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.
Dear Bryan, the .cif file is the final document which summarizes the results of a single-crystal X-ray structure determination. This is the key document which is e.g. deposited at the Cambridge Structural Database (CSD). For some fundamental information about .cif files please have a look at the following useful article:
The Crystallographic Information File (CIF)
Article The Crystallographic Information File (CIF)
Once you have the .cif file of a structurally characterized compound, you can not only visualize the molecular structure but also the crystals structure including inter-molecular hydrogen bonding networks. As a typical example please have a look at the following publication from our research group:
Supramolecular Layer Structures of Mn(II), Co(II), and Cu(II) Complexes with the 3-(1H-Benzotriazol-1-yl)propaneamide Ligand: Metal Coordination vs Hydrogen Bonding
Article Supramolecular Layer Structures of Mn(II), Co(II), and Cu(II...
This paper is freely available as public full text on RG. I hope this helps answering your interesting technical question. Good luck with your work and best wishes, Frank Edelmann
In addition to what Prof. Edelmann said (no doubt in a .cif file that has passed through a professional crystallographer), I can think of a couple of points which may cause disagreement between spectroscopic and crystallographic results.
1) Measurement temperature: the X-ray diffraction (XRD) data is normally acquired at rather low temperatures (often 170-120 K) to minimize atomic thermal motion. Therefore, it may be important to measure the spectra at the same temperature, as it affects interatomic distances and may even cause phase transitions. If measuring IR at low temperature is technically problematic, the XRD may be measured at ambient temperature.
2) Hydrogen bond strength: one must be careful using single crystal XRD structure to measure hydrogen-heteroatom distances. Routine XRD is a rather poor method to locate hydrogen atoms, because X-rays are scattered on electron density and hydrogens have the lowest density which fades on the background of neighboring heavier atoms, which possess more electrons. Furthermore, even if the electron density of hydrogen atom can be well located (high quality data), usually it will NOT correspond to the position of hydrogen nucleus because the electronegative atoms pull electron density. Therefore the O-H and N-H bonds determined by XRD are always shorter then determined by other methods, such as neutron diffraction or rotational spectroscopy.
The ways to overcome this shortcoming of XRD are to introduce the correction to H-heteroatom bond distances (e.g. in Mercury https://bip.weizmann.ac.il/course/structbioinfo/databases/CCDC_Mercury/mercury.3.143.html) or, even better in my opinion, only measure distances between the heavy atoms.
3) Purity of the sample: XRD structure will usually make an impression that the sample is pure, because it only "sees" the crystal itself but not anything amorphous that may surround the crystal, and small crystalline impurities attached to the main crystal will give only several reflections (signals) which would be discarded during data processing. I'm not familiar with single crystal IR techniques, but in principle IR should "see" both the crystalline and amorphous parts of the sample. Furthermore, of IR measurement is based on reflection rather then transmission, the surface of the sample will give much stronger contribution to the spectrum than the crystalline bulk. I could imagine that some water on the crystal surface, in combination with crystal surface imperfections, may result in obscuring the signals corresponding to H-bonded moieties. (On this point I have no experience, it's only thinking)
Regards,
-Evgeny
Dear Frank Edelmann:
Thanks for the information. I guess in the paper, .cif were used to justify the supramolecular packing style, by identifying intermolecular hydrogen bonding and pi-pi interaction.
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