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

Abstract

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.