June 29th, 2017
In 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.
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Posted in crystal_structure_mining | 8 Comments »
June 26th, 2017
About 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.
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Tags: 10.1021, Blog, chemical shift, chemical shift difference, chemical shifts, gas phase, Oxygen, Steve Bachrach
Posted in Interesting chemistry | 3 Comments »
June 18th, 2017
The iron complex shown below forms the basis for many catalysts.[cite]10.1002/anie.200502985[/cite] With iron, the catalytic behaviour very much depends on the spin-state of the molecule, which for the below can be either high (hextet) or medium (quartet) spin, with a possibility also of a low spin (doublet) state. Here I explore whether structural information in crystal structures can reflect such spin states.
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Tags: catalysis, Catalysts, Chemistry, energy, energy separations, energy span, Fe complex, Homogeneous catalysis, Kumada coupling, Organometallic chemistry, spin-state energy separations, Synergistic catalysis
Posted in crystal_structure_mining | 1 Comment »
June 10th, 2017
In 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.
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Tags: Alan Tongue, City: London, City: Paris, Company: Sun Microsystems, computing, Computing platforms, Country: Poland, Darek Bogdal, Guillaume Cottenceau, Java, Java platform, jmol, Person Travel, Roman law, Wyn Locke
Posted in Historical | 5 Comments »
June 8th, 2017
As 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.
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Tags: chemical content, chemical/x- media type, chemical/x-gaussian, Company: DataCite, Company: Google, digital repository search, domain-specific chemical content, media type, media:chemical/x-mnpub, media:chemical\/x\-gaussian*, Question, search definition, search engines, search string, search syntax, subject search
Posted in Chemical IT | 1 Comment »
June 2nd, 2017
In 2016, the world heard that gravitational waves had been detected and now a third instance is reported.‡ Given that the data associated with these detections are perhaps amongst the most important instances in recent times, I thought I might take a peek at how it was managed.
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Tags: Astronomy, Binary stars, Black holes, famous chemical controversy, General relativity, Gravitational wave, Gravity, Physics, search procedures, Technology/Internet, Wave
Posted in Chemical IT | 1 Comment »
June 1st, 2017
Conformational 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.
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Tags: Chemistry, chloroform solutions, Conformational isomerism, Crystal, crystallography, gas phase, Ian Bruno, Isomerism, Polymorphism, Ritonavir, S-centre, Tautomer
Posted in Chemical IT, crystal_structure_mining | No Comments »
May 29th, 2017
Derek 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).
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Tags: Company: CL ENGENHARIA, Derek, Derek Lowe, Lowe, search query
Posted in crystal_structure_mining | 2 Comments »
May 29th, 2017
The title here is taken from a presentation made by Ian Bruno from CCDC at the recent conference on Open Science. It also addresses the theme here of the issues that might arise in assigning identifiers for any given molecule.
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Tags: author, Bruno, chemical identifier, Digital Object Identifier, Ian Bruno, Identifier, InChI algorithm
Posted in Chemical IT | 2 Comments »
May 29th, 2017
As the Internet and its Web-components age, so early pages start to decay as technology moves on. A few posts ago, I talked about the maintenance of a relatively simple page first hosted some 21 years ago. In my notes on the curation, I wrote the phrase “Less successful was the attempt to include buttons which could be used to annotate the structures with highlights. These buttons no longer work and will have to be entirely replaced in the future at some stage.” Well, that time has now come, for a rather more crucial page associated with a journal article published more recently in 2009.[cite]10.1039/b810301a[/cite]
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Tags: Applet, compression algorithm, computing, Cross-platform software, HTML, HTML element, Internet Journal, Java, Java applet, Java platform, jmol, Markup languages, Open formats, publishers site, publishers systems, technology moves, Technology/Internet, the Internet Journal, Web browser, web technologies, Web-components age, XML, XSLT
Posted in Chemical IT | 8 Comments »