Multiscale Simulation and Modeling of Multilayer Heteroepitactic Growth of C60 on Pentacene.

We apply multiscale methods to describe the strained growth of multiple layers of C60 on a thin film of pentacene. We study this growth in the presence of a monolayer pentacene step to compare our simulations to recent experimental studies by Breuer and Witte of submonolayer growth in the presence of monolayer steps. The molecular-level details of this organic semiconductor interface have ramifications on the macroscale structural and electronic behavior of this system and allow us to describe several unexplained experimental observations for this system. The growth of a C60 thin film on a pentacene surface is complicated by the differing crystal habits of the two component species, leading to heteroepitactical growth. In order to probe this growth, we use three computational methods that offer different approaches to coarse-graining the system and differing degrees of computational efficiency. We present a new, efficient reaction-diffusion continuum model for 2D systems whose results compare well with mesoscale kinetic Monte Carlo (KMC) results for submonolayer growth. KMC extends our ability to simulate multiple layers but requires a library of predefined rates for event transitions. Coarse-grained molecular dynamics (CGMD) circumvents KMC's need for predefined lattices, allowing defects and grain boundaries to provide a more realistic thin film morphology. For multilayer growth, in this particularly suitable candidate for coarse-graining, CGMD is a preferable approach to KMC. Combining the results from these three methods, we show that the lattice strain induced by heteroepitactical growth promotes 3D growth and the creation of defects in the first monolayer. The CGMD results are consistent with experimental results on the same system by Conrad et al. and by Breuer and Witte in which C60 aggregates change from a 2D structure at low temperature to 3D clusters along the pentacene step edges at higher temperatures.

Transferable Molecular Model of Woven Covalent Organic Framework Materials.

Two woven covalent organic framework materials (COF-505 and COF-506) have been synthesized since 2016, and the latter demonstrated the ability to take up dyes and other small molecules. This opens the door to applications such as separations, sensing, and catalysis. However, accelerating the design of future woven materials by changing the chemistry of the "threads" will require a computational model for these materials. Since no such atomic-scale model exists, we have developed a protocol for optimizing a force field for woven materials which can be used as the input to molecular dynamics simulations. Their high density and elasticity made these COFs challenging to model at a semiempirical level. Our modeling approach required simultaneous optimization of lattice parameters and elasticity using density functional theory-derived energy barriers and available experimental results. We used this force field, parameterized to fit COF-505, without change, to predict the structure of COF-506. This model allowed us to predict an anisotropy in 505's elasticity and preferred directions for diffusion which cannot be seen experimentally. The pore size distribution for 506 is dominated by small pores (80% <10 Å dia.), though 5% of the pores are up to 20 Å in diameter. We confirmed the experimental result that gases (barring helium) do not diffuse appreciably in COF-505. We validated our (unaltered) force field model to accurately predict experimental uptake data for tetrahydrofuran and methyl orange dye in COF-506. We proposed an atomic-scale mechanism by which COF-505 becomes metallated and demetallated. In addition, in advance of experimental studies, we determined the ability of 505 to incorporate other metals, such as Zn and Fe, which might be considered artificial photosynthesis agents. These predictions validate that Cu was a particularly appropriate choice of metal center for the synthesis, showcasing the ability of this model to play a role in designing woven materials a priori.

Synthesis and Solution-Phase Characterization of Sulfonated Oligothioetheramides.

Nature has long demonstrated the importance of chemical sequence to induce structure and tune physical interactions. Investigating macromolecular structure and dynamics is paramount to understand macromolecular binding and target recognition. To that end, we have synthesized and characterized flexible sulfonated oligothioetheramides (oligo-TEAs) by variable temperature pulse field gradient (PFG) NMR, double electron-electron resonance (DEER), and molecular dynamics (MD) simulations to capture their room temperature structure and dynamics in water. We have examined the contributions of synthetic length (2-12mer), pendant group charge, and backbone hydrophobicity. We observe significant entropic collapse, driven in part by backbone hydrophobicity. Analysis of individual monomer contributions revealed larger changes due to the backbone compared to pendant groups. We also observe screening of intramolecular electrostatic repulsions. Finally, we comment on the combination of DEER and PFG NMR measurements via Stokes-Einstein-Sutherland diffusion theory. Overall, this sensitive characterization holds promise to enable de novo development of macromolecular structure and sequence-structure-function relationships with flexible, but biologically functional macromolecules.