Posts Tagged ‘Quantum chemistry’

Why do flowers such as roses, peonies, dahlias, delphiniums (etc), exhibit so many shades of colours?

Monday, June 18th, 2018
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It was about a year ago that I came across a profusion of colour in my local Park. Although colour in fact was the topic that sparked my interest in chemistry many years ago (the fantastic reds produced by diazocoupling reactions), I had never really tracked down the origin of colours in many flowers. It is of course a vast field. Here I take a look at just one class of molecule responsible for many flower colours, anthocyanidin, this being the sugar-free counterpart of the anthocyanins found in nature.

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What are the highest bond indices for main group and transition group elements?

Sunday, March 4th, 2018
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A bond index (BI) approximately measures the totals of the bond orders at any given atom in a molecule. Here I ponder what the maximum values might be for elements with filled valence shells.

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VSEPR Theory: Octet-busting or not with trimethyl chlorine, ClMe3.

Sunday, November 12th, 2017
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A few years back, I took a look at the valence-shell electron pair repulsion approach to the geometry of chlorine trifluoride, ClF3 using so-called ELF basins to locate centroids for both the covalent F-Cl bond electrons and the chlorine lone-pair electrons. Whereas the original VSEPR theory talks about five “electron pairs” totalling an octet-busting ten electrons surrounding chlorine, the electron density-based ELF approach located only ~6.8e surrounding the central chlorine and no “octet-busting”. The remaining electrons occupied fluorine lone pairs rather than the shared Cl-F regions. Here I take a look at ClMe3, as induced by the analysis of SeMe6.

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Elongating an N-B single bond is much easier than stretching a C-C single bond.

Tuesday, October 24th, 2017
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An N-B single bond is iso-electronic to a C-C single bond, as per below. So here is a simple question: what form does the distribution of the lengths of these two bonds take, as obtained from crystal structures? 

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The di-anion of dilithium (not the Star Trek variety): Another “Hyper-bond”?

Saturday, September 16th, 2017
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Early in 2011, I wrote about how the diatomic molecule Be2 might be persuaded to improve upon its normal unbound state (bond order ~zero) by a double electronic excitation to a strongly bound species. I yesterday updated this post with further suggestions and one of these inspired this follow-up.

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First, hexacoordinate carbon – now pentacoordinate oxygen?

Saturday, March 25th, 2017
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The previous post demonstrated the simple iso-electronic progression from six-coordinate carbon to five coordinate nitrogen. Here, a further progression to oxygen is investigated computationally.

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Reaction coordinates vs Dynamic trajectories as illustrated by an example reaction mechanism.

Monday, March 20th, 2017
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The example a few posts back of how methane might invert its configuration by transposing two hydrogen atoms illustrated the reaction mechanism by locating a transition state and following it down in energy using an intrinsic reaction coordinate (IRC). Here I explore an alternative method based instead on computing a molecular dynamics trajectory (MD).

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The H4 (2+) dication and its bonding.

Wednesday, February 15th, 2017
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This post arose from a comment attached to the post on Na2He and relating to peculiar and rare topological features of the electron density in molecules called non-nuclear attractors. This set me thinking about other molecules that might exhibit this and one of these is shown below.

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Molecule orbitals as indicators of reactivity: bromoallene.

Thursday, September 1st, 2016
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Bromoallene is a pretty simple molecule, with two non-equivalent double bonds. How might it react with an electrophile, say dimethyldioxirane (DMDO) to form an epoxide?[1] Here I explore the difference between two different and very simple approaches to predicting its reactivity. bromoallene

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References

  1. D. Christopher Braddock, A. Mahtey, H.S. Rzepa, and A.J.P. White, "Stable bromoallene oxides", Chemical Communications, vol. 52, pp. 11219-11222, 2016. http://dx.doi.org/10.1039/C6CC06395K

A periodic table for anomeric centres, this time with quantified interactions.

Monday, August 8th, 2016
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The previous post contained an exploration of the anomeric effect as it occurs at an atom centre X for which the effect is manifest in crystal structures. Here I quantify the effect, by selecting the test molecule MeO-X-OMe, where X is of two types:

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