Analysis of Diamondoid Mechanosynthesis Tooltip Pathologies Generated via a Distributed Computing Approach

Abstract

The results of a combined molecular dynamics/quantum chemistry pathology study of previously reported organic (diamondoid) tooltips for diamondoid mechanosynthesis (DMS) are presented. This study, employing the NanoHive@Home (NH@H) distributed computing project, produced 80,000 tooltip geometries used in 200,000 calculations optimized at either the RHF/3-21G or RHF/STO-3G levels of theory based on geometries obtained from high-energy molecular dynamics simulations to produce highly deformed starting geometries. These 200,000 calculations have been catalogued, grouped according to energies and geometries, and analyzed to consider potentially accessible defect structures (pathologies) for tooltip geometries either binding a carbon dimer (C 2 feedstock or not containing the transported dimer feedstock. The transport and deposition of feedstock and the stability of the tooltip between dimer "loading" cycles are important geometries that must be considered as part of a tooltip stability analysis. The NH@H framework is found to be a useful method both for the study of highly deforming covalent geometries and, using lower-temperature MD simulations, for generating and optimizing molecular conformations (demonstrated using biotin, n-heptane, and n-octane in this study). The results of the pathology survey are discussed and general considerations for the exploration of DMS tooltip usability are explored.