Orientation of non-spherical protonated water clusters revealed by infrared absorption dichroism

Abstract

Infrared continuum bands that extend over a broad frequency range are a key spectral signature of protonated water clusters. They are observed for many membrane proteins that contain internal water molecules, but their microscopic mechanism has remained unclear. Here we compute infrared spectra for protonated and unprotonated water chains, discs, and droplets from ab initio molecular dynamics simulations. The continuum bands of the protonated clusters exhibit significant anisotropy for chains and discs, with increased absorption along the direction of maximal cluster extension. We show that the continuum band arises from the nuclei motion near the excess charge, with a long-ranged amplification due to the electronic polarizability. Our experimental, polarization-resolved light–dark difference spectrum of the light-driven proton pump bacteriorhodopsin exhibits a pronounced dichroic continuum band. Our results suggest that the protonated water cluster responsible for the continuum band of bacteriorhodopsin is oriented perpendicularly to the membrane normal.

Salt Bridge in Aqueous Solution: Strong Structural Motifs but Weak Enthalpic Effect

“…The corresponding terms kosmotropic and chaotropic indicate that a specific ion can make the hydrogen bond network more rigid–kosmotropic or more flexible–chaotropic. An interesting related ongoing debate is whether the properties of solvating water molecules determine the behavior of proteins or whether the properties of the protein surface determine the behavior of the surrounding water (‘enslaved water’ versus ‘enslaving water’) 15 – 17 .…”

Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient

“…The complex exit cluster PLS, with Glu 194 and 204, has multiple tautomers for the proton loaded state. IR spectroscopy ( Daldrop et al, 2018 ) and simulations ( Bashford and Gerwert, 1992 ; Spassov et al, 2001 ; Phatak et al, 2008 ) support a protonated water stabilized by the two anionic glutamic acids, while the proton can also be trapped by a hydrogen bonded pair with one acid protonated and a water nearby ( Song et al, 2003 ; Phatak et al, 2008 ). An advantage of using a cluster PLS is that it can use the multiple ways to store the proton to be less sensitive to mutation.…”

The influence of molecular vicinity (expressed in terms of dielectric constant) on the infrared spectra of embedded species in ices and solid matrices

“…Such behavior might also be related with asymmetric band proles of such vibration modes in the ices. [45][46][47][48] The inset gure, with the spectrum prole, in the right part of Fig. 6 illustrates the inuence of water molecular cluster in the H 2 O n 1 band of typical water ice or liquid (taken from Choe et al 46 ).…”