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Wang Y, Liu L, Gao Y, Zhao J, Liu C, Gong L, Yang Z. Development of a QM/MM(ABEEM) method for the deprotonation of neutral and cation radicals in the G-tetrad and GGX(8-oxo-G) tetrad. Phys Chem Chem Phys 2023; 26:504-516. [PMID: 38084041 DOI: 10.1039/d3cp04357f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
The rapid deprotonation of G˙+ in the DNA strand impedes positive charge (hole) transfer, whereas the slow deprotonation rate of G˙+ in the G-tetrad makes it a more suitable carrier for hole conduction. The QM/MM(ABEEM) combined method, which involves the integration of QM and the ABEEM polarizable force field (ABEEM PFF), was developed to investigate the deprotonation of neutral and cation free radicals in the G-tetrad and GGX(8-oxo-G) tetrad (xanthine and 8-oxoguanine dual substituted G-tetrad). By incorporating valence-state electronegativity piecewise functions χ*(r) and implementing charge local conservation conditions, QM/MM(ABEEM) possesses the advantage of accurately simulating charge transfer and polarization effect during deprotonation. The activation energy calculated by the QM method of X˙ is the lowest among other bases in the GGX(8-oxo-G) tetrad, which is supported by the computation of the average electronegativity calculated by ABEEM PFF. By utilizing QM/MM(ABEEM) with a two-way free energy perturbation method, the deprotonation activation energy of X˙ in the GGX(8-oxo-G) tetrad is determined to be 33.0 ± 2.1 kJ mol-1, while that of G˙+ in the G-tetrad is 20.7 ± 0.6 kJ mol-1, consistent with the experimental measurement of 20 ± 1.0 kJ mol-1. These results manifest that X˙ in the GGX(8-oxo-G) tetrad exhibits a slower deprotonation rate than G˙+ in the G-tetrad, suggesting that the GGX(8-oxo-G) tetrad may serve as a more favorable hole transport carrier. Furthermore, the unequal average electronegativities of bases in the GGX(8-oxo-G) tetrad impede the deprotonation rate. This study provides a potential foundation for investigating the microscopic mechanism of DNA electronic devices.
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Affiliation(s)
- Yue Wang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Linlin Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Yue Gao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Jiayue Zhao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Cui Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Lidong Gong
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Zhongzhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
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Liu C, Jiang H, Li Y, Xue B, Yao YY, Yang ZZ. Development of a QM/MM(ABEEM) method combined with a polarizable force field to investigate the excision reaction mechanism of damaged thymine. Phys Chem Chem Phys 2023; 25:3432-3448. [PMID: 36637033 DOI: 10.1039/d2cp05873a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This paper focuses on the development of a quantum mechanics/molecular mechanics method using the ABEEM polarizable force field (QM/MM(ABEEM) method) to investigate the excision reaction mechanism of damaged thymine. This method does not simply combine the QM method with the polarizable force field. A valence electronegativity piecewise function with the distance between atoms as a variable is introduced to describe the atomic partial charges, and changes greatly during the reaction process. At the same time, the charge transfer effect is treated using the condition of local charge conservation. Compared with the traditional QM/MM method, the QM/MM(ABEEM) method can more accurately simulate the polarization effect and charge transfer effect in the reaction process. Focusing on the controversial problems of the excision of damaged bases, six reaction pathways were designed for monofunctional and difunctional deglycosylation of neutral bases and protonated bases. The results show that the QM/MM(ABEEM) method accurately simulates the polarization effect, charge transfer effect, activation energy and other properties of the reaction process. The process in which the active residue Asp activates the nucleophile H2O to attack the protonated base is the preferred path. The average activation energy and free activation energy of the protonated base are 7.00-14.00 kcal mol-1 lower than that of the neutral base. The study in this paper is helpful to understand the mechanism of repair enzymes in repairing bases.
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Affiliation(s)
- Cui Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - He Jiang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Yue Li
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Bing Xue
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Yu-Ying Yao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.
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Liu C, Ren Y, Gao XQ, Du X, Yang ZZ. Development of QM/MM (ABEEM polarizable force field) method to simulate the excision reaction mechanism of damaged cytosine. J Comput Chem 2022; 43:2139-2153. [PMID: 36151878 DOI: 10.1002/jcc.27008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/25/2022] [Accepted: 09/05/2022] [Indexed: 11/06/2022]
Abstract
DNA damages are regarded as having harmful effects on cell. The base excision repair mechanism combats these effects by removing damaged bases. The deglycosylation mechanism of excising damaged bases by DNA glycosylase and the state of the leaving base have been controversial. The enzymatic reaction of DNA glycosylase to remove the damaged bases involves not only the formation and breaking of chemical bonds, but also complex polarization effect and charge transfer, which cannot be accurately simulated by the QM/MM method combined with the fixed charge force field. This work has developed the ABEEM fluctuating polarizable force field combining with the QM method, that is (QM/MM[ABEEM]), to accurately simulate the proton transfer, charge transfer and the charge distribution. The piecewise function is used as the valence-state electronegativity in the QM/MM (ABEEM) to realize the accurate fitting of the charge distribution in reaction. And the charge transfer is accurately simulated by the local charge conservation conditions. Four deglycosylation mechanisms including the monofunctional and difunctional mechanisms of four neutral and protonated cytosine derivatives are explored. It is confirmed that the monofunctional mechanism of Asp-activated nucleophile water is a better deglycosylation mechanism and the base is protonated before the reaction occurs. Protonization of the base reduced the activation energy by 10.00-17.00 kcal/mol. Asp provides the necessary charge for the reaction, and DNA glycosylase preferentially cleaves ɛC. This work provides a theoretical basis for the research of excising damaged bases by DNA glycosylase.
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Affiliation(s)
- Cui Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
| | - Yang Ren
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
| | - Xiao-Qin Gao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
| | - Xue Du
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, People's Republic of China
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Pereira ES, Rodrigues GLS, Rocha WR. Electronic structure and mechanism for the uptake of nitric oxide by the Ru(iii) antitumor complex NAMI-A. RSC Adv 2021; 11:7381-7390. [PMID: 35423255 PMCID: PMC8695036 DOI: 10.1039/d0ra10622d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/05/2021] [Indexed: 11/24/2022] Open
Abstract
Nitric oxide (NO) has well known vasodilation effects in living organisms and its participation in the metastasis of cancer cells through the angiogenesis process has been demonstrated experimentally. Therefore, the uptake of NO has become one focus of investigation to produce anti-metastatic drugs. In this article we have investigated the uptake of NO by the ruthenium based metallodrug trans-tetrachloride(dimethylsulfoxide)imidazole ruthenate(iii) [Im]trans-[RuCl4(Im)(DMSO)], known as New Anti-tumor Metastasis Inhibitor-A (NAMI-A). Electronic structure calculations using Density Functional Theory, DFT, and State-Averaged Complete Active Space Self Consistent Field, SA-CASSCF, with second order perturbation theory corrections, NEVPT2 were carried out to investigate the mechanism involved in the uptake of NO by the Ru-based anticancer metallodrug NAMI-A. The calculations revealed that the reaction takes place at the triplet potential energy surface, with the singlet surface being ∼15 kcal mol-1 shifted to higher energies, and there is a surface crossing to form the most stable singlet product after the reaction takes place at the triplet surface. The spin pairing and electron transfer from the nitric oxide to the metallic fragment takes place at the region of the minimum energy crossing point between the two surfaces. The Ru-NO bond in the {Ru-NO}6 product has ∼10% of the RuIII-NO0 character. The SA-CASSCF/NEVPT2 calculations revealed that the uptake of NO by NAMI-A has a small energy barrier of ∼8 kcal mol-1 and, therefore a rate constant of 11.3 × 106 s-1 at 300 K. In addition, the reaction is thermodynamically favorable, with a Gibbs free energy of ∼30 kcal mol-1. These results show that the uptake of nitric oxide by the NAMI-A complex is kinetically and thermodynamically feasible in biological medium and, therefore, gives support to the anti-angiogenesis theory associated to the mode of action of NAMI-A and other related compounds.
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Affiliation(s)
- Eufrásia S Pereira
- Laboratório de Estudos Computacionais em Sistemas Moleculares, eCsMolab, Departamento de Química, ICEx, Universidade Federal de Minas Gerais 31270-901 Pampulha Belo Horizonte MG Brazil
| | - Gabriel L S Rodrigues
- Laboratório de Estudos Computacionais em Sistemas Moleculares, eCsMolab, Departamento de Química, ICEx, Universidade Federal de Minas Gerais 31270-901 Pampulha Belo Horizonte MG Brazil
| | - Willian R Rocha
- Laboratório de Estudos Computacionais em Sistemas Moleculares, eCsMolab, Departamento de Química, ICEx, Universidade Federal de Minas Gerais 31270-901 Pampulha Belo Horizonte MG Brazil
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Shi H, Gong LD, Liu C, Lu LN, Yang ZZ. ABEEM/MM OH - Models for OH -(H 2O) n Clusters and Aqueous OH -: Structures, Charge Distributions, and Binding Energies. J Phys Chem A 2020; 124:5963-5978. [PMID: 32520555 DOI: 10.1021/acs.jpca.0c03941] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Based on the atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM), two fluctuating charge models of OH--water system were proposed. The difference between these two models is whether there is charge transfer between OH- and its first-shell water molecules. The structures, charge distributions, charge transfer, and binding energies of the OH-(H2O)n (n = 1-8, 10, 15, 23) clusters were studied by these two ABEEM/MM models, the OPLS/AA force field, the OPLS-SMOOTH/AA force field, and the QM methods. The results demonstrate that two ABEEM/MM models can search out all stable structures just as the QM methods, and the structures and charge distributions agree well with those from the QM calculations. The structures, the charge transfer, and the strength of hydrogen bonds in the first hydration shell are closely related to the coordination number of OH-. Molecular dynamics simulations on the aqueous OH- solution are performed at 298 and 278 K using ABEEM/MM-I model. The MD results show that the populations of three-, four-, and five-coordinated OH- are 29.6%, 67.1%, and 3.4% at 298 K, respectively, and those of two-, three-, four-, and five-coordinated OH- are 10.8%, 44.9%, 39.2%, and 4.9% at 278 K, respectively; the average hydrogen bond lengths and the hydrogen bond angle in the first shell increase with the temperature decreasing.
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Affiliation(s)
- Hua Shi
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China.,School of Marine Science and Environment, Dalian Ocean University, Dalian 116023, People's Republic of China
| | - Li-Dong Gong
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China
| | - Cui Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China
| | - Li-Nan Lu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, People's Republic of China
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