MultiWfn is a very useful program for wavefunction analysis. You will need a .wfn or .wfx file that is computed by your electronic structure calculation software (e.g. I am using gaussian to compute this file) and the MultiWfn software can help you extract various information that could be usefull for your analyses. In this tutorial we will cover how to plot the Non-Covalent Interactions (NCI) as well as the critical bond points and paths that are present in our molecule, using the Atoms In Molecules (AIM) theory. MultiWfn has a very complete manual that can be accessed here and a very informative YouTube channel with lots of video tutorials that can be accessed here. I created this tutorial just to combine in an easy way two of the analyses that I usually do in my researchm without having to search thrpugh the whole manual or watch the youtube videos everytime, but please have a look at the original sources for further information!
Just a bit of Theory first
Alternatively, jump to the tutorial.
Topology analysis
The topology analysis technique proposed by Bader was firstly used for analyzing electron density in ”atoms in molecules” (AIM) theory, which is also known as ”the quantum theory of atoms in molecules” (QTAIM), this technique has also been extended to other real space functions, e.g. the first topology analysis research of ELF for small molecules is given by Silvi and Savin, see Nature, 371, 683. In topology analysis language, the points at where gradient norm of function value is zero (except at infinity) are called as critical points (CPs), CPs can be classified into four types according to how many eigenvalues of Hessian matrix of real space function are negative.
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(3,-3): All three eigenvalues of Hessian matrix of function are negative, namely the local maximum. For electron density analysis and for heavy atoms, the position of (3,-3) are nearly identical to nuclear positions, hence (3,-3) is also called nuclear critical point (NCP). Generally the number of (3,-3) is equal to the number of atoms, only in rarely cases the former can be more than (e.g. Li~2~) or less than (e.g. KrH^+^) the latter.
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(3,-1): Two eigenvalues of Hessian matrix of function are negative, namely the second-order saddle point. For electron density analysis, (3,-1) generally appears between attractive atom pairs and hence commonly called as bond critical point (BCP). The value of real space functions at BCP have great significance, for example the value of ρ and the sign of ∇2 at BCP are closely related to bonding strength and bonding type respectively in analogous bonding type (The Quantum Theory of Atoms in Molecules- From Solid State to DNA and Drug Design, p11); the potential energy density at BCP has been shown to be highly correlated with hydrogen bond energies Chem. Phys. Lett., 285, 170; local information entropy at BCP is a good indicator of aromaticity Phys. Chem. Chem. Phys., 12,4742.
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(3,+1): Only one eigenvalue of Hessian matrix of function is negative, namely first-order saddle point (like transition state in potential energy surface). For electron density analysis, (3,+1) generally appears in the center of ring system and displays steric effect, hence (3,+1) is often named as ring critical point (RCP).
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(3,+3): None of eigenvalues of Hessian matrix of function are negative, namely the local minimum. For electron density analysis, (3,+3) generally appears in the center of cage system (e.g. pyramid P4 molecule), hence is often referred to as cage critical point (CCP).
The maximal gradient path linking BCP and associated two local maxima of density is termed as “bond path”, which reveals atomic interaction path for all kinds of bonding. The collection of bond paths is known as molecular graph, which provides an unambiguous definition of molecular structure. Bond path can be straight line or curve, obviously for the latter case the length of bond path is longer than the sum of the distances between BCP and associated two (3,-3) CPs.
| CP type | Colour |
|---|---|
| nuclear | magenta |
| bond | orange |
| ring | yellow |
| cage | green |
Weak Interactions
Plot NCI
- Open Multiwfn and drag and drop your .wfn file.
- Write 20 from the main functions menu: Visual study of weak interaction
- Then choose the subfunction 1: Normal NCI analysis
- Choose the high quality grid by writing 3 (if your computer is slow, opt for a lower quality grid).
- After the completion of the process, write 2 in order to create a scatter map. The output.txt will be created in the Multiwfn working directory. Move it to your project’s working directory in order to save it. You may want to plot this scatter map later (not included in this tutorial).
- Write 3 in order to output the cube files. Similarly, the files func1.cub and func2.cub will be created in the Multiwfn working directory. Move them to your project’s working directory in order to save them.
- Copy the cube files to the VMD working directory.
- From the Multiwfn → examples folder, copy the RDGfill.vmd to the VMD working directory.
- Open VMD and run the script by writing at VMD’s black console screen
source RDGfill.vmd - In the VMD Represantations window, change the isovalue and any other parameter you want, in order to create high quality figures.
- See Figure 8 from this paper to interpret your results.
Display AIM Topology
- Open Multiwfn and drag and drop your .wfn file.
- Write 2 from the main functions menu: Topology Analysis
- Write 2 from the main functions menu: Search CPs from nuclear positions
- Write 3 from the main functions menu: Search CPs from midpoint from atom pairs
- Write 4 from the main functions menu: Search CPs from triangle center of three atoms
- Write 5 from the main functions menu: Search CPs from pyramid center of four atoms
- Write 8 and then 9 to generate the corresponding paths.
- Write 0 to print and visualize the paths and CPs.
- Click RETURN button in the GUI window.
- Write -4 and then 4 and 6 to write the CP.txt and CP.pdb files. Move them to your project’s working directory in order to save them.
- Copy CP.pdb and the AIM.vmd plotting script to your VMD folder.
- Open VMD and run the script by writing at VMD’s black console screen
source AIM.vmd - If you have already created the cube files from the previous section, invoke RDGfill.vmd to have them all in the same screen.