Archive for the ‘Interesting chemistry’ Category
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, Kilocalorie per mole, model is to calculate the free energy difference, Properties of water, the free energy, thermodynamics, Tritiated water
Posted in Interesting chemistry | 4 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, Hydrogen bond, Hydrogen peroxide, Inorganic solvents, Oxide, Oxidizing agents, Peroxide, Properties of water
Posted in General, Interesting chemistry | No Comments »
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[cite]10.1002/chem.201406383[/cite] 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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Tags:Ammonia, aqueous solutions, Bases, energy relative, free energy, Functional groups, Hydrogen bond, Hydronium, Hydroxides, Hydroxyl, Hydroxylamine, lowest energy form, Properties of water, Reducing agents, Self-ionization of water
Posted in General, Interesting chemistry | No Comments »
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, Hydride, Hydrogen bond, Hydronium, Hydroxide, Physical chemistry, Properties of water, self-ionization energy, Self-ionization of water
Posted in General, Interesting chemistry | 3 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, Hydrogen bond, Hydroxide, Lone pair, metal, Nitrile, relative free energy, search query
Posted in General, Interesting chemistry | 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, 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 »
Wednesday, 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 »
Wednesday, 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 »
Sunday, January 31st, 2016
Six years ago, I posted on the nature of a then recently reported[cite]10.1002/anie.200803859[/cite] Cr-Cr quintuple bond. The topic resurfaced as part of the discussion on a more recent post on NSF3, and a sub-topic on the nature of the higher order bonding in C2. The comment made a connection between that discussion and the Cr-Cr bond alluded to above. I responded briefly to that comment, but because I want to include 3D rotatable surfaces, I expand the discussion here and not in the comment.‡
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Tags:Chemical bond, chemical bonding, Electron, Electron configuration, energy, Molecular orbital, Multi-configurational self-consistent field, Quantum chemistry, quintuple bond, search term, Transition metal, Valence bond theory
Posted in General, Interesting chemistry | 6 Comments »
Sunday, January 10th, 2016
Earlier I explored models for the heteroaromatic electrophilic protiodecarboxylation of an 3-substituted indole, focusing on the role of water as the proton transfer and delivery agent. Next, came models for both water and the general base catalysed ionization of indolinones. Here I explore general acid catalysis by evaluating the properties of two possible models for decarboxylation of 3-indole carboxylic acid, one involving proton transfer (PT) from neutral water in the presence of covalent un-ionized HCl (1) and one with PT from a protonated water resulting from ionised HCl (2).
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Tags:Acid, Acids, bicyclic network, carboxylic acid, free energy, Functional groups, Hydrogen bond, Indole, transition state free energy
Posted in Interesting chemistry | 1 Comment »