Sysadmin: Revised formatting

2022-09-26T21:01:43Z

Revised formatting

← Older revision		Revision as of 21:01, 26 September 2022
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	HyperChem:		====== HyperChem ======

	This section depends on the need for quantum descriptors such as HOMO, LUMO, and Total energy.		This section depends on the need for quantum descriptors such as HOMO, LUMO, and Total energy.

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	<li><p>Select “ QSAR Properties” at the bottom</p></li>		<li><p>Select “ QSAR Properties” at the bottom</p></li>
	<li><p>In this window you can select any of the properties that you desired to compute by simply selecting the property and press compute. The value will be shown at the bottom of the “QSAR Properties” window.</p></li>		<li><p>In this window you can select any of the properties that you desired to compute by simply selecting the property and press compute. The value will be shown at the bottom of the “QSAR Properties” window.</p></li>
	<li><p>Scripts are also available to be written for Hyperchem if desired, you can do this via following Lesson 17 or 18 in this manual. <u>http://www.chemistry-software.com/pdf/Hyperchem_full_manual.pdf</u><br />		<li><p>Scripts are also available to be written for Hyperchem if desired, you can do this via following Lesson 17 or 18 in this manual. <u>http://www.chemistry-software.com/pdf/Hyperchem_full_manual.pdf</u></p>
	<~~br /~~>		<li><p>If manual doesn’t show up just google “Hyperchem Manual”</p></li></li>
	If manual doesn’t show up just google “Hyperchem Manual”</p></li>
	<li><p>If It says your Molecule has issues before Geometry optimization such as Valence error go to Select</p>		<li><p>If It says your Molecule has issues before Geometry optimization such as Valence error go to Select</p>
	<ol style="list-style-type: lower-alpha;">		<ul style="list-style-type: lower-alpha;">
	<li><p>Select All</p></li>		<li><p>Select All</p></li>
	<li><p>Select again</p></li>		<li><p>Select again</p></li>
	<li><p>“Add H & Model Build”</p></li></ol>		<li><p>“Add H & Model Build”</p></li></ul>
	</li>		</li>
	<li><p>This corrects the error</p></li>		<li><p>This corrects the error</p></li>
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	<li><p>If it doesn’t initially then try going to labels and pressing “none.” Then repeat steps 114 a-b</p></li>		<li><p>If it doesn’t initially then try going to labels and pressing “none.” Then repeat steps 114 a-b</p></li>
	<li><p>If that doesn’t work then select the semi-empirical. Once selected redo steps 114a-d</p></li>		<li><p>If that doesn’t work then select the semi-empirical. Once selected redo steps 114a-d</p></li>
	<li><p>Use RHF not UHF</p></li></ol>		<li><p>Use RHF not UHF<br /></p></li></ol>
	</li></ol>		</li></ol>

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2022-09-26T19:21:17Z

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HyperChem:

This section depends on the need for quantum descriptors such as HOMO, LUMO, and Total energy.

<ol>
<li>Open “HyperChem”</li>
<li>Open a file that has “.hin” extension</li>
<li>Press “Setup” on the tool bar</li>
<li>Press “Semi-empirical”</li>
<li>Press “RM1”</li>
<li>Press “OK</li>
<li>Press “Compute” on the tool bar</li>
<li>Select “Geometry Optimization”</li>
<li>For regular work make sure “Polak –Ribiere (Conjugate gradiant)” is selected.</li>
<li>Have 0.1 in the top bar of RMS gradiant and in the bottom bar 600.</li>
<li>Have “In vacuo” selected</li>
<li>For the “Screen refresh period” use 1 for cycles.</li>
<li>Steps 78-81 should be default settings</li>
<li>Press “OK”</li>
<li>Once the optimization has stopped (Numbers on the bottom right or left have stopped moving) then select “Compute”</li>
<li>Select “Properties”</li>
<li>All the information in “Properties” can be used as quantum descriptors if needed</li>
<li>By Pressing “Details” you will get more information and these are also used as descriptors if needed.</li>
<li>Exit out of “Properties”</li>
<li>Press “Compute”</li>
<li>Select “Orbitals”</li>
<li>the screen that pops up shows 2-4 different columns, the left being Alpha orbitals and the right being Beta orbitals. The pink/purple column is simply the orbitals above the HOMO-LUMO Gap, and the green is simply below the HOMO LUMO Gap</li>
<li>Each line in these columns gives you the energy in “eV” for that orbital.</li>
<li>If you zoom into the bottom most line of the pink/purple column that is LUMO- Lowest unoccupied molecular orbital. If you select the bottom most line of the pink/purple column, it will give you a value in the “Energy” bar as “eV”. That is LUMO.</li>
<li>If you zoom into the top most line of the green column that is HOMO- Highest Occupied Molecular Orbital. If you select the top most like of the green column it will give you a value in the “Energy” bar as “eV”. That is HOMO</li>
<li>The difference of these energies is the HOMO-LUMO Gap.</li>
<li>If desired, you can simply “Plot” isosurfaces of the orbital that is selected by pressing the “Plot” button on the bottom left of the Orbitals panal.</li>
<li>Press “OK” when done with this screen.</li>
<li>To get further Descriptors</li>
<li>Select “Compute”</li>
<li>Select “ QSAR Properties” at the bottom</li>
<li>In this window you can select any of the properties that you desired to compute by simply selecting the property and press compute. The value will be shown at the bottom of the “QSAR Properties” window.</li>
<li>Scripts are also available to be written for Hyperchem if desired, you can do this via following Lesson 17 or 18 in this manual. http://www.chemistry-software.com/pdf/Hyperchem_full_manual.pdf 
 
If manual doesn’t show up just google “Hyperchem Manual”</li>
<li>If It says your Molecule has issues before Geometry optimization such as Valence error go to Select
<ol style="list-style-type: lower-alpha;">
<li>Select All</li>
<li>Select again</li>
<li>“Add H & Model Build”</li></ol>
</li>
<li>This corrects the error</li>
<li>Additionally, If molecules are large and “Semi-Empirical” geometry optimization takes too much time then molecular mechanics is needed
<ol style="list-style-type: lower-alpha;">
<li>When doing the molecular mechanics it is necessary to make sure the atom “type” is corrected.</li>
<li>To check if atom type is correct go to “Display”
<ol style="list-style-type: lower-roman;">
<li>“Labels”</li>
<li>“type”</li></ol>
</li>
<li>If you see “**” on the atoms then hyperchem needs to recalculate the atoms to get C, H, O, and other atoms.
<ol style="list-style-type: lower-roman;">
<li>Go to “setup”</li>
<li>“Molecular Mechanics”</li>
<li>Select “MM+”</li>
<li>Click on “Options”</li>
<li>Press OK</li>
<li>Click on “Components”</li>
<li>Press OK</li>
<li>Then press “OK” on the same window you selected “MM+”</li>
<li>You should get a popup window saying the atom types are going to be recalculated</li>
<li>Press “OK”</li></ol>
</li>
<li>This should change the “**” to letters such as C, H, O</li>
<li>If it doesn’t initially then try going to labels and pressing “none.” Then repeat steps 114 a-b</li>
<li>If that doesn’t work then select the semi-empirical. Once selected redo steps 114a-d</li>
<li>Use RHF not UHF</li></ol>
</li></ol>

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