Problems, successes and challenges for the application of dispersion-corrected density-functional theory combined with dispersion-based implicit solvent models to large-scale hydrophobic self-assembly and polymorphism

Putting David Craig’s Legacy to Work in Nanotechnology and Biotechnology

“…The observation of interface regions provides strong verification of the assigned structures as the L and M polymorphs must smoothly mesh into each other, a feature which is very difficult to obtain as it requires perfect alignment of many aspects of the structures. [369] The calculations also yield the free energy of SAM formation. [253] This is evaluated using DFT in various forms.…”

“…This boundary appears between different polymorphs and shows one row of molecular structures in the low density 'L' polymorph plus several interface 'I' rows that in their middle take on the structure of the medium-density 'M' polymorph. [368,369] The molecular structures determined from modelling of large areas of the L and M polymorphs are shown, as is how they seamlessly meld together to form the interface layers. The L polymorph is observed for all odd-length chain molecules studied (lengths m from 11 to 19) [253,363,366,368] but not for the even chain Free-electron gas, exact description n molecule studied, 2H-C 12 P, [364,365] while three M polymorphs [253,364,365,368] of quite different form named M a , M b , and M c are observed for 2H-C 11 P, 2H-C 12 P, and 2H-C 13 P, respectively.…”

“…The calculated structures were obtained by optimizing five possible structures for the L polymorphs [363,366] and 40 possibilities for the M polymorphs. [363,369] These possibilities were obtained by considering various conformations of the chain kinks that occur as the alkyl chains come away from the porphyrin at an angle near 608 and must subsequently be bent back in order to lie flat on the surface. The 40 possibilities for the M polymorphs were obtained by varying kink-structure conformers and macrocycle rotation angles, first eliminating possibilities that cannot be shaped into a valid SAM.…”

“…Our work has focussed on the self-assembly of tetraalkylporphyrin molecules synthesized by Max Crossley on highly ordered pyrolytic graphite (HOPG) surfaces from solution in 1-phenyloctane, octanoic acid, or n-tetradecane. [253,[363][364][365][366][367][368] This involved measurement of STM images and the simulation [253,363,369] of the Gibbs free-energy of formation for a wide range of possible atomic structures for each image. The molecules considered are shown in Chart 2.…”

“…After optimization, only at most 22 stable SAMs were realised, named Ma to Mv. Structure assignment was made by comparing these structures to experiment, considering: [253,363,366,369] -Agreement of observed and calculated lattice parameters. To do this, new experimental techniques based on internal calibration and repeated measurements were developed to significantly reduce the experimental uncertainties in the lattice parameters, allowing for discrimination between the calculated structures.…”