Chematica: Difference between revisions

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{{Short description|Chemical synthesis software}}

{{advert|date=September 2014}}

{{Infobox software

| name = Chematica

| logo =

| screenshot =

| caption = software info GNU/Linux frontend

| developer = 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

| released = N/A

| frequently_updated = yes<!-- Release version update? Don't edit this page, just click on the version number! -->

| platform = [[Cross-platform]]

| language = English

| programming language = [[Python (programming language)|Python]], [[Java (programming language)|Java]], [[C++]], [[CoffeescriptCoffeeScript]]

| genre = [[Computer algebra system|Computer algebra]], [[List of numerical analysis software|numerical computations]], [[Information visualization]], [[List of statistical packages|statistics]], [[Graphical user interface|user interface creation]]

| license = [[Proprietary software|Proprietary]]

| website =

}}

'''Chematica''' is a software that uses algorithms and a collective database to predict synthesis pathways for molecules. The software development, led by Bartosz A. Grzybowski, was publicized in August 2012. In 2017, the software and database were wholly purchased by Merck KGaA | MRK.<ref name=MRK>[https://www.chemistryworld.com/news/merck-kgaa-to-buy-chematica/3007276.article Merck KGaA to buy Chematica], by Andy Extance, at ChemistryWorld; published May 12, 2017; retrieved January 1, 2019</ref><ref>{{Cite journal|last1=Klucznik|first1=Tomasz|last2=Mikulak-Klucznik|first2=Barbara|last3=McCormack|first3=Michael P.|last4=Lima|first4=Heather|last5=Szymkuć|first5=Sara|last6=Bhowmick|first6=Manishabrata|last7=Molga|first7=Karol|last8=Zhou|first8=Yubai|last9=Rickershauser|first9=Lindsey|last10=Gajewska|first10=Ewa P.|last11=Toutchkine|first11=Alexei|date=March 2018|title=Efficient Syntheses of Diverse, Medicinally Relevant Targets Planned by Computer and Executed in the Laboratory|journal=Chem|volume=4|issue=3|pages=522–532|doi=10.1016/j.chempr.2018.02.002|issn=2451-9294|doi-access=free}}</ref> Since the acquisition, the software has been made commercially available as Synthia.<ref>[https://www.sigmaaldrich.com/chemistry/chemical-synthesis/synthesis-software.html Synthia]</ref>

'''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. Press have dubbed the software as the "Google of chemistry"<ref name=kurzweilai>{{cite web|title=A ‘Google’ for chemistry invents best path to new compounds in seconds|url=http://www.kurzweilai.net/a-google-for-chemistry-invents-best-path-to-new-compounds-in-seconds|publisher=KurzweilAI.net|accessdate=25 August 2012}}</ref> and "chemical brain".<ref name=northwestern-ref>{{cite web|last=Fellman|first=Megan|title=Northwestern Scientists Create Chemical Brain|url=http://www.northwestern.edu/newscenter/stories/2012/08/scientists-create-chemical-brain-.html|publisher=Northwestern University Press|accessdate=25 August 2012}}</ref>

==Features==

The [[software]] was designed to combine long synthesis paths into shorter and more economical paths.<ref Thename=northwestern-ref>{{cite softwareweb|last=Fellman|first=Megan|title=Northwestern hasScientists theCreate potentialChemical to enhance a chemists quest for [[drug discovery]] and other industrially important chemicalsBrain|url=http://www.northwestern.edu/newscenter/stories/2012/08/scientists-create-chemical-brain-.html|publisher=Northwestern ThereUniversity arePress|accessdate=25 estimatedAugust seven million chemicals connected by the number of reactions and catalogues 86,000 chemical rules.2012}}</ref name=northwestern-ref />

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.<ref name=AngewChemIntEd_51_7928>{{cite journal|last=Grzybowski|first=Bartosz A. |author2=Kyle J. M. Bishop |author3=Mikołaj Kowalik |author4=Chris M. Gothard |author5=Aaron M. Drews |author6=Nosheen A. Gothard |author7=Alex Weckiewicz |author8=Patrick E. Fuller|title=Parallel Optimization of Synthetic Pathways within the Network of Organic Chemistry|journal=Angew. Chem. Int. Ed.|date=August 2012|volume=51|issue=32 |pages=7928–7932|doi=10.1002/anie.201202209|urlpmid=http://onlinelibrary.wiley.com/doi/10.1002/anie.201202209/abstract22807100 }}</ref>

OneA molecule can specifybe a moleculespecified in severalmultiple ways, including searching by [[Beilstein Registry Number]], [[CAS number|CAS registry number]], chemical name, [[SMILES]] structure, or by drawing the molecule diagram itself.<ref name=2012_Demo>{{cite video|title=Chematica Demonstration|| date=May 2012 |url=httphttps://www.youtube.com/watch?v=h7m8JCiGPFU}} {{Retrieved | accessdate=2013-04-09 }}</ref> 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.<ref name=2012_Demo />

The program also notes regulated and unregulated compounds, and uses specialized algorithms that avoid these. It also gives the classification and reasons for regulation.<ref name=2012_Demo />

===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.<ref name=northwestern-ref />

==References==

<references />

{{Reflist|2}}

[[Category:Chemical databases]]