An Empirical IR Frequency Map for Ester C═O Stretching Vibrations

Abstract

We present an approach for parametrizing spectroscopic maps of carbonyl groups against experimental IR absorption spectra. The model correlates electric fields sampled from molecular dynamics simulations with vibrational frequencies and line shapes in different solvents. We perform an exhaustive search of parameter combinations and optimize the parameter values for the ester carbonyl stretching mode in ethyl acetate by comparing to experimental FTIR spectra of the small molecule in eight different solvents of varying polarities. Hydrogen-bonding solvents require that the peaks are fit independently for each hydrogen bond ensemble to compensate for improper sampling in molecular dynamics simulations. Spectra simulated using the optimized electrostatic map reproduce C═O IR absorption spectra of ethyl acetate with a line center RMSD error of 4.9 cm(-1) over 12 different solvents whose measured line centers span a 45 cm(-1) range. In combination with molecular dynamics simulations, this spectroscopic map will be useful in interpreting spectra of ester groups in heterogeneous environments such as lipid membranes.

Dynamic effect of polymers at the surfactant–water interface: an ultrafast study

“…1A), containing ester carbonyls precisely located within the 1-nanometer interface between the hydrophilic and hydrophobic environments, and therefore these carbonyl groups report on local water environments. 26,27 Specifically, in this study two-dimensional infrared (2D IR) spectroscopy is used to measure the effects of acrylamide (AM) monomers and polyacrylamide (PAM) polymers (Fig. 1B and C) on the sub-picosecond frequency fluctuations of the carbonyls.…”

Site-Specific Peptide Probes Detect Buried Water in a Lipid Membrane

“…Agreement between computed and experimental line shapes implies that MD simulations accurately sample the molecular ensembles observed in the experiment. Over the past decade, these methods have proven useful in interpreting 2D IR spectra of biomolecules, as well as providing a quantitative framework for selecting potential isotope-labeled sites within proteins (47)(48)(49)(50)(51)(52)(53)(54)(55)(56). Here, we use 2D IR spectra of isotope-labeled pHLIP in combination with these computational tools to probe solvent penetration into a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayer surrounding a transmembrane peptide.…”

Solvent-Independent Anharmonicity for Carbonyl Oscillators

“…Other more sophisticated multi-parameter fitting methods have been introduced that also show that the effects are largely electrostatic in origin, and this is the primary application of these fits. 10,13–15 …”