Ab initio molecular dynamics free energy study of enhanced copper (II) dimerization on mineral surfaces

Leung, Kevin; Greathouse, Jeffery A.

doi:10.1038/s42004-022-00688-2

Ab initio molecular dynamics free energy study of enhanced copper (II) dimerization on mineral surfaces

Journal Article · Tue Jun 28 00:00:00 EDT 2022 · Communications Chemistry

DOI:https://doi.org/10.1038/s42004-022-00688-2· OSTI ID:1877140

^[1]; Greathouse, Jeffery A. ^[1]

Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

Understanding the adsorption of isolated metal cations from water on to mineral surfaces is critical for toxic waste retention and cleanup in the environment. Heterogeneous nucleation of metal oxyhydroxides and other minerals on material surfaces is key to crystal growth and dissolution. The link connecting these two areas, namely cation dimerization and polymerization, is far less understood. In this work we apply ab initio molecular dynamics calculations to examine the coordination structure of hydroxide-bridged Cu(II) dimers, and the free energy changes associated with Cu(II) dimerization on silica surfaces. The dimer dissociation pathway involves sequential breaking of two Cu²⁺-OH^– bonds, yielding three local minima in the free energy profiles associated with 0-2 OH^– bridges between the metal cations, and requires the design of a (to our knowledge) novel reaction coordinate for the simulations. Cu(II) adsorbed on silica surfaces are found to exhibit stronger tendency towards dimerization than when residing in water. Cluster-plus-implicit-solvent methods yield incorrect trends if OH^– hydration is not correctly depicted. The predicted free energy landscapes are consistent with fast equilibrium times (seconds) among adsorbed structures, and favor Cu²⁺ dimer formation on silica surfaces over monomer adsorption.

View Accepted Manuscript (DOE)

Research Organization:: Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division

Grant/Contract Number:: NA0003525

OSTI ID:: 1877140

Report Number(s):: SAND2022-8657J; 707638

Journal Information:: Communications Chemistry, Journal Name: Communications Chemistry Journal Issue: 1 Vol. 5; ISSN 2399-3669

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

References (64)

Unraveling the Coordination Geometry of Copper(II) Ions in Aqueous Solution through Absorption Intensity Gómez-Salces, Susana; Aguado, Fernando; Valiente, Rafael Angewandte Chemie International Edition, Vol. 51, Issue 37 https://doi.org/10.1002/anie.201202033	journal	August 2012
Investigations of water/oxide interfaces by molecular dynamics simulations Wang, Ruiyu; Klein, Michael L.; Carnevale, Vincenzo WIREs Computational Molecular Science, Vol. 11, Issue 6 https://doi.org/10.1002/wcms.1537	journal	June 2021
XAFS Spectroscopy Study of Cu(II) Sorption on Amorphous SiO2and γ-Al2O3: Effect of Substrate and Time on Sorption Complexes Cheah, Sing-Foong; Brown, Gordon E.; Parks, George A. Journal of Colloid and Interface Science, Vol. 208, Issue 1 https://doi.org/10.1006/jcis.1998.5678	journal	December 1998
Magnetic exchange coupling in Cu dimers studied with modern multireference methods and broken-symmetry coupled cluster theory Singh, Gurjot; Gamboa, Stefani; Orio, Maylis Theoretical Chemistry Accounts, Vol. 140, Issue 10 https://doi.org/10.1007/s00214-021-02830-0	journal	September 2021
Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set Kresse, G.; Furthmüller, J. Computational Materials Science, Vol. 6, Issue 1, p. 15-50 https://doi.org/10.1016/0927-0256(96)00008-0	journal	July 1996
Mono-, bi-, tetra- and polynuclear copper(II) halogenocarboxylates Melník, Milan Coordination Chemistry Reviews, Vol. 36, Issue 1 https://doi.org/10.1016/S0010-8545(00)80504-4	journal	February 1981
An X-ray absorption spectroscopy study of the structure and reversibility of copper adsorbed to montmorillonite clay Morton, John D.; Semrau, Jeremy D.; Hayes, Kim F. Geochimica et Cosmochimica Acta, Vol. 65, Issue 16 https://doi.org/10.1016/S0016-7037(01)00633-0	journal	August 2001
Characterization of Cu-complexes in smectite with different layer charge location: chemical, thermal and EXAFS studies Brigatti, Maria Franca; Colonna, S.; Malferrari, Daniele Geochimica et Cosmochimica Acta, Vol. 68, Issue 4 https://doi.org/10.1016/S0016-7037(03)00487-3	journal	February 2004
Reactivity descriptors of diverse copper-oxo species on ZSM-5 zeolite towards methane activation Wang, Guiru; Chen, Wei; Huang, Ling Catalysis Today, Vol. 338 https://doi.org/10.1016/j.cattod.2019.05.007	journal	November 2019
Copper sorption by the edge surfaces of synthetic birnessite nanoparticles Peña, Jasquelin; Bargar, John R.; Sposito, Garrison Chemical Geology, Vol. 396 https://doi.org/10.1016/j.chemgeo.2014.12.021	journal	March 2015
Copper complexation and solubility in high-temperature hydrothermal fluids: A combined study by Raman, X-ray fluorescence, and X-ray absorption spectroscopies and ab initio molecular dynamics simulations Schmidt, Christian; Watenphul, Anke; Jahn, Sandro Chemical Geology, Vol. 494 https://doi.org/10.1016/j.chemgeo.2018.07.018	journal	September 2018
Combined EXAFS and ab initio study of copper complex geometries adsorbed on natural illite Martins, David M. S.; Mirão, José P.; Göttlicher, Jörg Applied Clay Science, Vol. 152 https://doi.org/10.1016/j.clay.2017.10.034	journal	February 2018
Ethyl xanthate collector interaction with precipitated iron and copper hydroxides – Experiments and DFT simulations Sarvaramini, A.; Larachi, F.; Hart, B. Computational Materials Science, Vol. 120 https://doi.org/10.1016/j.commatsci.2016.04.023	journal	July 2016
Equilibrium isotopic fractionation of copper during oxidation/reduction, aqueous complexation and ore-forming processes: Predictions from hybrid density functional theory Sherman, David M. Geochimica et Cosmochimica Acta, Vol. 118 https://doi.org/10.1016/j.gca.2013.04.030	journal	October 2013
Surface complexation of heavy metal cations on clay edges: insights from first principles molecular dynamics simulation of Ni(II) Zhang, Chi; Liu, Xiandong; Lu, Xiancai Geochimica et Cosmochimica Acta, Vol. 203 https://doi.org/10.1016/j.gca.2017.01.014	journal	April 2017
Theoretical insights into the dimerization mechanism of aluminum species at two different pH conditions Jin, Xiaoyan; Liao, Rongbao; Zhang, Ting Inorganica Chimica Acta, Vol. 520 https://doi.org/10.1016/j.ica.2021.120311	journal	May 2021
Molecular-level investigation into copper complexes on vermiculite: Effect of reduction of structural iron on copper complexation Furnare, Luca J.; Vailionis, Arturas; Strawn, Daniel G. Journal of Colloid and Interface Science, Vol. 289, Issue 1 https://doi.org/10.1016/j.jcis.2005.03.068	journal	September 2005
Recyclable aqueous metal adsorbent: Synthesis and Cu(II) sorption characteristics of ternary nanocomposites of Fe3O4 nanoparticles@graphene–poly-N-phenylglycine nanofibers Kim, Hyeong Jin; Choi, Hyuk; Sharma, Abhishek Kumar Journal of Hazardous Materials, Vol. 401 https://doi.org/10.1016/j.jhazmat.2020.123283	journal	January 2021
Immobilized Co2+ and Cu2+ induced structural change of layered double hydroxide for efficient heterogeneous degradation of antibiotic Chen, Meiqing; Huang, Zhiyan; Liang, Shuling Journal of Hazardous Materials, Vol. 403 https://doi.org/10.1016/j.jhazmat.2020.123554	journal	February 2021
In Situ ²⁷ Al NMR Spectroscopy of Aluminate in Sodium Hydroxide Solutions above and below Saturation with Respect to Gibbsite Graham, Trent R.; Dembowski, Mateusz; Martinez-Baez, Ernesto Inorganic Chemistry, Vol. 57, Issue 19 https://doi.org/10.1021/acs.inorgchem.8b00617	journal	July 2018
Marcus Theory of Ion-Pairing Roy, Santanu; Baer, Marcel D.; Mundy, Christopher J. Journal of Chemical Theory and Computation, Vol. 13, Issue 8 https://doi.org/10.1021/acs.jctc.7b00332	journal	July 2017
Reaction Mechanisms of the Initial Oligomerization of Aluminophosphate Xiang, Yan; Xin, Liang; Deetz, Joshua D. The Journal of Physical Chemistry A, Vol. 120, Issue 18 https://doi.org/10.1021/acs.jpca.6b01058	journal	May 2016
Isomerism of Trimeric Aluminum Complexes in Aqueous Environments: Exploration via DFT-Based Metadynamics Simulation Lanzani, Giorgio; Seitsonen, Ari P.; Iannuzzi, Marcella The Journal of Physical Chemistry B, Vol. 120, Issue 45 https://doi.org/10.1021/acs.jpcb.6b08112	journal	November 2016
Combining Explicit Quantum Solvent with a Polarizable Continuum Model Provorse Long, Makenzie R.; Isborn, Christine M. The Journal of Physical Chemistry B, Vol. 121, Issue 43 https://doi.org/10.1021/acs.jpcb.7b06693	journal	October 2017
Ab Initio Molecular Dynamics Reveal Spectroscopic Siblings and Ion Pairing as New Challenges for Elucidating Prenucleation Aluminum Speciation Pouvreau, Maxime; Dembowski, Mateusz; Clark, Sue B. The Journal of Physical Chemistry B, Vol. 122, Issue 29 https://doi.org/10.1021/acs.jpcb.8b04377	journal	June 2018
Concerted Metal Cation Desorption and Proton Transfer on Deprotonated Silica Surfaces Leung, Kevin; Criscenti, Louise J.; Knight, Andrew W. The Journal of Physical Chemistry Letters, Vol. 9, Issue 18 https://doi.org/10.1021/acs.jpclett.8b02173	journal	August 2018
Separation and Sequential Recovery of Tetracycline and Cu(II) from Water Using Reusable Thermoresponsive Chitosan-Based Flocculant Ren, Kexin; Du, Hongwei; Yang, Zhen ACS Applied Materials & Interfaces, Vol. 9, Issue 11 https://doi.org/10.1021/acsami.7b00828	journal	March 2017
Roles of Water Molecules in Modulating the Reactivity of Dioxygen-Bound Cu-ZSM-5 toward Methane: A Theoretical Prediction Yumura, Takashi; Hirose, Yuuki; Wakasugi, Takashi ACS Catalysis, Vol. 6, Issue 4 https://doi.org/10.1021/acscatal.5b02477	journal	March 2016
Structure and dynamics of hydrated ions Ohtaki, Hitoshi.; Radnai, Tamas. Chemical Reviews, Vol. 93, Issue 3 https://doi.org/10.1021/cr00019a014	journal	May 1993
Potential of Mean Force Calculation from Molecular Dynamics Simulation of Asphaltene Molecules on a Calcite Surface Headen, Thomas F.; Boek, Edo S. Energy & Fuels, Vol. 25, Issue 2 https://doi.org/10.1021/ef1010385	journal	December 2010
Effects of ZSM-5 Zeolite Confinement on Reaction Intermediates during Dioxygen Activation by Enclosed Dicopper Cations Yumura, Takashi; Takeuchi, Mina; Kobayashi, Hisayoshi Inorganic Chemistry, Vol. 48, Issue 2 https://doi.org/10.1021/ic8010184	journal	January 2009
Elucidating the Bimodal Acid−Base Behavior of the Water−Silica Interface from First Principles Leung, Kevin; Nielsen, Ida M. B.; Criscenti, Louise J. Journal of the American Chemical Society, Vol. 131, Issue 51 https://doi.org/10.1021/ja906190t	journal	December 2009
Visualization of Aluminum Ions at the Mica Water Interface Links Hydrolysis State-to-Surface Potential and Particle Adhesion Legg, Benjamin A.; Baer, Marcel D.; Chun, Jaehun Journal of the American Chemical Society, Vol. 142, Issue 13 https://doi.org/10.1021/jacs.9b12530	journal	February 2020
Development and Validation of a ReaxFF Reactive Force Field for Cu Cation/Water Interactions and Copper Metal/Metal Oxide/Metal Hydroxide Condensed Phases van Duin, Adri C. T.; Bryantsev, Vyacheslav S.; Diallo, Mamadou S. The Journal of Physical Chemistry A, Vol. 114, Issue 35 https://doi.org/10.1021/jp102272z	journal	September 2010
Computational Molecular Simulation of the Oxidative Adsorption of Ferrous Iron at the Hematite (001)–Water Interface Kerisit, Sebastien; Zarzycki, Piotr; Rosso, Kevin M. The Journal of Physical Chemistry C, Vol. 119, Issue 17 https://doi.org/10.1021/jp512422h	journal	April 2015
Hydration of Copper(II): New Insights from Density Functional Theory and the COSMO Solvation Model Bryantsev, Vyacheslav S.; Diallo, Mamadou S.; van Duin, Adri C. T. The Journal of Physical Chemistry A, Vol. 112, Issue 38 https://doi.org/10.1021/jp804373p	journal	September 2008
Computational Study of Copper(II) Complexation and Hydrolysis in Aqueous Solutions Using Mixed Cluster/Continuum Models Bryantsev, Vyacheslav S.; Diallo, Mamadou S.; Goddard, William A. The Journal of Physical Chemistry A, Vol. 113, Issue 34 https://doi.org/10.1021/jp904816d	journal	August 2009
X-Ray Evidence for Metal-to-Metal Bonds in Cupric and Chromous Acetate Van Niekerk, J. N.; Schoening, F. R. L. Nature, Vol. 171, Issue 4340 https://doi.org/10.1038/171036a0	journal	January 1953
Pre-critical fluctuations and what they disclose about heterogeneous crystal nucleation Fitzner, Martin; Sosso, Gabriele C.; Pietrucci, Fabio Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-02300-x	journal	December 2017
A supramolecular lanthanide separation approach based on multivalent cooperative enhancement of metal ion selectivity Li, Xiao-Zhen; Zhou, Li-Peng; Yan, Liang-Liang Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-02940-7	journal	February 2018
Mineral dissolution and reprecipitation mediated by an amorphous phase Konrad-Schmolke, Matthias; Halama, Ralf; Wirth, Richard Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-03944-z	journal	April 2018
Evidence for auto-catalytic mineral dissolution from surface-specific vibrational spectroscopy Schaefer, Jan; Backus, Ellen H. G.; Bonn, Mischa Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-05762-9	journal	August 2018
Phosphorylation regulates the binding of intrinsically disordered proteins via a flexible conformation selection mechanism Liu, Na; Guo, Yue; Ning, Shangbo Communications Chemistry, Vol. 3, Issue 1 https://doi.org/10.1038/s42004-020-00370-5	journal	September 2020
Modelling nano-clusters and nucleation Catlow, C. Richard A.; Bromley, Stefan T.; Hamad, Said Phys. Chem. Chem. Phys., Vol. 12, Issue 4 https://doi.org/10.1039/B916069H	journal	January 2010
Interfacial reactions of Cu( ii ) adsorption and hydrolysis driven by nano-scale confinement Knight, Andrew W.; Ilani-Kashkouli, Poorandokht; Harvey, Jacob A. Environmental Science: Nano, Vol. 7, Issue 1 https://doi.org/10.1039/C9EN00855A	journal	January 2020
Interplay of physically different properties leading to challenges in separating lanthanide cations – an ab initio molecular dynamics and experimental study Leung, Kevin; Ilgen, Anastasia G.; Criscenti, Louise J. Physical Chemistry Chemical Physics, Vol. 23, Issue 10 https://doi.org/10.1039/D1CP00031D	journal	January 2021
Effects of nanoconfinement and surface charge on iron adsorption on mesoporous silica Greathouse, Jeffery A.; Duncan, Tyler J.; Ilgen, Anastasia G. Environmental Science: Nano, Vol. 8, Issue 7 https://doi.org/10.1039/D1EN00066G	journal	January 2021
Factors influencing Al3+-dimer speciation and stability from density functional theory calculations Bogatko, Stuart; Geerlings, Paul Physical Chemistry Chemical Physics, Vol. 14, Issue 22 https://doi.org/10.1039/c2cp40885f	journal	January 2012
Defining silica–water interfacial chemistry under nanoconfinement using lanthanides Ilgen, Anastasia G.; Kabengi, Nadine; Leung, Kevin Environmental Science: Nano, Vol. 8, Issue 2 https://doi.org/10.1039/d0en00971g	journal	January 2021
Why does the B3LYP hybrid functional fail for metals? Paier, Joachim; Marsman, Martijn; Kresse, Georg The Journal of Chemical Physics, Vol. 127, Issue 2 https://doi.org/10.1063/1.2747249	journal	July 2007
Redox potentials and pKa for benzoquinone from density functional theory based molecular dynamics Cheng, Jun; Sulpizi, Marialore; Sprik, Michiel The Journal of Chemical Physics, Vol. 131, Issue 15 https://doi.org/10.1063/1.3250438	journal	October 2009
Relativistic effects in a b i n i t i o effective core potentials for molecular calculations. Applications to the uranium atom Kahn, Luis R.; Hay, P. Jeffrey; Cowan, Robert D. The Journal of Chemical Physics, Vol. 68, Issue 5 https://doi.org/10.1063/1.436009	journal	March 1978
A first-principle calculation of the XANES spectrum of Cu ²⁺ in water La Penna, G.; Minicozzi, V.; Morante, S. The Journal of Chemical Physics, Vol. 143, Issue 12 https://doi.org/10.1063/1.4931808	journal	September 2015
Acidity constants from DFT-based molecular dynamics simulations Sulpizi, Marialore; Sprik, Michiel Journal of Physics: Condensed Matter, Vol. 22, Issue 28 https://doi.org/10.1088/0953-8984/22/28/284116	journal	June 2010
Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set Kresse, G.; Furthmüller, J. Physical Review B, Vol. 54, Issue 16, p. 11169-11186 https://doi.org/10.1103/PhysRevB.54.11169	journal	October 1996
From ultrasoft pseudopotentials to the projector augmented-wave method Kresse, G.; Joubert, D. Physical Review B, Vol. 59, Issue 3, p. 1758-1775 https://doi.org/10.1103/PhysRevB.59.1758	journal	January 1999
Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations Piaggi, Pablo M.; Valsson, Omar; Parrinello, Michele Physical Review Letters, Vol. 119, Issue 1 https://doi.org/10.1103/PhysRevLett.119.015701	journal	July 2017
Generalized Gradient Approximation Made Simple Perdew, John P.; Burke, Kieron; Ernzerhof, Matthias Physical Review Letters, Vol. 77, Issue 18, p. 3865-3868 https://doi.org/10.1103/PhysRevLett.77.3865	journal	October 1996
First Solvation Shell of the Cu(II) Aqua Ion: Evidence for Fivefold Coordination Pasquarello, A. Science, Vol. 291, Issue 5505 https://doi.org/10.1126/science.291.5505.856	journal	February 2001
Copper Sorption Mechanisms on Smectites Strawn, Daniel G.; Palmer, Noel E.; Furnare, Luca J. Clays and Clay Minerals, Vol. 52, Issue 3 https://doi.org/10.1346/CCMN.2004.0520307	journal	June 2004
First-Principles Molecular Dynamics Insight Into Fe²⁺ Complexes Adsorbed on Edge Surfaces of Clay Minerals Liu, Xiandong; Jan Meijer, Evert; Lu, Xiancai Clays and Clay Minerals, Vol. 60, Issue 4 https://doi.org/10.1346/CCMN.2012.0600401	journal	August 2012
Cadmium(II) Complexes Adsorbed on Clay Edge Surfaces: Insight From First Principles Molecular Dynamics Simulation Zhang, Chi; Liu, Xiandong; Lu, Xiancai Clays and Clay Minerals, Vol. 64, Issue 4 https://doi.org/10.1346/CCMN.2016.0640402	journal	August 2016
XAFS study of Cu model compounds and Cu ²⁺ sorption products on amorphous SiO ₂ , γ-Al ₂ O ₃ , and anatase Cheah, Sing-Foong; Brown, Gordon E.; Parks, George A. American Mineralogist, Vol. 85, Issue 1 https://doi.org/10.2138/am-2000-0113	journal	January 2000
Description of input and examples for PHREEQC version 3: a computer program for speciation, batch-reaction, one-dimensional transport, and inverse geochemical calculations Parkhurst, David L.; Appelo, C. A. J. https://doi.org/10.3133/tm6A43	report	January 2013

Similar Records

Anomalous adsorption of copper(II) on goethite

Journal Article · Tue Dec 24 23:00:00 EST 1996 · Journal of Colloid and Interface Science · OSTI ID:419831

Concerted Metal Cation Desorption and Proton Transfer on Deprotonated Silica Surfaces

Journal Article · Thu Aug 30 20:00:00 EDT 2018 · Journal of Physical Chemistry Letters · OSTI ID:1473940

Interplay of physically different properties leading to challenges in separating lanthanide cations – an ab initio molecular dynamics and experimental study

Journal Article · Wed Feb 10 19:00:00 EST 2021 · Physical Chemistry Chemical Physics. PCCP · OSTI ID:1770353

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Density functional theory
Geochemistry

Ab initio molecular dynamics free energy study of enhanced copper (II) dimerization on mineral surfaces

Citation Formats

References (64)

Similar Records

Related Subjects