Building Pillars of MesoScale Particles on a Surface

Let’s build layers of (macromolecular) material on a surface. If the material were lego pieces, then the amount of coverage at any given point would be precisely the number that fell there and connected (interlocked). In the simplest cases, you might imagine the same type of construction on a macromolecular scale surface with nano sized bricks. The trouble is that at that small length scale, particles are no longer rigid. The possibility of such softness allows for higher density layers and even a lack of certainty as to which layer you are in. This leads to a roughness in the surface due to the fact that the soft legos stack more in some places than others. Moreover, there will be regions without any legos at all which means that the surface will not be completely covered. This led us to ask: What is the surface coverage as a function of the amount of macromolecular material coated on the surface and the degree of softness of that material?

As in our recent work using tricked-up hard particles, we wondered whether we could answer this question without using explicit soft particle interactions. It does, indeed, appear to work in the sense that we are able to capture the differences in coverage of the surface between a metastable coverage in which particles once trapped at a site remain there, and the relaxed coverage in which particles are allowed to spread across the surface. We also found that relaxation leads to reduced coverage fractions rather than larger coverage as one might have expected a spreading of particles due to the relaxation.

This work was performed by my graduate student, Dr. Galen Craven, in collaboration with a research scientist in my group, Dr. Alex Popov. The title of the article is "Effective surface coverage of coarse grained soft matter.” The work was funded by the NSF. It was published on-line in J. Phys. Chem. B back in July, and I’ve been waiting to write this post hoping that it would hit the presses. Unfrotunately, it’s part of a Special Issue on Spectroscopy of Nano- and Biomaterials which hasn’t quite yet been published. But I hope that it will be soon! Click on the doi link to access the article.

Checks and Balances in Science… (#ACS #JPC-A #justpublished)

Science is self-correcting in a number of ways. It's true that sometimes the progress of science gets off the rails, seemingly falling into sink holes. Other times, it appears to find its course only through the jolt of a paradigm shift. However, most of the time, it moves forward with errors or missteps corrected naturally (or incrementally) by the community along the way. In our case, we recently made one (albeit small) such misstep. Specifically, in our recent article on roaming and transition state theory in the ketene isomerization reaction, we had a factor of 1/2 in the wrong place. (Check out my earlier blog post describing our earlier work.) Trouble was that the same factor had been mistyped in an earlier article by Gezelter and Miller, and we, like others before us, hadn't noticed it. Wiggins ran across our article before it was available in print, noticed the typo, and wrote to me about it. After some back and forth, including Miller, Gezelter and a few others, we agreed that the factor should have been there in the first place. The results of Gezelter and Miller's original article are o.k. because the typo was only in the text, not in their calculations. This left us wondering about our calculations. We reran them. The precise numbers changed, but fortunately all the qualitative results remained the same. Nevertheless, we just published a correction in the Journal of Physical Chemistry to clean up the issue and remove any doubt about the results.

Long story short, the scientific process worked. We published our results in an open setting. Someone across the Atlantic discovered an error that had endured in the literature through to us. He brought it to the attention of the community and us. We fixed it, and science moves on. There has been much talk in the common press in the past year about the persistence of errors in science. Indeed some of them persist because the internet tends to retain a memory of them. Sometimes searches find the article and not the subsequent correction. For the most part, though, these are rare events. I, like others, are just happy to get it right at the end of the day, and the scientific system works to help us get there.

The title of the article is "Correction to `Effects of Roaming Trajectories on the Transition State Theory Rates of a Reduced-Dimensional Model of Ketene Isomerization'" and the work was funded by the AFOSR. It was just published at J. Phys. Chem. A, 117, 10567 (2013).
Click on http://dx.doi.org/10.1021/jp408997z to access the article.

Roaming pathways and rates: A case study on ketene(#ACS #JPC-A #justpublished)

It's no surprise that chemists care about chemical reactions. We want to know both how the reactions take place—mechanism or pathway—and how much time it takes to happen—rates. One of the most successful, though approximate, theories has been transition state theory (TST), in part, because it provides an answer to both questions. You simply need to find the saddle (or col) on the potential energy landscape between reactants and products. That bottleneck, which can be described with varying levels of fanciness, gives you a sense of how the atoms in the reacting system have to distort so as to proceed to products. The energy of the bottleneck can be used in a well-known formula to obtain the rate. Recently, however, Joel Bowman and others have discovered the possibility that the reactants could avoid the bottleneck entirely. These roaming trajectories thus pose a challenge to TST, and have generated a lot of well-deserved buzz.

In those cases when roaming trajectories wander so far away from the transition state (bottleneck) that new product channels (such as radical molecules) become accessible, there is no doubt that everything goes topsy turvy. However, we were curious as to whether roaming trajectories would turn TST upside down even when such channels are not available. In recent work, we studied the ketene isomerization reaction—that is when it interconverts from one form to another—and found that it gave rise to roaming trajectories (such as the one pictured here.) Unfortunately, TST remains reasonable for this system as long as one is careful to generalize the dividing surface associated with the bottleneck so as to appropriately include roaming trajectories. So perhaps all remains good with TST after all?!

The title of the article is "Effects of Roaming Trajectories on the Transition State Theory Rates of a Reduced-Dimensional Model of Ketene Isomerization" and the work was funded by the AFOSR. It was released recently at J. Phys. Chem. A, ASAP (2013). (doi:10.1021/jp402322h) 

Click on http://dx.doi.org/10.1021/jp402322h to access the article.