Archive for April, 2016
Sunday, April 24th, 2016
The autoionization of water involves two molecules transfering a proton to give hydronium hydroxide, a process for which the free energy of reaction is well known. Here I ask what might happen with the next element along in the periodic table, F.
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Tags:dielectric, energy, Equilibrium chemistry, Fluorides, free energy, free energy barrier, Hydrogen bond, Hydronium, Inorganic solvents, Interesting chemistry, Lithium fluoride, low energy final geometry corresponds, Oxides, PH, Properties of water, Self-ionization of water, Water, Water model
Posted in Uncategorised | 10 Comments »
Friday, April 22nd, 2016
Earlier, I constructed a possible model of hydronium hydroxide, or H3O+.OH– One way of assessing the quality of the model is to calculate the free energy difference between it and two normal water molecules and compare the result to the measured difference. Here I apply a further test of the model using isotopes.
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Tags:dielectric, energy, free energy, Heat transfer, Heavy water, Interesting chemistry, Kilocalorie per mole, model is to calculate the free energy difference, Properties of water, the free energy, thermodynamics, Tritiated water
Posted in Uncategorised | 4 Comments »
Sunday, April 17th, 2016
I want to describe a recent attempt by a group of collaborators to share the research data associated with their just published article.[1]
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References
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C. Romain, Y. Zhu, P. Dingwall, S. Paul, H.S. Rzepa, A. Buchard, and C.K. Williams, "Chemoselective Polymerizations from Mixtures of Epoxide, Lactone, Anhydride, and Carbon Dioxide", Journal of the American Chemical Society, vol. 138, pp. 4120-4131, 2016. http://dx.doi.org/10.1021/jacs.5b13070
Tags:10.17616, Academic publishing, Chemical IT, DataCite, energy profile diagrams, Figshare, Identifiers, Open science, ORCiD, PDF, Scholarly communication, Technical communication, Technology/Internet, Web-enhanced object
Posted in Uncategorised | No Comments »
Saturday, April 16th, 2016
Scientists are familiar with the term data, at least in a scientific or chemical context, but appreciating metadata (meaning "after", or "beyond") is slightly more subtle, in the sense of using it to mean data about data. The challenge lies in clarifying where the boundary between data and its metadata lies and in specifying and controlling the vocabulary used for these metadata descriptions. Items in a chemical metadata dictionary might include e.g. subject classifications such as Organic Molecular Chemistry or identifiers such as InChIkey. But what could metametadata be? Here I briefly show some examples by way of illustration.
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Tags:Academic publishing, automated software analysis, BASE, chemical context, Chemical Database Service, Chemical IT, chemical metadata, chemical metadata dictionary, chemical space, City: Cambridge, Data dictionary, Data management, Identifiers, Knowledge representation, programmer, Registry of Research Data Repositories, search.datacite.org/api, SPECTRa, Technology/Internet
Posted in Uncategorised | No Comments »
Friday, April 15th, 2016
If H3N+-O– is viable compared with its tautomer H2N-OH when carrying water bridges, then why not try H2O+-O– vs HO-OH?
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Tags:Ammonia, Anions, free energy, General, Hydrogen bond, Hydrogen peroxide, Inorganic solvents, Interesting chemistry, Oxide, Oxidizing agents, Peroxide, Properties of water
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Friday, April 15th, 2016
In the previous post I described how hydronium hydroxide or H3O+…HO–, an intermolecular tautomer of water, has recently been observed captured inside an organic cage[1] and how the free-standing species in water can be captured computationally with the help of solvating water bridges. Here I explore azane oxide or H3N+-O–,‡ a tautomer of the better known hydroxylamine (H2N-OH).
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References
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M. Stapf, W. Seichter, and M. Mazik, "Unique Hydrogen‐Bonded Complex of Hydronium and Hydroxide Ions", Chemistry – A European Journal, vol. 21, pp. 6350-6354, 2015. http://dx.doi.org/10.1002/chem.201406383
Tags:Ammonia, aqueous solutions, Bases, energy relative, free energy, Functional groups, General, Hydrogen bond, Hydronium, Hydroxides, Hydroxyl, Hydroxylamine, Interesting chemistry, lowest energy form, Properties of water, Reducing agents, Self-ionization of water
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Thursday, April 14th, 2016
Ammonium hydroxide (NH4+…OH–) can be characterised quantum mechanically when stabilised by water bridges connecting the ion-pairs. It is a small step from there to hydronium hydroxide, or H3O+…OH–. The measured concentrations [H3O+] ≡ [OH–] give rise of course to the well-known pH 7 of pure water, and converting this ionization constant to a free energy indicates that the solvated ion-pair must be some ~19.1 kcal/mol higher in free energy than water itself.♣ So can a quantum calculation reproduce pH7 for water?
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Tags:Acid dissociation constant, Acids, Cations, chemical bonding, energy, Equilibrium chemistry, free energy, General, Hydride, Hydrogen bond, Hydronium, Hydroxide, Interesting chemistry, Physical chemistry, Properties of water, self-ionization energy, Self-ionization of water
Posted in Uncategorised | 3 Comments »
Wednesday, 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, Chemical IT, Embargo, Open access, Publishing, Royal Society of Chemistry, Technology/Internet, Uncharted, Uncharted Territory
Posted in Uncategorised | No Comments »
Friday, 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, General, Hydrogen bond, Hydroxide, Interesting chemistry, Lone pair, metal, Nitrile, relative free energy, search query
Posted in Uncategorised | 2 Comments »
Saturday, 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, Chemical IT, City: Erlangen, Country: Germany, Degree of a continuous mapping, Ferrocene, Hydrogen bond, individual search definition, Interesting chemistry, metal, overall search collection, Streitwieser, terminal H-positions, Torsion, X-ray
Posted in crystal_structure_mining | 6 Comments »