Self-Assembled Two-Dimensional Nanoporous Crystals as Molecular Sieves: Molecular Dynamics Studies of 1,3,5-Tristyrilbenzene-Cn Superstructures.

Due to their unique geometry complex, self-assembled nanoporous 2D molecular crystals offer a broad landscape of potential applications, ranging from adsorption and catalysis to optoelectronics, substrate processes, and future nanomachine applications. Here we report and discuss the results of extensive all-atom Molecular Dynamics (MD) investigations of self-assembled organic monolayers (SAOM) of interdigitated 1,3,5-tristyrilbenzene (TSB) molecules terminated by alkoxy peripheral chains Cn containing n carbon atoms (TSB3,5-Cn) deposited onto highly ordered pyrolytic graphite (HOPG). In vacuo structural and electronic properties of the TSB3,5-Cn molecules were initially determined using ab initio second order Møller-Plesset (MP2) calculations. The MD simulations were then used to analyze the behavior of the self-assembled superlattices, including relaxed lattice geometry (in good agreement with experimental results) and stability at ambient temperatures. We show that the intermolecular disordering of the TSB3,5-Cn monolayers arises from competition between decreased rigidity of the alkoxy chains (loss of intramolecular order) and increased stabilization with increasing chain length (afforded by interdigitation). We show that the inclusion of guest organic molecules (e.g., benzene, pyrene, coronene, hexabenzocoronene) into the nanopores (voids formed by interdigitated alkoxy chains) of the TSB3,5-Cn superlattices stabilizes the superstructure, and we highlight the importance of alkoxy chain mobility and available pore space in the dynamics of the systems and their potential application in selective adsorption.

Computer modeling of 2D supramolecular nanoporous monolayers self-assembled on graphite.

Nano-porous two-dimensional molecular crystals, self-assembled on atomically flat host surfaces offer a broad range of possible applications, from molecular electronics to future nano-machines. Computer-assisted designing of such complex structures requires numerically intensive modeling methods. Here we present the results of extensive, fully atomistic simulations of self-assembled monolayers of interdigitated molecules of 1,3,5-tristyrilbenzene substituted by C6 alkoxy peripheral chains (TSB3,5-C6), deposited onto highly-ordered pyrolytic graphite. Structural and electronic properties of the TSB3,5-C6 molecules were determined from ab initio calculations, then used in Molecular Dynamics simulations to analyze the mechanism of formation, epitaxy, and stability of the TSB3,5-C6 nanoporous superlattice. We show that the monolayer disordering results from the competition between flexibility of the C6 chains and their stabilization by interdigitation. The inclusion of guest molecules (benzene and pyrene) into superlattice nanopores stabilizes the monolayer. The alkoxy chain mobility and available pore space defines the systems dynamics, essential for potential application.

Molecular simulations of intermediate and long alkanes adsorbed on graphite: tuning of non-bond interactions.

The interplay between the torsional potential energy and the scaling of the 1-4 van der Waals and Coulomb interactions determines the stiffness of flexible molecules. In this paper we demonstrate for the first time that the precise value of the nonbond scaling factor (SF)--often a value assumed without justification--has a significant effect on the critical properties and mechanisms of systems undergoing a phase transition, and that, for accurate simulations, this scaling factor is highly dependent on the system under consideration. In particular, by analyzing the melting of n-alkanes (hexane C6, dodecane C12, tetracosane C24) on graphite, we show that the SF is not constant over varying alkane chain lengths when the structural correlated transformations are concerned. Instead, monotonic decrease of SF with the molecular length drives a cross-over between two distinct mechanisms for melting in such systems. In a broad sense we show that the choice for SF in any simulation containing adsorbed or correlated long molecules needs to be carefully considered.