Siddharth Ghule1,2, Soumya Ranjan Dash1,2, Sayan Bagchi1,2, Kavita Joshi1,2, Kumar Vanka1,2. 1. Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pashan, Pune 411008, India. 2. Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
Abstract
This study investigates four machine-learning (ML) models to predict the redox potentials of phenazine derivatives in dimethoxyethane using density functional theory (DFT). A small data set of 151 phenazine derivatives having only one type of functional group per molecule (20 unique groups) was used for the training. Prediction accuracy was improved by a combined strategy of feature selection and hyperparameter optimization, using the external validation set. Models were evaluated on the external test set containing new functional groups and diverse molecular structures. High prediction accuracies of R 2 > 0.74 were obtained on the external test set. Despite being trained on the molecules with a single type of functional group, models were able to predict the redox potentials of derivatives containing multiple and different types of functional groups with good accuracies (R 2 > 0.7). This type of performance for predicting redox potential from such a small and simple data set of phenazine derivatives has never been reported before. Redox flow batteries (RFBs) are emerging as promising candidates for energy storage systems. However, new green and efficient materials are required for their widespread usage. We believe that the hybrid DFT-ML approach demonstrated in this report would help in accelerating the virtual screening of phenazine derivatives, thus saving computational and experimental costs. Using this approach, we have identified promising phenazine derivatives for green energy storage systems such as RFBs.
This study investigates four machine-learning (ML) models to predict the redox potentials of phenazine derivatives in dimethoxyethane using density functional theory (DFT). A small data set of 151 phenazine derivatives having only one type of functional group per molecule (20 unique groups) was used for the training. Prediction accuracy was improved by a combined strategy of feature selection and hyperparameter optimization, using the external validation set. Models were evaluated on the external test set containing new functional groups and diverse molecular structures. High prediction accuracies of R 2 > 0.74 were obtained on the external test set. Despite being trained on the molecules with a single type of functional group, models were able to predict the redox potentials of derivatives containing multiple and different types of functional groups with good accuracies (R 2 > 0.7). This type of performance for predicting redox potential from such a small and simple data set of phenazine derivatives has never been reported before. Redox flow batteries (RFBs) are emerging as promising candidates for energy storage systems. However, new green and efficient materials are required for their widespread usage. We believe that the hybrid DFT-ML approach demonstrated in this report would help in accelerating the virtual screening of phenazine derivatives, thus saving computational and experimental costs. Using this approach, we have identified promising phenazine derivatives for green energy storage systems such as RFBs.
Today,
∼85% of the world’s energy demand is being
fulfilled by fossil fuels.[1,2] The limited supply of
fossil fuels and the ever-increasing population have raised concerns
that we might run out of fossil fuels sooner than expected.[1,3] Furthermore, electricity production from fossil fuels is one of
the major factors responsible for greenhouse gas emissions.[4] In this age, humanity faces two major challenges
of balancing increased energy demand while reducing the environmental
impact associated with energy production. In the past decades, investments
and research efforts in the green technology have been increased to
overcome these challenges.[5] Significant
progress has already been made to access renewable energy sources.[6,7] Renewable energy sources, being intermittent, require efficient
energy storage.[4] Improvements in the energy
storage technology would not only help in the adoption of renewable
energy but also help in making efficient use of non-renewable energy
sources. Historically, it has been more expensive to store energy
than to expand energy generation for handling increased demand.[8] Thus, grid systems employed today are likely
to fail when additional energy cannot be generated during peak demand.
The massive Texas Blackout in February 2021 is an example of such
a failure.[9] It suggests that an efficient
energy storage technology is urgently required. Unfortunately, only
1.0% of the energy consumed worldwide can be stored with the energy
storage technology accessible today.[10] Furthermore,
the contribution of electrochemical batteries to energy storage capacity
is less than 2.0%, even though most of the devices we use every day
include batteries.[8,10] Li-ion batteries are widely used
today due to their high energy density, high specific energy, long
cycle life, and fast charge–discharge cycle.[4,8,11] Unfortunately, Li-ion batteries suffer from
high production costs, safety issues, and high environmental impact.[2,12] Redox flow batteries (RFBs) have the potential to overcome drawbacks
of Li-ion batteries, owing to their high storage capacity, independent
control over storage capacity and power, fast responsiveness, ease
of scaling, room-temperature operation, cost-effectiveness, high round
trip efficiency, safety, and lower environmental impact.[13−26] RFBs are increasingly being used as energy storage devices in renewable
energy systems, thereby helping in the adoption of green energy.[15,22] A schematic diagram of the typical RFB is shown in Figure . The RFB consists of two storage
tanks containing cathode and anode redox-active species dissolved
in an electrolyte solution. The electrolyte solution in the positive
and negative compartments is termed catholyte and anolyte, respectively.
These storage tanks are connected to an electrochemical cell (or current
collector) via pumps. The electrochemical cell consists
of porous electrodes separated by an ion-selective membrane. During
operation, electrolytes containing redox-active species are pumped
to the electrochemical cell, where they undergo oxidation or reduction
depending on the charge/discharge cycle. Then, electrolytes are circulated
back to their storage tanks.[13,24] So far, transition
metal-based RFBs (such as vanadium, iron, and chromium) have found
some commercial success. However, their widespread adoption has been
limited mainly due to high production cost, toxicity, and cell component
corrosion associated with the use of transition-metal salts.[27,28] Therefore, RFBs containing organic redox-active species are being
heavily investigated due to their low production cost, access to a
massive space of electroactive compounds, and low environmental impact.[28,29] Many organic compounds such as quinones, viologens, flavins, thiazines,
imides, and their derivatives have been investigated for redox-active
species in both aqueous and non-aqueous RFBs.[27,30,31] However, non-aqueous RFBs offer large operating
voltage.[30] Recently, phenazine derivatives
have been shown to be promising redox-active candidates in non-aqueous
RFBs. Recent reports have revealed why phenazine derivatives are promising
redox-active candidates. Romadina et al. synthesized phenazine derivatives
having significantly negative redox potential.[32] RFBs require anolytes with high negative redox potential.
They showed that the non-aqueous RFB based on the synthesized phenazine
derivative is capable of achieving a potential of 2.3 V, high capacities,
>95% Coulombic efficiency, and good charge–discharge cycling
stability after the initial 20 cycles. Mavrandonakis and co-workers,
in their computational investigation, reported the most negative redox-active
candidate based on phenazine for non-aqueous RFBs.[27] They showed that tetra-amino-phenazine has 140 mV more
negative potential than N-methylphthalimide (MePht),
which has one of the most negative redox potentials reported so far
in RFBs.[33] They also proposed all-phenazine
RFB reaching a high potential of 2.83 V. Furthermore, the redox potential
of phenazine derivatives could be tuned easily with the addition of
appropriate electron-donating or electron-withdrawing functional groups.
The synthesis of phenazine derivatives is very economical than mining
transition metals. Therefore, phenazine derivatives are currently
being investigated as candidates for novel redox-active species.[27,32]
Figure 1
Schematic
diagram of a typical RFB.
Schematic
diagram of a typical RFB.These investigations remain primarily experimental. Unfortunately,
the vast chemical space offered by organic compounds cannot be explored
using experimental procedures. Quantum mechanical density functional
theory (DFT) computations have been used heavily in materials science
research due to high accuracy but are very slow and cannot screen
millions of molecules in a reasonable amount of time. Therefore, a
fast and reliable method to screen millions of compounds without compromising
accuracy is required. In this regard, machine-learning (ML) algorithms
have shown excellent predictive accuracies along with short development
and prediction times.[34−38] Therefore, ML models have been used extensively to screen millions
of molecules in materials science and drug discovery.[39−43] ML models generally require a large amount of data for accurate
predictions. When the quantity of data is limited, feature engineering
is employed to generate the most informative features. These features
are expected to capture the appropriate molecular information necessary
to predict the target quantity. Feature engineering requires domain
knowledge, relying on having access to experts.[44−46] In small data
sets, DFT-based or experimentally determined features have been used
due to their high accuracy. However, some reports also explore simple
features based on the molecular structure.[47−52]In this work, we investigated four ML models to predict the
redox
potentials of phenazine derivatives in the dimethoxyethane (DME) solvent.
The training-set containing 151 phenazine derivatives was obtained
from the previously reported DFT study having 189 phenazine derivatives
with only one type of functional group per molecule (20 unique functional
groups).[27] Molecular features were computed
from the optimized neutral structures using the RDKit python library.[53] Model accuracy was improved through feature
selection and hyperparameter optimization using the external validation
set. Then, the model performance was assessed on the external test-set
compiled from the literature consisting of new functional groups,
multiple functional groups, and diverse structures. Their redox potential
was computed using the DFT. The trained models were employed to predict
the redox potentials of randomly generated phenazine derivatives with
multiple functional groups. We also carried out feature importance
analysis and discussed the structure–functional relationship
of phenazine derivatives. Finally, promising candidates were identified
for the anolyte from the external test-set and multiple functional
group test-sets.
Materials and Methods
Computational Details
The redox potentials
of phenazine derivatives were computed using the DFT workflow described
in the paper by Mavrandonakis et al.[27] All
the DFT calculations were performed with Gaussian 09 software.[54] Geometry optimization of neutral and reduced
forms of phenazine and its derivatives were carried out in the gas
phase by employing B3LYP/6-31+G(d,p) level of theory.[55−58] Harmonic frequency analysis was performed for all the structures
to confirm them as minima. Solvation effects of DME were incorporated
during the single-point calculations using the M06-2X functional,[59] by employing the SMD solvation model (details
in the Supporting Information).[60,61] The term “Redox Potential” in this report corresponds
to the “Reduction Potential” with respect to unsubstituted
phenazine molecule (i.e., the parent phenazine). The redox potentials
of phenazine derivatives were computed using the following equations:where PZ symbolizes
the parent phenazine,
XPZ represents the substituted phenazine molecules, E1(ref)0 is
the reported redox potential of parent PZ,[27] ΔG(rxn,sol) corresponds to the
free energy change of the reaction, F is the Faraday
constant, n is number of electrons involved in the
reduction, and G(sol)0 represents the final composite free energy
of individual species, which was calculated by adding the free energy
contribution computed at the B3LYP level of theory, G(therm,gas)(B3LYP), to the single-point energies calculated at the M06-2X level of
theory: E(sol)M06-2X.
Data
Generation
Training-Set and Internal Test–Test
These data sets were obtained from work reported by Mavrandonakis
and co-workers.[27] In their report, the
redox potentials of 189 phenazine derivatives were computed using
DFT in the DME solvent. These DFT redox potentials were used as a
target property in this work during training and testing. 20 unique
electron-withdrawing and electron-donating functional groups were
present in the data set [−N(CH3)2, −NH2, −OH, −OCH3, −P(CH3)2, −SCH3, −SH, −CH3, −C6H5, −CH=CH2, −F, −Cl, −CHO, −COCH3, −CONH2, −COOCH3, −COOH,
−CF3, −CN, and −NO2]. It
should be noted that phenazine derivatives in this data set contain
only one type of functional group per molecule. The optimized 3D structures
of derivatives in neutral and in anionic states were also provided.
However, only neutral structures were used in this study. Unfortunately,
not all compounds were supplied with their neutral structure, those
compounds were modeled, and their optimized structures were added
to the data set. Next, 208 different types of features were generated
using the RDKit python library.[53] The list
of all features is given in Table S1 of Supporting Information. The features were scaled using the “StandardScaler” class of the scikit-learn library,[62] removing the mean and scaling each feature to
unit variance. Finally, the whole data set was shuffled and split
randomly into a training-set and test-set in an 8:2 ratio (151 samples
in the training-set and 38 samples in the test-set). A few phenazine
derivatives from the training-set/internal test-set are shown in Table .
Table 1
Representative Structures from Training-Set/Internal
Test-Seta
Mol IDs were assigned
to identify
derivatives from the corresponding data set.
Mol IDs were assigned
to identify
derivatives from the corresponding data set.
External Test-Set
This data set
was compiled from different reports studying various properties of
phenazine derivatives.[63−67] Their redox potentials were computed using DFT and used as a target
property during testing. We gathered a total of 30 phenazine derivatives.
Derivatives containing five or more substituted rings were removed.
Also, derivatives having drastically different neutral and anion structures
were removed. In the end, 22 diverse phenazine derivatives with multiple
types of functional groups remained in the external test-set. Table shows some of the
structures from this data set. It can be seen that this data set contains
unique and different structures compared to the training-set.
Table 2
Representative Structures from the
External Test-Seta
Mol IDs were assigned
to identify
derivatives from the corresponding data set.
Mol IDs were assigned
to identify
derivatives from the corresponding data set.
Multiple Functional Group
Test-Sets
This data set contains two test-sets: (i) two functional
group test-set
and (ii) three functional group test-set. These test-sets were generated
by randomly choosing the position and the type of the functional group
from this list [−N(CH3)2, −NH2, −OH, −OCH3, −P(CH3)2, −SCH3, −SH, −CH3, −C6H5, −CH=CH2, −F, −Cl, −CHO, −COCH3, −CONH2, −COOCH3, −COOH,
−CF3, −CN, and −NO2]. 20
derivatives having two different types of functional groups per molecule
were generated for two functional group test-set. Similarly, 20 derivatives
having three different types of functional groups per molecule were
generated for three functional group test-set. Their redox potentials
were computed using DFT and used as a target property during testing.
Five derivatives from two and three functional group test-sets were
removed to form an external validation set. Thus, the final size of
two and three functional group test-sets was reduced from 20 to 15.
In this report, the term “multiple” refers to the derivatives
containing different types and more than one functional group. Similarly,
the terms “two functional groups” and “three
functional groups” refer to the derivatives containing two
different types of functional groups and three different types of
functional groups per molecule, respectively. A few representative
structures from these test-sets are shown in Table .
Table 3
Representative Structures
from Multiple
Functional Group Test-Setsa
Mol IDs were assigned
to identify
derivatives from the corresponding data set.
Mol IDs were assigned
to identify
derivatives from the corresponding data set.
External Validation Set
An external
validation set of 10 phenazine derivatives was compiled from two and
three functional group test-sets. Five derivatives from two functional
group test-set and five derivatives from three functional group test-set
were selected. Their redox potentials were computed using DFT and
used as a target property. This validation set does not come from
the training-set. Therefore, it is termed as an external validation
set. It was used for feature selection and hyperparameter optimization.
External validation set improves generalization by transferring knowledge
from the test-set to models through hyperparameters.
Hyperparameter Optimization
Hyperparameters
of the models were optimized using the “GridSearchCV” class of the scikit-learn library.[62] During hyperparameter optimization, models were trained on the training-set
and evaluated on the external validation set. Mean squared error (MSE)
was used as an evaluation metric for hyperparameter optimization.
The grid of hyperparameters for each model is given in Table S2 of Supporting Information. The parameter grid was
adjusted manually.
ML Models
Following
four ML models
were investigated in this study. These models were chosen due to their
ability to generalize from small data sets. Models were implemented
with the scikit-learn python library.[62] First, models were trained on the training-set containing all 208
features, followed by hyperparameter optimization. Then, the models
were re-trained on different subsets of features to identify the set
of features having the highest average performance on the external
validation set. Once the optimum features were identified, hyperparameter
optimization was performed with the selected features to improve the
model performance further.
This is a probabilistic model related to the sparse
Bayesian learning (SBL) framework. It assumes axis-parallel, elliptical
Gaussian distribution for each coefficient. The precision of each
Gaussian distribution is drawn from the prior distribution (gamma
distribution); therefore, it can lead to sparser coefficients. Thus,
it is an effective tool to remove irrelevant features.[68,69]
Gaussian Process Regression (GP)
It is a nonparametric Bayesian model. The nonparametric Bayesian
model provides the probability distribution of parameters over all
possible functions that fit the data. The prior in a Gaussian process
is specified on the function space. Gaussian process prior is a multivariate
normal distribution whose mean is obtained from the data, and covariance
is specified using the kernel function. The hyperparameters of the
kernel are optimized during the training.[70,71] We used a combination of WhiteKernel and RBF kernel. WhiteKernel is used for specifying
the noise level, and RBF kernel is a very popular
kernel used in many algorithms.
Kernel
Ridge Regression (KRR)
It
is the extension of ridge regression with kernel trick. In ridge regression,
a linear model is leaned with the l2-norm regularization. Using the
kernel trick, KRR learns a linear function in the high dimensional
non-linear space without actually transforming the data.[72]
Support Vector Regression
(SVR)
This model is the regression form of the support vector
machine (SVM),
a popular algorithm for classification tasks. Analogous to the SVM,
SVR depends on the subset of training data and ignores the points
whose prediction is close to their true value. SVM also utilizes the
kernel trick and learns a hyperplane in the high dimensional space.[73]
Evaluation Metrics
The following
metrics were used for evaluating the model performance. In the formulas
below, N denotes the number of data points, ŷ denotes the predicted
value of ith sample, and the y denotes the corresponding true value.Coefficient of determination
(R2):whereMean
Squared Error (MSE):Mean Absolute Error (MAE):The use of terms “Accuracy”
and “Performance”
in this report is contextual and refers to one or more metrics defined
above.
Feature Selection
As the number of
features obtained from the RDKit library was more than the size of
training-set, it was necessary to implement a feature selection strategy.
It has been observed that the training-set containing more features
than data points leads to overfitting.[30] Feature selection was implemented using the “SelectKBest” class of the scikit-learn library.[74] The parameter “k” of the “SelectKBest” class was obtained by evaluating the
average performance of models on the external validation set at different
values of “k.” First, models were trained
on the training-set containing all features, followed by hyperparameter
optimization. Then, the models were re-trained on the subsets of features
selected using “SelectKBest” class
at different values of “k.” These values
for “k” were tested: 50, 75, 100, 125,
150, and 208. The average model performance at different values of
“k” on the external validation set
is shown in Table . It can be seen that the models trained on 100 selected features
show the highest average performance in terms of R2. Therefore, these 100 features were selected for the
subsequent analysis. The models trained on 100 selected features were
further improved through hyperparameter optimization.
Table 4
Average Model Performance on External
Validation Set at Different Values of “k”
values
of “k”
performance metric
50
75
100
125
150
208
R2
0.45
0.42
0.57
0.55
0.54
0.54
MSE
0.02
0.02
0.02
0.02
0.02
0.02
MAE
0.12
0.12
0.10
0.10
0.10
0.10
Feature Importance Analysis
Feature
importance analysis was performed using the technique known as permutation
importance. In this technique, values of the feature to be assessed
are randomly shuffled (permuted). Then, prediction accuracy is computed
on the shuffled data set. Shuffling feature values is equivalent to
replacing the feature with noise, thereby removing its information
from the data set. Therefore, the model is expected to perform poorly
on the shuffled data set if the feature is important. The degree of
importance depends on the amount of variation in the accuracy. This
technique does not re-train the model; therefore, a trained model
is required. The permutation importance was computed using “permutation_importance” class of the scikit-learn
library and the training-set.[75] This procedure
was repeated 100 times to obtain reliable estimates. The feature importance
scores were rescaled between 0 to 1. The mean and standard deviation
of the feature scores were reported. The mean feature score was used
for the ranking of individual features. The terms “Feature”
and “Descriptor” are used interchangeably in this report.
Results and Discussion
Test-Set
Performance
We assessed
the generalizability of the trained models (i.e., performance on the
unseen data) using internal and external test-sets. Please refer to Section for the preparation
of internal and external test-sets. As the internal test-set comes
from the same source, it is very similar to the training-set and contains
derivatives with only one type of functional group per molecule. However,
the external test-set is compiled from multiple sources, therefore,
it has very diverse phenazine derivatives with different types of
functional groups. It also contains functional groups and structures
not present in the training-set (e.g., −NHPh, −Br, and
extended conjugation). Figure shows the performance on the internal test-set, and Figure shows performance
on the external test-set. It can be seen that all models have excellent
accuracy on the internal test-set (R2 >
0.98) and high accuracy on the external test-set set (R2 > 0.74). The GP model achieved the highest R2 of 0.89 on the external test-set. After deep
analysis
in Section , it
was revealed that GP is not a stable model, whereas relatively low-performing
models KRR (R2 = 0.83) and SVR (R2 = 0.85) are more stable. Therefore, one should
be careful while using the high-performing model, and the stability
of the model should also be considered. The values of performance
metrics on internal and external tests are shown in Table . Such a performance on the
external test-set is surprising as models were trained on the phenazine
derivatives having only one type of functional group. These results
show that ML models are capable of generalizing from a very small
and simple data set.
Figure 2
Plots showing ML predictions on internal test-set (y-axis) vs DFT redox potentials (x-axis).
Gray dashed
line corresponds to the perfect predictions.
Figure 3
Plots
showing ML predictions on external test-set (y-axis)
vs DFT redox potentials (x-axis). Gray dashed
line corresponds to the perfect predictions.
Table 5
Values of Performance Metrics on Internal
and External Test-Setsa
Internal
test-set
External
test-set
Model name
R2
MSE
MAE
R2
MSE
MAE
ARDR
0.98
0.01
0.06
0.74
0.06
0.18
GP
0.99
0.01
0.05
0.89
0.03
0.11
KRR
0.98
0.01
0.05
0.83
0.04
0.14
SVR
0.98
0.01
0.07
0.85
0.03
0.13
Numbers were rounded upto two decimals.
Plots showing ML predictions on internal test-set (y-axis) vs DFT redox potentials (x-axis).
Gray dashed
line corresponds to the perfect predictions.Plots
showing ML predictions on external test-set (y-axis)
vs DFT redox potentials (x-axis). Gray dashed
line corresponds to the perfect predictions.Numbers were rounded upto two decimals.
Prediction on Multiple
Functional Group Test-Sets
Next, we assessed the model performance
on the phenazine derivatives
substituted with different types of functional groups per molecule.
These test-sets were generated randomly; please refer to Section for the generation
of this data set. Figures and 5 show the performance on the
derivatives containing two and three different functional groups,
respectively. It can be seen that the models performed reasonably
well (R2 > 0.7) even though molecules
used for the training had only one type of functional group per molecule.
In particular, GP model achieved the highest performance of R2 = 0.82 on two functional groups test-set.
However, automatic relevance determination regression (ARDR) achieved
the highest performance of R2 = 0.82 on
three functional groups test-set. A deeper analysis of GP and ARDR
in Section suggests
that GP and ARDR are not very reliable models. Although KRR and SVR
have relatively low performance, they are more reliable. Therefore,
one should be careful while using a high-performing model, and the
model’s reliability and stability should also be considered.
Nevertheless, these results again show the surprising generalization
power of ML models.
Figure 4
Plots showing ML predictions on two functional group test-set
(y-axis) vs DFT redox potentials (x-axis).
Gray dashed line corresponds to the perfect predictions.
Figure 5
Plots showing ML predictions on three functional group test-set
(y-axis) vs DFT redox potentials (x-axis). Gray dashed line corresponds to the perfect predictions.
Plots showing ML predictions on two functional group test-set
(y-axis) vs DFT redox potentials (x-axis).
Gray dashed line corresponds to the perfect predictions.Plots showing ML predictions on three functional group test-set
(y-axis) vs DFT redox potentials (x-axis). Gray dashed line corresponds to the perfect predictions.Furthermore, we added all 15 derivatives from two
functional group
test-set to the training-set and re-trained the models on this new
data set of 166 derivatives. The predictive performance of this combined
data set was assessed on the same data set of 15 derivatives containing
three different types of functional groups. The results of this analysis
are shown in Figure . It can be seen that the model performance has improved with the
addition of more data in the training-set.
Figure 6
Plots showing ML predictions
on three functional group test-set
(y-axis) vs DFT redox potentials (x-axis). The combined data set (training-set + two functional group
test-set) was used for the training. Gray dashed line corresponds
to the perfect predictions.
Plots showing ML predictions
on three functional group test-set
(y-axis) vs DFT redox potentials (x-axis). The combined data set (training-set + two functional group
test-set) was used for the training. Gray dashed line corresponds
to the perfect predictions.We carried
out feature importance analysis using permutation importance. Please
refer to Section for
the details on the technique. In order to understand how model performance
changes with the number of descriptors, we re-trained the models on
the subset of features and assessed their performance on the internal
test-set. Top 50 features based on their permutation importance score
were used. R2 was used as a performance
metric. The result of this analysis is shown in Figure . It can be seen that most of the models
show a jump in the R2 and have R2 > 0.9 around the top 10 features. The unusual
behavior of the GP model is attributed to the instability of the model
for a small number of features. The plots in Figure show the histograms of the top 10 important
features from each model. Although models show variation in feature
importance, they all agree in terms of the most important feature
that is, “PEOE_VSA1.” Interestingly,
most of the features in ARDR have small weights as ARDR tries to prune
the large number of irrelevant features, leading to a sparse model.[69,76] Five out of 10 features—“MaxAbsPartialCharge,” “PEOE_VSA1,” “fr_ArN,” “fr_NH0,”
and “fr_NH2” are common to all models.
Variations in the feature importance scores could be attributed to
the difference in the internal structures of the models. Here, we
discuss some of the common features from Figure .
Figure 7
R2 vs number of
descriptors. R2 was computed using the
internal test-set.
In this study, we identified a few issues with ARDR and GP. Despite
high predictive performance, ARDR is not a reliable model as it places
very high weight on one feature (i.e., “PEOE_VSA1”). Similarly, GP is not a reliable model as it becomes unstable
when the small number of features are used. We encountered divided
by zero errors in the kernel function during the analysis with the
GP model.
Figure 8
Top 10 features (y-axis) vs
mean feature importance
score (x-axis). Feature importance scores were rescaled
between 0 to 1. Error bars represent standard deviation from 100 repetitions.
R2 vs number of
descriptors. R2 was computed using the
internal test-set.
In this study, we identified a few issues with ARDR and GP. Despite
high predictive performance, ARDR is not a reliable model as it places
very high weight on one feature (i.e., “PEOE_VSA1”). Similarly, GP is not a reliable model as it becomes unstable
when the small number of features are used. We encountered divided
by zero errors in the kernel function during the analysis with the
GP model.Top 10 features (y-axis) vs
mean feature importance
score (x-axis). Feature importance scores were rescaled
between 0 to 1. Error bars represent standard deviation from 100 repetitions.
PEOE_VSA1
This is the sum of the
approximate accessible van der Waals surface area (i.e., VSA in Å2) of the atoms having partial charge less than −0.30.[77−79] The partial charges are computed using the partial equalization
of orbital electronegativities (PEOE) method developed by Gasteiger
and Marsili in 1980. Please refer to the discussion of MaxAbsPartialCharge descriptor for the PEOE method. Thus, this descriptor captures the
information related to molecular size and the number of electron-donating
functional groups.
MaxAbsPartialCharge
This is the
maximum value of the absolute Gasteiger partial charges present in
the molecule. In 1980, Gasteiger and Marsili gave the procedure to
calculate the partial charges in a molecule. That procedure is known
as PEOE. In this method, the charge is transferred between bonded
atoms until equilibrium. Gasteiger partial charges depend on the connectivity
and orbital electronegativity, thus capturing the electron-donating
and electron-withdrawing power of the atoms.[80] Electronegativity is essential information as electron-donating
groups decrease the redox potential, and electron-withdrawing groups
increase the redox potential.[27]
MinPartialCharge
This is the minimum
value of the Gasteiger partial charges present in the molecule. Please
refer to the discussion of MaxAbsPartialCharge descriptor
for the properties of Gasteiger partial charges.
fr_NH0
It is the number of tertiary
amines present in the molecule.
fr_
ArN
It is the number of N functional groups
attached to aromatic rings.
fr_NH2
It is the number of primary
amines.
NHOHCount
It is the number of N–H
and O–H bonds present in the molecule.From the analysis
in this section, we realized that there are some issues with the ARDR
and GP which are outlined below. One should be very careful while
using ARDR and GP models.
Issues with the ARDR
Model
As ARDR
is related to the SBL framework, it reduces the number of irrelevant
features. Unfortunately, in this case, ARDR has put a lot of weight
on only one feature, that is, “PEOE_VSA1”
(Figure ). Surprisingly,
ARDR also archives an accuracy of more than 0.95R2 only with the two features (Figure ). Although it has shown good performance
on the data set used in this work, it may not work for the broad chemical
space. This type of behavior reduces the reliability of the model.
Issues with the GP Model
From Figure , it can be seen
that the model’s accuracy decreases with more features, and
at around 10 features, there is a significant drop in the performance.
We also encountered divided by zero errors in the kernel function
during this analysis. This shows that GP may not be a very stable
model in this case.
Structure–Functional
Relationship
“PEOE_VSA1” is
the most important
descriptor common to all models. It is computed by summing over the
approximate accessible VSA (i.e., in Å2) of the atoms
having partial charge less than −0.30.[77−79] Thus, the “PEOE_VSA1” descriptor captures the information related
to molecular size and the number of electron-donating functional groups
present in the molecule. From Figure , we can see that the redox potential of phenazine
derivatives decreases with the increasing value of “PEOE_VSA1.” The Pearson correlation coefficient between
“PEOE_VSA1” and redox potential is
−0.69, supporting the the observation. We observed that the
value of “PEOE_VSA1” is higher for
the systems having delocalization of negative partial charge. The
delocalized system contains more atoms with the negative partial charge
than the corresponding localized system. Thus, the number of atoms
contributing to “PEOE_VSA1” in delocalized
systems is higher than localized ones. The effect of delocalization
of partial charge on “PEOE_VSA1” is
shown in Figure with a few examples from the training-set. Thus, for designing better
anolytes, it is suggested to increase the delocalization of negative
partial charge in the phenazine derivatives.
Figure 9
Redox potential vs“PEOE_VSA1.”
Figure 10
Examples
from the training-set showing the effect of charge delocalization
on “PEOE_VSA1.” Values of “PEOE_VSA1” and DFT redox potentials in volts are
also shown. Mol IDs were assigned to identify derivatives from the
corresponding data set.
Redox potential vs“PEOE_VSA1.”Examples
from the training-set showing the effect of charge delocalization
on “PEOE_VSA1.” Values of “PEOE_VSA1” and DFT redox potentials in volts are
also shown. Mol IDs were assigned to identify derivatives from the
corresponding data set.The redox potential
of phenazine derivative depends on the type
of functional group, the position of attachment, and the number of
functional groups. Two types of functional groups have been investigated
in this study: (i) electron-donating, and (ii) electron-withdrawing.
The redox potential of parent phenazine without any functional group
is −1.74 V. When the redox potential of the derivative decreases
(i.e., less than −1.74 V) after the attachment of functional
groups, then it is called a negative shift. Similarly, if it increases,
it is called a positive shift. The shift is quantified as the difference
between the redox potential of phenazine derivative and parent phenazine.
After sorting phenazine derivatives based on the redox potential,
it was observed that electron-donating groups show a negative shift,
whereas electron-withdrawing groups show a positive shift. Thus, the
shift corresponding to electron-donating groups is negative and electron-withdrawing
groups is positive. The redox potentials of phenazine derivatives
were computed using the approach discussed in Section . Equation shows that functional groups stabilizing the anionic
form of phenazine derivatives have high redox potential. In contrast,
those that destabilize the anionic form have low redox potential.
Therefore, electron-withdrawing groups show a positive shift as they
stabilize the anionic form, and electron-donating groups show a negative
shift as they destabilize the anionic form. A few examples showing
positive and negative shifts with respect to parent phenazine are
shown in Figure .
Figure 11
Examples showing positive and negative shifts with respect to parent
phenazine. DFT redox potentials and shifts in volts are also shown.
Mol IDs were assigned to identify derivatives from the corresponding
data set.
Examples showing positive and negative shifts with respect to parent
phenazine. DFT redox potentials and shifts in volts are also shown.
Mol IDs were assigned to identify derivatives from the corresponding
data set.In the case of derivatives with
multiple functional groups, if
all groups are similar, then shift also corresponds to their type.
For example, when the derivative contains all electron-donating groups,
it shows a negative shift. Similarly, the shift is positive when the
derivative contains all electron-withdrawing groups. A few examples
having similar types of functional groups are shown in Figure .
Figure 12
Examples showing the
effect of similar type of functional groups
on the redox potential. DFT redox potentials and shifts in volts are
also shown. Mol IDs were assigned to identify derivatives from the
corresponding data set.
Examples showing the
effect of similar type of functional groups
on the redox potential. DFT redox potentials and shifts in volts are
also shown. Mol IDs were assigned to identify derivatives from the
corresponding data set.When derivatives contain
more than one functional group that differ
in their type, the shift is determined by the group showing the highest
absolute shift in the corresponding single functional group derivative.
For example, derivative A in Table contains −NH2, an electron-donating
group which has a shift of −0.11 V and −Cl, an electron-withdrawing
group which has a shift of 0.13 V. The absolute of the shift for −Cl
is more than −NH2; therefore, derivative A shows
a positive shift of 0.03 V, supporting our claim. A similar analysis
is applicable to derivative B, which also shows a positive shift.
Derivative C contains −N(CH3)2 and −CH3, two electron-donating groups, and −CO(NH2), an electron-withdrawing group. An absolute shift of −N(CH3)2 is −0.24 V, which is the highest among
all three groups. Therefore, derivative C shows a negative shift of
−0.09 V. Derivative D contains −OCH3 and
−C6H5, two electron-donating groups,
and −CHO, one electron-withdrawing group. However, derivative
D shows a positive shift as the absolute shift of −CHO is more
than both electron-donating groups. Thus, the redox potential of phenazine
derivatives containing multiple functional groups is determined by
the relative strength of electron-donating or electron-withdrawing
power of the functional groups.
Table 6
Examples Showing
the Effect of Absolute
Values of Single Functional Group Shift on the Redox Potential of
Derivatives Containing Different Types of Functional Groupsa
DFT redox potentials and shifts
in volts are also shown. Mol IDs were assigned to identify derivatives
from the corresponding data set.
DFT redox potentials and shifts
in volts are also shown. Mol IDs were assigned to identify derivatives
from the corresponding data set.The effect of position on the redox potential of single functional
group derivatives has been studied by Mavrandonakis and co-workers.[27] They showed that the position does not have
a significant effect for electron-withdrawing groups. However, electron-donating
groups which are capable of intra-molecular hydrogen boding show more
negative shift when attached at position 2 compared to position 1.
The position numbers in phenazine derivatives are shown in Figure . They also investigated
the effect of the number of functional groups on redox potential.
It was shown that the addition of more electron-withdrawing groups
shifts the redox potential continuously toward positive values. However,
this effect is less significant for electron-donating groups. The
difference between the phenazine derivative with four amino groups
and eight amino groups is very small (∼0.05 V). The difference
between phenazine derivative with four cyano groups and eight cyano
groups is ∼1.23 V.
Figure 13
Numbering of the positions in phenazine derivatives.
Numbering of the positions in phenazine derivatives.
Identification of Promising
Phenazine Derivatives
for the Anolyte
In this section, we identify the top five
promising candidates for the anolyte using the trained ML models.
Models developed in this study are based on features that do not require
electronic structure calculations. Therefore, these models could screen
millions of molecules in a significantly small amount of time. Then,
experimentation or DFT calculations could be performed on the reduced
number of molecules to identify the best redox-active molecules, saving
computational and experimental costs. Using this hybrid DFT-ML approach,
we have identified promising phenazine derivatives for the anolyte
in RFBs. These promising candidates would provide a good starting
point for the experimentalists. Electron-donating molecules with negative
redox potential are preferred candidates for the anolyte. As KRR and
SVR are stable models, the predictions here are based on them. The
values of redox potentials are averaged over 100 independent iterations
of data splitting and model training. Table lists the top five phenazine derivatives
from the external test-set with the most negative redox potentials
obtained from DFT and two ML models. Four out of five predictions
from KRR and SVR match with DFT predictions. The top five promising
candidates from multiple functional groups test-sets are shown in
Tables S3–S5 Supporting Information.
Table 7
Top Five Anolyte Candidates Predicted
Using DFT, KRR, and SVR from the External Test-Seta
SVR and KRR were trained on the
phenazine derivatives containing single type of functional group per
derivative. Mol IDs and redox potentials predicted from DFT and ML
models are shown below the respective candidates. Mol IDs were assigned
to identify derivatives from the corresponding test-set. Derivatives
are arranged in increasing order of redox potential. Redox potentials
are given in the unit of volts.
SVR and KRR were trained on the
phenazine derivatives containing single type of functional group per
derivative. Mol IDs and redox potentials predicted from DFT and ML
models are shown below the respective candidates. Mol IDs were assigned
to identify derivatives from the corresponding test-set. Derivatives
are arranged in increasing order of redox potential. Redox potentials
are given in the unit of volts.
Conclusions
In this study, four ML models
were employed to predict the redox
potentials of phenazine derivatives in DME using DFT. Models were
trained on a small data set of 151 phenazine derivatives having only
one type of functional group per molecule (20 unique functional groups).
The trained models achieved high accuracies (R2 > 0.74) on internal and external test-sets containing
diverse
phenazine derivatives. We also showed that despite being trained on
derivatives with a single type of functional groups, models were able
to predict the redox potentials of the derivatives containing multiple
and different types of functional groups with good accuracies (R2 > 0.7). Feature selection and hyperparameter
optimization using the validation set were critical strategies for
performance improvement. Feature selection removed the unnecessary
and noisy features. Hyperparameter optimization using an external
validation set helped improve the generalizability of the models.
The addition of 15 derivatives from two functional group test-sets
in the training-set improved the accuracy on three functional group
test-sets. It was observed that the “PEOE_VSA1” descriptor was the most important molecular feature as it
contains information related to molecular size and the partial charges.
Deeper analysis showed that one should not rely only on the model
performance but also investigate the stability and reliability of
the models. Through the structure–functional relationship,
we observed that the redox potential of derivatives containing multiple
functional groups is influenced by the functional group having either
strong electron-donating or strong electron-withdrawing power. Models
developed in this study are based on features that do not require
electronic structure calculations. Therefore, these models could screen
millions of molecules in a significantly small amount of time. Then,
experimentation or DFT calculations could be performed on the screened
candidates to identify the best molecules, saving computational and
experimental costs. Using this hybrid DFT-ML approach, we have identified
promising phenazine derivatives for the anolyte in RFBs. These promising
candidates would provide a good starting point for the experimentalists.
This study shows that it is possible to develop reasonably accurate
ML models for complex quantities such as redox potential using small
and simple data sets.
Authors: Benjamin G Peyton; Connor Briggs; Ruhee D'Cunha; Johannes T Margraf; T Daniel Crawford Journal: J Phys Chem A Date: 2020-06-02 Impact factor: 2.781
Authors: Karlee P Castro; Tyler T Clikeman; Nicholas J DeWeerd; Eric V Bukovsky; Kerry C Rippy; Igor V Kuvychko; Gao-Lei Hou; Yu-Sheng Chen; Xue-Bin Wang; Steven H Strauss; Olga V Boltalina Journal: Chemistry Date: 2016-01-12 Impact factor: 5.236