Difference between revisions of "Jmol-Application/C2/Surfaces-and-Orbitals/English"
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− | '''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. | ||
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{| style="border-spacing:0;" | {| style="border-spacing:0;" | ||
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'''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.''' | ||
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If not, watch the relevant tutorials available at our website. | If not, watch the relevant tutorials available at our website. | ||
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* '''Ubuntu '''OS version. 12.04 | * '''Ubuntu '''OS version. 12.04 | ||
− | + | * '''Jmol '''version 12.2.2 and | |
− | * '''Jmol | + | * '''Java (JRE)''' version 7 |
− | + | ||
− | * '''Java ''' | + | |
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| 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. |
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− | Click on the modelkit menu. | + | Click on the '''modelkit menu.''' |
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− | | 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. |
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− | | 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'''. | ||
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− | | 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. |
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| 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 | + | Open modelkit menu and check against '''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;"| 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'''. | ||
+ | |||
To convert this into '''cyclopentane''', select '''Drag to bond''' option from the '''modelkit''' menu. | To convert this into '''cyclopentane''', select '''Drag to bond''' option from the '''modelkit''' menu. | ||
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− | | 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 |
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| 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'''. | ||
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| 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'''. | ||
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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. |
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| 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"'''. |
+ | |||
A sub-menu opens with many options. | A sub-menu opens with many options. | ||
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| 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.''' |
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| 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'''. |
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− | | 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. | ||
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| 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. | ||
+ | |||
Observe that the '''benzene '''model has become opaque. | Observe that the '''benzene '''model has become opaque. | ||
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| 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> | ||
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| 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. |
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| 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 file option in the menu 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 file option in the menu bar. | ||
+ | |||
Select 'New' and click on it. | Select 'New' and click on it. | ||
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| 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. |
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| 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.''' |
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| style="background-color:transparent;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type: 2 0 0 | | style="background-color:transparent;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Type: 2 0 0 | ||
| 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;"| To display ''''s' orbital. '''type 2 0 0 | | 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;"| To display ''''s' orbital. '''type 2 0 0 | ||
+ | |||
Numbers 2, 0, 0 represent''' n, l '''and '''m quantum numbers '''respectively. | Numbers 2, 0, 0 represent''' n, l '''and '''m quantum numbers '''respectively. | ||
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| 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 to execute the command. | | 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 to execute the command. | ||
+ | |||
We have '''s orbital''' displayed on the panel. | We have '''s orbital''' displayed on the panel. | ||
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| 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 command line is same for all '''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;"| The command line is same for all '''atomic orbitals.''' | ||
− | 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. | ||
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| 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. |
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| 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. |
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| 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'''. |
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− | | 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.''' |
+ | |||
'''Hybridized molecular orbitals '''such as '''sp<sup>3</sup>, sp<sup>2 '''</sup>and '''sp '''can be displayed using '''Jmol.''' | '''Hybridized molecular orbitals '''such as '''sp<sup>3</sup>, sp<sup>2 '''</sup>and '''sp '''can be displayed using '''Jmol.''' | ||
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− | | 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. |
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'''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.''' | ||
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| 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 sp3a''' | | 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 sp3a''' | ||
+ | |||
'''>> '''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''' |
+ | |||
Press '''Enter. ''' | 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;"| 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.''' |
|- | |- | ||
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'''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'''. | ||
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* 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.''' | ||
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| 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 | ||
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| 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 |
|- | |- | ||
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|} | |} | ||
+ | == |
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.
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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.
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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.
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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
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Press Enter key | Press Enter key to execute the command.
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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.
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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.
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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
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At the dollar prompt type lcaocartoon create sp3
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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. |
==