Rotational and translational diffusion of liquid n-hexane: EFP-based molecular dynamics analysis

Abstract

Molecular Dynamics (MD) simulations based upon the Effective Fragment Potential (EFP) method are utilized to provide a comprehensive assessment of diffusion in liquid n-hexane. We decompose translational diffusion into components along and orthogonal to the long axis of the molecule. Rotational diffusion is decomposed into tumbling and spinning motions about this axis. Our analysis yields four corresponding diffusion coefficients which are related to diagonal entries in the complete 6 ´ 6 diffusion tensor accounting for the three rotational and three translational degrees of freedom, and for the potential coupling between them. However, coupling between different degrees of freedom is expected to be minimal for a natural choice of molecular body-fixed axis, so then off-diagonal entries in the tensor are negligible. This expectation is supported by a hydrodynamic analysis of the diffusion tensor which treats the liquid surrounding the molecule being tracked as a viscous continuum. Thus, the EFP MD analysis provides a comprehensive characterization of diffusion, and also reveals expected shortcomings of the hydrodynamic treatment particularly for rotational diffusion.

Intermolecular interactions in clusters of ethylammonium nitrate and 1-amino-1,2,3-triazole

“…49–52 The EFP method was originally developed to describe aqueous solvent effects on biomolecular systems and chemical reaction mechanisms. More recently, the method has been generalized to evaluate intermolecular interactions in systems such as molecular clusters, 49,51 protein–ligand interactions, 75,76 diffusion in liquids, 77,78 and ILs. 4,79 The EFP method decomposes the fragment–fragment interaction energies into five terms as shown in eqn (1): Coulomb, charge transfer, exchange repulsion, dispersion and polarization, respectively.…”

The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems

“…The EFP method has been applied to various applications to study many important phenomena, including (a) the nature of the intermolecular interactions in molecular clusters via EFP−EFP calculations, 31−36 (b) modeling polarizable embedding through the interface of EFP with ab initio methods (QM-EFP) for an accurate explicit solvation approach, 10,16,37,38 (c) the highly scalable QM-based fragmentation method, EFMO, for large molecular species, and (d) molecular dynamics simulations of diffusion. 39,40 Prior to the work reported here, the MAKEFP component of the code involved significant I/O (i.e., writing data to files and later retrieving them). This was especially true for the CPHF and TDHF calculations.…”

“…Consequently, the MAKEFP step becomes a significant EFMO bottleneck. The EFP method has been applied to various applications to study many important phenomena, including (a) the nature of the intermolecular interactions in molecular clusters via EFP–EFP calculations, − (b) modeling polarizable embedding through the interface of EFP with ab initio methods (QM-EFP) for an accurate explicit solvation approach, ,,, (c) the highly scalable QM-based fragmentation method, EFMO, for large molecular species, and (d) molecular dynamics simulations of diffusion. , …”