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Computational Investigation of Hydrogen Abstraction from 2‐Aminoethanol by the 1,5‐Dideoxyribose‐5‐yl Radical: A Model Study of a Reaction Occurring in the Active Site of Ethanolamine Ammonia Lyase
Author(s) -
Semialjac Marija,
Schwarz Helmut
Publication year - 2004
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.200305773
Subject(s) - chemistry , conformational isomerism , hydrogen atom abstraction , moiety , enthalpy , protonation , hydrogen bond , computational chemistry , substrate (aquarium) , stereochemistry , hydrogen , medicinal chemistry , organic chemistry , thermodynamics , molecule , ion , physics , oceanography , geology
Hydrogen abstraction from 2‐aminoethanol by the 5′‐deoxyadenosyl radical, which is formed upon CoC bond homolysis in coenzyme B 12 , was investigated by theoretical means with employment of the DFT (B3LYP) and ab initio (MP2) approaches. As a model system for the 5′‐deoxyadenosyl moiety the computationally less demanding 1,5‐dideoxyribose was employed; two conformers, which differ in ring conformation (C2‐ and C3‐ endo ), were considered. If hydrogen is abstracted from “free” substrate by the C2‐ endo conformer of the 1,5‐dideoxyribose‐5‐yl radical, the activation enthalpy is 16.7 kcal mol −1 ; with the C3‐ endo counterpart, the value is 17.3 kcal mol −1 . These energetic requirements are slightly above the activation enthalpy limit (15 kcal mol −1 ) determined experimentally for the rate‐determining step of the sequence, that is, hydrogen delivery from 5′‐deoxyadenosine to the product radical. The activation enthalpy is lower when the substrate interacts with at least one amino acid from the active site. According to the computations, when a His model system partially protonates the substrate the activation enthalpy is 4.5 kcal mol −1 for the C3‐ endo conformer and 5.8 kcal mol −1 for the C2‐ endo counterpart. As hydrogen abstraction from the fully as well as the partially protonated substrate is preceded by the formation of quite stable encounter complexes, the actual activation barriers are around 13–15 kcal mol −1 . A synergistic interaction of 2‐aminoethanol with two amino acids where His partially protonates the NH 2 group and Asp partially deprotonates the OH group of the substrate results in an activation enthalpy of 12.4 kcal mol −1 for the C3‐ endo conformer and 13.2 kcal mol −1 for the C2‐ endo counterpart. However, if encounter complexes exist in the active site, the actual activation barriers are much higher (>25 kcal mol −1 ) than that reported for the rate‐determining step. These findings together with previous computations suggest that the energetics of the initial hydrogen abstraction decrease with an interaction of the substrate with only a protonating auxiliary, but for the rearrangement of the radical the synergistic effects of two auxiliaries are essential to pull the barrier below the limit of 15 kcal mol −1 .