Maximize Data Extraction (MDE) from a 1H NMR Spectrum

Here is a lesson I learnt over time while working on small molecules—my Elucidation Evolution.

Thinking back to when I started doing elucidations of unknowns, my mindset was to collect loads of data (NMR, MS, IR, etc.) whether I needed it or not. Initially inexperienced, I was extracting bits and pieces of information from various datasets and building up a list of fragments that needed to be combined together to form a candidate structure. Although this offered a means to practice and learn how to interpret a wide array of data, it was not an efficient approach to an elucidation.

Please note that there is value in collecting additional data to confirm or verify a candidate structure. However, for elucidation purposes, one should maximize data extraction while minimizing data collection.

As my skills grew, I felt more comfortable working with less data. I began to maximize the information I could extract from a simple 1H NMR, thus avoiding the need to collect and analyze “duplicate data”. (An example of duplicate data is a 1H NMR and a 1H-1H COSY.) Although 1H-1H COSY data could be valuable in cases with complicated resonances and a high degree of signal overlap, a 1H NMR could suffice in extracting structural information.

For the purpose of an elucidation, one should extract the following bits of information from a 1H NMR spectrum:

presence of proton resonances,

spectrum purity (identifying impurities or mixtures),

identifying aromatic and/or aliphatic protons,

presence of exchangeable protons,

chemical shifts,

proton count from integrals,

presence of symmetry,

coupling patterns and constants,

second-order effects.

TIP: Every bit of information helps. A negative result is also telling you something.

Maximize Data Extraction (MDE) from a 1H NMR Spectrum

Here is a lesson I learnt over time while working on small molecules—my Elucidation Evolution.

Thinking back to when I started doing elucidations of unknowns, my mindset was to collect loads of data (NMR, MS, IR, etc.) whether I needed it or not. Initially inexperienced, I was extracting bits and pieces of information from various datasets and building up a list of fragments that needed to be combined together to form a candidate structure. Although this offered a means to practice and learn how to interpret a wide array of data, it was not an efficient approach to an elucidation.

Please note that there is value in collecting additional data to confirm or verify a candidate structure. However, for elucidation purposes, one should maximize data extraction while minimizing data collection.

As my skills grew, I felt more comfortable working with less data. I began to maximize the information I could extract from a simple 1H NMR, thus avoiding the need to collect and analyze “duplicate data”. (An example of duplicate data is a 1H NMR and a 1H-1H COSY.) Although 1H-1H COSY data could be valuable in cases with complicated resonances and a high degree of signal overlap, a 1H NMR could suffice in extracting structural information.

For the purpose of an elucidation, one should extract the following bits of information from a 1H NMR spectrum:

presence of proton resonances,

spectrum purity (identifying impurities or mixtures),

identifying aromatic and/or aliphatic protons,

presence of exchangeable protons,

chemical shifts,

proton count from integrals,

presence of symmetry,

coupling patterns and constants,

second-order effects.

TIP: Every bit of information helps. A negative result is also telling you something.

Identifying Meta coupling in a 1H NMR Spectrum

In a substituted benzene ring, aromatic protons that are in the meta position can exhibit coupling to each other. This is referred to as meta or 4J coupling. The coupling pattern is typically a doublet with a coupling constant of ~2 Hz.

On the contrary, a spectrum without any meta coupling indicates a lack of protons in the meta position. Although a 2D COSY experiment can produce the same result, one can save time by looking for this information in a 1H NMR spectrum first.

Illustrated below is a portion of a 1H NMR spectrum for a substituted benzene ring. Proton A is a doublet with a 2.3 Hz coupling and proton B is also a doublet with 2.2 Hz coupling. Proton A and B are coupled to each other due to the similar coupling constant (+/- 0.2 Hz). Another indication of coupling is the slight tilt of the multiplets to each other.

TIP: Be careful on the extent of line broadening applied to the FID, too much and the meta coupling information can be lost.

Identifying Meta coupling in a 1H NMR Spectrum

In a substituted benzene ring, aromatic protons that are in the meta position can exhibit coupling to each other. This is referred to as meta or 4J coupling. The coupling pattern is typically a doublet with a coupling constant of ~2 Hz.

On the contrary, a spectrum without any meta coupling indicates a lack of protons in the meta position. Although a 2D COSY experiment can produce the same result, one can save time by looking for this information in a 1H NMR spectrum first.

Illustrated below is a portion of a 1H NMR spectrum for a substituted benzene ring. Proton A is a doublet with a 2.3 Hz coupling and proton B is also a doublet with 2.2 Hz coupling. Proton A and B are coupled to each other due to the similar coupling constant (+/- 0.2 Hz). Another indication of coupling is the slight tilt of the multiplets to each other.

TIP: Be careful on the extent of line broadening applied to the FID, too much and the meta coupling information can be lost.

Structural bias in an elucidation

A biased elucidation is an elucidation where the chemist makes certain assumptions about the data at hand based on a previous experience(s) and not deviating from it. Depending on the elucidation, it can be a good thing or a very bad thing. As a good thing, it can speed up the time spent on an elucidation. However, an incorrect assumption(s) can mean wasting time and frustration to the point of being unable to elucidate the compound.

Shown below is a correlation map for an unknown with a molecular formula of C14H9NO2. The hybridization states of all the carbons are sp2, the ring size is restricted to 5 and 6, and there is an exchangeable proton (OH or NH). How many structures can you draw that fit these restrictions? For clarity reasons, the atoms in red are the ones to be arranged.

The answer is 28.

Two answers are shown below. Which tautomer did you draw first? A common structural bias is to take the 5 sp2 carbons and the nitrogen and draw a pyridine ring – pyridine being a commonly encountered substituent. Here, structural bias for this unknown is a bad thing especially if you overlooked a possibility.

The reference listed is for the tautomer on the right side. In hindsight, it is commonly seen when a pyridine ring is conjugated with a carbonyl group(s).

TIP: The best approach is to not to encourage an outcome over another, that is, make no assumptions. For elucidations where the starting material is known, consider not viewing the starting material so as not to cloud the mind. Remember to cover all the bases so all possibilities are taken into account.

Structural bias in an elucidation

A biased elucidation is an elucidation where the chemist makes certain assumptions about the data at hand based on a previous experience(s) and not deviating from it. Depending on the elucidation, it can be a good thing or a very bad thing. As a good thing, it can speed up the time spent on an elucidation. However, an incorrect assumption(s) can mean wasting time and frustration to the point of being unable to elucidate the compound.

Shown below is a correlation map for an unknown with a molecular formula of C14H9NO2. The hybridization states of all the carbons are sp2, the ring size is restricted to 5 and 6, and there is an exchangeable proton (OH or NH). How many structures can you draw that fit these restrictions? For clarity reasons, the atoms in red are the ones to be arranged.

The answer is 28.

Two answers are shown below. Which tautomer did you draw first? A common structural bias is to take the 5 sp2 carbons and the nitrogen and draw a pyridine ring – pyridine being a commonly encountered substituent. Here, structural bias for this unknown is a bad thing especially if you overlooked a possibility.

The reference listed is for the tautomer on the right side. In hindsight, it is commonly seen when a pyridine ring is conjugated with a carbonyl group(s).

TIP: The best approach is to not to encourage an outcome over another, that is, make no assumptions. For elucidations where the starting material is known, consider not viewing the starting material so as not to cloud the mind. Remember to cover all the bases so all possibilities are taken into account.

13C NMR and Natural products

Looking for the next big pharmaceutical drug among natural products is a growing endeavour. However, a common drawback to working with natural products is the limited amount of sample.

With a sample limitation, acquiring a 13C NMR spectrum within a reasonable time can be an issue. Rather than wasting instrument time on a 13C NMR, one can save time by extracting the sum (or projection) of slices across a 2D NMR.

Using strychnine as an example, the diagram below is a comparison of two datasets. The top trace (green) is the sum of all the F1 slices from an HMBC and the bottom spectrum (blue) is an acquired 13C NMR. From the top trace, one can gather a good approximation on the minimum number of carbons for strychnine without resorting to acquiring a 13C NMR.

TIP: Be especially careful with quaternary and overlapping carbons as they may not be evident on an HMBC.