[Multiwfn+VMD] Plotting Crystal Hirshfeld Surface and Fingerprint Diagram – 2

This article is a supplement to the content of [Multiwfn+VMD] Plotting Crystal Hirshfeld Surface and Fingerprint Diagram. A preliminary analysis of intermolecular interactions has been completed, but how to specifically distinguish each type of interaction remains unclear. This article can be ignored if the study does not require the separation of these weak interactions. For consistency, this article still uses salicylic acid derivative single crystal (CCDC: 251741) as an example.Review1. Copy files: Copy the hirsh_rho.vmd from the Multiwfn examples\scripts\ directory to the VMD directory.2. Build cluster: Open the single crystal with Multiwfn, input 300-7-25-1-Enter sequentially, and record the atom numbers: 1-3,5,6,9-11,13,15,51,54,55,59,61,154. After inputting -2, name it cluster.pdb and press Enter, then close Multiwfn3. CalculateHirshfeld surface: Open cluster.pdb with Multiwfn, input 12-1-5 sequentially, input atom numbers: 1-3,5,6,9-11,13,15,51,54,55,59,61,154, press Enter, then input 0 and press Enter to complete the calculation.4. Plot fingerprint diagram: After the calculation is complete, input 20-0 to view the image.5. PlotHirshfeld surface diagram: In Multiwfn, input two -1 to go back two levels, then input -2 and 13 to export surf.cub and mapfunc.cub files, copy them to the VMD directory, open VMD and input source hirsh_rho.vmd and press Enter.Content:1. View O-H intermolecular hydrogen bonds: Do not close Multiwfn after completing the previous text, input 20 (content is Fingerprint plot and local contact analyses), and observe the interface below.(Here, 1 and 2 define the internal and external atom numbers or types. Since we are studying O-H hydrogen bonds, the internal atom is O, and the external is H as the research object.)a. Define internal atoms: Input 1 and press Enter, then press Enter again. Now let’s input the internal atom type, input O and press Enter, and return to the above interface.b. Define external atoms: Input 2 and press Enter, then press Enter again. Now let’s input the external atom type, input H and press Enter, returning to the above interface.c. Start calculation: Input 0 to start analysis.Here, it can be seen that O-H hydrogen bonds account for 17%. Input 0 to view the image.Here is the O-H hydrogen bond. However, careful observers will notice that the sharp spike above is not displayed. This is because we only calculated the case where the central molecule acts as the hydrogen bond acceptor, and the hydrogen atoms of the central molecule as the hydrogen bond donor were not calculated. Therefore, swapping the defined internal and external atoms will reveal another spike. If you find it troublesome, you can define both O and H as internal and external atoms to display them simultaneously.The method for calculating other N-H hydrogen bonds is the same.You can also view all intermolecular interactions. In this state, input -1 to go back one level, then select3 Calculate contact area between different elements to proceed.2. Face-to-face interactions (such as p-p stacking): First, determine the atom numbers: Open the previously exported cluster file cluster.pdb directly with Gaussview, check the Labels option.Here, the central molecule benzene ring atom numbers are 5,6,9,10,54,55, and the stacked benzene ring atom numbers are 7,8,189-192,34,35,52,53,56,57. Consistent with the above, after completing the calculation in Multiwfn, return to the upper layer, select 20 (content is Fingerprint plot and local contact analyses) and press Enter.a. Define internal atoms: Input 1 and press Enter, input the above central benzene ring atom numbers and press Enter, which are 5,6,9,10,54,55, and press Enter again to indicate no separate atom types are set.b. Define external atoms: Input 2 and press Enter, input the above stacked benzene ring atom numbers and press Enter, which are 7,8,189-192,34,35,52,53,56,57, and press Enter again to indicate no separate atom types are set.c. Start calculation: Input 0 to start analysis.Here, the p-p stacking accounts for a small proportion, only 6.91%. Input 0 to view the corresponding fingerprint diagram.This method can help us better identify the meanings of different scatter points in the fingerprint diagram, which is helpful for more detailed analysis. After viewing the scatter plot, input 4 to obtain the finger.pqr file, then use VMD to open the cluster.pdb file obtained in this article and the finger.pqr file to visually inspect this interaction area. Setting the Coloring Method to Charge and adjusting the drawing method and color scale can help distinguish the regions, which will not be elaborated here.