Wednesday, 27 April 2016

Water revisited: Molecule of the Month for May 2016

Over two years ago, in this series, I attempted to describe the unique role of the water molecule in Biology. Recently the world of Quantum Mechanics has collided with "classical" Biology in a way that could radically alter our thinking about many Biochemical phenomena, from catalysis and the mysteries of avian migration to electron transfer and photosynthesis. I don't intend to discuss these topics in this post, but a glance at the success of Jim Alkalili and JohnJoe McFadden's crusade to alert the world of the potential value of considering quantum level explanations for unexplained Biological phenomena, is gaining momentum! However in this post, I intend to combine a second look at water with a celebration of the 400th anniversary of the death of our greatest writer of English, William Shakespeare.  I have used some quotes from the cannon of the Bard in order  to structure this months return to water as my molecule of the month. [You will find a general introduction to water in my February 2014 blog post on water here.]

Smooth runs the water where the brook is deep

Briefly, water molecules comprise two atoms of hydrogen (white) and one of oxygen (red) in a relationship that is generally very stable. We know this from our own experiences: a glass of tap water brings no surprises! If we touch it, are we not cleansed? If we drink, it, is our thirst not quenched? Sorry, couldn't resist a little Shakespearean pastiche! The colourless, odourless liquid that is a glass of tap water just sits quietly in the glass: we are only aware of its presence when  it refracts incident light. Famously, a stick placed in water appears to bend away from the observer at the point of entry. [Do you know any liquids that bend a rod in the other direction? If not, look here. This is an excellent example of a robust physical model that allows predictions to be made]. Water may be a solid (ice is formed at temperatures below zero Celsius), liquid until 100 degrees Celsius, where it boils and forms a gas, steam. The inter-molecular forces that result in water adopting a relatively non-volatile liquid form at room temperature (or perhaps more importantly at 37 degrees Celsius) should be familiar to readers for my Blogs (take a look at this nice wiki site for a refresher). Perhaps the two features of water that are on the must learn list for Biochemists are its properties as a solvent,  as a model for understanding hydrogen bonding networks and polarisation effects in catalysis.

To unpathed waters, undreamed shores

The recent observation that water molecules trapped inside crystals of Beryl (this will be more familiar to you in its transparent, bright green form, as emerald: the formula for which is Be3Al2(Si O3)6) points to a quantum effect that I recently discussed in connection with a visiting speaker at Sheffield, Professor Nigel Scrutton, from the University of Manchester. Beryl crystals, under some conditions are arranged at the molecular level into structures that contain regular hexagonal cavities. These cavities are just large enough to trap a single water molecule. What was unexpected was that the hydrogens can exist at 1 of 6 different places in the crystal, giving rise to a new structural form for the water molecule. It has been suggested by the team at Oak Ridge National Laboratory led by physicist Alexander Kolesnikov in a recent publication that the hydrogens in water, inside the crystal lattice, can tunnel through the crystal "wall" in order to adopt this unusual conformation. I like this description of quantum tunneling from Forbes Magazine 

Tunneling is one of the strange and wonderful features of quantum mechanics, the type of physics that takes over at very small scales. When a particle like a hydrogen atom meets a wall, quantum tunneling allows it to sometimes go through without paying the energy toll classical physics would require for the atom to go over or around.

I can understand the principle of tunneling; and I respect the value of the  tunneling concept  in explaining otherwise inexplicable observations, but when I read abstracts like:

Using neutron scattering and ab initio simulations, we document the discovery of a new “quantum tunneling state” of the water molecule confined in 5 Å channels in the mineral beryl, characterized by extended proton and electron delocalization. We observed a number of peaks in the inelastic neutron scattering spectra that were uniquely assigned to water quantum tunneling. In addition, the water proton momentum distribution was measured with deep inelastic neutron scattering, which directly revealed coherent delocalization of the protons in the ground state,

Figure captionI have to sit down and think much harder than usual! But that's all part of the challenge and joy of Science! It has been demonstrated by Dudovich's group (and I am pretty sure others that I am ignorant of) experimentally that electrons tunnel through barriers: by measuring a photon emission that can only occur if an electron escapes from its "orbital" a group of scientists at the Weizmann Institute provided a nice quantitative demonstration of the extremely fast timescales of electron tunneling. Hydrogen atoms tunnel as well, but the dynamics and the distances are considerably smaller than the tunneling properties of electrons and require greater considerations of steric constraints in protein molecules. Nevertheless, we must consider the likely placing of an electron and a hydrogen more as a probability rather than as a fixed set of 3 dimensional coordinates. The structure adopted by this quantum state of water is best described by a smeared pair of concentric rings. The molecule can adopt 6 configurations at once. It is difficult (especially for me) to decide what impact this observation might have in Biology, but I believe Biologists need to start a greater level of dialogue with physicists, so we can evaluate these concepts more critically.

Cease thy counsel, for thy words fall into my ears as priceless as water into a sieve

My next quotation from Shakespeare perhaps anticipates the tunneling phenomenon. I am coming round to the view that was expressed by Nigel Scrutton when I last heard him speak. And it is that we often assume that we know everything about enzymes, but of course the smartest scientists know that just isn't true. In fact it reminds me of a non-Shakesperean quote that I have used before, attributed to Physics Nobel Laureate, Richard Feynman

Anyone who says they understand quantum mechanics, doesn't understand quantum mechanics

That is, we are still to fully appreciate the role of water in Biology. As Shakespeare says, it is a "priceless" commodity: it is the medium in which all intracellular and most intercellular events are orchestrated. In fact we go to special lengths to keep water out in order to contain it (eg by elaborating cell membranes and hydrophobic cavities in enzymes and active sites). But on the other hand the concentration of water molecules is around 55.5M. Hence, priceless water in a sieve! This dichotomy needs a resolution and this will come with time as we find explanations to accommodate the anomalies in Bio-molecular behaviour. And so to my final quote from the Bard of Stratford.

Glory is like a circle in the water, which never ceaseth to enlarge itself, till by broad spreading, it disperses to naught

Shakespeare was again prescient! Clearly the drop is the particle and the ripples the waves. He understood wave particle duality in quantum mechanics over 300 years before modern science. Maybe he was also hinting at the possibility of dispersion of interactions brought about by the multiple possibilities of the conformations of water. Let us celebrate William Shakespeare with a long cool glass of water and try to bring to Biochemistry the insight Shakespeare brought to human behaviour through his beautiful use of language!  

1 comment:

  1. Good post! I am also going to write a blog post

    about this... thanks

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