5

I'm using the modiagram package and I'm half-way through a text (so I'm eager to get this to work). Now I'm up to filling up p orbitals and hence the σ(pz) orbitals. I'm taught that the z axis is the bonding axis and that it is the p(z) orbitals that form the molecular sigma orbitals. modiagram assumed the x axis and p(x) orbitals. Is it possible to configuration or hack modiagram to have this suite my needs?

Also, is it possible to change the format of the labels from 2σ(x) to σ(2px)? Should this perhaps be a question on it's own?

I have actually read the code, but it's all new to me. I'd be glad for any kind of answer, be it hints on where to hack the .styfile or hints about the package.

Reading the code, I understand that it is around line 1150 I should focus for both problems but the code is all new to me and I'm embarrassed to say I don't understand it.

Here's a MWE on top of things.

\documentclass{article}

\usepackage{mhchem}
\usepackage{modiagram}

\begin{document}

\begin{center}
  \begin{MOdiagram}[names,labels,labels-fs=\footnotesize]
    \atom[\ce{C}]{left}{ 2s, 2p = {; up, up} }
    \atom[\ce{C}]{right}{ 2s, 2p = {; up, up} }
    \molecule[\ce{C2}]{ 2sMO, 2pMO = {; pair, pair} }
    \EnergyAxis[title=$E$]
  \end{MOdiagram}
\end{center}

N.B. Wouldn't it be great to have the $\sigma$ orbital be formatted
$\sigma_{2pz}$ or $\sigma_{2p_z}$ and the $\pi$ orbital $\pi_{2py}$ or
$\pi_{2p_y}$.

\end{document}
  • @clemens And a final thing: what are px, py and pz AOs named? – Mats Sep 6 '16 at 17:24
  • 1
    You mean the node names? The available ones are shown in the figure in section 3.3 (the naming scheme) – clemens Sep 6 '16 at 17:31
  • @clemens Sure they are. Sorry for being so sloppy. Thanks for the immediate help. How kind. Cheers – Mats Sep 6 '16 at 17:35
3

Thanks again for the feedback Clemens. Here are two examples of me using the \AO command which made it possible to customize the use modiagram and solve my problems.

\documentclass{article}
\usepackage{modiagram}
\usepackage[version=3]{mhchem}

\begin{document}

\begin{center}
  \begin{MOdiagram}[names,labels,labels-fs=\footnotesize]
    % left atom
    \AO[2sleft](1cm){s}[label={$2s_{2}$}]{1;pair} %AO1
    \AO[2pxleft](1.5cm){s}[label={$2p_x$}]{5;pair}
    \AO[2pyleft](2cm){s}[label={$2p_y$}]{5;up}
    \AO[2pzleft](1cm){s}[label={$2p_z$}]{5;up}    
    \node at (1cm, -1){\ce{O}};

    % right atom
    \AO[2sright](7cm){s}[label={$2s$}]{1;pair} % AO3
    \AO[2pxright](6.5cm){s}[label={$2p_x$}]{5;pair}
    \AO[2pyright](7cm){s}[label={$2p_y$}]{5;up}
    \AO[2pzright](7.5cm){s}[label={$2p_z$}]{5;up}
    \node at (7cm, -1){\ce{O}};

    % molecule
    \AO[sigma2](4.5cm){s}[label={$\sigma_{2s}$}]{0.5;pair} % AO5
    \AO[sigma2*](4.5cm){s}[label={$\sigma^*_{2s}$}]{1.5;pair}
    \AO[pi2x](4.2cm){s}[label={$\pi_{2p_x}$}]{4;pair} % AO7
    \AO[pi2y](4.8cm){s}[label={$\pi_{2p_y}$}]{4;pair}
    \AO[sigma2pz](4.5cm){s}[label={$\sigma_{2p_z}$}]{3;pair}

    \AO[pi2x*](4.2cm){s}[label={$\pi^*_{2p_x}$}]{7;up} % AO10
    \AO[pi2y*](4.8cm){s}[label={$\pi^*_{2p_y}$}]{7;up}
    \AO[sigma2pz*](4.5cm){s}[label={$\sigma^*_{2p_z}$}]{8;}
    \node at (4.5cm, -1){\ce{O2}};

    \draw[densely dotted,draw=black] (2sleft.0) -- (sigma2.180);
    \draw[densely dotted,draw=black] (2sleft.0) -- (sigma2*.180);
    \draw[densely dotted,draw=black] (2sright.180) -- (sigma2.0);
    \draw[densely dotted,draw=black] (2sright.180) -- (sigma2*.0);

    \draw[densely dotted,draw=black] (2pyleft.0) -- (pi2x.180);
    \draw[densely dotted,draw=black] (2pxright.180) -- (pi2y.0);
    \draw[densely dotted,draw=black] (2pyleft.0) -- (pi2x*.180);
    \draw[densely dotted,draw=black] (2pxright.180) -- (pi2y*.0);

    \draw[densely dotted,draw=black] (2pzleft.0) -- (sigma2pz*.180);
    \draw[densely dotted,draw=black] (2pzleft.0) -- (sigma2pz.180);
    \draw[densely dotted,draw=black] (2pzright.180) -- (sigma2pz*.0);
    \draw[densely dotted,draw=black] (2pzright.180) -- (sigma2pz.0);
    \EnergyAxis[title=$E$]
  \end{MOdiagram}
\end{center}


\begin{center}
  \begin{MOdiagram}[names,labels,labels-fs=\footnotesize]
    % left atom
    \AO[2sleft](1cm){s}[label={$2s_{2}$}]{.5;pair} %AO1
    \AO[2pxleft](1.5cm){s}[label={$2p_x$}]{3;up}
    \AO[2pyleft](2cm){s}[label={$2p_y$}]{3;up}
    \AO[2pzleft](1cm){s}[label={$2p_z$}]{3;}    
    \node at (1cm, -1){\ce{C}};
    \node[align=center,text width=2cm] at (1cm, -1.5cm){four valence $e^-$};

    % right atom
    \AO[2sp31](5.7cm){s}[label={$2sp^3$}]{2;up} % AO3
    \AO[2sp32](6.4cm){s}[label={$2sp^3$}]{2;up}
    \AO[2sp33](7.1cm){s}[label={$2sp^3$}]{2;up}
    \AO[2sp34](7.8cm){s}[label={$2sp^3$}]{2;up}
    \node at (7cm, -1.5cm){\itshape Hybrid orbitals};

    \draw[ultra thick,->](3cm, 1cm) -- (5cm, 1cm)
      node[midway,below]{\scriptsize\itshape hybridization};
    \EnergyAxis[title=$E$]
  \end{MOdiagram}
\end{center}

\end{document}

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