Multi-level Quantum Mechanics and Molecular Mechanics Study of Ring Opening Process of Guanine Damage by Hydroxyl Radical in Aqueous Solution

Abstract Combining multi-level quantum mechanics theories and molecular mechanics with an explicit water model, we investigated the ring opening process of guanine damage by hydroxyl radical in aqueous solution. The detailed, atomic-level ring-opening mechanism along the reaction pathway was reveale...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Peng Liu, Qiong Wang, Meixing Niu, Dunyou Wang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4bfb1fd80461469ca8e348c07186e63e
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:4bfb1fd80461469ca8e348c07186e63e
record_format	dspace
spelling	oai:doaj.org-article:4bfb1fd80461469ca8e348c07186e63e2021-12-02T15:06:26ZMulti-level Quantum Mechanics and Molecular Mechanics Study of Ring Opening Process of Guanine Damage by Hydroxyl Radical in Aqueous Solution10.1038/s41598-017-08219-z2045-2322https://doaj.org/article/4bfb1fd80461469ca8e348c07186e63e2017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-08219-zhttps://doaj.org/toc/2045-2322Abstract Combining multi-level quantum mechanics theories and molecular mechanics with an explicit water model, we investigated the ring opening process of guanine damage by hydroxyl radical in aqueous solution. The detailed, atomic-level ring-opening mechanism along the reaction pathway was revealed in aqueous solution at the CCSD(T)/MM levels of theory. The potentials of mean force in aqueous solution were calculated at both the DFT/MM and CCSD(T)/MM levels of the theory. Our study found that the aqueous solution has a significant effect on this reaction in solution. In particular, by comparing the geometries of the stationary points between in gas phase and in aqueous solution, we found that the aqueous solution has a tremendous impact on the torsion angles much more than on the bond lengths and bending angles. Our calculated free-energy barrier height 31.6 kcal/mol at the CCSD(T)/MM level of theory agrees well with the one obtained based on gas-phase reaction profile and free energies of solvation. In addition, the reaction path in gas phase was also mapped using multi-level quantum mechanics theories, which shows a reaction barrier at 19.2 kcal/mol at the CCSD(T) level of theory, agreeing very well with a recent ab initio calculation result at 20.8 kcal/mol.Peng LiuQiong WangMeixing NiuDunyou WangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Peng Liu Qiong Wang Meixing Niu Dunyou Wang Multi-level Quantum Mechanics and Molecular Mechanics Study of Ring Opening Process of Guanine Damage by Hydroxyl Radical in Aqueous Solution
description	Abstract Combining multi-level quantum mechanics theories and molecular mechanics with an explicit water model, we investigated the ring opening process of guanine damage by hydroxyl radical in aqueous solution. The detailed, atomic-level ring-opening mechanism along the reaction pathway was revealed in aqueous solution at the CCSD(T)/MM levels of theory. The potentials of mean force in aqueous solution were calculated at both the DFT/MM and CCSD(T)/MM levels of the theory. Our study found that the aqueous solution has a significant effect on this reaction in solution. In particular, by comparing the geometries of the stationary points between in gas phase and in aqueous solution, we found that the aqueous solution has a tremendous impact on the torsion angles much more than on the bond lengths and bending angles. Our calculated free-energy barrier height 31.6 kcal/mol at the CCSD(T)/MM level of theory agrees well with the one obtained based on gas-phase reaction profile and free energies of solvation. In addition, the reaction path in gas phase was also mapped using multi-level quantum mechanics theories, which shows a reaction barrier at 19.2 kcal/mol at the CCSD(T) level of theory, agreeing very well with a recent ab initio calculation result at 20.8 kcal/mol.
format	article
author	Peng Liu Qiong Wang Meixing Niu Dunyou Wang
author_facet	Peng Liu Qiong Wang Meixing Niu Dunyou Wang
author_sort	Peng Liu
title	Multi-level Quantum Mechanics and Molecular Mechanics Study of Ring Opening Process of Guanine Damage by Hydroxyl Radical in Aqueous Solution
title_short	Multi-level Quantum Mechanics and Molecular Mechanics Study of Ring Opening Process of Guanine Damage by Hydroxyl Radical in Aqueous Solution
title_full	Multi-level Quantum Mechanics and Molecular Mechanics Study of Ring Opening Process of Guanine Damage by Hydroxyl Radical in Aqueous Solution
title_fullStr	Multi-level Quantum Mechanics and Molecular Mechanics Study of Ring Opening Process of Guanine Damage by Hydroxyl Radical in Aqueous Solution
title_full_unstemmed	Multi-level Quantum Mechanics and Molecular Mechanics Study of Ring Opening Process of Guanine Damage by Hydroxyl Radical in Aqueous Solution
title_sort	multi-level quantum mechanics and molecular mechanics study of ring opening process of guanine damage by hydroxyl radical in aqueous solution
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/4bfb1fd80461469ca8e348c07186e63e
work_keys_str_mv	AT pengliu multilevelquantummechanicsandmolecularmechanicsstudyofringopeningprocessofguaninedamagebyhydroxylradicalinaqueoussolution AT qiongwang multilevelquantummechanicsandmolecularmechanicsstudyofringopeningprocessofguaninedamagebyhydroxylradicalinaqueoussolution AT meixingniu multilevelquantummechanicsandmolecularmechanicsstudyofringopeningprocessofguaninedamagebyhydroxylradicalinaqueoussolution AT dunyouwang multilevelquantummechanicsandmolecularmechanicsstudyofringopeningprocessofguaninedamagebyhydroxylradicalinaqueoussolution
_version_	1718388447070126080

Multi-level Quantum Mechanics and Molecular Mechanics Study of Ring Opening Process of Guanine Damage by Hydroxyl Radical in Aqueous Solution

Ejemplares similares