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Related Concept Videos

IR Spectrum Peak Splitting: Symmetric vs Asymmetric Vibrations01:08

IR Spectrum Peak Splitting: Symmetric vs Asymmetric Vibrations

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Identical bonds within a polyatomic group can stretch symmetrically (in-phase) or asymmetrically (out-of-phase). Similar to hydrogen bonding, these vibrations also influence the shape of the IR peak. Generally, asymmetric stretching frequencies are higher than symmetric stretching frequencies. For example, primary amines exhibit two distinct IR peaks between 3300–3500 cm−1 corresponding to the symmetric and asymmetric N-H stretching, while secondary amines exhibit a single...
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NMR Spectroscopy Of Amines

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In proton NMR spectroscopy, primary amines and secondary amines showcase their N–H protons as a broad signal in the chemical shift range between δ 0.5 and 5 ppm. The exact position in this range depends on several factors, including sample concentration, hydrogen bonding, and the type of solvent used. Since amine protons undergo fast proton exchange in solution, the protons are labile and therefore do not participate in any splitting with adjacent protons. Thus, the observed peak is...
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¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)01:20

¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)

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When proton-coupled carbon-13 spectra are simplified by a broadband proton decoupling technique, structural information about the coupled protons is lost. Distortionless enhancement by polarization transfer (DEPT) is a technique that provides information on the number of hydrogens attached to each carbon in a molecule. While the DEPT experiment utilizes complex pulse sequences, the pulse delay and flip angle are specifically manipulated. The resulting signals have different phases depending on...
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Mass Spectrometry of Amines01:19

Mass Spectrometry of Amines

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In mass spectroscopy, amines undergo fragmentation to give parent ions with odd molecule weights. This observed mass spectrum follows the nitrogen rule: a molecule with an odd number of nitrogen atoms produces a parent ion with an odd molecular weight. The remaining fragments have an even mass.
Amines undergo fragmentation through α cleavage, producing nitrogen-containing cations—iminium ions—and alkyl radicals. Mass spectra of aromatic and cyclic aliphatic amines exhibit...
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Mass Spectrometry: Amine Fragmentation00:55

Mass Spectrometry: Amine Fragmentation

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Amines can be identified using mass spectroscopy based on their characteristic fragmentation patterns. The molecular ions of amines undergo fragmentation via ⍺-cleavage. The ⍺-cleavage of the carbon-carbon bonds in amines generates an alkyl radical and resonance-stabilized nitrogen-containing cation.
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IR Frequency Region: X–H Stretching

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In IR spectroscopy, signals produced by the X−H bonds (such as C−H, O−H, or N−H) can be observed in the frequency range of  2700–4000 cm–1. The C−H stretching vibration forms sharp bands in the region 2850–3000 cm–1. The presence of the O−H stretching vibration leads to the forming of an absorption band in the frequency range 3650–3200 cm−1. At the same time, N−H stretching can be confirmed by absorption bands in...
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Dissecting amide-I vibrations in histidine dipeptide.

Xuan Zheng1, Nairong Yang1, Yanjun Hou1

  • 1College of Chemistry, Chemical Engineering and Environment, Fujian Province Key Laboratory of Modern Analytical Science and Separation Technology, Fujian Provincial Key Laboratory of Pollution Monitoring and Control, Minnan Normal University, Zhangzhou 363000, PR China.

Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
|February 7, 2023
PubMed
Summary

This study reveals the conformational preferences and amide-I vibrations of the histidine dipeptide (HISD) in different environments using computational methods. Findings aid in understanding and monitoring polypeptide structures and spectral interpretations.

Keywords:
Amide-I modeElectrostatic potentialHistidine dipeptideSecondary structureSolvent effect

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Area of Science:

  • Computational Chemistry
  • Biophysics
  • Spectroscopy

Background:

  • The histidine dipeptide (Ac-His-NHCH3, HISD) is a model compound for studying peptide structure.
  • Amide-I vibrations are sensitive to local conformation and environment.
  • Understanding conformational preferences is crucial for interpreting spectral data.

Purpose of the Study:

  • To investigate the amide-I vibrational characteristics of HISD.
  • To determine the conformational preferences of HISD in gas and solution phases.
  • To correlate vibrational frequencies with electronic structure and solvent effects.

Main Methods:

  • Ab initio calculations were employed to study HISD.
  • Wavefunction analyses were performed to understand electronic structure.
  • Free energy surfaces (FESs) were computed to map conformational landscapes in different solvents (CHCl3, DMSO, water).

Main Results:

  • HISD adopts C7eq conformation in CHCl3 and gas phase, while favoring β and PPII in DMSO and water, respectively.
  • The imidazole group sterically reduces accessible conformational states compared to ALAD.
  • Amide-I vibrations show secondary structure dependence and sensitivity to the environment.
  • Amide-I frequencies correlate linearly with atomic electrostatic potentials, explaining solvent-induced shifts.

Conclusions:

  • Computational methods reveal distinct conformational populations of HISD based on the environment.
  • Amide-I vibrational modes provide insights into secondary structure and solvent interactions.
  • These findings enhance the understanding of spectral interpretation for solvated polypeptides.