On the Diffusion of Acetonitrile in Nanoscale Amorphous Silica Pores. Understanding Anisotropy and the Effects of Hydrogen Bonding

Abstract

Molecular dynamics simulations are used to examine the diffusion of acetonitrile within ∼2.4 nm diameter amorphous silica pores with a focus on the mechanism. The role of the pore surface chemistry is examined by comparison of a hydrophilic, −OH terminated, silica pore with one that has hydrogen-bonding turned off and with an effectively hydrophobic pore obtained by setting all pore charges to zero. The anisotropy of diffusion, along and perpendicular to the pore axis, is examined through the mean-squared displacements. The origins of the anisotropy are investigated through the dependence on the acetonitrile position within the pore. The effect of hydrogen bonding of acetonitrile molecules to the hydrophilic pore surface is also probed. The simulations show that acetonitrile molecules do not diffuse axially next to the pore surface. Rather, axial diffusion is preceded by radial diffusion away from the pore surface. The same mechanism is observed for molecules independent of their hydrogen-bonding status to surface silanols though hydrogen-bonded molecules diffuse more slowly.

Single‐Molecule and Ensemble Diffusivities in Individual Nanopores with Spatially Dependent Mobility

“…Thus, molecules in region I must first move towards the high‐mobility region before any significant movement parallel to the surface can take place. Similar behavior was reported for neat acetonitrile at a silica surface …”

“…Similar behavior was reported for neat acetonitrile at as ilica surface. [52] The pore diffusion of ACN is enhanced with respect to diffusion in the bulk liquid, because the ACN molecules reside mostlyi nt he high-mobility region (region II) and in the bulk (region III) of the pore. In contrast, Wd iffusion resembles its bulk value, as Wm olecules largely avoid the low-and highmobility regionsI and II.…”

“…[47] Near as olid surface, the molecular diffusivity is known to be spatially dependent. [39,[48][49][50][51][52] It generally stemsf rom microheterogeneityi nduced by solvent molecules formingamore-ordereds tructure next to ah ard wall and from chemical surface modifications, which impart distinctm obility regions. (This phenomenons hould not be confused with the microheterogeneity that is also observedi n water/ACN( W/ACN) mixtures in the absence of any confinement due to the amphiphilic character of acetonitrile.…”

“…(This phenomenons hould not be confused with the microheterogeneity that is also observedi n water/ACN( W/ACN) mixtures in the absence of any confinement due to the amphiphilic character of acetonitrile. [53] )A ll these effects can be analyzed in detail by using MD simulations, [38][39][40][49][50][51][52] and the solute molecules can be accurately traced individually through all mobility regions. This allows ac omplete pore-level molecular exchange to be achieved and, thus, allows the long-time behavioro fD pore to be monitored.…”

Potential Role of Inorganic Confined Environments in Prebiotic Phosphorylation

“…The number of exploratory studies in confined systems within the realm of prebiotic chemistry is relatively small. Theoretical studies have been undertaken extensively outside the origins community [ 2 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 ], where the physicochemical properties of water in confinement and its implication on hydrogen bonding have been studied extensively. More recently, within the community, theoretical studies on confinement within layers of mackinawite were carried out where encouraging results have been obtained in terms of amino acid polymerization [ 13 , 14 , 15 ].…”