Previously, I showed how conjugation in dienes and diaryls can be visualised by inspecting bond lengths as a function of torsions. Here is another illustration, this time of the mesomeric resonance on a benzene ring induced by an electron donating substituent (an amino group) or an electron withdrawing substituent (cyano).
Archive for the ‘crystal_structure_mining’ Category
Mesomeric resonance in substituted benzenes: a crystallographic reality check.
Wednesday, August 26th, 2015A visualisation of the effects of conjugation; dienes and biaryls.
Tuesday, August 25th, 2015Here is another exploration of simple chemical concepts using crystal structures. Consider a simple diene: how does the central C-C bond length respond to the torsion angle between the two C=C bonds?
Intermolecular atom-atom bonds in crystals? The O…O case.
Saturday, July 25th, 2015I recently followed this bloggers trail; link1 → link2 to arrive at this delightful short commentary on atom-atom bonds in crystals[cite]10.1107/S2052252515002006[/cite] by Jack Dunitz. Here he discusses that age-old question (to chemists), what is a bond? Even almost 100 years after Gilbert Lewis’ famous analysis,[cite]10.1021/ja02261a002[/cite] we continue to ponder this question. Indeed, quite a debate on this topic broke out in a recent post here. My eye was caught by one example in Jack's article: "The close stacking of planar anions, as occurs in salts of croconic acid …far from producing a lowering of the crystal energy, this stacking interaction in itself leads to an increase by several thousand kJ mol−1 arising from Coulombic repulsion between the doubly negatively charged anions" I thought I might explore this point a bit further in this post.
The Bürgi–Dunitz angle revisited: a mystery?
Tuesday, May 12th, 2015The Bürgi–Dunitz angle is one of those memes that most students of organic chemistry remember. It hypothesizes the geometry of attack of a nucleophile on a trigonal unsaturated (sp2) carbon in a molecule such as ketone, aldehyde, ester, and amide carbonyl. Its value obviously depends on the exact system, but is generally taken to be in the range 105-107°. A very good test of this approach is to search the crystal structure database (this was how it was originally established[cite]10.1016/S0040-4020(01)90678-7[/cite]).
A new way of exploring the directing influence of (electron donating) substituents on benzene.
Friday, April 17th, 2015The knowledge that substituents on a benzene ring direct an electrophile engaged in a ring substitution reaction according to whether they withdraw or donate electrons is very old.[cite]10.1039/CT8875100258[/cite] Introductory organic chemistry tells us that electron donating substituents promote the ortho and para positions over the meta. Here I try to recover some of this information by searching crystal structures.
Halogen bonds 4: The strongest (?) halogen bond.
Sunday, December 7th, 2014
Continuing my hunt, here is a candidate for a strong(est?) halogen bond, this time between Se and I.[cite]10.1021/ic50038a006[/cite]. 
The features of interest include:
More simple experiments with crystal data. The pyramidalisation of nitrogen.
Saturday, November 1st, 2014We are approaching 1 million recorded crystal structures (actually, around 716,000 in the CCDC and just over 300,00 in COD). One delight with having this wealth of information is the simple little explorations that can take just a minute or so to do. This one was sparked by my helping a colleague update a set of interactive lecture demos dealing with stereochemistry. Three of the examples included molecules where chirality originates in stereogenic centres with just three attached groups. An example might be a sulfoxide, for which the priority rule is to assign the lone pair present with atomic number zero. The issue then arises as to whether this centre is configurationally stable, i.e. does it invert in an umbrella motion slowly or quickly. My initial intention was to see if crystal structures could cast any light at all on this aspect.
Amides and inverting the electronics of the Bürgi–Dunitz trajectory.
Thursday, June 26th, 2014
The Bürgi–Dunitz angle describes the trajectory of an approaching nucleophile towards the carbon atom of a carbonyl group. A colleague recently came to my office to ask about the inverse, that is what angle would an electrophile approach (an amide)? Thus it might approach either syn or anti with respect to the nitrogen, which is a feature not found with nucleophilic attack. 
My first thought was to calculate the wavefunction and identify the location and energy (= electrophilicity) of the lone pairs (the presumed attractor of an electrophile). But a better more direct approach soon dawned. A search of the crystal structure database. Here is the search definition, with the C=O-E angle, the O-E distance and the N-C=O-E torsion defined (also specified for R factor < 5%, no errors and no disorder). 
The first plot is of the torsion vs the distance, for E = H-X (X=O,F, Cl) 
Halogen bonds: Part 1.
Saturday, November 29th, 2014Halogen bonds are less familiar cousins to hydrogen bonds. They are defined as non-covalent interactions (NCI) between a halogen atom (X, acting as a Lewis acid, in accepting electrons) and a Lewis base D donating electrons; D….X-A vs D…H-A. They are superficially surprising, since both D and X look like electron rich species. In fact the electron distribution around X-X (A=X) is highly anisotropic, with the electron rich distribution (the "donor") being in a torus encircling the bond, and an electron deficient region (the "acceptor") lying along the axis of the bond.
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Tags:crystal structure search, D. Note, frequent commentator, Paul Schleyer
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