Novel Analysis of Cation Solvation Using a Graph Theoretic Approach

Abstract

A new method for analyzing molecular dynamics simulation data is employed to study the solvent shell structure and exchange processes of mono-, di-, and trivalent metal cations in water. The instantaneous coordination environment is characterized in terms of the coordinating waters' H-bonding network, orientations, mean residence times, and the polyhedral configuration. The graph-theory-based algorithm provides a rapid frame-by-frame identification of polyhedra and reveals fluctuations in the solvation shell shape--previously unexplored dynamic behavior that in many cases can be associated with the exchange reactions of water between the first and second solvation shells. Extended solvation structure is also analyzed graphically, revealing details of the hydrogen bonding network that have practical implications for connecting molecular dynamics data to ab initio cluster calculations. Although the individual analyses of water orientation, residence time, etc., are commonplace in the literature, their combination with graphical algorithms is new and provides added chemical insight.

ChemNetworks: A complex network analysis tool for chemical systems

“…In the former, the entire hydrogen bond network of the simulated water was first converted into a graph, wherein the oxygen atoms are vertices and the intermolecular hydrogen bonds between water molecules are edges. The PageRank of the solute was then used to investigate the specific organization patterns of water about a solute, and was shown to be an effective data‐mining tool for understanding solvation structure as a function of time . This algorithm is available within the moleculaRnetworks software program .…”

In situ quasi-elastic neutron scattering study on the water dynamics and reaction mechanisms in alkali-activated slags

“…It is noted that there are also Mg 2+ and Ca 2+ ions and aluminate monomers in the AAS pore solution, however, the H2O molecules solvating these ions/species are not considered here because these ions/monomers are at much lower concentrations compared with Na + and silicate species in the AAS pore solution. 71 The impact of Na + on water dynamics has been examined using MD simulations which revealed that the residence time of H2O molecules in the 1 st solvation shell of Na + is ~10-25 ps, 57,[68][69][70] suggesting that the H2O molecules solvating Na + ions should be assigned to the BWI. However, Figure 6a clearly shows that the BWI of the three NaOH solutions are similar despite their large difference in concentrations (~5.6, ~8.2 and ~10.0 M).…”

Statistical and image analysis for characterizing simulated atomic-scale damage in crystals

“…[17,18] This is in contrast to MD simulations of soft materials and clusters, where a number of structure analysis tools have been introduced. [5][6][7][8][9][10][11][12] Recognizing this need, as well as a current trend in combining statistical and materials analysis, [33] we have explored the use of an image analysis and a statistical technique to compare plastic damage profiles among MD simulations. For this study, the damage was created by straining bi-crystals containing symmetric tilt grain boundaries with different initial tilt angles.…”

“…For molecular and cluster structures, a number of methods have been developed for analyzing complex shapes. [5][6][7][8][9][10][11][12] Some of these methods use direct statistical analysis to discriminate between structures, while others use statistical comparisons to structural databases. For crystals, a number of schemes have been introduced that can efficiently identify defects such as shear bands, stacking faults and dislocations from atom coordinates.…”