Difference between revisions of "Jmol-Application/C2/Surfaces-and-Orbitals/English"
From Script | Spoken-Tutorial
Snehalathak (Talk | contribs) (Created page with ''''Title of script''': Surfaces and Orbitals '''Author: '''Snehalatha Kaliappan '''Keywords: '''Molecular visualization, 3D models of chemical structures, Alicyclic and Aromati…') |
|||
| (6 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
| − | '''Title of script''': Surfaces and Orbitals | + | |
| + | == '''Title of script''': Surfaces and Orbitals | ||
'''Author: '''Snehalatha Kaliappan | '''Author: '''Snehalatha Kaliappan | ||
'''Keywords: '''Molecular visualization, 3D models of chemical structures, Alicyclic and Aromatic molecules, surface topology, Atomic and Molecular orbitals, Video tutorial, Jmol tutorial. | '''Keywords: '''Molecular visualization, 3D models of chemical structures, Alicyclic and Aromatic molecules, surface topology, Atomic and Molecular orbitals, Video tutorial, Jmol tutorial. | ||
| − | |||
| − | |||
| − | |||
{| style="border-spacing:0;" | {| style="border-spacing:0;" | ||
| Line 25: | Line 23: | ||
* Create models of '''Alicyclic''' and '''Aromatic''' molecules. | * Create models of '''Alicyclic''' and '''Aromatic''' molecules. | ||
| + | |||
* Display different surfaces of molecules. | * Display different surfaces of molecules. | ||
| + | |||
* Display Atomic and Molecular orbitals. | * Display Atomic and Molecular orbitals. | ||
| − | |||
| − | |||
|- | |- | ||
| Line 35: | Line 33: | ||
'''Pre-requisites''' | '''Pre-requisites''' | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To follow this tutorial, you should know how to create and edit molecular models in '''Jmol Application.''' | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To follow this tutorial, you should know how to create and edit molecular models in '''Jmol Application.''' | ||
| − | |||
If not, watch the relevant tutorials available at our website. | If not, watch the relevant tutorials available at our website. | ||
| − | |||
| − | |||
| − | |||
|- | |- | ||
| Line 49: | Line 43: | ||
* '''Ubuntu '''OS version. 12.04 | * '''Ubuntu '''OS version. 12.04 | ||
| − | * '''Jmol | + | * '''Jmol '''version 12.2.2 and |
| − | * '''Java ''' | + | * '''Java (JRE)''' version 7 |
| − | + | ||
| − | + | ||
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Jmol panel | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Jmol panel | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| I have opened a new '''Jmol application''' window. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| I have opened a new '''Jmol application''' window. | ||
| − | |||
| − | |||
| − | |||
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Jmol panel | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Jmol panel | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Let us first create a model of''' cyclohexane.''' | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Let us first create a model of''' cyclohexane.''' | ||
| − | |||
| − | |||
| − | |||
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on the modelkit icon in the tool bar | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on the modelkit icon in the tool bar | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''modelkit menu'''. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''modelkit menu'''. | ||
| − | |||
A model of '''methane '''appears on the '''panel.''' | A model of '''methane '''appears on the '''panel.''' | ||
| Line 89: | Line 74: | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To do so, we will place the cursor on the '''hydrogen '''and click on it. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To do so, we will place the cursor on the '''hydrogen '''and click on it. | ||
| − | + | This is a model of '''ethane''' on screen. | |
| − | This is a model of ethane on screen | + | |
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the Ethane molecule >> Click on hydrogen. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the Ethane molecule >> Click on hydrogen. | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Repeat this step another 2 times and replace one '''hydrogen''' at a time with a '''methyl''' group. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Repeat this step another 2 times and replace one '''hydrogen''' at a time with a '''methyl''' group. | ||
| − | |||
Click on the '''hydrogens''' in such a way that the structure forms a circle. | Click on the '''hydrogens''' in such a way that the structure forms a circle. | ||
| Line 102: | Line 85: | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Rotate molecule '''tool and rotate the model. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Rotate molecule '''tool and rotate the model. | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now, rotate the structure on screen using the '''Rotate molecule '''tool. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now, rotate the structure on screen using the '''Rotate molecule '''tool. | ||
| − | |||
| − | |||
| − | |||
|- | |- | ||
| Line 111: | Line 91: | ||
| − | Click on the modelkit menu. | + | Click on the '''modelkit menu.''' |
|- | |- | ||
| Line 130: | Line 110: | ||
|- | |- | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on minimize option in the modelkit menu |
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Use minimize option in the modelkit menu to optimize the structure. | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Use minimize option in the '''modelkit menu''' to optimize the structure. |
|- | |- | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel. |
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The model of '''Cyclohexane''' is now, in its most stable “'''chair'''” '''conformation'''. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The model of '''Cyclohexane''' is now, in its most stable “'''chair'''” '''conformation'''. | ||
| Line 140: | Line 120: | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Open '''modelkit''' menu and scroll down to '''Drag to bond''' option. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Open '''modelkit''' menu and scroll down to '''Drag to bond''' option. | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Alternately, we can also use '''Drag to bond''' option in '''modelkit''' menu to create''' '''cyclic structures. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Alternately, we can also use '''Drag to bond''' option in '''modelkit''' menu to create''' '''cyclic structures. | ||
| − | |||
| − | |||
| − | |||
|- | |- | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel. |
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| I will use a model of pentane to demonstrate this feature. | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| I will use a model of '''pentane''' to demonstrate this feature. |
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Open new Jmol window with pentane structure. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Open new Jmol window with pentane structure. | ||
| − | + | Open modelkit menu and check against '''Drag to bond''' option. | |
| − | Open modelkit menu and check | + | |
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| This is a model of '''pentane''' on the '''panel'''. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| This is a model of '''pentane''' on the '''panel'''. | ||
| Line 167: | Line 143: | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Bring the cursor to other end of the chain and click on the carbon. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Bring the cursor to other end of the chain and click on the carbon. | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Without releasing the mouse button, bring the cursor to the '''carbon '''present at the other end of the chain. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Without releasing the mouse button, bring the cursor to the '''carbon '''present at the other end of the chain. | ||
| − | |||
Now release the mouse button. | Now release the mouse button. | ||
| Line 176: | Line 151: | ||
|- | |- | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now Let us go back to the '''Jmol panel '''with the model of '''cyclohexane'''. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now Let us go back to the '''Jmol panel '''with the model of '''cyclohexane'''. | ||
| − | |||
| − | |||
| − | |||
|- | |- | ||
| Line 212: | Line 180: | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on the bond between the next two alternate '''carbon''' atoms. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on the bond between the next two alternate '''carbon''' atoms. | ||
| − | We have a model of benzene on the panel. | + | We have a model of '''benzene''' on the '''panel'''. |
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Benzene. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Benzene. | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Do the energy minimization to get a '''stable''' '''conformation'''. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Do the energy minimization to get a '''stable''' '''conformation'''. | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on panel | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on panel | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Surface topology''' of the molecules can be displayed by using''' Jmol Application.''' | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Surface topology''' of the molecules can be displayed by using''' Jmol Application.''' | ||
| − | |||
To view different surfaces, open the pop-up menu. | To view different surfaces, open the pop-up menu. | ||
| − | Ensure that the modelkit menu is closed if it is open. | + | Ensure that the '''modelkit menu''' is closed, if it is open. |
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Right click to open Pop-up-menu | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Right click to open Pop-up-menu | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now, right-click on the panel, to open the Pop-up menu. | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now, right-click on the '''panel''', to open the Pop-up menu. |
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Scroll down to “Surfaces” | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Scroll down to “Surfaces” | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Scroll down and select | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Scroll down and select '''"Surfaces"'''. |
| Line 247: | Line 206: | ||
* '''Dot Surface''' | * '''Dot Surface''' | ||
| + | |||
* '''van der Waal's''' | * '''van der Waal's''' | ||
| + | |||
* and some others. | * and some others. | ||
| − | |||
| − | |||
|- | |- | ||
| Line 258: | Line 217: | ||
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Benzene. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Benzene. | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The model of '''Benzene | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The model of '''Benzene''' is displayed with a '''molecular surface.''' |
|- | |- | ||
| Line 268: | Line 227: | ||
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on Solvent accessible surface. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on Solvent accessible surface. | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| So, open the Pop-up menu again, and choose '''Dot | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| So, open the Pop-up menu again, and choose '''Dot Surface'''. |
|- | |- | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel. |
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can also make the surfaces opaque or translucent. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can also make the surfaces opaque or translucent. | ||
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Right click to open Pop-up-menu >> Select 'Surfaces' Scroll down >> Click on ''''Make Opaque'''' | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Right click to open Pop-up-menu >> Select 'Surfaces' Scroll down >> Click on ''''Make Opaque'''' | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To do so, open the Pop-up menu again | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To do so, open the Pop-up menu again. |
| + | |||
| + | Choose '''Surfaces''' and select '''Make Opaque''' option. | ||
| Line 287: | Line 248: | ||
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on “Off”. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on “Off”. | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| scroll down to '''Off''' and click on it. |
| + | Now, we have a model of '''benzene''' without any surfaces. | ||
<nowiki><<Pause>></nowiki> | <nowiki><<Pause>></nowiki> | ||
| Line 294: | Line 256: | ||
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Jmol panel. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Jmol panel. | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Jmol''' can display '''atomic''' and '''molecular | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Jmol''' can display '''atomic''' and '''molecular orbitals''' of molecules. |
| − | + | ||
| − | + | ||
| − | + | ||
|- | |- | ||
| Line 320: | Line 279: | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The''' console '''window opens on the screen. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The''' console '''window opens on the screen. | ||
| − | I am using''' Kmag''' | + | I am using''' Kmag Screen magnifier''' to magnify the '''console''' window. |
|- | |- | ||
| Line 328: | Line 287: | ||
| style="background-color:transparent;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The command line for atomic orbitals starts with '''isosurface phase atomicorbital. ''' | | style="background-color:transparent;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The command line for atomic orbitals starts with '''isosurface phase atomicorbital. ''' | ||
| − | At the $ prompt type | + | At the''' ($) dollar prompt''' type '''isosurface phase atomicorbital'''. |
| − | This is followed by '''quantum numbers n.l | + | This is followed by '''quantum numbers n. l''' and '''m''' that are specific for each '''atomic orbital.''' |
|- | |- | ||
| Line 345: | Line 304: | ||
We have '''s orbital''' displayed on the panel. | We have '''s orbital''' displayed on the panel. | ||
| − | |||
| − | |||
| − | |||
|- | |- | ||
| Line 355: | Line 311: | ||
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the console. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the console. | ||
| − | |||
Press up arrow key on the keyboard. | Press up arrow key on the keyboard. | ||
| Line 361: | Line 316: | ||
| − | To display the previous command on the console press up arrow key on the keyboard. | + | To display the previous command on the '''console''', press up arrow key on the keyboard. |
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Delete 2 0 0 and type 2 1 1 | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Delete 2 0 0 and type 2 1 1 | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Edit '''n, l '''and '''m '''numbers to | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Edit '''n, l '''and '''m '''quantum numbers to 2 1 1. |
|- | |- | ||
| Line 373: | Line 328: | ||
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Press up arrow key on the keyboard. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Press up arrow key on the keyboard. | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Press up arrow key again and edit '''n, l '''and '''m '''to 3 2 and -1. | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Press up arrow key again and edit '''n, l '''and '''m '''to 3 2 and -1. |
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Press enter key. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Press enter key. | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Press '''Enter '''key and see the ''''dxy' orbital '''on the '''Jmol panel.''' | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Press '''Enter '''key and see the ''''dxy' orbital '''on the '''Jmol panel.''' | ||
| − | |||
| − | |||
| − | |||
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel. | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can also save these images in different file formats like jpg, png or pdf. | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We can also save these images in different file formats like '''jpg, png''' or '''pdf'''. |
|- | |- | ||
| Line 390: | Line 342: | ||
'''Script commands for Atomic Orbitals. ''' | '''Script commands for Atomic Orbitals. ''' | ||
| − | |||
| − | |||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Here is a list of commands for all '''atomic orbitals (s, p, d, '''and '''f).''' | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Here is a list of commands for all '''atomic orbitals (s, p, d, '''and '''f).''' | ||
| Line 404: | Line 354: | ||
|- | |- | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel. |
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Here I | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Here I have opened a new '''Jmol panel''' and '''console''' to show how to display '''molecular orbitals.''' |
| Line 411: | Line 361: | ||
|- | |- | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on modelkit mode. |
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We have a model of methane on the panel. | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We have a model of '''methane''' on the panel. |
|- | |- | ||
| Line 422: | Line 372: | ||
'''Molecular Orbitals''' | '''Molecular Orbitals''' | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Linear Combination of Atomic Orbitals (LCAO)''' method is used to create '''molecular orbitals. ''' |
| − | + | ||
So, the command line starts with ''''lcaocartoon', '''followed by '''create '''and the name of the '''orbital.''' | So, the command line starts with ''''lcaocartoon', '''followed by '''create '''and the name of the '''orbital.''' | ||
| − | |||
| − | |||
| − | |||
|- | |- | ||
| Line 435: | Line 381: | ||
'''>> '''Press '''Enter ''' | '''>> '''Press '''Enter ''' | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| At the dollar prompt type''' lcaocartoon create sp3''' | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| At the '''dollar prompt''' type''' lcaocartoon create sp3''' |
| Line 441: | Line 387: | ||
|- | |- | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the Jmol panel. |
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Observe the model of '''methane '''with '''sp3 hybridized molecular orbitals.''' | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Observe the model of '''methane '''with '''sp3 hybridized molecular orbitals.''' | ||
|- | |- | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on Jmol panel. |
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To display '''sp2 hybridized molecular orbitals,''' we will take '''ethene '''as an example. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To display '''sp2 hybridized molecular orbitals,''' we will take '''ethene '''as an example. | ||
|- | |- | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Use “Open a file” option in the tool bar to open model of ethene. |
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| This is a molecule of '''ethene''' on the '''panel.''' | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| This is a molecule of '''ethene''' on the '''panel.''' | ||
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Ethene''' molecule has three '''sp2 hybridized molecular orbitals.''' They are named | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Ethene''' molecule has three '''sp2 hybridized molecular orbitals.''' They are named '''sp2a, sp2b '''and '''sp2c.''' |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type''' lcaocartoon create sp2a''' | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type''' lcaocartoon create sp2a''' | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| At the '''dollar prompt''', type''' lcaocartoon create sp2a '''and press '''Enter.''' |
| − | + | ||
| − | Observe the '''sp2 '''orbital on the | + | Observe the '''sp2 '''orbital on the '''ethene''' model on the panel. |
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Press the up arrow key. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Press the up arrow key. | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Press up arrow key and change '''sp2a''' to '''sp2b''' | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Press up arrow key and change '''sp2a''' to '''sp2b, '''press '''Enter.''' |
|- | |- | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Press the up arrow key. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Press the up arrow key. | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Again, press up arrow key and change '''sp2b''' to '''sp2c''' | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Again, press up arrow key and change '''sp2b''' to '''sp2c,''' press '''Enter.''' |
|- | |- | ||
| Line 502: | Line 443: | ||
* Create a model of '''cyclohexane''' and '''cyclopentane''' | * Create a model of '''cyclohexane''' and '''cyclopentane''' | ||
| + | |||
* Create a model of '''benzene''' | * Create a model of '''benzene''' | ||
| + | |||
* Display '''surface topology''' of molecules. | * Display '''surface topology''' of molecules. | ||
| − | |||
| − | |||
|- | |- | ||
| Line 511: | Line 452: | ||
'''Summary''' | '''Summary''' | ||
| − | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| * Display '''Atomic orbitals (s, p, d, f)''' | + | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| We also learnt to |
| + | * Display '''Atomic orbitals (s, p, d, f)''' | ||
* Display '''Molecular orbitals (sp3, sp2 and sp)''' by writing '''script commands''' on the '''console'''. | * Display '''Molecular orbitals (sp3, sp2 and sp)''' by writing '''script commands''' on the '''console'''. | ||
| − | |||
| − | |||
|- | |- | ||
| Line 523: | Line 463: | ||
* Create a model of '''2-Butene''' and display '''molecular orbitals.''' | * Create a model of '''2-Butene''' and display '''molecular orbitals.''' | ||
| + | |||
* Explore''' lcaocartoon '''command to change the color and size of '''molecular orbitals.''' | * Explore''' lcaocartoon '''command to change the color and size of '''molecular orbitals.''' | ||
| Line 535: | Line 476: | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Watch the video available at this URL. | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Watch the video available at this URL. | ||
| − | [http://spoken-tutorial.org/What http://spoken-tutorial.org/ | + | [http://spoken-tutorial.org/What http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial] |
It summarizes the Spoken Tutorial project | It summarizes the Spoken Tutorial project | ||
| Line 545: | Line 486: | ||
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The Spoken Tutorial Project Team: | | style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The Spoken Tutorial Project Team: | ||
| − | Conducts workshops using spoken tutorials | + | *Conducts workshops using spoken tutorials |
| − | + | ||
| − | + | ||
| − | + | *Gives certificates to those who pass an on-line test | |
| − | contact@spoken-tutorial.org | + | For more details, please write to contact@spoken-tutorial.org |
|- | |- | ||
| Line 566: | Line 505: | ||
|} | |} | ||
| + | == | ||
Latest revision as of 16:55, 1 September 2020
== Title of script: Surfaces and Orbitals
Author: Snehalatha Kaliappan
Keywords: Molecular visualization, 3D models of chemical structures, Alicyclic and Aromatic molecules, surface topology, Atomic and Molecular orbitals, Video tutorial, Jmol tutorial.
| |
|
|---|---|
| Slide Number 1
Title Slide |
Welcome to this tutorial on Surfaces and Orbitals in Jmol Application. |
| Slide Number 2
Learning Objectives |
In this tutorial, we will learn to,
|
| Slide Number 3
Pre-requisites |
To follow this tutorial, you should know how to create and edit molecular models in Jmol Application.
If not, watch the relevant tutorials available at our website. |
| Slide Number 4
System Requirement |
To record this tutorial, I am using
|
| Cursor on Jmol panel | I have opened a new Jmol application window. |
| Cursor on Jmol panel | Let us first create a model of cyclohexane. |
| Click on the modelkit icon in the tool bar | Click on modelkit menu.
A model of methane appears on the panel. |
| Cursor on Jmol panel | To create cyclohexane, we have to make a hydrocarbon chain of six carbon atoms. |
| Cursor on methane. | We will substitute the hydrogen in the model with a methyl group. |
| Cursor on the hydrogen of the methane.
Click on the hydrogen. |
To do so, we will place the cursor on the hydrogen and click on it.
This is a model of ethane on screen. |
| Cursor on the Ethane molecule >> Click on hydrogen. | Repeat this step another 2 times and replace one hydrogen at a time with a methyl group.
Click on the hydrogens in such a way that the structure forms a circle. |
| Click on Rotate molecule tool and rotate the model. | Now, rotate the structure on screen using the Rotate molecule tool. |
| Cursor on the butane structure | This is the structure of butane on the panel.
|
| Click on hydrogen at the end of the chain. | Click on hydrogen on any of the carbon atoms present at the end of the chain. |
| Cursor on pentane structure. | Here is a model of pentane on the panel. |
| Cursor on hydrogen atom. | Click on one of the hydrogens, that is close to the end of the carbon chain. |
| Cursor on Cyclohexane. | A model of cyclohexane is created on the panel. |
| Click on minimize option in the modelkit menu | Use minimize option in the modelkit menu to optimize the structure. |
| Cursor on the panel. | The model of Cyclohexane is now, in its most stable “chair” conformation. |
| Open modelkit menu and scroll down to Drag to bond option. | Alternately, we can also use Drag to bond option in modelkit menu to create cyclic structures. |
| Cursor on the panel. | I will use a model of pentane to demonstrate this feature. |
| Open new Jmol window with pentane structure.
Open modelkit menu and check against Drag to bond option. |
This is a model of pentane on the panel.
|
| Click on carbon at one end of the chain. | Place the cursor on the carbon present at one end of the chain.
Hold down the mouse button. |
| Bring the cursor to other end of the chain and click on the carbon. | Without releasing the mouse button, bring the cursor to the carbon present at the other end of the chain.
Now release the mouse button. |
| Cursor on the panel | We have a model of cyclopentane on the panel. |
| Cursor on the panel | Now Let us go back to the Jmol panel with the model of cyclohexane. |
| Cursor on Cyclohexane. | Let us now convert cyclohexane to a benzene ring.
We have to introduce double bonds at alternate positions in the cyclohexane ring. |
| Click on “modelkit” icon. | Open the modelkit menu. |
| Click on the bond between two carbon atoms. | Place the cursor on the bond between any two carbon atoms and click on it. |
| Cursor on cyclohexene. | We now have cyclohexene on the panel. |
| Cursor on the panel. | Next, we need to introduce two more double bonds in the structure, to convert it to benzene. |
| Click on the bond between next two carbon atoms >> Repeat the above step. | Click on the bond between the next two alternate carbon atoms.
We have a model of benzene on the panel. |
| Cursor on Benzene. | Do the energy minimization to get a stable conformation. |
| Cursor on panel | Surface topology of the molecules can be displayed by using Jmol Application.
To view different surfaces, open the pop-up menu. Ensure that the modelkit menu is closed, if it is open. |
| Right click to open Pop-up-menu | Now, right-click on the panel, to open the Pop-up menu. |
| Scroll down to “Surfaces” | Scroll down and select "Surfaces".
|
| Select “Molecular Surface”. | For demonstration purpose, I will select Molecular surface. |
| Cursor on Benzene. | The model of Benzene is displayed with a molecular surface. |
| Right click to open Pop-up-menu.
scroll down to 'Surfaces' |
Let us change it to another surface, say, Dot Surface. |
| Click on Solvent accessible surface. | So, open the Pop-up menu again, and choose Dot Surface. |
| Cursor on the panel. | We can also make the surfaces opaque or translucent. |
| Right click to open Pop-up-menu >> Select 'Surfaces' Scroll down >> Click on 'Make Opaque' | To do so, open the Pop-up menu again.
Choose Surfaces and select Make Opaque option.
|
| Right click to open Pop-up-menu. Scroll down to “Surfaces”. | To turn off the surface option, open the Pop-up menu and choose Surfaces. |
| Click on “Off”. | scroll down to Off and click on it.
Now, we have a model of benzene without any surfaces. <<Pause>> |
| Cursor on Jmol panel. | Jmol can display atomic and molecular orbitals of molecules. |
| Cursor on Jmol panel. | Atomic orbitals can be displayed on screen by writing commands on the console. |
| Click on file option in the menu bar.
|
Open a new Jmol window by clicking on File and New. |
| Scroll down the options in the 'File' menu.
Click on 'Console' option. |
Now open the console window by clicking on File and then on Console. |
| Cursor on the console. | The console window opens on the screen.
I am using Kmag Screen magnifier to magnify the console window. |
| On the console, at the $ prompt, type:
isosurface phase atomicorbital |
The command line for atomic orbitals starts with isosurface phase atomicorbital.
At the ($) dollar prompt type isosurface phase atomicorbital. This is followed by quantum numbers n. l and m that are specific for each atomic orbital. |
| Type: 2 0 0 | To display 's' orbital. type 2 0 0
|
| Press Enter key | Press Enter key to execute the command.
|
| Cursor on the console. | Here are few more examples of atomic orbitals and the corresponding script commands. |
| Cursor on the console.
Press up arrow key on the keyboard. |
The command line is same for all atomic orbitals.
|
| Delete 2 0 0 and type 2 1 1 | Edit n, l and m quantum numbers to 2 1 1. |
| Press Enter key. | Press Enter key and see the 'px' orbital on the Jmol panel. |
| Press up arrow key on the keyboard. | Press up arrow key again and edit n, l and m to 3 2 and -1. |
| Press enter key. | Press Enter key and see the 'dxy' orbital on the Jmol panel. |
| Cursor on the panel. | We can also save these images in different file formats like jpg, png or pdf. |
| Slide Number 5
Script commands for Atomic Orbitals. |
Here is a list of commands for all atomic orbitals (s, p, d, and f). |
| Slide Number 6
Types of Atomic Orbitals |
Shown on this slide are models of atomic orbitals.
They were created with the help of script commands written on the console. |
| Cursor on the panel. | Here I have opened a new Jmol panel and console to show how to display molecular orbitals.
|
| Click on modelkit mode. | We have a model of methane on the panel. |
| Cursor on methane. | Methane has molecular orbitals of the type sp3. |
| Slide number 7
Molecular Orbitals |
Linear Combination of Atomic Orbitals (LCAO) method is used to create molecular orbitals.
So, the command line starts with 'lcaocartoon', followed by create and the name of the orbital. |
| Type lcaocartoon create sp3a
|
At the dollar prompt type lcaocartoon create sp3
|
| Cursor on the Jmol panel. | Observe the model of methane with sp3 hybridized molecular orbitals. |
| Cursor on Jmol panel. | To display sp2 hybridized molecular orbitals, we will take ethene as an example. |
| Use “Open a file” option in the tool bar to open model of ethene. | This is a molecule of ethene on the panel. |
| Cursor on the panel | Ethene molecule has three sp2 hybridized molecular orbitals. They are named sp2a, sp2b and sp2c. |
| Type lcaocartoon create sp2a | At the dollar prompt, type lcaocartoon create sp2a and press Enter.
Observe the sp2 orbital on the ethene model on the panel. |
| Press the up arrow key. | Press up arrow key and change sp2a to sp2b, press Enter. |
| Press the up arrow key. | Again, press up arrow key and change sp2b to sp2c, press Enter. |
| Press the up arrow key. | Finally for the pi bond, edit the name of the orbital as pz. |
| Rotate the model. | On the panel, we have ethene molecule with all the molecular orbitals. |
| Slide number 8
Types of molecular orbitals |
This slide shows examples of few other molecules with molecular orbitals. |
| Slide number 9 | Explore the website for Jmol Script documentation for more information. |
| Slide Number 10
Summary |
Let's summarize.
In this tutorial we have learnt to
|
| Slide Number 11
Summary |
We also learnt to
|
| Slide Number 12
Assignment |
Here is an assignment
Refer the following link for list of commands. |
| Slide Number 13
Acknowledgement |
Watch the video available at this URL.
http://spoken-tutorial.org/What_is_a_Spoken_ Tutorial It summarizes the Spoken Tutorial project If you do not have good bandwidth, you can download and watch it |
| Slide Number 14 | The Spoken Tutorial Project Team:
For more details, please write to contact@spoken-tutorial.org |
| Slide number 15 | Spoken Tutorial Project is a part of the Talk to a Teacher project
It is supported by the National Mission on Education through ICT, MHRD, Government of India More information on this Mission is available at this link http://spoken-tutorial.org/NMEICT-Intro ] |
| This is Snehalatha from IIT Bombay signing off. Thank you for joining. |
==
