1
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Kunkel S, Brinschwitz KL, Richter TMM, Niewa R. Ammonothermal Synthesis and Characterization of First Amidozincate Hydroxides. Eur J Inorg Chem 2021. [DOI: 10.1002/ejic.202100348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sebastian Kunkel
- Institut für Anorganische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Kai L. Brinschwitz
- Institut für Anorganische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Theresia M. M. Richter
- Institut für Anorganische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Rainer Niewa
- Institut für Anorganische Chemie Universität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
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2
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Theoretical insight on the solvation properties of Zn2+ in pure liquid ammonia: A quantum mechanical molecular charges field molecular dynamics (QMCF-MD) study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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3
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Hou Z, Dong M, Xiong Y, Zhang X, Ao H, Liu M, Zhu Y, Qian Y. A High-Energy and Long-Life Aqueous Zn/Birnessite Battery via Reversible Water and Zn 2+ Coinsertion. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2001228. [PMID: 32510836 DOI: 10.1002/smll.202001228] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/13/2020] [Accepted: 04/28/2020] [Indexed: 05/12/2023]
Abstract
Aqueous rechargeable Zn/birnessite batteries have recently attracted extensive attention for energy storage system because of their low cost and high safety. However, the reaction mechanism of the birnessite cathode in aqueous electrolytes and the cathode structure degradation mechanics still remain elusive and controversial. In this work, it is found that solvation water molecules coordinated to Zn2+ are coinserted into birnessite lattice structure contributing to Zn2+ diffusion. However, the birnessite will suffer from hydroxylation and Mn dissolution with too much solvated water coinsertion. Through engineering Zn2+ primary solvation sheath with strong-field ligand in aqueous electrolyte, highly reversible [Zn(H2 O)2 ]2+ complex intercalation/extraction into/from birnessite cathode is obtained. Cathode-electrolyte interface suppressing the Mn dissolution also forms. The Zn metal anode also shows high reversibility without formation of "death-zinc" and detrimental dendrite. A full cell coupled with birnessite cathode and Zn metal anode delivers a discharge capacity of 270 mAh g-1 , a high energy density of 280 Wh kg-1 (based on total mass of cathode and anode active materials), and capacity retention of 90% over 5000 cycles.
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Affiliation(s)
- Zhiguo Hou
- Jiangsu University of Technology, Zhong Wu Road 1801, Changzhou, 213001, China
| | - Mengfei Dong
- Jiangsu University of Technology, Zhong Wu Road 1801, Changzhou, 213001, China
| | - Yali Xiong
- Jiangsu University of Technology, Zhong Wu Road 1801, Changzhou, 213001, China
| | - Xueqian Zhang
- Jiangsu University of Technology, Zhong Wu Road 1801, Changzhou, 213001, China
| | - Huaisheng Ao
- School of Chemistry and Materials, University of Science and Technology of China, Hefei, 230052, China
| | - Mengke Liu
- School of Chemistry and Materials, University of Science and Technology of China, Hefei, 230052, China
| | - Yongchun Zhu
- School of Chemistry and Materials, University of Science and Technology of China, Hefei, 230052, China
| | - Yitai Qian
- School of Chemistry and Materials, University of Science and Technology of China, Hefei, 230052, China
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4
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Guo W, Zhao B, Zhou Q, He Y, Wang Z, Radacsi N. Fe-Doped ZnO/Reduced Graphene Oxide Nanocomposite with Synergic Enhanced Gas Sensing Performance for the Effective Detection of Formaldehyde. ACS OMEGA 2019; 4:10252-10262. [PMID: 31460117 PMCID: PMC6648138 DOI: 10.1021/acsomega.9b00734] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 05/31/2019] [Indexed: 06/02/2023]
Abstract
Here, we report the synthesis of Fe-doped ZnO/reduced graphene oxide (rGO) nanocomposites for gas sensing applications via a one-pot hydrothermal process. A wide range of characterization techniques were used to confirm the successful fabrication of the nanocomposite material and to determine the surface area, the structural and morphological properties, the chemical composition, and the purity of the samples, such as Brunauer-Emmett-Teller, X-ray diffraction, Fourier transform infrared, Raman spectroscopy, scanning electron microscopy, transmission electron microscopy, UV-vis spectroscopy, and X-ray photoelectron spectroscopy techniques. The gas sensing performance to formaldehyde was studied thoroughly in a temperature-controlled test chamber. Compared to that of the bare ZnO and ZnO/rGO nanocomposites, the as-prepared 5 atom % Fe-doped ZnO/rGO nanocomposites presented significantly enhanced gas sensing performance to formaldehyde at relatively low temperatures. Whereas most formaldehyde sensors operate at 150 °C and can detect as low as 100 ppm concentrations, the presented sensor can detect 5 ppm formaldehyde at 120 °C. Its fast response-recovery time, high stability, and high selectivity make it an ideal sensor; however, it can exhibit degenerative gas sensing performance at elevated relative humidity. The enhanced gas sensing mechanism was explained as the synergic effect of rGO and Fe doping. The results demonstrate that Fe doping and decorating the nanocomposite with rGO are promising approaches for achieving a superior gas sensing performance for the development of ZnO gas sensors for the detection of formaldehyde.
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Affiliation(s)
- Weiwei Guo
- Chongqing
Key Laboratory of Catalysis and New Environmental Materials, College
of Environment and Resources, Chongqing
Technology and Business University, Chongqing 400067, People’s Republic of China
| | - Bangyu Zhao
- Chongqing
Key Laboratory of Catalysis and New Environmental Materials, College
of Environment and Resources, Chongqing
Technology and Business University, Chongqing 400067, People’s Republic of China
| | - Qilin Zhou
- Chongqing
Key Laboratory of Catalysis and New Environmental Materials, College
of Environment and Resources, Chongqing
Technology and Business University, Chongqing 400067, People’s Republic of China
| | - Youzhou He
- Chongqing
Key Laboratory of Catalysis and New Environmental Materials, College
of Environment and Resources, Chongqing
Technology and Business University, Chongqing 400067, People’s Republic of China
| | - Zhongchang Wang
- Department
of Quantum and Energy Materials, International
Iberian Nanotechnology Laboratory (INL), Avenida Mestre Jose Veiga, Braga 4715-330, Portugal
| | - Norbert Radacsi
- School
of Engineering, Institute for Materials and Processes, The University of Edinburgh, King’s Buildings, Edinburgh EH9 3FB, United
Kingdom
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5
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Lin C, Shinde SS, Li X, Kim DH, Li N, Sun Y, Song X, Zhang H, Lee CH, Lee SU, Lee JH. Solid-State Rechargeable Zinc-Air Battery with Long Shelf Life Based on Nanoengineered Polymer Electrolyte. CHEMSUSCHEM 2018; 11:3215-3224. [PMID: 30028577 DOI: 10.1002/cssc.201801274] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/19/2018] [Indexed: 06/08/2023]
Abstract
Zinc-air batteries (ZABs) are vulnerable to the ambient environment (e.g., humidity and CO2 ), and have serious selfdischarge issues, resulting in a short shelf life. To overcome these challenges, a near-neutral quaternary ammonium (QA) functionalized polyvinyl alcohol electrolyte membrane (different from conventional alkali-type membranes) has been developed. QA functionalization leads to the formation of interconnected nanochannels by creating hydrophilic/-phobic separations at the nanoscale. These nanochannels selectively transport OH- ions with a reduced migration barrier, while inhibiting [Zn(NH3 )6 ]2+ crossover. Owing to the superior water retention ability and enhanced chemical stability of the membrane, the solid-state zinc-air battery (SZAB) displays outstanding flexibility, a promising cycle lifetime, and a large volumetric energy density. More importantly, the self-discharge rate of SZAB is depressed to less than 7 % per month, and the fully dehydrated SZAB could recover its rechargeability upon replenishment of the solution of NH4 Cl.
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Affiliation(s)
- Chao Lin
- Department of Materials Science and Chemical Engineering, Hanyang University, Ansan, Gyeonggi-do, 15588, South Korea
| | - Sambhaji S Shinde
- Department of Materials Science and Chemical Engineering, Hanyang University, Ansan, Gyeonggi-do, 15588, South Korea
| | - Xiaopeng Li
- CAS Key Laboratory of Low-Carbon Conversion Science and Engineering, Shanghai Advanced Research Institute (SARI), Chinese Academy of Sciences (CAS), Shanghai, 201210, PR China
| | - Dong-Hyung Kim
- Department of Materials Science and Chemical Engineering, Hanyang University, Ansan, Gyeonggi-do, 15588, South Korea
| | - Nanwen Li
- Institute of Coal Chemistry, Chinese Academy of Sciences (CAS), Shanxi, 030001, PR China
| | - Yu Sun
- Institute for International Collaboration, Hokkaido University, Sapporo, Hokkaido, 060-0815, Japan
| | - Xiaokai Song
- School of Chemical & Environmental Engineering, Jiangsu University of Technology, Changzhou, 213001, PR China
| | - Haojie Zhang
- CAS Key Laboratory of Low-Carbon Conversion Science and Engineering, Shanghai Advanced Research Institute (SARI), Chinese Academy of Sciences (CAS), Shanghai, 201210, PR China
| | - Chi Ho Lee
- Department of Bionano Technology, and Department of Applied Chemistry, Hanyang University, Ansan, Gyeonggi-do, 15588, South Korea
| | - Sang Uck Lee
- Department of Bionano Technology, and Department of Applied Chemistry, Hanyang University, Ansan, Gyeonggi-do, 15588, South Korea
| | - Jung-Ho Lee
- Department of Materials Science and Chemical Engineering, Hanyang University, Ansan, Gyeonggi-do, 15588, South Korea
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6
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Nedjoua D, Krallafa AM. Temperature effect on the structure and conformational fluctuations in two zinc knuckles from the mouse mammary tumor virus. Comput Biol Chem 2018; 74:86-93. [PMID: 29567490 DOI: 10.1016/j.compbiolchem.2018.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 10/28/2017] [Accepted: 03/07/2018] [Indexed: 11/18/2022]
Abstract
Zinc fingers are small protein domains in which zinc plays a structural role, contributing to the stability of the zinc-peptide complex. Zinc fingers are structurally diverse and are present in proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription and translation, metabolism and signaling, cell proliferation, and apoptosis. Zinc fingers typically function as interaction modules and bind to a wide variety of compounds, such as nucleic acids, proteins, and small molecules. In this study, we investigated the structural properties, in solution, of the proximal and distal zinc knuckles of the nucleocapsid (NC) protein from the mouse mammary tumor virus (MMTV) (MMTV NC). For this purpose, we performed a series of molecular dynamics simulations in aqueous solution at 300 K, 333 K, and 348 K. The temperature effect was evaluated in terms of root mean square deviation of the backbone atoms and root mean square fluctuation of the coordinating residue atoms. The stability of the zinc coordination sphere was analyzed based upon the time profile of the interatomic distances between the zinc ions and the chelator atoms. The results indicate that the hydrophobic character of the proximal zinc finger is dominant at 333 K. The low mobility of the coordinating residues suggests that the strong electrostatic effect exerted by the zinc ion on its coordinating residues is not influenced by the increase in temperature. The evolution of the structural parameters of the coordination sphere of the distal zinc finger at 300 K gives us a reasonable picture of the unfolding pathway, as proposed by Bombarda and coworkers (Bombarda et al., 2005), which can predict the binding order of the four conserved ligand-binding residues. Our results support the conclusion that the structural features can vary significantly between the two zinc knuckles of MMTV NC.
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Affiliation(s)
- Drici Nedjoua
- LCPM, Department of Chemistry, University of Oran 1 Ahmed Benbella, PO Box 1524, El m'naouer, Oran, 31000, Algeria.
| | - Abdelghani Mohamed Krallafa
- LCPM, Department of Chemistry, University of Oran 1 Ahmed Benbella, PO Box 1524, El m'naouer, Oran, 31000, Algeria.
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7
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Clark S, Latz A, Horstmann B. Rational Development of Neutral Aqueous Electrolytes for Zinc-Air Batteries. CHEMSUSCHEM 2017; 10:4735-4747. [PMID: 28898553 PMCID: PMC5765460 DOI: 10.1002/cssc.201701468] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Indexed: 05/07/2023]
Abstract
Neutral aqueous electrolytes have been shown to extend both the calendar life and cycling stability of secondary zinc-air batteries (ZABs). Despite this promise, there are currently no modeling studies investigating the performance of neutral ZABs. Traditional continuum models are numerically insufficient to simulate the dynamic behavior of these complex systems because of the rapid, orders-of-magnitude concentration shifts that occur. In this work, we present a novel framework for modeling the cell-level performance of pH-buffered aqueous electrolytes. We apply our model to conduct the first continuum-scale simulation of secondary ZABs using aqueous ZnCl2 -NH4 Cl as electrolyte. We first use our model to interpret the results of two recent experimental studies of neutral ZABs, showing that the stability of the pH value is a significant factor in cell performance. We then optimize the composition of the electrolyte and the design of the cell considering factors including pH stability, final discharge product, and overall energy density. Our simulations predict that the effectiveness of the pH buffer is limited by slow mass transport and that chlorine-containing solids may precipitate in addition to ZnO.
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Affiliation(s)
- Simon Clark
- German Aerospace Center (DLR)Pfaffenwaldring 38–4070569StuttgartGermany
- Helmholtz Institute Ulm (HIU)Helmholtzstr. 1189081UlmGermany
| | - Arnulf Latz
- German Aerospace Center (DLR)Pfaffenwaldring 38–4070569StuttgartGermany
- Helmholtz Institute Ulm (HIU)Helmholtzstr. 1189081UlmGermany
- Ulm University (UUlm)Albert-Einstein-Allee 4789081UlmGermany
| | - Birger Horstmann
- German Aerospace Center (DLR)Pfaffenwaldring 38–4070569StuttgartGermany
- Helmholtz Institute Ulm (HIU)Helmholtzstr. 1189081UlmGermany
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8
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Prasetyo N, Utami W, Armunanto R, Hofer TS. Exploring structure and dynamics of solvated Ca(II) in liquid ammonia: A quantum mechanical charge field (QMCF) molecular dynamics simulation. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Moin ST, Hofer TS. Zinc- and copper-porphyrins in aqueous solution - two similar complexes with strongly contrasting hydration. MOLECULAR BIOSYSTEMS 2017; 12:2288-2295. [PMID: 27194391 DOI: 10.1039/c6mb00133e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We present detailed analysis of the hydration behavior of zinc and copper bound porphyrins treated via ab initio quantum mechanical charge field molecular dynamics which agrees well with available experimental data. The computed metal-water coordination in the case of zinc bound porphyrin demonstrates a strong association of water with zinc compared to the copper-water interaction which correlates well with the calculated free energy of binding. The H-bond dynamics in these hydrated systems yield weaker H-bond interactions as compared to that observed in the case of metal-free porphyrin; nevertheless, the effect of metal association with porphyrin resulted in shifts in the vibrational frequencies. These characteristic data suggest a contrasting behavior between these metalloporphyrins in solution which could also serve to correlate with the properties of biological systems.
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Affiliation(s)
- Syed Tarique Moin
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan.
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria.
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10
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Hitzenberger M, Hofer TS. The influence of metal-ion binding on the structure and surface composition of Sonic Hedgehog: a combined classical and hybrid QM/MM MD study. Phys Chem Chem Phys 2016; 18:22254-65. [DOI: 10.1039/c6cp03960j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The interaction of metal ions with Shh binding-sites and their structural impact are assessed via classical and quantum mechanical simulations.
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Affiliation(s)
- Manuel Hitzenberger
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- University of Innsbruck
- A-6020 Innsbruck
| | - Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- University of Innsbruck
- A-6020 Innsbruck
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11
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Tirler AO, Hofer TS. A Comparative Study of [CaEDTA](2-) and [MgEDTA](2-): Structural and Dynamical Insights from Quantum Mechanical Charge Field Molecular Dynamics. J Phys Chem B 2015; 119:8613-22. [PMID: 26090779 DOI: 10.1021/acs.jpcb.5b03938] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structure and dynamics of [MgEDTA](2-) and [CaEDTA](2-) complexes in aqueous solution have been investigated via quantum mechanical/molecular mechanical (QM/MM) simulations. While for the first a 6-fold octahedral complex has been observed, the presence of an additional coordinating water ligand has been observed in the latter case. Because of rapidly exchanging water molecules, this 7-fold coordination complex was found to form pentagonal bipyramidal as well as capped trigonal prismatic configurations along the simulation interchanging on the picosecond time scale. Also in the case of [MgEDTA](2-) a trigonal prismatic configuration has been observed for a very short time period of approximately 1 ps. This work reports for the first time the presence of trigonal prismatic structures observed in the coordination sphere of [MgEDTA](2-) and [CaEDTA](2-) complexes in aqueous solution. In addition to the detailed characterization of structure and dynamics of the systems, the prediction of the associated infrared spectra indicates that the ion-water vibrational mode found at approximately 250 cm(-1) provides a distinctive measure to experimentally detect the presence of the coordinating water molecule via low-frequency IR setups.
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Affiliation(s)
- Andreas O Tirler
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Thomas S Hofer
- Theoretical Chemistry Division Institute of General, Inorganic and Theoretical Chemistry University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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12
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Ikeda Y, Yasuda Y, Ohashi T, Yokohama H, Minoda S, Kobayashi H, Honma T. Dinuclear Bridging Bidentate Zinc/Stearate Complex in Sulfur Cross-Linking of Rubber. Macromolecules 2015. [DOI: 10.1021/ma502063m] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yuko Ikeda
- Graduate
School of Science and Technology, Kyoto Institute of Technology, Matsugasaki,
Sakyo, Kyoto 606-8585, Japan
| | - Yoritaka Yasuda
- Graduate
School of Science and Technology, Kyoto Institute of Technology, Matsugasaki,
Sakyo, Kyoto 606-8585, Japan
| | - Takumi Ohashi
- Graduate
School of Science and Technology, Kyoto Institute of Technology, Matsugasaki,
Sakyo, Kyoto 606-8585, Japan
| | - Hiroyuki Yokohama
- Graduate
School of Science and Technology, Kyoto Institute of Technology, Matsugasaki,
Sakyo, Kyoto 606-8585, Japan
| | - Shinya Minoda
- Graduate
School of Science and Technology, Kyoto Institute of Technology, Matsugasaki,
Sakyo, Kyoto 606-8585, Japan
| | - Hisayoshi Kobayashi
- Graduate
School of Science and Technology, Kyoto Institute of Technology, Matsugasaki,
Sakyo, Kyoto 606-8585, Japan
| | - Tetsuo Honma
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
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13
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14
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Schmidt TC, Paasche A, Grebner C, Ansorg K, Becker J, Lee W, Engels B. QM/MM investigations of organic chemistry oriented questions. Top Curr Chem (Cham) 2014; 351:25-101. [PMID: 22392477 DOI: 10.1007/128_2011_309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.
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Affiliation(s)
- Thomas C Schmidt
- Institut für Phys. und Theor. Chemie, Emil-Fischer-Strasse 42, Campus Hubland Nord, 97074, Würzburg, Germany
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15
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Tam HH, Asthagiri D, Paulaitis ME. Coordination state probabilities and the solvation free energy of Zn2+ in aqueous methanol solutions. J Chem Phys 2012; 137:164504. [DOI: 10.1063/1.4759452] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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16
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Hu J, Chen Q, Hu H, Chen X, Hu F, Yin Z. XAS investigation on the coordination structure and extraction mechanism of zinc(II) in ammoniacal solution. Sep Purif Technol 2012. [DOI: 10.1016/j.seppur.2012.08.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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17
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Zhang J, Yang W, Piquemal JP, Ren P. Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential. J Chem Theory Comput 2012; 8:1314-1324. [PMID: 22754403 PMCID: PMC3383645 DOI: 10.1021/ct200812y] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
As the second most abundant cation in human body, zinc is vital for the structures and functions of many proteins. Zinc-containing matrix metalloproteinases (MMPs) have been widely investigated as potential drug targets in a range of diseases ranging from cardiovascular disorders to cancers. However, it remains a challenge in theoretical studies to treat zinc in proteins with classical mechanics. In this study, we examined Zn(2+) coordination with organic compounds and protein side chains using a polarizable atomic multipole based electrostatic model. We find that polarization effect plays a determining role in Zn(2+) coordination geometry in both matrix metalloproteinase (MMP) complexes and in zinc-finger proteins. In addition, the relative binding free energies of selected inhibitors binding with MMP13 have been estimated and compared with experimental results. While not directly interacting with the small molecule inhibitors, the permanent and polarizing field of Zn(2+) exerts a strong influence on the relative affinities of the ligands. The simulation results also reveal the polarization effect on binding is ligand dependent and thus difficult to be incorporated into fixed-charge models implicitly.
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Affiliation(s)
- Jiajing Zhang
- Department of Biomedical Engineering, The University of Texas at Austin, TX 78712
| | - Wei Yang
- The Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306
| | - Jean-Philip Piquemal
- UPMC Univ. Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, TX 78712
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