ACTIVITY-1

CREATE AND EDIT MOLECULAR MODELS:

ASSIGNMENT QUESTIONS -1.1 :-
1. Create models of the following molecules,
2. 3-bromo-1-butanol and 2-amino-4-chloro-pentane
3. Do energy minimization and save the image in JPEG format.
4. Hint: Use "Save current view as an image" icon in the Tool bar.

3-Bromo 1-butanol Jmol 3-D

structure:-

PROCEDURE:-
1.First, you need to obtain the 3D structure of 3-bromo-1-butanol. You can
use a chemical database or a modeling software to create or find this
structure.

2.Save the 3D structure in a format that Jmol can read, such as a PDB or

MOL file .
3.Open Jmol and load the 3D structure file by using the open command
followed by the file name.

4. Once the structure is loaded, you can use various Jmol commands to
display and manipulate it. For instance, you can use the zoom command

to automatically fit the structure to the Jmol window .

5. You can also use the spacefill command to display the structure with
space-filling spheres, which can be helpful to visualize the molecular
volume and the positions of the atoms.

6. This is a basic procedure to display 3-bromo-1-butanol in Jmol.

7. Then we have to minimize it for that we have to right click on mouse

then we have select last option then after that we can see minimize.

8.After that according to question we have save it .

ASSIGNMENT QUESTIONS-1.2:-
1. Create models of the following molecules 2-amino-4-chloro-pentane.

2. Do energy minimization and save the image in JPEG format.

Hint: Use "Save current view as an image" icon in the Tool bar.

2-Amino-4-chloro-pentane :-
PROCEDURE:-
1.Launch Jmol by double-clicking on the Jmol icon or running the Jmol
executable file.

2.In the Jmol window, click on the "File" menu and select "Open".

3.In the "Open" dialog box, click on the "Load" button.

4.In the "Load" dialog box, select "URL" as the "Load from" option.

5.In the "URL" field, enter the following URL to load the pre-configured Jmol
script for 2-amino-4-chloropentane

6. Click on the "Load" button to load the Jmol script and display the 3D
structure of 2-amino-4-chloropentane

7.Then we have to minimize it for that we have to right click on mouse then
we have select last option then after that we can see minimize.After that
according to question we have save it .

ASSIGNMENT QUESTIONS-2.1 :-
1. Create the models of 2-fluoro-1,3-butadiene .

2. Use the Pop-up menu to change the display of the model to wireframe.

3. Do energy minimization and save the image in PDF format.

2-fluoro-1,3-butadiene:-

PROCEDURE:-
1.Open Jmol: Launch the Jmol application on your device or access the
web-based version.

2.Access Drawing Tools: In the Jmol interface, locate and access the
drawing tools. These tools may be labeled as "Draw" or represented by
icons like a pencil or a molecule sketcher.

3.Select Atom Types: Choose the appropriate atom types to draw the
molecule. For 2-fluoro-1,3-butadiene, you'll need carbon (C), hydrogen (H),
and fluorine (F) atoms.

4.Draw Carbon Skeleton: Begin by drawing the carbon skeleton of the

molecule. Draw four carbon atoms arranged in a chain with alternating
single and double bonds, representing the butadiene backbone.

5.Add Hydrogen Atoms: Attach hydrogen atoms to the carbon atoms to

satisfy their valency. Each carbon atom should have the appropriate
number of hydrogen atoms bonded to it to fill its valence shell.

6.Introduce Fluorine Atom: Identify the carbon atom where the fluorine
atom will be attached. Replace one of the hydrogen atoms bonded to this
carbon with a fluorine atom.

7.Refine Structure: Adjust the positions and orientations of atoms and

bonds to ensure the molecule's geometry is correct and satisfies standard
bond angles and lengths.

8.View the Molecule: After drawing the structure, the molecule should be
automatically displayed in the Jmol viewer window.

9.Interact with the Molecule: Utilize the controls provided in the Jmol
interface to interact with the molecule. You can rotate, zoom, and explore
the structure to examine its features
ASSIGNMENT QUESTIONS-2.2 :-
1. Create the models of 2-pentyne.

2. Use the Pop-up menu to change the display of the model to wireframe.

3. Do energy minimization and save the image in PDF format.

2-pentyne

PROCEDURE :-
1.Open Jmol: Launch the Jmol application on your device or access the
web-based version.

2.Access Drawing Tools: Locate and access the drawing tools within Jmol.
These tools may be labeled as "Draw" or represented by icons like a pencil
or a molecule sketcher.

3.Select Atom Types: Choose the appropriate atom types to draw the
molecule. For 2-pentyne, you'll need carbon (C) and hydrogen (H) atoms.

4.Draw Carbon Skeleton: Begin by drawing the carbon skeleton of the

molecule. Draw five carbon atoms arranged in a chain, representing the
pentane backbone.

5.Add Hydrogen Atoms: Attach hydrogen atoms to the carbon atoms to

satisfy their valency. Each carbon atom should have the appropriate
number of hydrogen atoms bonded to it to fill its valence shell.
6.Introduce Triple Bond: Identify the carbon-carbon bond where the triple
bond will be located. Draw a triple bond between the two carbon atoms to
represent the triple bond characteristic of an alkyne.

7.Refine Structure: Adjust the positions and orientations of atoms and

bonds to ensure the molecule's geometry is correct and satisfies standard
bond angles and lengths.

8.Name the Molecule: Optionally, label or annotate the molecule as "2-

Pentyne" or "Dimethylacetylene" to indicate its identity.

9.View the Molecule: After drawing the structure, the molecule should be
automatically displayed in the Jmol viewer window.

10.Interact with the Molecule: Utilize the controls provided in the Jmol
interface to interact with the molecule. You can rotate, zoom, and explore
the structure to examine its features.

ACTIVITY-2
MODIFY DISPLAY AND VIEW
ASSIGNMENT QUESTIONS -1:-
1. Create a model of 2-chloro-3-iodo-pentane.

2. Explore the 'Spin' option in the Pop-up menu.

3. Change the direction of spin to 'Z' axis and rate of spin to '40'.

4. Hint: Use Set Z Rate option

2-chloro 3-iodo pentane

PROCEDURE:-
1.Open Jmol: Launch the Jmol application on your device or access the
web-based version.

2.Access Drawing Tools: Locate and access the drawing tools within Jmol.
These tools may be labeled as "Draw" or represented by icons like a pencil
or a molecule sketcher.

3.Select Atom Types: Choose the appropriate atom types to draw the
molecule. For 2-chloro-3-iodopentane, you'll need carbon (C), hydrogen
(H), chlorine (Cl), and iodine (I) atoms.

4.Draw Carbon Skeleton: Begin by drawing the carbon skeleton of the

molecule. Draw five carbon atoms arranged in a chain, representing the
pentane backbone.

5.Add Hydrogen Atoms: Attach hydrogen atoms to the carbon atoms to

satisfy their valency. Each carbon atom should have the appropriate
number of hydrogen atoms bonded to it to fill its valence shell.

6.Introduce Chlorine and Iodine Atoms: Identify the carbon atoms where
the chlorine and iodine atoms will be attached. Draw a chlorine atom
bonded to the second carbon atom and an iodine atom bonded to the third
carbon atom.

7.Refine Structure: Adjust the positions and orientations of atoms and

bonds to ensure the molecule's geometry is correct and satisfies standard
bond angles and lengths.
8.View the Molecule: After drawing the structure, the molecule should be
automatically displayed in the Jmol viewer window.

ASSIGNMENT QUESTIONS-2 :-
1. Create a model of 3-amino-1-propanol.

2. Change the display to 'Sticks'.

3. Change the color of all the hydrogens in the model to 'Green'.

3-AMINO 1 PROPANOL

PROCEDURE:-
1.Open Jmol: Launch the Jmol application on your device or access the
web-based version.

2.Access Drawing Tools: Locate and access the drawing tools within Jmol.
These tools may be labeled as "Draw" or represented by icons like a pencil
or a molecule sketcher.

3.Select Atom Types: Choose the appropriate atom types to draw the
molecule. For 3-amino-1-propanal, you'll need carbon (C), hydrogen (H),
oxygen (O), and nitrogen (N) atoms.

4.Draw Carbon Skeleton: Begin by drawing the carbon skeleton of the

molecule. Draw three carbon atoms arranged in a chain, representing the
propanal backbone.

5.Add Functional Groups: Attach functional groups to the carbon skeleton.

Draw an oxygen atom bonded to the first carbon atom, representing the
aldehyde group (-CHO), and a nitrogen atom bonded to the second carbon
atom, representing the amino group (-NH2).

6.Add Hydrogen Atoms: Attach hydrogen atoms to the carbon, nitrogen,

and oxygen atoms to satisfy their valency. Each atom should have the
appropriate number of hydrogen atoms bonded to it to fill its valence shell.

7.Refine Structure: Adjust the positions and orientations of atoms and

bonds to ensure the molecule's geometry is correct and satisfies standard
bond angles and lengths.

8.View the Molecule: After drawing the structure, the molecule should be
automatically displayed in the Jmol viewer window.

ACTIVITY-3
MEASUREMENTS AND LABELING:
ASSIGNMENT QUESTIONS-1.1 :-
1. Create models of 1-butanoic acid

2. Optimize the structure by doing energy minimization.

3. Save the image .

1-BUTANOIC ACID

PROCEDURE:-
1.Open Jmol: Launch the Jmol application on your device or access the
web-based version.
2.Access Drawing Tools: Find and access the drawing tools within Jmol.
These tools might be labeled as "Draw" or represented by icons like a
pencil or a molecule sketcher.

3.Select Atom Types: Choose the appropriate atom types to draw the
molecule. For 1-butanoic acid, you'll need carbon (C), hydrogen (H), and
oxygen (O) atoms.

4.Draw Carbon Skeleton: Begin by drawing the carbon skeleton of the

molecule. Draw a chain of four carbon atoms, representing the butanoic
acid backbone.

5.Add Functional Groups: Attach the functional groups characteristic of

butanoic acid to the carbon skeleton. At one end of the chain, attach a
carboxylic acid group (-COOH), consisting of a carbon double-bonded to an
oxygen atom and single-bonded to a hydroxyl group (OH).

6.Add Hydrogen Atoms: Attach hydrogen atoms to the carbon and oxygen
atoms to satisfy their valency. Each atom should have the appropriate
number of hydrogen atoms bonded to it to complete its valence shell.

7.Refine Structure: Adjust the positions and orientations of atoms and

bonds to ensure the molecule's geometry is correct and satisfies standard
bond angles and lengths.

8.View the Molecule: Once you've drawn the structure, you can load it into
the Jmol viewer. Use the appropriate command to load the structure file or
input the drawn structure directly into the Jmol interface.

ASSIGNMENT QUESTIONS-1.2 :-
1. Create models of ethylacetate

2. Optimize the structure by doing energy minimization.

3. Save the image

ETHYLACETATE
PROCEDURE:-
1.Open Jmol: Launch the Jmol application on your device or access the
web-based version.

2.Access Drawing Tools: Find and access the drawing tools within Jmol.
These tools might be labeled as "Draw" or represented by icons like a
pencil or a molecule sketcher.

3.Select Atom Types: Choose the appropriate atom types to draw the
molecule. For ethyl acetate, you'll need carbon (C), hydrogen (H), and
oxygen (O) atoms.

4.Draw Carbon Skeleton: Begin by drawing the carbon skeleton of the

molecule. Draw two carbon atoms, representing the ethyl group attached
to the oxygen atom.

5.Add Functional Groups: Attach the functional groups characteristic of

ethyl acetate to the carbon skeleton. One carbon atom should have three
hydrogen atoms attached (representing the ethyl group), and the other
carbon atom should have a double bond to an oxygen atom (representing
the carbonyl group). Additionally, attach two more hydrogen atoms to the
oxygen atom to represent the remaining valences.

6.Add Hydrogen Atoms: Attach hydrogen atoms to the carbon and oxygen
atoms to satisfy their valency. Each atom should have the appropriate
number of hydrogen atoms bonded to it to complete its valence shell.

7.Refine Structure: Adjust the positions and orientations of atoms and

bonds to ensure the molecule's geometry is correct and satisfies standard
bond angles and lengths.

8.View the Molecule: Once you've drawn the structure, you can load it into
the Jmol viewer. Use the appropriate command to load the structure file or
input the drawn structure directly into the Jmol interface.
ASSIGNMENT QUESTIONS-2.1 :-
1. Create models of molecules with single and double bonds.

2. Measure bond lengths between the carbon atoms and compare them

MOLECULE WITH SINGLE AND DOUBLE

BOND

PROCEDURE:-
1.Open Jmol: Launch the Jmol application on your device or access the
web-based version.

2.Access Drawing Tools: Find and access the drawing tools within Jmol.
These tools might be labeled as "Draw" or represented by icons like a
pencil or a molecule sketcher.

3.Select Atom Types: Choose the appropriate atom types to draw the
molecule. For benzene, you'll need carbon (C) atoms.

4.Draw Carbon Skeleton: Begin by drawing the carbon skeleton of the

molecule. Draw a hexagon shape representing the six carbon atoms
bonded together in a ring.
4.Add Double Bonds: In benzene, each carbon atom forms a double bond
with one neighbouring carbon atom. Draw alternating double bonds
between the carbon atoms in the hexagon.

5.Add Hydrogen Atoms: Attach hydrogen atoms to each carbon atom to

satisfy their valency. Since each carbon atom in benzene forms three
sigma bonds (two to other carbons and one to hydrogen), add hydrogen
atoms accordingly.

6.Refine Structure: Adjust the positions and orientations of atoms and

bonds to ensure the molecule's geometry is correct and satisfies standard
bond angles and lengths.

7.View the Molecule: Once you've drawn the structure, you can load it into
the Jmol viewer. Use the appropriate command to load the structure file or
input the drawn structure directly into the Jmol interface.

ASSIGNMENT QUESTIONS-2.2 :-
1. Create models of molecules with single and triple bonds.

2. Measure bond lengths between the carbon atoms and compare them

MOLECULE WITH SINGLE AND

TRIPLE BOND
PROCEDURE:-
1.Open Jmol: Launch the Jmol application on your device or access the web-
based version.

2.Access Drawing Tools: Find and access the drawing tools within Jmol.
These tools might be labeled as "Draw" or represented by icons like a pencil
or a molecule sketcher.

3.Select Atom Types: Choose the appropriate atom types to draw the
molecule. For benzyne, you'll need carbon (C) atoms.

4.Draw Carbon Skeleton: Begin by drawing the carbon skeleton of the

molecule. Draw a straight line of three carbon atoms.

5.Add Triple Bonds: In benzyne, the central carbon forms a triple bond with
one of the adjacent carbons. Draw a triple bond between the second and
third carbon atoms.

6.Add Hydrogen Atoms: Attach hydrogen atoms to each carbon atom to

satisfy their valency. Since each carbon atom in benzyne forms two sigma
bonds (one to another carbon and one to hydrogen), add hydrogen atoms
accordingly.

7.Refine Structure: Adjust the positions and orientations of atoms and

bonds to ensure the molecule's geometry is correct and satisfies standard
bond angles and lengths.

8.View the Molecule: Once you've drawn the structure, you can load it into
the Jmol viewer. Use the appropriate command to load the structure file or
input the drawn structure directly into the Jmol interface.
 ACTIVITY-4
SCRIPT CONSOLE AND SCRIPT
COMMANDS:

ASSIGNMENT QUESTIONS -1 :-
1. Create a model of 3-methylpentane.

2. Use script commands to do the following.

* Change the color of all hydrogens to blue.

* Change the color of all the bonds to red.

* Set the molecule to spin on screen

3-METHYL PENTANE
PROCEDURE:-
1.Open Jmol: Launch the Jmol application on your device or access the
web-based version.

2.Access Drawing Tools: Find and access the drawing tools within Jmol.
These tools might be labeled as "Draw" or represented by icons like a
pencil or a molecule sketcher.

3.Select Atom Types: Choose the appropriate atom types to draw the
molecule. For 3-methylpentane, you'll need carbon (C) and hydrogen (H)
atoms.

4.Draw Carbon Skeleton: Begin by drawing the carbon skeleton of the

molecule. Draw a chain of five carbon atoms, representing the pentane
backbone.

5.Add Methyl Group: Identify the third carbon atom in the chain and draw a
methyl group (-CH3) attached to it. This represents the "3-methyl" part of
the molecule.

6.Add Hydrogen Atoms: Attach hydrogen atoms to the carbon atoms to

satisfy their valency. Each carbon atom should have the appropriate
number of hydrogen atoms bonded to it to complete its valence shell.

7.Refine Structure: Adjust the positions and orientations of atoms and

bonds to ensure the molecule's geometry is correct and satisfies standard
bond angles and lengths.

8.View the Molecule: Once you've drawn the structure, you can load it into
the Jmol viewer. Use the appropriate command to load the structure file or
input the drawn structure directly into the Jmol interface.

ACTIVITY-5
SURFACE AND ORBITALS:

ASSIGNMENT QUESTIONS -1:-

1. Create a model of 2-butene and display molecular orbitals.

2. Explore 'lcaocartoon' command to change the color and size of

molecular orbitals.

3. Refer the following link for list of commands.

2-BUTENE AND DISPLAYING THE
MOLECULAR ORBITALS

PROCEDURE:-
1.Open Jmol: Launch the Jmol application on your device or access the
web-based version.

2.Access Drawing Tools: Find and access the drawing tools within Jmol.
These tools might be labeled as "Draw" or represented by icons like a
pencil or a molecule sketcher.

3.Select Atom Types: Choose the appropriate atom types to draw the
molecule. For 2-butene, you'll need carbon (C) and hydrogen (H) atoms.

4.Draw Carbon Skeleton: Begin by drawing the carbon skeleton of the

molecule. Draw a chain of four carbon atoms, representing the butene
backbone.

5.Add Double Bond: Identify the second carbon atom in the chain and draw
a double bond between the second and third carbon atoms. This
represents the "2" position of the butene molecule.

6.Add Hydrogen Atoms: Attach hydrogen atoms to the carbon atoms to

satisfy their valency. Each carbon atom should have the appropriate
number of hydrogen atoms bonded to it to complete its valence shell.
7.Refine Structure: Adjust the positions and orientations of atoms and
bonds to ensure the molecule's geometry is correct and satisfies standard
bond angles and lengths.

8.View the Molecule: Once you've drawn the structure, you can load it into
the Jmol viewer. Use the appropriate command to load the structure file or
input the drawn structure directly into the Jmol interface.