DOI: 10.5061/dryad.9w0vt4btn
title: Directing selective solvent presentations at the electrochemical interfaces to enable initially anode-free sodium metal batteries

description: Initially, anode-free sodium metal batteries offer a high energy density
 at lower costs than lithium-ion batteries, making them a promising
 alternative for portable electronics, transportation, and power grids.
 However, side reactions at the electrode/electrolyte interface hinder
 their practical applications. Our study reveals that negative electrode
 stability is primarily influenced by the solvents in the cation’s first
 solvation shell, whereas positive electrode stability is dictated by
 weakly bonded solvents. Based on this insight, we introduce an electrolyte
 design strategy to selectively direct 2-methyltetrahydrofuran to the Na
 metal electrode and tetrahydrofuran to the NaNi1/3Fe1/3Mn1/3O2 positive
 electrode interface, optimizing stability for both electrodes. With this
 tailored electrolyte, we achieve an average Coulombic efficiency of 99.91%
 in Na-Cu cells for 400 cycles at 1 mA/cm2 with 1 mAh/cm2 and demonstrate
 stable Na plating/stripping for 5000 hours at 2 mA/cm2 with 2mAh/cm2 in
 Na-Na cells. Furthermore, an initially anode-free sodium metal battery
 with a positive electrode active material loading of 15.88 mg cm^-2^
 retains 90.9% of its capacity over 150 cycles at 110 mA g^-1^, even after
 aging, underscoring its potential for practical applications.
description: # Directing selective solvent presentations at the electrochemical
 interfaces to enable initially anode-free sodium metal batteries Dataset
 DOI: [10.5061/dryad.9w0vt4btn](10.5061/dryad.9w0vt4btn) ## Description of
 the data and file structure This document outlines the simulation and
 computational methods used in the paper “Directing Selective Solvent
 Presentations at Electrochemical Interfaces to Enable Initially Anode-Free
 Sodium Metal Batteries” to facilitate reproducibility of the reported
 results. All simulations were performed using GROMACS 2021.5 and Python
 3.11.5 ### Files and variables #### File: NC_codes.tar **Description:** 
 Text-based files (‘.gro’, ‘.ndx’, ‘.top’, ‘.itp’, ‘.mdp’, and ‘.xvg’) can
 be opened with standard text readers, while binary files (‘.tpr’, ‘.xtc’)
 require GROMACS to read or run the files.   * ‘.tpr’: Simulation input
 (coordinates, parameters, etc.)   * ‘.ndx’: Index groups of atoms or
 residues   * ‘.top’: System topology and parameters   * ‘.itp’: Modular
 topology components (parameters, atom types, bonds, angles, dihedrals,
 etc.)   * ‘.gro’: System structure (coordinates, atom type, box size)   *
 ‘.xtc’: Compressed trajectory file   * ‘.xvg’: Plot/graph data generated
 by GROMACS built-in functions #### Folder structure   * **analysis** =
 Python scripts for analyzing GROMACS output   * **bash_files** = Bash
 files for job submission (simulation runs and solvation free energy
 calculations)   * **force_fields** = Parameter files that define the force
 field of each molecule   * **MDP** = MDP files (energy minimization
 (**'em_steep.mdp'**), NVT and NPT equilibrations
 (**'nvt.mdp'** and **'npt.mdp'**), MD production
 (**'md.mdp'**), and a Perl script to create .mdp files for each
 lambda state (**'write_mdp.pl'**)) for standard simulation runs
   * **MDP_solv** = MDP files (energy minimization
 (**'em_steep.mdp'**), NVT and NPT equilibrations
 (**'nvt.mdp'** and **'npt.mdp'**), MD production
 (**'md.mdp'**), and a Perl script to create .mdp files for each
 lambda state (**'write_mdp.pl'**)) for solvation free energy
 calculations   * **packmol_files** = Packmol scripts and corresponding
 input/output for system generation      * **input_pdbs** = GROMACS input
 files (.pdb)      * **output_pdbs** = GROMACS output files (.pdb)      *
 **scripts** = Packmol scripts to generate systems   * **Replicate 1** =
 GROMACS input/output files for replicate 1      * **55TM18** = All
 simulation input/output files for 1.8M NaPF~6~ in THF/2-MeTHF (5:5) system
         * **equil** = GROMACS output files for energy minimization, NVT,
 and NPT equilibration steps         * **Lambda_nas** = GROMACS output
 files from Na^+^ solvation free energy calculations in multi-ion systems,
 named **Lambda_nas_0** through **Lambda_nas_25** (for each λ state)      
      * **EM** = GROMACS output files for energy minimization at each λ
 state (0–25)            * **NPT** = GROMACS output files for NPT
 equilibration at each λ state (0–25)            * **NVT** = GROMACS output
 files for NVT equilibration at each λ state (0–25)            *
 **Production_MD** = GROMACS output files for production runs at each λ
 state (0–25)         * **Lambda_pf6** = GROMACS output files from PF~6~^-^
 solvation free energy calculations in multi-ion systems,
 named **Lambda_pf6_0** through **Lambda_pf6_25** (for each λ state)      
      * **EM** = GROMACS output files for energy minimization at each λ
 state (0–25)            * **NPT** = GROMACS output files for NPT
 equilibration at each λ state (0–25)            * **NVT** = GROMACS output
 files for NVT equilibration at each λ state (0–25)            *
 **Production_MD** = GROMACS output files for production runs at each λ
 state (0–25)         * **md_nas** = .xvg output files from
 the **'Production*_*MD'** directories for each λ state (0–25),
 collected for Na^+^ solvation free energy analysis with *gmx bar*        
 * **md_pf6** = .xvg output files from the **'Production*_*MD'**
 directories for each λ state (0–25), collected for PF~6~^-^ solvation free
 energy analysis with *gmx bar*      * **Bulk** = GROMACS input/output
 files for single-ion and bulk systems         * **Bulk_55TM18** = All
 simulation input/output files for the THF/2-MeTHF (5:5) system, containing
 either one Na^+^, one PF~6~^-^, or the bulk system)            * **equil**
 = GROMACS output files for energy minimization, NVT, and NPT equilibration
 steps            * **Lambda_nas** = GROMACS output files from Na^+^
 solvation free energy calculations in single-ion systems,
 named **Lambda_nas_0** through **Lambda_nas_25** (for each λ state)      
         * **EM** = GROMACS output files for energy minimization at each λ
 state (0–25)               * **NPT** = GROMACS output files for NPT
 equilibration at each λ state (0–25)               * **NVT** = GROMACS
 output files for NVT equilibration at each λ state (0–25)               *
 **Production_MD** = GROMACS output files for production runs at each λ
 state (0–25)            * **Lambda_pf6** = GROMACS output files from
 PF~6~^-^ solvation free energy calculations in single-ion systems,
 named **Lambda_pf6_0** through **Lambda_pf6_25** (for each λ state)      
         * **EM** = GROMACS output files for energy minimization at each λ
 state (0–25)               * **NPT** = GROMACS output files for NPT
 equilibration at each λ state (0–25)               * **NVT** = GROMACS
 output files for NVT equilibration at each λ state (0–25)               *
 **Production_MD** = GROMACS output files for production runs at each λ
 state (0–25)            * **md_nas** = .xvg output files from
 the **'Production*_*MD'** directories for each λ state (0–25),
 collected for Na^+^ solvation free energy analysis with *gmx bar*        
    * **md_pf6** = .xvg output files from
 the **'Production*_*MD'** directories for each λ state (0–25),
 collected for PF~6~^-^ solvation free energy analysis with *gmx bar*      
      * **vacuum** = GROMACS input/output files of each solvent system used
 for solvation free energy corrections               * **equil** = GROMACS
 output files for energy minimization, NVT, and NPT equilibration steps
 \***Note: Only the folder structure for Replicate 1 (55TM18) is shown here
 in detail as an example. The corresponding directories in other replicates
 and systems (Replicate 2, 37TM18, 73TM18, M1, T18) follow the same nested
 structure and naming conventions.*   * **Replicate 2** = GROMACS
 input/output files for replicate 2 ###### Abbreviations   * **THF** =
 tetrahydrofuran   * **2-MeTHF** = 2-methyltetrahydrofuran   * **CIP** =
 Contact Ion Pairs   * **SSIP** = Solvent-Separated Ion Pairs   * **AGGs**
 = Aggregates   * **NAS** = Na^+^   * **MTR** = 2-MeTHF-R   * **MTS** =
 2-MeTHF-S \***Note on software: Some files (e.g., .log) are output logs
 generated by GROMACS. These are provided for reproducibility. The GROMACS
 software itself is not included in this dataset.* ## Code/software **1.**
 **Multi-ion systems** This directory contains all simulation input and
 output files for the five systems described in the paper   * 1.8M NaPF~6~
 in THF/2-MeTHF (3:7) in *37TM18*   * 1.8M NaPF~6~ in THF/2-MeTHF (5:5) in
 *55TM18*   * 1.8M NaPF~6~ in THF/2-MeTHF (7:3) in *73TM18*   * 1.0M
 NaPF~6~ in 2-MeTHF in *M1*   * 1.8M NaPF~6~ in THF in *T18* The script
 **‘run_sims.sh’** is provided, which conducts all equilibration and
 production MD steps to prepare initial configurations for further analysis
 using MDtraj The scripts **‘fep_nas.sh’** and **‘fep_pf6.sh’** are
 provided, which conduct the solvation free energy calculations for
 multi-ion systems **2.** **Single-ion systems** This directory contains
 all simulation input and output files for the five systems described in
 the paper   * 1 Na^+^ or 1 PF~6~^-^ in THF/2-MeTHF (3:7) in *37TM18*   * 1
 Na^+^ or 1 PF~6~^-^ in THF/2-MeTHF (5:5) in *55TM18*   * 1 Na^+^ or 1
 PF~6~^-^ in THF/2-MeTHF (7:3) in *73TM18*   * 1 Na^+^ or 1 PF~6~^-^ in
 2-MeTHF in *M1*   * 1 Na^+^ or 1 PF~6~^-^ in THF in *T18* The scripts
 **‘fep_nas.sh’** and **‘fep_pf6.sh’** are provided, which include the
 solvation free energy calculations for single-ion systems **3.** **Bulk
 systems** This directory contains all simulation input and output files
 for the five systems described in the paper   * THF/2-MeTHF (3:7) in
 *37TM18*   * THF/2-MeTHF (5:5) in *55TM18*   * THF/2-MeTHF (7:3) in
 *73TM18*   * 2-MeTHF in *M1*   * THF in *T18* The script **‘run_sims.sh’**
 is provided, which conducts all equilibration and production MD steps to
 prepare initial configurations for the solvation free energy corrections
 **4.** **Trajectory analysis scripts and data** The following are provided
 to aid with the reproducibility of Figures in the main text and
 Supplementary Information: **Figs. 2d, 2f, S6, S7, and S8** --&gt;
 **‘contact_type.py’** \* Calculates the number of P atoms of each contact
 type (SSIP, CIP, AGG, and weakly bonded solvent) \* Calculates the ratio
 of THF and 2-MeTHF in each solvation shell (SSIP, CIP, AGG) using a cutoff
 distance \* Identifies the type of solvent (THF or 2-MeTHF) around the P
 atom in each contact type \* The cutoff distances are set to 0.5, 0.5,
 0.4, 0.5, and 0.6 nm for Figs. 2d, 2f, S6 S7, and S8, respectively **Fig.
 S22** --&gt; **‘split.py’**_**‘plot_int.py’** \* Extracts md*.xvg files
 for cumulative simulation intervals (0–0.5 ns, 0–1.0 ns, …, 0–5.0 ns)
 using **‘split.py’** \* Runs *gmx bar* on md*.xvg of each interval to
 produce bar.xvg and bar_int.xvg \* Reads each bar_int.xvg file, extracts
 the value at λ = 25, and plots it as a function of sampling time to assess
 convergence using **‘plot_int.py’** **Fig. S25a** --&gt;
 **‘converge_p.py’** \* Calculates the percentage of each Na-P contact type
 (SSIP, CIP, AGG) as a function of simulation time, averaging results over
 two replicates **Fig. S25b** --&gt; **‘converge_o.py’** \* Calculates the
 Na-O coordination number as a function of simulation time, averaging
 results over two replicates