Posts Tagged ‘Chemistry’
Monday, November 27th, 2017
Previously: “Non-polar” species such as SeMe6, SMe6, ClMe3, ClMe5 all revealed interesting properties for the Se-C, S-C or Cl-C “single” bonds. The latter two examples in particular hinted at internal structures for these single bonds, as manifested by two ELF basins for some of the bonds. Here I take a look at the related molecule where a formal double bond between carbon and the central sulfur atom replacing the single-bond might also hint at octet expansions and hypervalence.
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Tags:Chemical bond, chemical bonding, Chemical polarity, Chemistry, double bond, Hypervalent molecule, Nature, single bond, Tetravalence, Valence
Posted in Hypervalency | No Comments »
Sunday, November 12th, 2017
A few years back, I took a look at the valence-shell electron pair repulsion approach to the geometry of chlorine trifluoride, ClF3 using so-called ELF basins to locate centroids for both the covalent F-Cl bond electrons and the chlorine lone-pair electrons. Whereas the original VSEPR theory talks about five “electron pairs” totalling an octet-busting ten electrons surrounding chlorine, the electron density-based ELF approach located only ~6.8e surrounding the central chlorine and no “octet-busting”. The remaining electrons occupied fluorine lone pairs rather than the shared Cl-F regions. Here I take a look at ClMe3, as induced by the analysis of SeMe6.
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Tags:Chemical bond, chemical bonding, Chemistry, Chlorine, Covalent bond, Lone pair, Oxidizing agents, Quantum chemistry, Stereochemistry, Valence, VSEPR theory
Posted in Chemical IT, Hypervalency | 5 Comments »
Tuesday, October 24th, 2017
An N-B single bond is iso-electronic to a C-C single bond, as per below. So here is a simple question: what form does the distribution of the lengths of these two bonds take, as obtained from crystal structures?
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Tags:bond, Bond valence method, Chemical bond, chemical bonding, Chemistry, Covalent bond, crystal structure, Nature, Quantum chemistry, search query
Posted in crystal_structure_mining | 2 Comments »
Thursday, September 21st, 2017
A recent article reports, amongst other topics, a computationally modelled reaction involving the capture of molecular hydrogen using a substituted borane (X=N, Y=C).[cite]10.1073/pnas.1709586114[/cite] The mechanism involves an initial equilibrium between React and Int1, followed by capture of the hydrogen by Int1 to form a 5-coordinate borane intermediate (Int2 below, as per Figure 11).‡ This was followed by assistance from a proximate basic nitrogen to complete the hydrogen capture via a TS involving H-H cleavage. The forward free energy barrier to capture was ~11 kcal/mol and ~4 kcal/mol in the reverse direction (relative to the species labelled Int1), both suitably low for reversible hydrogen capture. Here I explore a simple variation to this fascinating reaction.∞
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Tags:Ammonia borane, animation, Boranes, Chemistry, Cleaning Services, Company: React Group, free energy barrier, Hydroboration, Hydrogen, Matter
Posted in reaction mechanism | 1 Comment »
Saturday, September 16th, 2017
Early in 2011, I wrote about how the diatomic molecule Be2 might be persuaded to improve upon its normal unbound state (bond order ~zero) by a double electronic excitation to a strongly bound species. I yesterday updated this post with further suggestions and one of these inspired this follow-up.
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Tags:Be-Be double bond, Be-Be triple bond, Chemical bond, Chemistry, Cs-Cs double bond, Diatomic molecule, free energy, General chemistry, K-K double bond, Li-Li double bond, Molecular geometry, Oxygen, Province/State: Be2, Quantum chemistry, Rb-Rb double bond, Stereochemistry
Posted in Interesting chemistry | 3 Comments »
Tuesday, August 29th, 2017
Another selection (based on my interests, I have to repeat) from WATOC 2017 in Munich.
- Odile Eisenstein gave a talk about predicted 13C chemical shifts in transition metal (and often transient) complexes, with the focus on metallacyclobutanes. These calculations include full spin-orbit/relativistic corrections, essential when the carbon is attached to an even slightly relativistic element. She noted that the 13C shifts of the carbons attached to the metal fall into two camps, those with δ ~+80 ppm and those with values around -8 ppm. These clusters are associated with quite different reactivities, and also seem to cluster according to the planarity or non-planarity of the 4-membered ring. There followed some very nice orbital explanations which I cannot reproduce here because my note taking was incomplete, including discussion of the anisotropy of the solid state spectra. A fascinating story, which I add to here in a minor aspect. Here is a plot of the geometries of the 52 metallacyclobutanes found in the Cambridge structure database. The 4-ring can be twisted by up to 60° around either of the C-C bonds in the ring, and rather less about the M-C bonds. There is a clear cluster (red spot) for entirely flat rings, and perhaps another at around 20° for bent ones, but of interest is that it does form something of a continuum. What is needed is to correlate these geometries with the observed 13C chemical shifts to see if the two sets of clusters match. I include this here because in part such a search can be done in “real-time” whilst the speaker is presenting, and can then be offered as part of the discussion afterwards. It did not happen here because I was chairing the meeting, and hence concentrating entirely on proceedings!
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Tags:chemical shifts, Chemistry, City: Munich, Jan Jenson, metal fall, Munich, Odile Eisenstein, Quotation, speaker, Stefan Grimme, Transition metal, Walter Thiel, World Association of Theoretical and cOmputational Chemists
Posted in Interesting chemistry, WATOC reports | 6 Comments »
Sunday, 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 »
Thursday, 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 »
Saturday, 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 »