Archive for July, 2009

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

Wednesday, July 29th, 2009

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

dmol3, neutron scattering spectroscopy, povray, publications, qc/mm/md progs, quantum chemistry, supramolecular chemistry and molecular building blocks | Comments (1)

Some Light Science Reading. The Constellations: Sagittarius

Sunday, July 26th, 2009

As first appeared in the July 2009 edition of the Syracuse Astronomical Society newsletter The Astronomical Chronicle (PDF).

Image generated with Starry Night Pro 6, www.starrynight.com.

The Constellations, for all of their mythological, mystical, and ceremonial significance throughout human history, are also the bases for much of the scientific discovery (the Zodiac was a calendar long before it was ever used to identify the other kind of dates, and the backdrop of the unchanging Heavens served as the guide against which the motions of the planets were first tracked) that fueled our understanding of the universe before Edwin Hubble first exposed its true vastness by identifying the “Andromeda Nebula” as, in fact, a galaxy far outside of the Milky Way. The constellations have also served in a far more pragmatic capacity throughout human history as seasonal sign posts, simply marking times and locations for those on land and sea. Perhaps the most famous example of this in American History is the use of the Big Dipper as the marker by freed slaves traveling North along the Underground Railroad. The song “Follow the Drinkin’ Gourd” is not simply a series of verses, but is instead a set of instructions, with the “Drinkin’ Gourd” being the Big Dipper, the most easily recognizable asterism in the Northern Hemisphere (amateur astronomer or not) and pointer (by drawing an arrow from Merak to Dubhe) to the North Star Polaris, itself the most famous star of the Little Dipper (also known as Ursa Minor), an otherwise somewhat unimpressive constellation (certainly not as prominent in the North as the Big Dipper or the Cassiopeia “W” and, therefore, not as useful a sign post).

The Little Dipper is not the most prominent constellation in the Night Sky, but it serves as an important terrestrial marker because it includes Polaris among its member stars. Just as the Big Dipper is a prominent asterism that directs you to the Little Dipper, the Summer constellation Scorpius (which has been recognized specifically as a scorpion by many cultures for several millennia) can draw you to a slightly less prominent constellation to its West that is a sign post to a far more impressive marker than Polaris.

Sagittarius is an astronomy instructor’s dream constellation, as it wraps up a number of interesting topics of discussion in one easy-to-find location. To begin, the Centaur, a half-human/half-horse hybrid, is the perfect bridge between the fantastical world of mythology in all of its seeming ridiculousness and, well, the shining example of what might even be ridiculously possible as scientists learn more about DNA and biological engineering (as of this past May, we now can make monkeys that glow in the dark. That’s right, in the dark).

Second, Sagittarius provides its viewer another shining example of the difference between a constellation and an asterism. A constellation is, simply, a specific grouping of stars that everyone has agreed are, in fact, assigned to that particular constellation. This circular definition was finally laid flat by the International Astronomical Union in its defining of Constellation Boundaries, solidifying star groupings that go as far back as antiquity and as far forward as 1763 (the exploration of the Southern Hemisphere was not limited to the land and the sea). An asterism is, simply, a convenient grouping of stars that are NOT one of the 88 Official Constellations, with some asterisms being only fragments of a full Constellation (such as the Big Dipper, the most famous asterism in the Constellation Ursa Major) and some asterisms composed of parts of multiple Constellations (such as the Summer Triangle, composed of the stars Deneb (Cygnus), Altair (Aquila), and Vega (Lyra). At our latitude (Syracuse and Tully), we cannot even see the entire Constellation of Sagittarius, but have an excellent view during the Summer of one of the most modern of conveniences in the form of a Tea Pot (see below). We may seem a little ridiculous pointing out the tea pot, short and stout, with its handle (on the left or to the West) and its spout (on the right or to the East) at Darling Hill on a dark night, but you will not forget this asterism after it jumps out at you the first time. An important thing to remember is that any grouping of stars in the sky that helps YOU find what you are looking for is as significant an asterism as one you might find in any book. If an otherwise unlabeled grouping jumps out at you that helps you find your place in the Night Sky, put those informal naming rights to good use.

Image generated with Starry Night Pro 6, www.starrynight.com.

Third, the billowing steam from the spout of this tea pot marks a most important location to all 100 billion or more stars in our galaxy. The small darkened oval in the picture above marks the exact location of the center of the Milky Way galaxy (the tiny, fuzzy spec at its middle), meaning we are looking into the most dense region of the galaxy when we set our gazes at this region. Unfortunately, the city lights from Cortland wash the density of the Milky Way band at our South when we observe in Tully, although the full band of the Milky Way is prominent above us during the Summer.

Images from ircamera.as.arizona.edu.

Fourth, because we are looking into the heart of the Milky Way when we see the spout of the tea pot (as the image at right tries to show), we are looking into the densest region of stars we can see from Earth. As a result, this tea pot marks the location of a variety of Messier Objects and fainter nebulae far more numerous than even the largest variety pack the other Celestial Seasonings (pardon the tea pun) has to offer. The Trifid Nebula (M20), Lagoon Nebula (M8), Sagittarius Cluster (M22), Omega Nebula (M17), Black Swan Nebula (M18), M25, M23, M55, M54, M70, M28, M21, and M75 all reside within the Sagittarius boundary, while M6, M7, M16, and a host of other deep sky objects surround its borders in neighboring Scorpius, Ophiuchus, and Serpens Cauda.

When we observe during the Summer, I often recommend to new visitors with binoculars to simply point to the South, aim for the tea pot, and slowly scan. If your binoculars or telescope are anywhere near focused, you are guaranteed to find something within your field of view.

Mildly thirsty just thinking about it,
Damian

astronomy, free press, publications | Comments (0)

Investigation of Crystalline 2-Pyridone Using Terahertz Spectroscopy and Solid-State Density Functional Theory

Sunday, July 26th, 2009

Accepted in Chemical Physics Letters. A solid-state density functional theory (DFT) follow-up to the solution-phase 2-pyridone (2PD) study published by Motley and Korter previously. Much of the work-up for this paper was straightforward, run-of-the-mill calculation and correlation (on the theory side, anyway). The most difficult part of the analysis was the identification of the easiest way to present the normal mode analysis of the 2PD crystal cell.

In terahertz (THz) spectroscopy, one observes the lowest-frequency vibrational motions of molecules (if the molecule has low-lying vibrational modes, of course). In the solid-state (such as molecular crystals), one observes both low-lying molecular vibrational motions (if they exist) and the relative motions between molecules in the unit cell. The boilerplate separation of internal (intramolecular) and external (between-molecule) modes is performed (and presented) as follows:

A crystal unit cell containing M molecules with N atoms contains 3N-6M internal modes (those modes associated with intramolecular motions), 6M-3 external modes (those modes associated with relative motions between the M molecules, such as rotations and translations), and three acoustic modes.

Some molecules simply do not absorb in the THz region, so all assignments are for external motions (and one simply identifies molecules sliding along axes or spinning around their centers of mass in their lattice site). Some molecules are very strongly bound to neighboring molecules in their lattice sites, which results in significant changes to the mode energies of low-lying vibrational modes (these are far more complicated systems to perform assignments of and a few of these cases are being prepared for future publications). Some molecules are strongly bound in very localized ways in their crystal cell to neighboring molecules and are very weakly bound to other neighbors in other ways. In 2PD, chains of molecules are strongly bound through hydrogen bonding along the crystal c-axis (see the figure below) and only weakly interacting between chains. In the figure below, the blue and red chains are strongly coupled in-chain (hydrogen-bonding) and only weakly coupled (dispersion and van der Waals forces) between chains.

The assignment of the 2PD solid is simplified by two important facts. First, the two chains (red and blue) are related by symmetry (the unit cell contains two anti-parallel 2PD chains). Second, the chains are very weakly interacting.

What point 1 means is that the chains, if in isolation, would undergo the same vibrational motions at the same energies (as if the chains were simply chiral molecules).

What point 2 means is that these chains are, because they interact very weakly, approaching a limit where there can, in fact, be considered isolated chains so that the unit cell will contain vibrational motions that involve the two chains undergoing the same motion in-phase with respect to reach other (in-phase here meaning that, for instance, both of your lungs are expanding at the same time) and out-of-phase with respect each other (the hypothetical case where the left and right lobes are out-of-sync with one another).

For instance, if both chains are sliding along the crystal c-axis in a vibrational mode, that makes the mode the in-phase acoustic translation in c (because the whole cell is sliding in one direction). If the two chains are sliding in opposite directions with respect to each other, this makes the mode the optical translation in c (the center of mass of the cell stays put while the chains undergo out-of-phase motions).

This simplification for the 2PD assignment (and other solid-state molecular chains) turned out to be the mode assignment based on the treatment of not the in-cell contents of atoms and molecular fragments (if we kept ourselves to only viewing what is happening in the cell, for instance), but instead the relative motions of the chains, which requires ever-so-slightly thinking outside of the box.

Tanieka L. Motley, Damian G. Allis, and Timothy M. Korter*

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

Crystalline 2-pyridone has been investigated using terahertz vibrational spectroscopy in the range of 10 to 90 cm^-1 (0.3 to 2.7 THz). Solid-state density functional theory (B3LYP, BP, and PW91 with the 6-311G(d,p) basis set) was used to simulate and assign both observed terahertz spectral features and a previously published far-infrared spectrum up to 400 cm^-1. The PW91 functional was found to provide the best combination of crystal structure and vibrational frequency reproduction. Observed spectral features below 150 cm^-1 are assigned to intermolecular movements of the 2-pyridone chains within the unit cell. The use of independent intramolecular and intermolecular frequency scalars is proposed.

www.sciencedirect.com/science/journal/00092614
dx.doi.org/10.1016/j.cplett.2008.09.021
en.wikipedia.org/wiki/2-Pyridone
en.wikipedia.org/wiki/Density_functional_theory
en.wikipedia.org/wiki/Terahertz
en.wikipedia.org/wiki/Vibrational_spectroscopy
en.wikipedia.org/wiki/Hydrogen_bonds
en.wikipedia.org/wiki/Van_der_Waals_force
en.wikipedia.org/wiki/Chirality_(chemistry)
en.wikipedia.org/wiki/Phonon