Bioinorganic Chemistry - 1 | Inorganic Chemistry PDF Download

Biological inorganic chemistry (bio-inorganic chemistry) is the study of inorganic elements as they are utilized in biology. The main focus is on metal ions, where we are interested in their interaction with biological ligands and important chemical properties they are able to exhibit and impart to an organism. These properties include ligand binding, catalysis, regulation, sensing defense and structural support. Interdisciplinary field of chemistry which largely focuses on the role of metal ions in the living system.

Special Ligand

Porphine: Derivatives porphyrin ring

Preparation

Properties

• Macrocyclic ligand
• Aromatic (Planar, π conjugated double bonds, follows Huckel Rule) (4n + 2 = 22, n = 5)
• If HCHO is replaced by PhCHO, then at meso position H is replaced by Ph.
• It is rigid due to delocalization of π electrons.
• Porphine molecule consists of unsubstituted tetrapyrrole connected by methylidyne
• (CH) bridges and these positions are labeled as α, β, γ,δ or 5, 10, 15, 20 positions.
• (Numbering of carbon only)
• The porphyrin ring can accept two hydrogen ions to form the dictation or donate two protons to form dianion. In  metalloporphyrin complexes the inner H atoms are  replaced as proton by dipositive metal ions, therefore metal free porphyrin ligand has –2 charges
• Spectral Properties
  • NMR → 3 signal
  • 8H → attached to pyrrole    (8.8 ppm)
  • 2H → inner (attach to N)    (–2 to –3 ppm) 
  • 4H → of methylene bridges (4.4 ppm)
  • IR →   N–H stretching frequency  (3300 cm-1  )
  • UV → Two broad bands are absorbed

Note

• The U-V visible spectrum of highly conjugated porphyrin ligands exhibit a strong absorption band at about 400 nm (Soret Band or B band) and several weaker bands (Q bands) at higher wavelengths (450 to 750 nm).
• Both these bands arise from transition of electron from porphyrin π HOMO to the π^∗ LUMO
• It is the nature of metal center and substituents on ring that affect the energies of these transitions and intensities of bands
• Metals ions (d^o, d¹, d², d³ 𝑜𝑟 d¹⁰) in which dπ orbitals are relatively low in energy and do not form M → L π bonds and have little effect on porphyrin π − 𝜋^∗ energy  gap  in absorption spectrum while metal ions 𝑑^𝑛 (n = 4–9) have filled dπ orbitals form metal to ligand π–bonds, this results in an increase in porphyrin π to π* energy gap & cause hypsochromic (blue shift)

Metalloporphyrin

• The size of the cavity in the center of porphyrin ring is ideal for accommodation of metal ions of first transition series
• If the metal ion is too small the ring becomes ruffled to allow closer approach of nitrogen atoms to the metal ion, while if the metal ion is too large, it cannot fit into the cavity and occupies position above the ring which also becomes domed.
• Order of metal fitting inside the ring, according to size.

Spectral changes

• N–H stretching frequency disappears
• 2 signal in NMR
• Soret band becomes broad and Q band disappears

Note:

(S0 → S2) is the soret bond
(S0 → S1) is the Q-band

An electronic transition to higher energy state S2 is strongly allowed whereas an electronic transition to the lower energy mixed state S1 is weakly allowed

color of metalloporphyrin (either oxidized or reduced form) is due to 𝜋 (HOMO) to 𝜋* (LUMO) transitions with in porphine ring

Soret peak or soret band is an intense peak in the blue wavelength region of the visible spectrum.

HEME GROUP is a porphyrin ring with iron atom at center. The oxidation state may be +2 or +3.

Heme A: R1 =  (-CH = CH2), R2 = ( C18H30OH)
Heme B: R1 = R2 = (−CH = CH2)
Heme C: R1 = R2 = (−CH(CH3)𝑆 − 𝑃𝑟𝑜𝑡𝑒𝑖𝑛)
Chlorohemp:    R1 =(- C(H) = O) R2 = (-CH = CH2 )

Note:

• Type A hemes are found in cytochrome a
• Type B hemes are found in hemoglobin, myoglobin, peroxidase and cytochrome b.
• Type C themes are found in cytochrome c
• Chloroheme are found in chlorocruorin

All the biological uses of heme groups are important, but the most important is the binding of dioxygen molecules.

Myoglobin

• It is a Fe containing protein , Molecular wt. = 17000 Dalton.
• Coordinates O2 reversibly and controls its concentration in tissue .
• It has a protein chain containing 153 amino acids residues folded about single heme

This restricts the access to the iron atom (by a second heme) and reduces the probability of formation of hematin-like (Fe III dimer)

• In Mb, four coordination sites of Fe are attached to Nitrogen atom of four pyrrole rings, and the 5th coordination site is attached to the nitrogen of the imidazole ring of a proximal histidine of globin protein. The sixth vacant site translating to the imidazole nitrogen  is  vacant  and reserved for dioxygen.
• Mb contains iron (II) in high spin state d6 (HS).
• Iron (II) has a radius of approximately 92 pm in a pseudo octahedral environment (square pyramidal arrangement when O2 is removed) and the iron atom will not fit into the hole of porphyrin ring and it lies 42 pm above the plane of the nitrogen atom in porphyrin ring.

• When dioxygen molecule binds to Fe (II) it becomes low spin (d⁶) → t_2g6 (maximum CFSE → 2.4 Δo). The ionic radius of low spin iron (II) with coordination number 6 is only 75 pm.
• 
• Reason for radius decrease: We know that in octahedral complex, eg orbitals point towards ligands ,if they contain electron, then they will repel the ligands along co- ordinate axes, thus effective radius of iron (II) will be greater in high spin, but in low spin state all the electron are in t_2g so ligands approaches more closely hence ionic radius decrease.

Recent X-rays studies have shown that oxygen is bound in a bent fashion with an Fe– O–O bond angle at 130°.

Note:

• When oxygen or carbon-monoxide binds to 6th position, iron becomes coplanar with the porphyrin and the resulting complex is diamagnetic.
• CO is a strong enough ligand to force spin pairing and result back 𝜋–bonding stabilizes the complex.

An alternative description is often considered in which bonding is in terms of low spin Fe(III) co-ordinated by superoxide (02)