Photochemistry of Thymine in Protic Polar Nanomeric Droplets Using Electrostatic Embeding TD-DFT/MM
Thymine photochemistry is important for understanding DNA photodamage. In the gas phase, thymine undergoes a fast non-radiative decay from S<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-10-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/26/19/6021 |
| _version_ | 1797515941237489664 |
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| author | Miquel Huix-Rotllant |
| author_facet | Miquel Huix-Rotllant |
| author_sort | Miquel Huix-Rotllant |
| collection | DOAJ |
| description | Thymine photochemistry is important for understanding DNA photodamage. In the gas phase, thymine undergoes a fast non-radiative decay from S<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mn>2</mn></msub></semantics></math></inline-formula> to S<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mn>1</mn></msub></semantics></math></inline-formula>. In the S<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mn>1</mn></msub></semantics></math></inline-formula> state, it gets trapped for several picoseconds until returning to the ground-state S<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mn>0</mn></msub></semantics></math></inline-formula>. Here, we explore the electrostatic effects of nanomeric droplets of methanol and water on the excited states of thymine. For this purpose, we develop and implement an electrostatic embedding TD-DFT/MM method based on a QM/MM coupling defined through electrostatic potential fitting charges. We show that both in methanol and water, the mechanism is similar to the gas phase. The solvent molecules participate in defining the branching plane of S<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mn>0</mn></msub></semantics></math></inline-formula>/S<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mn>1</mn></msub></semantics></math></inline-formula> intersection and have a negligible effect on the S<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mn>1</mn></msub></semantics></math></inline-formula>/S<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mn>2</mn></msub></semantics></math></inline-formula> intersection. Despite the wrong topology of the ground/excited state intersections, electrostatic embedding TD-DFT/MM allows for a fast exploration of the potential energy surfaces and a qualitative picture of the photophysics of thymine in solvent droplets. |
| first_indexed | 2024-03-10T06:54:21Z |
| format | Article |
| id | doaj.art-b724cc8e84004327b442cd6f2a504aae |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T06:54:21Z |
| publishDate | 2021-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-b724cc8e84004327b442cd6f2a504aae2023-11-22T16:36:08ZengMDPI AGMolecules1420-30492021-10-012619602110.3390/molecules26196021Photochemistry of Thymine in Protic Polar Nanomeric Droplets Using Electrostatic Embeding TD-DFT/MMMiquel Huix-Rotllant0Aix-Marseille University, CNRS, ICR, 13397 Marseille, FranceThymine photochemistry is important for understanding DNA photodamage. In the gas phase, thymine undergoes a fast non-radiative decay from S<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mn>2</mn></msub></semantics></math></inline-formula> to S<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mn>1</mn></msub></semantics></math></inline-formula>. In the S<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mn>1</mn></msub></semantics></math></inline-formula> state, it gets trapped for several picoseconds until returning to the ground-state S<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mn>0</mn></msub></semantics></math></inline-formula>. Here, we explore the electrostatic effects of nanomeric droplets of methanol and water on the excited states of thymine. For this purpose, we develop and implement an electrostatic embedding TD-DFT/MM method based on a QM/MM coupling defined through electrostatic potential fitting charges. We show that both in methanol and water, the mechanism is similar to the gas phase. The solvent molecules participate in defining the branching plane of S<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mn>0</mn></msub></semantics></math></inline-formula>/S<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mn>1</mn></msub></semantics></math></inline-formula> intersection and have a negligible effect on the S<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mn>1</mn></msub></semantics></math></inline-formula>/S<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mn>2</mn></msub></semantics></math></inline-formula> intersection. Despite the wrong topology of the ground/excited state intersections, electrostatic embedding TD-DFT/MM allows for a fast exploration of the potential energy surfaces and a qualitative picture of the photophysics of thymine in solvent droplets.https://www.mdpi.com/1420-3049/26/19/6021electrostatic embeddingQM/MMconical intersectionsnucleobasesthymine |
| spellingShingle | Miquel Huix-Rotllant Photochemistry of Thymine in Protic Polar Nanomeric Droplets Using Electrostatic Embeding TD-DFT/MM Molecules electrostatic embedding QM/MM conical intersections nucleobases thymine |
| title | Photochemistry of Thymine in Protic Polar Nanomeric Droplets Using Electrostatic Embeding TD-DFT/MM |
| title_full | Photochemistry of Thymine in Protic Polar Nanomeric Droplets Using Electrostatic Embeding TD-DFT/MM |
| title_fullStr | Photochemistry of Thymine in Protic Polar Nanomeric Droplets Using Electrostatic Embeding TD-DFT/MM |
| title_full_unstemmed | Photochemistry of Thymine in Protic Polar Nanomeric Droplets Using Electrostatic Embeding TD-DFT/MM |
| title_short | Photochemistry of Thymine in Protic Polar Nanomeric Droplets Using Electrostatic Embeding TD-DFT/MM |
| title_sort | photochemistry of thymine in protic polar nanomeric droplets using electrostatic embeding td dft mm |
| topic | electrostatic embedding QM/MM conical intersections nucleobases thymine |
| url | https://www.mdpi.com/1420-3049/26/19/6021 |
| work_keys_str_mv | AT miquelhuixrotllant photochemistryofthymineinproticpolarnanomericdropletsusingelectrostaticembedingtddftmm |