Quantum-classical calculations of X-ray photoelectron spectra of polymers-Polymethyl methacrylate revisited.

In this work, we apply quantum mechanics/molecular mechanics (QM/MM) approach to predict core-electron binding energies and chemical shifts of polymers, obtainable via X-ray photoelectron spectroscopy(XPS), using polymethyl methacrylate as a demonstration example. The results indicate that standard parametrizations of the quantum part (basis sets, level of correlation) and the molecular mechanics parts (decomposed charges, polarizabilities, and capping technique) are sufficient for the QM/MM model to be predictive for XPS of polymers. It is found that the polymer environment produces contributions to the XPS binding energies that are close to monotonous with the number of monomer units, totally amounting to approximately an eV decrease in binding energies. In most of the cases, the order of the shifts is maintained, and even the relative size of the differential shifts is largely preserved. The coupling of the internal core-hole relaxation to the polymer environment is found to be weak in each case, amounting only to one or two tenths of an eV. The main polymeric effect is actually well estimated already at the frozen orbital level of theory, which in turn implies a substantial computational simplification. These conclusions are best represented by the cases where the ionized monomer and its immediate surrounding are treated quantum mechanically. If the QM region includes only a single monomer, a couple of anomalies are spotted, which are referred to the QM/MM interface itself and to the neglect of a possible charge transfer.

Studies of pH-Sensitive Optical Properties of the deGFP1 Green Fluorescent Protein Using a Unique Polarizable Force Field.

The aim of this study is to identify the responsible molecular forms for the pH dependent optical properties of the deGFP1 green fluorescent protein mutant. We have carried out static and dynamic type calculations for all four protonation states of the chromophore to unravel the contributions due to finite temperature and the flexible protein backbone on the pH dependent optical properties. In particular, we have used a combined molecular dynamics and density functional-molecular mechanics linear response approach by means of which the optical property calculations were carried out for the chromophore in the explicitly treated solvent and bioenvironment. Two different models were used to describe the environment-electronic embedding and polarizable electronic embedding-accounting for the polarization of the chromophore and the mutual polarization between the chromophore and the environment, respectively. For this purpose a polarizable force field was derived quantum mechanically for the protein environment by use of analytical response theory. While the gas-phase calculations for the chromophore predict that the induced red shift going from low to high pH is attributed to the change of molecular forms from neutral to zwitterionic, the two more advanced models that explicitly account for the protein backbone attribute the pH shift to a neutral to anionic conversion. Some ramifications of the results for the use of GFPs as pH sensors are discussed.