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    Computational Chemistry: Geometry Optimization Using Avogadro Software

    Uploaded by

    Anil Kumar
    The document describes using Avogadro software to model and optimize the geometry of water and hydrogen sulfide dimers and 2-nitrophenol. It outlines steps to build the molecular structures, set up force fields, and perform geometry optimizations. Geometry optimizations reveal intermolecular hydrogen bonding in the water dimer and intramolecular hydrogen bonding in 2-nitrophenol, but not in the hydrogen sulfide dimer due to weaker interactions. The energies of the optimized structures are reported.

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    © All Rights Reserved
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    Computational Chemistry: Geometry Optimization Using Avogadro Software

    Uploaded by

    Anil Kumar
    321 views7 pages
    The document describes using Avogadro software to model and optimize the geometry of water and hydrogen sulfide dimers and 2-nitrophenol. It outlines steps to build the molecular structures, set up force fields, and perform geometry optimizations. Geometry optimizations reveal intermolecular hydrogen bonding in the water dimer and intramolecular hydrogen bonding in 2-nitrophenol, but not in the hydrogen sulfide dimer due to weaker interactions. The energies of the optimized structures are reported.

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    10._Geometry_Optimization_Using_Avogadro_software_Final

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    The document describes using Avogadro software to model and optimize the geometry of water and hydrogen sulfide dimers and 2-nitrophenol. It outlines steps to build the molecular structures, set up force fields, and perform geometry optimizations. Geometry optimizations reveal intermolecular hydrogen bonding in the water dimer and intramolecular hydrogen bonding in 2-nitrophenol, but not in the hydrogen sulfide dimer due to weaker interactions. The energies of the optimized structures are reported.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    321 views7 pages

    Computational Chemistry: Geometry Optimization Using Avogadro Software

    Uploaded by

    Anil Kumar
    The document describes using Avogadro software to model and optimize the geometry of water and hydrogen sulfide dimers and 2-nitrophenol. It outlines steps to build the molecular structures, set up force fields, and perform geometry optimizations. Geometry optimizations reveal intermolecular hydrogen bonding in the water dimer and intramolecular hydrogen bonding in 2-nitrophenol, but not in the hydrogen sulfide dimer due to weaker interactions. The energies of the optimized structures are reported.

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    Computational Chemistry: Geometry optimization using

    Avogadro software
    Aim

    To create models and optimize the geometry of H2O and H2S dimers, and 2-nitrophenol as
    examples of inter- and intra-molecular hydrogen bonding respectively using Avogadro
    software.

    Course outcome

    Using the Avogadro software students will learn about modelling 3D structures of any
    molecule of interest. Also, they will learn the concept of geometry optimization and
    associated stabilization parameters like hydrogen bonding interaction.

    Geometry optimization

    The geometry optimization can be performed employing commonly used methods like
    steepest descent and conjugate gradient methods that are available in Avogadro software to
    calculate the energy of given molecular geometry along with the application of force field or
    molecular mechanics theory.

    The force field is represented as a collection of equations and associated constants that are
    designed with standard parameters to reproduce geometry and interpret the behaviour of
    atoms and molecules [Ref: https://doi.org/10.1016/j.colsurfb.2014.06.050].
    Modelling procedure

    Avogadro is open source software which is available to model chemical structures and
    predict their approximate energy values. Avogadro software can be downloaded from the
    https://avogadro.cc/.

    Representative examples of molecular systems considered in this demonstration are:-

    1. Comparison and modelling of water (H2O) dimer and H2S dimer to investigate the
    influence of intermolecular hydrogen bonding.

    2. Modelling of 2-nitrophenol to study the influence of intramolecular hydrogen bonding.

    These examples will provide clear understanding on the concept of hydrogen bonding that
    stabilizes the molecular systems.

    Step 1: Make sure that in “Settings” menu, the options “Display types”, “Draw settings” are
    enabled as shown below. In the “Display types” enable “Hydrogen bond” to visualize it in the
    optimized structure.

    Step 2: In the “Draw settings”, choose oxygen atom to model two water molecules placed
    close to each other as shown below.
    Step 3: In the “Extensions” main menu, choose “Molecular Mechanics” followed by “Setup
    force field” menu as shown below.

    Once it is chosen, the following screen appears with the option to choose the type of method.
    It is possible to perform geometry optimization after choosing the force field and algorithm,

    Step 4: Click “Optimize Geometry” in the “Extension” menu to perform geometry


    optimization.

    Step 5: Now the geometry optimization is performed for water dimer. The optimized
    geometry is displayed in the screen. One can visualize the dotted line which indicates the
    hydrogen bond between the oxygen atom of one water molecule to the hydrogen atom of
    another water molecule. This is an example of intermolecular hydrogen bonding as it
    involves two different molecules. Note the energy of the water dimer.
    Step 6: Now in the build option, choose “sulphur” to convert water dimer to H2S dimer.
    Remove “Adjust Hydrogens” option in the build menu and click oxygen atoms. Now the
    structure becomes H2S dimer as shown below.

    Step 7: Now perform geometry optimization as given in Step 4


    Note the difference in structure of H2S dimer and the energy.

    Question: What brings the change in bond length and bond angle between the two dimers,
    H2O and H2S? Explain why hydrogen bonding is missing in H2S dimer?

    Answer: The interactions between the H2S molecules are comparatively weaker (more like
    van der Waals interaction) than the interaction between the two H2O molecules. That is the
    reason the hydrogen bond is absent in H2S dimer. For the same reason, H2O is liquid and H2S
    is gas at room temperature.

    Note: The software is programmed in such a way that depending on the geometry criteria of
    the molecules, the presence of hydrogen bonding will be highlighted.

    Step 8: Draw 2-nitrophenol as shown below


    Step 9: Perform geometry optimization of 2-nitrophenol as given in Step 4. Once geometry
    optimization is performed, intramolecular hydrogen bonding between -OH and -NO2 groups
    can be visualized as a dotted line as shown below.

    Results:

    1. Visualize the geometry of H2O and H2S dimers.


    2. The energy of H2O dimer = _____________ and H2S dimer = _____________
    3. Visualize the geometry of 2-nitrophenol.
    4. The energy of 2-nitrophenol = _____________

    Happy Learning!!!!

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