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 ‘Coordination complex’
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 »
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 »
Bond stretch isomerism. Did this idea first surface 100 years ago?
Tuesday, February 9th, 2016The phenomenon of bond stretch isomerism, two isomers of a compound differing predominantly in just one bond length, is one of those chemical concepts that wax and occasionally wane.[cite]10.1016/S1631-0748(02)01380-2[/cite] Here I explore such isomerism for the elements Ge, Sn and Pb.
Tags:a Jahn-Teller, Bond length, chemical concepts, Chemical substance, Company: Ge, Coordination complex, energy, energy difference, Entertainment/Culture, Hydrogen bond, Isomer, Isomerism, Length, Molecular geometry, Organic chemistry, results of a search, search both bond stretch isomers, SN
Posted in crystal_structure_mining, Historical | 1 Comment »
Discovering chemical concepts from crystal structure statistics: The Jahn-Teller effect
Saturday, May 30th, 2015I am on a mission to persuade my colleagues that the statistical analysis of crystal structures is a useful teaching tool. One colleague asked for a demonstration and suggested exploring the classical Jahn-Teller effect (thanks Milo!). This is a geometrical distortion associated with certain molecular electronic configurations, of which the best example is illustrated by octahedral copper complexes which have a d9 electronic configuration. The eg level shown below is occupied by three electrons and which can therefore distort in one of two ways to eliminate the eg degeneracy by placing the odd electron into either a x2-y2 or a z2 orbital. Here I explore how this effect can be teased out of crystal structures.
Tags:basic search, Chemical bond, chemical bonding, Chemistry, classical Jahn-Teller, clear Jahn-Teller, Coordination chemistry, Coordination complex, Copper(II) nitrate, dynamic Jahn-Teller, Edward Teller, Inorganic chemistry, Jahn-Teller, Jahn–Teller effect, Metal ions in aqueous solution, search criteria, Technology/Internet, Transition metals
Posted in Chemical IT, crystal_structure_mining | 1 Comment »