those for the conformer Q9i+1 = 30u with the OCNH dihedral angle constrained to be 180u (XQ9i+1 = 30u planar form). (B) Calculations at the MP2/6-31G(d) level. Results for the three conformers of the terminal C0 methyl group are shown (mQ9i+1 = 0u; &Q9i+1 = 30u; NQ9i+1 = 60u) together with those for the conformer Q9i+1 = 0u with the OCNH dihedral angle constrained to be 180u (XQ9i+1 = 0u planar form). On the right, schematic drawings of the Q9i+1 conformers are shown (for a larger version, see Figure S1). (TIF) Figure S4 Pep model in vacuo: Dv9 variation as a function of y9. (A) Calculations for the conformer Q9i+1 = 60u at different levels of theory: NPBE0/6-31G(d), &PBE0/6- 31+G(d,p) and XPBE0/6-311+G(2d,2p) (B) Calculations at the MP2/6-31G(d,p) level for the three conformers of the terminal C0 methyl group: NQ9i+1 = 60u, &Q9i+1 = 30u and XQ9i+1 = 0u. (TIF) Figure S5 Pep model in vacuo: Dv9 variation as a function of y9. DFT calculations adopting the M05-2X functional. (TIF) Figure S6 Ala1 model in vacuo. Dependence of Dv on peptide conformation. (TIF) Figure S7 Dependence of Ni-Ni+1 (blue) and Ni-Hi+1 (green) on the y angle. (TIF) Figure S8 Ala1 model in vacuo. Dependence of hC on peptide conformation. (TIF) Figure S9 CSD small molecule structure survey. Depen- dence of peptide bond geometrical parameters on peptide conformation. (A) Dv variation as a function of y (B) hC variation as a function of y. (TIF) Figure S10 CSD small molecule structure survey of tertiary amides (see Table S1). Dependence of peptide bond geometrical parameters on peptide conformation. (A) Dv variation as a function of y (B) hC variation as a function of y. Only peptide planes in trans conformation were included in the analysis. Accurate peptide models were selected by restricting the survey References 1. Bra¨nde´n CI, Tooze J (1999) Introduction to Protein Structure. New York: Garland Publishing. 410 p. 2. Choudhary A, Gandla D, Krow GR, Raines RT (2009) Nature of amide carbonyl–carbonyl interactions in proteins. J Am Chem Soc 131: 7244–7246. 3. Shoulders MD, Satyshur KA, Forest KT, Raines RT (2010) Stereoelectronic and steric effects in side chains preorganize a protein main chain. Proc Natl Acad Sci U S A 107: 559–564. 4. Cieplak AS (1985) Solid-state conformations of linear oligopeptides and aliphatic amides. A model of chiral perturbation of a conjugated system. J Am Chem Soc 107: 271–273. 5. Rondan NG, Paddon-Row MN, Caramella P, Houk KN (1981) Nonplanar alkenes and carbonyls: a molecular distortion which parallels addition stereoselectivity. J Am Chem Soc 103: 2436–2438. 6. Jeffrey GA, Houk KN, Paddon-Row MN, Rondan NG, Mitra J (1985) Pyramidalization of carbonyl carbons in asymmetric environments: carboxyl- ates, amides, and amino acids. J Am Chem Soc 107: 321–326. 7. Greenberg A, Breneman CM, Liebman JF (2000) Amide linkage: selected structural aspects in chemistry, biochemistry, and materials science. New York: Wiley. 653 p. 8. Juranic N, Dannenberg JJ, Cornilescu G, Salvador P, Atanasova E, et al. (2008) Structural dependencies of protein backbone 2JNC9 couplings. Protein Sci 17: 768–776. Electronic Effects Governing Peptide Distortions to the structures determined at low temperature (T,200K) with an R-factor lower than 0.05. (TIF) Figure S11 NBO analysis of Pep at the PBE0 level. (A) Orbital interaction energy between the Ca s system and the CO p system as a function of y9 (m Ca-Cb sRCO p* + CO pRCa-Cb s*; N Ca-S sRCO p* + CO pRCa-S s*; X Ca-Ha sRCO p* + CO pRCa-Ha s*; & Sum of the above three contributions) (B) Orbital interaction energy for (m) Ca-X sRCO p* and (N) CO pRCa-X s* as a function of y9. With Ca-X we represent the sum of the three Ca-Cb, Ca-S, and Ca-Ha contributions. It is worth noting that, due to the non-perfect separation between s and p systems, the Ca substituent bonds interact also with the CO s bond. These small contributions are not included in the figure, explaining why some deviations from the ideal sinusoidal behavior can be found. (TIF) Figure S12 NBO analysis for different Dv9 values in two representative conformers of Ala1-Solv model. (A) Orbital interaction energy versus Dv9 for the Q = 2135u, y = 150u conformer (& Ca-Ha sRCO p*; % CO pRCa-Ha s*;¤ Ca- Cb sRCO p*;e CO pRCa-Cb s*;# N nRCO p*); (B) Orbital interaction energy versus Dv9 for the Q = 260u, y = 245u conformer (& N-Ca sRCO p*;% CO pRN-Ca s*;¤ Ca-Cb sRCO p*;e CO pRCa-Cb s*;# N nRCO p*). (TIF) Figure S13 Population of the CO nonbonding p* orbital (m) and the N n orbital (&) as a function of y9 in Pep. (TIF) Surveys of CSD small molecule crystal Table S1 structures. (DOCX) Acknowledgments The authors thank L. De Luca for technical assistance. 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Edison AS (2001) Linus Pauling and the planar peptide bond. Nat Struct Biol 8: 201–202. 14. Dunitz JD, Winkler FK (1975) Amide group deformation in medium-ring lactams. Acta Crystallogr B 31: 251–263. 15. Ramachandran GN, Kolaskar AS (1973) The non-planar peptide unit. Comparison of theory with crystal structure data. Biochim Biophys Acta 303: 385–388. 16. MacArthur MW, Thornton JM (1996) Deviations from planarity of the peptide bond in peptides and proteins. J Mol Biol 264: 1180–1195. 17. Chakrabarti P, Bernard M, Rees DC (1986) Peptide-bond distortions and the curvature of alpha-helices. Biopolymers 25: 1087–1093. PLoS ONE | www.plosone.org 9 September 2011 | Volume 6 | Issue 9 | e24533