Posts Tagged ‘pence’
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 10th, 2015
Previously on this blog: modelling the reduction of cinnamaldehyde using one molecule of lithal shows easy reduction of the carbonyl but a high barrier at the next stage, the reduction of the double bond. Here is a quantum energetic exploration of what might happen when a second LAH is added to the brew (the usual ωB97XD/6-311+G(d,p)/SCRF=diethyl ether).
In a comment at the end of the first post on this theme, I had noted some crystal structures containing in effect HxAl.Li(OR)y units (x=3,4; y=0-3), noting the variety of structural motifs. The current exploration does not even attempt to cover this range of possibilities, but it is informed by the types of weak interaction that these structures reveal. I will nevertheless accept that whatever pathway is revealed here is likely to represent an energetic upper bound and recognise that lower energy pathways may well exist but are yet to be explored.
- At the I12 stage, a second AlH4–.Li(OMe)2 is added and hydride transfer occurs antiperiplanar across the C=C bond (TS34-1). The computed free energy barrier ΔG298† is ~24 kcal/mol. The magnitude of this barrier corresponds to a relatively slow reaction occurring around room temperatures or slightly higher.
TS. Click for 3D
NCI Isosurface (green regions are dispersion stabilizing) Click for 3D
- A transient shallow intermediate I34-1 is formed in which the benzylic anion is stabilised by an adjacent solvated Li centre. The energy of this species (Table below) needs some explanation.‡ Can its free energy really be 1.5 kcal/mol higher than that of the preceding transition state? Yes, because its entropy is lower! The transition state is located on a total energy surface, which does not include thermal and entropic corrections; these are always applied AFTER the stationary points are located. If one inspects these total energies, I34-1 emerges as 1.2 kcal/mol lower than the preceding transition state. This sort of result serves to remind us of the dynamic nature of a potential energy surface, and that static energies may on occasion lead to odd results. Its geometry is shown below, and this too has an interesting feature. The C-H bond just created from the LAH is antiperiplanar to the benzylic anion (locked anti by the Li) and the resulting stereoelectronic effect reduces its C-H calculated[1] stretching wavenumber from the normal value of ~3100 cm-1 to 2231 cm-1, a remarkable reduction.
I34-1. Click for 3D
- The C-O-AlH3.Li(OMe)2 ligand now needs to rotate to I34-2 so that metal exchange on the benzylic carbon can occur, with Al displacing Li at that position. As with I34-1, the free energy of this species is actually slightly higher than that of TS34-1. Two AlH3 groups now exist at this stage (each of them formed by hydride donation as part of the reduction process, see below). A hydride transfer metathesis between them (H2Al-H-Al3 is actually a stable bridged species) will generate an AlH2 as part of the 5-ring aluminate ester in P34 and regenerate a molecule of LAH. Transition states for these processes (i.e. TS34-2) proved difficult to locate;† it may be that the ligand rotation and the hydride metathesis are part of the same concerted process but that is not proven yet.
I34-2. Click for 3D
- The final product prior to hydrolysis is appropriately exoenergic.
- I would also remark that many aspects of this reaction remain unexplored. For example, AlH4 can deliver up to four hydrides, becoming progressively substituted as Al(OR)nHy and in the process loosing Al-H…Li weak interactions. What influence this has on the barriers remains unknown.
In summary, the first step in the reduction of cinnamaldehyde to cinnamyl alcohol requires just one molecule of “LiAlH4” as reductant and has a very low barrier to reaction. To construct a reasonable model to account for the slower further reduction of the C=C bond requires adding a further LiAlH4, the key feature being the availability of a lithium centre to stabilise out the forming benzylic carbanion. No doubt even better models might include the effects of adding e.g. a third molecule of LAH, and a much more extensive exploration of the various conformational options. But I think the present model might be good enough to augment the apparently relatively limited mechanistic speculations found in text books on the topic.
†You sometimes see this phrase in articles reporting transition state location. What is means it that I tried a half-dozen what I thought were reasonable possibilities, and none of them satisfactorily converged. This semi-random exploration of the potential energy surface revealed a very flat energy potential, with lots of conformational possibilities. At this point, you have to decide whether it is worth the time to continue hunting.
References
- H.S. Rzepa, and H.S. Rzepa, "C 17 H 40 Al 2 Li 2 O 5", 2015. https://doi.org/10.14469/ch/191178
- H.S. Rzepa, and H.S. Rzepa, "C 17 H 40 Al 2 Li 2 O 5", 2015. https://doi.org/10.14469/ch/191172
- H.S. Rzepa, and H.S. Rzepa, "C 17 H 40 Al 2 Li 2 O 5", 2015. https://doi.org/10.14469/ch/191177
- H.S. Rzepa, and H.S. Rzepa, "C 17 H 40 Al 2 Li 2 O 5", 2015. https://doi.org/10.14469/ch/191181
- H.S. Rzepa, and H.S. Rzepa, "C 17 H 40 Al 2 Li 2 O 5", 2015. https://doi.org/10.14469/ch/191171
Tags:computed free energy barrier, energy, energy surface, final product, flat energy potential, free energy, lower energy pathways, metal exchange, pence, potential energy surface, reduction, Yes
Posted in reaction mechanism | No Comments »
Wednesday, April 1st, 2015
The reduction of cinnamaldehyde by lithium aluminium hydride (LAH) was reported in a classic series of experiments[1],[2],[3] dating from 1947-8. The reaction was first introduced into the organic chemistry laboratories here at Imperial College decades ago, vanished for a short period, and has recently been reintroduced again.‡ The experiment is really simple in concept; add LAH to cinnamaldehyde and you get just reduction of the carbonyl group; invert the order of addition and you additionally get reduction of the double bond. Here I investigate the mechanism of these reductions using computation (ωB97XD/6-311+G(d,p)/SCRF=diethyl ether).
The mechanism can be envisaged as proceeding through a 1,4-hydride attack (TS14) with a hidden intermediate (HI14) on the reaction path, or instead finding a pathway involving either one or two consecutive 1,2-attacks; TS12-1, TS12-2 via an explicit intermediate I12. Experiment shows that quenching with D2O at the end of the reduction to replace a C-Al with a C-D bond certainly seems to rule out the 1,4 route, since that would not lead to incorporation of deuterium at the benzylic position. So does the computational model reflect this reality?
I have chosen a model in which two dimethyl ether molecules solvate the lithium cation. The reactant itself has an interesting structure, in which two of the Al-H bonds form bridges to the Li, which ends up being five-coordinated. Further weak C-H…O=C hydrogen bonding is also observed. The NCI (non-covalent-interaction) surfaces are well worth inspecting (inspection notes: the NCI surrounding the Al has artefacts, since the value of the electron density surrounding the metal is lower than covalent density for the other elements. Click on the image below to load the 3D model).
Click for 3D
TS14 retains that C-H…O=C hydrogen bond, but the double Al-H-Li bridge is lost. The 8-ring for the TS allows the hydride transfer to be approximately linear, and the Bürgi-Dunitz angle of approach of the hydride to the double bond is 107.4°. Whilst the barrier is acceptably low, the reaction reaches a cul-de-sac down this path; it has no low energy escape route.
Click for 3D
TS12-1 loses the C-H…O=C hydrogen bond, but being 3.3 kcal/mol lower in free energy than TS14 fortunately provides a lower energy alternative to that cul-de-sac! The Bürgi-Dunitz angle is 112.0°.
TS12-2 is required to proceed further to the dihydrocinnamyl alcohol reduction product P12, and now we have to confront the nub of the problem. Why does this further reduction only proceed when the LAH is in excess? TS12-2 itself corresponds to an Al-H addition across a C=C double bond.[11]†, with a similar barrier to TS12-1. The answer to this conundrum is to recognise that I12 forms what is called a resting state for the reaction, and that to proceed further the reaction has to overcome the barrier from I12 to TS12-2. That barrier is 42.3 kcal/mol, far too high to proceed thermally. When one encounters an unreasonable barrier, one has to look very carefully at the model one has constructed for the process.
Click for 3D
Clearly, the model I used here is lacking something. Since the reaction only proceeds when LAH is in excess, we can formulate the hypothesis that further LAH must be added to the model, from which a more reasonable barrier might emerge. If I find out how that can be done, I will report back here.
‡ LAH as a reagent was originally available in powder form, which could be quite tricky to handle and could cause fires if not handled properly. The lab organiser Chris tells me it now comes in standard-sized pellets which are far easier and safer to handle in a laboratory, allowing its re-introduction.
†Biographical note. This footnote is added because I spent three years as a Ph.D. student trying to construct transition state models by measuring kinetic isotope effects. My failure to do so convincingly meant I decided to spend a further three years as a Post Doc inverting the concept by learning how to model transition states using quantum mechanical computation. I first applied these skills as an independent researcher to locating the transition state for Cl-H addition (vs Al-H in this post) across a C=C double bond and computing the associated isotope effects.[12] This article ends with the assertion that “SCF-MO calculations may provide a more rational basis for interpreting kinetic isotopes than the reverse procedure of attempting to establish a transition state model from the observed kinetic data.” It is nice to see that posterity has shown that this assessment was about right.
References
- R.F. Nystrom, and W.G. Brown, "Reduction of Organic Compounds by Lithium Aluminum Hydride. I. Aldehydes, Ketones, Esters, Acid Chlorides and Acid Anhydrides", Journal of the American Chemical Society, vol. 69, pp. 1197-1199, 1947. https://doi.org/10.1021/ja01197a060
- R.F. Nystrom, and W.G. Brown, "Reduction of Organic Compounds by Lithium Aluminum Hydride. II. Carboxylic Acids", Journal of the American Chemical Society, vol. 69, pp. 2548-2549, 1947. https://doi.org/10.1021/ja01202a082
- F.A. Hochstein, and W.G. Brown, "Addition of Lithium Aluminum Hydride to Double Bonds", Journal of the American Chemical Society, vol. 70, pp. 3484-3486, 1948. https://doi.org/10.1021/ja01190a082
- H.S. Rzepa, "C 13 H 24 Al 1 Li 1 O 3", 2015. https://doi.org/10.14469/ch/191154
- H.S. Rzepa, "C 13 H 24 Al 1 Li 1 O 3", 2015. https://doi.org/10.14469/ch/191148
- H.S. Rzepa, "C 13 H 24 Al 1 Li 1 O 3", 2015. https://doi.org/10.14469/ch/191152
- H.S. Rzepa, "C 13 H 24 Al 1 Li 1 O 3", 2015. https://doi.org/10.14469/ch/191149
- H.S. Rzepa, "C 13 H 24 Al 1 Li 1 O 3", 2015. https://doi.org/10.14469/ch/191151
- H.S. Rzepa, and H.S. Rzepa, "C 13 H 24 Al 1 Li 1 O 3", 2015. https://doi.org/10.14469/ch/191156
- H.S. Rzepa, "C 13 H 24 Al 1 Li 1 O 3", 2015. https://doi.org/10.14469/ch/191155
- H.S. Rzepa, "Gaussian Job Archive for C2H7Al", 2015. https://doi.org/10.6084/m9.figshare.1362146
- H.S. Rzepa, "MNDO SCF-MO calculations of kinetic isotope effects for dehydrochlorination reactions of chloroalkanes", Journal of the Chemical Society, Chemical Communications, pp. 939, 1981. https://doi.org/10.1039/c39810000939
Tags:Al-H-Li bridge, dihydrocinnamyl alcohol reduction product, free energy, Imperial College, independent researcher, low energy escape route, lower energy alternative, metal, pence
Posted in reaction mechanism | 5 Comments »
Sunday, March 15th, 2015
My previous posts have covered the ionization by a small number of discrete water molecules of the series of halogen acids, ranging from HI (the strongest, pKa -10) via HF (weaker, pKa 3.1) to the pseudo-halogen HCN (the weakest, pKa 9.2). Here I try out some even stronger acids to see what the least number of water molecule needed to ionize these might be.
Firstly what must surely be the ultimate acid H(CHB11Cl11), discovered by Christopher Reed[1] in 2006. This is so strong that it appears that it can even largely ionize itself; the form on the right (below) is the cationic acid, the form on the left is its anionic base. The proton itself is bridged[2] between the two in a manner similar to the structure of one form of HCl.4H2O reported in the earlier post on the topic.
Click for 3D
So it comes as no surprise‡ to find[3] that just one water molecule can also ionize H(CHB11Cl11) to the anionic form (CHB11Cl11)–.
Click for 3D
How about triflic acid, CF3SO2OH, pKa -16), which is also a fair bit more acidic than HI? Here, only three waters are needed (ωB97XD/6-311++G(2d,2p) prediction) to ionise to triflate anion.[4]
Click for 3D
So, if there a system which is ionised by precisely two water molecules I will record it here.
‡Perhaps also no surprise is that one H2S molecule can also perform this ionisation.[5] This leads us into another exploration, using molecules other than water to perform these ionisations.
References
- E.S. Stoyanov, S.P. Hoffmann, M. Juhasz, and C.A. Reed, "The Structure of the Strongest Brønsted Acid: The Carborane Acid H(CHB<sub>11</sub>Cl<sub>11</sub>)", Journal of the American Chemical Society, vol. 128, pp. 3160-3161, 2006. https://doi.org/10.1021/ja058581l
- Stoyanov, E.S.., Hoffmann, S.P.., Juhasz, M.., and Reed, C.A.., "CCDC 606170: Experimental Crystal Structure Determination", 2006. https://doi.org/10.5517/ccnbrwl
- H.S. Rzepa, "C 1 H 4 B 11 Cl 11 O 1", 2015. https://doi.org/10.14469/ch/191134
- H.S. Rzepa, "C 1 H 7 F 3 O 6 S 1", 2015. https://doi.org/10.14469/ch/191129
- H.S. Rzepa, "C 1 H 4 B 11 Cl 11 S 1", 2015. https://doi.org/10.14469/ch/191135
Tags:Christopher Reed, Ohio, pence
Posted in Interesting chemistry | 3 Comments »
Saturday, February 28th, 2015
Why is this post orphaned from the previous? In order to have the opportunity of noting that treating iodine computationally can be a little different from the procedures used for F, Cl and Br.
As the nuclear charge increases proceeding down the periodic table, the inner electron shells start becoming relativistic. Iodine is the first halogen where this might really start to matter.* There are two ways in which one can compute molecules with I; the first adopts the same procedure as for the earlier halogens, whereby all the electrons are described by basis functions (called an all-electron basis). This effect does not really include the effects of relativistic contractions on the inner (1s) shell unless special relativistic Hamiltonians are also used. The second replaces these inner cores with a pseudopotential, and this does incorporate some of the relativistic effects. To find out how much this might matter, I have included both types:
|
I |
| n |
I-H |
H-O |
| 1 |
1.637†/1.623‡ |
2.032/2.060[1] |
| 2 |
1.657/1.641 |
1.863/1.889[2] |
| 3 |
1.696/1.675 |
1.641/1.670[3] |
| 4 |
2.316/2.304 |
1.014/1.015[4] |
†Non-relativistic calculation with an all-electron 6-311G(d,p) basis on I, 6-311++G(2d,2p) on O and H. ‡Def2-TZVPPD basis, with pseudopotential just on I.
As with bromine, iodine shows a precipitous ionisation when the 4th water molecule is added. In the previous post, I compared this with pKa values, and a comment posted there reminded us that a pKa is measured for macroscopic bulk water and that all sorts of new effects due to free energy/entropy, continuum solvation and much else will take hold. But qualitatively at least, the ionisation of HI in a gas-phase cluster of water molecules seems to match the bulk properties. Relativistic effects do not appear to play a major role here.
*Whilst such effects can be prominent for I, arguably they actually start at Cl via an effect called spin-orbit (SO) coupling. This manifests in the calculation of chemical magnetic shieldings. If one uses standard GIAO NMR theories, one can calculate shieldings for e.g. C pretty accurately. But with Cl, the shieldings may be SO-perturbed by about 3ppm, with Br it’s about 12 ppm and with I it reaches 50 ppm![5]
References
- H.S. Rzepa, "H 3 I 1 O 1", 2015. https://doi.org/10.14469/ch/190924
- H.S. Rzepa, "H 5 I 1 O 2", 2015. https://doi.org/10.14469/ch/190921
- H.S. Rzepa, "H 7 I 1 O 3", 2015. https://doi.org/10.14469/ch/190925
- H.S. Rzepa, "H 9 I 1 O 4", 2015. https://doi.org/10.14469/ch/190927
- D.C. Braddock, and H.S. Rzepa, "Structural Reassignment of Obtusallenes V, VI, and VII by GIAO-Based Density Functional Prediction", Journal of Natural Products, vol. 71, pp. 728-730, 2008. https://doi.org/10.1021/np0705918
Tags:chemical magnetic shieldings, free energy/entropy, gas-phase cluster, Hawaii, pence
Posted in General, Interesting chemistry | No Comments »
Friday, February 27th, 2015
No doubt answers to the question posed in the previous post are already being obtained by experiment. Just in case that does not emerge in the next day or so, I offer a prediction here.
The methodology is the same as before, and I have not tried to look for new isomeric forms compared with the structures found with HCl. The method as before is DFT-based: ωB97XD/6-311++G(2d,2p). In the table below, I am recording the halogen-H distance and the distance from the same H to oxygen. You might also observe a more general principle here; first calibrate the method you intend to use with a system where there is an experimental answer. If the two match, use the same method to predict (extrapolate) to systems as yet unmeasured.
|
F |
Cl |
Br |
| n |
F-H, Å |
H-O |
Cl-H |
H-O |
Br-H |
H-O |
| 1 |
0.937 |
1.702[1] |
1.300 |
1.857 |
1.438 |
1.912[2] |
| 2 |
0.951 |
1.631[3] |
1.322 |
1.728 |
1.463 |
1.754[4] |
| 3 |
0.967 |
1.532[5] |
1.351 |
1.579 |
1.506 |
1.554[6] |
| 4 |
0.972 |
1.504[7] |
1.387 |
1.470 |
2.032 |
1.028[8] |
| 5 |
1.043 |
1.329[9] |
1.841 |
1.034 |
2.039 |
1.021[10] |
| 6 |
1.067 |
1.283[11] |
1.880 |
1.023 |
2.073 |
1.013[12] |
From the bond distances, one notices that “ionisation” is an abrupt discontinuous event, happening for four molecules with HBr, five molecules with HCl and more than six molecules with HF. This nicely parallels the pka values: HBr (pKa = -9.0) < HCl (pKa = -6.0) << HF (pKa = +3.1).
It is good to see that such a process modelled on the nanoscale using just a few discrete molecules can map onto the macroscopic scale of solutions.
Postscript: If you check on the structures of these systems (click on the pictures in the previous post) you will see that the discontinuous ionisation event occurs in a bicyclic system, with the water forming two separate rings. Evidence that this really is the structure of microsolvated species has recently been put forward[13].
References
- H.S. Rzepa, "H 3 F 1 O 1", 2015. https://doi.org/10.14469/ch/190911
- H.S. Rzepa, "H 3 Br 1 O 1", 2015. https://doi.org/10.14469/ch/190907
- H.S. Rzepa, "H 5 F 1 O 2", 2015. https://doi.org/10.14469/ch/190910
- H.S. Rzepa, "H 5 Br 1 O 2", 2015. https://doi.org/10.14469/ch/190909
- H.S. Rzepa, "H 7 F 1 O 3", 2015. https://doi.org/10.14469/ch/190912
- H.S. Rzepa, "H 7 Br 1 O 3", 2015. https://doi.org/10.14469/ch/190913
- H.S. Rzepa, "H 9 F 1 O 4", 2015. https://doi.org/10.14469/ch/190915
- H.S. Rzepa, "H 9 Br 1 O 4", 2015. https://doi.org/10.14469/ch/190916
- H.S. Rzepa, "H 11 F 1 O 5", 2015. https://doi.org/10.14469/ch/190918
- H.S. Rzepa, "H 11 Br 1 O 5", 2015. https://doi.org/10.14469/ch/190919
- H.S. Rzepa, "H 13 F 1 O 6", 2015. https://doi.org/10.14469/ch/190928
- H.S. Rzepa, "H 13 Br 1 O 6", 2015. https://doi.org/10.14469/ch/190917
- C. Pérez, J.L. Neill, M.T. Muckle, D.P. Zaleski, I. Peña, J.C. Lopez, J.L. Alonso, and B.H. Pate, "Water–Water and Water–Solute Interactions in Microsolvated Organic Complexes", Angewandte Chemie International Edition, vol. 54, pp. 979-982, 2014. https://doi.org/10.1002/anie.201409057
Tags:pence, Postscript
Posted in General, Interesting chemistry | 9 Comments »
Saturday, February 14th, 2015
According to Guggemos, Slavicek and Kresin, about 5-6![1]. This is one of those simple ideas, which is probably quite tough to do experimentally. It involved blasting water vapour through a pinhole, adding HCl and measuring the dipole-moment induced deflection by an electric field. They found “evidence for a noticeable rise in the dipole moment occurring at n≈5–6“.
Modelling the structures takes little time. So here are some ωB97XD/6-311++G(2d,2p) gas phase models. I state at the outset that these are not dynamic-stochastic models, averaged over many conformations, but a static picture of individual poses. As usual, click on individual images to obtain an interactive 3D model (Java required).‡
n=1.[2] Dipole moment 3.7D
n=2.[3] Dipole moment 2.4D. Note how the O…H bond becomes shorter.
n=3.[4] Dipole moment 2.5D. Note how the key O..H bond is contracting rapidly, as are the other H-bond interactions. This is the cyclic polarisation effect, where each bond influences the others. We are starting to approach the formation of H3O+ and Cl–!
n=4.[5] Dipole moment 2.3 D, We have two ways to add the next water molecule, firstly to try to stabilise the H3O+. Nope.
n=4,[5] Dipole moment 1.1 D. Better by solvating the Cl–! The proton originally attached to the Cl is now starting its transfer to the water to form that hydronium cation, but the dipole moment is not yet large.
n=5.[6] Dipole moment 4.7D. The ionisation is almost complete and the dipole moment is on the increase.
n=6.[7] The dipole moment is up to 8.2D and the three H-O bonds of the hydronium cation are almost all equal in length.
A cautionary observation though. The isomer below for n=6[8] is lower in energy by ΔG -1.2 kcal/mol, and its dipole moment is only 2.5D! The charges (summed onto heavy atoms) show the chloride to have -0.88 and the hydronium cation +0.88, so it is a true ion-pair, despite its dipole moment.
So these calculations do indeed appear to confirm that 5-6 water molecules are required to ionise HCl. But it does raise the interesting issue that even for n=6, there are poses for the assembly which have low dipole moments. Clearly of course the observed dipole moment is a dynamic average over many conformations of similar energy but the prediction that some of these may have low dipole moments should be noted.
‡ If you right-click in the 3D model area, you can bring down a list of vibrational modes for each complex from the first item of the pop-up menu that appears (labelled model). You might wish to e.g. explore how the H-Cl stretch vibration changes as the ionisation increases.
References
- N. Guggemos, P. Slavíček, and V.V. Kresin, "Electric Dipole Moments of Nanosolvated Acid Molecules in Water Clusters", Physical Review Letters, vol. 114, 2015. https://doi.org/10.1103/physrevlett.114.043401
- H.S. Rzepa, "H 3 Cl 1 O 1", 2015. https://doi.org/10.14469/ch/189758
- H.S. Rzepa, "H 5 Cl 1 O 2", 2015. https://doi.org/10.14469/ch/189760
- H.S. Rzepa, "H 7 Cl 1 O 3", 2015. https://doi.org/10.14469/ch/189759
- H.S. Rzepa, "H 9 Cl 1 O 4", 2015. https://doi.org/10.14469/ch/189763
- H.S. Rzepa, "H 11 Cl 1 O 5", 2015. https://doi.org/10.14469/ch/189756
- H.S. Rzepa, "H 13 Cl 1 O 6", 2015. https://doi.org/10.14469/ch/189761
- H.S. Rzepa, "H 13 Cl 1 O 6", 2015. https://doi.org/10.14469/ch/189764
Tags:energy, gas phase models, Java, pence, similar energy
Posted in Interesting chemistry, reaction mechanism | 1 Comment »
Monday, December 22nd, 2014
I started chemistry with a boxed set in 1962. In those days they contained serious amounts of chemicals, but I very soon ran out of most of them. Two discoveries turned what might have been a typical discarded christmas present into a lifelong career and hobby.
The first was 60 Stoke Newington High Street in north London, the home of Albert N. Beck, Chemist (or his son; my information comes from a historical listing of the shops present on the high street in 1921). I would set out from our home in London SW6 on the #73 bus route (top deck) and it would take about an hour to arrive. On entering the shop, I ventured down a set of stairs into the basement to replenish the chemicals with sensible stocks, and purchase the odd glassware, filter paper, etc. And then venture back across London carrying the proceeds of many weeks, possibly months worth of hoarded pocket-money (apart that is from 1 shilling every two weeks which I reserved for football at Craven Cottage). At some stage, health and safety legislated against 12-year-old boys (and certainly also girls) purchasing chemicals in this manner! However, I can assure you all that I never came to any harm with anything I purchased at A. N. Beck and Sons. Apart that is from giving my parents a good fright.
The second was coming across this book by A. J. Mee. I had thought it was well and truly lost; imagine my delight when I recently found it at home, complete with chemical stains, and dated as from a reprint in 1959.
On the inside cover, I found one shopping list from my expeditions to A. N. Beck and Sons. The price 1/6 is the representation of one shilling and six pence (more than the price of a football match, or perhaps £50 in today’s money? I think football was much cheaper then! Oh, 1/6 is 7.5p in the decimal currency of today, or £0.075). Note that iodine was one of the items purchased. And note the wish list at the bottom! I was clearly starting to do organic chemistry.
The pages of this book list 289 experiments, and I assiduously recorded a tick against all the ones I actually did. This is a typical page (click to expand).
Thus expt 205 is the preparation of 1,3,5-tribromobenzene from 1,3,5-tribromoaniline (ticked), followed by that of o-cresol from o-toluidine (ticked). You can see how all the aromatic rings are still represented by what now looks like cyclohexane. This book gave me many hours of delightful recreation (I have not counted the ticks, but I think I attempted around half the experiments). Note in particular the huge scale these experiments were done at; 18g of product (I suspect I must have scaled them down a fair bit in order to preserve pocket money). Expt 198 was that of benzidine, of which I do recollect preparing ~2g. No warnings then about the extremely carcinogenic nature of this substance! Chemistry has certainly changed since then.
Lost unfortunately is the laboratory book where I recorded my results, but one or two samples still exist!
Tags:A. N. Beck and Sons, Albert N. Beck, chemical stains, chemicals, chemist, christmas, Craven Cottage, GBP, London, pence, Shilling
Posted in Historical | 60 Comments »
Saturday, July 19th, 2014
Whilst clusters of carbon atoms are well-known, my eye was caught by a recent article describing the detection of a cluster of boron atoms, B40 to be specific.[1] My interest was in how the σ and π-electrons were partitioned. In a C40, one can reliably predict that each carbon would contribute precisely one π-electron. But boron, being more electropositive, does not always play like that. Having one electron less per atom, one might imagine that a fullerene-like boron cluster would have no π-electrons. But the element has a propensity[2] to promote its σ-electrons into the π-manifold, leaving a σ-hole. So how many π-electrons does B40 have? These sorts of clusters are difficult to build using regular structure editors, and so coordinates are essential. The starting point for a set of coordinates with which to compute a wavefunction was the supporting information. Here is the relevant page: 
The coordinates are certainly there (that is not always the case), but you have to know a few tricks to make them usable.
- Open Adobe Reader, select the coordinates and copy
- Paste into any application which recognises text. I used an old stalwart on the Mac, BBedit. It is reliable!
- But no, it produces a row of skull&crossbones characters (the authors of the program clearly have a sense of humour)
- Thinking that BBedit might have let me down (for the first time), I tried Word. A little less humour, but the same result.
- There are lots of web sites out there that claim to convert PDF files directly to Word files. Again, no luck, the coordinates are now entirely missing!
- Right, time for the big guns. Adobe Acrobat XI converts .PDF to .DOC, and (if you jump through a lot of hoops to register etc) they even give you a 30 day trial. Well, at least it gives numbers. But notice that the line breaks are missing, and all the numbers flow from one line to another.
- Another copy/paste from Word to BBedit, and now I have all the numbers, and adding 40 line breaks is all that is needed (there is sometimes some skill in knowing where to add them by the way).‡ The time taken from step 1 to step 7 was about 90 minutes (including a necessary cup of tea to recover from steps 1-5, and the realisation that the time was not wasted, since I could blog the experience!).
Well, I am sure you know what is coming next; my usual rant about how little most chemists truly value data and particularly its integrity and its semantics. And how little almost all journals understand data. Notice that the original article was published in Nature Chemistry. Note also a new journal from that stable, Scientific Data. The journal clearly thinks there is mileage in receiving scholarly articles about scientific data, and what they call data descriptors (they even got me to write a data descriptor a year or so back). Its a shame then that the same publisher allowed the decimation of the core data related to an article about B40.
They have a widely read blog, perhaps they can comment?
One more point to make about data: a phrase has recently been coined: deposition with recognition. Here, I show how my own data has been recognised:
There are various other ways as well, and perhaps I will leave this to another post. To return to the chemistry (where we should have been at the start). I ran the calculation (B3LYP+D3/TZVP) and published the newly enhanced data, citing it in the usual way.[3],[4]† To answer my question, for the D2d geometry, B40 has 24 π-electrons (there is some ambiguity, it could be 26). On average, the boron retains only ~0.65s, balanced by ~2.35p electrons. The most stable π-pair is shown below. At the centre of the ring is a strongly diatropic ring current (NICS = -42 ppm)[5] suggesting aromaticity (26 electrons = 4n+2).¶
I conclude by pondering whether the properties of any such boron cluster may in time prove to be directly related to the number of σ-to-π promotions.
‡ Sadly, line breaks in lists of atom coordinates date back to an era of about 50 years ago when text files were first treated differently from binary files. Three different “standards” emerged for specifying a line break (DOS, Mac and Unix) in a text file and much confusion has there been ever since when moving these text files across operating systems. The modern way of doing it is to make line breaks redundant by instead marking up the file. The standard chemical markup, invented in 1996, and formally published in 1999[6], is CML. You will find such CML coordinates in the deposited data from this calculation.[3] You will not have any problems with line breaks!
†Publication assigns a DataCite DOI. This takes about 48 hours to propagate to CrossRef, which is here used by the KCite WordPress plugin to retrieve the metadata and compose a citation. If KCite queries CrossRef before the metadata has propagated, it does not generate a citation. If you are reading this and see no citation, please revisit after 48 hours have elapsed.
¶The diatropicity is inverted to paratropicity (NICS = +28 ppm) when two electrons are removed to create the dication.[7] This inversion is normally a good test of aromaticity/antiaromaticity.
References
- H. Zhai, Y. Zhao, W. Li, Q. Chen, H. Bai, H. Hu, Z.A. Piazza, W. Tian, H. Lu, Y. Wu, Y. Mu, G. Wei, Z. Liu, J. Li, S. Li, and L. Wang, "Observation of an all-boron fullerene", Nature Chemistry, vol. 6, pp. 727-731, 2014. https://doi.org/10.1038/nchem.1999
- H.S. Rzepa, "The distortivity of π-electrons in conjugated boron rings", Physical Chemistry Chemical Physics, vol. 11, pp. 10042, 2009. https://doi.org/10.1039/b911817a
- H.S. Rzepa, "Gaussian Job Archive for B40", 2014. https://doi.org/10.6084/m9.figshare.1111454
- H.S. Rzepa, "B 40", 2014. https://doi.org/10.14469/ch/24884
- H.S. Rzepa, "Gaussian Job Archive for B40", 2014. https://doi.org/10.6084/m9.figshare.1111518
- P. Murray-Rust, and H.S. Rzepa, "Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles", Journal of Chemical Information and Computer Sciences, vol. 39, pp. 928-942, 1999. https://doi.org/10.1021/ci990052b
- H.S. Rzepa, "Gaussian Job Archive for B40(2+)", 2014. https://doi.org/10.6084/m9.figshare.1111534
Tags:Acrobat, Adobe, chemical markup, DOS, operating systems, PDF, pence, Unix
Posted in Chemical IT, Interesting chemistry | 2 Comments »
Saturday, July 12th, 2014
Computational quantum chemistry has made fantastic strides in the last 30 years. Often deep insight into all sorts of questions regarding reactions and structures of molecules has become possible. But sometimes the simplest of questions can prove incredibly difficult to answer. One such is how accurately can the boiling point of water be predicted from first principles? Or its melting point? Another classic case is why mercury is a liquid at room temperatures? The answer to that question (along with another, why is gold the colour it is?) is often anecdotally attributed to Einstein. More accurately, to his special theory of relativity.[1] But finally in 2013 a computational proof of this was demonstrated for mercury.[2] The proof was built up in three stages.
- Potential energy surfaces for the Hg2 dimer showed that inclusion of a relativistic Hamiltonian contracts the Hg-Hg distance by 0.2Å. This can be traced back to the value of the 1S0(6s2)→3P0(6s16p11/2) electronic excitation in the atom being 4.67eV, compared to a non-relativistic value of 3.40eV. This in turn is the result of the strong relativistic 6s shell contraction and hence stabilisation. But it has previously been shown that bulk mercury cannot be described by such a simple two-body interaction.
- Next many-body clusters of various sizes were built. This is a complex task, since for each size, various types of packing might be possible. The largest was a “two-layer Mackay icosahedron”, with 55 Hg atoms. These clusters however did not show any monotonic convergence to a clear melting point.
- Finally, using Monte Carlo (MC) simulations within a quantum diatomics-in-molecules (DIM) model and with periodic boundary conditions to simulate the bulk metal, it was possible to show that without a relativistic Hamiltonian, the predicted melting point was predicted as 355K (82°C) but when the relativistic effects were switched on, this decreased to 250K (-23°C). This lowering of 105K is dominated by scalar relativistic effects through many-body contributions.
- The experimental melting point is 234K. The density is well predicted as well (the non-relativistic model predicts mercury to be denser than it actually is).
What I did not get from this article is why mercury is such a very special case (i.e. why neither gold, m.p. 1337K nor thallium, m.p. 577K, are liquids at room temperature). No doubt someone will explain. In the past, gold and mercury were said to be the only two visual manifestations of Einstein’s special theory in every-day objects. I say the past, because mercury is now rarely seen in any every-day objects (digital thermometers have taken over, and the mercury barometer has long since gone). If anyone knows of other examples, do let us know.
References
- A. Einstein, "Ist die Trägheit eines Körpers von seinem Energieinhalt abhängig?", Annalen der Physik, vol. 323, pp. 639-641, 1905. https://doi.org/10.1002/andp.19053231314
- F. Calvo, E. Pahl, M. Wormit, and P. Schwerdtfeger, "Evidence for Low‐Temperature Melting of Mercury owing to Relativity", Angewandte Chemie International Edition, vol. 52, pp. 7583-7585, 2013. https://doi.org/10.1002/anie.201302742
Tags:bulk metal, pence, potential energy surfaces
Posted in General | 4 Comments »
