1
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He Y, Lu JB, Zhang YY, Hu HS, Li J. Structures of Th 4+ aqueous solutions: insights from AIMD and metadynamics simulations. Phys Chem Chem Phys 2024; 26:24447-24454. [PMID: 39263704 DOI: 10.1039/d4cp02512a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Solution chemistry of actinide ions is critical to understanding the solvation behaviors and hydrolysis process. Using tetravalent thorium ion Th4+ as a representative example, we investigate the local structures and dynamic behaviors of hydrated Th4+ ions by ab initio molecular dynamics (AIMD) simulations using the recently developed norm-conserving pseudopotentials and basis sets optimized for actinides (J.-B. Lu et al., J. Chem. Theory Comput. 2021, 17, 3360-3371). AIMD simulations reveal two distinct solvation shells, with the first shell comprising 9 water molecules at approximately rTh-O = 2.50 Å and exhibiting a tricapped trigonal prism geometry. These conclusions are confirmed through metadynamics simulations and further structural analysis. AIMD simulations also show the slight effect of temperature and counterions on the structure of the solution. The structured solvation shells of the highly charged Th4+ ion with the specific geometry, distinct from the structure of liquid water, lead to corresponding structural changes in the hydrogen bond network in water. Additionally, beyond the solvent-shared ion pair (SIP) state observed in the unbiased AIMD simulations, the metadynamics simulations reconstruct a two-dimensional free energy surface that clearly indicates the potential stability of the contact ion pair (CIP) state in the system with Cl- as a counterion. The findings in this work provide insights into the solution chemistry of actinides and serve as a reference for studying other actinide solution systems.
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Affiliation(s)
- Yang He
- Department of Chemistry and Engineering Research Center of Advanced Rare-Earth Materials of Ministry of Education, Tsinghua University, Beijing 100084, China.
| | - Jun-Bo Lu
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
- Fundamental Science Center of Rare Earths, Ganjiang Innovation Academy, Chinese Academy of Sciences, Ganzhou 341000, China
| | - Yang-Yang Zhang
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
| | - Han-Shi Hu
- Department of Chemistry and Engineering Research Center of Advanced Rare-Earth Materials of Ministry of Education, Tsinghua University, Beijing 100084, China.
| | - Jun Li
- Department of Chemistry and Engineering Research Center of Advanced Rare-Earth Materials of Ministry of Education, Tsinghua University, Beijing 100084, China.
- Department of Chemistry and Guangdong Provincial Key Laboratory of Catalytic Chemistry, Southern University of Science and Technology, Shenzhen 518055, China
- Fundamental Science Center of Rare Earths, Ganjiang Innovation Academy, Chinese Academy of Sciences, Ganzhou 341000, China
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2
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Juraskova V, Tusha G, Zhang H, Schäfer LV, Duarte F. Modelling ligand exchange in metal complexes with machine learning potentials. Faraday Discuss 2024. [PMID: 39308396 PMCID: PMC11417676 DOI: 10.1039/d4fd00140k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 07/31/2024] [Indexed: 09/25/2024]
Abstract
Metal ions are irreplaceable in many areas of chemistry, including (bio)catalysis, self-assembly and charge transfer processes. Yet, modelling their structural and dynamic properties in diverse chemical environments remains challenging for both force fields and ab initio methods. Here, we introduce a strategy to train machine learning potentials (MLPs) using MACE, an equivariant message-passing neural network, for metal-ligand complexes in explicit solvents. We explore the structure and ligand exchange dynamics of Mg2+ in water and Pd2+ in acetonitrile as two illustrative model systems. The trained potentials accurately reproduce equilibrium structures of the complexes in solution, including different coordination numbers and geometries. Furthermore, the MLPs can model structural changes between metal ions and ligands in the first coordination shell, and reproduce the free energy barriers for the corresponding ligand exchange. The strategy presented here provides a computationally efficient approach to model metal ions in solution, paving the way for modelling larger and more diverse metal complexes relevant to biomolecules and supramolecular assemblies.
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Affiliation(s)
- Veronika Juraskova
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK.
| | - Gers Tusha
- Center for Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany.
| | - Hanwen Zhang
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK.
| | - Lars V Schäfer
- Center for Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany.
| | - Fernanda Duarte
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK.
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3
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Boukar O, Fifen JJ, Conradie J, Conradie MM. Solvation energies of the ferrous ion in water and in ammonia at various temperatures. J Mol Model 2024; 30:52. [PMID: 38285315 DOI: 10.1007/s00894-024-05839-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/09/2024] [Indexed: 01/30/2024]
Abstract
CONTEXT The solvation of metal ions is crucial to understanding relevant properties in physics, chemistry, or biology. Therefore, we present solvation enthalpies and solvation free energies of the ferrous ion in water and ammonia. Our results agree well with the experimental reports for the hydration free energy and hydration enthalpy. We obtained [Formula: see text] kJ mol[Formula: see text] for the hydration free energy and [Formula: see text] kJ mol[Formula: see text] for the hydration enthalpy of ferrous ion in water at room temperature. At ambient temperature, we obtained [Formula: see text] kJ mol[Formula: see text] as the [Formula: see text] ammoniation free energy and [Formula: see text] kJ mol[Formula: see text] for the ammoniation enthalpy. In addition, the free energy of solvation is deeply affected when the temperature increases. This pattern can be attributed to the rise of entropy when the temperature rises. Besides, the temperature does not affect the ammoniation enthalpies and the hydration enthalpy of the [Formula: see text] ion. METHOD All the geometry optimizations are performed at the MP2 methods associated with the 6-31++g(d,p) basis set of Pople. solvated phase structures of [Formula: see text] ion in water or in ammonia are performed using the PCM model. The [Formula: see text] program suite was used to perform all the calculations. The program TEMPO was also used to evaluate the temperature sensitivity of the different obtained geometries.
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Affiliation(s)
- Ousman Boukar
- Department of Physics, Faculty of Science, University of Maroua, P.O. Box 46, Maroua, Cameroon.
| | - Jean Jules Fifen
- Quantum Theory and Aplications Unit, Department of Physics, Faculty of Science, The University of Ngaoundere, P.O. Box 454, Ngaoundere, Cameroon.
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, PO Box 339, Bloemfontein, 9300, South Africa
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4
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Yan Z, Di Y, Wang L, Fei P, Chen S, Yue X, Wang Y, Zuo Z, Lu J, Zhao Z. Mechanistic insight into homogeneous catalytic crosslinking behavior between cellulose and epoxide by explicit solvent models. Int J Biol Macromol 2023; 252:126093. [PMID: 37573910 DOI: 10.1016/j.ijbiomac.2023.126093] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/10/2023] [Accepted: 07/21/2023] [Indexed: 08/15/2023]
Abstract
Inspired by recent advances on functional modification of cellulosic materials, the crosslinking behaviors of epoxide with cellulose under the catalysis of different homogeneous catalysts including H2O, Brønsted acid, Brønsted base, Lewis acid and neutral salt were systematically investigated using density functional theory (DFT) methods with hybrid micro-solvation-continuum approach. The results showed that catalytic activity, reaction mechanism and regioselectivity are determined by the combined effect of catalyst type, electronic effect and steric hindrance. All the homogeneous catalysts have catalytic activity for the crosslinking reaction, which decreases in the order of NaOH > HCl > NCl3 > MCl2 > CH3COOH > NaCl (N = Fe3+, Al3+; M = Zn2+, Ca2+). Upon the catalysis of NaOH, hydroxyl group of cellulose is firstly deprotonated to form a carbanion-like intermediate which will further attack the less sterically hindered C atom of epoxide showing excellent regioselectivity. Acidic catalysts readily cause epoxide protonated, which suffers from nucleophilic attack of cellulose and forms the carbocation-like intermediate. Brønsted acid exhibits poor regioselectivity, however, Lewis acid shows an interesting balance between catalytic activity and regioselectivity for the crosslinking reaction, which may be attributed to the unique catalysis and stabilization effects of its coordinated H2O on the transition state structure.
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Affiliation(s)
- Zhifeng Yan
- College of Textile Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi, China; College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi, China; National Advanced Functional Fiber Innovation Center, Suzhou 215228, Jiangsu, China
| | - Youbo Di
- College of Textile Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi, China
| | - Le Wang
- College of Textile Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi, China
| | - Pengfei Fei
- College of Textile Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi, China
| | - Shaojie Chen
- College of Textile Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi, China
| | - Xiuping Yue
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi, China
| | - Yuping Wang
- National Advanced Functional Fiber Innovation Center, Suzhou 215228, Jiangsu, China
| | - Zhijun Zuo
- Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan 030024, Shanxi, China
| | - Jianjun Lu
- College of Textile Engineering, Taiyuan University of Technology, Taiyuan 030024, Shanxi, China; Key Laboratory of Coal Science and Technology of Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan 030024, Shanxi, China
| | - Zhou Zhao
- School of Textile science and engineering, Xi'an Polytechnic university, Xi'an 710048, Shaanxi, China.
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5
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Baker S, Pagotto J, Duignan TT, Page AJ. High-Throughput Aqueous Electrolyte Structure Prediction Using IonSolvR and Equivariant Graph Neural Network Potentials. J Phys Chem Lett 2023; 14:9508-9515. [PMID: 37845640 DOI: 10.1021/acs.jpclett.3c01783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Neural network potentials have recently emerged as an efficient and accurate tool for accelerating ab initio molecular dynamics (AIMD) in order to simulate complex condensed phases such as electrolyte solutions. Their principal limitation, however, is their requirement for sufficiently large and accurate training sets, which are often composed of Kohn-Sham density functional theory (DFT) calculations. Here we examine the feasibility of using existing density functional tight-binding (DFTB) molecular dynamics trajectory data available in the IonSolvR database in order to accelerate the training of E(3)-equivariant graph neural network potentials. We show that the solvation structure of Na+ and Cl- in aqueous NaCl solutions can be accurately reproduced with remarkably small amounts of data (i.e., 100 MD frames). We further show that these predictions can be systematically improved further via an embarrassingly parallel resampling approach.
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Affiliation(s)
- Sophie Baker
- Discipline of Chemistry, College of Engineering, Science and Environment, University of Newcastle, Callaghan, Newcastle, NSW 2308, Australia
| | - Joshua Pagotto
- School of Chemical Engineering, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Timothy T Duignan
- School of Chemical Engineering, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, Brisbane, QLD 4111, Australia
| | - Alister J Page
- Discipline of Chemistry, College of Engineering, Science and Environment, University of Newcastle, Callaghan, Newcastle, NSW 2308, Australia
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6
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Xie H, Ma S, Zhao Y, Zhou H, Tong Q, Chen Y, Zhang Z, Yu K, Lin Q, Kai L, Liu M, Yang J. Molecular Mechanisms of Mercury-Sensitive Aquaporins. J Am Chem Soc 2022; 144:22229-22241. [PMID: 36413513 DOI: 10.1021/jacs.2c10240] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Aquaporins are transmembrane channels that allow for the passive permeation of water and other small molecules across biological membranes. Their channel activities are sensitive to mercury ions. Intriguingly, while most aquaporins are inhibited by mercury ions, several aquaporins are activated by mercury ions. The molecular basis of the opposing aquaporin regulation by mercury remains poorly understood. Herein, we investigated AqpZ inhibition and AQP6 activation upon binding of mercury ions using solid-state NMR (ssNMR) and molecular dynamics (MD) simulations. Based on the structure of the Hg-AqpZ complex constructed by MD simulations and ssNMR, we identified that the pore closure was caused by mercury-induced conformational changes of the key residue R189 in the selectivity filter region, while pore opening was caused by conformational changes of residues H181 and R196 in the selectivity filter region in AQP6. Both conformational changes were caused by the disruption of the H-bond network of R189/R196 by mercury. The molecular details provided a structural basis for mercury-mediated functional changes in aquaporins.
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Affiliation(s)
- Huayong Xie
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Shaojie Ma
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China.,Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China.,Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - Yongxiang Zhao
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Hu Zhou
- Department of Biological Sciences, NUS Environmental Research Institute (NERI), National University of Singapore, Singapore 117411, Singapore
| | - Qiong Tong
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China.,Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - Yanke Chen
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Zhengfeng Zhang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China
| | - Kunqian Yu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China
| | - Qingsong Lin
- Department of Biological Sciences, NUS Environmental Research Institute (NERI), National University of Singapore, Singapore 117411, Singapore
| | - Lei Kai
- School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, P. R. China
| | - Maili Liu
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China.,Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P. R. China.,Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
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7
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Gregory KP, Elliott GR, Wanless EJ, Webber GB, Page AJ. A quantum chemical molecular dynamics repository of solvated ions. Sci Data 2022; 9:430. [PMID: 35864118 PMCID: PMC9304403 DOI: 10.1038/s41597-022-01527-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/30/2022] [Indexed: 12/29/2022] Open
Abstract
The importance of ion-solvent interactions in predicting specific ion effects in contexts ranging from viral activity through to electrolyte viscosity cannot be underestimated. Moreover, investigations of specific ion effects in nonaqueous systems, highly relevant to battery technologies, biochemical systems and colloid science, are severely limited by data deficiency. Here, we report IonSolvR – a collection of more than 3,000 distinct nanosecond-scale ab initio molecular dynamics simulations of ions in aqueous and non-aqueous solvent environments at varying effective concentrations. Density functional tight binding (DFTB) is used to detail the solvation structure of up to 55 solutes in 28 different protic and aprotic solvents. DFTB is a fast quantum chemical method, and as such enables us to bridge the gap between efficient computational scaling and maintaining accuracy, while using an internally-consistent simulation technique. We validate the database against experimental data and provide guidance for accessing individual IonSolvR records. Measurement(s) | solvation structure | Technology Type(s) | quantum chemistry computational method • Molecular Dynamics |
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Affiliation(s)
- Kasimir P Gregory
- Discipline of Chemistry, School of Environmental & Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia.,Department of Materials Physics, Research School of Physics, Australian National University, Canberra, ACT, 0200, Australia
| | - Gareth R Elliott
- Discipline of Chemistry, School of Environmental & Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Erica J Wanless
- Discipline of Chemistry, School of Environmental & Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Grant B Webber
- Discipline of Chemical Engineering, School of Engineering, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Alister J Page
- Discipline of Chemistry, School of Environmental & Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia.
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8
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Baolin K, Qin Z, Xianhai L, Zhihui S. Adsorption and solidification of cadmium by calcium sulfate dihydrate (gypsum) in an aqueous environment: a dispersion-corrected DFT and ab initio molecular dynamics study. Phys Chem Chem Phys 2022; 24:9521-9533. [PMID: 35388811 DOI: 10.1039/d1cp03964d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Phosphogypsum is a by-product of phosphoric acid production by a wet-process and can be used to prepare adsorption materials to treat Cd(II) in sewage. Its main component is calcium sulfate dihydrate (gypsum). In the present study, incorporation and adsorption of cadmium on gypsum in an aqueous environment have been investigated using dispersion-corrected density functional theory, and the effect of different vacancy defects on the adsorption and doping of Cd on gypsum was also studied. The results show that Cd impurity defects can form more easily in gypsum crystals with Ca vacancy defects. The increase in both calcium vacancy defects and sulfate vacancy defects is beneficial to the incorporation of Cd in calcium sulfate dihydrate. In addition, the calcium vacancy defects on the gypsum surface can promote the adsorption of Cd(II), while sulfate vacancy defects on the gypsum surface inhibit the adsorption of Cd(II). Therefore, increasing the Ca vacancy defects of gypsum will help in improving the adsorption and curing properties of phosphogypsum for cadmium.
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Affiliation(s)
- Ke Baolin
- Mining College, Guizhou University, Guiyang 550025, China.,National & Local Joint Laboratory of Engineering for Effective Utilization of Regional Mineral Resources from Karst Areas, Guizhou University, Guiyang 550025, China. .,Guizhou Key Laboratory of Comprehensive Utilization of Non-metallic Mineral Resources, Guizhou University, Guiyang 550025, China
| | - Zhang Qin
- National & Local Joint Laboratory of Engineering for Effective Utilization of Regional Mineral Resources from Karst Areas, Guizhou University, Guiyang 550025, China. .,Guizhou Key Laboratory of Comprehensive Utilization of Non-metallic Mineral Resources, Guizhou University, Guiyang 550025, China.,Guizhou Academy of Sciences, Guiyang 550001, China
| | - Li Xianhai
- Mining College, Guizhou University, Guiyang 550025, China.,National & Local Joint Laboratory of Engineering for Effective Utilization of Regional Mineral Resources from Karst Areas, Guizhou University, Guiyang 550025, China. .,Guizhou Key Laboratory of Comprehensive Utilization of Non-metallic Mineral Resources, Guizhou University, Guiyang 550025, China
| | - Shen Zhihui
- Mining College, Guizhou University, Guiyang 550025, China.,National & Local Joint Laboratory of Engineering for Effective Utilization of Regional Mineral Resources from Karst Areas, Guizhou University, Guiyang 550025, China. .,Guizhou Key Laboratory of Comprehensive Utilization of Non-metallic Mineral Resources, Guizhou University, Guiyang 550025, China
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9
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Jon JS, Ri WK, Sin KR, Son YC, Jo KW, Pak JS, Kim SJ, Ri YJ, An YC. Derivation of the solvation effect-incorporated Poisson-Boltzmann equation. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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10
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Saputri WD, Pranowo HD, Hofer TS. Can’t we negotiate the importance of electron correlation? HF vs RIMP2 in ab initio quantum mechanical charge field molecular dynamics simulations of Cu+ in pure liquid ammonia. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Han Y, Wang L, Guo X, Jiao T, Ding H. Enhanced adsorption efficiency of graphene oxide by electrostatic field for Hg(II) removal from water. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Lu C, Hu C, Ritt CL, Hua X, Sun J, Xia H, Liu Y, Li DW, Ma B, Elimelech M, Qu J. In Situ Characterization of Dehydration during Ion Transport in Polymeric Nanochannels. J Am Chem Soc 2021; 143:14242-14252. [PMID: 34431669 DOI: 10.1021/jacs.1c05765] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The transport of hydrated ions across nanochannels is central to biological systems and membrane-based applications, yet little is known about their hydrated structure during transport due to the absence of in situ characterization techniques. Herein, we report experimentally resolved ion dehydration during transmembrane transport using modified in situ liquid ToF-SIMS in combination with MD simulations for a mechanistic reasoning. Notably, complete dehydration was not necessary for transport to occur across membranes with sub-nanometer pores. Partial shedding of water molecules from ion solvation shells, observed as a decrease in the average hydration number, allowed the alkali-metal ions studied here (lithium, sodium, and potassium) to permeate membranes with pores smaller than their solvated size. We find that ions generally cannot hold more than two water molecules during this sterically limited transport. In nanopores larger than the size of the solvation shell, we show that ionic mobility governs the ion hydration number distribution. Viscous effects, such as interactions with carboxyl groups inside the membrane, preferentially hinder the transport of the mono- and dihydrates. Our novel technique for studying ion solvation in situ represents a significant technological leap for the nanofluidics field and may enable important advances in ion separation, biosensing, and battery applications.
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Affiliation(s)
- Chenghai Lu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Chengzhi Hu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Cody L Ritt
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
| | - Xin Hua
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Jingqiu Sun
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Hailun Xia
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Yingya Liu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Da-Wei Li
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Baiwen Ma
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Menachem Elimelech
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
| | - Jiuhui Qu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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13
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Dixon IM, Bonnet S, Alary F, Cuny J. Photoinduced Ligand Exchange Dynamics of a Polypyridyl Ruthenium Complex in Aqueous Solution. J Phys Chem Lett 2021; 12:7278-7284. [PMID: 34323082 DOI: 10.1021/acs.jpclett.1c01424] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The understanding of photoinduced ligand exchange mechanisms in polypyridyl ruthenium(II) complexes operating in aqueous solution is of crucial importance to rationalize their photoreactivity. Herein, we demonstrate that a synergetic use of ab initio molecular dynamics simulations and static calculations, both conducted at the DFT level, can provide a full understanding of photosubstitution mechanisms of a monodentate ligand by a solvent water molecule in archetypal ruthenium complexes in explicit water. The simulations show that the photoinduced loss of a monodentate ligand generates an unreactive 16-electron species in a hitherto undescribed pentacoordinated triplet excited state that converts, via an easily accessible crossing point, to a reactive 16-electron singlet ground state, which combines with a solvent water molecule to yield the experimentally observed aqua complex in less than 10 ps. This work paves the way for the rational design of novel photoactive metal complexes relevant for biological applications.
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Affiliation(s)
- Isabelle M Dixon
- Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, Laboratoire de Chimie et Physique Quantiques, 31062 Toulouse Cedex 9, France
| | - Sylvestre Bonnet
- Leiden Institute of Chemistry, Leiden University, 2300 RA Leiden, The Netherlands
| | - Fabienne Alary
- Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, Laboratoire de Chimie et Physique Quantiques, 31062 Toulouse Cedex 9, France
| | - Jérôme Cuny
- Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier, Laboratoire de Chimie et Physique Quantiques, 31062 Toulouse Cedex 9, France
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14
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Li M, Ren G, Yang W, Wang F, Ma N, Fan X, Pan Q. Modulation of High-Spin Co(II) in Li/Co-MOFs as Efficient Fenton-like Catalysts. Inorg Chem 2021; 60:12405-12412. [PMID: 34296855 DOI: 10.1021/acs.inorgchem.1c01632] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Developing high-performance catalysts toward the Fenton reaction is important for environmental protection and sustainable development, yet it is still challenging. The high-spin states of first-row transition metal atoms with tetrahedral coordination provide a flexible electronic environment to activate the catalyst and elevate its catalytic activity. As a type of material with adjustable structures, metal-organic frameworks (MOFs) are excellent candidate catalysts as they can accurately regulate the coordination configurations of metal ions. In this paper, we investigate and summarize the direct formation of bimetallic carboxylate Li/Co-MOFs with tetrahedral coordination metal centers in a mixed H2O/polar organic solvent system. The induction of Li(I) ions is manifested in the generation of hydroxides during the dissociation of the Co(II) solvation structure to trigger the tetrahedral coordination behavior of Co(II). These Li/Co-MOFs containing high-spin Co(II) centers can serve as highly efficient Fenton-like catalysts for organics. This study provides a promising strategy for rational design of MOF-based catalysts with high-spin metal centers for application in environment governance.
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Affiliation(s)
- Meiling Li
- Key Laboratory of Advanced Materials of Tropical Island Resources, Ministry of Education, College of Science, Hainan University, Haikou 570228, China
- School of Chemical Engineering and Technology, Hainan University, Haikou 570228, China
| | - Guojian Ren
- Key Laboratory of Advanced Materials of Tropical Island Resources, Ministry of Education, College of Science, Hainan University, Haikou 570228, China
| | - Weiting Yang
- Key Laboratory of Advanced Materials of Tropical Island Resources, Ministry of Education, College of Science, Hainan University, Haikou 570228, China
| | - Fuxiang Wang
- Key Laboratory of Advanced Materials of Tropical Island Resources, Ministry of Education, College of Science, Hainan University, Haikou 570228, China
| | - Nana Ma
- College of Chemistry and Chemical Engineering, Henan Normal University, XinXiang 453007, China
| | - Xiaolei Fan
- Department of Chemical Engineering and Analytical Science, School of Engineering, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Qinhe Pan
- Key Laboratory of Advanced Materials of Tropical Island Resources, Ministry of Education, College of Science, Hainan University, Haikou 570228, China
- School of Chemical Engineering and Technology, Hainan University, Haikou 570228, China
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15
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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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16
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Boukar O, Fifen JJ, Nsangou M, Ghalila H, Conradie J. Structures and relative stability of hydrated ferrous ion clusters and temperature effects. NEW J CHEM 2021. [DOI: 10.1039/d1nj01849c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Structures of solvated ferrous ion clusters have been investigated in the singlet and quintet spin states of the ferrous ion. Relative stabilities of isomers are also discussed at different temperatures.
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Affiliation(s)
- Ousman Boukar
- Department of Physics
- Faculty of Science
- University of Maroua
- Cameroon
| | - Jean Jules Fifen
- Quantum Theory and Aplications Unit
- Department of Physics
- Faculty of Science
- The University of Ngaoundere
- Ngaoundere
| | - Mama Nsangou
- Department of Physics
- Faculty of Science
- University of Maroua
- Cameroon
- Quantum Theory and Aplications Unit
| | - Hassen Ghalila
- Faculty of Science
- University of Tunis El Manar
- Tunis
- Tunisia
| | - Jeanet Conradie
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
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17
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Saputri WD, Pranowo HD, Schuler MJ, Hofer TS. Cu 2+ in liquid ammonia-The impact of solvent flexibility and electron correlation in ab initio quantum mechanical charge field molecular dynamics. J Comput Chem 2020; 41:2168-2176. [PMID: 32735755 DOI: 10.1002/jcc.26379] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/13/2020] [Indexed: 11/06/2022]
Abstract
The impact of solvent flexibility and electron correlation on the simulation results of Cu2+ in liquid ammonia has been investigated via an ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation approach. To achieve this, three different simulation systems were considered in this study, namely Cu2+ in rigid and flexible ammonia at Hartree-Fock (HF) level of theory, as well as resolution of identity second order Møller-Plesset (MP2) perturbation theory in the rigid body case. In all cases, a stable octahedral [Cu(NH3 )6 ]2+ complex subject to dynamic Jahn-Teller distortions without the occurrence of ligand exchange was observed. The Cu2+ - NH3 distance in the first shell agrees well with the experimental and other theoretical data. In all three cases, the structural data shows that the rigid-body ammonia model in conjunction with the HF level of theory provides accurate data for the first solvation shell, while at the same time, the computational demand and thus the achievable simulation time are much more beneficial. The vibrational analysis of the Cu2+ - NH3 interaction yields similar force constants in the three investigated systems indicating that there is no distinct difference on the dynamical properties of the first solvation shell. In addition to the QMCF MD simulations, a number of natural bond orbital (NBO) analyses were carried out, confirming the strong electrostatic character of the Cu2+ - NH3 interaction.
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Affiliation(s)
- Wahyu Dita Saputri
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Austrian-Indonesian Centre for Computational Chemistry, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Harno Dwi Pranowo
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Austrian-Indonesian Centre for Computational Chemistry, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Manuel J Schuler
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
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18
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Wang X, Toroz D, Kim S, Clegg SL, Park GS, Di Tommaso D. Density functional theory based molecular dynamics study of solution composition effects on the solvation shell of metal ions. Phys Chem Chem Phys 2020; 22:16301-16313. [PMID: 32647838 DOI: 10.1039/d0cp01957g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present an ab initio molecular dynamics study of the alkali metal ions Li+, Na+, K+ and Cs+, and of the alkaline earth metal ions Mg2+ and Ca2+ in both pure water and electrolyte solutions containing the counterions Cl- and SO42-. Simulations were conducted using different density functional theory methods (PBE, BLYP and revPBE), with and without the inclusion of dispersion interactions (-D3). Analysis of the ion-water structure and interaction strength, water exchange between the first and second hydration shell, and hydrogen bond network and low-frequency reorientation dynamics around the metal ions have been used to characterise the influence of solution composition on the ionic solvation shell. Counterions affect the properties of the hydration shell not only when they are directly coordinated to the metal ion, but also when they are at the second coordination shell. Chloride ions reduce the sodium hydration shell and expand the calcium hydration shell by stabilizing under-coordinated hydrated Na(H2O)5+ complexes and over-coordinated Ca(H2O)72+. The same behaviour is observed in CaSO4(aq), where Ca2+ and SO42- form almost exclusively solvent-shared ion pairs. Water exchange between the first and second hydration shell around Ca2+ in CaSO4(aq) is drastically decelerated compared with the simulations of the hydrated metal ion (single Ca2+, no counterions). Velocity autocorrelation function analysis, used to probe the strength of the local ion-water interaction, shows a smoother decay of Mg2+ in MgCl2(aq), which is a clear indication of a looser inter-hexahedral vibration in the presence of chloride ions located in the second coordination shell of Mg2+. The hydrogen bond statistics and orientational dynamics in the ionic solvation shell show that the influence on the water-water network cannot only be ascribed to the specific cation-water interaction, but also to the subtle interplay between the level of hydration of the ions, and the interactions between ions, especially those of opposite charge. As many reactive processes involving solvated metal ions occur in environments that are far from pure water but rich in ions, this computational study shows how the solution composition can result in significant differences in behaviour and function of the ionic solvation shell.
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Affiliation(s)
- Xiangwen Wang
- School of Biological and Chemical Sciences, Materials Research Institute, Thomas Young Centre, Queen Mary University of London, Mile End Road, E1 4NS, London, UK.
| | - Dimitrios Toroz
- School of Biological and Chemical Sciences, Materials Research Institute, Thomas Young Centre, Queen Mary University of London, Mile End Road, E1 4NS, London, UK.
| | - Seonmyeong Kim
- Center for THz-driven Biological Systems, Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Republic of Korea and Advanced Institutes of Convergence Technology, Seoul National University, Suwon-Si, Gyeonggi-do 16229, Republic of Korea
| | - Simon L Clegg
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Gun-Sik Park
- Center for THz-driven Biological Systems, Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Republic of Korea and Advanced Institutes of Convergence Technology, Seoul National University, Suwon-Si, Gyeonggi-do 16229, Republic of Korea
| | - Devis Di Tommaso
- School of Biological and Chemical Sciences, Materials Research Institute, Thomas Young Centre, Queen Mary University of London, Mile End Road, E1 4NS, London, UK.
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19
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Campisi S, Beevers C, Nasrallah A, Catlow CRA, Chan-Thaw CE, Manzoli M, Dimitratos N, Willock DJ, Roldan A, Villa A. DFT-Assisted Spectroscopic Studies on the Coordination of Small Ligands to Palladium: From Isolated Ions to Nanoparticles. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2020; 124:4781-4790. [PMID: 33828633 PMCID: PMC8016172 DOI: 10.1021/acs.jpcc.9b09791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/28/2019] [Indexed: 06/12/2023]
Abstract
A combination of experimental spectroscopies (UV-vis and Fourier-transform infrared) and computational modeling was used to investigate the coordination of small ligands (aminopropanol and propanediol) to Pd species during the metal nanoparticle formation process. Differences emerged between O- (propanediol) and N-containing (aminopropanol) ligands. In particular, a strong interaction between the NH amino group and Pd2+ ions could be inferred on the basis of spectroscopic evidences, which was corroborated by theoretical simulations, which confirmed the preferential coordination of aminopropanol through the NH group. This interaction seems to potentially cause the aminopropanol ligand to control the particle shape through a selective blocking of Pd(100) facets, which promote the growth on the Pd(111) facets.
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Affiliation(s)
- Sebastiano Campisi
- Dipartimento
di Chimica, Università degli Studi
di Milano, Via Golgi 19, I-20133 Milano, Italy
| | - Cameron Beevers
- Cardiff
Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, CF10 3AT Cardiff, U.K.
| | - Ali Nasrallah
- Cardiff
Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, CF10 3AT Cardiff, U.K.
| | - C. Richard A. Catlow
- Cardiff
Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, CF10 3AT Cardiff, U.K.
| | - Carine e. Chan-Thaw
- Dipartimento
di Chimica, Università degli Studi
di Milano, Via Golgi 19, I-20133 Milano, Italy
| | - Maela Manzoli
- Department
of Drug Science and Technology and NIS—Centre for Nanostructured
Interfaces and Surfaces, University of Turin, Via P. Giuria 9, 10125 Turin, Italy
| | - Nikolaos Dimitratos
- Dipartimento
di Chimica Industriale e dei Materiali, Alma Mater Studiorum Università di Bologna, Viale Risorgimento 4, 40136 Bologna, Italy
| | - David J. Willock
- Cardiff
Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, CF10 3AT Cardiff, U.K.
| | - Alberto Roldan
- Cardiff
Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, CF10 3AT Cardiff, U.K.
| | - Alberto Villa
- Dipartimento
di Chimica, Università degli Studi
di Milano, Via Golgi 19, I-20133 Milano, Italy
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20
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Koskamp J, Ruiz-Hernandez SE, Di Tommaso D, Elena AM, De Leeuw NH, Wolthers M. Reconsidering Calcium Dehydration as the Rate-Determining Step in Calcium Mineral Growth. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2019; 123:26895-26903. [PMID: 31737161 PMCID: PMC6849658 DOI: 10.1021/acs.jpcc.9b06403] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/15/2019] [Indexed: 06/10/2023]
Abstract
The dehydration of cations is generally accepted as the rate-limiting step in many processes. Molecular dynamics (MD) can be used to investigate the dynamics of water molecules around cations, and two different methods exist to obtain trajectory-based water dehydration frequencies. Here, these two different post-processing methods (direct method versus survival function) have been implemented to obtain calcium dehydration frequencies from a series of trajectories obtained using a range of accepted force fields. None of the method combinations reproduced the commonly accepted experimental water exchange frequency of 10-8.2 s-1. Instead, our results suggest much faster water dynamics, comparable with more accurate ab initio MD simulations and with experimental values obtained using neutron scattering techniques. We obtained the best agreement using the survival function method to characterize the water dynamics, and we show that different method combinations significantly affect the outcome. Our work strongly suggests that the fast water exchange kinetics around the calcium ions is not rate-limiting for reactions involving dissolved/solvated calcium. Our results further suggest that, for alkali and most of the earth alkali metals, mechanistic rate laws for growth, dissolution, and adsorption, which are based on the principle of rate-limiting cation dehydration, need careful reconsideration.
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Affiliation(s)
- Janou
A. Koskamp
- Department
of Earth Sciences-Geochemistry, Utrecht
University, 3584 CB Utrecht, The Netherlands
| | | | - Devis Di Tommaso
- Materials
Research Institute and School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, E1 4NS London, United Kingdom
| | | | - Nora H. De Leeuw
- Department
of Earth Sciences-Geochemistry, Utrecht
University, 3584 CB Utrecht, The Netherlands
- School
of Chemistry, Cardiff University, Main Building Park Place, Cardiff CF10 3AT, United Kingdom
| | - Mariette Wolthers
- Department
of Earth Sciences-Geochemistry, Utrecht
University, 3584 CB Utrecht, The Netherlands
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21
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Bachler J, Handle PH, Giovambattista N, Loerting T. Glass polymorphism and liquid-liquid phase transition in aqueous solutions: experiments and computer simulations. Phys Chem Chem Phys 2019; 21:23238-23268. [PMID: 31556899 DOI: 10.1039/c9cp02953b] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One of the most intriguing anomalies of water is its ability to exist as distinct amorphous ice forms (glass polymorphism or polyamorphism). This resonates well with the possible first-order liquid-liquid phase transition (LLPT) in the supercooled state, where ice is the stable phase. In this Perspective, we review experiments and computer simulations that search for LLPT and polyamorphism in aqueous solutions containing salts and alcohols. Most studies on ionic solutes are devoted to NaCl and LiCl; studies on alcohols have mainly focused on glycerol. Less attention has been paid to protein solutions and hydrophobic solutes, even though they reveal promising avenues. While all solutions show polyamorphism and an LLPT only in dilute, sub-eutectic mixtures, there are differences regarding the nature of the transition. Isocompositional transitions for varying mole fractions are observed in alcohol but not in ionic solutions. This is because water can surround alcohol molecules either in a low- or high-density configuration whereas for ionic solutes, the water ion hydration shell is forced into high-density structures. Consequently, the polyamorphic transition and the LLPT are prevented near the ions, but take place in patches of water within the solutions. We highlight discrepancies and different interpretations within the experimental community as well as the key challenges that need consideration when comparing experiments and simulations. We point out where reinterpretation of past studies helps to draw a unified, consistent picture. In addition to the literature review, we provide original experimental results. A list of eleven open questions that need further consideration is identified.
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Affiliation(s)
- Johannes Bachler
- Institute of Physical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria.
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22
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Kepp KP. Free Energies of Hydration for Metal Ions from Heats of Vaporization. J Phys Chem A 2019; 123:6536-6546. [DOI: 10.1021/acs.jpca.9b05140] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Kasper P. Kepp
- Technical University of Denmark, DTU Chemistry, Building 206, 2800 Kgs. Lyngby, DK, Denmark
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23
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Saputri WD, Wijaya K, Pranowo HD, Hofer TS. The Jahn-Teller effect in mixed aqueous solution: the solvation of Cu2+ in 18.6% aqueous ammonia obtained from ab initio quantum mechanical charge field molecular dynamics. PURE APPL CHEM 2019. [DOI: 10.1515/pac-2018-1115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
The solvation structure and dynamics of Cu2+ in 18.6 % aqueous ammonia have been investigated using an ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation approach at the Hartree–Fock (HF) level of theory applying the LANL2DZ ECP and Dunning DZP basis sets for Cu2+, ammonia and water, respectively. During a simulation time of 20 ps, only NH3 molecules are observed within the first solvation shell of Cu2+, resulting in the formation of an octahedral [Cu(NH3)6]2+ complex. While no exchange of these ligands with the second solvation shell are observed along the simulation, the monitoring of the associated N-Ntrans distances highlight the dynamics of the associated Jahn-Teller distortions, showing on average 2 elongated axial (2.19 Å) and 4 equatorial Cu–N bonds (2.39 Å). The observed structural properties are found in excellent agreement with experimental studies. In addition, an NBO analysis was carried out, confirming the strong electrostatic character of the Cu2+–NH3 interaction.
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Affiliation(s)
- Wahyu Dita Saputri
- Department of Chemistry , Universitas Gadjah Mada , Yogyakarta , Indonesia
- Austrian-Indonesian Centre for Computational Chemistry , Universitas Gadjah Mada , Yogyakarta , Indonesia
| | - Karna Wijaya
- Department of Chemistry , Universitas Gadjah Mada , Yogyakarta , Indonesia
| | - Harno Dwi Pranowo
- Department of Chemistry , Universitas Gadjah Mada , Yogyakarta , Indonesia
- Austrian-Indonesian Centre for Computational Chemistry , Universitas Gadjah Mada , Yogyakarta , Indonesia
| | - Thomas S. Hofer
- University of Innsbruck , Theoretical Chemistry Division , Innsbruck , Austria
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24
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Lynes O, Austin J, Kerridge A. Ab initio molecular dynamics studies of hydroxide coordination of alkaline earth metals and uranyl. Phys Chem Chem Phys 2019; 21:13809-13820. [PMID: 31210212 DOI: 10.1039/c9cp00142e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Ab initio molecular dynamics (AIMD) simulations of the Mg2+, Ca2+, Sr2+ and UO22+ ions in either a pure aqueous environment or an environment containing two hydroxide ions have been carried out at the density functional level of theory, employing the generalised gradient approximation via the PBE exchange-correlation functional. Calculated mean M-O bond lengths in the first solvation shell of the aquo systems compared very well to existing experimental and computational literature, with bond lengths well within values measured previously and coordination numbers in line with previously calculated values. When applied to systems containing additional hydroxide ions, the methodology revealed increased bond lengths in all systems. Proton transfer events (PTEs) were recorded and were found to be most prevalent in the strontium hydroxide systems, likely due to the low charge density of the ion and the consequent lack of hydroxide coordination. For all alkaline earths, intrashell PTEs which occurred outside of the first solvation shell were most prevalent. Only three PTEs were identified in the entire simulation data of the uranium dihydroxide system, indicating the clear impact of the increased charge density of the hexavalent uranium ion on the strength of metal-oxygen bonds in aqueous solution. Broadly, systems containing more charge dense ions were found to exhibit fewer PTEs than those containing ions of lower charge density.
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Affiliation(s)
- Olivia Lynes
- Department of Chemistry, Faraday Building, Lancaster University, Lancaster, LA1 4YB, UK.
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25
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Boukar O, Fifen JJ, Malloum A, Dhaouadi Z, Ghalila H, Conradie J. Structures of solvated ferrous ion clusters in ammonia and spin-crossover at various temperatures. NEW J CHEM 2019. [DOI: 10.1039/c9nj02462j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The solvated ferrous ion in ammonia is hexa-coordinated, irrespective of the temperature.
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Affiliation(s)
- Ousman Boukar
- Department of Physics
- Faculty of Science
- University of Maroua
- Maroua
- Cameroon
| | - Jean Jules Fifen
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Alhadji Malloum
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere
- Cameroon
| | | | - Hassen Ghalila
- Faculty of Science
- University of Tunis El Manar
- Tunis
- Tunisia
| | - Jeanet Conradie
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
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26
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Kepp KP. Thermochemically Consistent Free Energies of Hydration for Di- and Trivalent Metal Ions. J Phys Chem A 2018; 122:7464-7471. [DOI: 10.1021/acs.jpca.8b06674] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kasper P. Kepp
- DTU Chemistry, Technical University of Denmark, Building 206, 2800 Kgs. Lyngby, DK, Denmark
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27
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Croll TI. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr D Struct Biol 2018; 74:519-530. [PMID: 29872003 PMCID: PMC6096486 DOI: 10.1107/s2059798318002425] [Citation(s) in RCA: 1007] [Impact Index Per Article: 167.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 02/09/2018] [Indexed: 01/19/2023] Open
Abstract
This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density maps. ISOLDE combines interactive molecular-dynamics flexible fitting with modern molecular-graphics visualization and established structural biology libraries to provide an immersive interface wherein the model constantly acts to maintain physically realistic conformations as the user interacts with it by directly tugging atoms with a mouse or haptic interface or applying/removing restraints. In addition, common validation tasks are accelerated and visualized in real time. Using the recently described 3.8 Å resolution cryo-EM structure of the eukaryotic minichromosome maintenance (MCM) helicase complex as a case study, it is demonstrated how ISOLDE can be used alongside other modern refinement tools to avoid common pitfalls of low-resolution modelling and improve the quality of the final model. A detailed analysis of changes between the initial and final model provides a somewhat sobering insight into the dangers of relying on a small number of validation metrics to judge the quality of a low-resolution model.
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Affiliation(s)
- Tristan Ian Croll
- Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
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28
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Miyazaki M, Naito A, Ikeda T, Klyne J, Sakota K, Sekiya H, Dopfer O, Fujii M. Real-time observation of the photoionization-induced water rearrangement dynamics in the 5-hydroxyindole-water cluster by time-resolved IR spectroscopy. Phys Chem Chem Phys 2018; 20:3079-3091. [PMID: 29143839 DOI: 10.1039/c7cp06127g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solvation plays an essential role in controlling the mechanism and dynamics of chemical reactions in solution. The present study reveals that changes in the local solute-solvent interaction have a great impact on the timescale of solvent rearrangement dynamics. Time-resolved IR spectroscopy has been applied to a hydration rearrangement reaction in the monohydrated 5-hydroxyindole-water cluster induced by photoionization of the solute molecule. The water molecule changes the stable hydration site from the indolic NH site to the substituent OH site, both of which provide a strongly attractive potential for hydration. The rearrangement time constant amounts to 8 ± 2 ns, and is further slowed down by a factor of more than five at lower excess energy. These rearrangement times are slower by about three orders of magnitude than those reported for related systems where the water molecule is repelled from a repulsive part of the interaction potential toward an attractive well. The excess energy dependence of the time constant is well reproduced by RRKM theory. Differences in the reaction mechanism are discussed on the basis of energy relaxation dynamics.
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Affiliation(s)
- Mitsuhiko Miyazaki
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 R1-15, Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.
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29
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Hofer TS, Wiedemair MJ. Towards a dissociative SPC-like water model II. The impact of Lennard-Jones and Buckingham non-coulombic forces. Phys Chem Chem Phys 2018; 20:28523-28534. [DOI: 10.1039/c8cp04957b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dissociative water potential by Garofalini and coworkers has been re-formulated in the framework of the widely employed Lennard-Jones and Buckingham potentials, enhancing the transferability of the model to third party simulation programs.
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Affiliation(s)
- Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
| | - Martin J. Wiedemair
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
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30
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Saleh M, Hofer TS. Square planar or octahedral after all? The indistinct solvation of platinum(ii). Dalton Trans 2018; 47:13032-13045. [DOI: 10.1039/c8dt02169d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The solvation structures of Pd(ii) and Pt(ii) are typically reduced to the well-known square-planar structural motif, although it has been shown, in both experimental and theoretical investigations, that these solutes demonstrate the affinity to bind ligand molecules at elongated distance in axial coordination sites.
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Affiliation(s)
- Muhammad Saleh
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
| | - Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
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31
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Chakraborty S, Pallada S, Pedersen JT, Jancso A, Correia JG, Hemmingsen L. Nanosecond Dynamics at Protein Metal Sites: An Application of Perturbed Angular Correlation (PAC) of γ-Rays Spectroscopy. Acc Chem Res 2017; 50:2225-2232. [PMID: 28832106 DOI: 10.1021/acs.accounts.7b00219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metalloproteins are essential to numerous reactions in nature, and constitute approximately one-third of all known proteins. Molecular dynamics of proteins has been elucidated with great success both by experimental and theoretical methods, revealing atomic level details of function involving the organic constituents on a broad spectrum of time scales. However, the characterization of dynamics at biomolecular metal sites on nanosecond time scales is scarce in the literature. The aqua ions of many biologically relevant metal ions exhibit exchange of water molecules on the nanosecond time scale or faster, often defining their reactivity in aqueous solution, and this is presumably also a relevant time scale for the making and breaking of coordination bonds between metal ions and ligands at protein metal sites. Ligand exchange dynamics is critical for a variety of elementary steps of reactions in metallobiochemistry, for example, association and dissociation of metal bound water, association of substrate and dissociation of product in the catalytic cycle of metalloenzymes, at regulatory metal sites which require binding and dissociation of metal ions, as well as in the transport of metal ions across cell membranes or between proteins involved in metal ion homeostasis. In Perturbed Angular Correlation of γ-rays (PAC) spectroscopy, the correlation in time and space of two γ-rays emitted successively in a nuclear decay is recorded, reflecting the hyperfine interactions of the PAC probe nucleus with the surroundings. This allows for characterization of molecular and electronic structure as well as nanosecond dynamics at the PAC probe binding site. Herein, selected examples describing the application of PAC spectroscopy in probing the dynamics at protein metal sites are presented, including (1) exchange of Cd2+ bound water in de novo designed synthetic proteins, and the effect of remote mutations on metal site dynamics; (2) dynamics at the β-lactamase active site, where the metal ion appears to jump between the two adjacent sites; (3) structural relaxation in small blue copper proteins upon 111Ag+ to 111Cd2+ transformation in radioactive nuclear decay; (4) metal ion transfer between two HAH1 proteins with change in coordination number; and (5) metal ion sensor proteins with two coexisting metal site structures. With this Account, we hope to make our modest contribution to the field and perhaps spur additional interest in dynamics at protein metal sites, which we consider to be severely underexplored. Relatively little is known about detailed atomic motions at metal sites, for example, how ligand exchange processes affect protein function, and how the amino acid composition of the protein may control this facet of metal site characteristics. We also aim to provide the reader with a qualitative impression of the possibilities offered by PAC spectroscopy in bioinorganic chemistry, especially when elucidating dynamics at protein metal sites, and finally present data that may serve as benchmarks on a relevant time scale for development and tests of theoretical molecular dynamics methods applied to biomolecular metal sites.
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Affiliation(s)
- Saumen Chakraborty
- Department
of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| | - Stavroula Pallada
- ISOLDE/CERN, PH
Div, CH-1211 Geneve
23, Switzerland
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 København Ø, Denmark
| | - Jeppe T. Pedersen
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 København Ø, Denmark
| | - Attila Jancso
- Department
of Inorganic and Analytical Chemistry, University of Szeged, Dóm
tér 7, H-6720 Szeged, Hungary
| | - Joao G. Correia
- ISOLDE/CERN, PH
Div, CH-1211 Geneve
23, Switzerland
- Centro
de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, 2695-066 Bobadela, Portugal
| | - Lars Hemmingsen
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 København Ø, Denmark
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32
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Duster AW, Wang C, Garza CM, Miller DE, Lin H. Adaptive quantum/molecular mechanics: what have we learned, where are we, and where do we go from here? WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1310] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Adam W. Duster
- Chemistry Department University of Colorado Denver Denver CO USA
| | - Chun‐Hung Wang
- Chemistry Department University of Colorado Denver Denver CO USA
| | | | | | - Hai Lin
- Chemistry Department University of Colorado Denver Denver CO USA
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33
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Saleh M, Hofer TS. Palladium(ii) in liquid ammonia: an investigation of structural and dynamical properties by applying quantum mechanical charge field molecular dynamics (QMCF-MD). Dalton Trans 2017; 46:9630-9638. [DOI: 10.1039/c7dt01548h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structural and dynamical properties of Pd2+ in liquid ammonia have been investigated via quantum mechanical charge field molecular dynamics.
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Affiliation(s)
- Muhammad Saleh
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
| | - Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- Center for Chemistry and Biomedicine
- University of Innsbruck
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34
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Wiedemair MJ, Hofer TS. Towards a dissociative SPC-like water model – probing the impact of intramolecular Coulombic contributions. Phys Chem Chem Phys 2017; 19:31910-31920. [DOI: 10.1039/c7cp06191a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A modification of the dissociative Garofalini water model towards an SPC-like Coulombic formulation proved to enhance accuracy and transferability of this successful force field approach.
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Affiliation(s)
- Martin J. Wiedemair
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- University of Innsbruck
- 6020 Innsbruck
| | - Thomas S. Hofer
- Theoretical Chemistry Division
- Institute of General
- Inorganic and Theoretical Chemistry
- University of Innsbruck
- 6020 Innsbruck
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35
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Qiao B, Ferru G, Ellis RJ. Complexation Enhancement Drives Water-to-Oil Ion Transport: A Simulation Study. Chemistry 2016; 23:427-436. [DOI: 10.1002/chem.201604470] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Indexed: 01/14/2023]
Affiliation(s)
- Baofu Qiao
- Chemical Sciences and Engineering Division; Argonne National Laboratory; Argonne Illinois 60439 USA
| | - Geoffroy Ferru
- Chemical Sciences and Engineering Division; Argonne National Laboratory; Argonne Illinois 60439 USA
| | - Ross J. Ellis
- Chemical Sciences and Engineering Division; Argonne National Laboratory; Argonne Illinois 60439 USA
- Chemical Sciences Division; Oak Ridge National Laboratory; Oak Ridge Tennessee 37831 USA
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36
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Saleh M, Hofer TS. Structure and dynamics of Ni2+ in liquid ammonia: A quantum mechanical charge field molecular dynamics (QMCF-MD) study. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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37
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Wang YL, Wang Y, Yi HB. High-Order Ca(II)–Chloro Complexes in Mixed CaCl2–LiCl Aqueous Solution: Insights from Density Functional Theory and Molecular Dynamics Simulations. J Phys Chem A 2016; 120:5635-48. [DOI: 10.1021/acs.jpca.6b01694] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yu-Lin Wang
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
| | - Ying Wang
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
| | - Hai-Bo Yi
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People’s Republic of China
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38
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Andersson MP, Dideriksen K, Sakuma H, Stipp SLS. Modelling how incorporation of divalent cations affects calcite wettability-implications for biomineralisation and oil recovery. Sci Rep 2016; 6:28854. [PMID: 27352933 PMCID: PMC4926276 DOI: 10.1038/srep28854] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 06/10/2016] [Indexed: 11/09/2022] Open
Abstract
Using density functional theory and geochemical speciation modelling, we predicted how solid-fluid interfacial energy is changed, when divalent cations substitute into a calcite surface. The effect on wettability can be dramatic. Trace metal uptake can impact organic compound adsorption, with effects for example, on the ability of organisms to control crystal growth and our ability to predict the wettability of pore surfaces. Wettability influences how easily an organic phase can be removed from a surface, either organic compounds from contaminated soil or crude oil from a reservoir. In our simulations, transition metals substituted exothermically into calcite and more favourably into sites at the surface than in the bulk, meaning that surface properties are more strongly affected than results from bulk experiments imply. As a result of divalent cation substitution, calcite-fluid interfacial energy is significantly altered, enough to change macroscopic contact angle by tens of degrees. Substitution of Sr, Ba and Pb makes surfaces more hydrophobic. With substitution of Mg and the transition metals, calcite becomes more hydrophilic, weakening organic compound adsorption. For biomineralisation, this provides a switch for turning on and off the activity of organic crystal growth inhibitors, thereby controlling the shape of the associated mineral phase.
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Affiliation(s)
- M P Andersson
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Denmark
| | - K Dideriksen
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Denmark
| | - H Sakuma
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Denmark.,National Institute for Materials Science, Japan
| | - S L S Stipp
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Denmark
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39
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Chillemi G, Pace E, D'Abramo M, Benfatto M. Equilibrium between 5- and 6-Fold Coordination in the First Hydration Shell of Cu(II). J Phys Chem A 2016; 120:3958-65. [PMID: 27195961 DOI: 10.1021/acs.jpca.6b03569] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hydration structure dynamics of Cu(II) ion is characterized by a combination of classical molecular dynamics simulation and X-ray absorption near-edge spectroscopy. Previous experimental data have been analyzed on the basis of 5- or 6-fold first hydration structure, with a quite well-established equatorial structure. This 4-fold equatorial geometry has been our starting point to develop a simple but effective in silico model, which provides ab initio theoretical X-ray absorption spectra in very good agreement with the experimental data. Our results point out two equally populated 6- and 5-fold hydration structures with remarkable different water residence times of 5 and 98 ps, respectively, and a low free energy barrier between first and second hydration shell.
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Affiliation(s)
- Giovanni Chillemi
- SCAI SuperComputing Applications and Innovation Department , Cineca Via dei Tizii, 6. 00185 Rome, Italy
| | - Elisabetta Pace
- Laboratori Nazionali di Frascati-INFN , Post Office Box 13, 00044 Frascati, Italy
| | - Marco D'Abramo
- Dipartimento di Chimica, Università di Roma "La Sapienza" , Ple A. Moro 5, 00185 Rome, Italy
| | - Maurizio Benfatto
- Laboratori Nazionali di Frascati-INFN , Post Office Box 13, 00044 Frascati, Italy
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40
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Eppard E, Pèrez-Malo M, Rösch F. Improved radiolabeling of DOTATOC with trivalent radiometals for clinical application by addition of ethanol. EJNMMI Radiopharm Chem 2016; 1:6. [PMID: 29564383 PMCID: PMC5843808 DOI: 10.1186/s41181-016-0010-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/16/2016] [Indexed: 11/10/2022] Open
Abstract
Background Typically, metal-based radiopharmaceuticals are synthesized in aqueous solutions with no or low ethanol content. Labeling yields are defined by temperature, period of labeling, amount of precursor, pH etc. As recently observed, radiolabeling yields (RCY) seem to increase in the presence of non-aqueous solvents. Consequently, this effect was investigated systematically using ethanol as non-aqueous solvent (n-as), which is widely utilized in medicine, and DOTATOC as model compound. Methods To determine the impact of ethanol on the radiolabeling efficacy, "standard" labeling conditions of 68Ga-DOTATOC (95-100 °C, 10-15 min, 20-50 μg DOTATOC, aqueous solution), i.e. 10 nmol (2.9 μM, 14.2 μg), were modified in terms of lower temperature (70 °C) to achieve lower RCY (<75 %). From those lower RCY, positive effects of increasing amounts of ethanol (0-40 vol%) could directly be observed. Labeling parameters were finally evaluated in terms of shorter reaction time and lower amount of precursor. To investigate whether the effects observed are also true for other trivalent radiometals, labeling was also performed with 44Sc. Results For increasing amounts of ethanol, 68Ga-DOTATOC RCY at 70 °C improved significantly. RCY of ~95 % can be achieved within 10 min using 30 vol% ethanol compared to 46 % in the pure aqueous system. If "standard" temperatures of 95 °C are applied, high RCY of 89 % can be achieved within 5 min with much lower amounts of precursor, i.e. even at 0.93 nmol (0.3 μM, 1.3 μg). This also represents significantly increased specific activities. Similar behavior was observed for 44Sc where RCY increase successively with increasing amounts of ethanol. Conclusion There is clear experimental evidence, that adding more than 20 vol% ethanol to the reaction mixtures significantly improve labeling efficacies. This could be demonstrated for 68Ga-DOTATOC and 44Sc-DOTATOC in terms of temperature, time and concentration of required precursor. Whether this is a principal phenomenon with practical impact on the radiopharmaceutical chemistry of trivalent metals and whether this applies to other non-aqueous solvents as well - and what the physico-chemical reasons are, remains to be studied in more detail. Nevertheless, the effect observed here will improve 68Ga-DOTATOC labeling and may save at least half of the usually applied amount of precursor.
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Affiliation(s)
- Elisabeth Eppard
- Department of Nuclear Medicine, University Hospital Bonn, Sigmund-Freud-Strasse 25, D-53127 Bonn, Germany
| | - Marylaine Pèrez-Malo
- Institute of Nuclear Chemistry, Johannes Gutenberg-University, Fritz-Strassmann-Weg 2, D-55128 Mainz, Germany.,Department of Radiopharmacy, Isotopes Center, Havana, Ave. Monumental y Carr. La Rada km 31/2, Mayabeque, La Habana Cuba
| | - Frank Rösch
- Institute of Nuclear Chemistry, Johannes Gutenberg-University, Fritz-Strassmann-Weg 2, D-55128 Mainz, Germany
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41
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42
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Aono S, Mori T, Sakaki S. 3D-RISM-MP2 Approach to Hydration Structure of Pt(II) and Pd(II) Complexes: Unusual H-Ahead Mode vs Usual O-Ahead One. J Chem Theory Comput 2016; 12:1189-206. [PMID: 26863511 DOI: 10.1021/acs.jctc.5b01137] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Solvation of transition metal complexes with water has been one of the fundamental topics in physical and coordination chemistry. In particular, Pt(II) complexes have recently attracted considerable interest for their relation to anticancer activity in cisplatin and its analogues, yet the interaction of the water molecule and the metal center has been obscured. The challenge from a theoretical perspective remains that both the microscopic solvation effect and the dynamical electron correlation (DEC) effect have to be treated simultaneously in a reasonable manner. In this work we derive the analytical gradient for the three-dimensional reference interaction site model Møller-Plesset second order (3D-RISM-MP2) free energy. On the basis of the three-regions 3D-RISM self-consistent field (SCF) method recently proposed by us, we apply a new layer of the Z-vector method to the CP-RISM equation as well as point-charge approximation to the derivatives with respect to the density matrix elements in the RISM-CPHF equation to remarkably reduce the computational cost. This method is applied to study the interaction of H2O with the d(8) square planar transition metal complexes in aqueous solution, trans-[Pt(II)Cl2(NH3)(glycine)] (1a), [Pt(II)(NH3)4](2+) (1b), [Pt(II)(CN)4](2-) (1c), and their Pd(II) analogues 2a, 2b, and 2c, respectively, to elucidate whether the usual H2O interaction through O atom (O-ahead mode) or unusual one through H atom (H-ahead mode) is stable in these complexes. We find that the interaction energy of the coordinating water and the transition metal complex changes little when switching from gas to aqueous phase, but the solvation free energy differs remarkably between the two interaction modes, thereby affecting the relative stability of the H-ahead and O-ahead modes. Particularly, in contrast to the expectation that the O-ahead mode is preferred due to the presence of positive charges in 1b, the H-ahead mode is also found to be more stable. The O-ahead mode is found to be more stable than the H-ahead one only in 2b. The energy decomposition analysis (EDA) at the 3D-RISM-MP2 level revealed that the O-ahead mode is stabilized by the electrostatic (ES) interaction, whereas the H-ahead one is mainly stabilized by the DEC effect. The ES interaction is also responsible for the difference between the Pd(II) and Pt(II) complexes; because the electrostatic potential is more negative along the z-axis in the Pt(II) complex than in the Pd(II) one, the O-ahead mode prefers the Pd(II) complexes, whereas the H-ahead becomes predominant in the Pt(II) complexes.
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Affiliation(s)
- Shinji Aono
- Fukui Institute for Fundamental Chemistry, Kyoto University , Nishihiraki-cho, Takano, Sakyo-ku, Kyoto 606-8103, Japan
| | - Toshifumi Mori
- Institute for Molecular Science , Okazaki, Aichi 444-8585, Japan.,School of Physical Sciences, The Graduate University for Advanced Studies , Okazaki, Aichi 444-8585, Japan
| | - Shigeyoshi Sakaki
- Fukui Institute for Fundamental Chemistry, Kyoto University , Nishihiraki-cho, Takano, Sakyo-ku, Kyoto 606-8103, Japan
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43
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Mogami G, Suzuki M, Matubayasi N. Spatial-Decomposition Analysis of Energetics of Ionic Hydration. J Phys Chem B 2016; 120:1813-21. [DOI: 10.1021/acs.jpcb.5b09481] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- George Mogami
- Department
of Materials Processing, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan
- Frontier
Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Makoto Suzuki
- Department
of Materials Processing, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan
- Frontier
Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Nobuyuki Matubayasi
- Frontier
Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
- Division
of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements
Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
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44
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45
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Hofer TS, Tirler AO. Combining 2d-Periodic Quantum Chemistry with Molecular Force Fields: A Novel QM/MM Procedure for the Treatment of Solid-State Surfaces and Interfaces. J Chem Theory Comput 2015; 11:5873-87. [DOI: 10.1021/acs.jctc.5b00548] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thomas S. Hofer
- Theoretical Chemistry Division,
Institute for General Inorganic and Theoretical Chemistry, Center
for Chemistry and Biomedicine, University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Austria
| | - Andreas O. Tirler
- Theoretical Chemistry Division,
Institute for General Inorganic and Theoretical Chemistry, Center
for Chemistry and Biomedicine, University of Innsbruck, Innrain
80-82, A-6020 Innsbruck, Austria
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46
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Bukharov MS, Shtyrlin VG, Mamin GV, Stapf S, Mattea C, Mukhtarov AS, Serov NY, Gilyazetdinov EM. Structure and Dynamics of Solvation Shells of Copper(II) Complexes with N,O-Containing Ligands. Inorg Chem 2015; 54:9777-84. [DOI: 10.1021/acs.inorgchem.5b01467] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mikhail S. Bukharov
- A.M. Butlerov Chemistry Institute, Kazan Federal University, Kremlevskaya St. 18, 420008, Kazan, Russian Federation
| | - Valery G. Shtyrlin
- A.M. Butlerov Chemistry Institute, Kazan Federal University, Kremlevskaya St. 18, 420008, Kazan, Russian Federation
| | - Georgy V. Mamin
- Institute of Physics, Kazan Federal University, Kremlevskaya St. 18, 420008 Kazan, Russian Federation
| | - Siegfried Stapf
- Fachgebiet Technische Physik II/Polymerphysik,
Institute of Physics, Technische Universität Ilmenau, P.O. Box 100 565, 98684 Ilmenau, Germany
| | - Carlos Mattea
- Fachgebiet Technische Physik II/Polymerphysik,
Institute of Physics, Technische Universität Ilmenau, P.O. Box 100 565, 98684 Ilmenau, Germany
| | - Anvar Sh. Mukhtarov
- A.M. Butlerov Chemistry Institute, Kazan Federal University, Kremlevskaya St. 18, 420008, Kazan, Russian Federation
| | - Nikita Yu. Serov
- A.M. Butlerov Chemistry Institute, Kazan Federal University, Kremlevskaya St. 18, 420008, Kazan, Russian Federation
| | - Edward M. Gilyazetdinov
- A.M. Butlerov Chemistry Institute, Kazan Federal University, Kremlevskaya St. 18, 420008, Kazan, Russian Federation
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47
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Sripa P, Tongraar A, Kerdcharoen T. Structure and dynamics of the Li+ hydrates: A comparative study of conventional QM/MM and ONIOM-XS MD simulations. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2015.04.054] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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48
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Mereshchenko AS, Olshin PK, Karabaeva KE, Panov MS, Wilson RM, Kochemirovsky VA, Skripkin MY, Tveryanovich YS, Tarnovsky AN. Mechanism of Formation of Copper(II) Chloro Complexes Revealed by Transient Absorption Spectroscopy and DFT/TDDFT Calculations. J Phys Chem B 2015; 119:8754-63. [PMID: 26079181 DOI: 10.1021/acs.jpcb.5b03889] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Copper(II) complexes are extremely labile with typical ligand exchange rate constants on the order of 10(6)-10(9) M(-1) s(-1). As a result, it is often difficult to identify the actual formation mechanism of these complexes. In this work, using UV-vis transient absorption when probing in a broad time range (20 ps to 8 μs) in conjunction with DFT/TDDFT calculations, we studied the dynamics and underlying reaction mechanisms of the formation of extremely labile copper(II) CuCl4(2-) chloro complexes from copper(II) CuCl3(-) trichloro complexes and chloride ions. These two species, produced via photochemical dissociation of CuCl4(2-) upon 420 nm excitation into the ligand-to-metal-charge-transfer electronic state, are found to recombine into parent complexes with bimolecular rate constants of (9.0 ± 0.1) × 10(7) and (5.3 ± 0.4) × 10(8) M(-1) s(-1) in acetonitrile and dichloromethane, respectively. In dichloromethane, recombination occurs via a simple one-step addition. In acetonitrile, where [CuCl3](-) reacts with the solvent to form a [CuCl3CH3CN](-) complex in less than 20 ps, recombination takes place via ligand exchange described by the associative interchange mechanism that involves a [CuCl4CH3CN](2-) intermediate. In both solvents, the recombination reaction is potential energy controlled.
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Affiliation(s)
- Andrey S Mereshchenko
- †Institute of Chemistry, Saint-Petersburg State University, 198504 Saint-Petersburg, Russian Federation
| | - Pavel K Olshin
- †Institute of Chemistry, Saint-Petersburg State University, 198504 Saint-Petersburg, Russian Federation
| | - Kanykey E Karabaeva
- ‡Department of Chemistry and the Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Maxim S Panov
- †Institute of Chemistry, Saint-Petersburg State University, 198504 Saint-Petersburg, Russian Federation
| | - R Marshall Wilson
- ‡Department of Chemistry and the Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Vladimir A Kochemirovsky
- †Institute of Chemistry, Saint-Petersburg State University, 198504 Saint-Petersburg, Russian Federation
| | - Mikhail Yu Skripkin
- †Institute of Chemistry, Saint-Petersburg State University, 198504 Saint-Petersburg, Russian Federation
| | - Yury S Tveryanovich
- †Institute of Chemistry, Saint-Petersburg State University, 198504 Saint-Petersburg, Russian Federation
| | - Alexander N Tarnovsky
- ‡Department of Chemistry and the Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
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Frank P, Benfatto M, Qayyam M, Hedman B, Hodgson KO. A high-resolution XAS study of aqueous Cu(II) in liquid and frozen solutions: pyramidal, polymorphic, and non-centrosymmetric. J Chem Phys 2015; 142:084310. [PMID: 25725734 PMCID: PMC4349298 DOI: 10.1063/1.4908266] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 02/04/2015] [Indexed: 11/15/2022] Open
Abstract
High-resolution EXAFS (k = 18 Å(-1)) and MXAN XAS analyses show that axially elongated square pyramidal [Cu(H2O)5](2+) dominates the structure of Cu(II) in aqueous solution, rather than 6-coordinate JT-octahedral [Cu(H2O)6](2+). Freezing produced a shoulder at 8989.6 eV on the rising XAS edge and an altered EXAFS spectrum, while 1s → 3d transitions remained invariant in energy position and intensity. Core square pyramidal [Cu(H2O)5](2+) also dominates frozen solution. Solvation shells were found at ∼3.6 Å (EXAFS) or ∼3.8 Å (MXAN) in both liquid and frozen phases. However, MXAN analysis revealed that about half the time in liquid solution, [Cu(H2O)5](2+) associates with an axially non-bonding 2.9 Å water molecule. This distant water apparently organizes the solvation shell. When the 2.9 Å water molecule is absent, the second shell is undetectable to MXAN. The two structural arrangements may represent energetic minima of fluxional dissolved aqueous [Cu(H2O)5](2+). The 2.9 Å trans-axial water resolves an apparent conflict of the [Cu(H2O)5](2+) core model with a dissociational exchange mechanism. In frozen solution, [Cu(H2O)5](2+) is associated with either a 3.0 Å axial non-bonded water molecule or an axial ClO4(-) at 3.2 Å. Both structures are again of approximately equal presence. When the axial ClO4(-) is present, Cu(II) is ∼0.5 Å above the mean O4 plane. This study establishes [Cu(H2O)5](2+) as the dominant core structure for Cu(II) in water solution, and is the first to both empirically resolve multiple extended solution structures for fluxional [Cu(H2O)5](2+) and to provide direct evidence for second shell dynamics.
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Affiliation(s)
- Patrick Frank
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Maurizio Benfatto
- Laboratori Nazionali di Frascati-INFN, P.O. Box 13, 00044 Frascati, Italy
| | - Munzarin Qayyam
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, USA
| | - Keith O Hodgson
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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Eklund L, Hofer TS, Persson I. Structure and water exchange dynamics of hydrated oxo halo ions in aqueous solution using QMCF MD simulation, large angle X-ray scattering and EXAFS. Dalton Trans 2015; 44:1816-28. [PMID: 25473816 PMCID: PMC4281468 DOI: 10.1039/c4dt02580f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Theoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) has been applied in conjunction with experimental large angle X-ray scattering (LAXS) and EXAFS measurements to study structure and dynamics of the hydrated oxo chloro anions chlorite, ClO2(-), chlorate, ClO3(-), and perchlorate, ClO4(-). In addition, the structures of the hydrated hypochlorite, ClO(-), bromate, BrO3(-), iodate, IO3(-) and metaperiodate, IO4(-), ions have been determined in aqueous solution by means of LAXS. The structures of the bromate, metaperiodate, and orthoperiodate, H2IO6(3-), ions have been determined by EXAFS as solid sodium salts and in aqueous solution as well. The results show clearly that the only form of periodate present in aqueous solution is metaperiodate. The Cl-O bond distances in the hydrated oxo chloro anions as determined by LAXS and obtained in the QMCF MD simulations are in excellent agreement, being 0.01-0.02 Å longer than in solid anhydrous salts due to hydration through hydrogen bonding to water molecules. The oxo halo anions, all with unit negative charge, have low charge density making them typical structure breakers, thus the hydrogen bonds formed to the hydrating water molecules are weaker and more short-lived than those between water molecules in pure water. The water exchange mechanism of the oxo chloro anions resembles those of the oxo sulfur anions with a direct exchange at the oxygen atoms for perchlorate and sulfate. The water exchange rate for the perchlorate ion is significantly faster, τ0.5 = 1.4 ps, compared to the hydrated sulfate ion and pure water, τ0.5 = 2.6 and 1.7 ps, respectively. The angular radial distribution functions show that the chlorate and sulfite ions have a more complex water exchange mechanism. As the chlorite and chlorate ions are more weakly hydrated than the sulfite ion the spatial occupancy is less well-defined and it is not possible to follow any well-defined migration pattern as it is difficult to distinguish between hydrating water molecules and bulk water in the region close to the ions.
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Affiliation(s)
- Lars Eklund
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, P.O.Box 7015, SE-750 07 Uppsala, Sweden
| | - Tomas S. Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Ingmar Persson
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, P.O.Box 7015, SE-750 07 Uppsala, Sweden
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