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Showing posts from May, 2009

Testing the Razors

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As I wrote initially, I like the razors because they are easy to learn and use. I have simulated two molecules only, because they are the standard (minimal) test I perform on simulation software. I come from the old school, where simulation means generating a plot from chemical shift values (while the razors mainly estimate the chemical shifts from the structure). The first test is N,N-dimethylformamide. 1-H exp. calc. diff. 8.019 1.609 -6.41 2.970 3.001 0.031 2.883 3.001 0.118 13-C exp. calc. diff. 162.6 198.7 36.1 36.4 34.568 -1.9 31.3 34.568 3.3 The second test is ortho-dichloro-benzene. Simulated by iNMR: Simulated by HNMRazor:

Interview with Kevin Theisen

Kevin already told his story on the offcial website of iChemLabs . I was curious to know more details... Here is the first offical interview of my blog. OS: How much accurate are the predictions of the NMRazors? KT: The NMRazors are fairly accurate for most molecules. They will handle any molecule encountered in an undergraduate organic chemistry course. The NMRazors will be less accurate for molecules where complex anisotropic and 3D effects are present. I used several published references when developing the algorithms in the NMRazors and they are cited on the NMRazor website. OS: Programming is similar to chemical synthesis: there are starting materials and finished products. What were the staring material for the NMRazors? KT: When I first began programming chemistry applications, I started with a graph based depth-first search traversal of a database of reactions in order to optimize synthetic routes. A credible synthetic database was too expensive for me to obtain as an undergrad...

Unusual Solution

This is how I solved the problem of the razor. 1- I described the bug on my (this) blog. 2- It rang a bell into Kevin's mind; 3- Kevin recompiled both programs (1-H and 13-C). It may sound difficult for you, yet recompiling a program is very easy (provided you are the author, it can be a nightmare in other cases!). The new versions work and produce the desired plots. I will return on the subject with more articles. Thank you, Kevin!

We Insist!

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Maybe there is an error into the drawing module, or I haven't understood how to use it. Today I am going to bypass drawing with a clever trick. You can follow me step by step. 1) I open NHMRazor. 2) Command: Find Molecule. 3) I insert a molecular formula: C6H12. 4) I find 30 result: great! I scroll down the list and select 2-methyl-2-ene. 5) I click the button "Load". This loads the structure: We have almost done it! Next step: 6) A click on the triplet icon. 7) This time I don't select any solvent (who knows?) and assume that the default settings are OK. Final step: button OK... I am not showing the result because nothing has changed since yesterday ("The server has an error that is currently being fixed. Sorry for any inconvenience"). Have you ever played Myst? You know the feeling.

A Picture from Kevin Theisen

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Shaving with a new HNMRazor

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The NMR razors are simple and (probably) powerful applications that can simulate a spectrum directly from the molecular formula. For the user's point of view it works like a (very) simplified version of ChemDraw. When you have finished drawing the structure, you hit a button to simulate the spectrum. When you hit the button, the program asks you such spectroscopic details like solvent, temperature, magnetic field, etc.. When you have finished this further step, the razor calls home. Yes, because all you have downloaded is a graphic interface, the true program is running into a remote and ultra-secret location. I like this program because I have understood everything in 5 minutes. To start with, I have simulated the 1-H spectrum of ethyl acetate in CDCl3, at 200 MHz. Here it is: Well, you know, I am not a lucky guy! Enough for today. If you want to try by yourself: http://www.ichemlabs.com/content/nmrazors This morning I shaved my face with a Gillette blue II. It is as good as a Gil...

Off-Topic

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I am not particularly inclined to blog in May. Do you want to play with me ?