August 25th, 2013
The concept of a “hidden intermediate” in a reaction pathway has been promoted by Dieter Cremer[1] and much invoked on this blog. When I used this term in a recent article of ours[2], a referee tried to object, saying it was not in common use in chemistry. The term clearly has an image problem. A colleague recently sent me an article to read (thanks Chris!) about isotope effects in the epoxidation of ethene[3] and there I discovered a nice example of hidden intermediates which I share with you now.
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References
- E. Kraka, and D. Cremer, "Computational Analysis of the Mechanism of Chemical Reactions in Terms of Reaction Phases: Hidden Intermediates and Hidden Transition States", Accounts of Chemical Research, vol. 43, pp. 591-601, 2010. https://doi.org/10.1021/ar900013p
- H.S. Rzepa, and C. Wentrup, "Mechanistic Diversity in Thermal Fragmentation Reactions: A Computational Exploration of CO and CO<sub>2</sub> Extrusions from Five-Membered Rings", The Journal of Organic Chemistry, vol. 78, pp. 7565-7574, 2013. https://doi.org/10.1021/jo401146k
- T. Koerner, H. Slebocka-Tilk, and R.S. Brown, "Experimental Investigation of the Primary and Secondary Deuterium Kinetic Isotope Effects for Epoxidation of Alkenes and Ethylene with <i>m</i>-Chloroperoxybenzoic Acid", The Journal of Organic Chemistry, vol. 64, pp. 196-201, 1998. https://doi.org/10.1021/jo981652x
Tags: activation free energy, arrow pushing, curly arrow, dichloromethane solution, Dieter Cremer, hidden intermediate, model, using per-ethanoic acid
Posted in Curly arrows, reaction mechanism | 3 Comments »
August 18th, 2013
We have been experimenting with full-colour 3D printing of molecular objects. I thought I might here share some of our observations. Firstly, I list the software used:
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Tags: 3D colour printing, 3D printing, Bob Hanson, chemical models, EUR
Posted in Interesting chemistry | 21 Comments »
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
- 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", Journal of the American Chemical Society, vol. 135, pp. 11239-11246, 2013. https://doi.org/10.1021/ja404256s
Tags: above energy diagram, energy, energy transfer, energy transfer occurring, energy transfers, engineer, free energy
Posted in Interesting chemistry | 1 Comment »
July 27th, 2013
Valence shell electron pair repulsion theory is a simple way of rationalising the shapes of many compounds in which a main group element is surrounded by ligands. ClF3 is a good illustration of this theory.
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Tags: 2-electron-3-centre
Posted in Hypervalency, Interesting chemistry | 5 Comments »
July 18th, 2013
This potential example of a molecule on the edge of chaos was suggested to me by a student (thanks Stephen!), originating from an inorganic tutorial. It represents a class of Mo-complex ligated by two dithiocarbamate ligands and two aryl nitrene ligands (Ar-N:).
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Posted in Interesting chemistry | 2 Comments »
July 14th, 2013
I noted previously that some 8-ring cyclic compounds could exist in either a planar-aromatic or a non-planar-non-aromatic mode, the mode being determined by apparently quite small changes in a ring substituent. Hunting for other examples of such chemistry on the edge, I did a search of the Cambridge crystal database for metal sulfides.
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Tags: Cambridge, chemical reasons, metal, metal sulfides, neutral systems, transition metal series
Posted in Interesting chemistry | No Comments »
July 11th, 2013
The butterfly effect summarises how a small change to a system may result in very large and often unpredictable (chaotic) consequences. If the system is merely on the edge of chaos, the consequences are predictable, but nevertheless finely poised between e.g. two possible outcomes. Here I ask how a molecule might manifest such behaviour.
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Posted in Interesting chemistry | 5 Comments »
July 8th, 2013
A feature of a blog which is quite different from a journal article is how rapidly a topic might evolve. Thus I started a few days ago with the theme of dicarbon (C2), identifying a metal carbide that showed C2 as a ligand, but which also entrapped a single carbon in hexa-coordinated mode. A comment was posted bringing attention to the origins of the discovery of hexacoordinated carbon, and we moved on to exploring the valency in one such species (CLi6). Here I ask if hydrogen itself might exhibit such coordination.
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Tags: chemical shift, metal atoms, metal carbide
Posted in Hypervalency, Interesting chemistry | 2 Comments »
July 5th, 2013
The title of this post summarises the contents of a new molecular database: www.molecularspace.org[1] and I picked up on it by following the post by Jan Jensen at www.compchemhighlights.org (a wonderful overlay journal that tracks recent interesting articles). The molecularspace project more formally is called “The Harvard Clean Energy Project: Large-scale computational screening and design of organic photovoltaics on the world community grid“. It reminds of a 2005 project by Peter Murray-Rust et al at the same sort of concept[2] (the World-Wide-Molecular-Matrix, or WWMM[3]), although the new scale is certainly impressive. Here I report my initial experiences looking through molecularspace.org
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References
- https://doi.org/
- P. Murray-Rust, H.S. Rzepa, J.J.P. Stewart, and Y. Zhang, "A global resource for computational chemistry", Journal of Molecular Modeling, vol. 11, pp. 532-541, 2005. https://doi.org/10.1007/s00894-005-0278-1
- P. Murray-Rust, S.E. Adams, J. Downing, J.A. Townsend, and Y. Zhang, "The semantic architecture of the World-Wide Molecular Matrix (WWMM)", Journal of Cheminformatics, vol. 3, 2011. https://doi.org/10.1186/1758-2946-3-42
Tags: energy gap, energy levels, Google, Harvard, Jan Jensen, molecularspace site, opendata, Peter Murray-Rust, software agent acting, www.compchemhighlights.org, www.molecularspace.org
Posted in Chemical IT | 7 Comments »