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Zhu S, Yang R, Li HJW, Huang S, Wang H, Liu Y, Li H, Zhai T. Reconstructing Hydrogen-Bond Network for Efficient Acidic Oxygen Evolution. Angew Chem Int Ed Engl 2024; 63:e202319462. [PMID: 38286750 DOI: 10.1002/anie.202319462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 01/31/2024]
Abstract
Developing highly active oxygen evolution reaction (OER) catalysts in acidic conditions is a pressing demand for proton-exchange membrane water electrolysis. Manipulating proton character at the electrified interface, as the crux of all proton-coupled electrochemical reactions, is highly desirable but elusive. Herein we present a promising protocol, which reconstructs a connected hydrogen-bond network between the catalyst-electrolyte interface by coupling hydrophilic units to boost acidic OER activity. Modelling on N-doped-carbon-layer clothed Mn-doped-Co3O4 (Mn-Co3O4@CN), we unravel that the hydrogen-bond interaction between CN units and H2O molecule not only drags the free water to enrich the surface of Mn-Co3O4 but also serves as a channel to promote the dehydrogenation process. Meanwhile, the modulated local charge of the Co sites from CN units/Mn dopant lowers the OER barrier. Therefore, Mn-Co3O4@CN surpasses RuO2 at high current density (100 mA cm-2 @ ~538 mV).
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Affiliation(s)
- Shicheng Zhu
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P. R. China
| | - Ruoou Yang
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P. R. China
| | - Huang Jing Wei Li
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P. R. China
| | - Sirui Huang
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P. R. China
| | - Haozhi Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, and School of Materials Science and Engineering, Hainan University, Haikou, Hainan, 570228, P. R. China
| | - Youwen Liu
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P. R. China
| | - Huiqiao Li
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P. R. China
| | - Tianyou Zhai
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, P. R. China
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Bezabh HK, Chiou JC, Nigatu TA, Hagos TM, Jiang SK, Nikodimos Y, Taklu BW, Tsai MC, Su WN, Hwang BJ. In-Depth Insight into a Passive Film through Hydrogen-Bonding Network in an Aqueous Zinc Battery. ACS Appl Mater Interfaces 2023; 15:7949-7958. [PMID: 36729118 DOI: 10.1021/acsami.2c18154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Electrochemical stability and interfacial reactions are crucial for rechargeable aqueous zinc batteries. Electrolyte engineering with low-cost aqueous electrolytes is highly required to stabilize their interfacial reactions. Herein, we propose a design strategy using glutamic additive and its derivatives with modification of hydrogen-bonding network to enable Zn aqueous battery at a low concentration (2 m ZnSO4 + 1 m Li2SO4). Computational, in situ/ex situ spectroscopic, and electrochemical studies suggest that additives with moderate interactions, such as 0.1 mol % glutamic additive (G1), preferentially absorb on the Zn surface to homogenize Zn2+ plating and favorably interact with Zn2+ in bulk to weaken the interaction between H2O and Zn2+. As a result, uniform deposition and stable electrochemical performance are realized. The Zn||Cu half-cell lasts for more than 200 cycles with an average Coulombic efficiency (CE) of >99.32% and the Zn||Zn symmetrical cells for 1400 h with a low and stable overpotential under a current density of 0.5 mA cm-2, which is better than the reported results. Moreover, adding 0.1 mol % G1 to the Zn||LFP full cell improves its electrochemical performance with stable cycling and achieves a remarkable capacity of 147.25 mAh g-1 with a CE of 99.79% after 200 cycles.
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Affiliation(s)
- Hailemariam Kassa Bezabh
- Nano-electrochemistry Laboratory, Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei106, Taiwan
| | - Jeng-Chian Chiou
- Nano-electrochemistry Laboratory, Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei106, Taiwan
| | - Teshome Assefa Nigatu
- Nano-electrochemistry Laboratory, Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei106, Taiwan
| | - Teklay Mezgebe Hagos
- Nano-electrochemistry Laboratory, Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei106, Taiwan
| | - Shi-Kai Jiang
- Nano-electrochemistry Laboratory, Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei106, Taiwan
| | - Yosef Nikodimos
- Nano-electrochemistry Laboratory, Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei106, Taiwan
| | - Bereket Woldegbreal Taklu
- Nano-electrochemistry Laboratory, Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei106, Taiwan
| | - Meng-Che Tsai
- Nano-electrochemistry Laboratory, Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei106, Taiwan
| | - Wei-Nien Su
- Nano-electrochemistry Laboratory, Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei106, Taiwan
| | - Bing Joe Hwang
- Nano-electrochemistry Laboratory, Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei106, Taiwan
- Sustainable Energy Development Center, National Taiwan University of Science and Technology, Taipei106, Taiwan
- National Synchrotron Radiation Research Center (NSRRC), Hsinchu30076, Taiwan
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Zhang L, Liu Z, Yang C, García Sakai V, Tyagi M, Hong L. Conduction Mechanism in Graphene Oxide Membranes with Varied Water Content: From Proton Hopping Dominant to Ion Diffusion Dominant. ACS Nano 2022; 16:13771-13782. [PMID: 35993828 DOI: 10.1021/acsnano.2c00686] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Proton conductors, particularly hydrated solid membranes, have various applications in sensors, fuel cells, and cellular biological systems. Unraveling the intrinsic proton transfer mechanism is critical for establishing the foundation of proton conduction. Two scenarios on electrical conduction, the Grotthuss and the vehicle mechanisms, have been reported by experiments and simulations. But separating and quantifying the contributions of these two components from experiments is difficult. Here, we present the conductive behavior of a two-dimensional layered proton conductor, graphene oxide membrane (GOM), and find that proton hopping is dominant at low water content, while ion diffusion prevails with increasing water content. This change in the conduction mechanism is attributable to the layers of water molecules in GOM nanosheets. The overall conductivity is greatly improved by forming one layer of water molecules. It reaches the maximum with two layers of water molecules, resulting from creating a complete hydrogen-bond network within GOM. When more than two layers of water molecules enter the GOM nanosheets, inducing the breakage of the ordered lamellar structure, protons spread in both in-plane and out-of-plane directions inside the GOM. Our results validate the existence of two conduction mechanisms and show their distinct contributions to the overall conductivity. Furthermore, these findings provide an optimization strategy for the design of realizing the fast proton transfer in materials with water participation.
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Affiliation(s)
- Lei Zhang
- School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhuo Liu
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai National Center for Applied Mathematics (SJTU Center) and MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chenxing Yang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Victoria García Sakai
- Rutherford Appleton Laboratory, ISIS Neutron and Muon Facility, Science and Technology Facilities Council, Didcot OX11 0QX, United Kingdom
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Liang Hong
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai National Center for Applied Mathematics (SJTU Center) and MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
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Tanaka I, Nishinomiya R, Goto R, Shimazaki S, Chatake T. Recent structural insights into the mechanism of lysozyme hydrolysis. Acta Crystallogr D Struct Biol 2021; 77:288-292. [PMID: 33645532 PMCID: PMC7919404 DOI: 10.1107/s2059798321000346] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 01/11/2021] [Indexed: 11/29/2022]
Abstract
The complex of lysozyme with an N-acetylglucosamine tetramer shows a relatively strong hydrogen-bond network around a catalytic residue via high-resolution X-ray structural analysis. This indicates a potentially different hydrolysis mechanism to that through a glycosyl intermediate, and this is expected to be proved using neutron experiments. Lysozyme hydrolyzes the glycosidic bonds between N-acetylmuramic acid and N-acetylglucosamine in peptidoglycans located in the bacterial cell wall. The mechanism of the hydrolysis reaction of lysozyme was first studied more than 50 years ago; however, it has not yet been fully elucidated and various mechanisms are still being investigated. One reaction system that has commonly been proposed is that the lysozyme intermediate undergoes covalent ligand binding during hydrolysis. However, these findings resulted from experiments performed under laboratory conditions using fluorine-based ligands, which facilitate the formation of covalent bonds between the ligands and the catalytic side chain of lysozyme. More recently, high-resolution X-ray structural analysis was used to study the complex of lysozyme with an N-acetylglucosamine tetramer. As a result, the carboxyl group of Asp52 was found to form a relatively strong hydrogen-bond network and had difficulty binding covalently to C1 of the carbohydrate ring. To confirm this hydrogen-bond network, neutron test measurements were successfully performed to a resolution of better than 1.9 Å.
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Affiliation(s)
- Ichiro Tanaka
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
| | - Ryota Nishinomiya
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
| | - Ryosuke Goto
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
| | - Shun Shimazaki
- College of Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan
| | - Toshiyuki Chatake
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Osaka 590-0494, Japan
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Abstract
Water provides the driving force for the assembly and stability of many cellular components. Despite its impact on biological functions, a nanoscale understanding of the relationship between its structure and dynamics under soft confinement has remained elusive. As expected, water in contact with biological membranes recovers its bulk density and dynamics at ∼1 nm from phospholipid headgroups but surprisingly enhances its intermediate range order (IRO) over a distance, at least, twice as large. Here, we explore how the IRO is related to the water's hydrogen-bond network (HBN) and its coordination defects. We characterize the increased IRO by an alteration of the HBN up to more than eight coordination shells of hydration water. The HBN analysis emphasizes the existence of a bound-unbound water interface at ∼0.8 nm from the membrane. The unbound water has a distribution of defects intermediate between bound and bulk water, but with density and dynamics similar to bulk, while bound water has reduced thermal energy and many more HBN defects than low-temperature water. This observation could be fundamental for developing nanoscale models of biological interactions and for understanding how alteration of the water structure and topology, for example, due to changes in extracellular ions concentration, could affect diseases and signaling. More generally, it gives us a different perspective to study nanoconfined water.
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Affiliation(s)
- Fausto Martelli
- Hartree Centre, IBM Research Europe, Daresbury WA4 4AD, United Kingdom
| | - Jason Crain
- Hartree Centre, IBM Research Europe, Daresbury WA4 4AD, United Kingdom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Giancarlo Franzese
- Secció de Física Estadística i Interdisciplinària, Departament de Física de la Matèria Condensada, and Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, C. Martí i Franquès 1, 08028 Barcelona, Spain
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Wang X, He X. An Ab Initio QM/MM Study of the Electrostatic Contribution to Catalysis in the Active Site of Ketosteroid Isomerase. Molecules 2018; 23:E2410. [PMID: 30241317 DOI: 10.3390/molecules23102410] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/16/2018] [Accepted: 09/17/2018] [Indexed: 01/28/2023] Open
Abstract
The electric field in the hydrogen-bond network of the active site of ketosteroid isomerase (KSI) has been experimentally measured using vibrational Stark effect (VSE) spectroscopy, and utilized to study the electrostatic contribution to catalysis. A large gap was found in the electric field between the computational simulation based on the Amber force field and the experimental measurement. In this work, quantum mechanical (QM) calculations of the electric field were performed using an ab initio QM/MM molecular dynamics (MD) simulation and electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. Our results demonstrate that the QM-derived electric field based on the snapshots from QM/MM MD simulation could give quantitative agreement with the experiment. The accurate calculation of the electric field inside the protein requires both the rigorous sampling of configurations, and a QM description of the electrostatic field. Based on the direct QM calculation of the electric field, we theoretically confirmed that there is a linear correlation relationship between the activation free energy and the electric field in the active site of wild-type KSI and its mutants (namely, D103N, Y16S, and D103L). Our study presents a computational protocol for the accurate simulation of the electric field in the active site of the protein, and provides a theoretical foundation that supports the link between electric fields and enzyme catalysis.
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Ren TB, Xu W, Zhang QL, Zhang XX, Wen SY, Yi HB, Yuan L, Zhang XB. Enhancing the Anti-Solvatochromic Two-Photon Fluorescence for Cirrhosis Imaging by Forming a Hydrogen-Bond Network. Angew Chem Int Ed Engl 2018; 57:7473-7477. [PMID: 29682856 DOI: 10.1002/anie.201800293] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Indexed: 01/10/2023]
Abstract
Two-photon imaging is an emerging tool for biomedical research and clinical diagnostics. Electron donor-acceptor (D-A) type molecules are the most widely employed two-photon scaffolds. However, current D-A type fluorophores suffer from solvatochromic quenching in aqueous biological samples. To address this issue, we devised a novel class of D-A type green fluorescent protein (GFP) chromophore analogues that form a hydrogen-bond network in water to improve the two-photon efficiency. Our design results in two-photon chalcone (TPC) dyes with 0.80 quantum yield and large two-photon action cross section (210 GM) in water. This strategy to form hydrogen bonds can be generalized to design two-photon materials with anti-solvatochromic fluorescence. To demonstrate the improved in vivo imaging, we designed a sulfide probe based on TPC dyes and monitored endogenous H2 S generation and scavenging in the cirrhotic rat liver for the first time.
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Affiliation(s)
- Tian-Bing Ren
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Wang Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Qian-Ling Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Xing-Xing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Si-Yu Wen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Hai-Bo Yi
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Lin Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
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Abstract
Two polymorphs of the title compound, C10H9BO2, were prepared by recystallization from different solvents at room temperature. Both forms demonstrate nearly identical mol-ecular structures with all naphthalene group atoms located in one plane and all boronic acid atoms in another: the dihedral angles between these planes are 39.88 (5) and 40.15 (5)° for the two asymmetric mol-ecules of the ortho-rhom-bic form and 40.60 (3)° for the single asymmetric mol-ecule in the monoclinic form. In each extended structure, mol-ecules form dimers, connected via two O-H⋯O hydrogen bonds. The dimers are connected by further O-H⋯O hydrogen bonds, forming layered networks in the (001) plane and the (100) plane in the ortho-rhom-bic and monoclinic forms, respectively. The resulting layers are practically identical in both forms. However, these layers are shifted along the [010] axis in the two forms, resulting in a slightly more effective packing for monoclinic structure (packing index = 0.692) compared to the ortho-rhom-bic form (0.688).
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Affiliation(s)
- Kayleigh Bemisderfer
- Chemistry Department, SUNY Buffalo State, 1300 Elmwood Ave, Buffalo, NY 14222, USA
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Yajima T, Kimura M, Hori Y, Shiraiwa T. Structures of N-acetyl-DL-isoleucine, N-acetyl-DL-alloisoleucine and their ammonium salts; role of ammonium ions in crystal structure formation. Acta Crystallogr B Struct Sci Cryst Eng Mater 2016; 72:650-657. [PMID: 27484385 DOI: 10.1107/s2052520616007319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/02/2016] [Indexed: 06/06/2023]
Abstract
The crystal structures of N-acetyl-DL-isoleucine, N-acetyl-DL-alloisoleucine and their ammonium salts show that these four compounds exist as racemic compounds around room temperature. The two ammonium salts are arranged around a 21 screw axis, forming a helical column which consists of ammonium ions and single enantiomeric anions similar to the crystals of the ammonium salts of optically active N-acetyl-L-isoleucine and N-acetyl-D-alloisoleucine. The ammonium ion and the carboxylate ion in the helix are connected by three hydrogen bonds, the fourth hydrogen bond being formed between the ammonium ion and an external acetyl amino group of the neighboring helical column. The fourth hydrogen bond is formed between the ammonium ion and an external acetyl amino group of the neighboring 21 column. Ammonium N-acetyl-DL-alloisoleucinate was revealed to exist as an unstable racemic compound due to conformational similarity between the racemic and optically active compounds in the solid state and was optically resolved by fractional crystallization at 293 K.
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Affiliation(s)
- Tatsuo Yajima
- Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Makiko Kimura
- Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Yoshihiro Hori
- Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Tadashi Shiraiwa
- Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
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Kirov MV. Hydrogen-bond-reversal symmetry and its violation in ice nanotubes. Acta Crystallogr A Found Adv 2016; 72:395-405. [PMID: 27126117 DOI: 10.1107/s2053273316004368] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 03/14/2016] [Indexed: 11/10/2022]
Abstract
Recently, a new type of generalized symmetry of ice structures was introduced which takes into account the change of direction of all hydrogen bonds. The energy nonequivalence of pairs of configurations with opposite direction of all hydrogen bonds was established in the course of computer simulation of bilayer ice and other four-coordinated structures without `dangling' hydrogen atoms. In this article, the results of detailed investigations of the violation of the hydrogen-bond-reversal symmetry in ice nanotubes consisting of stacked n-membered rings are presented. A comprehensive classification of all possible hydrogen-bonding configurations and their division into two classes (antisymmetrical and non-antisymmetrical) are given. Attention is focused on the most stable configurations that have no longitudinally arranged water molecules. This restriction made the asymmetry very difficult to find. For example, it was established that the asymmetry (non-antisymmetrical configurations) in ice nanotubes with square, pentagonal and hexagonal cross sections appears only when the number of transverse rings in the unit cell is more than six. It is shown that this is related to the well known combinatorial problem of enumerating the symmetry-distinct necklaces of black and white beads. It was found that, among the ice nanotubes that had been considered, hydrogen-bond-reversal asymmetry is most conspicuous in wide nanotubes such as heptagonal and octagonal. In this case the asymmetry is observed for unit cells of any length. In order to verify the results of the symmetry analysis and to confirm the energy nonequivalence of some (non-antisymmetrical) configurations, approximate calculations of the binding energy have been performed using the package TINKER.
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Affiliation(s)
- Mikhail V Kirov
- Institute of the Earth Cryosphere SB RAS, Tyumen, 625000, Russian Federation
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11
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Onwukwe GU, Koski MK, Pihko P, Schmitz W, Wierenga RK. Structures of yeast peroxisomal Δ(3),Δ(2)-enoyl-CoA isomerase complexed with acyl-CoA substrate analogues: the importance of hydrogen-bond networks for the reactivity of the catalytic base and the oxyanion hole. ACTA ACUST UNITED AC 2015; 71:2178-91. [PMID: 26527136 DOI: 10.1107/s139900471501559x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/19/2015] [Indexed: 11/10/2022]
Abstract
Δ(3),Δ(2)-Enoyl-CoA isomerases (ECIs) catalyze the shift of a double bond from 3Z- or 3E-enoyl-CoA to 2E-enoyl-CoA. ECIs are members of the crotonase superfamily. The crotonase framework is used by many enzymes to catalyze a wide range of reactions on acyl-CoA thioesters. The thioester O atom is bound in a conserved oxyanion hole. Here, the mode of binding of acyl-CoA substrate analogues to peroxisomal Saccharomyces cerevisiae ECI (ScECI2) is described. The best defined part of the bound acyl-CoA molecules is the 3',5'-diphosphate-adenosine moiety, which interacts with residues of loop 1 and loop 2, whereas the pantetheine part is the least well defined. The catalytic base, Glu158, is hydrogen-bonded to the Asn101 side chain and is further hydrogen-bonded to the side chain of Arg100 in the apo structure. Arg100 is completely buried in the apo structure and a conformational change of the Arg100 side chain appears to be important for substrate binding and catalysis. The oxyanion hole is formed by the NH groups of Ala70 (loop 2) and Leu126 (helix 3). The O atoms of the corresponding peptide units, Gly69 O and Gly125 O, are both part of extensive hydrogen-bond networks. These hydrogen-bond networks are a conserved feature of the crotonase oxyanion hole and their importance for catalysis is discussed.
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Affiliation(s)
- Goodluck U Onwukwe
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - M Kristian Koski
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Petri Pihko
- Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland
| | - Werner Schmitz
- Department of Biochemistry and Molecular Biology, University of Würzburg, Biozentrum, Am Hubland, 97074 Würzburg, Germany
| | - Rik K Wierenga
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
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Jeyachandran YL, Meyer F, Nagarajan S, Benkert A, Bär M, Blum M, Yang W, Reinert F, Heske C, Weinhardt L, Zharnikov M. Ion-Solvation-Induced Molecular Reorganization in Liquid Water Probed by Resonant Inelastic Soft X-ray Scattering. J Phys Chem Lett 2014; 5:4143-4148. [PMID: 26278946 DOI: 10.1021/jz502186a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The molecular structure of liquid water is susceptible to changes upon admixture of salts due to ionic solvation, which provides the basis of many chemical and biochemical processes. Here we demonstrate how the local electronic structure of aqueous potassium chloride (KCl) solutions can be studied by resonant inelastic soft X-ray scattering (RIXS) to monitor the effects of the ion solvation on the hydrogen-bond (HB) network of liquid water. Significant changes in the oxygen K-edge emission spectra are observed with increasing KCl concentration. These changes can be attributed to modifications in the proton dynamics, caused by a specific coordination structure around the salt ions. Analysis of the spectator decay spectra reveals a spectral signature that could be characteristic of this structure.
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Affiliation(s)
- Yekkoni L Jeyachandran
- †Angewandte Physikalische Chemie, Universität Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
| | - Frank Meyer
- ‡Experimentelle Physik VII, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Sankaranarayanan Nagarajan
- †Angewandte Physikalische Chemie, Universität Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
| | - Andreas Benkert
- ‡Experimentelle Physik VII, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- §Institute for Photon Science and Synchrotron Radiation, Karlsruhe Institute of Technology (KIT), Hermann-v.-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Marcus Bär
- ∥Solar Energy Research, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
- ⊥Institut für Physik und Chemie, Brandenburgische Technische Universität Cottbus-Senftenberg, Platz der Deutschen Einheit 1, 03046 Cottbus, Germany
- #Department of Chemistry, University of Nevada, Las Vegas (UNLV), 4505 Maryland Parkway, Las Vegas, Nevada 89154-4003, United States
| | - Monika Blum
- #Department of Chemistry, University of Nevada, Las Vegas (UNLV), 4505 Maryland Parkway, Las Vegas, Nevada 89154-4003, United States
| | - Wanli Yang
- ∇Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Friedrich Reinert
- ‡Experimentelle Physik VII, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Clemens Heske
- §Institute for Photon Science and Synchrotron Radiation, Karlsruhe Institute of Technology (KIT), Hermann-v.-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- #Department of Chemistry, University of Nevada, Las Vegas (UNLV), 4505 Maryland Parkway, Las Vegas, Nevada 89154-4003, United States
- ○ANKA Synchrotron Radiation Facility, Karlsruhe Institute of Technology (KIT), Hermann-v.-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- ◆Institute for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology (KIT), Engesserstrasse 18/20, 76128 Karlsruhe, Germany
| | - Lothar Weinhardt
- §Institute for Photon Science and Synchrotron Radiation, Karlsruhe Institute of Technology (KIT), Hermann-v.-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- #Department of Chemistry, University of Nevada, Las Vegas (UNLV), 4505 Maryland Parkway, Las Vegas, Nevada 89154-4003, United States
- ○ANKA Synchrotron Radiation Facility, Karlsruhe Institute of Technology (KIT), Hermann-v.-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- ◆Institute for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology (KIT), Engesserstrasse 18/20, 76128 Karlsruhe, Germany
| | - Michael Zharnikov
- †Angewandte Physikalische Chemie, Universität Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
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Yokoyama T, Mizuguchi M, Nabeshima Y, Kusaka K, Yamada T, Hosoya T, Ohhara T, Kurihara K, Tanaka I, Niimura N. Hydrogen-bond network and pH sensitivity in human transthyretin. J Synchrotron Radiat 2013; 20:834-7. [PMID: 24121323 PMCID: PMC3795539 DOI: 10.1107/s090904951302075x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 07/25/2013] [Indexed: 05/20/2023]
Abstract
Transthyretin (TTR) is a tetrameric protein. TTR misfolding and aggregation are associated with human amyloid diseases. Dissociation of the TTR tetramer is believed to be the rate-limiting step in the amyloid fibril formation cascade. Low pH is known to promote dissociation into monomer and the formation of amyloid fibrils. In order to reveal the molecular mechanisms underlying pH sensitivity and structural stabilities of TTR, neutron diffraction studies were conducted using the IBARAKI Biological Crystal Diffractometer with the time-of-flight method. Crystals for the neutron diffraction experiments were grown up to 2.5 mm(3) for four months. The neutron crystal structure solved at 2.0 Å revealed the protonation states of His88 and the detailed hydrogen-bond network depending on the protonation states of His88. This hydrogen-bond network is involved in monomer-monomer and dimer-dimer interactions, suggesting that the double protonation of His88 by acidification breaks the hydrogen-bond network and causes the destabilization of the TTR tetramer. Structural comparison with the X-ray crystal structure at acidic pH identified the three amino acid residues responsible for the pH sensitivity of TTR. Our neutron model provides insights into the molecular stability related to amyloidosis.
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Affiliation(s)
- Takeshi Yokoyama
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Mineyuki Mizuguchi
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Yuko Nabeshima
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0914, Japan
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Taro Yamada
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Takaaki Hosoya
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
- College of Engineering, Ibaraki University, 4-12-1 Naka-Narusawa, Hitachi, Ibaraki 316-8511, Japan
| | - Takashi Ohhara
- Research Center for Neutron Science and Technology, Comprehensive Research Organization for Science and Society, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Kazuo Kurihara
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
| | - Ichiro Tanaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
- College of Engineering, Ibaraki University, 4-12-1 Naka-Narusawa, Hitachi, Ibaraki 316-8511, Japan
| | - Nobuo Niimura
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
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