Effects of ionization on stability of 1-methylcytosine — DFT and PCM studies
Consequences of ionization were studied by quantum-chemical methods (DFT and PCM) for 1-methylcytosine ( MC )—a model of the nucleobase cytosine ( C ) connected with sugar in DNA. For calculations, three prototropic tautomers (one amino and two imino forms) and two imino zwitterions were considered,...
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| Veröffentlicht in: | Journal of molecular modeling 2016-07, Vol.22 (7), p.146-146, Article 146 |
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| creator | Raczyńska, Ewa D. Michalec, Piotr Zalewski, Marcin Sapuła, Mariusz |
| description | Consequences of ionization were studied by quantum-chemical methods (DFT and PCM) for 1-methylcytosine (
MC
)—a model of the nucleobase cytosine (
C
) connected with sugar in DNA. For calculations, three prototropic tautomers (one amino and two imino forms) and two imino zwitterions were considered, including conformational or configurational isomerism of
exo
heterogroups. Ionization and interactions between neighboring groups affect intramolecular proton-transfers, geometric and thermodynamic parameters, and electron delocalization for individual isomers. We discovered that an imino isomer is present in the isomeric mixture in the highest amount for positively ionized
MC
. Its contribution in neutral and negatively ionized
MC
is considerably smaller. Acid-base parameters for selected radical ions were estimated in the gas phase and compared to those of neutral
MC
. Gas-phase acidity of radical cations is close to that of the conjugate acid of
MC
, and gas-phase basicity of radical anions is close to that of the conjugate base of
MC
. Various routes of amino-imino conversion between neutral and ionized isomers were considered. Energetic-barrier for intramolecular proton-transfer in
MC
is close to that in the parent system—formamidine. |
| doi_str_mv | 10.1007/s00894-016-3020-2 |
| format | Article |
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MC
)—a model of the nucleobase cytosine (
C
) connected with sugar in DNA. For calculations, three prototropic tautomers (one amino and two imino forms) and two imino zwitterions were considered, including conformational or configurational isomerism of
exo
heterogroups. Ionization and interactions between neighboring groups affect intramolecular proton-transfers, geometric and thermodynamic parameters, and electron delocalization for individual isomers. We discovered that an imino isomer is present in the isomeric mixture in the highest amount for positively ionized
MC
. Its contribution in neutral and negatively ionized
MC
is considerably smaller. Acid-base parameters for selected radical ions were estimated in the gas phase and compared to those of neutral
MC
. Gas-phase acidity of radical cations is close to that of the conjugate acid of
MC
, and gas-phase basicity of radical anions is close to that of the conjugate base of
MC
. Various routes of amino-imino conversion between neutral and ionized isomers were considered. Energetic-barrier for intramolecular proton-transfer in
MC
is close to that in the parent system—formamidine.</description><identifier>ISSN: 1610-2940</identifier><identifier>EISSN: 0948-5023</identifier><identifier>DOI: 10.1007/s00894-016-3020-2</identifier><identifier>PMID: 27259531</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Characterization and Evaluation of Materials ; Chemistry ; Chemistry and Materials Science ; Computer Appl. in Life Sciences ; Computer Applications in Chemistry ; Cytosine - analogs & derivatives ; Cytosine - chemistry ; Electrons ; Ions - chemistry ; Isomerism ; Models, Molecular ; Molecular Conformation ; Molecular Medicine ; Molecular Structure ; Original Paper ; Protons ; Quantum Theory ; Theoretical and Computational Chemistry ; Thermodynamics ; Water - chemistry</subject><ispartof>Journal of molecular modeling, 2016-07, Vol.22 (7), p.146-146, Article 146</ispartof><rights>The Author(s) 2016</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c442t-9af31ff3e800dbe39587982a637cc4b1f64afe5cf8aeab544148877b7ceb9e2b3</citedby><cites>FETCH-LOGICAL-c442t-9af31ff3e800dbe39587982a637cc4b1f64afe5cf8aeab544148877b7ceb9e2b3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00894-016-3020-2$$EPDF$$P50$$Gspringer$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00894-016-3020-2$$EHTML$$P50$$Gspringer$$Hfree_for_read</linktohtml><link.rule.ids>230,314,776,780,881,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27259531$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Raczyńska, Ewa D.</creatorcontrib><creatorcontrib>Michalec, Piotr</creatorcontrib><creatorcontrib>Zalewski, Marcin</creatorcontrib><creatorcontrib>Sapuła, Mariusz</creatorcontrib><title>Effects of ionization on stability of 1-methylcytosine — DFT and PCM studies</title><title>Journal of molecular modeling</title><addtitle>J Mol Model</addtitle><addtitle>J Mol Model</addtitle><description>Consequences of ionization were studied by quantum-chemical methods (DFT and PCM) for 1-methylcytosine (
MC
)—a model of the nucleobase cytosine (
C
) connected with sugar in DNA. For calculations, three prototropic tautomers (one amino and two imino forms) and two imino zwitterions were considered, including conformational or configurational isomerism of
exo
heterogroups. Ionization and interactions between neighboring groups affect intramolecular proton-transfers, geometric and thermodynamic parameters, and electron delocalization for individual isomers. We discovered that an imino isomer is present in the isomeric mixture in the highest amount for positively ionized
MC
. Its contribution in neutral and negatively ionized
MC
is considerably smaller. Acid-base parameters for selected radical ions were estimated in the gas phase and compared to those of neutral
MC
. Gas-phase acidity of radical cations is close to that of the conjugate acid of
MC
, and gas-phase basicity of radical anions is close to that of the conjugate base of
MC
. Various routes of amino-imino conversion between neutral and ionized isomers were considered. Energetic-barrier for intramolecular proton-transfer in
MC
is close to that in the parent system—formamidine.</description><subject>Characterization and Evaluation of Materials</subject><subject>Chemistry</subject><subject>Chemistry and Materials Science</subject><subject>Computer Appl. in Life Sciences</subject><subject>Computer Applications in Chemistry</subject><subject>Cytosine - analogs & derivatives</subject><subject>Cytosine - chemistry</subject><subject>Electrons</subject><subject>Ions - chemistry</subject><subject>Isomerism</subject><subject>Models, Molecular</subject><subject>Molecular Conformation</subject><subject>Molecular Medicine</subject><subject>Molecular Structure</subject><subject>Original Paper</subject><subject>Protons</subject><subject>Quantum Theory</subject><subject>Theoretical and Computational Chemistry</subject><subject>Thermodynamics</subject><subject>Water - chemistry</subject><issn>1610-2940</issn><issn>0948-5023</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><recordid>eNp9kc9OGzEQxi0EIhHwAL1Ue-xlYfxnd-1LpSolUCktHOjZ8jrjYLRZ07UXKZx4CJ6QJ8FRKGovSCONNN9vPlvzEfKJwikFaM4igFSiBFqXHBiUbI9MQQlZVsD4PpnSmuahEjAhJzHeAQBlVV0xdkgmrGGVqjidkl_nzqFNsQiu8KH3jyblVuSKybS-82mzlWi5xnS76ewmheh7LF6enovv85vC9MvievYz0-PSYzwmB850EU_e-hH5PT-_mV2Wi6uLH7Nvi9IKwVKpjOPUOY4SYNkiV5VslGSm5o21oqWuFsZhZZ00aNpKCCqkbJq2sdgqZC0_Il93vvdju8alxT4NptP3g1-bYaOD8fp_pfe3ehUetJCKQy2ywZc3gyH8GTEmvfbRYteZHsMYNW0UV8B5zTJKd6gdQowDuvdnKOhtFHoXhc5R6G0Uervz-d__vW_8PXwG2A6IWepXOOi7MA59vtkHrq-dVZWJ</recordid><startdate>20160701</startdate><enddate>20160701</enddate><creator>Raczyńska, Ewa D.</creator><creator>Michalec, Piotr</creator><creator>Zalewski, Marcin</creator><creator>Sapuła, Mariusz</creator><general>Springer Berlin Heidelberg</general><scope>C6C</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20160701</creationdate><title>Effects of ionization on stability of 1-methylcytosine — DFT and PCM studies</title><author>Raczyńska, Ewa D. ; Michalec, Piotr ; Zalewski, Marcin ; Sapuła, Mariusz</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c442t-9af31ff3e800dbe39587982a637cc4b1f64afe5cf8aeab544148877b7ceb9e2b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Characterization and Evaluation of Materials</topic><topic>Chemistry</topic><topic>Chemistry and Materials Science</topic><topic>Computer Appl. in Life Sciences</topic><topic>Computer Applications in Chemistry</topic><topic>Cytosine - analogs & derivatives</topic><topic>Cytosine - chemistry</topic><topic>Electrons</topic><topic>Ions - chemistry</topic><topic>Isomerism</topic><topic>Models, Molecular</topic><topic>Molecular Conformation</topic><topic>Molecular Medicine</topic><topic>Molecular Structure</topic><topic>Original Paper</topic><topic>Protons</topic><topic>Quantum Theory</topic><topic>Theoretical and Computational Chemistry</topic><topic>Thermodynamics</topic><topic>Water - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Raczyńska, Ewa D.</creatorcontrib><creatorcontrib>Michalec, Piotr</creatorcontrib><creatorcontrib>Zalewski, Marcin</creatorcontrib><creatorcontrib>Sapuła, Mariusz</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Journal of molecular modeling</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Raczyńska, Ewa D.</au><au>Michalec, Piotr</au><au>Zalewski, Marcin</au><au>Sapuła, Mariusz</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Effects of ionization on stability of 1-methylcytosine — DFT and PCM studies</atitle><jtitle>Journal of molecular modeling</jtitle><stitle>J Mol Model</stitle><addtitle>J Mol Model</addtitle><date>2016-07-01</date><risdate>2016</risdate><volume>22</volume><issue>7</issue><spage>146</spage><epage>146</epage><pages>146-146</pages><artnum>146</artnum><issn>1610-2940</issn><eissn>0948-5023</eissn><abstract>Consequences of ionization were studied by quantum-chemical methods (DFT and PCM) for 1-methylcytosine (
MC
)—a model of the nucleobase cytosine (
C
) connected with sugar in DNA. For calculations, three prototropic tautomers (one amino and two imino forms) and two imino zwitterions were considered, including conformational or configurational isomerism of
exo
heterogroups. Ionization and interactions between neighboring groups affect intramolecular proton-transfers, geometric and thermodynamic parameters, and electron delocalization for individual isomers. We discovered that an imino isomer is present in the isomeric mixture in the highest amount for positively ionized
MC
. Its contribution in neutral and negatively ionized
MC
is considerably smaller. Acid-base parameters for selected radical ions were estimated in the gas phase and compared to those of neutral
MC
. Gas-phase acidity of radical cations is close to that of the conjugate acid of
MC
, and gas-phase basicity of radical anions is close to that of the conjugate base of
MC
. Various routes of amino-imino conversion between neutral and ionized isomers were considered. Energetic-barrier for intramolecular proton-transfer in
MC
is close to that in the parent system—formamidine.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>27259531</pmid><doi>10.1007/s00894-016-3020-2</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Characterization and Evaluation of Materials Chemistry Chemistry and Materials Science Computer Appl. in Life Sciences Computer Applications in Chemistry Cytosine - analogs & derivatives Cytosine - chemistry Electrons Ions - chemistry Isomerism Models, Molecular Molecular Conformation Molecular Medicine Molecular Structure Original Paper Protons Quantum Theory Theoretical and Computational Chemistry Thermodynamics Water - chemistry |
| title | Effects of ionization on stability of 1-methylcytosine — DFT and PCM studies |
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