May 25th, 2017
It is a sign of the times that one travels to a conference well-connected. By which I mean email is on a constant drip-feed, with venue organisers ensuring each delegate receives their WiFi password even before their room key. So whilst I was at a conference espousing the benefits of open science, a nice example of open collaboration was initiated as a result of a received email.‡
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Tags: animation, chemical reactions, City: Cupertino, Company: Cupertino Elec, Company: Firefox Communic, Computer Hardware - NEC, computing, detective, Digital media, Drip, Electronic documents, Electronic publishing, Email, HTML, Imperial College, Linux, operating system, Password, Person Location, Steven Kirk, Technology/Internet, XML
Posted in Chemical IT | No Comments »
May 23rd, 2017
This is taking place in the idyllic surroundings of the Niederwald forest, Rüdesheim, Germany. Here I highlight only aspects of the first three talks.
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Tags: article processing charges, Bad Kreuznach, chemical shift, chemical terms, City: Rüdesheim, Country: Germany, Hesse, Hesse-Nassau, Ian Bruno, Jeremy Frey, Klaus Tochtermann, Leah McEwen, Martin Hicks, metadata tools, Niederwald, Niederwalddenkmal, Quotation, Rüdesheim, Rüdesheim am Rhein, Rüdesheim an der Nahe, Rheingau-Taunus-Kreis, Rhine, Richard Kidd, spectroscopy, States of Germany, Stuart Chalk, Technology/Internet
Posted in Chemical IT | 1 Comment »
May 6th, 2017
Mention carbon dioxide (CO2) to most chemists and its properties as a metal ligand are not the first aspect that springs to mind. Here thought I might take a look at how it might act as such.
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Tags: Carbon, Carbon Capture & Storage, carbon dioxide, chemical bonding, Chemistry, Environment, Ligand, ligand-metal coordination, metal, metal ligand, Propellants, Search queries, search query, short metal-centroid distance
Posted in crystal_structure_mining | 2 Comments »
April 28th, 2017
Research data (and its management) is rapidly emerging as a focal point for the development of research dissemination practices. An important aspect of ensuring that such data remains fit for purpose is identifying what curation activities need to be associated with it. Here I revisit one particular case study associated with the molecular structure of a product identified from a photolysis reaction[cite]10.1126/science.1188002[/cite] and the curation of the crystallographic data associated with this study.
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Tags: assigned chemical name, author, chemical name, chemical name synonym, chemical names, chemical structures, editor, indicated chemical name synonym, Knowledge, radiation, Research, Scientific method, Technology/Internet, X-ray
Posted in Chemical IT, crystal_structure_mining | 5 Comments »
April 17th, 2017
Following on from my re-investigation of close hydrogen bonding contacts to the π-face of alkenes, here now is an updated scan for H-bonds to alkynes. The search query (dataDOI: 10.14469/hpc/2478) is similar to the previous one:
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Tags: alkene, alkyne, Functional groups, intra-molecular search, search query
Posted in crystal_structure_mining | 1 Comment »
April 15th, 2017
Back in the early 1990s, we first discovered the delights of searching crystal structures for unusual bonding features.[cite]10.1039/P29940000703[/cite] One of the first cases was a search for hydrogen bonds formed to the π-faces of alkenes and alkynes. In those days the CSD database of crystal structures was a lot smaller (<80,000 structures; it’s now ten times larger) and the search software less powerful. So here is an update.
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Tags: calculated energy, chemical bonding, Chemistry, Crystal, crystallography, energy, energy calculation, Intermolecular forces, Nature, search query, search software, Supramolecular chemistry
Posted in crystal_structure_mining | 2 Comments »
April 13th, 2017
Layer stacking in structures such as graphite is well-studied. The separation between the π-π planes is ~3.35Å, which is close to twice the estimated van der Waals (vdW) radius of carbon (1.7Å). But how much closer could such layers get, given that many other types of relatively weak interaction such as hydrogen bonding can contract the vdW distance sum by up to ~0.8Å or even more? This question was prompted by the separation calculated for the ion-pair cyclopropenium cyclopentadienide (~2.6-2.8Å).
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Tags: Carbon, chemical bonding, Chemistry, Cyclopentadienyl anion, Graphite, Hydrogen bond, Intermolecular forces, Nature, Organic chemistry, search query, Stacking, Supramolecular chemistry, VDW
Posted in crystal_structure_mining | 1 Comment »
April 11th, 2017
Following my conformational exploration of enols, here is one about a much more common molecule, a carboxylic acid.
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Tags: Acid, Alcohols, carboxylic acid, Chemistry, Enol, Functional groups, Organic chemistry, search uses
Posted in crystal_structure_mining | No Comments »
April 9th, 2017
Both the cyclopropenium cation and the cyclopentadienide anion are well-known 4n+2-type aromatic ions, but could the two together form an ion-pair?
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Tags: Anions, Aromatization, Cation–pi interaction, Chemistry, Cyclopentadienyl anion, Ion, Ion association, potential energy surface, Simple aromatic rings
Posted in crystal_structure_mining, Interesting chemistry | 6 Comments »
April 6th, 2017
Enols are simple compounds with an OH group as a substituent on a C=C double bond and with a very distinct conformational preference for the OH group. Here I take a look at this preference as revealed by crystal structures, with the theoretical explanation.
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Tags: Chemical bond, chemical bonding, Chemistry, Conformational isomerism, constrained search, Enol, free energy, Gauche effect, Hydrogen bond, Isomerism, Java, Physical organic chemistry, search query, Stereochemistry, Supramolecular chemistry
Posted in crystal_structure_mining, reaction mechanism | 2 Comments »