The physical properties and function of biological tissues depend critically upon the hydration of proteins; in particular, their thermal, mechanical, and chemical stability. Here, we show quantitatively how thermal, mechanical, and chemical conditions can denature a protein. An elastic instability criterion is applied to localised ab initio quantum mechanics simulations of water and amide bond energies to predict both denaturing conditions and the effect of water on the glass transition temperature of a protein. The kinetics of bond instability for denaturation over a wide range of time scales is quantified by an expression for a second order phase change using parameters derived directly from the quantum simulations. We also show how the zero point energy of vibrations in a potential energy well of intermolecular bonding can differentiate between crystal and amorphous states of matter and their corresponding transition temperatures; this is illustrated by calculating the crystal melt and glass transition temperatures of water.