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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 bizarre construction of a molecule with a hydrogen bonded interplay between a phenol and a pyridine. The crystal construction title 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 strong N-H traces 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 route of movement between the 2 nitrogen atoms. This function was largely unexplained on the time of publication (1975) and certainly to this present day. Right here I supply a potential perception into this enigma.

The standard construction is proven under exhibiting 4 N-H bonds and 4 H…N hydrogen bonds.

So now for the outcomes of some calculations. Computed at varied B3LYP(±GD3BJ)/Def2-SVPP/Def2-TZVPP ranges (Desk, FAIR knowledge DOI: 10.14469/hpc/10406), the situated minimal within the complete vitality, saddle=0, corresponds to the standard 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 element 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 the next diploma of cost separation while 3 superficially seems to scale back the diploma of cost separation in comparison with 1. In reality, the three-dimensional construction of 1 permits the adverse ion to stack above the optimistic ion, thus really reaching minimal separation of expenses.

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

The lesson learnt from the earlier publish is that the place of protons as decided by quantum-chemical geometry location utilizing minimisation of the overall computed vitality could be deceptive. Higher maybe to make use of the computed free vitality? When that is performed, as we noticed within the earlier publish, the transition state for proton switch as situated within the complete vitality floor can even have a free vitality that’s decrease than that of the overall vitality 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 a few pressure constants being adverse. 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 fascinating asymmetry.

The traditional vibrational modes for these three -ve pressure 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 prime, the place one pair of hydrogens present little movement and the opposite pair entails a lot higher 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 can 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
-1984.441075(11.9)
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
-1986.690265(14.1)

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 vitality than the third order saddle level! Standard knowledge is that the upper the order of the saddle level, the upper ought to its vitality be! I’m not conscious of anybody reporting an inverse statement earlier than. The impact nevertheless is solvation and in addition basis-set dependent, since including dichloromethane as a continuum solvent adjustments the free vitality minimal from the third to the second-order saddle level. It would nicely even be depending on the density purposeful methodology.

What are we to conclude? The free vitality boundaries for all of the proton switch saddle factors computed above are usually not that small, being ≥ 10 kcal/mol. However at room temperatures, these exchanges will in actual fact be quick kinetic processes and the measured impartial diffraction construction might nicely emerge as averaged not directly. The free energies of the upper order saddle factors suggests the dynamics of this method might in actual fact 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 publish has DOI: 10.14469/hpc/10512

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