Hi,
I am studying the mechanism of an enzyme catalyed reaction where a bond is broken between two glucopyranose molecules and a hydrogen (proton) is transferred from one of the residues (Amino acid No. 205), and also a covalent bond is formed between one glucose residues and an amino acid( Amino acid No. 120). I have generated the reactants and products as per the reaction and on calculating the TS, the TS energy also looks reasonable but the problem is that in the TS I want the proton to be somewhere between the donor and acceptor. However, the proton forms a complete hydrogen bond with the acceptor just like in the product state. Could any one tell me why am I getting such a TS? I am using GGA BLYP functionals and DNP 3.5 basis set.
I have also attached reactant, product, TS and TS_search.xtd file.
Thanks in advance for help.
Regards
BHARAT
I am studying the mechanism of an enzyme catalyed reaction where a bond is broken between two glucopyranose molecules and a hydrogen (proton) is transferred from one of the residues (Amino acid No. 205), and also a covalent bond is formed between one glucose residues and an amino acid( Amino acid No. 120). I have generated the reactants and products as per the reaction and on calculating the TS, the TS energy also looks reasonable but the problem is that in the TS I want the proton to be somewhere between the donor and acceptor. However, the proton forms a complete hydrogen bond with the acceptor just like in the product state. Could any one tell me why am I getting such a TS? I am using GGA BLYP functionals and DNP 3.5 basis set.
I have also attached reactant, product, TS and TS_search.xtd file.
Thanks in advance for help.
Regards
BHARAT
