Posts Tagged ‘Cambridge’
Thursday, April 18th, 2019
The topic of this post originates from a recent article which is attracting much attention.[1] The technique uses confined light to both increase the spatial resolution by around three orders of magnitude and also to amplify the signal from individual molecules to the point it can be recorded. To me, Figure 3 in this article summarises it nicely (caption: visualization of vibrational normal modes). Here I intend to show selected modes as animated and rotatable 3D models with the help of their calculation using density functional theory (a mode of presentation that the confinement of Figure 3 to the pages of a conventional journal article does not enable).
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References
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J. Lee, K.T. Crampton, N. Tallarida, and V.A. Apkarian, "Visualizing vibrational normal modes of a single molecule with atomically confined light", Nature, vol. 568, pp. 78-82, 2019. http://dx.doi.org/10.1038/s41586-019-1059-9
Tags:anionic metal surface, Cambridge, chemical bonding, Chemistry, dihedral, energy, flat metal surface, metal, Natural sciences, Neutral Quartet, Physical sciences, Raman scattering, Raman spectroscopy, Resonance, spectroscopy, steric repulsion energy
Posted in Interesting chemistry | No Comments »
Thursday, November 12th, 2015
Derek Lowe has a recent post entitled “Another Funny-Looking Structure Comes Through“. He cites a recent medchem article[1] in which the following acetal sub-structure appears in a promising drug candidate (blue component below). His point is that orally taken drugs have to survive acid (green below) encountered in the stomach, and acetals are famously sensitive to hydrolysis (red below). But if X=NH2, compound “G-5555” is apparently stable to acids.[1] So I pose the question here; why?
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References
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C.O. Ndubaku, J.J. Crawford, J. Drobnick, I. Aliagas, D. Campbell, P. Dong, L.M. Dornan, S. Duron, J. Epler, L. Gazzard, C.E. Heise, K.P. Hoeflich, D. Jakubiak, H. La, W. Lee, B. Lin, J.P. Lyssikatos, J. Maksimoska, R. Marmorstein, L.J. Murray, T. O’Brien, A. Oh, S. Ramaswamy, W. Wang, X. Zhao, Y. Zhong, E. Blackwood, and J. Rudolph, "Design of Selective PAK1 Inhibitor G-5555: Improving Properties by Employing an Unorthodox Low-pKa Polar Moiety", ACS Medicinal Chemistry Letters, vol. 6, pp. 1241-1246, 2015. http://dx.doi.org/10.1021/acsmedchemlett.5b00398
Tags:Cambridge, Derek Lowe, HTML, HTML element, medchem, medical chemistry
Posted in reaction mechanism | 2 Comments »
Thursday, October 1st, 2015
A fascinating re-examination has appeared[1] of a reaction first published[2] in 1960 by Wittig and then[3] repudiated by him in 1964 since it could not be replicated by a later student. According to the new work, the secret to a successful replication seems to be the presence of traces of a nickel catalyst (originally coming from e.g. a nickel spatula?). In this recent article[1] a mechanism for the catalytic cycle is proposed. Here I thought I might explore this mechanism using calculations to see if any further insights might emerge.
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References
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S.A. Künzi, J.M. Sarria Toro, T. den Hartog, and P. Chen, "Nickel‐Catalyzed Cyclopropanation with NMe4OTf and nBuLi", Angewandte Chemie International Edition, vol. 54, pp. 10670-10674, 2015. http://dx.doi.org/10.1002/anie.201505482
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V. Franzen, and G. Wittig, "Trimethylammonium‐methylid als Methylen‐Donator", Angewandte Chemie, vol. 72, pp. 417-417, 1960. http://dx.doi.org/10.1002/ange.19600721210
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G. Wittig, and D. Krauss, "Cyclopropanierungen bei Einwirkung von N‐Yliden auf Olefine", Justus Liebigs Annalen der Chemie, vol. 679, pp. 34-41, 1964. http://dx.doi.org/10.1002/jlac.19646790106
Tags:activation free energy barriers, Cambridge, energy, energy relative, nickel-carbene product
Posted in Interesting chemistry, reaction mechanism | No Comments »
Sunday, September 6th, 2015
An article entitled “Four Decades of the Chemistry of Planar Hypercoordinate Compounds“[1] was recently reviewed by Steve Bacharach on his blog, where you can also see comments. Given the recent crystallographic themes here, I thought I might try a search of the CSD (Cambridge structure database) to see whether anything interesting might emerge for tetracoordinate carbon.
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References
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L. Yang, E. Ganz, Z. Chen, Z. Wang, and P.V.R. Schleyer, "Four Decades of the Chemistry of Planar Hypercoordinate Compounds", Angewandte Chemie International Edition, vol. 54, pp. 9468-9501, 2015. http://dx.doi.org/10.1002/anie.201410407
Tags:Angle, Cambridge, chemical bonding, Cycloalkane, Cyclopropane, HTML, HTML element, Ligand, metal, search definition, search results, search software, Steve Bacharach
Posted in Chemical IT, crystal_structure_mining | No Comments »
Friday, June 26th, 2015
Open principles in the sciences in general and chemistry in particular are increasingly nowadays preached from funding councils down, but it can be more of a challenge to find innovative practitioners. Part of the problem perhaps is that many of the current reward systems for scientists do not always help promote openness. Jean-Claude Bradley was a young scientist who was passionately committed to practising open chemistry, even though when he started he could not have anticipated any honours for doing so. A year ago a one day meeting at Cambridge was held to celebrate his achievements, followed up with a special issue of the Journal of Cheminformatics. Peter Murray-Rust and I both contributed and following the meeting we decided to help promote Open Chemistry via an annual award to be called the Bradley-Mason prize. This would celebrate both “JC” himself and Nick Mason, who also made outstanding contributions to the cause whilst studying at Imperial College. The prize was initially to be given to an undergraduate student at Imperial, but was also extended to postgraduate students who have promoted and showcased open chemistry in their PhD researches.
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Tags:Cambridge, chemical data, Chemistry Central, Collective intelligence, Crowdsourcing, Doctor of Philosophy, Education, European Union, France, GITHUB INC., Imperial College, Jean Claude Bradley, lab on a chip, Lyon, Nick Mason, Nonprofit technology, Open content, Peter Murray-Rust, reward systems, Technology/Internet, Tom Arrow, Tom Phillips, Wikimedia Foundation, wikipedia, World Wide Web, young scientist
Posted in Bradley-Mason Prize for Open Chemistry, Chemical IT | 1 Comment »
Sunday, April 13th, 2014
Around 100 tons of the potent antimalarial artemisinin is produced annually; a remarkable quantity given its very unusual and fragile looking molecular structure (below). When I looked at this, I was immediately struck by a thought: surely this is a classic molecule for analyzing stereoelectronic effects (anomeric and gauche). Here this aspect is explored.
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Tags:C7 Lp, Cambridge, stereo-electronics
Posted in crystal_structure_mining, Interesting chemistry | No Comments »
Wednesday, June 5th, 2013
In a time of change, we often do not notice that Δ = ∫δ. Here I am thinking of network bandwidth, and my personal experience of it over a 46 year period.
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Tags:acoustic coupler, Addison-Wesley, Austin Texas, BT, building I, California, Cambridge, computing, electronics, ethernet, Global Intelligence, Google, Historical, Imperial College, Leeds, London, New York, operating system, quantum chemical calculations, Samuel Butler, United Kingdom, University College London
Posted in Uncategorized | 4 Comments »