The effects of loading up lots of dispersion attractions (between t-butyl groups) into a compact molecule has the interesting consequence of allowing two “non-bonded” hydrogen atoms to approach to ~1.5Å of each other, thus creating the appearance of a “bond” where one normally would not be found. Can such an effect be injected into other combinations of two atoms, say H and F? Here I briefly explore this notion.
Dispersion “bonds” not involving hydrogen. A Cl…Cl candidate?
June 29th, 2017In the previous post, I noted the crystallographic detection of an unusually short non-bonded H…H contact of ~1.5Å, some 0.9Å shorter than twice the van der Waals radius of hydrogen (1.2Å, although some sources quote 1.1Å which would make the contraction ~0.7Å). This was attributed to dispersion attractions accumulating in the rest of the molecule. I asked myself what the potential might be for other elements to reveal significantly contracted non-bonded distances as a result of dispersive attractions.
Dispersion “bonds”: a new example with an ultra-short H…H distance.
June 26th, 2017About 18 months ago, there was much discussion on this blog about a system reported by Bob Pascal and co-workers containing a short H…H contact of ~1.5Å[cite]10.1021/ja407398w[/cite]. In this system, the hydrogens were both attached to Si as Si-H…H-Si and compressed together by rings. Now a new report[cite]10.1021/jacs.7b01879[/cite] and commented upon by Steve Bachrach, claims a similar distance for hydrogens attached to carbon, i.e. C-H…H-C, but without the ring compression.
Twenty one years of chemistry-related Java apps: RIP Java?
June 10th, 2017In an earlier post, I lamented the modern difficulties in running old instances of Jmol, an example of an application program written in the Java programming language. When I wrote that, I had quite forgotten a treasure trove of links to old Java that I had collected in 1996-7 and then abandoned. Here I browse through a few of the things I found.
How to search data repositories for FAIR chemical content and data: SubjectScheme
June 8th, 2017As data repositories start to flourish, it is reasonable to ask questions such as what sort of chemistry can be found there and how can I find it? Here I give an updated[cite]10.1515/ci-2016-3-408[/cite] worked example of a digital repository search for chemical content and also pose an important issue for the chemistry domain.
Tautomeric polymorphism.
June 1st, 2017Conformational polymorphism occurs when a compound crystallises in two polymorphs differing only in the relative orientations of flexible groups (e.g. Ritonavir).[cite]10.1039/D1SC06074K[/cite] At the Beilstein conference, Ian Bruno mentioned another type; tautomeric polymorphism, where a compound can crystallise in two forms differing in the position of acidic protons. Here I explore three such examples.
CH⋅⋅⋅π Interactions between methyl and carbonyl groups in proteins: a small molecule check.
May 29th, 2017Derek Lowe highlights a recent article[cite]10.1002/anie.201702626[/cite] postulating CH⋅⋅⋅π interactions in proteins. Here I report a quick check using the small molecule crystal structure database (CSD).