ArticleThe Journal of chemical physics2012
Quantification of transition dipole strengths using 1D and 2D spectroscopy for the identification of molecular structures via exciton delocalization: application to α-helices.
Article in The Journal of chemical physics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
- Multidimensional Infrared Spectroscopy as a Bioanalytical Technique.Chemical reviews · 2026Review
- Advances in Probing Amyloid Heterogeneity Using Vibrational Spectroscopy and Imaging.The journal of physical chemistry. B · 2025Review
- Refining Structural Analysis of Proteins: Automated Methods to Measure Transition Dipole Strength of Single Residues.The journal of physical chemistry. B · 2025Article
- Transition Dipole Strength as a Quantitative Tool for Protein Secondary Structure Analysis.The journal of physical chemistry. B · 2025Article
- Modeling Infrared Spectroscopy of Nucleic Acids: Integrating Vibrational Non-Condon Effects with Machine Learning Schemes.Journal of chemical theory and computation · 2024Article
- Suppressing sidechain modes and improving structural resolution for 2D IR spectroscopy via vibrational lifetimes.The Journal of chemical physics · 2024Article
- Simultaneously Measured Kinetics of Two Amyloid Polymorphs Using Cross Peak Specific 2D IR Spectroscopy.The journal of physical chemistry letters · 2023Article
- Increasing Pump-Probe Signal toward Asymptotic Limits.The journal of physical chemistry. B · 2023Review
- Probing local changes to α-helical structures with 2D IR spectroscopy and isotope labeling.Biophysical journal · 2023Article
- Determining the impact of gold nanoparticles on amyloid aggregation with 2D IR spectroscopy.The Journal of chemical physics · 2023Article
- Spectrophotometric Concentration Analysis Without Molar Absorption Coefficients by Two-Dimensional-Infrared and Fourier Transform Infrared Spectroscopy.Analytical chemistry · 2022Article
- Applications of Single-Molecule Vibrational Spectroscopic Techniques for the Structural Investigation of Amyloid Oligomers.Molecules (Basel, Switzerland) · 2022Review
- Vibrational couplings between protein and cofactor in bacterial phytochrome Agp1 revealed by 2D-IR spectroscopy.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Metastable intermediate during hIAPP aggregation catalyzed by membranes as detected with 2D IR spectroscopy.RSC chemical biology · 2022Article
- Coherent response of the electronic system driven by non-interfering laser pulses.Nature communications · 2022Article
- Investigating the effects of N-terminal acetylation on KFE8 self-assembly with 2D IR spectroscopy.Biophysical journal · 2022Article
- Cross-α/β polymorphism of PSMα3 fibrils.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Application of 2D IR Bioimaging: Hyperspectral Images of Formalin-Fixed Pancreatic Tissues and Observation of Slow Protein Degradation.The journal of physical chemistry. B · 2021Article
- Protein Dynamics by Two-Dimensional Infrared Spectroscopy.Annual review of analytical chemistry (Palo Alto, Calif.) · 2021Article
- Shot-to-shot 2D IR spectroscopy at 100 kHz using a Yb laser and custom-designed electronics.Optics express · 2020Article
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2 authors.
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Abstract
Vibrational and electronic transition dipole strengths are often good probes of molecular structures, especially in excitonically coupled systems of chromophores. One cannot determine transition dipole strengths using linear spectroscopy unless the concentration is known, which in many cases it is not. In this paper, we report a simple method for measuring transition dipole moments from linear absorption and 2D IR spectra that does not require knowledge of concentrations. Our method is tested on several model compounds and applied to the amide I(') band of a polypeptide in its random coil and α-helical conformation as modulated by the solution temperature. It is often difficult to confidently assign polypeptide and protein secondary structures to random coil or α-helix by linear spectroscopy alone, because they absorb in the same frequency range. We find that the transition dipole strength of the random coil state is 0.12 ± 0.013 D(2), which is similar to a single peptide unit, indicating that the vibrational mode of random coil is localized on a single peptide unit. In an α-helix, the lower bound of transition dipole strength is 0.26 ± 0.03 D(2). When taking into account the angle of the amide I(') transition dipole vector with respect to the helix axis, our measurements indicate that the amide I(') vibrational mode is delocalized across a minimum of 3.5 residues in an α-helix. Thus, one can confidently assign secondary structure based on exciton delocalization through its effect on the transition dipole strength. Our method will be especially useful for kinetically evolving systems, systems with overlapping molecular conformations, and other situations in which concentrations are difficult to determine.
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