Development of New Transferable Coarse-Grained Models of Hydrocarbons

Abstract

We have utilized an approach that integrates molecular dynamics (MD) simulations with particle swarm optimization (PSO) to accelerate the development of coarse-grained (CG) models of hydrocarbons. Specifically, we have developed new transferable CG beads, which can be used to model the hydrocarbons (C5 to C17) and reproduce their experimental properties with good accuracy. First, the PSO method was used to develop the CG beads of the decane model represented with a 2:1 (2-2-2-2-2) mapping scheme. This was followed by the development of the nonane model described with hybrid 2-2-3-2 and 3:1 (3-3-3) mapping schemes. The force-field parameters for these three CG models were optimized to reproduce four experimentally observed properties including density, enthalpy of vaporization, surface tension, and self-diffusion coefficient at 300 K. The CG MD simulations conducted with these new CG models of decane and nonane, at different timesteps, for various system sizes, and at a range of different temperatures, were able to predict their density, enthalpy of vaporization, surface tension, self-diffusion coefficient, expansibility, and isothermal compressibility with good accuracy. Moreover, a comparison of structural features obtained from the CG MD simulations and the CG beads of mapped all-atom trajectories of decane and nonane showed very good agreement. To test the chemical transferability of these models, we have constructed the models for hydrocarbons ranging from pentane to heptadecane, by using different combinations of the CG beads of decane and nonane. The properties of pentane to heptadecane predicted by these new CG models showed excellent agreement with the experimental data.

Development of transferable coarse-grained models of amino acids

“…In addition to utilizing the water models developed by Bejagam, et al 33 in order to create amino acid models for use with explicit solvent, we were interested in using other CG models that members of our lab had recently developed: CG models for hydrocarbons 47,48 and benzene. 33 of heavy atoms represented in a given bead in the models developed is four (4:1 beads), as can be seen in the mapping schemes given in Table A1.1 in the appendix.…”

“…This methodology was successfully used in our group to develop the hydrocarbon models. 47 determine what subsequent steps should be taken in the model parameterization. Tuning the interaction parameters with the water model also could be evaluated.…”

“…Regarding the other beads in the CG model, the middle side chain bead was modeled with the same non-bonded parameters as the NC (nitrogen plus Cα) bead of the backbone, and the inner side chain bead was modeled with the same non-bonded parameters as those of the two-carbon C2M bead previously developed by a member of the group from modeling hydrocarbons. 47 Because of the structure of the asparagine side chain, it was necessary to model the entire side chain as one bead as shown in Figure 7(a) above. Experimental values of acetamide were used for optimizing the non-bonded parameters.…”

“…The inner bead was modeled with the same parameters as the C2M bead obtained in previous work. 47 Propionamide was used as the analogue for glutamine as it represents the side chain very accurately as can be seen in Figure 11. Its melting point is 81 °C (354 K), 52 so all simulations were run at 356 K to target experimental thermodynamic properties of the liquid phase for optimizing the CG force field parameters.…”

“…al. 47 Yet because of the slight difference between the inner side chain bead and the outer side chain bead, as shown in Figure 14, we decided to model the inner side chain bead as different from the outer side chain bead. The side chain of leucine had to be modeled as one bead because of the bond pattern.…”