ArticleThe Journal of chemical physics2013
Electrostatic frequency shifts in amide I vibrational spectra: direct parameterization against experiment.
Article in The Journal of chemical physics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Using Multiple Isotope-Labeled Infrared Spectra for the Structural Characterization of an Intrinsically Disordered Peptide.The journal of physical chemistry. B · 2025Article
- Membrane Interactions Drive Hydrogen-Bond Dynamics in the pH-Low Insertion Peptide (pHLIP).The journal of physical chemistry letters · 2025Article
- Development and Characterization of Electrodes for Surface-Specific Attenuated Total Reflection Two-Dimensional Infrared Spectroelectrochemistry.The journal of physical chemistry. C, Nanomaterials and interfaces · 2023Article
- Structural Dependence of Extended Amide III Vibrations in Two-Dimensional Infrared Spectra.The journal of physical chemistry letters · 2023Article
- Intermediate Antiparallel Fibrils in Aβ40 Dutch Mutant Aggregation: Insights from Nanoscale Infrared Spectroscopy.The journal of physical chemistry. B · 2023Article
- Intermediate antiparallel fibrils in Aβ40 Dutch mutant aggregation: nanoscale insights from AFM-IR.bioRxiv : the preprint server for biology · 2023Article
- AIM: A Mapping Program for Infrared Spectroscopy of Proteins.Journal of chemical theory and computation · 2022Article
- Label-Free Infrared Spectroscopic Imaging Reveals Heterogeneity of β-Sheet Aggregates in Alzheimer's Disease.The journal of physical chemistry letters · 2021Article
- Computational IR Spectroscopy of Insulin Dimer Structure and Conformational Heterogeneity.The journal of physical chemistry. B · 2021Article
- Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.Chemical reviews · 2020Review
- Site-Specific Peptide Probes Detect Buried Water in a Lipid Membrane.Biophysical journal · 2019Article
- Equilibrium versus Nonequilibrium Peptide Dynamics: Insights into Transient 2D IR Spectroscopy.The journal of physical chemistry. B · 2018Review
- Refinement of Peptide Conformational Ensembles by 2D IR Spectroscopy: Application to Ala‒Ala‒Ala.Biophysical journal · 2018Article
- Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments.Chemical Society reviews · 2018Review
- Coordination to lanthanide ions distorts binding site conformation in calmodulin.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Hydration of the Carboxylate Group in Anti-Inflammatory Drugs: ATR-IR and Computational Studies of Aqueous Solution of Sodium Diclofenac.ACS omega · 2018Article
- Simple Quantum Dynamics with Thermalization.The journal of physical chemistry. A · 2018Article
- Not All β-Sheets Are the Same: Amyloid Infrared Spectra, Transition Dipole Strengths, and Couplings Investigated by 2D IR Spectroscopy.The journal of physical chemistry. B · 2017Article
- The dynamics of peptide-water interactions in dialanine: An ultrafast amide I 2D IR and computational spectroscopy study.The Journal of chemical physics · 2017Article
- Structural and Spectroscopic Properties of Assemblies of Self-Replicating Peptide Macrocycles.ACS nano · 2017Article
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2 authors.
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Abstract
The interpretation of protein amide I infrared spectra has been greatly assisted by the observation that the vibrational frequency of a peptide unit reports on its local electrostatic environment. However, the interpretation of spectra remains largely qualitative due to a lack of direct quantitative connections between computational models and experimental data. Here, we present an empirical parameterization of an electrostatic amide I frequency map derived from the infrared absorption spectra of 28 dipeptides. The observed frequency shifts are analyzed in terms of the local electrostatic potential, field, and field gradient, evaluated at sites near the amide bond in molecular dynamics simulations. We find that the frequency shifts observed in experiment correlate very well with the electric field in the direction of the C=O bond evaluated at the position of the amide oxygen atom. A linear best-fit mapping between observed frequencies and electric field yield sample standard deviations of 2.8 and 3.7 cm(-1) for the CHARMM27 and OPLS-AA force fields, respectively, and maximum deviations (within our data set) of 9 cm(-1). These results are discussed in the broader context of amide I vibrational models and the effort to produce quantitative agreement between simulated and experimental absorption spectra.
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