Challenges in Simulating Light-Induced Processes in DNA
In this contribution, we give a perspective on the main challenges in performing theoretical simulations of photoinduced phenomena within DNA and its molecular building blocks. We distinguish the different tasks that should be involved in the simulation of a complete DNA strand subject to UV irradia...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2016-12-01
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| Series: | Molecules |
| Subjects: | |
| Online Access: | http://www.mdpi.com/1420-3049/22/1/49 |
| _version_ | 1819100651564564480 |
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| author | Philipp Marquetand Juan J. Nogueira Sebastian Mai Felix Plasser Leticia González |
| author_facet | Philipp Marquetand Juan J. Nogueira Sebastian Mai Felix Plasser Leticia González |
| author_sort | Philipp Marquetand |
| collection | DOAJ |
| description | In this contribution, we give a perspective on the main challenges in performing theoretical simulations of photoinduced phenomena within DNA and its molecular building blocks. We distinguish the different tasks that should be involved in the simulation of a complete DNA strand subject to UV irradiation: (i) stationary quantum chemical computations; (ii) the explicit description of the initial excitation of DNA with light; (iii) modeling the nonadiabatic excited state dynamics; (iv) simulation of the detected experimental observable; and (v) the subsequent analysis of the respective results. We succinctly describe the methods that are currently employed in each of these steps. While for each of them, there are different approaches with different degrees of accuracy, no feasible method exists to tackle all problems at once. Depending on the technique or combination of several ones, it can be problematic to describe the stacking of nucleobases, bond breaking and formation, quantum interferences and tunneling or even simply to characterize the involved wavefunctions. It is therefore argued that more method development and/or the combination of different techniques are urgently required. It is essential also to exercise these new developments in further studies on DNA and subsystems thereof, ideally comprising simulations of all of the different components that occur in the corresponding experiments. |
| first_indexed | 2024-12-22T01:06:10Z |
| format | Article |
| id | doaj.art-29949107b71c4aaea1d89d4be2deaa18 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-12-22T01:06:10Z |
| publishDate | 2016-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-29949107b71c4aaea1d89d4be2deaa182022-12-21T18:44:04ZengMDPI AGMolecules1420-30492016-12-012214910.3390/molecules22010049molecules22010049Challenges in Simulating Light-Induced Processes in DNAPhilipp Marquetand0Juan J. Nogueira1Sebastian Mai2Felix Plasser3Leticia González4Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, AustriaInstitute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, AustriaInstitute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, AustriaInstitute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, AustriaInstitute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, AustriaIn this contribution, we give a perspective on the main challenges in performing theoretical simulations of photoinduced phenomena within DNA and its molecular building blocks. We distinguish the different tasks that should be involved in the simulation of a complete DNA strand subject to UV irradiation: (i) stationary quantum chemical computations; (ii) the explicit description of the initial excitation of DNA with light; (iii) modeling the nonadiabatic excited state dynamics; (iv) simulation of the detected experimental observable; and (v) the subsequent analysis of the respective results. We succinctly describe the methods that are currently employed in each of these steps. While for each of them, there are different approaches with different degrees of accuracy, no feasible method exists to tackle all problems at once. Depending on the technique or combination of several ones, it can be problematic to describe the stacking of nucleobases, bond breaking and formation, quantum interferences and tunneling or even simply to characterize the involved wavefunctions. It is therefore argued that more method development and/or the combination of different techniques are urgently required. It is essential also to exercise these new developments in further studies on DNA and subsystems thereof, ideally comprising simulations of all of the different components that occur in the corresponding experiments.http://www.mdpi.com/1420-3049/22/1/49DNAphotochemistryexcited statessimulationelectronic structureab initio molecular dynamicsQM/MMtheoretical chemistry |
| spellingShingle | Philipp Marquetand Juan J. Nogueira Sebastian Mai Felix Plasser Leticia González Challenges in Simulating Light-Induced Processes in DNA Molecules DNA photochemistry excited states simulation electronic structure ab initio molecular dynamics QM/MM theoretical chemistry |
| title | Challenges in Simulating Light-Induced Processes in DNA |
| title_full | Challenges in Simulating Light-Induced Processes in DNA |
| title_fullStr | Challenges in Simulating Light-Induced Processes in DNA |
| title_full_unstemmed | Challenges in Simulating Light-Induced Processes in DNA |
| title_short | Challenges in Simulating Light-Induced Processes in DNA |
| title_sort | challenges in simulating light induced processes in dna |
| topic | DNA photochemistry excited states simulation electronic structure ab initio molecular dynamics QM/MM theoretical chemistry |
| url | http://www.mdpi.com/1420-3049/22/1/49 |
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