Abstract:

This dataset includes configuration, parameter, and production files for a molecular dynamics simulation of water or n-hexane and CH3(CH2-O-CH2)mCH3 chain conformations using GROMACS. GROMACS version 4.5.3 was used for parallel tempering simulations from 256-550K temperature with 32 replicas (where m=11 and m=21) and 40 replicas (where m=31). This dataset supports the book chapter: Chaudhari, M. I. and Pratt, L. R. (2014) Microstructures of Capped Ethylene Oxide Oligomers in Water and N-Hexane, in Oil Spill Remediation: Colloid Chemistry-Based Principles and Solutions (eds P. Somasundaran, P. Patra, R. S. Farinato and K. Papadopoulos), John Wiley and Sons, Inc, Hoboken, NJ. doi: 10.1002/9781118825662.ch11

Suggested Citation:

Chaudhari, Mangesh, and Lawrence Pratt. 2017. Dataset for: Microstructures of capped ethylene oxide oligomers in water and n-hexane. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N72N507M

Publications:

Chaudhari, M. I., Holleran, S. A., Ashbaugh, H. S., & Pratt, L. R. (2013). Molecular-scale hydrophobic interactions between hard-sphere reference solutes are attractive and endothermic. Proceedings of the National Academy of Sciences, 110(51), 20557–20562. doi:10.1073/pnas.1312458110

Chaudhari, M. I., & Pratt, L. R. (2014). Microstructures of Capped Ethylene Oxide Oligomers in Water and N -Hexane . Oil Spill Remediation, 247–257. doi:10.1002/9781118825662.ch11

Purpose:

This project determined microstructural features of CH3(CH2-O-CH2)mCH3 used in dispersant materials that are used in response to oil spills.

Data Parameters and Units:

molecule type, nr, type, resnr, residue, atom, cgnr, charge, mass, bonds, integrator, dt, nsteps, nstxtcout, nstxout, nstvout, nstlog, nstenergy, ns_type, pbc, rcoulomb, rvdw, DispCorr, rlist, coulombypte, fourierspacing, fourier_nx, fourier_ny, fourirer_nz, pme_order, optimize_fft, tcoupl, tc_grps, tau_t, ref_t, Pcoupl, Pcoupltype, tau_p, compressibility, ref_p, gen_vel, gen_temp, gen_seed, connstraints, constraint_algorithm, #mols, position restraint for each water oxygen (fcs, fcy, fcz)

Methods:

Two different simulation techniques were used for the molecular dynamics calculations. The first class of calculations used parallel tempering to achieve enhanced sampling of the mixing characteristics with water or n-hexane solvent, and of CH3(CH2-O-CH2)mCH3 chain conformations. The second class of simulations obtained higher spatial resolution in the loop closure region using the windowing stratification method.

Individual Files: