MrPIXEL: automated execution of Pixel calculations via the Mercury interface

Abstract

The interpretation of crystal structures in terms of intermolecular interaction energies enables phase stability and polymorphism to be rationalized in terms of quantitative thermodynamic models, while also providing insight into the origin of physical and chemical properties including solubility, compressibility and host–guest formation. The Pixel method is a semi-empirical procedure for the calculation of intermolecular interactions and lattice energies based only on crystal structure information. Molecules are represented as blocks of undistorted ab initio molecular electron and nuclear densities subdivided into small volume elements called pixels. Electrostatic, polarization, dispersion and Pauli repulsion terms are calculated between pairs of pixels and nuclei in different molecules, with the accumulated sum equating to the intermolecular interaction energy, which is broken down into physically meaningful component terms. The MrPIXEL procedure enables Pixel calculations to be carried out with minimal user intervention from the graphical interface of Mercury, which is part of the software distributed with the Cambridge Structural Database (CSD). Following initial setup of a crystallographic model, one module assigns atom types and writes necessary input files. A second module then submits the required electron-density calculation either locally or to a remote server, downloads the results, and submits the Pixel calculation itself. Full lattice energy calculations can be performed for structures with up to two molecules in the crystallographic asymmetric unit. For more complex cases, only molecule–molecule energies are calculated. The program makes use of the CSD Python API, which is also distributed with the CSD.

Mapping the cooperativity pathways in spin crossover complexes

“…In this study the cluster radius was 20 Å, and the molecular electron densities were obtained in steps of 0.08 Å from GAUSSIAN-09 with the 6-31G** basis set at the B3LYP level of theory. 52 The PIXEL calculations themselves were accomplished with the CLP-PIXEL suite within the MrPIXEL interface 53 using a condensation level of 4 ( i.e. the original pixels from GAUSSIAN were combined into 4 × 4 × 4 blocks of dimension 0.32 Å).…”

“…The implementation used for the present work reflects these limitations. However, the methods described in ref. 53 would enable calculations on more complex structures to be carried out, while those of ref.…”

Towards Computational Screening for New Energetic Molecules: Calculation of Heat of Formation and Determination of Bond Strengths by Local Mode Analysis

“…For lattice enthalpies calculated using PIXEL ( Gavezzotti, 2005 ), calculations were set up using MrPIXEL ( Reeves et al, 2020 ) within the Mercury interface, distributed with the Cambridge Structural Database (CSD) ( Macrae et al, 2008 ; Groom et al, 2016 ). Hydrogen atom positions were set to the CSD normalised positions.…”

Hidden Solvates and Transient Forms of Trimesic Acid

“…An analysis of all the known alcohol solvates and the geometry of the framework reveals that there is a correlation between the length of the solvent and the degree to which the ring system is distorted; the longer the alcohol, the more distorted (Figure 4d). We have calculated the intermolecular energies for the series using PIXEL [24][25][26], and these are shown in Table 1 and Figure 5. Despite the distortions to the ring system, the energy of the TMA framework is reasonably consistent.…”

“…Table 1. The intermolecular energies for each solvate calculated by PIXEL [24][25][26] and partitioned into different contributions of coulombic, polarization, dispersion and repulsion. An image of the particular interaction (a-e) is found in Figure 5.…”