A three dimensional illustration of various clusters of atoms.

Edit and compile if you like:
% Clusters of atoms% Author: Agustin E. Bolzan\documentclass{article}\usepackage[gray]{xcolor}\usepackage{tikz,pgffor}\usepackage[active,tightpage]{preview}\PreviewEnvironment{tikzpicture}\setlength\PreviewBorder{5pt}%\usetikzlibrary{shadows}\begin{document}%\begin{figure}\centering\begin{tikzpicture}%\draw[help lines] (0,0) grid (10,10); %used just for visualising the positions of objects during construction\begin{scope}[yshift=-180,yslant=0.5,xslant=-1]%the rectangular surface onto which the clusters are located\filldraw[black!10,very thick] (0.5,1) rectangle (10,7);%circle circumventing the smallest cluster\node[circle,circular glow,fill=red!20,draw=red,thick]at (4.1,4.9) {\phantom{perimetro}};\end{scope}%atom clusters are rotated for a better visualisation\begin{scope}[rotate around = {-5:(0,0,0)}]%text describing the objects in the picture\draw[-latex,thick] (6,3) node[right,text width=3cm]{$\mathsf{potent\; perimeter\; sites}$} to [out=180,in=0] (4.5,1);\draw[-latex,thick](3,-1)node[right]{$\mathsf{Non-metallic\; molecule}$} to[out=180,in=0] (2.6,-3);\draw[-latex,thick](-3,-1)node[above]{$\mathsf{extra \; electron}$} to[out=-90,in=180] (-1.4,-2);%now we start with the clusters (maybe this code could be improved by a tikz expert)%the layers are built starting from the very lowest one%largest cluster
Click to download: clusters-of-atoms.tex • clusters-of-atoms.pdf
Open in Overleaf: clusters-of-atoms.tex