ReviewThe journal of physical chemistry. B2009
Empirical amide I vibrational frequency map: application to 2D-IR line shapes for isotope-edited membrane peptide bundles.
Review in The journal of physical chemistry. B, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
52 citing papers in PubMed.
- Multidimensional Infrared Spectroscopy as a Bioanalytical Technique.Chemical reviews · 2026Review
- NIR-responsive mild photothermal hydrogels for multimodal antibacterial therapy, immunomodulation, and regenerative repair of MRSA-infected wounds.Journal of nanobiotechnology · 2026Article
- IR Spectroscopy: From Experimental Spectra to High-Resolution Structural Analysis by Integrating Simulations and Machine Learning.The journal of physical chemistry. B · 2025Article
- Using Multiple Isotope-Labeled Infrared Spectra for the Structural Characterization of an Intrinsically Disordered Peptide.The journal of physical chemistry. B · 2025Article
- Chasing weakly-bound biological water in aqueous environment near the peptide backbone by ultrafast 2D infrared spectroscopy.Communications chemistry · 2024Article
- Probing Ion Configurations in the KcsA Selectivity Filter with Single-Isotope Labels and 2D IR Spectroscopy.Journal of the American Chemical Society · 2023Article
- Reconstructing the infrared spectrum of a peptide from representative conformers of the full canonical ensemble.Communications chemistry · 2023Article
- Origin of thiocyanate spectral shifts in water and organic solvents.The Journal of chemical physics · 2022Article
- Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.Chemical reviews · 2020Review
- Photo-initiated rupture of azobenzene micelles to enable the spectroscopic analysis of antimicrobial peptide dynamics.RSC advances · 2020Article
- Development of Vibrational Frequency Maps for Nucleobases.The journal of physical chemistry. B · 2019Article
- Interspecies Bombolitins Exhibit Structural Diversity upon Membrane Binding, Leading to Cell Specificity.Biophysical journal · 2019Article
- Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy.Chemical reviews · 2017Review
- Computing infrared spectra of proteins using the exciton model.Journal of computational chemistry · 2017Article
- Interplay between Hydrogen Bonding and Vibrational Coupling in Liquid N-Methylacetamide.The journal of physical chemistry letters · 2017Article
- Refining Disordered Peptide Ensembles with Computational Amide I Spectroscopy: Application to Elastin-Like Peptides.The journal of physical chemistry. B · 2016Article
- Kinetic Isotope Effect Provides Insight into the Vibrational Relaxation Mechanism of Aromatic Molecules: Application to Cyano-phenylalanine.The journal of physical chemistry letters · 2016Article
- How Sensitive is the Amide I Vibration of the Polypeptide Backbone to Electric Fields?Chemphyschem : a European journal of chemical physics and physical chemistry · 2015Article
- An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution.Biophysical journal · 2015Article
- Histidine Orientation Modulates the Structure and Dynamics of a de Novo Metalloenzyme Active Site.Journal of the American Chemical Society · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
The amide I vibrational mode, primarily associated with peptide-bond carbonyl stretches, has long been used to probe the structures and dynamics of peptides and proteins by infrared (IR) spectroscopy. A number of ab initio-based amide I vibrational frequency maps have been developed for calculating IR line shapes. In this paper, a new empirical amide I vibrational frequency map is developed. To evaluate its performance, we applied this map to a system of isotope-edited CD3-zeta membrane peptide bundles in aqueous solution. The calculated 2D-IR diagonal line widths vary from residue to residue and show an asymmetric pattern as a function of position in the membrane. The theoretical results are in fair agreement with experiments on the same system. Through analysis of the computed frequency time-correlation functions, it is found that the 2D-IR diagonal widths are dominated by contributions from the inhomogeneous frequency distributions, from which it follows that these widths are a good probe of the extent of local structural fluctuations. Thus, the asymmetric pattern of line widths follows from the asymmetric structure of the bundle in the membrane.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.