Description of QMC Visualizations

Quantum Monte Carlo molecular simulation methods usually involve placement of electrons around nuclei, and the optimization of their position in order to lower the energy of the system. During the optimization, the electrons are propagated on arbitrary time scales. We visualize the the resulting electron trajectories (called walkers) by connecting electron positions, effectively leaving a trace path in space. This allows chemists to visualize the path of the electrons during chemical reactions. We can also color the walkers based on the energy state of the molecule; this allows chemists to understand the change in energies based on the positions of the electrons.

Plot of multiple electron trajectories (walkers) Plot of multiple electrons (colored by energy) and volume rendering of electron density.

Electron structure bases molecular simulation methods generate 3D spatial electron distributions around a molecule. It can be challenging to understand the spatial distribution; we use a variety of standard techniques to look at this data. First we use a conventional 2D contour plot to show density slices in a plane. We then look at 3D isocontours of electric potential of the molecules. These surfaces can be colored by the electron density; this reveals the polarization of the molecule.

2D contours of electron density 3D iso-contours of potential Potential iso-contours colored by electron density

Bonding patterns in large molecules reveal chemical properties. Conventional approaches to visualizing bond length take cross sections and show numerical plots of variation in length across the sections. Instead, one can choose to color bonds in a molecule according to their length. While this presents a qualitative representation of the data, such visualizations are much more effective in depicting equidistant or oscillatory trends (in bonding) in graphene-like molecules. This is shown for the triangulene and hexagulene structures. Such visualizations help chemists in gaining insights into electron distribution and physical activity of the edge vs. the core of the molecule. Such comparisons can be conducted not just across different molecules, but also the same molecule in different electronic states. This is demonstrated for both of the previous molecules in singlet and septet states.

Plot of bondlength for triangulene Plot of difference in bondlength for different energy states

Large graphene-like molecules with zig-zag edges are capable of carying unpaired electrons along the edges. This results in magnetization of the molecule; one can also think of this as the presence of vector spin data, which can be depicted visually. Visualization of this information helps chemists understand the spatial mapping and trends in spin information for large molecules.

Spin information overlaid on triangulene Spin information overlaid on acene