Previously, I explored (computationally) the normal vibrational modes of Co(II)-tetraphenylporphyrin (CoTPP) as a “flattened” species on copper or gold surfaces for comparison with those recently imaged[cite]10.1038/s41586-019-1059-9[/cite]. The initial intent was to estimate the “flattening” energy. There are six electronic possibilities for this molecule on a metal surface. Respectively positively, or negatively charged and a neutral species, each in either a low or a high-spin electronic state. I reported five of these earlier, finding each had quite high barriers for “flattening” the molecule. For the final 6th possibility, the triplet anion, the SCF (self-consistent-field) had failed to converge, but for which I can now report converged results.†
Posts Tagged ‘metal’
Imaging normal vibrational modes of a single molecule of CoTPP: a mystery about the nature of the imaged species.
Thursday, April 25th, 2019Tags:019-1059-9, 10.1038, Biomolecules, Chelating agents, chemical bonding, Chemical compounds, Chemistry, Coordination chemistry, Coordination complex, Copper, copper metal surface, Cu–CO, E-type, energy, free energy, higher energy, impossible free energy, Inorganic chemistry, Jahn–Teller effect, lowest energy electronic state, Metabolism, metal, metal surface, modest planarisation energy, Molecule, Natural sciences, Physical sciences, planarisation, Porphyrin, reasonable energy, Resonance, Solid-state chemistry, sufficient energy, Teller, Tetraphenylporphyrin
Posted in Interesting chemistry | 1 Comment »
Imaging vibrational normal modes of a single molecule.
Thursday, April 18th, 2019The topic of this post originates from a recent article which is attracting much attention.[cite]10.1038/s41586-019-1059-9[/cite] The technique uses confined light to both increase the spatial resolution by around three orders of magnitude and also to amplify the signal from individual molecules to the point it can be recorded. To me, Figure 3 in this article summarises it nicely (caption: visualization of vibrational normal modes). Here I intend to show selected modes as animated and rotatable 3D models with the help of their calculation using density functional theory (a mode of presentation that the confinement of Figure 3 to the pages of a conventional journal article does not enable).
Tags:anionic metal surface, Cambridge, chemical bonding, Chemistry, dihedral, energy, flat metal surface, metal, Natural sciences, Neutral Quartet, Physical sciences, Raman scattering, Raman spectroscopy, Resonance, spectroscopy, steric repulsion energy
Posted in Interesting chemistry | No Comments »
Hypervalent hydrogen?
Saturday, January 13th, 2018I discussed the molecule the molecule CH3F2- a while back. It was a very rare computed example of a system where the added two electrons populate the higher valence shells known as Rydberg orbitals as an alternative to populating the C-F antibonding σ-orbital to produce CH3– and F–. The net result was the creation of a weak C-F “hyperbond”, in which the C-F region has an inner conventional bond, with an outer “sheath” encircling the first bond. But this system very easily dissociates to CH3– and F– and is hardly a viable candidate for experimental detection. In an effort to “tune” this effect to see if a better candidate for such detection might be found, I tried CMe3F2-. Here is its story.
Tags:Antibonding molecular orbital, candidate for experimental detection, chemical bonding, chemical shift, Chemistry, metal, Molecular orbital, Nature
Posted in Hypervalency | 2 Comments »
How does carbon dioxide coordinate to a metal?
Saturday, May 6th, 2017Mention 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.
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 »
Silyl cations?
Thursday, March 23rd, 2017It is not only the non-classical norbornyl cation that has proved controversial in the past. A colleague mentioned at lunch (thanks Paul!) that tri-coordinate group 14 cations such as R3Si+ have also had an interesting history.[cite]10.1021/ja990389u[/cite] Here I take a brief look at some of these systems.
Tags:2-Norbornyl cation, Carbocations, chemical bonding, Chemistry, metal, Physical organic chemistry, Reactive intermediates, search query, tri-coordinate
Posted in crystal_structure_mining | 8 Comments »
Pyrophoric metals + the mechanism of thermal decomposition of magnesium oxalate.
Sunday, March 19th, 2017A pyrophoric metal is one that burns spontaneously in oxygen; I came across this phenomenon as a teenager doing experiments at home. Pyrophoric iron for example is prepared by heating anhydrous iron (II) oxalate in a sealed test tube (i.e. to 600° or higher). When the tube is broken open and the contents released, a shower of sparks forms. Not all metals do this; early group metals such as calcium undergo a different reaction releasing carbon monoxide and forming calcium carbonate and not the metal itself. Here as a prelude to the pyrophoric reaction proper, I take a look at this alternative mechanism using calculations.
Tags:Aluminium, calculated free energy barrier, Carbon monoxide, Chemical elements, Chemistry, higher activation energy, Iron, Matter, metal, metal oxalates, Oxide, pyrophoric metal, Pyrophoricity, Reducing agents
Posted in crystal_structure_mining, reaction mechanism | 1 Comment »
Molecules of the year? Pnictogen chains and 16 coordinate Cs.
Monday, December 19th, 2016I am completing my survey of the vote for molecule of the year candidates, which this year seems focused on chemical records of one type or another.
Tags:chemical publishing, chemical records, human chemical perception, Matter, metal, Molecule, Nature, search query, search software, Voting
Posted in crystal_structure_mining, Interesting chemistry | 2 Comments »
Molecule of the year? “CrN123”, a molecule with three different types of Cr-N bond.
Friday, December 16th, 2016Here is a third candidate for the C&EN “molecule of the year” vote. This one was shortlisted because it is the first example of a metal-nitrogen complex exhibiting single, double and triple bonds from different nitrogens to the same metal[cite]10.1039/c5sc04608d[/cite] (XUZLUB has a 3D display available at DOI: 10.5517/CC1JYY6M). Since no calculation of its molecular properties was reported, I annotate some here.
Tags:10.14469, chemical shifts, expert chemical knowledge, metal, metal-nitrogen complex exhibiting single, search query
Posted in crystal_structure_mining, Interesting chemistry | 10 Comments »
The largest C-C-C angle?
Tuesday, November 1st, 2016I am now inverting the previous question by asking what is the largest angle subtended at a chain of three connected 4-coordinate carbon atoms? Let’s see if further interesting chemistry can be unearthed.
Tags:Angle, metal, Subtended angle
Posted in crystal_structure_mining, Interesting chemistry | 1 Comment »
A wider look at π-complex metal-alkene (and alkyne) compounds.
Monday, June 13th, 2016Previously, 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.
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
Posted in crystal_structure_mining | No Comments »