Full-colour 3D printing of molecular models and orbitals (wavefunctions).

August 18th, 2013

We have been experimenting with full-colour 3D printing of molecular objects. I thought I might here share some of our observations. Firstly, I list the software used:

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Molecule-sized pixels.

August 11th, 2013

The ultimate reduction in size for an engineer is to a single molecule. It’s been done for a car; now it has been reported for the pixel (picture-element).[cite]10.1021/ja404256s[/cite]

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The Amsterdam Manifesto on Data Citation Principles

July 31st, 2013

The Amsterdam manifesto espouses the principles of citable open data. It is a short document, and it is worth re-stating its eight points here:

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VSEPR Theory: A closer look at chlorine trifluoride, ClF3.

July 27th, 2013

Valence shell electron pair repulsion theory is a simple way of rationalising the shapes of many compounds in which a main group element is surrounded by ligands. ClF3 is a good illustration of this theory.

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The butterfly effect in chemistry: bimodal bond angles.

July 18th, 2013

This potential example of a molecule on the edge of chaos was suggested to me by a student (thanks Stephen!), originating from an inorganic tutorial. It represents a class of Mo-complex ligated by two dithiocarbamate ligands and two aryl nitrene ligands (Ar-N:).Mo

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The butterfly effect in chemistry: Bimodal M~S bonds?

July 14th, 2013

I noted previously that some 8-ring cyclic compounds could exist in either a planar-aromatic or a non-planar-non-aromatic mode, the mode being determined by apparently quite small changes in a ring substituent. Hunting for other examples of such chemistry on the edge, I did a search of the Cambridge crystal database for metal sulfides. 

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The butterfly effect in chemistry: aromaticity on the edge of chaos.

July 11th, 2013

The butterfly effect summarises how a small change to a system may result in very large and often unpredictable (chaotic) consequences. If the system is merely on the edge of chaos, the consequences are predictable, but nevertheless finely poised between e.g. two possible outcomes. Here I ask how a molecule might manifest such behaviour.

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Hexacoordinate hydrogen.

July 8th, 2013

A feature of a blog which is quite different from a journal article is how rapidly a topic might evolve. Thus I started a few days ago with the theme of dicarbon (C2), identifying a metal carbide that showed C2 as a ligand, but which also entrapped a single carbon in hexa-coordinated mode. A comment was posted bringing attention to the origins of the discovery of hexacoordinated carbon, and we moved on to exploring the valency in one such species (CLi6). Here I ask if hydrogen itself might exhibit such coordination.

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150,000,000 DFT calculations on 2,300,000 compounds!

July 5th, 2013

The title of this post summarises the contents of a new molecular database: www.molecularspace.org[cite]10.1021/jz200866s[/cite] and I picked up on it by following the post by Jan Jensen at www.compchemhighlights.org (a wonderful overlay journal that tracks recent interesting articles). The molecularspace project more formally is called “The Harvard Clean Energy Project: Large-scale computational screening and design of organic photovoltaics on the world community grid“. It reminds of a 2005 project by Peter Murray-Rust et al at the same sort of concept[cite]10.1007/s00894-005-0278-1[/cite] (the World-Wide-Molecular-Matrix, or WWMM[cite]10.1186/1758-2946-3-42[/cite]), although the new scale is certainly impressive. Here I report my initial experiences looking through molecularspace.org

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Is CLi6 hypervalent?

July 5th, 2013

A comment made on the previous post on the topic of hexa-coordinate carbon cited an article entitled “Observation of hypervalent CLi6 by Knudsen-effusion mass spectrometry“[cite]10.1038/355432a0[/cite] by Kudo as a amongst the earliest of evidence that such species can exist (in the gas phase). It was a spectacular vindication of the earlier theoretical prediction[cite]10.1021/ja00379a051[/cite],[cite]10.1021/ja00356a045[/cite] that such 6-coordinate species are stable with respect to dissociation to CLi4 and Li2.

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