Posts Tagged ‘dielectric’
Saturday, December 24th, 2016
The previous posts produced discussion about the dipole moments of highly polar molecules. Here to produce some reference points for further discussion I look at the dipole moment of glycine, the classic zwitterion (an internal ion-pair).
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Tags:aqueous solution, Chemical polarity, Chemistry, dielectric, Dipole, Electric dipole moment, Electromagnetism, Interesting chemistry, Magnetism, Moment, Nature, Physical quantities, Physics, Potential theory, zwitterion
Posted in crystal_structure_mining | 1 Comment »
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 »
Wednesday, November 12th, 2014
In London, one has the pleasures of attending occasional one day meetings at the Burlington House, home of the Royal Society of Chemistry. On November 5th this year, there was an excellent meeting on the topic of Challenges in Catalysis, and you can see the speakers and (some of) their slides here. One talk on the topic of Direct amide formation – the issues, the art, the industrial application by Dave Jackson caught my interest. He asked whether an amide could be formed directly from a carboxylic acid and an amine without the intervention of an explicit catalyst. The answer involved noting that the carboxylic acid was itself a catalyst in the process, and a full mechanistic exploration of this aspect can be found in an article published in collaboration with Andy Whiting's group at Durham.[1] My after-thoughts in the pub centered around the recollection that I had written some blog posts about the reaction between hydroxylamine and propanone. Might there be any similarity between the two mechanisms?
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References
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H. Charville, D.A. Jackson, G. Hodges, A. Whiting, and M.R. Wilson, "The Uncatalyzed Direct Amide Formation Reaction – Mechanism Studies and the Key Role of Carboxylic Acid H‐Bonding", European Journal of Organic Chemistry, vol. 2011, pp. 5981-5990, 2011. http://dx.doi.org/10.1002/ejoc.201100714
Tags:Andy Whiting, Dave Jackson, dielectric, Durham, energy profile, free energy barrier, London, non-polar solution, PDF, Royal Society of Chemistry
Posted in reaction mechanism | 6 Comments »
Monday, December 3rd, 2012
I promised that the follow-up to on the topic of Birch reduction would focus on the proton transfer reaction between the radical anion of anisole and a proton source, as part of analysing whether the mechanistic pathway proceeds O or M.
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Tags:Birch reduction, dielectric, energy, free energy, free energy barrier, Hammonds postulate, proton transfer, Reaction Mechanism, Tutorial material
Posted in Uncategorised | 2 Comments »
Saturday, December 1st, 2012
The Birch reduction is a classic method for partially reducing e.g. aryl ethers using electrons (from sodium dissolved in ammonia) as the reductant rather than e.g. dihydrogen. As happens occasionally in chemistry, a long debate broke out over the two alternative mechanisms labelled O (for ortho protonation of the initial radical anion intermediate) or M (for meta protonation). Text books seem to have settled down of late in favour of O. Here I take a look at the issue myself.
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Tags:dielectric, energy, free energy, Reaction Mechanism, Tutorial material
Posted in Uncategorised | 2 Comments »
Monday, July 16th, 2012
Singleton and co-workers have produced some wonderful work showing how dynamic effects and not just transition states can control the outcome of reactions. Steve Bachrach’s blog contains many examples, including this recent one.
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Tags:dielectric, energy surface, final product, Interesting chemistry, Molecular dynamics, potential energy surface, Reaction Mechanism, Singleton & co., Steve Bachrach, substitution products
Posted in Uncategorised | 3 Comments »
Saturday, April 9th, 2011
Understanding why and how proteins fold continues to be a grand challenge in science. I have described how Wrinch in 1936 made a bold proposal for the mechanism, which however flew in the face of much of then known chemistry. Linus Pauling took most of the credit (and a Nobel prize) when in a famous paper[1] in 1951 he suggested a mechanism that involved (inter alia) the formation of what he termed α-helices. Jack Dunitz in 2001[2] wrote a must-read article[3] on the topic of “Pauling’s Left-handed α-helix” (it is now known to be right handed). I thought I would revisit this famous example with a calculation of my own and here I have used the ωB97XD/6-311G(d,p) DFT procedure[4] to calculate some of the energy components of a small helix comprising (ala)6 in both left and right handed form.
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References
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L. Pauling, R.B. Corey, and H.R. Branson, "The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain", Proceedings of the National Academy of Sciences, vol. 37, pp. 205-211, 1951. http://dx.doi.org/10.1073/pnas.37.4.205
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J.D. Dunitz, "Pauling's Left-Handed α-Helix", Angewandte Chemie International Edition, vol. 40, pp. 4167-4173, 2001. http://dx.doi.org/10.1002/1521-3773(20011119)40:22<4167::AID-ANIE4167>3.0.CO;2-Q
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K.S. Thanthiriwatte, E.G. Hohenstein, L.A. Burns, and C.D. Sherrill, "Assessment of the Performance of DFT and DFT-D Methods for Describing Distance Dependence of Hydrogen-Bonded Interactions", Journal of Chemical Theory and Computation, vol. 7, pp. 88-96, 2010. http://dx.doi.org/10.1021/ct100469b
Tags:alpha-helix, aqueous solutions, chiroptical, conformational analysis, dielectric, energy, energy components, high energy species, Historical, Interesting chemistry, Jack Dunitz, Julia Contreras-Garcia, protein, solvation algorithms, Tutorial material, watoc11
Posted in Uncategorised | 4 Comments »
Friday, January 7th, 2011
This story starts with a calixarene, a molecule (suitably adorned with substituents) frequently used as a host to entrap a guest and perchance make the guest do something interesting. Such a calixarene was at the heart of a recent story where an attempt was made to induce it to capture cyclobutadiene in its cavity.
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Tags:animation, calixarene, chiral, dielectric, free energy barrier, gas phase, gas phase model, Interesting chemistry, pericyclic, proton transfer, watoc11, zwitterionic
Posted in Uncategorised | 2 Comments »