Chem 211 Report

NiFe Hydrogenase
[NiFe] Hydrogenase
• Normally found in prokaryots
• Reversibly converts atomic hydrogen into
hydrogen gas
• Method of energy storage and utilization in
hydrogen-metabolizing microorganisms

2H2 ↔ 2H+ + e-
 • Bimetallic (Ni and Fe)
• Ni is attached to 4 Cys residues and Fe is
attached to 2 CO and CN
Active Site • Only the Ni involved in the reaction
• Has different conformations
• Ni3+ is present in the active form
• Square planar geometry
 [NiFe]
Hydrogenase
 x
S

y S
S Ni
z

NiS4
s pz
px py

E 2C4 C2 2C2’ 2C2” i 2S4 σh 2σv 2σd RR

s 4 0 0 2 0 0 0 4 2 0 A1g + B1g + Eu
px 4 0 0 2 0 0 0 4 2 0 A1g + B1g + Eu
py 4 0 0 -2 0 0 0 4 -2 0 A2g + B2g + Eu
pz 4 0 0 -2 0 0 0 -4 2 0 A2u + B2u + Eg
 E 2C4 C2 2C2’ 2C2” i 2S4 σh 2σv 2σd RR
s s1 s2 s3 s1 s2 s3 s2 s1 s1 s2 A1g + B1g + Eu
s4 s3 s4 s4 s3 s4
px x1 x2 x3 x1 x2 x3 x2 x1 x1 x2 A1g + B1g + Eu
x4 x3 x4 x4 x3 x4
NiS4
py y1 y2 y3 -y1 -y2 y3 y2 y1 -y1 -y2 A2g + B2g + Eu
y4 -y3 -y4 y4 -y3 -y4
pz z1 z2 z3 -z1 -z2 -z3 -z2 -z1 z1 z2 A2u + B2u + Eg
z4 -z3 -z4 -z4 z3 z4
 A1g = 4s1 + 4s2 + 4s3 + 4s4
= ½ (s1 + s2 + s3 + s4)

B1g = 4s1 - 4s2 + 4s3 - 4s4

NiS4 (s) = ½ (s1 - s2 + s3 - s4)

Eu = 2s1 – 2s3 ; 2s2 - 2s4

= 1/√2 (s1 – s3) ; 1/√2(s2 - s4)
 A1g = 4px1 + 4px2 + 4px3 + 4px4
= ½ (px1 + px2 + px3 + px4)

B1g = 4px1 - 4px2 + 4px3 - 4px4

NiS4 (px) = ½ (px1 - px2 + px3 - px4)

Eu = 2px1 – 2px3 ; 2px2 – 2px4

= 1/√2 (px1 – px3) ; 1/√2(px2 – px4)
 A2g = 4py1 + 4py2 + 4py3 + 4py4
= ½ (py1 + py2 + py3 + py4)

B2g = 4py1 – 4py2 + 4py3 – 4py4

NiS4 (py) = ½ (py1 – py2 + py3 – py4)

Eu = 2py1 – py3 ; 2py2 – 2py4

= 1/√2 (py1 – py3) ; 1/√2(py2 – py4)
 A2u = 4pz1 + 4pz2 + 4pz3 + 4pz4
= ½ (pz1 + pz2 + pz3 + pz4)

B2u = 4pz1 – 4pz2 + 4pz3 – 4pz4

NiS4 (pz) = ½ (pz1 – pz2 + pz3 – pz4)

Eg = 2pz1 – 2pz3 ; 2pz2 – 2pz4

= 1/√2 (pz1 – pz3) ; 1/√2(pz2 – pz4)
D4h

Eu A2u

B2g Eg A1g B1g

A1g
 A1g (s-s) B2g (py – xy) Eg (pz – xz/yz)*

A1g (px – x2+y2) B1g (px – x2 – y2) Eu (s – px/py)

Combined
Orbitals

A2u (pz - pz)

 A1g*
A2u*
Eu *
A1g*
B1g*

Eu A2u B2g*

Eg*
B2g Eg A1g B1g

A1g
Eg B1g B1g A2g B2u

B2g
Eu Eu Eu Eg
B1g
A1g A1g B2g A2u
A1g

Eu

A2u

A1g
Maleonitriledithiolate
• Commonly used as a dithiolate
model system
• Only the p orbitals are available for
binding for the S atom
 z

y
Ni
x

Ni(mnt)2-
px pz
py

E C2(z) C2(y) C2(x) i σ (xy) σ (xz) σ (yz) RR

px 4 -2 -2 0 0 2 2 -4 2B3u + B1g + B2g
py 4 -2 -2 0 0 -2 -2 4 2B3g + B1u + B2u
pz 4 2 2 0 0 2 2 4 2Ag + B1u + B2u
 z

y
Ni
x

Ni(mnt)2-
px pz
py

E C2(z) C2(y) C2(x) i σ (xy) σ (xz) σ (yz) RR

px x1 -x1 -x3 x3 -x3 x3 x1 -x1 2B3u + B1g + B2g
py y1 -y1 -y3 y3 y3 -y3 -y1 y1 2B3g + B1u + B2u
pz z1 z1 z3 z3 z3 z3 z1 z1 2Ag + B1u + B2u
 px
B3u = x1 –(-x1) – (-x3) + x3 –(-x3) + x3 + x1 – (-x1) = 4x1 + 4x3
B1g = x1 -x1 – (-x3) - x3 +(-x3) + x3 - x1 – (-x1) = 0
B2g = x1 –(-x1) + (-x3) - x3 +(-x3) - x3 + x1 – (-x1) = 4x1 - 4x3

py
B3g = y1 –(-y1) – (-y3) + y3 + y3 – (-y3) – (-y1) + y1 = 4y1 + 4y3
Ni(mnt)2-
B1u = y1 +(-y1) – (-y3) - y3 - y3 – (-y3) + (-y1) + y1 = 0
B2u = y1 –(-y1) + (-y3) - y3 - y3 + (-y3) – (-y1) + y1 = 4y1 - 4y3

pz
Ag = z1 + z1 + z3 + z3 + z3 + z3 + z1 + z1 = 4z1 + 4z3
B1u = z1 + z1 - z3 - z3 - z3 - z3 + z1 + z1 = 4z1 - 4z3
B2u = z1 - z1 + z3 - z3 - z3 + z3 - z1 + z1 = 0
 B3u = 2/√2 (x1 + x3) B2g = 1/√2 (x1 - x3)

B3g = 2/√2 (y1 + y3) B2u = 1/√2 (y1 – y3)

Ni(mnt)2-

Ag = 2/√2 (z1 + z3) B1u = 1/√2 (z1 - z3)

Ni(mnt)2-

B3u B2u B1u

B1g B2g B3g Ag Ag

Ag
 B3u (px - px)* B2g (px -xz )*

Ag (pz – z2) B1u (pz – pz)

Combined
Orbitals

B3g (py - yz) B2u (py - py)

 B3u*

B2u*
B2g*

B3g*
B3u B2u B1u
B1u*

B1g B2g B3g Ag Ag Ag*

Ag
Ag B2g B2u B1u

B1u
B3g B3u B3g Ag
B2g

B2u

B3u
A1g*
A2u*
B3u*
Eu*
A1g* B2u*

B1g* B2g*

B2g* B3g*

Eg* B1u*

Ag*

Eg Ag

B2g B1u

B1g B3g

A1g B2g

Eu B2u

A2u B3u
NiS4 Ni(mnt)2-
A1g
[NiFe] Hydrogenase
Reaction
• [NiFe] center is not the final electron acceptor in
the enzyme
• [FeS] clusters are also involved in the reaction
but their actual contribution is unknown
• [NiFe] center should be in a paramagnetic
(active) state for the reaction to occur
• H2 is taken by the [NiFe] center, and is split
heterolytically
• Electrons are transferred from [FeS] clusters until
it arrives at the distal [FeS] cluster
 Kampa, M. (2012). The electronic and geometric
structure of [NiFe] hydrogenase studied by theoretical
spectroscopy (Doctoral dissertation). Rheinischen
Friedrich-Wilhelms-Universitat Bonn.
Bruschi M, Zampella G, Fantucci P, De Gioia L. (2005).
DFT investigations of models related to the active site
of [NiFe] and [Fe] hydrogenases. Coordination
Chemistry Reviews 249: 1620-1640.
References Brazzolotto D, et al. (2016). Nickel-centered proton
reduction catalysis in a model of [NiFe] hydrogenase.
Nature Chemistry 8: 1054-1060

Bagyinka, C. (2014). How does the [NiFe] hydrogenase

enzyme work? International Journal of Hydrogen
Energy 39: 18521-18532