Article
Multidisciplinary Sciences
Ye Tian, Jiani Hong, Duanyun Cao, Sifan You, Yizhi Song, Bowei Cheng, Zhichang Wang, Dong Guan, Xinmeng Liu, Zhengpu Zhao, Xin-Zheng Li, Li-Mei Xu, Jing Guo, Ji Chen, En-Ge Wang, Ying Jiang
Summary: The nature of hydrated proton on solid surfaces has been visualized using cryogenic qPlus-based atomic force microscopy. Eigen cations self-assemble into monolayer structures with local order, while Zundel cations form long-range ordered structures stabilized by nuclear quantum effects. It is found that Zundel configuration is preferred over Eigen on Pt(111), but such preference is absent on Au(111).
Article
Chemistry, Multidisciplinary
Christian Lorent, Vladimir Pelmenschikov, Stefan Frielingsdorf, Janna Schoknecht, Giorgio Caserta, Yoshitaka Yoda, Hongxin Wang, Kenji Tamasaku, Oliver Lenz, Stephen P. Cramer, Marius Horch, Lars Lauterbach, Ingo Zebger
Summary: A new experimental setup was developed to study metalloenzymes in detail, allowing the controlled preparation and characterization of catalytic intermediates using various spectroscopic techniques. By investigating two O-2-tolerant [NiFe]-hydrogenases as model systems, detailed insights into the catalytic mechanisms and vibrational fingerprints were revealed. Additionally, the study highlighted the importance of complementing X-ray crystallographic data with spectroscopic analyses.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Jifu Duan, Anja Hemschemeier, David J. Burr, Sven T. Stripp, Eckhard Hofmann, Thomas Happe
Summary: In this study, the crystal structures of CN--treated [FeFe]-hydrogenase CpI from Clostridium pasteurianum were obtained, revealing that extrinsic CN- binds to the open coordination site of the cofactor. The binding of CN- leads to conformational changes in conserved residues within the proton transfer pathway, potentially facilitating efficient proton transfer. This observation provides important insights into the mechanism of CN- inhibition and proton transfer in hydrogenases.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Applied
Gabriel Luna-Lopez, Raquel Sainz, Ana M. Coito, Charlotte Pichon, Ana Iglesias-Juez, Ines A. C. Pereira, Antonio L. De Lacey, Marcos Pita
Summary: In order to tackle the challenge of diminishing the high potentials required for the reaction, a combination of a redox biocatalyst and an inorganic semiconductor has been studied. The system, based on a photocathode made of copper gallium sulfide and Desulfovibrio vulgaris Hildenborough NiFeSe-hydrogenase, can produce photoelectrochemical biocatalytic proton reduction to H2 without any sacrificial agent while providing an approximately 400 mV decrease of the applied potential.
Article
Biochemistry & Molecular Biology
Gabriel Luna-Lopez, Melisa del Barrio, Jennifer Fize, Vincent Artero, Ana Margarida Coito, Ines A. C. Pereira, Jose Carlos Conesa, Ana Iglesias-Juez, Antonio L. De Lacey, Marcos Pita
Summary: Clean energy vectors are required to achieve a fossil fuel-free society, reducing both greenhouse effect and pollution. Electrochemical water splitting provides a clean method to obtain green hydrogen, but efficient electrocatalysts are needed to avoid high overpotentials. The combination of inorganic semiconductors with biocatalysts offers an alternative approach for photoelectrochemical H2 production.
BIOELECTROCHEMISTRY
(2023)
Article
Chemistry, Physical
Yvonne Rippers, Barbara Procacci, Neil T. Hunt, Marius Horch
Summary: This study presents a computational approach for simulating and analyzing static 2D-IR spectra of [NiFe] hydrogenases and similar organometallic systems. By accurately reproducing experimental spectra, it reveals the crucial role of the [NiFe] core in shaping the enzymatic potential energy surface and provides molecular information not accessible by experiments.
Article
Chemistry, Physical
Yangfan Li, Shijie Xie, Xingmiao Huang, Wenjing Song, Chuncheng Chen, Hua Sheng, Jincai Zhao
Summary: Investigating aqueous CO2 reduction on catalysts with redox-noninnocent ligands is essential as they promote CO2 reduction while avoiding H2 evolution. By using rapid-scan FT-IR in external reflection mode, the researchers monitored the pathway of CO2 reduction on iron porphyrin in real-time. They discovered that the protonation of the porphyrin nitrogen, coupled with first-electron reduction of [Fe(II)TAPP](0), avoids the formation of Fe-H structure, and the protonated porphyrin-N acts as a proton relay for efficient inner-sphere proton transfer to activated CO2 molecules. This study provides experimental evidence of proton migration pathway via reduced porphyrin ligands and has implications for the design of catalysts with high CO2 reduction selectivity.
APPLIED CATALYSIS B-ENVIRONMENTAL
(2023)
Article
Chemistry, Inorganic & Nuclear
Georgia R. F. Orton, Sara Belazregue, Jeremy K. Cockcroft, Frantisek Hartl, Graeme Hogarth
Summary: In this study, [FeFe]-ase biomimics were synthesized and their molecular structures were reported. The protonation and re-dox chemistry of these biomimics were investigated to evaluate their activity as catalysts for H2 oxidation. The results showed that the protonation products were solvent dependent, with nitrogen being the favored site of protonation in d6-acetone. A preliminary H2 oxidation study of one of the biomimics was conducted, which revealed a turnover of approximately 2.3 mol of H2 consumed per mole of the biomimic.
JOURNAL OF ORGANOMETALLIC CHEMISTRY
(2023)
Review
Chemistry, Inorganic & Nuclear
James A. Birrell, Patricia Rodriguez-Macia, Edward J. Reijerse, Maria Alessandra Martini, Wolfgang Lubitz
Summary: This review provides an overview of the research history and progress on hydrogenases, focusing on their structure, mechanism of action, and catalytic cycle. It compares the studies on the simple enzyme containing the active site H-cluster and enzymes containing additional iron-sulfur clusters.
COORDINATION CHEMISTRY REVIEWS
(2021)
Article
Chemistry, Multidisciplinary
Weixing Li, Denis S. Tikhonov, Melanie Schnell
Summary: Proton transfer via tunneling is a fundamental quantum-mechanical phenomenon, as demonstrated by rotational spectroscopy measurements on the complex of formic acid dimer with fluorobenzene. The presence of fluorobenzene does not quench the double proton transfer in the formic acid dimer, but instead decreases its tunneling splitting. Calculations suggest that fluorobenzene's weak binding does not affect the activation energy of proton transfer, but does slow down the proton transfer motion during the reaction.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Physical
Ilnaz T. Rakipov, Artem A. Petrov, Aydar A. Akhmadiyarov, Artashes A. Khachatrian, Mikhail A. Varfolomeev
Summary: This work evaluates and analyzes the intermolecular interactions of amides in solution, focusing on the absorption frequencies of the C = O groups. Infrared spectroscopy is used to measure the frequencies in different solvents. The study shows that solvation effects have a similar impact on the C = O frequencies of various amides and highlights the cooperative effects of hydrogen bonding in associated solvent environments.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Multidisciplinary
Jakob Heller, Wai Kit Tang, Ethan M. Cunningham, Ephrem G. Demissie, Christian van der Linde, Wing Ka Lam, Milan Oncak, Chi-Kit Siu, Martin K. Beyer
Summary: Infrared multiple photon spectroscopy was used to probe the structure of hydrated singly charged aluminum ions. The Al-H vibration frequency is highly sensitive to the hydrogen bonding network, and the hydride can act as a double hydrogen bond acceptor. The onset of hydrogen bonding and disappearance of the free Al-H stretch coincides with the onset of hydrogen evolution.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Electrochemistry
Yuanming Wang, Yunhong Song, Chunling Ma, Hong-qi Xia, Ranran Wu, Zhiguang Zhu
Summary: In this study, researchers demonstrated the different biological and electrochemical properties of hydrogenase by constructing and immobilizing truncated hydrogenases on electrodes. Analysis of the characteristics of truncated hydrogenases revealed different activities in H-2 oxidation, with the dimer showing significant oxidation current.
ELECTROCHIMICA ACTA
(2021)
Article
Spectroscopy
Xiao Luo, Wei Shi, Yunfan Yang, Yuzhi Song, Yongqing Li
Summary: In their experiment, Song et al. successfully synthesized two novel molecules BtyC-1 and BtyC-2 and observed different fluorescence peaks in each molecule. By studying the excited state intramolecular proton transfer (ESIPT) mechanisms, they found that the differences in the photochemical and photophysical properties of BtyC-1 and BtyC-2 are mainly due to the variations in hydrogen bonding interactions in their excited states.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Chemistry, Physical
Shaoguang Zhang, Serge Ruccolo, Anna Fryszkowska, Artis Klapars, Nicholas Marshall, Neil A. Strotman
Summary: An electrochemical activation method for galactose oxidase (GOase) was developed to replace the expensive horseradish peroxidase activator in large-scale pharmaceutical processes. The study showed that the electron-transfer rates between GOase and various mediators depend on both the redox potential of the mediator and the pH. The electrochemical GOase activation method was successfully applied to the aerobic oxidation of benzyl alcohol derivatives and other compounds, including a key step in the biocatalytic cascade for the HIV therapeutic islatravir.
Review
Chemistry, Multidisciplinary
Shun Hirota, Satoshi Nagao
Summary: Cytochrome c is a multifunctional water-soluble heme protein that plays important roles in apoptosis and the mitochondrial respiratory chain. Through 3D domain swapping, cytochrome c molecules can form oligomers and polymers. Cytochrome c interacts with cardiolipin on the inner mitochondrial membrane, and its peroxidase activity increases when interacting strongly with cardiolipin.
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN
(2021)
Review
Chemistry, Multidisciplinary
Hulin Tai, Shun Hirota, Sven T. Stripp
Summary: Hydrogenases are metalloenzymes capable of efficiently catalyzing proton reduction and hydrogen oxidation. This Account discusses the use of photochemistry and infrared spectroscopy to study the dynamic hydrogen-bonding changes in [NiFe]- and [FeFe]-hydrogenases, revealing distinct structures and functions in these systems.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Multidisciplinary Sciences
Masaru Yamanaka, Tsuyoshi Mashima, Michio Ogihara, Mei Okamoto, Takayuki Uchihashi, Shun Hirota
Summary: Ferritin can form a hydrogel from concentrated apoferritin solutions through acid denaturation and subsequent neutralization, with a water content of approximately 80%. The hydrogel exhibits stability and the ability to adsorb and release metal ions, demonstrating a unique property of ferritin as a potential material for future biomaterial design.
Article
Biochemical Research Methods
Takahiro Imanishi, Koji Nishikawa, Midori Taketa, Katsuhiro Higuchi, Hulin Tai, Shun Hirota, Hironobu Hojo, Toru Kawakami, Kiriko Hataguchi, Kayoko Matsumoto, Hideaki Ogata, Yoshiki Higuchi
Summary: This study investigated the binding state of CO with the hydrogenase in Citrobacter sp. S-77 using activity assays, spectroscopic techniques, and X-ray crystallography. The results showed a positive correlation between CO tolerance and oxygen tolerance in [NiFe]-hydrogenases.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2022)
Review
Chemistry, Multidisciplinary
Sven T. Stripp, Benjamin R. Duffus, Vincent Fourmond, Christophe Leger, Silke Leimkueshler, Shun Hirota, Yilin Hu, Andrew Jasniewski, Hideaki Ogata, Markus W. Ribbe
Summary: Gases like H-2, N-2, CO2, and CO are important feedstock for green energy conversion and as sources of nitrogen and carbon. However, their industrial transformation and production require significant energy input, whereas nature efficiently converts them at ambient conditions using gas-processing metalloenzymes (GPMs). In this review, the importance of the cofactor/protein interface in GPMs is emphasized, and the effects of second and outer coordination sphere on catalytic activity are discussed.
Article
Chemistry, Multidisciplinary
Naoki Shibata, Yoshiki Higuchi, Bernhard Krautler, Tetsuo Toraya
Summary: The X-ray structures of coenzyme B-12 (AdoCbl)-dependent eliminating isomerases complexed with adenosylmethylcobalamin (AdoMeCbl) have been determined. The Co-C bond in diol dehydratase (DD) is not activated even in the presence of substrate. In ethanolamine ammonia-lyase (EAL), the bond is elongated in the absence of substrate, and in the presence of substrate, the complex likely exists in both pre- and post-homolysis states. The flexibility and rigidity of the active sites in the two enzymes may reflect the tightness of adenine binding.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Article
Chemistry, Physical
Mohan Zhang, Hulin Tai, Sachiko Yanagisawa, Masaru Yamanaka, Takashi Ogura, Shun Hirota
Summary: The peroxidase activity of cytochrome c increases when Met80 dissociates from the heme iron, which is related to the initial cyt c membrane permeation step of apoptosis. This study analyzed the resonance Raman spectra of Met80-depleted horse cytochrome c (M80A cyt c) to understand the heme ligand properties of Met80-dissociated cyt c. The results showed that the frequencies of Fe-His stretching and Fe-O2 stretching modes of M80A cyt c were higher than other His-ligated heme proteins, indicating strong heme coordination and the imidazolate character of His18. Moreover, the frequencies of the oxygenated species of M80A cyt c were observed to have a positive linear relationship, suggesting that the Fe-O and O-O bonds are important for the peroxidase activity when Met80 dissociates from the heme iron.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Multidisciplinary
Yue Cui, Li Zhang, Jing Liu, Taozhe Zhang, Aya Sugahara, Atsuya Momotake, Yasuhiko Yamamoto, Zong-wan Mao, Hulin Tai
Summary: In this study, an artificial DNAzyme composed of cobalt-protoporphyrin IX (CoPP) and G-quadruplex DNA was constructed to catalyze photo-induced H2 production. The G-quadruplex DNA significantly enhanced the photocatalytic H2 production for CoPP, and the DNAzyme exhibited an optimal acid-base equilibrium with a pKa value of 7.60 +/- 0.05, which is attributed to the balance between Co(III)-H- and Co(I) states. These findings demonstrate the potential of using DNAzymes for direct conversion of solar energy to H2 from water.
Article
Chemistry, Multidisciplinary
Jing Liu, Taozhe Zhang, Jinyang Feng, Yue Cui, Li Zhang, Yunong Wang, Meiyu Cui, Donghao Li, Hulin Tai
Summary: It is discovered that N-acetylated microperoxidase-11 and G-quadruplex DNA can form a stable peptide-hemin/DNA hybrid-complex, and the peroxidase activity at the interface between hemin and the G-quartet planes exponentially increases with increasing K-a value.
CHEMICAL COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Shun Hirota, Chun-Liang Chiu, Chieh-Ju Chang, Pei-Hua Lo, Tien Chen, Hongxu Yang, Masaru Yamanaka, Tsuyoshi Mashima, Cheng Xie, Hiroshi Masuhara, Teruki Sugiyama
Summary: The spatial and temporal control of amyloid fibril formation of cytochrome c was achieved using a combined method of disulfide bond cross-linking of cysteine-introduced variants and optical trapping. It was identified that the structural change in the region containing Ala83 is essential for amyloid fibril formation.
CHEMICAL COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Cheng Xie, Hiromitsu Shimoyama, Masaru Yamanaka, Satoshi Nagao, Hirofumi Komori, Naoki Shibata, Yoshiki Higuchi, Yasuteru Shigeta, Shun Hirota
Summary: Research has shown that enhancing the hydrogen bond network at the hinge region can stabilize the structure of myoglobin dimer, further supporting the connection between myoglobin dimer and monomer through 3D domain swapping.
Review
Chemistry, Multidisciplinary
Shun Hirota, Tsuyoshi Mashima, Naoya Kobayashi
Summary: Supramolecules, formed by assembly of multiple molecules through noncovalent interactions, exhibit unique properties and have applications in both biology and chemistry. The design and creation of supramolecular proteins are leading to the development of new enzymes, biomaterials, and drug delivery systems. Studies on the regulation of supramolecular proteins are increasing, with methods like disulfide bond and metal coordination being utilized for their construction.
CHEMICAL COMMUNICATIONS
(2021)
