Posts Tagged ‘chem’

The Many Guises of Aromaticity » American Scientist

Friday, January 23rd, 2015

The Many Guises of Aromaticity #Resonance is hyped; hence, many proposals for compounds w/ it that aren’t benchstable

Today, an inflation of hype threatens this beautiful concept. Molecules constructed in silico are extolled as possessing surfeits of aromaticity—“doubly aromatic” is a favorite descriptor. Yet the molecules so dubbed have precious little chance of being made in bulk in the laboratory. One can smile at the hype, a gas of sorts, were it not for its volume. A century and a half after the remarkable suggestion of the cyclic structure of benzene, the conceptual value of aromaticity—so useful, so chemical—is in a way dissolving in that hype. Or so it seems to me.

Bench-Stable, Bottleable

Computers made the determination of the structure of molecules in crystals easy—what took half a year in 1960 takes less than an hour today. They also made computations of the stability of molecules facile.

Whoa! What do you mean by stability? Usually what’s computed is stability with respect to decomposition to atoms. But that is pretty meaningless; for instance, of the four homonuclear diatomic molecules (composed of identical atoms) that are most stable with respect to atomization, N2,C2, O2, and P2, two (C2 and P2) are not persistent. You will never see a bottle of them. Nor the tiniest crystal. They are reactive, very much so. In chemistry it’s the barriers to reaction that provide the opportunity to isolate a macroscopic amount of a compound. Ergo the neologism, “bench-stable.” “Bottleable” is another word for the idea. A lifetime of a day at room temperature allows a competent graduate student at the proverbial bench to do a crystal structure and take an NMR scan of a newly made compound. Or put it into a bottle and keep it there for a day, not worrying that it will turn into brown gunk.


Atomdroid: A Computational Chemistry Tool for Mobile Platforms

Friday, May 2nd, 2014

Little Interactions Mean a Lot » American Scientist

Saturday, March 1st, 2014

Little Interactions Mean a Lot. Nice overview of small energies determining structure, eg ~5kcal/mol hbond #chem 1/2

Little Interactions Mean a Lot. C18H38 alkane is a great example: 2 gauche turns allow a kink & favorable folding-over VDW interactions 2/2


What is big from one perspective is small from another, and energy can be measured in a variety of ways. By “big energies,” I mean those equal or greater than about 1 electron volt per molecule, which is equal to 23.1 kilocalories per mole, or 96.5 kilojoules per mole. A photon of yellow light has an energy of about 2.1 electron volts.

In theoretical chemistry, I was looking for molecules that in one bonding arrangement could be at least 1 electron volt per molecule more stable than in an alternative configuration, or that would require an activation energy (the barrier to a reaction taking place) that is at least 1 electron volt lower than a competing reaction, thus proceeding much more expeditiously. I knew that the strength of the hydrogen bonds that hold together the base pairs of the DNA in my body are, per pair of atoms involved, at least an order of magnitude smaller than 1 electron volt. So are the “dispersion” forces (more on these in a moment) that make the molecules around me–be they acetaminophen or ethanol–solids and liquids rather than gases. …

In addition to the hydrogen bonding mentioned earlier, there are other small forces, like multipole interactions that convert an asymmetry of the way electrons are distributed in a molecule into forces between them. And dispersion forces, which are responsible for molecules and atoms condensing and eventually freezing.


Prototypical hydrogen bonding, the noncovalent bond associated with wet hair and brushes, occurs when the hydrogen of a polar
oxygen-hydrogen (O-H) or nitrogen-hydrogen (N-H) bond comes near an electron source, typically the lone pair of electrons of a nearby oxygen or nitrogen atom. …
Despite such disagreement on origins, there is no disagreement at all on the magnitude of the energy involved, generally less than 5 kilocalories per mole. Small again, but there are oh-so-many of them.

Small energies play out in other interesting ways in some of the simplest organic molecules: the unbranched long-chain hydrocarbons, such as the liquid to waxy “normal” alkanes, which are written chemically as CH3(CH2)nCH3. The molecules in gasoline belong to this family with n = 6 or so; increasing n from six leads to diesel fuel, jet fuel, oil, and lubricants…..At each interior point in the hydrocarbon chain, for every four carbons, a choice is available between an extended conformation, which chemists refer to as all-anti, and two mirror-image curled-up forms, known as gauche conformations. …
The energy difference between the two conformations is truly minuscule. The gauche geometry is merely about one kilocalorie per mole in energy above the global minimum of the anti form; ….

That kinking costs energy, but only a wee amount–each gauche turn has an associated penalty of about 1 kilocalorie per mole. What is accomplished by the kink ….
the second part of the chain is brought near the first. In that conformation, or actually in a family of conformations looking roughly like that, there is a new source of stabilization that is unavailable in the extended, all-anti geometry: attractive dispersion forces between the two parts of the chain.

Small as they individually are, dispersion interactions add up. For an isolated molecule, for some n in CH3(CH2)n CH3 for example, the energy lowering (stabilization) in dispersion interaction will win out over the increase in energy (destabilization) in kinking, the latter accomplished by two or more gauche conformations along the chain.

To my knowledge, Jonathan Goodman first wrote down this idea in 1999. Theory in his and others’ hands confirmed the notion: For
CH3(CH2)nCH3, the crossover from extended to kinked (and eventually curled in a more complex way) comes at around n = 16, or 18 carbon atoms. Remarkably, the experimental proof for this hypothesis has recently come forward, in work by N. O. B. Lüttschwager and


Maillard Reaction | Chemical & Engineering News

Saturday, April 14th, 2012

3 favorite chemical reactions

Combustion | Chemical & Engineering News

Saturday, April 14th, 2012

3 favorite chemical reactions

Diels-Alder Reaction | Chemical & Engineering News

Saturday, April 14th, 2012
3 favorite chemical reactions

Long Live the Intermediate! » American Scientist

Saturday, April 14th, 2012