Example: Atoms and orbitals

% Example drawings to help explain the VSEPR atom model to high school
% students. Although the actual model is three dimensional, these drawings
% are deliberately presented as two dimensional to gently introduce them to the
% concepts, before advancing to three dimensional models.

%
% Authors: Berteun Damman & Arne Röhrs

\documentclass{article}
\usepackage{tikz}

\usepackage[version=3]{mhchem}



\pgfdeclarelayer{background}
\pgfdeclarelayer{foreground}

\pgfsetlayers{background,main,foreground}

% For black & white suggestions are black!95 for the electron
% and a white background, or a simple shade for the orbitals.
\colorlet{electron}{blue!75}

\tikzset{orbital/.style={thick,draw=blue,fill opacity=.60}}
% Styles for orbitals with 0, 1 and 2 atoms respectively.
\tikzset{orbital 0/.style={orbital,fill=blue!25}}
\tikzset{orbital 1/.style={orbital,fill=blue!66}}

\tikzset{orbital 2/.style={orbital,fill=blue}}
\tikzset{atomcore/.style={shape=circle,thick,draw=red!40,minimum size=7mm,
    font=\large\color{red!70!gray},fill=red!20,inner sep=0pt}}

\def\orbheight{1.2}
\def\orbwidth{.6}

% Parameters: #1 Rotation of the orbital
%             #2 Coordinate where the orbital should be attached
%             #3 Number of electrons to draw in the orbital

\newcommand{\orbital}[3]{
    \begin{scope}[rotate=#1,shift=(#2)]
        % These points define the curve for the orbital.
        \coordinate (c1) at (-\orbwidth, .6 * \orbheight);
        \coordinate (c2) at (-\orbwidth, \orbheight);
        \coordinate (c3) at (\orbwidth, \orbheight);
        \coordinate (c4) at (\orbwidth, .6 * \orbheight);
        \coordinate (top) at (0,\orbheight);

        %Coordinates of the electrons

        \coordinate (e1) at (0, 0.45*\orbheight);
        \coordinate (e2) at (0, 0.75*\orbheight);
    \end{scope}

  % These are drawn on a background layer, so orbitals
  % can overlap without covering the electrons, which
  % visualises the role electrons play in chemical bonds.
  \begin{pgfonlayer}{background}

      \draw[orbital #3] (#2) .. controls (c1) and (c2) .. (top) ..
            controls (c3) and (c4) .. (#2);
  \end{pgfonlayer}

  % Draw the electrons
  \ifnum#3>0
      \foreach \n in {1,...,#3} {

          \shade[ball color=electron] (e\n) circle (1mm);
      }
  \fi
}

% This allows to quickly place an atom.

% Parameters: #1 (Optional) Name of the center node
%             #2 Text for the center node
%             #3 A list of rotation-angle/anchor/number of electrons
\newcommand{\Atom}[3][AtomNode]{
  \node[atomcore] (#1) {\ce{#2}};
  \foreach \ang/\anchor/\n in {#3} {

      \orbital{\ang}{#1.\anchor}{\n}
  }
}

\begin{document}
    \pagestyle{empty}
    
    
% Note: Cells of matrices cannot contain layered pictures,
% therefore we use some old-fashioned scopes.
\begin{tikzpicture}

    \Atom{B}{90/west/2,0/north/1,270/east/0,180/south/1}
    \begin{scope}[xshift=4cm]
        \Atom{H}{0/north/1}

    \end{scope}
    \begin{scope}[yshift=-4cm]
        \Atom{C}{90/west/1,0/north/1,270/east/1,180/south/1}

        \begin{scope}[xshift=4cm]
            \Atom{Cl}{90/west/2,0/north/2,270/east/2,180/south/1}
        \end{scope}

    \end{scope}
\end{tikzpicture}

\medskip

\begin{tikzpicture}

    \Atom{Cl}{90/west/2,0/north/2,270/east/1,180/south/2}
    \begin{scope}[xshift=2.2cm]
        \Atom{H}{90/west/1}

    \end{scope}
\end{tikzpicture}

\medskip

\begin{tikzpicture}

    \Atom{O}{45/north west/2,315/north east/1,225/south east/1,135/south west/2}
    \begin{scope}[xshift=3.0cm]
        \Atom{O}{45/north west/1,315/north east/2,225/south east/2,135/south west/1}

    \end{scope}

    \begin{scope}[xshift=7.0cm]
        \Atom{O}{45/north west/2,315/north east/1,225/south east/1,135/south west/2}

        \begin{scope}[xshift=1.6cm]
            \Atom{O}{45/north west/1,315/north east/2,225/south east/2,135/south west/1}
        \end{scope}

    \end{scope}
\end{tikzpicture}

\end{document}