UV Absorption Spectra of TAMRA and TAMRA Labeled Peptides: A Combined Density Functional Theory and Classical Molecular Dynamics Study

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388955%3A_____%2F25%3A00618968" target="_blank" >RIV/61388955:_____/25:00618968 - isvavai.cz</a>
Alternative codes found
RIV/60461373:22340/25:43933353
Result on the web
<a href="https://hdl.handle.net/11104/0365767" target="_blank" >https://hdl.handle.net/11104/0365767</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1002/jcc.70096" target="_blank" >10.1002/jcc.70096</a>

Result language
angličtina
Original language name
UV Absorption Spectra of TAMRA and TAMRA Labeled Peptides: A Combined Density Functional Theory and Classical Molecular Dynamics Study
Original language description
This study explores the structural and electronic factors affecting the absorption spectra of 5-carboxy-tetramethylrhodamine (TAMRA) in water, a widely used fluorophore in imaging and molecular labeling in biophysical studies. Through molecular dynamics (MD) simulations and density functional theory (DFT) calculations, we examine TAMRA UV absorption spectra together with TAMRA-labeled peptides (Arg(9), Arg(4), Lys(9)). We found that DFT calculations with different functionals underestimate TAMRA maximum UV absorption peak by similar to 100 nm, resulting in the maximum at ca. 450 nm instead of the experimental value of ca. 550 nm. However, incorporating MD simulation snapshots of TAMRA in water, the UV maximum peak shifts and is in close agreement with the experimental results due to the rotation of TAMRA N(CH3)(2) groups, effectively captured in MD simulations. The method is used to estimate the UV absorption spectra of TAMRA-labeled peptides, matching experimental values.
Czech name
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Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
10403 - Physical chemistry

Project
<a href="/en/project/GF22-27317K" target="_blank" >GF22-27317K: Functionalization of biomaterial surfaces by bioactive substances: from fundamentals to application</a><br>
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year
2025
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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