Acid dissociation mechanisms of Si(OH)4 and Al(H2O)63+ in aqueous solution

Liu, Xiandong; Lu, Xiancai; Meijer, Evert Jan; Wang, Rucheng; Zhou, Huiqun

doi:10.1016/j.gca.2009.10.032

Cited by 37 publications

(30 citation statements)

References 44 publications

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“…Based on this, the uncertainty of free-energy values is estimated to have an upper limit of about 1.8 kcal/mol. This error is similar to those in our previous studies (Liu et al, 2010(Liu et al, , 2011a(Liu et al, , 2011b.…”

Section: Free Energy Calculationsupporting

confidence: 93%

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Atomic scale structures of interfaces between kaolinite edges and water

Liu

Wang

et al. 2012

Geochimica et Cosmochimica Acta

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This paper reports the atomic scale structures of kaolinite edge surfaces in contact with water. The commonly occurring edge surfaces are investigated (i.e. (0 1 0) and (1 1 0)) by using first principles molecular dynamics (FPMD) technique. For (1 1 0)-type edge surface, there are two different surface topologies (denoted as (1 1 0)-1 and (1 1 0)-2) and they are considered separately.By using constrained FPMD technique, the free-energy changes for the leaving processes of water ligands of O-sheet Al cations have been calculated and thus, the coordination states of those Al cations are determined. The results show that for (0 1 0) and (1 1 0)-2 edges, both the 5 and 6-fold coordination states are possible whereas for (1 1 0)-1 edges, only the 6-fold states are stable. Based on the analyses of H-bonding structures at the interfaces, the surface acid/base reactive sites are illustrated. (1) T-sheet groups are "Si-OH, behaving as both proton donors and acceptors. (2) Bridging oxygen At (0 1 0) and (1 1 0)-2 edges, these sites are inaccessible from the water and thus, they are not effective reactive sites. At (1 1 0)-1 edges, the bridging oxygen atoms are proton accepting sites. (3) O-sheet groups At (0 1 0) and (1 1 0)-2 edges, for 6-fold Al cases, the active surface groups are "Al-(OH)(OH 2 ) and for the 5-fold Al cases, the active surface groups are "Al-(OH). At (1 1 0)-1 edges, the active site is "Al-OH 2 . This study provides fundamental structural properties for understanding the interface chemistry of widely occurring 1:1 type phyllosilicates.

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Section: Free Energy Calculationsupporting

confidence: 93%

“…This functional can also nicely predict free energy changes of proton transfer processes in aqueous systems (e.g. Sprik, 2000;Sulpizi and Sprik, 2008;Liu et al, 2010). BLYP has been widely employed in simulation studies of silicates, e.g.…”

Section: Car-parrinello MDmentioning

confidence: 99%

Atomic scale structures of interfaces between kaolinite edges and water

Liu

Wang

et al. 2012

Geochimica et Cosmochimica Acta

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“…The acidity constants of edge groups are necessary for determining the protonation states at certain pH levels. Previous studies have proved that acidity values can be predicted accurately with FPMD (e.g., Sulpizi and Sprik, 2008;Liu et al, 2010Liu et al, , 2011; thus, these calculations will be performed in future studies. Non-sub (0 1 0) 3.0 ± 0.9 5.0 ± 0.6 Non-sub (1 1 0) unstable 3.8 ± 0.3 T-sub (0 1 0) 2.8 ± 0.9 4.0 ± 0.8 T-sub (1 1 0) --O-sub (0 1 0) unstable 7.5 ± 0.6 O-sub (1 1 0) 2.1 ± 0.9 2.6 ± 0.7…”

Section: Discussionmentioning

confidence: 97%

Atomic-scale structures of interfaces between phyllosilicate edges and water

Liu

Meijer

et al. 2012

Geochimica et Cosmochimica Acta

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We report first-principles molecular dynamics (FPMD) studies on the structures of interfaces between phyllosilicate edges and water. Using FPMD, the substrates and solvents are simulated at the same first-principles level, and the thermal motions are sampled via molecular dynamics. Both the neutral and charged silicate frameworks are considered, and for charged cases, the octahedral (Mg for Al) and tetrahedral (Al for Si) substitutions are taken into account. For all frameworks, we focus on the commonly occurring (0 1 0)-and (1 1 0)-type edge surfaces.With constrained FPMD, we calculated the free energy of the leaving processes of coordinated water of octahedral cations; therefore, the coordination states of those edge cations are determined. For (0 1 0)-type edges, both the 5-and 6-fold coordination states of Al are stable and occur with a similar probability, whereas only the 5-fold coordination is stable for Mg cations. For (1 1 0)-type edges, only the 6-fold states of Al cations are stable. However, for Mg cations, both coordination states are stable. In the 5-fold case, the solvent water molecules form H-bonds with the bridging oxygen atoms (i.e., "MgAOASi"). The free energy results indicate that there should be a considerable number of 5-fold coordinated octahedral sites (i.e., "MgAOH/ "AlAOH) at the interfaces. The interfacial structures and acid/base groups were determined by detailed H-bonding analyses.(1) Bridging oxygen sites. For (0 1 0) edges, the bridging oxygen atoms are not effective proton-accepting sites because they are inaccessible from the solvent. For (1 1 0) edges, the oxygen atoms of neutral and octahedrally substituted frameworks (i.e., "MAOASi" for M@Al/Mg) are proton-accepting sites. For T-sheet substituted cases, the bridging oxygen site becomes a proton-donating group (i.e., "AlAOHASi") through the capture of a proton. (2) T-sheet groups. All T-sheet edge groups are "MAOH (M@Si/Al) and act as both proton donors and acceptors. (3)O-sheet groups. For (0 1 0) edges with 6-fold Al, the active surface groups include "AlA(OH)(H 2 O) and "AlA(OH) 2 , whereas for Mg cations, the edge group is "MgA(OH 2 ) 2 . For 5-fold coordination, the active groups are "AlAOH. At (1 1 0) edges, proton-donating sites include "AlAOH, "AlAOH 2 and "MgAOH 2 groups. Overall, our results reveal the significant effects of isomorphic substitutions on the interfacial structures, and the models provide a molecular-level basis for understanding relevant interfacial processes.

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“…(1) Peptide backbone angle sampling [36,37]; (2) Nucleoside [38], protein [39] and fullerene [40,41] insertion into a lipid bilayer; (3) Interactions of small molecules with polymers in water [42,43]; (4) Molecule/ion transport through protein complexes [44][45][46][47] and DNA superstructures [48]; (5) Calculation of octanol-water partition coefficients [49,50]; (6) Large-scale protein conformational changes [51]; (7) Protein-nanotube [52] and nanotube-nanotube [53] association.…”

Section: The Adaptive Biasing Force Algorithmmentioning

confidence: 99%

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

Abrams

Bussi

2013

Entropy

396

405

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Abstract:We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In collective-variable biasing, we first discuss methods stemming from thermodynamic integration that use mean force biasing, including the adaptive biasing force algorithm and temperature acceleration.We then turn to methods that use bias potentials, including umbrella sampling and metadynamics. We next consider parallel tempering and replica-exchange methods.We conclude with a brief presentation of some combination methods.

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Acid dissociation mechanisms of Si(OH)4 and Al(H2O)63+ in aqueous solution

Cited by 37 publications

References 44 publications

Atomic scale structures of interfaces between kaolinite edges and water

Atomic scale structures of interfaces between kaolinite edges and water

Atomic-scale structures of interfaces between phyllosilicate edges and water

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

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