Provided Files

We provide three groups of data in this archive: the raw simulation trajectories from our papers, CSV files of the shape data from the simulations, and equilibrated structures from pulled from our simulations. These are provided as a series of ZIP compressed folders. Due to the size, the raw trajectories are bundled as individual ZIP folders for each simulation while the other groups of data are provided in their own ZIP folders, labelled "Shape_Analysis" and "Equilibrated_Structures".

Raw Trajectories

These subdirectories provide the files necessary for loading our raw trajectories. We performed five simulations and have files for each. Each ZIP compressed folder contains five files from each simulation. A summary of the provided files is given in Table 1.

Table 1: Naming conventions and description of simulation files

The prefix of each file specifies which simulation the file is referring to. Specifications of the file prefixes and a brief summary of all simulations is provided in Table 2. The ZIP compressed folders are named according to the second column of Table 2. We provide a more thorough description of the simulations at the end of this document and we refer readers to Ref. 3 for complete details on the simulations.

Table 2: Table of simulation names and force fields

The OPLS force field lacks native parameters for the sulfonate moiety, parameters for this group were taken from literature. Charges and intramolecular parameters (bond stretching, etc) were taken from Ref. 4, while Lennard-Jones parameters were taken from Ref. 5, both provided below.

1. Canongia Lopes, J.N.; Padua, A.A.H.; Shimizu, K. Molecular force field for ionic liquids IV: Trialkylimidazolium and alkoxycarbonyl-imidazolium cations; alkylsulfonate and alkylsulfate anions. J. Phys. Chem. B 20, 112, 5039-5046.
2. Rios-Lopez, M.; Mendez-Bermudez, J.G.; Dominguez, H. New Force field parameters for the sodium dodecyl sulfate and alpha olefin sulfonate anionic surfactants. J. Phys. Chem. B 2018, 122, 4558-4565.

We also provide MDP files which are common to all simulations, which are provided in the archive as individual files outside of ZIP folders. The MDP file is the GROMACS file used to specify the options utilized in the simulation and therefore these serve as references of the exact options set for each simulation. Each simulation used the same MDP file so only two are provided. The MDP file information is provided in Table 3. Note that semicolons are the MDP files comment operator so any line starting with a semicolon has been commented out.

Table 3: Description of the provided MDP files

Simulations were performed using the 2019 version of GROMACS, which provides excellent documentation and so we refer readers to their website for details about each file type. There are several options for reading and analyzing GROMACS trajectories, including the Python package MDAnalysis and the free program VMD. The provided files should be more than sufficient to read in the trajectory via whatever interface the user prefers. Note that the inclusion of both the “-prod1.tpr” and “-RotAuto.tpr” files is redundant as either can be used to provide the necessary information to read the XTC trajectory files. We have included them mostly for completeness and out of an abundance of caution.

When accessing the trajectories, it is often useful to know the residue names and/or the atom names. The residue names are given below with the common name of the molecule on the left and the residue name used by the simulations on the right.

• water - SOL
• AOT - AOT
• isooctane - ISO

Note that the sodium cation was considered a part of the AOT residue for the purposes of these simulations. It simplified packing the initial structures greatly and only impacts the residue name given to sodium. Users just need to be aware of that fact.

Atom names are recorded most effectively in the PDB files found in the “Equilibrated_Structures”. All OPLS simulations used the same atom names for all residues as the only difference between these simulations were the partial charges on each atom. The OPLS atom names are generally different than the CHARMM atom names. The CHARMM atom names between the CHARMM and CHARMM-4P are identical except for the water atom names, where we switch between a 3-site and 4-site water model.

"Equilibrated_Structures" Directory

We have created sets of 20 frames for each simulation taken from the production run of our simulation. The structures may be used as pre-equilibrated starting structures of a w₀ = 5 reverse micelle for each force field we utilized. These frames were generated using a k-means clustering, implemented via the Scikit-Learn Python package based on the CPE and convexity measured at the 5^th, outermost surface (see Ref. 3 for more details about surfaces). This has the effect of generating a set of frames which are as different from each other as possible while also spanning the entire range of observed shapes. They therefore represent a highly diverse set of starting structures, which may or may not be important to someone interested in simulating AOT reverse micelles.

We also note that these files serve as a reference for the atom naming conventions used in each simulation.

Files are named with a prefix specifying the simulation, a middle portion indicating that the file is part of the equilibrated structures, and a suffix specifying the cluster and frame number, mostly for debugging and logging purposes. For example, consider a file named below.

CHARMM_EqStructures.k15_f96324.pdb

This indicates that the frame is from the CHARMM simulations, is an equilibrated structure, representing the 16th k-means cluster (they are numbered starting from 0), and is the 96,324^th frame of the CHARMM simulation.

The files have been extensively commented to indicate where they come from, give a short summary of the system, and detail the shape data at this particular frame.

"Shape_Analysis" Directory

We provide the shape data for each simulation, analyzed at all frames, in a simple CSV files for convenience. Because the curvature data is relatively larger and, as we showed in Ref. 1, not usually necessary and especially not in the case of AOT reverse micelles, we have separated the data into 3 files for each simulation: CPE and convexity data in one CSV file, the mean curvature data in its own CSV file, and the Gaussian curvature data in its own CSV file. Each file is given a suffix as shown below:

• CPE and Convexity data: -.CandC.csv
• mean curvature: -.mean.csv
• Gaussian curvature: -.gauss.csv

For the CandC files, the columns are given by Table 4.

Table 4: Data in each column for the convexity and CPE files (-.CandC.csv)

Data in each column for the CandC files

We remind the user that the curvature is a distribution of values computed over each vertex of the Delauney triangulated surface which results from using the Willard-Chandler algorithm to compute the interface for a given group of atoms. The number of vertices is not constant over time but we generally found it to be somewhere around ~3,000 points. To conserve space, we reduced this to a distribution characterized by 9 percentile values. These values include the median and 25^th and 75^th percentile so that the median and interquartile range can be computed. Columns for the mean curvature files is given by 5.

Table 5: Data in each column for mean curavture files (-.mean.csv)

Columns for the Gaussian curvature files is given by Table 6.

Table 6: Data in each column for Gaussian curvature files (-.gauss.csv)

Simulation Details

System Stoichiometry

The stoichiometry of the reverse micelle is kept constant across all simulations, only changing the force field used to describe the system. The stoichiometry is provided in Table 7.

Table 7: Molecular stoichiometry

The more experimentally relevant or experimentally "preferred" values that this stoichiometry yields are provided on the right in Table 8.

Table 8: Some key values of the reverse micelle

Simulations and Force Fields

The simulations are varied by the force fields used. A full accounting of the details can be found in Ref 3. Non-standard parameters used in this work are provided in a program agnostic format in the supplementary information (SI) attached to Ref 3. The parameters for AOT in GROMACS-style parameter files are provided on the Levinger GitHub page. A brief overview of simulations was provided in Table 2 above.

The CM5 and RESP atomic charges were calculated using the Multiwfn program based on DFT calculations for a single geometry of AOT. As the names imply, the OPLS-CM5 force field uses the CM5 method of computing partial charges, while the OPLS-RESP method uses the restricted electrostatic potential mapping (RESP) method of computing partial charges. Please see Ref. 3 for further details and the appropriate citations.

A reminder that the MDP files are provided as a more complete record of what options were used for the simulations, but a brief overview is provided here. The shape analyses we performed were based on a 1 μs simulation with frames saved every 8 ps. To accomodate calculating the rotational autocorrelation functions of water, a short extension was also performed. This was a 100 ns extension, with frames saved every 0.1 ps. Both simulations were held at a constant 1 bar and 298 K pressure and temperature using a Parrinello-Rahman barostat and velocity-rescale thermostat. Electrostatics were computed using the Particle Mesh Ewald scheme.

Shape Analyses

The shape analyses we used have been extensively documented in Refs 1-3. An example of the code needed to compute these values is provided on the Levinger GitHub page Levinger GitHub page.

References

The simulations presented here have been used in the following manuscripts:

1. Gale, C. D.; Derakhshani-Molayousefi, M.; Levinger, N. E. How To Characterize Amorphous Shapes: The Tale of a Reverse Micelle. J. Phys. Chem. B 2022, 126 (4), 953-963. DOI: 10.1021/acs.jpcb.1c09439
2. Gale, C. D.; Levinger, N. E. Predicting the Geometry of Core-Shell Structures: How a Shape Changes with Constant Added Thickness. J. Phys. Chem. B 2024, 128 (5), 1317-1324. DOI: 10.1021/acs.jpcb.3c07652
3. Gale, C. D.; Derakhshani-Molayousefi, M.; Levinger, N. E. Shape of AOT Reverse Micelles: The Mesoscopic Assembly is More Than the Sum of the Parts. Submitted to J. Phys. Chem. B, 2024, 128 (26), 6410-6421. DOI: 10.1021/acs.jpcb.4c02569

Ref. 1 develops the shape-measuring methods which form the basis of this series of works. Ref. 2 develops a model for how the coordinate-pair eccentricity, one of my shape-measuring methods, is expected to change with size, e.g. as a shell is "grown" onto an arbitrary core, providing a reference for comparison. Ref. 3 uses the methods and ideas developed in the previous references to fully explore the shape of AOT reverse micelles.

Ref. 1 used only the first 100 ns of the CHARMM simulation. Ref. 2 used the full 1 *μ*s of only the CHARMM simulation. Ref. 3 used the full time of all simulations.