diffraction – welcome to somewhereville (.com)

"I'm high on life… and PCP." – Mitch Hedberg

In press, in the Journal of Physical Chemistry A. If the current rosters of pending manuscripts and calculations are any indication, this PCP paper will mark the near end of my use of DMol³ for the prediction (and experimental assignment) of terahertz (THz) spectra (that said, it is still an excellent tool for neutron scattering spectroscopy and is part of several upcoming papers).

While the DMol³ vibrational energy (frequency) predictions are generally in good agreement with experiment (among several density functionals, including the BLYP, BOP,VWN-BP, and BP generalized gradient approximation density functionals), the use of the difference-dipole method for the calculation of infrared intensities has shown itself to be of questionable applicability when the systems being simulated are charged (either molecular salts (such as PCP.HCl) or zwitterions (such as the many amino acid crystal structures)). The previously posted ephedrine paper (in ChemPhysChem) is most interesting from a methodological perspective for the phenomenal agreement in both mode energies AND predicted intensities obtained using Crystal06, another solid-state density functional theory program (that has implemented hybrid density functionals, Gaussian-type basis sets, cell parameter optimization and, of course, a more theoretically sound prediction of infrared intensities by way of Born charges). The Crystal06 calculations take, on average, an order of magnitude longer to run than the comparable DMol³ calculations, but the slight additional gain in accuracy for good density functionals, the much greater uniformity of mode energy predictions across multiple density functionals (when multiple density functionals are tested), and the proper calculation of infrared intensities all lead to Crystal06 being the new standard for THz simulations.

After a discussion with a crystallographer about what theoreticians trust and what they don't in a diffraction experiment, the topic of interatomic separation agreement between theory and experiment came up in the PCP.HCl analysis performed here (wasn't Wayne). As the position of hydrogen atoms in an X-ray diffraction experiment are categorically one of those pieces of information solid-state theoreticians do NOT trust when presented with a cif file, I reproduce a snippet from the paper considering this difference below (and, generally, one will not find comparisons of crystallographically-determined hydrogen positions and calculated hydrogen positions in any of the THz or inelastic neutron scattering spectroscopy papers found on this blog).

The average calculated distance between the proton and the Cl^– ion is 2.0148 Angstroms, an underestimation of nearly 0.13 Angstroms when compared to the experimental data. This deviation is likely strongly tied to the uncertainly in the proton position as determined by the X-ray diffraction experiment and is, therefore, not used as a proper metric of agreement between theory and experiment. The distance from the nitrogen atom to the Cl^– ion has been determined to be an average of 3.0795 Angstroms, which is within 0.002 Angstroms of the experimentally determined bond length. This proper comparison of heavy atom positions between theory and experiment indicates that this interatomic separation has been very well predicted by the calculations.

Patrick M. Hakey, Matthew R. Hudson, Damian G. Allis, Wayne Ouellette, and Timothy M. Korter

Department of Chemistry, Syracuse University, Syracuse, NY 13244-4100

The terahertz (THz) spectrum of phencyclidine hydrochloride from 7.0 – 100.0 cm^-1 has been measured at cryogenic (78 K) temperature. The complete structural analysis and vibrational assignment of the compound have been performed employing solid-state density functional theory utilizing eight generalized gradient approximation density functionals and both solid-state and isolated-molecule methods. The structural results and the simulated spectra display the substantial improvement obtained by using solid-state simulations to accurately assign and interpret solid-state THz spectra. A complete assignment of the spectral features in the measured THz spectrum has been completed at a VWN-BP/DNP level of theory, with the VWN-BP density functional providing the best-fit solid-state simulation of the experimentally observed spectrum. The cryogenic THz spectrum contains eight spectral features that, at the VWN-BP/DNP level, consist of fifteen infrared-active vibrational modes. Of the calculated modes, external crystal vibrations are predicted to account for 42% of the total spectral intensity.

Accepted in Physical Chemistry Chemical Physics. Quite possibly the hardest-fought article within the peer review process I've found myself on the revision-side of, with an interesting debate between we authors and two crystallography reviewers occurring over three total revisions (and, it should be noted, two of the three original reviewers accepted the article without any revision, so this really was a debate between we authors and the crystallography reviewers).

To briefly summarize (as the content of the controversy is part of ongoing work), the paper includes an inelastic neutron scattering (INS) spectrum at 25 K, a new X-ray diffraction study at 90 K, and 77 K and 293 K Raman spectra. The INS spectrum and 77 K Raman spectrum contain a feature at 450 cm^-1 that does not occur at higher temperature and that is not predicted by the solid-state density functional theory simulation with the 90 K structure. The proposed argument is that a proton is either shifted from an alanine -NH₃⁺ group to a nitrate oxygen (which the crystallography reviewers generally refused to accept as a reasonable explanation) or the potential energy surface for this proton between the -NH₃⁺ and nitrate oxygen is changed considerably due to contraction of the unit cell at low temperature (which our 90 K crystal structure does not show and so, if it occurs, must occur at lower temperature).

The disagreement between ourselves and the crystallography reviewers concerns the use of the 90 K structure as a basis for proposing full proton motion from alanine to nitrate. On the one hand, the 90 K structure solves with the protons on the alanine and so, to the extent that one can extrapolate from a single point, there is a notable absence of crystallographic data to confirm that proton motion is occurring. On the other hand, the spectroscopic change (new peak at 450 cm^-1) is entirely consistent with the proposed proton motion to the nitrate OR the marked change in the shape of the potential well for the proton motion between the -NH₃⁺ and nitrate oxygen. We expect this mystery to be solved with a very low temperature neutron diffraction study to determine exactly where the proton resides at 25 (or so) K.

Matthew R. Hudson, Damian G. Allis, Wayne Ouellette, and Bruce S. Hudson

Department of Chemistry, 1-014 Center for Science and Technology, Syracuse University, Syracuse, NY 13244-4100, USA

Keywords: L-alanine alaninium nitrate, amino acid salt, nonlinear optical material, vibrational spectroscopy, inelastic neutron scattering spectroscopy, solid-state density functional theory

Abstract: The 2:1 amino acid salt of L-alanine with nitric acid was crystallized and the vibrational spectrum measured at 25 K by incoherent inelastic neutron scattering (INS) spectroscopy. The spectrum was simulated using solid-state density functional theory based on a new 90 K structure determination. A feature observed at approximately 450 cm-1 in the experimental spectrum of L-alanine alaninium nitrate is noticeably absent in the calculation. Further investigation by Raman spectroscopy reveals spectral differences between the spectra at 77 and 293 K. The nature of these spectral changes and the disagreement between the INS spectrum and its simulation are discussed in relation to a possible structural change at low (< 90 K) temperature.

www.rsc.org/publishing/journals/cp/Index.asp
en.wikipedia.org/wiki/Crystallography
en.wikipedia.org/wiki/Inelastic_neutron_scattering
en.wikipedia.org/wiki/Raman_spectroscopy
en.wikipedia.org/wiki/Density_functional_theory
en.wikipedia.org/wiki/Alanine
en.wikipedia.org/wiki/Nitrate
en.wikipedia.org/wiki/Potential_energy_surface
en.wikipedia.org/wiki/Neutron_diffraction

Tag: diffraction

Examination of Phencyclidine Hydrochloride via Cryogenic Terahertz Spectroscopy, Solid-State Density Functional Theory, and X-Ray Diffraction

Low-Temperature X-ray Structure Determination and Inelastic Neutron Scattering Spectroscopic Investigation of L-Alanine Alaninium Nitrate, a Homologue of a Ferroelectric Material

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