Software that can predict organic reaction products is a hotly pursued but unsolved challenge because of its obvious potential in pharmaceutical industry. However, stereochemistry is not included in the vast majority of the previous efforts, although its control is often the most challenging and interesting part of organic reactions. This is not an accidental omission but maybe an inherent problem of molecule representations in computer. The molecule representation methods (strings, tables, matrix etc.) used by programmers differ from those of chemists, which may be the reason that the software can not fully take advantage of the knowledges and wisdoms of chemists.
VirtualChemist is an organic reaction software suite focusing on stereochemistry. A new design (
https://www.jstage.jst.go.jp/article/jccjie/8/0/8_2021-0050/_article ) was proposed to translate molecule Lewis structure to machine readable format data. Using Lewis formula as the only user input, which can be either an existing molecule or a molecule unknown yet,
(1).
Model Kit can generate the molecule 3D structure. With sigma-bond rotation and "Flip" functionality, it can present conformational isomers.
(2).
Stereoisomer can identify all the stereocenters and configurational isomers for the compounds with tetrahedral carbon stereocenters. It can also handle molecules with carbon-carbon and carbon-nitrogen double bond stereocenters.
(3).
Tautomer can simulate the practice of chemists writing acid/base catalyzed tautomerization and enumerate all the tautomers.
(4).
Reaction Stereochemistry is a mechanism-based organic reaction software focusing on stereochemistry, It can track molecular 3D configuration changes in every elementary reaction step.
The demo videos show the basic graphic user interfaces of the software and its basic functionalities.
There are two versions of the software, free version and commercial version. The table below summarizes the major differences between the two versions.
| Model Kit | Stereoisomer and Reaction Stereochemistry | Tautomer |
| Free | Commercial | Free | Commercial | Free | Commercial |
| conformational isomer | only one | one or more | only one | one or more |
|
|
| configurational isomer |
|
| only one | one or more |
|
|
| reaction set |
|
|
|
| only one | one or more |
| user enter Lewis Formula | no | yes | no | yes | no | yes |
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ProcessEngineer is an open-source petro-chemical process simulation software (https://www.gitlink.org.cn/yuming086/petrochemical-process-simulation-software). With the help of Microsoft Visual Studio, its C++ source codes can be read, modified, and re-compiled.
CompressorDynamics, developed based on
ProcessEngineer, may be useful for centrifugal compressor surge analysis as well as the start-up and shutdown simulations of centrifugal compressors.