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8/4/2019 Handout Lecture May12
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Gr
o u p 5 AEl e m e n t s
-
n s 2 p 3 v al e n c e e l e c t r on c onf i g u
r a t i on
N
N onm e
t al s
P A s
M e t al o
i d
S b
M e t al s
Bi
S e l e c t e d
ph y s i c al pr o p e r t i e s , s o ur c e s ,
an d m e t h o d s of pr e p ar a t i on-T a b l e
1 9 .1
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Gr o u p 5 A e l e m
e n t s c anf or mm ol e c ul e s i n v ol vi n g
3 , 5 , or 6 c o v al e n t b on d s t o t h e Gr o u p 5 A a t om
MX
3 : NH
3 ,P H
3 , NF
3 ,A s Cl 3 ,A s F 3
c on t ai n al on e p ai r of e l e c t r on s ( L e wi s b a s e )
MX
5 : P F 5 ,P Cl 5 , S b Cl 5 ,A s F 5
t h e s m al l a t omi c s i z e of ni t r o g e nm ak e s i t d i f f i c ul t t o
a c c omm o d a t e 5 c o v al e n t b
on d s ( pr e d i c
t i on of
V S EP Rm o d e
l )
MX
6 :
MX
5 + X-
MX
6 -
e . g .P F 5 + F - P F
6 - ( ph o s ph o
r o u s h e x af l u or i d e ani on )
A s F 5 + F - A s F 6
-
( Ar s e n
i c h e x af l u or i d e ani on )
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MX
3
an d MX
5 a
r e v e r y s t r on g e l e c t r on a c c e p t or s
H e e g e r ,M
a c Di ar mi d ,
S h i r ak a w a ( 1 9 7 7 )
2 0 0 0
N o b e l P r i z e
i n Ch e mi s t r y
σRT =
1 0 -1 2
s / c m
σRT =
1 0 4
s / c m
m e t al l i c p ol y
m e r s ! ! +
A s F 6
-
A s F 6
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Th e C
h e mi s t r y of Ni t r o g e
n
• El e m e n t al ni t r o g e n e xi s t s a s N2 m ol e c ul e
s
N
N ,
2 π
b on d s
9 4 1 k J / m ol
b on d e n e r g y
• O
t h e r e l e m e n t s i n Gr o u p 5 A d on o t f or m
π b on d s ,
b u t
e xi s t a s a g gr e g a t e s wi t h s i n gl e b on d s ( e . g .P 4 ,A s 4 ,
e t c . )
• Th e s t r on g N
N b on d m ak e s N2 v e r y u
nr e a c t i v e
t o w ar d m o s t o t h e r s u b s t an c e s ( i n e r t a t m o s ph e r e )
• M
an y N- c on t ai ni n g c om p o u
n d s d e c om p o s e
e x o t h e r m i c a l l y t o
N2 ,r e l e a s i n g e n e r g y
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Ex a
m pl e s :
N2 O ( g ) N2
( g ) + 1 / 2 O2 ( g )
∆ H=- 8
2 k J / m ol
N2 H4 ( g ) N
2 ( g ) + 2 H2 ( g )
∆ H=- 9
5 k J / m ol
( h y d r az i n e )
4 C 3 H 5 N 3 O 9 (
l ) 6 N2 ( g ) +
1 2 C O2 ( g )
( Ni t r o gl y c e r i n e )
+ 1 0 H2
O ( g ) + O2 ( g ) + En e r g y !
4 m o l e s o f l i q u i d 2
9 m o l e s o f g a s s e s w
i t h
l a
r g e b o n d e n er
g i e s !
2 C 7 H 5 N 3 O 6 (
s ) 1 2 C O ( g
) + 5 H2 ( g ) + 3 N2 ( g )
( t r i ni t r o t ol u e n e ,T
NT )
+ 2 C ( s )
+ En e r g y !
2 m o l e s o f s o l i d 2
0 m o l e
s o f g a s s e s +
e n er g
y !
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S om eI m p or t an
t R e a c t i on
s
1 . Ni t r o g
e ni s “ f i x e d ” i n d
u s t r i a l l yi n t h e H a b e r pr o c e s s un d e r h i gh
t e m p e
r a t ur e a n d h e a t ,
a n d wi t h a c a t a l y s t ( s e e F i g .1 9 . 6 ) :
2 .F ur t h e r i n d u s t r i a l r e a c
t i on s c on v e r t NH 3 t o N O , N O2 ,
a n d H N O 3 ,
e . g . ( O s t w a l d pr o c e s s ) :
4 NH 3 ( g ) +
5 O2 ( g )
4 N O ( g ) + 6 H2 O ( g )
n i t r i c o x i d e
3 . N O c a n a l s o b e m a d e
d i r e c t l yf r om N2
a t h i gh t e m p e r a t ur e s ( l i k e i n
a ni n t e r n
a l c om b u s t i on e
n gi n e ) :
N2 ( g ) + O2
( g )
2 N O ( g )
N2 ( g ) +
3 H2 ( g )
2 NH 3 ( g )
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H a b er P r o
c e s s
O
s t w al d P r
o c e s s
F
i g .1 9 . 6
F i g .1 9 .1 0
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AF ew
I m p or t an t C om p o
un d s of Ni t r o g en
1 .Amm oni a , NH
3 .F i r s t
s u b s t a n c e f or m e d wh e n a t m o s p
h e r i c N2 i s
u s e d t om a k e N- c on t a i ni n g c om p o un d
s .Ann u a l m ul t i mi l l i on- t on
pr o d u c t i onf or u s e i nf
e r t i l i z e r s , e x pl o s i v e s ,r a y on , a n d
p ol ym e r s
s u c h a
s n yl on , ur e a -f or m a l d e h y d e r e s i n s , a n d a c r yl i c s .
2 .H y d r az i n e , N2 H4 . U s e d i nr o c k e t s a s a pr o p e l l a n t , a n d a s a s t a r t i n g
p oi n t f or a n t i t u b e r c ul i n d r u g s .
3 . Ni t r i c
oxi d e ( N O ) ,ni t r o g e n d i oxi d e ( N O2 ) , an d ni t r
i c a c i d ( H N O 3 ) .
U s e d i nf e r t i l i z e r m a n uf a c t ur e ,n yl on pr o d u c t i on ,m e t a
l e t c h i n g ,
e x pl o s
i v e s i n d u s t r y , a n d b i ol o gi c a l s i g
n a l i n g , a m on g o
t h e r t h i n g s .
4 .Ami n o a c i d s ,H
3 N+ - C
H ( R ) - C O O- ( R
= on e of 2 0 d i f f e r e n t or g a ni c
gr o u p s ) . O c c ur i n e v e r
y or g a ni s m , b o t
h f r e e a n d l i nk e d t o g e t h e r i n t o
pr o t e i n s .E s s e n t i a l t o g
r o w t h a n d f un c t i on of a l l c e l l s .
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Ni t r i
c Oxi d eM O
Di a gr am
r e a
d h i gh l i gh t on
p a g e
8 8 1
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Ni t r o g en Oxi d e
s ( s e e
T a b l e
1 9 .2 )
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S e e F i g
1 9 .1 1
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T h eNi t r o g e
n C y cl e
• Al l l i f e r e q ui r e s ni t r o g
e n c om p o un d s , e . g . pr o t e i n s a n d
n u c l e i c a c i d s .
• Ai r , wh i c h i s 7 9 % N2 g a s ,i s t h e m a j or
r e s e r v oi r of ni t r o g e n .
• M o s t o
r g a ni s m s c a nn o
t u s e ni t r o g e ni n
t h i s f or m .
• P l a n t s
m u s t s e c ur e t h e i r ni t r o g e ni n" f i x e d " f or m ,i . e . ,i n c or p or a t e d i n
c om p o u
n d s s u c h a s :
ni t r a t e i on
s ( N O 3 - )
a mm oni a
( NH 3 )
ur e a ( NH2
) 2 C O
• Ani m a
l s s e c ur e t h e i r n
i t r o g e n c om p o u
n d s f r om pl a n t s
( or a ni m a l s t h a t
h a v e f e d
on pl a n t s ) .
• F o ur p
r o c e s s e s a r e i n v ol v e d i n t h e c y c
l i n g of ni t r o g e n
t h r o u gh t h e
Bi o s ph e
r e :
n i t r o g e n f
i x a t i o n
d e c a y
n i t r i f i c a t i o n
d e n i t r i f i c a
t i o n
• Mi c r o or g a ni s m s pl a y a m a j or r ol e i n e a c h of t h e s e .
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T h
eNi t r o g en C y cl e
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Ni t r o g e nF
i x a t i on
N2 i s q ui t e i n e r t .T o a c t i v a t e i t r e q ui r e s
s u b s t a n t i a l e n e r g y .
T h r e e pr o c e s s e s a r e r e s
p on s i b l e f or m o
s t of t h e ni t r o g e
nf i x a t i oni n t h e
b i o s ph e r e :
- a t m o s ph e r i c f i x a t i on b yl i gh t ni n g
- b
i ol o gi c a l f i x a t i o
n b ymi c r o b e s
-i n d u s t r i a l f i x a t i on ( H a b e r pr o c e s s )
A t m o s
ph e r i c F i x a t i on
• T h e e n or m o u s e n e r g y of l i gh t ni n g b r
e a k s ni t r o g e nm
ol e c ul e s a n d
e n a b l e s t h e i r a t om s t o c om b i n e wi t h ox
y g e ni n t h e a i r ,
f or mi n g
ni t r o g e
n oxi d e s .
• T h e s e d i s s ol v e i nr a i n a n d a r e c a r r i e d
t o t h e e a r t h .
• A t m o s ph e r i c ni t r o g e nf i x a t i on pr o b a b l y c on t r i b u t e s 5 - 8 % of t h e t o t a l
ni t r o g e
nf i x e d .
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Ni t
r o g e nF i x a t i on ( c on t )
Bi ol o gi c al F i x a t i on
• Onl y c e r t a i n b a c t e r i a h a v e t h e a b i l i t y
t of i xni t r o g e n .
• Bi ol o gi c a l ni t r o g e nf i x a t i onr e q ui r e s a c om pl e x s e t of
e nz ym e s a n d
a h u g e
e x p e n d i t ur e of A
T P .
• M a n y
l i v e i n a s ym b i o t i c r e l a t i on s h i p
wi t h pl a n t s of t h e l e g um e
f a mi l y ( e . g . , s o y b e a n s ,
a l f a l f a ) .
• S om e
ni t r o g e n-f i xi n g
b a c t e r i a l i v e f r e
e i n t h e s oi l .
• Al t h o
u gh t h e f i r s t s t a b l e pr o d u c t of t h
e pr o c e s s i s a mm oni a , t h i s i s
q ui c k l y
i n c or p or a t e d i n
t o pr o t e i n a n d o t h e r or g a ni c ni t r
o g e n
c om p o un d s .
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Ni t r o g e nF i x a t i on ( c on t )
I n d u s t r i al F i x a t i on ( t h
e H a b e r pr o c e s s )
• Un d e r
gr e a t pr e s s ur e ,
a t a t e m p e r a t ur e
of 6 0 0 ° C , a n d wi t h t h e u s e of a
c a t a l y s t
, a t m o s ph e r i c ni t r o g e n a n d h y d r
o g e n ( u s u a l l y d e r i v e d f r om
n a t ur a l
g a s or p e t r ol e um
) c a n b e c om b i n e d t of or m a mm
oni a ( NH 3 ) .
• Amm oni a c a n b e u s e d
d i r e c t l y a s f e r t i l i z e r , b u t m o s t o
f i t s i s f ur t h e r
pr o c e s s e d t o ur e a a n d a mm oni umni t r a t
e ( NH4 N O 3 ) .
D e c a
y
• T h e pr o t e i n s m a d e b y
pl a n t s e n t e r a n d
p a s s t h r o u gh f o
o d w e b s j u s t a s
c a r b oh y
d r a t e s d o .
• M e t a b
ol i s m pr o d u c e s
o t h e r or g a ni c ni t r o g e n c om p o un
d s t h a t r e t ur n t o
t h e e n vi r onm e n t , c h i e f l yi n e x c r e t i on s ( e . g .m a n ur e ! ) .
• T h e f i n a l b e n e f i c i a r i e s of t h e s e m a t e r i
a l s a r e mi c r o or g
a ni s m s of
d e c a y .T h e y b r e a k d o wn t h e m ol e c ul e s
i n e x c r e t i on s a n
d d e a d
or g a ni s m s i n t o a mm oni a .
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Ni t r i f i c a
t i on
• Amm oni a c a n b e t a k e
n u p d i r e c t l y b y
pl a n t s - u s u a l l y
t h r o u gh t h e i r
r o o t s .H
o w e v e r ,m o s t o
f t h e a mm oni a p
r o d u c e d b y d e c a yi s c on v e r t e d
i n t oni t r a t e s ( N O 3 - ) a n d
ni t r i t e s ( N O2 - ) b y b a c t e r i a .
• S u c h b a c t e r i a a r e c a l l e d n i t r i f y i n g b a c t e r i a .T h r o u gh t h e i r a c t i vi t i e s
( wh i c h
s u p pl y t h e m wi t h a l l t h e i r e n e r g
yn e e d s ) ,ni t r o g
e ni s m a d e
a v a i l a b
l e t o t h e r o o t s of pl a n t s .
D e ni t r i f i c a t i on
• T h e t h r e e pr o c e s s e s a b o v e r e m o v e N2
f r om t h e a t m o s ph e r e a n d p a s s
i t t h r o u
gh e c o s y s t e m s .
• D e n i t r i f i c a t i o nr e d u c e s ni t r a t e s t o N2 , t h u s r e pl e ni s h i n g t h e
a t m o s p
h e r e .
• On c e
a g a i n , b a c t e r i a a
r e t h e a g e n t s .T h e yl i v e d e e pi n
s oi l a n d i n
a q u a t i c
s e d i m e n t s wh e r e c on d i t i on s a r e
a n a e r o b i c .T h e y u s e ni t r a t e s a s
a n a l t e r
n a t i v e t o ox y g e nf or t h e f i n a l e l e c t r on a c c e p t or i n t h e i r
r e s pi r a t i on .
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M e c h a ni s m pr o p o s e d f or r e d u c t i on of ni t r i t e b y t h e h e m e c d 1 - c on t a i ni n g
ni t r i t e r e d u c t a s e s b a s e d
on t h e X-r a y s t r u c t ur e of t h e T .
p a n t o s p h er a
e nz ym e .
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T h
eNi t r o g en C y cl e
I n d u s t r i a
l
F i x a t i on
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Ar e t h e d e ni t r i f i e r
s k e e pi n g u
p ?
• A gr i c ul t ur e m a yn o w b e r e s p on s i b l e f or on e -h al f of t h e ni t r o g e n
f i x a t i on
on e a r t h t h r o u g
h
- t h e u s e of f e r t i l i z e r s pr o d u c e d
b yi n d u s t r i a l f i x
a t i on
- t h e gr o wi n g of l e g um e s l i k e s o y b e a n s a n d a l f a l f a .
• T h i s h
a s a m e a s ur a b l e
i m p a c t on t h e n
a t ur a l ni t r o g e n c y c l e .
• Ar e t h
e d e ni t r i f i e r s k e e pi n g t h e ni t r o g e n c y c l e i n b a l a n c e ? P r o b a b l y
n o t .T h e r e a r e s om e c l e a r e x a m pl e s of n
i t r o g e n e nr i c h m
e n t i n
e c o s y s t e m s .
• On e e x a m pl e : " b l o om s " of a l g a e i nl a k e s a n d r i v e r s a r
e b e i n gr e p or t e d
a s ni t r o g e nf e r t i l i z e r s l e
a c h f r om t h e s oi l of a d j a c e n t f a r
m s ( a n d l a wn s )
• T a l e n t e d s c i e n t i s t s of a l l t y p e s ( b i ol o g
i s t s , c h e mi s t s , g
e ol o gi s t s ,
d o c t or s , a t m o s ph e r i c s c i e n t i s t s , e n gi n e e
r s , e t c . ) a r e n e e d
e d t o
un d e r s t a n d t h e s e pr o c e s
s e s a n d h e l p g ui d e u s t o a b e t t e r b a l a n c e .
Th e s e
mi gh t b e y o
ur j o b s ! ! !