Concentration-dependent like-charge pairing of guanidinium ions and effect of guanidinium chloride on the structure and dynamics of water from all-atom molecular dynamics simulation

Abstract

An all-atom molecular dynamics simulation shows concentration-dependent like-charge ion pairing of the guanidinium ion in an aqueous solution of guanidinium chloride. We have observed two types of like-charge ion pairing for guanidinium ions, namely, stacked ion pairs and solvent-separated ion pairs. Interestingly, both of these like-charge ion-pair formations are dependent on the concentration of guanidinium chloride in water. The probability of stacked like-charge ion-pair formation decreases, whereas, the probability of solvent-separated like-charge pairing increases as the concentration of guanidinium chloride increases, which is shown from radial distribution functions and is confirmed from the energy calculations. Besides like-charge ion-pair formation, we also investigated guanidinium chloride induced changes in water structure. Hydrogen-bond analysis indicates that guanidinium chloride does not alter the strict-hydrogen-bonding patterns of water, whereas, it breaks the bend-hydrogen bond and the non-hydrogen-bonding patterns. Tetrahedral order, nearest neighbor orientation, and distance distribution of water molecules around a probe water molecule show the extent of water structure distortion.

Dowser++, a new method of hydrating protein structures

“…Figure shows oxygen‐oxygen radial distribution functions, obtained from molecules placed by Dowser++ into protein structures from the united data set. The radial distribution function in Figure 7 has a sharp peak at 2.8 Å and another peak of a lower height at 4.6 Å due to tetrahedral arrangement of water . This is in approximate agreement with obtained from experimental diffraction results for liquid water .…”

“…The radial distribution function in Figure 7 has a sharp peak at 2.8 Å and another peak of a lower height at 4.6 Å due to tetrahedral arrangement of water. 29,30 This is in approximate agreement with g OO r ð Þ obtained from experimental diffraction results for liquid water. 31-34 Thus it appears that the placed water molecules are not overcrowded, judging by the position of the first pick, but distributed rather similarly to the liquid state.…”

Unexpected Like-Charge Self-Assembly of a Biguanide-Based Antimicrobial Polyelectrolyte

“…The intrachain (and we will see later the interchain as well) association observed in the PHMB chain can be related to the remarkable like-charge pairing properties demonstrated for free guanidinium ions in previous experimental and computational studies. − According to these studies, the association of the like-charged cations stems from hydrophobic attraction which overcomes the electrostatic repulsion. In particular, it was shown that hydrogen bonds are formed between the oxygen atoms of the water molecules and the nitrogen atoms of the ions but not between the water and the carbon atoms (despite their relative high charge) and therefore the cations (which have a planar symmetry) behave as hydrophobic surfaces .…”

Effects of Concentration on Like-Charge Pairing of Guanidinium Ions and on the Structure of Water: An All-Atom Molecular Dynamics Simulation Study

“…In this case, when n < 4, we have used proper normalization (see Bandyopadhyay et al 60 for details). So, the rapid decrease in ⟨q 4 ⟩ as a function of GdmCl concentration that was observed earlier 51 should not be attributed to breaking of tetrahedral network of water but, on the contrary, it is due to selection of wrong water neighbors. Those water molecules residing in the second shell of a central water molecule contribute to the decrease in ⟨q 4 ⟩.…”