Supporting Information ligo(-aryl glycines): A ew Twist on Structured Peptoids eel H. Shah, Glenn L. Butterfoss,, Khanh guyen, Barney Yoo, Richard Bonneau,, Dallas L. Rabenstein, and Kent Kirshenbaum*, Department of Chemistry, ew York University, ew York, Y 10003. Center for Genomics & Systems Biology, ew York University, ew York, Y 10003. Courant Institute of Mathematical Sciences, Department of Computer Science, ew York University, ew York, Y 10003. Department of Chemistry, University of California, Riverside, California 92521. Email: kent@nyu.edu S1
Table of Contents Chemical Structures Table S1. -substituted glycine monomer units. S4 Scheme S1. Structures of linear peptoid oligomers. S5 Scheme S2. Structures of cyclic peptoid oligomers and their linear precursors. S5 Characterization Data Table S2. Characterization of -methylacetanilides by mass spectrometry. S6 Table S3. Characterization of peptoid oligomers by mass spectrometry. S6 Table S4. Characterization of peptoid oligomers by analytical RP-HPLC. S7-S8 Crystallographic Data Figure S1. Crystal structures of peptoid dimer 11 showing hydrogen bonding. S9 Figure S2. Crystal structures of cyclic hexamer 17. S10 uclear Magnetic Resonance (MR) Spectra Table S5. MR analysis of cis/trans isomer ratios for compounds 1, 2, 4, 6, and 8. S11 Figures S3-S4. MR spectra of compound 1. S12-S13 Figures S5-S6. MR spectra of compound 2. S14-S15 Figures S7. MR spectra of compound 4. S16 Figure S8-S9. MR spectra of compound 6. S17-S18 Figure S10-S11. MR spectra of compound 8. S19-S20 Scheme S3. Distinctive E patterns in oligo(-aryl glycines) S21 Figure S12. 1-D MR of dimer 11 in acetonitrile-d 3. S21 Figure S13. 1-D MR of dimer 11 in methanol-d 4. S22 Figure S14. 2-D ESY traces of dimer 11 in methanol-d 4. S22-23 Figure S15. 1-D MR of trimer 13 in acetonitrile-d 3 S24 Figure S16. 1-D MR of trimer 13 in methanol-d 4. S24 Figure S17. 2-D ESY traces trimer 13 in methanol-d 4. S25-S28 Figure S18. 1-D MR spectra of hexamer 17. S29 Figure S19. 2-D HSQC spectra of hexamer 17. S30 Figure S20. 2-D CSY spectra of hexamer 17. S31 Figure S21. 2-D RESY spectrum of hexamer 17. S32 Figure S22. 1-D MR spectra of hexamer 18. S33 S2
Figure S23. 2-D HSQC spectra of hexamer 18. Figure S24. 2-D CSY spectra of hexamer 18. Figure S25. 2-D CSY/RESY overlay spectra of hexamer 18. Figure S26. MR-based model of cyclic hexamer 18. Computational Data Figure S27. Conformational analysis of -methylacetanilide. Figure S28. Energy surface plots for the conformational analysis of compound 16. Complete reference: Gaussian 2003 S34 S35 S36 S37 S38 S39 S40 S3
Table S1. -substituted glycine monomer units. Monomer Designator H 2 phe = -(phenyl)glycine np = -(4-hydroxy-3-nitrophenyl)glycine dmp = -(3,4-dimethylphenyl)glycine spe = (S)--(1-phenylethyl)glycine S4
Scheme S1. Structures of linear peptoid oligomers. H 2 H H 2 H 2 H 2 2 2 11 H 12 H 13 H 2 H 2 14 15 Scheme S2. Structures of cyclic peptoid oligomers and their linear precursors. H H PyBP DIEA DMF 3 4 2 5 1 6 17 H H PyBP DIEA DMF 3 2 1 4 6 5 18 S5
Table S2. Characterization of -methylacetanilides by electrospray mass spectrometry. Expected bserved Mass Compound ame Mass (M+H) + 1 -Methyl-acetanilide 149.19 150.0 2 -(3,4-Dimethyl-phenyl)--methyl-acetamide 177.12 178.1 4 -Methyl--(4-nitro-phenyl)-acetamide 194.19 195.0 6 -(4-Methoxy-phenyl)--methyl-acetamide 179.22 180.0 8 -(4-Fluoro-phenyl)--methyl-acetamide 167.18 168.0 Table S3. Characterization of peptoid oligomers by electrospray mass spectrometry. ote that Ac = -terminal acetyl, c = cyclic oligomer, all linear oligomers have C- terminal amides. Compound Sequence Formula Calc. m/z bs. m/z Ion 11 Ac-np-phe C 18 H 18 4 6 386.12 12 dmp-np-phe C 26 H 27 5 6 505.20 13 Ac-dmp-np-phe C 28 H 29 5 7 547.21 14 Ac(phe) 4 C 34 H 33 5 5 591.25 15 Ac(phe) 6 C 50 H 47 7 7 857.35 17 c(spe-phe-spe) 2 C 56 H 58 6 6 910.44 18 c(spe-spe-spe- phe-phe-spe) C 56 H 58 6 6 910.44 387.1 M+H + 409.1 M+a + 506.3 M+H + 528.3 M+a + 548.2 M+H + 570.3 M+a + 591.9 M+H + 613.9 M+a + 858.1 M+H + 880.1 M+a + 911.1 M+H + 933.2 M+a + 911.2 M+H + 933.2 M+a + S6
Table S4. Characterization of peptoid oligomers by analytical RP-HPLC. Analytical Reverse Phase High Performace Liquid Chromatography of purified oligomers (5-95% acetonitrile in water, 10 minutes, 214 nm): Compound RP-HPLC Chromatogram Retention Time 1.4 1.2 1.0 0.8 11 AU 0.6 4.125 min 0.4 0.2 0.0 0 1 2 3 4 5 6 7 8 9 10 Minutes Det 166 080207 dmpnpphe 080207 dmpnpphe 1.0 0.8 5.342 min 12 AU 0.6 (This oligomer 0.4 was not purified.) 0.2 0.0 1.0 1.5 2.0 2.5 3.0 3.5 4.0 4.5 5.0 5.5 6.0 6.5 7.0 7.5 8.0 8.5 9.0 9.5 10.0 Minutes 1.6 1.4 1.2 1.0 13 AU 0.8 5.942 min 0.6 0.4 0.2 0.0 0 1 2 3 4 5 6 7 8 9 10 Minutes S7
0.45 0.40 0.35 0.30 14 AU 0.25 0.20 6.133 min 0.15 0.10 0.05 0.00 0 1 2 3 4 5 6 7 8 9 10 Minutes 1.2 1.0 0.8 15 AU 0.6 7.033 min 0.4 0.2 0.0 0 1 2 3 4 5 6 7 8 9 10 Minutes 1.4 1.2 1.0 17 AU 0.8 8.402 min 0.6 0.4 0.2 0.0 0 1 2 3 4 5 6 7 8 9 10 Minutes 0.6 0.5 0.4 18 AU 0.3 8.192 min 0.2 0.1 0.0 0 1 2 3 4 5 6 7 8 9 10 Minutes S8
Figure S1. Crystal structures of peptoid dimer 11 showing intermolecular hydrogen bonding. H--- distance = 1.973 Å --- distance = 2.814 Å H--- angle = 159.33º H--- distance = 1.780 Å --- distance = 2.603 Å H--- angle = 142.24º S9
Figure S2. Crystal structures of cyclic hexamer 17 showing unit cell and crystal packing. S10
MR Analysis of cis/trans isomerization in -methylacetanilides All small molecules were analyzed by 1 H-MR at 500 MHz. Cis and trans isomers were identified by distinctive 2-D ESY cross-peaks, and the amide conformer ratios were obtained by integration of the acetyl-methyl peaks of each isomer. A comparison of the experimental and computational data in Table S5 supports the general trend shown in Table 1 of the main text. Electron-donating substituents increase the trans-amide preference, whereas electron-withdrawing substituents decrease this preference. The reduced magnitude of the energetic preference from theoretical to experimental analysis may reflect the ability of a polar solvent to disrupt electronic effects. Table S5. MR analysis of cis/trans isomer ratios for compounds 1, 2, 4, 6, and 8. Compound Structure % trans in Methanol-d 4 ΔE cis-trans (kcal/mol) HF level of theory 1 92.9 % 3.43 2* 96.5% 3.52 2 4** n/a 1.35 6 95.7 % 3.55 F 8 91.9 % 3.05 * Due to peak overlap, the cis/trans isomer ratio for compound 2 is an approximate value. ** A cis/trans isomer ratio could not be determined for compound 4 due to exchange-broadened, exchange-averaged resonance of the acetyl-methyl peaks. Qualitative evaluation of peak intensities suggests that the cis-amide isomer is slightly more populated for this compound than for compounds 1, 2, 6, and 8, with a dominant trans-amide preference (See Fig. S7). S11
Figure S3. 1-D MR spectra of compound 1 at 25 C in methanol-d 4 (500 MHz). There are two resonances for the acetyl methyl protons, a strong resonance at 1.836 ppm and a less intense resonance at 2.275 ppm. The more intense resonance is for the trans isomer, as evidenced by E cross peaks in the 2D ESY spectrum (Fig. S4). S12
Figure S4. 2-D BASHD-ESY of compound 1 (acetyl-methyl region) plus traces through the ESY spectrum at 1.84 ppm and 2.28 ppm. 1.84 ppm 2.28 ppm The negative E at 7.28,7.295 ppm indicates that the resonance at 1.84 ppm is for the trans conformation. Positive cross peaks are observed between the weaker resonance at 2.274 ppm and the trans resonance at 1.84 ppm in the 2D spectrum, indicating these two resonances are linked by chemical exchange. The chemical exchange connectivity between the resonances at 1.84 and 2.28 ppm provides evidence that the resonance at 2.28 ppm is for the cis isomer. Similar results were obtained for the -methyl resonance, i.e. exchange cross peaks were observed between the strong resonance at 3.235 ppm and the much weaker resonance at 3.393 ppm in the ESY spectrum, and negative Es were observed between the resonance at 3.24 ppm and the aromatic resonances at 7.28 and 7.296 ppm. S13
Figure S5. 1-D MR spectra of compound 2 at 25 C in methanol-d 4 (500 MHz). Acetyl-methyl (trans) Acetyl-methyl (cis) Residual solvent -methyl (trans) -methyl (cis) S14
Figure S6. 2-D BASHD-ESY of compound 2 (acetyl-methyl region). The various resonances for compound 2 were assigned as for compound 1. The acetyl-methyl resonance (Figure S5) for the cis isomer is on the shoulder of the resonance for the two methyl groups on the aromatic ring, and the -methyl resonance for cis isomer is on the shoulder of the residual solvent resonance, making it difficult to obtain accurate integrals computationally. Thus, the relative ratios were only approximately determined. S15
Figure S7. 1-D MR spectra of compound 4 at varying temperatures in methanol-d 4 (500 MHz). Temperature = 45 ºC Temperature = 35 ºC The resonance for the acetyl methyl protons was found to be broad at 25 o C, suggesting exchange averaging of the cis and trans resonances. Spectra were then measured as a function of temperature. The resonance broadened even further at 15 o C and became more narrow at 35 o C and 45 o C, confirming that an exchange-broadened, exchangeaveraged resonance is being observed. Thus, it is not possible to determine accurately the populations of the cis and trans isomers for compound 4. The width at half height of the acetyl methyl resonance was 30.9 Hz at 15 o C, 25.1 Hz at 25 o C, 11.5 Hz at 35 o C and 7.6 Hz at 45 o C. Temperature = 15 ºC Temperature = 15 ºC S16
Figure S8. 1-D MR spectra of compound 6 at 25 C in methanol-d 4 (500 MHz). There are tw o resonances for the acetyl methyl protons in the 1D spectrum, at 1.831 ppm and 2.262 ppm. Likewise, there are two resonances for the -methyl protons at 3.296 and 3.366 ppm. In each case the more intense resonance is for the trans isomer, as evidenced by negative E cross peaks to the aromatic resonances at 7.194 ppm and 7.211 ppm. S17
Figure S9. Below, 2-D BASHD-ESY of compound 6 (acetyl-methyl region). Above, traces through the ESY spectrum at 1.83 ppm. Exchange cross peaks Shown are traces through the ESY spectrum at 1.83 ppm, showing negative Es to the aromatic resonances at 7.194 ppm and 7.211 ppm. The trace also shows a positive exchange cross peak at 2.262 ppm, which establishes connectivity by chemical exchange between the more intense resonance at 1.83 ppm and the less intense resonance at 2.262 ppm. Similar results were obtained for the -methyl resonance, i.e. exchange cross peaks were observed between the two resonances at 3.296 ppm and 3.366 ppm. S18
Figure S10. 1-D MR spectra of compound 8 at 25 C in methanol-d 4 (500 MHz). There are two resonances for the acetyl methyl protons, a strong resonance at 1.833 ppm and a less intense resonance at 2.264 ppm. S19
Figure S11. Below, 2-D BASHD-ESY of compound 8 (acetyl-methyl region). Above, traces through ESY spectrum at 1.833 ppm. As described in detail for compound 1, a negative E at 7.313 ppm provides evidence that the more intense acetyl methyl resonance (1.833 ppm) is from the trans isomer, and exchange cross peaks in the 2D ESY spectra indicate the less intense resonance (2.264 ppm) corresponds to the cis isomer. The cross peaks are clearly observed in the traces taken through the ESY spectrum at 1.833 ppm. S20
Scheme S3. Distinctive E patterns in oligo(-aryl glycines) cis-amide Es trans-amide Es The backbone amide-bond preference of oligo(-aryl glycines) can be defined by the distinct pattern of Es present in either cis-amide or trans-amide bonds. ote that in both cases, the backbone methylene protons will show an E cross-peak with the aromatic ortho protons of that same monomer unit. For a cis-amide bond conformation, the methylene protons of one monomer unit with interact with those of an adjacent monomer. For a trans-amide bond conformation, the methylene protons of one monomer unit will show an E cross-peak with the aromatic ortho-protons of the adjacent monomer unit in the C-terminal direction. Figure S12. 1-D MR of dimer 11 at 25 C in acetonitrile-d 3 (500 MHz). S21
Figure S13. 1-D MR of dimer 11 at 25 C in methanol-d (500 MHz). 4 Figure S14. 2-D ESY traces of dimer 11 at 25 C in methanol-d 4 (500 MHz). Trace through ESY spectrum at 1.885 ppm shows Es between the -acetyl protons (1) and aromatic ortho-protons (6 and 9), establishing a trans-amide bond at this site. S22
Traces through ESY spectrum at 8.13 ppm and 7.64 ppm, respectively, show Es from the aromatic ortho-protons (9 and 6) to -acetyl protons (1) and methylene protons (2). These crosspeaks verify that the resonances are from the same isomer, and allow for conclusive resonance assignment, differentiating methylene protons 2 and 3. Trace through ESY spectrum at 4.17 ppm, shows Es from the methylene protons (2) to aromatic protons (10-14) from the same residue and to aromatic ortho-protons (6 and 9) from the adjacent residue. These cross-peaks establish that these residues are joined by a trans-amide bond. These E experiments identify the major conformer has having trans-amide bonds throughout the backbone. This conformer has a relative abundance of approximately 93%. S23
Figure S15. 1-D MR of trimer 13 at 25 C in acetonitrile-d (500 MHz) 3 Figure S16. 1-D MR of trimer 13 at 0 ºC in methanol-d 4 (500 MHz) 15 12 10 11 13 9 4 3 2 S24
Figure S17. 2-D ESY traces of trimer 13 at 0 ºC in methanol-d 4 (500 MHz). Trace through ESY spectrum at 1.85 ppm shows Es between the -acetyl protons (1) and aromatic ortho-protons (9 and 11), establishing a trans-amide bond at this site. Traces through ESY spectrum at 7.06 ppm (first two) and 7.12 ppm (second two) show Es between both aromatic protons (9 and 11, top and bottom, respectively) to the -acetyl protons (1) and also to backbone methylene protons (2). Proton 11 also exhibits Es to the two aryl methyl groups 5 and 6. 11 9 2 1 S25
2 Trace through ESY spectrum at 4.15 ppm shows Es between the methylene protons (2) and aromatic ortho-protons (9 and 11 of the first residue). Es are also present between the methylene protons (2) and aromatic ortho-protons (12 and 15 of the second residue) establishing a trans-amide bond at this second site. 5,6 15 12 11 9 Traces through ESY spectrum at 8.05 ppm (15, at left) and 7.53 ppm (12, at right) indicate Es from both aromatic protons to methylene protons 2 and 3 of adjacent residues. 3 2 3 2 S26
Trace through ESY spectrum at 4.20 ppm shows Es from methylene protons (3) to ortho protons (12 and 15) and aromatic protons (16-20), establishing a trans-amide bond at this site.. Weak Es are also evident between backbone protons 3 and ortho protons (9 and 11). 15 12 16-20 11 9 Traces through ESY spectrum at 7.43 ppm, 7.46 ppm, and 7.49 ppm (all for protons 16-20) show Es between these protons and backbone methylene protons 3 and 4 of adjacent residues. In addition, the traces at 7.46 and 7.49 indicate Es between these aromatic protons and aryl methyl groups 5 and 6. 7.43 ppm 7.46 ppm 4 3 4 3 5,6 S27
7.49 ppm 4 3 5,6 1 Trace through ESY spectrum at 4.36 ppm shows an E between backbone methylene protons (4) and aromatic protons (16-20). 16-20 Trace through ESY spectrum at 2.26 ppm shows Es between aryl methyl protons (5 and 6) and aromatic protons (10 and 11). Trace through ESY spectrum at 7.19 ppm shows Es between aromatic proton (10) and aryl methyl protons (5 and 6). 10 11 5,6 S28
Figure S18. 1-D MR spectra of hexamer 17 at 25 C in chloroform-d (500 MHz). S29
Figure S19. 2-D HSQC spectra of hexamer 17 at 25 C in chloroform-d (500 MHz). ote that hexamer 17 exists as two conformers in solution, with one significantly more dominant than the other. The chemical shifts of the 1-phenyl-ethyl methine protons suggest that the side chains are associated with cis-amide bonds, consistent with the crystal structure. S30
Figure S20. 2-D CSY spectra of hexamer 17 at room temperature in chloroform-d (500 MHz). S31
Figure S21. 2-D RESY spectrum of hexamer 17 at 25 C in chloroform-d (500 MHz). ote: positive phase in black, negative phase in red. The significant number of exchange cross-peaks (negative phase) supports the presence of two conformers in dynamic equilibrium. S32
Figure S22. 1-D MR spectra of hexamer 18 at 25 C in acetonitrile-d 3 (500 MHz). ote that each number refers to a specific residue. (a) and (b) designate backbone methylene protons, ( ) designates a side chain methyne proton, and (*) designates a side chain methyl group S33
Figure S23. 2-D HSQC spectra of hexamer 18 at 25 C in acetonitrile-d 3 (500 MHz). As discussed in the main text, this spectrum shows a distinct grouping of carbon-proton crosspeaks which aids in the differentiation of -aryl and -alkyl monomer units and cis- and trans-amide bonds. S34
Figure S24. 2-D CSY spectra of hexamer 18 at 25 C in acetonitrile-d 3 (500 MHz). S35
Figure S25. 2-D CSY(blue) / RESY(black and red) overlay spectra of hexamer 18 at 25 C in acetonitrile-d 3 (500 MHz). The overlay spectra shown here clearly indicate the unique through-space E cross-peaks (black) that do not correspond to protons with through-bond correlation (blue). In the spectrum above, the cross-peaks boxed in red clearly indicate which residues bear 1-phenylethyl side chains. The cross-peak boxed in red in the spectrum on the left shows a strong E between methine proton 2 and backbone methylene protons 1a and 1b, indicating that the amide bond between these residues is in a trans- geometry. S36
Figure S26. MR-based model of cyclic hexamer 18. This model describes one possible backbone configuration for cyclic hexamer 18 that reflects the 1-D and 2-D MR data shown above. S37
Figure S27. Conformational analysis of -methylacetanilide. 12 HF Relative Energy (kcal/mol) 10 8 6 4 B3LYP MP2 2 0 0 20 40 60 80 Chi1 ote that for the solid-line plots, ω was fixed at 180º (trans-amide bond), and for the dashed-line plots, ω was fixed at 0º (cis-amide bond). S38
Figure S28. Energy surface plots for the conformational analysis of compound 16. S39
Complete reference for Gaussian 2003: Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, Jr., J. A.; Vreven, T.; Kudin, K..; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega,.; Petersson, G. A.; akatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; akajima, T.; Honda, Y.; Kitao,.; akai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev,.; Austin, A. J.; Cammi, R.; Pomelli, C.; chterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas,.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; rtiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; anayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; and Pople, J. A.; Gaussian, Inc., Wallingford CT, 2004. S40