Estimating p<i>K</i><sub>a</sub> Values for Pentaoxyphosphoranes

Davies, John E.; Doltsinis, Nikos L.; Kirby, Anthony J.; Roussev, Christo D.; Sprik, Michiel

doi:10.1021/ja025779m

Cited by 119 publications

(161 citation statements)

References 25 publications

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“…This approach has been successfully applied in some cases, e.g. water (Sprik, 2000) and pentaoxyphosphoranes (Davies et al, 2002;Doltsinis and Sprik, 2003).…”

Section: Methods Of Constraintmentioning

confidence: 99%

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

Liu

Meijer

et al. 2010

Geochimica et Cosmochimica Acta

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Silicic acid and the hexa-aqua of Al 3+ are fundamental model aqueous species of chemical importance in nature. In order to investigate their hydroxyl dissociation mechanisms, Car-Parrinello molecular dynamics (CPMD) simulations were carried out, which allow treating the solutes and solvents on the same footing. The method of constraint was employed to trigger the reactions by taking coordination number as the reaction coordinate and the thermodynamic integration was used to obtain the free-energy profiles. The approximate transition states were located and the reactant and product states were also characterized. The free-energy changes of dissociation are found about 15.0 kcal/mol and 7.7 kcal/mol for silicic acid and Al-aqua, respectively. From the simulation results, the first pKas were calculated by using two approaches, which are based on the pristine thermodynamic relation and the RDF (radial distribution function)-free energy relation, respectively. Because of more uncertainties involved in the RDF way, it is suggested that the pristine way should be favored, which shows an error margin of 1 pKa unit. This study provides an encouraging basis for applying the present methodology to predict acidity constants of those groups that are difficult to measure experimentally.

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“…This approach has been successfully applied in some cases, e.g. water (Sprik, 2000) and pentaoxyphosphoranes (Davies et al, 2002;Doltsinis and Sprik, 2003).…”

Section: Methods Of Constraintmentioning

confidence: 99%

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

Liu

Meijer

et al. 2010

Geochimica et Cosmochimica Acta

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“…Other studies have shown this type of proton transfer can be controlled by constraining the proton coordination number of O w . 45, 51 The contribution of entropy to ∆F is small, at least in P-O s bond breaking (see reaction maxima in Figure 8a). The experimental results of George et al 9 indicate that the entropy contribution in pyrophosphate hydrolysis is -1.4 kcal/mol at 298 K. The solvent structure in our final configuration is not fully relaxed, since the displacement of the metaphosphate has created a small cavity.…”

Section: A Properties Of Triphosphate Molecules and Solvatedmentioning

confidence: 99%

ATP Hydrolysis in Water − A Density Functional Study

2003

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Adenosine 5′-triphosphate (ATP) is a basic energy carrier in cellular metabolism. As a high-energy intermediate, it provides a way to convert energy from one biochemical process to another via an environment-dependent hydrolysis reaction. Two paths for ATP hydrolysis in water with Mg 2+ are studied here using the density functional method: an associative reaction involving a nucleophilic attack of one water molecule, and a dissociative reaction involving a scission of the terminal bridging P-O bond. The latter has an activation energy of 35 kcal/mol, where 25 kcal/mol can be assigned to the P-O bond breaking and 10 kcal/mol to the artificial stability of PO 3 -resulting from the small size and the short time scale of the simulation. The path and energy barrier (39 kcal/mol) of the less-favorable associative reaction suggest that it is possible only under conditions where the lytic water is already deprotonated to OH -. The Mg cation elongates the terminal bridging P-O bond when forming a bidentate chelate with the two terminal phosphates. Additional constrained displacements of Mg 2+ with respect to the nearest phosphate oxygens show that a direct electrophilic attack of Mg toward a bridging O is possible.

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“…Since that encouraging study, the methodology has been applied on more complicated condensed phase systems, e.g. pentaoxyphosphoranes (Davies et al, 2002;Doltsinis and Sprik, 2003), Al-aqua and Si(OH) 4 (Liu et al, 2010a), and carbonic acid conformers (Liu et al, 2010b). Recently, Churakov and Kosakowski (2010) employed FPMD to study the transfer events of excess protons occurring in the interlayer regions of smectites and found that similar to the bulk, the proton transfer processes are barrier free.…”

Section: Introductionmentioning

confidence: 99%

Acidities of confined water in interlayer space of clay minerals

Liu

Wang

et al. 2011

Geochimica et Cosmochimica Acta

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The acid chemistry of confined waters in smectite interlayers have been investigated with first principles molecular dynamics (FPMD) simulations. Aiming at a systematic picture, we establish the model systems to take account of the three possible controlling factors: layer charge densities (0 e, 0.5 e and 1.0 e per cell), layer charge locations (tetrahedral and octahedral) and interlayer counterions (Na + and Mg 2+). For all models, the interlayer structures are characterized in detail. Na + and Mg 2+show significantly different hydration characteristics: Mg 2+ forms a rigid octahedral hydration shell and resides around the midplane, whereas Na + binds to a basal oxygen atom and forms a very flexible hydration shell, which consists of five waters on average and shows very fast water exchanges. The method of constraint is employed to enforce the water dissociation reactions and the thermodynamic integration approach is used to derive the free-energy values and the acidity constants. Based on the simulations, the following points have been gained. (1) The layer charge is found to be the direct origin of water acidity enhancement in smectites because the neutral pore almost does not have influences on water dissociations but all charged pores do. (2) With a moderate charge density of 0.5 e per cell, the interlayer water shows a pKa value around 11.5. While increasing layer charge density to 1.0 e, no obvious difference is found for the free water molecules. Since 1.0 e is at the upper limit of smectites' layer charge, it is proposed that the calculated acidity of free water in octahedrally substituted Mg 2+ -smectite, 11.3, can be taken as the lower limit of acidities of free waters. (3) In octahedrally and tetrahedrally substituted models, the bound waters of Mg 2+ show very low pKa values: 10.1 vs 10.4. This evidences that smectites can also promote the dissociations of the coordinated waters of metal cations. The comparison between the two Mg 2+ -smectites reveals that different layer charge locations do not lead to obvious differences for bound and free water acidities.

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Estimating pK_a Values for Pentaoxyphosphoranes

Cited by 119 publications

References 25 publications

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

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

ATP Hydrolysis in Water − A Density Functional Study

Acidities of confined water in interlayer space of clay minerals

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Estimating pKa Values for Pentaoxyphosphoranes

Cited by 119 publications

References 25 publications

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

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

ATP Hydrolysis in Water − A Density Functional Study

Acidities of confined water in interlayer space of clay minerals

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Product

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Estimating pK_a Values for Pentaoxyphosphoranes