I am trying to correlate the IR spectrum and single crystallography data.
In single crystal IR spectra, I found some inter-molecular hydrogen bonds were stronger (from wavenumber shift), and I think the different hydrogen bond strengths are due to different crystal packing. (At least in single molecule quantum calculations, the -OH wavenumbers are mostly the same)
Is it reasonable that I run QM/MM based on the single crystal molecular geometries (.cif files) and calculate the -OH vibration (freq) to correlate with experimental IR data?
I am not familiar of how single crystal technician actually grab the .cif data, so I am wondering if the cif. files that I received are actually reflecting the molecular packing in real.
Hi Bright Emenike,
1. I did my best while designing the molecules, such as breaking resonance structure between substitutions and -OH…; The single molecules in QM are having mostly same -OH frequency; In very diluted IR sample, the frequencies were mostly the same as well.
2. Yes my hypothesis was now based on the crystal packing style. But I want to confirm the cif reflects actual molecular packing, if yes, then I’ll only continue QM/MM based on cif geometries.
Thanks.
Hello dear RG members,
the strength of hydrogen bonds in solid state structures is indeed strongly influenced by the donor(D)-acceptor(A) distances in a D-H...A bridge.
https://doi.org/10.1002/(SICI)1097-0134(19990515)35:33.0.CO;2-V
The D...A distances in strong hydrogen bonds are at 230-250pm and lead to a lengthening of the O-H bond and a shift to smaller frequencies. The D...A distances in weak hydrogen bonds are at 270-300pm.
Thus, it makes sense to look precisely at the chemical environment of the OH groups within the solid state structure and to take it into account for quantum chemical calculations. The .cif file contains the coordinates of all atoms within the unit cell. With appropriate programs, e.g. DIAMOND, the structure can be visualized and distances to neighboring atoms can be determined. However, the .cif file does not contain any direct information about bond lengths and molecular packing, but these result from the atomic coordinates and symmetry encodings.
I hope that my contribution can help.
Dear Florian Morsbach:
Thanks, this is a very helpful reference to me.
And yes, I'm aware of the missing bond length of -XH in single crystal x-ray, I think in my case, QM/MM will solve the problem. But I'll also think about ssNMR as well.