Condensed concepts

Tomorrow I am giving a talk A unified picture of hydrogen bonding and proton transfer via a two state Hamiltonian. It is based on this paper.  The main point is A simple model Hamiltonian • with just two parameters • i s physically and chemically transparent g ives • a unified picture of different types of H-bonds and of proton transfer • insight into the H-bond puzzle • a semi-quantitative description of empirical correlations between bond lengths, binding energies, vibrational frequencies….

How do enzymes work? Are they any different from other catalysts? The traditional view is no. They simply lower the energy barrier of the transition state between the reactants and products. The only difference from man-made catalysts is that due to their complexity (and evolution) enzymes can lower this barrier by more than an eV leading to an increase in reaction rate by tens of orders of magnitude. In the traditional view the only role of the dynamics of the nuclei in the enzyme is that statistical thermal fluctuations provide access to the transition state. Furthermore, quantum dynamics of the nuclei does not play any significant role. Tunneling below the barrier may provide small corrections to the reaction rate for light nuclei such in proton, hydrogen, or hydride (hydrogen anion) transfer reactions. Over the past decade some people have been advocating a radical non-traditional view of how (some) enzymes work. They claim that non-trivial (and non-local) dynamics plays a k

At the workshop today Tom Markland gave a nice talk on work described in a recent PNAS paper Unraveling quantum effects in water using isotopic fractionation . It turns out that the amount of deuterium in liquid water depends on the temperature at which the water was condensed. This can be measured very accurately and has proven to be a sensitive probe in climate change studies (see for example, figure 1 in this Nature  paper ). For most temperatures there is a preference for HOD to reside in the liquid rather than the vapour phase. This is a purely quantum effect! According to the Born-Oppenheimer approximation the intermolecular and intramolecular interaction potentials for H2O and HOD are identical. However, different isotopic masses lead to different vibrational frequencies, zero point energies, and free energies. Calculating the free energy of the liquid phase where one treats the H and D atoms fully quantum mechanically is a highly non-trivial exercise. Markland has done t

T his week I am in Colorado at the  Telluride Science Research Center  for the workshop on Condensed Phase Dynamics.  Many of my favourite theoretical chemical physicists are here so I am really looking forward to it. I am going to give a talk based on my recent paper about hydrogen bonding.

Bill Parson has published a nice book Modern Optical Spectroscopy: with examples from biochemistry and biophysics. I like it because it includes real experimental data from a range of specific biomolecular systems. It covers all the important topics and is not scared of a full quantum mechanical treatment. Hence, it has a good balance of theory and experiment. It is also available as an e-book.

There is an interesting article Entropy: Order or information by Arieh Ben-Naim in the Journal of Chemical Education. He points out two related and common misconceptions about entropy: mixing is always irreversible (and so must involve an increase in entropy) entropy is related to disorder This is illustrated with the three processes of mixing shown below. All involve mixing, but only the first is irreversible. What determines the entropy change is not the mixing (or amount of disorder) but the change in volume of each gas. That can be related to information (or ignorance) about the state of the gas molecules.

One should be careful about comparing apples and oranges! There is a helpful and interesting article in Science Comparing Photosynthetic and Photovoltaic Efficiencies and Recognizing the Potential for Improvement written by an Aussie Rules football team (18 co-authors!). It points out that quantifying the efficiency of photosynthesis is not completely straightforward. It is sometimes claimed that it has evolved to have an optimum efficiency and that it has a quantum efficiency of 100% because every photon that is absorbed produces a desired chemical product. The authors state: For comparison with PV electrolysis over an annual cycle, the energy efficiency of photosynthesis is a more useful parameter and is defined as the energy content (heat of combustion of glucose to CO 2   and liquid H 2 O at STP) of the biomass that can be harvested annually divided by the annual solar irradiance over the same area. Using this definition, solar energy conversion efficiencies for crop plants

I had a nice visit this morning at University of Washington with Jim Mayer who has worked extensively on coupled electron-proton transfer [see this post for an earlier discussion]. Here are a few things I learnt. CPET is involved in one of the most important processes in biology, whereby we get all of our oxygen! This is the Kok S-state mechanism of Photosystem II: the amino acid tyrosine-Z is oxidised to yield a neutral tyrosyl radical. Specifically, the electron is transferred 14 Angstroms (i.e. a long way!) to a photoexcited chlorophyll radical and the proton is transferred across a hydrogen bond to a nearby histidine residue (e.g. see this 2003 PNAS paper  for evidence). It is important to note that the proton and the electron are spatially separated and "attached" to different atoms. Nevertheless, their motion is concerted , i.e. the transfer is not sequential. A major question concerns whether this process is adiabatic or non-adiabatic. Uncertainty about the ans

A series of earlier posts have considered how the excited dynamics of a range of organic dyes is determined by the viscosity of the solvent. This essentially determines the friction associated with torsional motion on the excited state potential energy surface. Seth Olsen brought to my attention a very nice paper from 1987. Torsional dynamics of molecules on barrierless potentials in liquids. II. Test of theoretical models by Ben-Amotz, D. and Harris, C. They test three alternative models, comparing to experimental data for auramine O and Crystal Violet. Thus this paper is very similar to the 2000 paper by  van der Meer, Zhang, and Glasbeek that I discussed in   an earlier post . They find experimentally that the excited state lifetime scales with the solvent viscosity. This scaling is required by the Smoluchowski equation (for overdamped stochastic motion in an external potential), regardless of the form of the potential energy. The experimental data is most consistent wit

Take a deep breath. You just created an entangled quantum state! There is a really interesting paper on the arXiv Quantum entanglement and Hund's rule are determinants to respiration Cedric Weber, David D. O'Regan, Nicholas D. M. Hine, Peter B. Littlewood, Gabriel Kotliar, Mike C. Payne They use DFT-DMFT (Density Functional Theory + Dynamical Mean-Field Theory) to study the binding of oxygen and carbon monoxide to iron-porphyrin ( heme ). This is the process by which respiration occurs. Oxygen binds reversibly to the heme group in myoglobin. Unfortunately, CO does not bind reversibly and you die! [Aside: Haemoglobin consists of four myoglobin molecules and they exhibit some interesting and important collective behaviour ( allostery ) first elucidated by Linus Pauling (who else!) from simple thermodynamic considerations. This is nicely described in Thermal Physics by Kittel and Kroemer]. This new work shows that as the iron atom Hund's rule coupling J varies

Many physics exam questions I set are meant to be "simple" and "easy", i.e. they aim to test understanding rather than the ability to -do complicated algebra/calculus -regurgitate large amounts of information Hence, always look for a simple way to solve the problem. Never think "It can't be that simple", e.g., just plugging numbers into a single equation  or just restating in different terms/words the answer to a previous part of the question. If your answer involves pages of algebra you are almost certainly on the wrong track... Try and be neat enough that the examiner can actually understand what you have done. Clearly explain what you are doing, including stating assumptions and results you are using. Don't just write lines of equation. Don't try and fake derivations. Include and keep track of physical units in all calculations. Clearly label axes and scales of all graphs. Don't waffle. If you don't have an explanatio

I think the Figure below is a really nice one which compares the variation of the superconducting order parameter on the Fermi surfaces for four different classes of superconductor: a. elemental b. cuprates c. MgB2 d. iron pnictides The figure is taken from a 2010 Perspective in Nature by Igor Mazin. A recent post considered how to unify b. and d.

There is a good editorial in the Journal of Chemical Education   Cherry Picking: Why We Must Not Let Negativity Dominance Affect Our Interactions with Students by Melanie M. Cooper She emphasizes how it is easy to get discouraged by just a few students whose performance,  preparation, actions, or attitude is disappointing to us. Furthermore, what is even worse is if that small minority ends up changing how and what we teach or what attitude we have to the majority of students. I thought the following line was particularly important: We must teach the students we have, not the students we want (or the students we imagine we were back in the mists of time).

I have been reading through a very interesting review paper Mott-Anderson Transition in Molecular Conductors: Influence of Randomness on Strongly Correlated Electrons in the κ-(BEDT-TTF)2X System by Takahiko Sasaki It reviews some very nice experiments done by Sasaki and collaborators where they used X-ray irradiation to systematically vary the amount of disorder. There are several things I find puzzling about the experimental results for X=Cu[N(CN)2]Br.  I also think they are inconsistent with the offered interpretation in terms of Anderson localisation. It is observed that irradiation does longer than 200 hours drive the material from a metallic phase to a Mott insulating phase. First, I don't think invoking Anderson localization is relevant because the amount of disorder is relatively small , compared to the electronic bandwidth. Specifically, even for doses of 200 hours the sample is still a superconductor [probably d-wave] with a Tc of about 6 K, reduced from about 12

I think I heard a distinguished mathematical ecologist claim that there are very few actual systems which do behave like the simple textbook models. Hence, I was very interested to see in Science this week a really nice experimental paper Generic Indicators for Loss of Resilience Before a Tipping Point Leading to Population Collapse  by Lei Dai, Daan Vorselen, Kirill S. Korolev, and Jeff Gore Theory predicts that the approach of catastrophic thresholds in natural systems (e.g., ecosystems, the climate) may result in an increasingly slow recovery from small perturbations, a phenomenon called critical slowing down. We used replicate laboratory populations of the budding yeast Saccharomyces cerevisiae for direct observation of critical slowing down before population collapse. We mapped the bifurcation diagram experimentally and found that the populations became more vulnerable to disturbance closer to the tipping point. Fluctuations of population density increased in size and durati

Previously I have posted about the importance of choosing a good title for your paper. Perhaps on a lighter note, I stumbled across this , which shows that sometimes people use really creative titles.