Molecular Structure and Absorption Spectra

The full electromagnetic spectrum includes radio waves on one end (long wavelength, low frequency, low energy) and gamma rays on the other (short wavelength, high frequency, high energy). Between the two extremes, we find, in order from lowest energy to highest energy: microwavesinfrared, visible light, ultraviolet, and x-rays. Although they have been placed in respective spectrums, there’s no universal agreement on all the boundaries, so many of these bands overlap. A changing magnetic field can cause a change in an electric field, and a changing electric field can cause a change in a magnetic field. We can see how electromagnetic waves occur in nature by observing the reciprocating nature of these two fields. Electromagnetic waves can even travel through a vacuum since each oscillating field causes oscillations in the other field completely independent of matter. Through a vacuum, all electromagnetic waves travel at a fixed speed:

c = 3.00 × 108 m/s

regardless of their frequency. Infrared (IRspectroscopy measures molecular vibrations, which can be seen as bond stretching, bending, or combinations of different vibrational modes.4 To record an IR spectrum, infrared light is passed through a sample, and the absorbance is measured. By determining what bonds exist within a molecule, we hope to infer the functional groups in the molecule. The infrared light range runs from λ = 700 nm to 1 mm, but the useful absorptions for spectroscopy occur at wavelengths of 2500 to 25,000 nm. On an IR spectrum, we use an analog of frequency called wavenumber. The standard range corresponding to 2500 to 25,000 nm is 4000 to 400 cm–1. The molecules enter excited vibrational states when light within these wavenumbers is absorbed.

Wavenumbers (cm–1) are an analog of frequency.

f = c/λ

Whereas

wavenumber = 1/λ

When the whole molecule moves as a whole, more complex vibration patterns can be seen and this typically occurs in the 1500 to 400 cm–1 range. Since the specific absorbance pattern is characteristic of each individual molecule, this region is known as the fingerprint region Spectroscopy experts can use this region to identify a substance. For an absorption to be recorded, the vibration must result in a change in the bond dipole moment. This means that molecules that do not experience a change in dipole moment, such as those composed of atoms with the same electronegativity or molecules that are symmetrical, do not exhibit absorption. For example, we cannot get an absorption from O2 or Br2, but we can from HCl or CO. Symmetric bonds, such as the triple bond in acetylene (C2H2), will also be silent. Symmetric stretches do not show up in IR spectra because they involve no net change in dipole movement. Infrared spectroscopy is best used for identification of functional groups. The most important peaks to know are:

  • O–H (broad around 3300 cm–1)
  • N–H (sharp around 3300 cm–1)
  • C=O (sharp around 1750 cm–1)

UV spectra are obtained by passing ultraviolet light through a sample that is usually dissolved in an inert, non- absorbing solvent, and recording the absorbance. The absorbance is then plotted against wavelength. The absorbance is caused by electronic transitions between orbitals. The biggest piece of information we get from this technique is the wavelength of maximum absorbance, which tells us the extent of conjugation within conjugated systems: the more conjugated the compound, the lower the energy of the transition and the greater the wavelength of maximum absorbance. UV spectroscopy works because molecules with π-electrons or nonbonding electrons can be excited by ultraviolet light to higher-energy antibonding orbitals. Molecules with a lower energy gap between highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) are more easily excited and can absorb longer wavelengths (lower frequencies) with lower energy. UV spectroscopy is most useful for studying compounds containing double bonds and/or heteroatoms with lone pairs that create conjugated systems. Molecules with unhybridized p-orbitals are known as conjugated molecules.4 These molecules can also be excited by ultraviolet light and the conjugation shifts the absorption spectrum. This results in a higher maximum wavelengths and lower frequencies. Larger conjugated molecules sometimes even absorb light in the visible range, leading to color. Because the technique for UV spectroscopy can also be used at visible wavelengths, it is sometimes called UV–Vis spectroscopy.

Nuclear magnetic resonance (NMR) spectroscopy is a non-invasive and non-destructive spectroscopic technique that allows determination of the constitution and relative configuration of molecules, the characterization of the dynamic three-dimensional (3D) conformation of molecules, and their interaction with other molecules. NMR spectroscopy detects the characteristics of nuclear spins; the most commonly studied nuclei are the spin-1/2-particles 1H, 13C, 15N, and 31P. NMR observables sensitively depend on their chemical surroundings of individual atoms. Therefore, NMR spectroscopy can derive information about the conformational dynamics and interactions of molecules in solution and at ambient temperature. In addition, thermodynamic and kinetic information about the interaction of molecules can be derived on a per-atom basis. Each peak or group of peaks that are part of a multiplet represents a single group of equivalent protons. The relative area of each peak reflects the ratio of the protons producing each peak. The position of the peak (upfield or downfield) is due to shielding or deshielding effects, which reflect the chemical environment of the protons

Now, let’s make it a little more interesting. Consider a compound containing protons that are within three bonds of each other: in other words, a compound in which there are hydrogens on two adjacent atoms. When we have two protons in such close proximity to each other that are not magnetically identical, spin–spin coupling (splitting) occurs.

 

References

1) Handel, S. (1995). Timbre perception and auditory object identification. Hearing, 425-461.

2) Strutt (Lord Rayleigh), John William (1896). MacMillan & Co, ed. The Theory of Sound. 2 (2 ed.). p. 154.

3) Halliday, David; Resnick, Robert; Walker, Jerl (2005), Fundamental of Physics (7th ed.), USA: John Wiley and Sons, Inc.,

4) James D. Ingle, Jr. and Stanley R. Crouch, Spectrochemical Analysis, Prentice Hall, 1988

5) Lekner, John (1987). Theory of Reflection, of Electromagnetic and Particle Waves. Springer.

6) Hecht, Eugene (1987). “5.4.3”. Optics (2nd ed.). Addison Wesley. pp. 160–1

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