HomeChemistry3-Methyl-5-phenylpyrazole: a crystallographic enigma? | Henry Rzepa's Weblog

3-Methyl-5-phenylpyrazole: a crystallographic enigma? | Henry Rzepa’s Weblog

Beforehand, I explored the weird construction of a molecule with a hydrogen bonded interplay between a phenol and a pyridine. The crystal construction identify was RAKQOJ and it had been reported as having virtually symmetrical N…H…O hydrogen bonds. This function had been decided utilizing neutron diffraction crystallography, which is assumed very dependable at figuring out proton positions. One other compound with these traits is 3-methyl-5-phenylpyrazole or MEPHPY01.[1] Right here the neutron examine confirmed it to apparently have the construction represented under, the place the stable N-H strains point out a proton equidistant between two nitrogens.

Inspection of the ORTEP plot exhibits a really odd function; the thermal elipsoids (purple arrow) for 2 of the N-H-N motifs are kind of spherical, indicating little thermal movement (the temperature of the dedication just isn’t famous, and is assumed as most likely room temperature) however the different two (magenta arrows) are extremely elongated within the course of movement between the 2 nitrogen atoms. This function was largely unexplained on the time of publication (1975) and certainly to today. Right here I provide a attainable perception into this enigma.

The traditional construction is proven under displaying 4 N-H bonds and 4 H…N hydrogen bonds.

So now for the outcomes of some calculations. Computed at numerous B3LYP(±GD3BJ)/Def2-SVPP/Def2-TZVPP ranges (Desk, FAIR information DOI: 10.14469/hpc/10406), the situated minimal within the complete power, saddle=0, corresponds to the traditional proton-localized construction proven above, the place all 4 hydrogens are firmly hooked up to the 4 nitrogen atoms by an everyday bond and the distances are 1.032 for the NH and 1.855Å for the hydrogen bond it kinds. A zwitterionic isomer contains the ion-pair proven under, examples of every part of that are identified within the CSD (crystal construction database). 

There are 3 ways of distributing this motif, of which solely 1 is secure to proton switch. Construction 2 has a better diploma of cost separation while 3 superficially seems to cut back the diploma of cost separation in comparison with 1. The truth is, the three-dimensional construction of 1 permits the destructive ion to stack above the optimistic ion, thus truly reaching minimal separation of costs.

The stacking additionally is dependent upon the kind of calculation. If dispersion correction is included, the fragrant faces stack instantly above one another (as above). If omitted, the stacking truly corresponds extra intently to that noticed within the reported crystal construction, for the reason that attraction between faces happens not solely inside a construction however between adjoining buildings within the stable state (one thing not modelled when the dispersion correction is utilized solely to a single unit).

The lesson learnt from the earlier put up is that the place of protons as decided by quantum-chemical geometry location utilizing minimisation of the full computed power is likely to be deceptive. Higher maybe to make use of the computed free power? When that is accomplished, as we noticed within the earlier put up, the transition state for proton switch as situated within the complete power floor can even have a free power that’s decrease than that of the full power minimal. So, for MEPHPY01, a stationary level by which all 4 hydrogens correspond to the apparently symmetrical experimental neutron diffraction construction emerges as saddle=3, corresponding to 3 drive constants being destructive. The bond lengths for this geometry happen in pairs, two with NH 1.25/N…H 1.30 and two with 1.28/1.28, revealing attention-grabbing asymmetry.

The traditional vibrational modes for these three -ve drive constants are proven under. The primary (ν 1315i cm-1) exhibits all 4 hydrogens exchanging between nitrogens, a quadruple proton switch. The second (ν 896i cm-1) exhibits a double proton switch between one pair exchanging between two nitrogens and the final (ν 801i cm-1) is analogous in type, however exhibits the opposite pair exchanging between a second totally different pair of nitrogens. These final two vibrational modes correspond to the very thermal ellipsoids seen within the crystal construction diagram on the high, the place one pair of hydrogens present little movement and the opposite pair includes a lot larger movement between a pair of nitrogen atoms.This may correspond to formation of a species exhibiting two standard NH…H hydrogen bonds and two symmetrical N…H…N models.


Two additional stationary factors similar to saddle=2 and saddle=1 may also be situated (Desk).

stationary factors B3LYP+GD3BJ/gasoline B3LYP+GD3BJ/DCM B3LYP/gasoline
SVPP, saddle=0, impartial -1984.448365(0.0) -1984.460070(0.0) -1984.241838(0.0)
SVPP, saddle=0, ion-pair -1984.426827(13.5) -1984.439305(13.0) -1984.218379(14.7)
TZVPP, saddle=0, impartial -1986.712743(0.0) -1986.725277 (0.0) -1986.509333(0.0)
TZVPP, saddle=0, ion-pair -1986.688467(15.2) -1986.703562 (13.6)  -1986.481384(17.5)

SVPP, saddle=1 -1984.428898(12.1) -1984.442004(11.3) -1984.220238(13.6)
SVPP, saddle=2 -1984.430085(11.5) -1984.442986(10.7) -1984.220968(13.1)
SVPP, saddle=3 -1984.431457(10.6)
1315, 896, 801
970, 603, 294
-1984.223176 (11.7)
1335, 782, 760
TZVPP, saddle=1 -1986.691518(13.2)
TZVPP, saddle=2 -1986.689979(14.3)
TZVPP, saddle=3

Now right here is the wacky factor. On the gasoline section SVPP foundation set ± dispersion ranges, these lower-order saddle factors are literally HIGHER in free power than the third order saddle level! Standard knowledge is that the upper the order of the saddle level, the upper ought to its power be! I’m not conscious of anybody reporting an inverse remark earlier than. The impact nevertheless is solvation and in addition basis-set dependent, since including dichloromethane as a continuum solvent adjustments the free power minimal from the third to the second-order saddle level. It’d nicely even be depending on the density purposeful technique.

What are we to conclude? The free power boundaries for all of the proton switch saddle factors computed above should not that small, being ≥ 10 kcal/mol. However at room temperatures, these exchanges will in reality be quick kinetic processes and the measured impartial diffraction construction might nicely emerge as averaged in a roundabout way. The free energies of the upper order saddle factors suggests the dynamics of this technique might in reality be very complicated and really totally different from any “regular” hydrogen bonded system. That is clearly not the ultimate phrase but, but it surely does trace that the proton switch dynamics of 3-Methyl-5-phenylpyrazole could also be a system very nicely value taking a look at once more! And certainly exploring how strong the results famous above are to totally different density functionals.

This put up has DOI: 10.14469/hpc/10512



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