Utilization of Compounds from Undergraduate Research To Exemplify

Chapter 4

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Utilization of Compounds from Undergraduate Research To Exemplify Concepts in NMR Spectroscopy J. Thomas Ippoliti,* Rebecca L. Kummer, Sarah N. Larson, Andrew K. Peterson, and Olga Y. Zamulko Department of Chemistry, University of St. Thomas, 2115 Summit Ave., St. Paul, Minnesota 55105, United States *E-mail: [email protected]

The 1H NMR spectra of compounds that were synthesized as part of undergraduate research projects are utilized as examples to illustrate numerous concepts that are taught in an Organic Spectroscopy course. The compounds and their spectra discussed here illustrate: Karplus curve concepts in cyclohexane rings, sigma bond anisotropy, fluorine splitting, magnetic inequivalence leading to 2nd order spectra and inverted triplets, anisotropy effects of sterically crowded aromatic rings, and the effect of hindered rotation on chemical shift. These spectra serve as excellent teaching tools.

Introduction One of the best ways to teach a concept in NMR spectroscopy is by using real life examples. Students who perform undergraduate research in organic synthesis learn many principles in NMR spectroscopy by utilizing this technique to support proposed structures of synthesized compounds. These same compounds also serve as excellent examples to demonstrate concepts in an organic spectroscopy course. All the compounds shown in this chapter were synthesized as part of undergraduate research projects, with their 1H NMR spectra being used in an undergraduate organic spectroscopy course. Each section is labeled with a set of concepts and then an example from an undergraduate research project is utilized to demonstrate those concepts.

© 2016 American Chemical Society Soulsby et al.; NMR Spectroscopy in the Undergraduate Curriculum: Upper-Level Courses and Across the Curriculum Volume 3 ... ACS Symposium Series; American Chemical Society: Washington, DC, 2016.

Compound 1: Coupling Constant Dependency on Dihedral Angle – Karplus Curve and Sigma Bond Anisotropy


The 1H NMR signals from protons on a cyclohexane ring exemplify the dependence of dihedral angle on coupling constants when there is a large substituent present so that one conformation is preferred. These signals also demonstrate the anisotropic effect of sigma bonds, since the axial protons in the shielding cone of the sigma bond are upfield from the equatorial protons on the same carbon. Compound 1 shown in Figure 1 illustrates these principles (1).

Figure 1. Structure of Compound 1.

The partial 1H NMR spectrum of compound 1 is shown in Figure 2.

Figure 2. The cyclohexyl region of Compound 1 in d6-DMSO.

H1 is the proton that is the farthest downfield in the spectrum due to its proximity to the nitrogen atom. This proton is also in the axial position since the large benzimidazole group effectively locks the ring in the chair conformation. It is split by the two vicinal axial protons (H3) into a large triplet with coupling constant of 11.8 Hz and into a smaller triplet of 3.7 Hz by the two equatorial protons (H2). A tree diagram describing this splitting is seen in Figure 3a. These spectra illustrate the dependency of the coupling constant on the dihedral angle as illustrated by the Karplus curve (Figure 3b). For H1, the coupling constant of Jax-ax = 11.8 Hz reflects the dihedral angle of 180°. The equatorial protons have a dihedral angle of 60° and therefore have a smaller coupling of Jax-eq = 3.7 Hz. 54 Soulsby et al.; NMR Spectroscopy in the Undergraduate Curriculum: Upper-Level Courses and Across the Curriculum Volume 3 ... ACS Symposium Series; American Chemical Society: Washington, DC, 2016.


Figure 3. a) Tree diagram for H1 of compound 1 with coupling constants of 11.8 Hz and 3.7 Hz; b) A general Karplus curve illustrating the relationship between dihedral angle and 3-bond (3J) coupling constant in Hz.

The fact that the two equatorial protons (H2) are upfield from the axial protons (H3) also illustrates the effect of the shielding cones of the sigma bonds in the cyclohexane ring, as shown in Figure 4.

Figure 4. Diagram illustrating the shielding and deshielding regions of the sigma bond in cyclohexane.

55 Soulsby et al.; NMR Spectroscopy in the Undergraduate Curriculum: Upper-Level Courses and Across the Curriculum Volume 3 ... ACS Symposium Series; American Chemical Society: Washington, DC, 2016.


The proton that should be the most shielded, and thus upfield according to the cones shown in Figure 4, is the axial proton, which is furthest from the benzimidazole substituent and is labeled H4 (Figure 2). This is confirmed by its integration value of one and its observed splitting pattern. Geminal and vicinal axial coupling constants are often of the same magnitude, in this case about 13 Hz. Since there are three protons, one geminal and two vicinal axial, that have a large coupling constants (12.96 Hz) and two protons, vicinal equatorial, that have a small coupling constants (3.66 Hz), a clean quartet of triplets is observed (Figure 5a). It is instructive to have students draw a tree diagram, as shown in Figure 5b, for this signal (or the analogous signal for H6).

Figure 5. a) Expanded region of the 1H NMR of 1. b) Tree diagram for H4.


Compound 2: Olefin Splitting Patterns, Long Range 4J Coupling, 19F Splitting and Magnetic Inequivalence


Compound 2 illustrates several important concepts in NMR spectroscopy. Its full spectrum is shown in Figure 6.

Figure 6. Structure and full 1H NMR spectrum of compound 2 with assignments. Analysis of the splitting patterns of the olefin proton signals in Figure 7 reveals the size of the different coupling constants for cis and trans protons, as well as long range allylic coupling (4J). This example also demonstrates how the assignment of these protons is definitive based on the coupling constants measured.

Figure 7. Expanded region of the 1H NMR spectrum of compound 2. The actual coupling constants are shown in Figure 8 and illustrate the size of cis versus trans coupling constants, as well as the long range allylic coupling inherent to freely rotating terminal alkenes. The size of the four bond coupling (4J) is on the order of the two bond geminal coupling (2J) constant for sp2 carbons, which leads to apparent quartets. 57 Soulsby et al.; NMR Spectroscopy in the Undergraduate Curriculum: Upper-Level Courses and Across the Curriculum Volume 3 ... ACS Symposium Series; American Chemical Society: Washington, DC, 2016.


Figure 8. Diagram showing measured coupling constants for compound 2.

Second order splitting patterns are quite common when large substituents are vicinally located on a two carbon chain. In compound 2, the allyloxy and the substituted phenoxy are the two large groups. In this case, the splitting patterns for the two methylenes, B and C, appear as inverted triplets with extra peaks in the middle instead of a clean triplet as one would expect in a normal straight chain compound (Figure 9). These inverted triplets are sometimes referred to as “Batman” peaks by the author when teaching this topic.

Figure 9. Partial spectrum of compound 2 showing the second order spitting patterns of B and C.



This pattern is the result of conformational averaging with the most highly populated conformation having the big substituents anti to one another, as shown in the Newman projection in Figure 10. In this conformation, it is clear that the two highlighted protons have different dihedral angles to the same vicinal proton and thus different coupling constants as illustrated by arrows in Figure 10. This results in second order spectra because, although the protons are chemically shift equivalent, they are magnetically non-equivalent.

Figure 10. Newman projection for compound 2 illustrating the different dihedral angles between the protons circled and the same vicinal proton.

A second example of magnetically non-equivalent protons in the same molecule is seen when examining the aromatic proton splitting pattern (Figure 11). These protons are chemically shift equivalent but magnetically non-equivalent due to the different coupling with the 19F atoms. This results in a second order spectrum and gives rise to extra lines so that a simple doublet is not observed. It gives the classic AA′XX′ with 19F as the other spin-active nuclei (X). The pattern can be predicted exactly using quantum mechanics (2).

Figure 11. Partial 1H NMR spectrum of the aromatic region of compound 2. 59 Soulsby et al.; NMR Spectroscopy in the Undergraduate Curriculum: Upper-Level Courses and Across the Curriculum Volume 3 ... ACS Symposium Series; American Chemical Society: Washington, DC, 2016.

Compound 3: Diastereotopic Protons in Molecules with No Stereogenic Centers, Magnetic Anisotropy Due to Aromatic Rings


The 1H NMR spectrum of compound 3 displays several important NMR concepts (3). One such concept in spectroscopy concerns diastereotopic protons. Diastereotopic protons are most easily recognized by first identifying stereogenic centers within a molecule, then finding methylene protons in the molecule. A less common type of diastereotopic protons, however, arises from molecules that have no stereogenic center, and thus are much more difficult to spot. As shown in Figure 12, this is the case in compound 3.

Figure 12. Partial 1H NMR spectrum of compound 3.

It is instructive to show students the structure of compound 3 and ask them to pick out the diastereotopic protons. In fact, this molecule has two equivalent sets of diastereotopic protons, the methylenes on each of the ethyl groups (only one methylene group shown) and the methyls of each isopropyl group (only one set of methyl groups shown). A common way to determine if protons are diastereotopic is to replace one of them with a deuterium and then identify and assign all stereogenic centers. Next, the other proton is replaced with a deuterium and again all of the stereogenic centers are assigned. If the two isomers are diastereomers then they are diastereotopic. When this process is carried out for the methylenes of the ethyl group in compound 3, two diastereomers are formed (Figure 13). 60 Soulsby et al.; NMR Spectroscopy in the Undergraduate Curriculum: Upper-Level Courses and Across the Curriculum Volume 3 ... ACS Symposium Series; American Chemical Society: Washington, DC, 2016.


Figure 13. Replacement of each diastereotopic proton of the methylenes illustrating their diastereomeric relationship.

Note that replacement of just one of the protons of the methylene with a deuterium creates two stereogenic centers! This is also the case for the methyl groups of the isopropyl group as well, Figure 14.

Figure 14. Replacement of each diastereotopic proton of the methyl groups illustrating the diastereomeric relationship.

The anisotropic effect of the benzene ring in compound 3 is clearly seen for the methyl of the ethyl group (Figure 15). The signal appears as a triplet and its chemical shift of 0.13 ppm is dramatically upfield from the protons of a typical methyl of an ethyl group. Since chemical shift is a result of conformational averaging, the methyl of the ethyl group spends a considerable amount of time over the middle of two benzene rings, resulting in it being shielded by the aromatic systems as illustrated in Figure 15. 61 Soulsby et al.; NMR Spectroscopy in the Undergraduate Curriculum: Upper-Level Courses and Across the Curriculum Volume 3 ... ACS Symposium Series; American Chemical Society: Washington, DC, 2016.


Figure 15. Two conformational isomers demonstrating the conformations in which the methyl is over an aromatic ring and the partial spectrum of 3 showing the methyl signal at 0.13 ppm.

Compound 4: Two Bond 19F-1H Coupling and Restricted Rotation Finally, compound 4 illustrates the principles of restricted rotation and two bond 19F-1H coupling. Figure 16 shows the large triplet caused by the 19F-1H coupling constant of 75.1 Hz. The large size of the chlorine atoms in compound 4 restricts the rotation around the aryl-nitrogen bond by sterically bumping into the other aromatic ring. This makes the protons labeled a and b in Figure 17 diastereotopic, with quite different chemical shifts. Another way to describe this is to define proton a has having a cis relationship to the other aromatic ring with respect to the heterocyclic five membered ring, while proton b has a trans relationship. This provides very different chemical environments that are not interchangeable by rotation.



Figure 16. The partial 1H NMR spectrum of compound 4 illustrating the large 19F-1H coupling constant of 75.1 Hz.

Figure 17. The partial 1H NMR spectrum of compound 4 illustrating the diastereomeric nature of protons labeled a and b.

Conclusions The 1H NMR spectra of molecules synthesized by undergraduate students can serve as excellent examples of concepts and principles taught in an organic spectroscopy course. The examples illustrated here show the common splitting patterns of cyclohexane ring protons, demonstrating the dependence of coupling constant on dihedral angle, anisotropic effects, terminal olefin proton splitting patterns, 19F-1H coupling, magnetically non-equivalent protons, and diastereotopic protons. 63 Soulsby et al.; NMR Spectroscopy in the Undergraduate Curriculum: Upper-Level Courses and Across the Curriculum Volume 3 ... ACS Symposium Series; American Chemical Society: Washington, DC, 2016.

Experimental General Remarks All reagents were purchased from Sigma Aldrich unless otherwise specified. All reagents were used as purchased without further purification. Column chromatography was performed with the Biotage Isolera One. 1H NMR spectra were recorded on a JEOL ECS400 NMR spectrometer (4). Compounds 1 and 3 were synthesized according procedures in references (1) and (3) respectively.


5-(2-(Allyloxy)ethoxy)-2-bromo-1,3-difluorobenzene (2) A two-step synthesis was followed to synthesize 2 as shown in Figure 18.

Figure 18. Synthetic route to compound 2. In a flame-dried 500 mL round bottom flask was added 2-(allyloxy)ethanol (5.06 g, 49.54 mmol) and anhydrous diethyl ether (70 mL) via syringe. Triethylamine (7.44 g, 73.53 mmol) was added to the round bottom flask and the solution was stirred. In a flame-dried 150 mL Erlenmeyer flask, p-toluenesulfonyl chloride (13.10 g, 68.71 mmol) was dissolved in anhydrous diethyl ether (100 mL). The tosyl solution then was added via cannula to the reaction flask and the reaction was stirred under a nitrogen atmosphere for 12 hours. After 12 hours the triethylamine hydrochloride salt was removed by gravity filtration and the solution was washed with 1% HCl solution (2 x 100 mL), distilled water (2 x 100 mL), concentrated NH4OH (100 mL), and 10% NaOH solution (100 mL). It was dried with sodium sulfate, filtered and concentrated by rotary evaporation. The tosylate was placed under vacuum to remove residual solvent, yielding an oil that was used in the next step without further purification. In a 25 mL round bottom flask was added 4-bromo-2,6-difluorophenol (0.51 g, 2.44 mmol), N,N-dimethylformamide (3 mL), and potassium carbonate (0.38 g, 2.75 mmol). The solution was stirred for 10-15 minutes. In a separate vial, 2-(allyloxy)ethyl 4-methylbenzenesulfonate (1.06 g, 4.14 mmol) was dissolved in 1.5 mL DMF. The tosyl solution was added dropwise via syringe into the reaction flask, and the reaction solution was stirred under nitrogen for 48 h. 64

Soulsby et al.; NMR Spectroscopy in the Undergraduate Curriculum: Upper-Level Courses and Across the Curriculum Volume 3 ... ACS Symposium Series; American Chemical Society: Washington, DC, 2016.

After 48 h, distilled water (10 mL) and brine (3 mL) was added, and the solution was extracted with ethyl acetate (3 x 13 mL). The combined organic layers were dried with sodium sulfate and filtered. The product was concentrated via rotary evaporation. The product had an Rf = 0.62 (in 4:1 petroleum ether : ethyl acetate) with impurities at 0.40, 0.36, and 0.06. The product was purified using a 100 g SNAP column on a Biotage automated chromatography instrument to yield 2 as a colorless oil (0.65 g, 2.22 mmol, 91%)


1-Cyclopropyl-2-(4-(difluoromethoxy)-3-ethoxyphenyl)-3-(2,4,6trichlorophenyl)imidazolidin-4-one (4) Compound 4 was isolated as an unexpected product from the attempted reductive amination reaction shown in Figure 19.

Figure 19. Synthetic route to compound 4. 4-(Difluoromethoxy)-3-ethoxybenzaldehyde (171 mg, 0.791 mmol) was dissolved in THF (5 mL, 61.6 mmol) and transferred via pipette to a 50 mL round bottom flask containing a stir bar. While stirring, 2-(cyclopropylamino)-N-(2,4,6-trichlorophenyl)acetamide (209 mg, 0.719 mmol) was added to the flask and the reaction mixture, and the reaction was stirred for 20 min. After 20 minutes, one drop of acetic acid was added to catalyze the reaction, and the mixture was stirred for a further 30 min. Sodium triacetoxyborohydride (231 mg, 1.08 mmol) was added to the reaction mixture, the flask was sealed under N2, and stirred at RT for 12 h. 35 drops of 10% NaOH and water (6 mL) were added until the white solid at the bottom of the flask dissolved. The mixture was extracted with dichloromethane (3 x 60 mL). The organic layers were combined, dried over K2CO3, and filtered into a 100 mL round bottom flask. The solvent was removed via rotary evaporation, giving 320 mg of a yellow oil. TLC (70:30 hexanes:ethyl acetate) showed the presence of 5 different compounds (Rf values: 0.07, 0.13, 0.28, 0.40 and 0.49). The product at Rf =0.28 (4) was isolated. Compound 4: 1H NMR (400 MHz): δ 7.30 (d, J = 2.2 Hz, 1H), 7.23 (d, J = 2.2 Hz, 1H), 7.22-7.21 (m, 1H), 7.22-7.21 (m, 1H), 7.12 (s, 1H), 7.12 (s, 1H), 6.95 (d, J = 8.1 Hz, 1H), 6.95 (d, J = 8.1 Hz, 1H), 6.86 (d, J = 8.2 Hz, 1H), 6.86 (d, J = 8.2 Hz, 1H), 6.54 (t, J = 75.1 Hz, 1H), 6.54 (t, J = 75.1 Hz, 1H), 5.73 (s, 1H), 5.73 (s, 1H), 4.02 (q, J = 7.0 Hz, 2H), 4.02 (q, J = 7.0 Hz, 2H), 3.93 (dd, J = 15.1, 0.7 Hz, 1H), 3.93 (dd, J = 15.1, 0.7 Hz, 1H), 3.59 (d, J = 15.2 Hz, 1H), 3.59 (d, J = 15.2 Hz, 1H), 2.03-2.00 (m, 1H), 2.03-2.00 (m, 1H), 1.56 (s, 5H), 1.56 (s, 5H), 1.41 (t, J = 7.0 Hz, 3H), 1.41 (t, J = 7.0 Hz, 3H), 0.89-0.85 (m, 1H), 65

Soulsby et al.; NMR Spectroscopy in the Undergraduate Curriculum: Upper-Level Courses and Across the Curriculum Volume 3 ... ACS Symposium Series; American Chemical Society: Washington, DC, 2016.

0.89-0.85 (m, 1H), 0.45 (td, J = 8.1, 4.8 Hz, 2H), 0.45 (td, J = 8.1, 4.8 Hz, 2H), 0.25-0.21 (m, 1H), 0.25-0.21 (m, 1H). 2D COSY, HMQC, HMBC, and IR spectra were also obtained to characterize the product.

References 1.


2. 3.

4.

Cuevas-Yañez, E.; Serrano, J. M.; Huerta, G.; Muchowski, J. M.; CruzAlmanza, R. Copper carbenoid mediated N-alkylation of imidazoles and its use in a novel synthesis of bifonazole. Tetrahedron 2004, 60, 9391–9396. Gunther, H. NMR Spectroscopy, 3rd ed.; Wiley-VCH: Weinheim, Germany, 2013; pp 192−210. Qin, X. Photochromic Naphthopyran Compounds: Compositions and Articles Containing Those Naphthopyran Compounds, U.S. Patent US007008568, 2006. NSF Grant: CHE-0959322, MRI-R2: Acquisition of 400 MHz Nuclear Magnetic Resonance (NMR)Spectrometer.


Utilization of Compounds from Undergraduate Research To Exemplify

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