View source for Frequency Calculations on a Small System (high level vs. ONIOM)

The aim of this page is to compare the results of frequency calculations on bicyclo(10,2,2)hexadeca-1(15),12(16)13-triene between those given by [http://www.ch.ic.ac.uk/wiki/index.php/First_steps_with_ONIOM_:_excited_state_of_Bicyclo(10%2C2%2C2)Hexadeca-1(15)%2C12(16)13-triene ONIOM], CASSCF(6,6)/6-31G* on the whole molecule, benzene in isolation and the modes from the ONIOM calculation that are associated with the high level system.  

We chose bicyclo(10,2,2)hexadeca-1(15),12(16)13-triene as our small system (it being the subject of a previous discussion: https://www.ch.ic.ac.uk/wiki/index.php/First_steps_with_ONIOM_:_excited_state_of_Bicyclo%2810%2C2%2C2%29Hexadeca-1%2815%29%2C12%2816%2913-triene). The high level method and basis set was chosen as b3lyp/6-31g(d), and the ONIOM layers as b3lyp/6-31g(d):amber.

<h2>Input and Output</h2>

<h4>ONIOM Input files</h4>

This is the original input file prior to assigning atomic charges for amber: [[Media:0raw.gjf]]

To find the charges: <br/>
1. Export the .com file to a cluster folder. <br/>
2. In the route section specify "#p oniom(b3lyp/6-31g(d):amber=qeq) geom=connectivity pop=full". The "amber=qeq" part of the job finds atomic charges using the qeq method (more information: http://www.gaussian.com/g_tech/g_ur/k_mm.htm). <br/>
3. Run the input file on the cluster. <br/>
4. As with GFP (https://www.ch.ic.ac.uk/wiki/index.php/GFP_:_Green_Fluorescent_Protein), open the .log file in an nedit window using X11 and copy all the missing charges (lines 5353 to 5392, sanity check line 5393). Paste into another nedit window displaying the input file from step 2, remove the "=qeq" keyword and save. <br/>

This is the end result: [[Media:1charges.gjf]]

<h4>ONIOM Frequency Calculations</h4>

Now run an "opt freq" calculation on the file 1charges.com. Output: [[Media:2optfreq.log]] <br/>
The formatted checkpoint files displays vibrations in GaussView 3.0, 4.1 or 5.0

Using the .chk file created, you can now run a "freq=sortmodes" calculation. This keyword prints frequencies according to ONIOM layer. Output: [[Media:3sortmodes.log]]

The main comparison we want to make between the two methods looks at the modes of the model to determine whether they compare well with those from the high level method. In an ONIOM input, the modes of the model are list with the keyword "freq=modelmodes". We've included the keyword "HPmodes" to print frequencies to a high level of precision. Output: [[Media:4modelmodes.log]]

<h4>High level input files</h4>

Quite simply, here is the input file for subsequent high level calculations: [[Media:high_level.gjf]]. The input orientation is taken from the optimisation of the ONIOM model.

<h4>High level Frequency Calculations</h4>

Here is the output from the "freq=hpmodes" calculation: [[Media:freq.log]]

There is no need to do a "sortmodes" or a "modelmodes" calculation since the input is all high level.

<h2>Comparison</h2>

Here is the list of frequencies calculated in 4modelmodes.log (i.e.: those associated with the model region):

<pre>
                          16        22        23        32        33
                           A         A         A         A         A
       Frequencies ---   409.0098  596.6039  665.1594  852.8351  865.1841
    Reduced masses ---     2.7051    2.5761    6.3022    1.4695    1.4536
   Force constants ---     0.2666    0.5402    1.6428    0.6297    0.6411
 Percent ModelSys  ---    68.1034   59.3840   86.7469   55.3040   61.8052
 Percent RealSys   ---    31.8966   40.6160   13.2531   44.6960   38.1948
    IR Intensities ---     0.0044   14.5668    0.0873    0.3912    0.2297

                          39        40        50        51        53
                           A         A         A         A         A
       Frequencies ---   970.2333  974.0159 1060.5563 1170.0279 1237.9576
    Reduced masses ---     1.2998    1.3634    2.6869    1.3712    1.2316
   Force constants ---     0.7209    0.7621    1.7806    1.1060    1.1121
 Percent ModelSys  ---    97.5852   99.5046   91.8918   98.5451   90.2186
 Percent RealSys   ---     2.4148    0.4954    8.1082    1.4549    9.7814
    IR Intensities ---     0.4089    0.0260    1.4967    0.8189    0.1163

                          54        65        87        90       111
                           A         A         A         A         A
       Frequencies ---  1245.8430 1382.6152 1663.4285 1717.0543 3182.3831
    Reduced masses ---     1.7658    1.2489    5.8710    5.1623    1.0877
   Force constants ---     1.6148    1.4066    9.5713    8.9674    6.4901
 Percent ModelSys  ---    52.3621   83.1773   70.9507   72.4910   99.9995
 Percent RealSys   ---    47.6379   16.8227   29.0493   27.5090    0.0005
    IR Intensities ---     1.0287    0.0037    0.0585    0.1809   16.7578

                        112       113       114
                           A         A         A
       Frequencies ---  3183.6449 3199.7525 3201.5732
    Reduced masses ---     1.0880    1.0954    1.0957
   Force constants ---     6.4971    6.6079    6.6172
 Percent ModelSys  ---    99.9953   99.9935   99.9992
 Percent RealSys   ---     0.0047    0.0065    0.0008
    IR Intensities ---     0.1514   51.4042    0.1518
</pre>

The corresponding modes in freq.log are given below:

<pre>
                          16         22	         23	  32	   33	  
                           A          A	          A	   A	    A
       Frequencies ---   387.9463   579.8860   655.1341 845.7905  862.0594
    Reduced masses ---     3.0546   2.2340     6.5555   1.3171    2.2789
   Force constants ---     0.2709   0.4426     1.6577  0.5551    0.9978
    IR Intensities ---     0.0170   11.5675    0.0301   0.8178    0.2188
                         
                           39	     40        50        51         53	
 			    A	      A         A         A	     A	  
       Frequencies ---   962.9661  972.9108 1112.6678   1124.2976 1189.9051 
    Reduced masses ---     1.3543    2.4918   1.3162    1.5015    1.3452 
   Force constants ---     0.7399    1.3897   0.9601    1.1182    1.1222 
    IR Intensities ---     0.1082    0.0529   0.9758    1.1525    0.0894 

                         54	   65         87	   90       111    
   			 A   	   A          A	            A        A    
       Frequencies ---  1208.0237  1336.8959  1525.1812 1664.6934 3192.0631 
    Reduced masses ---    1.4300     1.1364   1.0934      5.7955    1.0956
   Force constants ---    1.2295   1.1967     1.4986      9.4625    6.5774
    IR Intensities ---    0.8899   0.6101     3.0594      2.7069   35.0614 


                         112       113       114
                           A         A         A
       Frequencies ---  3195.4208 3198.2576 3221.8400
    Reduced masses ---     1.0939    1.0946    1.0960
   Force constants ---     6.5811    6.5966    6.7032
    IR Intensities ---    45.5175    1.8373   20.4506
</pre>

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