DiTe2: Calculating the diffusion tensor for flexible molecules

Abstract

We report on an extended hydrodynamic modeling of the friction tensorial properties of flexible molecules including all types of natural, Z‐Matrix like, internal coordinates. We implement the new methodology by extending and updating the software DiTe [Barone et al. J. Comput. Chem. 30, 2 (2009)]. DiTe (DIffusion TEnsor) implements a hydrodynamic modeling of the generalized translational, rotational, and configurational friction and diffusion tensors of flexible molecules in which flexibility is described in terms of dihedral angles. The new tool, DiTe2, has been renewed to include also stretching and bending types of internal mobility. Furthermore, DiTe2 is able to calculate the friction and diffusion tensors along collective (or reaction) coordinates defined as linear combinations of the internal natural ones. A number of tests are reported to show the new features of DiTe2. As leitmotiv for the tests, the calmodulin protein is taken into consideration, described both at all‐atom and coarse‐grained levels. © 2018 Wiley Periodicals, Inc.

Multiscale modeling of reaction rates: application to archetypal SN2 nucleophilic substitutions

“…The evaluation of the dissipative properties was based on a hydrodynamic approach. 24 The system, immersed in a homogeneous isotropic fluid of known viscosity, is described as a set of rigid fragments (made of atoms or groups of atoms) connected via different types of joints allowing for stretching, bending and torsional motions. Internal coordinates can be defined as linear combinations of such Z-Matrix like degrees of freedom, and the friction tensor elements along these generalized coordinates can be evaluated.…”

“…The DiTe2 software recently developed in our laboratory, 24 allows to compute the friction along generalized internal coordinates defined as linear combinations of internal coordinates, q, i.e. s = j cjqj, where the coefficients of the combination are those provided by Equation 9.…”

“…Using the map between Cartesian and Z-Matrix coordinates (see ref. 24 where the partial derivatives ∂R/∂qj are computed analytically in DiTe2, 24 while the partial derivatives ∂qj/∂s can be obtained numerically from the qj(s) plots once the reaction coordinate has been built from the IRC reaction path. In the Appendix it is shown as a weak hydrodynamic coupling is observed between the rigid-body like motions of the system and s. This justifies the employment of the 1D Fokker-Planck operator in Equation 2, where just the internal friction coefficient enters in the expression.…”

“…1,9,19 However, for a chemist it is more natural to reason in terms of internal degrees of freedom (bonds, bond angles, and torsion angles). For this purpose, we have recently developed a software tool, DiTe2, 24 for the calculation of the diffusion tensor of flexible molecules. As discussed in the next Section, DiTe2 allows to compute diffusive properties along collective coordinates defined as linear combinations of Z-Matrix-like internal coordinates.…”

Stochastic modeling of macromolecules in solution. I. Relaxation processes

“…via the Rotne-Prager model. 71,87 For the sake of completeness, the table below compares the principal values of the rotational diffusion tensor of 2-alanine calculated with and without hydrodynamic interactions using, respectively, effective radii of 0.5 Å and 2.0 Å. The principal values are of the same order…”