title: Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer.
abstract: The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between nonreactive and reactive conformations leading to the photolesion. Moreover, our nonadiabatic simulations show that most of the photoexcited reactive conformations return to standard B-DNA conformations after an ultrafast nonradiative decay to the ground state. This work highlights the importance of dynamical effects (free energy, excited-state dynamics) for the study of photochemical reactions in biological systems.
authors: Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid , ES-28049 Madrid, Spain.|Molecular Modelling Group, Center of Molecular Biology Severo Ochoa (CSIC-UAM) , ES-28049 Madrid, Spain.
authors: Jesús I
authors: JI
authors: Mendieta-Moreno
authors: Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid , ES-28049 Madrid, Spain.
authors: Daniel G
authors: DG
authors: Trabada
authors: Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid , ES-28049 Madrid, Spain.|Molecular Modelling Group, Center of Molecular Biology Severo Ochoa (CSIC-UAM) , ES-28049 Madrid, Spain.|Departamento de Biotecnología, Universidad Francisco de Vitoria , ctra. Pozuelo-Majadahonda, km 1,800, 28223 Pozuelo de Alarcón, Madrid, Spain.
authors: Jesús
authors: J
authors: Mendieta
authors: Department of Physics, West Virginia University , Morgantown, West Virginia 26506-6315, United States.
authors: James P
authors: JP
authors: Lewis
authors: Molecular Modelling Group, Center of Molecular Biology Severo Ochoa (CSIC-UAM) , ES-28049 Madrid, Spain.
authors: Paulino
authors: P
authors: Gómez-Puertas
authors: Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid , ES-28049 Madrid, Spain.
authors: José
authors: J
authors: Ortega
mesh_terms: D003503:Cyclobutanes / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D055668:Photochemical Processes; D011740:Pyrimidine Dimers / Q000737:chemistry*; D011789:Quantum Theory
chemical_list: D003503:Cyclobutanes; D011740:Pyrimidine Dimers