Difference between revisions of "Avogadro/C2/Create-Surfaces/English-timed"

From Script | Spoken-Tutorial
Jump to: navigation, search
(Created page with " {| border=1 ! <center>Time</center> ! <center>Narration</center> |- |00:01 | Warm greetings everyone. Welcome to this tutorial on '''Create surfaces.''' |- | 00:07 | In th...")
 
Line 10: Line 10:
 
|-
 
|-
 
|  00:07
 
|  00:07
−
| In this tutorial, we will learn to:  View properties of the molecule
+
| In this tutorial, we will learn to:  view properties of the molecule,
  
 
|-
 
|-
 
| 00:13
 
| 00:13
−
| Label the atoms with '''partial charge'''
+
| label the atoms with '''partial charge''',
  
 
|-
 
|-
 
| 00:17
 
| 00:17
−
| Create '''Van der waals '''surface
+
| create '''Van der waals '''surface,
  
 
|-
 
|-
 
| 00:20
 
| 00:20
−
| Color the surface according to the '''electrostatic potential''' energies.
+
| color the surface according to the '''electrostatic potential''' energies.
  
 
|-
 
|-
 
| 00:25
 
| 00:25
−
| Here I am using '''Ubuntu Linux '''OS version. 14.04
+
| Here, I am using '''Ubuntu Linux '''OS version. 14.04,
  
 
'''Avogadro''' version 1.1.1.
 
'''Avogadro''' version 1.1.1.
Line 32: Line 32:
 
|-
 
|-
 
|00:35
 
|00:35
−
| To follow this tutorial, you should be familiar with: '''Avogadro '''interface.
+
| To follow this tutorial, you should be familiar with '''Avogadro '''interface.
  
 
|-
 
|-
Line 48: Line 48:
 
|-
 
|-
 
| 00:57
 
| 00:57
−
|Click on '''Build''' menu then click on '''Insert ->fragment'''
+
|Click on '''Build''' menu, then click on '''Insert ->fragment'''.
  
 
|-
 
|-
Line 64: Line 64:
 
|-
 
|-
 
| 01:17
 
| 01:17
−
| A model of '''n-butane''' is displayed on the panel.
+
| A model of '''n-butane''' is displayed on the '''panel'''.
  
 
|-
 
|-
Line 84: Line 84:
 
|-
 
|-
 
| 01:39
 
| 01:39
−
|'''Molecule Properties''' window opens with information such as,
+
|'''Molecule Properties''' window opens with information such as:
  
 
'''IUPAC Molecule Name''', '''Molecular weight''', '''Chemical Formula''', '''Dipole moment''' etc.
 
'''IUPAC Molecule Name''', '''Molecular weight''', '''Chemical Formula''', '''Dipole moment''' etc.
Line 94: Line 94:
 
|-
 
|-
 
|  01:57
 
|  01:57
−
| Similarly to view the '''Atom Properties''': Click on '''Atom properties''' option from the '''properties''' menu.
+
| Similarly to view the '''Atom Properties''', click on '''Atom properties''' option from the '''properties''' menu.
  
 
|-
 
|-
 
|  02:04
 
|  02:04
−
| A table opens with values of properties such as: '''Element''', '''Type''', '''Valence''', '''Formal charge''' etc for each atom in the molecule.
+
| A '''table''' opens with values of properties such as: '''Element''', '''Type''', '''Valence''', '''Formal charge''' etc for each atom in the molecule.
  
 
|-
 
|-
Line 114: Line 114:
 
|-
 
|-
 
| 02:33
 
| 02:33
−
| Click on '''Display settings''': From the '''Display Types''' list, check the box against '''Label.'''  
+
| Click on '''Display settings''' from the '''Display Types''' list, check the box against '''Label.'''  
  
 
|-
 
|-
Line 142: Line 142:
 
|-
 
|-
 
|  03:22
 
|  03:22
−
| Because of the '''inductive effect''' '''carbons''' close to '''chlorine''' become more positive.
+
| Because of the '''inductive effect''', '''carbons''' close to '''chlorine''' become more positive.
  
 
|-
 
|-
 
| 03:28
 
| 03:28
−
| We have also an option to label the bonds. Click on the '''bond labels '''text box.
+
| We have also an option to label the '''bond'''s. Click on the '''bond labels '''text box.
  
 
|-
 
|-
Line 175: Line 175:
 
|-
 
|-
 
|  04:12
 
|  04:12
−
| Another very useful feature of '''Avogadro''', is the ability to create surfaces.
+
| Another very useful feature of '''Avogadro''' is, the ability to create surfaces.
  
 
|-
 
|-
 
| 04:18
 
| 04:18
−
|The option for creating surfaces is available in the '''extensions''' menu.  
+
|The option for creating surfaces is available in the '''Extensions''' menu.  
  
 
|-
 
|-
 
|  04:24
 
|  04:24
−
| Click on '''extensions''' menu, then click on '''create surfaces''' option.  
+
| Click on '''Extensions''' menu, then click on '''Create Surfaces''' option.  
  
 
|-
 
|-
 
| 04:30
 
| 04:30
−
|A '''create surface '''dialog box''' '''opens on the screen.
+
|A '''Create Surface '''dialog box opens on the '''screen'''.
  
 
|-
 
|-
 
|  04:34
 
|  04:34
−
| Surface type drop-down has two options: '''Van der waals''' and '''electro-static potential'''.
+
| '''Surface Type''' drop-down has two options: '''Van der waals''' and '''electro-static potential'''.
  
 
|-
 
|-
 
|  04:42
 
|  04:42
−
| '''Electrostatic potential surfaces''' are not yet supported in '''Avogadro'''.
+
| Electrostatic potential surfaces are not yet supported in Avogadro.
  
 
|-
 
|-
 
|  04:48
 
|  04:48
−
| Choose '''Van der waals '''option. In the '''Color By''' drop down select '''Nothing'''.  
+
| Choose '''Van der waals '''option. In the '''Color By''' drop down, select '''Nothing'''.  
  
 
|-
 
|-
 
| 04:55
 
| 04:55
−
| Set '''Resolution''' to '''Medium'''
+
| Set '''Resolution''' to '''Medium'''.
  
 
|-
 
|-
Line 215: Line 215:
 
|-
 
|-
 
|  05:07
 
|  05:07
−
| The '''van der waals''' surface is displayed on the Panel.
+
| The '''Van der waals''' surface is displayed on the panel.
  
 
|-
 
|-
Line 223: Line 223:
 
|-
 
|-
 
|  05:19
 
|  05:19
−
| To change the surface settings: Click on the spanner symbol corresponding to surfaces.
+
| To change the surface settings, click on the spanner symbol corresponding to '''Surfaces'''.
  
 
|-
 
|-
 
| 05:26
 
| 05:26
−
| A surface setting dialog box opens. Drag the '''slider''' to adjust the '''opacity'''.
+
| A '''Surface Settings''' dialog box opens. Drag the '''slider''' to adjust the '''opacity'''.
  
 
|-
 
|-
 
| 05:34
 
| 05:34
−
| In the '''Render '''drop-down there are different display options to choose such as:
+
| In the '''Render '''drop-down, there are different display options to choose such as:
  
 
'''Fill''',''' lines''' and '''points'''.
 
'''Fill''',''' lines''' and '''points'''.
Line 241: Line 241:
 
|-
 
|-
 
|  05:45
 
|  05:45
−
| To change the color of the surface: Click on the box filled with color next to '''positive''' option.
+
| To change the color of the surface, click on the box filled with color next to '''Positive''' option.
  
 
|-
 
|-
Line 249: Line 249:
 
|-
 
|-
 
|  06:00
 
|  06:00
−
| Next from the '''Create surface''' window: Choose '''Electrostatic potential''' from the '''Color by''' drop-down.
+
| Next, from the '''Create surface''' window, choose '''Electrostatic potential''' from the '''Color by''' drop-down.
  
 
|-
 
|-
Line 265: Line 265:
 
|-
 
|-
 
| 06:21
 
| 06:21
−
| On the '''panel '''we see the surface of '''1-chloro butane'''  Colored according to the '''electro-static potential values''' of atoms.
+
| On the '''panel, '''we see the surface of '''1-chloro butane''', colored according to the '''electro-static potential value'''s of atoms.
  
 
|-
 
|-
Line 273: Line 273:
 
|-
 
|-
 
|06:37
 
|06:37
−
|They are also used in predicting the behavior of molecules
+
|They are also used in predicting the behavior of molecules.
  
 
|-
 
|-
Line 297: Line 297:
 
|-
 
|-
 
| 07:12
 
| 07:12
−
| Let's summarize. In this tutorial we have learnt to: View properties of the molecule.
+
| Let's summarize. In this tutorial, we have learnt to: view properties of the molecule,
  
 
|-
 
|-
 
| 07:20
 
| 07:20
−
| Label the atoms with '''partial charge'''.
+
| label the atoms with '''partial charge''',
  
 
|-
 
|-
 
|07:24
 
|07:24
−
| Create '''Van der waals '''surface
+
| create '''Van der waals '''surface,
  
 
|-
 
|-
 
|07:27
 
|07:27
−
|Color the surface according to the '''electrostatic potential''' energies.
+
|color the surface according to the '''electrostatic potential''' energies.
  
 
|-
 
|-
 
|  07:33
 
|  07:33
−
| As an assignment : Compare the reactivity of '''acetaldehyde''' and '''formamide''' using '''electro-static potential surface'''.
+
| As an assignment: compare the reactivity of '''acetaldehyde''' and '''formamide''' using '''electro-static potential surface'''.
  
 
|-
 
|-
Line 333: Line 333:
 
|-
 
|-
 
|08:02
 
|08:02
−
|Hence '''Acetaldehyde''' is more reactive than '''Formamide'''.
+
|Hence, '''Acetaldehyde''' is more reactive than '''Formamide'''.
  
 
|-
 
|-
 
|  08:07
 
|  08:07
−
| This video summarizes the Spoken Tutorial project. If you do not have good bandwidth, you can download and watch it.
+
| This video summarizes the '''Spoken Tutorial''' project. If you do not have good '''bandwidth''', you can download and watch it.
  
 
|-
 
|-

Revision as of 16:46, 5 June 2018

Time
Narration
00:01 Warm greetings everyone. Welcome to this tutorial on Create surfaces.
00:07 In this tutorial, we will learn to: view properties of the molecule,
00:13 label the atoms with partial charge,
00:17 create Van der waals surface,
00:20 color the surface according to the electrostatic potential energies.
00:25 Here, I am using Ubuntu Linux OS version. 14.04,

Avogadro version 1.1.1.

00:35 To follow this tutorial, you should be familiar with Avogadro interface.
00:41 If not, for relevant tutorials, please visit our website.
00:47 Here I have opened the Avogadro window.
00:51 Insert a molecule of butane from Insert Fragment Library.
00:57 Click on Build menu, then click on Insert ->fragment.
01:04 Double click on alkanes folder to open. Select butane.cml.
01:11 Click on Insert button.
01:14 Close the dialog box.
01:17 A model of n-butane is displayed on the panel.
01:21 Clear the selection using Select none option from the Select menu.
01:26 Let us display molecular properties of the molecule.
01:30 Click on View menu, select Properties option.
01:35 From the sub-menu, click on Molecule Properties.
01:39 Molecule Properties window opens with information such as:

IUPAC Molecule Name, Molecular weight, Chemical Formula, Dipole moment etc.

01:54 Click on OK to close the window.
01:57 Similarly to view the Atom Properties, click on Atom properties option from the properties menu.
02:04 A table opens with values of properties such as: Element, Type, Valence, Formal charge etc for each atom in the molecule.
02:17 Close the dialog box.
02:20 Explore other properties like Angle, Torsion and Conformer from the list.
02:27 Let us now learn to label the atoms in the molecule with partial charge.
02:33 Click on Display settings from the Display Types list, check the box against Label.
02:43 Click on the Spanner symbol on the right side of Label check box.
02:48 Label Settings window opens.
02:51 Click on Partial charge option from atom labels text drop down. Now all the atoms in the molecule are labeled with partial charge.
03:01 The partial charge distribution helps to predict the reactivity of the carbon atoms.
03:07 Inductive effect can be explained by labeling the atoms with partial charge.
03:14 Replace a hydrogen with chlorine. Notice the change in the value of partial charge along the carbon chain.
03:22 Because of the inductive effect, carbons close to chlorine become more positive.
03:28 We have also an option to label the bonds. Click on the bond labels text box.
03:35 The drop-down menu has options to label the bonds.
03:39 Click on bond length. The bond lengths for all the bonds are displayed on the panel.
03:46 To change the color of the labels, click on the box filled with color.
03:51 Select the color from the Select atoms label color window. Click on OK button.
03:59 We can shift the labels in X, Y and Z direction.
04:04 Click on the increment or decrement buttons in the label shift menu.

Close the dialog box.

04:12 Another very useful feature of Avogadro is, the ability to create surfaces.
04:18 The option for creating surfaces is available in the Extensions menu.
04:24 Click on Extensions menu, then click on Create Surfaces option.
04:30 A Create Surface dialog box opens on the screen.
04:34 Surface Type drop-down has two options: Van der waals and electro-static potential.
04:42 Electrostatic potential surfaces are not yet supported in Avogadro.
04:48 Choose Van der waals option. In the Color By drop down, select Nothing.
04:55 Set Resolution to Medium.
04:58 Iso value to zero. Click on Calculate button.
05:04 Close the dialog box.
05:07 The Van der waals surface is displayed on the panel.
05:11 Van der waals surface is a representation of surface through which a molecule interacts with other molecules.
05:19 To change the surface settings, click on the spanner symbol corresponding to Surfaces.
05:26 A Surface Settings dialog box opens. Drag the slider to adjust the opacity.
05:34 In the Render drop-down, there are different display options to choose such as:

Fill, lines and points.

05:42 The default option is fill.
05:45 To change the color of the surface, click on the box filled with color next to Positive option.
05:52 Select the color from the basic color chart by clicking on the color. Click on OK button.
06:00 Next, from the Create surface window, choose Electrostatic potential from the Color by drop-down.
06:07 Set the resolution to medium. Set the Iso value to 0.02.
06:14 Setting low Iso value gives a finer surface.
06:18 Click on Calculate button.
06:21 On the panel, we see the surface of 1-chloro butane, colored according to the electro-static potential values of atoms.
06:31 Electrostatic potential surface illustrates charge distributions of the molecule.
06:37 They are also used in predicting the behavior of molecules.
06:42 By default, areas of high electronegativity are colored in red and least in blue.
06:49 Here are a few more examples of molecules with electro-static potential surfaces.
06:56 Aniline and cyclohexylamine.
07:00 The electron density on the Nitrogen of cyclohexylamine is more localized than it is in aniline.
07:08 Hence cyclohexylamine is a stronger base.
07:12 Let's summarize. In this tutorial, we have learnt to: view properties of the molecule,
07:20 label the atoms with partial charge,
07:24 create Van der waals surface,
07:27 color the surface according to the electrostatic potential energies.
07:33 As an assignment: compare the reactivity of acetaldehyde and formamide using electro-static potential surface.
07:43 Label the atoms with partial charge.
07:47 Your completed assignment should look as follows.
07:51 Negative charge indicated in red is more localized on the oxygen atom of acetaldehyde.
07:58 The Negative charge is more delocalized in formamide.
08:02 Hence, Acetaldehyde is more reactive than Formamide.
08:07 This video summarizes the Spoken Tutorial project. If you do not have good bandwidth, you can download and watch it.
08:15 We conduct workshops using Spoken Tutorials and give certificates. Please contact us.
08:22 The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India
08:29 This tutorial is contributed by Viswa Janani Vasudhevan and Snehalatha Kaliappan.

Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14

Retrieved from "https://script.spoken-tutorial.org/index.php?title=Avogadro/C2/Create-Surfaces/English-timed&oldid=43340"