Chematica

Chematica is a software/database that uses algorithms and a collective database of 250 years of organic chemical information to predict and provide synthesis pathways for molecules. The software development, led by Bartosz A. Grzybowski, took place for a decade when it was finally publicized in August, 2012.

Chematica
Developer(s)Elizabeth Wylie, Matthew Wampler-Doty, Ling Su, Andrea Cadeddu, Aaron Oppenheimer, Patrick Fuller, Malous Kossarian, Chris Gothard, Nosheen Gothard, Kamel Meguellati, Mikolaj Kowalik, Kyle Bishop, Bartosz Grzybowski
Initial releaseN/A
Written inPython, Java, C++, Coffeescript
PlatformCross-platform
Available inEnglish
TypeComputer algebra, numerical computations, Information visualization, statistics, user interface creation
LicenseProprietary

In 2017, the software and database were wholly purchased by Merck KGaA | MRK.[1][2] The software has been made available commercially since the acquisition as Synthia.[3]

Features

The software was designed to combine long synthesis paths into shorter and more economical paths. The software has the potential to enhance a chemists quest for drug discovery and other industrially important chemicals. There are estimated seven million chemicals connected by the number of reactions and catalogues 86,000 chemical rules.[4] The software complements other attempts such as manual searching or semi-automated search tools that use back-tracking to assess each possible step. Back-tracking has been found to be inefficient as even a five-step synthesis amounts to 1019 possible pathways.[5]

One can specify a molecule in several ways, including searching by Beilstein Registry Number, CAS registry number, chemical name, SMILES structure, or by drawing the molecule diagram itself.[6] It supports optimization of reactions by cost. One can scale node sizes by molecular weight, product occurrence, and reactant occurrence. The program also supports 3D modeling of individual molecules, as well as labeling of functional groups.[6]

The program also notes regulated and unregulated compounds, and uses specialized algorithms that avoid these. It also gives the classification and reasons for regulation.[6]

One-Pot Reactions

The software has the potential to determine synthesis pathways that can take place through a "one-pot" reaction, where all starting chemicals are mixed simultaneously to achieve final product, thereby eliminating any purification and need for multiple steps.[4]

References
  1. Merck KGaA to buy Chematica, by Andy Extance, at ChemistryWorld; published May 12, 2017; retrieved January 1, 2019
  2. Klucznik, Tomasz; Mikulak-Klucznik, Barbara; McCormack, Michael P.; Lima, Heather; Szymkuć, Sara; Bhowmick, Manishabrata; Molga, Karol; Zhou, Yubai; Rickershauser, Lindsey; Gajewska, Ewa P.; Toutchkine, Alexei (March 2018). "Efficient Syntheses of Diverse, Medicinally Relevant Targets Planned by Computer and Executed in the Laboratory". Chem. 4 (3): 522–532. doi:10.1016/j.chempr.2018.02.002. ISSN 2451-9294.
  3. Synthia
  4. Fellman, Megan. "Northwestern Scientists Create Chemical Brain". Northwestern University Press. Retrieved 25 August 2012.
  5. Grzybowski, Bartosz A.; Kyle J. M. Bishop; Mikołaj Kowalik; Chris M. Gothard; Aaron M. Drews; Nosheen A. Gothard; Alex Weckiewicz; Patrick E. Fuller (August 2012). "Parallel Optimization of Synthetic Pathways within the Network of Organic Chemistry". Angew. Chem. Int. Ed. 51 (32): 7928–7932. doi:10.1002/anie.201202209. PMID 22807100.
  6. Chematica Demonstration. May 2012. Retrieved 2013-04-09.
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