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    Lecture No. 3 - Optimization II

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    XarOon
    The document provides instructions for students on performing conformational analysis calculations using computational chemistry software. It outlines two problems - calculating the inversion barrier of ammonia by optimizing planar and pyramidal structures, and calculating the rotation barrier of ethane by optimizing staggered and eclipsed conformations. Students are asked to perform the calculations using different basis sets and report the results. The document teaches how to scan bond lengths and angles through the Z-matrix and perform relaxed and rigid scans on a water molecule as an example.

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    Lecture No. 3 - Optimization II

    Uploaded by

    XarOon
    36 views15 pages
    The document provides instructions for students on performing conformational analysis calculations using computational chemistry software. It outlines two problems - calculating the inversion barrier of ammonia by optimizing planar and pyramidal structures, and calculating the rotation barrier of ethane by optimizing staggered and eclipsed conformations. Students are asked to perform the calculations using different basis sets and report the results. The document teaches how to scan bond lengths and angles through the Z-matrix and perform relaxed and rigid scans on a water molecule as an example.

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    Lecture No. 3_Optimization II.ppt

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    The document provides instructions for students on performing conformational analysis calculations using computational chemistry software. It outlines two problems - calculating the inversion barrier of ammonia by optimizing planar and pyramidal structures, and calculating the rotation barrier of ethane by optimizing staggered and eclipsed conformations. Students are asked to perform the calculations using different basis sets and report the results. The document teaches how to scan bond lengths and angles through the Z-matrix and perform relaxed and rigid scans on a water molecule as an example.

    Copyright:

    © All Rights Reserved
    Download as PPT, PDF, TXT or read online from Scribd
    Download as ppt, pdf, or txt
    36 views15 pages

    Lecture No. 3 - Optimization II

    Uploaded by

    XarOon
    The document provides instructions for students on performing conformational analysis calculations using computational chemistry software. It outlines two problems - calculating the inversion barrier of ammonia by optimizing planar and pyramidal structures, and calculating the rotation barrier of ethane by optimizing staggered and eclipsed conformations. Students are asked to perform the calculations using different basis sets and report the results. The document teaches how to scan bond lengths and angles through the Z-matrix and perform relaxed and rigid scans on a water molecule as an example.

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    Part II

    Geometry optimization and


    conformational analysis,
    Scan of bond lengths, bond
    angles and dihedral angles
    through Z-Matrix and
    redundant coordinates
    Dr. Mazhar Amjad Gilani

    COMSATS University Islamabad, Lahore Campus

    12-09-18
    Learning Objectives:

    1. Conformational Analysis???

    2. How to Scan along bond length??

    3. How to Scan along bond angle???


    application of mathematical
    models and simulations to
    chemical problems using
    computers
    Conformers VS. Configurations

     The spatial arrangement of atoms of molecules.

     Conformations are determined by energy, so the essence of the


    required calculations is to compare energies of different molecular
    structures.
    Problem 1: The inversion barrier of ammonia
    (planar versus pyramidal)

     The "umbrella" inversion barrier in ammonia, is the difference in energy between


    the pyramidal and the planar structures of the ammonia molecule.

    For both structures, it is important to optimize the geometry.


    Problem 1…………….

    Make input files for both planar as well as pyramidal


    structures

    Submit the Gaussian calculation.

    Open the output file in Notepad and verify that the


    run terminated successfully and that convergence
    was accomplished.

    Open the output file in GaussView in order to


    observe the optimized structure.

    Go to RESULTS tab and note the energy.


    Assignment # 01 (2.5 Marks)
    Problem # 2: Rotation barrier of ethane
    Make input files for both eclipsed as well as
    staggered conformations

    Submit the Gaussian calculation.

    Open the output file in Notepad and verify that the


    run terminated successfully and that convergence
    was accomplished.

    Open the output file in GaussView in order to


    observe the optimized structure.

    Go to RESULTS tab and note the energy.


    Assignment # 02 (2.5 Marks)
    Perform geometry optimization calculations of the staggered and the eclipsed
    conformations of ethane using the Hartree-Fock method and the following
    basis sets: STO-3G, 3-21G, 6-31G(d) and the 6-31G(d, p).

    Tabulate the energy, C-C bond length and C-C-H bond angle for each structure,
    and the energy difference between the staggered and the eclipsed conformations.

    Compare the results with the experimental data.

    Is there any significant improvement with the larger basis sets?


    Tutorial: Scan of Bond Lengths
    through Z-matrix
    Types of Scan: RIGID Vs. RELAXED

    Example of Water molecule


    Tutorial: Scan of Bond Angles
    through Z-matrix

    Example of Water molecule


    Thanks a lot

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