Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations.

Area of Science:

• Computational chemistry
• Biophysics
• Molecular dynamics

Background:

• Understanding molecular rotational dynamics is crucial in biophysics.
• Anisotropic rotational diffusion describes complex molecular motion.
• Existing methods may have limitations in accuracy and applicability.

Purpose of the Study:

• To present a novel method for calculating the fully anisotropic rotational diffusion tensor.
• To validate the method using molecular dynamics simulations.
• To compare simulation-derived tensors with hydrodynamic predictions.

Main Methods:

• Fitting the time-dependent covariance matrix of quaternions describing rigid-body rotational dynamics.
• Utilizing explicit analytical expressions for covariances derived by Favro.
• Employing optimal rigid-body superposition for molecular structure alignment.
• Determining the rotational diffusion tensor via fitting or Laplace transformation and matrix diagonalization.

Main Results:

• The method successfully calculates anisotropic rotational diffusion tensors from simulation trajectories.
• Analytical expressions for uncertainty quantification were derived and compared with Brownian dynamics simulations.
• Microsecond-scale trajectories of B-DNA dodecamer and myoglobin were analyzed.
• Calculated tensors showed good agreement with hydrodynamic predictions.

Conclusions:

• The presented method provides an accurate way to determine anisotropic rotational diffusion tensors from molecular dynamics simulations.
• This approach is applicable to complex biological molecules.
• The findings support the utility of molecular dynamics simulations in predicting molecular rotational behavior.