USING HYPERCHEM

l>Using HyperChem

Using HyperChem

HyperChem is a package for performing Molecular Mechanics,Molecular Dynamics and ab initio calculations forchemical systems.

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The first screen that one sees on starting up the packagelooks as follows:

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First, I will describe how khổng lồ vì chưng a simple Molecular Mechanicscalculation for a simple molecule, H2O. First, we needlớn "create" the molecule. This is done by selecting Build: Default Element : và selecting O for Oxygene - thescreen looks as follows:

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After returning to the main screen, make sure the

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button is selected andclick the left mouse button on the main drawing area. You willget the following image of an Oxygene atom:

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If you vì chưng not, you may need lớn select Display : RenderingOptions : Rendering Method : Balls & Cylinders (seescreen shot below):

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Now select Build : Add Hydrogens and themolecule turns into lớn a water molecule:

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Now "select" the molecule you created by clicking Select: Select All . The molecule should turn green. Now select from the thực đơn Setup: Periodic Box. You will see the following screen:

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Enter the desired dimensions in the periodic box (12x12x12Angstrom in the case above) and click OK. You get a boxwith 58 "solvent" molecules, which happen lớn be waterin this case. Select from the thực đơn Select : ComplementSelection và the image inside your drawing area should look asfollows:

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Now delete all the added solvent molecules by pressing the"Delete" on the keyboard. You can verify that there isa box now by setting the Rendering mode (see above)lớn "Sticks" và making sure that the "ShowPeriodic Box" Option is checked (under Display). Thescreen (after rotating using the

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tool) looks like this:

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Now select the water atom & duplicate as many times as youwant using Edit : Copy : Past (or CTRL-CCTRL-V).

To cài đặt a Molecular Dynamics Calculation using the MM+ forcefield, select Setup : Molecular Mechanics from the mainmenu and cliông chồng on the MM+ force field button:

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After this, you are ready to run a simulation using Compute: Molecular Dynamics và filling out the appropriate options onthe screen:

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HyperChem will likely complain that the simulation isunstable, because of the poor initial configuration (whichprobably has overlaps & a very high energy). You can fix thisby running a cycle of energy minimization by selecting Compute: Geometry Optimization, which will minimize the energy ofthe selected molecules by shifting them around. You will need torun for some time và collect averages of the energy.

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Ab Initio Calculations

The application of ab initio calculations lớn simpleelectronic structure calculations will be illustrated below forthe simple case of determining the potential energy curve sầu as afunction of bond length for the molecule O2. The firststep is to thiết lập two O atoms in the main simulation box, at adistance (in the case below) of 1.18329 Angstrom.

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Different distance can be obtained by selecting one of theatoms and displacing it (Edit : Translate). Thenext step is khổng lồ "Setup" the ab initio calculations.The following menu pops up:

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Select the basis set desired, and also click on "Options"to lớn get to the following menu:

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The "Total charge" entry is for the wholemolecule (0 in this case) & the "UHF" or"RHF" denote unrestricted và restrictedHartree-Fochồng calculations, respectively. For molecules such as O2,RHF calculations are appropriate, since there are no loneelectrons.

After the calculations have sầu been phối up, you can proceed lớn Compute: Single Point khổng lồ obtain the total energy of theconfiguration. To see details on the results of the calculation,you will need to select File : Start Log to keepyour calculations in a tệp tin of your choice. The following is ansection of the log file for the O2 calculations:


Bond Distance, (Angstrom) Energy (Mcal/mol)
0.8 -92.80
0.85 -92.97
0.90 -93.09
0.95 -93.17
1.00 -93.22
1.05 -93.26
1.10 -93.28
1.15 -93.29
1.20 -93.30
1.25 -93.30
1.30 -93.05
1.35 -93.08
1.40 -93.10
1.50 -93.14

A "Geometry Optimization" gives an equilibrium bonddistance of 1.242 Angstrom for the molecule. The behavior of theenergy at longer distances is a little strange (can you guesswhy?). The experimental value for the bond length is 1.208Angstrom.