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Way Down There in the Pores

Let’s get physical-organic. A big topic of research in recent years has been the properties of liquids and solids under boundary conditions. By that sweeping statement, I mean questions such as “When does a small cluster of metal atoms start to act like a small piece of bulk metal? Why is there a transition, and what happens below it?” Or “What’s different about atoms/molecules in a crystal when they’re at a corner and not surrounded by so many of their kind? Are they the first ones to dissolve or react?” And another: “How do water atoms act differently when they’re in the first layer of a surface – against air, against the wall of a container, against an immiscible liquid, or in the first layer of a hydration shell? Do things dissolved in such zones change reactivities?”

There are plenty of such topics, and plenty of reasons, as you do the thought experiments, to expect interesting and unusual behavior. But for many years it was next to impossible to get experimental data on such things. Pioneers like Langmuir and Blodgett (among others) opened up surface chemistry as a field, but it’s fair to say that for a long time after them it remained pretty empirical. Good examples are industrial catalyst design and pharmaceutical formulations. We know for certain that particle sizes and compositions make huge differences in catalyst turnover numbers, fouling, and selectivity, as well as in drug dissolution rates and bioavailabilities. But a lot of what was discovered over the years was done by sheer experimentation while hunting for trends and empirical rules. Science was waiting on the tools to study physical behavior and structure at these difficult scales.

Here’s a current example from a group at Manchester (a university with a storied history in structural and nano-chemistry). It uses MCM-41, an industrial catalyst and catalyst support developed at Mobil, which is a bit like a zeolite (although those have aluminum in their structure and thus contain acidic centers, while MCM-41 is pretty much all silicate). It’s full of long empty pores, several nanometers across, a stack-of-tubes arrangement that you also see in some metal-organic frameworks and mesoporous materials in general. These hollow tubes fill with solvent, naturally, but on that scale, the solvent is not exactly just plain bulk liquid. It doesn’t have the room to be. So what is it?

People have studied this sort of thing with simulations, but when you take X-ray diffraction structures of such things (as with MOFs), you usually just get disordered solvent that can’t be refined (and whose noisy data indeed sometimes have to be tossed out, computationally, to get the rest of the structure to solve well). When the solvent molecules do refine well, they tend to be rather closely associated with the surface of relatively narrow pores and cavities, a bit more like the structure of a freestanding metal complex. But MCM-41 is too large for that and too small to be “normal” solvent. Simulations have suggested various poses for solvents like benzene – sometimes they’re flat against the pore walls in the first layer, and sometimes they come out tilted, and there are various proposals for how they stack in the layers after that.

This paper take benzene-soaked MCM-41 and gets neutron scattering data, which as I understand it is not a lot of fun (and can be obtained at relatively few locations around the world as well). The model that fits the experimental data best has benzene molecules arranged in the pore as concentric cylindrical shells, which needless to say is not what you would expect to see if you could peer inside a bottle of bulk benzene. In an 18A pore, there’s room for four of these layers. They’re definitely affected by contact with the pore wall, but in a complicated way. The closest benzenes to the wall tend to be canted at about a 40-degree angle relative to the silicate surface, but the ones a bit further out, while also definitely more constricted than a bulk phase, tend to be more perpendicular to the wall (plus or minus some wiggle room). And the ones beyond that are flat parallel to the (now distant) wall, and by this point you’re talking about benzene molecules that are mainly reacting to the presence of other structurally ordered (or semi-ordered) benzene molecules. In fact, that last interaction sounds like the “edge-to-face” orientation often seen with the aromatic rings of drug structures in protein binding pockets.

Shown is a simulation fitted to the experimental data, to give you an idea of the scale we’re talking about. The red stuff is the silicate of MCM41, and the grey-and-white are the benzenes. We’re looking down a pore, with a slice taken out of the structure. If you squint, you can actually see some of the layering – it’s messy, but it’s a far less random mess than bulk solvent. Diffusion of solute molecules is going to be a very different thing in such an environment, and reactivities can change because the energetic background of solvation has changed. Moving solvent molecules around is a big influence (both enthalpically and entropically) on the thermodynamics of a reaction, and this sort of confinement is a direct way to affect that. If we can get a better handle on it, we have possibilities to do types of chemistry we might never be able to access otherwise.

9 comments on “Way Down There in the Pores”

  1. Uncle Al says:

    Aromatic pi-stacking is shown not to exist (DOI:10.1039/c2sc20045g vs. DOI:10.1063/1.2011396 ). Given no pi-stacking, it would be silly to FT the distribution, seeking spacing and orientation periodicities (versus the surrounding lattice)/

    How much oxygen is in there? Oxygen can inappropriately touch benzene.

    1. Chemperor says:

      As an apologist for the pi-stacking community, I’d have to respectfully disagree with the conclusion that “pi-stacking is shown not to exist”. There is some debate (highlighted very well in the references that you’ve provided) that the term “pi-stacking” might be something of a misnomer and too often implies a simplistic face-to-face interaction, but the abundance of crystallographic evidence supporting aromatic-aromatic interactions (particularly “slipped” or offset rings) is too compelling to ignore. I fear that this debate is beginning to descend into semantics, much like the debate over the nature and definition of H-bonding seems to have become rather arbitrary in recent years. Many chemists might not be able to explicitly define pi interactions or hydrogen bonding, but they know them when they see them (to paraphrase the late Justice Potter Stewart).

  2. Gene says:

    P-Chem = hard
    O-Chem = hard
    P-Chem + O-Chem = Pass the tequila

    1. fajensen says:

      -> Run the Tequila + MCM-41 through the relevant neutron spallation source instrument.

      Somebody is bound to do it eventually, even if it is mostly because any science paper including alcohol will be widely reported and the PR-people like to clock up some “visibility” metrics.

      Netron Spallation Machines are huge, physics experiments (almost), and very expensive to build and run. The global consensus is to have about one per continent to cover materials research needs. The EU site will be the ESS in Lund, Sweden. We are hoping to fire it up sometime around 2020-2025.

  3. olver says:

    Hi Derek
    I did my Ph.D. at Georgetown, right down the street from NIST, Gaithersburg. I did some SANS work there in the mid 90’s last century. This was the time when one could just drive onto the NIST campus and park right next to the reactor. no Q’s asked.
    I would say that was fun.

    The lecture by W. Phillips, after that thing in Stockholm, a couple years later, 1998 I think, was only by RSVP and you were thoroughly checked at the campus entrance.

    Cheers oliver

  4. Synthon says:

    I’ve been interested in reactions on simple mesoporous silica for a long time but never had much opportunity to research it. For example absorb benzene on silica and mix with bromine on silica and bromination happens very rapidly but with no selectivity. With chlorine the reaction is over with one shake. Gary Posner did lot of work 30 years ago or so and other have found it good for Michael additions.

  5. gippgig says:

    OTBMBOI (Off topic but may be of interest):
    The Drug Development Paradigm in Oncology
    Proceedings of a Workshop

  6. gippgig says:

    …and then there’s:
    Examining the Impact of Real-World Evidence on Medical Product Development
    1. Incentives: Proceedings of a Workshop-in Brief

  7. Barry says:

    two molecules of water can’t form ice
    at best, they share a single hydrogen
    no less than five could possibly suffice
    to sketch the unit right tetrahedron
    thereafter, each incomer’s free to dock
    if its kinetic energy’s alright
    forsaking role as gas for role as rock
    to claim a free coordination site
    six vertices in six directions grow
    each independently hews to the norm
    as building blocks march outwards, row by row
    defining a new snowflake’s starry form
    reductionism picks a thing apart
    to grasp it by the method of Descartes

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