Posts Tagged ‘Supramolecular chemistry’
Sunday, March 24th, 2019
There is a predilection amongst chemists for collecting records; one common theme is the length of particular bonds, either the shortest or the longest. A particularly baffling type of bond is that between the very electronegative F atom and an acid hydrogen atom such as that in OH. Thus short C-N…HO hydrogen bonds are extremely common, as are C-O…HO.‡ But F atoms in C-F bonds are largely thought to be inert to hydrogen bonding, as indicated by the use of fluorine in many pharmaceuticals as inert isosteres.[1] Here I do an up-to-date search of the CSD crystal structure database, which is now on the verge of accumulating 1 million entries, to see if any strong C-F…HO hydrogen bonding may have been recently discovered.
The search query uses the CF…HO distance as one variable, and the C-F-H angle as the second. The first diagram shows just intermolecular interactions, up to a distance of 2.7Å which is the sum of the van der Waals radii of the two elements. The hot spot occurs at this value, and an angle of ~95°.
The intra-molecular plot shows a similar value for the most common F…H distance, with the interesting variation that the angle subtended at F is about 80°.
The outlier at the short end of the spectrum (arrow) was observed in 2014[2] with the structure shown below. It is indeed the current record holder by some margin! This length by the way is however a great deal longer than the shortest O…HO hydrogen bonds, which can be in the region of 1.2Å (with the proton sometimes symmetrically disposed between the two oxygen atoms). The value is also very similar to the record holder for the shortest C-H…H-C interaction.
It is always useful to check up on crystallographic hydrogen atom positions using a quantum calculation, so here is one at the ωB97XD/Def2-TZVPP level (Data DOI: 10.14469/hpc/5131) which replicates the values nicely.
ωB97XD/Def2-TZVPP Calculation
A QTAIM analysis of the critical points shows that the F…H BCP has a high value of ρ(r) (most hydrogen bonds only reach about 0.03 au).
NBO analysis indicates the E(2) perturbation energy for donation from an F lone pair into the H-O σ* orbital is 21.2 kcal/mol, which indicates a strong H-bond (typical C-O…HO values are 18-22 kcal/mol). The F…H bond order is 0.05.
This molecule has another interesting property, also noted in the original article;[2] the shift in wavenumber of the O-H stretching vibration. Most hydrogen bonds are characterised by the shift (mostly red and recently discovered blue shifts) that occurs in the OH group when it hydrogen bonds. These shifts are typically 100-200 cm-1 but in this molecule there is no shift, which is described as “exceptional”.
The 1H NMR shift of the OH proton is observed at δ 4.8 ppm, with the value calculated here (ωB97XD/Def2-TZVPP) being 4.75 ppm. A very large H-F coupling was observed of 68 Hz, again a very high value for a “through space” hydrogen bond.
So another record for the molecule makers to try to break!
‡Respectively 7142 and 31428 intermolecular (3859 and 10602 intra) examples using the same search parameters as above, with the shortest values being ~1.28 and ~1.2Å. 
References
- S. Purser, P.R. Moore, S. Swallow, and V. Gouverneur, "Fluorine in medicinal chemistry", Chem. Soc. Rev., vol. 37, pp. 320-330, 2008. https://doi.org/10.1039/b610213c
- M.D. Struble, C. Kelly, M.A. Siegler, and T. Lectka, "Search for a Strong, Virtually “No‐Shift” Hydrogen Bond: A Cage Molecule with an Exceptional OH⋅⋅⋅F Interaction", Angewandte Chemie International Edition, vol. 53, pp. 8924-8928, 2014. https://doi.org/10.1002/anie.201403599
Tags:Chemical bond, chemical bonding, Chemical elements, Chemistry, Fluorine, Hydrogen, Hydrogen bond, Intermolecular forces, Natural sciences, perturbation energy, pharmaceuticals, Physical sciences, Refrigerants, search parameters, search query, Supramolecular chemistry
Posted in crystal_structure_mining | No Comments »
Saturday, April 15th, 2017
Back in the early 1990s, we first discovered the delights of searching crystal structures for unusual bonding features.[1] One of the first cases was a search for hydrogen bonds formed to the π-faces of alkenes and alkynes. In those days the CSD database of crystal structures was a lot smaller (<80,000 structures; it’s now ten times larger) and the search software less powerful. So here is an update.
The search query (dataDOI:10.14469/hpc/2473) is shown below:
- A mid-point (centroid) of a C-C bond (of any type) is defined, but the carbons are each restricted to being 3-coordinate, with the substituents R being either C or H.
- The distance to a hydrogen (attached to group QA, where QA is any one of N,O,F,Cl, i.e. acidic H) is defined.
- The properties of the alkene are defined by the sines of the two angles subtended at the centroid. This defines how perpendicular the QA-H hydrogen bond is to the C-C bond.
- Four torsions R-C-centroid-H are defined by their sines. The mean of the absolute values of these will define how orthogonal the approach of the hydrogen to the π-π plane is.
- Further constraints in the search are no disorder, no errors, R < 0.05, the H atom position is normalised and this position is defined as being <2.5Å from the C-C bond centroid, which is ~0.3Å < the sum of the van der Waals values for C and H.
The first search is limited to intermolecular contacts between the C-C bond and the H and reveals that for most of the 18 hits, the H approach is close to perpendicular to the centroid but the inclination to the π-π plane is more scattered. The most interesting (shortest H…centroid contact of ~2.22Å, orthogonal approach) can be inspected as KANYAA (dataDOI: 10.5517/CC8JRQ7).
When the search is repeated for intramolecular contacts, rather shorter distances are obtained for 88 hits and with more variation in the angles of approach. The most interesting candidate (blue dots) is IGELAJ[2] (dataDOI: 10.5517/CC14PBW1 ) which has the very short intramolecular H approach of 1.90Å to the C-C centroid corresponding to ~2.04Å to the carbons, a contraction of ~0.8Å from the van der Waals sum.
The authors remarked[2] “that it possesses a better defined intramolecular hydrogen bond compared to the usual molecules for which it is noted“. They also note JOCQEX, which is present in the above plot, but for which there is a non-orthogonal approach of the hydrogen bond to the π-π plane. The authors do not mention TIBCUD[3] (dataDOI: 10.5517/CCPL0FP), which has a similar close approach of 1.92Å to the C-C centroid, but at an angle inclined to the C-C axis.
IGELAJ, as an intramolecular H-bond, was amenable to calculation of its geometry and properties (inter-molecular interactions would ideally require the periodic lattice to be computed), with the observation[3] that “another test was to compare the energy calculation of IGELAJ to a non-hydrogen-bound version where the OH bond is rotated 180°” and “the results predict IGELAJ to be 7.30 kcal more stable than the non-hydrogen-bound version”. This value, if correct, is indeed typical of a very strong hydrogen bond!
Pedant (curious?) as I am, I wanted to be clear what kind of calculated energy was being reported. Was it the difference in total energies, or the energies corrected for ZPE (zero-point-energy) as ΔH or the free energies for which entropy is included as ΔG? The article[3] itself is unclear on this aspect and no energies are reported in the supporting information. This is an illustration that “supporting information” in most current incarnations may often not provide crucial information; only a full deposition as the management of research (RDM) of FAIR data can provide. This process is illustrated for my own calculations of this system (ωB97XD/Def2-TZVPP, dataDOIs: 10.14469/hpc/2474, 10.14469/hpc/2475), which reveals that ΔG298 4.8 kcal/mol and ν 3761 cm-1. In comparison when the OH bond is rotated 180° the wavenumber goes up 3956 cm-1, a difference of 195 cm-1 is calculated, which is indeed a large red-shift. But the “non-hydrogen-bound version where the OH bond is rotated 180°” is not a valid reference point for a non-hydrogen bonded isomer, since it manifests instead as a transition state for OH rotation with νi 166 cm-1, there being no minimum other than the π-facially hydrogen bonded one (dataDOI: 10.14469/hpc/2476). So, for the lack of a suitable reference system, we cannot conclude what the strength of this particular hydrogen bond is, nor make any conclusions about it being unusually strong.
So IGELAJ holds the current record for the shortest π-facial hydrogen bond to an alkene, but not necessarily the strongest! I wonder if this record might be broken with the aid of further computational design and prediction?
References
- H.S. Rzepa, M.H. Smith, and M.L. Webb, "A crystallographic AM1 and PM3 SCF-MO investigation of strong OH ⋯π-alkene and alkyne hydrogen bonding interactions", J. Chem. Soc., Perkin Trans. 2, pp. 703-707, 1994. https://doi.org/10.1039/p29940000703
- M.D. Struble, M.G. Holl, G. Coombs, M.A. Siegler, and T. Lectka, "Synthesis of a Tight Intramolecular OH···Olefin Interaction, Probed by IR,<sup>1</sup>H NMR, and Quantum Chemistry", The Journal of Organic Chemistry, vol. 80, pp. 4803-4807, 2015. https://doi.org/10.1021/acs.joc.5b00470
- B. Ndjakou Lenta, K.P. Devkota, B. Neumann, E. Tsamo, and N. Sewald, "4-(1,1-Dimethylprop-2-enyl)-1,3,5-trihydroxy-2-(3-methylbut-2-enyl)-9<i>H</i>-xanthen-9-one", Acta Crystallographica Section E Structure Reports Online, vol. 63, pp. o1629-o1631, 2007. https://doi.org/10.1107/s1600536807009907
Tags:calculated energy, chemical bonding, Chemistry, Crystal, crystallography, energy, energy calculation, Intermolecular forces, Nature, search query, search software, Supramolecular chemistry
Posted in crystal_structure_mining | 2 Comments »
Thursday, April 13th, 2017
Layer stacking in structures such as graphite is well-studied. The separation between the π-π planes is ~3.35Å, which is close to twice the estimated van der Waals (vdW) radius of carbon (1.7Å). But how much closer could such layers get, given that many other types of relatively weak interaction such as hydrogen bonding can contract the vdW distance sum by up to ~0.8Å or even more? This question was prompted by the separation calculated for the ion-pair cyclopropenium cyclopentadienide (~2.6-2.8Å).
The search query for the Cambridge structure database is shown below.
The query (dataDOI: 10.14469/hpc/2471) defines centroids for two benzenoid rings, both comprising only 3-coordinated carbons. The sine of an angle subtended at each centroid to the other and to one ring carbon attempts to track how parallel the two rings are (strictly speaking, 12 such angles should be included). If the sines of both angles are 1.00, then the two centroids overlap orthogonally. A search constrained to no disorder, no errors and R < 0.05 reveals 1107 hits at a centroid-centroid distance of < 3.5Å. The colour code (red) indicates the distances in the range 3.4-3.5Å, which matches that of graphite, while distances down to 3.2Å (yellow-green) are not uncommon.
Here is another way of representing these results, in which the centroid-centroid distances (measured from the positions of 12 carbon atoms and hence statistically more reliable than any individual atom pair distance) are multiplied by either sin(ANGa) or sin(ANGb). The number of occurrences with distances < 3.2Å is less than 32 (out of 1107).
Taking a look at some of these outliers, PAZJEG has two entries, one with a short distance (dataDOI: 10.5517/ccsffzl) and one with a normal distance[1], which does tend to cast doubt on the former.
ZOMSEB[2], DataDOI: 10.5517/CCZS2MF) appears to have the planes of the molecules stacked ~2.5Å apart.
OXUDES02[cite10.1016/j.poly.2016.09.046[/cite], DataDOI: 10.5517/CCDC.CSD.CC1MBBFQ) has a separation of ~2.6Å.
Verifying these and other outliers would require expert inspection of the crystallographic data and its refinement. This might require access to the hkl structure factors, data which are now being “strongly encouraged”‡ for deposition with the CSD, but which are not present for most structures deposited before ~2016. In extreme cases, the original diffraction images collected by the cameras would allow for a fully independent re-analysis, data which however is rarely if ever deposited.
So the separation of π-π stacked six-membered benzenoid rings is only infrequently less than ~3.2Å in measured crystal structures. There are hints it might reach as short as ~2.6Å, but such examples with values significantly less than 3.2Å do require expert validation before they can be called real.
‡See structuredepositioninformation/ “We strongly encourage data to be deposited either with imbedded structure factor data or with an associated FCF or HKL structure factor file.”
References
- J. Rogan, D. Poleti, and L. Karanović, "Synthesis, Structure, and Thermal Properties of Two New Inorganic‐organic Framework Compounds: Hexaaqua(<i>μ</i><sub>2</sub>‐1,2,4,5‐benzenetetracarboxylato)‐bis(<i>N</i>,<i>N′</i>‐1,10‐phenathroline)dicobalt(II) Dihydrate and Hexaaqua(<i>μ</i><sub>2</sub>‐1,2,4,5‐benzenetetracarboxylato)‐bis(<i>N</i>,<i>N′</i>‐2,2′‐dipyridylamine)dinickel(II) Tetrahydrate", Zeitschrift für anorganische und allgemeine Chemie, vol. 632, pp. 133-139, 2005. https://doi.org/10.1002/zaac.200500292
- P. Das, C.K. Jain, S.K. Dey, R. Saha, A.D. Chowdhury, S. Roychoudhury, S. Kumar, H.K. Majumder, and S. Das, "Synthesis, crystal structure, DNA interaction and in vitro anticancer activity of a Cu(<scp>ii</scp>) complex of purpurin: dual poison for human DNA topoisomerase I and II", RSC Adv., vol. 4, pp. 59344-59357, 2014. https://doi.org/10.1039/c4ra07127a
Tags:Carbon, chemical bonding, Chemistry, Cyclopentadienyl anion, Graphite, Hydrogen bond, Intermolecular forces, Nature, Organic chemistry, search query, Stacking, Supramolecular chemistry, VDW
Posted in crystal_structure_mining | 1 Comment »
Thursday, April 6th, 2017
Enols are simple compounds with an OH group as a substituent on a C=C double bond and with a very distinct conformational preference for the OH group. Here I take a look at this preference as revealed by crystal structures, with the theoretical explanation.
First, a search of the Cambridge structure database (CDS), using the search query shown below (DOI: 10.14469/hpc/2429)
The first search (no errors, no disorder, R < 0.05) is unconstrained in the sense that the HO group is free to hydrogen bond itself. The syn conformer has the torsion of 0° and it has a distinct preponderance over the anti isomer (180°). There is the first hint that the most probable C=C distance for the syn isomer may be longer than that for the anti, but this is not yet entirely convincing.
To try to make it so, a constrained search is now performed, in which only structures where the HO group has no contact (hydrogen bonding) interaction are included. This is achieved using a “Boolean” search;
The number of hits approximately halves, but the proportion of syn examples increases considerably. There is an interesting double “hot-spot” distribution, which amplifies the lengthening of the C=C bond compared to the anti orientation.
The next constraint added is that the data collection must be <100K (to reduce thermal noise) which reduces the hits considerably but now shows the lengthening of the C=C bond for the syn isomer very clearly.
A final plot is of the C=C length vs the C-O length (no temperature, but HO interaction constraint). If there were no correlation, the distribution would be ~circular. In fact it clearly shows that as the C=C bond lengthens, the C-O bond contracts.
Now for some calculations (ωB97XD/Def2-TZVPP, DOI: 10.14469/hpc/2429) which reveal the following:
- The free energy of the syn isomer is 1.2 kcal/mol lower than that of the syn. The effect is small, and hence easily masked by other interactions such as hydrogen bonding to the OH group. Hence the reason why removing such interactions from the search above increased the syn population compared to anti.
- The syn C=C bond length (1.325Å) is longer than the anti (1.322Å).
- The syn isomer has one unique σO-Lp/σ*C-C NBO orbital interaction (below) with a value of E(2) 7.7 kcal/mol, which is absent in the anti form. As it happens, a πO/π*C=C interaction is present in both forms but is also stronger in the syn isomer (E(2)= 46.8 vs 44.2 kcal/mol).
| unoccupied NBO, σ*C-C |
|
| Occupied NBO, σO-Lp |
 |
- The overlap of the filled σO-Lp with the empty σ*C-C orbital is shown below (blue overlaps with purple, red overlaps with orange).
To view the overlap in rotatable 3D, click on any of the colour diagrams above.‡
It is nice to see how experiment (crystal structures) and theory (the calculation of geometries and orbital interactions) can quickly and simply be reconciled. Both these searches and the calculations can be done in just one day of “laboratory time” and I think it would make for an interesting undergraduate chemistry lab experiment.
‡ This visualisation uses Java. Increasingly this browser plugin is becoming more onerous to activate (because of increased security) and some browsers do not support it at all. The macOS Safari browser is one that still does, but you do have to allow it via the security permissions.
Tags:Chemical bond, chemical bonding, Chemistry, Conformational isomerism, constrained search, Enol, free energy, Gauche effect, Hydrogen bond, Isomerism, Java, Physical organic chemistry, search query, Stereochemistry, Supramolecular chemistry
Posted in crystal_structure_mining, reaction mechanism | 2 Comments »
Saturday, December 31st, 2016
My holiday reading has been Derek Lowe’s excellent Chemistry Book setting out 250 milestones in chemistry, organised by year. An entry for 1920 entitled hydrogen bonding seemed worth exploring in more detail here.
As with many historical concepts, it can often take a few years to coalesce into something we would readily recognise today, and hydrogen bonds are no exception. Wikipedia is another source of the history and it cites a 1912 article as the origin of the term in relation to the solvation of amines[1] but also notes that the better known setting of water occurs later in 1920.[2] Here I try to capture the essence of the concept with a few diagrams taken from these two articles.
Firstly “The state of amines in aqueous solution“[1] which is mostly concerned with the measurement of ionization constants of primary, secondary and tertiary amines. It boils down to the below:
and the connection to ionization is laid out as:
Since in 1912, Lewis’ electron pair theory of the covalent bond had not yet emerged, the authors use the terms “strong union” and “weak union”, and of course it is the “weak union” that we now know of as the hydrogen bond. Some other comments about this seminal diagram:
- The article contains the very explicit and modern term stereochemical, which is used in a manner that suggests it was already common.‡ But there is only a hint at most that the nitrogen atoms might be tetrahedral, or that the “weak union” between (what we now think of as the lone pair on) the nitrogen and the hydrogen of the water is directional.
- The second weak union between the tetramethyl ammonium (which we now describe as a cation) and the hydroxide (now described as an anion; both terms are however implied by the description strong electrolyte) is probably not what we would now call a hydrogen bond, more an intimate ion-pair.
The second article in 1920 on water itself[2] is post-Lewis, but perhaps applied in a manner which we would not entirely agree with nowadays. Thus dinitrogen, N≡N is shown as below with just a single connecting bond.
Then we get the interaction between ammonia and water,† analogous to the example shown above:
and for water itself:♠
which in each case shows the central hydrogen having what we now call a valence shell of four electrons,♣ and hence more equivalent to the “strong unions” above. This shows that in 1920 chemists were rapidly adopting Lewis’ representations, but not always entirely successfully.
On balance, I think the 1912 article sets out the modern concept of a hydrogen bond representing a weak union to a hydrogen rather better than the Latimer and Rodebush attempt (at least diagrammatically).
‡Stereochemical notation is discussed in this post, and it dates from the 1930s.
†The modern take is explored here, in which the equilibrium set up between a “weak union” between ammonia and water (the weak electrolyte) and an isomeric “strong union” which represents ionization into an ammonium hydroxide ion-pair (the strong electrolyte) is favoured for the former by ΔG ~6 kcal/mol.
♠The equilibrium between a “weak union” of two water molecules and the fully ionized strong union of hydronium hydroxide favours the former by ΔG ~23 kcal/mol.
♣ This 1920 representation does imply symmetry for the hydrogen, being ~equally disposed between the two oxygens. We now know that such symmetric hydrogen bonding is not unusual (see this post for how to fine-tune a hydrogen bond into this situation) but rather than requiring four electrons as implied in the diagram above, it is now better described as a three-centre-two-electron bond instead.
References
- T.S. Moore, and T.F. Winmill, "CLXXVII.—The state of amines in aqueous solution", J. Chem. Soc., Trans., vol. 101, pp. 1635-1676, 1912. https://doi.org/10.1039/ct9120101635
- W.M. Latimer, and W.H. Rodebush, "POLARITY AND IONIZATION FROM THE STANDPOINT OF THE LEWIS THEORY OF VALENCE.", Journal of the American Chemical Society, vol. 42, pp. 1419-1433, 1920. https://doi.org/10.1021/ja01452a015
Tags:10.1021, aqueous solution, Chemical bond, chemical bonding, Chemistry, Derek Lowe, Hydrogen, Hydrogen bond, Intermolecular forces, Lowe's, Nature, Supramolecular chemistry
Posted in Historical | 2 Comments »
Saturday, December 31st, 2016
My holiday reading has been Derek Lowe’s excellent Chemistry Book setting out 250 milestones in chemistry, organised by year. An entry for 1920 entitled hydrogen bonding seemed worth exploring in more detail here.
As with many historical concepts, it can often take a few years to coalesce into something we would readily recognise today, and hydrogen bonds are no exception. Wikipedia is another source of the history and it cites a 1912 article as the origin of the term in relation to the solvation of amines[1] but also notes that the better known setting of water occurs later in 1920.[2] Here I try to capture the essence of the concept with a few diagrams taken from these two articles.
Firstly “The state of amines in aqueous solution“[1] which is mostly concerned with the measurement of ionization constants of primary, secondary and tertiary amines. It boils down to the below:
and the connection to ionization is laid out as:
Since in 1912, Lewis’ electron pair theory of the covalent bond had not yet emerged, the authors use the terms “strong union” and “weak union”, and of course it is the “weak union” that we now know of as the hydrogen bond. Some other comments about this seminal diagram:
- The article contains the very explicit and modern term stereochemical, which is used in a manner that suggests it was already common.‡ But there is only a hint at most that the nitrogen atoms might be tetrahedral, or that the “weak union” between (what we now think of as the lone pair on) the nitrogen and the hydrogen of the water is directional.
- The second weak union between the tetramethyl ammonium (which we now describe as a cation) and the hydroxide (now described as an anion; both terms are however implied by the description strong electrolyte) is probably not what we would now call a hydrogen bond, more an intimate ion-pair.
The second article in 1920 on water itself[2] is post-Lewis, but perhaps applied in a manner which we would not entirely agree with nowadays. Thus dinitrogen, N≡N is shown as below with just a single connecting bond.
Then we get the interaction between ammonia and water,† analogous to the example shown above:
and for water itself:♠
which in each case shows the central hydrogen having what we now call a valence shell of four electrons,♣ and hence more equivalent to the “strong unions” above. This shows that in 1920 chemists were rapidly adopting Lewis’ representations, but not always entirely successfully.
On balance, I think the 1912 article sets out the modern concept of a hydrogen bond representing a weak union to a hydrogen rather better than the Latimer and Rodebush attempt (at least diagrammatically).
‡Stereochemical notation is discussed in this post, and it dates from the 1930s.
†The modern take is explored here, in which the equilibrium set up between a “weak union” between ammonia and water (the weak electrolyte) and an isomeric “strong union” which represents ionization into an ammonium hydroxide ion-pair (the strong electrolyte) is favoured for the former by ΔG ~6 kcal/mol.
♠The equilibrium between a “weak union” of two water molecules and the fully ionized strong union of hydronium hydroxide favours the former by ΔG ~23 kcal/mol.
♣ This 1920 representation does imply symmetry for the hydrogen, being ~equally disposed between the two oxygens. We now know that such symmetric hydrogen bonding is not unusual (see this post for how to fine-tune a hydrogen bond into this situation) but rather than requiring four electrons as implied in the diagram above, it is now better described as a three-centre-two-electron bond instead.
References
- T.S. Moore, and T.F. Winmill, "CLXXVII.—The state of amines in aqueous solution", J. Chem. Soc., Trans., vol. 101, pp. 1635-1676, 1912. https://doi.org/10.1039/ct9120101635
- W.M. Latimer, and W.H. Rodebush, "POLARITY AND IONIZATION FROM THE STANDPOINT OF THE LEWIS THEORY OF VALENCE.", Journal of the American Chemical Society, vol. 42, pp. 1419-1433, 1920. https://doi.org/10.1021/ja01452a015
Tags:10.1021, aqueous solution, Chemical bond, chemical bonding, Chemistry, Derek Lowe, Hydrogen, Hydrogen bond, Intermolecular forces, Lowe's, Nature, Supramolecular chemistry
Posted in Historical | 2 Comments »
Wednesday, June 22nd, 2016
I previously used data mining of crystal structures to explore the directing influence of substituents on aromatic and heteroatomatic rings. Here I explore, quite literally, a different angle to the hydrogen bonding interactions between a benzene ring and OH or NH groups.
I start by defining a benzene ring with a centroid. The distance is from that centroid to the H atom of an OH or NH group and the angle is C-centroid-H. To limit the search to approach of the OH or NH group more or less orthogonal to the ring, the absolute value of the torsion between the centroid-H vector and the ring C-C vector is constrained to lie between 70-100° (the other constraints being no disorder, no errors, T < 140K and R < 0.05).[1]
The above shows the results for NH groups interacting with the aromatic ring. The maximum distance 2.8Å is more or less the van der Waals contact distance between a hydrogen and a carbon and as you can see the contacts "funnel down" to the centroid at < 2.1Å. The shortest distance[2] is for ammonium tetraphenylborate, which you can view in e.g. spacefill mode here[3]
The other interesting close contact derives from a protonated pyridine[4], which can in turn be viewed here.[5] The main message from the distribution shown above is that as the distances between the HN and the centroid get shorter, the "trajectory" of approach remains orthogonal to the ring (the angle defined above remains ~90°) and heads towards the centroid of the π-cloud. The hotspot itself (red, ~2.6Å) also lies along this trajectory.
Recollect that when I used such hydrogen bonding to see if crystal structures discriminate between the ortho or meta positions of a ring carrying an electron donating substituent, it was the distance from a HO to the carbon that was measured as the discriminator. So it's a faint surprise to find that with HN, and without the necessary perturbation of an electron donating substituent, the intrinsic preference seems to be for the ring centroid and not any specific carbon atom of the ring.
So how about the OH group? There are in fact rather fewer examples, and so the statistics are a bit less clear-cut. But there is a tantalising suggestion that this time, the trajectory is not ~90° but rather less, implying that the destination is no longer the centroid of the π-cloud but one of the carbon atoms of the ring itself. For those who like to "read between the lines" and spot things that are absent rather than present, you may have asked yourself why I did not use NH probes in my earlier post. Well, it appears that the NH group is less effective at e.g. o/p discrimination than is an OH group.
I can only speculate as to the origins (real or not) of the difference in behaviour between OH and NH groups towards a phenyl π-face. Perhaps it is simply bias in the CSD database? Or might there be electronic origins? Time to end with that phrase "watch this space".
References
- H. Rzepa, "How does an OH or NH group approach an aromatic ring to hydrogen bond with its Ï-face?", 2016. https://doi.org/10.14469/hpc/673
- T. Steiner, and S.A. Mason, "Short N<sup>+</sup>—H...Ph hydrogen bonds in ammonium tetraphenylborate characterized by neutron diffraction", Acta Crystallographica Section B Structural Science, vol. 56, pp. 254-260, 2000. https://doi.org/10.1107/s0108768199012318
- Steiner, T.., and Mason, S.A.., "CCDC 144361: Experimental Crystal Structure Determination", 2000. https://doi.org/10.5517/cc4v6tz
- O. Danylyuk, B. Leśniewska, K. Suwinska, N. Matoussi, and A.W. Coleman, "Structural Diversity in the Crystalline Complexes of <i>para</i>-Sulfonato-calix[4]arene with Bipyridinium Derivatives", Crystal Growth & Design, vol. 10, pp. 4542-4549, 2010. https://doi.org/10.1021/cg100831c
- Danylyuk, O.., Lesniewska, B.., Suwinska, K.., Matoussi, N.., and Coleman, A.W.., "CCDC 819118: Experimental Crystal Structure Determination", 2011. https://doi.org/10.5517/ccwhc5w
Tags:10.1021, 10.1107, 10.5517, aromaticity, benzene, Centroid, chemical bonding, data mining, Functional groups, Hydrogen bond, Physical organic chemistry, Pyridine, Simple aromatic rings, Supramolecular chemistry
Posted in Chemical IT, crystal_structure_mining | 3 Comments »
The intra-molecular plot shows a similar value for the most common F…H distance, with the interesting variation that the angle subtended at F is about 80°.
The outlier at the short end of the spectrum (arrow) was observed in 2014[2] with the structure shown below. It is indeed the current record holder by some margin! This length by the way is however a great deal longer than the shortest O…HO hydrogen bonds, which can be in the region of 1.2Å (with the proton sometimes symmetrically disposed between the two oxygen atoms). The value is also very similar to the record holder for the shortest C-H…H-C interaction.
