Posts Tagged ‘Molecule’
Thursday, April 25th, 2019
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[1]. 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.†
| charge |
Spin
Multiplicity
|
ΔG, Twisted Ph,
Hartree |
ΔG, “flattened”,
Hartree |
ΔΔG,
kcal/mol
|
| -1 |
Triplet |
-3294.68134 (C2) |
-3294.64735 (C2v) |
21.3 |
| -3294.60006 (Cs) |
51.0 |
| -3294.37012 (D2h) |
195.3 |
| Singlet |
-3294.67713 (S4) |
-3294.39418 (D4h) |
175.6 |
| -3294.39321 (D2h) |
178.2 |
| -3294.56652 (D2) |
69.4 |
| FAIR data at DOI: 10.14469/hpc/5486 |
I am exploring the so-called “flattened” mode, induced by the voltage applied at the tip of the STM (scanning-tunnelling microscope) probe and which causes the phenyl rings to rotate as per above. This rotation in turn causes the hydrogen atom-pair encircled above to approach each other very closely.‡ To avoid these repulsions, the molecule buckles into one of two modes. The first causes the phenyl rings to stack up/down/up/down. The second involves an all-up stacking, as shown below. Although these are in fact 4th-order saddle points as isolated molecules, the STM voltage can inject sufficient energy to convert these into apparently stable minima on the metal surface.
All syn mode, Triplet anion
The up/down/up/down “flattened” form (below) shows a much more modest planarisation energy than all the other charged/neutral states reported in the previous post, whereas the all-up isomer (which on the face of it looks a far easier proposition to come into close contact with a metal surface) is far higher in free energy.
The caption to Figure 3 in the original article[1] does not explicitly mention the nature of the metal surface on which the vibrations were recorded, but we do get “The intensity in the upper right corner of the 320-cm−1 map is from a neighbouring Cu–CO stretch” which suggests it is in fact a copper surface. Coupled with the other observation that in “contrast to gold, the Kondo resonance of cobalt disappears on Cu(100), suggesting that it acquires nearly a full electron from the metal (see Extended Data Fig. 2),” the model below of a triplet-state anion on the Cu surface seems the most appropriate.
Syn/anti mode, Triplet anion with C2v symmetry
There is one final remark made in the article worth repeating here: “This suggests that the vibronic functions are complex-valued in this state, as expected for Jahn–Teller active degenerate orbitals of the planar porphyrin.26” Orbital degeneracy can only occur if the molecule has e.g. D4h point group symmetry, whereas the triplet anion stationary-point shown in the figure above has only C2v symmetry for which no orbital degeneracies (E) are expected. Enforcing D4h symmetry on Co(II) tetraphenylporphyrin results in eight pairs of H…H contacts of 1.34Å,‡ which is an impossibly short distance (the shortest known is ~1.5Å). Moreover this geometry has an equally impossible free energy 176 kcal/mol above the relaxed free molecule. Visually from Figure 3, the H…H contact distance looks even shorter (below, circled in red)! A D2h form (with no E-type orbitals) can also be located.
 Singlet, Calculated with D4h symmetry. Click for vibrations. |
 Singlet, Calculated with D2h symmetry. Click for vibrations. |
 Taken from Figure 3 (Ref 1). |
These totally flat species are calculated to be at 13 or 12th-order saddle points, with the eight most negative force constants having vectors which correspond to up/down avoidance motions of the proximate hydrogen pairs encircled above and the remaining being buckling modes of the entire ring.
So to the mystery, being the nature of the “flattened” CoTPP on the copper metal surface, as represented in Figure 3 of the article.[1] Is it truly flat, as implied by the article? If so, the energy of such a species would be beyond the limits of what is normally considered feasible. Moreover, it would represent a species with truly mind-blowing short H…H contacts. Or could it be a saddle-shaped geometry, where the phenyl rings are not lying flat in contact with the metal but interacting via the phenyl para-hydrogens? That geometry has not only a much more reasonable energy above the unflattened free molecule, but also acceptable H…H contacts (~2.0.Å) However, would such a shape correspond to the visualised vibrational modes also shown in Figure 3? I have a feeling that there must be more to this story.
†These convergence problems were solved by improving the basis set via adding “diffuse” functions, as in (u)ωB97XD/6-311+G(d,p). ‡If the crystal structure for these species is flattened without geometry optimisation, the H-H distance is around 0.8Å
References
- J. Lee, K.T. Crampton, N. Tallarida, and V.A. Apkarian, "Visualizing vibrational normal modes of a single molecule with atomically confined light", Nature, vol. 568, pp. 78-82, 2019. https://doi.org/10.1038/s41586-019-1059-9
Tags: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 »
Monday, June 18th, 2018
It was about a year ago that I came across a profusion of colour in my local Park. Although colour in fact was the topic that sparked my interest in chemistry many years ago (the fantastic reds produced by diazocoupling reactions), I had never really tracked down the origin of colours in many flowers. It is of course a vast field. Here I take a look at just one class of molecule responsible for many flower colours, anthocyanidin, this being the sugar-free counterpart of the anthocyanins found in nature.
These vary widely in the substituent around the aromatic rings, but here I take a look at just three differing substitutions. Thus pelargonidin has just one OH on ring C (R1‘, R3‘=H, see crystal structure[1]), cyanidin has two (R5‘=H, see crystal structure[2]) and is found in red roses, dahlia, peonies etc. Finally delphinidin (no crystal structure available) has three OHs in that region and is found in yes, delphiniums but also grape skins etc. Below is a colour table that allows one to relate the electronic transitions in a molecule to the observed colour, which of course is due to removal (absorption) of wavelength of light leaving us to see all the remaining wavelengths.
Next I show the computed UV/visible spectra of these three species (ωB97XD/6-311G(d,p)/SCRF=water)‡. Click on any image to se a 3D model of the molecule.
Note how in the visible region, all have a very simple (monochromatic) single electronic transition comprising mostly the HOMO→LUMO excitation.
Click to view 3D model of the HOMO
Click to view 3D model of the LUMO
Now, λmax can be predicted quite poorly using most DFT methods, but the trends should be better predicted. Thus the change induced by adding two hydroxy groups is ~7nm, which is in effect how the colour seen in a flower can be tuned to display different shades.
Next, pH. Using delphinidin, under basic conditions one can remove a proton from the cationic species to produce a neutral quinone. In fact, any one of five OH groups could have its proton removed and so it is of some interest to compare the relative energies of the five isomers so produced.
| Position proton removed |
Relative ΔG298, kcal/mol |
| 4′ |
0.0 |
| 5 |
3.8 |
| 7 |
4.7 |
| 3′ |
11.8 |
| 5′ |
22.2 |
In fact, one species only would have the major Boltzmann population (4′) and so we need only look at its UV/Visible predicted spectrum. This is shifted 17nm towards the red, thus producing a blue colour in what remains after it is absorbed. The absorption (ε) also increases significantly. Indeed the very striking colour of blue delphiniums (one of my favourite flowers) must be produced by such pH control in the plant. Given the presence of delphinidin in many grape skins, the next time I drink a glass of red wine, I will see if it turns blue upon adding some NaOH!
‡FAIR data doi: 10.14469/hpc/4473
References
- N. Saito, and K. Ueno, "The Crystal and Molecular Structure of Pelargonindin Bromide Monohydrate", HETEROCYCLES, vol. 23, pp. 2709, 1985. https://doi.org/10.3987/r-1985-10-2709
- K. Ueno, and N. Saito, "Cyanidin bromide monohydrate (3,5,7,3',4'-pentahydroxyflavylium bromide monohydrate)", Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry, vol. 33, pp. 114-116, 1977. https://doi.org/10.1107/s0567740877002702
Tags:Anthocyanidin, Anthocyanin, Chemistry, Delphinidin, HOMO/LUMO, Major, Molecular electronic transition, Molecule, Nature, PH indicators, Quantum chemistry, spectroscopy, Ultraviolet–visible spectroscopy
Posted in Interesting chemistry | 4 Comments »
Wednesday, April 18th, 2018
The molecules below were discussed in the previous post as examples of highly polar but formally neutral molecules, a property induced by aromatisation of up to three rings. Since e.g. compound 3 is known only in its protonated phenolic form, here I take a look at the basicity of the oxygen in these systems to see if deprotonation of the ionic phenol form to the neutral polar form is viable.
The equilibrium being considered is shown below for compound 2:
The energetics of this equilibrium shown below, computed at the ωB97XD/Def2-TZVPPD/SCRF=water level and for which the FAIR data DOI is 10.14469/hpc/4073
For 1: X=Cl, the energy is shown below as a function of the O….H distance. Proton abstraction from HCl is exothermic by ~25 kcal/mol.
For 2: X=Cl, the exothermicity increases by only ~5 kcal/mol , despite the apparent aromatisation of a further ring. It is also worth noting that this is greater basicity than that of e.g. water, where around 4-5 water molecules acting in concert are required to deprotonate HCl.
For 1: X=OH, the proton abstraction from water is mildly endothermic by about 13 kcal/mol; indeed there is no energy minimum for carbonyl protonation and instead a relatively strong hydrogen bond to the water is formed instead.
For 2: X=OH the endothermicity is reduced to ~9 kcal/mol.
For 1: X=CH3, deprotonation of methane is now strongly endothermic by ~40 kcal/mol.
So the molecules 1 – 2 above are clearly not superbases, which perhaps augers well for being able to deprotonate the ionic phenols into these neutral but highly polar molecules.
Tags:Antiseptics, Aromatization, Chemistry, energy, energy minimum, Hydrogen, Molecule, Neurotoxins, Science
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Sunday, March 4th, 2018
A bond index (BI) approximately measures the totals of the bond orders at any given atom in a molecule. Here I ponder what the maximum values might be for elements with filled valence shells.
Following Lewis in 1916[1] who proposed that the full valence shell for main group elements should be 2 (for the first two elements) and 8 (the “octet“), Bohr (1922[2]), Langmuir (1919-1921[3]) and Bury (1921[4]) extended this rule to include 18 (the transition series) and 32 (the lanthanides and actinides). If we assume no contributions from higher Rydberg shells (thus 3s, 3p, 3d for carbon etc) and an electron pair model for orbital population (which amounts to the single-determinantal model), then the maximum bond index for hydrogen (and helium) would be 1, it would be 4 for main group elements, and then what?
For the special case of hydrogen, I have previously identified (for a hypothetical species) a bond index of 1.33, due mostly to a high Rydberg occupancy of 1.19e. The more normal BI is <1.0, as noted for this hexacoordinated hydride system. My current estimate for the maximum bond index for main group elements is <4.5. Thus for SF6, it has the value of ~4.33 and that includes a modest occupancy of Rydberg shells of 0.36e = 0.18 BI. Exclude these and it is close to 4.
Move on from group 16 to group 6 and you get compounds such as Me4CrCrMe44- or ReMe82- where the metal bond indices are ~6.5.‡ Compounds such as Cr(Me)6 (BI = 5.6) and W(Me)6 (BI = 6.1) are rather lower. This is a long way from 18/2 = 9. The lanthanides and actinides[5] are unlikely to reveal many large BIs (32/2= 16 maximum value) since they are often ionic and the wavefunctions may be too complex to allow a simple index such as a BI to be safely computed.
So if we are hunting for record BIs, the transition elements are the place to hunt. Can a BI of 6.5 be beaten? Can it even approach 9, its maximum value? Does anyone know of candidate molecules?
‡FAIR Data doi: 10.14469/hpc/3352.
References
- G.N. Lewis, "THE ATOM AND THE MOLECULE.", Journal of the American Chemical Society, vol. 38, pp. 762-785, 1916. https://doi.org/10.1021/ja02261a002
- N. Bohr, "Der Bau der Atome und die physikalischen und chemischen Eigenschaften der Elemente", Zeitschrift f�r Physik, vol. 9, pp. 1-67, 1922. https://doi.org/10.1007/bf01326955
- I. Langmuir, "Types of Valence", Science, vol. 54, pp. 59-67, 1921. https://doi.org/10.1126/science.54.1386.59
- C.R. Bury, "LANGMUIR'S THEORY OF THE ARRANGEMENT OF ELECTRONS IN ATOMS AND MOLECULES.", Journal of the American Chemical Society, vol. 43, pp. 1602-1609, 1921. https://doi.org/10.1021/ja01440a023
- P. Pyykkö, C. Clavaguéra, and J. Dognon, "The 32‐Electron Principle", Computational Methods in Lanthanide and Actinide Chemistry, pp. 401-424, 2015. https://doi.org/10.1002/9781118688304.ch15
Tags:Atom, Chemical bond, chemical bonding, chemical properties, Chemistry, metal bond indices, Molecule, Nature, Quantum chemistry, Residential REITs, Resonance, Tennessine, Valence, Valence electron
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Friday, March 10th, 2017
George Olah passed away on March 8th. He was part of the generation of scientists in the post-war 1950s who had access to chemical instrumentation that truly revolutionised chemistry. In particular he showed how the then newly available NMR spectroscopy illuminated structures of cations in solvents such “Magic acid“. The obituaries will probably mention his famous “feud” with H. C. Brown over the structure of the norbornyl cation (X=CH2+), implicated in the mechanism of many a solvolysis reaction that characterised the golden period of physical organic chemistry just before and after WWII.
The dispute between Olah and Brown was not played on a pitch using quite the same goal posts. Olah did much of his work in magic acid and Brown did his in aqueous solutions. I was involved in a tiny way when the discussion about the precise character of the norbornyl cation was reaching its peak in the mid 1970s. At the time, I was working with Michael Dewar, who was himself not shy in joining in the fun and sometimes very acrimonious disputes at conferences. We contributed by calculating the so-called core-electron carbon ESCA spectrum.[1] History records that we came down on the wrong side,‡ by suggesting that this form of spectroscopy supported Brown rather than Winstein/Olah on the basis of a 6:1 spectral deconvolution (classical) rather than 5:2 (non-classical). More recently of course the crystal structure of the parent cation itself has been shown to be non-classical[2] (there are other crystal structures which differ in respect to having one or more additional methyl groups[3]). For a 3D model of norbornyl cation, see DOI: 10.5517/CCZ21LN. This still leaves the issue (very slightly) open for the structure of the solvated cation when formed in water!
When I started to teach a course in molecular modelling, I touched briefly on how modelling could contribute and whilst updating the notes in the 1990s, wondered why the boron analogue had never been so studied (X=BH2). Unlike the crystallographically difficult norbornyl ion-pair, the iso-electronic boron species would be neutral and not need a counter-ion. Perhaps it might be a more manageable molecule? Checking the Cambridge structural database, such a species has never been reported!† So here as my homage to Olah, I report its calculated structure (b2plypd3/Def2-TZVPP, DOI: 10.14469/hpc/2236).
The norbornyl cation has symmetrical C-C bridging distances of ~1.80±0.02Å and a basal C-C distance of ~1.39±0.02Å. The calculated values for the boron equivalent are 2.16Å and 1.36Å respectively, with all positive force constants. B-C bonds are normally 1.66-1.72Å, significantly longer than C-C bonds, which makes the longer B-C lengths in this example unsurprising. More interestingly, the species has one vibrational normal mode (ν 203 cm-1) which corresponds to the [1,2] shift of the BH2 group across the basal C-C. For a classical species, this vibrational motion would correspond to a transition state (an imaginary vibration) but for a non-classical species it is of course real. In this sense it is analogous to the so-called real Kekulé mode in non-classical benzene, which “equilibrates” the two classical Kekulé structures. The corresponding calculated vibration for the norbornyl cation itself is ν 194 cm-1 (DOI: 10.14469/hpc/2238).
Of course, the entire controversy over the structure of this species is littered with comparisons between not quite similar systems, differing in a methyl group more or less. So morphing a C+ to a B might be seen as quite a large change. But perhaps if it had been crystallised in say the 1960s, would the subsequent debates have taken a different turn?
‡ We were also wrong about the symmetry of the Diels-Alder cyclisation, which is nowadays accepted to be synchronous rather than asynchronous for simple Diels-Alder reactions. But that is another story.
†GAXLIA is perhaps the closest analogue.[4],
References
- M.J.S. Dewar, R.C. Haddon, A. Komornicki, and H. Rzepa, "Ground states of molecules. 34. MINDO/3 calculations for nonclassical ions", Journal of the American Chemical Society, vol. 99, pp. 377-385, 1977. https://doi.org/10.1021/ja00444a012
- F. Scholz, D. Himmel, F.W. Heinemann, P.V.R. Schleyer, K. Meyer, and I. Krossing, "Crystal Structure Determination of the Nonclassical 2-Norbornyl Cation", Science, vol. 341, pp. 62-64, 2013. http://dx.doi.org/10.1126/science.1238849
- T. Laube, "Redetermination of the Crystal Structure of the 1,2,4,7‐<i>anti</i>‐tetramethylbicyclo[2.2.1]heptan‐2‐yl cation at 110 K", Helvetica Chimica Acta, vol. 77, pp. 943-956, 1994. https://doi.org/10.1002/hlca.19940770407
- P.J. Fagan, E.G. Burns, and J.C. Calabrese, "Synthesis of boroles and their use in low-temperature Diels-Alder reactions with unactivated alkenes", Journal of the American Chemical Society, vol. 110, pp. 2979-2981, 1988. https://doi.org/10.1021/ja00217a053
Tags:2-Norbornyl cation, aqueous solutions, Chemical bond, chemical instrumentation, Chemistry, George Andrew Olah, George Olah, Ion association, Magic acid, Michael Dewar, Molecule, Nature, Physical organic chemistry, Reactive intermediates, spectroscopy
Posted in Interesting chemistry | 18 Comments »
Wednesday, February 15th, 2017
This post arose from a comment attached to the post on Na2He and relating to peculiar and rare topological features of the electron density in molecules called non-nuclear attractors. This set me thinking about other molecules that might exhibit this and one of these is shown below.
The topology of the electron density is described by just four basic types, designed formally by the notation [3,-3], [3,-1], [3,1] and [3,3] and more colloquially by the terms nuclear attractor (NNA), line (or bond) critical point, a ring critical point and a cage critical point respectively. Mostly, the nuclear critical points coincide exactly with the actual nuclear positions, but more rarely these points are not found centered at a nucleus. It was such an NNA that was suggested as a comment on the post on Na2He. There I replied that another example of an NNA is to be found in H3+ and so its a short step to take a look at H42+ in a tetrahedral arrangement (DOI: 10.14469/hpc/2165). Since only two electrons are available for bonding, it is tempting to represent it as below, with dashed partial bonds connnecting the six edges of the tetrahedron and is associated with real normal vibrational modes; ν 416, 1490 and 1861 cm-1. A brief search on Scifinder, which appears to reference this species as hydrogen, ion (H42+), does not identify any publications associated with it (there are studies on H41+ however); if any reader here knows of any discussion please alert us!
Analysing the density however gives a different result. A NNA is located at the centre of the tetrahedron and a line (bond) critical point connects this to each of the four hydrogen nuclei. This result is similar to the obtained for H3+. It is rather odd that these non-nuclear attractors have not entered into the vocabulary used to describe the bonding in simple molecules, but this picture is certainly different from the more empirical dashed lines between the four nuclei that one is instinctively drawn to use (above).
The ELF analysis (performed using multiWFN) is more interesting. The nuclear basins associated with the hydrogens reveal each has 0.425e, but the central one (green below) has its own basin with 0.301e.
The NICS value associated with the non-nuclear attractor is -27 ppm, which is indicative of strong spherical aromaticity.
All of which goes to show that even the simplest of molecular species may still have properties that are unexpected or certainly not well-known!
Tags:Attractor, brief search, Chemistry, Electron, Electron density, Hydrogen, Molecule, Nature, Physics, Quantum chemistry
Posted in Interesting chemistry | 11 Comments »
Friday, January 20th, 2017
This is one of those posts of a molecule whose very structure is interesting enough to merit a picture and a 3D model. The study[1] reports a molecular knot with the remarkable number of eight crossings.
The DOI for the 3D model is 10.5517/CCDC.CSD.CC1M85Y0 (or click on the image above). Such topology intersects with work we did a few years back on high-order crossings in fully conjugated π-systems[2], which were then illustrated[3] with hypothetical charged higher order annulenes exhibiting linking numbers Lk of up to 6π. A fully π-conjugated system, also with a linking number in the π-framework of 6π but in the form of a trefoil braid was even suggested on this blog, with a common feature of a central templating atom (a cation rather than an anion). Another example of a previously reported pentadecanuclear manganese metallacycle[4] was also assigned a linking number of 6π.
The molecule above is not completely π-conjugated around the braid and so special properties related to aromaticity and associated ring currents resulting from the topology of the cyclic conjugation[5] are not expected to accrue in the eight-crossing molecular braid[1]. We might also look forward to examples of the characterisation of braids with an odd-number of crossings such as trefoils, pentafoils, heptafoils, etc, as associated with the name Möbius.
References
- J.J. Danon, A. Krüger, D.A. Leigh, J. Lemonnier, A.J. Stephens, I.J. Vitorica-Yrezabal, and S.L. Woltering, "Braiding a molecular knot with eight crossings", Science, vol. 355, pp. 159-162, 2017. https://doi.org/10.1126/science.aal1619
- S.M. Rappaport, and H.S. Rzepa, "Intrinsically Chiral Aromaticity. Rules Incorporating Linking Number, Twist, and Writhe for Higher-Twist Möbius Annulenes", Journal of the American Chemical Society, vol. 130, pp. 7613-7619, 2008. https://doi.org/10.1021/ja710438j
- C.S. Wannere, H.S. Rzepa, B.C. Rinderspacher, A. Paul, C.S.M. Allan, H.F. Schaefer, and P.V.R. Schleyer, "The Geometry and Electronic Topology of Higher-Order Charged Möbius Annulenes", The Journal of Physical Chemistry A, vol. 113, pp. 11619-11629, 2009. https://doi.org/10.1021/jp902176a
- H.S. Rzepa, "Linking Number Analysis of a Pentadecanuclear Metallamacrocycle: A Möbius-Craig System Revealed", Inorganic Chemistry, vol. 47, pp. 8932-8934, 2008. https://doi.org/10.1021/ic800987f
- P.L. Ayers, R.J. Boyd, P. Bultinck, M. Caffarel, R. Carbó-Dorca, M. Causá, J. Cioslowski, J. Contreras-Garcia, D.L. Cooper, P. Coppens, C. Gatti, S. Grabowsky, P. Lazzeretti, P. Macchi, . Martín Pendás, P.L. Popelier, K. Ruedenberg, H. Rzepa, A. Savin, A. Sax, W.E. Schwarz, S. Shahbazian, B. Silvi, M. Solà, and V. Tsirelson, "Six questions on topology in theoretical chemistry", Computational and Theoretical Chemistry, vol. 1053, pp. 2-16, 2015. https://doi.org/10.1016/j.comptc.2014.09.028
Tags:Cheminformatics, Chemistry, Drug discovery, Education, Matter, Molecule, Nature, spectroscopy, Structure validation, π-systems
Posted in Interesting chemistry | 3 Comments »
Monday, December 19th, 2016
I 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.
The first article[1] reports striving towards creating a molecule covering a complete column of the period table. In this case, group 7, containing N, P, As, Sb, Bi and Mc. Only the first four of these were incorporated, although the prospects of extending this to five seem good (and to six extremely unlikely). The structure of this pnictogen chain is referenced here: DOI: 10.5517/CCDC.CSD.CC1LHPJ9 and I have demurred from a calculation.
The second article[2] relates to what might be called hypercoordination, and the achievement of what is felt is a maximum value of 16 to a single metal. I thought I might approach this one by searching the Cambridge structure database (CSD) by specifying any metal with a coordination number 16 as the search query. However, I was foiled in this query because the search software (Conquest) allows a maximum value of only 15! So instead I list the total number of hits retrieved for coordination numbers of 10-15: 25224, 4753, 8856, 2492, 839, 348 respectively.
These totals have to be taken with some caution; the coordination number of what may often be very weak interactions may be often determined by human chemical perception rather than hard and fast rules. Nevertheless, the assignment of 348 molecules to having a coordination number of 15 is still a remarkably high number. If I can persuade CCDC to allow searches with 16, who knows what other candidates might emerge to rival this one, DOI: CCDC.CSD.CC1KFCQ2
The final candidate[3] is the only one where no measured coordinates are reported, with the title “Preparation of an ion with the highest calculated proton affinity: ortho-diethynylbenzene dianion”. There high level theoretical and computational modelling is reported to which I cannot add anything useful.
The common theme emerging of my review is that most of the candidates have crystal structures to which I have been able to occasionally add some computed quantum mechanical properties to try to tease out some other aspects of their character. It is also nice to be able to cite a persistent identifier (DOI) that leads directly to the 3D coordinates for the structures. My first ever post to this blog in 2008 addressed one solution on how such immediacy might be achieved and it is nice to see this now as a mainstream aspect of chemical publishing.
References
- A. Hinz, A. Schulz, and A. Villinger, "Synthesis of a Molecule with Four Different Adjacent Pnictogens", Chemistry – A European Journal, vol. 22, pp. 12266-12269, 2016. https://doi.org/10.1002/chem.201601916
- D. Pollak, R. Goddard, and K. Pörschke, "Cs[H<sub>2</sub>NB<sub>2</sub>(C<sub>6</sub>F<sub>5</sub>)<sub>6</sub>] Featuring an Unequivocal 16-Coordinate Cation", Journal of the American Chemical Society, vol. 138, pp. 9444-9451, 2016. https://doi.org/10.1021/jacs.6b02590
- B.L.J. Poad, N.D. Reed, C.S. Hansen, A.J. Trevitt, S.J. Blanksby, E.G. Mackay, M.S. Sherburn, B. Chan, and L. Radom, "Preparation of an ion with the highest calculated proton affinity: ortho-diethynylbenzene dianion", Chemical Science, vol. 7, pp. 6245-6250, 2016. https://doi.org/10.1039/c6sc01726f
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 »