Role of Host Layer Flexibility in DNA Guest Intercalation Revealed by Computer Simulation of Layered Nanomaterials

Abstract

Layered double hydroxides (LDHs) have been shown to form staged intermediate structures in experimental studies of intercalation. However, the mechanism by which staged structures are produced remains undetermined. Using molecular dynamics simulations, we show that LDHs are flexible enough to deform around bulky intercalants such as deoxyribonucleic acid (DNA). The flexibility of layered materials has previously been shown to affect the pathway by which staging occurs. We explore three possible intermediate structures which may form during intercalation of DNA into Mg2Al LDHs and study how the models differ energetically. When DNA strands are stacked directly on top of each other, the LDH system has a higher potential energy than when they are stacked in a staggered or interstratified structure. It is generally thought that staged intercalation occurs through a Daumas-Herold or a Rudorff model. We find, on average, greater diffusion coefficients for DNA strands in a Daumas-Herold configuration compared to a Rudorff model and a stage-1 structure. Our simulations provide evidence for the presence of peristaltic modes of motion within Daumas-Herold configurations. This is confirmed by spectral analysis of the thickness variation of the basal spacing. Peristaltic modes are more prominent in the Daumas-Herold structure compared to the Rudorff and stage-1 structures and support a mechanism by means of which bulky intercalated molecules such as DNA rapidly diffuse within an LDH interlayer.

Recent Advances in Stimuli‐Responsive Photofunctional Materials Based on Accommodation of Chromophore into Layered Double Hydroxide Nanogallery

“…Such strategy for construction of PCL material is based on the fact that the LDH nanosheets are flexible enough to deform over interlayer bulky guests, and slipping of LDH layer can occur on increasing the external pressure, which can further influence the host-guest interactions [21]. In addition, the long-chain BTZB anion has four rotatable aromatic amine units, and thus its molecular conformation and intermolecular interactions can be tuned more easily by external perturbations than the rigid molecules.…”

“…A previous review on LDH-based fluorescent materials has mainly summarized the preparation method and tunable photoluminescent properties [19]. Recently, the host-guest stimuli-responsive luminescent materials have also been studied successively, since the orientation mode of the interlayer chromophores and hostguest interaction can be changed upon external stimuli [20,21]. In addition, new physical/chemical phenomena have also been obtained based on the theoretical calculations for these hybrid nanomaterials.…”

Green Rust: The Simple Organizing &lsquo;Seed&rsquo; of All Life?&nbsp;&nbsp;<strong> </strong>

“…[153,154] So, a 1 µm GRcarb would be about 100 nm thick and comprise ~130 double layers overall. [154,155,156,157,158] The height of the hydroxyl interlayer galleries is ~0.30 nm, allowing them perhaps to act as anion and proton channels. And the Fe 2+ -Fe 3+ distance of ~0.33 nm along the iron layers would allow electron hopping by quantum tunneling, though a small proportion of electrons could also jump across the layers.…”

Bio-Layered Double Hydroxides Nanohybrids for Theranostics Applications

“…3C) [54,55]. As a result of molecular dynamic modeling, it was found that the LDH layers are flexible enough to deform around bulky DNA molecules.…”