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Sep 05, 2012 Organic, chem Structure, calculator,.

Synthesis and Use of New Heterocyclic and polymers for the Protection of Steel in Acid Medium

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Aug 03, 2009 reaction calculator for organic synthesis.

I think that every synthetic organic chemist should take a look at in Angewandte Chemie. It’s on the application of computer algorithms to planning synthetic routes, which is a subject that’s been worked on for fifty years or more – without, it has to be said, making too much of an impression on working organic chemists. But after reading this paper, from Bartosz Grzybowski and co-workers at the Polish Academy of Sciences, I’m convinced that that is going to change. I don’t know if this particular software, or even this particular computational approach (which I last is going to do it, although they both look very promising. But to a first approximation, those conditions don’t matter – what seems inescapable to me is that the generation of synthetic routes in organic chemistry is subject to automation, and we are getting very close to seeing this put into use.

Most important name reactions and keywords for the field of organic synthesis.

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Organic chemistry: “R and S naming”

Can type in the reagents used for an organic chemical reaction and the products.

We publish practical and reliable organic, organometallic and inorganic chemical synthesis, reactions and procedures deposited by synthetic chemists..."


The database is designed to be searched for kinetics data based on the specific reactants involved, for reactions resulting in specified products, for all the reactions of a particular species, or for various combinations of these..." Chemical Kinetics Database For more information see or the



Multimedia Chemical Kinetics Database on Oxygenated VOC's Gas Phase Reactions (Text & Images).

Organic chemistry: “R and S naming problems”.

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But these now seem like solvable problems, and that’s what I want to emphasize. There seems to be no reason why time, money, and effort cannot continue to make this sort of approach work better and better – and it’s already working better than most people realize. In fact, I’m willing to stipulate that software will, in fact, eventually (how soon?) turn out to provide plausible synthetic routes to most compounds that you give it, with the definition of “most” becoming progressively more stringent as time goes on. So where exactly does that leave us organic chemists?

Well, back in the 1960s, it took an R. B. Woodward (or someone at his level, and there weren’t too damn many of those) to look at some honking big alkaloid and figure out a way that it could be made. There were fewer reactions to choose from, and analytical techniques were (by our standards) quite primitive, so just figuring out that you’d made what you thought you’d made at each step could be a major challenge all by itself. But the science has advanced greatly – we have a lot more bond-forming reactions than we used to, and a lot of elegant ways to set stereochemistry that just weren’t available. And we have far better ways to know just what our reactions have produced, to make sure that we’re on the right track.

Examples of "Synthetic Organic Chemistry I" Course Lectures include  For more information see ; ;
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  • Organic chemistry: Three types of SN2 reaction

    Organic chemistry: “Stereochemistry”. Stereochemistry. carbons ("") vs. molecules. molecules. and . R and S naming

  • Organic chemistry: “SN2, SN1, E2, and E1 reactions”

    Organic chemistry: “More on SN2, SN1, E2, and E1 reactions”

  • Organic chemistry: “Radical reactions”.

    Organic chemistry: “”. Addition reactions with alkenes: addition of H2 (hydrogenation); addition of HX (). vs. anti-.

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Organic chemistry: “Retro Diels-Alder reaction”.

One response in the total synthesis community has been to turn to making even larger and more complicated molecules, but that (at least to me) tends to reduce to the “find new chemistry” rationale, and there may be easier or more direct ways to find new chemistry. That, though, looks like the place to be in general. All those transformations that have been painstakingly entered into this software were discovered by organic chemists themselves – and no one knew that there was such a thing as a Friedel-Crafts reaction or a Suzuki coupling until those reaction were discovered. Each new reaction opens up a new part of the world to the techniques of organic chemistry. If it does, in the end, come down to software for reaction planning, then each new reaction that’s discovered will suddenly expand the capability of that program, and it will be able to generate good synthetic routes to things that it couldn’t before (and neither could anyone else).

Organic chemistry: “ reactions”.

And this isn’t a purely academic debate either. The fact that synthesis has become a victim of its own success has had a huge (and many would say detrimental) impact on the economy. It’s very similar to what happened with software and programming, with many software jobs getting outsourced because of their evolution into plug-and-play protocols.

Organic Chemistry Portal - Reactions

CROs such as Cyclofluidic have started to capitalise on this by adapting batch chemistry to flow. The beauty of this is that after the right protocol has been found you have complete reliability over your product. Syntheses of a dozen steps can now be performed over as many hours leading to huge cost savings downstream.

Organic reaction mechanisms - Organic Chemistry Help!

In 2011 Zen19D reached 5 dan in Go (scale of 1-9 for professionals). 5 years later, AlphaGo is the best Go player that has ever existed. Although I would estimate that synthesis is a tougher problem than Go (mostly because of imperfect/incomplete information in the literature and complicated stereoelectronic and functional group compatibility issues), Go was a MUCH tougher problem than chess, and chess was a MUCH tougher problem then checkers, and checkers was a MUCH tougher problem than [so on and so forth]. Many AI experts thought we were decades from a computer that could defeat a 9 dan professional without handicaps. Point is, AI almost always progresses faster than you think. As it gets better at what it does, it gets better at getting better at what it does. Programs for organic synthesis are no different. If a program can be the approximate equivalent of an undergraduate today, it will be a graduate student in 5 years, and a professor 2 years after that, then one month later it’s hanging Baran’s Ingenol synthesis up on it’s refrigerator, patting him on the head and telling him how cute it was that he came up with that all on his own. But most practitioners will bury their head in the sand here and insist that they could never be replaced by computers.

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