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Schmahl S, Horn F, Jin J, Westphal H, Belder D, Asmis KR. Online-Monitoring of the Enantiomeric Ratio in Microfluidic Chip Reactors Using Chiral Selector Ion Vibrational Spectroscopy. Chemphyschem 2024; 25:e202300975. [PMID: 38418402 DOI: 10.1002/cphc.202300975] [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: 12/18/2023] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024]
Abstract
A novel experimental approach for the rapid online monitoring of the enantiomeric ratio of chiral analytes in solution is presented. The charged analyte is transferred to the gas phase by electrospray. Diastereomeric complexes are formed with a volatile chiral selector in a buffer-gas-filled ion guide held at room temperature, mass-selected, and subsequently spectrally differentiated by cryogenic ion trap vibrational spectroscopy. Based on the spectra of the pure complexes in a small diastereomer-specific spectral range, the composition of diastereomeric mixtures is characterized using the cosine similarity score, from which the enantiomeric ratio in the solution is determined. The method is demonstrated for acidified alanine solutions and using three different chiral selectors (2-butanol, 1-phenylethanol, 1-amino-2-propanol). Among these, 2-butanol is the best choice as a selector for protonated alanine, also because the formation ratio of the corresponding diastereomeric complexes is found to be independent of the nature of the enantiomer. Subsequently, a microfluidic chip is implemented to mix enantiomerically pure alanine solutions continuously and determine the enantiomeric ratio online with minimal sample consumption within one minute and with competitive accuracy.
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Affiliation(s)
- Sonja Schmahl
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstraße 2, 04103, Leipzig, Germany
| | - Francine Horn
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstraße 2, 04103, Leipzig, Germany
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Jiaye Jin
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstraße 2, 04103, Leipzig, Germany
| | - Hannes Westphal
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, 04103, Leipzig, Germany
| | - Detlev Belder
- Institut für Analytische Chemie, Universität Leipzig, Linnéstraße 3, 04103, Leipzig, Germany
| | - Knut R Asmis
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstraße 2, 04103, Leipzig, Germany
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2
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Disassembly of Amyloid Fibril with Infrared Free Electron Laser. Int J Mol Sci 2023; 24:ijms24043686. [PMID: 36835098 PMCID: PMC9967569 DOI: 10.3390/ijms24043686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Amyloid fibril causes serious amyloidosis such as neurodegenerative diseases. The structure is composed of rigid β-sheet stacking conformation which makes it hard to disassemble the fibril state without denaturants. Infrared free electron laser (IR-FEL) is an intense picosecond pulsed laser that is oscillated through a linear accelerator, and the oscillation wavelengths are tunable from 3 μm to 100 μm. Many biological and organic compounds can be structurally altered by the mode-selective vibrational excitations due to the wavelength variability and the high-power oscillation energy (10-50 mJ/cm2). We have found that several different kinds of amyloid fibrils in amino acid sequences were commonly disassembled by the irradiation tuned to amide I (6.1-6.2 μm) where the abundance of β-sheet decreased while that of α-helix increased by the vibrational excitation of amide bonds. In this review, we would like to introduce the IR-FEL oscillation system briefly and describe combination studies of experiments and molecular dynamics simulations on disassembling amyloid fibrils of a short peptide (GNNQQNY) from yeast prion and 11-residue peptide (NFLNCYVSGFH) from β2-microglobulin as representative models. Finally, possible applications of IR-FEL for amyloid research can be proposed as a future outlook.
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3
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Andersson Å, Yatsyna V, Linares M, Rijs A, Zhaunerchyk V. Indication of 3 10-Helix Structure in Gas-Phase Neutral Pentaalanine. J Phys Chem A 2023; 127:938-945. [PMID: 36669091 PMCID: PMC9900583 DOI: 10.1021/acs.jpca.2c07863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We investigate the gas-phase structure of the neutral pentaalanine peptide. The IR spectrum in the 340-1820 cm-1 frequency range is obtained by employing supersonic jet cooling, infrared multiphoton dissociation, and vacuum-ultraviolet action spectroscopy. Comparison with quantum chemical spectral calculations suggests that the molecule assumes multiple stable conformations, mainly of two structure types. In the most stable conformation theoretically found, the N-terminus forms a C5 ring and the backbone resembles that of an 310-helix with two β-turns. Additionally, the conformational preferences of pentaalanine have been evaluated using Born-Oppenheimer molecular dynamics, showing that a nonzero simulation time step causes a systematic frequency shift.
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Affiliation(s)
- Åke Andersson
- Department
of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Vasyl Yatsyna
- Department
of Physics, University of Gothenburg, 41296 Gothenburg, Sweden,FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands,Laboratoire
de Chimie Physique Moléculaire, École
Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Mathieu Linares
- Laboratory
of Organic Electronics and Group of Scientific Visualization Department
of Science and Technology (ITN), Linköping
University, 601 74 Norrköping, Sweden
| | - Anouk Rijs
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands,Division
of BioAnalytical Chemistry, AIMMS Amsterdam Institute of Molecular
and Life Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV, Amsterdam, The Netherlands,
| | - Vitali Zhaunerchyk
- Department
of Physics, University of Gothenburg, 41296 Gothenburg, Sweden,
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Okumura H, Kawasaki T, Nakamura K. Probing protein misfolding and dissociation with an infrared free-electron laser. Methods Enzymol 2022; 679:65-96. [PMID: 36682873 DOI: 10.1016/bs.mie.2022.08.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Misfolding is observed in the mutant proteins that are causative for neurodegenerative disorders such as polyglutamine diseases. These proteins are prone to aggregate in the cytoplasm and nucleus of cells. To reproduce cells with the aggregated proteins, gene expression system is usually applied, in which the expression construct having the mutated DNA sequence of the interest is transfected into cells. The transfected DNA is finally converted into the mutant protein, which is gradually aggregated in the cells. In addition, a simple method to prepare the cells having aggregates inside has been recently applied. Peptides were first aggregated by incubating them in water. The aggregates are spontaneously taken up by cells because aggregated proteins generally transfer between cells. Peptides with different degrees of aggregation can be made by changing the incubation times and temperatures, which enables to examine contribution of aggregation to the toxicity to the recipient cells. Moreover, such cells can be used for therapeutic researches of diseases in which aggregates are involved. In this chapter, we show methods to induce aggregation of peptides. The functional analyses of the cells with aggregates are also described. Then, experimental dissociation of the aggregates produced using this method by mid infrared free electron laser irradiation and its theoretical support by molecular dynamics simulation are introduced as the therapeutic research for neurodegenerative disorders.
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Affiliation(s)
- Hisashi Okumura
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Takayasu Kawasaki
- Accelerator Laboratory, High Energy Accelerator Research Organization, Tsukuba, Ibaraki, Japan
| | - Kazuhiro Nakamura
- Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, Maebashi, Gunma, Japan.
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5
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Jindo M, Nakamura K, Okumura H, Tsukiyama K, Kawasaki T. Application study of infrared free-electron lasers towards the development of amyloidosis therapy. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:1133-1140. [PMID: 36073871 PMCID: PMC9455209 DOI: 10.1107/s1600577522007330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 07/15/2022] [Indexed: 05/27/2023]
Abstract
Amyloidosis is known to be caused by the deposition of amyloid fibrils into various biological tissues; effective treatments for the disease are little established today. An infrared free-electron laser (IR-FEL) is an accelerator-based picosecond-pulse laser having tunable infrared wavelengths. In the current study, the irradiation effect of an IR-FEL was tested on an 11-residue peptide (NFLNCYVSGFH) fibril from β2-microglobulin (β2M) with the aim of applying IR-FELs to amyloidosis therapy. Infrared microspectroscopy (IRM) and scanning electron microscopy showed that a fibril of β2M peptide was clearly dissociated by IR-FEL at 6.1 µm (amide I) accompanied by a decrease of the β-sheet and an increase of the α-helix. No dissociative process was recognized at 6.5 µm (amide II) as well as at 5.0 µm (non-specific wavelength). Equilibrium molecular dynamics simulations indicated that the α-helix can exist stably and the probability of forming interchain hydrogen bonds associated with the internal asparagine residue (N4) is notably reduced compared with other amino acids after the β-sheet is dissociated by amide I specific irradiation. This result implies that N4 plays a key role for recombination of hydrogen bonds in the dissociation of the β2M fibril. In addition, the β-sheet was disrupted at temperatures higher than 340 K while the α-helix did not appear even though the fibril was heated up to 363 K as revealed by IRM. The current study gives solid evidence for the laser-mediated conversion from β-sheet to α-helix in amyloid fibrils at the molecular level.
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Affiliation(s)
- Mikiko Jindo
- Department of Chemistry, Faculty of Science Division I, Tokyo University of Science, 1–3 Kagurazaka, Tokyo 184-8501, Japan
| | - Kazuhiro Nakamura
- Department of Laboratory Sciences, Gunma University, Graduate School of Health Sciences, 3-39-22, Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Hisashi Okumura
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Department of Structural Molecular Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
| | - Koichi Tsukiyama
- Department of Chemistry, Faculty of Science Division I, Tokyo University of Science, 1–3 Kagurazaka, Tokyo 184-8501, Japan
- IR Free Electron Laser Research Center, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Takayasu Kawasaki
- IR Free Electron Laser Research Center, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- Accelerator Laboratory, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
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6
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Wang H, Heger M, Al-Jabiri MH, Xu Y. Vibrational Spectroscopy of Homo- and Heterochiral Amino Acid Dimers: Conformational Landscapes. Molecules 2021; 27:38. [PMID: 35011269 PMCID: PMC8746356 DOI: 10.3390/molecules27010038] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/15/2021] [Accepted: 12/19/2021] [Indexed: 12/19/2022] Open
Abstract
The homo- and heterochiral protonated dimers of asparagine with serine and with valine were investigated using infrared multiple-photon dissociation (IRMPD) spectroscopy. Extensive quantum-chemical calculations were used in a three-tiered strategy to screen the conformational spaces of all four dimer species. The resulting binary structures were further grouped into five different types based on their intermolecular binding topologies and subunit configurations. For each dimer species, there are eight to fourteen final conformational geometries within a 10 kJ mol-1 window of the global minimum structure for each species. The comparison between the experimental IRMPD spectra and the simulated harmonic IR features allowed us to clearly identify the types of structures responsible for the observation. The monomeric subunits of the observed homo- and heterochiral dimers are compared to the corresponding protonated/neutral amino acid monomers observed experimentally in previous IRMDP/rotational spectroscopic studies. Possible chirality and kinetic influences on the experimental IRMPD spectra are discussed.
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Affiliation(s)
| | | | | | - Yunjie Xu
- Department of Chemistry, University of Alberta, Edmonton, Alberta, AB T6G 2G2, Canada; (H.W.); (M.H.); (M.H.A.-J.)
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Andersson Å, Poline M, Houthuijs KJ, van Outersterp RE, Berden G, Oomens J, Zhaunerchyk V. IRMPD Spectroscopy of Homo- and Heterochiral Asparagine Proton-Bound Dimers in the Gas Phase. J Phys Chem A 2021; 125:7449-7456. [PMID: 34428065 PMCID: PMC8419839 DOI: 10.1021/acs.jpca.1c05667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 08/11/2021] [Indexed: 12/16/2022]
Abstract
We investigate gas-phase structures of homo- and heterochiral asparagine proton-bound dimers with infrared multiphoton dissociation (IRMPD) spectroscopy and quantum-chemical calculations. Their IRMPD spectra are recorded at room temperature in the range of 500-1875 and 3000-3600 cm-1. Both varieties of asparagine dimers are found to be charge-solvated based on their IRMPD spectra. The location of the principal intramolecular H-bond is discussed in light of harmonic frequency analyses using the B3LYP functional with GD3BJ empirical dispersion. Contrary to theoretical analyses, the two spectra are very similar.
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Affiliation(s)
- Åke Andersson
- Department
of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
| | - Mathias Poline
- Department
of Physics, Stockholm University, 10691 Stockholm, Sweden
| | - Kas J. Houthuijs
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Rianne E. van Outersterp
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Giel Berden
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Jos Oomens
- FELIX
Laboratory, Institute for Molecules and Materials, Radboud University, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands
| | - Vitali Zhaunerchyk
- Department
of Physics, University of Gothenburg, 41296 Gothenburg, Sweden
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8
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Polewski L, Springer A, Pagel K, Schalley CA. Gas-Phase Structural Analysis of Supramolecular Assemblies. Acc Chem Res 2021; 54:2445-2456. [PMID: 33900743 DOI: 10.1021/acs.accounts.1c00080] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Ion mobility spectrometry and gas-phase IR action spectroscopy are two structure-sensitive mass-spectrometric methods becoming more popular recently. While ion mobility spectrometry provides collision cross sections as a size and shape dependent parameter of an ion of interest, gas-phase spectroscopy identifies functional groups and is capable of distinguishing different isomers. Both methods have recently found application for the investigation of supramolecular assemblies. We here highlight several aspects.Starting with the characterization of switching states in azobenzene photoswitches as well as redox-switchable lasso-type pseudorotaxanes, structures of isomers can be distinguished and mechanistic details analyzed. Ion mobility mass spectrometry in combination with gas-phase H/D-exchange reactions unravels subtle structural details as described for the chiral recognition of crown ether amino acid complexes. Gas-phase IR spectroscopy allows identification of details of the binding patterns in dimeric amino acid clusters as well as the serine octamer. This research can be extended into the analysis of peptide assemblies that are of medical relevance, for example, in Alzheimer's disease, and into a general hydrophobicity scale for natural as well as synthetic amino acids. The development of ultracold gas-phase spectroscopy that for example makes use of ions trapped in liquid helium droplets provides access to very well resolved spectra. The combination of ion mobility separation of ions with subsequent spectroscopic analysis even permits separation of different isomers and studying them separately with respect to their structure. This represents a great advantage of these gas-phase methods over solution experiments, in which the supramolecular complexes under study typically equilibrate and thus prevent a separate investigation of different isomers. At the end of this overview, we will discuss larger and more complex supramolecules, among them giant halogen-bonded cages and complex intertwined topologies such as molecular knots and Solomon links.
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Affiliation(s)
- Lukasz Polewski
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 20-22, 14195 Berlin, Germany
| | - Andreas Springer
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 20-22, 14195 Berlin, Germany
| | - Kevin Pagel
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 20-22, 14195 Berlin, Germany
| | - Christoph A. Schalley
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 20-22, 14195 Berlin, Germany
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9
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Chiavarino B, Sinha RK, Crestoni ME, Corinti D, Filippi A, Fraschetti C, Scuderi D, Maitre P, Fornarini S. Binding Motifs in the Naked Complexes of Target Amino Acids with an Excerpt of Antitumor Active Biomolecule: An Ion Vibrational Spectroscopy Assay. Chemistry 2021; 27:2348-2360. [PMID: 33175428 DOI: 10.1002/chem.202003555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/30/2020] [Indexed: 11/06/2022]
Abstract
The structures of proton-bound complexes of 5,7-dimethoxy-4H-chromen-4-one (1) and basic amino acids (AAs), namely, histidine (His) and lysine (Lys), have been examined by means of mass spectrometry coupled with IR ion spectroscopy and quantum chemical calculations. This selection of systems is based on the fact that 1 represents a portion of glabrescione B, a natural small molecule of promising antitumor activity, while His and Lys are protein residues lining the cavity of the alleged receptor binding site. These species are thus a model of the bioactive adduct, although clearly the isolated state of the present study bears little resemblance to the complex biological environment. A common feature of [1+AA+H]+ complexes is the presence of a protonated AA bound to neutral 1, in spite of the fact that the gas-phase basicity of 1 is comparable to those of Lys and His. The carbonyl group of 1 acts as a powerful hydrogen-bond acceptor. Within [1+AA+H]+ the side-chain substituents (imidazole group for His and terminal amino group for Lys) present comparable basic properties to those of the α-amino group, taking part to a cooperative hydrogen-bond network. Structural assignment, relying on the comparative analysis of the infrared multiple photon dissociation (IRMPD) spectrum and calculated IR spectra for the candidate geometries, derives from an examination over two frequency ranges: 900-1800 and 2900-3700 cm-1 . Information gained from the latter one proved especially valuable, for example, pointing to the contribution of species characterized by an unperturbed carboxylic OH or imidazole NH stretching mode.
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Affiliation(s)
- Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Rajeev K Sinha
- Department of Atomic and Molecular Physics, Manipal University, Manipal, 576104, Karnataka, India
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Antonello Filippi
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Caterina Fraschetti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
| | - Debora Scuderi
- Institut de Chimie Physique, UMR8000, CNRS, Université Paris-Saclay, 91405, Orsay, France
| | - Philippe Maitre
- Institut de Chimie Physique, UMR8000, CNRS, Université Paris-Saclay, 91405, Orsay, France
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli studi di Roma La Sapienza, P.le A. Moro 5, 00185, Roma, Italy
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10
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Ren J, Zhang XY, Kong XL. Structure of protonated heterodimer of proline and phenylalanine: Revealed by infrared multiphoton dissociation spectroscopy and theoretical calculations. CHINESE J CHEM PHYS 2020. [DOI: 10.1063/1674-0068/cjcp2006089] [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]
Affiliation(s)
- Juan Ren
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xian-yi Zhang
- School of Physics and Electronic Information, Anhui Normal University, Anhui Normal University, Wuhu 241000, China
| | - Xiang-lei Kong
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
- Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
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