Structural evolution of amino acid crystals under stress from a non-empirical density functional

Abstract

Use of the non-local correlation functional vdW-DF (from 'van der Waals density functional'; Dion M et al 2004 Phys. Rev. Lett. 92 246401) has become a popular approach for including van der Waals interactions within density functional theory. In this work, we extend the vdW-DF theory and derive the corresponding stress tensor in a fashion similar to the LDA and GGA approach, which allows for a straightforward implementation in any electronic structure code. We then apply our methodology to investigate the structural evolution of amino acid crystals of glycine and l-alanine under pressure up to 10 GPa-with and without van der Waals interactions-and find that for an accurate description of intermolecular interactions and phase transitions in these systems, the inclusion of van der Waals interactions is crucial. For glycine, calculations including the vdW-DF (vdW-DF-c09x) functional are found to systematically overestimate (underestimate) the crystal lattice parameters, yet the stability ordering of the different polymorphs is determined accurately, at variance with the GGA case. In the case of l-alanine, our vdW-DF results agree with recent experiments that question the phase transition reported for this crystal at 2.3 GPa, as the a and c cell parameters happen to become equal but no phase transition is observed.

Nonlocal van der Waals functionals: The case of rare-gas dimers and solids

“…Note that the method of Román-Pérez and Soler also leads to an efficient calculation of the contribution of the nonlocal term to the KS-DFT potential (needed for the forces) and stress tensor. 69,70 In our implementation, the nonlocal term is evaluated using only the smooth part of the electron density of the GAPW method. However, in Ref.…”

Simple way to apply nonlocal van der Waals functionals within all-electron methods

“…Also, in Ref. 45, the formula for the contribution to the stress tensor was derived. For these reasons, the RPS method is the preferred one compared to the others that have been proposed.…”

“…However, for the geometry optimization with the forces and stress tensor, 45 the complete potential is required, therefore it is still desirable to have access to v v NL c,disp requires the calculation of dρ s /dρ, which is trivially done with Eq. (6) of the present scheme.…”

“…For the RPS method, the subroutines available in the QUAN-TUM ESPRESSO code 45,63 were used and modified. The FFT were done using version 3.3.5 of the FFTW software package, 64 which is efficiently parallelized with MPI.…”

Mechanical properties of hydrogenated bilayer graphene

“…In all cases, a kinetic energy cutoff of 40 Ryd was used. The vdW stress components were calculated using the method of Sabatini et al 54 as implemented in PWscf. All atomic forces during relaxation were converged to within 0.0001 a.u For all structures, a 1×1 in-plane unit cell was used.…”