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Chemfig Package
Chemfig Package
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Chemg Package
Zachary Morseth
Minnesota State University-Moorhead
May 3, 2011
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Outline
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Chemg is a package written for drawing molecules and other A important aspects of chemistry using the LTEXcode.
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Chemg is a package written for drawing molecules and other A important aspects of chemistry using the LTEXcode.
To add the package, type: \usepackage{chemfig} into the preamble of your document. This will also automatically load the tikz package (a very powerful graphics representation program).
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Outline
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
The syntax for drawing gures using Chemg is \chemfig{<code>} The code will describe the atoms to draw and their spatial arrangment (angles, distance, bond type, etc.).
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
The syntax for drawing gures using Chemg is \chemfig{<code>} The code will describe the atoms to draw and their spatial arrangment (angles, distance, bond type, etc.). A more detailed example of the code is: \chemfig{<atom1><bond type> [<angle>,<coeff>,<n1>,<n2>,<tikz code>]<atom2>} With this code in hand, it is possible to draw an innite number of dierent molecules.
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Outline
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Water Molecule
To draw a water molecule, we will use Chemg to specify the arrangement of the atoms. The code is: \chemfig{H-O-H}
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Water Molecule
To draw a water molecule, we will use Chemg to specify the arrangement of the atoms. The code is: \chemfig{H-O-H} H O H
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Water Molecule
To draw a water molecule, we will use Chemg to specify the arrangement of the atoms. The code is: \chemfig{H-O-H} H O H We can also change the distance of the bond using the command \setatomsep{2em}
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Water Molecule
To draw a water molecule, we will use Chemg to specify the arrangement of the atoms. The code is: \chemfig{H-O-H} H O H We can also change the distance of the bond using the command \setatomsep{2em} H O H
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Specifying Angles
In Chemg, predened angles are specied in multiples of 45 degrees.
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Specifying Angles
In Chemg, predened angles are specied in multiples of 45 degrees. For example, to specify an angle measure of 90 degrees, we input [2] in the optional argument. The default value for no input is 0 degrees.
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Specifying Angles
In Chemg, predened angles are specied in multiples of 45 degrees. For example, to specify an angle measure of 90 degrees, we input [2] in the optional argument. The default value for no input is 0 degrees. There is also a way to introduce absolute angles in the interval [0, 360). The code for this is: [:<absolute angle>]
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Specifying Angles
In Chemg, predened angles are specied in multiples of 45 degrees. For example, to specify an angle measure of 90 degrees, we input [2] in the optional argument. The default value for no input is 0 degrees. There is also a way to introduce absolute angles in the interval [0, 360). The code for this is: [:<absolute angle>] Additionally, angles can be dened relative to the preceding bond. The code for this is: [::<relative angle>]
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Ethane Molecule
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Ethane Molecule
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Outline
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Drawing Rings
In addition to drawing linear and branched molecules, Chemg can also construct a variety of dierent molecules containing rings. The code for drawing a ring is: \chemfig{*n(<code for the molecule>)}
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Drawing Rings
In addition to drawing linear and branched molecules, Chemg can also construct a variety of dierent molecules containing rings. The code for drawing a ring is: \chemfig{*n(<code for the molecule>)} To draw rings composed of 6 carbon atoms, we will use the code: \chemfig{*6(------)}, \chemfig{*6(--(-Cl)-=-=)}
Cl
Zachary Morseth Chemg Package MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Drawing Rings
To combine multiple rings together, as in the case of phtalic anhydride, we use the code: \chemfig{*6(=*5(-(=O)-O-(=O)-)-=-=-)}
O O O
Zachary Morseth Chemg Package MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
The code for the benzene ring is \chemfig{*6(=-=-=-)} The code for the oxalane-2,5-dione is \chemfig{*5(-(=O)-O-(=O)--)} O
O
Zachary Morseth Chemg Package MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Drawing Caeine
O H3 C N N CH3
N CH3
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Drawing Caeine
O H3 C N N CH3
N CH3
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Adrenaline
Now, lets take a look at how to construct the chemical structure for adrenaline piece by piece. OH HO
HN HO CH3
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Drawing Adrenaline
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Drawing Adrenaline
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Drawing Adrenaline
Draw the skeleton structure: \chemfig{*6(-=-=-=)} HO Add hydroxyl substituents to skeleton stucture: HO
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Drawing Adrenaline
Draw the skeleton structure: \chemfig{*6(-=-=-=)} HO Add hydroxyl substituents to skeleton stucture: HO \chemfig{*6((-HO)-=-=-(-HO)=}
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Drawing Adrenaline
Next, we must add the branched chain to our structure (using relative angles for ease): HO HN HO CH3
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Drawing Adrenaline
Next, we must add the branched chain to our structure (using relative angles for ease): HO HN HO CH3 The code for this step is: \chemfig{*6((-HO)-=-(--[::-60][::-60]HN-[::+60]CH_3)=-(-HO)=)}
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Drawing Adrenaline
Lastly, we must add in the cram bond for the added hydroxyl substituent.
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Drawing Adrenaline
Lastly, we must add in the cram bond for the added hydroxyl substituent. To illustrate the use of cram bonds: The code for A B is \chemfig{A<B}
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Drawing Adrenaline
Lastly, we must add in the cram bond for the added hydroxyl substituent. To illustrate the use of cram bonds: The code for A B is \chemfig{A<B} OH HO HO HN CH3
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Drawing Adrenaline
Lastly, we must add in the cram bond for the added hydroxyl substituent. To illustrate the use of cram bonds: The code for A B is \chemfig{A<B} OH HO HO Th nal code for the structure is: \chemfig{*6((-HO)-=-(-(<[::60]OH)[::-60]-[::-60]HN-[::+60]CH_3)=-(-HO)=)}
Zachary Morseth Chemg Package MSUM
HN
CH3
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
O \chemfig{*6(-=-(-O-[::-60](=[::-60]O)[::+60])=(-(=[::+60])-[::-60]OH)-=)}
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Drawing Camphor
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Drawing Camphor
Here is the code for drawing camphor: \quad \setcrambond{3pt}{}{} \chemfig{<[:10](>[:85,1.8]?(-[:160,0.6])-[:20,0.6])>[:-10] -[:60](=[:30,0.6]O)-[:170]?(-[:30,0.6])-[:190]-[:240]} Note: The ? character is used to create a hook between an atom and a distant atom.
Zachary Morseth Chemg Package MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Outline
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Chemical Reactions
Another important feature of chemg is the ability to write chemical reactions, which show how a set of reactants reaches a nal product.
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Chemical Reactions
Another important feature of chemg is the ability to write chemical reactions, which show how a set of reactants reaches a nal product. As an example, consider the reaction
H3 C
Cl
AlCl3
+ HCl
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
The code for the previous chemical reaction (the alkylation of benzene) is: \setatomsep{2em}\chemfig{**6(------)} \hspace{.2cm} + \hspace{.2cm} \chemfig{H_3C-Cl} \hspace{.2cm} $\xrightarrow{\chemfig{AlCl_3}}$ \hspace{.2cm} \chemfig{**6(-(-)-----)} \hspace{.1cm} + \hspace{.1cm} \chemfig{HCl}
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Drawing Viagara
O H N O S N N H3 C O CH3 CH3 N O CH3 N N
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
The code for the drug Viagara is: \setatomsep{2.2em} \chemfig{N*6((-H_3C)---N(-S(=[::+120]O)(=[::+0]O) -[::-60]*6(-=-(-O-[::-60]-[::+60]CH_3)= (-*6(=N-*5(-(--[::-60]-[::+60]CH_3) =N-N(-CH_3)-=)--(=O)-N(-H)-))-=))---)}
MSUM
Introduction
Syntax
Drawing Molecules
Drawing Rings
Chemical Reactions
Thank You!
MSUM