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. 2018 May 28;23(6):1292. doi: 10.3390/molecules23061292

Expectation-Maximization Model for Substitution of Missing Values Characterizing Greenness of Organic Solvents

Gabriela Łuczyńska 1,2, Francisco Pena-Pereira 3, Marek Tobiszewski 4, Jacek Namieśnik 4,*
PMCID: PMC6100055  PMID: 29843437

Abstract

Organic solvents are ubiquitous in chemical laboratories and the Green Chemistry trend forces their detailed assessments in terms of greenness. Unfortunately, some of them are not fully characterized, especially in terms of toxicological endpoints that are time consuming and expensive to be determined. Missing values in the datasets are serious obstacles, as they prevent the full greenness characterization of chemicals. A featured method to deal with this problem is the application of Expectation-Maximization algorithm. In this study, the dataset consists of 155 solvents that are characterized by 13 variables is treated with Expectation-Maximization algorithm to predict missing data for toxicological endpoints, bioavailability, and biodegradability data. The approach may be particularly useful for substitution of missing values of environmental, health, and safety parameters of new solvents. The presented approach has high potential to deal with missing values, while assessing environmental, health, and safety parameters of other chemicals.

Keywords: E-M algorithm, green analytical chemistry, missing data prediction, solvents, sustainability assessment

1. Introduction

Green Chemistry has been defined as the “design of chemical products and processes to reduce or eliminate the use and generation of hazardous substances” [1]. With this aim, Anastas and Warner, introduced, in 1998, the twelve principles of Green Chemistry that charted a path towards sustainability in chemical processes [1]. Several principles of Green Chemistry point out the need to eliminate or replace solvents by less harmful alternatives [2]. Particularly, the 5th principle of Green Chemistry specifically recommends the use of innocuous solvents when avoiding the use of solvents is not possible. The employment of harmful solvents is also indirectly discouraged, as can be deduced from additional principles, such as waste prevention (1st principle) and the prevention or minimization of potential chemical accidents (12th principle) that are associated to their use. Furthermore, advances toward the design of safer chemicals (4th principle) that at the end of their function can be transformed into innocuous non-persistent products (10th principle), and importantly, renewable feedstocks, rather than depleting non-renewable resources (7th principle), are highly recommended [3,4].

Organic solvents are increasingly used in scientific and technological activities, with an estimated worldwide consumption of roughly 30 million metric tons per year [5]. Apart from the steady increase of solvent consumption in the last years, especially worrisome is the fact that certain solvents of very high concern are still being widely used. Thus, the implementation of solventless process is strongly advisable from the point of view of Green Chemistry. While remarkable efforts have been made in certain areas toward the implementation of solventless processes (e.g., solventless sample preparation approaches [6] and greener reactions under solvent free conditions [7]), these strategies are, in general terms, still far from reaching the desired level of implementation. Alternatively, the minimization of solvent consumption and/or the replacement of hazardous solvents by cleaner alternatives are highly recommended strategies to reduce the risks that are associated to solvent usage [8,9]. In this vein, a number of solvent selection guides have been reported in the literature for a convenient selection of alternatives to harmful solvents [10,11,12,13,14,15,16,17,18]. However, the lack of relevant data, such as physicochemical properties and environmental impact, might hinder their implementation in scientific and technological processes [19]. The problem of missing data in solvents assessments is managed by default, substitution with value for nearest neighbor (homologue), and substitution with mean value for the entire chemical class [20].

Expectation-Maximization (E-M) algorithm [21] was developed in the 1970‘s and it is widely applied in different branches of sciences as the tool for the substitution of missing values [22]. It is applied to deal with missing values for the characterization of patients to predict breast cancer recurrence [23]. The algorithm is used to predict missing values in genetic arrays [24]. Application in chemistry include the prediction of missing data in environmental monitoring [25] or to construct regression models in the case of missing data in the raw dataset [26]. Other applications of E-M algorithm for predictions in the chemistry related field include the prediction of biomarkers essentiality [27] or the prediction of peptide bounding [28].

The aim of the study is to substitute missing values in the dataset characterizing organic solvents with the application of E-M algorithm, and to find relations between the characteristics from the estimated distribution. Toxicity, biodegradability, and bioavailability parameters are predicted with E-M algorithm.

2. Materials and Methods

2.1. Dataset

The dataset consists of 155 solvents that are described by 13 variables. The values of variables are extracted mainly from the Handbook of Physical-Chemical Properties and Environmental Fate for Organic Chemicals [29] and from material safety data sheets of solvents. Physicochemical properties include melting point, boiling point, vapor pressure, density, water solubility, Henry’s law constant, logarithms of octanol-water partitioning coefficient, and logarithm of octanol-air partitioning coefficient. Also, toxicity towards rodents when being administered orally (Oral LD50), toxicity towards rodents via inhalation exposure pathway (Inhalation LC50), toxicity towards fish (Fish LC50), half-life time needed for biodegradation, and logarithm of bioconcentration factors were taken as variables for analysis.

Solvents included in the dataset are compounds of different chemical classes–from hydrocarbons, terpenes, chlorinated solvents to alcohols, ketones, ethers, and esters and carboxylic acids. 85 out of the 155 solvents were fully characterized in terms of abovementioned variables, whereas the dataset contained at least one gap in case of the remaining solvents.

2.2. E-M Model

To complete the data we use E-M algorithm. This algorithm consists of two steps: an Expectation step or the E-step and a Maximization step or the M-step.

We observe a data y=(y1,,yn), where yi are realizations of a random vector Y, i=1,,n. Let Y has the probability distribution function depending on a vector of unknown parameters Ψ.

Let X be a k dimensional random vector corresponding to a complete-data x=(x1,,xn), where xi are realizations of X, i=1,,n. We consider the case where the vector X has multivariate normal distribution, which means that Ψ=(μ,Σ), where μ is a vector of means and Σ is a covariance matrix.

Suppose that there are G groups with distinct missing patterns. Then, the observed-data log likelihood can be expressed as

logL(Ψ)=Σg=1GlogLg(Ψ). (1)

The likelihood function for gth group formed from the observed data yg=(y1g,,yngg) is, discarding a proportionality constant, given by

Lg(Ψ)=|Σg|ng2exp{12Σi=1ng(yigμg)TΣg1(yigμg)} (2)

An estimate Ψ^ of Ψ can be obtained by solving the log likelihood equation

logL(Ψ)Ψ=0 (3)

The E-M algorithm approaches the problem of solving the incomplete-data log likelihood Equation (3) indirectly by proceeding iteratively in terms of complete-data log likelihood function logLc(Ψ), where

Lc(Ψ)=|(2π)kΣ|n2exp{12Σi=1n(xiμ)TΣ1(xiμ)} (4)

The E-step calculates the conditional expectation of the complete-data log likelihood, EΨ(0)(logLc(Ψ)|y), given the observed data and the parameter estimates. Then, the M-step finds the parameter estimates to maximize the complete-data log likelihood from the E-step.

The steps are carried out until the value of

L(Ψ(k+1))L(Ψ(k)) (5)

is smaller than arbitrarily amount in case of convergence of the sequence of likelihood values (L(Ψ(k)))k. The extended description of this procedure can be found in Supplementary Material. More details for normal distribution can be found in [30].

2.3. Dataset Preparation

We consider 155 solvents that are described by 13 attributes, which are listed in Table 1. Some chemical compounds do not have the value for the parameter “Inhalation LC50”, because they are not volatile, so there is no possibility to be intoxicated via inhalation. We decided to give them values 5001. This is the expert judgment caused by the threshold of danger to the environment. According to Globally Harmonized System of Classification and Labelling of Chemicals, the values above 5000 ppm are not characterized as “harmful if inhaled” [31].

Table 1.

Basic statistics of the dataset.

Variable Mean Std. Dev. Variance Minimum Maximum N N Missing
Melting point (°C) −43.901 48.728 2374.453 −140 49.52 152 3
Boiling point (°C) 142.385 68.626 4709.488 20 323 155 0
Density (g cm−3) 0.952 0.214 0.046 0.62 1.68 155 0
Water solubility (mg dm−3) 116,796.63 244,339.68 5.97 × 1010 0.000927 1,000,000 155 0
Vapor pressure (Pa) 11,901.626 28,631.781 8.2 × 108 0 241,900 155 0
Henry law constant (Pa m3 mol−1) 60,736.714 267,946.02 7.18 ×1 010 8.03×10−6 2,219,017 153 2
log KOW 2.229 2.352 5.531 −2.32 8.73 155 0
log KOA 4.434 1.999 3.995 1.451 12.101 152 3
Oral LD50 (mg kg−1) 3667.383 4658.48 21,701,436 5 31,500 120 35
Inhalation LC50 (ppm) 10,532.284 18,252.957 3.33 × 108 34 123,000 109 46
Fish LC50 (mg dm−3) 970.096 2813.093 7,913,490 0.1 16,700 98 57
BOD t1/2 [days] 55.360 127.192 16,178 1 800 93 62
log BCF 1.154 1.016 1.032 −1.63 4.7 151 4

LD50: lethal dose administered orally to rodents that kills half of population; LC50: toxicity towards rodents via inhalation exposure pathway; Std. Dev.: Standard Deviation; Kow: octanol-water partitioning coefficient; KOA: octanol-air partitioning coefficient; BOD: biodegradation half-life; BCF: bioconcentration factor.

3. Results and Discussion

3.1. Basic Statistics

Table 1 shows the basic statistics of investigated dataset, including the number of missing data (N missing). For boiling point, density, water solubility, vapor pressure, and log KOW, all of the values are available. The biggest problems with data availability are in case of Oral LD50, inhalation LC50, fish LC50, and BOD t1/2 (biodegradation half-life), as they are characterized by a big fraction of missing values.

3.2. Predictions with Bayesian Model

Application of E-M Algorithm

To complete the data set, we use the programming language SAS 4GL. There is a proper procedure in SAS, called PROC MI, which performs the E-M algorithm by function EM. The extensive description of this procedure can be found in [32].

We assume that the random vector X corresponding to a complete-data vector x has the multivariate normal distribution, X ~N(µ,Σ) where µ is a vector of means and Σ is a covariance matrix. To approach that assumption, we use a logarithmic transformation of the properties Henry’s law constant, Oral LD50, Inhalation LC50, fish LC50, and BOD t1/2.

In this case, we have to find a parameter Ψ = (µ, Σ) where µ is a vector of means and Σ is a covariance matrix of the unknown distribution. The initial estimates Ψ(0) are the means and the standard deviations from available cases. The correlations are set to zero.

On the prepared set, we carry out the E-M algorithm in SAS. To satisfy the convergence requirement the difference (5) has to be smaller than 0.0001. The method converges after 69 iterations. It means that

L(Ψ(69)) − L(Ψ(68)) < 0.0001 (6)

due to (5). Thereby, we received the completion of the data set. The most important thing is that we received full information about the set by finding the distribution of the data, N(µ,Σ). The E-M algorithm evaluated the parameters µ and Σ. Despite the Mardia’s kurtosis test has not shown that the data has a multivariate normal distribution we think that such a model gives a good approximation of relations. We will find these relations using principal component analysis (PCA) [33]. Table 2 shows the obtained results of first three principal components.

Table 2.

The results of data treatment with principal component analysis. Dark red is for very negative values, yellow is for neutral values and green stands for positive values.

Comp. 1 Comp. 2 Comp. 3
Melting point −0.4448 −0.1465 −0.0451
Boiling point −0.4963 −0.0883 0.0598
Density −0.0607 −0.0709 −0.4854
Water solubility 0.1150 −0.3744 0.0708
Vapor pressure 0.3478 0.0295 −0.0888
log Henry law const 0.1247 0.5103 0.0289
log KOW −0.2462 0.4340 0.1635
log KOA −0.4352 −0.1795 0.1165
log Oral LD50 −0.0528 0.0933 0.5678
log Inhalation LC50 0.2287 0.0600 0.4662
log fish LC50 0.1673 −0.2642 0.2638
log BOD t1/2 0.0848 0.2915 −0.3085
log BCF −0.2492 0.4202 0.0174

The first three components explain 65.9% of variability of the raw dataset. Fourth principal component explained 8.4% of variability, and it was decided not to include it in the assessment result. The first component consists of melting point, boiling point, vapor pressure, and log KOA, and it explains 26.2% of the initial variability. This component can be identified as responsible for the characterization of solvents in terms of their basic physicochemical properties, especially volatility. The second component is loaded with Henry’s law constant, log Kow, and log BCF, and it explains 24.4% of variability. This relation can be explained by the polarity of solvents. All three variables are related to interphase transfer and the ability to be transferred out of water. Apart from these three variables, weaker negative loading (−0.3774) is observed for water solubility, which additionally supports the polarity related origin of this group. The third component is formed by inhalation and oral toxicities and the negative loading of density. It carries 15.3% of initial dataset variability. It can be defined as toxicity relation and the presence of density in this group is due to the fact that more toxic solvents are usually more dense (i.e., chlorinated solvents).

The prediction of missing values are presented in Table 3—shaded are modeled with the E-M algorithm, whereas non-shaded are input data. Algorithm allows to substitute missing values for alkyl glycerol esters (numbers 15–29 in the Table 3), bio-based solvents originating from biodiesel production. Glycerol is formed as a byproduct during biodiesel production, and it is a platform molecule for the synthesis of its alkylated ester derivatives [34]. Because they originate from renewable resource, undergo biodegradation, and are low cost, they are potentially attractive from a Green Chemistry point of view. However, they are not fully characterized in terms of their toxicology or environmental fate related properties. The means of completed values are of 2017 mg kg−1 LD50 by oral administration (mean for solvents with available data—3667 mg kg−1), 13945 ppm of LC50 by inhalation (mean for solvents with available data—4658 ppm), 158 mg dm−3 of LC50 towards fish (mean for solvents with available data—970 mg dm−3), 1.96 days of biodegradability half-lifes (mean for solvents with available data—55 days), and 0.46 of logarithm of bioconcentration factors (mean for solvents with available data—1.15). According to Globally Harmonized System of Classification and Labelling of Chemicals, oral toxicity of >2000 mg kg−1 and inhalation toxicity of >5000 ppm indicate that they are chemicals of low acute toxicity. The predicted results show that alkyl glycerol esters may be toxic (especially towards fish) and they should be characterized in this manner to confirm their green status. Other predicted that missing values show that alkyl glycerol esters are biodegradable and they do not undergo bioaccumulation.

Table 3.

Input and completed values (shaded) for solvents that were not fully characterized. Green color indicate predicted values.

Solvent CAS Number Oral LD50 (mg kg−1) Inhalation LC50 (ppm) Fish LC50 (mg dm−3) BOD t1/2 (days) log BCF
1 Cyclopentane 287-92-3 11,400 57,377 100 10.6 1.61
2 Octane 111-65-9 7930 25,260 100 13.7 3.289
3 Nonane 111-84-2 218 3200 6.5 16.4 2.651
4 Decane 124-18-5 5000 1369 500 40.0 2.158
5 Tridecane 629-50-5 5000 41 0.9 18.2 2.979
6 Tetradecane 629-59-4 15,000 5001 1000 38.7 3.036
7 Pentadecane 629-62-9 5000 5001 100.1 39.6 2.34
8 1-pentene 109-67-1 3197 21,800 90.7 17.0 1.349
9 1-hexene 646-04-8 10,000 32,000 5.6 10.7 1.91
10 1-heptene 592-76-7 5000 27,986 175 12.6 2.372
11 1-octene 111-66-0 10,000 8500 6.8 9.3 2.819
12 1-nonene 124-11-8 4390 7116 5.0 9.6 3.266
13 Pentanol 71-41-0 2200 6119 370 4 0.463
14 oleic alcohol 143-28-2 9604 13,049 46.7 9.0 2.623
15 1,3-di-iso-propoxy-2-propanol 13021-54-0 1267 2725 33.5 1.6 0.5
16 1,3-dimethoxypropan-2-ol 1393 3794 104.7 2.5 0.5
17 1,3-di-n-butoxy-2-propanol 1130 885 69.4 2.1 0.603
18 1-ethoxy-3-iso-propoxy-2-propanol 1256 1889 377.7 4.3 0.5
19 1-methoxy-3-(propan-2-yloxy)propan-2-ol 1498 2945 160.8 2.1 0.5
20 1-n-butoxy-3-ethoxy-2-propanol 2220 2347 232.2 1.8 0.5
21 1-n-butoxy-3-iso-propoxy-2-propanol 3047 4273 188.0 1.5 0.168
22 1-n-butoxy-3-methoxy-2-propanol 1883 2582 197.6 2.1 0.5
23 1-tert-butoxy-3-ethoxy-2-propanol 2568 4601 97.1 1.3 0.5
24 1-tert-butoxy-3-methoxy-2-propanol 1477 3305 35.3 1.4 0.5
25 3-butoxypropane-1,2-diol 3875 2818 203.4 1.5 0.5
26 3-ethoxypropane-1,2-diol 2538 2663 186.2 1.9 0.5
27 3-methoxypropane-1,2-diol 2081 1985 272.4 2.6 0.5
28 3-n-butoxy-1-tert-butoxy-2-propanol 5660 5167 51.7 1.4 0.517
29 Isopropylidene glycerol 100-79-8 7000 167,197 16,700 1.3 0.125
30 Methoxycyclopentane 5614-37-9 1500 5250 34.9 6.6 0.721
31 Benzyl ethyl ether 539-30-0 2428 2625 38.6 6.6 1.374
32 1,2,3-trimethoxypropane 1305 2815 135.8 5.3 0.5
33 1,2,3-tri-n-butoxypropane 4390 5001 261.2 4.5 2.276
34 2-methylfuran 1965 9352 94.3 16.0 0.725
35 2-methyltetrahydrofuran 4500 24,083 319.6 6.4 0.343
36 3-n-butoxy-1-tert-butoxy-2-methoxypropane 2392 1656 95.4 2.9 1.094
37 Isosorbide dimethyl ether 1545 18,269 213.8 4.9 0.5
38 Dioxolane 646-06-0 2833 3,7363 31.0 6.1 0.149
39 Benzaldehyde 100-52-7 1300 1304 1.07 10 1.1
40 gamma-valerolactone 108-29-2 2800 1186 756.6 7.8 0.5
41 Dihydrolevoglucosenone 2021 2916 59.3 4.4 0.5
42 1,8-cineole 470-82-6 2480 1000 102 26.4 1.41
43 3-carene 13466-78-9 4800 8800 17.9 28 2.673
44 Neryl acetate 141-12-8 4550 5001 41.7 8.7 2.365
45 Propionic acid 79-19-4 3500 5422 51 1 0
46 Ethyl formate 1850 9800 276.6 15 0.5
47 Butyl levulinate 2052-15-5 5000 5001 26.3 3.3 0.278
48 Ethyl levulinate 539-88-8 5000 4735 121.3 3.3 0.5
49 Glycerol triacetate 102-76-1 3000 5001 72.5 2.2 0.5
50 Methyl caprylate 111-11-5 10,800 9987 95 7.0 1.856
51 Methyl lactate 27871-49-4 5000 1350 828.6 11.8 0.5
52 Methyl levulinate 624-45-3 2051 2888 92.7 3.4 0.5
53 Methyl linoleate 112-63-0 3977 5001 4.5 20.4 3.051
54 Isopropyl myristate 110-27-0 8348 11,207 8.4 10.7 3.07
55 Methyl oleate 112-62-9 2000 5001 6.1 18.9 2.694
56 Methyl palmitate 112-39-0 4786 5001 1.8 9.4 2.789
57 Isopropyl palmitate 142-91-6 17,781 45,414 50.3 13.0 1.725
58 Methyl stearate 112-61-8 5237 5001 2.8 10.4 1.46
59 Tributyl 2-acetylcitrate 77-90-7 31,500 226,174 60 14 1.6
60 Benzyl benzoate 120-51-4 1700 665 6.2 5.3 2.357
61 cis-1,2-dichloroethene 156-59-2 1393 13,700 54.2 180 1.18
62 1,1-dichloroethane 75-34-3 725 13,000 100.0 154 1.24
63 1,1,1,2-tetrachloroethane 630-20-6 670 2100 20 134.0 1.559
64 1-chloropropane 540-54-5 2000 14,034 117.8 30 0.763
65 1-chlorobutane 109-69-3 2670 11,879 101.2 18.2 1.333
66 1-chloropentane 543-59-9 3379 11,804 27.8 10.5 1.402
67 Dimethyl sulphide 75-18-3 535 5156 87.1 10.7 0.561
68 Dimethyl sulfoxide 67-68-5 2758 4291 36.9 1.6 0.349
69 Diethylamine 109-89-7 540 4000 218.5 5.0 0.21
70 2-pyrrolidone 616-45-5 2030 1083 152.5 2.5 0.5

Esters (mainly methyl or isopropyl esters of fatty acids) are characterized by low completed inhalation toxicity, rather low oral toxicity, but they some have low values (at the level of single mg dm−3) of toxicity towards fish, which suggest they are potential threats to aquatic life. Their completed values suggest that they are biodegradable, with half-lifes at the level of few to 20 days. Gamma valerolactone is considered to be green solvent, and recently it gained much attention [35]. E-M algorithm showed that LC50 by inhalation is 1186 ppm and LC50 towards fish is 756.6 mg dm−3 and biodegradability half-life is 7.8 days. These values suggest that this compound is not very toxic and it undergoes biodegradation.

Chloropropane, chlorobutane, and chloropentane are characterized by mean predicted missing value of inhalation LC50 = 12572 ppm, which is in accordance with available values for cis-1,2-dichloroethene (13,700 ppm) and 1,1-dichloroethane (13,000 ppm). The completed values show that they are slightly less toxic than the mean of the entire dataset. Mean value of LC50 towards fish is 82 mg dm−3, what shows they can be toxic to fish as the mean value of this parameters equals to 970 mg dm−3. Biodegradability half-lifes are predicted to be 18.2 and 10.5 days for 1-chlorobutane and 1-chloropentane, respectively. This value for 1-chloropropane of 30 days is available in the original dataset. What is more, the completed value for 1,1,2,2-tetrachloroethane is equal to 134 days. Chlorinated solvents are not concerned as green solvents and predicted missing values confirm this statement.

To obtain the information about the standard errors bootstrap analysis is performed [36]. The results of analysis are presented in Table 4. Standard errors are small for almost all of the variables. Only those variables, which do not contain data gaps and are not transformed, have the high standard errors.

Table 4.

Standard errors of predictions calculated with bootstrap.

Variable Mean Mean Error
Melting point (°C) −43.1378 −0.0056
Boiling point (°C) 142.3852 −0.4245
Density (g cm−3) 0.9521 −0.0005
Water solubility (mg dm−3) 116,796.6328 −279.7044
vapor pressure (Pa) 11,901.6258 403.5914
Henry law constant (Pa m3 mol−1) 2.4677 0.0955
log KOW 2.2285 0.0125
log KOA 4.4644 −0.0269
Oral LD50 (mg kg−1) 7.6122 −0.0093
Inhalation LC50 (ppm) 8.2734 0.0014
Fish LC50 (mg dm−3) 4.2248 −0.0069
BOD t1/2 (days) 2.2431 0.0065
log BCF 1.1450 0.0076

4. Conclusions

E-M algorithm is useful in predicting of organic solvents missing parameters. Algorithm allows for completing 35 values of LD50 by oral administration to rodents, 46 values of LC50 by inhalation, 57 values of LC50 towards fish, 57 values of biodegradability, and 62 values of bioconcentration factors. Some of the solvents that are considered in this study are promising from the Green Chemistry point of view, even though they have not been fully characterized yet.

E-M algorithm can be useful in characterization of other novel, potential green alternatives of other chemicals. It is important for the characterization of chemicals for their rapid screening.

Acknowledgments

F.P.-P. thanks Xunta de Galicia for financial support as a postdoctoral researcher of the I2C program. Authors would like to express their gratitude to Karol Dziedziul for pointing to E-M algorithm and for his precious remarks and suggestions.

Supplementary Materials

The following are available online. E-M algorithm description.

Author Contributions

G.Ł. performed the calculations with PCA and E-M algorithm, and wrote substantial part of paper, F.P.-P. prepared the dataset and wrote substantial part of paper, M.T. prepared the dataset, interpreted the results and wrote substantial part of paper, J.N. was guiding the research.

Funding

This research received no external funding.

Conflicts of Interest

Authors declare no conflict of interests

Footnotes

Sample Availability: Samples of the compounds are not available from the authors.

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