Posts Tagged ‘gas phase’

Dispersion “bonds”: a new example with an ultra-short H…H distance.

Monday, June 26th, 2017
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About 18 months ago, there was much discussion on this blog about a system reported by Bob Pascal and co-workers containing a short H…H contact of ~1.5Å[1]. In this system, the hydrogens were both attached to Si as Si-H…H-Si and compressed together by rings. Now a new report[2] and commented upon by Steve Bachrach, claims a similar distance for hydrogens attached to carbon, i.e. C-H…H-C, but without the ring compression.

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References

  1. J. Zong, J.T. Mague, and R.A. Pascal, "Exceptional Steric Congestion in anin,in-Bis(hydrosilane)", Journal of the American Chemical Society, vol. 135, pp. 13235-13237, 2013. http://dx.doi.org/10.1021/ja407398w
  2. S. Rösel, H. Quanz, C. Logemann, J. Becker, E. Mossou, L. Cañadillas-Delgado, E. Caldeweyher, S. Grimme, and P.R. Schreiner, "London Dispersion Enables the Shortest Intermolecular Hydrocarbon H···H Contact", Journal of the American Chemical Society, vol. 139, pp. 7428-7431, 2017. http://dx.doi.org/10.1021/jacs.7b01879

Tautomeric polymorphism.

Thursday, June 1st, 2017
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Conformational polymorphism occurs when a compound crystallises in two polymorphs differing only in the relative orientations of flexible groups (e.g. Ritonavir). At the Beilstein conference, Ian Bruno mentioned another type;  tautomeric polymorphism, where a compound can crystallise in two forms differing in the position of acidic protons. Here I explore three such examples.

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What is the (calculated) structure of a norbornyl cation anion-pair in water?

Saturday, April 1st, 2017
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In a comment appended to an earlier post, I mused about the magnitude of the force constant relating to the interconversion between a classical and a non-classical structure for the norbornyl cation. Most calculations indicate the force constant for an “isolated” symmetrical cation is +ve, which means it is a true minimum and not a transition state for a [1,2] shift. The latter would have been required if the species equilibrated between two classical carbocations. I then pondered what might happen to both the magnitude and the sign of this force constant if various layers of solvation and eventually a counter-ion were to be applied to the molecule, so that a bridge of sorts between the different states of solid crystals, superacid and aqueous solutions might be built.

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A 5-high straight flush of water-ionised acids?

Tuesday, March 17th, 2015
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I do not play poker, and so I had to look up a 5-4-3-2-1(A), which Wikipedia informs me is a 5-high straight flush, also apparently known as a steel wheel. In previous posts  I have suggested acids which can be ionised by (probably) 5, 4, 3 or  1 discrete water molecules in the gas phase; now to try to track down  a candidate for ionisation by the required two water molecules to form that straight flush.

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Is CLi6 hypervalent?

Friday, July 5th, 2013
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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+", Journal of the American Chemical Society, 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", Journal of the American Chemical Society, vol. 105, pp. 5930-5932, 1983. http://dx.doi.org/10.1021/ja00356a045

Why is the carbonyl IR stretch in an ester higher than in a ketone?

Thursday, February 28th, 2013
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Infra-red spectroscopy of molecules was introduced 110 years ago by Coblentz[1] as the first functional group spectroscopic method (” The structure of the compound has a great influence on the absorption spectra. In many cases it seems as though certain bonds are due to certain groups.“). It hangs on in laboratories to this day as a rapid and occasionally valuable diagnostic tool, taking just minutes to measure. Its modern utility rests on detecting common functional groups, mostly based around identifying the nature of double or triple bonds, and to a lesser extent in differentiating between different kinds of C-H stretches[2] (and of course OH and NH). One common use is to identify the environment of carbonyl groups, C=O. These tend to come in the form of aldehydes and ketones, esters, amides, acyl halides, anhydrides and carbonyls which are part of small rings. The analysis is performed by assigning the value of the C=O stretching wavenumber to a particular range characteristic of each type of compound. Thus ketones are said to inhabit the range of ~1715-1740 cm-1 and simple esters come at ~1740-1760 cm-1, some 20-30 cm-1 higher. Here I try to analyse how this difference arises.

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References

  1. W.W. Coblentz, "Infra-red Absorption Spectra: I. Gases", Physical Review (Series I), vol. 20, pp. 273-291, 1905. http://dx.doi.org/10.1103/PhysRevSeriesI.20.273
  2. J.L. Arbour, H.S. Rzepa, J. Contreras-García, L.A. Adrio, E.M. Barreiro, and K.K.M. Hii, "Silver-Catalysed Enantioselective Addition of OH and NH Bonds to Allenes: A New Model for Stereoselectivity Based on Noncovalent Interactions", Chemistry - A European Journal, vol. 18, pp. 11317-11324, 2012. http://dx.doi.org/10.1002/chem.201200547

Joining up the pieces. Peroxidation of ethyne.

Monday, July 9th, 2012
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Sometimes, connections between different areas of chemistry just pop out (without the help of semantic web tools, this is called serendipity). So here, I will try to join up some threads which emerge from previous posts.

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A golden age for (computational) spectroscopy.

Monday, April 2nd, 2012
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I mentioned in my last post an unjustly neglected paper from that golden age of 1951-1953 by Kirkwood and co. They had shown that Fischer’s famous guess for the absolute configurations of organic chiral molecules was correct. The two molecules used to infer this are shown below.

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Do electrons prefer to move in packs of 4, 6 or 8 during proton exchange in a calixarene?

Friday, January 7th, 2011
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This story starts with a calixarene, a molecule (suitably adorned with substituents) frequently used as a host to entrap a guest and perchance make the guest do something interesting. Such a calixarene was at the heart of a recent story where an attempt was made to induce it to capture cyclobutadiene in its cavity.

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Bio-renewable green polymers: Stereoinduction in poly(lactic acid)

Saturday, July 24th, 2010
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Lactide is a small molecule made from lactic acid, which is itself available in large quantities by harvesting plants rather than drilling for oil. Lactide can be turned into polymers with remarkable properties, which in turn degrade down easily back to lactic acid. A perfect bio-renewable material!

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