The formation of 2D surface-confined supramolecular porous networks is scientifically and technologically appealing, notably for hosting guest species and confinement phenomena. In this study, we report a scanning tunneling microscopy (STM) study of the self-assembly of a tripod molecule specifically equipped with pyridyl functional groups to steer a simultaneous expression of lateral pyridyl-pyridyl interactions and Cu-pyridyl coordination bonds. The assembly protocols yield a new class of porous open assemblies, the formation of which is driven by multiple interactions. The tripod forms a purely porous organic network on Ag(111), phase α, in which the presence of the pyridyl groups is crucial for porosity, as confirmed by molecular dynamics and Monte Carlo simulations. Additional deposition of Cu dramatically alters this scenario. For submonolayer coverage, three different porous phases coexist (i.e., β, γ, and δ). Phases β and γ are chiral and exhibit a simultaneous expression of lateral pyridyl-pyridyl interactions and twofold Cu-pyridyl linkages, whereas phase δ is just stabilized by twofold Cu-pyridyl bonds. An increase in the lateral molecular coverage results in a rise in molecular pressure, which leads to the formation of a new porous phase (ε), only coexisting with phase α and stabilized by a simultaneous expression of lateral pyridyl-pyridyl interactions and threefold Cu-pyridyl bonds. Our results will open new avenues to create complex porous networks on surfaces by exploiting components specifically designed for molecular recognition through multiple interactions.

The behavior of a multiwalled carbon nanotube functionalized by magnetic nanoparticles through triethylene glycol chains is studied using molecular dynamics simulations. Particular attention is paid to the effect of magnetic anisotropy of nanoparticles which significantly affects the behavior of the system under an external magnetic field. The magnetization reversal process is coupled with the standard atomistic molecular dynamics equations of motion by utilizing the Neel–Brown model and the overdamped Langevin dynamics for description of the inertless magnetization displacements. The key results obtained in this study concern: an energetic profile of the system accompanying transition of a magnetic nanoparticle from the vicinity of the nanotube tip to its sidewall, that is from the capped configuration to the uncapped one; range of the magnetic anisotropy constant in which the system performs structural rearrangements under the external magnetic fields; range of the magnetic field strengths necessary for triggering the structural rearrangements; and other effects like magnetic heating observed during the interaction of the system with the magnetic field. The determined properties of the studied system strongly suggest its application in the area of nanomedicine as a drug targeting and delivery nanovehicle.

A lattice Monte Carlo (MC) model was proposed with the aim of understanding the factors affecting the chiral self-assembly of tripod-shaped molecules in two dimensions. To that end a system of flat symmetric molecules adsorbed on a triangular lattice was simulated by using the canonical ensemble method. Special attention was paid to the influence of size and composition of the building block on the morphology of the adsorbed overlayer. The obtained results demonstrated a spontaneous self-assembly into extended chiral networks with hexagonal cavities, highlighting the ability of the model to reproduce basic structural features of the corresponding experimental systems. The simulated assemblies were analyzed with respect to their structural and energetic properties resulting in quantitative estimates of the unit cell parameters and mean potential energy of the adsorbed layer. The predictive potential of the model was additionally illustrated by comparison of the obtained superstructures with the recent STM images that have been recorded for different organic tripod-shaped molecules adsorbed at the liquid/pyrolytic graphite interface.

The interactions of divalent calcium ions with a single α-L-guluronate anion and oligo(α-L-guluronate) chain have been studied in terms of the 'hybrid' molecular dynamics technique in which the selected parts of the system are treated with different level of theory (DFT-MD). The simulations were focused on obtaining the free energy profiles designed to clarify the possible calcium binding modes. In all considered cases, the calcium ion is coordinated by carboxyl oxygen atoms and water molecules exclusively. The results allowed for (i) determining the dentacy of calcium binding; (ii) estimating the calcium binding/unbinding-related free energy profiles; and (iii) positive verification of the previously [J. Comput. Chem. 2011, 32, 2988] proposed modification of the egg-box model describing the calcium alginate/guluronate structure. Additionally, the findings indicate that the polarization of the carboxyl group induced by the presence of Ca(2+) ion causes the increase of the free energy barrier separating the 'free' and 'bound' states of Ca(2+), in comparison to the classical biomolecular force fields (GROMOS/SPC and GLYCAM/TIP3P).

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We studied the permeability of graphene sheets with designed nanopores using the classical molecular dynamics. To characterize the energy profile for transmission we calculated the potential of the mean force. A high selectivity for methane + butane mixture with the hydrogen-passivated pore diameter of 0.32 nm was found where the volume exclusion mechanism governs the separation process. In the case of a slightly larger pore diameter of 0.64 nm the same alkane mixture separates completely unexpectedly: a larger butane molecule permeates much faster than a small methane one. The blocking effect of the permeation path by a larger mixture component when it worked like a cork was also observed. This is a promising perspective for using graphene to design intelligent membranes which can maintain a constant composition of mixtures in the permeable area.

The hexopyranose mutarotation is an important focus for carbohydrate chemistry for more than 150 years. The paper describes the results of advanced computational studies aimed at elucidating the ring-opening reaction of glucose. Molecular simulations based on the combination of the DFT method with the molecular dynamics formalism allowed for a detailed insight into the mechanism of the process accompanied by the information of the kinetic and dynamic nature. The results indicate that the process is initiated by deprotonation of the anomeric hydroxyl group by water molecules and the subsequent proton transfer to the ring oxygen atom. The latter event has been identified as a 'bottleneck' of the process triggering the ring cleavage. The most time-consuming steps of the ring-opening reaction are the orientational rearrangements of water molecule(s) participating in the proton transfer(s) and the final extension of the newly-formed aldehyde chain. The orientational preferences of the aldehyde group present in the acyclic form of D-hexopyranoses are responsible for the anomeric equilibrium characteristics.