Will the correct structure please stand up? … Part 2

Part 1 presented a challenge to determine an experiment to distinguish two very similar products from each other, namely 3-methyl-5-(pyridin-2-yloxy)pyridine and 5'-methyl-2H-1,3'-bipyridin-2-one. The products have identical formula weights and the LC/MS and 1H NMR are too similar to draw any conclusion from.

 

The first step is to determine what is different between the two products and then identify an experiment specifically designed to focus on that difference. The obvious difference between the two products is the position of the oxygen atom—an ester group verse a carbonyl group. An FT-IR experiment, as commented by the reader Felipe A., can be used to sort out the products.

 

Other experiments can include the use of reducing agents, 15N NMR, 1H -13C HMBC, 1D NOE, 1H-1H TOCSY, MS2, etc. Note free water, acids and sample concentration can inhibit the use of some of these experiments.

 

A 13C NMR experiment may appear to be another good choice when trying to identify a carbonyl group. However, the carbonyl is part of a conjugated system and so the 13C chemical shift is expected around 160 ppm, which also happens to be expected for the 13C chemical shift of the O-C=N group on the other product.

Will the correct structure please stand up? … Part 2

Part 1 presented a challenge to determine an experiment to distinguish two very similar products from each other, namely 3-methyl-5-(pyridin-2-yloxy)pyridine and 5'-methyl-2H-1,3'-bipyridin-2-one. The products have identical formula weights and the LC/MS and 1H NMR are too similar to draw any conclusion from.

 

The first step is to determine what is different between the two products and then identify an experiment specifically designed to focus on that difference. The obvious difference between the two products is the position of the oxygen atom—an ester group verse a carbonyl group. An FT-IR experiment, as commented by the reader Felipe A., can be used to sort out the products.

 

Other experiments can include the use of reducing agents, 15N NMR, 1H -13C HMBC, 1D NOE, 1H-1H TOCSY, MS2, etc. Note free water, acids and sample concentration can inhibit the use of some of these experiments.

 

A 13C NMR experiment may appear to be another good choice when trying to identify a carbonyl group. However, the carbonyl is part of a conjugated system and so the 13C chemical shift is expected around 160 ppm, which also happens to be expected for the 13C chemical shift of the O-C=N group on the other product.

Examining the IR pattern for C=O vibrations

Infrared (IR) spectrometry is an excellent diagnostic tool for identifying, or lack of, a carbonyl functional group(s). Carbonyl stretching vibration absorbs between 1900-1600 cm-1—a region where few other functional groups absorb. In addition, the carbonyl vibration is typically intense and thus easy to spot.

The gas phase FT-IR spectra, shown below, represent five carbonyl bands differing in the neighbouring atoms: acid halide, carboxylic acid, ester, ketone and amide. The general pattern can be used to suggest a carbonyl group based on the wavenumber.

TIP: conjugated carbonyl groups and hydrogen bonding will typically shift the C=O band to a lower frequency. Ring strain and heteroatoms will shift the C=O band to a higher frequency.

Examining the IR pattern for C=O vibrations

Infrared (IR) spectrometry is an excellent diagnostic tool for identifying, or lack of, a carbonyl functional group(s). Carbonyl stretching vibration absorbs between 1900-1600 cm-1—a region where few other functional groups absorb. In addition, the carbonyl vibration is typically intense and thus easy to spot.

The gas phase FT-IR spectra, shown below, represent five carbonyl bands differing in the neighbouring atoms: acid halide, carboxylic acid, ester, ketone and amide. The general pattern can be used to suggest a carbonyl group based on the wavenumber.

TIP: conjugated carbonyl groups and hydrogen bonding will typically shift the C=O band to a lower frequency. Ring strain and heteroatoms will shift the C=O band to a higher frequency.

Examining IR spectra for the presence of OH

Infrared (IR) spectrometry can serve as a simple method to gather information on the presence of OH. Characteristic OH absorptions occur around the ranges of 3700-3200 cm-1 (OH stretching) and 1200-1000 cm-1 (OH bending). In the case of hydrogen-bonded OH, the band in the region 3700-3200 cm-1 generally appears broad and sometimes can go unnoticed.

Below is the IR spectrum for butanoic acid. The presence of the two bands at 3582 cm-1 and 1150 cm-1 suggest that an OH group is present.

 

 

TIP: An incorrect interpretation may occur for samples that contain impurities with OH groups, for example, water.

Examining IR spectra for the presence of OH

Infrared (IR) spectrometry can serve as a simple method to gather information on the presence of OH. Characteristic OH absorptions occur around the ranges of 3700-3200 cm-1 (OH stretching) and 1200-1000 cm-1 (OH bending). In the case of hydrogen-bonded OH, the band in the region 3700-3200 cm-1 generally appears broad and sometimes can go unnoticed.

Below is the IR spectrum for butanoic acid. The presence of the two bands at 3582 cm-1 and 1150 cm-1 suggest that an OH group is present.

 

 

TIP: An incorrect interpretation may occur for samples that contain impurities with OH groups, for example, water.

IR, NMR and MS of a Sulfonyl Chloride compound

The best use of a set of tools for a structure elucidation are those that have a general target or goal in mind. Random experiments for the sake of collecting data are a sure sign of inexperience. With that said, Infrared (IR) spectroscopy is a great tool for identifying or confirming a functional group(s). It is an under utilized tool that can complement information from NMR and MS.

The IR, NMR and MS spectra for butane-1-sulfonyl chloride are shown below.

Sulfonyl chloride exhibits strong characteristic bands in the IR region of 1410-1370 and 1204-1166 cm-1. The alkane CH stretching bands appear around 3000-2800 cm-1.

The MS illustrates two ions at m/z 57 and 99. The ion peak at m/z 57 is characteristic of a hydrocarbon chain. The ion peak at m/z 99, although weak, is characteristic for a sulfonyl chloride group and exhibits an A+2 peak at m/z 101 due to the 37Cl isotope.

The 1H NMR spectrum exhibits 4 distinct multiplets attributed to the hydrocarbon chain. The deshielded multiplet at 3.68 ppm indicates the presence of a strong-electron withdrawing atom or group.

Using any 2 of the 3 techniques can facilitate the elucidation process and assist in confirming the structure.

IR, NMR and MS of a Sulfonyl Chloride compound

The best use of a set of tools for a structure elucidation are those that have a general target or goal in mind. Random experiments for the sake of collecting data are a sure sign of inexperience. With that said, Infrared (IR) spectroscopy is a great tool for identifying or confirming a functional group(s). It is an under utilized tool that can complement information from NMR and MS.

The IR, NMR and MS spectra for butane-1-sulfonyl chloride are shown below.

Sulfonyl chloride exhibits strong characteristic bands in the IR region of 1410-1370 and 1204-1166 cm-1. The alkane CH stretching bands appear around 3000-2800 cm-1.

The MS illustrates two ions at m/z 57 and 99. The ion peak at m/z 57 is characteristic of a hydrocarbon chain. The ion peak at m/z 99, although weak, is characteristic for a sulfonyl chloride group and exhibits an A+2 peak at m/z 101 due to the 37Cl isotope.

The 1H NMR spectrum exhibits 4 distinct multiplets attributed to the hydrocarbon chain. The deshielded multiplet at 3.68 ppm indicates the presence of a strong-electron withdrawing atom or group.

Using any 2 of the 3 techniques can facilitate the elucidation process and assist in confirming the structure.