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
The rapid deprotonation of G&z.rad; + in the DNA strand impedes positive charge (hole) transfer, whereas the slow deprotonation rate of G&z.rad; + 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...
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| Veröffentlicht in: | Physical chemistry chemical physics : PCCP 2023-12, Vol.26 (1), p.54-516 |
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| creator | Wang, Yue Liu, Linlin Gao, Yue Zhao, Jiayue Liu, Cui Gong, Lidong Yang, Zhongzhi |
| description | The rapid deprotonation of G&z.rad;
+
in the DNA strand impedes positive charge (hole) transfer, whereas the slow deprotonation rate of G&z.rad;
+
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&z.rad; 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&z.rad; in the GGX(8-oxo-G) tetrad is determined to be 33.0 ± 2.1 kJ mol
−1
, while that of G&z.rad;
+
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&z.rad; in the GGX(8-oxo-G) tetrad exhibits a slower deprotonation rate than G&z.rad;
+
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.
The unequal average electronegativity within GGX(8-oxo-G) tetrad impedes deprotonation and reduces competition with hole transfer, ultimately enhancing hole transfer efficiency. |
| doi_str_mv | 10.1039/d3cp04357f |
| format | Article |
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+
in the DNA strand impedes positive charge (hole) transfer, whereas the slow deprotonation rate of G&z.rad;
+
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&z.rad; 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&z.rad; in the GGX(8-oxo-G) tetrad is determined to be 33.0 ± 2.1 kJ mol
−1
, while that of G&z.rad;
+
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&z.rad; in the GGX(8-oxo-G) tetrad exhibits a slower deprotonation rate than G&z.rad;
+
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.
The unequal average electronegativity within GGX(8-oxo-G) tetrad impedes deprotonation and reduces competition with hole transfer, ultimately enhancing hole transfer efficiency.]]></description><identifier>ISSN: 1463-9076</identifier><identifier>EISSN: 1463-9084</identifier><identifier>DOI: 10.1039/d3cp04357f</identifier><identifier>PMID: 38084041</identifier><language>eng</language><publisher>England: Royal Society of Chemistry</publisher><subject>Activation energy ; Cations ; Charge transfer ; Electronegativity ; Free energy ; Free radicals ; Mathematical analysis ; Perturbation methods</subject><ispartof>Physical chemistry chemical physics : PCCP, 2023-12, Vol.26 (1), p.54-516</ispartof><rights>Copyright Royal Society of Chemistry 2024</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c296t-3a3d8ac00cf2efe97b132482c0d255b33b8d745a07068a862fc959aac72ff14f3</cites><orcidid>0000-0001-9575-2288 ; 0000-0002-6767-2915 ; 0000-0003-2979-2040</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27901,27902</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38084041$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wang, Yue</creatorcontrib><creatorcontrib>Liu, Linlin</creatorcontrib><creatorcontrib>Gao, Yue</creatorcontrib><creatorcontrib>Zhao, Jiayue</creatorcontrib><creatorcontrib>Liu, Cui</creatorcontrib><creatorcontrib>Gong, Lidong</creatorcontrib><creatorcontrib>Yang, Zhongzhi</creatorcontrib><title>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</title><title>Physical chemistry chemical physics : PCCP</title><addtitle>Phys Chem Chem Phys</addtitle><description><![CDATA[The rapid deprotonation of G&z.rad;
+
in the DNA strand impedes positive charge (hole) transfer, whereas the slow deprotonation rate of G&z.rad;
+
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&z.rad; 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&z.rad; in the GGX(8-oxo-G) tetrad is determined to be 33.0 ± 2.1 kJ mol
−1
, while that of G&z.rad;
+
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&z.rad; in the GGX(8-oxo-G) tetrad exhibits a slower deprotonation rate than G&z.rad;
+
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.
The unequal average electronegativity within GGX(8-oxo-G) tetrad impedes deprotonation and reduces competition with hole transfer, ultimately enhancing hole transfer efficiency.]]></description><subject>Activation energy</subject><subject>Cations</subject><subject>Charge transfer</subject><subject>Electronegativity</subject><subject>Free energy</subject><subject>Free radicals</subject><subject>Mathematical analysis</subject><subject>Perturbation methods</subject><issn>1463-9076</issn><issn>1463-9084</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><recordid>eNpd0U1L7DAUBuAginrVjXsl4GYUqkmTNulyHMcqOKig4K5k8oGVthmT9HLv0n9uZqojuEo4eXJOwgvAIUbnGJHiQhG5QJRkzGyAXUxzkhSI0831nuU74I_3bwghnGGyDXYIjwBRvAs-rvRf3dhFq7sArYECPs4uZrPR-HI6nZ3CVodXq6CxDoZXDZVeOBtsJ0JtuyXvdB-caKDoFJRD1QlVS9F4WHerO2USdDRqZcryZcQT-88m5Skc6vtgy0SuD77WPfB8PX2a3CR39-XtZHyXyLTIQ0IEUVxIhKRJtdEFm2OSUp5KpNIsmxMy54rRTCCGci54nhpZZIUQkqXGYGrIHhgNfeMX3nvtQ9XWXuqmEZ22va_SAsVBjGEW6ckv-mZ718XXLRXFPKMkj-psUNJZ75021cLVrXD_K4yqZTDVFZk8rIK5jvj4q2U_b7Va0-8kIjgagPNyffqTLPkE3-qP_A</recordid><startdate>20231221</startdate><enddate>20231221</enddate><creator>Wang, Yue</creator><creator>Liu, Linlin</creator><creator>Gao, Yue</creator><creator>Zhao, Jiayue</creator><creator>Liu, Cui</creator><creator>Gong, Lidong</creator><creator>Yang, Zhongzhi</creator><general>Royal Society of Chemistry</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7SR</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>JG9</scope><scope>L7M</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0001-9575-2288</orcidid><orcidid>https://orcid.org/0000-0002-6767-2915</orcidid><orcidid>https://orcid.org/0000-0003-2979-2040</orcidid></search><sort><creationdate>20231221</creationdate><title>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</title><author>Wang, Yue ; Liu, Linlin ; Gao, Yue ; Zhao, Jiayue ; Liu, Cui ; Gong, Lidong ; Yang, Zhongzhi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c296t-3a3d8ac00cf2efe97b132482c0d255b33b8d745a07068a862fc959aac72ff14f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Activation energy</topic><topic>Cations</topic><topic>Charge transfer</topic><topic>Electronegativity</topic><topic>Free energy</topic><topic>Free radicals</topic><topic>Mathematical analysis</topic><topic>Perturbation methods</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wang, Yue</creatorcontrib><creatorcontrib>Liu, Linlin</creatorcontrib><creatorcontrib>Gao, Yue</creatorcontrib><creatorcontrib>Zhao, Jiayue</creatorcontrib><creatorcontrib>Liu, Cui</creatorcontrib><creatorcontrib>Gong, Lidong</creatorcontrib><creatorcontrib>Yang, Zhongzhi</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Engineered Materials Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>Materials Research Database</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>MEDLINE - Academic</collection><jtitle>Physical chemistry chemical physics : PCCP</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wang, Yue</au><au>Liu, Linlin</au><au>Gao, Yue</au><au>Zhao, Jiayue</au><au>Liu, Cui</au><au>Gong, Lidong</au><au>Yang, Zhongzhi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>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</atitle><jtitle>Physical chemistry chemical physics : PCCP</jtitle><addtitle>Phys Chem Chem Phys</addtitle><date>2023-12-21</date><risdate>2023</risdate><volume>26</volume><issue>1</issue><spage>54</spage><epage>516</epage><pages>54-516</pages><issn>1463-9076</issn><eissn>1463-9084</eissn><abstract><![CDATA[The rapid deprotonation of G&z.rad;
+
in the DNA strand impedes positive charge (hole) transfer, whereas the slow deprotonation rate of G&z.rad;
+
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&z.rad; 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&z.rad; in the GGX(8-oxo-G) tetrad is determined to be 33.0 ± 2.1 kJ mol
−1
, while that of G&z.rad;
+
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&z.rad; in the GGX(8-oxo-G) tetrad exhibits a slower deprotonation rate than G&z.rad;
+
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.
The unequal average electronegativity within GGX(8-oxo-G) tetrad impedes deprotonation and reduces competition with hole transfer, ultimately enhancing hole transfer efficiency.]]></abstract><cop>England</cop><pub>Royal Society of Chemistry</pub><pmid>38084041</pmid><doi>10.1039/d3cp04357f</doi><tpages>13</tpages><orcidid>https://orcid.org/0000-0001-9575-2288</orcidid><orcidid>https://orcid.org/0000-0002-6767-2915</orcidid><orcidid>https://orcid.org/0000-0003-2979-2040</orcidid></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1463-9076 |
| ispartof | Physical chemistry chemical physics : PCCP, 2023-12, Vol.26 (1), p.54-516 |
| issn | 1463-9076 1463-9084 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_2902967717 |
| source | Royal Society Of Chemistry Journals 2008-; Alma/SFX Local Collection |
| subjects | Activation energy Cations Charge transfer Electronegativity Free energy Free radicals Mathematical analysis Perturbation methods |
| title | 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 |
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