Proton transfers from and to biomolecules

What are proton transfers?

Proton transfers happen between acids and bases when a proton moves from the acidic molecule or part of a molecule to the basic molecule or the basic part of a molecule. Protons are the nuclei of hydrogen atoms and therefore the lightest atom nuclei in chemistry. They are positively charged and prefer places where free or lone electron pairs are around. Acids have a weakly bound proton, and bases have an attractive free electron pair. Water is both an acid and a base. Here is the pair of acetic acid and water:

The pH is used to measure how acidic an aqueous solution is. The larger the number, the less acidic it is. Pure water has a pH around 7.

Why do we need to simulate proton transfers?

How to simulate proton transfers in solution

Protons are very light particles. They do not exactly follow the classical (Newton's) laws of motion. In principle, quantum mechanics can describe exactly the behaviour of protons. There are many methods to do quantum mechanical calculations:

• Ab initio calculations look for the ground state (or a particular excited state) of small molecules from 'first principles' (physical laws). In principle, they can be done as exactly as required. Only very small systems possible (some dozen atoms).
• Semi-empirical calculations are similar to the ab initio calculations, but the most time-consuming parts of the calculation are omitted, and empirical values are inserted instead. Larger systems possible (some hundred atoms).
• Density functional calculations do the most time-consuming part of the more accurate ab-initio calculations only approximately, but can be still more accurate than the fastest ab initio calculations. Quite large systems possible (some dozen to some hundred atoms).
• Quantum dynamics describes the motion of a molecular system instead of looking for a stable state. Some few particles can be calculated (note that an atom consists of more than one particle: the nucleus and the electrons).
• Mixed simulations: some particles of interest (protons or electrons) are calculated quantum mechanically. The large environment is simulated using molecular dynamics. Large systems possible (some ten thousand atoms) while the part of interest is still described as accurately as required. Many problems are still to solve.

Here are some examples

Two pictures of a crystal (benzoic acid, 25 unit cells) in water Van der Waals representation Ball and stick representation

Movies of proton transfers: Benzoic acid hexamer 500 K Formic acid - water dimer 300 K

Select the movie or picture and click once more to start the movie

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Salomon Billeter, 30-Sept-97