Solid-State DFT Of The THz Spectrum Of HMX Is (In) Science!

Six years as a card-carrying member finally paid off this week as my new favorite editor Gilbert Chin selected the HMX THz DFT paper (posted below) that just came out in J. Phys. Chem. A as an AOK Editor’s Choice in Science magazine. So far as I know, this page is publicly accessible without subscription, although I do encourage you to join the A.A.A.S. and help us all push this boulder that is U.S. research up the North face of Mt. Everest.

So what?” you may ask. Terahertz (THz) spectroscopy is a technique that allows one to study vibrations in the zero-ish to few hundred wavenumber region, which is exactly where molecules undergo their largest-amplitude, lowest-frequency motions. I made mention back in an NCSA Access Magazine article concerning the same subject (regarding neutron spectroscopy) that…

“Molecules feel the same physical constraints from crystal packing that someone on the subway would from other passengers. If you take that person on the subway and put them on a bumpy track, where they move and how far they move will be determined by where everyone else is. Their restricted motion on a crowded subway will look very different to an observer than their motion on a bumpy track if the car was empty of other people. We see those differences when comparing vibrational spectra of isolated molecules with crystalline solids and, therefore, learn about the environment of the molecule in the crystal.”

When the molecules aren’t involved in strong electrostatic interactions, the high frequency molecular vibrational modes in crystals usually occur close to the gas-phase molecular vibrational frequency. That is to say, peaks shift somewhat, but they usually reside close to their gas-phase values. In the low-frequency molecular modes (to 300 cm-1 or so), having an array of neighboring molecules closely spaced to one another DOES affect the positions of molecular vibrations, because these large-amplitude motions occur in constrained environments. There’s a difference between kicking out your leg and twiddling your fingers in an elevator. Further, the molecular vibrations within a molecular crystal cell are not only a result of molecular motions, but also the relative motions between neighboring molecules, which isolated-molecule calculations, surprise, can’t account for. Having two neighboring molecules rotate clockwise is different than having one rotate clockwise and the other counterclockwise. The 3 translational and 3 rotational motions molecular vibrational spectroscopists throw out in their 3n-6 mode count are THE motions of impact in the phonon region. In the figure below, the red lines are the molecular normal modes calculated at a VWNBP/DNP level of theory. The blue lines are the normal modes of the crystal cell at the same theory level, which show much more structure. The smooth blue line is a simple Lorentzian lineshape of the calculated solid-state modes.

So, for the scientists who didn’t go “well, yeah”, it is shown that theory-based solid-state THz spectroscopy assignments are suspect (at best, useless at worst) when not performed by solid-state quantum chemical methods. For everyone else, there’s little need to detail in this day and age the utility of detecting high-energy explosives by… non-invasive spectroscopic (at a distance!) methods.

I also find it mildly amusing that the experimental THz piece is under physics, and the theoretical THz piece is under chemistry.

www.sciencemag.org/content/vol311/issue5761/twil.dtl
pubs.acs.org/journals/jpcafh/index.html
access.ncsa.uiuc.edu/Stories/crystalforms

The Inelastic Neutron Scattering Spectrum Of Cs2[B12H12]: Reproduction Of Its Solid-State Vibrational Spectrum By Periodic DFT

In press, available from the Journal of Physical Chemistry A. The INS experiment was carried out using the TOSCA instrument across the pond at the ISIS facility of the Rutherford Appleton Laboratory. The solid-state calculations were performed, as usual, with DMol3 from Accelrys. The paper was presented originally at the 2005 ACS DC meeting, available in the posters page on this site. Another example of theory and vibrational spectroscopy generating a far more complete picture than crystallography alone.

D. G. Allis and B. S. Hudson

Abstract: The inelastic neutron scattering (INS) spectrum of polycrystalline Cs2[B12H12] is assigned through 1200 cm-1 based on aqueous and solid-state Raman/IR measurements and normal mode analyses from solid-state density functional theory. The Cs+ cations are responsible for frequency shifts of the internal cage vibrational modes and Ih cage mode splittings due to the crystal Th site symmetry. These changes to the [B12H12]-2 molecular modes make isolated molecule calculations inadequate for use in complete assignments. Solid-state calculations reveal that 30/40 cm-1 shifts of Tg/Hg molecular modes are responsible for structure in the INS spectrum unobserved by optical methods or in aqueous solutions.

www.isis.rl.ac.uk/molecularspectroscopy/tosca
www.isis.rl.ac.uk
www.accelrys.com

Nanotech Gallery And Development Migration To nanoENGINEER-1

Yes, yes, I know. After all, I do work for the company. Why WOULDN’T I use the program?! The development of nanoENGINEER-1 is going tremendously well. Now on the verge of another alpha release, I decided, in the interest of seeing what kind of imagery functionality the package might benefit from, to see if I could make the old Nanotech Gallery happen with the new software.

I could not be happier with the results.

The problems to date are all with Povray. That is, my amateur understanding of it. As an order of alignment, I was doing all of my graphic work with VMD, which is still the method of choice for biomolecular images (mostly because I’m still using NAMD/Charmm for my occasional forays into drug development). It’s a tall order to replicate the quality of graphics VMD is capable of, but it’s clear (to me, anyway) that nE-1 is more than up to the challenge.