April 13th, 2016
Publishing embargoes seem a relatively new phenomenon, probably starting in areas of science when the data produced for a scientific article was considered more valuable than the narrative of that article. However, the concept of the embargo seems to be spreading to cover other aspects of publishing, and I came across one recently which appears to take such embargoes into new and uncharted territory.
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Tags: Academic publishing, Embargo, Open access, Publishing, Royal Society of Chemistry, Technology/Internet, Uncharted, Uncharted Territory
Posted in Chemical IT | No Comments »
April 8th, 2016
Previously, I looked at models of how ammonia could be protonated by water to form ammonium hydroxide. The energetic outcome of my model matched the known equilbrium in water as favouring the unprotonated form (pKb ~4.75). I add here two amines for which R=Me3Si and R=CN. The idea is that the first will assist nitrogen protonation by stabilising the positive centre and the second will act in the opposite sense; an exploration if you like of how one might go about computationally designing a non-steric superbasic amine that becomes predominantly protonated when exposed to water (pKb <1)† and is thus more basic than hydroxide anion in this medium.
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Tags: Acid, Acid dissociation constant, Amide, Amine, Ammonia, Ammonium, Bases, City: Cambridge, energy, from non-protic solution, Functional groups, Hydrogen bond, Hydroxide, Lone pair, metal, Nitrile, relative free energy, search query
Posted in General, Interesting chemistry | 2 Comments »
April 2nd, 2016
A celebration of the life and work of the great chemist Paul von R. Schleyer was held this week in Erlangen, Germany. There were many fantastic talks given by some great chemists describing fascinating chemistry. Here I highlight the presentation given by Andy Streitwieser on the topic of organolithium chemistry, also a great interest of Schleyer's over the years. I single this talk out since I hope it illustrates why people still get together in person to talk about science.
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Tags: Centroid, chemical effect, chemical insights, chemical interpretation, City: Erlangen, Country: Germany, Degree of a continuous mapping, Ferrocene, Hydrogen bond, individual search definition, metal, overall search collection, Streitwieser, terminal H-positions, Torsion, X-ray
Posted in Chemical IT, crystal_structure_mining, Interesting chemistry | 6 Comments »
March 28th, 2016
Augmented reality, a superset if you like of virtual reality (VR), has really been hitting the headlines recently. Like 3D TV, its been a long time coming! Since ~1994 or earlier, there have been explorations of how molecular models can be transferred from actual reality to virtual reality using conventional computers (as opposed to highly specialised ones). It was around then that a combination of software (Rasmol) and hardware (Silicon Graphics, and then soon after standard personal computers with standard graphics cards) became capable of such manipulations. VRML (virtual reality modelling language) also proved something of a false start‡ So have things changed?
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Tags: Augmented reality, chemical article, Company: Microsoft, Company: Silicon Graph, for 3D printing, Google Cardboard, jmol, RasMol, User interface techniques, Virtual reality, VRML
Posted in Chemical IT, General | No Comments »
March 20th, 2016
This is a corollary to the previous post‡ exploring how many molecules are needed to ionise HCl. Here I am asking how many water molecules are required to form the ionic ammonium hydroxide from ammonia and water.
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Tags: Ammonia, Ammonium, Ammonium hydroxide, Bases, dilute solutions, free energy difference, Hydroxides, Ion, Properties of water
Posted in General | No Comments »
March 16th, 2016
At the ACS conference, I have attended many talks these last four days, but one made some “connections” which intrigued me. I tell its story (or a part of it) here.
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Tags: Archive formats, chemical structure, ELN, Nuclear magnetic resonance, PDF, research data management, spectroscopy, suitable processing software, XML, Zip
Posted in Chemical IT | 1 Comment »
March 7th, 2016
The upcoming ACS national meeting in San Diego has a CINF (chemical information division) session entitled "Global initiatives in research data management and discovery". I have highlighted here just one slide from my contribution to this session, which addresses the discovery aspect of the session.
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Tags: Academic publishing, chemical, chemical information division, Chemical nomenclature, chemical structures, Chemical substance, chemical/x-wavefunction, Cheminformatics, City: San Diego, content media, data repository search, format type chemical/x-* , Identifiers, Imperial College, Imperial College London, International Chemical Identifier, JSON, media types, multipurpose internet media extensions, ORCiD, PDF, potential such systems, research data management, Search queries, Technical communication, Technology/Internet
Posted in Chemical IT | 2 Comments »
March 2nd, 2016
The upcoming ACS national meeting in San Diego has a CHED (chemical education division) session entitled Implementing Discovery-Based Research Experiences in Undergraduate Chemistry Courses. I had previously explored what I called extreme gauche effects in the molecule F-S-S-F. Here I take this a bit further to see what else can be discovered about molecules containing bonds between group 16 elements (QA= O, S, Se, Te).
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Tags: City: San Diego, metal, non-metal, Singular spectrum analysis, Time series analysis
Posted in crystal_structure_mining, Interesting chemistry | No Comments »
February 24th, 2016
At the precise moment I write this, there is information about 108,230,950 organic and inorganic chemical substances from the World's disclosed chemistry. So it was with a sense of curiosity that I came across this article in the American Mineralogist[cite]/10.2138/am-2015-5417[/cite] entitled "Earth’s “missing” minerals" (the first in a series of articles apparently planned on the topic of the missing ones). The abstract is particularly interesting and whilst I encourage you to go read the article itself, I will quote some eye-catching observations from just this abstract:
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Tags: inorganic chemical substances, Mineral, Mineralogist, natural products
Posted in Interesting chemistry | No Comments »
February 21st, 2016
Hypervalency is defined as a molecule that contains one or more main group elements formally bearing more than eight electrons in their valence shell. One example of a molecule so characterised was CLi6[cite]10.1038/355432a0[/cite] where the description "“carbon can expand its octet of electrons to form this relatively stable molecule“ was used. Yet, in this latter case, the octet expansion is in fact an illusion, as indeed are many examples that are cited. The octet shell remains resolutely un-expanded. Here I will explore the tiny molecule CH3F2- where two extra electrons have been added to fluoromethane.
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Tags: Antibonding molecular orbital, Atomic orbital, Block, chemical bonding, Covalent bond, energy, Hypervalent molecule, hypervalent systems, Molecular orbital, Molecular orbital diagram, Octet rule, Periodic table, Valence
Posted in Bond slam, Hypervalency | 1 Comment »