Location via proxy:   [ UP ]  
[Report a bug]   [Manage cookies]                
Scribd Logo
Upload

Welcome to Scribd!

  • 171 views

    Molcalc Activities

    Uploaded by

    maugonzalezsuarez
    The document describes methods for using molecular modeling and quantum calculation software to determine properties of diatomic, triatomic molecules and simple chemical reactions. It also describes methods for investigating trends in acid molecules and conjugated alkene systems by calculating molecular properties including bond distances, angles, orbital energies and vibrational frequencies. Calculated values are compared to accepted data to validate the computational methods.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd

    Molcalc Activities

    Uploaded by

    maugonzalezsuarez
    171 views4 pages
    The document describes methods for using molecular modeling and quantum calculation software to determine properties of diatomic, triatomic molecules and simple chemical reactions. It also describes methods for investigating trends in acid molecules and conjugated alkene systems by calculating molecular properties including bond distances, angles, orbital energies and vibrational frequencies. Calculated values are compared to accepted data to validate the computational methods.

    Copyright

    © © All Rights Reserved

    Available Formats

    PDF, TXT or read online from Scribd

    Did you find this document useful?

    Is this content inappropriate?

    The document describes methods for using molecular modeling and quantum calculation software to determine properties of diatomic, triatomic molecules and simple chemical reactions. It also describes methods for investigating trends in acid molecules and conjugated alkene systems by calculating molecular properties including bond distances, angles, orbital energies and vibrational frequencies. Calculated values are compared to accepted data to validate the computational methods.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    171 views4 pages

    Molcalc Activities

    Uploaded by

    maugonzalezsuarez
    The document describes methods for using molecular modeling and quantum calculation software to determine properties of diatomic, triatomic molecules and simple chemical reactions. It also describes methods for investigating trends in acid molecules and conjugated alkene systems by calculating molecular properties including bond distances, angles, orbital energies and vibrational frequencies. Calculated values are compared to accepted data to validate the computational methods.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    of 4

    Molecular Orbital Calculations of Molecules I.

    Diatomics, Triatomics and Reactions


    Object: The purpose of this exercise is to use molecular modeling /quantum
    calculation software to determine molecular energies, orbital shapes, thermo-
    dynamic parameters, and vibrational wavenumbers of three simple molecules
    (a homonuclear diatomic molecule, a heteronuclear diatomic molecule, and a
    triatomic molecule) and to use quantum -calculated thermodynamic data to de-
    termine the reaction enthalpy for a simple chemical reaction.

    Method:

    1. Using an appropriate web browser connect to The Molecule Calculator


    (MolCalc) web site (http://dgu.ki.ku.dk/molcalc).
    2. Familiarize yourself with the molecule-building tools in the entry page
    (JSmol).
    3. Construct a homonuclear diatomic molecule with the molecule-building
    function.
    4. Click on “Calculate” to find the minimum energy of this molecule. Note
    that two types of calculations are invoked in GAMESS carry out these
    calculations;

    (a) The GAMESS program computes the molecular orbitals and orbital
    energies at the RHF/STO-3G level of theory. (RHF = restricted
    Hartree-Fock and STO-3G is the basis set of atomic orbitals).
    (b) The GAMESS program computes thermodynamic properties, vibra-
    tional frequencies and vibrational modes using the semi-empirical
    method PM3.

    5. Click on “Thermodynamics” and write down the values for:


    (a) Heat of formation (compare to the accepted value).
    (b) Enthalpy
    (c) Entropy
    (d) Translational enthalpy
    (e) Rotational enthalpy
    (f) Vibrational enthalpy
    (g) Translational entropy
    (h) Rotational entropy
    (i) Vibrational entropy
    6. Click on “Molecular Orbitals” and “View” the orbitals.

    1
    (a) Construct an energy level diagram of the valence molecular orbitals.
    (b) Write down the energies of the highest occupied molecular orbital
    (HOMO) and the lowest unoccupied molecular orbital (LUMO).
    (c) Calculate the wavelength of light that would be needed to induce a
    HOMO → LUMO transition.
    (d) Sketch the shapes of the HOMO and LUMO.
    7. Click on “Vibrational frequencies” and view the animated vibrational mo-
    tions.
    (a) Write down the vibrational frequencies and compare to the accepted
    values.
    8. Repeat steps 4-7 for a heteronuclear diatomic molecule and for a triatomic
    molecule.
    9. Write down a simple chemical reaction of molecules made up of elements
    with Z < 18.

    (a) Construct each of the reactant and product molecules using JSmol.
    (b) Determine the calculated heat of formation of each molecule.
    (c) Calculate the enthalpy of your reaction using Hess’s law.
    (d) Compare your reaction enthalpy to that obtained from thermody-
    namic tables.

    2
    Molecular Orbital Calculations of Molecules II.
    Acids and Alkenes
    Object: The purposes of this exercise are twofold: (1) to use molecular mod-
    eling/quantum calculation software to determine some molecular properties of
    a series of acids and to generalize the effect of changing a parameter of the acid
    molecules in the series on the calculated molecular properties; and (2) to use
    molecular modeling/quantum calculation software to determine some molecular
    properties of a series of conjugated alkenes and to determine the orbital energies
    and shapes of the molecular orbitals involved in the conjugated π system.

    Method 1—property trends of acid molecules:

    1. Using an appropriate web browser connect to The Molecule Calculator


    (MolCalc) web site (http://dgu.ki.ku.dk/molcalc).
    2. Familiarize yourself with the molecule-building tools in the entry page
    (JSmol).
    3. Choose an acid from the following list: H2 CO3 , H2 SiO3 , H3 PO4 , H3 PO3 ,
    H2 SO4 , H2 SO3 (Note: H3 PO3 is a diprotic acid).
    4. Build the structure of the acid molecule you choose using the JSmol tools.
    5. Click on “Minimise” to optimize the shape of the molecule using the Merck
    Molecular Force Field (MMFF).
    6. Click on “Calculate” to find the minimum energy of this molecule. Note
    that two types of calculations are invoked in GAMESS carry out these
    calculations;
    (a) The GAMESS program computes the molecular orbitals and orbital
    energies at the RHF/STO-3G level of theory. (RHF = restricted
    Hartree-Fock and STO-3G is the basis set of atomic orbitals).
    (b) The GAMESS program computes thermodynamic properties, vibra-
    tional frequencies and vibrational modes using the semi-empirical
    method PM3.
    7. Measure and record two bond distances (rO−H and rX=O ), one bond angle
    (O=X-O), and one dihedral angle (O=X-O-H).
    8. Click on “Molecular Orbitals” and “View” the orbitals.
    (a) Record the energies of the highest occupied molecular orbital (HOMO)
    and the lowest unoccupied molecular orbital (LUMO).
    (b) Calculate the wavelength of light that would be needed to induce a
    HOMO → LUMO transition.
    (c) Sketch the shapes of the HOMO and LUMO.

    3
    9. Click on “Vibrational frequencies” and view the animated vibrational mo-
    tions.

    (a) Record two vibrational frequencies (wavenumbers): ṽO−H and ṽX=O

    10. Click on “New Molecule” and rebuild the same acid molecule, but replace
    one of the hydroxyl (OH) groups with a methyl (CH3 ) group. “Minimise”
    and “Calculate” this new acid molecule.
    11. Repeat steps 7-9 for the new acid molecule and record the appropriate
    molecular properties.

    12. Repeat step 10, but before you “Minimise” and “Calculate,” substitute
    one of the methyl hydrogens with another nonmetal element available in
    the element list.
    13. Repeat steps 7-9 for the new acid molecule and record the appropriate
    molecular properties.

    You might also like