Posts Tagged ‘energy’

More simple experiments with crystal data. The pyramidalisation of nitrogen.

Saturday, November 1st, 2014

We 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.

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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. amide 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). search   The first plot is of the torsion vs the distance, for E = H-X (X=O,F, Cl) amides

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Ribulose-1,5-bisphosphate + carbon dioxide → carbon fixation!

Sunday, April 20th, 2014

Ribulose-1,5-bisphosphate reacts with carbon dioxide to produce 3-keto-2-carboxyarabinitol 1,5-bisphosphate as the first step in the biochemical process of carbon fixation. It needs an enzyme to do this (Ribulose-1,5-bisphosphate carboxylase/oxygenase, or RuBisCO) and lots of ATP (adenosine triphosphate, produced by photosynthesis). Here I ask what the nature of the uncatalysed transition state is, and hence the task that might be facing the catalyst in reducing the activation barrier to that of a facile thermal reaction. I present my process in the order it was done.

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Enantioselective epoxidation of alkenes using the Shi Fructose-based catalyst. An undergraduate experiment.

Tuesday, April 15th, 2014

The journal of chemical education can be a fertile source of ideas for undergraduate student experiments. Take this procedure for asymmetric epoxidation of an alkene.[1] When I first spotted it, I thought not only would it be interesting to do in the lab, but could be extended by incorporating some modern computational aspects as well. 

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References

  1. A. Burke, P. Dillon, K. Martin, and T.W. Hanks, "Catalytic Asymmetric Epoxidation Using a Fructose-Derived Catalyst", J. Chem. Educ., vol. 77, pp. 271, 2000. http://dx.doi.org/10.1021/ed077p271

What is the best way of folding a straight chain alkane?

Sunday, April 6th, 2014

In the previous post, I showed how modelling of unbranched alkenes depended on dispersion forces. When these are included, a bent (single-hairpin) form of C58H118 becomes lower in free energy than the fully extended linear form. Here I try to optimise these dispersion forces by adding further folds to see what happens.

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Modelling the geometry of unbranched alkanes.

Saturday, March 29th, 2014

By about C17H36, the geometry of “cold-isolated” unbranched saturated alkenes is supposed not to contain any fully anti-periplanar conformations. [1] Indeed, a (co-crystal) of C16H34 shows it to have two-gauche bends.[2]. Surprisingly, the longest linear alkane I was able to find a crystal structure for, C28H58 appears to be fully extended[3],[4] (an early report of a low quality structure for C36H74[5] also appears to show it as linear). Here I explore how standard DFT theories cope with these structures.

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References

  1. N.O.B. Lüttschwager, T.N. Wassermann, R.A. Mata, and M.A. Suhm, "The Last Globally Stable Extended Alkane", Angew. Chem. Int. Ed., vol. 52, pp. 463-466, 2012. http://dx.doi.org/10.1002/anie.201202894
  2. N. Cocherel, C. Poriel, J. Rault-Berthelot, F. Barrière, N. Audebrand, A.M.Z. Slawin, and L. Vignau, "New 3π-2Spiro Ladder-Type Phenylene Materials: Synthesis, Physicochemical Properties and Applications in OLEDs", Chemistry - A European Journal, vol. 14, pp. 11328-11342, 2008. http://dx.doi.org/10.1002/chem.200801428
  3. S.C. Nyburg, and A.R. Gerson, "Crystallography of the even n-alkanes: structure of C20H42", Acta Cryst Sect B, vol. 48, pp. 103-106, 1992. http://dx.doi.org/10.1107/S0108768191011059
  4. R. Boistelle, B. Simon, and G. Pèpe, "Polytypic structures of n-C28H58 (octacosane) and n-C36H74 (hexatriacontane)", Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry, vol. 32, pp. 1240-1243, 1976. http://dx.doi.org/10.1107/S0567740876005025
  5. H.M.M. Shearer, and V. Vand, "The crystal structure of the monoclinic form of n-hexatriacontant", Acta Crystallographica, vol. 9, pp. 379-384, 1956. http://dx.doi.org/10.1107/S0365110X5600111X

Caesium trifluoride: could it be made?

Saturday, November 23rd, 2013

Mercury (IV) tetrafluoride attracted much interest when it was reported in 2007[1] as the first instance of the metal being induced to act as a proper transition element (utilising d-electrons for bonding) rather than a post-transition main group metal (utilising just s-electrons) for which the HgF2 dihalide would be more normal (“Is mercury now a transition element?”[2]). Perhaps this is the modern equivalent of transmutation! Well, now we have new speculation about how to induce the same sort of behaviour for caesium; might it form CsF3 (at high pressures) rather than the CsF we would be more familiar with.[3] Here I report some further calculations inspired by this report.

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References

  1. X. Wang, L. Andrews, S. Riedel, and M. Kaupp, "Mercury Is a Transition Metal: The First Experimental Evidence for HgF4", Angew. Chem. Int. Ed., vol. 46, pp. 8371-8375, 2007. http://dx.doi.org/10.1002/anie.200703710
  2. W.B. Jensen, "Is Mercury Now a Transition Element?", J. Chem. Educ., vol. 85, pp. 1182, 2008. http://dx.doi.org/10.1021/ed085p1182
  3. M. Miao, "Caesium in high oxidation states and as a p-block element", Nature Chem, vol. 5, pp. 846-852, 2013. http://dx.doi.org/10.1038/nchem.1754

Patterns of behaviour: serendipity in action for enantiomerisation of F-S-S-Cl

Thursday, September 19th, 2013

Paul Schleyer sent me an email about a pattern he had spotted, between my post on F3SSF and some work he and Michael Mauksch had done 13 years ago with the intriguing title “Demonstration of Chiral Enantiomerization in a Four-Atom Molecule“.[1] Let me explain the connection, but also to follow-up further on what I discovered in that post and how a new connection evolved.FSSF3-gen

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References

  1. P.V.R. Schleyer, and M. Mauksch, "Demonstration of Chiral Enantiomerization in a Four‐Atom Molecule ", Angewandte Chemie International Edition, 2000. http://doi.org/d8g2nw

Molecule-sized pixels.

Sunday, August 11th, 2013

The ultimate reduction in size for an engineer is to a single molecule. It’s been done for a car; now it has been reported for the pixel (picture-element).[1]

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References

  1. J.E. Kwon, S. Park, and S.Y. Park, "Realizing Molecular Pixel System for Full-Color Fluorescence Reproduction: RGB-Emitting Molecular Mixture Free from Energy Transfer Crosstalk", J. Am. Chem. Soc., vol. 135, pp. 11239-11246, 2013. http://dx.doi.org/10.1021/ja404256s

Is CLi6 hypervalent?

Friday, July 5th, 2013

A comment made on the previous post on the topic of hexa-coordinate carbon cited an article entitled “Observation of hypervalent CLi6 by Knudsen-effusion mass spectrometry[1] by Kudo as a amongst the earliest of evidence that such species can exist (in the gas phase). It was a spectacular vindication of the earlier theoretical prediction[2],[3] that such 6-coordinate species are stable with respect to dissociation to CLi4 and Li2.

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References

  1. H. Kudo, "Observation of hypervalent CLi6 by Knudsen-effusion mass spectrometry", Nature, vol. 355, pp. 432-434, 1992. http://dx.doi.org/10.1038/355432a0
  2. E.D. Jemmis, J. Chandrasekhar, E.U. Wuerthwein, P.V.R. Schleyer, J.W. Chinn, F.J. Landro, R.J. Lagow, B. Luke, and J.A. Pople, "Lithiated carbocations. The generation, structure, and stability of CLi5+", J. Am. Chem. Soc., vol. 104, pp. 4275-4276, 1982. http://dx.doi.org/10.1021/ja00379a051
  3. P.V.R. Schleyer, E.U. Wuerthwein, E. Kaufmann, T. Clark, and J.A. Pople, "Effectively hypervalent molecules. 2. Lithium carbide (CLi5), lithium carbide (CLi6), and the related effectively hypervalent first row molecules, CLi5-nHn and CLi6-nHn", J. Am. Chem. Soc., vol. 105, pp. 5930-5932, 1983. http://dx.doi.org/10.1021/ja00356a045