ArticleThe journal of physical chemistry. B2020
The Amide I Spectrum of Proteins-Optimization of Transition Dipole Coupling Parameters Using Density Functional Theory Calculations.
Article in The journal of physical chemistry. B, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 9 papers.
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9 citing papers in PubMed.
- Optimized histidine-specific isotopic labeling in proteins overproduced in Escherichia coli.Protein science : a publication of the Protein Society · 2026Article
- VeloxChem: Large-Scale DFT Calculations of Geometric Derivatives up to Second Order for Simulation of IR Spectra.The journal of physical chemistry. A · 2026Article
- IR Spectroscopy: From Experimental Spectra to High-Resolution Structural Analysis by Integrating Simulations and Machine Learning.The journal of physical chemistry. B · 2025Article
- First Vibrational Fingerprint ofBiosensors · 2025Article
- Ordered Aggregates of Fmoc-Diphenylalanine at Alkaline pH as a Precursor of Fibril Formation and Peptide Gelation.The journal of physical chemistry. B · 2025Article
- Physicochemical Properties, Functionalities, and Antioxidant Activity of Protein Extracts from New Zealand Wild Sea Cucumbers (Foods (Basel, Switzerland) · 2024Article
- Non-orthogonal Configuration Interaction Study on the Effect of Thermal Distortions on the Singlet Fission Process in Photoexcited Pure and B,N-Doped Pentacene Crystals.The journal of physical chemistry. C, Nanomaterials and interfaces · 2023Article
- Vibrational exciton delocalization precludes the use of infrared intensities as proxies for surfactant accumulation on aqueous surfaces.Chemical science · 2021Article
- On the Secondary Structure of Silk Fibroin Nanoparticles Obtained Using Ionic Liquids: An Infrared Spectroscopy Study.Polymers · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The amide I region of the infrared spectrum is related to the protein backbone conformation and can provide important structural information. However, the interpretation of the experimental results is hampered because the theoretical description of the amide I spectrum is still under development. Quantum mechanical calculations, for example, using density functional theory (DFT), can be used to study the amide I spectrum of small systems, but the high computational cost makes them inapplicable to proteins. Other approaches that solve the eigenvalues of the coupled amide I oscillator system are used instead. An important interaction to be considered is transition dipole coupling (TDC). Its calculation depends on the parameters of the transition dipole moment. This work aims to find the optimal parameters for TDC in three major secondary structures: α-helices, antiparallel β-sheets, and parallel β-sheets. The parameters were suggested through a comparison between DFT and TDC calculations. The comparison showed a good agreement for the spectral shape and for the wavenumbers of the normal modes for all secondary structures. The matching between the two methods improved when hydrogen bonding to the amide oxygen was considered. Optimal parameters for individual secondary structures were also suggested.
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