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Wang K, Yang S, Yu X, Bai M, Ye H, Xu Y, Zhao L, Wu D, Li X, Weng L, Li Y. Microplastics degradation stimulated by in-situ bioelectric field in agricultural soils. ENVIRONMENT INTERNATIONAL 2023; 177:108035. [PMID: 37329759 DOI: 10.1016/j.envint.2023.108035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/15/2023] [Accepted: 06/09/2023] [Indexed: 06/19/2023]
Abstract
Bioelectric field is a stimulated force to degrade xenobiotic pollutants in soils. However, the effect of bioelectric field on microplastics (MPs) aging is unclear. The degradation behavior of polyvinyl chloride (PVC), polyethylene (PE) and polylactic acid (PLA) was investigated in an agricultural soil microbial electrochemical system in which bioelectric field was generated in-situ by native microbes. Based on the density function theory, the energy gaps between the highest and the lowest occupied molecular orbitals of the three polymers with periodic structure were 4.20, 7.24 and 10.09 eV respectively, and further decreased under the electric field, indicating the higher hydrolysis potential of PLA. Meanwhile, the mass loss of PLA in the closed-circuit group (CC) was the highest on day 120, reaching 8.94%, which was 3.01-3.54 times of that without bioelectric field stimulation. This was mainly due to the enrichment of plastic-degrading bacteria and a robust co-occurrence network as the deterministic assembly process, e.g., the abundance of potential plastic-degrading bacteria on the surface of PLA and PVC in the CC increased by 1.92 and 1.30 times, respectively, compared to the open-circuit group. In terms of functional genes, the xenobiotic biodegradation and metabolism capacity of plasticsphere in the CC were stronger than that in soil, and determined by the bioaccessibility of soil nitrogen and carbon. Overall, this study explored the promoting effect of bioelectric field on the degradation of MPs and reveled the mechanism from quantum chemical calculations and microbial community analysis, which provides a novel perception to the in-situ degradation of MPs.
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Affiliation(s)
- Kai Wang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Side Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Xin Yu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Mohan Bai
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Huike Ye
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Yan Xu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Lixia Zhao
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Dan Wu
- Tianjin Eco-Environmental Monitoring Center, Tianjin 300191, China.
| | - Xiaojing Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China.
| | - Liping Weng
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs / Key Laboratory of Original Agro-Environmental Pollution Prevention and Control, MARA / Tianjin Key Laboratory of Agro-Environment and Agro-Product Safety, Tianjin 300191, China
| | - Yongtao Li
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
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Spicher S, Caldeweyher E, Hansen A, Grimme S. Benchmarking London dispersion corrected density functional theory for noncovalent ion-π interactions. Phys Chem Chem Phys 2021; 23:11635-11648. [PMID: 33978015 DOI: 10.1039/d1cp01333e] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The strongly attractive noncovalent interactions of charged atoms or molecules with π-systems are important binding motifs in many chemical and biological systems. These so-called ion-π interactions play a major role in enzymes, molecular recognition, and for the structure of proteins. In this work, a molecular test set termed IONPI19 is compiled for inter- and intramolecular ion-π interactions, which is well balanced between anionic and cationic systems. The IONPI19 set includes interaction energies of significantly larger molecules (up to 133 atoms) than in other ion-π test sets and covers a broad range of binding motifs. Accurate (local) coupled cluster values are provided as reference. Overall, 19 density functional approximations, including seven (meta-)GGAs, eight hybrid functionals, and four double-hybrid functionals combined with three different London dispersion corrections, are benchmarked for interaction energies. DFT results are further compared to wave function based methods such as MP2 and dispersion corrected Hartree-Fock. Also, the performance of semiempirical QM methods such as the GFNn-xTB and PMx family of methods is tested. It is shown that dispersion-uncorrected DFT underestimates ion-π interactions significantly, even though electrostatic interactions dominate the overall binding. Accordingly, the new charge dependent D4 dispersion model is found to be consistently better than the standard D3 correction. Furthermore, the functional performance trend along Jacob's ladder is generally obeyed and the reduction of the self-interaction error leads to an improvement of (double) hybrid functionals over (meta-)GGAs, even though the effect of the SIE is smaller than expected. Overall, the double-hybrids PWPB95-D4/QZ and revDSD-PBEP86-D4/QZ turned out to be the most reliable among all assessed methods for the description of ion-π interactions, which opens up new perspectives for systems where coupled cluster calculations are no longer computationally feasible.
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Affiliation(s)
- Sebastian Spicher
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Eike Caldeweyher
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany.
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Wan Z, Wang QD. Accurate prediction of enthalpy of formation combined with AM1 method and molecular descriptors. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Fishing wild-type sparing inhibitors of proto-oncogene c-met variants in renal cell carcinoma from a curated tyrosine kinase inhibitor pool using analog-sensitive kinase technology. Biochimie 2018; 152:188-197. [DOI: 10.1016/j.biochi.2018.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/09/2018] [Indexed: 12/25/2022]
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Zhao Y, Jiao Y, Sun F, Liu X. Revisiting the molecular mechanism of acquired resistance to reversible tyrosine kinase inhibitors caused by EGFR gatekeeper T790M mutation in non-small-cell lung cancer. Med Chem Res 2018. [DOI: 10.1007/s00044-018-2224-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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6
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Yang X, Yang F, Wu RZ, Yan CX, Zhou DG, Zhou PP, Yao X. Linear σ-hole⋯C O⋯σ-hole intermolecular interactions between carbon monoxide and dihalogen molecules XY (X, Y = Cl, Br). J Mol Graph Model 2017; 76:419-428. [DOI: 10.1016/j.jmgm.2017.07.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/23/2017] [Accepted: 07/25/2017] [Indexed: 12/21/2022]
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López E, Lucas JM, de Andrés J, Albertí M, Bofill JM, Aguilar A. The role of Li + ions in the gas phase dehydrohalogenation and dehydration reactions of i-C 3H 7Br and i-C 3H 7OH molecules studied by radiofrequency-guided ion beam techniques and ab initio methods. J Chem Phys 2017; 146:134301. [DOI: 10.1063/1.4979296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- E. López
- Departament de Ciència de Materials i Química Física, Institut de Química Teòrica i Computacional, Universitat de Barcelona, Martí i Franquès, 1, 08028 Barcelona, Spain
| | - J. M. Lucas
- Departament de Ciència de Materials i Química Física, Institut de Química Teòrica i Computacional, Universitat de Barcelona, Martí i Franquès, 1, 08028 Barcelona, Spain
| | - J. de Andrés
- Departament de Ciència de Materials i Química Física, Institut de Química Teòrica i Computacional, Universitat de Barcelona, Martí i Franquès, 1, 08028 Barcelona, Spain
| | - M. Albertí
- Departament de Ciència de Materials i Química Física, Institut de Química Teòrica i Computacional, Universitat de Barcelona, Martí i Franquès, 1, 08028 Barcelona, Spain
| | - J. M. Bofill
- Departament de Química Inorgànica i Química Orgànica, Institut de Química Teòrica i Computacional, Universitat de Barcelona, Martí i Franquès, 1, 08028 Barcelona, Spain
| | - A. Aguilar
- Departament de Ciència de Materials i Química Física, Institut de Química Teòrica i Computacional, Universitat de Barcelona, Martí i Franquès, 1, 08028 Barcelona, Spain
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Yang X, Yan CX, Yang F, Zhou DG, Zhou PP, Liu S. Linear σ-Hole Bonding Dimers and Trimers Between Dihalogen Molecules XY (X, Y=Cl, Br) and Carbon Monoxide. ChemistrySelect 2017. [DOI: 10.1002/slct.201700075] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xing Yang
- State Key Laboratory of Applied Organic Chemistry; Key Laboratory of NonferrousMetal Chemistry and Resources Utilization of Gansu Province; College ofChemistry and Chemical Engineering; Lanzhou University; 222 South TianshuiRoad 730000 Lanzhou P. R. China
| | - Chao-Xian Yan
- State Key Laboratory of Applied Organic Chemistry; Key Laboratory of NonferrousMetal Chemistry and Resources Utilization of Gansu Province; College ofChemistry and Chemical Engineering; Lanzhou University; 222 South TianshuiRoad 730000 Lanzhou P. R. China
| | - Fan Yang
- State Key Laboratory of Applied Organic Chemistry; Key Laboratory of NonferrousMetal Chemistry and Resources Utilization of Gansu Province; College ofChemistry and Chemical Engineering; Lanzhou University; 222 South TianshuiRoad 730000 Lanzhou P. R. China
| | - Da-Gang Zhou
- State Key Laboratory of Applied Organic Chemistry; Key Laboratory of NonferrousMetal Chemistry and Resources Utilization of Gansu Province; College ofChemistry and Chemical Engineering; Lanzhou University; 222 South TianshuiRoad 730000 Lanzhou P. R. China
| | - Pan-Pan Zhou
- State Key Laboratory of Applied Organic Chemistry; Key Laboratory of NonferrousMetal Chemistry and Resources Utilization of Gansu Province; College ofChemistry and Chemical Engineering; Lanzhou University; 222 South TianshuiRoad 730000 Lanzhou P. R. China
| | - Shubin Liu
- Research Computing Center; University of North Carolina; Chapel Hill, NC 27599 USA
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dos Santos RB, Rivelino R, Mota FDB, Kakanakova-Georgieva A, Gueorguiev GK. Feasibility of novel (H3C)nX(SiH3)3−ncompounds (X = B, Al, Ga, In): structure, stability, reactivity, and Raman characterization from ab initio calculations. Dalton Trans 2015; 44:3356-66. [DOI: 10.1039/c4dt03406f] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stability of the (H3C)nX(SiH3)3−ncompounds.
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Affiliation(s)
- Renato B. dos Santos
- Instituto de Física
- Universidade Federal da Bahia
- 40210-340 Salvador
- Brazil
- Department of Physics
| | - R. Rivelino
- Instituto de Física
- Universidade Federal da Bahia
- 40210-340 Salvador
- Brazil
| | - F. de Brito Mota
- Instituto de Física
- Universidade Federal da Bahia
- 40210-340 Salvador
- Brazil
| | | | - G. K. Gueorguiev
- Department of Physics
- Chemistry and Biology (IFM)
- Linköping University
- 581 83 Linköping
- Sweden
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Mezei PD, Csonka GI, Ruzsinszky A, Sun J. Accurate, Precise, and Efficient Theoretical Methods To Calculate Anion−π Interaction Energies in Model Structures. J Chem Theory Comput 2014; 11:360-71. [DOI: 10.1021/ct5008263] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Pál D. Mezei
- Department
of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, H-1521 Budapest, Hungary
| | - Gábor I. Csonka
- Department
of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, H-1521 Budapest, Hungary
| | - Adrienn Ruzsinszky
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Jianwei Sun
- Department of Physics, Temple University, Philadelphia, Pennsylvania 19122, United States
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Suresh DM, Amalanathan M, Sebastian S, Sajan D, Hubert Joe I, Bena Jothy V, Nemec I. Vibrational spectral investigation and natural bond orbital analysis of pharmaceutical compound 7-Amino-2,4-dimethylquinolinium formate - DFT approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 115:595-602. [PMID: 23872018 DOI: 10.1016/j.saa.2013.06.077] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Revised: 06/14/2013] [Accepted: 06/19/2013] [Indexed: 06/02/2023]
Abstract
The molecular geometry, the normal mode frequencies and corresponding vibrational assignments, natural bond orbital analysis and the HOMO-LUMO analysis of 7-Amino-2,4-dimethylquinolinium formate in the ground state were performed by B3LYP levels of theory using the 6-31G(d) basis set. The optimised bond lengths and bond angles are in good agreement with the X-ray data. The vibrational spectra of the title compound which is calculated by DFT method, reproduces vibrational wave numbers and intensities with an accuracy which allows reliable vibrational assignments. The possibility of N-H⋯O hydrogen bonding was identified using NBO analysis. Natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction.
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Affiliation(s)
- D M Suresh
- Department of Physics, Government Arts College, Udhagamandalam, Tamil Nadu, India
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12
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CHENG CHENG, ZHANG MIN, SHENG LI. AB INITIO AND DFT STUDY OF NON-COVALENT INTERACTIONS BETWEEN RARE GAS ATOMS AND AROMATIC RINGS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613500120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this paper, the weak interaction between aromatic rings (ARs) and rare gas (Rg) atoms has been studied using ab initio calculation and density functional theory (DFT). The augmented Dunning basis sets were used, and the convergence test was performed up to aug-cc-pV5Z. Among the computationally feasible methods, ωB97XD performed the best for these non-covalent systems. NBO analysis was performed to investigate the nature of the Rg/AR interactions. In this type of weak interaction, the induced and instantaneous dipole and charge transfer character both contribute to the interaction energies and equilibrium distances.
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Affiliation(s)
- CHENG CHENG
- Department of Chemistry, Natural Science Research Center, Academy of Fundamental and Interdisciplinary Sciences, Harbin Institute of Technology, Harbin 150080, P. R. China
| | - MIN ZHANG
- Department of Chemistry, Natural Science Research Center, Academy of Fundamental and Interdisciplinary Sciences, Harbin Institute of Technology, Harbin 150080, P. R. China
| | - LI SHENG
- Department of Chemistry, Natural Science Research Center, Academy of Fundamental and Interdisciplinary Sciences, Harbin Institute of Technology, Harbin 150080, P. R. China
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Iwata S. Dispersion energy evaluated by using locally projected occupied and excited molecular orbitals for molecular interaction. J Chem Phys 2012; 135:094101. [PMID: 21913747 DOI: 10.1063/1.3629777] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The dispersion terms are evaluated with the perturbation theory based on the locally projected molecular orbitals. A series of model systems, including some of the S22 set, is examined, and the calculated binding energies are compared with the published results. The basis set dependence is also examined. The dispersion energy correction is evaluated by taking into account the double excitations only of the dispersion type electron configurations and is added to the 3rd order single excitation perturbation energy, which is a good approximation to the counterpoise (CP) corrected Hartree-Fock (HF) binding energy. The procedure is the approximate "CP corrected HF + D" method. It ensures that the evaluated binding energy is approximately free of the basis set superposition error without the CP procedure. If the augmented basis functions are used, the evaluated binding energies for the predominantly dispersion-bound systems, such as rare gas dimers and halogen bonded clusters, agree with those of the reference calculations within 1 kcal mol(-1) (4 kJ mol(-1)). The limitation of the present method is also discussed.
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Affiliation(s)
- Suehiro Iwata
- Toyota Physical and Chemical Research Institute, Nagakute, Aichi 480-1192, Japan.
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14
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A theoretical study of the hydrogen bonding properties of H2BNH2: Some considerations on the basis set superposition error issue. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.04.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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15
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Quiñonero D, Estarellas C, Frontera A, Deyà PM. A methodological analysis for the assessment of non-covalent π interactions. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.04.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Zhou PP, Qiu WY, Liu S, Jin NZ. Halogen as halogen-bonding donor and hydrogen-bonding acceptor simultaneously in ring-shaped H3N·X(Y)·HF (X = Cl, Br and Y = F, Cl, Br) complexes. Phys Chem Chem Phys 2011; 13:7408-18. [PMID: 21423995 DOI: 10.1039/c1cp00025j] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of ring-shaped molecular complexes formed by H(3)N, HF and XY (X = Cl, Br and Y = F, Cl, Br) have been investigated at the MP2/aug-cc-pVTZ level of theory. Their optimized geometry, stretching mode, and interaction energy have been obtained. We found that each complex possesses two red-shifted hydrogen bonds and one red-shifted halogen bond, and the two hydrogen bonds exhibit strong cooperative effects on the halogen bond. The cooperativity among the NH(3)···FH, FH···XY and H(3)N···XY interactions leads to the formations of these complexes. The AIM analysis has been performed at the CCSD(T)/aug-cc-pVQZ level of theory to examine the topological characteristics at the bond critical point and at the ring critical point, confirming the coexistence of the two hydrogen bonds and one halogen bond for each complex. The NBO analysis carried out at the B3LYP/aug-cc-pVTZ level of theory demonstrates the effects of hyperconjugation, hybridization, and polarization coming into play during the hydrogen and halogen bonding formations processes, based on which a clockwise loop of charge transfer was discovered. The molecular electrostatic potential has been employed to explore the formation mechanisms of these molecular complexes.
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Affiliation(s)
- Pan-Pan Zhou
- Department of Chemistry, State Key Laboratory of Applied Organic Chemistry, Lanzhou University, 222 South Tianshui Road, Lanzhou 730000, PR China
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