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Shiery RC, Cooper KA, Cantu DC. Computational Prediction of All Lanthanide Aqua Ion Acidity Constants. Inorg Chem 2021; 60:10257-10266. [PMID: 34214391 DOI: 10.1021/acs.inorgchem.1c00662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The protonation state of lanthanide-ligand complexes, or lanthanide-containing porous materials, with many Brønsted acid sites can change due to proton loss/gain reactions with water or other heteroatom-containing compounds. Consequently, variations in the protonation state of lanthanide-containing species affect their molecular structure and desired properties. Lanthanide(III) aqua ions undergo hydrolysis and form hydroxides; they are the best characterized lanthanide-containing species with multiple Brønsted acid sites. We employed constrained ab initio molecular dynamics simulations and electronic structure calculations to determine all acidity constants of the lanthanide(III) aqua ions solely from computation. The first, second, and third acidity constants of lanthanide(III) aqua ions were predicted, on average, within 1.2, 2.5, and 4.7 absolute pKa units from experiment, respectively. A table includes our predicted pKa values alongside most experimentally measured pKa values known to date. The approach presented is particularly suitable to determine the Brønsted acidity of lanthanide-containing systems with multiple acidic sites, including those whose measured acidity constants cannot be linked to specific acid sites.
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Affiliation(s)
- Richard C Shiery
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557, United States
| | - Kyle A Cooper
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557, United States
| | - David C Cantu
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada 89557, United States
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2
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Thomsen B, Shiga M. Nuclear quantum effects on autoionization of water isotopologs studied by ab initio path integral molecular dynamics. J Chem Phys 2021; 154:084117. [PMID: 33639728 DOI: 10.1063/5.0040791] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In this study, we investigate the nuclear quantum effects (NQEs) on the acidity constant (pKA) of liquid water isotopologs under the ambient condition by path integral molecular dynamics (PIMD) simulations. We compared simulations using a fully explicit solvent model with a classical polarizable force field, density functional tight binding, and ab initio density functional theory, which correspond to empirical, semiempirical, and ab initio PIMD simulations, respectively. The centroid variable with respect to the proton coordination number of a water molecule was restrained to compute the gradient of the free energy, which measures the reversible work of the proton abstraction for the quantum mechanical system. The free energy curve obtained by thermodynamic integration was used to compute the pKA value based on probabilistic determination. This technique not only reproduces the pKA value of liquid D2O experimentally measured (14.86) but also allows for a theoretical prediction of the pKA values of liquid T2O and aqueous HDO and HTO, which are unknown due to their scarcity. It is also shown that the NQEs on the free energy curve can result in a downshift of 4.5 ± 0.9 pKA units in the case of liquid water, which indicates that the NQEs plays an indispensable role in the absolute determination of pKA. The results of this study can help inform further extensions into the calculation of the acidity constants of isotope substituted species with high accuracy.
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Affiliation(s)
- Bo Thomsen
- CCSE, Japan Atomic Energy Agency, 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
| | - Motoyuki Shiga
- CCSE, Japan Atomic Energy Agency, 178-4-4, Wakashiba, Kashiwa, Chiba 277-0871, Japan
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3
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Wang R, Carnevale V, Klein ML, Borguet E. First-Principles Calculation of Water p Ka Using the Newly Developed SCAN Functional. J Phys Chem Lett 2020; 11:54-59. [PMID: 31834803 DOI: 10.1021/acs.jpclett.9b02913] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Acid/base chemistry is an intriguing topic that still constitutes a challenge for computational chemistry. While estimating the acid dissociation constant (or pKa) could shed light on many chemistry processes, especially in the fields of biochemistry and geochemistry, evaluating the relative stability between protonated and nonprotonated species is often very difficult. Indeed, a prerequisite for calculating the pKa of any molecule is an accurate description of the energetics of water dissociation. Here, we applied constrained molecular dynamics simulations, a noncanonical sampling technique, to investigate the water deprotonation process by selecting the OH distance as the reaction coordinate. The calculation is based on density functional theory and the newly developed SCAN functional, which has shown excellent performance in describing water structure. This first benchmark of SCAN on a chemical reaction shows that this functional accurately models the energetics of proton transfer reactions in an aqueous environment. After taking Coulomb long-range corrections and nuclear quantum effects into account, the estimated water pKa is only 1.0 pKa unit different from the target experimental value. Our results show that the combination of SCAN and constrained MD successfully reproduces the chemistry of water and constitutes a good framework for calculating the free energy of chemical reactions of interest.
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Affiliation(s)
- Ruiyu Wang
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
- Center for Complex Materials from First-Principles (CCM) , Temple University , 1925 North 12th Street , Philadelphia , Pennsylvania 19122 , United States
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science , Temple University , Philadelphia , Pennsylvania 19122 , United States
- Department of Biology , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Michael L Klein
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
- Center for Complex Materials from First-Principles (CCM) , Temple University , 1925 North 12th Street , Philadelphia , Pennsylvania 19122 , United States
- Institute for Computational Molecular Science , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Eric Borguet
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
- Center for Complex Materials from First-Principles (CCM) , Temple University , 1925 North 12th Street , Philadelphia , Pennsylvania 19122 , United States
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4
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Determination of pKa Values via ab initio Molecular Dynamics and its Application to Transition Metal-Based Water Oxidation Catalysts. INORGANICS 2019. [DOI: 10.3390/inorganics7060073] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The p K a values are important for the in-depth elucidation of catalytic processes, the computational determination of which has been challenging. The first simulation protocols employing ab initio molecular dynamics simulations to calculate p K a values appeared almost two decades ago. Since then several slightly different methods have been proposed. We compare the performance of various evaluation methods in order to determine the most reliable protocol when it comes to simulate p K a values of transition metal-based complexes, such as the here investigated Ru-based water oxidation catalysts. The latter are of high interest for sustainable solar-light driven water splitting, and understanding of the underlying reaction mechanism is crucial for their further development.
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5
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Sandmann N, Bachmann J, Hepp A, Doltsinis NL, Müller J. Copper(ii)-mediated base pairing involving the artificial nucleobase 3H-imidazo[4,5-f]quinolin-5-ol. Dalton Trans 2019; 48:10505-10515. [DOI: 10.1039/c9dt02043h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A highly stabilizing Cu(ii)-mediated base pair is introduced into DNA using a large artificial nucleobase.
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Affiliation(s)
- Nikolas Sandmann
- Institut für Anorganische und Analytische Chemie
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Jim Bachmann
- Institut für Festkörpertheorie and Center for Multiscale Theory and Computation
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Alexander Hepp
- Institut für Anorganische und Analytische Chemie
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Nikos L. Doltsinis
- Institut für Festkörpertheorie and Center for Multiscale Theory and Computation
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
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Matsui T, Shigeta Y, Morihashi K. Assessment of Methodology and Chemical Group Dependences in the Calculation of the pKa for Several Chemical Groups. J Chem Theory Comput 2017; 13:4791-4803. [DOI: 10.1021/acs.jctc.7b00587] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Toru Matsui
- Department
of Chemistry, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Yasuteru Shigeta
- Center
for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Kenji Morihashi
- Department
of Chemistry, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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7
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Zhu G, Kang X, Zhou S, Tang X, Sha M, Cui Z, Xu X. Molecular insight into the microstructure and microscopic dynamics of pyridinium ionic liquids with different alkyl chains based on temperature response. RSC Adv 2017. [DOI: 10.1039/c6ra26866h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
High temperature is advantageous to the aggregation of the polar regions as well as the nonpolar regions of pyridinium ionic liquids.
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Affiliation(s)
- Guanglai Zhu
- Institute of Atomic and Molecular Physics
- Anhui Normal University
- Wuhu 241000
- China
| | - Xianqu Kang
- Institute of Atomic and Molecular Physics
- Anhui Normal University
- Wuhu 241000
- China
| | - Siwen Zhou
- Institute of Atomic and Molecular Physics
- Anhui Normal University
- Wuhu 241000
- China
| | - Xiaoshuan Tang
- Institute of Atomic and Molecular Physics
- Anhui Normal University
- Wuhu 241000
- China
| | - Maolin Sha
- Department of Chemistry and Chemical Engineering
- Hefei Normal University
- Hefei 230061
- China
| | - Zhifeng Cui
- Institute of Atomic and Molecular Physics
- Anhui Normal University
- Wuhu 241000
- China
| | - Xinsheng Xu
- Institute of Atomic and Molecular Physics
- Anhui Normal University
- Wuhu 241000
- China
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8
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Thapa B, Schlegel HB. Theoretical Calculation of pKa’s of Selenols in Aqueous Solution Using an Implicit Solvation Model and Explicit Water Molecules. J Phys Chem A 2016; 120:8916-8922. [DOI: 10.1021/acs.jpca.6b09520] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Bishnu Thapa
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - H. Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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9
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Thapa B, Schlegel HB. Density Functional Theory Calculation of pKa’s of Thiols in Aqueous Solution Using Explicit Water Molecules and the Polarizable Continuum Model. J Phys Chem A 2016; 120:5726-35. [DOI: 10.1021/acs.jpca.6b05040] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Bishnu Thapa
- Chemistry Department, Wayne State University, Detroit, Michigan 48202, United States
| | - H. Bernhard Schlegel
- Chemistry Department, Wayne State University, Detroit, Michigan 48202, United States
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Xue XS, Wang Y, Yang C, Ji P, Cheng JP. Toward Prediction of the Chemistry in Ionic Liquids: An Accurate Computation of Absolute pKa Values of Benzoic Acids and Benzenethiols. J Org Chem 2015; 80:8997-9006. [DOI: 10.1021/acs.joc.5b00693] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiao-Song Xue
- State
Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation
Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China
| | - Ya Wang
- State
Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation
Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China
| | - Chen Yang
- State
Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation
Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China
| | - Pengju Ji
- Center
of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jin-Pei Cheng
- State
Key Laboratory of Elemento-organic Chemistry, Collaborative Innovation
Center of Chemical Science and Engineering (Tianjin), College of Chemistry, Nankai University, Tianjin 300071, China
- Center
of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing 100084, China
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11
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Thermodynamic properties and microstructures of the mixture of N-butylpyridinium tetrafluoroborate with acetonitrile studied by molecular dynamics simulation. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2015.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Thapa B, Schlegel HB. Calculations of pKa's and redox potentials of nucleobases with explicit waters and polarizable continuum solvation. J Phys Chem A 2014; 119:5134-44. [PMID: 25291241 DOI: 10.1021/jp5088866] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The SMD implicit solvation model augmented with one and four explicit water molecules was used to calculate pKa's and redox potentials of N-methyl-substituted nucleic acid bases guanine, adenine, cytosine, thymine, and uracil. Calculations were carried out with the B3LYP/6-31+G(d,p) level of theory. The same numbers of water molecules were hydrogen bonded to the neutral, protonated, and deprotonated nucleobases in their unoxidized and oxidized forms. The improvement in pKa1 involving neutrals and cations was modest. By contrast, the improvement in pKa2 involving neutrals and anions was quite significant, reducing the mean absolute error from 4.6 pKa units with no waters, to 2.6 with one water and 1.7 with four waters. For the oxidation of nucleobases, adding explicit waters did little to improve E(X(•),H(+)/XH), possibly because both species in the redox couple are neutral molecules at pH 7.
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Affiliation(s)
- Bishnu Thapa
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - H Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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13
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Yang C, Xue XS, Li X, Cheng JP. Computational Study on the Acidic Constants of Chiral Brønsted Acids in Dimethyl Sulfoxide. J Org Chem 2014; 79:4340-51. [DOI: 10.1021/jo500158e] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Chen Yang
- State Key
Laboratory of Elemento-Organic
Chemistry, Department of Chemistry, and Collaborative Innovation Center
of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Xiao-Song Xue
- State Key
Laboratory of Elemento-Organic
Chemistry, Department of Chemistry, and Collaborative Innovation Center
of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Xin Li
- State Key
Laboratory of Elemento-Organic
Chemistry, Department of Chemistry, and Collaborative Innovation Center
of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Jin-Pei Cheng
- State Key
Laboratory of Elemento-Organic
Chemistry, Department of Chemistry, and Collaborative Innovation Center
of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
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14
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Hassanali AA, Cuny J, Verdolino V, Parrinello M. Aqueous solutions: state of the art in ab initio molecular dynamics. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2014; 372:20120482. [PMID: 24516179 DOI: 10.1098/rsta.2012.0482] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The simulation of liquids by ab initio molecular dynamics (AIMD) has been a subject of intense activity over the last two decades. The significant increase in computational resources as well as the development of new and efficient algorithms has elevated this method to the status of a standard quantum mechanical tool that is used by both experimentalists and theoreticians. As AIMD computes the electronic structure from first principles, it is free of ad hoc parametrizations and has thus been applied to a large variety of physical and chemical problems. In particular, AIMD has provided microscopic insight into the structural and dynamical properties of aqueous solutions which are often challenging to probe experimentally. In this review, after a brief theoretical description of the Born-Oppenheimer and Car-Parrinello molecular dynamics formalisms, we show how AIMD has enhanced our understanding of the properties of liquid water and its constituent ions: the proton and the hydroxide ion. Thereafter, a broad overview of the application of AIMD to other aqueous systems, such as solvated organic molecules and inorganic ions, is presented. We also briefly describe the latest theoretical developments made in AIMD, such as methods for enhanced sampling and the inclusion of nuclear quantum effects.
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Affiliation(s)
- Ali A Hassanali
- Department of Chemistry and Applied Biosciences, ETH Zurich and Università della Svizzera Italiana, , via G. Buffi 13, 6900 Lugano, Switzerland
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Xue XS, Yang C, Li X, Cheng JP. Computational Study on the pKa Shifts in Proline Induced by Hydrogen-Bond-Donating Cocatalysts. J Org Chem 2014; 79:1166-73. [DOI: 10.1021/jo402605n] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Xiao-Song Xue
- State Key Laboratory of Elemento-Organic
Chemistry, Collaborative Innovation Center of Chemical Science and
Engineering, Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Chen Yang
- State Key Laboratory of Elemento-Organic
Chemistry, Collaborative Innovation Center of Chemical Science and
Engineering, Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Xin Li
- State Key Laboratory of Elemento-Organic
Chemistry, Collaborative Innovation Center of Chemical Science and
Engineering, Department of Chemistry, Nankai University, Tianjin 300071, China
| | - Jin-Pei Cheng
- State Key Laboratory of Elemento-Organic
Chemistry, Collaborative Innovation Center of Chemical Science and
Engineering, Department of Chemistry, Nankai University, Tianjin 300071, China
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Xue XS, Yang C, Li X, Cheng JP. Computation of standard equilibrium acidity of C–H acids in ionic media: shedding light on predicting changes of chemical behavior by switching solvent system from molecular to ionic. Org Chem Front 2014. [DOI: 10.1039/c3qo00070b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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