.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "api/gallery/photochem/fluorescence/plot_01_stokes_shift.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_photochem_fluorescence_plot_01_stokes_shift.py>`
        to download the full example code.

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

.. _sphx_glr_api_gallery_photochem_fluorescence_plot_01_stokes_shift.py:


Stokes shift: fluorescence is emitted at longer wavelength than it is absorbed
================================================================================

Stokes (1852) found that quinine solution absorbs invisible ultraviolet
light and re-emits it as blue light -- always at longer wavelength than
the exciting light. The excited molecule relaxes vibrationally (and its
solvent reorganizes) before emitting, so emission starts from a lower
energy than absorption ended at.
:func:`~chemistrykit.photochem.stokes_shift` gives the gap in
wavenumbers. The bands below are model Gaussian spectra with maxima near
those of quinine sulfate in dilute acid (about 350 nm and 450 nm).

.. GENERATED FROM PYTHON SOURCE LINES 16-48



.. image-sg:: /api/gallery/photochem/fluorescence/images/sphx_glr_plot_01_stokes_shift_001.png
   :alt: Stokes shift of a quinine-like fluorophore
   :srcset: /api/gallery/photochem/fluorescence/images/sphx_glr_plot_01_stokes_shift_001.png
   :class: sphx-glr-single-img


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

 .. code-block:: none

    Stokes shift: 6349 cm^-1 (100 nm)






|

.. code-block:: Python

    import matplotlib.pyplot as plt
    import numpy as np

    from chemistrykit.photochem import stokes_shift

    lam_abs, lam_em = 350.0, 450.0  # nm
    wavenumber = np.linspace(16000.0, 34000.0, 800)  # cm^-1
    nu_abs, nu_em = 1e7 / lam_abs, 1e7 / lam_em
    absorption = np.exp(-(((wavenumber - nu_abs) / 2000.0) ** 2))
    emission = np.exp(-(((wavenumber - nu_em) / 2000.0) ** 2))

    shift = stokes_shift(lam_abs, lam_em)
    print(f"Stokes shift: {shift:.0f} cm^-1 ({lam_em - lam_abs:.0f} nm)")

    fig, ax = plt.subplots()
    ax.plot(1e7 / wavenumber, absorption, label="absorption")
    ax.plot(1e7 / wavenumber, emission, label="fluorescence")
    ax.annotate(
        "",
        xy=(lam_em, 1.03),
        xytext=(lam_abs, 1.03),
        arrowprops={"arrowstyle": "->"},
    )
    ax.text(0.5 * (lam_abs + lam_em), 1.06, f"Stokes shift = {shift:.0f} cm$^{{-1}}$", ha="center")
    ax.set_ylim(0, 1.15)
    ax.set_xlabel("Wavelength (nm)")
    ax.set_ylabel("Normalized intensity")
    ax.set_title("Stokes shift of a quinine-like fluorophore")
    ax.legend(loc="upper right")
    fig.tight_layout()

    plt.show()


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

   **Total running time of the script:** (0 minutes 0.041 seconds)


.. _sphx_glr_download_api_gallery_photochem_fluorescence_plot_01_stokes_shift.py:

.. only:: html

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

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

      :download:`Download Jupyter notebook: plot_01_stokes_shift.ipynb <plot_01_stokes_shift.ipynb>`

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

      :download:`Download Python source code: plot_01_stokes_shift.py <plot_01_stokes_shift.py>`

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

      :download:`Download zipped: plot_01_stokes_shift.zip <plot_01_stokes_shift.zip>`


.. only:: html

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

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_