Loading…
Estimate of the Reorganization Energy for Charge Transfer in DNA
The solvent reorganization energy λs can have a significant effect on the activation energy for charge transfer in DNA and its dependence on donor (D)−acceptor (A) distance R DA. To estimate λs and the resulting effective contribution β s to the falloff parameter β for the overall transfer rate cons...
Saved in:
| Published in: | The journal of physical chemistry. B 2003-03, Vol.107 (11), p.2595-2601 |
|---|---|
| Main Authors: | , , , |
| Format: | Article |
| Language: | English |
| Citations: | Items that this one cites Items that cite this one |
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| cited_by | cdi_FETCH-LOGICAL-a361t-944874b835f96b6b32d277455b0dc11cc40e35957c4d8b02f66d1221defde6a63 |
|---|---|
| cites | cdi_FETCH-LOGICAL-a361t-944874b835f96b6b32d277455b0dc11cc40e35957c4d8b02f66d1221defde6a63 |
| container_end_page | 2601 |
| container_issue | 11 |
| container_start_page | 2595 |
| container_title | The journal of physical chemistry. B |
| container_volume | 107 |
| creator | Siriwong, Khatcharin Voityuk, Alexander A Newton, Marshall D Rösch, Notker |
| description | The solvent reorganization energy λs can have a significant effect on the activation energy for charge transfer in DNA and its dependence on donor (D)−acceptor (A) distance R DA. To estimate λs and the resulting effective contribution β s to the falloff parameter β for the overall transfer rate constant, the Poisson equation was solved numerically for several systems representing DNA duplexes, 5‘-GGGT n GGG-3‘, in a realistically structured heterogeneous dielectric, as determined by molecular dynamics (MD) simulations. The charge transfer was modeled primarily for holes localized on single guanine bases. Effects of thermal fluctuations on λs were taken into account via structures for a given duplex sampled from MD trajectories. Calculated values of λs were found to be rather insensitive to thermal fluctuations of the DNA fragments but depended in crucial fashion on details of the dielectric model (shape and dielectric constants of various zones) that was used to describe the polarization response of the DNA and its environment to the charge transfer. λs was calculated to increase rapidly at small R DA values ( |
| doi_str_mv | 10.1021/jp027052q |
| format | article |
| fullrecord | <record><control><sourceid>acs_cross</sourceid><recordid>TN_cdi_crossref_primary_10_1021_jp027052q</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>d294811847</sourcerecordid><originalsourceid>FETCH-LOGICAL-a361t-944874b835f96b6b32d277455b0dc11cc40e35957c4d8b02f66d1221defde6a63</originalsourceid><addsrcrecordid>eNptj8FOhDAURRujiePowj_oxoUL9LXQFnZOEEaTiRrBuGwKtAyoMLaYOH69GCazcvFy3-Lk5h6EzglcEaDkut0AFcDo5wGaEUbBG08c7n5OgB-jE-daAMpoyGfoJnFD86EGjXuDh7XGz7q3teqaHzU0fYeTTtt6i01vcbxWttY4t6pzRlvcdPj2YXGKjox6d_psl3P0kiZ5fOetHpf38WLlKZ-TwYuCIBRBEfrMRLzghU8rKkTAWAFVSUhZBqB9FjFRBlVYADWcV4RSUmlTaa64P0eXU29pe-esNnJjx-F2KwnIP3W5Vx9Zb2IbN-jvPajsm-TCF0zmT5nMIF9mryyV6chfTLwqnWz7L9uNJv_0_gJavWWv</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype></control><display><type>article</type><title>Estimate of the Reorganization Energy for Charge Transfer in DNA</title><source>American Chemical Society:Jisc Collections:American Chemical Society Read & Publish Agreement 2022-2024 (Reading list)</source><creator>Siriwong, Khatcharin ; Voityuk, Alexander A ; Newton, Marshall D ; Rösch, Notker</creator><creatorcontrib>Siriwong, Khatcharin ; Voityuk, Alexander A ; Newton, Marshall D ; Rösch, Notker</creatorcontrib><description>The solvent reorganization energy λs can have a significant effect on the activation energy for charge transfer in DNA and its dependence on donor (D)−acceptor (A) distance R DA. To estimate λs and the resulting effective contribution β s to the falloff parameter β for the overall transfer rate constant, the Poisson equation was solved numerically for several systems representing DNA duplexes, 5‘-GGGT n GGG-3‘, in a realistically structured heterogeneous dielectric, as determined by molecular dynamics (MD) simulations. The charge transfer was modeled primarily for holes localized on single guanine bases. Effects of thermal fluctuations on λs were taken into account via structures for a given duplex sampled from MD trajectories. Calculated values of λs were found to be rather insensitive to thermal fluctuations of the DNA fragments but depended in crucial fashion on details of the dielectric model (shape and dielectric constants of various zones) that was used to describe the polarization response of the DNA and its environment to the charge transfer. λs was calculated to increase rapidly at small R DA values (<15 Å), and accordingly the falloff parameter β s (defined as a local function of R DA) decreases appreciably with increasing R DA (from 1.0 Å-1 with only one intermediate base pair between D and A to 0.15 Å-1 for systems with five intervening pairs). Calculated λs values were accurately fitted (standard deviation of ∼0.5 kcal/mol) to a linear function of 1/R DA, including all cases except contact (R DA = 3.4 Å), where some overlap of D and A sites may occur. A linear fit to an exponential (of form exp(−βs R DA)) gave comparable accuracy for the entire R DA range. λs based on D and A holes delocalized over two adjacent guanine bases was uniformly ∼12 kcal/mol smaller than the corresponding results for holes localized on single guanines, almost independent of R DA. The internal reorganization energy for hole transfer between GC pairs was calculated at 16.6 kcal/mol at the B3LYP/6-31G* level.</description><identifier>ISSN: 1520-6106</identifier><identifier>EISSN: 1520-5207</identifier><identifier>DOI: 10.1021/jp027052q</identifier><language>eng</language><publisher>American Chemical Society</publisher><ispartof>The journal of physical chemistry. B, 2003-03, Vol.107 (11), p.2595-2601</ispartof><rights>Copyright © 2003 American Chemical Society</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a361t-944874b835f96b6b32d277455b0dc11cc40e35957c4d8b02f66d1221defde6a63</citedby><cites>FETCH-LOGICAL-a361t-944874b835f96b6b32d277455b0dc11cc40e35957c4d8b02f66d1221defde6a63</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>315,786,790,27957,27958</link.rule.ids></links><search><creatorcontrib>Siriwong, Khatcharin</creatorcontrib><creatorcontrib>Voityuk, Alexander A</creatorcontrib><creatorcontrib>Newton, Marshall D</creatorcontrib><creatorcontrib>Rösch, Notker</creatorcontrib><title>Estimate of the Reorganization Energy for Charge Transfer in DNA</title><title>The journal of physical chemistry. B</title><addtitle>J. Phys. Chem. B</addtitle><description>The solvent reorganization energy λs can have a significant effect on the activation energy for charge transfer in DNA and its dependence on donor (D)−acceptor (A) distance R DA. To estimate λs and the resulting effective contribution β s to the falloff parameter β for the overall transfer rate constant, the Poisson equation was solved numerically for several systems representing DNA duplexes, 5‘-GGGT n GGG-3‘, in a realistically structured heterogeneous dielectric, as determined by molecular dynamics (MD) simulations. The charge transfer was modeled primarily for holes localized on single guanine bases. Effects of thermal fluctuations on λs were taken into account via structures for a given duplex sampled from MD trajectories. Calculated values of λs were found to be rather insensitive to thermal fluctuations of the DNA fragments but depended in crucial fashion on details of the dielectric model (shape and dielectric constants of various zones) that was used to describe the polarization response of the DNA and its environment to the charge transfer. λs was calculated to increase rapidly at small R DA values (<15 Å), and accordingly the falloff parameter β s (defined as a local function of R DA) decreases appreciably with increasing R DA (from 1.0 Å-1 with only one intermediate base pair between D and A to 0.15 Å-1 for systems with five intervening pairs). Calculated λs values were accurately fitted (standard deviation of ∼0.5 kcal/mol) to a linear function of 1/R DA, including all cases except contact (R DA = 3.4 Å), where some overlap of D and A sites may occur. A linear fit to an exponential (of form exp(−βs R DA)) gave comparable accuracy for the entire R DA range. λs based on D and A holes delocalized over two adjacent guanine bases was uniformly ∼12 kcal/mol smaller than the corresponding results for holes localized on single guanines, almost independent of R DA. The internal reorganization energy for hole transfer between GC pairs was calculated at 16.6 kcal/mol at the B3LYP/6-31G* level.</description><issn>1520-6106</issn><issn>1520-5207</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2003</creationdate><recordtype>article</recordtype><recordid>eNptj8FOhDAURRujiePowj_oxoUL9LXQFnZOEEaTiRrBuGwKtAyoMLaYOH69GCazcvFy3-Lk5h6EzglcEaDkut0AFcDo5wGaEUbBG08c7n5OgB-jE-daAMpoyGfoJnFD86EGjXuDh7XGz7q3teqaHzU0fYeTTtt6i01vcbxWttY4t6pzRlvcdPj2YXGKjox6d_psl3P0kiZ5fOetHpf38WLlKZ-TwYuCIBRBEfrMRLzghU8rKkTAWAFVSUhZBqB9FjFRBlVYADWcV4RSUmlTaa64P0eXU29pe-esNnJjx-F2KwnIP3W5Vx9Zb2IbN-jvPajsm-TCF0zmT5nMIF9mryyV6chfTLwqnWz7L9uNJv_0_gJavWWv</recordid><startdate>20030320</startdate><enddate>20030320</enddate><creator>Siriwong, Khatcharin</creator><creator>Voityuk, Alexander A</creator><creator>Newton, Marshall D</creator><creator>Rösch, Notker</creator><general>American Chemical Society</general><scope>BSCLL</scope><scope>AAYXX</scope><scope>CITATION</scope></search><sort><creationdate>20030320</creationdate><title>Estimate of the Reorganization Energy for Charge Transfer in DNA</title><author>Siriwong, Khatcharin ; Voityuk, Alexander A ; Newton, Marshall D ; Rösch, Notker</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a361t-944874b835f96b6b32d277455b0dc11cc40e35957c4d8b02f66d1221defde6a63</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2003</creationdate><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Siriwong, Khatcharin</creatorcontrib><creatorcontrib>Voityuk, Alexander A</creatorcontrib><creatorcontrib>Newton, Marshall D</creatorcontrib><creatorcontrib>Rösch, Notker</creatorcontrib><collection>Istex</collection><collection>CrossRef</collection><jtitle>The journal of physical chemistry. B</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Siriwong, Khatcharin</au><au>Voityuk, Alexander A</au><au>Newton, Marshall D</au><au>Rösch, Notker</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Estimate of the Reorganization Energy for Charge Transfer in DNA</atitle><jtitle>The journal of physical chemistry. B</jtitle><addtitle>J. Phys. Chem. B</addtitle><date>2003-03-20</date><risdate>2003</risdate><volume>107</volume><issue>11</issue><spage>2595</spage><epage>2601</epage><pages>2595-2601</pages><issn>1520-6106</issn><eissn>1520-5207</eissn><notes>ark:/67375/TPS-S0TGSW5F-F</notes><notes>istex:2986A07B7ACC1E9103F1A0AE3C2C8883345A742D</notes><abstract>The solvent reorganization energy λs can have a significant effect on the activation energy for charge transfer in DNA and its dependence on donor (D)−acceptor (A) distance R DA. To estimate λs and the resulting effective contribution β s to the falloff parameter β for the overall transfer rate constant, the Poisson equation was solved numerically for several systems representing DNA duplexes, 5‘-GGGT n GGG-3‘, in a realistically structured heterogeneous dielectric, as determined by molecular dynamics (MD) simulations. The charge transfer was modeled primarily for holes localized on single guanine bases. Effects of thermal fluctuations on λs were taken into account via structures for a given duplex sampled from MD trajectories. Calculated values of λs were found to be rather insensitive to thermal fluctuations of the DNA fragments but depended in crucial fashion on details of the dielectric model (shape and dielectric constants of various zones) that was used to describe the polarization response of the DNA and its environment to the charge transfer. λs was calculated to increase rapidly at small R DA values (<15 Å), and accordingly the falloff parameter β s (defined as a local function of R DA) decreases appreciably with increasing R DA (from 1.0 Å-1 with only one intermediate base pair between D and A to 0.15 Å-1 for systems with five intervening pairs). Calculated λs values were accurately fitted (standard deviation of ∼0.5 kcal/mol) to a linear function of 1/R DA, including all cases except contact (R DA = 3.4 Å), where some overlap of D and A sites may occur. A linear fit to an exponential (of form exp(−βs R DA)) gave comparable accuracy for the entire R DA range. λs based on D and A holes delocalized over two adjacent guanine bases was uniformly ∼12 kcal/mol smaller than the corresponding results for holes localized on single guanines, almost independent of R DA. The internal reorganization energy for hole transfer between GC pairs was calculated at 16.6 kcal/mol at the B3LYP/6-31G* level.</abstract><pub>American Chemical Society</pub><doi>10.1021/jp027052q</doi><tpages>7</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1520-6106 |
| ispartof | The journal of physical chemistry. B, 2003-03, Vol.107 (11), p.2595-2601 |
| issn | 1520-6106 1520-5207 |
| language | eng |
| recordid | cdi_crossref_primary_10_1021_jp027052q |
| source | American Chemical Society:Jisc Collections:American Chemical Society Read & Publish Agreement 2022-2024 (Reading list) |
| title | Estimate of the Reorganization Energy for Charge Transfer in DNA |
| url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-09-21T14%3A35%3A45IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-acs_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Estimate%20of%20the%20Reorganization%20Energy%20for%20Charge%20Transfer%20in%20DNA&rft.jtitle=The%20journal%20of%20physical%20chemistry.%20B&rft.au=Siriwong,%20Khatcharin&rft.date=2003-03-20&rft.volume=107&rft.issue=11&rft.spage=2595&rft.epage=2601&rft.pages=2595-2601&rft.issn=1520-6106&rft.eissn=1520-5207&rft_id=info:doi/10.1021/jp027052q&rft_dat=%3Cacs_cross%3Ed294811847%3C/acs_cross%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-a361t-944874b835f96b6b32d277455b0dc11cc40e35957c4d8b02f66d1221defde6a63%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_id=info:pmid/&rfr_iscdi=true |