The d-blo[g]ck

some chemistry and other points of scientific interest

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Too many compounds

2 July, 2011 (14:34) | chemistry, Organic Synthesis, Uncategorized | 2 comments

Kodadek posits that combinatorial chemistry should be applied to large unbiased libraries for de novo screening efforts as was originally intended, in order to overcome the limitations of current compound collections. Basically he cites two ways to accomplish this; 1) diversity-oriented synthesis (DOS) which prepares libraries of compounds with varied structural motifs and 2) big, and I mean BIG, compound libraries with numbers described in scientific notation.


For those of you who don’t know what combinatorial chemistry is; it’s basically hedging your bets on drug discovery. It entails using synth-bots, automation, and algorithmic synth design to produce large libraries of potential “lead compounds”. Lead compounds are those bare bone drug prototype molecules that don’t necessarily work well, but do illicit something similar to the desired response at the target receptor. These leads are later derivatized into yet another large library of similar analogues that are “high-throughput screened” against cell lines, en vitro targets, and animals.

Typical combinatorial libraries contain anywhere from a few hundred to a few thousand compounds (usually produced in microgram quantities). Recent developments point to the fact that many of our compound libraries should in fact contain more like a few hundred thousand to a few million compounds. This helps alleviate something we call combinatorial bias, human creativity getting in the way of a truly algorithmic approach to drug discovery.

Finding a molecule to fit a receptor site can be thought of as trying to force a metric nut onto a standard bolt. Not an easy task. Combinatorial chemistry in essence tries to accomplish that by trying out several million different nuts all differing by 0.0001 mm.

Carbonic acid isolated!? surely you jest

13 January, 2011 (19:18) | chemistry, exciting science, spectroscopy | 4 comments

Gas-phase carbonic acid isolated and characterized for the first time

This experiment not only is of high importance for basic research but also for astronomy. The identification of gas-phase carbonic acid in the atmosphere of celestial bodies may be facilitated by the detailed spectra of gas-phase carbonic acid described in this study. “Conditions in space environments suggest that gas-phase carbonic acid may be found in the coma of comets or the poles of Mars,” says Thomas Loerting. “However, infrared spectra currently measured in extraterrestrial environments are still too imprecise to be comparable to the results produced in our laboratory.”

The isolation of carbonic acid has always been a wild goose chase. On thermodynamic grounds carbonic acid should decompose to carbon dioxide and water outside of aqueous solution. It does; past treatments of the system didn’t account for the possibility of phenomena like dimerization into metastable species.

Glass pulls crystal symmetry phase trick

13 January, 2011 (18:27) | chemistry, materials | 1 comment

The physical properties of silica glass have long eluded materials chemists. This article is two years old but is still a worthy read:

Dual Personality of Glass Explained at Last

silicon dioxide icosahedron

This geometry is incapable of slotting together, or tessellating, to form the regular 3D lattice characteristic of a solid. But equally they cannot move around freely because they are larger than the original particles.

Royall thinks that the molecules of real glass takes on the same icosahedral structure, leaving it unable to crystallize into a solid, but not free enough to have liquid-like properties.

Cosmic strings, molecular orbitals, crystal behavior…symmetry always seems to have a part to play in the goings on of the universe.


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