Isotopically-Labeled Solid-State Vibrational Mode Energies And Intensities In Crystal09 – A Simple How-To

The generation of isotopically-substituted molecular crystal spectra has become a point of interest, which means blog post. To be clear, this is for cases where isotopic substitution does not affect the crystal geometry – the crystal cell does not change significantly upon deuteration (and for those who believe isotopic substitution never leads to significant changes in the solid, I refer you Zhou, Kye, and Harbison’s article on Isotopomeric Polymprphism and their work on 4-methylpyridine pentachlorophenol, which changes dramatically upon deuteration. I beat on this point because blindly assuming of the crystal cell geometry in such cases will produce spectra noticeably different than measured. It’s NOT the calculation’s fault!).

The generation of isotopically-substituted spectra and intensities in Crystal09 is trivial provided that you KEEP THE FREQINFO.DAT FILE. In fact, you need keep ONLY the FREQINFO.DAT to generate these spectra, which greatly reduces file transfer loads and allows for the scripted calculation of new vibrational spectra and thermodynamic data post-frequency calculation.

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25 November 2010 Cover Art For The Journal Of Physical Chemistry A – “Computation Of Deuterium Isotope Perturbation Of 13C NMR Chemical Shifts of Alkanes: A Local Mode Zero Point Level Approach”

A bit of a sneak preview and a chance to get a second use out of an instructive pair of potentials. This new cover for an upcoming article by Kin Yang and Bruce Hudson expands upon the previous Deuterium-for-Hydrogen substitution study summarized on the blog page (and in a publication of the same name) Vicinal Deuterium Perturbations on Hydrogen NMR Chemical Shifts in Cyclohexanes. In brief, exchanging a hydrogen for a deuterium alters 13C NMR spectra because the deuterium, being twice the mass, has a narrower nuclear probability distribution. If the C-H/D stretching potential were harmonic (symmetric on both the elongation and contraction sides), this would produce no effect. As this stretching potential is anharmonic (as shown below and the background of the above image), the actual average positions of the D and H differ slightly (but enough!), with the C-D bond being, on average, slightly shorter than C-H (something that a quantum chemical calculation will not tell you without treating the nuclei as quantum mechanical objects). Different average bond length, different affect on a bound 13C.

A bit more explanation can be found at

The studies continue, limited largely by the number of simple hydrocarbons with high-quality NMR spectra (and selective deuteration).