View source for Optimisation of the geometry of the molecule


== Optimization of the geometry of a molecule ==


<p>Now we are going to optimize the geometry of our molecule </p>

<h4>Calculations with HF and the DFT</h4>

<p>As previously, click on '''Calculate''' --> '''Gaussian''', click on '''Job style''' and now select '''Optimization'''. Keep the optimization in a minimum, and then click on '''Method''' and choose Hartree-Fock with a basis set of 3-21G or 6-21G.<br/>
Then click on '''Title''' and enter the title of your file, and click on '''Link 0'''. In this part you have to type your file name after %chk. Then click on '''Edit''' and '''save''' on Gaussian. A third window should appear, in which you have to enter the file name, take the same as you enter after %chk.</p>

<p>You created a file .com (check if everything is registering in your folder). Now everything is ready to be calculated by Gaussian.<br/>
Open a '''Terminal''' window and enter the name of your file, press enter and it would be start the calculation. At the end you should find the results in the file .log that you can open with the '''TextEdit''' application.</p>

<p>Do the same with the DFT method.</p>

<h4>What can you see in the file .log ?</h4>
<p>This file .log is going to condense all the information concerning the molecule before and after the optimization.<br/>
That's why you will find the informations of the spatial position of the atom first in the originate geometry and then in the optimized geometry. Furthermore, Gaussian checks if there is a stationary point or not. So to get this information, search this part of the file (Optimization of Propene, DFT 6-21G): </p>

<pre>
Optimization completed.
    -- Stationary point found.
                           ----------------------------
                           !   Optimized Parameters   !
                           ! (Angstroms and Degrees)  !
 --------------------------                            --------------------------
 ! Name  Definition              Value          Derivative Info.                !
 --------------------------------------------------------------------------------
 ! R1    R(1,2)                  1.0883         -DE/DX =   -0.0001              !
 ! R2    R(1,3)                  1.086          -DE/DX =   -0.0001              !
 ! R3    R(1,4)                  1.3382         -DE/DX =    0.0                 !
 ! R4    R(4,5)                  1.0901         -DE/DX =   -0.0001              !
 ! R5    R(4,6)                  1.5145         -DE/DX =   -0.0002              !
 ! R6    R(6,7)                  1.0976         -DE/DX =   -0.0001              !
 ! R7    R(6,8)                  1.0945         -DE/DX =   -0.0001              !
 ! R8    R(6,9)                  1.0976         -DE/DX =   -0.0001              !
 ! A1    A(2,1,3)              116.1865         -DE/DX =    0.0                 !
 ! A2    A(2,1,4)              121.9746         -DE/DX =    0.0001              !
 ! A3    A(3,1,4)              121.8389         -DE/DX =   -0.0001              !
 ! A4    A(1,4,5)              118.7541         -DE/DX =   -0.0001              !
 ! A5    A(1,4,6)              124.9684         -DE/DX =    0.0                 !
 ! A6    A(5,4,6)              116.2775         -DE/DX =    0.0001              !
 ! A7    A(4,6,7)              111.4927         -DE/DX =    0.0                 !
 ! A8    A(4,6,8)              111.5201         -DE/DX =   -0.0001              !
 ! A9    A(4,6,9)              111.4922         -DE/DX =    0.0                 !
 ! A10   A(7,6,8)              107.4812         -DE/DX =    0.0001              !
 ! A11   A(7,6,9)              107.1385         -DE/DX =    0.0                 !
 ! A12   A(8,6,9)              107.4799         -DE/DX =    0.0001              !
 ! D1    D(2,1,4,5)            179.9991         -DE/DX =    0.0                 !
 ! D2    D(2,1,4,6)             -0.0025         -DE/DX =    0.0                 !
 ! D3    D(3,1,4,5)             -0.0006         -DE/DX =    0.0                 !
 ! D4    D(3,1,4,6)            179.9977         -DE/DX =    0.0                 !
 ! D5    D(1,4,6,7)             59.7949         -DE/DX =    0.0                 !
 ! D6    D(1,4,6,8)            179.9473         -DE/DX =    0.0                 !
 ! D7    D(1,4,6,9)            -59.9023         -DE/DX =    0.0                 !
 ! D8    D(5,4,6,7)           -120.2067         -DE/DX =    0.0                 !
 ! D9    D(5,4,6,8)             -0.0543         -DE/DX =    0.0                 !
 ! D10   D(5,4,6,9)            120.0961         -DE/DX =    0.0                 !
 --------------------------------------------------------------------------------
</pre>
[[See other results]]
<p>The different R are the different bond length between the atoms and you can check with showing the labels. A corresponds to the angle, and D the dihedral angle.</p>


----

'''Definition break''' 
''<p>What is a stationary point ?<br/>
A stationary point is a point of the potential energy surface where the forces are zero, so it corresponds to have a null gradient too. If your optimization is successful Gaussian have to locate a stationary point, but this stationary point could be a minimum or a saddle point, and so it could be not what you expected.</p>''

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<h4>Transition state optimization</h4>
<p>To optimize the geometry of the molecule, you have check '''Opt''' --> '''minimum''' in the Job style. But you can also optimize a geometry of a transition state, and to explain it to Gaussian you just have to ask for an '''Opt''' --> '''TS (berny)'''. And in the Chapter Frequency calculations we will see more about this.</p>