Posts Tagged ‘Matter’
Saturday, February 24th, 2018
Another post inspired by a comment on an earlier one; I had been discussing compounds of the type I.In (n=4,6) as possible candidates for hypervalency. The comment suggests the below as a similar analogue, deriving from observations made in 1989.[1]
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References
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Y. Mazaki, and K. Kobayashi, "Structure and intramolecular dynamics of bis(diisobutylselenocarbamoyl) triselenide as identified in solution by the 77Se-NMR spectroscopy", Tetrahedron Letters, vol. 30, pp. 2813-2816, 1989. http://dx.doi.org/10.1016/S0040-4039(00)99132-9
Tags:C, chemical bonding, Chemistry, free energy, Hypervalency, Hypervalent molecule, Matter, Molecular geometry, Nature, Nitrogen
Posted in Uncategorised | 3 Comments »
Friday, February 16th, 2018
Last year, this article[1] attracted a lot of attention as the first example of molecular helium in the form of Na2He. In fact, the helium in this species has a calculated‡ bond index of only 0.15 and it is better classified as a sodium electride with the ionisation induced by pressure and the presence of helium atoms. The helium is neither valent, nor indeed hypervalent (the meanings are in fact equivalent for this element). In a separate blog posted in 2013, I noted a cobalt carbonyl complex containing a hexacoordinate hydrogen in the form of hydride, H–. A comment appended to this blog insightfully asked about the isoelectronic complex containing He instead of H–. Here, rather belatedly, I respond to this comment!
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References
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X. Dong, A.R. Oganov, A.F. Goncharov, E. Stavrou, S. Lobanov, G. Saleh, G. Qian, Q. Zhu, C. Gatti, V.L. Deringer, R. Dronskowski, X. Zhou, V.B. Prakapenka, Z. Konôpková, I.A. Popov, A.I. Boldyrev, and H. Wang, "A stable compound of helium and sodium at high pressure", Nature Chemistry, vol. 9, pp. 440-445, 2017. http://dx.doi.org/10.1038/nchem.2716
Tags:chemical bonding, Chemical elements, chemical shift, Chemistry, helium, Hydride, Hydrogen, Hypervalency, Hypervalent molecule, Matter, Metal hydrides, Reducing agents, Transition metal hydride
Posted in Uncategorised | 4 Comments »
Sunday, December 17th, 2017
Alkalides are anionic alkali compounds containing e.g. sodide (Na–), kalide (K–), rubidide (Rb–) or caeside (Cs–). Around 90 examples can be found in the Cambridge structure database (see DOI: 10.14469/hpc/3453 for the search query and results). So what about the ammonium analogue, ammonide (NH4–)? A quick search of Scifinder drew a blank! So here I take a look at this intriguingly simple little molecule.‡
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Tags:Alkalide, Ammonium, Anions, Atomic physics, Chemistry, electron gas, energy, free-electron gas, Hypervalency, Jahn-Teller, kinetic energy density, Matter, Nitrogen, potential energy surface, search query
Posted in Uncategorised | 2 Comments »
Thursday, September 21st, 2017
A recent article reports, amongst other topics, a computationally modelled reaction involving the capture of molecular hydrogen using a substituted borane (X=N, Y=C).[1] The mechanism involves an initial equilibrium between React and Int1, followed by capture of the hydrogen by Int1 to form a 5-coordinate borane intermediate (Int2 below, as per Figure 11).‡ This was followed by assistance from a proximate basic nitrogen to complete the hydrogen capture via a TS involving H-H cleavage. The forward free energy barrier to capture was ~11 kcal/mol and ~4 kcal/mol in the reverse direction (relative to the species labelled Int1), both suitably low for reversible hydrogen capture. Here I explore a simple variation to this fascinating reaction.∞
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References
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L. Li, M. Lei, Y. Xie, H.F. Schaefer, B. Chen, and R. Hoffmann, "Stabilizing a different cyclooctatetraene stereoisomer", Proceedings of the National Academy of Sciences, vol. 114, pp. 9803-9808, 2017. http://dx.doi.org/10.1073/pnas.1709586114
Tags:Ammonia borane, animation, Boranes, Chemistry, Cleaning Services, Company: React Group, free energy barrier, Hydroboration, Hydrogen, Matter
Posted in reaction mechanism | 1 Comment »
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 »
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 »
Tuesday, February 14th, 2017
I analysed the bonding in chlorine trifluoride a few years back in terms of VSEPR theory. I noticed that several searches on this topic which led people to this post also included a query about the differences between it and the bromine analogue. For those who posed this question, here is an equivalent analysis.
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Tags:Bromine, Bromine trifluoride, Chemical elements, Chemistry, Chlorine, Fluorides, Halogens, Interesting chemistry, Interhalogen compounds, Matter, Oxidizing agents, VSEPR theory
Posted in Uncategorised | 1 Comment »
Saturday, February 11th, 2017
On February 6th I was alerted to this intriguing article[1] by a phone call, made 55 minutes before the article embargo was due to be released. Gizmodo wanted to know if I could provide an (almost)† instant‡ quote. After a few days, this report of a stable compound of helium and sodium still seems impressive to me and I now impart a few more thoughts here.
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References
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X. Dong, A.R. Oganov, A.F. Goncharov, E. Stavrou, S. Lobanov, G. Saleh, G. Qian, Q. Zhu, C. Gatti, V.L. Deringer, R. Dronskowski, X. Zhou, V.B. Prakapenka, Z. Konôpková, I.A. Popov, A.I. Boldyrev, and H. Wang, "A stable compound of helium and sodium at high pressure", Nature Chemistry, vol. 9, pp. 440-445, 2017. http://dx.doi.org/10.1038/nchem.2716
Tags:10.1038, Atom, Chemical elements, chemical phenomenon, Chemistry, Company: P. Acucar-CBD, Electride, Electron, Food Retail & Distribution - NEC, helium, Hydrogen, Interesting chemistry, Matter, Oxygen, Physics, social media
Posted in Bond slam, crystal_structure_mining | 11 Comments »
Friday, January 20th, 2017
This is one of those posts of a molecule whose very structure is interesting enough to merit a picture and a 3D model. The study[1] reports a molecular knot with the remarkable number of eight crossings.
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References
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J.J. Danon, A. Krüger, D.A. Leigh, J. Lemonnier, A.J. Stephens, I.J. Vitorica-Yrezabal, and S.L. Woltering, "Braiding a molecular knot with eight crossings", Science, vol. 355, pp. 159-162, 2017. http://dx.doi.org/10.1126/science.aal1619
Tags:Cheminformatics, Chemistry, Drug discovery, Education, Interesting chemistry, π-systems, Matter, Molecule, Nature, spectroscopy, Structure validation
Posted in Uncategorised | 3 Comments »