Diborane Structure and Bonding

 Structure and Bonding of Diborane (B₂H₆)

Boron is an electron deficient element. Due to its electron deficient character, the trivalent boron leads to dimerization to form diborane (B₂H₆). If we assumed that, the structure of diborane (B₂H₆) is similar to single bond structure of ethane (C₂H₆), then this assumption is rejected because single bond structure of ethane (C₂H₆) contains 14 electrons [(4+4 = 8 electrons from two carbon atoms) and (1x6 = 6 electrons from six hydrogen atoms)] but in diborane there are only 12 electrons [(3+3 = 6 electrons from two boron atoms) and (1x6 = 6 electrons from six hydrogen atoms)].

If we further assumed that, diborane (B₂H₆) molecule contains two one-electron bonds in its structure, to account for 12 electrons then diborane (B₂H₆) must be paramagnetic but actual fact that, the diborane (B₂H₆) molecule is diamagnetic. So, this assumption is also rejected.

Again, if we further assumed that, the diborane (B₂H₆) molecule contain two-electron three-centred bond (2e-3c bond), then the problem has been solved.

Electron diffraction study and other physical studies indicate the below structure for the molecule of diborane (B₂H₆).

Two B―H―B bridges joined the two B atoms. The B―H bridge bond length (1.33 A⁰) are longer than B―H terminal bond length (1.19 A⁰). The B―B distance is 1.77 A⁰. Specific heat measurement data confirm that the two bridging H-atoms are in a plane perpendicular to the rest of the molecule and prevent rotation between the two B-atoms.

Raman spectroscopy confirm that four terminal H-atoms are in a different environment from two bridging H-atoms. It is also confirmed by the fact that, methylation of diborane (B₂H₆) with B(CH₃)₃ produced tetramethyl diborane [(CH₃)₄B₂H₂], further attempt for methylation breaking the molecule into B(CH₃)₃ fragments. Four terminal H-atoms which are linked to B-atoms by normal covalent bonds, means two-electron two-centred bond (2e-2c) are replaced on methylation. The two bridging H-atoms, which are not methylated are connected through peculiar two-electron three-centred (2e-3c) bonds. The whole structure of diborane (B₂H₆) molecule can be explained as follows.

Electron configuration of boron is----

1s² 2s² 2p³

So, boron contains three electrons in its outermost shell. Two boron atoms of diborane (B₂H₆) molecule undergoes sp³ hybridisation. Two sp³ hybrid orbitals of each boron atoms overlap with the 1s orbitals of two terminal H-atoms.

The other two sp³ hybrid orbitals of one B atom overlap with two other sp³ hybrid orbitals of another B atom through the 1s orbitals of the two bridging H-atoms. As a result of these overlap, there formed total two B―H―B two-electron three-centred (2e-3c) bonds.

Such type of bond or molecular orbital has banana shape, so these bent bonds are called banana bonds.

Molecular orbital approach of diborane (B₂H₆) molecule---

Molecular orbital approach of diborane molecule begin with four roughly sp³ hybrid orbitals of each boron atoms and the 1s atomic orbitals of six hydrogen atoms. Two sp³ hybrid orbitals of each boron overlap with two 1s atomic orbitals of two hydrogen atoms and formed four terminal B―H bonds (covalent bonds, 2e-2c bonds). Due to this overlap four bonding and four anti bonding molecular orbitals are formed by four sp³ hybrid orbitals of two boron (two sp³ hybrid orbitals of each boron) and four 1s atomic orbitals of four hydrogen atoms. The four bonding molecular orbitals are occupied by eight electrons (four electrons from two boron atoms and four electrons from four hydrogen atoms). Remaining four sp³ hybrid orbital of two boron (two sp³ hybrid orbitals from each boron) and two 1s atomic orbitals of remaining two hydrogen atoms forms two sets of B―H―B bridge bonds (2e-3c bonds). Due to this overlap three sets of molecular orbitals are formed. One set of bonding molecular orbitals, one set of nonbonding molecular orbitals and one set of antibonding molecular orbitals. Remaining four electrons (two from two boron atoms and two from two hydrogen atoms) occupied the lowest energy bonding molecular orbitals.

The molecular orbital diagram of diborane (B₂H₆) molecule----

   

 BORON

Symbol --- B

Abundance --- 0.00086% in earth’s crust

Allotropes --- α-rhombohedral, β-rhombohedral, β-tetragonal

Physical state --- solid

Colour --- black brown

Discovery --- Gay-Lussac and Thenard (1808)

First isolation --- Humphry Davy

Atomic no --- 5

Atomic weight --- 10.81

Period --- 2

Group --- 13 or IIIA

Block --- p

Known isotopes --- ₅B⁸, ₅B⁹, ₅B¹⁰, ₅B¹¹, ₅B¹², ₅B¹³, ₅B¹⁴, ₅B¹⁵, ₅B¹⁶

Stable isotopes --- ₅B¹⁰, ₅B¹¹

Isotopic abundance --- ₅B¹⁰ (19.7%), ₅B¹¹ (80.3%)

Melting Point --- 2348 K (2075 ⁰C)

Boiling Point --- 4198 K (3925 ⁰C)

Density --- 2.45 g/cm³

Density --- 2.08 g/cm³ (liquid)

Electron configuration --- [He] 2s² 2p¹

Electrons per shell --- 2 (1 st shell), 3 (2 nd shell)

Oxidation state --- +3

Valance --- 3

Electronegativity --- 2.04

Electron affinity --- 26.4 KJ/mol

Ionisation energy --- 800 KJ/mol (1 st), 2426 KJ/mol (2 nd), 3659 KJ/mol (3 rd), 25000 KJ/mol (4 th)

Atomic radius --- 90 pm

Covalent radius --- 84 pm

Van der Waals radius --- 192 pm

Ionic radius (B³⁺) --- 27 pm

E⁰(V) --- -0.89 [B³⁺+3e = B(s)]

Crystal structure --- rhombohedral

Heat of fusion --- 50 KJ/mol

Heat of vaporization --- 507 KJ/mol

ΔH⁰_atomisation --- 565 KJ/mol

Molar heat capacity --- 11.08 J/(mol-K)

Specific heat --- 1030 J/ (Kg K)

Thermal expansion --- 5-7 μm/ (m K)

Thermal conductivity --- 27.4 W/ (m K)

Molar volume --- 4.39 x 10^-6

Speed of sound --- 16200 m/s

Magnetic type --- diamagnetic

Lattice angles --- 1.01334, 1.01334, 1.01334

Lattice constants --- 506 pm, 506 pm, 506 pm

Quantum numbers --- ²P_1/2

Neutron cross section --- 760

Neutron mass absorption --- 2.4

Electrical conductivity --- 0.0001 S/m

Electrical resistivity --- 10⁶ Ωm

Mohs hardness --- 9.5

Bulk modulus --- 320 GPa

Vickers hardness --- 49000 MPa

Nitrolim calcium cyanamide

 NITROLIM or CALCIUM CYANAMIDE

Nitrolim or calcium cyanamide is one of the most important fertilizers in the present day, contain about 20% of nitrogen. The formula of nitrolim or calcium cyanamide is CaNCN or CaCN₂ and it is represented as N≡C―N=Ca or [(Ca²⁺) (^-N=C=N^-)], it is a derivative of cyanamide, N≡C―NH₂. Nitrolim is grey powdered fertilizer.

When limestone means calcium oxide (CaO) and coke (C) heated in an electric furnace at about 2000⁰C, calcium carbide (CaC₂) is formed.

At 2000⁰C,   CaO + 3C ------> CaC₂ + CO

When this calcium carbide (CaC₂) treated with nitrogen (N₂), calcium cyanamide or nitrolim is formed, this reaction is highly exothermic.

CaC₂ + N₂ -------> CaNCN + C       ΔH = - 72.7 Kcal

Some important considerations during this manufacturing process are---

Temperature: Since the reaction is exothermic, so according to Le-chatelier principle, this reaction is highly favorable at low temperature, but this off set the activation energy of the reaction.

Activator: CaF₂ is used as an activator to overcome the above difficulty. At low temperature, CaF₂ activates the process of the reaction at a reasonably in speed.

Fixation: Nitrogen (N₂) fixation limit cannot pass over 85% limit.

Raw Materials

Raw materials required for the manufactured of nitrolim or calcium cyanamide are calcium carbide (CaC₂) [which is prepared from lime stone or calcium oxide (CaO) and coke (C)] and nitrogen (N₂).

Manufacturing Process

Powdered calcium carbide (CaC₂) along with CaF₂ (activator) are taken in the electric furnace fitted with pipe to get supply of nitrogen (N₂). In the electric furnace, the central carbon electrode is connected to high voltage mains. When the temperature of the electric furnace reaches to 900⁰C, highly exothermic reaction leading to the formation of the calcium cyanamide or nitrolim. Allowing the reaction to continue by its own liberated heat at about 40-60 hours for completion. During this process temperature is maintained at about 1000⁰C. After completion the reaction solid chank are taken out, and then disintegrated, powdered. Now first water is sprayed over the powdered to destroy any residual carbide and then spray oil. The grey powdered thus obtained is suitable for use.

Uses of Nitrolim or Calcium Cyanamide

Nitrolim or calcium cyanamide is used as a fertilizer due to its slow conversion into ammonia (NH₃) and nitrate (NO₃^-). So, it is a good fertilizer as its effects are prolonged nature.

Action of Calcium Cyanamide or Nitrolim as Fertilizer

In the soil, when finely powdered nitrolim is applied, it gets hydrolyzed to calcium hydroxide [Ca(OH)₂] and urea (H₂N―CO―NH₂). This hydrolysis process is catalysed by soil catalysis or microorganisms, which are present in the soil.

CaCN₂ + 4H₂O ------> Ca(OH)₂ + CO(NH₂)₂ + H₂O

Or, CaCN₂ + 3H₂O ------> Ca(OH)₂ + CO(NH₂)₂

The urea formed in this process, is then hydrolysed with the help of enzyme urease into ammonia. The ammonia is then converted to nitrates by oxidation with the help of enzyme of bacteria.

CO(NH₂)₂ + H₂O ------> CO + 2NH₃

2NH₃ + 3O₂ -----> 2NO₂^- . 2H₂O + 2H⁺ + Energy

2NO₂^- + O₂ -------> 2NO₃^- + Energy

Albendazole and Mebendazole

 Synthesis of Albendazole and Mebendazole

Albendazole

Albendazole is a benzimidazole derivative, widely used across the globe for the treatment of neurocysticerosis and echinococcosis and other intestinal nematode infection. Albendazole is found to be quite effective as a single dose treatment for ascariasis. Albendazole is also found in the treatment of infection caused by various worms such as roundworm, whipworm, threadworm and hookworm. A recommended multi dose therapy with albendazole is found to be very effective in the complete eradication of pinworm chlonorchiasis and capillariasis.

Synthesis of Albendazole

Albendazole is prepared by three steps----

Step – 1-----

In this step at first, 3-chloro-6-nitroacetanilide is reacted with propyl mercaptan, as a result 3-propylthio-6-nitroacetanilide is formed. The nitro group present at position 6 in 3-propylthio-6-nitroacetanilide is reduced by hydrogen in presence of palladium on carbon (Pd-C) as a catalyst. As a result, 4-(propylthio)-o-phenylenediamine is formed.

Step – 2-----

In this step, s-methylisothiourea sulfate is reacted with methylchloro formate in presence of NaOH at p^H 8. As a result, methyl-s-methylthiourea carboxylate is formed.

Step – 3------

In the final step, 4-(propylthio)-o-phenylenediamine formed in step–1 and methyl-s-methylthiourea carboxylate formed in step–2, are reacted. As a result, albendazole is formed.

Mebendazole

Mebendazole is also a benzimidazole derivative, widely used across the globe for the treatment of infection caused by hookworm, pinworm, roundworm, whipworm, guinea worm. Mebendazole is used for the treatment of infection caused by Trichuris trichiura, Enterobius vermicularis. Mebendazole is also used as an alternative medicine for Visceral Larva Migrans. Mebendazole is found very effective against nematodes and cestodes.

Synthesis of Mebendazole

Mebendazole is prepared by three steps---

Step – 1-----

In this step at first, 4-chlorobenzophenone reacted with mixed acid (HNO₃+H₂SO₄), as a result 4-chloro-3-nitrobenzophenone is formed. Now 4-chloro-3-nitrobenzophenone reacted with ammonia in presence of methanol at 125⁰C. As a result, 4-amino-3-nitrobenzophenone is produced. The nitro group present at position 3 in 4-amino-3-nitrobenzophenone is reduced by hydrogen in presence of palladium on carbon (Pd-C) as a catalyst. As a result, diaminobenzophenone is formed.

Step – 2-----

In this step, s-methylisothiourea sulfate reacted with methylchloro formate in presence of NaOH at p^H 8. As a result, methyl-s-methylthiourea carboxylate is produced.

Step – 3-----

In the final step, diaminobenzophenone formed in step-1 and methyl-s-methylthiourea carboxylate formed in step-2 are reacted. As a result, mebendazole is formed.

 

 NEOPRENE RUBBER

Neoprene rubber is a type of synthetic rubber which is made by several chloroprene monomer unit. Over a wide range of temperature neoprene maintains its flexibility and exhibits high chemical stability. In market neoprene rubber available in both form, such as solid form and latex form and used in a variety of application.

In the manufacture of neoprene rubber, the raw materials required are acetylene (C₂H₂) and hydrochloric acid (HCl). Acetylene (C₂H₂) is washed by concentrated sulfuric acid (H₂SO₄) for purification. In presence of cuprous chloride (CuCl) pure acetylene (C₂H₂) dimerised to vinyl acetylene (CH₂=CH―C≡CH). During this process some amount of divinyl acetylene is also produced, which is separate from vinyl acetylene immediately as an immiscible oil, because this divinyl acetylene violently active compound.

If pure acetylene gas rapidly sweeping through a catalyst solution [this catalyst solution contains concentrated solution of CuCl and NH₄Cl at ordinary temperature] then the formation of divinyl acetylene is avoided.

Now the mixture of vinyl acetylene with some amount of divinyl acetylene and some amount of unreacted acetylene is cooled. Due to cooling unreacted acetylene separated as a gas and the mixture of vinyl acetylene and divinyl acetylene are condensed. Now the vinyl acetylene in gas form is passed through a solution of CuCl and concentrated hydrochloric acid (HCl) at 30⁰C. As a result, chloroprene is formed which is the monomeric unit of neoprene rubber.

Now this chloroprene vapour which contain some amount of HCl gas is allowed to cool. As a result, chloroprene condenses to liquid form from vapour form and HCl gas separated which is reused. At ordinary temperature the emulsion polymerization of chloroprene gives neoprene. This emulsion polymerization process is very rapid and this polymerization process follows free radical mechanism pathway.

To increase the plasticity and stabilization of the polymer, tetraethyl thiuram disulphide is added after the polymerization process.

Neoprene can be vulcanized by the following ways----

By heating alone.

By used of ZnO and MgO as a vulcanizing agent.

By used of antimony sulphide.

Properties of Neoprene rubber

Chemically neoprene rubber very closely related to natural rubber, neoprene rubber has higher elongation percentage than natural rubber but tensile strength of neoprene rubber is lower than natural rubber. Neoprene rubber is soluble in polar solvent and it has good weathering resistance. Neoprene rubber is not attacked by alkali below 50% strength and it is resistance to vegetable and mineral oils and also resistance to oxidising agents such as oxygen and ozone and in high temperature.

Application of Neoprene rubber

Neoprene rubber has various uses such as, for making gaskets in oil refining plants, for making various standard engineering material, in conveyor belts, for printing rollers and for making rubber cements.

Hemerythrin

 Hemerythrin (H_r)

Hemerythrin (H_r) is a nonheme iron containing protein which is a dioxygen-binding pigment found in marine invertebrates, such as sipunculids (peanut marine worms). Hemerythrin (H_r) has some similarities with hemoglobin (H_b) and myoglobin (M_b), and also has some differences with hemoglobin (H_b) and myoglobin (M_b). Several oligomers of hemerythrin (H_r) are known, among them diiron subunit is common. Like both hemoglobin (H_b) and myoglobin (M_b), hemerythrin (H_r) also contains Fe (II) which binds oxygen molecule reversibly, but when hemerythrin (H_r) oxidized to methemerythrin Fe (III), it does not bind dioxygen. There are monomeric, dimeric, trimeric, and tetrameric forms in the tissues with lower molecular weight and octameric form with a molecular weight of about 108,000 which transport dioxygen in the blood. Hemoglobin (H_b) contains four chains, every chain is very similar to the single chain of myoglobin (M_b), and octameric form of hemerythrin (H_r) contains eight subunits very similar in quaternary structure to myohemerythrin. In case of binding of dioxygen there are major differences between hemoglobin (H_b) and hemerythrin (H_r). In hemerythrin (H_r), whether it is in monomeric form or in octameric form each dioxygen binding site contains two Fe (II) atoms, and the reaction takes place via an oxidation-reduction reaction to form Fe (III) and peroxide (O―O)^2-. Oxyhemerythrin is diamagnetic in nature with antiferromagnetically coupled Fe (III). In oxyhemerythrin, two Fe (III) atoms are in different environments proved by Mössbauer spectroscopy.

The active site of the reduced deoxy form of hemerythrin (H_r) contains two Fe (II) atoms, separated by roughly 3.25 – 3.5 A⁰. In the deoxy form of hemerythrin (H_r), the core is asymmetric, one Fe (II) atom have five coordination sites, this Fe (II) atom linked with two histidine side-chain residue, and bridged by one hydroxo group derived from water and aspartate and glutamate, whereas other Fe (II) atom have six coordination sites, this Fe (II) atom linked with three histidine side-chain residue, and bridged by one hydroxo group derived from water and aspartate and glutamate.

Deoxyhemerythrin

Peroxide ion [ (O―O)^2- ] means dioxygen binds at the vacant site [that Fe (II) atom, which have five coordination sites, so one site is vacant] of the deoxy form of hemerythrin (H_r) and the proton from the hydroxo bridge transferred to the bound O₂ (peroxide ion or dioxygen) as two electrons from the Fe₂⁴⁺ core are transferred to O₂ (peroxide ion or dioxygen), thus reducing it.

Oxyhemerythrin

So, in the oxyhemerythrin both Fe (III) atoms have six coordination sites. One Fe (III) atom linked with two histidine side-chain residues, one peroxide ion (O―O)^2-, and bridged by one oxygen atom derived from water and aspartate and glutamate, other Fe (III) atom linked with three histidine side-chain residues and bridged by one oxygen atom derived from water and aspartate and glutamate.

Binding of Dioxygen to Hemerythrin (H_r)

 

 Peptide Synthesis

Peptide

Peptides are polymers of amino acids containing from 2 to 50 individual units.

The individual amino acids are connected by amide linkages (which are commonly known as peptide linkages) from the amino group of one unit to the carboxyl group of another.

The main structural features of the peptides are that they have a free amino group on one end which is called the N-terminus and a free carboxylic group on the other which is called C-terminus.

They are named from N-terminus to C-terminus through the sequential listing of the names of amino acids. [ Peptides structures are always written with the N-terminal unit on the left and the C-terminal unit on the right]. This is done by replacing the ending -ine by -yl in the names of all amino acids excepting the C-terminus. Quite often the names of the peptides are abbreviated by using three letter abbreviations for amino acids.

H₃N⁺―CH₂―CONH―CH₂―COO^-

Glycylglycine (Gly.Gly)

H₃N⁺―CH₂―CONH―CH(CH₃)―CONH―CH(CH₂OH)―COO^-

Glycylalanylserine (Gly.Al.Ser)

Peptide synthesis

We know that peptides are polyamides and can be synthesized by the stepwise condensation in which the amino group of one amino acid is condensed with the carboxylic group of a second amino acid and then so on.

Let us consider the synthesis of a simple dipeptide glycylalanine (Gly-Ala).

Such a direct approach will give four different dipeptides. So, the problem of forming an amide linkage by direct treatment may be removed by the formation of acyl halide.

R―COOH + SOCl₂ ------> R―CO―Cl

R―CO―Cl + R'―NH₂ ------> R―CO―NH―R'

But the amino acid can not be converted into an acyl halide, polymerization would result.

The general method that has been developed to avoid these difficulties involves the use of protecting groups. Protecting groups have been developed for both the amino and carboxy groups.

Peptide synthesis using protecting Amino group:-

Among the many amino protecting groups that have been developed, we shall discuss only two, the benzyloxy carbonyl (carbobenzoxy) and the t-butoxy carbonyl group.

In organic synthesis, generally amino group is protected by acetylation or benzoylation. Neither method is suitable here because hydrolysis of the amide linkage to the protective groups also cleaves the peptide bonds.

a) Carbobenzoxy protection:---

b) The t-butoxy carbonyl group is introduced by treating the amino acid with t-butoxy carbonyl oximino phenyl acetonitrile (BOC-on):---

The t-butoxy carbonyl group is removed by treating the protected amino acid or peptide with anhydrous acid, such as CF₃COOH or HCl in CH₃COOH.

C-Terminus protecting agent:---

Protecting agent is benzyl alcohol:---

Preparation of glycylalanine:---

Recently it has been shown that step B can be avoided by treating the protected amino acid with the second molecule of free amino acid in presence of D.C.C (Dicyclohexyl carbodi imide) which is a dehydrating agent of choice for direct conversion of acids into esters and amides.

Protection of -NH₂ group:---

Condensation with glycine in presence of D.C.C---

Deprotection:---