Another really short lit link post.

A cavity QED approach to magnetic resonance that was just published - figured a few of you might be interested in this sort of thing. 

In other news, have a fair amount of NMR data myself to work through and understand.  Speaking of which, back to it. Read more!

Still alive....

You can cue the "Portal" song here - trying to not fall entirely away from this blog, especially as the most entertaining time of the year approaches for the chemical blogosphere.

Here's something for the quantum mechanics & photosynthesis fans - Excitation Energy Transfer in a Classical Analogue of Photosynthetic Antennae from J. Phys. Chem. B.  

I may have more to say about this and other things in the future.  In other news, I suppose we'll all be really careful with our supplemental information sections in the future........ Read more!

Back again....

Yet another "quantum effects in photosynthesis" paper.

Waiting for the rampant speculation that can arise from this paper, as well.

Off to troubleshooting the remainder of my afternoon! Read more!

Trifling Thoughts.

1.) I really was hoping to go for a couple of more years before having to deal with a poorly behaving high-power RF amplifier.

2.) Whenever someone says that quantum mechanics should be understood at an intuitive level, I wonder if they never had to occasionally take solace in the mathematics earlier on in their education.  While it was fleeting during intro E&M at university, the intermediate E&M class did have me routinely finding some sanity in mathematics.  Perhaps my intuition is just exceptionally poor, of course. 

3.)  Given all the hoo-ha about AFM recently, I thought this was interesting and timely.

And there's a good ending point for today......


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A bit overdue, I suppose.

It seems that I have neglected you, dear blog.  I would express my regret, but, well, I've been busy.  I do hope that any occasional visitors have been having themselves a healthy, enjoyable, and productive 2013.

In any case, research is progressing to the point to where critical experiments will be run within the next few months, and presuming that my calculations are not too far off, we should obtain a reasonable amount of interesting data that will be published not long thereafter.   Which should help with the entire "what to do next?" conundrum.

However, before I meander to other topics, an observation - the one thing that keeps biochemistry challenging is that your samples are never entirely happy.  You can purify it to some vague approximation of homogenity, put it in a buffer it likes, add cryoprotectant, and flash freeze in countless little aliquots for storage at -80 degrees Celsius.  And when someone takes out an untouched aliquot 3 years later to check its viabiity, they find it's.....reluctantly alive.  You compare it to a sample made of protein you prepared a week ago, it's clearly working nowhere near its potential.  Now, I had the occasion to stop by my old grad school lab the other year, and the one student working on my old project is still using the small molecule ligands that was synthesized by myself and another student ~ 10 years ago. And that sample was not aliquoted out in tiny volumes, each one to only be used once, rest assured. 

Onto said other topics......

- I have to say I am extremely tickled and intrigued by the idea of approaching quantum mechanics as a certain generalization of probability theory.  It's probably a good thing I have no intentions of being a faculty member anywhere, as I'd probably try to pull off a presentation like this to students. 

- I sort of postponed my entire relativistic quantum chemistry self-study program.  I will get back to it.  One of these days.

- I am finding myself in the position where I need to start doing some serious practical and theoretical NMR teaching to a very small audience, though.   The whiteboards in lab are going to get messy, I suspect.

- Should probably start microblogging more often, to boot. 

Anyway, going to try and chime in more regularly here over the upcoming weeks and months. 




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Quantum biology - A Rose By Any Other Name?

I believe I may have off-handedly mentioned some of this work somewhere in a blog comment semi-recently, but I suppose some further thoughts would not be out of place at this time.  I bring it up because of this preprint and this article about said preprint.

Clearly, on one level, quantum mechanics - via chemistry - underlies biology.  This is, I suspect, a fairly unoffensive statement.  Chemical reactions are quantitatively studied in a quantum mechanical framework, and I don't see biochemical reactions being much different. 

On another level, direct appeal to quantum mechanical behavior to explain biology can seem kind of silly.  Biology is slow, wet, messy, and takes place at a whole bunch of time and length scales.  I imagine many of us recall the exercise - likely done in an introductory general chemistry course, at least in my experience - where one calculates the de Broglie wavelength for an electron and then, say, a baseball. 

Of course, when one looks at table 1 in the preprint, a light goes on.  Long-range electron transfer in proteins?  The role of tunneling in enzyme catalysis?  Vision - which involves the photochemistry of a protein-immobilized chromophore?  Photosynthesis?  A proposed radical spin mechanism for avian magnetoreception? 

This all reeks of physical(ly predisposed) chemists trying to get their dirty mitts onto a whole lot of funding.  Not that there's anything wrong with that, mind you - I'm presently trying to work "quantum biology" into my CV/resume as we speak. 

But for sake of argument, let's take a look at the Fenna-Matthews-Olsen (FMO) protein from a green sulfur bacterium where quantum effects were observed via 2D electronic spectroscopy.

Yep, definitely a protein.  But what's all of that inside the protein?

Why, it looks like the protein is the wrapping for a photochemically delicious filling of chlorophyll molecules!  I could envision that this is the sort of environment which would be conducive for maintaining some sort of quantum mechanical excitation. 

But what about - for instance - microtubules, which some have suggested play a role in consciousness via quantum mechanical effects?  Why, there's even GTP (GDP) known to associate with tubulin in the structure!  Let's take a look -

Hmmm.  Let's focus on the GTP and GDP, so how about….

Well, that was kind of anticlimactic.  That's it?  That is somehow supposed to sustain and nurture our very consciousness from the harsh decoherent world out there?  I find myself skeptical. 

I suppose that is as good a place to end as any.  I may or may not have more to say in the future after I've had a chance to properly consume and digest the preprint.  While I do find the idea of nature exploiting exciton transport, radical spin pair chemistry, proton tunneling, and so on incredibly exciting - I don't think taking that and wantonly speculating is the best route.   

FYI - This was also mostly a chance to play around some more with UCSF Chimera.  Just started using it a bit earlier this year, so if anyone has any tips or list of useful tricks, please share!  The structures were generated with this program using PDB ID 3ENI (FMO protein) and 1JFF (tubulin).  Read more!

Quantum Chemistry on the Cheap.

I am not liking this new Blogger interface.  I suppose it will become more familiar with time, which I might take as a reason to post more.  In any case.....

The main reason for this post is to alert those who haven't heard/seen - the January 2012 issue of Chemical Reviews is the free sample issue available to non-subscribers, and contains the (near) latest in quantum chemistry.  I know there's a tiny bit of interest in what can actually be done with these methods by some, and - at least from my POV - yet another delightful article from Pekka Pyykkö, whose material I always find interesting and readable. 

Anyway, the rest of the month, I will be mired in tremendous experimental effort.  Not going off the grid, but more "locked in an NMR room until I finally keel over in exhaustion."  Wish me luck. Read more!

You spin me right round baby.....

I saw this come up in the comments here, and figured that it would make for a cute post. I will start off with the mundane, though.

One is frequently asked to picture electromagnetic radiation as an oscillating wave, with the electric and magnetic fields orthogonal to one another as it propagates. This, I imagine, does not come as a surprise to anyone reading this.

As is propagated in the above link, the NMR experiment is presented as utilizing radiofrequency (RF) waves to tickle the nuclear spin magnetic moments. Of course, that leads to the question presented in that post – how does an RF wave (with a wavelength on the order of meters) get absorbed at the scale of a single nucleus? One might also ask an analogous question on the other end of the experiment when one is recording a signal on your nearest friendly NMR spectrometer.

Now, for two related things to think about –

The first is the oft-neglected sibling in the magnetic resonance community, electron magnetic resonance (EMR, also known as ESR or EPR depending on who you speak to). One of the fun little things that you can shovel a sample into is a flat sample cell. This is exactly what it sounds like – your sample is basically sandwiched between two planes of quartz. It is helpful since you can position your sample (typically aqueous in this case, as they’re notoriously lossy) at a point of maximum magnetic field (high B1) and minimal electric field (low E1), which keeps the resonator Q-factor high as well as keeping your sample from heating up, which can make for sad spectroscopic pandas.

The second is the development of so-called “Low-E” probes for the biological solid state NMR community. Given that they are not infrequently studying aqueous samples with some amount of salts (aka lossy as hell), and the traditional need for high power decoupling to get adequately resolved spectra, minimizing sample heating has been a major focus of effort within the community. The result here is a probe that minimizes heating from the electric field, actually using some insights from the EMR/EPR/ESR community.

Now, if we think about what’s going on here….they’re trying to minimize the influence of the electric field (E1) by either judicious sample placement or probe design. We know from basic electromagnetism that an EM wave is composed of both electric and magnetic field components. It would seem that the absorption of EM radiation in magnetic resonance is not necessary for a successful experiment. It would, in fact, appear to be the case that what is important is the magnetic field that is generated by an appropriate EM source (RF for NMR/MRI, microwave for EMR) for the magnetic resonance experiment. The electric field appears to simply be a source of woe and frustration.

Of course, as noted in the comments to the above link, this is not new thinking. Hoult and his collaborators have been working on this topic in various ways and manners for over two decades now. There’s also that fun paper by Hanson regarding the necessity of quantum mechanics for understanding magnetic resonance. And more recently, there’s been a rather lengthy (and somewhat dense – I have a copy printed out, haven’t had a chance to really dig into it just yet) article on virtual photons in magnetic resonance, following up on Hoult’s suggestion from a while back.

Alright, back to things.... Read more!