Logic Puzzle #13: Extra Correlations on the HSQC Spectrum … Solution

The intensity of a correlation in relation to other correlations on a 2D NMR spectrum can be just as important in a structure elucidation as assessing the position and phase of a correlation. The example below presents one such case.

From the 1H-13C HSQC in the previous post, the correlations differ significantly in intensity. The weaker correlations can be attributed to long-range couplings, more specifically, 2J coupling responses. In addition to the 1H integrals, the carbons at 121 and 134 ppm are probably CH’s (4 CH’s in total) and probably not CH2’s. Two potential fragments are shown below and here.

 
I would like to send out a special thanks to Sarah T. for discussing the idea with me.

Logic Puzzle #13: Extra Correlations on the HSQC Spectrum

A 1H-13C HSQC is frequently used to assist in assigning a carbon as CH, CH2 or CH3 (additional blog here). The purpose of this puzzle is to examine a non-standard assignment.

The 1H-13C HSQC below shows 2 correlations for each carbon at 121 and 134 ppm. Given also the information on the 1H integrals on the F2 axis, are the carbons at 121 and 134 ppm really CH2’s?

 

Logic Puzzle #12: Torsion Angle and Coupling … Solution

Couplings can be affected by the torsion angle. The couplings can be expressed mathematically with a cos θ relationship. At certain values of θ, the couplings are expected to be relatively weaker to non-existent.

Based on the torsion angle, fragment B is expected to exhibit a prominent coupling between the red and gold nuclei. Fragment A, exhibiting a torsion angle of 90º, will generally lead to a weak or non-evident coupling on an NMR spectrum.

At the initial stages of an elucidaton of an unknown structure, the torsion angle(s) is usually not known. As such, an elucidator must be prepared to expect the unexpected coupling(s). 

Logic Puzzle #12: Torsion Angle and Coupling

For a simple case, the torsion angle (or dihedral angle) is described as the angle between 4 contiguous atoms or 3 successive bonds. In NMR, the magnitude of the coupling is directly related to the torsion angle between the vicinal nuclei (see the Karplus equation for more details).

Below are two animations, A and B, for identical fragments differing only in the torsion angle. Assuming the following fragments exhibit a rigid geometry, which torsion angle would generally contribute to a prominent coupling between the red and gold nuclei?

A (torsion angle at 90º)                 B (torsion angle at 35º)

                     

Logic Puzzle #11: Pairwise Correlation Confidence … Solution

Long range 2D NMR experiments do not necessarily provide information about all the connectivities. The following structure elucidation problem set is one such example.

Based on the 1H-13C HMBC shown below, there is no evident correlation between the 1H at 5.31 ppm and the 13C at 21.1 ppm. Note the green box describes the region of interest.

The correlation between the methyl 1H at 2.15 ppm and 13C at 84.7 ppm (indicated by the purple arrow and the red bonds below) is a weak 4J coupling (also denoted as a W-coupling or M-coupling). The coupling arises from the individual methyl protons rotating and interacting through a W-relationship (or M-)with the carbon. This coupling is not evident for the methine 1H at 5.31 ppm and the 13C at 21.1 ppm.

 
Thank you Serge for your comment.

Logic Puzzle #11: Pairwise Correlation Confidence

Typical for long range 2D NMR experiments, spectral data may exhibit more than one correlation for two coupled nuclei (e.g. A to B and B to A). The pairwise correlations offer an extra degree of confidence in the interpretation.  

For the following fragment, an 1H-13C HMBC correlation exists for the 1H 2.15 ppm to 13C 84.7 ppm (represented by the purple arrow in the diagram below).

 
Is the pairwise correlation for the 1H 5.31 ppm to 13C 21.1 ppm evident?

 
A special thanks goes to Gene M. for pointing me to the data.

Logic Puzzle #10: Deciphering the Fragment Pattern using 2D NMR Data … Solution

Like any new process, it takes some practice to extract, understand and convert the information presented from a set of experimental NMR datasets into a fragment.

The only fragment that can accommodate the set of restrictions from a 1H-13C HSQC and HMBC is 2,3-dimethylbutane-1,1-diyl. The green arrows illustrate the 2-3JCH coupling responses extracted from an HMBC experiment.

 

Logic Puzzle #10: Deciphering the Fragment Pattern using 2D NMR Data

The goal of this puzzle is to conceptualize a fragment(s) from the given information.

In the following example, a set of protonated sp3 carbons were extracted from an HSQC experiment (not shown). The green arrows represent the 2-3JCH coupling responses extracted from an HMBC experiment. Based on these restrictions, what fragment(s) supports the data?

Note there is an open valence off one of the carbon atoms.

Logic Puzzle #7: Almost Missed It … Solution 2

With intense solvent signals present on a spectrum, a smaller signal(s) can easily be missed. If 2D NMR data is available, then this extra information can assist in clarifying whether a small signal(s) is obscured by larger signals.

On the 1H-13C HMBC below, the correlations for CDCl3/CHCl3 (due to 1J coupling responses and more) are more intense in comparison to the weak correlation at approximately 6.9 and 77.3 ppm. In this case, the weak correlation is attributed to a quaternary carbon obscured by a set of intense solvent signals.

 

Logic Puzzle #4: Correlating to the Correct 13C Signal … Solution

The goal of this puzzle is to resolve the ambiguity exhibited within a 2D NMR spectrum and thus provide the correct signal correlation. Although this exercise may seem a trivial one, it is important to go over the rationale when correlating one signal to another.

For the following 1H-13C HSQC-DEPT NMR spectrum it is important to note that the 2 correlations are phased positively (red) and thus represent either a CH or CH3 group and not a CH2. Next, one must ensure that the carbons at 61.5 and 62.2 ppm are 1 carbon each. Although this detail is not certain, we will assume this to be the case. Finally, it is best to start with the easy part first. The 1H signal at 3.50 ppm is correlated to the 13C signal at 62.2 ppm. By process of elimination, one can conclude that the 1H signal at 2.73 ppm is correlated to the 13C signal at 61.5 ppm (see this post for more details).

Ambiguity in correlating 1D and 2D NMR data can routinely occur. Some extra steps that can help avoid this issue are re-aligning the data and/or re-processing the ‘raw’ data with different parameters.

 

Logic Puzzle #4: Correlating to the Correct 13C Signal … Solution

The goal of this puzzle is to resolve the ambiguity exhibited within a 2D NMR spectrum and thus provide the correct signal correlation. Although this exercise may seem a trivial one, it is important to go over the rationale when correlating one signal to another.

For the following 1H-13C HSQC-DEPT NMR spectrum it is important to note that the 2 correlations are phased positively (red) and thus represent either a CH or CH3 group and not a CH2. Next, one must ensure that the carbons at 61.5 and 62.2 ppm are 1 carbon each. Although this detail is not certain, we will assume this to be the case. Finally, it is best to start with the easy part first. The 1H signal at 3.50 ppm is correlated to the 13C signal at 62.2 ppm. By process of elimination, one can conclude that the 1H signal at 2.73 ppm is correlated to the 13C signal at 61.5 ppm (see this post for more details).

Ambiguity in correlating 1D and 2D NMR data can routinely occur. Some extra steps that can help avoid this issue are re-aligning the data and/or re-processing the ‘raw’ data with different parameters.

 

Logic Puzzle #4: Correlating to the Correct 13C Signal

The goal of this puzzle is to resolve the ambiguity exhibited within a 2D NMR spectrum and thus provide the correct signal correlation.

The following 1H-13C HSQC-DEPT NMR spectrum shows two one-bond correlations linked to the 1H signals 2.75 and 3.50 ppm and two closely spaced 13C signals at 61.5 and 62.2 ppm. Does the 1H signal at 2.75 ppm correlate to the 13C signal at 61.5 ppm or the one at 62.2 ppm?

Note: the blue line was added to help align the correlation to the F1 domain.

Logic Puzzle #4: Correlating to the Correct 13C Signal

The goal of this puzzle is to resolve the ambiguity exhibited within a 2D NMR spectrum and thus provide the correct signal correlation.

The following 1H-13C HSQC-DEPT NMR spectrum shows two one-bond correlations linked to the 1H signals 2.75 and 3.50 ppm and two closely spaced 13C signals at 61.5 and 62.2 ppm. Does the 1H signal at 2.75 ppm correlate to the 13C signal at 61.5 ppm or the one at 62.2 ppm?

Note: the blue line was added to help align the correlation to the F1 domain.

Logic Puzzle #1: The Missing Link

A great skill to master is the capability to conceptualize a fragment or structure directly off a spectrum without resorting to paper-and-pen work. This skill is learnt through lots of practice. Whenever partial information is available, an elucidator can conjure up a mental image of possibilities and should it be required instinctively hunt for any missing data.

In the following example, a set of fragments including 13C and 1H chemical shifts and long-range coupling information were extracted from an HMBC experiment (not shown). The green arrows represent the 2-3J coupling responses between the 3 equivalent methyl groups and the carbonyl’s quaternary carbon. Based on these restrictions, what fragment(s) support the data and is there anything missing?

To accommodate these restrictions, three potential fragments, assigned A, B and C, are shown below. Fragment A can be disregarded on the basis of the carbon valence. Fragment B is not a good candidate because the CH3 chemical shifts do not support the presence of an adjacent heteroatom. Fragment C seems to be the most logical choice. However, there is a missing quaternary carbon. The next step is to re-evaluate the NMR data in search of a weak 13C signal at ~40 ppm.

Logic Puzzle #1: The Missing Link

A great skill to master is the capability to conceptualize a fragment or structure directly off a spectrum without resorting to paper-and-pen work. This skill is learnt through lots of practice. Whenever partial information is available, an elucidator can conjure up a mental image of possibilities and should it be required instinctively hunt for any missing data.

In the following example, a set of fragments including 13C and 1H chemical shifts and long-range coupling information were extracted from an HMBC experiment (not shown). The green arrows represent the 2-3J coupling responses between the 3 equivalent methyl groups and the carbonyl’s quaternary carbon. Based on these restrictions, what fragment(s) support the data and is there anything missing?

To accommodate these restrictions, three potential fragments, assigned A, B and C, are shown below. Fragment A can be disregarded on the basis of the carbon valence. Fragment B is not a good candidate because the CH3 chemical shifts do not support the presence of an adjacent heteroatom. Fragment C seems to be the most logical choice. However, there is a missing quaternary carbon. The next step is to re-evaluate the NMR data in search of a weak 13C signal at ~40 ppm.

Signals can simply disappear on a DEPT-135 experiment

There are many advantages in working with a 1H-13C HSQC-DEPT spectrum over a 13C DEPT-135 and a 1H-13C HSQC (see Post 1 & Post 2). In most cases, a 1H-13C HSQC-DEPT is more valuable than either one of those experiments.

The aliphatic region of a 1H-13C HSQC-DEPT is spectrum below. Two coincidental carbon signals are overlapping at 38.51 ppm, one pertaining to a CH while the other a CH2 group. The DEPT-135, attached to the F1 domain, exhibits a weak 13C signal that can easily be misconstrued, for example as an impurity, if not for the extra information from the 2D NMR experiment.

Signals can simply disappear on a DEPT-135 experiment

There are many advantages in working with a 1H-13C HSQC-DEPT spectrum over a 13C DEPT-135 and a 1H-13C HSQC (see Post 1 & Post 2). In most cases, a 1H-13C HSQC-DEPT is more valuable than either one of those experiments.

The aliphatic region of a 1H-13C HSQC-DEPT is spectrum below. Two coincidental carbon signals are overlapping at 38.51 ppm, one pertaining to a CH while the other a CH2 group. The DEPT-135, attached to the F1 domain, exhibits a weak 13C signal that can easily be misconstrued, for example as an impurity, if not for the extra information from the 2D NMR experiment.

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.

Ah Sugar, Sugar … Residue

Sugar residues (saccharides) can be tough to elucidate. They tend to have 1H NMR spectrum with overlapping and sometimes poorly-resolved 1H signals, and the 2D NMR data presents lots of ambiguous assignments. With a little practice, an elucidator can quickly pick out a sugar moiety based on a minimal amount of NMR data.

For a given set of atoms with known 13C chemical shifts (shown below), a hexopyranoside sugar moiety is evident even without any long-range coupling information. The general pattern is as follows: a CH at ~100 ppm, 4 CHs between ~70 to 77 ppm, a CH2 at ~60 ppm, 6 O atoms and 4 H atoms. Note: the H atoms count may vary depending on the number of connection points.

An example sugar, phenyl hexapyranoside, with 13C chemical shifts is presented below.