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Zhang Y, Zhang F, Li L, Liu F, Wang A. Highly Chemoselective Reduction of Amides to Amines over a Ruthenium‐Molybdenum Bimetallic Catalyst. ChemistrySelect 2022. [DOI: 10.1002/slct.202203030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yue Zhang
- CAS Key Laboratory of Science and Technology on Applied Catalysis Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Fan Zhang
- CAS Key Laboratory of Science and Technology on Applied Catalysis Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Lin Li
- CAS Key Laboratory of Science and Technology on Applied Catalysis Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Fei Liu
- CAS Key Laboratory of Science and Technology on Applied Catalysis Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 P. R. China
| | - Aiqin Wang
- CAS Key Laboratory of Science and Technology on Applied Catalysis Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 P. R. China
- State Key Laboratory of Catalysis Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 P. R. China
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Zhang Y, Li L, Liu F, Qi H, Zhang L, Guan W, Liu Y, Wang A, Zhang T. Synergy between Ru and WO x Enables Efficient Hydrodeoxygenation of Primary Amides to Amines. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Yue Zhang
- CAS Key Laboratory of Science and Technology on Applied Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Li
- CAS Key Laboratory of Science and Technology on Applied Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Fei Liu
- CAS Key Laboratory of Science and Technology on Applied Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Haifeng Qi
- CAS Key Laboratory of Science and Technology on Applied Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leilei Zhang
- CAS Key Laboratory of Science and Technology on Applied Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Weixiang Guan
- CAS Key Laboratory of Science and Technology on Applied Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yuefeng Liu
- Dalian National Laboratory for Clean Energy, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Aiqin Wang
- CAS Key Laboratory of Science and Technology on Applied Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Tao Zhang
- CAS Key Laboratory of Science and Technology on Applied Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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Dörner S, Schwob L, Atak K, Schubert K, Boll R, Schlathölter T, Timm M, Bülow C, Zamudio-Bayer V, von Issendorff B, Lau JT, Techert S, Bari S. Probing Structural Information of Gas-Phase Peptides by Near-Edge X-ray Absorption Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:670-684. [PMID: 33573373 DOI: 10.1021/jasms.0c00390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Near-edge X-ray absorption mass spectrometry (NEXAMS) is an action-spectroscopy technique of growing interest for investigations into the spatial and electronic structure of biomolecules. It has been used successfully to give insights into different aspects of the photodissociation of peptides and to probe the conformation of proteins. It is a current question whether the fragmentation pathways are sensitive toward effects of conformational isomerism, tautomerism, and intramolecular interactions in gas-phase peptides. To address this issue, we studied the cationic fragments of cryogenically cooled gas-phase leucine enkephalin ([LeuEnk+H]+) and methionine enkephalin ([MetEnk+H]+) produced upon soft X-ray photon absorption at the carbon, nitrogen, and oxygen K-edges. The interpretation of the experimental ion yield spectra was supported by density-functional theory and restricted-open-shell configuration interaction with singles (DFT/ROCIS) calculations. The analysis revealed several effects that could not be rationalized based on the peptide's amino acid sequences alone. Clear differences between the partial ion yields measured for both peptides upon C 1s → π*(C═C) excitations in the aromatic amino acid side chains give evidence for a sulfur-aromatic interaction between the methionine and phenylalanine side chain of [MetEnk+H]+. Furthermore, a peak associated with N 1s → π*(C═N) transitions, linked to a tautomeric keto-to-enol conversion of peptide bonds, was only present in the photon energy resolved ion yield spectra of [MetEnk+H]+.
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Affiliation(s)
- Simon Dörner
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Lucas Schwob
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Kaan Atak
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Kaja Schubert
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Rebecca Boll
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- European XFEL, Holzkoppel 4, 22869 Schenefeld, Germany
| | - Thomas Schlathölter
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands
| | - Martin Timm
- Abteilung Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Christine Bülow
- Abteilung Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Vicente Zamudio-Bayer
- Abteilung Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - Bernd von Issendorff
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 3, 79104 Freiburg, Germany
| | - J Tobias Lau
- Abteilung Hochempfindliche Röntgenspektroskopie, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 3, 79104 Freiburg, Germany
| | - Simone Techert
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Institut für Röntgenphysik, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Sadia Bari
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
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Al-Zaqri N, Khatib T, Alsalme A, Alharthi FA, Zarrouk A, Warad I. Synthesis and amide imidic prototropic tautomerization in thiophene-2-carbohydrazide: XRD, DFT/HSA-computation, DNA-docking, TG and isoconversional kinetics via FWO and KAS models. RSC Adv 2020; 10:2037-2048. [PMID: 35494597 PMCID: PMC9048253 DOI: 10.1039/c9ra09831c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 12/24/2019] [Indexed: 11/21/2022] Open
Abstract
Thiophene-2-carbohydrazide as a novel small-molecule amide tautomer has been synthesized with an acceptable yield under microwave radiation (MW) conditions. The amide imidic thiophene-2-carbohydrazide prototropic tautomerization via single proton intramigration was computed using the DFT B3LYP/6-311G(d,p) level of theory. The endo-isomer amide structure of thiophene-2-carbohydrazide was proved by XRD and is considered to be the kinetically favored isomer. The DFT-structure parameters were compared to their corresponding XRD-experimental parameters. Several H-bond interactions were detected in the crystal lattice experimentally using the XRD-packing model then correlated to MEP and HSA calculations. The manual and calculated electronic parameters such as, frontier molecular orbital energies, excitation energy, absorption, dipole moment, DOS, GRD quantum parameters and TD-SCF/B3LYP were DFT computed. The thiophene-2-carbohydrazide isomers together with their prototropic (E)/(Z)-thiophene-2-carbohydrazonic acid tautomers were docked against 1BNA DNA. FWO and KAS isoconversional kinetic methods were applied, and the thermal behavior and estimated Ea–α relations were determined. Thiophene-2-carbohydrazide as a novel small-molecule amide tautomer has been synthesized with an acceptable yield under microwave radiation (MW) conditions.![]()
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Affiliation(s)
- Nabil Al-Zaqri
- Department of Chemistry, College of Science, King Saud University P. O. Box 2455 Riyadh 11451 Saudi Arabia
| | - Tamer Khatib
- Department of Energy Engineering and Environment, An-Najah National University Nablus 97300 Palestine
| | - Ali Alsalme
- Department of Chemistry, College of Science, King Saud University P. O. Box 2455 Riyadh 11451 Saudi Arabia
| | - Fahad A Alharthi
- Department of Chemistry, College of Science, King Saud University P. O. Box 2455 Riyadh 11451 Saudi Arabia
| | - Abdelkader Zarrouk
- Laboratory of Materials, Nanotechnology and Environment, Faculty of Science, Mohammed V University 4Av. Ibn Battuta, B. P. 1014 Rabat Morocco
| | - Ismail Warad
- Department of Chemistry and Earth Sciences, Qatar University PO Box 2713 Doha Qatar .,Department of Chemistry, Science College, An-Najah National University P. O. Box 7 Nablus Palestine
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Mateo-Marti E, Prieto-Ballesteros O, Muñoz Caro G, González-Díaz C, Muñoz-Iglesias V, Gálvez-Martínez S. Characterizing Interstellar Medium, Planetary Surface and Deep Environments by Spectroscopic Techniques Using Unique Simulation Chambers at Centro de Astrobiologia (CAB). Life (Basel) 2019; 9:life9030072. [PMID: 31510002 PMCID: PMC6789534 DOI: 10.3390/life9030072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/21/2019] [Accepted: 08/28/2019] [Indexed: 11/16/2022] Open
Abstract
At present, the study of diverse habitable environments of astrobiological interest has become a major challenge. Due to the obvious technical and economical limitations on in situ exploration, laboratory simulations are one of the most feasible research options to make advances both in several astrobiologically interesting environments and in developing a consistent description of the origin of life. With this objective in mind, we applied vacuum and high pressure technology to the design of versatile simulation chambers devoted to the simulation of the interstellar medium, planetary atmospheres conditions and high-pressure environments. These simulation facilities are especially appropriate for studying the physical, chemical and biological changes induced in a particular sample by in situ irradiation or physical parameters in a controlled environment. Furthermore, the implementation of several spectroscopies, such as infrared, Raman, ultraviolet, etc., to study solids, and mass spectrometry to monitor the gas phase, in our simulation chambers, provide specific tools for the in situ physico-chemical characterization of analogues of astrobiological interest. Simulation chamber facilities are a promising and potential tool for planetary exploration of habitable environments. A review of many wide-ranging applications in astrobiology are detailed herein to provide an understanding of the potential and flexibility of these unique experimental systems.
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Affiliation(s)
- Eva Mateo-Marti
- Centro de Astrobiología (CSIC-INTA), Ctra. Ajalvir, Km. 4, 28850-Torrejón de Ardoz, Spain.
| | | | - Guillermo Muñoz Caro
- Centro de Astrobiología (CSIC-INTA), Ctra. Ajalvir, Km. 4, 28850-Torrejón de Ardoz, Spain.
| | | | | | - Santos Gálvez-Martínez
- Centro de Astrobiología (CSIC-INTA), Ctra. Ajalvir, Km. 4, 28850-Torrejón de Ardoz, Spain.
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Sanchez-Arenillas M, Mateo-Marti E. Pyrite surface environment drives molecular adsorption: cystine on pyrite(100) investigated by X-ray photoemission spectroscopy and low energy electron diffraction. Phys Chem Chem Phys 2018; 18:27219-27225. [PMID: 27711447 DOI: 10.1039/c6cp03760g] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We have demonstrated that the annealing process for cleaning pyrite surfaces is a critical parameter in promoting ordering on the surface and driving surface reactivity. Furthermore, we describe a spectroscopic surface characterization of the presence or absence of the surface ordering, as indicated by the Low Energy Electron Diffraction (LEED) pattern, as a function of the surface annealing process. Complementary X-ray photoemission spectroscopy (XPS) results provide evidence that longer annealing processes of over 3 hours repair the sulfur vacancies in the pyrite, making FeS species partially disappear in favor of FeS2 species. These features play an important role in molecular adsorption. We show that in the case of the cystine amino acid on the (100) pyrite surface, the substrate structure is responsible for the chemical adsorption form. The presence of an ordered structure on the surface, as indicated by the LEED pattern, favors the cystine NH3+ chemical form, whereas the absence of the surface ordering promotes cystine NH2 adsorption due to the sulfur-deficient surface. The cystine molecule could then act by changing its chemical functionalities to compensate for the iron surface coordination. The chemical molecular adsorption form can be selected by the surface annealing conditions, implying that environmental conditions could drive molecular adsorption on mineral surfaces. These findings are relevant in several surface processes, and they could play a possible role in prebiotic chemistry surface reactions and iron-sulfur scenarios.
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Affiliation(s)
- M Sanchez-Arenillas
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, 28850 Madrid, Spain.
| | - E Mateo-Marti
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, 28850 Madrid, Spain.
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Insight into bio-metal interface formation in vacuo: interplay of S-layer protein with copper and iron. Sci Rep 2015; 5:8710. [PMID: 25736576 PMCID: PMC4348631 DOI: 10.1038/srep08710] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 01/30/2015] [Indexed: 11/08/2022] Open
Abstract
The mechanisms of interaction between inorganic matter and biomolecules, as well as properties of resulting hybrids, are receiving growing interest due to the rapidly developing field of bionanotechnology. The majority of potential applications for metal-biohybrid structures require stability of these systems under vacuum conditions, where their chemistry is elusive, and may differ dramatically from the interaction between biomolecules and metal ions in vivo. Here we report for the first time a photoemission and X-ray absorption study of the formation of a hybrid metal-protein system, tracing step-by-step the chemical interactions between the protein and metals (Cu and Fe) in vacuo. Our experiments reveal stabilization of the enol form of peptide bonds as the result of protein-metal interactions for both metals. The resulting complex with copper appears to be rather stable. In contrast, the system with iron decomposes to form inorganic species like oxide, carbide, nitride, and cyanide.
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