Absorption Spectroscopy: Relationship of Transition Type to Molecular Structure
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A very wide range of organic and inorganic substances can be analyzed using UV and visible absorption spectroscopy. The wavelengths, intensities, and fine structure of the absorption bands are determined by the structures of the neutral or ionic species concerned. For almost all substances, UV and visible absorption spectra are caused by electronic transitions. A spectrum may contain more than one region of absorption, known as a band or band system, as molecules may undergo a range of different electronic transitions.
To a first approximation, electronic transitions may be described as involving different combinations of orbitals: bonding (e.g., σ and π for organic molecules), so-called nonbonding (n), and antibonding (e.g., σ* and π*) orbitals. A simple bonding-to-antibonding promotion model of electronic transitions is an oversimplification that does not adequately explain the spectra of all compounds – for example, benzene, porphyrins (e.g., in heme groups), and proteins – but transitions are commonly and usefully characterized as being, for example, π → π* or n → π* in character, and detailed assignments are possible using combinations of experimental spectroscopy and computational chemistry (Atkins and Friedman 2011). However, detailed analysis and computational studies may show that excited electronic states have mixed orbital character, as in some ruthenium and platinum complexes of biological interest (Campagna et al. 2007; Mackay et al. 2009).
At the wavelengths, λ, that are commonly used for absorption spectrophotometry (λ = 170–800 nm), electronic transitions are commonly associated with conjugated regions of organic molecules, or with metal complexes. The structural components that cause absorption are often referred to as chromophores. Conjugated chromophores can be linear, as in β-carotene, or cyclic, as in purine and pyrimidine bases, heme groups, and the amino acids that have aromatic side chains. The chromophores may consist entirely of CH groups or may include heteroatoms such as nitrogen, sulfur, or oxygen. Typically, the longest absorption wavelength (lowest energy) increases with the length or, for cyclic systems, the size of the chromophore (Atkins and Friedman 2011; Atkins and de Paula 2006).
At wavelengths greater than 200 nm, most absorption spectra of organic molecules are dominated by transitions in which electrons are redistributed between π and π* orbitals; these are known as π → π* transitions. However, heteroatoms introduce so-called nonbonding or n-orbitals or lone pairs to the chromophore. These are σ-type orbitals that can give rise to n → π* transitions in an absorption spectrum (Hollas 2004). The transitions are typically weaker than π → π* transitions and are often suppressed in hydrogen-bonding solvents such as water, but they may be seen when the accompanying π → π* transitions are weak or when they occur in a different wavelength range. n → π* transitions make an appreciable contribution to the absorption spectra of some proteins, and give rise to the color of some compounds such as trans-azobenzene, and may become more prominent in circular dichroism (CD) spectra (Nordén et al. 2010).
As discussed above, absorption wavelengths are sensitive to the extent of conjugation in a chromophore. They are also sensitive to interactions between neighboring chromophores in the same molecule (intramolecular), or in neighboring molecules (intermolecular). Examples of intramolecular coupling between chromophores include π stacking of aromatic residues in proteins and nucleic acids, and strong interactions between peptide n → π* transitions in protein α-helices. Examples of intermolecular coupling include π stacking of ligands bound externally to DNA and the effects of intercalation between DNA base pairs on the spectroscopy of the ligand.
- Atkins PW, de Paula J (2006) Physical chemistry, 8th edn. Oxford University Press, OxfordGoogle Scholar
- Atkins PW, Friedman RS (2011) Molecular quantum mechanics, 5th edn. Oxford University Press, OxfordGoogle Scholar
- Bell S (2006) Forensic chemistry. Prentice Hall, Upper Saddle RiverGoogle Scholar
- Hollas JM (2004) Modern spectroscopy, 4th edn. Wiley, ChichesterGoogle Scholar
- Nordén B, Rodger A, Dafforn TR (2010) Linear dichroism and circular dichroism: a textbook on polarized spectroscopy. Royal Society of Chemistry, Cambridge, MAGoogle Scholar