Ionic-Liquid

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(1) Force field parameters for Zhiping Liu and CL&P FF, for several cations and anion (2) Relevant input files to run Molecular Dynamics (MD) simulations using GROMACS (3) Relevant input files to run Monte Carlo (MC) simulations using CASSANDRA for phase equilibria calculations.

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# Ionic Liquid #

This repository is created by **Utkarsh Kapoor**, as part of the Ph.D. disseration, for the purpose of contributing to the ionic liquid research community; and allowing the user to get acquainted with running simulations. It contains:

* Force Field Parameters  
	1. Zhiping Liu United Atom FF  
	2. CL&P All Atom FF  
* Input Files for running MD simulations using GROMACS
* CASSANDRA input files for running MC Simulations for Phase Equilibria Properties

##### Utkarsh Kapoor, Oklahoma State University #####

## Download ##

git clone https://github.com/utkarsk/Ionic-Liquid.git

## Force Field Parameters Available ##

#### Zhiping Liu United Atom FF ####

* Cations  
	* 1-ethyl-3-methylimidazolium [EMIM]
	* 1-butyl-3-methylimidazolium [BMIM]
	* 1-hexyl-3-methylimidazolium [HMIM]
	* 1-octyl-3-methylimidazolium [OMIM]
	
* Anions
	* chloride [Cl]
	* methylsulfate [MeSO4]
	* bis(trifluoromethylsulfonyl)amide [NTf2]
	* acetate [OAC]
	* trifluoroacetate [TFA]
	* trifluoromethanesulfonate [TFS]

#### CL&P All Atom FF ####

* Cations 
	* 1,3 dimethylimidazolium     [MMIM]
	* 1-ethyl-3-methylimidazolium [EMIM]
	* 1-butyl-3-methylimidazolium [BMIM]
	* 1-hexyl-3-methylimidazolium [HMIM]
	* 1-octyl-3-methylimidazolium [OMIM]
	* 1-decyl-3-methylimidazolium [DMIM]
	* 1-dodecyl-3-methylimidazolium [XMIM]
	
* Anions
	* 1-n-octylsulfate [OtSO4]
	* chloride [Cl]
	* methylsulfate [MeSO4]
	* dimethylphosphate [Me2PO4]
	* acetate [OAC]
	* bis(trifluoromethylsulfonyl)amide [NTf2]
	* trifluoroacetate [TFA]
	* trifluoromethanesulfonate [TFS]
	* tris(pentafluoroethyl)trifluorophosphate [eFAP]
	* tetraborofluorate [BF4]
	* hexafluorophosphate [PF6]
	* dicyanamide [DCA]
	
#### Extra Force Field Parameters ####

* Gas Solutes
	* carbon dioxide [CO2]  (from the works of Shi and Maginn)
	* sulfur dioxide [SO2]  (from the works of Shi and Maginn)
	* ammonia [NH3]         (from the works of Shi and Maginn)
	* methane [CH4]         (from TRaPPE)

* Others
	* 1-n-octanol [C8H17OH]  (CL&P)
	* n-octane [C8H18]	     (CL&P)
	* water [H2O]            (SPC/E)

## GROMACS Input Files Available ##

* MDP Files
	* minimize (minimization using steepest descend)
	* annealing (to remove bad energy contacts)
	* nvt_eq (relaxation in NVT ensemble)
	* npt_eq (relaxation in NPT ensemble)
	* npt_prod (Production run - used for analysis)

* TOP Files (only for reference)
	* a top file for [BMIM]Cl[NTf2] mixture for using Zhiping Liu FF
	* a top file for [XMIM][OtSO4] for using CL&P FF

## CASSANDRA Input Files Available ##

* MCF (Molecular connectivity file)
	* 1-butyl-3-methylimidazolium [BMIM]        (Zhiping Liu FF)
	* chloride [Cl]                             (Zhiping Liu FF)
	* bis(trifluoromethylsulfonyl)amide [NTf2]  (Zhiping Liu FF)
	* methylsulfate [MeSO4]                     (Zhiping Liu FF)
	* carbon dioxide [CO2]                      (from the works of Shi and Maginn)
	* methane [CH4]                             (from TRaPPE)

* INP (INPUT file)
	* Gibbs Ensemble Monte Carlo (GEMC_NPT) Simulation (Both Equilibration and Production)
		* For Pure Gas Solubility in [BMIM]Cl[NTf2] mixture at a particular pressure
		* For Mixture of CO2/CH4 Solubility in [BMIM]Cl[NTf2] mixture at 100 bar pressure

* PDB 
	* Since CASSANDRA requires atom connectivity information, unlike GROMACS

## PDB Files Available ##
All the relevant cation, anion and gas solute mentioned above, PDB files are provided.

## Input Files for doing Thermodynamic Integration using MD in GROMACS ##
* MDP Files (for initial state only)
	* minimize
	* annealing 
	* nvt_eq
	* npt_eq 
	* npt_prod

* TOP Files (only for reference)
	* a top file for CO2 + [BMIM]Cl[NTf2] mixture for using Zhiping Liu FF

## References ##
U. Kapoor and J. K. Shah "Effect of Molecular Solvents of Varying Polarity on the Self-Assembly of 1-n-Dodecyl-3- methylimidazolium Octylsulfate Ionic Liquid" [J. Theor. Comput. Chem. 2018, 17, 1840004-1-1840004-26](https://www.worldscientific.com/doi/pdf/10.1142/S0219633618400047)

U. Kapoor and J. K. Shah "Thermophysical Properties of Imidazolium-Based Binary Ionic Liquid Mixtures Using Molecular Dynamics Simulations" [J. Chem. Eng. Data, 2018, 63 (7), 2512-2521](https://pubs.acs.org/doi/abs/10.1021/acs.jced.7b01028)

U. Kapoor and J. K. Shah "Globular, Sponge-like to Layer-like Morphological Transition in 1-n-Alkyl-3-methylimidazolium Octylsulfate Ionic Liquid Homologous Series" [J. Phys. Chem. B, 2018, 122(1), 213-228](https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b08397)

U. Kapoor and J. K. Shah "Preferential Ionic Interactions and Microscopic Structural Changes Drive Nonideality in Binary Ionic Liquid Mixtures as Revealed from Molecular Simulations" [Ind. Eng. Chem. Res., 2016, 55 (51), 13132-1314](https://pubs.acs.org/doi/abs/10.1021/acs.iecr.6b03314)

U. Kapoor "Ionic Liquids: The Importance of Local Structures at Micro-and Mesoscale and Descriptors to Tune Them" (https://drive.google.com/file/d/1WCsQEjGhEi6eLN-0bW4XQ7-B2sqojDOu/view?usp=sharing) or (https://hdl.handle.net/11244/320939)

## About ##

Contributing Authors: Utkarsh Kapoor and Jindal K. Shah, Oklahoma State University

Contact: utkarsh.kapoor@okstate.edu

Funding: Gratitude is expressed to the National Science Foundation (NSF ACI-1339785 and NSF CBET-1706978) for funding the project.

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