Introduction to CrystalExplorer, Hirshfeld surfaces, interaction energies, energy frameworks and more
What is CrystalExplorer?
CrystalExplorer is a computational tool for investigating intermolecular interactions and packing in molecular crystalline materials using Hirshfeld surface analysis, as well as powerful tools to generate molecular surfaces based on quantum mechanical property densities. It has been created bearing in mind the desire of researchers to access useful chemical information about molecular crystal structures, in a reasonable amount of time, and on their laptop or desktop computer.
Mapping molecular properties and other distance- and curvature-related metrics on Hirshfeld surfaces, CrystalExplorer provides unique insights into the in-crystal environment. It can also readily display and quantify voids -- 'empty' spaces -- in crystal structures. The most recent version of this software, CrystalExplorer17, implements the accurate and efficient calculation of intermolecular interaction energies, energy frameworks and lattice energies.
Getting Started
All of the documentation for CrystalExplorer is available online via the 'Documentation' link at www.crystalexplorer.net, and the best place to start is the Quick Start Guide, which describes in detail most of the basic functionality:
In the first exercise of this tutorial you will become familiar with most of the items in the Quick Start Guide, using one of the CIF files mentioned below.
For more detailed descriptions of the more advanced options you will also need to refer to the Online User Manual:
After gaining a reasonable familiarity with basic CrystalExplorer functions, this workshop tutorial consists of several more exercises, each based on one or two crystal structures, and focusing on the extraction of meaningful conclusions relating to why the molecules pack as they do, and what might be inferred about bulk properties.
For the purposes of this tutorial all calculations will be performed using wavefunctions computed at the HF/3-21G level with the ab initio program Tonto included with the CrystalExplorer distribution. If you have a version of Gaussian on your computer by all means use that for wavefunction calculation. And bear in mind that all interaction energies computed using these electron densities are those from the CE-HF model.
When you have more time -- and perhaps better computing resources, including access to Gaussian -- it would be worthwhile repeating these calculations using B3LYP/6-31G(d,p) wavefunctions and CE-B3LYP model energies.
Crystal structure data: CIF files
CrystalExplorer only accepts Crystallographic Information Files (CIF files) as input. The required CIF files for this Tutorial can be downloaded from the Cambridge Structural Database (CSD) Teaching Subset, accessed via the WebCSD portal: www.ccdc.cam.ac.uk/structures/
Required CIF Files
Below is a list of CIF files in the CSD Teaching Subset that include reasonably small molecules, and for which CrystalExplorer calculations on a laptop or desktop can be performed in a reasonable time, using Tonto for wavefunction calculation. Entries in bold have been used as the basis for tutorial exercises.
| Files | Files |
|---|---|
| ACETAC07 acetic acid | HCLBNZ11 hexachlorobenzene |
| ACETYL03 acetylene -- neutron | HIXHIF05 acetone |
| ALOXAN alloxan | LIKSAZ acetonitrile hydrofluoric acid |
| ALUCAL05 D-alanine | LIKSIH borazine |
| BARBAD01 barbituric acid dihydrate | NAPHTA12 naphthalene |
| BENZEN benzene | PHENOL03 phenol Z' = 3 |
| CAACTY cyanoacetylene | PYRDNA01 pyridine Z' = 4 |
| CEKGUU01 trimethylamine | QQQCIS01 cyclopropane |
| CLMETH chloromethane | TELXAJ 2-butyne-1,4-diol |
| CYACAC cyanoacetic acid Z' = 2 | TIVWOL tetramethylsilane @ 0.58 GPa |
| DERWAY trans,trans-1,3,5,7-octatetraene | TOLUEN toluene Z' = 2 |
| FLUREN01 fluorene | UREAXX urea |
| FUYVUQ03 ammonia borane | ZEXQAU 1,3,5-tricyanobenzene |
| GLYCIN glycine | ZZZKDW01 carbon tetraiodide |
| GURNEN formaldehyde ethyne | ZZZSAE01 cyclooctatetraene |