Posts Tagged ‘Jack Dunitz’
Saturday, July 25th, 2015
I recently followed this bloggers trail; link1 → link2 to arrive at this delightful short commentary on atom-atom bonds in crystals[1] by Jack Dunitz. Here he discusses that age-old question (to chemists), what is a bond? Even almost 100 years after Gilbert Lewis’ famous analysis,[2] we continue to ponder this question. Indeed, quite a debate on this topic broke out in a recent post here. My eye was caught by one example in Jack's article: "The close stacking of planar anions, as occurs in salts of croconic acid …far from producing a lowering of the crystal energy, this stacking interaction in itself leads to an increase by several thousand kJ mol−1 arising from Coulombic repulsion between the doubly negatively charged anions" I thought I might explore this point a bit further in this post.
(more…)
References
-
J.D. Dunitz, "Intermolecular atom–atom bonds in crystals?", IUCrJ, vol. 2, pp. 157-158, 2015. http://dx.doi.org/10.1107/S2052252515002006
-
G.N. Lewis, "THE ATOM AND THE MOLECULE.", Journal of the American Chemical Society, vol. 38, pp. 762-785, 1916. http://dx.doi.org/10.1021/ja02261a002
Tags:Carbon, Cations, Chemical bond, Chemical IT, control search, Croconic acid, crystal energy, crystal structure search, Gilbert Lewis, Interesting chemistry, intermolecular search, Jack Dunitz, overall energy balance, Proton
Posted in crystal_structure_mining | 1 Comment »
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.
(more…)
References
-
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
-
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
-
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 »