General Applicable Frequency Map for the Amide-I Mode in β-Peptides

Cai, Kezhou; Du, Fenfen; Zheng, Xuan; Liu, Jia; Zheng, Ren-Hui; Zhao, Juan; Wang, Jianping

doi:10.1021/acs.jpcb.5b11643

Cited by 17 publications

(6 citation statements)

References 92 publications

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“…The application of VSMs of amide modes is not limited to polypeptides and proteins composed of -amino acids. Recently, Wang and coworkers theoretically determined the coefficients to calculate the amide I frequency of N-ethylpropionamide (NEPA), a model compound of -amino acid, based on electrostatic potentials on the N, H, C and O atoms of the peptide unit, 331 and the calculated linear spectra of NEPA in three different solvents were in reasonable agreement with the experimental results. They also computed the coupling strengths of the amide I and II modes for five helical -peptide conformers, 332,333 and showed that the coupling strengths for shorter inter-amide distances cannot be described well by the TDC model.…”

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confidence: 60%

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

et al. 2020

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Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and inter-protein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an allencompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semi-empirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository website (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-theart multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.

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confidence: 60%

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

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“…70,71 Similarly, to IR spectra of natural proteins and peptides, the amide I and II absorption bands, originating mainly from C]O stretching and N-H bending vibrations ($1651 and $1540 cm À1 ) of the peptide backbone were considered. [72][73][74] The amide I vibration depends on the backbone structure and is commonly used for secondary structure analysis by tting with components bands or by decomposing into basis spectra. 75 The most intense contribution of deconvoluted amide I band of 1 in HFIP is at 1648 cm À1 which could be assigned to a random coil conformation (Table S1 †).…”

Section: Structure and Morphologymentioning

confidence: 99%

Membrane active Janus-oligomers of β³-peptides

et al. 2020

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“…This work drove the early development and subsequent widespread use of IR spectroscopy for structural analysis. − (2) In turn, spectroscopic models that facilitate the interpretation of amide I spectra were extensively developed. Models for similar carbonyl stretches in ketones, acetyls, aldehydes, and esters remain comparatively undeveloped. ,− (3) With some exceptions, the protein backbone represents a uniform array of oscillators with one-to-one correspondence between oscillators and protein residues. Backbone CO stretches are vibrationally coupled and form delocalized modes that reflect the underlying arrangement of the oscillators, namely the protein structure. ,− …”

Section: Introductionmentioning

confidence: 99%

An Empirical IR Frequency Map for Ester C═O Stretching Vibrations

2016

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We present an approach for parametrizing spectroscopic maps of carbonyl groups against experimental IR absorption spectra. The model correlates electric fields sampled from molecular dynamics simulations with vibrational frequencies and line shapes in different solvents. We perform an exhaustive search of parameter combinations and optimize the parameter values for the ester carbonyl stretching mode in ethyl acetate by comparing to experimental FTIR spectra of the small molecule in eight different solvents of varying polarities. Hydrogen-bonding solvents require that the peaks are fit independently for each hydrogen bond ensemble to compensate for improper sampling in molecular dynamics simulations. Spectra simulated using the optimized electrostatic map reproduce C═O IR absorption spectra of ethyl acetate with a line center RMSD error of 4.9 cm(-1) over 12 different solvents whose measured line centers span a 45 cm(-1) range. In combination with molecular dynamics simulations, this spectroscopic map will be useful in interpreting spectra of ester groups in heterogeneous environments such as lipid membranes.

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General Applicable Frequency Map for the Amide-I Mode in β-Peptides

Cited by 17 publications

References 92 publications

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

Membrane active Janus-oligomers of β³-peptides

An Empirical IR Frequency Map for Ester C═O Stretching Vibrations

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General Applicable Frequency Map for the Amide-I Mode in β-Peptides

Cited by 17 publications

References 92 publications

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction

Membrane active Janus-oligomers of β3-peptides

An Empirical IR Frequency Map for Ester C═O Stretching Vibrations

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Membrane active Janus-oligomers of β³-peptides