Sunday, August 20, 2006

Frontiers of Chemistry:
A recent issue of Nature Magazine (August 3,2006) has an article on the "relevance of chemistry". This comes at a time when chemistry is increasingly seen as less exciting than physics, biology, astronomy,etc.. Other disciples are seen as "nibbling away at the edges of chemistry", and because chemistry is so important to industry, "the scientific enterprise that fuels industry" according to the article, it may be that chemistry is only "a form of engineering- a quest for particular solutions to particular problems".
The article above tries to set forth some of the big problems that working chemists see as important. Hence its title, 'What Chemists want To Know'. One of the core problems is, of course, the chemistry of life. As the article states,
"...many of the gaps in scientific understanding of the fundamental processes of molecular biology, such as protein folding, genetic encoding of biomolecular function, and highly selective molecular recognition, are fundamentally chemical problems."
The article go on to say that despite the misconceptions of many (most ?) molecular biologists that,
"Scientific understanding is still not good enough to provide a rational and predictive basis for the kind of molecular scale interventions needed in biomedicine and drug development."
The article goes on to mention that processes such as signal transduction are making chemistry part of information science. This leads via the study of self assembly to the information science of self organization in general.
Another of the frontiers is the design of "chemical learning systems" that can be "trained". This merges into neurobiology at its edges. There is also the unresolved problem of the interface between structure and function, and this is "...often possible only for relatively simple, small molecules-and even then there are many details of the problem that have yet to be clarified."
The article further goes on to state that "the dynamic behavior of molecules can play as big a role in their reactivity as their molecular structure.", and that, "the interactions between biomolecules aren't simply a matter of fitting a key into a lock".
As an aside I can see this as something that used to bother me a a chemist/biochemist. No matter the "perfect fit" of things such as an enzyme and substrate what are the stochastic probabilities of a proper conformational "fit" in the environment of a cell ?
It may be that the newer view of reactions as, "how the molecule's peptide chain negotiates a trajectory across this energy landscape so that it ends up in a 'valley' corresponding to the correct conformation" may contain many parts of the solution to this problem. In other words, the dynamics are key.
Some chemical reactions, but only the simpler ones, are now susceptible to guidance across an energy landscape by methods such as lasers. This comes back to the eternal problem of chemical synthesis- how to "assemble atoms into new molecules in a predictable and effective way". To be cynical about it- how to avoid the sludge that is only 1% desired product.
The estimate is that the number of possible molecules that could be made of the size of a typical drug is about 10 to the 40th power. The number of known natural chemical compounds and artificial ones doesn't even come close to 1% of that number.
The article ends with an aesthetic justification of the small problem approach of most chemistry today because,
" chemistry, as in any science, the biggest breakthroughs often come from unexpected directions"

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