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Infrared spectroscopy, also known as vibrational spectroscopy, is mainly used to determine the types of bonds and functional groups in molecules. In aldehydes and ketones, the carbonyl (C=O) bond shows an absorption around 1710 cm-1. The C=O bond vibration of an aldehyde occurs at lower frequencies than that of a ketone. In addition to the C=O absorption in an aldehyde, the aldehydic C–H bond also gives two peaks in the 2700–2800 cm-1 range. This absorption, coupled with the...
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Vanillin—a flavoring agent in vanilla, cinnamaldehyde—a molecule responsible for the distinct smell of cinnamon, and acetone—a strong-smelling ingredient in nail polish removers, all belong to a class of carbonyl compounds called aldehydes and ketones (Figure 1). Although both aldehydes and ketones contain the characteristic carbonyl (C=O) bond, their chemical structures vary with respect to the groups directly attached to the carbonyl carbon.
In aldehydes (Figures 1a and 1b),...
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IR Spectroscopy: Molecular Vibration Overview01:24

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When Infrared (IR) radiation passes through a covalently bonded molecule, the bonds transition from lower to higher vibrational levels. The fundamental vibrational motions that result in infrared absorption can be classified as stretching or bending vibrations.
Stretching vibrations are vibrational motions that occur along the bond line, changing the bond length or distance between two bonded atoms. They are further distinguished as symmetric or asymmetric. In symmetric stretching, the...
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IR Frequency Region: Alkene and Carbonyl Stretching01:29

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Double bonds in alkenes and carbonyl compounds exhibit stretching frequencies in the diagnostic region of the IR spectrum. In addition, alkenes exhibit vinylic C–H stretching and C–H out-of-plane bending absorptions that are useful for identifying substitution patterns.
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IR Frequency Region: Alkyne and Nitrile Stretching01:22

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Both alkyne (C≡C) and nitrile (C≡N) functional groups contain triple bonds and show stretching absorptions around the wavenumber range of 2100 to 2300 cm−1 in the diagnostic region of the IR spectra.
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Spectroscopy of Carboxylic Acid Derivatives01:26

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Infrared spectroscopy is primarily used to determine the types of bonds and functional groups. In carboxylic acid derivatives, a typical carbonyl bond absorption is observed around 1650–1850 cm−1. For esters, the absorption is recorded at around 1740 cm−1, while acid halides show the absorption at about 1800 cm−1. Another acid derivative, the acid anhydrides, exhibit two carbonyl absorption around 1760 cm−1 and 1820 cm−1, arising from the symmetrical and...
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Using Alizarin Red Staining to Detect Chemically Induced Bone Loss in Zebrafish Larvae
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Structural and Vibrational Characterizations of Alizarin Red S.

César A N Catalán1, Licínia L G Justino2, Rui Fausto2,3

  • 1Cátedra de Química General, Instituto de Química Inorgánica, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, San Miguel de Tucumán 4000, Argentina.

Molecules (Basel, Switzerland)
|August 14, 2025
PubMed
Summary

Theoretical calculations investigated alizarin red S (ARS) salts and anions. This research provides insights into ARS structures and aids in identifying different ARS species.

Keywords:
DFT calculationsalizarin red Sharmonic force fieldsmolecular and electronic structurevibrational analysis

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Area of Science:

  • Computational chemistry
  • Spectroscopy
  • Materials science

Background:

  • Alizarin red S (ARS) is a dye with applications in various fields.
  • Understanding the structural and electronic properties of ARS and its salts is crucial for its applications.
  • Theoretical investigations can complement experimental data for a comprehensive analysis.

Purpose of the Study:

  • To theoretically investigate the structures of isolated alizarin red S anion, and its anhydrous and monohydrated sodium salts.
  • To assign the experimental infrared spectrum of ARS in the solid phase.
  • To evaluate the impact of counterions and hydration on ARS properties.

Main Methods:

  • Density Functional Theory (DFT) framework (B3LYP/6-311++G** calculations).
  • Scaled Quantum Mechanics Force Field (SQMFF) methodology.
  • Atoms in Molecules (AIM) theory analysis.

Main Results:

  • Theoretical structures were determined for the isolated anion, and anhydrous and monohydrated sodium salts of ARS.
  • Experimental infrared spectrum was assigned, and force constants were determined.
  • Quantum chemical calculations showed good agreement with experimental NMR and UV-visible spectra.
  • The influence of Na+ and water on ARS properties was evaluated.
  • HOMO-LUMO gap was determined to assess relative reactivity.

Conclusions:

  • The study provides extended information on alizarin red S.
  • The obtained theoretical data can be used for the fast identification of anhydrous and monohydrated sodium salts and the isolated anion of ARS.