Archive for December, 2017
Tuesday, December 26th, 2017
Recollect the suggestion that diazomethane has hypervalent character[1]. When I looked into this, I came to the conclusion that it probably was mildly hypervalent, but on carbon and not nitrogen. Here I try some variations with substituents to see what light if any this casts.
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References
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M.C. Durrant, "A quantitative definition of hypervalency", Chemical Science, vol. 6, pp. 6614-6623, 2015. http://dx.doi.org/10.1039/C5SC02076J
Tags:chemical bonding, Chemistry, diazo, Diazo compounds, Diazomethane, diazomethane-like systems, Functional groups, Hypervalency, Hypervalent molecule, Molecular geometry, Organic chemistry, Recollects
Posted in Uncategorised | 8 Comments »
Saturday, December 23rd, 2017
In the previous post, I referred to a recently published review on hypervalency[1] which introduced a very simple way (the valence electron equivalent γ) of quantifying the effect. Diazomethane was cited as one example of a small molecule exhibiting hypervalency (on nitrogen) by this measure. Here I explore the effect of substituting diazomethane with cyano and nitro groups.‡
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References
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M.C. Durrant, "A quantitative definition of hypervalency", Chemical Science, vol. 6, pp. 6614-6623, 2015. http://dx.doi.org/10.1039/C5SC02076J
Tags:candidate for hypervalent carbon, chemical bonding, Hypervalency, Hypervalent molecule, Interesting chemistry, Molecular geometry
Posted in Uncategorised | No 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 »
Friday, December 8th, 2017
An article with the title shown above in part recently appeared.[1] Given the apparent similarity of HF1- to CH3F1- and CH3F2-, the latter of which I introduced on this blog previously, I thought it of interest to apply my analysis to HF1-.
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References
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M. Liu, H. Chen, C. Chin, T. Huang, Y. Chen, and Y. Wu, "Identification of a Simplest Hypervalent Hydrogen Fluoride Anion in Solid Argon", Scientific Reports, vol. 7, 2017. http://dx.doi.org/10.1038/s41598-017-02687-z
Tags:Hypervalency
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Thursday, December 7th, 2017
FAIR data is increasingly accepted as a description of what research data should aspire to; Findable, Accessible, Inter-operable and Re-usable, with Context added by rich metadata (and also that it should be Open). But there are two sides to data, one of which is the raw data emerging from say an instrument or software simulations and the other in which some kind of model is applied to produce semi- or even fully processed/interpreted data. Here I illustrate a new example of how both kinds of data can be made to co-exist.
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Tags:Chemical IT, computing, Context, data, Data management, Information, Knowledge, Raw data, software simulations, Technology/Internet
Posted in crystal_structure_mining | No Comments »
Saturday, December 2nd, 2017
For around 16 years, Floyd Romesberg’s group has been exploring un-natural alternatives (UBPs) to the Watson-Crick base pairs (C-G and A-T) that form part of the genetic code in DNA. Recently they have had remarkable success with one such base pair, called X and Y (for the press) and dNaMTP and d5SICSTP (in scholarly articles).[1],[2] This extends the genetic coding from the standard 20 amino acids to the possibility of up to 172 amino acids. Already, organisms engineered to contain X-Y pairs in their DNA have been shown to express entirely new (and un-natural) proteins.
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References
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A.W. Feldman, M.P. Ledbetter, Y. Zhang, and F.E. Romesberg, "Reply to Hettinger: Hydrophobic unnatural base pairs and the expansion of the genetic alphabet", Proceedings of the National Academy of Sciences, vol. 114, 2017. http://dx.doi.org/10.1073/pnas.1708259114
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D.A. Malyshev, K. Dhami, H.T. Quach, T. Lavergne, P. Ordoukhanian, A. Torkamani, and F.E. Romesberg, "Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet", Proceedings of the National Academy of Sciences, vol. 109, pp. 12005-12010, 2012. http://dx.doi.org/10.1073/pnas.1205176109
Tags:Base pair, Biology, DNA, Floyd Romesberg, Gene, genetic code, Genetics, Interesting chemistry, Molecular biology, Molecular genetics, Nucleic acids, Nucleotide, Synthetic genomics
Posted in Uncategorised | 3 Comments »