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Inorganic Biochemistry notes
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INORGANIC BIOCHEMISTRYLECTURE 1
COORDINATION COMPOUNDS
− complex = a central metal atom surrounded by ligands
− ligand = any molecule or ion that can exist independently of the metal
− changing the metal → changing the functionality
− inner-sphere complex = the ligands are attached directly to the central metal → the ligands form
the primary coordination sphere of the complex and their number is called the coordination
number of the central metal ion
− outer-sphere complex = the product of the association of the complex cations with anionic ligands
− donation of the electron density from the ligands to the metals → ligands are generally electron
donors (Lewis bases) in bound formation with the central metal (Lewis acid)
− coordination number:
o size and oxidation state of the metal centre → large radii favour high coordination numbers
o steric interactions between the ligands: bulky ligands → low coordination number &
charged ligands → low coordination number due to electrostatic repulsion
o electronic interactions (way more important):
• left in a period → high coordination number due to the larger metal ion radius
• metals with few valence electrons → high coordination number since they can
accept more ligand electrons
• right in a period → low coordination number due to the smaller metal ion radius,
electron rich metals so they don’t want more ligand electrons
− complex geometry → see Figure
− formulas:
o [] = the metal + the groups
that are bound to the
metal atom (inner sphere)
o first the metal symbol, then
the ligands
o () = the groups that are not
bound to the metal
o cationic counterions go
before the complex and
anionic after
(Xc)n[central atom(ligands) n]c(Xc)n
− nomenclature:
o name first the positive
complex/counterion, and then the negative complex/counterion
o ligand names (alphabetical order) are followed by the name of the metal
o oxidation number (Roman) in parentheses or the overall complex charge (Arabic)
, o single atoms & homonuclear negative counterions: -ide
o complex negative counter ions: -ate
o bridging ligands: m-
o more ligands of 1 type: mono-, di-, tri-, tetra-, penta-, hexa-, etc.
o in case of confusion: bis-, tris-, tetrakis-, pentakis-, hexakis-, etc.
− ηx(2) = when a ligand is bound with x atoms to the metal (a double bond that can be donated to the
metal centre)
− μn = when a ligand is bound to x metal centers (bridging them)
− isomerism:
o cis = the ligands are next to each other & trans = the ligands are opposite of each other
o behave differently in chemical reactions
o different physical properties
o a triangular plane within the 3 same ligands → meridial/mer = intersecting with the metal
ion & facial/fac = not intersecting with the metal ion
− chirality: at least 4 different ligands, but also 2 bidentate ligands (exam: determine whether a
complex is chiral or not and why, don't need to know whether it's R or S)
− Berry pseudorotation = chirality in 5-membered complexes, their geometry is fluctional, not locked,
ligands can move around and the conformation changes very quickly, separation impossible
THERMODYNAMICS of COMPLEX FORMATION
− if something happens spontaneously,
it’s because it’s energetically
favourable (lowest energy) → doesn’t
mean it is happening fast
− finding out what’s the rate-
determining step → energetically most
difficult to pass, but very important
− catalysis:
o higher yields in less time
o better enantioselectivity →
less costs
− understanding biological processes:
o how does nature work so efficiently
o how can we mimic nature and what do we need for that
o can it be done in a simpler way, in a lab/factory
→ detailed knowledge of all reaction steps, intermediates, and reaction rates, particularly the rate-
determining step, is necessary
− reaction mechanisms information:
o type of reactants and products + their stoichiometry
o information about K – equilibria = [C]/[A][B], k – reaction rate and RDS
o influence of concentration, temperature, and pressure
o influence of steric and electronic effects, ligands (can be used to control reactions –
steer/block)
, o detection of reaction intermediates in the too fast reactions → NMR, UV-vis, IR, EPR or
theoretical models that help to explain the mechanism
− thermodynamics vs. kinetics:
o reaching the energetical barrier →
ΔGf, activation energy
o ΔG0 = –RT ln (Keq) = ΔH0 – TΔS0
o if the K value is high, it doesn't
mean the reaction is fast
o second activation energy → very
high, the thermodynamics doesn’t
change, but the kinetics is very
different
o Keq = kf/kb
o if you want ΔG0 to be negative, H
should be negative, S should be
positive (more disorder), lower the temperature
− Eyring plot:
o nothing can measure the transition step (too fast)
o determine the rate (k) first to determine the RDS
o measure rates k at different temperatures → plot ln (k/T) against 1/T → information about
activation enthalpy and entropy of the RDS
o reaction is generally favoured if ΔH < 0 and ΔS > 0
− reaction rates:
o rate = d[C]/dt = kobs[A][B]
o rate equation gives information about which components are involved in the RDS
o rate equations can't be used to draw conclusions about a reaction mechanism → the
solvent may play a role and the reaction steps may not be linked to the RDS
− techniques:
o inert behaviour (t1/2 > 1 min) → NMR, EPR, UV-vis, fluorescence, pH measurements for
slower reactions
o labile behaviour (t1/2 << 1 ms) → stop-flow measurements, rapid mixing, fast
spectroscopies, relaxation techniques for fast reactions
− complex formation:
o Kf = formation constant, indicates binding strength of the new ligand relative to the old one,
it does not say anything about the rate kf of substitution, don’t include water in the
formation const. equation (set to 1 by definition)
o addition of multiple ligands: stepwise formation constants, overall formation constant βn is
the product of the stepwise constants
o K value decreases since in every step we have less ligands to exchange and the equilibrium
can go back the more we add → if this doesn’t occur, major change in electronic or
geometrical structure
o Jahn-Teller effect → ligands are bound more strongly to the copper centre, but only the first
4
− chelate & macrocyclic effects:
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