Bayesian Optimization-Assisted Screening to Identify Improved Reaction Conditions for Spiro-Dithiolane Synthesis
Abstract
:1. Introduction
2. Results and Discussion
2.1. BO-Assisted Multiparameter Screening of Sulfurization of 2 in 2 g Scale and Scale-Up
2.2. Proposed Reaction Mechanism
3. Materials and Methods
3.1. General Experimental Details
3.2. Typical Synthetic Procedure for Spiro-Dithiolane 1 in Two Grams Scale (Table 1, Entry 16)
3.3. Synthetic Procedure for Spiro-Dithiolane 1 in Twenty Grams Scale (Table 1, Entry 17)
3.4. Synthetic Procedure for Spiro-Dithiolane 1 in a Hundred Grams Scale (Table 1, Entry 18)
3.5. Code: Latin Hypercube Sampling (LHS) Using pyDOE2
import pyDOE2 as doe |
from sklearn.preprocessing import MinMaxScaler |
import pandas as pd |
import random |
boundary = pd.DataFrame({‘paramA’:[2,9],’paramB’:[0.4,3.2],’paramC’:[0.6,3.6],’paramD’:[0.5,6.5]}) |
lhs = doe.lhs(4, samples = 5, criterion = ‘center’, random_state = 1) |
scaler = MinMaxScaler() |
min_max = scaler.fit(boundary) |
value = pd.DataFrame(min_max.inverse_transform(lhs), columns=boundary.columns) |
print(value) |
3.6. Code: Bayesian Optimization Using GPyOpt for Entries 2–8 in Table 1
import numpy as np | ||
import GPy | ||
import GPyOpt | ||
X = np.array | ([[6.5, 1.2, 2.4, 3.5], | |
[4.5, 2.4, 2.4, 1.5], | ||
[5.5, 1.2, 3.0, 5.5], | ||
[5.5, 2.4, 1.2, 3.5], | ||
[6.5, 1.8, 3.0, 1.5], | ||
[4.5, 1.8, 1.2, 5.5], | ||
[5.8, 2.2, 1.9, 3.4], | ||
[6.2, 2.5, 1.5, 3.2]]) | ||
Y = -np.array([65, 51, 39, 76, 66, 52, 78, 74])[:, np.newaxis] | ||
initial_x = X | ||
initial_y = Y | ||
bounds = | [{‘name’: ‘current’, ‘type’: ‘continuous’, ‘domain’: (2,9)}, | |
{‘name’: ‘Init_molarity’, ‘type’: ‘continuous’, ‘domain’: (0.4,3.2)}, | ||
{‘name’: ‘electrolyte’, ‘type’: ‘continuous’, ‘domain’: (0.6,3.6)}, | ||
{‘name’: ‘time’, ‘type’: ‘continuous’, ‘domain’: (0.5,6.5)}] | ||
myBopt = GPyOpt.methods.BayesianOptimization(f=None, | ||
domain=bounds, | ||
X = initial_x, | ||
Y = initial_y, | ||
acquisition_type=‘EI’, | ||
) | ||
next_x = myBopt.suggest_next_locations() | ||
print(next_x) |
3.7. Code: Bayesian Optimization Using GPyOpt for Entries 9–16 in Table 1
import numpy as np | ||
import GPy | ||
import GPyOpt | ||
X = np.array | ([[5.5, 2.36, 2.1, 1.1], | |
[2.7, 1.8, 3.3, 2.3], | ||
[6.9, 0.68, 2.7, 3.5], | ||
[8.3, 2.92, 0.9, 5.9], | ||
[4.1, 1.24, 1.5, 4.7], | ||
[6.7, 0.77, 2.7, 3.3], | ||
[6.5, 1.36, 2.0, 2.2]]) | ||
Y = -np.array([67, 31, 68, 48, 66, 70, 78])[:, np.newaxis] | ||
initial_x = X | ||
initial_y = Y | ||
bounds = | [{‘name’: ‘current’, ‘type’: ‘continuous’, ‘domain’: (2,9)}, | |
{‘name’: ‘Init_molarity’, ‘type’: ‘continuous’, ‘domain’: (0.4,3.2)}, | ||
{‘name’: ‘electrolyte’, ‘type’: ‘continuous’, ‘domain’: (0.6,3.6)}, | ||
{‘name’: ‘time’, ‘type’: ‘continuous’, ‘domain’: (0.5,6.5)}] | ||
myBopt = GPyOpt.methods.BayesianOptimization(f=None, | ||
domain=bounds, | ||
X = initial_x, | ||
Y = initial_y, | ||
acquisition_type=‘EI’, | ||
) | ||
next_x = myBopt.suggest_next_locations() | ||
print(next_x) |
3.8. Code: Calculation of Correlation Coefficient Using Pandas
import pandas as pd | |
import seaborn as sns | |
import matplotlib.pyplot as plt | |
from matplotlib import rcParams | |
NaSH = [5.5, 2.7, 6.9, 8.3, 4.1, 6.7, 6.5, 7.0] | |
H2O = [2.36, 1.8, 0.68, 2.92, 1.24, 0.77, 1.36, 0.42] | |
sulfur = [2.1, 3.3, 2.7, 0.9, 1.5, 2.7, 2.0, 1.3] | |
toluene = [1.1, 2.3, 3.5, 5.9, 4.7, 3.3, 2.2, 1.1] | |
result = [67, 31, 68, 48, 66, 70, 78, 89] | |
df = pd.DataFrame({“NaSH”:NaSH, | |
“H2O”:H2O, | |
“sulfur”:sulfur, | |
“toluene”:toluene, | |
“result”:result, | |
}) | |
sns.heatmap(df.corr(), cmap=“magma”, annot=True, fmt=“1.1f”) |
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
References
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Entry | NaSH aq. | Sulfur (eq.) | 2 Concentration in Toluene (M) | %Conversion Yield (% GC Yield of 1) | Note | |
---|---|---|---|---|---|---|
(eq.) | Concentration in H2O (M) | |||||
1 | 6.0 | 11.9 | 3.0 | 1.71 | 68 | Previous optimized conditions |
2 | 6.5 | 14.8 | 2.4 | 1.19 | 65 | ITS prepared by random sampling |
3 | 4.5 | 7.4 | 2.4 | 2.78 | 51 | |
4 | 5.5 | 14.8 | 3.0 | 0.76 | 39 | |
5 | 5.5 | 7.4 | 1.2 | 1.19 | 76 | |
6 | 6.5 | 9.8 | 2.0 | 2.78 | 66 | |
7 | 4.5 | 9.8 | 1.2 | 0.76 | 52 | |
8 | 5.8 | 8.1 | 1.4 | 1.22 | 78 a | Estimated conditions by BO and entries 2–7 |
9 | 5.5 | 5.3 | 2.1 | 4.54 | 67 | ITS prepared by LHS |
10 | 2.7 | 7.0 | 3.3 | 2.16 | 31 | |
11 | 6.9 | 18.4 | 2.7 | 1.42 | 68 | |
12 | 8.3 | 4.3 | 0.9 | 0.84 | 48 | |
13 | 4.1 | 10.0 | 1.5 | 1.06 | 66 | |
14 | 6.7 | 16.2 | 2.7 | 1.50 | 70 | Estimated conditions by BO and entries 9–13 |
15 | 6.5 | 9.2 | 2.0 | 2.26 | 78 | Estimated conditions by BO and entries 9–14 |
16 | 7.0 | 29.8 | 1.3 | 4.54 | 89 b | Estimated conditions by BO and entries 9–15 |
17 | 7.0 | 29.8 | 1.3 | 4.54 | 87 b | 20 g of 2 Overhead stirrer motor (210 rpm) based on entry 16 |
18 | 7.0 | 29.8 | 1.3 | 4.54 | 81 b | 100 g of 2 Overhead stirrer motor (210 rpm) based on entry 16 |
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Kondo, M.; Wathsala, H.D.P.; Ishikawa, K.; Yamashita, D.; Miyazaki, T.; Ohno, Y.; Sasai, H.; Washio, T.; Takizawa, S. Bayesian Optimization-Assisted Screening to Identify Improved Reaction Conditions for Spiro-Dithiolane Synthesis. Molecules 2023, 28, 5180. https://doi.org/10.3390/molecules28135180
Kondo M, Wathsala HDP, Ishikawa K, Yamashita D, Miyazaki T, Ohno Y, Sasai H, Washio T, Takizawa S. Bayesian Optimization-Assisted Screening to Identify Improved Reaction Conditions for Spiro-Dithiolane Synthesis. Molecules. 2023; 28(13):5180. https://doi.org/10.3390/molecules28135180
Chicago/Turabian StyleKondo, Masaru, Hettiarachchige Dona Piyumi Wathsala, Kazunori Ishikawa, Daisuke Yamashita, Takeshi Miyazaki, Yoji Ohno, Hiroaki Sasai, Takashi Washio, and Shinobu Takizawa. 2023. "Bayesian Optimization-Assisted Screening to Identify Improved Reaction Conditions for Spiro-Dithiolane Synthesis" Molecules 28, no. 13: 5180. https://doi.org/10.3390/molecules28135180
APA StyleKondo, M., Wathsala, H. D. P., Ishikawa, K., Yamashita, D., Miyazaki, T., Ohno, Y., Sasai, H., Washio, T., & Takizawa, S. (2023). Bayesian Optimization-Assisted Screening to Identify Improved Reaction Conditions for Spiro-Dithiolane Synthesis. Molecules, 28(13), 5180. https://doi.org/10.3390/molecules28135180