利用 ISIS Draw 繪製 2D 化學結構 Ta-Wei Li NCTU. Today ’ s Job Practice ISIS Draw Basic –...

利用 ISIS Draw繪製 2D化學結構

Ta-Wei Li

NCTU

Today’s Job

Practice ISIS Draw Basic– Aromatic Compounds– Basic Aliphatic Compounds

Draw 2D Chemical Structure Draw 2/3D Chemical Structure

Basic Strategy for ISIS Draw (1)

All atoms are carbons unless you specify otherwise.

Click benzene of the template-tool icons on the horizontal tool bar:

To place this template anywhere, just click an empty area.

Basic Strategy for ISIS Draw (2)

Click benzene Icon again Then move the mouse to one bond of the

previous benzene Click the bond After attachment, one can obtain naphthalene

molecule

Select, Copy and Paste

Click the 「 Select 」 tool that appears on the tool bar

– Understand the difference among Then, move the mouse to naphthalene Click the mouse and circle naphthalene like

Select “Edit” “Copy” and “Edit” “Paste” Move the 2nd naphthalene to a empty space

Resizing Structures

To resize a structure, select it, then drag one of the corner handles

To scale a structure, select it, and then choose Object > Scale > Percent. Enter a number - without a % sign - to scale the structure.

Rotate Molecule – 2D & 3D

Click the 「 2D Rotate 」 tool that appears on the tool bar

– Understand the difference between

Click the mouse to select one of two naphthalene molecules, like

Try to rotate the selected molecule in 2D direction or 3D direction

Drawing Bonds

To draw bonds, click a bond tool on the tool bar, such as

Then move the mouse to any atom of the 2nd naphthalene, such as

Click the mouse to sprout a bond from a atom Keep adding a bond to every atom (except two

bridge atoms)

Drawing Atoms

To draw an atom, click Then move the mouse to any sprouted bond of

the 2nd naphthalene, such as Click the mouse See a text entry field and choose H from a list

H

Deleting atoms, bonds, and structures

Select one or more atoms, bonds, or structures. Then, do one of the following:– Press the Delete key.– Choose Edit > Cut.

To delete atoms or bonds one at a time, click , then click an atom or bond.

Change Bond Type

Click benzene Icon again Click any empty area to get

benzene Use right mouse button to click

one bond and select “Edit Bond”

In the folder of “Bond”, please select “Single/Aromatic” to get 1.5 bond drawn as the down right figure

Generate Chemical Names

Draw a chemical compound as the right pictures

Select the whole molecule

Click on

Automatically Create H Atoms

Select p-Xylene and click on the right button of the mouse

Select “Edit Molecule…” On the “Atom” Folder,

Select “Auto position” to create the H atoms automatically.

ISIS Draw Practice 1

Please draw following molecular structures (20%)

H

H H

H

H

H

Fe

CH

CHCH

CHCHCH

ISIS Draw Practice 2

Please draw the line structures of the following three molecule and show their molecular formulas and IUPAC names (30%)

Express Moles and Charges

Press

Type 「 H2SO4 」

Type 「 H+ 」

Type 「 SO42- 」 ?

Use Superscript to Express Charge

Press

Type

SO4\S2-\S

\S : superscript.

You must use a capital S.

SO42-

Express Free Radical and Isotope

Press

Type 「 Cl. 」

Type 「 15O 」

Cl

O15

Draw Alkane, Alkene, Alkyne (1)

To draw bonds, press a bond tool on the tool bar, such as

Next, drag the mouse onto the double-bond tool

Release the mouse and the cursor indicates that you can draw double bonds

Draw Alkane, Alkene, Alkyne (2)

To place this double bond anywhere, just click an empty area and then drag the mouse for the direction of the bond

Click and move the mouse to any end of the double bond

See a text entry field and type CH2 Do the same input to another end of the double

bond to get CH2 CH2

Draw Alkane, Alkene, Alkyne (3)

With the choice of , move the mouse to the double bond area, such as

Click once to get

Click twice to get

CH2 CH2

CH CH

CH3 CH3

Explicitly Show C atom of CO2

First draw Then change single

bonds into double bonds Add C atom in the center

of CO2 molecule – Click– Click the center of CO2,

select “more”– In “Symbol” of the “Atom”

folder, select “C(show)” to show C atom explicitly

Clean CO2 molecule

Add O atoms in the two ends of CO2 as

Select the whole CO2 molecule Click “Object” “Clean Molecule” to get the

proper molecular model of CO2

COO

CO

O

Sprout Hydrogen

To draw chain molecules, click a chain tool on the tool bar, such as

Select the whole molecule Click 「 Object 」 「 Edit

Molecule 」 In

「 Hydrogen 」 of 「 Atom 」 folder, select 「 Auto position 」

CH3

CH

2

CH2

CH

2

CH2

CH

2

CH2

CH

2

CH3

Draw Vitamin K (1)

To draw chain molecules, click a chain tool on the tool bar, such as

Click an empty area and then drag until a 10-atom chain appears

Move the mouse to the 4th atom and click it to sprout a bond, such as

Move the mouse to the 8th atom and click it to sprout a bond, such as

Draw Vitamin K (2)

Move the mouse to the 3rd bond and click it to create a double bond, such as

Click and move the mouse to the 10th atom, and then type H, such as

Question 1 : What should be the groups in the two red squares?

H

H

Draw Vitamin K (3)

Click and move the mouse to the left corner above of 6th atom such as

Click there as the start point of a bracket and drag the mouse to the right corner below

Chose “multiple group” in Bracket type and type “3” in Repeat count

Click “Apply” and close the window to get

H

H3

Draw Vitamin K (4)

Please finish the following picture

Chemistry Information of Vitamin K

Select 「 Vitamin K 」 molecule Then select 「 Chemistry 」「 Calculate Mol

Values 」「 Calculate 」 to show the chemistry information of Vitamin K– Molecular Weight– Molecular Formula– Molecular Composition

ISIS Draw Practice 3

Please draw and clean the molecular structure of Vitamin K, and then show its molecular information including molecular weight and molecular formula. (10%)

Please draw the line structures of the following two molecule and show their molecular formulas and IUPAC names (10%)

Draw 2/3D Chemical Structure (1)

Click Click an empty area as the start point and then

drag until a 4-atom chain appears Click the rotation tool Click any part of the molecule and drag the

mouse to rotate the molecule, such as

Draw 2/3D Chemical Structure (2)

Click the up-wedge tool Click the 2nd atom and drag the up-wedge bond

to the correct direction, such as

implies the bond above the molecular plane

Draw 2/3D Chemical Structure (3)

Press and drag the mouse to the down-wedge tool

Click the 2nd atom and drag the down-wedge bond to the right direction, such as

implies the bond below the molecular plane

Draw 2/3D Chemical Structure (4)

Click the down-wedge bond again to change its direction from to

Please finish the following picture

Draw Cyclohexane (1)

Click cyclohexane of the template-tool icons on the horizontal tool bar

Click an empty area and click the rotation tool to rotate cyclohexane to get

Select the up-wedge tool and click cyclcohexane to get

Draw Cyclohexane (2)

Select the up-bond tool

Click the Cyclohexane to get

Draw Cyclohexane (3)

Click “Templates” “Rings” Among various rings, click Please try to finish the following picture

ISIS Draw Practice 4

請畫出 CH2CCCCH2 化合物的 2/3D 的結構圖。 (10%)

請畫出下列化合物的順式 2/3D 結構圖。 (10%)

CH CH

CH2

CH3CH3

ISIS Draw Practice 5

Please draw following molecular structures (10%)

O

H

O O

H

O O OH+

32PO4

ISIS Draw Homework

Finish ISIS Draw practice 1, 2, 3, 4, and 5, and save the file as “ isisHW.skc ”

請在今天（ 2 月 24 日）午夜十二點將 “ isisHW.skc”上傳至 http://bb.nctu.edu.tw

– 2 月 24 日午夜十二點以前繳交，滿分為 100 分– 3 月 3 日午夜十二點以前繳交，滿分為 80 分– 3 月 3 日午夜十二點以後就不需要繳交，以 0 分計算