Kinetics and thermodynamics of the reaction between the •OH radical and adenine – a theoretical investigation

TY - JOUR

T1 - Kinetics and thermodynamics of the reaction between the •OH radical and adenine – a theoretical investigation

AU - Milhøj, Birgitte Olai

AU - Sauer, Stephan P. A.

PY - 2015/6/18

Y1 - 2015/6/18

N2 - The accessibility of all possible reaction paths for the reaction between the nucleobase adenine and the •OH radical is investigated through quantum chemical calculations of barrier heights and rate constants at the ωB97X-D/6-311++G(2df,2pd) level with Eckart tunneling corrections. First the computational method is validated by considering the hydrogen abstraction from the heterocyclic N9 nitrogen in adenine as a test system. Geometries for all molecules in the reaction are optimized with four different DFT exchange-correlation functionals (B3LYP, BHandHLYP, M06-2X, and ωB97X-D), in combination with Pople and Dunning basis sets, all of which have been employed in similar investigations in the literature. Improved energies are obtained through single point calculations with CCSD(T) and the same basis sets, and reaction rate constants are calculated for all methods both without tunneling corrections and with the Wigner, Bell, and Eckart corrections. In comparison to CCSD(T)//BHandHLYP/aug-cc-pVTZ reference results, the ωB97X-D/6-311++G(2df,2pd) method combined with Eckart tunneling corrections provides a sensible compromise between accuracy and time. Using this method, all subreactions of the reaction between adenine and the •OH radical are investigated. The total rate constants for hydrogen abstraction and addition for adenine are predicted with this method to be 1.06 × 10-12 and 1.10 × 10-12 cm3 molecules-1 s-1, respectively. Abstractions of H61 and H62 contribute the most, while only addition to the C8 carbon is found to be of any significance, in contrast to previous claims that addition is the dominant reaction pathway. The overall rate constant for the complete reaction is found to be 2.17 × 10-12 cm3 molecules-1 s-1, which agrees exceptionally well with experimental results.

AB - The accessibility of all possible reaction paths for the reaction between the nucleobase adenine and the •OH radical is investigated through quantum chemical calculations of barrier heights and rate constants at the ωB97X-D/6-311++G(2df,2pd) level with Eckart tunneling corrections. First the computational method is validated by considering the hydrogen abstraction from the heterocyclic N9 nitrogen in adenine as a test system. Geometries for all molecules in the reaction are optimized with four different DFT exchange-correlation functionals (B3LYP, BHandHLYP, M06-2X, and ωB97X-D), in combination with Pople and Dunning basis sets, all of which have been employed in similar investigations in the literature. Improved energies are obtained through single point calculations with CCSD(T) and the same basis sets, and reaction rate constants are calculated for all methods both without tunneling corrections and with the Wigner, Bell, and Eckart corrections. In comparison to CCSD(T)//BHandHLYP/aug-cc-pVTZ reference results, the ωB97X-D/6-311++G(2df,2pd) method combined with Eckart tunneling corrections provides a sensible compromise between accuracy and time. Using this method, all subreactions of the reaction between adenine and the •OH radical are investigated. The total rate constants for hydrogen abstraction and addition for adenine are predicted with this method to be 1.06 × 10-12 and 1.10 × 10-12 cm3 molecules-1 s-1, respectively. Abstractions of H61 and H62 contribute the most, while only addition to the C8 carbon is found to be of any significance, in contrast to previous claims that addition is the dominant reaction pathway. The overall rate constant for the complete reaction is found to be 2.17 × 10-12 cm3 molecules-1 s-1, which agrees exceptionally well with experimental results.

KW - Faculty of Science

KW - Radiation Damage

KW - DNA

KW - Adenine

KW - OH radical

KW - Kinetics

KW - DFT calculations

KW - Thermodynamics

KW - Quantum Chemistry

KW - Computational Chemistry

KW - Coupled Cluster

U2 - 10.1021/acs.jpca.5b02711

DO - 10.1021/acs.jpca.5b02711

M3 - Journal article

C2 - 25985211

SN - 1089-5639

VL - 119

SP - 6516

EP - 6527

JO - Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory

JF - Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory

IS - 24

ER -