Stereoelectronic effects galore: bis(trifluoromethyl)trioxide.

August 4th, 2016
No Gravatar

Here is a little molecule that can be said to be pretty electron rich. There are lots of lone pairs present, and not a few electron-deficient σ-bonds. I thought it might be fun to look at the stereoelectronic interactions set up in this little system.

Read the rest of this entry »

Managing (open) NMR data: a working example using Mpublish.

August 1st, 2016
No Gravatar

In March, I posted from the ACS meeting in San Diego on the topic of Research data: Managing spectroscopy-NMR, and noted a talk by MestreLab Research on how a tool called Mpublish in the forthcoming release of their NMR analysis software Mestrenova could help. With that release now out, the opportunity arose to test the system.

Read the rest of this entry »

Anomeric effects at carbon involving lone pairs originating from one or two nitrogens.

July 8th, 2016
No Gravatar

The previous post looked at anomeric effects set up on centres such as B, Si or P, and involving two oxygen groups attached to these atoms. Here I vary the attached groups to include either one or two nitrogen atoms.[1]

Read the rest of this entry »

References

  1. Henry Rzepa., "Anomeric effects at carbon, involving lone pairs originating from one or two nitrogens", 2016. http://dx.doi.org/10.14469/hpc/936

Anomeric effects at boron, silicon and phosphorus.

July 1st, 2016
No Gravatar

The anomeric effect occurs at 4-coordinate (sp3) carbon centres carrying two oxygen substituents and involves an alignment of a lone electron pair on one oxygen with the adjacent C-O σ*-bond of the other oxygen. Here I explore whether other centres can exhibit the phenomenon. I start with 4-coordinate boron, using the crystal structure search definition below (along with R < 0.1, no disorder, no errors).[1]anomeric-bo-sq

Read the rest of this entry »

References

  1. Henry Rzepa., "Anomeric effects at boron, silicon and phosphorus.", 2016. http://dx.doi.org/10.14469/hpc/696

How does an OH or NH group approach an aromatic ring to hydrogen bond with its π-face?

June 22nd, 2016
No Gravatar

I previously used data mining of crystal structures to explore the directing influence of substituents on aromatic and heteroaromatic rings. Here I explore, quite literally, a different angle to the hydrogen bonding interactions between a benzene ring and OH or NH groups.

Read the rest of this entry »

Exploring the electrophilic directing influence of heteroaromatic rings using crystal structure data mining.

June 21st, 2016
No Gravatar

This is a follow-up to the post on exploring the directing influence of (electron donating) substituents on benzene[1] with the focus on heteroaromatic rings such indoles, pyrroles and group 16 analogues (furans, thiophenes etc).

Read the rest of this entry »

References

  1. H.S. Rzepa, "Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases", J. Chem. Educ., vol. 93, pp. 550-554, 2016. http://dx.doi.org/10.1021/acs.jchemed.5b00346

Why is the carbonyl IR stretch in an ester higher than in a ketone: crystal structure data mining.

June 18th, 2016
No Gravatar

In this post, I pondered upon the C=O infra-red spectroscopic properties of esters, and showed three possible electronic influences:

Read the rest of this entry »

A wider look at π-complex metal-alkene (and alkyne) compounds.

June 13th, 2016
No Gravatar

Previously, I looked at the historic origins of the so-called π-complex theory of metal-alkene complexes. Here I follow this up with some data mining of the crystal structure database for such structures.

Read the rest of this entry »

A wider look at chlorine trifluoride: crystal structures and data mining.

June 10th, 2016
No Gravatar

A while ago, I explored how the 3-coordinate halogen compound ClF3 is conventionally analyzed using VSEPR (valence shell electron pair repulsion theory). Here I (belatedly) look at other such tri-coordinate halogen compounds using known structures gleaned from the crystal structure database (CSD).

Read the rest of this entry »

500 chemical twists: a (chalk and cheese) comparison of the impacts of blog posts and journal articles.

June 3rd, 2016
No Gravatar

The title might give it away; this is my 500th blog post, the first having come some eight years ago. Very little online activity nowadays is excluded from measurement and so it is no surprise that this blog and another of my "other" scholarly endeavours, viz publishing in traditional journals, attract such "metrics" or statistics. The h-index is a well-known but somewhat controversial measure of the impact of journal articles; here I thought I might instead take a look at three less familiar ones – one relating to blogging, one specific to journal publishing and one to research data.

Read the rest of this entry »