# Challenges in Simulating Light-Induced Processes in DNA

^{*}

## Abstract

**:**

## 1. Introduction

## 2. Potential Energy Surfaces

## 3. Excitation Process

## 4. Nuclear Dynamics

## 5. Probe Processes

## 6. Analysis of the Results

## 7. Conclusions

## Acknowledgments

## Author Contributions

## Conflicts of Interest

## Abbreviations

MDPI | Multidisciplinary Digital Publishing Institute |

DOAJ | directory of open access journals |

DNA | deoxyribonucleic acid |

UV | ultraviolet |

DFT | density functional theory |

DFTB | density functional tight binding |

TDDFT | time-dependent density functional theory |

CC2 | approximate coupled cluster |

ADC | algebraic diagrammatic construction |

CIS(D) | perturbatively-corrected configuration interaction with single excitations |

CASSCF | complete active space self-consistent field |

CASPT2 | complete active space perturbation theory of second order |

MRCI | multireference configuration interaction |

QM | quantum mechanics |

MM | molecular mechanics |

DMRG | density matrix renormalization group |

FCIQMC | full configuration interaction quantum Monte Carlo |

MCTDH | multi-configurational time-dependent Hartree |

SHARC | surface hopping including arbitrary couplings |

## References

- Görner, H. New trends in photobiology: Photochemistry of DNA and related biomolecules: Quantum yields and consequences of photoionization. J. Photochem. Photobiol. B
**1994**, 26, 117–139. [Google Scholar] [CrossRef] - Shukla, M.K.; Leszczynski, J. Radiation Induced Molecular Phenomena in Nucleic Acids; Springer: Berlin, Germany, 2008. [Google Scholar]
- Crespo-Hernández, C.E.; Cohen, B.; Hare, P.M.; Kohler, B. Ultrafast Excited-State Dynamics in Nucleic Acids. Chem. Rev.
**2004**, 104, 1977–2020. [Google Scholar] [CrossRef] [PubMed] - Middleton, C.T.; de La Harpe, K.; Su, C.; Law, Y.K.; Crespo-Hernández, C.E.; Kohler, B. DNA Excited-State Dynamics: From Single Bases to the Double Helix. Ann. Rev. Phys. Chem.
**2009**, 60, 217–239. [Google Scholar] [CrossRef] [PubMed] - Barbatti, M.; Borin, A.C.; Ullrich, S. (Eds.) Photoinduced Phenomena in Nucleic Acids; Topics in Current Chemistry; Springer: Berlin/Heidelberg, Germany, 2015.
- Improta, R.; Santoro, F.; Blancafort, L. Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases. Chem. Rev.
**2016**, 116, 3540–3593. [Google Scholar] [CrossRef] [PubMed] - Sancar, A. Mechanisms of DNA Repair by Photolyase and Excision Nuclease (Nobel lecture). Angew. Chem. Int. Ed.
**2016**, 55, 8502–8527. [Google Scholar] [CrossRef] [PubMed] - Crespo-Hernández, C.E.; Martínez-Fernández, L.; Rauer, C.; Reichardt, C.; Mai, S.; Pollum, M.; Marquetand, P.; González, L.; Corral, I. Electronic and Structural Elements That Regulate the Excited-State Dynamics in Purine Nucleobase Derivatives. J. Am. Chem. Soc.
**2015**, 137, 4368–4381. [Google Scholar] [CrossRef] [PubMed] - Mai, S.; Pollum, M.; Martínez-Fernández, L.; Dunn, N.; Marquetand, P.; Corral, I.; Crespo-Hernández, C.E.; González, L. The Origin of Efficient Triplet State Population in Sulfur-Substituted Nucleobases. Nat. Commun.
**2016**, 7, 13077. [Google Scholar] [CrossRef] [PubMed] - Rauer, C.; Nogueira, J.J.; Marquetand, P.; González, L. Cyclobutane Thymine Photodimerization Mechanism Revealed by Nonadiabatic Molecular Dynamics. J. Am. Chem. Soc.
**2016**. [Google Scholar] [CrossRef] [PubMed] - Cohen, A.J.; Mori-Sánchez, P.; Yang, W. Challenges for Density Functional Theory. Chem. Rev.
**2012**, 112, 289–320. [Google Scholar] [CrossRef] [PubMed] - Lu, Y.; Lan, Z.; Thiel, W. Computational Modeling of Photoexcitation in DNA Single and Double Strands. In Photoinduced Phenomena in Nucleic Acids II; Topics in Current Chemistry; Springer: Berlin/Heidelberg, Germany, 2014; Volume 356, pp. 89–122. [Google Scholar]
- Kedziora, G.S.; Barr, S.A.; Berry, R.; Moller, J.C.; Breitzman, T.D. Bond breaking in stretched molecules: Multi-reference methods versus density functional theory. Theor. Chem. Acc.
**2016**, 135, 79. [Google Scholar] [CrossRef] - Zelený, T.; Ruckenbauer, M.; Aquino, A.J.; Müller, T.; Lankaš, F.; Dršata, T.; Hase, W.L.; Nachtigallová, D.; Lischka, H. Strikingly Different Effects of Hydrogen Bonding on the Photodynamics of Individual Nucleobases in DNA: Comparison of Guanine and Cytosine. J. Am. Chem. Soc.
**2012**, 134, 13662–13669. [Google Scholar] [CrossRef] [PubMed] - Sponer, J.; Riley, K.E.; Hobza, P. Nature and magnitude of aromatic stacking of nucleic acid bases. Phys. Chem. Chem. Phys.
**2008**, 10, 2595–2610. [Google Scholar] [CrossRef] [PubMed] - Conti, I.; Nenov, A.; Hofinger, S.; Flavio Altavilla, S.; Rivalta, I.; Dumont, E.; Orlandi, G.; Garavelli, M. Excited state evolution of DNA stacked adenines resolved at the CASPT2//CASSCF/Amber level: From the bright to the excimer state and back. Phys. Chem. Chem. Phys.
**2015**, 17, 7291–7302. [Google Scholar] [CrossRef] [PubMed] - Benda, Z.; Szalay, P.G. Characterization of the excited states of DNA building blocks: A coupled cluster computational study. Phys. Chem. Chem. Phys.
**2016**, 18, 23596–23606. [Google Scholar] [CrossRef] [PubMed] - Spata, V.A.; Lee, W.; Matsika, S. Excimers and Exciplexes in Photoinitiated Processes of Oligonucleotides. J. Phys. Chem. Lett.
**2016**, 7, 976–984. [Google Scholar] [CrossRef] [PubMed] - Ludwig, A.; Maurer, J.; Mayer, B.W.; Phillips, C.R.; Gallmann, L.; Keller, U. Breakdown of the Dipole Approximation in Strong-Field Ionization. Phys. Rev. Lett.
**2014**, 113, 243001. [Google Scholar] [CrossRef] [PubMed] - Sándor, P.; Tagliamonti, V.; Zhao, A.; Rozgonyi, T.; Ruckenbauer, M.; Marquetand, P.; Weinacht, T. Strong Field Molecular Ionization in the Impulsive Limit: Freezing Vibrations with Short Pulses. Phys. Rev. Lett.
**2016**, 116, 063002. [Google Scholar] [CrossRef] [PubMed] - Kotur, M.; Weinacht, T.C.; Zhou, C.; Matsika, S. Strong-Field Molecular Ionization from Multiple Orbitals. Phys. Rev. X
**2011**, 1, 021010. [Google Scholar] [CrossRef] - Ruckenbauer, M.; Mai, S.; Marquetand, P.; González, L. Revealing Deactivation Pathways Hidden in Time-Resolved Photoelectron Spectra. Sci. Rep.
**2016**, 6, 35522. [Google Scholar] [CrossRef] [PubMed] - Löwdin, P. Correlation Problem in Many-Electron Quantum Mechanics I. Review of Different Approaches and Discussion of Some Current Ideas. Adv. Chem. Phys.
**1959**, 2, 207–322. [Google Scholar] - Lasorne, B.; Worth, G.A.; Robb, M.A. Excited-state dynamics. WIREs Comput. Mol. Sci.
**2011**, 1, 460–475. [Google Scholar] [CrossRef] - Granucci, G.; Persico, M.; Zoccante, A. Including quantum decoherence in surface hopping. J. Chem. Phys.
**2010**, 133, 134111. [Google Scholar] [CrossRef] [PubMed] - Subotnik, J.E.; Jain, A.; Landry, B.; Petit, A.; Ouyang, W.; Bellonzi, N. Understanding the Surface Hopping View of Electronic Transitions and Decoherence. Annu. Rev. Phys. Chem.
**2016**, 67, 387–417. [Google Scholar] [CrossRef] [PubMed] - Plasser, F.; Lischka, H. Analysis of Excitonic and Charge Transfer Interactions from Quantum Chemical Calculations. J. Chem. Theory Comput.
**2012**, 8, 2777–2789. [Google Scholar] [CrossRef] [PubMed] - Mai, S.; Müller, T.; Marquetand, P.; Plasser, F.; Lischka, H.; González, L. Perturbational Treatment of Spin-Orbit Coupling for Generally Applicable High-Level Multi-Reference Methods. J. Chem. Phys.
**2014**, 141, 074105. [Google Scholar] [CrossRef] [PubMed] - Richings, G.W.; Worth, G.A. A Practical Diabatisation Scheme for Use with the Direct-Dynamics Variational Multi-Configuration Gaussian Method. J. Phys. Chem. A
**2015**, 119, 12457–12470. [Google Scholar] [CrossRef] [PubMed] - Amadei, A.; Linssen, A.B.M.; Berendsen, H.J.C. Essential dynamics of proteins. Proteins Struct. Funct. Bioinf.
**1993**, 17, 412–425. [Google Scholar] [CrossRef] [PubMed] - Plasser, F.; Aquino, A.J.A.; Lischka, H.; Nachtigallová, D. Electronic Excitation Processes in Single-Strand and Double-Strand DNA: A Computational Approach. In Photoinduced Phenomena in Nucleic Acids II; Topics in Current Chemistry; Springer: Berlin/Heidelberg, Germany, 2014; Volume 356, pp. 1–37. [Google Scholar]
- Emanuele, E.; Markovitsi, D.; Millié, P.; Zakrzewska, K. UV Spectra and Excitation Delocalization in DNA: Influence of the Spectral Width. ChemPhysChem
**2005**, 6, 1387–1392. [Google Scholar] [CrossRef] [PubMed][Green Version] - Bittner, E.R.; Czader, A. Quantum Mechanics in Biology: Photoexcitations in DNA. In Energy Transfer Dynamics in Biomaterial Systems; Burghardt, I., May, V., Micha, D.A., Bittner, E.R., Eds.; Number 93 in Springer Series in Chemical Physics; Springer: Berlin Heidelberg, Germany, 2009; pp. 103–126. [Google Scholar]
- Patwardhan, S.; Tonzani, S.; Lewis, F.D.; Siebbeles, L.D.A.; Schatz, G.C.; Grozema, F.C. Effect of Structural Dynamics and Base Pair Sequence on the Nature of Excited States in DNA Hairpins. J. Phys. Chem. B
**2012**, 116, 11447–11458. [Google Scholar] [CrossRef] [PubMed] - Lan, Z.; Fabiano, E.; Thiel, W. Photoinduced Nonadiabatic Dynamics of Pyrimidine Nucleobases: On-the-Fly Surface-Hopping Study with Semiempirical Methods. J. Phys. Chem. B
**2009**, 113, 3548–3555. [Google Scholar] [CrossRef] [PubMed] - Starikov, E.B.; Cuniberti, G.; Tanaka, S. Conformation Dependence of DNA Exciton Parentage. J. Phys. Chem. B
**2009**, 113, 10428–10435. [Google Scholar] [CrossRef] [PubMed] - Alexandrova, A.N.; Tully, J.C.; Granucci, G. Photochemistry of DNA Fragments via Semiclassical Nonadiabatic Dynamics. J. Phys. Chem. B
**2010**, 114, 12116–12128. [Google Scholar] [CrossRef] [PubMed] - Dou, Y.; Liu, Z.; Yuan, S.; Zhang, W.; Tang, H.; Zhao, J.; Fang, W.; Lo, G.V. Dynamics of laser-excited stacked adenines: Semiclassical simulations. Int. J. Biol. Macromol.
**2013**, 52, 358–367. [Google Scholar] [CrossRef] [PubMed] - Lei, Y.; Yuan, S.; Dou, Y.; Wang, Y.; Wen, Z. Detailed Dynamics of the Nonradiative Deactivation of Adenine: A Semiclassical Dynamics Study. J. Phys. Chem. A
**2008**, 112, 8497–8504. [Google Scholar] [CrossRef] [PubMed] - Mitrić, R.; Werner, U.; Wohlgemuth, M.; Seifert, G.; Bonačić-Koutecký, V. Nonadiabatic Dynamics within Time-Dependent Density Functional Tight Binding Method. J. Phys. Chem. A
**2009**, 113, 12700–12705. [Google Scholar] [CrossRef] [PubMed] - Lange, A.W.; Rohrdanz, M.A.; Herbert, J.M. Charge-transfer excited states in a pi-stacked adenine dimer, as predicted using long-range-corrected time-dependent density functional theory. J. Phys. Chem. B
**2008**, 112, 6304–6308. [Google Scholar] [CrossRef] [PubMed] - Aquino, A.J.A.; Nachtigallova, D.; Hobza, P.; Truhlar, D.G.; Hättig, C.; Lischka, H. The charge-transfer states in a stacked nucleobase dimer complex: A benchmark study. J. Comput. Chem.
**2011**, 32, 1217–1227. [Google Scholar] [CrossRef] [PubMed] - Improta, R. Photophysics and Photochemistry of Thymine Deoxy-Dinucleotide in Water: A PCM/TD-DFT Quantum Mechanical Study. J. Phys. Chem. B
**2012**, 116, 14261–14274. [Google Scholar] [CrossRef] [PubMed] - Raeber, A.E.; Wong, B.M. The importance of short- and long-range exchange on various excited state properties of DNA monomers, stacked complexes, and Watson-Crick pairs. J. Chem. Theory Comput.
**2015**, 11, 2199–2209. [Google Scholar] [CrossRef] [PubMed] - Sun, H.; Zhang, S.; Zhong, C.; Sun, Z. Theoretical study of excited states of DNA base dimers and tetramers using optimally tuned range-separated density functional theory. J. Comput. Chem.
**2016**, 37, 684–693. [Google Scholar] [CrossRef] [PubMed] - Sobolewski, A.L.; Domcke, W.; Hättig, C. Tautomeric selectivity of the excited-state lifetime of guanine/cytosine base pairs: The role of electron-driven proton-transfer processes. Proc. Natl. Acad. Sci. USA
**2005**, 102, 17903–17906. [Google Scholar] [CrossRef] [PubMed] - Nachtigallová, D.; Hobza, P.; Ritze, H.H. Electronic splitting in the excited states of DNA base homodimers and -trimers: An evaluation of short-range and Coulombic interactions. Phys. Chem. Chem. Phys.
**2008**, 10, 5689–5697. [Google Scholar] [CrossRef] [PubMed] - Plasser, F.; Aquino, A.J.A.; Hase, W.L.; Lischka, H. UV Absorption Spectrum of Alternating DNA Duplexes. Analysis of Excitonic and Charge Transfer Interactions. J. Phys. Chem. A
**2012**, 116, 11151–11160. [Google Scholar] [CrossRef] [PubMed] - Ramazanov, R.R.; Maksimov, D.A.; Kononov, A.I. Noncanonical Stacking Geometries of Nucleobases as a Preferred Target for Solar Radiation. J. Am. Chem. Soc.
**2015**, 137, 11656–11665. [Google Scholar] [CrossRef] [PubMed] - Szalay, P.G.; Watson, T.; Perera, A.; Lotrich, V.; Bartlett, R.J. Benchmark studies on the building blocks of DNA. 3. Watson-crick and stacked base pairs. J. Phys. Chem. A
**2013**, 117, 3149–3157. [Google Scholar] [CrossRef] [PubMed] - Groenhof, G.; Schäfer, L.V.; Boggio-Pasqua, M.; Goette, M.; Grubmüller, H.; Robb, M.A. Ultrafast Deactivation of an Excited Cytosine-Guanine Base Pair in DNA. J. Am. Chem. Soc.
**2007**, 129, 6812–6819. [Google Scholar] [CrossRef] [PubMed] - Hudock, H.R.; Levine, B.G.; Thompson, A.L.; Satzger, H.; Townsend, D.; Gador, N.; Ullrich, S.; Stolow, A.; Martínez, T.J. Ab Initio Molecular Dynamics and Time-Resolved Photoelectron Spectroscopy of Electronically Excited Uracil and Thymine. J. Phys. Chem. A
**2007**, 111, 8500–8508. [Google Scholar] [CrossRef] [PubMed] - Barbatti, M.; Aquino, A.J.A.; Szymczak, J.J.; Nachtigallová, D.; Hobza, P.; Lischka, H. Relaxation Mechanisms of UV-Photoexcited DNA and RNA Nucleobases. Proc. Natl. Acad. Sci. USA
**2010**, 107, 21453–21458. [Google Scholar] [CrossRef] [PubMed] - Barbatti, M.; Aquino, A.J.A.; Szymczak, J.J.; Nachtigallová, D.; Lischka, H. Photodynamical simulations of cytosine: Characterization of the ultrafast bi-exponential UV deactivation. Phys. Chem. Chem. Phys.
**2011**, 13, 6145–6155. [Google Scholar] [CrossRef] [PubMed] - Richter, M.; Marquetand, P.; González-Vázquez, J.; Sola, I.; González, L. Femtosecond Intersystem Crossing in the DNA Nucleobase Cytosine. J. Phys. Chem. Lett.
**2012**, 3, 3090–3095. [Google Scholar] [CrossRef] [PubMed] - Richter, M.; Mai, S.; Marquetand, P.; González, L. Ultrafast Intersystem Crossing Dynamics in Uracil Unravelled by Ab Initio Molecular Dynamics. Phys. Chem. Chem. Phys.
**2014**, 16, 24423–24436. [Google Scholar] [CrossRef] [PubMed] - Mai, S.; Richter, M.; Marquetand, P.; González, L. The DNA Nucleobase Thymine in Motion—Intersystem Crossing Simulated with Surface Hopping. Chem. Phys.
**2016**. [Google Scholar] [CrossRef] - Perun, S.; Sobolewski, A.L.; Domcke, W. Ab Initio Studies on the Radiationless Decay Mechanisms of the Lowest Excited Singlet States of 9H-Adenine. J. Am. Chem. Soc.
**2005**, 127, 6257–6265. [Google Scholar] [CrossRef] [PubMed] - Olaso-González, G.; Merchán, M.; Serrano-Andrés, L. The role of adenine excimers in the photophysics of oligonucleotides. J. Am. Chem. Soc.
**2009**, 131, 4368–4377. [Google Scholar] [CrossRef] [PubMed] - Blancafort, L.; Voityuk, A.A. Exciton delocalization, charge transfer, and electronic coupling for singlet excitation energy transfer between stacked nucleobases in DNA: An MS-CASPT2 study. J. Chem. Phys.
**2014**, 140, 095102. [Google Scholar] [CrossRef] [PubMed] - Yu, H.; Sánchez-Rodríguez, J.A.; Pollum, M.; Crespo-Hernández, C.E.; Mai, S.; Marquetand, P.; González, L.; Ullrich, S. Internal Conversion and Intersystem Crossing Pathways in UV Excited, Isolated Uracils and Their Implications in Prebiotic Chemistry. Phys. Chem. Chem. Phys.
**2016**, 18, 20168–20176. [Google Scholar] [CrossRef] [PubMed] - Mai, S.; Marquetand, P.; González, L. Intersystem Crossing Pathways in the Noncanonical Nucleobase 2-Thiouracil: A Time-Dependent Picture. J. Phys. Chem. Lett.
**2016**, 7, 1978–1983. [Google Scholar] [CrossRef] [PubMed] - Kistler, K.A.; Matsika, S. Three-state conical intersections in cytosine and pyrimidinone bases. J. Chem. Phys.
**2008**, 128, 215102. [Google Scholar] [CrossRef] [PubMed] - Barbatti, M.; Szymczak, J.J.; Aquino, A.J.A.; Nachtigallová, D.; Lischka, H. The decay mechanism of photoexcited guanine—A nonadiabatic dynamics study. J. Chem. Phys.
**2011**, 134, 014304. [Google Scholar] [CrossRef] [PubMed] - Barbatti, M.; Lan, Z.; Crespo-Otero, R.; Szymczak, J.J.; Lischka, H.; Thiel, W. Critical Appraisal of Excited State Nonadiabatic Dynamics Simulations of 9H-Adenine. J. Chem. Phys.
**2012**, 117, 22A503. [Google Scholar] [CrossRef] [PubMed] - Barbatti, M.; Lischka, H. Nonadiabatic Deactivation of 9H-Adenine: A Comprehensive Picture Based on Mixed Quantum-Classical Dynamics. J. Am. Chem. Soc.
**2008**, 130, 6831–6839. [Google Scholar] [CrossRef] [PubMed] - Banyasz, A.; Gustavsson, T.; Onidas, D.; Changenet-Barret, P.; Markovitsi, D.; Improta, R. Multi-pathway excited state relaxation of adenine oligomers in aqueous solution: A joint theoretical and experimental study. Chem. Eur. J.
**2013**, 19, 3762–3774. [Google Scholar] [CrossRef] [PubMed] - Plasser, F.; Crespo-Otero, R.; Pederzoli, M.; Pittner, J.; Lischka, H.; Barbatti, M. Surface Hopping Dynamics with Correlated Single-Reference Methods: 9H-Adenine as a Case Study. J. Chem. Theory Comput.
**2014**, 10, 1395–1405. [Google Scholar] [CrossRef] [PubMed] - Plasser, F.; Lischka, H. Electronic excitation and structural relaxation of the adenine dinucleotide in gas phase and solution. Photochem. Photobiol. Sci.
**2013**, 12, 1440–1452. [Google Scholar] [CrossRef] [PubMed] - Boggio-Pasqua, M.; Groenhof, G.; Schäfer, L.V.; Grubmüller, H.; Robb, M.A. Ultrafast deactivation channel for thymine dimerization. J. Am. Chem. Soc.
**2007**, 129, 10996–10997. [Google Scholar] [CrossRef] [PubMed] - Banyasz, A.; Douki, T.; Improta, R.; Gustavsson, T.; Onidas, D.; Vayá, I.; Perron, M.; Markovitsi, D. Electronic Excited States Responsible for Dimer Formation upon UV Absorption Directly by Thymine Strands: Joint Experimental and Theoretical Study. J. Am. Chem. Soc.
**2012**, 134, 14834–14845. [Google Scholar] [CrossRef] [PubMed] - Lu, Y.; Lan, Z.; Thiel, W. Hydrogen Bonding Regulates the Monomeric Nonradiative Decay of Adenine in DNA Strands. Angew. Chem. Int. Ed. Engl.
**2011**, 50, 6864–6867. [Google Scholar] [CrossRef] [PubMed] - Lu, Y.; Lan, Z.; Thiel, W. Monomeric adenine decay dynamics influenced by the DNA environment. J. Comp. Chem.
**2012**, 33, 1225–1235. [Google Scholar] [CrossRef] [PubMed] - Mai, S.; Richter, M.; Marquetand, P.; González, L. Excitation of Nucleobases from a Computational Perspective II: Dynamics. In Photoinduced Phenomena in Nucleic Acids I; Barbatti, M., Borin, A.C., Ullrich, S., Eds.; Topics in Current Chemistry; Springer: Berlin/Heidelberg, Germany, 2014; Volume 355, pp. 99–153. [Google Scholar]
- Senn, H.M.; Thiel, W. QM/MM Methods for Biomolecular Systems. Angew. Chem. Int. Ed.
**2009**, 48, 1198–1229. [Google Scholar] [CrossRef] [PubMed] - Foloppe, N.; MacKerell, A.D., Jr. All-Atom Empirical Force Field for Nucleic Acids: I. Parameter Optimization Based on Small Molecule and Condensed Phase Macromolecular Target Data. J. Comput. Chem.
**2000**, 21, 86–104. [Google Scholar] [CrossRef] - MacKerell, A.D., Jr.; Banavali, N.K. All-Atom Empirical Force Field for Nucleic Acids: II. Application to Molecular Dynamics Simulations of DNA and RNA in Solution. J. Comput. Chem.
**2000**, 21, 105–120. [Google Scholar] [CrossRef] - Wang, J.; Cieplak, P.; Kollman, P.A. How Well Does a Restrained Electrostatic Potential (RESP) Model Perform in Calculating Conformational Energies of Organic and Biological Molecules? J. Comput. Chem.
**2000**, 21, 1049–1074. [Google Scholar] [CrossRef] - Pérez, A.; Marchán, I.; Svozil, D.; Sponer, J.; Cheatham, T.E., III; Laughton, C.A.; Orozco, M. Refinement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers. Biophys. J.
**2007**, 92, 3817–3829. [Google Scholar] [CrossRef] [PubMed] - Curutchet, C.; Muñoz Losa, A.; Monti, S.; Kongsted, J.; Scholes, G.D.; Mennucci, B. Electronic energy transfer in condensed phase studied by a polarizable QM/MM model. J. Chem. Theory Comput.
**2009**, 5, 1838–1848. [Google Scholar] [CrossRef] [PubMed] - Savelyev, A.; MacKerell, A.D., Jr. All-atom polarizable force field for DNA based on the classical drude oscillator model. J. Comput. Chem.
**2014**, 35, 1219–1239. [Google Scholar] [CrossRef] [PubMed] - Olsen, J.M.H.; Steinmann, C.; Ruud, K.; Kongsted, J. Polarizable density embedding: A new QM/QM/ MM-based computational strategy. J. Phys. Chem. A
**2015**, 119, 5344–5355. [Google Scholar] [CrossRef] [PubMed] - Wesolowski, T.A.; Shedge, S.; Zhou, X. Frozen-Density Embedding Strategy for Multilevel Simulations of Electronic Structure. Chem. Rev.
**2015**, 115, 5891–5928. [Google Scholar] [CrossRef] [PubMed] - Mendieta-Moreno, J.I.; Trabada, D.G.; Mendieta, J.; Lewis, J.P.; Gómez-Puertas, P.; Ortega, J. Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer. J. Phys. Chem. Lett.
**2016**, 7, 4391–4397. [Google Scholar] [CrossRef] [PubMed] - Barbatti, M. Photorelaxation induced by water-chromophore electron transfer. J. Am. Chem. Soc.
**2014**, 136, 10246–10249. [Google Scholar] [CrossRef] [PubMed] - White, S.R.; Martin, R.L. Ab initio quantum chemistry using the density matrix renormalization group. J. Chem. Phys.
**1999**, 110, 4127. [Google Scholar] [CrossRef] - Marti, K.H.; Reiher, M. The Density Matrix Renormalization Group Algorithm in Quantum Chemistry. Z. Phys. Chem.
**2010**, 224, 583. [Google Scholar] [CrossRef] - Olivares-Amaya, R.; Hu, W.; Nakatani, N.; Sharma, S.; Yang, J.; Chan, G.K.L. The ab-initio density matrix renormalization group in practice. J. Chem. Phys.
**2015**, 142. [Google Scholar] [CrossRef] [PubMed] - Booth, G.H.; Thom, A.J.W.; Alavi, A. Fermion Monte Carlo without fixed nodes: A game of life, death, and annihilation in Slater determinant space. J. Chem. Phys.
**2009**, 131, 054106. [Google Scholar] [CrossRef] [PubMed] - Hattig, C. Structure optimizations for excited states with correlated second-order methods: CC2 and ADC(2). Adv. Quantum Chem.
**2005**, 50, 37–60. [Google Scholar] - Bostrom, J.; Aquilante, F.; Pedersen, T.B.; Lindh, R. Analytical gradients of hartree-fock exchange with density fitting approximations. J. Chem. Theory Comput.
**2013**, 9, 204–212. [Google Scholar] [CrossRef] [PubMed] - Zuehlsdorff, T.J.; Hine, N.D.M.; Spencer, J.S.; Harrison, N.M.; Riley, D.J.; Haynes, P.D. Linear-scaling time-dependent density-functional theory in the linear response formalism. J. Chem. Phys.
**2013**, 139. [Google Scholar] [CrossRef] [PubMed][Green Version] - Müller, T. Large-Scale Parallel Uncontracted Multireference-Averaged Quadratic Coupled Cluster: The Ground State of the Chromium Dimer Revisited. J. Phys. Chem. A
**2009**, 113, 12729. [Google Scholar] [CrossRef] [PubMed] - Isborn, C.M.; Luehr, N.; Ufimtsev, I.S.; Martínez, T.J. Excited-State Electronic Structure with Configuration Interaction Singles and Tamm–Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units. J. Chem. Theory Comput.
**2011**, 7, 1814–1823. [Google Scholar] [CrossRef] [PubMed] - Kubař, T.; Elstner, M. Efficient algorithms for the simulation of non-adiabatic electron transfer in complex molecular systems: Application to DNA. Phys. Chem. Chem. Phys.
**2013**, 15, 5794–5813. [Google Scholar] [CrossRef] [PubMed] - Sisto, A.; Glowacki, D.R.; Martinez, T.J. Ab initio nonadiabatic dynamics of multichromophore complexes: A scalable graphical-processing-unit-accelerated exciton framework. Acc. Chem. Res.
**2014**, 47, 2857–2866. [Google Scholar] [CrossRef] [PubMed] - Handley, C.M.; Popelier, P.L.A. Potential Energy Surfaces Fitted by Artificial Neural Networks. J. Phys. Chem. A
**2010**, 114, 3371–3383. [Google Scholar] [CrossRef] [PubMed] - Vitek, A.; Stachon, M.; Kromer, P.; Snael, V. Towards the Modeling of Atomic and Molecular Clusters Energy by Support Vector Regression. In Proceedings of the International Conference on Intelligent Networking and Collaborative Systems (INCoS), Xi’an, China, 9–11 September 2013; pp. 121–126.
- Behler, J. Constructing high-dimensional neural network potentials: A tutorial review. Int. J. Quantum Chem.
**2015**, 115, 1032–1050. [Google Scholar] [CrossRef] - Gastegger, M.; Marquetand, P. High-Dimensional Neural Network Potentials for Organic Reactions and an Improved Training Algorithm. J. Chem. Theory Comput.
**2015**, 11, 2187–2198. [Google Scholar] [CrossRef] [PubMed] - Gastegger, M.; Kauffmann, C.; Behler, J.; Marquetand, P. Comparing the accuracy of high-dimensional neural network potentials and the systematic molecular fragmentation method: A benchmark study for all-trans alkanes. J. Chem. Phys.
**2016**, 144, 194110. [Google Scholar] [CrossRef] [PubMed] - Ramakrishnan, R.; von Lilienfeld, O.A. Machine Learning, Quantum Mechanics, and Chemical Compound Space. arXiv
**2016**. [Google Scholar] - Barbatti, M.; Sen, K. Effects of different initial condition samplings on photodynamics and spectrum of pyrrole. Int. J. Quantum Chem.
**2016**, 116, 762–771. [Google Scholar] [CrossRef] - Dahl, J.P.; Springborg, M. The Morse oscillator in position space, momentum space, and phase space. J. Chem. Phys.
**1987**, 88, 4535–4547. [Google Scholar] [CrossRef][Green Version] - Marazzi, M.; Mai, S.; Roca-Sanjuán, D.; Delcey, M.G.; Lindh, R.; González, L.; Monari, A. Benzophenone Ultrafast Triplet Population: Revisiting the Kinetic Model by Surface-Hopping Dynamics. J. Phys. Chem. Lett.
**2016**, 7, 622–626. [Google Scholar] [CrossRef] [PubMed] - Szymczak, J.J.; Barbatti, M.; Lischka, H. Mechanism of Ultrafast Photodecay in Restricted Motions in Protonated Schiff Bases: The Pentadieniminium Cation. J. Chem. Theory Comput.
**2008**, 4, 1189–1199. [Google Scholar] [CrossRef] [PubMed] - Lan, Z.; Lu, Y.; Fabiano, E.; Thiel, W. QM/MM Nonadiabatic Decay Dynamics of 9H-Adenine in Aqueous Solution. ChemPhysChem
**2011**, 12, 1989–1998. [Google Scholar] [CrossRef] [PubMed] - Isborn, C.M.; Götz, A.W.; Clark, M.A.; Walker, R.C.; Martínez, T.J. Electronic absorption spectra from MM and ab initio QM/MM molecular dynamics: Environmental effects on the absorption spectrum of photoactive yellow protein. J. Chem. Theory Comput.
**2012**, 8, 5092–5106. [Google Scholar] [CrossRef] [PubMed] - Ruckenbauer, M.; Barbatti, M.; Sellner, B.; Muller, T.; Lischka, H. Azomethane: Nonadiabatic Photodynamical Simulations in Solution. J. Phys. Chem. A
**2010**, 114, 12585–12590. [Google Scholar] [CrossRef] [PubMed] - Ruckenbauer, M.; Barbatti, M.; Müller, T.; Lischka, H. Nonadiabatic Photodynamics of a Retinal Model in Polar and Nonpolar Environment. J. Phys. Chem. A
**2013**, 117, 2790–2799. [Google Scholar] [CrossRef] [PubMed] - Tannor, D. Introduction to Quantum Mechanics: A Time-Dependent Perspective; University Science Books: Sausalito, CA, USA, 2006. [Google Scholar]
- Mitrić, R.; Petersen, J.; Bonačić-Koutecký, V. Laser-field-induced surface-hopping method for the simulation and control of ultrafast photodynamics. Phys. Rev. A
**2009**, 79, 053416. [Google Scholar] [CrossRef] - Richter, M.; Marquetand, P.; González-Vázquez, J.; Sola, I.; González, L. SHARC: Ab Initio Molecular Dynamics with Surface Hopping in the Adiabatic Representation Including Arbitrary Couplings. J. Chem. Theory Comput.
**2011**, 7, 1253–1258. [Google Scholar] [CrossRef] [PubMed] - Marquetand, P.; Richter, M.; González-Vázquez, J.; Sola, I.; González, L. Nonadiabatic Ab Initio Molecular Dynamics Including Spin-Orbit Coupling and Laser Fields. Faraday Discuss.
**2011**, 153, 261–273. [Google Scholar] [CrossRef] [PubMed] - Bajo, J.J.; González-Vázquez, J.; Sola, I.; Santamaria, J.; Richter, M.; Marquetand, P.; González, L. Mixed Quantum-Classical Dynamics in the Adiabatic Representation to Simulate Molecules Driven by Strong Laser Pulses. J. Phys. Chem. A
**2012**, 116, 2800–2807. [Google Scholar] [CrossRef] [PubMed] - Fiedlschuster, T.; Handt, J.; Schmidt, R. Floquet surface hopping: Laser-driven dissociation and ionization dynamics of H
_{2}^{+}. Phys. Rev. A**2016**, 93, 053409. [Google Scholar] [CrossRef] - Fiedlschuster, T.; Handt, J.; Gross, E.K.U.; Schmidt, R. Surface hopping methodology in laser-driven molecular dynamics. arXiv
**2016**. [Google Scholar] - Barbatti, M.; Granucci, G.; Persico, M.; Ruckenbauer, M.; Vazdar, M.; Eckert-Maksić, M.; Lischka, H. The on-the-fly surface-hopping program system Newton-X: Application to ab initio simulation of the nonadiabatic photodynamics of benchmark systems. J. Photochem. Photobiol. A
**2007**, 190, 228–240. [Google Scholar] [CrossRef] - Hemmers, O.A.; Lindle, D.W. Photoelectron spectroscopy and the dipole approximation. AIP Conf. Proc.
**2001**, 576, 189–192. [Google Scholar] - Meyer, H.D.; Gatti, F.; Worth, G.A. Multidimensional Quantum Dynamics; Chapter 2; Wiley-VCH Verlag GmbH & Co. KGaA: Weinheim, Germany, 2009; pp. 9–15. [Google Scholar]
- Picconi, D.; Lami, A.; Santoro, F. Hierarchical transformation of Hamiltonians with linear and quadratic couplings for nonadiabatic quantum dynamics: Application to the ππ
^{*}nπ^{*}internal conversion in thymine. J. Chem. Phys.**2012**, 136, 224104. [Google Scholar] [CrossRef] [PubMed] - Assmann, M.; Köppel, H.; Matsika, S. Photoelectron Spectrum and Dynamics of the Uracil Cation. J. Phys. Chem. A
**2015**, 119, 866–875. [Google Scholar] [CrossRef] [PubMed] - Wang, H.; Thoss, M. Multilayer formulation of the multiconfiguration time-dependent Hartree theory. J. Chem. Phys.
**2003**, 119, 1289–1299. [Google Scholar] [CrossRef] - Burghardt, I.; Meyer, H.D.; Cederbaum, L.S. Approaches to the approximate treatment of complex molecular systems by the multiconfiguration time-dependent Hartree method. J. Chem. Phys.
**1999**, 111, 2927–2939. [Google Scholar] [CrossRef] - Richings, G.; Polyak, I.; Spinlove, K.; Worth, G.; Burghardt, I.; Lasorne, B. Quantum dynamics simulations using Gaussian wavepackets: The vMCG method. Int. Rev. Phys. Chem.
**2015**, 34, 269–308. [Google Scholar] [CrossRef] - Martínez, T.J.; Ben-Nun, M.; Levine, R.D. Multi-Electronic-State Molecular Dynamics: A Wave Function Approach with Applications. J. Phys. Chem.
**1996**, 100, 7884–7895. [Google Scholar] [CrossRef] - Makhov, D.V.; Glover, W.J.; Martinez, T.J.; Shalashilin, D.V. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics. J. Chem. Phys.
**2014**, 141, 054110. [Google Scholar] [CrossRef] [PubMed] - Asturiol, D.; Lasorne, B.; Worth, G.A.; Robb, M.A.; Blancafort, L. Exploring the sloped-to-peaked S2/S1 seam of intersection of thymine with electronic structure and direct quantum dynamics calculations. Phys. Chem. Chem. Phys.
**2010**, 12, 4949–4958. [Google Scholar] [CrossRef] [PubMed] - Karplus, M.; McCammon, J.A. Molecular dynamics simulations of biomolecules. Nat. Struct. Biol.
**2002**, 9, 646. [Google Scholar] [CrossRef] [PubMed] - Barbatti, M. Nonadiabatic dynamics with trajectory surface hopping method. WIREs Comput. Mol. Sci.
**2011**, 1, 620–633. [Google Scholar] [CrossRef] - Wang, L.; Akimov, A.; Prezhdo, O.V. Recent Progress in Surface Hopping: 2011–2015. J. Phys. Chem. Lett.
**2016**, 7, 2100–2112. [Google Scholar] [CrossRef] [PubMed] - Christ, C.D.; Mark, A.E.; van Gunsteren, W.F. Basic ingredients of free energy calculations: A review. J. Comput. Chem.
**2010**, 31, 1569–1582. [Google Scholar] [CrossRef] [PubMed] - Abedi, A.; Maitra, N.T.; Gross, E.K.U. Exact Factorization of the Time-Dependent Electron-Nuclear Wave Function. Phys. Rev. Lett.
**2010**, 105, 123002. [Google Scholar] [CrossRef] [PubMed] - Berne, B.J.; Thirumalai, D. On the Simulation of Quantum Systems: Path Integral Methods. Annu. Rev. Phys. Chem.
**1986**, 37, 401–424. [Google Scholar] [CrossRef] - Curchod, B.F.E.; Tavernelli, I. On trajectory-based nonadiabatic dynamics: Bohmian dynamics versus trajectory surface hopping. J. Chem. Phys.
**2013**, 138, 184112. [Google Scholar] [CrossRef] [PubMed] - Habershon, S.; Manolopoulos, D.E.; Markland, T.E.; Miller, T.F., III. Ring-Polymer Molecular Dynamics: Quantum Effects in Chemical Dynamics from Classical Trajectories in an Extended Phase Space. Annu. Rev. Phys. Chem.
**2013**, 64, 387–413. [Google Scholar] [CrossRef] [PubMed] - Doltsinis, N. Computational Nanoscience: Do It Yourself; NIC Series; John von Neumann Institute for Computing: Jülich, Geramny, 2006; Volume 31, pp. 389–409. [Google Scholar]
- Broeckhove, J.; Lathouwers, L. (Eds.) Time-Dependent Quantum Molecular Dynamics; Springer: New York, NY, USA, 1992.
- Thompson, D.L. (Ed.) Modern Methods for Multidimensional Dynamics Computations in Chemistry; World Scientific: Singapore, 1998.
- Lischka, H.; Dallos, M.; Szalay, P.G.; Yarkony, D.R.; Shepard, R. Analytic Evaluation of Nonadiabatic Coupling Terms at the MR-CI Level. I. Formalism. J. Chem. Phys.
**2004**, 120, 7322–7329. [Google Scholar] [CrossRef] [PubMed] - Hammes-Schiffer, S.; Tully, J.C. Proton transfer in solution: Molecular dynamics with quantum transitions. J. Chem. Phys.
**1994**, 101, 4657–4667. [Google Scholar] [CrossRef] - Plasser, F.; Ruckenbauer, M.; Mai, S.; Oppel, M.; Marquetand, P.; González, L. Efficient and Flexible Computation of Many-Electron Wave Function Overlaps. J. Chem. Theory Comput.
**2016**, 12, 1207. [Google Scholar] [CrossRef] [PubMed] - Köppel, H.; Domcke, W.; Cederbaum, L.S. Multimode Molecular Dynamics Beyond the Born-Oppenheimer Approximation. In Advances in Chemical Physics; John Wiley & Sons Inc.: Hoboken, NJ, USA, 1984; Volume 57, pp. 59–246. [Google Scholar]
- Mai, S.; Marquetand, P.; González, L. A general method to describe intersystem crossing dynamics in trajectory surface hopping. Int. J. Quantum Chem.
**2015**, 115, 1215–1231. [Google Scholar] [CrossRef] - Mai, S.; Marquetand, P.; Richter, M.; González-Vázquez, J.; González, L. Singlet and Triplet Excited-State Dynamics Study of the Keto and Enol Tautomers of Cytosine. ChemPhysChem
**2013**, 14, 2920–2931. [Google Scholar] [CrossRef] [PubMed] - Berera, R.; Grondelle, R.; Kennis, J.T.M. Ultrafast transient absorption spectroscopy: Principles and application to photosynthetic systems. Photosynth. Res.
**2009**, 101, 105–118. [Google Scholar] [CrossRef] [PubMed] - Monti, S.; Chiorboli, C. Transient Absorption Spectroscopy. In The Exploration of Supramolecular Systems and Nanostructures by Photochemical Techniques; Lecture Notes in Chemistry 78; Ceroni, P., Ed.; Springer: Berlin, Germany, 2012. [Google Scholar]
- Davydova, D.; de la Cadena, A.; Akimov, D.; Dietzek, B. Transient absorption microscopy: Advances in chemical imaging of photoinduced dynamics. Laser Photonics Rev.
**2016**, 10, 62–81. [Google Scholar] [CrossRef] - Pollum, M.; Martínez-Fernández, L.; Crespo-Hernández, C.E. Photochemistry of Nucleic Acid Bases and Their Thio- and Aza-Analogues in Solution. In Photoinduced Phenomena in Nucleic Acids I; Barbatti, M., Borin, A.C., Ullrich, S., Eds.; Topics in Current Chemistry; Springer: Berlin/Heidelberg, Germany, 2014; Volume 356, pp. 245–327. [Google Scholar]
- Chen, J.; Zhang, Y.; Kohler, B. Excited States in DNA Strands Investigated by Ultrafast Laser Spectroscopy. In Photoinduced Phenomena in Nucleic Acids; Topics in Current Chemistry; Springer: Berlin/Heidelberg, Germany 2014; Volume 356, pp. 39–87. [Google Scholar]
- Petit, A.S.; Subotnik, J.E. Calculating time-resolved differential absorbance spectra for ultrafast pump-probe experiments with surface hopping trajectories. J. Chem. Phys.
**2014**, 141, 154108. [Google Scholar] [CrossRef] [PubMed] - Stolow, A. Femtosecond Time-Resolved Photoelectron Spectroscopy of Polyatomic Molecules. Annu. Rev. Phys. Chem.
**2003**, 54, 89–119. [Google Scholar] [CrossRef] [PubMed] - Schwell, M.; Hochlaf, M. Photoionization Spectroscopy of Nucleobases and Analogues in the Gas Phase Using Synchrotron Radiation as Excitation Light Source. In Photoinduced Phenomena in Nucleic Acids I; Topics in Current Chemistry; Springer: Berlin/Heidelberg, Germany, 2014; Volume 355, pp. 155–208. [Google Scholar]
- Xu, J.; Blaga, C.I.; Agostini, P.; DiMauro, L.F. Time-resolved molecular imaging. J. Phys. B At. Mol. Opt. Phys.
**2016**, 49, 112001. [Google Scholar] [CrossRef] - Oana, C.M.; Krylov, A.I. Dyson orbitals for ionization from the ground and electronically excited states within equation-of-motion coupled-cluster formalism: Theory, implementation, and examples. J. Chem. Phys.
**2007**, 127, 234106. [Google Scholar] [CrossRef] [PubMed] - Hudock, H.R.; Martínez, T.J. Excited-State Dynamics of Cytosine Reveal Multiple Intrinsic Subpicosecond Pathways. ChemPhysChem
**2008**, 9, 2486–2490. [Google Scholar] [CrossRef] [PubMed] - Arbelo-González, W.; Crespo-Otero, R.; Barbatti, M. Steady and Time-Resolved Photoelectron Spectra Based on Nuclear Ensembles. J. Chem. Theory Comput.
**2016**. [Google Scholar] [CrossRef] [PubMed] - Ruckenbauer, M.; Mai, S.; Marquetand, P.; González, L. Photoelectron spectra of 2-thiouracil, 4-thiouracil, and 2,4-dithiouracil. J. Chem. Phys.
**2016**, 144, 074303. [Google Scholar] [CrossRef] [PubMed] - Oana, C.M.; Krylov, A.I. Cross sections and photoelectron angular distributions in photodetachment from negative ions using equation-of-motion coupled-cluster Dyson orbitals. J. Chem. Phys.
**2009**, 131, 124114. [Google Scholar] [CrossRef] [PubMed] - Gozem, S.; Gunina, A.O.; Ichino, T.; Osborn, D.L.; Stanton, J.F.; Krylov, A.I. Photoelectron Wave Function in Photoionization: Plane Wave or Coulomb Wave? J. Phys. Chem. Lett.
**2015**, 6, 4532–4540. [Google Scholar] [CrossRef] [PubMed] - Burkey, R.S.; Cantrell, C.D. Discretization in the quasi-continuum. J. Opt. Soc. Am. B
**1984**, 1, 169–175. [Google Scholar] [CrossRef] - Engel, V. Femtosecond Pump/Probe Experiments and Ionization: The Time Dependence of the Total Ion Signal. Chem. Phys. Lett.
**1991**, 178, 130–134. [Google Scholar] [CrossRef] - Seel, M.; Domcke, W. Femtosecond Time-Resolved Ionization Spectroscopy of Ultrafast Internal-Conversion Dynamics in Polyatomic Molecules: Theory and Computational Studies. J. Chem. Phys.
**1991**, 95, 7806–7822. [Google Scholar] [CrossRef] - Mitrić, R.; Petersen, J.; Wohlgemuth, M.; Werner, U.; Bonačić-Koutecký, V.; Wöste, L.; Jortner, J. Time-Resolved Femtosecond Photoelectron Spectroscopy by Field-Induced Surface Hopping. J. Phys. Chem. A
**2011**, 115, 3755–3765. [Google Scholar] [CrossRef] [PubMed] - Marante, C.; Argenti, L.; Martín, F. Hybrid Gaussian-B-spline basis for the electronic continuum: Photoionization of atomic hydrogen. Phys. Rev. A
**2014**, 90, 012506. [Google Scholar] [CrossRef] - Nesbet, R.K. Stieltjes imaging method for computation of oscillator-strength distributions for complex atoms. Phys. Rev. A
**1976**, 14, 1065–1081. [Google Scholar] [CrossRef] - Cacelli, I.; Carravetta, V.; Rizzo, A.; Moccia, R. The calculation of photoionisation cross sections of simple polyatomic molecules by L2 methods. Phys. Rep.
**1991**, 205, 283–351. [Google Scholar] [CrossRef] - Werner, U.; Mitrić, R.; Bonačić-Koutecký, V. Simulation of time resolved photoelectron spectra with Stieltjes imaging illustrated on ultrafast internal conversion in pyrazine. J. Chem. Phys.
**2010**, 132, 174301. [Google Scholar] [CrossRef] [PubMed] - Cukras, J.; Coriani, S.; Decleva, P.; Christiansen, O.; Norman, P. Photoionization cross section by Stieltjes imaging applied to coupled cluster Lanczos pseudo-spectra. J. Chem. Phys.
**2013**, 139. [Google Scholar] [CrossRef] [PubMed] - Spanner, M.; Patchkovskii, S. One-Electron Ionization of Multielectron Systems in Strong Nonresonant Laser Fields. Phys. Rev. A
**2009**, 80, 063411. [Google Scholar] [CrossRef] - Spanner, M.; Patchkovskii, S.; Zhou, C.; Matsika, S.; Kotur, M.; Weinacht, T.C. Dyson Norms in XUV and Strong-Field Ionization of Polyatomics: Cytosine and Uracil. Phys. Rev. A
**2012**, 86, 053406. [Google Scholar] [CrossRef] - Spanner, M.; Patchkovskii, S. Molecular Strong Field Ionization and High Harmonic Generation: A Selection of Computational Illustrations. Chem. Phys.
**2013**, 414, 10–19. [Google Scholar] [CrossRef] - Tagliamonti, V.; Sándor, P.; Zhao, A.; Rozgonyi, T.; Marquetand, P.; Weinacht, T. Nonadiabatic dynamics and multiphoton resonances in strong-field molecular ionization with few-cycle laser pulses. Phys. Rev. A
**2016**, 93, 051401. [Google Scholar] [CrossRef] - Li, Q.; Giussani, A.; Segarra-Martí, J.; Nenov, A.; Rivalta, I.; Voityuk, A.A.; Mukamel, S.; Roca-Sanjuán, D.; Garavelli, M.; Blancafort, L. Multiple Decay Mechanisms and 2D-UV Spectroscopic Fingerprints of Singlet Excited Solvated Adenine-Uracil Monophosphate. Chem. Eur. J.
**2016**, 22, 7497–7507. [Google Scholar] [CrossRef] [PubMed] - Marangos, J.P. Development of high harmonic generation spectroscopy of organic molecules and biomolecules. J. Phys. B At. Mol. Opt. Phys.
**2016**, 49, 132001. [Google Scholar] [CrossRef] - Schreier, W.J.; Schrader, T.E.; Koller, F.O.; Gilch, P.; Crespo-Hernández, C.E.; Swaminathan, V.N.; Charell, T.; Zinth, W.; Kohler, B. Thymine Dimerization in DNA Is an Ultrafast Photoreaction. Science
**2007**, 315, 625–629. [Google Scholar] [CrossRef] [PubMed] - Billinghurst, B.E.; Oladepo, S.A.; Loppnow, G.R. pH-Dependent UV Resonance Raman Spectra of Cytosine and Uracil. J. Phys. Chem. B
**2009**, 113, 7392–7397. [Google Scholar] [CrossRef] [PubMed] - Nielsen, L.M.; Hoffmann, S.V.; Nielsen, S.B. Probing electronic coupling between adenine bases in RNA strands from synchrotron radiation circular dichroism experiments. Chem. Commun.
**2012**, 48, 10425–10427. [Google Scholar] [CrossRef] [PubMed] - Lorenz, U.J.; Zewail, A.H. Biomechanics of DNA structures visualized by 4D electron microscopy. Proc. Natl. Acad. Sci. USA
**2013**, 110, 2822–2827. [Google Scholar] [CrossRef] [PubMed] - Wu, X.; Karsili, T.N.V.; Domcke, W. Excited-State Deactivation of Adenine by Electron-Driven Proton-Transfer Reactions in Adenine-Water Clusters: A Computational Study. ChemPhysChem
**2016**, 17, 1298–1304. [Google Scholar] [CrossRef] [PubMed] - Nogueira, J.J.; Oppel, M.; González, L. Enhancing intersystem crossing in phenotiazinium dyes by intercalation into DNA. Angew. Chem. Int. Ed.
**2015**, 54, 4375–4378. [Google Scholar] [CrossRef] [PubMed] - Lavery, R.; Moakher, M.; Maddocks, J.H.; Petkeviciute, D.; Zakrzewska, K. Conformational analysis of nucleic acids revisited: Curves+. Nucleic Acids Res.
**2009**, 37, 5917–5929. [Google Scholar] [CrossRef] [PubMed] - Lu, X.J.; Olson, W.K. 3DNA: A versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nat. Protoc.
**2008**, 3, 1213–1227. [Google Scholar] [CrossRef] [PubMed] - Bignon, E.; Gattuso, H.; Morell, C.; Dehez, F.; Georgakilas, A.G.; Monari, A.; Dumont, E. Correlation of bistranded clustered abasic DNA lesion processing with structural and dynamic DNA helix distortion. Nucleic Acids Res.
**2016**, 44, 8588–8599. [Google Scholar] [CrossRef] [PubMed] - Nogueira, J.J.; González, L. Molecular dynamics simulations of binding modes between methylene blue and DNA with alternating GC and at sequences. Biochemistry
**2014**, 53, 2391–2412. [Google Scholar] [CrossRef] [PubMed] - Kurtz, L.; Hofmann, A.; de Vivie-Riedle, R. Ground state normal mode analysis: Linking excited state dynamics and experimental observables. J. Chem. Phys.
**2001**, 114, 6151–6159. [Google Scholar] [CrossRef] - Plasser, F.; Barbatti, M.; Aquino, A.J.A.; Lischka, H. Excited-State Diproton Transfer in [2,2′-Bipyridyl]-3,3′-diol: The Mechanism Is Sequential, Not Concerted. J. Phys. Chem. A
**2009**, 113, 8490–8499. [Google Scholar] [CrossRef] [PubMed] - Cremer, D.; Pople, J.A. General definition of ring puckering coordinates. J. Am. Chem. Soc.
**1975**, 97, 1354–1358. [Google Scholar] [CrossRef] - Boeyens, J.C.A. The conformation of six-membered rings. J. Cryst. Mol. Struct.
**1978**, 8, 317. [Google Scholar] [CrossRef] - Martin, R.L. Natural transition orbitals. J. Chem. Phys.
**2003**, 118, 4775–4777. [Google Scholar] [CrossRef] - Head-Gordon, M.; Grana, A.; Maurice, D.; White, C. Analysis of Electronic Transitions as the Difference of Electron Attachment and Detachment Densities. J. Phys. Chem.
**1995**, 99, 14261–14270. [Google Scholar] [CrossRef] - Plasser, F.; Bäppler, S.A.; Wormit, M.; Dreuw, A. New tools for the systematic analysis and visualization of electronic excitations. II. Applications. J. Chem. Phys.
**2014**, 141, 024107. [Google Scholar] [CrossRef] [PubMed] - Bäppler, S.A.; Plasser, F.; Wormit, M.; Dreuw, A. Exciton analysis of many-body wave functions: Bridging the gap between the quasiparticle and molecular orbital pictures. Phys. Rev. A
**2014**, 90, 052521. [Google Scholar] [CrossRef] - Luzanov, A.V.; Zhikol, O.A. Electron Invariants and Excited State Structural Analysis for Electronic Transitions Within CIS, RPA, and TDDFT Models. Int. J. Quant. Chem.
**2010**, 110, 902–924. [Google Scholar] [CrossRef] - Plasser, F.; Granucci, G.; Pittner, J.; Barbatti, M.; Persico, M.; Lischka, H. Surface hopping dynamics using a locally diabatic formalism: Charge transfer in the ethylene dimer cation and excited state dynamics in the 2-pyridone dimer. J. Chem. Phys.
**2012**, 137, 22A514. [Google Scholar] [CrossRef] [PubMed] - Voityuk, A.A. Fragment transition density method to calculate electronic coupling for excitation energy transfer. J. Chem. Phys.
**2014**, 140, 244117. [Google Scholar] [CrossRef] [PubMed] - Plasser, F.; Thomitzni, B.; Bäppler, S.A.; Wenzel, J.; Rehn, D.R.; Wormit, M.; Dreuw, A. Statistical analysis of electronic excitation processes: Spatial location, compactness, charge transfer, and electron-hole correlation. J. Comp. Chem.
**2015**, 36, 1609–1620. [Google Scholar] [CrossRef] [PubMed] - Baer, M. Beyond Born-Oppenheimer: Electronic Nonadiabatic Coupling Terms and Conical Intersections; John Wiley & Sons: Hoboken, NJ, USA, 2006. [Google Scholar]
- Thiel, A.; Köppel, H. Proposal and numerical test of a simple diabatization scheme. J. Chem. Phys.
**1999**, 110, 9371–9383. [Google Scholar] [CrossRef] - Mai, S.; Marquetand, P.; González, L. Non-Adiabatic Dynamics in SO
_{2}: II. The Role of Triplet States Studied by Surface-Hopping Simulations. J. Chem. Phys.**2014**, 140, 204302. [Google Scholar] [CrossRef] [PubMed] - Plasser, F.; Lischka, H. Semiclassical dynamics simulations of charge transport in stacked pi-systems. J. Chem. Phys.
**2011**, 134, 34309. [Google Scholar] [CrossRef] [PubMed]

© 2016 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC-BY) license ( http://creativecommons.org/licenses/by/4.0/).

## Share and Cite

**MDPI and ACS Style**

Marquetand, P.; Nogueira, J.J.; Mai, S.; Plasser, F.; González, L.
Challenges in Simulating Light-Induced Processes in DNA. *Molecules* **2017**, *22*, 49.
https://doi.org/10.3390/molecules22010049

**AMA Style**

Marquetand P, Nogueira JJ, Mai S, Plasser F, González L.
Challenges in Simulating Light-Induced Processes in DNA. *Molecules*. 2017; 22(1):49.
https://doi.org/10.3390/molecules22010049

**Chicago/Turabian Style**

Marquetand, Philipp, Juan J. Nogueira, Sebastian Mai, Felix Plasser, and Leticia González.
2017. "Challenges in Simulating Light-Induced Processes in DNA" *Molecules* 22, no. 1: 49.
https://doi.org/10.3390/molecules22010049