UV Absorption Spectra of TAMRA and TAMRA Labeled Peptides: A Combined Density Functional Theory and Classical Molecular Dynamics Study.
Copyright policy )UV Absorption Spectra of TAMRA and TAMRA Labeled Peptides: A Combined Density Functional Theory and Classical Molecular Dynamics Study.
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 (Arg9, Arg4, Lys9). We found that DFT calculations with different functionals underestimate TAMRA maximum UV absorption peak by ~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 Academy of Sciences Czech Republic
- University of Chemistry and Technology Czech Republic
- Jagiellonian University Poland
- Ruđer Bošković Institute Croatia
- Academy of Sciences Library Czech Republic
time- dependent density functional theory, Rhodamines, molecular dynamics simulations, Molecular Dynamics Simulation, UV absorption spectra, time-dependent density functional theory, fluorescent probes, gaussian-basis sets, correlation-energy, orbital methods, Spectrophotometry, Ultraviolet, Peptides, approximation, Density Functional Theory, Research Article, Fluorescent Dyes
time- dependent density functional theory, Rhodamines, molecular dynamics simulations, Molecular Dynamics Simulation, UV absorption spectra, time-dependent density functional theory, fluorescent probes, gaussian-basis sets, correlation-energy, orbital methods, Spectrophotometry, Ultraviolet, Peptides, approximation, Density Functional Theory, Research Article, Fluorescent Dyes
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