Henry Rzepa's Blog

Back in early 2012, I pondered about the relationships between a science-based blog post and a science-based journal article[1]. This was in part induced by my discovering a blog plugin called Kcite, which allow a journal articles to be appended to the blog in the form of a numbered reference list. The only required input for Kcite was the DOI of the article (as you can see earlier in this paragraph). For around 500 posts after that moment, I always strove to add such references to my posts. Around 2016, I started including references to data in the form of repository DOIs to sit alongside the journal references, but this feature stopped working a year or two later because of changes in the metadata resolved by the DOI. Kcite itself lasted until January 2024 for this blog, when a required update to the software running the blog (WordPress) meant that it no longer worked and had to be removed as a plugin. Two years ago, Rogue Scholar (Science blogging on steroids) started coming along to the rescue.[2] ,[3] It provides some amazing automated features and infrastructure to blogs; I will illustrate from those listed on the top page of Rogue Scholar itself: (more…)

References

1. H. Rzepa, "The blog post as a scientific article: citation management", 2012. https://doi.org/10.59350/3pbz1-vcd67
2. M. Fenner, "Automatically list all your publications in your blog", 2013. https://doi.org/10.53731/axtz227-73n18e7
3. M. Fenner, "Rogue Scholar now shows citations of science blog posts", 2025. https://doi.org/10.53731/4bvt3-hmd07

X-ray crystallography is the technique of using the diffraction of x-rays by the electrons in a molecule to determine the positions of all the atoms in that molecule. Quantum theory teaches us that the electrons are to be found in shells around the atomic nuclei. There are two broad types, the outermost shell (also called the valence shell) and all the inner or core shells. The density of the core electrons is much higher (more compact) than the more diffuse valence shell for all but the hydrogen atom, which only has valence electrons. How does this relate to x-ray diffraction by electrons? Well, core electrons, because of their relative compactness, diffract X-rays more strongly than the valence electrons. This compactness of the core also means that its electron density distribution can be well (but not exactly) approximated by a sphere, with the nucleus at the centre of that sphere. And from this it follows that the density for each atom can be treated independently, the so-called IAM or independent atom model. For example all the carbon atoms in a molecule are approximated as having the same value for the electron density of their core shell. But the IAM approximation is much less good for hydrogen atoms, especially when they are attached to very polar atoms (Li, O, F, etc) and even atoms such as carbon or oxygen have noticeable deviations as illustrated in  figure 1 below. [1]

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References

1. F. Kleemiss, O.V. Dolomanov, M. Bodensteiner, N. Peyerimhoff, L. Midgley, L.J. Bourhis, A. Genoni, L.A. Malaspina, D. Jayatilaka, J.L. Spencer, F. White, B. Grundkötter-Stock, S. Steinhauer, D. Lentz, H. Puschmann, and S. Grabowsky, "Accurate crystal structures and chemical properties from NoSpherA2", Chemical Science, vol. 12, pp. 1675-1692, 2021. https://doi.org/10.1039/d0sc05526c

Starting around 2016, journal publishers started including mandatory “Data Availability” statements as part of research articles; a typical (dated) example is linked here, including guidelines for how to cite the data itself. I wrote about these aspects last year in a blog post for the RSC journal Digital Discovery[1] and here I follow up with more news.

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References

1. H. Rzepa, "The evolving roles of data and citations in journal articles", 2024. https://doi.org/10.26434/chemrxiv-2024-dz2dv