June 21st, 2016
This is a follow-up to the post on exploring the directing influence of (electron donating) substituents on benzene[cite]10.1021/acs.jchemed.5b00346[/cite] with the focus on heteroaromatic rings such indoles, pyrroles and group 16 analogues (furans, thiophenes etc).
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Tags: Asymmetric hydrogenation, benzene, benzo, Electrophile, Furan, Indole, Pyridine, Pyrrole, search query, Simple aromatic rings, Substitution reaction, Thiophene
Posted in crystal_structure_mining | No Comments »
June 18th, 2016
In this post, I pondered upon the C=O infra-red spectroscopic properties of esters, and showed three possible electronic influences:
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Tags: Ester, Functional groups, Infra-Red
Posted in Chemical IT, crystal_structure_mining | 1 Comment »
June 13th, 2016
Previously, I looked at the historic origins of the so-called π-complex theory of metal-alkene complexes. Here I follow this up with some data mining of the crystal structure database for such structures.
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Tags: alkene, alkene-metal complex, alkyne, Bond length, Carbon–carbon bond, Chemical bond, chemical bonding, Cluster chemistry, Conquest structure editor, Coordination complex, data mining, double bond, editor, filled metal orbital, metal, metal-alkene complexes, metal-alkyne complexes, metal-carbon bonds, Pi backbonding, search query, Structural formula, Transition metal alkyne complex
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June 10th, 2016
A while ago, I explored how the 3-coordinate halogen compound ClF3 is conventionally analyzed using VSEPR (valence shell electron pair repulsion theory). Here I (belatedly) look at other such tri-coordinate halogen compounds using known structures gleaned from the crystal structure database (CSD).
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Tags: chemical phenomena, data mining, equivalent search, Halogen, search query specifies 7A
Posted in crystal_structure_mining | 1 Comment »
June 3rd, 2016
The title might give it away; this is my 500th blog post, the first having come some eight years ago. Very little online activity nowadays is excluded from measurement and so it is no surprise that this blog and another of my "other" scholarly endeavours, viz publishing in traditional journals, attract such "metrics" or statistics. The h-index is a well-known but somewhat controversial measure of the impact of journal articles; here I thought I might instead take a look at three less familiar ones – one relating to blogging, one specific to journal publishing and one to research data.
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Tags: Country: Svalbard and Jan Mayen, CrossRef, head of information resources, HTML, Imperial College, librarian, online activity, Online Usage, PDF, researcher, search engines, usage statistics portal
Posted in Chemical IT | 4 Comments »
May 30th, 2016
This is a follow-up to one aspect of the previous two posts dealing with nucleophilic substitution reactions at silicon. Here I look at the geometries of 5-coordinate compounds containing as a central atom 4A = Si, Ge, Sn, Pb and of the specific formula C34AO2 with a trigonal bipyramidal geometry. This search arose because of a casual comment I made in the earlier post regarding possible cooperative effects between the two axial ligands (the ones with an angle of ~180 degrees subtended at silicon). Perhaps the geometries might expand upon this comment?
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Tags: Anomer, Anomeric effect, Carbohydrate chemistry, Carbohydrates, Ligand, Molecular geometry, Physical organic chemistry, Stereochemistry, Stereoelectronic effect, Trigonal bipyramidal molecular geometry
Posted in Chemical IT, crystal_structure_mining | 3 Comments »
May 27th, 2016
In the previous post, I explored the mechanism for nucleophilic substitution at a silicon centre proceeding via retention of configuration involving a Berry-like pseudorotation. Here I probe an alternative route involving inversion of configuration at the Si centre. Both stereochemical modes are known to occur, depending on the leaving group, solvent and other factors.[cite]10.1016/S0040-4020(01)89077-3[/cite],[cite]10.1021/ja01006a024[/cite],[cite]10.1021/ja00784a081[/cite]
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Tags: Brook rearrangement, energy, free energy, Leaving group, Nucleophilic substitution, Pseudorotation, Si centre, SNi, Substitution reactions, Walden inversion
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May 25th, 2016
The substitution of a nucleofuge (a good leaving group) by a nucleophile at a carbon centre occurs with inversion of configuration at the carbon, the mechanism being known by the term SN2 (a story I have also told in this post). Such displacement at silicon famously proceeds by a quite different mechanism, which I here quantify with some calculations.
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Tags: Berry mechanism, Elimination reaction, energy, energy barrier, energy profile, free energy, Leaving group, lower energy orientation, Molecular geometry, Organic reactions, overall free energy, Pseudorotation, search query, SN2 reaction, Stereochemistry, Trigonal bipyramidal molecular geometry
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May 24th, 2016
I occasionally post about "RDM" (research data management), an activity that has recently become a formalised essential part of the research processes. I say recently formalised, since researchers have of course kept research notebooks recording their activities and their data since the dawn of science, but not always in an open and transparent manner. The desirability of doing so was revealed by the 2009 "Climategate" events. In the UK, Climategate was apparently the catalyst which persuaded the funding councils (such as the EPSRC, the Royal Society, etc) to formulate policies which required all their funded researchers to adopt the principles of RDM by May 2015 and in their future researches. An early career researcher here, anxious to conform to the funding body instructions, sent me an email a few days ago asking about one aspect of RDM which got me thinking.
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Tags: Academic publishing, chemical identifiers, chemical names and chemical terms, chemical tagger page, CrossRef, Data management, Data management plan, DataCite, Identifiers, ORCiD, RDM, researcher, Royal Society, Singular spectrum analysis, Technical communication, Technology/Internet
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May 11th, 2016
I have previously commented on the Bürgi–Dunitz angle, this being the preferred approach trajectory of a nucleophile towards the electrophilic carbon of a carbonyl group. Some special types of nucleophile such as hydrazines (R2N-NR2) are supposed to have enhanced reactivity[cite]10.1016/S0040-4020(01)93101-1[/cite] due to what might be described as buttressing of adjacent lone pairs. Here I focus in on how this might manifest by performing searches of the Cambridge structural database for intermolecular (non-bonded) interactions between X-Y nucleophiles (X,Y= N,O,S) and carbonyl compounds OC(NM)2.
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Tags: Bases, Bürgi–Dunitz angle, Carbonyl, Electrophile, Ester, Flippin–Lodge angle, Functional groups, hydrazine, non-metal attachments, Nucleophile, Physical organic chemistry, search query, Superbase
Posted in Chemical IT, crystal_structure_mining | 1 Comment »