Single-file diffusion through inhomogeneous nanopores

Crystalline Bis-urea Nanochannel Architectures Tailored for Single-File Diffusion Studies

Urea is a versatile building block that can be modified to self-assemble into a multitude of structures. One-dimensional nanochannels with zigzag architecture and cross-sectional dimensions of only ∼3.7 Å × 4.8 Å are formed by the columnar assembly of phenyl ether bis-urea macrocycles. Nanochannels formed by phenylethynylene bis-urea macrocycles have a round cross-section with a diameter of ∼9.0 Å. This work compares the Xe atom packing and diffusion inside the crystalline channels of these two bis-ureas using hyperpolarized Xe-129 NMR. The elliptical channel structure of the phenyl ether bis-urea macrocycle produces a Xe-129 powder pattern line shape characteristic of an asymmetric chemical shift tensor with shifts extending to well over 300 ppm with respect to the bulk gas, reflecting extreme confinement of the Xe atom. The wider channels formed by phenylethynylene bis-urea, in contrast, present an isotropic dynamically average electronic environment. Completely different diffusion dynamics are revealed in the two bis-ureas using hyperpolarized spin-tracer exchange NMR. Thus, a simple replacement of phenyl ether with phenylethynylene as the rigid linker unit results in a transition from single-file to Fickian diffusion dynamics. Self-assembled bis-urea macrocycles are found to be highly suitable materials for fundamental molecular transport studies on micrometer length scales.

Differential binding of bispyridinium oxime drugs with acetylcholinesterase

AIM

To performe a time-dependent topographical delineation of protein-drug interactions to gain molecular insight into the supremacy of Ortho-7 over HI-6 in reactivating tabun-conjugated mouse acetylcholinesterase (mAChE).

METHODS

We conducted all-atom steered molecular dynamics simulations of the two protein-drug complexes. Through a host of protein-drug interaction parameters (rupture force profiles, hydrogen bonds, water bridges, hydrophobic interactions), geometrical, and orientation ordering of the drugs, we monitored the enzyme's response during the release of the drugs from its active-site.

RESULTS

The results show the preferential binding of the drugs with the enzyme. The pyridinium ring of HI-6 shows excellent complementary binding with the peripheral anionic site, whereas one of two identical pyridinium rings of Ortho-7 has excellent binding compatibility in the enzyme active-site where it can orchestrate the reactivation process. We found that the active pyridinium ring of HI-6 undergoes a complete turn along the active site axis, directed away from the active-site region during the course of the simulation.

CONCLUSION

Due to excellent cooperative binding of Ortho-7, as rendered by several cation-pi interactions with the active-site gorge of the enzyme, Ortho-7 may be a more efficient reactivator than HI-6. Our work supports the growing body of evidence that the efficacy of the drugs is due to the differential bindings of the oximes with AChE and can aid to the rational design of oxime drugs.

Subdiffusion in time-averaged, confined random walks

Certain techniques characterizing diffusive processes, such as single-particle tracking or molecular dynamics simulation, provide time averages rather than ensemble averages. Whereas the ensemble-averaged mean-squared displacement (MSD) of an unbounded continuous time random walk (CTRW) with a broad distribution of waiting times exhibits subdiffusion, the time-averaged MSD, delta2, does not. We demonstrate that, in contrast to the unbounded CTRW, in which delta2 is linear in the lag time Delta, the time-averaged MSD of the CTRW of a walker confined to a finite volume is sublinear in Delta, i.e., for long lag times delta2 approximately Delta1-alpha. The present results permit the application of CTRW to interpret time-averaged experimental quantities.