138
M. M. Kabanda and K. P. Otukile
and the subsequent structures. The overall energetic values are however significantly
different; the RC to TS1 barrier is much lower than the energy required for the
formation of TS1-t from RC-t. In this reaction, the rate determining step corresponds
to TS3, which lies 41.689 kcal/mol above the free reactants. An analysis of the E
and G values suggests that the reaction is always endothermic and endergonic.
Therefore, the large barrier height and the endergenicity of the reaction implies that
it may be both kinetically and thermodynamically unfavourable pathway.
3.4 NH 2 CSNH 2 + ClCH 2 COOH Reaction Mechanism
in Water Solution
Geometry optimisations in solution were performed to investigate the geometric and
energetic differences that might be due to solute solvent interaction. The geometry
of the RC complex is water solution is similar to that in vacuo, however, the H-bond
lengths are such that the N10–H11···O2 is longer in water solution (1.960 Å) than in
vacuo (1.856 Å) and the O3–H6···S7 H-bond is shorter in in water solution (2.143 Å)
than in vacuo (2.154). The TS1 structure is also similar between the results in water
solution and in vacuo, characterised by the breaking of the C4–Cl5 bond and the
concomitant formation of the C4–S7 bond. The C4–Cl5 bond distance is shorter in
water solution (2.275 Å) than in vacuo (2.408 Å). The C4–S7 bond distance is longer
in water solution (2.379 Å) than in vacuo (2.164 Å). These results suggest that in
solution the transition state is closer to the reactant geometry than in vacuo. As with
the results in vacuo, the geometry features of IM1 obtained here are essentially the
same as those obtained for the reaction between NHCSHNH 2 and ClCH 2 COOH.
Consequently, all the subsequent reaction steps and geometries (second transition
state, second intermediate, third transition state and products) are structurally and
energetically similar for the two mechanisms in water solution and therefore are not
discussed further in this work.
In the presence of the bulk solvent (Table 1), the reaction barrier is reduced from
30.880 to 18.231 kcal/mol. The determining factor for barrier reduction could be the
formation of H-bond networks involving the transition state structure and the solvent molecules [48–53]. Interestingly, the relative stability of the third transition state
structure does not change significantly between the results in vacuo (41.689 kcal/mol)
and the results in water solution (41.968 kcal/mol). Moreover, the result suggests that,
as it is in vacuo, the step IM2 → TS3 is the energetically most costly step, and it
involves the H11 proton transfer from N10 to O3 and the subsequent formation
of the tetrahedral C2 carbon atom. The overall reaction is endothermic and endergonic, which means that the reaction of thiourea and chloroacetic acid may not be
thermodynamically preferred in the presence of bulk water solvent.
M. M. Kabanda and K. P. Otukile
and the subsequent structures. The overall energetic values are however significantly
different; the RC to TS1 barrier is much lower than the energy required for the
formation of TS1-t from RC-t. In this reaction, the rate determining step corresponds
to TS3, which lies 41.689 kcal/mol above the free reactants. An analysis of the E
and G values suggests that the reaction is always endothermic and endergonic.
Therefore, the large barrier height and the endergenicity of the reaction implies that
it may be both kinetically and thermodynamically unfavourable pathway.
3.4 NH 2 CSNH 2 + ClCH 2 COOH Reaction Mechanism
in Water Solution
Geometry optimisations in solution were performed to investigate the geometric and
energetic differences that might be due to solute solvent interaction. The geometry
of the RC complex is water solution is similar to that in vacuo, however, the H-bond
lengths are such that the N10–H11···O2 is longer in water solution (1.960 Å) than in
vacuo (1.856 Å) and the O3–H6···S7 H-bond is shorter in in water solution (2.143 Å)
than in vacuo (2.154). The TS1 structure is also similar between the results in water
solution and in vacuo, characterised by the breaking of the C4–Cl5 bond and the
concomitant formation of the C4–S7 bond. The C4–Cl5 bond distance is shorter in
water solution (2.275 Å) than in vacuo (2.408 Å). The C4–S7 bond distance is longer
in water solution (2.379 Å) than in vacuo (2.164 Å). These results suggest that in
solution the transition state is closer to the reactant geometry than in vacuo. As with
the results in vacuo, the geometry features of IM1 obtained here are essentially the
same as those obtained for the reaction between NHCSHNH 2 and ClCH 2 COOH.
Consequently, all the subsequent reaction steps and geometries (second transition
state, second intermediate, third transition state and products) are structurally and
energetically similar for the two mechanisms in water solution and therefore are not
discussed further in this work.
In the presence of the bulk solvent (Table 1), the reaction barrier is reduced from
30.880 to 18.231 kcal/mol. The determining factor for barrier reduction could be the
formation of H-bond networks involving the transition state structure and the solvent molecules [48–53]. Interestingly, the relative stability of the third transition state
structure does not change significantly between the results in vacuo (41.689 kcal/mol)
and the results in water solution (41.968 kcal/mol). Moreover, the result suggests that,
as it is in vacuo, the step IM2 → TS3 is the energetically most costly step, and it
involves the H11 proton transfer from N10 to O3 and the subsequent formation
of the tetrahedral C2 carbon atom. The overall reaction is endothermic and endergonic, which means that the reaction of thiourea and chloroacetic acid may not be
thermodynamically preferred in the presence of bulk water solvent.