Molecular dynamics simulation of organic crystals: introducing the CLP-dyncry environment

Abstract

The CLP‐dyncry molecular dynamics (MD) program suite and force field environment is introduced and validated with its ad hoc features for the treatment of organic crystalline matter. The package, stemming from a preliminary implementation on organic liquids (Gavezzotti & Lo Presti, 2019), includes modules for the preliminary generation of molecular force field files from ab initio derived force constants, and for the preparation of crystalline simulation boxes from general crystallographic information, including Cambridge Structural Database CIFs. The intermolecular potential is the atom–atom Coulomb–London–Pauli force field, well tested as calibrated on sublimation enthalpies of organic crystals. These products are then submitted to a main MD module that drives the time integration and produces dynamic information in the form of coordinate and energy trajectories, which are in turn processed by several kinds of crystal‐oriented analytic modules. The whole setup is tested on a variety of bulk crystals of rigid, non‐rigid and hydrogen‐bonded compounds for the reproduction of radial distribution functions and of crystal‐specific collective orientational variables against X‐ray data. In a series of parallel tests, some advantages of a dedicated program as opposed to software more oriented to biomolecular simulation (Gromacs) are highlighted. The different and improved view of crystal packing that results from joining static structural information from X‐ray analysis with dynamic upgrades is also pointed out. The package is available for free distribution with I/O examples and Fortran source codes.

Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K

“…To shed light on the possible nature of our models’ inability to account for the observed residual features, we performed classical molecular dynamics (MD) simulations on crystalline 1-MUR with the MiCMoS package [ 49 , 50 , 51 , 52 ]. Full details of the procedure are documented in Section S3 Supplementary Materials .…”

Dynamic simulation of orientational disorder in organic crystals: methyl groups, trifluoromethyl groups and whole molecules

“…A computational box for the crystal model is set up by an appropriate number of repetitions of the unit cell along the three directions of space (MiCMoS module Boxcry), and module Pretop provides a template for the force field 'topology' file. In our case, the only allowed intramolecular degree of freedom is the torsional CH 3 or CF 3 motion, described by the usual (Gavezzotti & Lo Presti, 2019) cosine potential functions (see also the supporting information, passim). Ordinary NPT runs (constant number of particles, pressure and temperature) with periodic boundary conditions are then carried out under the MI-LJC intermolecular potential until a steady state (equilibration) is reached, after which the distribution of torsion angles or of whole-molecule orientations is analyzed.…”

Resonance between dithiocarbamates and thioureide mesomeres coupled to metal−hydrogen anagostic bond transforming under pressure

“…The crystal intermolecular energies were calculated with the MiCMoS platform. 54,55 Atomic positions were first retrieved from the CIF files for the measurements at 0.…”