Resonant Soft X-ray Scattering Reveals the Distribution of Dopants in Semicrystalline Conjugated Polymers
Data files
Jan 08, 2025 version files 83.10 GB
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Atomic_Force_Microscopy_(AFM).zip
5.65 MB
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Computational_Polarized_Resonant_Soft_X-Ray_Scattering_(P-RSoXS).zip
61.33 GB
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DopantModeling.yml
10.82 KB
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Experimental_Polarized_Resonant_Soft_X-Ray_Scattering_(P-RSoXS).zip
14.56 GB
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Grazing_Incidence_Wide_Angle_X-Ray_Scattering_(GIWAXS).zip
858.40 MB
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Near-Edge_X-Ray_Absorbance_Fine_Structure_(NEXAFS).zip
6.35 GB
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README.md
22.29 KB
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UV_Vis_Spectroscopy.zip
263.53 KB
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X-Ray_Photoelectron_Spectroscopy_(XPS).zip
1.56 MB
Abstract
The distribution of counterions and dopants within electrically doped semicrystalline conductive polymers, such as poly(3-hexylthiophene-2,5-diyl) (P3HT), plays a pivotal role in charge transport. The distribution of counterions in doped films of P3HT with controlled crystallinity was examined using polarized resonant soft X-ray scattering (P-RSoXS). The changes in scattering of doped P3HT films containing trifluoromethanesulfonimide (TFSI−) and 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ•−) as counterions to the charge carriers revealed distinct differences in their nanostructure. The scattering anisotropy of P-RSoXS from doped blends of P3HT was examined as a function of the soft X-ray absorption edge and found to vary systematically with the composition of crystalline and amorphous domains and by the identity of the counterion. A computational methodology was developed and used to simulate the soft X-ray scattering as a function of morphology and molecular orientation of the counterions. Modeling of the P-RSoXS at N and F K-edges was consistent with a structure where the conjugated plane of F4TCNQ•− aligns perpendicularly to that of the P3HT backbone in ordered domains. In contrast, TFSI− was distributed more uniformly between domains with no significant molecular alignment. The approach developed here demonstrates the capabilities of P-RSoXS in identifying orientation, structural, and compositional distributions within doped conjugated polymers using a computational workflow that is broadly extendable to other soft matter systems.
README: Resonant Soft X-ray Scattering Reveals the Distribution of Dopants in Semicrystalline Conjugated Polymers
https://doi.org/10.5061/dryad.6t1g1jx65
Description of the data and file structure
This work focuses on the analysis of Polarized Resonant Soft X-Ray Scattering (P-RSoXS) from a conjugated polymer, poly(3-hexylthiophene-2,5-diyl) (P3HT), doped with two distinct small molecules: trifluoromethanesulfonimide (TFSI⁻) and 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ•⁻). A digital twin of the material system was developed to simulate the P-RSoXS experiments. To support the model's development, various physical characterization methods were employed, including Atomic Force Microscopy (AFM) to assess sample surface morphology, Grazing Incidence Wide Angle X-Ray Scattering (GIWAXS) to determine crystal orientation distribution, UV-vis spectroscopy to evaluate sample crystallinity, and X-Ray Photoelectron Spectroscopy (XPS) to analyze chemical composition.
Analysis code, provided in Jupyter notebooks, parses data, performs analyses, and generates plots featured in the article and/or inputs for modeling software. Additional model inputs, such as complex refractive indices, inform how the material interacts with X-rays. Scripts for simulating refractive indices and corresponding Jupyter notebooks for analysis are provided. Custom software and scripts to construct the models and simulate the resultant scattering are provided. Finally, Jupyter notebooks for analyzing the experimental and simulated P-RSoXS in an identical manner are provided, facilitating direct comparisons as detailed in the corresponding article.
Files and variables
File: UV_Vis_Spectroscopy.zip
Description:
Subfolder(s):
- Figure 2 Crystallinity Versus P3HT Blend Composition
- Contains
.csv
files of UV-vis absorbance spectra (absorbance and wavelength in nm) for various P3HT blend formulations. This data is used to generate Figure 2 in the article. A Jupyter notebook (Spano_Model_Fitting.ipynb
) parses the data, calculates blend crystallinities, and generates the plot shown in Figure 2.
- Contains
File: X-Ray_Photoelectron_Spectroscopy_(XPS).zip
Description:
All .xlsx
and .xls
files were exported directly from XPS instrument software (Thermo Scientific Avantage 5.9925).
Subfolder(s):
Figure 3 Dopant Concentration Versus P3HT Blend Composition
- Depth profile data includes etch time (s) and atomic percent (%) for analyzed elements. The Jupyter notebook (
Dopant_Quantification_From_XPS.ipynb
) parses the data and produces the plot shown in Figure 3.
- Depth profile data includes etch time (s) and atomic percent (%) for analyzed elements. The Jupyter notebook (
Figure S2 XPS Depth Profile of LiTFSI Exchanged, 100% Regioregular P3HT Film
- Contains survey spectra data, with intensity (counts/s) as a function of binding energy (eV) and etch time (s). The Jupyter notebook (
XPS_Depth_Profile_of_LiTFSI_Exchanged_100pct_Regioregular_P3HT_Film.ipynb
) parses the data and generates the plot shown in Figure S2.
- Contains survey spectra data, with intensity (counts/s) as a function of binding energy (eV) and etch time (s). The Jupyter notebook (
Figure S3 Quantified XPS Depth Profile of F4TCNQ Vapor Doped P3HT
- Depth profile data includes etch time (s) and atomic percent (%) for analyzed elements. The Jupyter notebook (
F4TCNQ_Vapor_Doping_Penetration_Depth.ipynb
) parses the data and generates the plots shown in Figure S3.
- Depth profile data includes etch time (s) and atomic percent (%) for analyzed elements. The Jupyter notebook (
Figure S4 Quantified XPS Depth Profile of Doped, TFSI- Anion Exchanged P3HT
- Depth profile data includes etch time (s) and atomic percent (%) for analyzed elements. The Jupyter notebook (
TFSI_Anion_Exchange_Penetration_Depth.ipynb
) parses the data and generates the plots shown in Figure S4.
- Depth profile data includes etch time (s) and atomic percent (%) for analyzed elements. The Jupyter notebook (
Figure S6 XPS Survey Spectra of F4TCNQ Surface Layer on P3HT
- Contains survey spectra data, with intensity (counts/s) as a function of binding energy (eV) and etch time (s). The Jupyter notebook (
Dopant_Quantification_From_XPS.ipynb
) parses the data and produces the plot shown in Figure S6.
- Contains survey spectra data, with intensity (counts/s) as a function of binding energy (eV) and etch time (s). The Jupyter notebook (
File: Atomic_Force_Microscopy_(AFM).zip
Description:
Contains .ibw
files used to generate the figures indicated by subfolder names. AFM data from the .ibw
files were visualized with Gwyddion, an open-source software for data visualization and analysis.
Subfolder(s):
- Figure S1 Atomic Force Microscopy of Least and Most Crystalline P3HT Blend
- Figure S5 Atomic Force Microscopy of F4TCNQ Vapor-Doped and TFSI- Anion Exchanged Films
File: Grazing_Incidence_Wide_Angle_X-Ray_Scattering_(GIWAXS).zip
Description:
Folder(s):
- Doped Blends
- Contains GIWAXS data for various P3HT blends doped with TFSI⁻ or F4TCNQ•-. Each blend includes three GIWAXS datasets corresponding to grazing incidence angles of 0.1°, 0.05°, and 0.13°. Each dataset contains a
.tif
file and a.txt
metadata file, following the naming convention:{Sample_ID}_{incidence_angle}_{exposure_time}_{beamline-generated_ID}_0001.tif
.
- Contains GIWAXS data for various P3HT blends doped with TFSI⁻ or F4TCNQ•-. Each blend includes three GIWAXS datasets corresponding to grazing incidence angles of 0.1°, 0.05°, and 0.13°. Each dataset contains a
- lab6_cal
- Contains GIWAXS data for LaB6 at an incidence angle of 3° (rocked continuously by 0.5°) with an exposure time of 10 seconds. This dataset is used as a reference for determining beam center and sample-to-detector distance.
- Neutral_Blends
- Similar structure to "Doped Blends," containing GIWAXS data for undoped P3HT blends.
- Processed_Datasets
- Contains
.nc
(NetCDF) files with processed GIWAXS data outputs, generated using the Jupyter notebookGIWAXS_Analysis.ipynb
.
- Contains
File(s):
- GIWAXS_Analysis.ipynb
- Utilizes GIWAXS_Tools to import, analyze, and process GIWAXS data from the SSRL 11-3 beamline instrument. Outputs are saved as
.nc
files in the "Processed_Datasets" folder. Parts or all of Figure S7, Figure S8, and Figure S11 are generated by this notebook.
- Utilizes GIWAXS_Tools to import, analyze, and process GIWAXS data from the SSRL 11-3 beamline instrument. Outputs are saved as
File: Near-Edge_X-Ray_Absorbance_Fine_Structure_(NEXAFS).zip
Description:\
Folder(s):
- Optical Constants Database P3HT
- "P3HT_db" is a folder containing experimentally derived absorbance spectra for P3HT at the C K-edge, provided in both
.txt
and.csv
formats. - The Jupyter notebook (
kkcalc_P3HT_C_K_Edge_Calculation.ipynb
) processes the absorbance spectra by (1) normalizing to the bare atom scattering factors pre- and post-edge, (2) re-normalizing to absorbance, (3) calculating reflectance, and (4) saving the outputs as.txt
files in the same directory. - Additional Jupyter notebooks (
kkcalc_P3HT_F_K_Edge_Calculation.ipynb
andkkcalc_P3HT_N_K_Edge_Calculation.ipynb
) calculate the expected absorbance and reflectance for other relevant edges, saving results to.txt
files.
- "P3HT_db" is a folder containing experimentally derived absorbance spectra for P3HT at the C K-edge, provided in both
- Avogadro_Structures
- This folder contains
.cml
files generated using Avogadro, a molecular visualization software. These files represent the 3D structures of dopant molecules. The atom positions in these.cml
files were used as starting inputs for Quantum Espresso relaxation calculations.
- This folder contains
- mbxas_spectra
- This folder contains output files from MBXAS, a tool for calculating X-ray absorbance spectra. The Jupyter notebook (
mbxas_plotting.ipynb
) processes these output files to generate plots of absorbance spectra and saves the plots as.tiff
files. Results are included for F4TCNQ, KTFSI, and NaTFSI. These results are supplementary to X-ray absorbance spectra calculated using the XSpectra module of Quantum Espresso and are not used for results presented in the corresponding article main text.
- This folder contains output files from MBXAS, a tool for calculating X-ray absorbance spectra. The Jupyter notebook (
- Quantum_ESPRESSO_HPC
- Contains input and output files for calculating electronic configurations for various unit cells of different chemical species and core-hole configuration-specific absorbance spectra.
- Folder(s):
- Pseudopotentials
- Contains original pseudopotential files (from the SSSP Efficiency Library) and custom core-hole pseudopotential files. Core-hole pseudopotentials were created by modifying the original pseudopotential inputs and regenerating
.UPF
files using Quantum Espresso'sld1.x
module. These files are required for X-ray absorbance spectrum calculations.
- Contains original pseudopotential files (from the SSSP Efficiency Library) and custom core-hole pseudopotential files. Core-hole pseudopotentials were created by modifying the original pseudopotential inputs and regenerating
- F4TCNQ
- Configuration files for neutral F4TCNQ (not used in the corresponding article). Includes folders named "Relaxation" with input files (
.in
), bash scripts (job.s
) for SLURM submission, and output files reporting relaxed atomic positions. Also includes subfolders for X-ray absorbance spectra calculations at the C, N, and F K-edges, with Python scripts (generate_*_input_files.py
) to generate SCF and XSpectra input files, bash scripts for job submission to SLURM, and output files. The following subfolders in this section have the same structure.
- Configuration files for neutral F4TCNQ (not used in the corresponding article). Includes folders named "Relaxation" with input files (
- Reduced_F4TCNQ
- Configuration and output files for NEXAFS calculations of F4TCNQ•- (used in the corresponding article).
- TFSI
- Configuration and output files for NEXAFS calculations of TFSI- (not used in the corresponding article).
- TFSI_2
- Configuration and output files for NEXAFS calculations of TFSI- (used in the corresponding article).
- P3HT_3
- Configuration and output files for NEXAFS calculations of four π-stacked 8-mers of 3-hexylthiophene (3HT), sampling only the Γ-point.
- P3HT_4
- Configuration and output files for NEXAFS calculations of four π-stacked 8-mers of 3HT, sampling a 2×2×2 k-point grid.
- P3HT_5
- Configuration and output files for NEXAFS calculations of a non-π-stacked 8-mer of 3HT, sampling only the Γ-point (used in the main text of the corresponding article).
- P3HT_6
- Configuration and output files for NEXAFS calculations of a non-π-stacked 8-mer of 3HT, sampling a 2×2×2 k-point grid.
- Jupyter_Notebooks
- Contains Jupyter notebooks for parsing XSpectra output files, performing calculations (normalization, reflectance, contrast), and generating plots for the corresponding article.
- File(s):
Simulated_2x2x2k_P3HT_C_K_Edge_Refractive_Indices.ipynb
- Parts or all of Figure S13 are generated by this notebook.
Simulated_F4TCNQ_C_K_Edge_Refractive_Indices.ipynb
- Parts or all of Figure S15 and Figure S25 are generated by this notebook.
Simulated_F4TCNQ_F_K_Edge_Refractive_Indices.ipynb
- Parts or all of Figure S17 and Figure S27 are generated by this notebook.
Simulated_F4TCNQ_N_K_Edge_Refractive_Indices.ipynb
- Parts or all of Figure S16 and Figure S26 are generated by this notebook.
Simulated_P3HT_C_K_Edge_Refractive_Indices.ipynb
- Parts or all of Figure 4, Figure 7, Figure S5, Figure S12, and Figure S24 are generated by this notebook.
Simulated_P3HT_S_K_Edge_Refractive_Indices.ipynb
- Parts or all of Figure S14 are generated by this notebook.
Simulated_Pi_Stacked_2x2x2k_P3HT_C_K_Edge_Refractive_Indices.ipynb
- Parts or all of Figure S11 are generated by this notebook.
Simulated_Pi_Stacked_P3HT_C_K_Edge_Refractive_Indices.ipynb
- Parts or all of Figure S10 are generated by this notebook.
Simulated_Reduced_F4TCNQ_C_K_Edge_Refractive_Indices.ipynb
- Parts or all of Figure S18 and Figure S28 are generated by this notebook.
Simulated_Reduced_F4TCNQ_F_K_Edge_Refractive_Indices.ipynb
- Parts or all of Figure S20 and Figure S30 are generated by this notebook.
Simulated_Reduced_F4TCNQ_N_K_Edge_Refractive_Indices.ipynb
- Parts or all of Figure S19 and Figure S29 are generated by this notebook.
Simulated_TFSI_C_K_Edge_Refractive_Indices.ipynb
- Parts or all of Figure S21 and Figure S31 are generated by this notebook.
Simulated_TFSI_F_K_Edge_Refractive_Indices.ipynb
- Parts or all of Figure S23 and Figure S33 are generated by this notebook.
Simulated_TFSI_N_K_Edge_Refractive_Indices.ipynb
- Parts or all of Figure S22 and Figure S32 are generated by this notebook.
- kkcalc
- Local copy of kkcalc, used for calculating complex refractive indices from NEXAFS. Dependency for notebooks in "Jupyter_Notebooks".
File: Experimental Polarized Resonant Soft X-Ray Scattering (P-RSoXS).zip
Description:\
Folder(s):
- SST-1 September 2022 RSoXS Data
- Contains subfolders with raw P-RSoXS datasets generated by the SST-1 beamline instrument. Data is in the native output format of the beamline instrument, optimized for parsing with PyHyperScattering.
- Processed_Experimental_Datasets
- Contains
.nc
files that are outputs from the batch analysis performed inPyHyperScattering_Batch_Processing.ipynb
. These files are used for further processing and plot generation.
- Contains
File(s):
Mosaic_Figures.ipynb
- Reads
.nc
files in "Processed_Experimental_Datasets" to generate various plots. Parts or all of Figure 6, Figure 9, Figure 10, and Figure S35 - Figure S39 and are generated by this notebook.
- Reads
PyHyperScattering_Batch_Processing.ipynb
- Uses PyHyperScattering to batch process P-RSoXS datasets output by the SST-1 beamline. Saves processed data to "Processed_Experimental_Datasets" as
.nc
files.
- Uses PyHyperScattering to batch process P-RSoXS datasets output by the SST-1 beamline. Saves processed data to "Processed_Experimental_Datasets" as
PyHyperScattering_Single_Processing.ipynb
- Uses PyHyperScattering to import P-RSoXS data files and perform detailed analysis on individual scans. Parts or all of Figure 4, Figure 7, and Figure S34 are generated by this notebook.
SST1_Nov2022_WAXS_mask.hdf
- Mask file created using Nika, an open-source software for analyzing X-ray scattering data in Igor Pro. Used in
PyHyperScattering_Batch_Processing.ipynb
andPyHyperScattering_Single_Processing.ipynb
to exclude specific regions of the X-ray scattering detector during analysis.
- Mask file created using Nika, an open-source software for analyzing X-ray scattering data in Igor Pro. Used in
File: Computational_Polarized_Resonant_Soft_X-Ray_Scattering_(P-RSoXS).zip
Description:
- Subfolder(s):
- Simulation_Outputs
- Contains P-RSoXS simulation files, including Python scripts for setting up and running CyRSoXS simulations.
- Subfolders include "full_sims", "full_sims_dopant_x0p8", "full_sims_dopant_x1p2", "full_sims_polymer_x0p8", and "full_sims_polymer_x1p2". These subfolders contain simulation files which use distinct refractive indices for dopants or polymers, scaled by 0.8 or 1.2 to simulate ±20% changes in dopant concentration or polymer density. Further subfolders within each are "C_1s", "F_1s", and "N_1s". These contain simulations performed at the C, F, and N K-edges, respectively.
cyrsoxs.{instance_id}.out
files are log files generated to capture console outputs when run on High Performance Computing (HPC) nodes.{instance_id}
is a numerical ID generated by the system.- There are further subfolders "C_1s", "F_1s", and "N_1s", which are specific to the elemental edge at which the simulations within are carried out.
- Within each elemental edge subfolder,
params.py
andrun.py
files are included to set up and run the CyRSoXS simulations. Theparams.py
file contains user-specified parameters used by DopantModeling for morphology generation. Therun.py
script sweeps over different simulation parameters, including the center-to-center distance of fibrils, the type of dopant, the distribution of dopant across P3HT crystalline/amorphous domains, and the orientation of the dopant relative to the polymer, and uses NRSS to run the simulation. - The simulation outputs are saved in nested directories which follow the parameter sweep structure. Key files and outputs include:
params.py
,run.py
: Setup and execute simulations with parameter sweeps over fibril spacing, dopant type, dopant distribution, and dopant orientation.- "HDF5" folder: Contains
.h5
simulation output files, parsed using PyHyperScattering. - "0_reduced"-prefixed folder: Contains plots of processed data, generated by
PyHyperScattering_Batch_CyRSoXS.ipynb
. config.txt
,CyRSoXS.log
: Metadata files for simulation configuration and execution details.mat*_checkH5.png
: Morphology visualizations for vacuum, crystalline P3HT, amorphous P3HT, and dopants. These plots are generated by NRSS as an optional check that models are generated as expected.Material*.txt
: Contain energy- and orientation-dependent refractive indices for vacuum, crystalline P3HT, amorphous P3HT, and dopants.parameters_doped.txt
,parameters_undoped.txt
: Metadata on model properties before and after dopant addition.
- Simulation_Results
- Contains analyzed simulation results in
.nc
format, created byPyHyperScattering_Batch_CyRSoXS.ipynb
. Note that "C_1s_10_c2c_single", "best_match_10_c2c", "*_F4TCNQ_orientation_10_c2c", and "theta_orientation" folders were created manually and individual.nc
files were copied within from other folders. These folders are used for generating plots in Figure 7, Figure 9, Figure 10, and Figure S9, respectively. - Folders have name nomenclature as
{elemental edge}_{polymer/dopant}_{x0p8/x1p2}_{center-to-center distance}
.{elemental edge}
refers to the elemental edge at which those simulations were performed.{polymer/dopant}_{x0p8/x1p2}
refers to the specific set of refractive indices used in those simulations. For example, "polymer_x0p8" would refer to using P3HT refractive indices that have been scaled by 0.8. Similar interpretation can be applied to other folder names. The corresponding refractive indices can be found in...\Computational Polarized Resonant Soft X-Ray Scattering (P-RSoXS)\DopantModeling\data
.{center-to-center distance}
refers to the distance between fibrils in the model and correlates with the model's mole fraction crystallinity.
.nc
files have the naming convention{elemental edge}_{CMF}_{dopant}_{dopant orientation}_{CDF/uniform}.nc
.{elemental edge}
refers to the elemental edge at which those simulations were performed.{CMF}
(Crystalline Mole Fraction): Refers to the mole fraction of crystalline P3HT in the model before the addition of dopants. This parameter reflects the initial crystallinity of the polymer matrix.{dopant}
Specifies the type of dopant in the model. Examples include:Reduced_F4TCNQ_C_Kedge
: F4TCNQ•⁻ dopant.TFSI_2_C_Kedge
: TFSI⁻ dopant.vacuum
: Represents an undoped or empty system.
{dopant orientation}
: Describes the alignment of the dopant relative to crystalline P3HT within the same voxel. Possible orientations include:- ISO (isotropic): Dopants are randomly oriented.
- ISO_S0: Dopants are randomly oriented with an alignment parameter (S) of 0, indicating no preferred alignment.
- PAR (parallel): Dopants are aligned parallel to the crystalline P3HT.
- PERP (perpendicular): Dopants are aligned orthogonally to the crystalline P3HT.
{CDF/uniform}
(crystalline dopant fraction or uniform): Refers to the distribution of dopants in the simulation:- CDF (Crystalline Dopant Fraction): Describes the mole fraction of total dopant within voxels that contain crystalline P3HT.
- uniform: Indicates that dopants are evenly distributed across the entire morphology, regardless of crystalline regions.
- File(s):
PyHyperScattering_Batch_CyRSoXS.ipynb
- Parses simulation outputs in "Simulation_Outputs", analyzes the data, and saves results to "Simulation_Results" in
.nc
format. Generates plots saved in "0_reduced"-prefixed folders and creates subfolders for analyzed data. Parts or all of Figure 7, Figure 9, Figure 10, Figure S9, and Figure S40 - Figure S60 are generated by this notebook.
File: DopantModeling.yml
Description: DopantModeling.yml
contains the specifications for the Python environment used to perform modeling, data analysis, and visualization related to this study. This environment was created and managed using Conda.
Code/software
- NIST RSoXS Simulation Suite (NRSS) 0.1.0: Used to simulate P-RSoXS data. This includes CyRSoXS, a virtual RSoXS beamline instrument.
- PyHyperScattering v0.2.3: Used to parse experimental P-RSoXS data files.
- DopantModeling v1.0.0: A custom tool developed specifically for this work to generate input models for CyRSoXS simulations.
- Quantum ESPRESSO v.6.8:
- PWscf module: Used for atomic position relaxation and subsequent SCF calculations to obtain core-hole configuration-specific electronic configurations.
- XSpectra module: Used to calculate X-ray absorbance spectra for specific core-hole configurations.
- GIWAXS_Tools v1.0.0: Used for analyzing GIWAXS data and calculating P3HT (020) orientational distributions.
- kkcalc 0.7.5: Used for normalizing calculated X-ray absorbance spectra to absorbance and calculating reflectance using the Kramers-Kronig relations.
- Gwyddion: Used for plotting AFM data.
- Nika: Used for creating mask files for regions of the P-RSoXS X-ray detector.
- Avogadro: Used for initial 3D visualization and atomic coordinates of dopant molecules prior to relaxation calculations.
- MBXAS: Used for supplementary calculation of X-ray absorbance spectra. Available through the Molecular Foundry at Lawrence Berkeley National Laboratory.
Additional Code
- The remaining scripts and workflows used for data parsing, analysis, and plotting are provided within Jupyter notebooks. These are described in detail in the Files and Variables section of this README.
Access information
Other publicly accessible locations of the data:
- P3HT refractive indices are available through the Optical-Constants-Database
- Pseudopotential files are available through the SSSP Efficiency Library
Methods
Materials and Processing Conditions. Low number-average molecular mass regioregular (RRe) P3HT [4.5 kg/mol, dispersity (Đ) = 1.6], high molecular mass RRe P3HT (23 kg/mol, Đ = 1.8), and regiorandom (RRa) P3HT (16.3 kg/mol, Đ = 2.5) (Figure 2), were dissolved in an equal-volume mixture of chlorobenzene and dichlorobenzene. P3HT solutions of varying blend composition were drop cast onto substrates to form (700 to 1000) nm thick films. P3HT films were doped in an inert nitrogen glovebox atmosphere, enclosing the film and ≈3 mg of F4TCNQ crystals within a jar in the orientation depicted in Figure 3.36 The jar was heated to 200 °C for 45 min, allowing for sublimation of F4TCNQ to oxidize the P3HT film. TFSI−-containing samples were formed by anion exchange from immersion in a concentrated LiTFSI solution (0.03 mass fraction in acetonitrile) for 120 min at 60 °C. Table S1 in the corresponding article summarizes the varying P3HT blend compositions utilized in this study, resultant levels of aggregation, and dopant counterion concentrations.
Atomic Force Microscopy. An Asylum MFP-3D atomic force microscope was used in tapping mode to examine the surface roughness of the P3HT blend films. The AFM tip was a silicon cantilever with a resonance frequency of approximately 61 kHz and a spring constant of about 1.6 N/m.
UV−Vis Absorbance Spectroscopy. All ultraviolet−visible (UV−vis) spectra were acquired using an Agilent Technologies Cary 60 UV−vis spectrometer. Samples were drop cast from solution onto quartz substrates to form optically transparent films. Spectra for P3HT films of varying composition were fit to the Spano model via a custom Python script to quantify aggregate mole fractions.
X-ray Photoelectron Spectroscopy. X-ray photo-electron spectroscopy (XPS) measurements were performed using an Escalab Xi+ Spectrometer from ThermoFisher Scientific. The spectrometer operated under a high vacuum condition of 10−6 Pa and utilized a monochromatic aluminum Kα X-ray source. To stabilize charge during the measurements, we used a dual ion-electron low-energy flood source. For acquiring survey spectra, we set the pass energy to 100 eV and conducted five scans at intervals of 0.25 eV, each with a dwell time of 50 ms. Depth profiling was done using an ion gun with a 1000-atom Ar+ cluster and an ion energy of 6000 eV. Ion sputtering covered a square region measuring (1.5 × 1.5) mm2. Within this area, we collected photoexcited electrons from the inner (400 × 400) μm2 region to selectively isolate signal from crater centers. All spectra are presented in the Supporting Information along with an AFM images of the topography of the films.
Grazing Incidence Wide Angle X-ray Scattering. Grazing incidence wide-angle X-ray scattering (GIWAXS) was performed at the BioPACFIC MIP user facilities at UC Santa Barbara and experimental station 11-3 at the Stanford Synchrotron Radiation Lightsource. Angle-resolved GIWAXS scans were acquired with 120 s exposures at grazing incidence angles of 0.05°, 0.10°, and 0.13° using an X-ray energy of 12.7 keV. 2D detector images were remapped to q-space using Nika and the WAXSTools Igor packages. Partial pole figure analysis was done using GIWAXS_Tools, a custom open-source software.
Resonant Soft X-ray Scattering. Polarized resonant soft X-ray scattering (P-RSoXS) experiments were performed at the Spectroscopy Soft and Tender (SST-1) beamline funded and operated by the National Institute of Standards and Technology (NIST) at the National Synchrotron Light Source II (NSLS-II). Data reduction was performed using PyHyperScattering, an open source package for hyperspectral scattering reduction and analysis. Thin film samples on transparent silicon nitride windows were mounted normal to the incident X-ray beam with samples measured in transmission mode under high vacuum conditions.
Computation of Near Edge X-ray Absorption Fine Structure. Near edge X-ray absorption fine structure (NEXAFS) simulations were carried out using the PWscf and XSpectra software packages of the Quantum ESPRESSO distribution. The simulation process consists of (1) sourcing equilibrated or equilibrating atomic coordinates for a given molecule, (2) obtaining the electronic structure for each core-hole configuration of the molecule, and calculating the polarization-dependent X-ray absorbance spectra for each core-hole configuration. The configuration-specific spectra are offset by their relative total energies. The sum of spectra for each polarization direction are offset to experimental absorption onsets (e.g., the C 1s → π*C=C peak measured at 285.25 eV) to obtain oriented NEXAFS. The NEXAFS are normalized to the bare atom scattering factors to obtain the imaginary component of the refractive indices, β, which can be used to solve for the real portion, δ, using the Kramers−Kronig relations. To calculate P3HT NEXAFS, atomic coordinates for unit cells of low-energy crystalline polymorphs of P3HT were sourced from literature. We adopt the approach of using a supercell consisting of 3-hexylthiophene 8-mer with periodic boundary conditions to represent a single polymer chain. This is consistent with prior work demonstrating that 6 repeat units is sufficient to isolate adjacent core-hole excitons. Our tests also confirmed that π-stacking effects are minimal and that k-point sampling density variations produce negligible spectral changes (Figures S10−S13). This further confirms that the chosen supercell is sufficient to capture key attributes of the simulated NEXAFS.
For the simulations involving dopant counterions, atomic coordinates were geometrically optimized through a relaxation calculation in Quantum ESPRESSO. A single dopant molecule within a sufficiently large cubic lattice was used to ensure the isolation of core-hole exciton effects. The optimization process employed the generalized gradient approximation (GGA), following the Perdew−Burke−Ernzerhof (PBE) scheme, and utilized a plane-wave cutoff energy of 30 Ry.
P-RSoXS Simulations. P-RSoXS simulations were carried out using the NIST RSoXS Simulation Suite (NRSS) which incorporates tools to validate input models and CyRSoXS, a virtual beamline instrument. Simulated morphologies were generated using DopantModeling, a custom open-source software developed specifically for this work.