Chematica software and computer cluster studies database since 1760 of 7 million organic chemicals with 7 million reactions to automatically find valuable practical recipes: Rich Murray 2012.08.27

[Rich Murray-2]

Chematica software and computer cluster studies database since 1760 of
 7 million organic chemicals with 7 million reactions to automatically
find valuable practical recipes: Rich Murray 2012.08.27

With exponential speed, we'll see this automatization of innovative
research and engineering of practical, highly valuable chemical,
biological, mathematical and physical science and technology knowledge
on a global network level, like Wikipedia encyclopedia...

http://phys.org/news/2012-08-google-steroids-scientists-chemical-brain.html#nwlt

'Google on steroids': Scientists create chemical brain
August 22, 2012

Northwestern University scientists have connected 250 years of organic
chemical knowledge into one giant computer network -- a chemical
Google on steroids.

This "immortal chemist" will never retire and take away its knowledge
but instead will continue to learn, grow and share.

A decade in the making, the software optimizes syntheses of drug
molecules and other important compounds, combines long (and expensive)
syntheses of compounds into shorter and more economical routes and
identifies suspicious chemical recipes that could lead to chemical
weapons.

"I realized that if we could link all the known chemical compounds and
reactions between them into one giant network, we could create not
only a new repository of chemical methods but an entirely new
knowledge platform where each chemical reaction ever performed and
each compound ever made would give rise to a collective 'chemical
brain,'" said Bartosz A. Grzybowski, who led the work. "The brain then
could be searched and analyzed with algorithms akin to those used in
Google or telecom networks."

Called Chematica, the network comprises some seven million chemicals
connected by a similar number of reactions. A family of algorithms
that searches and analyzes the network allows the chemist at his or
her computer to easily tap into this vast compendium of chemical
knowledge. And the system learns from experience, as more data and
algorithms are added to its knowledge base.

Details and demonstrations of the system are published in three
back-to-back papers in the Aug. 6 issue of the journal Angewandte
Chemie. Grzybowski is the senior author of all three papers.
He is the Kenneth Burgess Professor of Physical Chemistry and Chemical
Systems Engineering in the Weinberg College of Arts and Sciences and
the McCormick School of Engineering and Applied Science.

In the Angewandte paper titled "Parallel Optimization of Synthetic
Pathways Within the Network of Organic Chemistry," the researchers
have demonstrated algorithms that find optimal syntheses leading to
drug molecules and other industrially important chemicals. "The way we
coded our algorithms allows us to search within a fraction of a second
billions of chemical syntheses leading to a desired molecule,"
Grzybowski said. "This is very important since within even a few
synthetic steps from a desired target the number of possible syntheses
is astronomical and clearly beyond the search capabilities of any
human chemist."

Chematica can test and evaluate every possible synthesis that exists,
not only the few a particular chemist might have an interest in. In
this way, the algorithms find truly optimal ways of making desired
chemicals. The software already has been used in industrial settings,
Grzybowski said, to design more economical syntheses of companies'
products.

Synthesis can be optimized with various constraints, such as avoiding
reactions involving environmentally dangerous compounds. Using the
Chematica software, such green chemistry optimizations are just one
click away.

Another important area of application is the shortening of synthetic
pathways into the so-called "one-pot" reactions. One of the holy
grails of organic chemistry has been to design methods in which all
the starting materials could be combined at the very beginning and
then the process would proceed in one pot -- much like cooking a stew
-- all the way to the final product.

The Northwestern researchers detail how this can be done in the
Angewandte paper titled "Rewiring Chemistry: Algorithmic Discovery and
Experimental Validation of One-Pot Reactions in the Network of Organic
Chemistry." The chemists have taught their network some 86,000
chemical rules that check -- again, in a fraction of a second --
whether a sequence of individual reactions can be combined into a
one-pot procedure.

Thirty predictions of one-pot syntheses were tested and fully
validated. Each synthesis proceeded as predicted and had excellent
yields. In one striking example, Grzybowski and his team synthesized
an anti-asthma drug using the one-pot method. The drug typically would
take four consecutive synthesis and purification steps. "Our
algorithms told us this sequence could be combined into just one step,
and we were naturally curious to check it out in a flask," Grzybowski
said. "We performed the one-pot reaction and obtained the drug in
excellent yield and at a fraction of the cost the individual steps
otherwise would have accrued."

The third area of application is the use of the Chematica network
approach for predicting and monitoring syntheses leading to chemical
weapons. This is reported in the Angewandte paper titled "Chemical
Network Algorithms for the Risk Assessment and Management of Chemical
Threats." "Since we now have this unique ability to scrutinize all
possible synthetic strategies, we also can identify the ones that a
potential terrorist might use to make a nerve gas, an explosive or
another toxic agent," Grzybowski said. Algorithms known from game
theory first are applied to identify the strategies that are hardest
to detect by the federal government -- the use of substances, for
example, such as kitchen salt, clarifiers, grain alcohol and a
fertilizer, all freely available from a local convenience store.
Characteristic combinations of seemingly innocuous chemicals, such as
this example, are red flags. This strategy is very different from the
government's current approach of monitoring and regulating individual
substances, Grzybowski said. Chematica can be used to monitor patterns
of chemicals that together become suspicious, instead of monitoring
individual compounds.

Grzybowski is working with the federal government to implement the
software. Chematica now is being commercialized. "We chose this name,"
Grzybowski said, "because networks will do to chemistry what
Mathematica did to scientific computing. Our approach will accelerate
synthetic design and discovery and will optimize synthetic practice at
large." Journal reference: Angewandte Chemie Provided by Northwestern
University

Read more at: http://phys.org/news/2012-08-google-steroids-scientists-chemical-brain.html#jCp

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