Chemistry rich diagrams: do crystal structures carry spin information? Iron-di-imine complexes.

June 18th, 2017
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The iron complex shown below forms the basis for many catalysts.[1] With iron, the catalytic behaviour very much depends on the spin-state of the molecule, which for the below can be either high (hextet) or medium (quartet) spin, with a possibility also of a low spin (doublet) state. Here I explore whether structural information in crystal structures can reflect such spin states.

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References

  1. M.P. Shaver, L.E.N. Allan, H.S. Rzepa, and V.C. Gibson, "Correlation of Metal Spin State with Catalytic Reactivity: Polymerizations Mediated by α-Diimine–Iron Complexes", Angewandte Chemie International Edition, vol. 45, pp. 1241-1244, 2006. http://dx.doi.org/10.1002/anie.200502985

Twenty one years of chemistry-related Java apps: RIP Java?

June 10th, 2017
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In an earlier post, I lamented the modern difficulties in running old instances of Jmol, an example of an application program written in the Java programming language. When I wrote that, I had quite forgotten a treasure trove of links to old Java that I had collected in 1996-7 and then abandoned. Here I browse through a few of the things I found.

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How to search data repositories for FAIR chemical content and data: SubjectScheme

June 8th, 2017
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As data repositories start to flourish, it is reasonable to ask questions such as what sort of chemistry can be found there and how can I find it? Here I give an updated[1] worked example of a digital repository search for chemical content and also pose an important issue for the chemistry domain.

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References

  1. H.S. Rzepa, A. Mclean, and M.J. Harvey, "InChI As a Research Data Management Tool", Chemistry International, vol. 38, 2016. http://dx.doi.org/10.1515/ci-2016-3-408

Research data: Gravitational waves as an example from the astrophysics community.

June 2nd, 2017
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In 2016, the world heard that gravitational waves had been detected and now a third instance is reported. Given that the data associated with these detections are perhaps amongst the most important instances in recent times, I thought I might take a peek at how it was managed.

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Tautomeric polymorphism.

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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CH⋅⋅⋅π Interactions between methyl and carbonyl groups in proteins: a small molecule check.

May 29th, 2017
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Derek Lowe highlights a recent article[1] postulating CH⋅⋅⋅π interactions in proteins. Here I report a quick check using the small molecule crystal structure database (CSD).

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References

  1. F.A. Perras, D. Marion, J. Boisbouvier, D.L. Bryce, and M.J. Plevin, "Observation of CH⋅⋅⋅π Interactions between Methyl and Carbonyl Groups in Proteins", Angewandte Chemie International Edition, 2017. http://dx.doi.org/10.1002/anie.201702626

Challenges in reliably representing the chemistry of crystal structures.

May 29th, 2017
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The title here is taken from a presentation made by Ian Bruno from CCDC at the recent conference on Open Science. It also addresses the theme here of the issues that might arise in assigning identifiers for any given molecule.

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Curating a nine year old journal FAIR data table.

May 29th, 2017
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As the Internet and its Web-components age, so early pages start to decay as technology moves on. A few posts ago, I talked about the maintenance of a relatively simple page first hosted some 21 years ago. In my notes on the curation, I wrote the phrase “Less successful was the attempt to include buttons which could be used to annotate the structures with highlights. These buttons no longer work and will have to be entirely replaced in the future at some stage.” Well, that time has now come, for a rather more crucial page associated with a journal article published more recently in 2009.[1]

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References

  1. H.S. Rzepa, "Wormholes in chemical space connecting torus knot and torus link π-electron density topologies", Physical Chemistry Chemical Physics, vol. 11, pp. 1340, 2009. http://dx.doi.org/10.1039/b810301a

Conference report: an example of collaborative open science (reaction IRCs).

May 25th, 2017
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It is a sign of the times that one travels to a conference well-connected. By which I mean email is on a constant drip-feed, with venue organisers ensuring each delegate receives their WiFi password even before their room key. So whilst I was at a conference espousing the benefits of open science, a nice example of open collaboration was initiated as a result of a received email.

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