Molecular Dynamics Simulations of the Interfacial Behavior of Small Molecules in Complex Multiphase Systems

Author:Li Jing

Supervisor:cao da peng zhang xian ren


Degree Year:2018





In a complex system,there are usually several different phases,which coexist with the interface.In natural world,most events occur on the interface,such as the formation of bubbles,the transmembrane of drug molecules and the separation of gases.In recent years,despite the rapid development of experimental methods enables us to observe directly the nanoscale structures.The current experimental technology restrict the direct observation of most interfacial processes on the atom-and molecule-sized scales.For most of such phenomena,the dynamic process and mechanism occurring in nanoscale interface are often far from being well understood.Therefore,atomistic molecular dynamics simulations are used to study the interfacial behavior of small molecules to supplement the deficiency in the experiment,mainly including the following five aspects:(1)The formation and stabilization mechanism of the bulk nanobubbles.It is very controversial whether bulk nanobubbles are stable or not.Atomistic molecular dynamics simulations are employed to find that amphiphilic molecules play an important role in the stability of nanobubbles.An interesting reversible dissolution-nanobubble-dissolution transition for gas molecules in DAM/water mixtures appears as the fraction of DAM increases.The re-entrant dissolution behavior indicating the crucial,dual roles of amphiphilic molecules in producing and stabilizing bulk nanobubbles.In general,when a small fraction of DAMs are added to the water,the DAM acts as surfactants to promote the formation of bubbles.While as the concentration of DAM increases to a certain value,DAM starts to behave as the co-solvent to promote the dissolution of the gas because the solubility of gas is much higher in DAM than in water.By studying the phase transition behavior of methane gas molecules in three different amphiphilic molecules aqueous solution,we believe that the reversible dissolution-nanobubble-dissolution transition for gas molecules in aqueous solution containing DAM is a universal phenomenon.(2)The phase transition between nanodroplets and nanobubbles under high gas-liquid interfacial tension.Atomistic molecular dynamics simulations were used to study the state of the gas molecules nanoclusters forming in an aqueous solution.Through simulations on both the bulk phase(where a negative pressure is applied to balance the additional pressure caused by the tension to the nanoclusters)and interface phase,we prove that when the curvature radius of the nanoclusters is relatively large,the nanoclusters are present in the form of nanobubbles.Whereas,when the curvature radius of the nanoclusters is small,the nanoclusters are present in the form of nanodroplets.In the absence of external surfactants or other conditions that can reduce the surface tension,high density nanoparticles may be the reason for the stability of the bulk nanobubbles.This may also be the reason why ultrasound probe,which is sensitive to minute quantities of gas and used to detect the structure of nanoclusters,fails to find any stable nanobubbles.(3)Gas supersaturation leads to decoupling of bilayer leaflets and forming nitrogen nanobubbles in membrane.Atomistic molecular dynamics simulation results demonstrate that by crossing a small energy barrier,excess nitrogen molecules could enter the lipid bilayer,for which the hydrophobic core serves as a potential well for gas enrichment.At a rather low nitrogen supersaturation,gas molecules in the membrane are dispersed in the hydrophobic region of the bilayer,with a slight increase of membrane thickness.But as the level of gas supersaturation reaches a threshold,accumulation of N2 molecules in the bilayer center causes the two leaflets to be decoupled and the formation of nanobubbles.Therefore,we propose a nucleation mechanism for bubble formation in supersaturated solution of inert gas:cell membrane acts as a potential well for gas enrichment,being an ideal location for forming nanobubbles that induce membrane damage at high level of gas supersaturation.(4)The essential influence of cholesterol on insertion of the GPI anchors into plasma membranes.Atomistic molecular dynamics simulations and free energy calculations demonstrate that in the presence of cholesterol,the tails of GPI anchors are able to penetrate inside the core of the lipid membrane spontaneously with a three-step mechanism,while in the absence of cholesterol no spontaneous insertion was observed.We ascribe the failure of insertion to the strong thermal fluctuation of lipid molecules in cholesterol-free bilayer,which generates a repulsive force in entropic origin.In the presence of cholesterol,however,the fluctuation of lipids is strongly reduced,thus decreasing the barrier for the anchor insertion.Based on this observation,we propose a hypothesis that addition of cholesterol creates vertical creases in membranes for the insertion of acyl chains.Moreover,we find that the GPI anchor could also spontaneously inserted into the boundary between cholesterol-rich and cholesterol-depleted domains.(5)Hydrogen bond networks of glycol molecules on ZIF-8 surfaces as semipermeable films for efficient carbon capture.Molecular dynamics simulations and free energy analysis reveal that the formation of two-layer ordered hydrogen bond(HB)networks of glycol molecules on the ZIF-8 surface is the physical origin of the high efficiency of using ZIF-8/glycol slurry for carbon capture.It is found that the film composed of two-layer HB networks acts as a selective gatekeeper,allowing the penetration of CO2 molecules but efficiently blocking CH4.The interaction between the HB forming solvent(glycol molecules)and ZIF-8 is the key to the formation of the semipermeable film,while the solute-solvent interaction is essential for film crossing.