Journal innovations – the next step is augmented reality?

August 17th, 2016
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In the previous post, I noted that a chemistry publisher is about to repeat an earlier experiment in serving pre-prints of journal articles. It would be fair to suggest that following the first great period of journal innovation, the boom in rapid publication “camera-ready” articles in the 1960s, the next period of rapid innovation started around 1994 driven by the uptake of the World-Wide-Web. The CLIC project[1] aimed to embed additional data-based components into the online presentation of the journal Chem Communications, taking the form of pop-up interactive 3D molecular models and spectra. The Internet Journal of Chemistry was designed from scratch to take advantage of this new medium.[2] Here I take a look at one recent experiment in innovation which incorporates “augmented reality”.[3]

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References

  1. D. James, B.J. Whitaker, C. Hildyard, H.S. Rzepa, O. Casher, J.M. Goodman, D. Riddick, and P. Murray‐Rust, "The case for content integrity in electronic chemistry journals: The CLIC project", New Review of Information Networking, vol. 1, pp. 61-69, 1995. http://dx.doi.org/10.1080/13614579509516846
  2. S.M. Bachrach, and S.R. Heller, " The Internet Journal of Chemistry: A Case Study of an Electronic Chemistry Journal ", Serials Review, vol. 26, pp. 3-14, 2000. http://dx.doi.org/10.1080/00987913.2000.10764578
  3. S. Ley, B. Musio, F. Mariani, E. Śliwiński, M. Kabeshov, and H. Odajima, "Combination of Enabling Technologies to Improve and Describe the Stereoselectivity of Wolff–Staudinger Cascade Reaction", Synthesis, 2016. http://dx.doi.org/10.1055/s-0035-1562579

Chemistry preprint servers (revisited).

August 16th, 2016
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This week the ACS announced its intention to establish a “ChemRxiv preprint server to promote early research sharing“. This was first tried quite a few years ago, following the example of especially the physicists. As I recollect the experiment lasted about a year, attracted few submissions and even fewer of high quality. Will the concept succeed this time, in particular as promoted by a commercial publisher rather than a community of scientists (as was the original physicists model)?

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

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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A periodic table for anomeric centres.

August 6th, 2016
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In the last few posts, I have explored the anomeric effect as it occurs at an atom centre X. Here I try to summarise the atoms for which the effect is manifest in crystal structures.

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Stereoelectronic effects galore: bis(trifluoromethyl)trioxide.

August 4th, 2016
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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.

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

August 1st, 2016
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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.

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

July 8th, 2016
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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]

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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
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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

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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
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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.

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

June 21st, 2016
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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).

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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