Posts Tagged ‘Chemistry’
Friday, May 22nd, 2015
As I have noted elsewhere, Gilbert N. Lewis wrote a famous paper entitled “the atom and the molecule“, the centenary of which is coming up.[1] In a short and rarely commented upon remark, he speculates about the shared electron pair structure of acetylene, R-X≡X-R (R=H, X=C). It could, he suggests, take up three forms. H-C:::C-H and two more which I show as he drew them. The first of these would now be called a bis-carbene and the second a biradical.
In 1916, it was too early for Lewis to speculate what the geometries of such species might be, and in particular the C…C (or generalising, X…X) distance, and the two angles, one for each X. Well, we do not need to speculate, we can perform a search of the crystal structure database. Here it is (R < 0.05, no errors, no disorder):
A little more explanation of this 4-dimensional plot is needed:
- The two angles are plotted as X and Y.
- The X…X distance is plotted as colour, with red representing the longest distances and blue the shortest
- The size of each “bin” is represented by the radius of the circle; small circles represent few examples, larger circles represent more examples in each “bin” defined by a regular range of angles.
There are one or two off-diagonal “outliers”, each of which probably deserves individual inspection. But dealing just with the obvious clusters, the overwhelmingly largest is for both angles of ~180°, and these are the triple bonds we know and love. As far as I know, Lewis was the first to propose a triple bond between two atoms, but if anyone reading this blog knows of an antecedent, do let me know. The next cluster is for angles of ~109° and these are clearly bis-carbenes. These all occur when X ≠ C. There are two small clusters worthy of note; one ~130° and one ~90°. The latter are mostly Pb-Pb and Sn-Sn, where the bonding is unhybridised pure p.
One of the limitations of searching for crystal structures is that the spin state of each molecule is never given. The biradical structure given by Lewis could well have a triplet ground state, and perhaps that might have very characteristic angles (~130° ?). It would be great to identify a genuine example of this biradical form!
As usual, the search itself took around 10 minutes, and it provides much interesting food for thought; not bad for a 100-year-old idea!
References
- G.N. Lewis, "THE ATOM AND THE MOLECULE.", Journal of the American Chemical Society, vol. 38, pp. 762-785, 1916. https://doi.org/10.1021/ja02261a002
Tags:Carbene, Carbenes, Chemistry, Cluster chemistry, food, Functional groups, Gilbert N. Lewis, Non-Kekulé molecule, Organic chemistry, Organic compounds
Posted in Chemical IT, Historical, Interesting chemistry | 1 Comment »
Tuesday, May 12th, 2015
The 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[1]).
The search is defined as follows
- R can be either H or C
- The carbon is constrained to 3-coordinate
- The carbonyl oxygen is constrained to 1-coordinate
- QA can be any of N, O, S, Cl, F.
- QB can be any of H (aldehyde), C (ketone), N (amide), O (ester) or S (thioester).
- The distance QA…C is constrained to any intermolecular non-bonded contact ≤ the sum of the van der Waals radii of the two atoms involved and the angle QA…C=O is the Bürgi–Dunitz angle.
- I have also added a torsion constraint to specify that Nu has got to be ± 20° from orthogonality to the plane of the carbonyl to allow it to attack the π* orbital.
- The crystallographic R factor must be < 0.05, no disorder, no crystallographic errors and the temperature is either any or < 120K.
With no temperature specified, 6994 hits are obtained as below. So the most probable angle (red spot) is ~90°.
One important change to the search is to decrease the temperature to 120K, since structures will have less vibrational noise. The number of hits decreases to 1279, but the most probable angle if anything reduces slightly.
So we have something of a mystery; this crystallographic data shows an angle of approach about 15° less than the oft quoted value. Here are some thoughts:
- This search is the average for all types of carbonyl, whereas the original suggestion was constrained to four types of nucleophiles and simple ketones.
- This search extends the interacting distance of the nucleophile and the carbon out to 3.5Å which is significantly longer than the normally considered length of ~2.85Å. The hotspots occur at about 3.15Å and not 2.85Å.
- There is obviously considerably more data available in 2015 than in 1974, and in particular at low temperature.
- The Bürgi–Dunitz angle is in fact one of two defining the trajectory, the other being the Flippin–Lodge angle which defines the displacement towards R or QB. The search above gives no direct information about this angle, but the torsion is related since it is constrained to bisect the C=O to within ± 20° and hence bisect the groups R and QB.
- An angle of ≤ 90° does not match to the normal explanation, which is that the nucleophile attacks the π* orbital, each lobe of which “leans out” from the centre at about 105° rather than leaning in at ≤ 90°.
- Decreasing the torsion range to ± 5° at 120K gives 592 hits with a hot spot at 95°
- Also constraining the distance QA…C to be 0.3Å less than the van der Waals sum at 120K gives 59 hits with a hot spot at 95° and 2.9Å.
Well, to get to the bottom of this will require reducing the scope of both QA and QB, to find which if any of discrete values for these two variables can indeed give an angle of 105-107°. This would make for quite a good student group project; I expect a group of 8 students could sort this out quite quickly!
References
- H. B:urgi, J. Dunitz, J. Lehn, and G. Wipff, "Stereochemistry of reaction paths at carbonyl centres", Tetrahedron, vol. 30, pp. 1563-1572, 1974. https://doi.org/10.1016/s0040-4020(01)90678-7
Tags:alkene, Bürgi–Dunitz angle, Carbonyl, Chemistry, Functional groups, Group of Eight, Ketone, Organic chemistry, Organic compounds, Stall
Posted in Chemical IT, crystal_structure_mining | 3 Comments »
Sunday, April 26th, 2015
Allotropes are differing structural forms of the elements. The best known example is that of carbon, which comes as diamond and graphite, along with the relatively recently discovered fullerenes and now graphenes. Here I ponder whether any of the halogens can have allotropes.
Firstly, I am not aware of much discussion on the topic. But ClF3 is certainly well-known, and so it is trivial to suggest BrBr3, i.e. Br4 as an example of a halogen allotrope. Scifinder for example gives no literature hits on such a substance (either real or as a calculation; it is not always easy nowadays to tell which). So, is it stable? A B3LYP+D3/6-311++G(2d,2p) calculation reveals a free energy barrier of 17.2 kcal/mol preventing Br4 from dissociating to 2Br2.[1] The reaction however is rather exoenergic, and so to stand any chance of observing Br4, one would probably have to create it at a low temperature. But say -78° would probably be low enough to give it a long lifetime; perhaps even 0°.
So how to make it? This is pure speculation, but the red colour of bromine originates from (weak, symmetry forbidden) transitions, with energies calculated (for the 2Br2 complex) as 504, 492nm. Geometry optimisation of the first singlet excited state of 2Br2 produces the structure below, not that different from Br4.
At least from these relatively simple calculations, it does seem as if an allotrope of bromine might be detectable spectroscopically, if not actually isolated as a pure substance.
References
- H.S. Rzepa, "Br4", 2015. https://doi.org/10.14469/ch/191228
Tags:Allotropy, Bromine, Carbon, Chemical elements, Chemistry, free energy barrier, Fullerene, Halogen, Hypobromite, Matter, Nonmetals, Oxidizing agents, Oxygen, pence
Posted in reaction mechanism | 11 Comments »
Friday, April 17th, 2015
The 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.[1] 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.
I conducted the following search:
- Any electron donating group as a ring substituent, defined by any of the elements N, O, F, S, Cl, Br.
- A distance from the H of an OH fragment (as a hydrogen bonder to the aryl ring) to the ortho position relative to the electron donating group.
- A similar distance to the meta position.
- The |torsion angle| between the aryl plane and the C…H axis to be constrained to 90° ± 20.
- Restricting the H…C contact distance to the van der Waals sum of the radii -0.3Å (to capture only the stronger interactions)
- The usual crystallographic requirements of R < 0.1, no disorder, no errors and normalised H positions.
The result of such a search is seen below. The red line indicates those hits where the distance from the H to the ortho and meta positions is equal. In the top left triangle, the distance to ortho is shorter than to meta (and the converse in the bottom right triangle). You can see that both the red hot-spot and indeed the majority of the structures conform to ortho direction (of π-facial ) hydrogen bonding.
Here is a little calculation, optimising the position that HBr adopts with respect to bromobenzene. You can see that the distance discrimination towards ortho is ~ 0.17Å, a very similar value to the “hot-spot” in the diagram above.
This little search of course has hardly scratched the surface of what could be done. Changing eg the OH acceptor to other electronegative groups. Restricting the wide span of N, O, F, S, Cl, Br. Probing rings bearing two substituents. What of the minority of points in the bottom right triangle; are they true exceptions or does each have extenuating circumstances? Why do many points actually lie on the diagonal? Can one correlate the distances with the substituent? Is there a difference between intra and intermolecular H-bonds? What of electron withdrawing groups?
The above search took perhaps 20 minutes to define and optimise, and it gives a good statistical overview of this age-old effect. It is something every new student of organic chemistry can try for themselves! If you run an introductory course in organic aromatic chemistry, or indeed a laboratory, try to see what your students come up with!
References
- H.E. Armstrong, "XXVIII.—An explanation of the laws which govern substitution in the case of benzenoid compounds", J. Chem. Soc., Trans., vol. 51, pp. 258-268, 1887. https://doi.org/10.1039/ct8875100258
Tags:above search, Aromatic compounds, aromaticity, Birch reduction, Chemistry, electron donating, Electrophile, Electrophilic aromatic substitution, Ether, Functional groups, little search, Organic chemistry, Physical organic chemistry, Substitution reactions
Posted in Chemical IT, crystal_structure_mining | 1 Comment »
Sunday, April 12th, 2015
Sodium borohydride is the tamer cousin of lithium aluminium hydride (LAH). It is used in aqueous solution to e.g. reduce aldehydes and ketones, but it leaves acids, amides and esters alone. Here I start an exploration of why it is such a different reducing agent.
Initially, I am using Li, not Na (X=Li), to enable a more or less equal comparison with LAH, with water molecules to solvate rather than ether (n=2,3,5) and R set to Me. First, n=2, for which the IRC is shown below. In this model, we will assume that the carbonyl has not first reacted with water to form a gem-diol. The free energy barrier is 9.6 kcal/mol (ωB97XD/6-311+G(d,p)/SCRF=water) which corresponds to a very fast reaction at room temperatures.
The immediate product is, if anything, more interesting than the transition state[1] with quite a stretched length for the newly formed C-H bond and predicted stretching wavenumber for this bond of 2137 cm-1. This effect is similar to that seen for the LAH reduction of cinnamaldehyde, and is due to stereoelectronic antiperiplanar alignment of the oxyanionic oxygen lone pair with the C-H bond. This species is also some 6.5 kcal/mol higher in energy than the reactant, and is clearly not the final product of the reaction (which must contain e.g. B-O bonds), the mechanism for which will not be investigated here immediately.
For n=3, we see new solvation patterns, including a dihydrogen bond formed between water and the borohydride at the transition state; ΔG† is 10.0 kcal.mol.
Click for 3D.
Finally, n=5, where the TS is showing a cage-like structure of complex weak interactions, ΔG† is 11.3 kcal.mol. We see a model where inclusion of explicit solvent molecules can have a significant influence on the size of the barrier obtained.
Click for 3D
NCI surface. Click for 3D. Blue=strong attractions, green=weak.
| n |
ΔG298‡ |
FAIR Data citation |
| 2 |
9.6 |
[2] |
| 3 |
10.0 |
[3] |
| 5 |
11.3 |
[4] |
With a mechanistic prototype now identified, it is time to start varying some of the parameters, such as X and R. This will enable us to assess the models built here to see if they reflect reality.
References
- H.S. Rzepa, and H.S. Rzepa, "C 2 H 12 B 1 Li 1 O 3", 2015. https://doi.org/10.14469/ch/191186
- H.S. Rzepa, and H.S. Rzepa, "C 2 H 12 B 1 Li 1 O 3", 2015. https://doi.org/10.14469/ch/191188
- H.S. Rzepa, and H.S. Rzepa, "C 2 H 14 B 1 Li 1 O 4", 2015. https://doi.org/10.14469/ch/191189
- H.S. Rzepa, and H.S. Rzepa, "C 2 H 18 B 1 Li 1 O 6", 2015. https://doi.org/10.14469/ch/191192
Tags:aqueous solution, Chemical bond, chemical bonding, Chemistry, Electronic effect, energy, final product, free energy barrier, Hydride, Hydrogen bond, immediate product, Lithium aluminium hydride, reduction
Posted in reaction mechanism | 2 Comments »
