In order to describe possible reaction mechanisms involving amino acids, and the evolution of the protonation state of amino acid side chains in solution, a reactive force field (ReaxFF-based description) for peptide and protein simulations has been developed as an expansion of the previously reported glycine parameters. This expansion consists of adding to the training set more than five hundred molecular systems, including all the amino acids and some short peptide structures, which have been investigated by means of quantum mechanical calculations. The performance of this ReaxFF protein force field on a relatively short time scale (500 ps) is validated by comparison with classical non-reactive simulations and experimental data of well characterized test cases, comprising capped amino acids, peptides, and small proteins, and reaction mechanisms connected to the pharmaceutical sector. A good agreement of ReaxFF predicted conformations and kinetics with reference data is obtained.

The superlative strength-to-weight ratio of carbon fibers (CFs) can substantially reduce vehicle weight and improve energy efficiency. However, most CFs are derived from costly polyacrylonitrile (PAN), which limits their widespread adoption in the automotive industry. Extensive efforts to produce CFs from low cost, alternative precursor materials have failed to yield a commercially viable product. Here, we revisit PAN to study its conversion chemistry and microstructure evolution, which might provide clues for the design of low-cost CFs. We demonstrate that a small amount of graphene can minimize porosity/defects and reinforce PAN-based CFs. Our experimental results show that 0.075 weight % graphene-reinforced PAN/graphene composite CFs exhibits 225% increase in strength and 184% enhancement in Young’s modulus compared to PAN CFs. Atomistic ReaxFF and large-scale molecular dynamics simulations jointly elucidate the ability of graphene to modify the microstructure by promoting favorable edge chemistry and polymer chain alignment.

Using reactive molecular dynamics (RMD), we present an atomistic insight into the interaction between water molecules and acidic centers of H-ZSM-5 zeolite. The reactive force field method, ReaxFF, was used to evaluate the adsorption and diffusion of water as well as to study the protonation of water molecules inside zeolite channels. The existing Si/Al/O/H parameters were refitted against DFT calculations to improve the ReaxFF description of interaction between water molecules and the acidic sites of zeolites. The diffusion coefficient of water in the zeolite obtained from refitted parameters is in excellent agreement with experimental results. The molecular dynamics (MD) simulations indicate that protonation of water molecules and acidity of the zeolite catalyst depend on water loadings and temperature and the observed trends compare favorably with existing experimental and theoretical studies. At higher water loadings, protonation of water molecules is more frequent leading to formation and growth of protonated water clusters inside zeolite channels. From the analysis of various reaction channels that were observed during the simulations, we found that such water clusters have relatively short life due to frequent interchange of protons and water molecules among the water clusters. Such proton hopping events play a key role in moving the protons between different acidic centers of zeolite. These simulations show the capability of ReaxFF in providing atomistic details of complex chemical interactions between the water phase and solid acid zeolites.