Stuck on a Structure Elucidation problem? You need Out of the Box thinking, right?

Attempting a challenging structure elucidation of an unknown and being unable to solve the problem can put a damper on a hectic workload and possibly on your skills as an elucidator. Emotionally, the excitement of working on a challenging elucidation problem leads into frustration -- results are what count. Subsequently, the elucidator faces the following choices:

-collect more data,

-question the data or the instrument or the instrument operator,

-discard everything and start from scratch,

-leave it alone for a few days and then come back to it with a clear mind,

-hand it off for someone else to do,

-forget about it and pretend it never existed, or

-file it in the cabinet under the X-file for another day.

The diagram below presents the situation whereby an elucidator is fixated on a core fragment and thus unable to budge from the enclosed Structural Bias box. A classic example is the elucidation of a synthetic product whereby the chemist synthesized an unknown compound far from what he/she intended. The elucidator then falls for the bias of a specific fragment upon seeing the synthetic route.

How to avoid the Structural Bias box? There is no easy answer (or answers) other than to simply broaden your scope of knowledge. Definitely, the willingness and enthusiasm to never give up is a plus while ensuring every idea is panned out to its fullest. Also, be sure to be open to more than one solution as you venture outside of your comfort zone. Explore the literature and databases in search of that elusive tidbit that could unlock the missing piece. Finally, focus on piecing the data together in new and creative ways.

Stuck on a Structure Elucidation problem? You need Out of the Box thinking, right?

Attempting a challenging structure elucidation of an unknown and being unable to solve the problem can put a damper on a hectic workload and possibly on your skills as an elucidator. Emotionally, the excitement of working on a challenging elucidation problem leads into frustration -- results are what count. Subsequently, the elucidator faces the following choices:

-collect more data,

-question the data or the instrument or the instrument operator,

-discard everything and start from scratch,

-leave it alone for a few days and then come back to it with a clear mind,

-hand it off for someone else to do,

-forget about it and pretend it never existed, or

-file it in the cabinet under the X-file for another day.

The diagram below presents the situation whereby an elucidator is fixated on a core fragment and thus unable to budge from the enclosed Structural Bias box. A classic example is the elucidation of a synthetic product whereby the chemist synthesized an unknown compound far from what he/she intended. The elucidator then falls for the bias of a specific fragment upon seeing the synthetic route.

How to avoid the Structural Bias box? There is no easy answer (or answers) other than to simply broaden your scope of knowledge. Definitely, the willingness and enthusiasm to never give up is a plus while ensuring every idea is panned out to its fullest. Also, be sure to be open to more than one solution as you venture outside of your comfort zone. Explore the literature and databases in search of that elusive tidbit that could unlock the missing piece. Finally, focus on piecing the data together in new and creative ways.

t-Butyl group towers over other 1H resonances

Like a methoxy group, a t-Butyl group stands out over other 1H resonances. For organic compounds, the 1H resonance for a t-Butyl group generally towers over other 1H resonances because it integrates to ~9 protons (assuming the presence of 1 t-Butyl group and no overlap with other resonances). The basic 1H NMR pattern of the CH3 groups is a typical singlet, although not always the case, and ranging in chemical shift between 0.5 and 2.0 ppm. The 13C NMR spectrum shows the CH3 resonances between 20 and 42 ppm.

The 1H NMR spectra below illustrates the 3 patterns for a t-Butyl group to be on the lookout for.

t-Butyl group towers over other 1H resonances

Like a methoxy group, a t-Butyl group stands out over other 1H resonances. For organic compounds, the 1H resonance for a t-Butyl group generally towers over other 1H resonances because it integrates to ~9 protons (assuming the presence of 1 t-Butyl group and no overlap with other resonances). The basic 1H NMR pattern of the CH3 groups is a typical singlet, although not always the case, and ranging in chemical shift between 0.5 and 2.0 ppm. The 13C NMR spectrum shows the CH3 resonances between 20 and 42 ppm.

The 1H NMR spectra below illustrates the 3 patterns for a t-Butyl group to be on the lookout for.

The advantages of overlaying an HSQC spectrum with an HMBC spectrum

When trying to elucidate an unknown structure using 2D NMR information, an elucidator gains an advantage by analyzing all of the NMR data as a whole rather than as individual pieces. Although complicated at first, this different perspective at viewing the NMR data can facilitate the elucidation process.

The following list are a few advantages for overlaying (also referred to as collect or dual mode) an HSQC with an HMBC:

HMBC correlations can be used to differentiate overlapping HSQC correlations (and vice versa),

by lining-up the correlations for both experiments, fragments can be quickly pieced together,

the number of HMBC correlations per HSQC correlation can be determined easily,

quaternary carbons can be directly differentiated and viewed alongside the protonated carbons.

Shown below are the spectral data of a 1H NMR, an 1H-13C HSQC (green) and an 1H-13C HMBC (red) for an indole group (assigned chemical shifts are shown in blue). The different correlation colours enable the elucidator to simply distinguish the 2D NMR experiments. Carbons 111, 119.4, 119.8, 121 and 125 ppm, shown in green, are the protonated carbons from the HSQC data, thus differentiating the quaternary carbons at 116 and 128.5 ppm. The 13C resonance at 111 ppm shows 2 1H correlations: 7.17 and 7.34 ppm (illustrated with black arrows). The 1H resonance at 7.34 ppm (13C at 111 ppm) shows 3 13C correlations: 119.4, 121 and 128 ppm.

The advantages of overlaying an HSQC spectrum with an HMBC spectrum

When trying to elucidate an unknown structure using 2D NMR information, an elucidator gains an advantage by analyzing all of the NMR data as a whole rather than as individual pieces. Although complicated at first, this different perspective at viewing the NMR data can facilitate the elucidation process.

The following list are a few advantages for overlaying (also referred to as collect or dual mode) an HSQC with an HMBC:

HMBC correlations can be used to differentiate overlapping HSQC correlations (and vice versa),

by lining-up the correlations for both experiments, fragments can be quickly pieced together,

the number of HMBC correlations per HSQC correlation can be determined easily,

quaternary carbons can be directly differentiated and viewed alongside the protonated carbons.

Shown below are the spectral data of a 1H NMR, an 1H-13C HSQC (green) and an 1H-13C HMBC (red) for an indole group (assigned chemical shifts are shown in blue). The different correlation colours enable the elucidator to simply distinguish the 2D NMR experiments. Carbons 111, 119.4, 119.8, 121 and 125 ppm, shown in green, are the protonated carbons from the HSQC data, thus differentiating the quaternary carbons at 116 and 128.5 ppm. The 13C resonance at 111 ppm shows 2 1H correlations: 7.17 and 7.34 ppm (illustrated with black arrows). The 1H resonance at 7.34 ppm (13C at 111 ppm) shows 3 13C correlations: 119.4, 121 and 128 ppm.

Using complementary elucidation tools to solve for an unknown structure

MS and NMR are complementary tools for structure elucidation. Knowing when to apply which tool can assist an elucidator in solving for an unknown structure quickly and with less frustration. Although the sample data below is for a simple organic structure, it is working through many simple examples that one refines the skills needed for elucidation(s) on a bigger scale.

With the available spectral data below, the steps outlined for elucidating an unknown are as follows:

1. extract peak information from the spectral data,

2. piece together the fragments to build a complete structure,

3. finally, verify that the candidate structure(s) is consistent with all the spectral data. If more than one structure fits the data, then look into collecting additional data.

Below are three spectra for an unknown compound: an EI MS, a 1H NMR and a 13C NMR. Although additional information can be extracted from the spectral data, an explanation follows to some of the obvious bits of information that can be extracted at a first pass. The MS shows pairs of ion clusters at approximately equal intensity for m/z pairs 79/81, 93/95 and 133/135, thus indicating the presence of a bromine atom. The molecular ion is most likely the ion peak at m/z 133. The nitrogen rule indicates that the unknown contains an odd number of nitrogen atoms. The 1H NMR spectrum shows 2 triplets at a 1:1 ratio and coupled to each other. The 13C NMR shows 3 carbon peaks at 21, 24 and 117 ppm, thus indicating 3 carbon atoms.

The structural pieces are a bromine atom (79 Da), a nitrogen atom (14 Da), -CH2-CH2- group (28 Da) and a third carbon (12 Da). The candidate structure that fits the data is 3-bromopropanenitrile (133 Da).