Abstract
N-protonation of amides is critical in numerous biological processes, including amide bonds proteolysis and protein folding, as well as in organic synthesis as a method to activate amide bonds towards unconventional reactivity. A computational model enabling prediction of protonation at the amide bond nitrogen atom along the C–N rotational pathway is reported. Notably, this study provides a blueprint for the rational design and application of amides with a controlled degree of rotation in synthetic chemistry and biology.
The amide bond is one of the most important functional groups in chemistry and biology.1 The nN → π*C=O conjugation and the resulting planarity controls the vast majority of chemico-physical properties of amides (Fig. 1).2 In contrast to planar amides, distorted amides have received much less attention3 despite their profound implications for structure,4 reactivity5 and wide significance in biology and medicinal chemistry6 (amide bond proteolysis,6a isomerization of cis-trans peptides,6b protein splicing,6c β-lactam antibiotics,6d conformational preferences of peptides,6e generation of new pharmacophores and lead structures6f). More fundamentally, non-planar amides that are characterized by ground-state distortion provide crucial insight into the amide bond resonance, including the long-standing question of structural factors governing the O- vs. N-protonation switch.7 N-protonation of amides is critical in numerous biological processes, including amide bonds proteolysis8 and protein folding,9 as well as in organic synthesis as a method to activate amide bonds towards unconventional reactivity.10,11 N-protonation results in disruption of the amide bond resonance, which has been used to catalyze isomerization of amides12 and promote reactions of C–N bonds adjacent to the carbonyl group.10,11 At present, the structural factors that govern the N- vs. O-protonation aptitude are poorly understood.
Fig. 1.
(a) Resonance description of amides. (b) Geometric changes resulting in non-planarity. (c) Conformational restriction of amides.
Herein, we present an efficient computational model that allows to predict the likelihood that a given amide can be protonated at the nitrogen atom, and disclose how one may predict the reactive properties of amides along the C–N rotational pathway from simple calculation of structural properties. This approach makes the amide bond distortion models developed by Greenberg13 generally applicable to accurately predict the reactive properties of amide linkages.1–12 We expect that these findings will enable synthetic and medicinal chemists to utilize amides with a controlled degree of rotation as versatile intermediates and target lead structures in organic synthesis.14,15
We designed a model series of amides in which the overall sum of carbon atoms forming the core scaffold is between five and ten (Scheme 1). These compounds are based on the highly promising one-carbon bridged 1-azabicyclo scaffold (Fig 1c).10,11 The compounds have been selected on the basis of their synthetic accessibility and distortion range of amide bonds. The conceptual advantage of using one-carbon bridged twisted amides (cf. two-carbon or larger bridge analogues)13a,b stems from their better hydrolytic profile,16 their successful use as a platform for discovery of new reactivity of amide bonds,10,11 and accessibility of diverse ring systems that span the whole spectrum of the amide bond distortion.17 Crucially, our approach determines the relationship between distortion and energetic parameters in readily-accessible amide models that (i) are non-planar in the ground-state conformation;1–5 and (ii) have already been synthesized in a laboratory environment and validated experimentally (cf. two-carbon or larger bridge analogues).13a,b As a key design element, we hypothesized that mapping the amide bond distortion along energetic parameters of amide bonds over sufficiently large distortion range would allow for elucidating the role of strain and the nN → π*C=O delocalization on the N-protonation of amide linkages.
Scheme 1.
Structures of model lactams calculated in the current study.
We first established geometric changes that occur upon the amide bond rotation in the series.18 Total energies as well as selected structural parameters are listed in Table 1. The results validate the use of small- and medium-sized one-carbon bridged twisted amides10,11 as models for a systematic study of geometric changes that occur during the amide bond rotation.1–12 The selected set covers the whole spectrum of the amide bond distortion geometries. The twist angle changes from essentially planar to fully perpendicular (τ = 11.32-90.0°), while the pyramidalization at nitrogen varies from essentially sp2 to fully sp3 hybridized nitrogen (χN = 5.99-71.44°). In contrast, the pyramidalization at carbon remains relatively unchanged (χC = 0.0-15.42°) with the carbonyl carbon essentially planar in the series, which is consistent with previous observations regarding amide bond distortion.3,4 In agreement with the amide bond distortion parameters, the length of the N–C(O) bond varies between 1.474 Å and 1.365 Å, while the length of the C=O bond is between 1.201 Å and 1.233 Å.
Table 1. Energies and Selected Geometric Parametersa.
| Amide | −ET (corr) [au] | N–C(O) [Å] | C=O [Å] | τ [deg] | χN [deg] |
|---|---|---|---|---|---|
| A | 362.90686 | 1.474 | 1.201 | 90.00 | 71.44 |
| B | 402.08837 | 1.447 | 1.209 | 65.40 | 63.10 |
| C | 441.25388 | 1.446 | 1.212 | 90.00 | 53.20 |
| D | 402.07156 | 1.422 | 1.207 | 38.23 | 57.48 |
| E | 441.26376 | 1.401 | 1.218 | 36.90 | 47.69 |
| F | 480.42708 | 1.391 | 1.225 | 41.78 | 36.01 |
|
| |||||
| G | 519.59194 | 1.409 | 1.223 | 47.52 | 41.78 |
| H | 480.44070 | 1.381 | 1.223 | 21.97 | 32.11 |
| I | 519.59957 | 1.372 | 1.230 | 25.53 | 17.39 |
| J | 519.60699 | 1.365 | 1.228 | 11.32 | 5.99 |
| K | 558.75395 | 1.378 | 1.231 | 37.94 | 14.10 |
| L | 558.77041 | 1.367 | 1.233 | 18.84 | 12.19 |
Computed using MP2/6-311++G(d,p) level. See ESI for full details.
The approach verifies structural changes that occur with the N–C(O) bond rotation as a function of the twist angle and the pyramidalization at nitrogen. Most importantly, a plot of N–C(O) bond length versus the sum of twist angles and nitrogen pyramidalization (Στ+χN) gives an excellent linear correlation over the observed range of amide bond geometries (R2 = 0.97, Fig. 2). Plots of N–C(O) bond length versus twist angle (R2 = 0.87) and nitrogen pyramidalization (R2 = 0.88) give scattered correlations in the series (not shown). In agreement with the classical resonance,1,2,7c disruption of the nN → π*C=O delocalization results in a significant lengthening of the N–C(O) bond, while the C=O bond experiences minor shortening.
Fig. 2.
Correlation of N–C(O) bond length [Å] to the sum of twist and pyramidalization at nitrogen angles (Στ+χN).
Importantly, the results demonstrate that description of the amide bond distortion by additive twist angle/pyramidalization at nitrogen parameters (i.e. the sum of twist and nitrogen pyramidalization angles (Στ+χN)) provides a more accurate representation of the geometric properties than the twist angle or the pyramidalization at nitrogen alone. Previous studies demonstrated that 1-azabicyclo[3.3.1]nonan-2-one (X-ray of a phenyl analogue: τ = 20.8°; χN = 48.8°; χC = 5.9°; Στ+χN = 69.6°)10c and derivatives of one-carbon bridged amides containing the [4.3.1] ring system (X-ray of an aryl analogue: τ = 42.8°; χN = 34.1°; χC = 16.5°; Στ+χN = 76.9°)10b feature amide bonds that are predominantly protonated at nitrogen.10,11 It was thus proposed that a twist angle of as low as approx. 40-50° may be sufficient to promote N-protonation of amide bonds.10a–c Additionally, earlier reports by Brown demonstrated that extended 2-quinuclidone analogues favor N-alkylation ([3.2.2] amide ring system, X-ray: τ = 33.2°; χN = 52.8°; χC = 11.0°; Στ+χN = 86.0°) or O-alkylation ([3.3.2] ring system, X-ray: τ = 15.3°; χN = 38.6°; χC = 4.3°; Στ+χN = 53.9°);3a detailed experimental results not disclosed. The additive (Στ+χN) parameter normalizes these results and reveals that a (Στ+χN) value of 60-70° appears to be close to a barrier between N- vs. O-protonation of amides. Note that this value is much lower than the distortion that would correspond to a fully perpendicular amide bond (Στ+χN = 150.0°), which has been proposed to be required for N-protonation.11a–c,3 In addition, these structural features indicate that an increase of the amide bond distortion results in a significant lengthening of the N–C(O) bond, while the C=O bond remains relatively unchanged, providing a strong support for the classical resonance.1,2,7c
Having validated our model, we addressed the key question of structural factors governing the O- vs. N-protonation switch in amides. As predicted by the resonance, planar amides undergo protonation at oxygen (formamide: O- vs. N-protonation is favored by ca. 11.5 kcal/mol).1,2 O-protonation of planar amides shortens the N–C(O) bond and significantly reinforces the double bond character of amides (RE of O-protonated amides of ca. 40 kcal/mol).19
Table 2 lists proton affinities (PA) and differences between N- and O-protonation affinities (ΔPA) in the series of studied lactams.13a,b Most importantly, there is an excellent linear correlation between proton affinity difference and the sum of twist and pyramidalization at nitrogen angles (R2 = 0.98, Fig. 3), which can be compared with the correlation between proton affinity difference and twist angles (R2 = 0.90) and the correlation between proton affinity difference and pyramidalization at nitrogen angles (R2 = 0.86). This finding validates the use of additive descriptors of the geometric transformations of amide bonds to predict reactive properties of non-planar amides (vide supra). Importantly, this equation provides a very useful tool to predict N- vs. O-protonation sites of amides as only a single determination of the amide bond geometry is required from the X-ray crystallography or calculations to provide a reliable prediction of ΔPA.1,2 Since our calculations have already shown that (Στ+χN) can be correlated with the N–C(O) bond lengths (vide supra), this can be used in conjunction with amide bond distortion parameters to accurately predict ΔPA in one-carbon bridged amides.20 Overall, this finding provides a compelling argument to the long-standing question of structural factors governing the O- vs. N-protonation switch in non-planar lactams, and determines that (Στ+χN) of ca. 50-60° should be sufficient to promote N-protonation of amides.1,3–5,10,11,13 The N- vs. O-cross-over point in the studied series of lactams is located around the geometry region defined by the [5.4.1] ring system.
Table 2. Proton Affinities and Differences in Proton Affinitiesa.
| Entry | Amide | NPA [kcal/mol] | OPA [kcal/mol] | ΔPA [kcal/mol] |
|---|---|---|---|---|
| 1 | A | 223.9 | 186.4 | 37.5 |
| 2 | B | 224.6 | 200.9 | 23.7 |
| 3 | C | 227.9 | 202.6 | 25.4 |
| 4 | D | 218.7 | 204.6 | 14.2 |
| 5 | E | 219.1 | 211.5 | 7.7 |
| 6 | F | 220.7 | 216.4 | 4.3 |
|
| ||||
| 7 | G | 225.5 | 215.0 | 10.6 |
| 8 | H | 211.8 | 217.0 | -5.3 |
| 9 | I | 215.2 | 219.7 | -4.5 |
| 10 | J | 206.0 | 218.8 | -12.8 |
| 11 | K | 220.7 | 219.8 | 0.9 |
| 12 | L | 209.2 | 222.0 | -12.8 |
Computed using MP2/6-311++G(d,p) level. See ESI for full details.
Fig. 3.
Correlation of ΔPA to the sum of twist and pyramidalization at nitrogen angles (Στ+χN).
In conclusion, we have presented an efficient model enabling to predict the likelihood that a given amide can be protonated at the nitrogen atom. This study provides a compelling answer to the long-standing question of structural factors governing the N- vs. O-protonation switch in non-planar amides.1,2,10,11,13 The (Στ+χN) value of around 50-60° appears to be close to a barrier between N- vs. O-protonation of amides. This is much lower than the distortion that would correspond to a fully perpendicular amide bond (Στ+χN = 150.0°), which has been proposed to be required for efficient N-protonation. Given the availability of distorted amides in moderate distortion range,3–5 our data suggest that a wide range of amide analogues can be readily applied for probing the unconventional reactivity of amide bonds via N-protonation, including in biological contexts. We expect that the understanding provided for the amide bond protonation will enable the rational application of non-planar amides with a controlled-degree of rotation in organic synthesis and medicinal chemistry. Further studies on the effect of functional groups on the N-/O-protonation aptitude of non-planar amides are ongoing and these results will be reported shortly.
Supplementary Material
Acknowledgments
We thank the Centre for Networking and Supercomputing (grant number WCSS159), NIH (grant number GM-49093 to J.A.) and Rutgers University (M.S.) for support.
Footnotes
Electronic Supplementary Information (ESI) available. See DOI: 10.1039/b000000x/
References
- 1.Greenberg A, Breneman CM, Liebman JF. The Amide Linkage: Structural Significance in Chemistry, Biochemistry, and Materials Science. Wiley; 2000. [Google Scholar]
- 2.Selected studies: Kemnitz CR, Loewen MJ. J Am Chem Soc. 2007;129:2521. doi: 10.1021/ja0663024.Mujika JI, Matxain JM, Eriksson LA, Lopez X. Chem Eur J. 2006;12:7215. doi: 10.1002/chem.200600052.Glover SA, Rosser AA. J Org Chem. 2012;77:5492. doi: 10.1021/jo300347k.Mujika JI, Mercero JM, Lopez X. J Am Chem Soc. 2005;127:4445. doi: 10.1021/ja044873v.Wang QP, Bennet AJ, Brown RS, Santarsiero BD. J Am Chem Soc. 1991;113:5757.Otani Y, Nagae O, Naruse Y, Inagaki S, Ohno M, Yamaguchi K, Yamamoto G, Uchiyama M, Ohwada T. J Am Chem Soc. 2003;125:15191. doi: 10.1021/ja036644z.Yamada S. Angew Chem, Int Ed. 1993;32:1083.Yamada S. J Org Chem. 1996;61:941.Ly T, Krout M, Pham DK, Tani K, Stoltz BM, Julian RR. J Am Chem Soc. 2007;129:1864. doi: 10.1021/ja067703m.
- 3.For reviews, see: Szostak M, Aubé J. Chem Rev. 2013;113:5701. doi: 10.1021/cr4000144.Szostak M, Aubé J. Org Biomol Chem. 2011;9:27. doi: 10.1039/c0ob00215a.Hall HK, Jr, El-Shekeil A. Chem Rev. 1983;83:549.Pace V, Holzer W, Olofsson B. Adv Synth Catal. 2014;356:3686.
- 4.Lease TG, Shea KJ. Advances in Theoretically Interesting Molecules. Vol. 2 JAI Press Inc.; 1992. A Compilation and Analysis of Structural Data of Distorted Bridgehead Olefins and Amides. [Google Scholar]
- 5.(a) Clayden J, Moran WJ. Angew Chem, Int Ed. 2006;45:7118. doi: 10.1002/anie.200603016. [DOI] [PubMed] [Google Scholar]; (b) Clayden J. Nature. 2012;481:274. doi: 10.1038/481274a. [DOI] [PubMed] [Google Scholar]; (c) Aubé J. Angew Chem, Int Ed. 2012;51:3063. doi: 10.1002/anie.201108173. [DOI] [PubMed] [Google Scholar]
- 6.Lead references: Amide bond proteolysis: Somayaji V, Brown RS. J Org Chem. 1986;51:2676.Cis-trans isomerization: Liu J, Albers MW, Chen CM, Schreiber SL, Walsh CT. Proc Natl Acad Sci USA. 1990;87:2304. doi: 10.1073/pnas.87.6.2304.Protein splicing: Romanelli A, Shekhtman A, Cowburn D, Muir TW. Proc Natl Acad Sci USA. 2004;101:6397. doi: 10.1073/pnas.0306616101.β-Lactam antibiotics: Georg GI. The Organic Chemistry of Beta-Lactams. Wiley-VCH; 1992. Conformational preferences of peptides: Hosoya M, Otani Y, Kawahata M, Yamaguchi K, Ohwada T. J Am Chem Soc. 2010;132:14780. doi: 10.1021/ja1017877.Chemical space: Burke MD, Schreiber SL. Angew Chem, Int Ed. 2003;43:46. doi: 10.1002/anie.200300626.
- 7.(a) Greenberg A. The Amide Linkage as a Ligand-Its Properties and the Role of Distortion. In: Greenberg A, Breneman CM, Liebman JF, editors. The Amide Linkage: Structural Significance in Chemistry, Biochemistry, and Materials Science. Wiley; 2000. [Google Scholar]; (b) Wiberg KB. Acc Chem Res. 1999;32:922. [Google Scholar]; (c) Bennet AJ, Somayaji V, Brown RS, Santarsiero BD. J Am Chem Soc. 1991;113:7563. [Google Scholar]
- 8.(a) Brown RS, Bennet AJ, Slebocka-Tilk H. Acc Chem Res. 1992;25:482. [Google Scholar]; (b) Radzicka A, Wolfenden R. J Am Chem Soc. 1996;118:6105. [Google Scholar]
- 9.(a) Ramachandran GN. Biopolymers. 1968;6:1494. doi: 10.1002/bip.1968.360061013. [DOI] [PubMed] [Google Scholar]; (b) MacArthur MW, Thornton JM. J Mol Biol. 1996;264:1180. doi: 10.1006/jmbi.1996.0705. [DOI] [PubMed] [Google Scholar]; (c) Chalupsky J, Vondrasek J, Spirko V. J Phys Chem A. 2008;112:693. doi: 10.1021/jp0750699. [DOI] [PubMed] [Google Scholar]; (d) Shin SBY, Yoo B, Todaro LJ, Kirshenbaum K. J Am Chem Soc. 2007;129:3218. doi: 10.1021/ja066960o. [DOI] [PubMed] [Google Scholar]
- 10.Lei Y, Wrobleski AD, Golden JE, Powell DR, Aubé J. J Am Chem Soc. 2005;127:4552. doi: 10.1021/ja050214m.Szostak M, Yao L, Day VW, Powell DR, Aubé J. J Am Chem Soc. 2010;132:8336. doi: 10.1021/ja101690u.Sliter B, Morgan J, Greenberg A. J Org Chem. 2011;76:2770. doi: 10.1021/jo200195a.For examples of electrophilic reactivity of twisted amides, see: Szostak M, Yao L, Aubé J. J Am Chem Soc. 2010;132:2078. doi: 10.1021/ja909792h.Szostak M, Aubé J. J Am Chem Soc. 2009;131:13246. doi: 10.1021/ja906471q.Szostak M, Aubé J. Chem Commun. 2009:7122. doi: 10.1039/b917508c.
- 11.Selected examples of non-planar amides: Tani K, Stoltz BM. Nature. 2006;441:731. doi: 10.1038/nature04842.Kirby AJ, Komarov IV, Wothers PD, Feeder N. Angew Chem, Int Ed. 1998;37:785. doi: 10.1002/(SICI)1521-3773(19980403)37:6<785::AID-ANIE785>3.0.CO;2-J.Komarov IV, Yanik S, Ishchenko AY, Davies JE, Goodman JM, Kirby AJ. J Am Chem Soc. 2015;137:926. doi: 10.1021/ja511460a.Bashore CG, Samardjiev IJ, Bordner J, Coe JW. J Am Chem Soc. 2003;125:3268. doi: 10.1021/ja028152c.Lease TG, Shea KJ. J Am Chem Soc. 1993;115:2248.Ribelin TP, Judd AS, Akritopoulou-Zanze I, Henry RF, Cross JL, Whittern DN, Djuric SW. Org Lett. 2007;9:5119. doi: 10.1021/ol7023373.
- 12.Cox C, Lectka T. Acc Chem Res. 2000;33:849. doi: 10.1021/ar990165g. [DOI] [PubMed] [Google Scholar]
- 13.Greenberg A, Venanzi CA. J Am Chem Soc. 1993;115:6951.Greenberg A, Moore DT, DuBois TD. J Am Chem Soc. 1996;118:8658.Morgan J, Greenberg A. J Chem Thermodyn. 2014;73:206.This elegant manuscript reports selected structural parameters of various bridged lactams using rapid DFT (B3LYP/6-31G*) method. For a discussion of the O- vs. N-protonation aptitute of amides, see: Morgan J, Greenberg A, Liebman JF. Struct Chem. 2012;23:197.
- 14.Lead references on bridged lactams in medicinal chemistry: Aszodi J, Rowlands DA, Mauvais P, Collette P, Bonnefoy A, Lampilas M. Bioorg Med Chem Lett. 2004;14:2489. doi: 10.1016/j.bmcl.2004.03.004.Mangion IK, Ruck RT, Rivera N, Huffman MA, Shevlin M. Org Lett. 2011;13:5480. doi: 10.1021/ol202195n.Brouillette WJ, Grunewald GL, Brown GB, DeLorey TM, Akhtar MS, Liang G. J Med Chem. 1989;32:1577. doi: 10.1021/jm00127a029.Buynak JD, Rao AS, Adam G, Nidamarthy SD, Zhang H. J Am Chem Soc. 1998;120:6846.
- 15.Lead references on bridged lactams in total synthesis: Belmar J, Funk RL. J Am Chem Soc. 2012;134:16941. doi: 10.1021/ja307277w.Zuo Z, Xie W, Ma D. J Am Chem Soc. 2010;132:13226. doi: 10.1021/ja106739g.
- 16.Szostak M, Yao L, Aubé JJ. J Org Chem. 2009;74:1869. doi: 10.1021/jo802192v. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 17.Winkler FK, Dunitz JD. J Mol Biol. 1971;59:169. doi: 10.1016/0022-2836(71)90419-0. Winkler-Dunitz distortion parameters: τ (twist angle), χN (pyramidalization at N) and χC (pyramidalization at C) describe the magnitude of rotation around the N–C(O) bond, pyramidalization at N and C; τ is 0° for planar amide bonds and 90° for fully orthogonal bonds; χN and χC are 0° for planar bonds, and 60° for fully pyramidalized amide bonds. [DOI] [PubMed] [Google Scholar]
- 18.Ab inito molecular orbital calculations were carried out at the readily accessible and practical MP2/6-311++G(d,p) level. This method has been shown to be accurate in predicting properties and resonance energies of amides2c,13a (e.g. resonance energy, N,N-dimethyl-acetamide: experimental value of 16.8±1.3 kcal/mol; calculated value of 16.4 kcal/mol). This method was further verified by obtaining good correlations between the calculated structures and available X-ray structures in the series (see the Electronic Supplementary Information, ESI, for details).
- 19.Only few examples of N-protonated amides have been reported to date. For lead references, see: Cox C, Wack H, Lectka T. Angew Chem, Int Ed. 1999;38:798. doi: 10.1002/(SICI)1521-3773(19990315)38:6<798::AID-ANIE798>3.0.CO;2-W. (b) Ref. 11b.
- 20.A plot of ΔPA to (Στ+χN) for larger bridge 2-qunuclidone analogues reported by Greenberg13b gives a linear correlation (R2 = 0.94), with a cross-over point around the [3.3.1] derivative ((Στ+χN) = 71.8°).13b Note that in the studied series of amides, τ gives a more reliable prediction of ΔPA than χN if these parameters are used separately.
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