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, Multimodal interaction, Nuclear magnetic resonance, open source chemical structure editors, Sonification, spectroscopy, stereochemical utilities
Posted in Interesting chemistry | No Comments »
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, 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 Chemical IT | 2 Comments »
March 25th, 2017
The previous post demonstrated the simple iso-electronic progression from six-coordinate carbon to five coordinate nitrogen. Here, a further progression to oxygen is investigated computationally.
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Tags: animation, Chemical bond, Chemistry, Matter, Nitrogen, Quantum chemistry
Posted in Bond slam, Hypervalency | 4 Comments »
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
- M. Malischewski, and K. Seppelt, "Crystal Structure Determination of the Pentagonal‐Pyramidal Hexamethylbenzene Dication C<sub>6</sub>(CH<sub>3</sub>)<sub>6</sub><sup>2+</sup>", Angewandte Chemie International Edition, vol. 56, pp. 368-370, 2016. https://doi.org/10.1002/anie.201608795
Tags: aromatic systems, Chemistry, Hexacoordinate, Hypotheses, Matter, Molecular geometry, Stereochemistry
Posted in Bond slam, crystal_structure_mining, Hypervalency, Interesting chemistry | 1 Comment »
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
- 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. https://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 »
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 »
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 »
March 16th, 2017
This is a spin-off from the table I constructed here for further chemical examples of the classical/non-classical norbornyl cation conundrum. One possible entry would include the transition state for inversion of methane via a square planar geometry as compared with e.g. NiH4 for which the square planar motif is its minimum. So is square planar methane a true transition state for inversion (of configuration) of carbon?
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Tags: Chemistry, Methane, Molecular geometry, Orbital hybridisation, Planar, Square planar molecular geometry, Stereochemistry
Posted in reaction mechanism | 2 Comments »