Pure compound property prediction¶
Introduction¶
The Property Prediction program in ADF provides quick, accurate estimates for many important pure component physical properties. At its core, the Property Prediction program maps various QSPR descriptors of an input molecule onto a single numerical value, the property estimate. Many of these property models rely on easy-to-evaluate QSPR descriptors and numerically straightforward computations, meaning that an estimate can be provided for every property in << 1s per molecule. The general expression for the models used in the Property Prediction program is as follows:
where f is a function that transforms the property value space, g is a function that maps QSPR descriptors onto a numerical value, and h is a function which also captures temperature-dependence of certain properties by including temperature, T, as an input. Additionally, C is a constant, \(n_i\) refers to QSPR values of QSPR descriptor i, and \(c_i\) and \(d_i\) are fitted coefficients corresponding to each QSPR descriptor i.
The accuracy of the property estimates depends on the nature/complexity of the input molecular structure. For many common organic structures, the property estimates should be reasonably accurate. However, as is always the case with QSPR models, the Property Prediction program will likely lose accuracy for molecules outside its training domain, i.e., for molecules that are very “dissimilar” to compounds which occur in the training set. In general, the program can be used for molecules with the following atom types:
| Accepted atom types | Example functional groups which can be used with atom type |
|---|---|
| H | Alkanes, Alkenes, Alkynes, Aldehydes, Amides, Amines, Aromatics, Carboxylic Acids, Hydroxides, Sulfides, Thiols |
| C | Acid chlorides, Alkanes, Alkenes, Alkynes, Aldehydes, Amides, Aromatics, Carboxylic Acids, Esters, Ethers, Ketones, C-X (halogens) |
| N | Amides, Amines, Aromatics, Cyanides, Imines, Nitro groups |
| O | Acid chlorides, Aldehydes, Amides, Aromatics, Carboxylic Acids, Esters, Ethers, Ketones, Nitro groups |
| F | -CF, -CF2, -CF3 |
| S | Sulfides, Thiols |
| Cl | Acid chlorides, -CCl, -CCl2, -CCl3 |
| Br | -CBr |
| I | -CI |
A brief description of molecule types for which this method will not work well is given in the General warnings section. Common molecules for which this method will fail are: (1) those that contain only one non-hydrogen atom, e.g., Methane or Water; (2) those that contain atoms not listed in the table above.
Available properties¶
The Property Prediction program can predict the values of various pure component physical properties. These properties can be of interest themselves or can be used in conjunction with other COSMO-RS property calculations (e.g., to calculate the solubility of a solid in a liquid, we must know the enthalpy of fusion and melting point of the solid – both of these properties can be estimated with the Property Prediction program). The available properties and their units are listed below:
| Property Name | Units | Additional Information | Typical error |
|---|---|---|---|
| Boiling point | K | at 1 atm | 15 K |
| Critical Pressure | bar | 1.5 bar | |
| Critical Temperature | K | 30 K | |
| Critical Volume | L/mol | 0.02 L/mol | |
| Dielectric Constant | 3 | ||
| Ideal Gas Entropy | J/(mol K) | at 298.15 K and 1 bar | 20 J/(mol K) |
| Flash point | K | 15 K | |
| Gibbs Energy Ideal Gas | kJ/mol | at 298.15 K and 1 bar | 25 kJ/mol |
| Enthalpy of Combustion | kJ/mol | at 298.15 K | 50 kJ/mol |
| Std. Enthalpy of Formation | kJ/mol | at 298.15 K and 1 bar | 30 kJ/mol |
| Enthalpy of Fusion | kJ/mol | at Normal Melting Point | 4 kJ/mol |
| Enthalpy of Form. Ideal Gas | kJ/mol | at 298.15 K and 1 bar | 25 kJ/mol |
| Enthalpy of Sublimation | kJ/mol | 5 kJ/mol | |
| Melting point | K | at 1 atm | 35 K |
| Liquid Molar volume | L/mol | at 298.15 K | 0.005 L/mol |
| (Liquid Density) | kg/L | at 298.15 K | uses Liquid Molar Volume |
| Liquid Vapor Pressure | bar | 10-30% | |
| Parachor | 7 | ||
| Solubility Parameter | (MPa)^1/2 | at 298.15 K | 0.7 |
| Triple point temperature | K | 35 K | |
| Van der Waals Area | Ų | 6 Ų | |
| Van der Waals Volume | ų | 3 ų |
Running the Property Prediction program¶
The Property Prediction program can be run from the command line. The following general flags are used by the program:
| Flag | Purpose | Example |
|---|---|---|
| -h [–help] | Produces help message | $ADFBIN/prop_prediction –help |
| -s [–smiles] | Input molecule as SMILES sting | $ADFBIN/prop_prediction –smiles <SMILES> … |
| -m [–mol] | Input molecule as .mol file | $ADFBIN/prop_prediction –mol <mol file> … |
| –temperature | Set temperature/range (K) | $ADFBIN/prop_prediction –temperature 298.15 … |
| -n | number of steps for temperature range | $ADFBIN/prop_prediction –n 20 … |
| -d [–display] | Display calculated properties | $ADFBIN/prop_prediction –d … |
| -o [–output] | Write output to file | $ADFBIN/prop_prediction –o <output file> … |
Note, if no output flag is supplied, then the results are written to a file called CRSKF by default. Additionally, the user may enter as many compounds as desired on the command line in either of the two available input formats.
The program can be run in 2 ways:
- Estimating all available properties for every molecule
- Estimating specific properties for every molecule
To estimate all properties for every input compound, simply execute the program with all molecules specified on the command line. Don’t forget that the -d flag is required to display the results in the terminal. An example of this is below.
$ADFBIN/prop_prediction --smiles CCCCCCO -o example.crskf -temperature 298.15 -temperature 398.15 -n 20 -d
Boiling point at standard pressure :
CCCCCCO 435.777 K
Critical pressure :
CCCCCCO 34.3493 bar
Critical temperature :
CCCCCCO 576.466 K
Critical volume :
CCCCCCO 0.404124 L/mol
Liquid density :
CCCCCCO 0.79182 kg/L
Dielectric constant :
CCCCCCO 10.9512
Absolute entropy of an ideal gas at 298.15 K and 1 bar :
CCCCCCO 439.885 J/(mol K)
Flash point :
CCCCCCO 342.271 K
Gibbs energy of formation for an ideal gas at 298.15 K and 1 bar :
CCCCCCO -131.869 kJ/mol
Net enthalpy of combustion at 298.15 K :
CCCCCCO -3678.12 kJ/mol
Standard state enthalpy of formation at 298.15 K and 1 bar :
CCCCCCO -384.388 kJ/mol
Enthalpy of fusion at normal melting point :
CCCCCCO 18.5054 kJ/mol
Enthalpy of formation for an ideal gas 298.15 K :
CCCCCCO -316.821 kJ/mol
Enthalpy of sublimation :
CCCCCCO 80.9799 kJ/mol
Melting point at 1 atm :
CCCCCCO 231.141 K
Liquid molar volume :
CCCCCCO 0.128949 L/mol
Parachor :
CCCCCCO 289.059
Solubility parameter :
CCCCCCO 10.1294 (MPa)^0.5
Triple point temperature :
CCCCCCO 230.404 K
Van der Waals area :
CCCCCCO 171.059 Å^2
Van der Waals volume :
CCCCCCO 120.519 Å^3
Liquid vapor pressure :
Molecule: CCCCCCO
Temperature (K) Vapor pressure (bar)
298.15 0.001229
303.15 0.001809
308.15 0.002623
313.15 0.003750
318.15 0.005289
323.15 0.007362
328.15 0.010123
333.15 0.013757
338.15 0.018487
343.15 0.024582
348.15 0.032357
353.15 0.042182
358.15 0.054484
363.15 0.069757
368.15 0.088563
373.15 0.111537
378.15 0.139394
383.15 0.172929
388.15 0.213022
393.15 0.260644
398.15 0.316852
For most applications, it is not necessary to calculate all of the available physical properties (although doing so is practically just as fast). In these cases, additional property flags need to be specified on the command line to restrict the program to calculating only certain physical properties. For example, if we were doing solid/liquid solubility calculations on Ibuprofen and Paracetamol, we would require the Enthalpy of Fusion and the Melting Point of both compounds. To calculate only these two properties, we simply have to add the two property flags “-hfusion” and “-meltingpoint” to the command line. Using the .mol file for Ibuprofen and the SMILES string for Paracetamol, we execute the following:
$ADFBIN/prop_prediction -d -m Ibuprofen.mol -s 'CC(=O)NC1=CC=C(C=C1)O' -hfusion -meltingpoint
Enthalpy of fusion at normal melting point :
CC(=O)NC1=CC=C(C=C1)O 33.0298 kJ/mol
Ibuprofen.mol 24.0336 kJ/mol
Melting point at 1 atm :
CC(=O)NC1=CC=C(C=C1)O 469.282 K
Ibuprofen.mol 331.887 K
Index of property keys¶
The available properties and their corresponding property flags are listed below:
| Property Name | Property Flag |
|---|---|
| Boiling point | -boilingpoint |
| Critical Pressure | -criticalpressure |
| Critical Temperature | -criticaltemp |
| Critical Volume | -criticalvol |
| Dielectric Constant | -dielectricconstant |
| Ideal Gas Entropy | -entropygas |
| Flash point | -flashpoint |
| Gibbs Energy Ideal Gas | -gidealgas |
| Enthalpy of Combustion | -hcombust |
| Std. Enthalpy of Formation | -hformstd |
| Enthalpy of Fusion | -hfusion |
| Enthalpy of Form. Ideal Gas | -hidealgas |
| Enthalpy of Sublimation | -hsublimation |
| Melting point | -meltingpoint |
| Liquid Molar volume | -molarvol |
| (Liquid Density) | -molarvol |
| Liquid Vapor Pressure | -vaporpressure |
| Parachor | -parachor |
| Solubility Parameter | -solubilityparam |
| Triple point temperature | -tpt |
| Van der Waals Area | -vdwarea |
| Van der Waals Volume | -vdwvol |
General warnings¶
This method will fail for the following types of molecules:
- Those that contain only one non-hydrogen atom (e.g., Methane or Water). However, experimental data is ample for these small molecules. The vapor pressure model is the exception in that it can represent such small structures.
- Those that contain atoms or substructures that are not listed in the Accepted atom types table above.
- Polymers and Ionic Liquids
This method will lose accuracy for some properties in the following domains:
- Molecules with many different types of functional groups
- Molecules that are extremely light (< 3 non-Hydrogen atoms) or heavy (> 30 non-Hydrogen atoms)