.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "api/gallery/structure/vsepr/plot_03_hypervalent_molecules.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_api_gallery_structure_vsepr_plot_03_hypervalent_molecules.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_api_gallery_structure_vsepr_plot_03_hypervalent_molecules.py:


Musher's hypervalent molecules: main-group centres beyond the octet
===================================================================

James Musher (1969) grouped molecules such as :math:`\mathrm{PCl_5}`,
:math:`\mathrm{SF_6}`, :math:`\mathrm{ClF_3}` and the xenon fluorides into
one class: *hypervalent* molecules, whose central main-group atom appears
to hold more than the eight electrons of Lewis's octet. Counting the
Lewis electrons around the central atom (two per bond plus two per lone
pair) gives 10 or 12 for all of them.

Whatever the bonding explanation (d-orbital participation, or the
three-centre four-electron bond favoured today), VSEPR domain counting
predicts their shapes. This example builds six hypervalent molecules
with
:func:`~chemistrykit.structure.systems.vsepr.build_vsepr_molecule`,
counts the electrons around each central atom, and confirms each shape's
symmetry with
:func:`~chemistrykit.structure.systems.point_group.determine_point_group`.

.. GENERATED FROM PYTHON SOURCE LINES 23-51

.. code-block:: Python

    import matplotlib.pyplot as plt

    from chemistrykit.structure.systems.point_group import determine_point_group
    from chemistrykit.structure.systems.vsepr import VSEPRGeometry, build_vsepr_molecule
    from chemistrykit.structure.visualizers.structure_plots import plot_molecule_3d

    # name: (steric number, lone pairs, central atom, ligand, bond length in A, expected point group)
    hypervalent = {
        "PCl5": (5, 0, "P", "Cl", 2.07, "D3h"),
        "SF4": (5, 1, "S", "F", 1.60, "C2v"),
        "ClF3": (5, 2, "Cl", "F", 1.65, "C2v"),
        "XeF2": (5, 3, "Xe", "F", 1.98, "D_inf_h"),
        "SF6": (6, 0, "S", "F", 1.56, "Oh"),
        "XeF4": (6, 2, "Xe", "F", 1.95, "D4h"),
    }

    molecules = {}
    for name, (sn, lp, central, ligand, length, expected) in hypervalent.items():
        molecule = build_vsepr_molecule(sn, lp, bond_length=length, central_symbol=central, ligand_symbol=ligand)
        molecules[name] = molecule
        n_bonds = sn - lp
        electrons = 2 * n_bonds + 2 * lp  # single bonds: one shared pair each
        group = determine_point_group(molecule).group_name
        shape = VSEPRGeometry(sn, lp).shape_name
        print(f"{name:5s}: {electrons:2d} electrons around {central:2s} (octet exceeded by {electrons - 8}), AX{n_bonds}E{lp} {shape}, point group {group}")
        assert electrons > 8
        assert group == expected, (name, group)





.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    PCl5 : 10 electrons around P  (octet exceeded by 2), AX5E0 trigonal bipyramidal, point group D3h
    SF4  : 10 electrons around S  (octet exceeded by 2), AX4E1 seesaw, point group C2v
    ClF3 : 10 electrons around Cl (octet exceeded by 2), AX3E2 T-shaped, point group C2v
    XeF2 : 10 electrons around Xe (octet exceeded by 2), AX2E3 linear, point group D_inf_h
    SF6  : 12 electrons around S  (octet exceeded by 4), AX6E0 octahedral, point group Oh
    XeF4 : 12 electrons around Xe (octet exceeded by 4), AX4E2 square planar, point group D4h




.. GENERATED FROM PYTHON SOURCE LINES 52-53

The six shapes, all derived from the five- and six-domain polyhedra:

.. GENERATED FROM PYTHON SOURCE LINES 53-62

.. code-block:: Python


    fig = plt.figure(figsize=(12, 8))
    for i, (name, molecule) in enumerate(molecules.items(), start=1):
        ax = fig.add_subplot(2, 3, i, projection="3d")
        plot_molecule_3d(molecule, ax=ax)
        ax.set_title(f"{name} ({2 * (hypervalent[name][0])} e around {hypervalent[name][2]})", fontsize=10)
    fig.suptitle("Hypervalent molecules: more than an octet, shapes still from VSEPR")
    fig.tight_layout()
    plt.show()



.. image-sg:: /api/gallery/structure/vsepr/images/sphx_glr_plot_03_hypervalent_molecules_001.png
   :alt: Hypervalent molecules: more than an octet, shapes still from VSEPR, PCl5 (10 e around P), SF4 (10 e around S), ClF3 (10 e around Cl), XeF2 (10 e around Xe), SF6 (12 e around S), XeF4 (12 e around Xe)
   :srcset: /api/gallery/structure/vsepr/images/sphx_glr_plot_03_hypervalent_molecules_001.png
   :class: sphx-glr-single-img






.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 0.221 seconds)


.. _sphx_glr_download_api_gallery_structure_vsepr_plot_03_hypervalent_molecules.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example

    .. container:: sphx-glr-download sphx-glr-download-jupyter

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    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_03_hypervalent_molecules.py <plot_03_hypervalent_molecules.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_03_hypervalent_molecules.zip <plot_03_hypervalent_molecules.zip>`


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 .. rst-class:: sphx-glr-signature

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