myChemistry

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\begin{rxn}[,.7]

\setatomsep{1.5em}\footnotesize

\reactant[,a]{

\chemfig{C(-[4]*6(=-=-=-))(-[2]*6(=-=-=-))(-[6,,,2]HO)-C(-[2]CH_3) (-[6]OH)-CH_3}

}

\arrow[a.20]{}{}

\reactant[20]{

\chemfig{C(-[4]*6(=-=-=-))(-[2]*6(=-=-=-))(-[@{e1}6,,,2]H_2@{e2}

\chembelow{O}{\oplus})-C(-[2]CH_3)(-[6]OH)-CH_3}\elmove{e1}

{10:4mm}{e2}{-10:4mm}

}

\arrow[,,1.42]{$-\ce{H2O}$}{}

\reactant{

\chemfig{\chembelow{C}{\oplus}(-[4]*6(=-=-=-))(-[2]

*6(=-=-=-))-C(-[2]CH_3)(-[6]OH)-CH_3}

}

\arrow[a.-20,-|>]{}{}

\reactant[-20]{

\chemfig{C(-[4]*6(=-=-=-))(-[2]*6(=-=-=-))(-[6,,,2]HO)-C(-[2]CH_3) (-[@{e3}6]@{e4}\chembelow{O}{\oplus}H_2)-CH_3}\elmove{e3}

{170:4mm}{e4}{-170:4mm}

}

\arrow[,,1.42]{$-\ce{H2O}$}{}

\reactant{

v1.5.1

April 27th 2011

Clemens Niederberger

Examples

C O H

C CH3

OH CH3

C O⊕ H2

C CH3

OH CH3

−H₂O

C⊕ C CH3

OH CH3

C O H

C CH3

O⊕H2

CH3

−H₂O

C O H

C⊕ CH3

CH3

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Since the documentation is already long enough, I decided to provide an extra file containing only examples and a few words where to find possibly interesting code.

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myChemistryv1.5.1 Example Schemes Examples

Example Schemes

1 Addition Reaction . . . 3

2 Mesomerism . . . 4

3 The Titlepage . . . 6

4 Condensation Reaction . . . 7

5 Substitution vs. Elimination . . . 8

6 Scheme with three Lines . . . 9

7 Hydratisation . . . 11

8 Esterification . . . 13

9 Electrophilic Addition . . . 15

10 Activation of Fatty Acids . . . 17

11 Change the layout with TikZ . . . 19

12 Claisen-Kondensation . . . 21

13 Extensive Synthesis. . . 24

1 Addition Reaction

A simple reaction scheme with two different products.

Reaction scheme 1Addition Reaction

O +H^⊕

OH

⊕

OH













OH

R 1,2-adduct

R OH

1,4-adduct

1 \b e g i n{r x n s c h e m e}[ , H ]{ A d d i t i o n R e a c t i o n }

2 \r e a c t a n t{ \c h e m f i g{ = _ [ : : - 3 0 ] - [ : : 6 0 ] ( = [ : : 6 0 ] O ) -[:: -60]}

}

3 \a r r o w{ $+ \Hpl$ }{}

4 \m e s o m e r i c[ , rf ]{

5 \r e a c t a n t{ \c h e m f i g{ = _ [ : - 3 0 ] - [ : : 6 0 ] ( - [ : : 6 0 ] OH ) ( -[:: -120 ,.3 , , , w h i t e ]\o p l u s) -[:: -60]} }

6 \m a r r o w[ b e l o w ]

7 \r e a c t a n t[ b e l o w ]{ \c h e m f i g{\oplus-[6 ,.3 , , , w h i t e ] - [ : - 3 0 ] = _ [ : : 6 0 ] ( - [ : : 6 0 ] OH ) -[:: -60]} }

8 }

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myChemistryv1.5.1 2 Mesomerism Examples

9 \b r a n c h[ r i g h t = of rf , , y s h i f t =3 em ]{

10 \a r r o w{}{}

11 \r e a c t a n t{ \c h e m n a m e{\c h e m f i g{ = _ [ : - 3 0 ] - [ : : 6 0 ] ( - [ : : 6 0 ] OH ) ( -[:: -120] R ) -[:: -60]}}{1 ,2 - a d d u c t } }

12 }

13 \b r a n c h[ r i g h t = of rf , , y s h i f t = -5 em ]{

14 \a r r o w{}{}

15 \r e a c t a n t{ \c h e m n a m e{\c h e m f i g{ R

- [ 6 ] - [ : - 3 0 ] = _ [ : : 6 0 ] ( - [ : : 6 0 ] OH ) -[:: -60]}}{1 ,4 - a d d u c t } }

16 }

17 \end{r x n s c h e m e}

2 Mesomerism

Reaction scheme 2Mesomerism

benzene1

Br

bromobenzene2 Br2/AlBr3

−AlBr₄

Br H

⊕

⊕ Br H

⊕

 Br H











−H^⊕

If you put something relative to an arrow you might have to consider, that the arrow’s anchor point is in the middle of the arrow. That’s why \mesomeric is shifted with yshift=-2.5emin line 9.

1 \b e g i n{r x n s c h e m e}[ , H , ,.8]{ M e s o m e r i s m }

2 \s e t a t o m s e p{1.6 em }

3 % main r e a c t i o n :

4 \r e a c t a n t[ , s t a r t ]{ \c h e m n a m e{\c h e m f i g{*6( -= -=( -[ , , , , w h i t e ]\p h a n t o m{ Br }) -=) }}{ b e n z e n e \c o m p o u n d{ b e n z e n e }}

}

5 \a r r o w[ , ,2.8]{}{}

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myChemistryv1.5.1 3 The Titlepage Examples

6 \r e a c t a n t{ \c h e m n a m e{\c h e m f i g{*6( -= -=( - Br ) -=) }}{

b r o m o b e n z e n e \c o m p o u n d{ b r o m o b e n z e n e }} }

7 % b r a n c h :

8 \a r r o w[ s t a r t . below , , , p f e i l _ a ]{\ce{ Br 2 / AlBr 3}}{$ -\ce{ AlBr 4\om}$}

9 \m e s o m e r i c[p f e i l _ a . b e l o w, m e s o m e r i s m , x s h i f t =8.5 em ,y s h i f t

= -2.5 em]{

10 \r e a c t a n t{

11 \c h e m f i g{ * 6 ( = [ @ { e 1}] -= -( -[:120] Br ) ( -[:60] H ) -( -[: -30 ,.4 , , , w h i t e ]\o p l u s) -[ @ { e 2}]) }

12 \e l m o v e{ e 1 } { 6 0 : 4 mm }{ e 2 } { 0 : 4 mm }

13 }

14 \m a r r o w

16 \c h e m f i g{*6( -( -[:90 ,.4 , , , w h i t e ]\o p l u s) -[ @ { e 4 } ] = [ @ { e 3}] -( -[:120] Br ) ( -[:60] H ) -=) }

17 \e l m o v e{ e 3 } { 1 8 0 : 4 mm }{ e 4 } { 1 5 0 : 4 mm }

18 }

19 \m a r r o w

21 \c h e m f i g{*6( -= -( -[: -150 ,.4 , , , w h i t e ]\o p l u s) -( -[:120]

Br ) ( -[:60] H ) -=) }

22 }

23 }

24 % last a r r o w i n s i d e a branch , s i n c e it c a n n o t be s h i f t e d by i t s e l f :

25 \b r a n c h[ a b o v e = of m e s o m e r i s m , , x s h i f t =7.5 em ]{

26 \a r r o w[ a b o v e ]{$ -\Hpl$}{}

27 }

3 The Titlepage

1 \b e g i n{rxn}[ ,.7]

2 \s e t a t o m s e p{1.5 em }\f o o t n o t e s i z e

3 % r e a c t i o n a b o v e :

4 \r e a c t a n t[ , a ]{ \c h e m f i g{ C ( -[4]*6(= -= -= -) ) ( -[2]*6(= -= -= -) ) ( -[6 , , ,2] HO ) - C ( -[2] CH _3) ( -[6] OH ) - CH _3} }

5 \a r r o w[ a . 4 5 ] { } { }

6 \r e a c t a n t[ 4 5 ] { \c h e m f i g{ C ( -[4]*6(= -= -= -) ) ( -[2]*6(= -= -= -) ) ( -[ @ { e 1}6 , , ,2] H _2 @ { e 2}\c h e m b e l o w{ O }{\o p l u s}) - C ( -[2]

CH _3) ( -[6] OH ) - CH _3}\e l m o v e{ e 1 } { 1 0 : 4 mm }{ e 2}{ -10:4 mm } }

7 \a r r o w[ , ,1.42]{$ -\ce{ H 2 O } $ } { }

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myChemistryv1.5.1 3 The Titlepage Examples Reaction scheme 3The Titlepage

C O H

C CH3

OH CH3

C O⊕ H2

C CH3

OH CH3

−H₂O

C⊕ C CH3

OH CH3

C O H

C CH3

O⊕H2

CH3

−H₂O

C O H

C⊕ CH3

CH3

8 \r e a c t a n t{ \c h e m f i g{\c h e m b e l o w{ C }{\o p l u s}( -[4]*6(= -= -= -) ) ( -[2]*6(= -= -= -) ) - C ( -[2] CH _3) ( -[6] OH ) - CH _3} }{}

9 % g o i n g down :

10 \a r r o w[ a . -45 , -| >]{}{}

11 \r e a c t a n t[ -45]{ \c h e m f i g{ C ( -[4]*6(= -= -= -) )

( -[2]*6(= -= -= -) ) ( -[6 , , ,2] HO ) - C ( -[2] CH _3) ( -[ @ { e 3}6] @ { e 4}\c h e m b e l o w{ O }{\o p l u s} H _2) - CH _3}\e l m o v e{ e 3 } { 1 7 0 : 4 mm }{ e 4 } { - 1 7 0 : 4 mm } }

12 \a r r o w[ , ,1.42]{$ -\ce{ H 2 O } $ } { }

13 \r e a c t a n t{ \c h e m f i g{ C ( -[4]*6(= -= -= -) ) ( -[2]*6(= -= -= -) ) ( -[6 , , ,2] HO ) -\c h e m b e l o w{ C }{\o p l u s}( -[2] CH _3) - CH _3} }

14 \end{rxn}

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myChemistryv1.5.1 4 Condensation Reaction Examples

4 Condensation Reaction

Reaction scheme 4Condensation Reaction CH₂OH

OH

+

OH H2

C O

H H2O

CH2

O CH₂ OH OH

CH2O 200^◦C

CH2

OH OH CH2OH

OH

+

OH

H H2O

1 \b e g i n{r x n s c h e m e}[ , H ]{ C o n d e n s a t i o n R e a c t i o n }

2 \r e a c t a n t{\c h e m f i g{**6( - - -( - CH _2 OH ) -( - OH ) - -) }}

3 \c h e m a n d

4 \r e a c t a n t{\c h e m f i g{**6( - - - -( - OH ) -( - HOCH _2) -) }}

5 \a r r o w[ , -+ >]{}{\ce{ H 2 O }}

6 \r e a c t a n t{\c h e m f i g{**6( - - -( - CH _2 -[: -30] O - [ : 3 0 ] CH _2 -[: -30]**6( - - - - -( - OH ) -) ) -( - OH ) - -) }}

7 \a r r o w[ -90 , -+ > , , dec ] { } { \ce{ CH 2 O }}

8 \a n y w h e r e{ dec .180 , , x s h i f t = -.2 em }{\SI{ 2 0 0 } { \ c e l s i u s }}

9 \r e a c t a n t[ -90 , t a r g e t ]{\c h e m f i g{**6( - - -( - CH _2 -[: -30]**6( - - - - -( - OH ) -) ) -( - OH ) - -) }}

10 \b r a n c h[ left = of t a r g e t ]{

11 \r e a c t a n t{\c h e m f i g{**6( - - -( - CH _2 OH ) -( - OH ) - -) }}

12 \c h e m a n d

13 \r e a c t a n t{\c h e m f i g{**6( - - - -( - OH ) -( - H ) -) }}

14 \a r r o w[ , -+ >]{}{\ce{ H 2 O }}

15 }

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myChemistryv1.5.1 5 Substitution vs. Elimination Examples

5 Substitution vs. Elimination

Reaction scheme 5Substitution vs. Elimination H

C

β

H

H C

α H H X

E2

H C H

C H H

+ X + O

H H

H C H

H X

SN2 H C H

H C

H H OH

+ X H O

You may see in line 20 that the\elmovecommands are put inside of\anywhere. This is necessary in order to produce the right scheme. But this time you can position\anywhere literally anywhere.

1 \n e w c o m m a n d*\ s c r o m {\s c r i p t s t y l e\o m i n u s}

2 \b e g i n{r x n s c h e m e}[ , H ]{ S u b s t i t u t i o n vs . E l i m i n a t i o n }

3 % f i r s t r e a c t i o n :

4 \r e a c t a n t[ , s t a r t _ a ]{\c h e m f i g{ @ { H } H -[ @ { b 1}: -60]\c h e m a b o v e { C }{\s c r i p t s t y l e\beta}( <[: -100] H ) ( <:[: -150] H ) -[ @ { b 2}]\c h e m a b o v e{ C }{\s c r i p t s t y l e\a l p h a}( <[:20] H ) ( <:[:60]

H ) -[ @ { b 3}: -60] @ { X 1} X }}

5 \a r r o w{ E 2}{}

6 \r e a c t a n t{\c h e m f i g{ H - [ : 6 0 ] C ( -[:120] H ) = C ( -[:60] H ) -[: -60] H }}

7 \c h e m a n d

8 \r e a c t a n t{\ce{ X \om}}

9 \c h e m a n d

10 \r e a c t a n t{\c h e m f i g{ O ( -[:60] H ) -[: -60] H }}

11 % s e c o n d r e a c t i o n :

12 \r e a c t a n t[ s t a r t _ a . -90 , s t a r t _ b , y s h i f t = -4 em ]{\c h e m f i g{ H -[: -60] C ( <[: -100] H ) ( <:[: -150] H ) - @ { C } C ( <[:20] H ) ( <:[:60] H ) -[ @ { b 4}: -60] @ { X 2} X }}

13 \a r r o w{ S $_\ text { N } $ 2 } { }

14 \r e a c t a n t{\c h e m f i g{ H -[: -60] C ( <[: -100] H ) ( <:[: -150] H ) - C ( <[: -80] H ) ( <:[: -30] H ) -[:60] OH }}

15 \c h e m a n d

16 \r e a c t a n t{\ce{ X \om}}

17 % n u c l e o p h i l e / base :

18 \a n y w h e r e{ s t a r t _ b .135 , nuc , x s h i f t = -3 em , y s h i f t =2 em }{\

c h e m f i g{ H - @ { O }\c h e m a b o v e{\l e w i s{026 , O }}{\h s p a c e{5 mm }\

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myChemistryv1.5.1 6 Scheme with three Lines Examples

s c r o m }}}

19 % e l e c t r o n m o v e m e n t s :

20 \a n y w h e r e{ nuc .0}{

21 \e l m o v e{ O } { 9 0 : 1 . 5 cm }{ H } { 1 8 0 : 1 cm }

22 \e l m o v e{ b 1 } { 6 0 : 1 cm }{ b 2 } { 9 0 : 5 mm }

23 \e l m o v e{ b 3 } { - 1 7 0 : 5 mm }{ X 1 } { 1 8 0 : 5 mm }

24 \e l m o v e{ O }{ -90:1 cm }{ C } { 1 0 0 : 1 . 5 cm }

25 \e l m o v e{ b 4 } { - 1 7 0 : 5 mm }{ X 2 } { 1 8 0 : 5 mm }

26 }

6 Scheme with three Lines

Reaction scheme 6Scheme with three Lines

EtO O

Br O O Et

+ O N K

⊕

O

O N O O Et

O O Et

O

B R−X

O N R

O O Et

O

H^⊕/H₂O

O N R

O C O2

H

O C O2

H

O

−CO₂ H^⊕ H₂O R

H CO2

NH3⊕

1 \n e w c o m m a n d*\ s c r o m {\s c r i p t s t y l e\o m i n u s}

2 \n e w c o m m a n d*\ s c r o p {\s c r i p t s t y l e\o p l u s}

3 \b e g i n{r x n s c h e m e}{ S c h e m e with t h r e e L i n e s }

4 \s e t a t o m s e p{1.5 em }

5 \f o o t n o t e s i z e

6 \r e a c t a n t[ , s t a r t ]{\c h e m f i g{ EtO - ( = [ 2 ] O ) -[: -60]( - Br ) - [ : - 1 2 0 ] ( = [ 6 ] O ) -[4] EtO }}

7 \c h e m a n d

8 \r e a c t a n t{\c h e m f i g{*6( -= -= -*5( -(= O ) -\c h e m a b o v e{\l e w i s {4: , N }}{\ s c r o m }( -[4 ,.7 , , , draw = none ]\c h e m a b o v e{ K }{\

s c r o p }) -(= O ) - -) =) }}

9 \a r r o w{}{}

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myChemistryv1.5.1 7 Hydratisation Examples

10 \r e a c t a n t{\c h e m f i g{*6( -= -= -*5( -(= O ) - N

( -( -[:: -60](=[:: -60] O ) -[::60] EtO ) - [ : : 6 0 ] ( = [ : : 6 0 ] O ) -[:: -60] EtO ) -(= O ) - -) =) }}

11 % newline , s t a r t e d with \ a n y w h e r e :

12 \a n y w h e r e{ s t a r t . -90 , a , x s h i f t = -4 em , y s h i f t = -5 em }{}

13 \a r r o w[ a .0 , ,.6]{\c h e m a b o v e{\l e w i s{0: , B }}{\ s c r o m }}{}

14 \a r r o w{\ce{ R - X }}{}

15 \r e a c t a n t{\c h e m f i g{*6( -= -= -*5( -(= O ) - N ( -( -[4] R ) ( - [ : : - 6 0 ] ( = [ : : - 6 0 ] O ) -[::60] EtO ) - [ : : 6 0 ] ( = [ : : 6 0 ] O ) -[:: -60] EtO ) -(= O ) - -) =) }}

16 \a r r o w[ , ,1.25]{\Hpl/\ce{ H 2 O }}{}

17 \r e a c t a n t{\c h e m f i g{*6( -= -= -*5( -(= O ) - N ( -( -[4] R )

( - [ : : - 6 0 ] ( = [ : : - 6 0 ] O ) -[::60] HO _2 C ) - [ : : 6 0 ] ( = [ : : 6 0 ] O ) -[:: -60] HO _2 C ) -(= O ) - -) =) }}

18 % newline , s t a r t e d with \ a n y w h e r e :

19 \a n y w h e r e{ a . -90 , b , y s h i f t = -7 em }{}

20 \a r r o w[ b . 0 ] { \ce{ - CO 2 } } { }

21 \a r r o w{\Hpl}{\ce{ H 2 O }}

22 \r e a c t a n t{\c h e m f i g{ R -( -[6] H ) ( -[2] C | O _2\om) - NH _3\op}}

7 Hydratisation

A scheme with transition states.

For this example we first declare a style for the delocalized double bonds:

1 \ p g f d e c l a r e d e c o r a t i o n { d d b o n d }{ i n i t i a l }{%

2 \ s t a t e { i n i t i a l }[ w i d t h =2 pt ]{%

3 \ p g f p a t h l i n e t o {\ p g f p o i n t {2 pt }{0 pt }}%

4 \ p g f p a t h m o v e t o {\ p g f p o i n t {1.5 pt }{2 pt }}%

5 \ p g f p a t h l i n e t o {\ p g f p o i n t {2 pt }{2 pt }}%

6 \ p g f p a t h m o v e t o {\ p g f p o i n t {2 pt }{0 pt }}%

7 }%

8 \ s t a t e { f i n a l }{%

9 \ p g f p a t h l i n e t o {\ p g f p o i n t d e c o r a t e d p a t h l a s t }%

10 }%

11 }%

12 \ t i k z s e t { l d d b o n d /. s t y l e ={ decorate , d e c o r a t i o n = d d b o n d }}%

13 \ t i k z s e t { r d d b o n d /. s t y l e ={ decorate , d e c o r a t i o n ={ ddbond , m i r r o r }}}%

Now the delocalized double bond can be used viaChemFig’s fifth option (see theChem- Figmanual):

1 \c h e m f i g{ -[ , , , , l d d b o n d ] -[ , , , , r d d b o n d ]}

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myChemistryv1.5.1 7 Hydratisation Examples Reaction scheme 7Hydratisation

R2C O H

O H

slow R2C

O H δ⊕ H

O H A

δ













‡

(general transition state, acid cat.)

R2C O

⊕

H₂ OH −

H_⊕

R₂C OH OH H²O

R2C OH O R2C

O H B

δ⊕

H

O

δ













‡

(general transition state, base cat.) R2C O slow

H O

H

Further we define the two commands

1 \n e w c o m m a n d*\ delm {\e n s u r e m a t h{\ text {\tiny$\d e l t a\o m i n u s

$}}}%

2 \n e w c o m m a n d*\ delp {\e n s u r e m a t h{\ text {\tiny$\d e l t a\o p l u s

$}}}%

to use the partial charges without effort.

Then the whole code looks like follows:

1 \b e g i n{r x n s c h e m e}{ H y d r a t i s a t i o n }

2 \r e a c t a n t[ , c a r b o n y l _ A ]{\c h e m f i g{ R _2 C = O }}

3 \a n y w h e r e{ a b o v e = of c a r b o n y l _ A }{\c h e m f i g{ H -[: -30] O - [ : 3 0 ] H }}

4 \a r r o w[ , <= >]{\tiny slow }{}

5 \t r a n s i t i o n[ , t r a n s i t i o n _ A ]{\c h e m f i g{ R _2 C ( -[2 , ,2 , , d e n s e l y d o t t e d ]\c h e m a b o v e{ O }{\ delp } ( - [ : 1 5 0 ] H ) -[:30] H )

-[: -30 ,1.15 , , , l d d b o n d ] O -[6 , , , , d e n s e l y d o t t e d ] H -[ , , , , d e n s e l y d o t t e d ]\c h e m a b o v e{ A }{\ delm }}}

6 \a n y w h e r e{ b e l o w = of t r a n s i t i o n _ A , , text w i d t h =3 cm }{(

g e n e r a l t r a n s i t i o n state , acid cat .) }

7 \a r r o w[ , <= > ,.7]{}{}

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myChemistryv1.5.1 7 Hydratisation Examples

8 \r e a c t a n t{\c h e m f i g{ R _2 C ( -[:60]\c h e m a b o v e{ O }{\s c r i p t s t y l e

\o p l u s} H _2) -[: -60] OH }}

9 \a r r o w[ b e l o w right , <= > ,.7]{$ -\Hpl$}{}

10 \r e a c t a n t[ b e l o w r i g h t ]{\c h e m f i g{ R _2 C ( -[:60] OH ) -[: -60] OH }}

11 \a r r o w[ b e l o w left , <= > ,.7]{}{\ce{ H 2 O }}

12 \r e a c t a n t[ b e l o w left , zw ]{\c h e m f i g{ R _2 C ( -[:60] OH ) -[: -60] O

|\om}}

13 \a r r o w[ left , <= > ,.7]{}{}

14 \t r a n s i t i o n[ left , t r a n s i t i o n _ B ]{\c h e m f i g{ R _2 C ( -[2 , ,2 , , d e n s e l y d o t t e d ] O ( -[:150] H -[4 , , , , d e n s e l y d o t t e d ]\

c h e m a b o v e{ B }{\ delp }) -[:30] H ) -[: -30 ,1.15 , , , l d d b o n d ]\

c h e m a b o v e{ O }{\ delm } -[6 , , , , draw = none ]\p h a n t o m{ H }}}

15 \a n y w h e r e{ b e l o w = of t r a n s i t i o n _ B , , text w i d t h =3 cm }{(

g e n e r a l t r a n s i t i o n state , base cat .) }

16 \a r r o w[ left , <= >]{\tiny l a n g s a m }{}

17 \r e a c t a n t[ left , c a r b o n y l _ B ]{\c h e m f i g{ R _2 C = O }}

18 \a n y w h e r e{ a b o v e = of c a r b o n y l _ B }{\c h e m f i g{ H -[: -30] O - [ : 3 0 ] H }}

You can see that\anywherewas used several times, either to place molecules or to label molecules.

(13)

myChemistryv1.5.1 8 Esterification Examples

8 Esterification

Reaction scheme 8Esterification

H C O O H

H2SO4HSO4

protolysis H C

O H

⊕

O H

H C O

⊕

H O H













H O

CH3 addition

H C O

H O

⊕CH₃ O H

H

protolysis

H C O

H O CH3

O

⊕

H H

−H2O

elimination

H C O H

⊕

O CH3

H C O

⊕

H O CH3













HSO4 H2SO4

H C O O CH3

1 \b e g i n{rxn}{ E s t e r i f i c a t i o n }

2 \r e a c t a n t{\c h e m f i g{ H - C ( = [ : 6 0 ] O ) -[: -60] O - H }}

3 \a r r o w[ , -+ > ,1.2 , p r o t o l y s i s ]{\ce{ H 2 SO 4 } } { \ce{ HSO 4\om}}

4 \a n y w h e r e{ b e l o w = of p r o t o l y s i s , , y s h i f t =1 em }{\tiny p r o t o l y s i s }

5 \m e s o m e r i c{

6 \r e a c t a n t{\c h e m f i g{ H - @ { a 2} C ( -[:60] O - H ) ( -[:30 ,.5 , , , draw

= none ]{\s c r i p t s t y l e\o p l u s}) -[: -60] O - H }}

7 \m a r r o w

8 \r e a c t a n t{\c h e m f i g{ H - C ( = [ : 6 0 ] \c h e m a b o v e{ O }{\

s c r i p t s t y l e\o p l u s} - H ) -[: -60] O - H }}

9 }

10 \b r a n c h[ below , , x s h i f t = -5 em ]{

11 \a r r o w[ below , <= >]{\tiny a d d i t i o n }{\c h e m f i g{ H - [ : 1 2 0 ] @ { a 1} O - [ : 6 0 ] CH _3}}

12 \r e a c t a n t[ b e l o w ]{

13 \c h e m f i g{ H - C ( -[2] O - [ : 3 0 ] H ) ( -\c h e m a b o v e{ O }{\

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myChemistryv1.5.1 8 Esterification Examples

s c r i p t s t y l e\o p l u s}( -[:60] CH _3) -[: -60] H ) -[6] O -[: -30] H }

14 \e l m o v e{ a 1 } { 9 0 : 1 . 5 cm }{ a 2 } { 0 : 3 cm }

15 }

16 }

17 \b r a n c h[ left , , y s h i f t = -3.5 em ]{

18 \a r r o w[ left , <= >]{}{\tiny p r o t o l y s i s }

19 }

20 \r e a c t a n t[ left ]{

21 \c h e m f i g{ H - C ( -[2] O - [ : 3 0 ] H ) ( - O - CH _3) -[ @ { b 1}6] @ { a 3}\

c h e m a b o v e{ O }{\h s p a c e*{ -4 mm }\s c r i p t s t y l e\o p l u s }( -[: -150] H ) -[: -30] H }

22 \e l m o v e{ b 1 } { 0 : 5 mm }{ a 3 } { 2 0 : 5 mm }

23 }

24 \a r r o w[ below , <= >]{\ce{ - H 2 O }}{\tiny e l i m i n a t i o n }

25 \m e s o m e r i c[ below , , x s h i f t =6 em ]{

26 \r e a c t a n t{\c h e m f i g{ H - C ( -[:60] O - H ) ( -[ ,.5 , , , draw = none ]{\

s c r i p t s t y l e\o p l u s}) -[: -60] O - CH _3}}

27 \m a r r o w

28 \r e a c t a n t{\c h e m f i g{ H - C ( = [ : 6 0 ] \c h e m a b o v e{ O }{\

s c r i p t s t y l e\o p l u s} - H ) -[: -60] O - CH _3}}

29 }

30 \a r r o w[ , -+ > ,1.2]{\ce{ HSO 4\om}}{\ce{ H 2 SO 4}}

31 \r e a c t a n t{\c h e m f i g{ H - C ( = [ : 6 0 ] O ) -[: -60] O - CH _3}}

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myChemistryv1.5.1 9 Electrophilic Addition Examples

9 Electrophilic Addition

This scheme forms a circle.

Reaction scheme 9Electrophilic Addition C

C + Br Br fast

C

C Br Br

−Br slow

C⊕

C Br

carbenium ion

C C⊕Br bromonium ion

slow

−Br

C

⊕

C Br carbenium ion

1 \b e g i n{r x n s c h e m e}[ , H ]{ E l e c t r o p h i l i c A d d i t i o n }

2 \s e t a r r o w l e n g t h{3 em }

3 \r e a c t a n t{\c h e m f i g{ >[: -20] C ( <[:40]) =[6] C ( <[: -130])

<[: -20]}}

4 \c h e m a n d[ , plus ]

5 \r e a c t a n t{\c h e m f i g{\l e w i s{246 , Br } -\l e w i s{026 , Br }}}

6 \a r r o w[ plus . -90 , <= >]{\f o o t n o t e s i z e fast }{}

7 \r e a c t a n t[ -90 , a t t a c k ]{\c h e m f i g{ >[: -20] C ( <[:40]) =[ @ { db }6]

C ( <[: -130]) <[: -20]}}

8 \a n y w h e r e{ r i g h t = of a t t a c k }{

9 \c h e m f i g{ @ { Br 1}\l e w i s{246 , Br } -[ @ { b 2}] @ { Br 2}\l e w i s{026 , Br }}

10 \e l m o v e{ db } { 2 0 : 5 mm }{ Br 1 } { 1 3 5 : 5 mm }

11 \e l m o v e{ b 2 } { - 1 2 0 : 5 mm }{ Br 2 } { - 1 2 0 : 5 mm }

12 }

13 % to the left :

14 \a r r o w[ a t t a c k . -135 , <= > ,2]{\ce{ - Br \om}}{\f o o t n o t e s i z e slow }

15 \r e a c t a n t[ -135 , c a r b e n i u m _ a ]{\v f l i p n e x t\c h e m f i g{ -[: -30]\

c h e m b e l o w{ C }{\s c r i p t s t y l e\o p l u s} ( - [ : 3 0 ] ) -[6] C

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myChemistryv1.5.1 9 Electrophilic Addition Examples

( <[: -150]) ( <:[: -100]) -[: -30]\l e w i s{137 , Br }}}

16 \a n y w h e r e{ b e l o w = of c a r b e n i u m _ a }{\f o o t n o t e s i z e c a r b e n i u m ion }

17 \a r r o w[ , < <= >]{}{}

18 \r e a c t a n t[ , b r o m o n i u m ]{\c h e m f i g{ >:[: -60] C ? ( < [ : 1 6 0 ] ) -[6] C ( <[: -110]) ( <:[: -150]) -[:30]\l e w i s{17 , Br }? -[4 ,.5 , , , draw = none ]{\s c r i p t s t y l e\o p l u s}}}

19 \a n y w h e r e{ b e l o w = of b r o m o n i u m , , y s h i f t =.35 em }{\

f o o t n o t e s i z e b r o m o n i u m ion }

20 % to the r i g h t :

21 \a r r o w[ a t t a c k . -45 , <= > ,2]{\f o o t n o t e s i z e slow }{\ce{ - Br \om }}

22 \r e a c t a n t[ -45 , c a r b e n i u m _ b ]{\c h e m f i g{ -[: -30]\c h e m a b o v e{ C }{\s c r i p t s t y l e\o p l u s} ( - [ : 3 0 ] ) -[6] C ( <:[: -150])

( <[: -100]) -[: -30]\l e w i s{157 , Br }}}

23 \a n y w h e r e{ b e l o w = of c a r b e n i u m _ b }{\f o o t n o t e s i z e c a r b e n i u m ion }

24 \a r r o w[ left , < <= >]{}{}

25 \m C s e t u p{ r e s e t }

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myChemistryv1.5.1 10 Activation of Fatty Acids Examples

10 Activation of Fatty Acids

Reaction scheme 10 Activation of Fatty Acids

O P O

O

O P O

O

O P O

O

O CH₂ O

OH OH

N N

N NH2

N

ATP

R C O O H

fatty acid

O P O

O

O P O

O O pyrophosphate PPi

+ R C

O O P

O O

O CH2

ribose adenine

acyl-AMP

H2O

2HO P O

O O

Pi

CoA S H AMP

R C O

S CoA

acyl-SCoA

1 \def\ s c r o m {\s c r i p t s t y l e\o m i n u s}

2 \b e g i n{r x n s c h e m e}[ , H ]{ A c t i v a t i o n of F a t t y A c i d s }

3 \r e a c t a n t[ , ATP ]{\c h e m f i g{\c h e m a b o v e{ O }{\h s p a c e*{ -5 mm }\

s c r o m } - P ( = [ 2 ] O ) ( -[6]\c h e m b e l o w{ O }{\ s c r o m }) -O - P ( = [ 2 ] O ) ( -[6]\c h e m b e l o w{ O }{\ s c r o m }) - @ { O 1} O -[ @ { b 1}] @ { P } P ( = [ 2 ] O ) ( -[6]\c h e m b e l o w{ O }{\ s c r o m }) -O - CH

_2 -[6 ,1.5 ,1]( -[6 ,.5]) ( -[:20 ,1.3] O ?[ a ]) <[7]( -[2 ,.5]) ( -[6] OH ) -[ , , , , line w i d t h =3 pt ]( -[2 ,.5]) ( -[6] OH ) >[1]?[ a

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myChemistryv1.5.1 10 Activation of Fatty Acids Examples

]( -[6 ,.5]) -[2 ,1.5] N ?[ b ] - [ : 1 8 ] ( [ : 3 0 ] * 6 ( - N = - N =( - NH _2) -=) ) - [ : 9 0 ] - [ : 1 6 2 ] N = ^ [ : - 1 2 6 ] ? [ b ]}}

4 \a n y w h e r e{ b e l o w r i g h t = of ATP , , x s h i f t = -4 em , y s h i f t =3 em }{\

b f s e r i e s ATP }

5 \a r r o w[ below , ,1.5]{\c h e m n a m e{\c h e m f i g{ R - C (=[: -60] O ) -[:60] @ { O 2} O -[ @ { b 2}] H }}{ f a t t y acid }}{}

6 \b r a n c h[ on c h a i n = g o i n g b e l o w ]{

7 \r e a c t a n t[ , p y r o p h o s p h a t ]{

8 \c h e m f i g{\c h e m a b o v e{ O }{\h s p a c e*{ -5 mm }\ s c r o m } - P ( = [ 2 ] O ) ( -[6]\c h e m b e l o w{ O }{\ s c r o m }) -O - P ( = [ 2 ] O ) ( -[6]\

c h e m b e l o w{ O }{\ s c r o m }) -\c h e m a b o v e{ O }{\h s p a c e*{5 mm }\ s c r o m }}

9 \e l m o v e{ b 1 } { 1 0 0 : 1 cm }{ O 1 } { 9 0 : 5 mm }

10 \e l m o v e{ O 2 } { 1 3 5 : 1 cm }{ P }{ -135:1 cm }

11 \e l m o v e{ b 2}{ -90:5 mm }{ O 2}{ -60:5 mm }

12 }

13 \a n y w h e r e{ b e l o w = of p y r o p h o s p h a t }{ p y r o p h o s p h a t e PP $_\

text { i }$}

14 \c h e m a n d

15 \r e a c t a n t[ , acyl - amp ]{\c h e m f i g{ R - @ { C } C (=[: -60] O ) -[ @ { b 3 } : 6 0 ] @ { O 3} O - P ( -[6]\c h e m b e l o w{ O }{\ s c r o m }) ( = [ 2 ] O ) -O - CH _2 -[6 , ,1 ,1] r | ibos | e -[2 ,1.05 ,3 ,1] A | d e n i n e }}

16 \a n y w h e r e{ b e l o w = of acyl - amp }{\b f s e r i e s acyl - AMP }

17 }

18 \b r a n c h[ on c h a i n = g o i n g below , , x s h i f t = -8 em ]{

19 \a r r o w[ b e l o w ]{\ce{ H 2 O }}{}

20 \r e a c t a n t[ below , Pi ] { 2 ~ \c h e m f i g{ HO - P ( = [ 2 ] O ) ( -[6]\

c h e m b e l o w{ O }{\ s c r o m }) - O }}

21 \a n y w h e r e{ b e l o w r i g h t = of Pi }{ P $_\ text { i }$}

22 }

23 \b r a n c h[ , , x s h i f t =4 em ]{

24 \a r r o w[ below , -+ >]{\c h e m f i g{ CoA - @ { S } S -[ @ { b 4}: -60] H }}{

AMP }

25 \r e a c t a n t[ below , acyl - SCoA ]{

26 \c h e m f i g{ R - C (=[: -60] O ) -[:60] S - CoA }

27 \e l m o v e{ S } { 1 3 5 : 2 cm }{ C }{ -135:1 cm }

28 \e l m o v e{ b 3}{ -45:5 mm }{ O 3}{ -70:7 mm }

29 \e l m o v e{ b 4 } { - 1 2 0 : 7 mm }{ S }{ -100:5 mm }

30 }

31 \a n y w h e r e{ b e l o w = of acyl - SCoA }{ acyl - SCoA }

32 }

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myChemistryv1.5.1 11 Change the layout with TikZ Examples

11 Change the layout with TikZ

Reaction scheme 11 Change the layout with TikZ Alkyl

l Acy

O P O

O O

NH2

Phosphatidylethanolamine

N-acyltransferase

Alkyl l Acy

O P O

O O

N H

O

N-arachidonoyl-PE

Phospholipase D

HO

N H

O

Anandamide

This is an example for the usage of the <tikz> option. Please take a closer look at lines5,7,11 and 15.

1 \b e g i n{r x n s c h e m e}{ C h a n g e the l a y o u t with \ TikZ }

2 \ c o l o r l e t { m C g r e e n }{ g r e e n !50! gray }

3 \ c o l o r l e t { m C b l u e }{ cyan !50! gray }

4 \ c o l o r l e t { m C r e d }{ m a g e n t a !50! gray }

(20)

myChemistryv1.5.1 12 Claisen-Kondensation Examples

5 \ t i k z s e t { r e a c t a n t /. s t y l e ={ draw =#1 , fill =#1!10 , m i n i m u m w i d t h =.8\ t e x t w i d t h , i n n e r sep =1 em , r o u n d e d c o r n e r s }}

6 \m C s e t u p{ a r r o w l e n g t h =3 em , a r r o w l i n e = very t h i c k }

7 \r e a c t a n t[ , ,r e a c t a n t = m C g r e e n]{

8 \c h e m n a m e{\c h e m f i g{ Alky | l - -[6]( -[4 , , ,2] Acy | l ) -[6] - O - P ( = [ 2 ] O ) ( -[6] O |\om) -O -[: -30] -[:30] -[: -30] NH _ 2 } } { \ b f s e r i e s P h o s p h a t i d y l e t h a n o l a m i n e }

9 }

10 \a r r o w[ b e l o w ] { } { \t e x t i t{ N } - a c y l t r a n s f e r a s e }

11 \r e a c t a n t[ below , ,r e a c t a n t = m C b l u e]{

12 \c h e m n a m e{\c h e m f i g{ Alky | l - -[6]( -[4 , , ,2] Acy | l ) -[6] - O - P ( = [ 2 ] O ) ( -[6] O |\om) -O - [: - 3 0] - [: 30 ] -[ : -3 0] \c h e m b e l o w{ N }{ H } - [ : 3 0 ] ( = [ 2 ] O )

-[ : -30 ] -[: 30] - [: -3 0] -[ :30 ]=_ - [: -3 0] -[ :30 ]=_ - [: -6 0]

- [ : : - 6 0 ] = _ [ : 1 8 0 ] - [ : : - 3 0 ] - [ : : 6 0 ] = _ [ : 1 8 0 ] - [ : : - 3 0 ] - [ : : 6 0 ] - [ : : - 6 0 ] - [ : : 6 0 ] - [ 6 ] } } { \b f s e r i e s\t e x t i t{ N } - a r a c h i d o n o y l - PE }

13 }

14 \a r r o w[ b e l o w ]{}{ P h o s p h o l i p a s e D }

15 \r e a c t a n t[ below , ,r e a c t a n t = m C r e d]{

16 \c h e m n a m e{\c h e m f i g{ HO - [: - 30 ] -[ :3 0] - [ : -3 0] \c h e m b e l o w{ N }{ H } - [ : 3 0 ] ( = [ 2 ] O )

-[ : -30 ] -[: 30 ] - [: -3 0] -[ :30 ]=_ - [: -3 0] -[ :30 ]=_ - [: -6 0]

- [ : : - 6 0 ] = _ [ : 1 8 0 ] - [ : : - 3 0 ] - [ : : 6 0 ] = _ [ : 1 8 0 ] - [ : : - 3 0 ] - [ : : 6 0 ] - [ : : - 6 0 ] - [ : : 6 0 ] - [ 6 ] } } { \b f s e r i e s A n a n d a m i d e }

17 }

18 \m C s e t u p{ r e s e t }

12 Claisen-Kondensation

1 \b e g i n{r x n s c h e m e}{ Claisen - K o n d e n s a t i o n }

2 \ c o l o r l e t { m C r e d }{ red !50! gray }

3 \s e t a t o m s e p{1.5 em }

4 % E r g e b n i s :

5 \b r a n c h[ , one , draw = mCred , fill = m C r e d !10 , r o u n d e d corners , i n n e r sep =.5 em ]{

6 \r e a c t a n t{\c h e m f i g{ [ : 3 0 ] - ( = [ 2 ] O ) -[: -30] O - -[: -30]}}

7 \c h e m a n d

8 \r e a c t a n t{\c h e m f i g{ [ : 3 0 ] - ( = [ 2 ] O ) -[: -30] O - -[: -30]}}

9 \a r r o w[ , ,2]{\ce{ N a O E t } , \ce{ EtOH }}{}

10 \r e a c t a n t{\c h e m f i g{ [ : 3 0 ] - ( = [ 2 ] O ) -[: -30] -(=[2] O ) -[: -30]

O - -[: -30]}}

(21)

Reaction scheme 12 Claisen-Kondensation O

O

+ O

O

NaOEt, EtOH O O

O

OEt

O O







+ EtOH

O O

O

O O

H H O

O + OEt

O O O









H^⊕, H2O O O

O

(22)

11 }

12 % M e c h a n i s m u s :

13 \b r a n c h[ -90 , , x s h i f t = -13.5 em ]{

14 \a r r o w[ -90 , <= >]{\ce{{}\om OEt }}{}

15 }

16 \m e s o m e r i c[ -90 , two , x s h i f t =4.5 em ]{

17 \r e a c t a n t{\c h e m f i g{[:30]( -[:150 ,.3 , , , draw = none ] @ { C 1}\

s c r i p t s t y l e\o m i n u s) -(=[2] O ) -[: -30] O - -[: -30]}}

18 \m a r r o w

19 \r e a c t a n t{\c h e m f i g{ [ : 3 0 ] = ( - [ 2 ] O |\om) -[: -30] O - -[: -30]}}

20 }

21 \c h e m a n d

22 \r e a c t a n t{\ce{ EtOH }}

23 \b r a n c h[ two . -90 , three , x s h i f t = -5.5 em ]{

24 \a r r o w[ -90 , <= > , , , both ]{\c h e m f i g[][ s c a l e = . 7 ] { [ : 3 0 ] - @ { C 2 } ( = [ @ { b 1}2] O@ { O 1}) -[: -30] O - -[: -30]}}{}

25 }

26 \r e a c t a n t[ t h r e e . -90]{\c h e m f i g{ -( -[ @ { b 2}2] @ { O 2} O |\om) ( - [ 6 ] - [: -3 0 ] (= [ 6] O ) -[:30] O - [ : - 3 0 ] - [ : 3 0 ] ) -[ @ { b 3}] @ { O 3}

O - [ : 3 0 ] - [ : - 3 0 ] } }

27 \a r r o w[ , <= >]{}{}

28 \r e a c t a n t[ , four ]{\c h e m f i g{ [ : 3 0 ] - ( = [ 2 ] O ) -[: -30] @ { C 3}( -[: -120] H ) ( -[ @ { b 4}: -60] H@ { H }) -(=[2] O ) -[: -30] O - -[: -30]}}

29 \c h e m a n d

30 \r e a c t a n t{\c h e m f i g{\om @ { O 4} OEt }}

31 \a r r o w[ four . - 9 0 ] { } { }

32 \m e s o m e r i c[ -90]{

33 \r e a c t a n t{\c h e m f i g{ [ : 3 0 ] - ( = [ 2 ] O ) -[: -30]=( -[2] O |\om) -[: -30] O - -[: -30]}}

34 \m a r r o w

35 \r e a c t a n t{\c h e m f i g{ [ : 3 0 ] - ( = [ 2 ] O ) -[: -30]( -[6 ,.3 , , , draw = none ]\s c r i p t s t y l e\o m i n u s) -(=[2] O ) -[: -30] O - -[: -30]}}

36 \m a r r o w

37 \r e a c t a n t{\c h e m f i g{[:30] -( -[2] O |\om) = [ : - 3 0 ] - ( = [ 2 ] O ) -[: -30] O - -[: -30]}}

38 }

39 \a r r o w[ -90]{\Hpl, \ce{ H 2 O }}{}

40 \r e a c t a n t[ -90]{\c h e m f i g{ [ : 3 0 ] - ( = [ 2 ] O ) -[: -30] -(=[2] O ) -[: -30] O - -[: -30]}}

41 \a n y w h e r e{ one .0}{

42 \e l m o v e{ C 1 } { - 1 0 0 : 2 cm }{ C 2}{ -90:2 cm }

43 \e l m o v e{ b 1 } { 1 0 : 5 mm }{ O 1 } { 0 : 5 mm }

44 \e l m o v e{ O 2 } { 1 8 0 : 5 mm }{ b 2 } { 1 8 0 : 5 mm }

(23)

myChemistryv1.5.1 13 Extensive Synthesis Examples

45 \e l m o v e{ b 3 } { 8 0 : 5 mm }{ O 3 } { 9 0 : 5 mm }

46 \e l m o v e{ b 4 } { 0 : 5 mm }{ C 3 } { 0 : 7 mm }

47 \e l m o v e{ O 4}{ -90:1 cm }{ H }{ -45:1 cm }

48 }

13 Extensive Synthesis

As last example we can create extensive syntheses, using the\mergecommand.

1 \b e g i n{r x n s c h e m e}[ , , ,.8]{ E x t e n s i v e S y n t h e s i s }

2 \s e t a t o m s e p{1.5 em }

3 \b r a n c h[ , s t a r t _ left ]{

4 \r e a c t a n t{\c h e m f i g{ = _ [ : : 3 0 ] - [ : : - 6 0 ] - [ : : 6 0 ] ( - [ : : - 6 0 ] ) ( - [ : : 1 2 0 ] ) -[::0] OH }}

5 \a r r o w[ b e l o w ]{\ce{ HBr }}{}

6 \r e a c t a n t[ b e l o w ]{\c h e m f i g{ Br

- [ : : 3 0 ] - [ : : - 6 0 ] = _ [ : : 6 0 ] ( - [ : : - 6 0 ] ) - [ : : 6 0 ] } }

7 }

8 \b r a n c h[ r i g h t = of s t a r t _ left , s t a r t _ center , y s h i f t =1 em ]{

9 \r e a c t a n t{\c h e m n a m e{\c h e m f i g[][ s c a l e =.8]{**6( - -( - SO _2 Cl ) - - -( -) -) }}{ t o s y l e c h l o r i d e }}

10 \a r r o w[ b e l o w ]{\ce{ NaOH }}{\ce{ Zn }}

11 \r e a c t a n t[ b e l o w ]{\c h e m f i g[][ s c a l e =.8]{**6( - -( - SO _2 Na ) - - -( -) -) }}

12 }

13 \b r a n c h[ r i g h t = of s t a r t _ center , s t a r t _ right , x s h i f t =3 em , y s h i f t = -10 em ]{

14 \r e a c t a n t{\c h e m n a m e{\c h e m f i g{ - [ : : 3 0 ] ( - [ : : 6 0 ] )

= _ [ : : - 6 0 ] - [ : : 6 0 ] COOH }}{3 - methyl -2 - b u t e n o i c acid }}

15 \a r r o w[ b e l o w ]{\ce{ CH 3 OH }}{}

16 \r e a c t a n t[ b e l o w ]{\c h e m f i g{ - [ : : 3 0 ] ( - [ : : 6 0 ] )

= _ [ : : - 6 0 ] - [ : : 6 0 ] CO _2 CH _3}}

17 }

18 \b r a n c h[ b e l o w = of s t a r t _ left , t a r g e t _ one , x s h i f t =5 em , y s h i f t

= -5 em ]{

19 \r e a c t a n t{\c h e m f i g[][ s c a l e =.8]{**6( - -( - SO

_ 2 - [ : 3 0 ] - [ : : - 6 0 ] = _ [ : : 6 0 ] ( - [ : : 6 0 ] ) -[:: -60]) - - -( -) -) }}

20 }

21 \b r a n c h[ b e l o w = of t a r g e t _ one , t a r g e t _ two , x s h i f t =6 em , y s h i f t

= -6 em ]{

22 \m e s o m e r i c{\c h e m f i g[][ s c a l e = . 8 ] { - [ : : 3 0 ] ( - [ : : 6 0 ] )

= ^ [ : : - 6 0 ] - [ : : 6 0 ] ( - [ : : 6 0 ] S ( = [ : : 9 0 ] O ) ( = [ : : - 9 0 ] O ) -[::0]**6( - - -( -) - - -) ) -[:: -60]( -[::0]) ( -[:: -120])

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Reaction scheme 13 Extensive Synthesis

OH

HBr

Br

SO2Cl

tosyle chloride Zn NaOH

SO2Na

COOH 3-methyl-2-butenoic acid

CH3OH

CO2CH3 SO2

S

O O

CO2CH3













KOH

COOH trans-chrysanthemum acid

NaOCH3

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-[::60]( -[::60 ,.5 , , , w h i t e ]\o m i n u s) -[:: -60] CO _2 CH _3}}

23 \a r r o w[ below , , . 5 ] { } { }

24 \a r r o w[ below , ,.5]{\ce{ KOH }}{}

25 \r e a c t a n t[ b e l o w ]{\c h e m n a m e{\c h e m f i g{ -[:: -30]( -[:: -60])

= ^ [ : : 6 0 ] > [ : : - 6 0 ] ( - [ : : 9 0 , 1 . 2 ] )

- [ : : 3 0 , 1 . 2 ] ( - [ : : 1 2 0 , 1 . 2 ] ( - [ : : - 6 0 ] ) -[::0]) <:[:: -30]

COOH }}{\emph{ t r a n s } - c h r y s a n t h e m u m acid }}

26 }

27 \m e r g e{ t a r g e t _ one }{ s t a r t _ left }{ s t a r t _ c e n t e r }

28 \m e r g e[\ce{ N a O C H 3}]{ t a r g e t _ two }{ t a r g e t _ one }{ s t a r t _ r i g h t }

Let’s go through the code, piece by piece.

1 \b e g i n{r x n s c h e m e}[ , , ,.8]{ E x t e n s i v e S y n t h e s i s }

2 \s e t a t o m s e p{1.5 em }

3 \b r a n c h[ , s t a r t _ left ]{

4 \r e a c t a n t{\c h e m f i g{ = _ [ : : 3 0 ] - [ : : - 6 0 ] - [ : : 6 0 ] ( - [ : : - 6 0 ] ) ( - [ : : 1 2 0 ] ) -[::0] OH }}

5 \a r r o w[ b e l o w ]{\ce{ HBr }}{}

6 \r e a c t a n t[ b e l o w ]{\c h e m f i g{ Br

- [ : : 3 0 ] - [ : : - 6 0 ] = _ [ : : 6 0 ] ( - [ : : - 6 0 ] ) - [ : : 6 0 ] } }

7 }

In lines1and2we begin the environment and make sure, that the formulæ don’t become to big. In lines 3 to 7 the first two reactants are written (lines 4 and 6) and connected with an arrow (line5).

OH

HBr

Br

8 \b r a n c h[ r i g h t = of s t a r t _ left , s t a r t _ center , y s h i f t =1 em ]{

9 \r e a c t a n t{\c h e m n a m e{\c h e m f i g[][ s c a l e =.8]{**6( - -( - SO _2 Cl ) - - -( -) -) }}{ t o s y l e c h l o r i d e }}

10 \a r r o w[ b e l o w ]{\ce{ NaOH }}{\ce{ Zn }}

11 \r e a c t a n t[ b e l o w ]{\c h e m f i g[][ s c a l e =.8]{**6( - -( - SO _2 Na ) - - -( -) -) }}

12 }

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myChemistryv1.5.1 13 Extensive Synthesis Examples In the following lines8 to 12, we create the second branch of the synthesis.

OH

HBr

Br

SO2Cl

tosyle chloride ZnNaOH

SO2Na

13 \b r a n c h[ r i g h t = of s t a r t _ center , s t a r t _ right , x s h i f t =3 em , y s h i f t = -10 em ]{

14 \r e a c t a n t{\c h e m n a m e{\c h e m f i g{ - [ : : 3 0 ] ( - [ : : 6 0 ] )

= _ [ : : - 6 0 ] - [ : : 6 0 ] COOH }}{3 - methyl -2 - b u t e n o i c acid }}

15 \a r r o w[ b e l o w ]{\ce{ CH 3 OH }}{}

16 \r e a c t a n t[ b e l o w ]{\c h e m f i g{ - [ : : 3 0 ] ( - [ : : 6 0 ] )

= _ [ : : - 6 0 ] - [ : : 6 0 ] CO _2 CH _3}}

17 }

18 \b r a n c h[ b e l o w = of s t a r t _ left , t a r g e t _ one , x s h i f t =5 em , y s h i f t

= -5 em ]{

19 \r e a c t a n t{\c h e m f i g[][ s c a l e =.8]{**6( - -( - SO

_ 2 - [ : 3 0 ] - [ : : - 6 0 ] = _ [ : : 6 0 ] ( - [ : : 6 0 ] ) -[:: -60]) - - -( -) -) }}

20 }

In lines 13 to 20 we create the third branch and the product of the first two branches.

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OH

HBr

Br

SO2Cl

tosyle chloride NaOH Zn

SO2Na

COOH 3-methyl-2-butenoic acid

CH3OH

CO2CH3 SO2

21 \b r a n c h[ b e l o w = of t a r g e t _ one , t a r g e t _ two , x s h i f t =6 em , y s h i f t

= -6 em ]{

22 \m e s o m e r i c{\c h e m f i g[][ s c a l e = . 8 ] { - [ : : 3 0 ] ( - [ : : 6 0 ] )

= ^ [ : : - 6 0 ] - [ : : 6 0 ] ( - [ : : 6 0 ] S ( = [ : : 9 0 ] O ) ( = [ : : - 9 0 ] O ) -[::0]**6( - - -( -) - - -) ) -[:: -60]( -[::0]) ( -[:: -120]) -[::60]( -[::60 ,.5 , , , w h i t e ]\o m i n u s) -[:: -60] CO _2 CH _3}}

23 \a r r o w[ below , , . 5 ] { } { }

24 \a r r o w[ below , ,.5]{\ce{ KOH }}{}

25 \r e a c t a n t[ b e l o w ]{\c h e m n a m e{\c h e m f i g{ -[:: -30]( -[:: -60])

= ^ [ : : 6 0 ] > [ : : - 6 0 ] ( - [ : : 9 0 , 1 . 2 ] )

- [ : : 3 0 , 1 . 2 ] ( - [ : : 1 2 0 , 1 . 2 ] ( - [ : : - 6 0 ] ) -[::0]) <:[:: -30]

COOH }}{\emph{ t r a n s } - c h r y s a n t h e m u m acid }}

26 }

In lines21 to 26 we create the last branch.

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CO2CH3 SO2

S

O O

CO2CH3













KOH

COOH trans-chrysanthemum acid

Finally, the different branches are merged, the second merging arrow gets a label and the environment is ended.

27 \m e r g e{ t a r g e t _ one }{ s t a r t _ left }{ s t a r t _ c e n t e r }

28 \m e r g e[\ce{ N a O C H 3}]{ t a r g e t _ two }{ t a r g e t _ one }{ s t a r t _ r i g h t }