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Computational two-dimensional infrared spectroscopy without maps: N-methylacetamide in water.
Pierre-André Cazade1, Tristan Bereau, Markus Meuwly
1Department of Chemistry, University of Basel , Klingelbergstrasse 80, 4056 Basel, Switzerland.
The Journal of Physical Chemistry. B
|April 2, 2014
Summary
This study computed two-dimensional infrared spectra for N-methylacetamide (NMAH) and N-methylacetamide-d3 (NMAD) using various electrostatic models. Point charge models offer a good balance of accuracy and computational efficiency for simulating these systems.
Area of Science:
- Computational chemistry
- Spectroscopy
- Molecular dynamics
Background:
- Two-dimensional infrared (2D IR) spectroscopy is a powerful technique for studying molecular dynamics.
- Accurate force fields are crucial for reliable simulations of 2D IR spectra.
- Different electrostatic models, such as point charge (PC) and multipolar (MTP) representations, can impact simulation outcomes.
Purpose of the Study:
- To compute and analyze the 2D IR spectra of N-methylacetamide (NMAH) and N-methylacetamide-d3 (NMAD) in water and heavy water.
- To evaluate the performance of different force field parametrizations, from standard point charge (PC) to multipolar (MTP) models, in reproducing experimental 2D IR spectra.
- To investigate the influence of electrostatic model choice on the frequency-frequency correlation function (FFCF) and its time scales.
Main Methods:
- Calculated 2D IR spectra using force field parametrizations including PC and MTP electrostatic models.
- Optimized nonbonded parameters for MTP models using thermodynamic data.
- Determined frequency trajectories and FFCFs from explicit frequency calculations on approximately 10^6 snapshots, avoiding traditional mapping approaches.
- Analyzed FFCFs to identify rapid and longer time scales, comparing simulation results with experimental data.
Main Results:
- FFCFs exhibit a rapid time scale (around 50 fs) followed by one or two longer time scales (up to 2-3 ps), consistent with experimental observations.
- All interaction models, when fitted empirically, yield three time scales in the FFCF.
- Simulations using PC models show good agreement with experimental correlation times (0.7-1 ps) when assuming two time scales and fixing the short time scale.
- MTP models result in longer decay times and reduced FFCF amplitudes compared to PC models.
- PC-based models demonstrate comparable performance to MTP-based models for NMAD in D2O.
Conclusions:
- Point charge (PC) models provide a reliable and computationally efficient approach for simulating 2D IR spectra of N-methylacetamide (NMAH) and N-methylacetamide-d3 (NMAD), particularly for NMAD in D2O.
- The choice of electrostatic model influences the longer time scales and amplitudes in the FFCF.
- PC models are recommended for investigations involving peptide and protein simulations due to their good performance and efficiency.
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