Finally! A Good Use For The Nano Gallery (Kudos To nanosonic.com)

An unlabeled version of the fused-diamondoid-carbon-nanotube-van-der-waals-crimp-junction found a home in the NanoSonic Nanotechnology Coloring Book, page 8 (I show it below (with mine shown a little more nano-sized)). I think that’s pretty hip.

Kudos to Tom Moore for pointing it out.

Cover Art For The 7 May 2010 Issue Of The Journal Of Organic Chemistry – Notes On Presentation

The cover art for the 7 May 2010 issue of the Journal of Organic Chemistry accompanies the article by (2nd semester organic chemistry professor, co-author, and 2010 American Chemical Society James Flack Norris Award in Physical Organic Chemistry recipient) John E. Baldwin and Alexey P. Kostikov entitled “On the Stereochemical Characteristic of the Thermal Reactions of Vinylcyclobutane.”

This Perspective outlines the stereochemical and mechanistic complexities inherent in the thermal reactions converting vinylcyclobutane to cyclohexene, butadiene, and ethylene. The structural isomerization and the fragmentation processes seem, at first sight, to be obvious and simple. When considered more carefully and investigated with the aid of deuterium-labeled stereochemically well-defined vinylcyclobutane derivatives there emerges a complex kinetic situation traced by 56 structure-to-structure transformations and 12 independent kinetic parameters. Experimental determinations of stereochemical details of stereomutations and [1,3] carbon sigmatropic shifts are now being pursued and will in time contribute to gaining relevant evidence casting light on the reaction dynamics involved as flexible short-lived diradical intermediates trace the paths leading from one d2-labeled vinylcyclobutane starting material to a mixture of 16 structures.

The cover image is meant to convey as much useful information as possible without any verbiage, although this is clearly not a concept meant to be crystal clear to a non-chemist (but kudos if you got the idea without my having to address it).

Included below are the four iterations involved in the cover draft, between which a considerable amount of verbal back-and-forth occurred (that is discussed briefly) to get what was intended to be presented. The iterations are provided both to show how different visions of what might be seen as the most-key of the key points change as content is presented to the client/researcher and, frankly, these all involved quite a bit of busy work and it seems a shame to not have them floating around somewhere accessible.

The original cover idea (above) was quite mundane but provided a bit more information (cryptic as it may appear to the non-mechanistic organic chemist) about what might be occurring in the absence of a brief read of the introduction of the article. This image emphasizes that a constant rearrangement occurs of the vinylcyclobutane (by the many, many arrows and the four different arrangements of deuteriums in the rearrangement) but does not address that the other 12 structures are products of reactions that are generated as the vinylcyclobutane rearranges and undergoes other but simultaneous intramolecular reactions. The absence of the connection between the rearrangement and the formation of products (which include the vinylcyclobutanes) removed this first iteration from the final running.

The second iteration (above) is a significant (well, I think so) improvement in the getting-across of the business end of the research. The vinylcyclobutane rearrangement is still central to the preferred emphasis of the cover (soon to go away) and the connection between the rearrangement and the formation of products is now hinted at directly by the use of the faded arrows. The second-tier information passed along in this image is that the vinylcyclobutane is one of the products, which is not stressed in the image (by the inclusion of four additional arrows from the central graphic (and, with that addition, the inclusion of arrows feeding the vinylcyclobutanes back into the center). If this had been an Angew. Chemie article, the circular design would have been a perfect fit.

It was at this point that a new piece of content was provided in the form of a medium-resolution digital photo of a piece of artwork by Anne Baldwin. The artwork was chosen as much for the colors as for the chaotic quality of the swirls, which was the one aspect of the entire process that the previous two images did not address and which Dr. Baldwin saw as the more significant point to convey. Some Gaussian blurring and a Gaussian basis set later, the new reactant/product combination as scrambled to complement the background and to make clear that one molecule (that at the arrow) lead to everything else in the image, including itself. The slight red halo around the deuterium (dark blue) is a result of an overlay of the blue spheres and red spheres rendered with slightly larger radii.

The arrow color and shading was stolen from Jean-Michel Folon. Example (The Cry) below. If you’ve one of the copies of La morte di un albero (mine is #630), see Comme un aimant (1971).

I admittedly prefer this (that is, the above cover idea) to the final version as the arrow indicates the forward direction of reactions and adds a hint of symmetry to an otherwise jumbled image.

As for the selected cover image (and final iteration, above), the considerable real estate taken up by the vinylcyclobutane in the previous image is recovered, which highlights the starting molecule differently and has the arrow simply angled into a less-busy space.

The final selection may make more sense in light of the image Baldwin chose to use for the graphical abstract.

A word to the perspective cover artist – This is a point that should be obvious but is often not until it is made obvious by an editor when it is much too late. Your images should be as LARGE as possible. Each of the images above is a 200 MB Photoshop file that would print without pixilation or granularity at 600 dpi on a 24” x 36” poster.

Terahertz Spectroscopic Investigation Of S-(+)-Ketamine Hydrochloride And Vibrational Assignment By Density Functional Theory, “Function Follows Functional Follows Formalism”

Accepted in the Journal of Physical Chemistry A, with my fingers crossed for pulling off the rare double-header in an upcoming print edition of the journal (having missed it by three intermediate articles with the Cs2B12H12 and HMX papers back in 2006 (you’d keep track, too). A fortuitous overlap of scheduled defense dates between P. Hakey, Ph.D. and M. Hudson, A.B.D.). A brief summary of interesting points from this study is provided below, including what I think is a useful point about how to most easily interpret AND represent solid-state vibrational spectra for publications.

1. AS USUAL, YOU CANNOT USE GAS-PHASE CALCULATIONS TO ASSIGN SOLID-STATE TERAHERTZ SPECTRA. It will take a phenomenal piece of data and one helluvan interpretation to convince me otherwise. As a more subtle point (for those attempting an even worse job of vibrational mode assignment), if the molecule exists in its protonated form in the solid-state, do not use the neutral form for your gas-phase calculation (this is a point that came up as part of an MDMA re-assignment published (and posted here) previously).

2. It is very difficult to find what I would consider to be “complete data sets” for molecules and solids being studied by spectroscopic and computational methods. For many molecular solids, the influences of thermal motion are not important to providing a proper vibrational analysis by solid-state density functional theory methods. Heating a crystal may make spectral lines broader, but phase changes and unusual spectral features do not often result when heating a sample from cryogenic (say, liquid nitrogen) to room temperature. Yes, there are thousands of cases where this is not true, but several fold more cases where it is. We are fortunate to live in a temperature regime where characterization is reasonably straightforward and yet we can modify a system to observe its subtle changes under standard laboratory conditions. The THz spectrum of S-(+)-Ketamine Hydrochloride gets a bit cleaner upon cooling, which makes the assignment easier. As the ultimate goal is to be able to characterize these systems in a person’s pocket instead of their liquid nitrogen thermos, the limited observed change to the spectrum upon cooling is important to note.

3. Crystal06 vs. DMol3 – This paper contains what is hoped to be a level, pragmatic discussion about the strengths and weaknesses of computational tools available to terahertz spectroscopists for use in their efforts to assign spectra. This type of discussion is, as a computational chemist using tools and not developing tools, a touchy subject to present on not because of the finger-pointing of limitations with software, but because the Crystal06 team and Accelrys (through Delley’s initial DMol3 code) clearly are doing things that the vast majority of their users (myself included) could in no way do by themselves. The analysis for the theory-minded terahertz spectroscopist is presented comparing two metrics – speed and functionality (specifically, infra-red intensity prediction). What is observed as the baseline is that both DMol3 and Crystal06 make available density functionals and basis sets that, when used at high levels of theory and rigorous convergence criteria, produce simulated terahertz spectra with vibrational mode energies that are in good (if not very good) agreement with each other. For the terahertz spectroscopist, Crystal06 provides as output (although this is system size- and basis set size-dependent) rigorous infrared intensity predictions for vibrational modes, inseparable from mode energy as “the most important” pieces of information for mode assignments. While DMol3 does not produce infrared intensities (the many previous terahertz papers I’ve worked on employed difference-dipole calculations that are, at best, a guesstimate), DMol3 produces very good mode energy predictions in 1/6th to (I’ve seen it happen) 1/10th the time of a comparable Crystal06 calculation. This is the reason DMol3 has been the go-to program for all of the neutron scattering spectroscopy papers cited on this blog (where intensity is determined by normal mode eigenvectors, which are provided by both (and any self-respecting quantum chemical code) programs).

Now, it should be noted that this difference in functionality has NOTHING to do with formalism. Both codes are excellent for what they are intended to do. To the general assignment-minded spectroscopist (the target audience of the Discussion in the paper), any major problem with Crystal06 likely originates with the time to run calculations (and, quite frankly, the time it takes to run a calculation is the worst possible reason for not running a calculation if you need that data. Don’t blame the theory, blame the deadline). In my past exchanges with George Fitzgerald of Accelrys, the issue of DMol3 infrared intensities came up as a feature request that would greatly improve the (this) user experience and Dr. Fitzgerald is very interested (of course) in making a great code that much better. Neither code will be disappearing from my toolbox anytime soon.

4. The Periodicity Of The Molecular Solid Doesn’t Care What The Space Group Is – One of the more significant problems facing the assignment-minded spectroscopist is the physical description of molecular motion in a vibrational mode. In the simplest motions involving the most weakly interacting molecules, translational and rotational motions are often quite easy to pick out and state as such. When the molecules are very weakly interacting, often the intramolecular vibrational modes are easy to identify as well, as they are largely unchanged from their gas-phase descriptions. In ionic solids or strongly hydrogen-bonded systems, it is often much harder to separate out individual molecular motions from “group modes” involving the in- and out-of-phase motions of multiple molecules. In the unit cells of molecular solids, it can be the case that these group modes appear, by inspection, to be extremely complicated, sometimes too involved to easily describe in the confines of a table in a journal article.

S-(+)-Ketamine Hydrochloride is one such example where a great simplification in vibrational mode description comes from thinking, well, “outside the box.” The image below shows two cells and the surrounding molecules of S-(+)-Ketamine Hydrochloride. As it is difficult to see why the mode descriptions are complex from just an image, assume that I am right in this statement of complexity. Part of this complexity comes from the fact that the two molecules in the unit cell are not strongly interacting, instead packed together by van der Waals and dispersion forces more than anything else. The key to a greatly simplified assignment comes from the realization that the most polar fragments of these molecules are aligned on the edges of the unit cell.

An alternate view of molecular vibrational motion comes from considering not the contents of the defined unit cell but the hydrogen-bonding and ionic bonding arrangement that exists between pairs of molecules between unit cells. The colorized image below shows two distinct chains (red and blue) that, when the predicted vibrational modes are animated, become trivial to characterize as the relative motions of a hydrogen/ionic-bonded chain. Rotational motions appear as spinning motions of the chains, translational motions as either chain sliding motions or chain breathing modes. It appears as a larger macromolecule undergoing very “molecular” vibrations. In optical vibrational spectroscopy, selection rules and the unit cell arrangement do not produce in- and out-of-phase motions of the red and blue chains, as only one “chain” exists in the periodicity of the unit cell. In neutron scattering spectroscopy, these relative motions between red and blue would appear in the phonon region. This same discussion was had, in part, in a previous post on the solid-state terahertz assignment of ephedrine (with a nicer picture).

So, look at the cell contents, then see if there’s more structure than crystal packing would indicate. It greatly simplifies the assignment (which, in turn. greatly simplifies the reader’s digestion of the vibrational motions).

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

Department of Chemistry, Syracuse University, Syracuse, New York 13244-4100

Abstract: The terahertz (THz) spectrum of (S)-(+)-ketamine hydrochloride has been investigated from 10 to 100 cm-1 (0.3-3.0 THz) at both liquid-nitrogen (78 K) and room (294 K) temperatures. Complete solid-state density functional theory structural analyses and normal-mode analyses are performed using a single hybrid density functional (B3LYP) and three generalized gradient approximation density functionals (BLYP, PBE, PW91). An assignment of the eight features present in the well-resolved cryogenic spectrum is provided based upon solid-state predictions at a PW91/6-31G(d,p) level of theory. The simulations predict that a total of 13 infrared- active vibrational modes contribute to the THz spectrum with 26.4% of the spectral intensity originating from external lattice vibrations.

pubs.acs.org/journal/jpcafh
www.somewhereville.com/?p=29
www.somewhereville.com/?p=26
www.somewhereville.com/?p=126
en.wikipedia.org/wiki/Density_functional_theory
en.wikipedia.org/wiki/Ketamine
www.crystal.unito.it
accelrys.com/products/materials-studio/quantum-and-catalysis-software.html
en.wikipedia.org/wiki/Time_domain_terahertz_spectroscopy
en.wikipedia.org/wiki/Computational_chemistry
accelrys.com
en.wikipedia.org/wiki/Inelastic_neutron_scattering
en.wikipedia.org/wiki/Vibrational_spectroscopy
www.somewhereville.com/?p=680