Chemists detail reasons behind H2O’s central role in chemistry of life

By Robert Sanders, Public Affairs

22 March 2001 | Much of the chemistry of life starts with a simple reaction in water — the plucking of a proton or hydrogen ion from weak acids like nucleic acids and some amino acids, the building blocks of DNA and proteins.

Berkeley theoretical chemist David Chandler and his colleagues have now described how this basic ionization reaction takes place.

“Ionization is just pulling protons off of molecules, and shuttling protons around an aqueous solution is basic to life,” Chandler said.

The molecular details of these ionization processes have never been measured before because the event is so rare — once an hour for any given molecule — and when it does happen it's over quickly, on the order of a trillionth of a second. Yet, the separation of a proton — a hydrogen atom missing its one electron — from a molecule is the essential first step in all acid/base chemical reactions.

All organic molecules consist of a tinker-toy backbone of mostly carbon, nitrogen and oxygen with lots of hydrogen atoms stuck on like Christmas ornaments. When weak acids or bases land in a pool of water, according to the team's calculations, these hydrogen atoms act as if they were connected by rubber bands to the backbone atoms, constantly flying outward and snapping back.

Every so often, the surrounding water molecules, each with a small electric field, line up and create a large field that pulls the hydrogen ion farther from the parent molecule than usual — as much as five neighbors away. Most of the time, the electric field quickly dies away and the proton snaps back.
“The electric field vanishes rapidly — it only lives for tens of femtoseconds — and then the proton just comes sweeping back because there is this strong electrical attraction from the chemical bond,” he said. A femtosecond is a millionth of a billionth of a second.

Once every billionth of a second or so, however, the pathway back to association — a wire of hydrogen bonds — breaks, and a free proton is created.

“The proton is pulled far away 100s and 100s of times without leading to auto-dissociation,” Chandler said. “This is the part that is surprising and that people didn't know. What finally leads to dissociation is, somewhere along this wire of hydrogen bonds, when there just happens to be a big electric field that's driven the proton away, by accident the hydrogen bond wire breaks and this proton is stuck off in left field.”

Once the proton is liberated, it wanders through the liquid, free to participate in many other chemical reactions until it recombines with an hydroxide ion to make water again.

This detailed picture comes from the team's calculations on what happens in pure water, which can be considered a weak acid. Chandler and his team calculated these detailed reactions by rethinking statistical mechanics — the branch of physical chemistry that deals with the chances of going from one state to another, such as from a neutral molecule in water to an ionized molecule.

“Defining a pathway between one state and another is a very famous optimization problem, and our technique is part of the solution to that general class of problems,” Chandler said. “This is a big generalization of thermodynamics and statistical mechanics.”