Role of host layer flexibility in DNA guest intercalation revealed by computer simulation of layered nanomaterials.
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.
Thyveetil
Mary-Ann
MA
Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom.
Coveney
Peter V
PV
Greenwell
H Christopher
HC
Suter
James L
JL
D000536:Aluminum Hydroxide / Q000737:chemistry*; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004058:Diffusion; D004338:Drug Combinations; D007364:Intercalating Agents / Q000737:chemistry*; D008276:Magnesium Hydroxide / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D049329:Nanostructures / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D014961:X-Ray Diffraction
D004338:Drug Combinations; D007364:Intercalating Agents; C013591:aluminum hydroxide, magnesium hydroxide, drug combination; D000536:Aluminum Hydroxide; D004247:DNA; D008276:Magnesium Hydroxide