Convergence behaviour of solvation shells in simulated liquids

Kalayan, Jas; Henchman, Richard H.

doi:10.1039/d0cp05903j

Cited by 5 publications

(9 citation statements)

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“…Debate exists in whether 90–110% of the average between the first and second peak of the RDF is too arbitrary when defining “insertion” and “deletion”, as shown in Figure . In previous research on the convergence behavior of solvation shells in condensed phases, the cutoffs were also selected arbitrarily and scaled up as the solvent molecule radii increases . Indeed, there is sensitivity to the choice of insertion and deletion, but we feel our choice is reasonable and reproducible, given that RDFs can be easily generated.…”

Section: Resultsmentioning

confidence: 99%

“…In previous research on the convergence behavior of solvation shells in condensed phases, the cutoffs were also selected arbitrarily and scaled up as the solvent molecule radii increases. 58 Indeed, there is sensitivity to the choice of insertion and deletion, but we feel our choice is reasonable and reproducible, given that RDFs can be easily generated. Overall, this strategy of defining water insertion/deletion cutoffs has been shown to control the error in a reasonable range for multiple ions.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

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Systematic Evaluation of Ion Diffusion and Water Exchange

Merz

2022

J. Chem. Theory Comput.

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As a fundamental property of all fluids, diffusion plays myriad roles in both science and our daily lives. Diffusive properties of many liquids including water have been extensively studied both experimentally and theoretically, while for transition metal ions, there exist significant experimental data that have not been extensively studied theoretically. Hence, high-confidence predictions for challenging systems like radioactive ions that are biohazardous cannot be reliably generated. In this work, a workflow named ISAIAH (Ion Simulation using AMBER for dIffusion Action when Hydrated) was designed to accurately simulate the diffusion coefficients of 15 monoatomic ions with charges varying from −1 to +3 in four water models. As the results indicate, good agreement with experimental values was achieved, leading us to select 239 Pu 4+ (for which no experimental data are available) as a candidate ion to make a theoretical prediction of its diffusion coefficient in water. Among all the force field parameter sets, the ones parametrized using an augmented 12-6-4 Lennard-Jones (LJ) potential showed lower average unsigned errors (AUE) for ions of various radii and electron configurations relative to some 12-6 LJ parameters. This observation agrees well with the fact that diffusion is affected by both the hydration free energy (HFE) and the ion-oxygen distance (IOD) between solute and solvent molecules, both of which are handled well by the 12-6-4 model.

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Section: Resultsmentioning

confidence: 99%

Section: ■ Results and Discussionmentioning

confidence: 99%

Systematic Evaluation of Ion Diffusion and Water Exchange

Merz

2022

J. Chem. Theory Comput.

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“…To calculate the free energy of hydrated proteins, we only consider water molecules in the coordination shell of the protein as depicted in Figure 1(A) . Although longer‐range effects may be present, causing water molecules to be perturbed beyond the protein surface, 68 , 93 , 94 they are weak and difficult to account for because of statistical noise involving a large number of molecules. To analyze the different types of water molecules, we group them according to the nearest non‐water UA (Figure 1(B) ), whether in the protein or an ion, and the nearest residue, defined as the residue that contains the nearest UA.…”

Section: Methodsmentioning

confidence: 99%

Total free energy analysis of fully hydrated proteins

et al. 2022

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The total free energy of a hydrated biomolecule and its corresponding decomposition of energy and entropy provides detailed information about regions of thermodynamic stability or instability. The free energies of four hydrated globular proteins with different net charges are calculated from a molecular dynamics simulation, with the energy coming from the system Hamiltonian and entropy using multiscale cell correlation. Water is found to be most stable around anionic residues, intermediate around cationic and polar residues, and least stable near hydrophobic residues, especially when more buried, with stability displaying moderate entropy-enthalpy compensation. Conversely, anionic residues in the proteins are energetically destabilized relative to singly solvated amino acids, while trends for other residues are less clear-cut. Almost all residues lose intraresidue entropy when in the protein, enthalpy changes are negative on average but may be positive or negative, and the resulting overall stability is moderate for some proteins and negligible for others. The free energy of water around single amino acids is found to closely match existing hydrophobicity scales. Regarding the effect of secondary structure, water is slightly more stable around loops, of intermediate stability around β strands and turns, and least stable around helices. An interesting asymmetry observed is that cationic residues stabilize a residue when bonded to its N-terminal side but destabilize it when on the Cterminal side, with a weaker reversed trend for anionic residues.

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“…In a recent QM/MM MD study 43 of aqueous F − , Cl − , and Br − , the application of a cutoff criterion based on the respective RDFs g(r) resulted in coordination numbers (CNs) showing notable deviations from experimental estimates, while other structural properties such as the average first shell ionoxygen distance were found in good agreement with experimental and theoretical reference data. In order to improve the determination of the CN in case of these more complex hydrogen-bonded complexes, an alternative definition of the first shell neighbors based on the relative angular distance (RAD) algorithm introduced by Higham and Henchman 44 was employed. This framework is based on the geometric concept of the solid angle Ω, which quantifies the field of view of a given object, e.g., an atom of a solvent molecule, from a predefined reference point, which, in this case, represents the solute.…”

Section: Introductionmentioning

confidence: 99%

“…Alternatively, a less-tight criterion referred to as RAD open has been introduced, in which the search is continued even though closer ligands are identified as blocked. 44 A key advantage of the RAD algorithm is the classification of first shell ligands without the requirement of any predetermined cutoff criterion solely on the basis of geometric properties of the coordination complex. By applying this alternative characterization of first shell ligands, a much better agreement in the CN with experimental reference data could be achieved when analyzing F − , Cl − , and Br − in aqueous solution 43 as well as when characterizing pure liquid systems.…”

Section: Introductionmentioning

confidence: 99%

Characterization of the Coordination and Solvation Dynamics of Solvated Systems─Implications for the Analysis of Molecular Interactions in Solutions and Pure H₂O

Listyarini,

Kriesche,

Hofer

2024

J. Chem. Theory Comput.

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The characterization of solvation shells of atoms, ions, and molecules in solution is essential to relate solvation properties to chemical phenomena such as complex formation and reactivity. Different definitions of the first-shell coordination sphere from simulation data can lead to potentially conflicting data on the structural properties and associated ligand exchange dynamics. The definition of a solvation shell is typically based on a given threshold distance determined from the respective solute−solvent pair distribution function g(r) (i.e., GC). Alternatively, a nearest neighbor (NN) assignment based on geometric properties of the coordination complex without the need for a predetermined cutoff criterion, such as the relative angular distance (RAD) or the modified Voronoi (MV) tessellation, can be applied. In this study, the effect of different NN algorithms on the coordination number and ligand exchange dynamics evaluated for a series of monatomic ions in aqueous solution, carbon dioxide in aqueous and dichloromethane solutions, and pure liquid water has been investigated. In the case of the monatomic ions, the RAD approach is superior in achieving a well separated definition of the first solvation layer. In contrast, the MV algorithm provides a better separation of the NNs from a molecular point of view, leading to better results in the case of solvated CO 2 . When analyzing the coordination environment in pure water, the cutoff-based GC framework was found to be the most reliable approach. By comparison of the number of ligand exchange reactions and the associated mean ligand residence times (MRTs) with the properties of the coordination number autocorrelation functions, it is shown that although the average coordination numbers are sensitive to the different definitions of the first solvation shell, highly consistent estimates for the associated MRT of the solvated system are obtained in the majority of cases.

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Convergence behaviour of solvation shells in simulated liquids

Abstract: A convenient way to analyse solvent structure around a solute is to use solvation shells, whereby solvent position around the solute is discretised by the size of a solvent molecule,...

Cited by 5 publications

References 79 publications

Systematic Evaluation of Ion Diffusion and Water Exchange

Systematic Evaluation of Ion Diffusion and Water Exchange

Total free energy analysis of fully hydrated proteins

Characterization of the Coordination and Solvation Dynamics of Solvated Systems─Implications for the Analysis of Molecular Interactions in Solutions and Pure H₂O

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Convergence behaviour of solvation shells in simulated liquids

Abstract: A convenient way to analyse solvent structure around a solute is to use solvation shells, whereby solvent position around the solute is discretised by the size of a solvent molecule,...

Cited by 5 publications

References 79 publications

Systematic Evaluation of Ion Diffusion and Water Exchange

Systematic Evaluation of Ion Diffusion and Water Exchange

Total free energy analysis of fully hydrated proteins

Characterization of the Coordination and Solvation Dynamics of Solvated Systems─Implications for the Analysis of Molecular Interactions in Solutions and Pure H2O

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Product

Resources

About

Characterization of the Coordination and Solvation Dynamics of Solvated Systems─Implications for the Analysis of Molecular Interactions in Solutions and Pure H₂O