Osmotic pressure: Thermodynamic basis and units of measurement

Janáček, Karel; Sigler, Karel

doi:10.1007/bf02816331

Cited by 16 publications

(18 citation statements)

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“…9, 19 The force exerted on the FBP was written out at every time step and averaged over 20 ns blocks. This average force was then converted to a pressure by dividing by the surface area of the semi-permeable membrane, and this pressure was converted to the molal osmotic coefficient (ϕ) according to the equation: 1–2 …”

Section: Methodsmentioning

confidence: 99%

“…It thus provides a reasonably direct measure of the extent to which solute-solute interactions are net attractive (ϕ<1) or repulsive (ϕ>1) in aqueous solution. 1–2 Importantly, there is a considerable amount of experimental osmotic coefficient data available in the literature, which provide, in principle, a means of parameterizing the strengths of solute-solute interactions for a wide range of molecule types. These data have only recently begun to be exploited in simulation, using a MD setup proposed by Murad and Powles 3 and implemented by Luo and Roux, who used it to parameterize ion-ion interactions for NaCl and KCl.…”

Section: Introductionmentioning

confidence: 99%

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Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations

Miller

Lay

et al. 2017

J. Chem. Theory Comput.

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There is a small, but growing, body of literature describing the use of osmotic coefficient measurements to validate and reparameterize simulation force fields. Here we have investigated the ability of five very commonly used force field and water model combinations to reproduce the osmotic coefficients of seven neutral amino acids and five small molecules. The force fields tested include AMBER ff99SB-ILDN, CHARMM36, GROMOS54a7, and OPLS-AA, with the first of these tested in conjunction with the TIP3P and TIP4P-Ew water models. In general, for both the amino acids and the small molecules, the tested force fields produce computed osmotic coefficients that are lower than experiment; this is indicative of excessively favorable solute-solute interactions. The sole exception to this general trend is provided by GROMOS54a7 when applied to amino acids: in this case, the computed osmotic coefficients are consistently too high. Importantly, we show that all of the force fields tested can be made to accurately reproduce the experimental osmotic coefficients of the amino acids when minor modifications – some previously reported by others and some that are new to this study – are made to the van der Waals interactions of the charged terminal groups. Special care is required, however, when simulating Proline with a number of the force fields, and a hydroxyl-group specific modification is required in order to correct Serine and Threonine when simulated with AMBER ff99SB-ILDN. Interestingly, an alternative parameterization of the van der Waals interactions in the latter force field, proposed by the Nerenberg and Head-Gordon groups, is shown to immediately produce osmotic coefficients that are in excellent agreement with experiment. Overall, this study reinforces the idea that osmotic coefficient measurements can be used to identify general shortcomings in commonly used force fields’ descriptions of solute-solute interactions, and further demonstrates that modifications to van der Waals parameters provides a simple route to optimizing agreement with experiment.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations

Miller

Lay

et al. 2017

J. Chem. Theory Comput.

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“…the area of the x-y plane. The molal osmotic coefficient was then derived from the average osmotic pressure according to the equation: 51–52

φ = \frac{π \cdot V_{w}}{R \cdot T \cdot m \cdot v \cdot M_{w}}

where V W is the partial molal volume of water (taken to be 0.018 L·mol −1 ), R is the gas constant, T is the temperature, m is the molality (determined, as noted above, by counting the number of water molecules in the central region of the system), M W is the molecular weight of water (0.018013 kg·mol −1 ), and ν is the van’t Hoff factor (1 for neutral amino acids, 2 for charged amino acids, since they are accompanied by a counterion). For a very lucid derivation of the above relationship, see Janáček and Sigler.…”

Section: Methodsmentioning

confidence: 99%

“…For a very lucid derivation of the above relationship, see Janáček and Sigler. 52 The computed osmotic coefficients were averaged over the 100 ns production period of the simulation, and errors were reported as standard deviations of the osmotic coefficients computed in five 20 ns blocks.…”

Section: Methodsmentioning

confidence: 99%

Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization

2016

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Recent molecular dynamics (MD) simulations of proteins have suggested that common force fields overestimate the strength of amino acid interactions in aqueous solution. In an attempt to determine the causes of these effects, we have measured the osmotic coefficients of a number of amino acids using the AMBER ff99SB-ILDN force field with two popular water models, and compared the results with available experimental data. With TIP4P-Ew water, interactions between aliphatic residues agree well with experiment, but interactions of the polar residues serine and threonine are found to be excessively attractive. For all tested amino acids, the osmotic coefficients are lower when the TIP3P water model is used. Additional simulations performed on charged amino acids indicate that the osmotic coefficients are strongly dependent on the parameters assigned to the salt ions, with a reparameterization of the sodium:carboxylate interaction reported by the Aksimentiev group significantly improving description of the osmotic coefficient for glutamate. For five neutral amino acids, we also demonstrate a decrease in solute-solute attractions using the recently reported TIP4P-D water model and using the KBFF force field. Finally, we show that for four two-residue peptides improved agreement with experiment can be achieved by re-deriving the partial charges for each peptide.

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“…The molecular modeling [96] for akaganeite formation creates an osmotic gradient between the hydrated shells surrounding the akaganeite and the surrounding water body [108]. Osmotic theory would expect the Cl − ions to migrate from the akaganeite water shell (and ionic layer) into the surrounding water body [108,109].…”

Section: Desalination Associated With Nacl Concentration In the Pore mentioning

confidence: 99%

Desalination of Water Using ZVI (Fe0)

Antia¹

2015

Water

196

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Batch treatment of water (0.2 to 240 L) using Fe 0 (44,000-77,000 nm) in a diffusion environment operated (at −8 to 25 °C) using: (a) no external energy; (b) pressurized (<0.1 MPa) air; (c) pressurized (<0.1 MPa) acidic gas (CO2); (d) pressurized (<0.1 MPa) anoxic gas (N2); (e) pressurized (<0.1 MPa) anoxic, acidic, reducing gas (H2 + CO + CO2 + CH4 + N2), reduces the salinity of water. Desalination costs increase with increasing NaCl removal. The cost of reducing water salinity from: (i) 2.65 to 1.55 g·L . Desalination is accompanied by the removal, from the water, of one or more of: nitrate, chloride, fluoride, sulphate, phosphate, As, B, Ba, Ca, Cd, Co, Cu, Fe, Mg, Mn, Na, Ni, P, S, Si, Sr, Zn. The rate of desalination is enhanced by increasing temperatures and increasing HCO3 − /CO3 2− concentrations. The rate of desalination decreases with increasing SO4 2− removal under acidic, or pH neutral, operating conditions.

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Osmotic pressure: Thermodynamic basis and units of measurement

Cited by 16 publications

References 1 publication

Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations

Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations

Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization

Desalination of Water Using ZVI (Fe0)

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