New Haven, Conn. -- This week in Science, Yale researchers present "roadmaps" showing that shared protons, a common loose link between two biological molecules, simply vibrate between the molecules as a local oscillator, rather than intimately entangling with the molecular vibrations of the attached molecules.
Led by Professor Mark Johnson in the Department of Chemistry, the new data reveal distinct, isolated vibrational patterns, solely associated with the bridging proton, that change dramatically according to the chemical properties of the tethered molecules.
In effect, the paper reports clear "roadmaps" for the widely varying, characteristic vibrational frequencies that occur when an excess proton binds together simple nitrogen and oxygen containing molecules.
Rather than studying the proton-trapped pairs of molecular in crystals or in solution at room temperature, as has been common in the past, Johnsons team made their measurements of proton interactions with 18 simple molecules by isolating them in the gas-phase and cooling them to about 50 Kelvin by taking advantage of recent advances in argon nanomatrix spectroscopy.
"Historically it has been very difficult to isolate the signature of an excess proton in a complex environment like a cell membrane, and say with confidence Aha, I have one," said Johnson. "The proton is in constant motion in a warm, disordered medium, which causes its natural vibrational frequency to spread out over a huge spectral range. As a result, its signature is often thought to comprise the continuous junk background in the vibrational spectra of protonated samples."
"When we cool the isolated systems, the protons sing out their sharp vibrational frequencies, and therefore provide clear signatures that are characteristic of each kind of interaction," said Johnson.