Other systems, such as convoluted protein Ilomastat structures or DNA, would be more complex to analyze (due to kinetic hindrance

of side-chain interactions, for example), but similar looped structures exist [26–28] and are also dictated by a balance of thermal and mechanical contributions [29–31]. While linear carbon chains have been experimentally attained, such a closed carbyne has yet to be synthesized. However, recent developments of carbon materials such as annulenes [32–34] and extended porphyrins [35] suggest that carbon may allow such  atomistic control’ and design of such molecular structures. Similar folded/looped atomistic structures include molecular knots [36, 37], Temsirolimus purchase foldamers [38, 39], and cyclic heterostructures [39–42]. The use of homogeneous carbon eliminates the effects of more complex structures (such as torsional rigidity or steric interactions). However, while carbyne is used here as an idealized model system, the general behavior can serve as an analog

to such systems and reflect the dynamics at a molecular scale. Methods Full atomistic simulations are implemented using classical MD, utilizing the first-principle-based ReaxFF potential [43, 44], known to provide an accurate account of the chemical/mechanical behavior of carbon nanostructures [21, 45–49]. Due to a bond order-based formulation, PFT�� research buy ReaxFF can reflect the bond hybridization of the polyyne structure Sorafenib purchase of carbyne, as well as the effect of other valence terms (angle and torsion), without explicit parameterization [45]. It is noted that at such a scale, electron behavior may play a critical role. For example, a previous

study demonstrated that in linear carbon chains, a local perturbation through the displacement of a single atom creates atomic force and charge density Friedel-like oscillations [50]. Other electron-dependent effects may include Jahn-Teller distortions [51] or Möbius topologies [52, 53]. While such complex behavior is incapable of being replicated by MD potentials, it is deemed sufficient for the current scope of length and temperature effects on unfolding. A time step is chosen to be on the order of a fraction of femtoseconds (0.1 × 10-15 s) to ensure the stability and reflect the high vibrational frequency of the acetylene groups of carbyne. All simulations are subject to a canonical (NVT) ensemble, with varying prescribed temperature (10 to 800 K), performed using the massively paralyzed modeling code LAMMPS (http://​lammps.​sandia.​gov/​) [54]. As carbyne has been stated to take either a cumulene (=C = C=) or a polyyne form (-C ≡ C-), small test structures (rings with n = 20 and n = 36) were minimized using ReaxFF to check the relative energetic stability of each structure (Figure 2).