First, a very brief history of scholarly publishing, starting in 1665[cite]10.1098/rstl.1665.0001[/cite] when scientific journals started to be published by learned societies. This model continued until the 1950s, when commercial publishers such as Pergamon Press started with their USP (unique selling point) of rapid time to publication of ~3 months,[cite]10.1016/0040-4020(57)85003-0[/cite] compared to typical times for many learned society publishers of 2 years or longer. Fast forward another 50 years or so, and the commercial publishers were now dominating the scene, but the business model was still based on institutional subscriptions, whereby the institution rather than authors paid the costs of publication. As the number of journals expanded, even well-off institutions had to make difficult decisions on which subscriptions to keep and which to cancel. By the late 1990s the delivery model was changing from print to online, but the overall issue was that many scientists around the world no longer had access to many journals.
Scholarly journals vs Scholarly Blogs.
January 12th, 2024Macrocyclic peptide antibiotics – now Zosurabalpin – then antibacterial agents based on cyclic D,L-α-peptide architectures.
January 8th, 2024Zosurabalbin[cite]10.1038/s41586-023-06873-0[/cite],[cite]10.1093/ofid/ofad500.1754[/cite], is receiving a great deal of attention as a new class of antibiotic which can target infections for which current treatment options are inadequate. It is a cyclic peptide and seeing this triggered memory of an earlier such species reported way back in 1995[cite]10.1002/anie.199500931[/cite],[cite]10.1038/35086601[/cite]. This octa-peptide (YIJDIE, DOI: 10.5517/cc58gxs) was presumed to function in a novel manner, having linear water channels wide enough to form a molecular nanoscale pipe for a stream of water molecules to flow along. When inserted into the bacterial cell membrane via its lipophilic sidechains, it drained the bacterium of its cell water within seconds, thus killing it. A 3D model shows the effect very clearly.
Molecules of the year 2023 – part 2. A FAIR data comment on a Strontium Metallocene.
December 29th, 2023I will approach this example of a molecule-of-the-year candidate – in fact the eventual winner in the reader poll – from the point of view of data. Its a metallocene arranged in the form of a ring comprising 18 sub-units.[cite]10.1038/s41586-023-06192-4[/cite] Big enough to deserve a 3D model rather than the static images you almost invariably get in journals (and C&EN). So how does one go to the journal and acquire the coordinates for such a model?
Molecules of the year: 2023
December 28th, 2023The Science education unit at the ACS publication C&EN publishes its list of molecules of the year (as selected by the editors and voted upon by the readers) in December. Here are some observations about three of this year’s batch. Read the rest of this entry »
The journey from Journal “ESI” to FAIR data objects: An eighteen year old (continuing) experiment.
December 10th, 2023Around 1996, journals started publishing what became known as “ESI” or electronic supporting information, alongside the articles themselves, as a mechanism for exposing the data associated with the research being reported and exploiting some of the new opportunities offered by the World Wide Web. From the outset, such ESI was expressed as a paginated Acrobat file, with the Web being merely a convenient document delivery mechanism. Such ESI would eventually reach more than 1000 such pages in length in some chemistry articles. The richer opportunities of Web interactivity were far less exploited. I have written about various aspects of this throughout this blog[cite]10.59350/qypm4-qfv97[/cite],[cite]10.59350/cqesx-a0e83[/cite],[cite]10.59350/z9g5j-r2p69[/cite], together with one early compendium of our own data examples.[cite]10.59350/wczky-8sf79[/cite] Here I update that compendium starting from 2005 to the current 2023 and add further information, being the current state of curation of some of these early examples. Curation became necessary because many of the earlier examples were no longer functional due to changes in the way journals expose these data objects or indeed changes at the data repository end of things over this 18 year period.
A trip down memory lane: An online departmental connection map from 1989.
December 7th, 2023In 2023, we very much take for granted that everyone and pretty much everything is online. But it was not always so and when I came across an old plan indicating how the chemistry department at Imperial College was connected in 1989, I was struck by how much has happened in the 34 years since. Nowadays all the infrastructures needed are effectively “built in” to the building when it is constructed and few are even aware of them. But in 1989 that was not at all true.
Two influential textbooks – “Mee” and “Mellor”.
November 11th, 2023I am a member of the Royal Society of Chemistry’s Historical group. Amongst other activities, it publishes two editions of a newsletter each year for its members. A new theme was recently launched asking for contributions on the topic of “two influential books” and shortly to appear in the winter 2023 edition will be the following recollections by myself (reprinted here with permission).
More examples of “double-headed” curly arrows: S and C Nucleophiles attacking acetyl chloride
October 12th, 2023In an earlier post on this topic,[cite]10.59350/f00wf-5tq46[/cite]‡ I described how the curly-arrows describing the mechanism of a nucleophilic addition at a carbonyl group choreograph in two distinct ways, as seen in red or blue below. The arrows in red can be described as firstly addition to the carbonyl group to form either a transient intermediate (a two-step process) or instead a formal transition state state as a concerted single-step mechanism. The blue arrows do the reverse; firstly elimination and then followed by addition. I will use the shorthand AE for the first type and EA for the second type. Here I explore some more nucleophiles to see which of these two mechanisms they follow. Data for these results can be found at 10.14469/hpc/13171
N- carbon ylid: This is a very facile (low-barrier) reaction with a C-O bond length response that initially increases steeply, followed by a more modest decline and hence corresponds to an AE mechanism.
Improving the Science blog – The Rogue Scholar service.
September 12th, 2023Some 13 years ago, I speculated about the longevity of the type of science communication then (and still now) represented by Blogs. I noted one new project called ArchivePress that was looking into providing solutions equivalent to what scientific journals have done for some 350 years of science communication. The link to ArchivePress no longer works, but details of the project can still be found here. Since then the technology and infrastructure has moved on, with a new backbone provided by the use of persistent identifiers (PIDs) in the form of DOIs. The PID ecosystem is now extensive and so a revival of the concept has recently been launched called The Rogue Scholar. Here I take a look at some of is features and illustrate these with application to this blog.
The “double-headed” curly arrow as used in mechanistic representations.
August 29th, 2023The schematic representation of a chemical reaction mechanism is often drawn using a palette of arrows connecting or annotating the various molecular structures involved. These can be selected from a chemical arrows palette, taken for this purpose from the commonly used structure drawing program Chemdraw. Explanations of how to apply the individual arrows are not always easy to find however! Circled in red are the ones to be discussed here, although most carry fascinating and often subtle meanings!‡
