Commonly misused terms and expressions in chemistry

Several technical terms in the field of chemistry may be misused or confused with other similar terms. Such use may seem appropriate and barely register as problematic, especially if frequently used in informal settings where everyone understands what you mean. But they would be inappropriate in formal scientific communication. Here are some common errors of this type I have observed researchers make.

FRET

FRETis a common phenomenon that is used to monitor structural and chemical changes in a fluorescent system. Very often, FRET is expanded as “fluorescence resonance energy transfer.” However, did you know that this expanded form is often considered incorrect by many scientists? Fluorescence is a radiative process, wherein electrons are transferred from the S1 level to the S0 level while emitting radiation (fluorescence radiation). FRET, on the other hand, is totally dependent on the location, structure, and distance between the donor and acceptor and is not a radiative process. That is to say, the fluorescence from the donor is transferred to the acceptor through non-radiative dipole-dipole coupling. Because of its sensitivity to distance, FRET is often known as the spectroscopic ruler! Wondering what the correct full form is? It is “Förster resonance energy transfer” (after the name of the discoverer, Theodor Förster).

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Photoluminescence and fluorescence

Photoluminescence (PL) and fluorescence are often used interchangeably and inconsistently. But is that okay? No. Photoluminescence includes both fluorescence and phosphorescence. For some classes of compounds (e.g., quantum dots), we do refer to the spectrum recorded in the fluorescence spectrometer as the PL spectrum. In other cases, where phosphorescence is not likely to occur at the temperature of fluorescence measurement, the spectra are simply referred to as fluorescence spectra. While some species can emit both phosphorescence and fluorescence at the temperature of fluorescence measurement, the former cannot be segregated in a steady-state spectrometer (hence, use “PL” rather than categorize a priori). Therefore, one must be very careful while labeling such spectra (i.e., do we wish to indicate fluorescence or PL?).

Theoretical chemistry and computational chemistry

These two terms might sound similar to you, and indeed, they are often used interchangeably. But they have different meanings! Theoretical chemistry involves the development of theoretical methods to predict the outcomes of experiments. This often includes developing theoretical models and computer programs/software/algorithms that can be used to answer questions about molecular behavior under different reaction conditions. In contrast, computational chemistry involves application of the models and software developed by theoretical chemists and analysis of the results obtained. For example, the DFT is used in almost every field of chemistry, and when authors describe DFT-based studies, they often refer to the approach they use as being a theoretical one. However, this is incorrect! DFT calculations are actually a computational approach.

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Protecting and deprotecting in organic synthesis

The presence of two reactive functional groups on a compound often necessitates the “protection” of one of the functional groups to ensure that the reaction involves only the desired functional group, after which the protecting group is removed. This last removal step is often referred to as deprotection. For example, if you use methyl ester as a protecting group, you may call the step “deprotection of methyl ester” or “methyl ester deprotection.” However, are you really deprotecting the protecting group (methyl ester) itself? No! you are removing the protecting group and deprotecting the original functional group or the original functional group-bearing compound. Hence, it is best to say “deprotection of the methyl ester-protected carboxylic acid” or simply, “removal of the methyl ester group.”

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Energy diagrams

In papers discussing energy diagrams, we often come across expressions like “energy of A decreases/increases.” Without looking at the diagram, can we really ascertain the stability status (which is directly related to the energy) of species A? No! The energy scale is rather different from our conventional scales, where terms like “increase” and “decrease” have straightforward meanings. The confusion arises because these energies comprise negative values also. Thus, if the energy changes from −10 to −20 eV, the absolute value increases, but the energy actually decreases. An easy way to avoid this confusion is to say that the energy becomes “more negative” or “less negative,” as the case may be.