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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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2
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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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3
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Hybrid DFT study on non-covalent interactions and their influence on pKa's of magnesium-carboxylate complexes. J Mol Graph Model 2018; 85:13-24. [DOI: 10.1016/j.jmgm.2018.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/18/2018] [Accepted: 07/09/2018] [Indexed: 01/15/2023]
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4
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Prabhakar S, Melnik R. Influence of Mg2+, SO42− and Na+ ions of sea water in crude oil recovery: DFT and ab initio molecular dynamics simulations. Colloids Surf A Physicochem Eng Asp 2018. [DOI: 10.1016/j.colsurfa.2017.12.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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5
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Betelu S, Rodrigues R, Seron A, Chauvet F, Ignatiadis I, Tzedakis T. Linear sweep voltammetry coupled to a quartz crystal microbalance for investigating the catalytic activity of the Mg(II)–water electrochemical system and managing the Mg oxy-hydroxide hydration state. Electrochem commun 2017. [DOI: 10.1016/j.elecom.2017.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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6
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Bernasconi L, Kazaryan A, Belanzoni P, Baerends EJ. Catalytic Oxidation of Water with High-Spin Iron(IV)–Oxo Species: Role of the Water Solvent. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00568] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Leonardo Bernasconi
- STFC
Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, United Kingdom
| | - Andranik Kazaryan
- Theoretical
Chemistry Section, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Paola Belanzoni
- Department
of Chemistry, Biology and Biotechnology, University of Perugia and Institute of Molecular Science and Technologies (ISTM-CNR), Via Elce
di Sotto 8, I-06123 Perugia, Italy
| | - Evert Jan Baerends
- Theoretical
Chemistry Section, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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7
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Peltzer RM, Eisenstein O, Nova A, Cascella M. How Solvent Dynamics Controls the Schlenk Equilibrium of Grignard Reagents: A Computational Study of CH3MgCl in Tetrahydrofuran. J Phys Chem B 2017; 121:4226-4237. [DOI: 10.1021/acs.jpcb.7b02716] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Raphael M. Peltzer
- Department
of Chemistry and Centre for Theoretical and Computational Chemistry
(CTCC), University of Oslo, Postbox 1033 Blindern, 0315 Oslo, Norway
| | - Odile Eisenstein
- Department
of Chemistry and Centre for Theoretical and Computational Chemistry
(CTCC), University of Oslo, Postbox 1033 Blindern, 0315 Oslo, Norway
- Institut
Charles Gerhardt, UMR 5253 CNRS-Université de Montpellier, Université de Montpellier, cc 1501, Place E. Bataillon, 34095 Montpellier, France
| | - Ainara Nova
- Department
of Chemistry and Centre for Theoretical and Computational Chemistry
(CTCC), University of Oslo, Postbox 1033 Blindern, 0315 Oslo, Norway
| | - Michele Cascella
- Department
of Chemistry and Centre for Theoretical and Computational Chemistry
(CTCC), University of Oslo, Postbox 1033 Blindern, 0315 Oslo, Norway
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8
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Bekçioğlu-Neff G, Allolio C, Desmukh YS, Hansen MR, Sebastiani D. Dynamical Dimension to the Hofmeister Series: Insights from First-Principles Simulations. Chemphyschem 2016; 17:1166-73. [DOI: 10.1002/cphc.201501150] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Indexed: 11/05/2022]
Affiliation(s)
- Gül Bekçioğlu-Neff
- Institut für Chemie; Martin-Luther-Universität Halle-Wittenberg; Von-Danckelmann-Platz 4 06120 Halle (Saale) Germany
- Physics Department; Freie Universität Berlin; Arnimallee 14 14195 Berlin Germany
| | - Christoph Allolio
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; Flemingovo nám 2 16610 Prague 6 Czech Republic
| | - Yogesh S. Desmukh
- Department of Biobased Materials; Maastricht University; P.O. Box 616 6200MD Maastricht The Netherlands
- Wavin Technology and Innovation; P.O. Box 173 8000 AD Zwolle The Netherlands
| | - Michael Ryan Hansen
- Institut für Physikalische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstrasse 28/30 Münster Germany
| | - Daniel Sebastiani
- Institut für Chemie; Martin-Luther-Universität Halle-Wittenberg; Von-Danckelmann-Platz 4 06120 Halle (Saale) Germany
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9
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Jia GZ, Liu S, Liu FH, Liu JC. Ion–Water Cooperative Interactions in Aqueous Solutions of MgCl2by Dielectric Spectroscopy. J DISPER SCI TECHNOL 2015. [DOI: 10.1080/01932691.2015.1010728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Jackson VE, Felmy AR, Dixon DA. Prediction of the pKa's of aqueous metal ion +2 complexes. J Phys Chem A 2015; 119:2926-39. [PMID: 25721568 DOI: 10.1021/jp5118272] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aqueous metal ions play an important role in many areas of chemistry. The acidities of [Be(H2O)4](2+), [M(H2O)6](2+), M = Mg(2+), Mn(2+), Fe(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), and Hg(2+), and [M(H2O)n](2+), M = Ca(2+) and Sr(2+), n = 7 and 8, complexes have been predicted using density functional theory, second-order Møller-Plesset perturbation theory (MP2), and coupled cluster CCSD(T) theory in the gas phase. pKa's in aqueous solution were predicted by using self-consistent reaction field (SCRF) calculations with different solvation models. The most common binding motif of the majority of the metal +2 complexes is coordination number (CN) 6, with each hexaaquo cluster having reasonably high symmetry for the best arrangement of the water molecules in the first solvation shell. Be(2+) is tetracoordinated, but a second solvation shell of 8 waters is needed to predict the pKa. The Ca(2+) and Sr(2+) aquo clusters have a coordination number of 7 or 8 as found in terms of the energy of the reaction M(H2O)7(2+) + H2O → M(H2O)8(2+) and the pKa values. The calculated geometries are in reasonable agreement with experiment. The SCRF calculations with the conductor-like screening model (COSMO), and the conductor polarized continuum model (CPCM) using COSMO-RS radii, consistently agree best with experiment at the MP2/aug-cc-pVDZ and CCSD(T)/aug-cc-pVDZ levels of theory. The CCSD(T) level provides the most accurate pKa's, and the MP2 level also provides reliable predictions. Our predictions were used to elucidate the properties of metal +2 ion complexes. The pKa predictions provide confirmation of the size of the first solvation shell sizes. The calculations show that it is still difficult to predict pKa's using this cluster/implicit solvent approach to better than 1 pKa unit.
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Affiliation(s)
- Virgil E Jackson
- †Department of Chemistry, The University of Alabama, Shelby Hall, Tuscaloosa, Alabama 35487-0336, United States
| | - Andrew R Felmy
- ‡Fundamental Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - David A Dixon
- †Department of Chemistry, The University of Alabama, Shelby Hall, Tuscaloosa, Alabama 35487-0336, United States
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11
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Lu X, Gaus M, Elstner M, Cui Q. Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications. J Phys Chem B 2014; 119:1062-82. [PMID: 25178644 PMCID: PMC4306495 DOI: 10.1021/jp506557r] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
We report the parametrization of
the approximate density functional
theory, DFTB3, for magnesium and zinc for chemical and biological
applications. The parametrization strategy follows that established
in previous work that parametrized several key main group elements
(O, N, C, H, P, and S). This 3OB set of parameters can thus be used
to study many chemical and biochemical systems. The parameters are
benchmarked using both gas-phase and condensed-phase systems. The
gas-phase results are compared to DFT (mostly B3LYP), ab initio (MP2 and G3B3), and PM6, as well as to a previous DFTB parametrization
(MIO). The results indicate that DFTB3/3OB is particularly successful
at predicting structures, including rather complex dinuclear metalloenzyme
active sites, while being semiquantitative (with a typical mean absolute
deviation (MAD) of ∼3–5 kcal/mol) for energetics. Single-point
calculations with high-level quantum mechanics (QM) methods generally
lead to very satisfying (a typical MAD of ∼1 kcal/mol) energetic
properties. DFTB3/MM simulations for solution and two enzyme systems
also lead to encouraging structural and energetic properties in comparison
to available experimental data. The remaining limitations of DFTB3,
such as the treatment of interaction between metal ions and highly
charged/polarizable ligands, are also discussed.
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Affiliation(s)
- Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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12
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Kılıç M, Ensing B. Acidity constants of lumiflavin from first principles molecular dynamics simulations. Phys Chem Chem Phys 2014; 16:18993-9000. [DOI: 10.1039/c4cp01450b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DFT-based molecular dynamics simulations predict the acidity of lumiflavin in different redox states.
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Affiliation(s)
- Murat Kılıç
- Van't Hoff Institute for Molecular Science
- University of Amsterdam
- Amsterdam, The Netherlands
| | - Bernd Ensing
- Van't Hoff Institute for Molecular Science
- University of Amsterdam
- Amsterdam, The Netherlands
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13
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Chatterjee A, Dixit MK, Tembe BL. Solvation Structures and Dynamics of the Magnesium Chloride (Mg2+–Cl–) Ion Pair in Water–Ethanol Mixtures. J Phys Chem A 2013; 117:8703-9. [PMID: 23829688 DOI: 10.1021/jp4031706] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anupam Chatterjee
- Department of Chemistry, Indian Institute of Technology, Bombay, Powai, Mumbai
400076, India
| | - Mayank Kumar Dixit
- Department of Chemistry, Indian Institute of Technology, Bombay, Powai, Mumbai
400076, India
| | - B. L. Tembe
- Department of Chemistry, Indian Institute of Technology, Bombay, Powai, Mumbai
400076, India
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14
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Bernasconi L, Baerends EJ. A Frontier Orbital Study with ab Initio Molecular Dynamics of the Effects of Solvation on Chemical Reactivity: Solvent-Induced Orbital Control in FeO-Activated Hydroxylation Reactions. J Am Chem Soc 2013; 135:8857-67. [DOI: 10.1021/ja311144d] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Leonardo Bernasconi
- STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, OX11 0QX,
United Kingdom
| | - Evert Jan Baerends
- Theoretical
Chemistry Section, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081
HV Amsterdam, The Netherlands
- WCU program at Department of Chemistry, Pohang University of Science and Technology, Pohang
790-784, South Korea
- Chemistry
Department, Faculty
of Science, King Abdulaziz University,
Jeddah 21589, Saudi Arabia
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15
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Steegstra P, Ahlberg E. Influence of oxidation state on the pH dependence of hydrous iridium oxide films. Electrochim Acta 2012. [DOI: 10.1016/j.electacta.2012.04.143] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Multiligand zinc(II) hydroxide complexes: Zn(OH)2X2Y and Zn(OH)2X1,2Y2; X=H2O, CH3OH and Y=NH3, C5H5N. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2011.12.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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Johnsson ACJH, Camerani MC, Abbas Z. Combined Electrospray-Scanning Mobility Particle Sizer (ES-SMPS) and Time-Resolved Synchrotron Radiation-Small-Angle X-ray Scattering (SR-SAXS) Investigation of Colloidal Silica Aggregation. Part II. Influence of Aggregation Initiator on Gel Stability. J Phys Chem B 2011; 115:9547-55. [DOI: 10.1021/jp2032753] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Zareen Abbas
- Department of Chemistry, University of Gothenburg, Gothenburg, Sweden
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18
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Pannetier F, Ohanessian G, Frison G. Comparison between α- and β-carbonic anhydrases: can Zn(His)3(H2O) and Zn(His)(Cys)2(H2O) sites lead to equivalent enzymes? Dalton Trans 2011; 40:2696-8. [PMID: 21298147 DOI: 10.1039/c0dt01454k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Large models of α- and β-carbonic anhydrases were compared using DFT calculations. They indicate similar acidity of the coordinated water molecule and zinc affinity. This explains their similar mechanism of action, despite the wide difference in their first coordination sphere.
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Affiliation(s)
- Florent Pannetier
- Laboratoire des Mécanismes Réactionnels, Département de Chimie, Ecole Polytechnique and CNRS, 91128 Palaiseau Cedex, France
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19
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Bernasconi L, Belanzoni P, Baerends EJ. An abiotic analogue of the diiron(iv)oxo “diamond core” of soluble methane monooxygenase generated by direct activation of O2 in aqueous Fe(ii)/EDTA solutions: thermodynamics and electronic structure. Phys Chem Chem Phys 2011; 13:15272-82. [DOI: 10.1039/c1cp21244c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Hu W, Tong W, Li L, Zheng J, Li G. Cation non-stoichiometry in multi-component oxide nanoparticles by solution chemistry: a case study on CaWO4 for tailored structural properties. Phys Chem Chem Phys 2011; 13:11634-43. [DOI: 10.1039/c0cp02153a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Liu X, Lu X, Wang R, Meijer EJ. Understanding hydration of Zn2+ in hydrothermal fluids with ab initio molecular dynamics. Phys Chem Chem Phys 2011; 13:13305-9. [DOI: 10.1039/c0cp03005h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Park JM, Boero M. Protonation of a hydroxide anion bridging two divalent magnesium cations in water probed by first-principles metadynamics simulation. J Phys Chem B 2010; 114:11102-9. [PMID: 20695500 DOI: 10.1021/jp102991f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The protonation of a hydroxide anion (OH(-)) located between two magnesium cations (Mg(2+)) in aqueous solution has been investigated by first-principles metadynamics simulation. We observe that the complex Mg(2+)-OH(-)-Mg(2+) is stabilized by the coparticipation of the hydroxide anion to the first hydration shells of both the Mg(2+) cations. Contrary to the cases of OH(-) in pure water, the transfer of protons in the presence of the divalent metal ions turns out to be a slow chemical event. This can be ascribed to the decreased proton affinity of the bridging OH(-). Metadynamics simulation, used to overcome the difficulty of the long time scale required by the protonation of the bridging OH(-), has shown that the system possesses a great stability on the reactant state, characterized by a bioctahedral (6,6) solvation structure around the two Mg(2+) cations. The exploration of the free energy landscape shows that this stable bioctahedral configuration converts into a lower coordinated (5,6) structure, leading to a proton transfer from a water molecule belonging to the first solvation shell of the Mg(2+) ion having the lower coordination to the bridging OH(-); the free energy barrier for the protonation reaction is 11 kcal/mol, meaning that the bridging hydroxide is a weak base. During the proton transfer, the bridging OH(-) reverts to an H(2)O molecule, and this breaks the electrostatic coupling of the two Mg(2+) ions, which depart independently with their own hydration shells, one of which is entirely formed by water molecules. The second one carries the newly created OH(-). Our results show that the flexibility in the metal coordination plays a crucial role in both the protonation process of the bridging OH(-) and the separation of the metal cations, providing useful insight into the nature of proton transfer in binuclear divalent metal ions, with several biological implications, such as, for instance, transesterification of catalytic RNA.
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Affiliation(s)
- Jung Mee Park
- Department of Chemistry, Sungkyunkwan University, Suwon, Gyeonggi, 440-746, Korea.
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23
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Ayala R, Spezia R, Vuilleumier R, Martínez JM, Pappalardo RR, Sánchez Marcos E. An Ab Initio Molecular Dynamics Study on the Hydrolysis of the Po(IV) Aquaion in Water. J Phys Chem B 2010; 114:12866-74. [DOI: 10.1021/jp1010956] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Regla Ayala
- Departamento Química Inorgánica, Universidad Sevilla, CSIC, ICMSE, Seville 41012, Spain, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, UMR 8587 CNRS, Bat Maupertuis, Bd F. Mitterrand 91025 Evry, Cedex, France, Département de Chimie de l’École Normale Supérieure, 24 rue Lhomond, 75005 Paris, and Departamento Química Física, Universidad Sevilla, E-41012 Seville, Spain
| | - Riccardo Spezia
- Departamento Química Inorgánica, Universidad Sevilla, CSIC, ICMSE, Seville 41012, Spain, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, UMR 8587 CNRS, Bat Maupertuis, Bd F. Mitterrand 91025 Evry, Cedex, France, Département de Chimie de l’École Normale Supérieure, 24 rue Lhomond, 75005 Paris, and Departamento Química Física, Universidad Sevilla, E-41012 Seville, Spain
| | - Rodolphe Vuilleumier
- Departamento Química Inorgánica, Universidad Sevilla, CSIC, ICMSE, Seville 41012, Spain, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, UMR 8587 CNRS, Bat Maupertuis, Bd F. Mitterrand 91025 Evry, Cedex, France, Département de Chimie de l’École Normale Supérieure, 24 rue Lhomond, 75005 Paris, and Departamento Química Física, Universidad Sevilla, E-41012 Seville, Spain
| | - José Manuel Martínez
- Departamento Química Inorgánica, Universidad Sevilla, CSIC, ICMSE, Seville 41012, Spain, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, UMR 8587 CNRS, Bat Maupertuis, Bd F. Mitterrand 91025 Evry, Cedex, France, Département de Chimie de l’École Normale Supérieure, 24 rue Lhomond, 75005 Paris, and Departamento Química Física, Universidad Sevilla, E-41012 Seville, Spain
| | - Rafael R. Pappalardo
- Departamento Química Inorgánica, Universidad Sevilla, CSIC, ICMSE, Seville 41012, Spain, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, UMR 8587 CNRS, Bat Maupertuis, Bd F. Mitterrand 91025 Evry, Cedex, France, Département de Chimie de l’École Normale Supérieure, 24 rue Lhomond, 75005 Paris, and Departamento Química Física, Universidad Sevilla, E-41012 Seville, Spain
| | - Enrique Sánchez Marcos
- Departamento Química Inorgánica, Universidad Sevilla, CSIC, ICMSE, Seville 41012, Spain, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, Université d’Evry Val d’Essonne, UMR 8587 CNRS, Bat Maupertuis, Bd F. Mitterrand 91025 Evry, Cedex, France, Département de Chimie de l’École Normale Supérieure, 24 rue Lhomond, 75005 Paris, and Departamento Química Física, Universidad Sevilla, E-41012 Seville, Spain
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Callahan KM, Casillas-Ituarte NN, Roeselová M, Allen HC, Tobias DJ. Solvation of magnesium dication: molecular dynamics simulation and vibrational spectroscopic study of magnesium chloride in aqueous solutions. J Phys Chem A 2010; 114:5141-8. [PMID: 20201546 DOI: 10.1021/jp909132a] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Magnesium dication plays many significant roles in biochemistry. While it is available to the environment from both ocean waters and mineral salts on land, its roles in environmental and atmospheric chemistry are still relatively unknown. Several pieces of experimental evidence suggest that contact ion pairing may not exist at ambient conditions in solutions of magnesium chloride up to saturation concentrations. This is not typical of most ions. There has been disagreement in the molecular dynamics literature concerning the existence of ion pairing in magnesium chloride solutions. Using a force field developed during this study, we show that contact ion pairing is not energetically favorable. Additionally, we present a concentration-dependent Raman spectroscopic study of the Mg-O(water) hexaaquo stretch that clearly supports the absence of ion pairing in MgCl(2) solutions, although a transition occurring in the spectrum between 0.06x and 0.09x suggests a change in solution structure. Finally, we compare experimental and calculated observables to validate our force field as well as two other commonly used magnesium force fields, and in the process show that ion pairing of magnesium clearly is not observed at higher concentrations in aqueous solutions of magnesium chloride, independent of the choice of magnesium force field, although some force fields give better agreement to experimental results than others.
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Affiliation(s)
- Karen M Callahan
- Environmental Molecular Science Institute and Department of Chemistry, University of California, Irvine, California 92697, USA
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25
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Fujiwara T, Mochizuki Y, Komeiji Y, Okiyama Y, Mori H, Nakano T, Miyoshi E. Fragment molecular orbital-based molecular dynamics (FMO-MD) simulations on hydrated Zn(II) ion. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.03.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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Brüssel M, Zahn S, Hey-Hawkins E, Kirchner B. Theoretical Investigation of Solvent Effects and Complex Systems: Toward the calculations of bioinorganic systems from ab initio molecular dynamics simulations and static quantum chemistry. ADVANCES IN INORGANIC CHEMISTRY 2010. [DOI: 10.1016/s0898-8838(10)62003-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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27
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Cramer CJ, Truhlar DG. Density functional theory for transition metals and transition metal chemistry. Phys Chem Chem Phys 2009; 11:10757-816. [PMID: 19924312 DOI: 10.1039/b907148b] [Citation(s) in RCA: 1079] [Impact Index Per Article: 71.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We introduce density functional theory and review recent progress in its application to transition metal chemistry. Topics covered include local, meta, hybrid, hybrid meta, and range-separated functionals, band theory, software, validation tests, and applications to spin states, magnetic exchange coupling, spectra, structure, reactivity, and catalysis, including molecules, clusters, nanoparticles, surfaces, and solids.
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Affiliation(s)
- Christopher J Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455-0431, USA.
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Munitz N, Avital Y, Pines D, Nibbering ETJ, Pines E. Cation-Enhanced Deprotonation of Water by a Strong Photobase. Isr J Chem 2009. [DOI: 10.1560/ijc.49.2.261] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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29
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Grigoriev FV, Golovacheva AY, Romanov AN, Kondakova OA, Sulimov VB. The thermodynamic characteristics of formation of organic molecule complexes with the magnesium ion in water: The results of quantum-chemical modeling. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2009. [DOI: 10.1134/s0036024409040098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Chen X, Wu G, Wu B, Duncombe BJ, Stace AJ. Enhanced Acidity of Zn2+ in the Presence of Small Numbers of Water Molecules. J Phys Chem B 2008; 112:15525-8. [DOI: 10.1021/jp8086804] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Xiaojing Chen
- Department of Physical Chemistry, School of Chemistry, The University of Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Guohua Wu
- Department of Physical Chemistry, School of Chemistry, The University of Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Bohan Wu
- Department of Physical Chemistry, School of Chemistry, The University of Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Bridgette J. Duncombe
- Department of Physical Chemistry, School of Chemistry, The University of Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Anthony J. Stace
- Department of Physical Chemistry, School of Chemistry, The University of Nottingham, University Park, Nottingham, NG7 2RD, U.K
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Bühl M, Golubnychiy V. On the Intermediacy of Chlorinated Alkylcobalt Complexes in the Reductive Dehalogenation of Chloroalkenes. A First-Principles Molecular Dynamics Study. Organometallics 2007. [DOI: 10.1021/om7007474] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael Bühl
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Volodymyr Golubnychiy
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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32
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Ikeda T, Boero M, Terakura K. Hydration properties of magnesium and calcium ions from constrained first principles molecular dynamics. J Chem Phys 2007; 127:074503. [PMID: 17718616 DOI: 10.1063/1.2768063] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
We studied the solvation structures of the divalent metal cations Mg(2+) and Ca(2+) in ambient water by applying a Car-Parrinello-based constrained molecular dynamics method. By employing the metal-water oxygen coordination number as a reaction coordinate, we could identify distinct aqua complexes characterized by structural variations of the first coordination shell. In particular, our estimated free-energy profile clearly shows that the global minimum for Mg(2+) is represented by a rather stable sixfold coordination in the octahedral arrangement, in agreement with experiments. Conversely, for Ca(2+) the free-energy curve shows several shallow local minima, suggesting that the hydration structure of Ca(2+) is highly variable. Implications for water exchange reactions are also discussed.
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Affiliation(s)
- Takashi Ikeda
- Quantum Beam Science Directorate, Japan Atomic Energy Agency (JAEA), 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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Louwerse MJ, Jan Baerends E. Oxidative properties of FeO2+: electronic structure and solvation effects. Phys Chem Chem Phys 2007; 9:156-66. [PMID: 17164898 DOI: 10.1039/b613182d] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An electronic structure analysis is provided of the action of solvated FeO(2+), [FeO(H(2)O)(5)](2+), as a hydroxylation catalyst. It is emphasized that the oxo end of FeO(2+) does not form hydrogen bonds (as electron donor and H-bond acceptor) with H-bond donors nor with aliphatic C-H bonds, but it activates C-H bonds as an electron acceptor. It is extremely electrophilic, to the extent that it can activate even such poor electron donors as aliphatic C-H bonds, the C-H bond orbital acting as electron donor in a charge transfer type of interaction. Lower lying O-H bonding orbitals are less easily activated. The primary electron accepting orbital in a water environment is the 3sigma*alpha orbital, an antibonding combination of Fe-3d(z(2)) and O-2p(z), which is very low-lying relative to the pi*alpha compared with, for example, the sigma* orbital in O(2) relative to its pi*. This is ascribed to relatively small Fe-3d(z(2)) with O-2p(z) overlap, due to the nodal structure of the 3d(z(2)).The H-abstraction barrier is very low in the gas phase, but it is considerably enhanced in water solvent. This is shown to be due to strong screening effects of the dielectric medium, leading to relative destabilization of the levels of the charged [FeO(H(2)O)(5)](2+) species compared to those of the neutral substrate molecules, making it a less effective electron acceptor. The solvent directly affects the orbital interactions responsible for the catalytic reaction.
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Affiliation(s)
- Manuel J Louwerse
- Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
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