Document Type : Research Paper
School of Pharmacy, Mashhad University of Medical Science, Mashhad, Iran.
Department of Medicinal Chemistry, School of Pharmacy & Avicenna Pharmaceutical Research Center, Mashhad University of Medical Science, Mashhad, Iran.
Departments of Bio & Chemical Engineering, University of Illinois at Chicago, Chicago, IL 60607-7052 USA.
Diamondoids are cage-like saturated hydrocarbons consisting of fused cyclohexane rings. The Diamondoids family of compounds is one of the best candidates for molecular building blocks (MBBs) in nanotechnology to construct organic nanostructures compared to other MBBs known so far. The challenge is to find a route for self-assembly of these cage hydrocarbons and their applications in the bottom-up synthesis. In this paper, a DNA-based self-assembly technique called “DNA Bridge-based Self-assembly” (DBS) is introduced to self-assemble the diamondoid molecules based upon a bottomup strategy. The results of our computations and simulations with different molecular mechanical force fields (MM+, AMBER, BIO+, and OPLS) and different optimization algorithms (Polak-Ribiere, Fletcher- Reeves, and block-diagonal Newton-Raphson) furthermore confirm the feasibility of the formation of such hybrid nanoarchitecture.