ArticleThe journal of physical chemistry. B2006
Simulation protocols for coherent femtosecond vibrational spectra of peptides.
Article in The journal of physical chemistry. B, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
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- Cross-α/β polymorphism of PSMα3 fibrils.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- AI-based spectroscopic monitoring of real-time interactions between SARS-CoV-2 and human ACE2.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Near-Ultraviolet Circular Dichroism and Two-Dimensional Spectroscopy of Polypeptides.Molecules (Basel, Switzerland) · 2021Article
- Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.Chemical reviews · 2020Review
- Modeling the vibrational couplings of nucleobases.The Journal of chemical physics · 2020Article
- Perspective: Quantum mechanical methods in biochemistry and biophysics.The Journal of chemical physics · 2016Article
- Histidine Orientation Modulates the Structure and Dynamics of a de Novo Metalloenzyme Active Site.Journal of the American Chemical Society · 2015Article
- Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations.The Journal of chemical physics · 2014Article
- Disentangling Peptide Configurations via Two-Dimensional Electronic Spectroscopy: Ab Initio Simulations Beyond the Frenkel Exciton Hamiltonian.The journal of physical chemistry letters · 2014Article
- Study of the γD-crystallin protein using two-dimensional infrared (2DIR) spectroscopy: experiment and simulation.The journal of physical chemistry. B · 2013Article
- Two-dimensional stimulated resonance Raman spectroscopy study of the Trp-cage peptide folding.Physical chemistry chemical physics : PCCP · 2013Article
- Simulations of Two-dimensional Infrared and Stimulated Resonance Raman Spectra of Photoactive Yellow Protein.Chemical physics · 2013Article
- Monitoring the folding of Trp-cage peptide by two-dimensional infrared (2DIR) spectroscopy.The journal of physical chemistry. B · 2013Article
- Simulations of the two-dimensional electronic spectroscopy of the photosystem II reaction center.The journal of physical chemistry. A · 2013Article
- Thermally induced protein unfolding probed by isotope-edited IR spectroscopy.The journal of physical chemistry. B · 2012Article
- Frequency distribution of the amide-I vibration sorted by residues in amyloid fibrils revealed by 2D-IR measurements and simulations.The journal of physical chemistry. B · 2012Article
- Environment Polarity in Proteins Mapped Noninvasively by FTIR Spectroscopy.The journal of physical chemistry letters · 2012Article
- Development and validation of transferable amide I vibrational frequency maps for peptides.The journal of physical chemistry. B · 2011Article
- Discriminating early stage A{beta}42 monomer structures using chirality-induced 2DIR spectroscopy in a simulation study.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
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Authors and funding
4 authors.
Funding
Abstract
Two algorithms for simulating the response of peptides to sequences of IR pulses are developed and applied to N-methyl acetamide (NMA) and a 17 residue alpha-helical peptide (YKKKH17) in D(2)O. A fluctuating vibrational-exciton Hamiltonian for the amide I mode is constructed from molecular dynamics trajectories. Coupling with the environment is described using a density functional theory electrostatic map. The cumulant expansion of Gaussian fluctuation incorporates motional narrowing due to fast frequency fluctuations and is adequate for NMA and for isotopically labeled bands in large peptides. Real-space truncation of the scattering matrix of the nonlinear exciton equations significantly reduces the computational cost, making it particularly attractive for slow fluctuations in large globular proteins.
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