Posts Tagged ‘X-ray’

A short non-bonding H…H interaction (continued)

Wednesday, October 2nd, 2013

This is a continuation of the discussion started on Steve Bachrach’s blog about a molecule with a very short H…H interaction involving two Si-H groups with enforced proximity. It had been inferred from the X-ray structure[1] that the H…H distance was in the region of 1.50Å. It’s that cis-butene all over again! So is that H…H region a bond? Is it attractive or repulsive? Go read Steve’s blog first.



  1. J. Zong, J.T. Mague, and R.A. Pascal, " Exceptional Steric Congestion in an in , in -Bis(hydrosilane) ", J. Am. Chem. Soc., pp. 130827160143003, 2013.

X-ray analysis and absolute configuration determination using porous complexes.

Wednesday, April 17th, 2013

This is another in the occasional series of “what a neat molecule”. In this case, more of a “what a neat idea”. The s-triazine below, when coordinated to eg ZnI2, forms what is called a metal-organic-framework, or MOF. A recent article[1] shows how such frameworks can be used to help solve a long-standing problem in structure determination, how to get a crystal structure on a compound that does not crystallise on its own.



  1. Y. Inokuma, S. Yoshioka, J. Ariyoshi, T. Arai, Y. Hitora, K. Takada, S. Matsunaga, K. Rissanen, and M. Fujita, "X-ray analysis on the nanogram to microgram scale using porous complexes", Nature, vol. 495, pp. 461-466, 2013.

To be cyclobutadiene, or not to be, that is the question? You decide.

Thursday, March 21st, 2013

A quartet of articles has recently appeared on the topic of cyclobutadiene.[1],[2],[3],[4]. You will find a great deal discussed there, but I can boil it down to this essence. Do the following coordinates (obtained from a (disordered) previously published[5] x-ray refinement) correspond to a van der Waals complex of 1,3-dimethyl cyclobutadiene and carbon dioxide, or do they instead represent a covalent interaction between these two components resulting in a compound with the chemical name 2-oxabicyclo[2.2.0]hex-5-en-3-one (i.e. not a cyclobutadiene)?



  1. H.S. Rzepa, "A Computational Evaluation of the Evidence for the Synthesis of 1,3-Dimethylcyclobutadiene in the Solid State and Aqueous Solution", Chemistry - A European Journal, vol. 19, pp. 4932-4937, 2013.
  2. M. Shatruk, and I.V. Alabugin, "Reinvestigation of “Single-Crystal X-ray Structure of 1,3-dimethylcyclobutadiene”", Chemistry - A European Journal, vol. 19, pp. 4942-4945, 2013.
  3. Y. Legrand, D. Dumitrescu, A. Gilles, E. Petit, A. van der Lee, and M. Barboiu, "A Constrained Disorder Refinement: “Reinvestigation of “Single-Crystal X-ray Structure of 1,3-Dimethylcyclobutadiene” by M. Shatruk and I. V. Alabugin”", Chemistry - A European Journal, vol. 19, pp. 4946-4950, 2013.
  4. Y. Legrand, D. Dumitrescu, A. Gilles, E. Petit, A. van der Lee, and M. Barboiu, "Reply to A Computational Evaluation of the Evidence for the Synthesis of 1,3-Dimethylcyclobutadiene in Solid State and Aqueous Solution-Beyond the Experimental Reality", Chemistry - A European Journal, vol. 19, pp. 4938-4941, 2013.
  5. Y. Legrand, A. van der Lee, and M. Barboiu, "Single-Crystal X-ray Structure of 1,3-Dimethylcyclobutadiene by Confinement in a Crystalline Matrix", Science, vol. 329, pp. 299-302, 2010.

Helically conjugated molecules. A follow-up to [144]-annulene.

Tuesday, February 12th, 2013

An extensive discussion developed regarding my post on a fascinating helical [144]-annulene. Topics included the nature of the ring current sustained by the π-electrons and in particular the bond-length alternation around the periphery and whether this should alter if the electron count were to be changed to that of a 4n+2 system (i.e. a dication). Whilst the [144]-annulene itself is hypothetical, it emerged that some compounds known as expanded porphyrins have very similar (albeit smaller scale) helical structures. X-ray structures for two such provide useful reality checks on the calculations. Here‡ I include the (3D) coordinates of these two systems so that you can explore for yourself their helicity.


Alkyne metathesis: a comparison with alkene metathesis.

Monday, October 8th, 2012

Metathesis reactions are a series of catalysed transformations which transpose the atoms in alkenes or alkynes. Alkyne metathesis is closely related to the same reaction for alkenes, and one catalyst that is specific to alkynes was introduced by Schrock (who with Grubbs won the Nobel prize for these discoveries) and is based on tungsten (M=W(OR)3).


Streptomycin: a case study in the progress of science.

Monday, May 28th, 2012

Streptomycin is an antibiotic active against tuberculosis, and its discovery has become something of a cause célèbre. It was first isolated on October 19, 1943 by a graduate student Albert Schatz in the laboratory of Selman Waksman at Rutgers University. I want to concentrate in this post on its molecular structure. Its initial isolation was followed by an extraordinarily concentrated period of about three years devoted to identifying that structure, culminating in a review of this chemistry in 1948 by Lemieux and Wolfram. This review presents the structure as shown below (left). The modern rendering on the right is based on a crystal structure done in 1978.


Computers 1967-2011: a personal perspective. Part 4. Moore’s Law and Molecules.

Friday, October 28th, 2011

Moore’s law describes a long-term trend in the evolution of computing hardware, and it is often interpreted in terms of processing speed. Here I chart this rise in terms of the size of computable molecules. By computable I mean specifically how long it takes to predict the geometry of a given molecule using a quantum mechanical procedure.


Hafnium and Niels Bohr

Sunday, June 5th, 2011

In 1923, Coster and von Hevesey (DOI: 10.1038/111182a0) claimed discovery of the element Hafnium, atomic number 72 (latin Hafnia, meaning Copenhagen, where the authors worked) on the basis of six lines in its X-ray spectrum. The debate had long raged as to whether (undiscovered) element 72 belonged to the rare-earth group 3 of the periodic table below yttrium, or whether it should be placed in group 4 below zirconium. Establishing its chemical properties finally placed it in group 4. Why is this apparently arcane and obscure re-assignment historically significant? Because, in June 1922, in Göttingen, Niels Bohr had given a famous series of lectures now known as the Bohr Festspiele on the topic of his electron shell theory of the atom. Prior to giving these lectures he had submitted his collected thoughts in January 1922[1].



  1. N. Bohr, "Der Bau der Atome und die physikalischen und chemischen Eigenschaften der Elemente", Z. Physik, vol. 9, pp. 1-67, 1922.

Déjà vu all over again. Are H…H interactions attractive or repulsive?

Tuesday, May 31st, 2011

The Pirkle reagent is a 9-anthranyl derivative (X=OH, Y=CF3). The previous post on the topic had highlighted DIST1, the separation of the two hydrogen atoms shown below. The next question to ask is how general this feature is. Here we take a look at the distribution of lengths found in the Cambridge data base, and focus on another interesting example.


The colour of Monastral blue (part 2).

Monday, April 4th, 2011

Andy Mclean posted a comment to my story of copper phthalocyanine (Monastral blue). The issue was its colour, and more specifically why this pigment has two peaks λmax 610 and 710nm making it blue. The first was accurately reproduced by calculation on the monomer, but the second was absent with such a model. Andy suggested this latter was due to stacking. Here, the calculated spectrum of a stacked dimer is explored.