In this step, you will add a simple molecule — H₂O — as your answer. You will learn how to:

• Open and close MarvinSketch.
• Add common atoms to your answer.
• Zoom in and out.

Questions that require you to use MarvinSketch display a frame in your assignment just like the one below.

1. To answer the question, first open MarvinSketch. Click Open MarvinSketch or click anywhere in the MarvinSketch frame. MarvinSketch opens in a new window, displaying toolbars and a drawing area. [notes]
2. First, add a hydrogen atom. In the MarvinSketch window, click . Move the pointer over the drawing area. Notice that the symbol for the hydrogen atom follows the pointer.
3. Click anywhere in the drawing area to add the hydrogen atom. Notice that MarvinSketch displays H⁺. For some questions, MarvinSketch calculates charges or the required number of hydrogen atoms for you.
4. Click to zoom in. Click to zoom out. Select a different zoom level from the zoom level list . The zoom level does not affect the scoring of your answer.
5. Click Discard Changes. The MarvinSketch window closes without saving your changes to the assignment question.
6. Click Open MarvinSketch to open MarvinSketch again. Notice that your previous changes are not displayed.
7. Now, add an oxygen atom. Click , and then click anywhere in the drawing area. Notice that MarvinSketch displays H₂O. This is because MarvinSketch automatically added the required number of hydrogen atoms.
8. Click Apply Changes. The MarvinSketch window closes and the question in the assignment is updated with your answer.

When you are ready to continue, click Submit.

In this step, you will add less commonly used atoms: Au and the generic halogen X. You will learn how to:

• Add any element from a Periodic Table to your answer.
• Add generic query atoms to your answer.

In addition to the common elements displayed in the MarvinSketch toolbar, you can add any element known to chemists by selecting it from a Periodic Table. In this first part, you will add gold to your answer.

MarvinSketch Help Click Open MarvinSketch. Use MarvinSketch to draw the chemical structure. Click Finished when you are done.

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Click . In the Periodic Table that displays, click (row 6, column 11). Close the Periodic System window. Click anywhere in the drawing area to add the gold atom. Click Apply Changes.

You can also add some special atom types for generalized problems. In this part, you will add a generic halogen atom: the mysterious element X.

MarvinSketch Help Click Open MarvinSketch. Use MarvinSketch to draw the chemical structure. Click Finished when you are done.

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Click . Click the Advanced tab. Under Generic query atoms, click X. Close the Periodic System window. Click anywhere in the drawing area to add the atom. Click Apply Changes.

When you are ready to continue, click Submit.

In this step, you will learn how to draw structures with bonds of different types. You will learn how to:

• Draw a structure with a single bond.
• Replace an atom with an atom of a different element.
• Change the type of bond in a structure.
• Draw a chain of carbon atoms in one step.

Tip: For many actions in MarvinSketch, colored semicircles are displayed when you move the pointer to help you identify a targeted atom or bond before you click.

First, you will draw a single bond.

MarvinSketch Help Click Open MarvinSketch. Use MarvinSketch to draw the chemical structure. Click Finished when you are done.

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Click the bond tool . Move the pointer over the drawing area. Notice that a single line follows the pointer. Click anywhere in the drawing area. Notice that MarvinSketch automatically added a carbon atom at each end of the bond, and then added the required hydrogen atoms. Carbon is always added as the default atom when you are drawing a structure in MarvinSketch. Click Apply Changes.

Next, you will draw a structure and replace one of the carbon atoms with oxygen.

MarvinSketch Help Click Open MarvinSketch. Use MarvinSketch to draw the chemical structure. Click Finished when you are done.

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Click the bond tool . Click anywhere in the drawing area. Click . Click one of the carbon atoms in the drawing area. Notice that the carbon atom is replaced by an oxygen atom and the number of required hydrogen atoms is updated. Click Apply Changes.

Next, you will draw a structure and change the bond to a double bond.

MarvinSketch Help Click Open MarvinSketch. Use MarvinSketch to draw the chemical structure. Click Finished when you are done.

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Click the bond tool . Click anywhere in the drawing area. Click the arrow on the right side of the bond tool and select Double. Notice that the bond tool now displays as . Click the single bond that you drew. Notice that the single bond is replaced by a double bond and the number of required hydrogen atoms is updated. Click Apply Changes.

Next, you will draw a chain of carbon atoms.

MarvinSketch Help Click Open MarvinSketch. Use MarvinSketch to draw the chemical structure. Click Finished when you are done.

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Click . Click and drag in the drawing area until the number 6 is displayed. As you drag, the number under the pointer displays how many carbon atoms will be included in the chain you are drawing. When you release the mouse button, notice that a chain of 6 carbon atoms is drawn, along with the needed hydrogens. Click Apply Changes.

When you are ready to continue, click Submit.

In this step, you will learn how to modify some properties of atoms in your drawing. You will learn how to:

• Specify the charge of an atom.
• Add lone pairs of electrons to an atom.
• Add unpaired electrons to an atom (radical notation).

First, you will add a sodium atom and change its charge (i.e., remove or add electrons).

MarvinSketch Help Click Open MarvinSketch. Use MarvinSketch to draw the chemical structure. Click Finished when you are done.

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Click . In the Periodic Table, click (row 3, column 1). Click anywhere in the drawing area to add the sodium atom. Right-click the sodium atom. Select Charge > +1. Notice that the atom changes to Na+. Click , and then click the sodium atom. Notice that the charge increases by 1. Click , and then click the sodium atom. Notice that the charge decreases by 1. Click Apply Changes.

Next, you will add 2 lone pairs of electrons to a carbon atom.

MarvinSketch Help Click Open MarvinSketch. Use MarvinSketch to draw the chemical structure. Click Finished when you are done.

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Click . Click anywhere in the drawing area to add the carbon atom. Click the arrow on the right side of the lone pairs tool and select 2 Lone Pairs. Click the carbon atom. Notice that the two lone pairs are displayed in your drawing as two pairs of dots. Click Apply Changes.

Next, you will use a keyboard shortcut to add a nitrogen atom, add a single electron to the atom, and then add 2 lone pairs.

MarvinSketch Help Click Open MarvinSketch. Use MarvinSketch to draw the chemical structure. Click Finished when you are done.

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Type N. Notice that the symbol under the pointer changes to N. You can type an element symbol in MarvinSketch to change the selected element. Click anywhere in the drawing area to add the nitrogen atom. Right-click the nitrogen atom and select Radical > Monovalent. Notice that a single electron was added to the atom and is indicated by a dot. Click the arrow on the right side of the radical tool and select Switch Radical. Click the nitrogen atom. Notice that the electron was removed. Click the nitrogen atom again. Notice that the electron was added. Click the arrow on the right side of the lone pairs tool and select 2 Lone Pairs. Click the nitrogen atom. Notice that the two lone pairs were added. Click Apply Changes.

When you are ready to continue, click Submit.

MarvinSketch questions can require you to create different kinds of drawings. Depending on the requirements of the question, you might be required to add hydrogen atoms to your drawing explicitly, or they might be added implicitly.

Structure showing implicit hydrogens for all atoms

Skeletal structure showing implicit hydrogens for heteroatoms.

Structure showing one explicit hydrogen.

In this step, you will learn how to determine when you need to add hydrogen atoms explicitly, and when MarvinSketch adds them implicitly. You will learn how to:

• Draw a structure in MarvinSketch when hydrogens are added implicitly.
• Draw a structure in MarvinSketch when you must add all hydrogens.
• Draw a structure in MarvinSketch when you must add only some hydrogens.

In the following parts, you will draw the same ethanol molecule, but because of the way each question is configured, you might have to use different procedures.

First, you will draw C₂H₅OH in a MarvinSketch question typical of organic chemistry, where MarvinSketch adds the hydrogen atoms implicitly for you.

MarvinSketch Help Click Open MarvinSketch. Use MarvinSketch to draw the chemical structure. Click Finished when you are done.

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Click the bond tool . Click anywhere in the drawing area. Notice that MarvinSketch automatically adds a carbon atom at each end of the bond, and then lists the required hydrogen atoms. Now you know that this MarvinSketch question will add hydrogen atoms implicitly for you. Click . Click and drag starting at one of the carbon atoms and moving away from the structure. When the O symbol displays under your pointer, release the mouse button to draw your oxygen atom and its bond to the carbon atom. Click Apply Changes.

Next, you will draw the skeletal formula of C₂H₅OH using exactly the same procedure. Also common in organic chemistry, when MarvinSketch is configured to draw a skeletal formula, it adds the hydrogen atoms implicitly for any heteroatoms.

MarvinSketch Help Click Open MarvinSketch. Use MarvinSketch to draw the chemical structure. Click Finished when you are done.

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Click the bond tool . Click anywhere in the drawing area. Notice that this is a skeletal formula and the carbon atoms and implicit hydrogens attached to the carbon atoms are not labeled. Now that you know that this MarvinSketch question will add hydrogen atoms implicitly for your heteroatoms. Click . Click and drag starting at one of the carbon atoms and moving away from the structure. When the O symbol displays under your pointer, release the mouse button to draw your oxygen atom and its bond to the carbon atom. Click Apply Changes.

Next, you will draw a complete structural formula of C₂H₅OH. You will need to add every atom explicitly. You use the same procedure when adding atoms to a Lewis structure.

MarvinSketch Help Click Open MarvinSketch. Use MarvinSketch to draw the chemical structure. Click Finished when you are done.

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Click the bond tool . Click anywhere in the drawing area. Notice that the carbon atoms are labeled, but no implicit hydrogen atoms are displayed. Now you know that this MarvinSketch question requires you to add all hydrogen atoms explicitly . Click . Click and drag starting at one of the carbon atoms to draw your oxygen atom and its bond to the carbon. Click . Click and drag starting at each of the carbons and the oxygen to draw your hydrogen atoms and their bonds. Add 1 hydrogen to the oxygen, 2 hydrogens to the adjacent carbon, and 3 hydrogens to the final carbon. Click Apply Changes.

Sometimes, a question might require you to do something different from what you would expect. For example, you might see a question like this:

MarvinSketch Help Click Open MarvinSketch. Use MarvinSketch to draw the chemical structure. Click Finished when you are done.

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Click the bond tool . Click anywhere in the drawing area. Notice that MarvinSketch automatically adds a carbon atom at each end of the bond, and then lists the required hydrogen atoms. Click . Click and drag starting at one of the carbon atoms to draw your oxygen atom and its bond to the carbon. MarvinSketch adds the hydrogen atom implicitly for you. But the question asks you to show this hydrogen explicitly since it is not attached to a carbon. If you submitted your answer now, it would be marked incorrect. Click . Click and drag starting at the oxygen to draw your hydrogen atom and its bond. Click Apply Changes.

When you are ready to continue, click Submit.

When you are drawing in MarvinSketch, you often need to edit your drawing to rearrange or remove items. Additionally, some MarvinSketch questions might start with a drawing instead of an empty drawing area, and require you to change the drawing in some way.

In this step, you will learn how to edit your drawing. You will learn how to:

• Select structures and parts of structures.
• Delete parts of your drawing.
• Undo changes in your drawing.
• Move and rotate parts of your drawing.
• Copy and paste parts of your drawing.
• "Clean" your drawing for a polished appearance.

In each part of this step, MarvinSketch starts with a drawing that you must edit.

First, you will select parts of a drawing and delete them.

MarvinSketch Help

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Click the arrow on the right side of the selection tool and select Rectangle Selection. Drag the pointer diagonally across the triangular structure to select it. Notice that the selected parts of your drawing are highlighted in color. Click an atom. Notice that your previous selection changes and only the atom you clicked is selected. Hold down SHIFT and click a different atom. Notice that both atoms are selected. Click the arrow on the right side of the selection tool and select Lasso Selection. Drag the pointer in a circle around the triangular structure to select it. Click the arrow on the right side of the selection tool and select Structure Selection. Click any part of the cross-shaped structure. Notice that the entire structure is selected. Click or press DELETE to delete the structure. Click Apply Changes.

Next, you will use the Erase button to delete items without first selecting them. You can click individual items, or you can drag the pointer to delete multiple items just like the rectangle selection tool.

MarvinSketch Help

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Click . Click the carbon atom on the top of the triangular structure. Click one of the bonds in the square structure. Drag the pointer over the cross-shaped structure to delete 4 of the carbon atoms. Click Apply Changes.

Next, you will make a copy of one of the structures in your drawing.

MarvinSketch Help

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Click the arrow on the right side of the selection tool and select Structure Selection. Click any part of the triangular structure. Click or press CTRL+C. Click or press CTRL+V. Move the pointer over the drawing area and click to paste a copy of the triangular structure. Click Apply Changes.

Next, you will move and rotate structures in your drawing.

MarvinSketch Help

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Click the arrow on the right side of the selection tool and select Structure Selection. Click any part of the rectangular structure. Move the pointer towards the center of the selection until a square is displayed; then, drag the selection to move it in the drawing area. Click any part of the cross-shaped structure. Move the pointer towards the center of the selection until a rotation cue is displayed; then, drag the selection to rotate it around its center. Click any part of the triangular structure. Move the pointer towards the center of the selection until a square is displayed; then, hold the CTRL key and drag the selection to copy it. Click Apply Changes.

Next, you will use tools that help improve the structure display by aligning your structures in regular geometric patterns. You do not have to use these tools, and they do not affect the scoring of your answers.

MarvinSketch Help

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Click the arrow on the right side of the selection tool and select Rectangle Selection. Move the pointer over one of the outer atoms in the cross-shaped structure. Drag the atom over one of the carbons in the triangular structure until colored semicircles display around your pointer and the carbon, and then release the mouse button. Notice that the carbon you moved replaces the carbon in the triangular structure. Click . Notice that your image is redrawn. All of your structures are chemically unchanged. Right-click a bond in the diamond-shaped structure, and select Align > Horizontally. The structure is rotated so the selected bond is horizontal. Click Apply Changes.

When you are ready to continue, click Submit.

In the previous step, you learned that some MarvinSketch questions will provide a drawing that you must edit, instead of starting with a blank drawing area. This initial drawing is called a template. In this step, you will learn about answering MarvinSketch questions with templates that include mapping numbers, and how to avoid some common mistakes that can cause your answer to marked incorrect. You will learn how to:

• Recognize questions that label atoms with mapping numbers.
• Avoid common mistakes that can change or remove mapping numbers.
• Restore mapping numbers if they are changed or removed.
• Restore a drawing to its original state.
• Work with mapped atoms and cleanup and rotation.

For some questions — typically when drawing resonance structures, reaction mechanisms, hybridization states, chiral centers, and reaction centers — the relative position of each atom is important, even for structures that otherwise exhibit symmetry. In order for MarvinSketch to identify individual atoms in these questions, the atoms are labeled with mapping numbers that are displayed near the atom. If these numbers are changed or removed, your answer will be marked incorrect even if it is otherwise correct.

First, you will learn how to recognize and answer questions that use atom mapping numbers.

MarvinSketch Help

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Notice that three of the atoms display mapping numbers. Delete one of the oxygens and add a new oxygen atom in its place. Notice that the new oxygen atom does not display a mapping number. Your answer will be marked incorrect without the original mapping number. Click Restore Template. Notice that the drawing reverts to the initial drawing provided by the question and displays the mapping numbers. Replace the lower-right oxygen with a nitrogen, and then change the nitrogen back to an oxygen. Notice that the new oxygen atom does not display a mapping number. Your answer will be marked incorrect without the original mapping number. Right-click the oxygen you added, and click Map > M2. This sets the mapping number to 2. Use this method only when you know the correct mapping number for an atom. Change the bond type for the top oxygen atom (1) to a double bond. Click Apply Changes.

Next, you will answer a question requiring you to make changes to specific parts of the structure:

MarvinSketch Help

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Notice that the top oxygen is numbered 1. Click . Notice that the structure is rotated so the atoms are in different locations. Your answer would be marked incorrect if you followed the directions now, because the atom at the top is different than it was originally. Click Restore Template. Change the bond type for the top oxygen atom (1) to a double bond. Click . Notice that even though the structure is rotated, your change is made for the correct atom. Click Apply Changes.

When you are ready to continue, click Submit.

In this step, you will learn how to answer questions involving reactions. You will learn how to:

• Answer reaction questions showing structural change.
• Answer reaction questions showing the flow of electrons.

First, you will learn how to answer questions about reactions at the structural level.

1. Click Open MarvinSketch or click anywhere in the MarvinSketch frame.
2. Draw a new structure to the right of the arrow that has the same atom types in the same relative order as the structure on the left. Tip: Use the copy and paste tools.
3. In the structure on the right, change the double bond to a single bond.
4. Click Apply Changes.

Next, you will learn how to answer questions about reactions at the electronic level.

1. Click Open MarvinSketch or click anywhere in the MarvinSketch frame.
2. Click the arrow on the right side of the electron flow tool and select 2 Electrons.
3. Click the Mg atom on the left.
4. Click the O atom on the left. Notice that the curved arrow shows the movement of two electrons from the magnesium to the oxygen atom. For the reaction to be correct, you need to change the charges of the magnesium and oxygen atoms on the right.
5. Right-click the Mg atom on the right, and then select Charge > +2.
6. Right-click the O atom on the right, and then select Charge > -2.
7. Click Apply Changes.

Next, you will show how a bond is formed between two fluorine atoms.

1. Click Open MarvinSketch or click anywhere in the MarvinSketch frame.
2. Use the lone pairs tool to add three lone pairs to each of the four F atoms.
3. Use the radical tool to add a single (monovalent) dot to each of the two F atoms on the left.
4. Add a single bond between the two F atoms on the right.
5. Click the arrow on the right side of the electron flow tool and select 1 Electron.
6. Click the upper F atom on the left.
7. Move the pointer toward the midpoint of the two F atoms on the left until a dashed line is displayed between the atoms (illustration). Click the dashed line.
8. Click the lower F atom on the left.
9. Move the pointer toward the midpoint of the two F atoms on the left until a dashed line is displayed between the atoms, and then click the dashed line.
10. Click Apply Changes.

When you are ready to continue, click Submit.

In this step, you will learn about two advanced features of MarvinSketch: shortcuts to aromatize or de-aromatize structures, and 3-dimensional modeling. You will learn how to:

• Convert structures between aromatic and non-aromatic representations.
• Work with structures in 3 dimensions.

First, you will convert a drawing to aromatic representation and back to a non-aromatic representation.

MarvinSketch Help

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Change three of the bonds to double bonds so you have alternating single and double bonds. Click . Notice that the bonds are now displayed as an aromatic ring. Click . Notice that the aromatic ring is now displayed as alternating single and double bonds. Click Apply Changes.

Next, you will work with a structure in 3 dimensions.

MarvinSketch Help

Click Open MarvinSketch or click anywhere in the MarvinSketch frame. Right-click an empty location in the drawing area and select Transform > Rotate in 3D. Drag the pointer around the drawing area to rotate the entire drawing in 3 dimensions. Notice that the structure is not a cube but is actually flat. Click . Rotate the structure in 3D again. Notice that the structure is now a cube. Replace two diametrically opposed C atoms with N atoms. Click Apply Changes.

When you are ready to continue, click Submit. This completes your MarvinSketch tutorial.