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Markus Meuwly

Publications and source records attributed to Markus Meuwly.

3 recordsLinked to original sources

2D IR spectra of cyanide in water investigated by molecular dynamics simulations

Using classical molecular dynamics simulations, the 2D infrared (IR) spectroscopy of CN − solvated in D 2 O is investigated. Depending on the force field parametrizations, most of which are based on multipolar interactions for the CN − molecule, the frequency-frequency correlation function and observables computed from it differ. Most notably, models based on multipoles for CN − and TIP3P for water yield quantitatively correct results when compared with experiments. Furthermore, the recent finding that T 1 times are sensitive to the van der Waals ranges on the CN − is confirmed in the present study. For the linear IR spectrum, the best model reproduces the full widths at half maximum almost quantitatively (13.0 cm −1 vs. 14.9 cm −1 ) if the rotational contribution to the linewidth is included. Without the rotational contribution, the lines are too narrow by about a factor of two, which agrees with Raman and IR experiments. The computed and experimental tilt angles (or nodal slopes) α as a function of the 2D IR waiting time compare favorably with the measured ones and the frequency fluctuation correlation function is invariably found to contain three time scales: a sub-ps, 1 ps, and one on the 10-ps time scale. These time scales are discussed in terms of the structural dynamics of the surrounding solvent and it is found that the longest time scale (≈10 ps) most likely corresponds to solvent exchange between the first and second solvation shell, in agreement with interpretations from nuclear magnetic resonance measurements.

Journal of Chemical Physics

Molecular dynamics simulation of nitric oxide in myoglobin

The infrared (IR) spectroscopy and ligand migration of photodissociated nitric oxide (NO) in and around the active sites in myoglobin (Mb) are investigated. A distributed multipolar model for open-shell systems is developed and used, which allows one to realistically describe the charge distribution around the diatomic probe molecule. The IR spectra were computed from the trajectories for two conformational substates at various temperatures. The lines are narrow (width of 3–7 cm –1 at 20–100 K), in agreement with the experimental observations where they have widths of 4–5 cm –1 at 4 K. It is found that within one conformational substate (B or C) the splitting of the spectrum can be correctly described compared with recent experiments. Similar to photodissociated CO in Mb, additional substates exist for NO in Mb, which are separated by barriers below 1 kcal/mol. Contrary to full quantum mechanical calculations, however, the force field and mixed QM/MM simulations do not correctly describe the relative shifts between the B- and C-states relative to gas-phase NO. Free energy simulations establish that NO preferably localizes in the distal site and the barrier for migration to the neighboring Xe4 pocket is Δ G B→C = 1.7–2.0 kcal/mol. The reverse barrier is Δ G B←C = 0.7 kcal/mol, which agrees well with the experimental value of 0.7 kcal/mol, estimated from kinetic data.

Journal of Physical Chemistry

Structure, spectroscopy and dynamics of layered H2O and CO2 ices

Molecular dynamics simulations of structural, spectroscopic and dynamical properties of mixed water–carbon dioxide (H 2 O–CO 2 ) ices are discussed over temperature ranges relevant to atmospheric and astrophysical conditions. The simulations employ multipolar force fields to represent electrostatic interactions which are essential for spectroscopic and dynamical investigations. It is found that at the water/CO 2 interface the water surface acts as a template for the CO 2 component. The rotational reorientation times in both bulk phases agree well with experimental observations. A pronounced temperature effect on the CO 2 reorientation time is observed between 100 K and 200 K. At the interface, water reorientation times are nearly twice as long compared to water in the bulk. The spectroscopy of such ices is rich in the far-infrared region of the spectrum and can be related to translational and rotational modes. Furthermore, spectroscopic signatures mediated across the water/CO 2 interface are found in this frequency range (around 440 cm −1 ). These results will be particularly important for new airborne experiments such as planned for SOFIA.

Physical Chemistry Chemical Physics