The Molecule in Water
Draft for the author's reading and rewriting. Established science throughout; the framing and the leaps are the author's.
The medium of water is one of the most ubiquitous substances we often take for granted. Water is everywhere in our surround and humans may never afford to be far removed from a source of water.
Water is one of the most interesting substances in the universe, with a molecular geometry and thermodynamics which allows for three separate phase transitions.
Water is used everywhere across my books as a medium which allows for the creating of many metaphors and which accommodates many different forms and dynamics of fluid/wave systems.
One of my favorite books is “If nothing else will level you, water will” by poet A.R. Ammons.
Every chapter that follows takes place in water. Not beside it, not over it — in it. The pairing, the charged membrane, the electrostatic protein: each is a relation staged inside a medium, and the medium is never neutral scenery. This chapter looks at the medium itself, because the flat reading of water — the background liquid in the diagram, drawn as empty blue — is the oldest flat reading in biology. Water is called the universal solvent, and the phrase is almost right in a way worth pausing over. No other liquid dissolves more different substances [3]. But the interesting fact is not what water dissolves. It is what water refuses to dissolve, and how both the yes and the no are the same property seen from two sides.
The molecule: a bent magnet for charge
One oxygen, two hydrogens. That is the whole inventory, and it should not be enough to run a planet. What makes it enough is how the electrons are shared. Oxygen holds the shared electrons closer to itself than hydrogen does, so the molecule is not evenly charged: the oxygen end sits slightly negative, the two hydrogens slightly positive. And the molecule is bent — the two O–H arms meet at an angle of about 104.5 degrees, not opposite each other [2]. A straight molecule's slight charges would cancel; a bent one's do not. The result is a permanent electric dipole, a molecule the size of a few tenths of a nanometre that behaves like a small permanent magnet for charge. This is the atomic structure doing one job: making every water molecule reach, permanently, for every charged thing near it. The dielectric strength, the ordered shells around proteins and membranes — both chapters that follow stand on this one bent geometry [1].
The geometry: a tetrahedron that does not close
Each water molecule has four arms: the two hydrogens, which offer positive charge, and the two lone pairs on the oxygen, which offer negative. Four arms, pushing apart, pointing to the corners of a tetrahedron. This is worth noticing in a book that keeps finding its architecture in shapes: the first shape life builds with is the tetrahedron, not by choice but by arithmetic — four arms, mutual repulsion, the tetrahedron is what remains. In ice, each molecule uses all four arms to grip four neighbours, and the grip locks into an open, hexagonal lattice — the reason snowflakes carry six arms, and the reason ice floats: the open lattice holds the molecules farther apart than the jostling liquid, so the solid is the lighter phase [2]. In liquid water the same geometry survives in broken form — each molecule holds three to four neighbours at any instant, trading them billions of times per second. The tetrahedron is the plan; the liquid is the plan, interrupted.
The thermodynamics: bonds that pay for everything
A hydrogen bond is weak — roughly a twentieth of a covalent bond — and it lasts a few picoseconds. Water's thermodynamics is the accounting of these small, temporary bonds made in enormous numbers. Heat capacity: to raise water's temperature you must break bonds as well as speed molecules, so water soaks up heat and lets go of it slowly — the reason the body holds its temperature and the sea holds the climate. Evaporation: to leave the liquid, a molecule must break every bond it holds, which is why sweat cools and why the oceans do not boil away. And then the hydrophobic effect, the no side of the solvent. Water cannot bond to an oily surface, so the molecules against that surface lose their choice of neighbours and arrange themselves more orderly than they would like — an entropy debt. The way the debt is paid is for the oily things to huddle together and expose the least surface. Nothing attracts them; the water's own demand for its geometry pushes them together [1, 4]. This one effect folds every protein and builds every membrane in this book. The solvent dissolves by charge and assembles by exclusion — both, in the same liquid.
The phases: the same molecule, three arrangements
At ordinary pressures water shows three phases — ice, liquid, vapour — and the transitions between them are the phase changes this book keeps meeting in other materials. Melt at 0 °C, boil at 100 °C, and between them no sharp border: the liquid is already a shifting mixture of locally ordered regions and free molecules, which is why the phase transition into ice can happen suddenly once nucleation begins. The anomalies are the teaching: solid less dense than liquid; melting point higher than a molecule this light has any right to; liquid surviving to depths of the ocean and into cells that never freeze. Every one of them traces back to the hydrogen bond — the same weak arm that pays the thermodynamic bills sets where the phase lines fall [2, 3]. And the transitions are reversible and ordinary: no exotic physics, no rarity. What is remarkable is that a molecule this simple holds a phase diagram this generous — three stable phases at the temperatures of a small planet, each one a different answer to the same tetrahedral geometry.
So, the so-called universal solvent says yes to almost anything charged, and its no — the hydrophobic exclusion — is the yes that builds the architecture. The medium is not between the molecules of life. It is one of the parties to every relation they hold.
Water has a relationship with electromagnetic charge and bears a close relationship to how other physiological substances either attract or repel water.
Water becomes a shadowy architect in molecular design and is a critically important shape agent.
References (to be checked against the originals)
- Ball, P. (2008). Water as an active constituent in cell biology. Chemical Reviews 108, 74–108.
- Pauling, L. (1960). The Nature of the Chemical Bond, 3rd ed. Cornell University Press.
- Ball, P. (1999). Life's Matrix: A Biography of Water. University of California Press.
- Chaplin, M. (2006). Do we underestimate the importance of water in cell biology? Nature Reviews Molecular Cell Biology 7, 861–866.