My major was polymer and now my project is polymer. I don’t quite care the InChI campaign much. I don’t know what is so importance in the reactions published on JACS or JOC. I don’t know how to design a molecule, or I cannot make sure the molecules can be synthesized. I certainly cannot meet any standard of a chemist.
I certainly cannot meet any standard of physics either because my maths is weak.
To let my future look less pessimistic I should be strong at at least one aspect as soon as possible. I choose chemistry. So…
If you are a synthetic chemist, would you please try to answer my questions?
How can I be synthetically proficient, capable of designing molecules that are synthesizable, and when designing them also knowing the reactions needed?
What molecule did you synthesize? What is that project about? How did you know you needed this structure? How did you also know you could synthesize this molecule with acceptable yield? What reactions were involved in the synthesis?
Why do you think you have this ability?
Let me think of the highest standard I can think of: suppose I am applying for a postdoc in a total synthesis group! Then, to meet the standard:
Is it enough that I read thoroughly a textbook of organic synthesis, many times? As I know, a thick book can well be filled up with only named reactions. And there are new reactions coming out every day from JOC and JACS and Angew Chem. These are not in the textbooks of organic synthesis. Do I also need to know most, if not all, of the named reactions in mind? Do I need to review some partial history of organic synthesis, that is, a lot of JOC or JACS papers? What should I read further if I have read Organic Chemistry and Theoretical/Physical Organic Chemistry? Is theories important in organic synthesis?
How do you comment on a new reaction published on JACS or JOC or a new total synthesis on Angew. Chem., besides quick and high yield and stereoselective and short path? What’s so funny in this kind of papers?
Why click chemistry is good? What is difficult before the invention of click chemistry? And why that difficult task is also important?
When do you feel a kind of freedom playing around organic synthetic chemistry? When do you feel no real difficulty in organic synthesis? How can I achieve this status?
I don’t think you should expect to know all possible reactions, but it obviously helps to have a very good knowledge. Beyond that you need access to tools like Beilstein Crossfire and "SciFinder"http://www.cas.org/products/scifindr/index.html from the Chemical Abstracts Service.
I guess it’s like going on a journey. It helps if you have a good knowledge of where you’re going and the various routes you can follow, but for the detail you will want to have some good maps to guide you.
I know this two resource. When you invent a molecule, you will consider how to break it into parts that can be coupled by reactions you know. If you still have to search for possible reactions on SciFinder, it is much harder to invent a molecule. And by ‘invent’ I mean there’s no earlier paper describing the synthesis of that.
So I guess to have some kind of freedom in designing a molecules one should have known a certain number of reaction. What’s that number? Was an ordinary textbook of organic synthesis enough? Plus a book of named reaction? Plus some research on literature?
And, if you are good at organic synthesis, what do you think you are actually good at? What eases you in organic synthesis?
I’m not a synthetic goddess like some of the natural products folk, but as far as DESIGNING molecules goes: know your application. Think about what you want from the material. Would air/water/thermal/photostability be necessary for the purpose you have in mind? Solubility? If you want an electron acceptor for solar cells, for instance, you need it to absorb a lot of visible light and be photostable with a reasonably low-lying LUMO. So you take a basic dye structure and tack on electron-withdrawing groups—in positions you know are synthetically feasible—and then you go about making it. Then test for photostability and check out the electrochemistry and device performance. If something is amiss, go back to the drawing board and figure out how to tune the properties of what you’re making.
It does help to be familiar with the literature in your field. It also helps to know some basic organic chemistry. Understand what conditions certain functional groups can and cannot tolerate. At least be aware of which reactions you’re good with. If you can rock out some Sonogashiras, design materials that will let you use them. As far as finding reactions, Scifinder will get you through a lot…don’t expect to be able to make up reaction conditions off the top of your head at first. That may take a few years. Don’t expect amazing yields every time—those come with a lot of experience. Don’t let failure get to you—you will experience a lot of it. :)
Thanks a lots Sherman! You simply answered my question! The following isn’t really a further question, but only something more to say.
As a materials scientist I should and do know the physicochemical aspects of my fields, i.e. the structure-function relationship. So I suppose I will know what structures I need in my field. The obstacles are often rather the synthetic difficulties. You can imagine a perfect structure for some application but that has not been realized only because its hard to synthesis. So what we have to know is not only a structure, but a synthesizable structure in particular. This rely on our synthesis knowledge and skills thus raising my questions in the post.
Thank you again.
Andrew, let me give you my view on the whole matter; and by that I mean partly my own personal view (I am rather a jack of all trades guy), as well as my experience here in industry (BASF, that is):
You say your background is polymers, and more from a material science point. This is an awesome starting point because it gives you broad overview over many things, as well as a solid foundation for what may actually be needed by a customer, or what problems they will have.
What I would suggest you do check out is not the same that someone doing chemistry in pharma would do: it does not matter if you know all the syntheses and pathways and reagents, as your selection of what is economically reasonable will be much more limited if material price is an issue. Pharma prices are not really determined by their synthetic routes as much as clinical research and marketing.
So it would be best to get a good overview over simple chemistry, simple routes which would work in an industrial setting, and that often means “no solvents” = and who learns this stuff at university? noone.
Learn about polymer engineering, and reaction engineering — this way you will be able to understand what it takes to go from idea to product. And you will make lots of friends if you actually know these things.
Start to think about chemistry from the viewpoint of a being living in nanometer and micrometer scales, rather than angstroms like most organic chemists do.
Or in short: embrace what you are trained for. Extent this different point of view and do not try to become another “bad” organic chemist. ;)
Words of wisdom, Daniel. Words of wisdom!
This post was published quiet a long time ago. I have determined to forget difficult organic synthesis and concentrate in material physics. Nowadays chemical structures seems to less important compared with topology at multiple scales. I feel easier than other to study this physics.
But you provided a complete thought which supports my decision. It’s very encouraging. Thank you!
Andrew, long ago does not mean anything anymore. Or it does, depending on your school of thought. Nevertheless, the questions you were asking are timeless, I believe. And there is more to it than just the simple question about chemistry. ;)