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Supporting Information for Unraveling the Molecular Recognition of Amino Acid Derivatives by a Macrocyclic Pseudopeptidic Receptor: ESI-MS, NMR, Fluorescence and Molecular Modeling Studies. Ignacio Alfonso, * M. Isabel Burguete, 2 Francisco Galindo, 2 * Santiago V. Luis, 2 * Laura Vigara, 2 Departamento de Química Biológica y Modelización Molecular, Instituto de Química Avanzada de Cataluña, Consejo Superior de Investigaciones Científicas (IQAC-CSIC), C/Jordi Girona 8-26, E- 834, Barcelona, Spain. 2 Departamento de Química Inorgánica ; Universitat Jaume I de Castellón; Av. Sos Baynat, s/n, E- 27, Castellón, Spain * Authors to whom correspondence should be addressed E-mail: ignacio.alfonso@iqac.csic.es ; luiss@qio.uji.es ; francisco.galindo@qio.uji.es Table of contents: NMR spectra of the receptor (Figure S) S2 Concentration dependence of NMR signals of (Figure S2) S3 Concentration dependence of NMR signals of Z-Phe- (Figure S3) S4 NMR spectra of the receptor with an excess of Z-L-Phe- (Figure S4) S5 NMR titration plots of the receptor with Z-Phe- (Figure S5) S6 Job plot of the complex between and Z-L-Phe- (Figure S6) S6 NMR titration plots of the receptor with Z-Ala- (Figure S7) S7 NMR titration plots of the receptor with Boc-Phe- (Figure S8) S7 NMR titration plots of the receptor with Z-Phg- (Figure S9) S8 NMR titration plots of the receptor with Boc-Phg- (Figure S) S8 D RESY spectra of the receptor with an excess of Z-L-Phe- (Figure S) D RESY spectra of the receptor with an excess of Z-D-Phe- (Figure S2) D RESY spectra of the receptor with an excess of Z-L-Ala- (Figure S3) Time resolved fluorescence measurements Molecular Mechanics Calculations S9 S S S2 S5 S-

Figure S. NMR spectra of the receptor ( mm, 5 Mz, CDCl 3, 33 K) S-2

8.5 8. δ (ppm) 7.5 7. d (N) d (C9) d (C7) 6.5 6..85.35.85 2.35 -logc (M) Figure S2. Plot of NMR chemical shift of selected signals versus log[concentration] for receptor (5 Mz, CDCl 3, 33 K). S-3

mm 2 mm mm Figure S3. NMR spectra of Z-L-Phe- at different concentrations (5 Mz, CDCl 3, 33 K) S-4

Figure S4. NMR spectra of the receptor ( mm, 5 Mz, CDCl 3, 33 K) in the presence of 8 equivalents of Z-L-Phe- S-5

Complexes Z-Phe- Complexes Z-Phe-.8.8 complex.6.4 3 (L) N (L) 3 (D) N (D) complex.6.4 9 (L) (L) 9 (D) (D).2.2 5 5 2 Eq Phe 5 5 2 Eq Phe Figure S5. NMR titration plots of the receptor ( mm, 5 Mz, CDCl 3, 33 K) with both enantiomers of Z-Phe-.8.7 δ (9) * X ().6.5.4.3.2...2.3.4.5.6.7.8.9 X (Phe) Figure S6. Job plot of the complex between and Z-L-Phe-, using 9 NMR signal of the receptor (5 Mz, CDCl 3, 33 K) S-6

Complexes Z-Ala-.8 complex.6.4 3 (L-Ala) N (L-Ala) 3 (D-Ala) N (D-Ala).2 5 5 2 25 3 35 Eq. Z-Ala- Figure S7. NMR titration plots of the receptor ( mm, 5 Mz, CDCl 3, 33 K) with both enantiomers of Z-Ala- Conplexes Boc-Phe-.8 complex.6.4 complex 3(L) complex 3(D) complex N(L) complex N(D).2 5 5 2 Eq. Boc-Phe- Figure S8. NMR titration plots of the receptor ( mm, 5 Mz, CDCl 3, 33 K) with both enantiomers of Boc-Phe- S-7

CyValA3Nap-Z-DL-Phg.8.8 complex.6.4 3 (L) 3 (D) complex.6.4 N (L) N (D).2.2 2 3 4 5 6 Eq Z-Phg- 2 3 4 5 6 Eq Z-Phg- Figure S9. NMR titration plots of the receptor ( mm, 5 Mz, CDCl 3, 33 K) with both enantiomers of Z-Phg- Complexes Boc-Phg-.8 complex.6.4.2 complex 3(L) complex 3(D) complex N(L) complex N(D) complex 9(L) complex 9(D) 5 5 2 Eq. Boc-Phg- Figure S. NMR titration plots of the receptor ( mm, 5 Mz, CDCl 3, 33 K) with both enantiomers of Boc-Phg- S-8

E D A B C E B A C D E D A B C E B A C D E 9 7 N B A C 3 D 5 6 2, 3 9. ppm (t) 8. 7. 6. 5. 4. 3. 2... Figure S.. NMR (lower trace) and D RESY spectra of the receptor ( mm, 5 Mz, CDCl 3, 33 K) in the presence of 8 equivalents of Z-L-Phe- upon irradiation on 9 (upper trace) or 2/3 (middle trace) S-9

Cbz N N N N N Ph N N N N N Figure S2. NMR (lower trace) and D RESY spectra of the receptor ( mm, 5 Mz, CDCl 3, 33 K) in the presence of 2 equivalents of Z-D-Phe- upon irradiation on 9 (upper trace) or 2/3 (middle trace) proton signals S-

Me Cbz N N N N N Me N N N N N Figure S3. NMR (lower trace) and D RESY spectra of the receptor ( mm, 5 Mz, CDCl 3, 33 K) in the presence of 2 equivalents of Z-L-Ala- upon irradiation on 9 (upper trace) or 2/3 (middle trace) proton signals S-

Time-Resolved Fluorescence Measurements The Stern-Volmer relationship (equation S) describes both static and dynamic quenching of the fluorescence, where K SV is the Stern-Volmer constant. Examination the fluorescence intensity is not enough to ascertain which quenching mode is operating. Calculation of the fluorescence lifetime of receptor in the absence (τ ) and in the presence (τ) of quencher allows for discriminating between both modes of quenching, since τ /τ = would indicate static quenching whereas F /F = τ /τ would mean dynamic deactivation of the excited state (hence no complexation in the ground state). F F Eq. S. = + K [ S] SV To prove the non-collisional quenching at 39 nm in the case of, the excited state lifetime of exciplex of was measured by means of single photon counting, in the absence and in the presence of several concentrations of substrate. The emission decays were fitted to a multiexponential model (equation S2). In all the cases fittings resulted purely monoexponential (α=), and for all the concentrations of added substrate the fluorescence lifetime remained at τ =. ns, independently on the concentration of quencher, which is an unambiguous proof of the formation of a ground state complex and no deactivation through collisions during the lifetime of the excited state (see Figures S4 and S5). Eq. S2. F i ( t ) = Σα e ( t / τ ) i Lakowicz, J. R. Principles of Fluorescence Spectroscopy, Springer, New York, 26. S-2

5 4 Q =. M τ =.4 ns 5 4 Q =.3 M τ =. ns Counts 3 2 Counts 3 2 Weighted residuals 3 2 - -2-3 25 3 35 4 25 3 35 4 Channels A Weighted residuals 3 2 - -2-3 25 3 35 4 25 3 35 4 Channels B 5 4 Q =.26 M τ =.99 ns 5 4 Q =.4 M τ =.2 ns Counts 3 2 Counts 3 2 Weighted residuals 3 2 - -2-3 25 3 35 4 25 3 35 4 Channels C Weighted residuals 3 2 - -2-3 25 3 35 4 25 3 35 4 Channels D 5 4 Q =.53 M τ =. ns 5 4 Q =.66 M τ =. ns Counts 3 2 Counts 3 2 Weighted residuals 3 2 - -2-3 25 3 35 4 25 3 35 4 Channels E Weighted residuals 3 2 - -2-3 25 3 35 4 25 3 35 4 Channels F 5 4 Q =.8 M τ =. ns 5 4 Q =.93 M τ =. ns Counts 3 2 Counts 3 2 Weighted residuals 3 2 - -2-3 25 3 35 4 25 3 35 4 Channels G Weighted residuals 3 2 - -2-3 25 3 35 4 25 3 35 4 Channels Figure S4. Fluorescence intensity decay profiles of (.3x -4 M, dichloromethane, 25ºC) monitored at 39 nm (exc. 3 nm) in the absence (A) and in the presence (B-) of Z-L-Phe-. Concentrations of titrant indicated in the graphs. Nanoseconds per channel =5.62939x -2. Also shown the incident light pulse and the weighted residuals. S-3

Figure S5. Fluorescence lifetime of (.3x -4 M, dichloromethane, 25ºC) monitored at 39 nm (exc. 3 nm) as a function of [Z-L-Phe-]. S-4

Molecular Mechanics Calculations All the molecular mechanics calculations were performed with MACRMDEL 7. using AMBER* as the force field and GB/SA simulation of chloroform as solvent. An initial Monte Carlo conformational search was carried out with the receptor alone through the modification of the torsional angles automatically setup by the program, and convergence was obtained after performing 2 cycles of steps departing from different conformers in each case and using simulation of chloroform. The global minimum obtained in this way was used as starting structures for preparing the three different supramolecular complexes with the different receptor-substrate dispositions (complexes Type I-III). Two molecules of the corresponding carboxylate were manually placed at both faces of the macrocycle and the amine nitrogen atoms of the receptor were replaced by ammonium-type (protonated). The salts thus obtained were fully minimized without restrictions using the same force field (AMBER*, GB/SA for chloroform). In order to ensure the validity of these minima, they were used as starting structures for molecular dynamics simulations, which were carried out using the following conditions: temperature = 3 K, length of simulation = 5 ns with.5 fs steps, SAKE was used to constraint the length of bonds to hydrogen and 2 structures were sampled. We did not observe fundamental changes of the minima during those dynamic simulations. Table S: Relative energies (kcal/mol, AMBER* force-field as implemented in Macromodel, CCl 3 solvent) of the complexes shown in Figure 2 Type I Type II Type III Relative Energy.26 2.55. S-5

Table S2: Measured distances (Å) for the -bonding and π-π interactions of the minimized structures. Atoms from the receptor are shown in italics. atom pairs receptor face Type I Type II Type III N + - - concave.85.93.78 2.5.74 2.2 2.76 amiden- - concave 2.23.92 2.3 C= -N(Z) concave 2.4-2.6 Naph Ar concave 4.5-3.49 N + - - convex -.88.8 amiden- - convex - - 2.4 Naph Ar convex 3.5 3.43 3.29 Table S3: Inter-atomic distances (Å), measured in the minimized structures, for the protons showing REs effects in the D RESY spectra. nly the intermolecular contacts are shown, and atoms from the receptor are shown in italics. protons Type I Type II Type III RESY 9-Cα 4.7 4.43 5.89 weak 9-Cβ 5.26 >6.5 4.4 weak 9-ortoAr- 3.36, 4.8 >6.5 3.53, 3.85 medium 9-N 5.75 5.2 5.75 weak 9-C2 >7. 4.6 4.4 medium 2-Cα 2.2 3.22 2.5, 3.2 strong 2-Cβ 4.34 2.3 3.26 medium 2-ortoAr- 2.79 3.37 3.26 strong 2-N 3.26 2.76 3.58 medium 2-C2 5.45 4.64 4.87 medium S-6

Type I C 4.275 -.429 2.328 C 5.37 -.49.25 C 4.665 -.963.5 C 3.34 -.374 -.57 C 2.464 -.36.976 C 2.98 -.872 2.28 C 2.79 -.82 -.42 C.52-2.349 -.469 C.68-2.34 -.332 C.2 -.88.864 C.7 -.626.976 N -.5 -.45 2.2 C -.59.368 2.246 C -.99.868.884 N -.59.59 -.87 C -.775.67 -.556-2.76.822.74 C -.37 -.29-3.595 C 3.592 -.768-2.698 N 4.4 -.4-2.97 C 3.249.8-2.86 C.966.642-3.658 N.922.6-2.945.86.947-4.82 C 4.43 2.7-3.258 C -.476 -.484-2.589 C -.54.45 3.355 C 4.838.878-4.625 C 3.356 3.328-3.92 C -2.942.9 3.729 C -.825.973 4.65 4.656 -.57 3.293 6.9 -.79.36 5.385 -.35 -.823 2.357 -.839 3.25. -2.739-2.44 -.352-2.73 -.438.449-2.64 2.94 -.843-2.23.77.25.245.224.48.9 2.94-2.93 -.457 2.572 -.827 -.576 -.5 -.6.524 -.76-2.846.98 -.648 -.244 -.97-4.39 -.683.776-4.67 2.972-2.53-3.579 4.459-2.462-2.68 4.56 -.426-3.95 4.957 -.239-2.34 2.972.94 -.789.63 -.67 -.982 4.958 2.77-2.489-2.47 -.7-3.64 -.22 -.436-2.78 -.962 2.348 2.98 5.464 2.774-4.837 4..785-5.46 5.522. -4.668 4.22 4.26-3.353 2.876 3.459-2.98 2.556 3.373-3.964-2.923 2.669 4.536-3.549.42 4.93-3.49 2.369 2.885 -.97.732 5.46.267.85 4.527 -.28.25 5.7 C 5.7628 3.5937 2.38 C 5.3488 4.2337.48 C 3.998 4.4847.9258 C 3.38 4.37.8688 C 3.468 3.4727 3.428 C 4.858 3.247 3.2628 C.568 4.3647.658 C.48 3.4987.4668 C.258 2.27.728.3268.5987.8938.78.8 -.2 N -.46 3.79.34 C -.9482 4.7677 -.3682-2.32 4.8657 -.3352 -.277 5.624 -.865 C -2.8752 6.277 -.692 C -4.3632 6.697 -.3552 C -4.8372 5.6587.8968 C -6.262 5.5737.548 C -7.252 5.947.578 C -6.6662 6.327 -.932 C -5.2952 6.47 -.3462 6.8 3.4 2.484 6.6 4.545.388 3.648 4.995 -.3 2.697 3.67 3.84 5.5 2.75 4.89.45 5.452.37.933 4.96 2.54.58 3.74 -.487 -.2 3..763-2.695 6.394 -.68-2.457 6.96.46-4.54 5.397.692-6.593 5.248 2.44-8.239 5.84.357-7.42 6.587 -.884-4.983 6.729-2.342 C 6.785-3.694 3.327 C 5.429-3.483 3.582 C 4.467-4.22 2.89 C 4.838-5.75.936 C 6.2-5.383.697 C 7.69-4.649 2.385 C 3.782-5.949.79 C 2.989-5.58.22 C 3.83-4.579 -.98 4.96-4.2 -.793 3.3-4.76-2.9 N.773-5.72 -.276 C.558-5.562.326 -.49-6.89 -.268.426-4.936.353 C -.75-6.222.446 C -2.388-4.87.548 C -2.73-4.327.79 C -3.369-3.88.883 C -3.67-2.37.725 C -3.34-2.93 -.52 C -2.75-4.44 -.66 7.547-3. 3.868 5.9-2.73 4.326 3.4-4.38 3. 6.522-6.27.95 8.239-4.82 2.8 3.87-6.394.93 4.226-6.83.68 2.696-4.23.743.86-6.286 -.9 -.54-6.687.443-2.398-6.96 -.9-2.497-4.877 2.76-3.629-2.674 2.87-4.7 -.39.795-3.585-2.344 -.438-2.453-4.554 -.597 S-7

Type II C 2.44.56 2.46 C 3.3.48.366 C 3.8.574.358 C.945 -.29.388 C.49 -.23.474 C.34.75 2.55 C.687 -.226 -.67 C.75-2.27 -.458 C -.7-2.39.658 C -. -.49.493 C -.386 -.73 2.238 N -2.92.23.36 C -3.632.594.644 C -4.425.75.338 N -3.677.65 -.88 C -4.288.65-2.42-5.67.99.35 C -2.458 -.77-3.837 C 2.383 -.78-2.6 N 2.3.85-2.642 C.6.943-2.78 C -.34.69-3.56 N -.298.225-3.33.224 -.398-4.595 C.465 2.259-3.465 C -3.72 -.53-3.26 C -3.658.99 2.46 C.997 2.79-4.9 C.348 3.35-3.479 C -5.49 2.83 3.66 C -2.626.988 3.6 2.65 2.269 3.28 4.2 2.3.339 3.86.55 -.458.639.843 3.376.56-2.98 -.22 -.928-2.872.78 -.9 -.267 3.232 -.964 -.636 2.45-2.89 -.79.372 -.7.46.453-4.98 -.25 2.26-2.672.533 -.758-4.5.63-2.62-5.393.483-2.64-2.98 -.7-4.453-2.688.66-4.539.934 -.898-2.727 3.453 -.462 -.888 2.74.72-3.64 2.963.86-2.3.644.53 -.756 -.45.744-2.82 2.33 2.69-2.856-4.59 -.785-3.772-3.556 -.434-2.422-3.433 2.74.75 2.46 3.35-5.29.9.77-5.6 2.85.329-4.959.664 4.24-4.3.95 3.626-2.443 -.574 2.936-3.973-5.58 3.29 3.654-5.355.36 3.75-5.839 2.297 2.293-2.733 2.932 4.8 -.582.996 3.29-2.75.42 4.33 C -5.839 4.254 -.47 C -5.478 4.557 -.56 C -4.52 4.867.49 C -3.62 4.857 -.84 C -3.54 4.566-2.57 C -4.869 4.27-2.473 C -.72 5.58 -.492 C -.74 4.84.4 C -.68 2.68 -.85 -.69 2.389 -.223 -.42.777.38 N.33 4.463.737 C.745 4.547 2.27 2.43 4.94 2.93.5 4.385 2.97 C 2.429 5.37 3.497 C 3.9 5.66 3.552 C 4.59 6.353 2.55 C 5.877 6.672 2.557 C 6.64 6.34 3.666 C 6.36 5.65 4.79 C 4.678 5.295 4.658-6.885 4.8 -.75-6.24 4.552.64-3.885 5.2.89-2.787 4.556-2.96-5.49 4.36-3.53 -.694 6.4.36 -.3 5.292 -.45 -.685 4.9.329.978 4.627.6 2.23 4.495 4.23.848 6.224 3.783 3.932 6.66.625 6.347 7.29.723 7.7 6.56 3.72 6.632 5.326 5.6 4.28 4.755 5.5 C -6.45-2.952-3.85 C -5.426-3.894-3.94 C -4.872-4.456-2.763 C -5.326-4.88 -.49 C -6.345-3.34 -.395 C -6.96-2.57-2.542 C -4.72-4.76 -.256 C -3.35-4.2.68 C -3.47-2.643.485-4.4-2.389.53-2.835 -.74 -. N -2.738-4.89.95 C -.52-5.429.5 -.7-5.886 2.288 -.98-5.59.75 C.325-6.37 2.267 C.34-5.284.985 C 2.6-5.337.85 C 3.8-4.342.62 C 3.255-3.278.494 C 2.44-3.2 2.626 C.492-4.27 2.866-6.892-2.58-4.72-5.57-4.95-4.98-4.65-5.2-2.862-6.75-2.82 -.45-7.7 -.822-2.452-4.63-5.8 -.436-5.48-4.69.65-2.7-4.48 -.837-3.75-4.774 2.3.395-7.29.55.535-6.79 3.277 2.6-6.7.38 3.739-4.394 -.3 4. -2.49.3 2.545-2.366 3.327.854-4.4 3.762 S-8

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