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http://hdl.handle.net/1942/31171
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DC Field | Value | Language |
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dc.contributor.author | Paloncyova, M. | - |
dc.contributor.author | Tornmalm, J. | - |
dc.contributor.author | Sen, S. | - |
dc.contributor.author | Piguet, J. | - |
dc.contributor.author | Widengren, J. | - |
dc.contributor.author | KNIPPENBERG, Stefan | - |
dc.date.accessioned | 2020-05-21T09:53:59Z | - |
dc.date.available | 2020-05-21T09:53:59Z | - |
dc.date.issued | 2020 | - |
dc.date.submitted | 2020-05-19T13:14:59Z | - |
dc.identifier.citation | JOURNAL OF PHYSICAL CHEMISTRY C, 124 (10) , p. 5829 -5837 | - |
dc.identifier.uri | http://hdl.handle.net/1942/31171 | - |
dc.description.abstract | The photoisomerization scheme of the cyanine-based 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine (DiD) probe was investigated by means of molecular modeling techniques, accounting for differences between the potential energy surfaces in the ground and excited states. Starting from the trans conformation, the photoisomerization path to the cis conformation and its dependence on the acyl tail lengths of the probe were evaluated. Moreover, the ground-state conformational distribution was investigated and suitable topologies were built for the ground- and excited-state molecular dynamics (MD) calculations. A protocol for simulations in solvents and in liquid-disordered lipid bilayers was worked out. In a kinetic analysis, the decay of the excited singlet (S1) state via radiative and nonradiative decays and via dihedral twisting is discussed. The twisting of one of the dihedral angles in the S1 state is found to be faster than the direct decay rate, which explains the relatively low fluorescence quantum yield of the compound. The molecular dynamics simulations show that in lipid bilayers, the DiD probe with methyl groups as acyl tails from the headgroup brings the highest level of photoisomerization, while a compound with acyl tails of 18 carbon atoms does not isomerize at all. | - |
dc.description.sponsorship | The Swedish National Infrastructure for Computing (SNIC) is acknowledged for the computational time granted through the medium allocations 3-397, 3-156, 3-396, 3-23, 3-398, and 3394 in 2018. The Flemish Supercomputer Centre (VSC) (Flanders, Belgium) and the Herculesstichting (Flanders, Belgium) are acknowledged for the generously allocated computational time on the Tier-1 cluster Breniac as well as the Tier-2 cluster Thinking. M.P. acknowledges the Special Research Fund (BOF) of Hasselt University (Belgium) for her research stay in November 2018 and support from ERDF/ESF Project no. CZ.02.1.01/0.0/0.0/16_019/0000754. J.W. acknowledges support from the Swedish Foundation for Strategic research (SSF ITM17-0491). S.K. is grateful to the Czech Science Foundation through grant 17-21122S. | - |
dc.language.iso | en | - |
dc.publisher | AMER CHEMICAL SOC | - |
dc.rights | 2020 American Chemical Society | - |
dc.subject.other | Force-Field | - |
dc.subject.other | Fluorescent Proteins | - |
dc.subject.other | Viscosity | - |
dc.subject.other | Cholesterol | - |
dc.subject.other | States | - |
dc.subject.other | Isomerization | - |
dc.subject.other | Photophysics | - |
dc.subject.other | Polymethine | - |
dc.subject.other | Temperature | - |
dc.subject.other | Simulation | - |
dc.title | Photoisomerization of DiD: Molecular Dynamics Calculations Reveal the Influence of Tail Lengths | - |
dc.title | Photoisomerization of DiD: Molecular Dynamics Calculations Reveal the Influence of Tail Lengths | - |
dc.type | Journal Contribution | - |
dc.identifier.epage | 5837 | - |
dc.identifier.issue | 10 | - |
dc.identifier.spage | 5829 | - |
dc.identifier.volume | 124 | - |
local.format.pages | 9 | - |
local.bibliographicCitation.jcat | A1 | - |
dc.description.notes | Knippenberg, S (reprint author), KTH Royal Inst Technol, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden.; Knippenberg, S (reprint author), Hasselt Univ, Biomed Res Inst, B-3590 Diepenbeek, Belgium.; Knippenberg, S (reprint author), Hasselt Univ, Theoret Phys, B-3590 Diepenbeek, Belgium.; Knippenberg, S (reprint author), Palacky Univ, Fac Sci, Reg Ctr Adv Technol & Mat, Dept Phys Chem, Olomouc 77146, Czech Republic.; Knippenberg, S (reprint author), Univ Antwerp, Res Grp PLASMANT, Dept Chem, B-2610 Antwerp, Belgium. | - |
dc.description.notes | stefan.knippenberg@upol.cz | - |
dc.description.other | Knippenberg, S (reprint author), KTH Royal Inst Technol, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden; Hasselt Univ, Biomed Res Inst, B-3590 Diepenbeek, Belgium; Hasselt Univ, Theoret Phys, B-3590 Diepenbeek, Belgium; Palacky Univ, Fac Sci, Reg Ctr Adv Technol & Mat, Dept Phys Chem, Olomouc 77146, Czech Republic; Univ Antwerp, Res Grp PLASMANT, Dept Chem, B-2610 Antwerp, Belgium. stefan.knippenberg@upol.cz | - |
local.publisher.place | 1155 16TH ST, NW, WASHINGTON, DC 20036 USA | - |
local.type.refereed | Refereed | - |
local.type.specified | Article | - |
dc.source.type | Article | - |
dc.identifier.doi | 10.1021/acs.jpcc.9b10322 | - |
dc.identifier.isi | WOS:000526394800037 | - |
dc.contributor.orcid | Widengren, Jerker/0000-0003-3200-0374 | - |
dc.identifier.eissn | 1932-7455 | - |
local.provider.type | wosris | - |
item.fullcitation | Paloncyova, M.; Tornmalm, J.; Sen, S.; Piguet, J.; Widengren, J. & KNIPPENBERG, Stefan (2020) Photoisomerization of DiD: Molecular Dynamics Calculations Reveal the Influence of Tail Lengths. In: JOURNAL OF PHYSICAL CHEMISTRY C, 124 (10) , p. 5829 -5837. | - |
item.accessRights | Restricted Access | - |
item.contributor | Paloncyova, M. | - |
item.contributor | Tornmalm, J. | - |
item.contributor | Sen, S. | - |
item.contributor | Piguet, J. | - |
item.contributor | Widengren, J. | - |
item.contributor | KNIPPENBERG, Stefan | - |
item.fulltext | With Fulltext | - |
item.validation | ecoom 2021 | - |
crisitem.journal.issn | 1932-7447 | - |
crisitem.journal.eissn | 1932-7455 | - |
Appears in Collections: | Research publications |
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paloncyova.pdf Restricted Access | Published version | 2.83 MB | Adobe PDF | View/Open Request a copy |
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