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Hyper Chem

This document provides instructions for using HyperChem software to analyze the electronic structure and vibrational spectrum of formaldehyde, perform molecular dynamics simulations of a tetrapeptide and ribosomal protein. The procedures involve building and optimizing the geometry of formaldehyde using RHF/6-31G*, then calculating its molecular orbitals, vibrational frequencies and spectra. Molecular dynamics simulations at 0K and 300K are run on the tetrapeptide using MM+, and a ribosomal protein file is loaded and simulated at 300K for 1ps. Total energies are recorded from the optimizations and simulations.

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Karlina Noordiningsih
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186 views

Hyper Chem

This document provides instructions for using HyperChem software to analyze the electronic structure and vibrational spectrum of formaldehyde, perform molecular dynamics simulations of a tetrapeptide and ribosomal protein. The procedures involve building and optimizing the geometry of formaldehyde using RHF/6-31G*, then calculating its molecular orbitals, vibrational frequencies and spectra. Molecular dynamics simulations at 0K and 300K are run on the tetrapeptide using MM+, and a ribosomal protein file is loaded and simulated at 300K for 1ps. Total energies are recorded from the optimizations and simulations.

Uploaded by

Karlina Noordiningsih
Copyright
© © All Rights Reserved
Available Formats
Download as DOC, PDF, TXT or read online on Scribd
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HYPERCHEM Exercise

Part A: Study the electronic structure and vibrational spectrum of formaldehyde


O

Procedures:
Step 1: Build up the structure of the formaldehyde.

Formaldehyde

1. Run HYPERCHEM software in the start menu.

H
2. Double click the drawing tool to open the elements table dialogue box and select carbon atom.

Close the element table.


(Drawing tool)
3. L-click the cursor on the workspace. A carbon atom will appear.
(Make sure drawing tool is selected. R-click on the atom if you want to delete it)
4. Repeat (2) and choose oxygen instead of carbon. Move the cursor to the carbon centre and drag the
mouse from the carbon centre to an empty workspace. (A single bond is created between carbon
atom and oxygen atom.)
5. L-click the bond between carbon and oxygen to create a double bond.
6. L-click on Build in the menu bar and switch on add H & model build (i.e. make sure a tick
appeared on the left of this function.).
Step 2: Optimize the structure using RHF and 6-31G* basis set.
7. L-Click on Setup in the menu bar and L-click ab Initio;
L-Click on 6-31G*; then, L-Click on Options button;
Select RHF, set Charge to 0 and Multiplicity to 1 (default for charge 0);
L-Click OK buttons after modifications were done.
8. L-Click on Compute in the menu bar and select Geometry Optimization;
Select Polak-Ribiere and set RMS gradient to 0.05 and max cycles to 60;
L-Click OK button (The calculation will be started. Repeat the step till Conv=YES appears in the
status line.).

Record the energy appeared in the status line


9. L-Click on Compute in the menu bar and select Orbitals.

Record energy levels and point groups of required molecular orbitals (MO)
(Optional: You can draw the contour plot of the selected orbital and visualize the shape of the orbital.)
10.

L-Click on Compute in the menu bar and select Vibrations.

11.

L-Click on Compute in the menu bar and select Vibrational Spectrum.

Record the frequencies of different vibrational modes and their corresponding


oscillator strengths.
(Optional: You can turn on animate vibrations, select any vibrational modes, and L-Click on OK
button. The molecule begins to vibrate. To suspend the animation, L-Click on Cancel button.)

Part B: Molecular Dynamics of Tetrapeptide


1. L-click Databases on the menu bar. Choose Amino Acids.
2. Select Beta sheet.
3. L-click Ala, Tyr, Asp and Gly to create tetrapeptide Ala-Tyr-Asp-Gly.
4. L-click on rotate-out-of-plane tool and use it to rotate the molecule to a proper angle for
observation and measurements.
(Rotate-out-of-plane tool)
5. L-Click on Setup in the menu bar and L-click Molecular Mechanics;
L-Click on MM+;
L-Click OK buttons after modifications were done.
6. L-Click on Compute in the menu bar and select Geometry Optimization;
7. Record the total energies.
8. L-Click on Compute in the menu bar and L-click Molecular Dynamics;
Run molecular dynamics at 0K and 300K with constant temperature.
Simulation Time: 1ps
9. Record the total energies.

Part C: Molecular Dynamics of Ribosomal Protein


Procedures:
10. Use a web-browser and Go to http://yangtze.hku.hk/lecture_notes.htm.
11. R-click the title labeled Download molecule and save it in a folder in your local disk (C:\).
12. L-click on File in the menu bar and select open to load in the molecule.
(You should notify that this file has extension filename .ENT and is in PDB format.)
13. L-click on rotate-out-of-plane tool and use it to rotate the molecule to a proper angle for
observation and measurements.
(Rotate-out-of-plane tool)
14. L-Click on Setup in the menu bar and L-click Molecular Mechanics;
L-Click on MM+;
L-Click OK buttons after modifications were done.
15. L-Click on Compute in the menu bar and L-click Molecular Dynamics;
Run molecular dynamics at 300K with constant temperature.
Simulation Time: 1ps
16. Record the total energy.

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