained by the cooperative stretching dynamics of the proposed HBNs that are formed involving the intramolecular HBN of α-CD and the intermolecular hydrogen bonds (HBs) between α-CD and RBAs. Furthermore, the rarely observed low barrier HBs (LBHBs) are suggested to be present in the HBNs. It is believed that the present complex anions can serve as a facilely accessible and informative model for studying HBNs in the future. Hydrogen bond networks and low barrier hydrogen bonds are demonstrated in the complex anions formed between α-cyclodextrin and benzoic acids.![]()
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Affiliation(s)
- Zhisheng Lai
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Minhui Shen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Yong Shen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Yu-Xin Ye
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Fang Zhu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Jianqiao Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China
| | - Gangfeng Ouyang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry/KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen UniversityGuangzhou510006China,College of Chemistry, Center of Advanced Analysis and Gene Sequencing, Zhengzhou UniversityZhengzhou450001China,Guangdong Provincial Key Laboratory of Emergency Testing for Dangerous Chemicals, Guangdong Institute of Analysis (China National Analytical Center Guangzhou), Guangdong Academy of SciencesGuangzhou510070China
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Méndez-Morales T, Montes-Campos H, Pérez-Rodríguez M, Piñeiro MM. Evaluation of hydrogen storage ability of hydroquinone clathrates using molecular simulations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119487] [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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3
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Xiang BL, Fu L, Li Y, Liu Y. A New Fe(III)/MOF-5(Ni) Catalyst for Highly Selective Synthesis of Catechol from Phenol and Hydrogen Peroxide. ChemistrySelect 2019. [DOI: 10.1002/slct.201803445] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Bai-lin Xiang
- College of Chemistry Engineering; Xiangtan University, Xiangtan; Hunan 411105 China
- College of Chemistry and Materials Engineering; Huaihua University, Huaihua; Hunan 418000 China
| | - Lin Fu
- College of Chemistry Engineering; Xiangtan University, Xiangtan; Hunan 411105 China
| | - Yongfei Li
- College of Chemistry Engineering; Xiangtan University, Xiangtan; Hunan 411105 China
| | - Yuejin Liu
- College of Chemistry Engineering; Xiangtan University, Xiangtan; Hunan 411105 China
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4
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Comesaña A, Pérez-Rodríguez M, Fernández-Fernández AM, Piñeiro MM. A description of hydroquinone clathrates using molecular dynamics: Molecular model and crystalline structures for CH4and CO2guests. J Chem Phys 2018; 148:244502. [PMID: 29960310 DOI: 10.1063/1.5027807] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- A. Comesaña
- Universidade de Vigo, Departamento de Física Aplicada, Campus Lagoas-Marcosende, E36310 Vigo, Spain
| | - M. Pérez-Rodríguez
- Universidade de Vigo, Departamento de Física Aplicada, Campus Lagoas-Marcosende, E36310 Vigo, Spain
| | | | - M. M. Piñeiro
- Universidade de Vigo, Departamento de Física Aplicada, Campus Lagoas-Marcosende, E36310 Vigo, Spain
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5
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Celis-Salazar PJ, Epley CC, Ahrenholtz SR, Maza WA, Usov PM, Morris AJ. Proton-Coupled Electron Transport in Anthraquinone-Based Zirconium Metal–Organic Frameworks. Inorg Chem 2017; 56:13741-13747. [DOI: 10.1021/acs.inorgchem.7b01656] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Charity C. Epley
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | | | - William A. Maza
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Pavel M. Usov
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Amanda J. Morris
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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6
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Frampton CS, Gall JH, MacNicol DD. Total CCl 4 guest alignment in a quasiracemic clathrate closely related to Dianin's compound. CrystEngComm 2017. [DOI: 10.1039/c7ce01275f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the trigonal CCl4quasiracemic clathrate, space group R3, formed from host components S-(−)-Dianin's compound, 4, and its (+)-2R,4R 2-nor methyl analogue, 2, the unprecedented complete ordering of a C–Cl bond of the guest with respect to the c-axial direction and the participation of an unexpected host conformation is reported for the first time.
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Affiliation(s)
| | - James H. Gall
- Department of Chemistry
- University of Glasgow
- Glasgow G12 8QQ
- UK
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7
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Evans JD, Jelfs KE, Day GM, Doonan CJ. Application of computational methods to the design and characterisation of porous molecular materials. Chem Soc Rev 2017; 46:3286-3301. [DOI: 10.1039/c7cs00084g] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Composed from discrete units, porous molecular materials (PMMs) possess properties not observed for conventional, extended solids. Molecular simulations provide crucial understanding for the design and characterisation of these unique materials.
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Affiliation(s)
- Jack D. Evans
- Chimie ParisTech
- PSL Research University
- CNRS
- Institut de Recherche de Chimie Paris
- 75005 Paris
| | - Kim E. Jelfs
- Department of Chemistry
- Imperial College London
- South Kensington
- London
- UK
| | - Graeme M. Day
- Computational Systems Chemistry
- School of Chemistry
- University of Southampton
- Highfield
- Southampton
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Clausen HF, Jørgensen MRV, Cenedese S, Schmøkel MS, Christensen M, Chen YS, Koutsantonis G, Overgaard J, Spackman MA, Iversen BB. Host perturbation in a β-hydroquinone clathrate studied by combined X-ray/neutron charge-density analysis: implications for molecular inclusion in supramolecular entities. Chemistry 2014; 20:8089-98. [PMID: 24828367 DOI: 10.1002/chem.201400129] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Indexed: 11/06/2022]
Abstract
X-ray/neutron (X/N) diffraction data measured at very low temperature (15 K) in conjunction with ab initio theoretical calculations were used to model the crystal charge density (CD) of the host-guest complex of hydroquinone (HQ) and acetonitrile. Due to pseudosymmetry, information about the ordering of the acetonitrile molecules within the HQ cavities is present only in almost extinct, very weak diffraction data, which cannot be measured with sufficient accuracy even by using the brightest X-ray and neutron sources available, and the CD model of the guest molecule was ultimately based on theoretical calculations. On the other hand, the CD of the HQ host structure is well determined by the experimental data. The neutron diffraction data provide hydrogen anisotropic thermal parameters and positions, which are important to obtain a reliable CD for this light-atom-only crystal. Atomic displacement parameters obtained independently from the X-ray and neutron diffraction data show excellent agreement with a |ΔU| value of 0.00058 Å(2) indicating outstanding data quality. The CD and especially the derived electrostatic properties clearly reveal increased polarization of the HQ molecules in the host-guest complex compared with the HQ molecules in the empty HQ apohost crystal structure. It was found that the origin of the increased polarization is inclusion of the acetonitrile molecule, whereas the change in geometry of the HQ host structure following inclusion of the guest has very little effect on the electrostatic potential. The fact that guest inclusion has a profound effect on the electrostatic potential suggests that nonpolarizable force fields may be unsuitable for molecular dynamics simulations of host-guest interaction (e.g., in protein-drug complexes), at least for polar molecules.
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Affiliation(s)
- Henrik F Clausen
- Center for Materials Crystallography, Department of Chemistry and iNANO, Aarhus University (Denmark)
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Nemkevich A, Spackman MA, Corry B. Simulations of guest transport in clathrates of Dianin's compound and hydroquinone. Chemistry 2013; 19:2676-84. [PMID: 23297109 DOI: 10.1002/chem.201202035] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 10/31/2012] [Indexed: 11/06/2022]
Abstract
Clathrates have been proposed for use in a variety of applications including gas storage, mixture separation and catalysis due to the potential for controlled guest diffusion through their porous lattices. Here molecular dynamics simulations are employed to study guest transport in clathrates of hydroquinone (HQ) and Dianin's compound (DC). Systems investigated were HQ with methanol and acetonitrile, and DC with methanol and ethanol. Simulations were set up with one guest in the pore, two guests in the pore and one vacancy in the pore and a filled pore, and free-energy barriers for movement between cavities of the pore were estimated for all cases. Comparison between these simulations indicates that guest transport most likely proceeds by molecules moving from full to empty cavities consecutively, one by one, rather than in a concerted manner. Thus, the presence of empty cavities is very important for guest transport, which becomes more energetically demanding in fully loaded systems. Flexibility of the host can assist guest transport. In the studied DC clathrates transport occurs via an intermediate conformation in which the hydroxyl group of the alcohol guest molecule participates in the hydrogen-bonded ring of the host. We also address the issue of the number of methanol guest molecules that DC accommodates, for which conflicting information exists. We found that this is likely to be temperature dependent and suggest that under some conditions the system is most likely non-stoichiometric.
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Affiliation(s)
- Alexandra Nemkevich
- School of Chemistry and Biochemistry, University of Western Australia, Australia
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Nemkevich A, Corry B, Spackman MA. Computational study of methyl group dynamics in the hydroquinoneclathrate of acetonitrile. Phys Chem Chem Phys 2012; 14:1570-2. [DOI: 10.1039/c2cp23384c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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