Archive for March, 2017
Friday, March 31st, 2017
Nowadays, data supporting most publications relating to the synthesis of organic compounds is more likely than not to be found in associated “supporting information” rather than the (often page limited) article itself. For example, this article[1] has an SI which is paginated at 907; almost a mini-database in its own right!† Here I ponder whether such dissemination of data is FAIR (Findable, accessible, interoperable and re-usable).[2]
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References
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J.M. Lopchuk, K. Fjelbye, Y. Kawamata, L.R. Malins, C. Pan, R. Gianatassio, J. Wang, L. Prieto, J. Bradow, T.A. Brandt, M.R. Collins, J. Elleraas, J. Ewanicki, W. Farrell, O.O. Fadeyi, G.M. Gallego, J.J. Mousseau, R. Oliver, N.W. Sach, J.K. Smith, J.E. Spangler, H. Zhu, J. Zhu, and P.S. Baran, "Strain-Release Heteroatom Functionalization: Development, Scope, and Stereospecificity", Journal of the American Chemical Society, vol. 139, pp. 3209-3226, 2017. http://dx.doi.org/10.1021/jacs.6b13229
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M.D. Wilkinson, M. Dumontier, I.J. Aalbersberg, G. Appleton, M. Axton, A. Baak, N. Blomberg, J. Boiten, L.B. da Silva Santos, P.E. Bourne, J. Bouwman, A.J. Brookes, T. Clark, M. Crosas, I. Dillo, O. Dumon, S. Edmunds, C.T. Evelo, R. Finkers, A. Gonzalez-Beltran, A.J. Gray, P. Groth, C. Goble, J.S. Grethe, J. Heringa, P.A. ’t Hoen, R. Hooft, T. Kuhn, R. Kok, J. Kok, S.J. Lusher, M.E. Martone, A. Mons, A.L. Packer, B. Persson, P. Rocca-Serra, M. Roos, R. van Schaik, S. Sansone, E. Schultes, T. Sengstag, T. Slater, G. Strawn, M.A. Swertz, M. Thompson, J. van der Lei, E. van Mulligen, J. Velterop, A. Waagmeester, P. Wittenburg, K. Wolstencroft, J. Zhao, and B. Mons, "The FAIR Guiding Principles for scientific data management and stewardship", Scientific Data, vol. 3, 2016. http://dx.doi.org/10.1038/sdata.2016.18
Tags:Carbon, chemical databases, chemical graveyard, Chemical IT, chemical spectra, Chemistry, digital signature, Nature, Organic, Organic chemistry, Organic compound, Organic food, search engines, Technology/Internet
Posted in Uncategorised | 3 Comments »
Friday, March 31st, 2017
Occasionally one comes across a web site that manages to combine being unusual, interesting and also useful. Thus www.molinsight.net is I think a unique chemistry resource for blind and visually impaired students.
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Tags:Chemistry, Electromagnetic radiation, Infrared, Infrared spectroscopy, Interesting chemistry, Multimodal interaction, Nuclear magnetic resonance, open source chemical structure editors, Sonification, spectroscopy, stereochemical utilities
Posted in Uncategorised | No Comments »
Thursday, March 30th, 2017
In an era when alternative facts and fake news afflict us, the provenance of scientific data becomes ever more important. Especially if that data is available as open access and exploitable by others for both valid scientific reasons but potentially also by those with other motives. Here I consider the audit trail that might serve to establish data provenance in one typical situation in chemistry, the acquisition of NMR instrumental data.
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Tags:Acquisition, Archival science, author, Chemical IT, collection software, Company: NMR, data, Data management, data processing software, Evidence law, instrument data collection software, local authentication systems, Mestrenova, MestreNova system, Nuclear magnetic resonance, principal investigator, Provenance, Scientific method, service manager, spectrometer software, supervisor, Technology/Internet, Terminology
Posted in Uncategorised | 2 Comments »
Saturday, March 25th, 2017
A few years back I followed a train of thought here which ended with hexacoordinate carbon, then a hypothesis rather than a demonstrated reality. That reality was recently confirmed via a crystal structure, DOI:10.5517/CCDC.CSD.CC1M71QM[1]. Here is a similar proposal for penta-coordinate nitrogen.
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References
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M. Malischewski, and K. Seppelt, "Crystal Structure Determination of the Pentagonal‐Pyramidal Hexamethylbenzene Dication C6(CH3)62+", Angewandte Chemie International Edition, vol. 56, pp. 368-370, 2016. http://dx.doi.org/10.1002/anie.201608795
Tags:aromatic systems, Chemistry, Hexacoordinate, Hypervalency, Hypotheses, Interesting chemistry, Matter, Molecular geometry, Stereochemistry
Posted in Bond slam, crystal_structure_mining | 1 Comment »
Thursday, March 23rd, 2017
It is not only the non-classical norbornyl cation that has proved controversial in the past. A colleague mentioned at lunch (thanks Paul!) that tri-coordinate group 14 cations such as R3Si+ have also had an interesting history.[1] Here I take a brief look at some of these systems.
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References
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J.B. Lambert, Y. Zhao, H. Wu, W.C. Tse, and B. Kuhlmann, "The Allyl Leaving Group Approach to Tricoordinate Silyl, Germyl, and Stannyl Cations", Journal of the American Chemical Society, vol. 121, pp. 5001-5008, 1999. http://dx.doi.org/10.1021/ja990389u
Tags:2-Norbornyl cation, Carbocations, chemical bonding, Chemistry, metal, Physical organic chemistry, Reactive intermediates, search query, tri-coordinate
Posted in crystal_structure_mining | 8 Comments »
Monday, March 20th, 2017
The example a few posts back of how methane might invert its configuration by transposing two hydrogen atoms illustrated the reaction mechanism by locating a transition state and following it down in energy using an intrinsic reaction coordinate (IRC). Here I explore an alternative method based instead on computing a molecular dynamics trajectory (MD).
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Tags:animation, chemical reaction, Chemistry, computational chemistry, computed potential energy surface, energy, Gaseous signaling molecules, Hydrogen, kinetic energy, kinetic energy contributions, Methane, Molecular dynamics, Physical chemistry, Quantum chemistry, Reaction coordinate, simulation, Theoretical chemistry
Posted in reaction mechanism | 2 Comments »
Sunday, March 19th, 2017
The Wikipedia entry on peroxydisulfate is quite short (as of today). But I suspect this article may change things.[1].
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References
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M.A. Keller, D. Kampjut, S.A. Harrison, and M. Ralser, "Sulfate radicals enable a non-enzymatic Krebs cycle precursor", Nature Ecology & Evolution, vol. 1, 2017. http://dx.doi.org/10.1038/s41559-017-0083
Tags:Interesting chemistry, metal salts, Peroxydisulfate
Posted in crystal_structure_mining | No Comments »
Sunday, March 19th, 2017
A pyrophoric metal is one that burns spontaneously in oxygen; I came across this phenomenon as a teenager doing experiments at home. Pyrophoric iron for example is prepared by heating anhydrous iron (II) oxalate in a sealed test tube (i.e. to 600° or higher). When the tube is broken open and the contents released, a shower of sparks forms. Not all metals do this; early group metals such as calcium undergo a different reaction releasing carbon monoxide and forming calcium carbonate and not the metal itself. Here as a prelude to the pyrophoric reaction proper, I take a look at this alternative mechanism using calculations.
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Tags:Aluminium, calculated free energy barrier, Carbon monoxide, Chemical elements, Chemistry, higher activation energy, Iron, Matter, metal, metal oxalates, Oxide, pyrophoric metal, Pyrophoricity, Reducing agents
Posted in crystal_structure_mining, reaction mechanism | 1 Comment »