Chemoselective Reactivity of Bifunctional Cyclooctynes on Si(001)

Transcription

1 Supporting Information for: Chemoselective Reactivity of Bifunctional Cyclooctynes on Si(001) M. Reutzel 1, N. Münster 2, M. A. Lipponer 1, C. Länger 3, U. Höfer 1, U. Koert 2,, and M. Dürr 3, 1 Fachbereich Physik und Zentrum für Materialwissenschaften, Philipps-Universität, D Marburg, Germany 2 Fachbereich Chemie, Philipps-Universität, D Marburg, Germany 3 Institut für Angewandte Physik, Justus-Liebig- Universität Giessen, D Giessen, Germany Corresponding authors: koert@chemie.uni-marburg.de (U.K.), michael.duerr@ap.physik.uni-giessen.de (M.D.) S1

2 This Supporting Information includes (I) Experimental details on XPS and molecular beam experiments including XPS data and fitting parameters on cyclooctyne ether 1 and ester 2 adsorption (II) Coverage dependent XPS measurements of cyclooctyne ether 1 on Si(001) (III) STM height profiles on the adsorption configuration of cyclooctyne ether 1 (IV) Details on synthetic route for synthesis of the cyclooctyne derivatives used I EXPERIMENTAL DETAILS N XPS AND MLECULAR BEAM EXPER- IMENTS In the XPS spectra, the energetic position of the core-level peaks was calibrated with respect to the binding energy of the Si 2p(3/2) peak (99.4 ev). The width of the peaks was fitted by a sum of voigt profiles. The lorentzian part was attributed to the natural line width of the 1s (0.165 ev) [1] and C 1s (0.095 ev) [2] electrons and the gaussian part was assigned to line broadening effects of the experimental set-up. The fitting parameters are summarized in Tab. S1. The measurements of the normalized initial sticking coefficient s 0 /s max were performed by means of molecular beam techniques [3]. In the case of cyclooctyne, a combination of optical second-harmonic generation (SHG) and Auger-electron spectroscopy was employed for measuring the initial sticking probability. In the SHG experiment, chopped 800 nm pulses (60 fs pulse duration, 82 MHz repetition rate) of a Ti:Sapphire oscillator were focused Table S1: 1s and C 1s core-level binding energies, FWHM, and intensity ratios of cyclooctyne ether 1 and cyclooctyne ester 2 adsorbed on Si(001) (300 K spectra). 1s C 1s C--C C= C= C-C- C-C-C C-C-Si Cyclooctyne Ether 1 E B (ev) FWHM (ev) rel. Intensity Cyclooctyne Ester 2 E B (ev) FWHM (ev) rel. Intensity S2

3 on the sample in s-polarization and the frequency doubled p-polarized light was separated from its fundamental by optical filters and detected by lock-in techniques [4]. surface coverage, the surface SH response χ (2) s For low is proportional to the number of quenched dangling bond orbitals and thus on the number of adsorbed molecules [5, 6]. In an isothermal adsorption experiment, the initial slope χ (2) s / t of the decreasing SH signal can thus be correlated to the initial sticking coefficient s 0 χ (2) s / t. These results were confirmed by means of Auger electron spectroscopy, when the integral of the carbon peak (KLL line) was measured at a given dose of cyclooctyne and was found to be independent on surface temperature. II CVERAGE DEPENDENT XPS MEASUREMENTS F CYCLCTYNE ETHER N Si(001) Coverage dependent XPS measurements were performed in order to elucidate the chemoselective adsorption at high surface coverage. In Fig. S1, XPS spectra of the 1s region of cyclooctyne ether on Si(001) are shown as a function of cyclooctyne ether dose. With increasing dose, the signal intensity increases. For the first three spectra (blue), the binding energy stays constant; further dosing leads to a shift of the spectra to higher binding energies. Such a shift of the 1s spectrum of the ether group is well known for the transition from monolayer to multilayer adsorption (compare grey line, [7, 8]). Annealing the sample to 300 K backs this interpretation: after annealing, the binding energy is again the same as in the sub-monolayer regime, the signal intensity (red area) is also the same as obtained for the highest intensity of the spectrum without shift of the binding energy (blue area). Thus, with increasing dose first the monolayer of cyclooctyne ether on Si(001) is formed and further dosing leads to weakly bound adsorbates in a second an further layers. These weakly bound molecules can be desorbed at 300 K, but the covalently attached monolayer stays on the surface. For the C 1s spectra, qualitatively the same behavior was observed. S3

4 1s Intensity (arb. u., arb. offs.) 300 K 80 K Coverage Annealing Binding Energy (ev) Figure S1: XPS spectra of cyclooctyne ether on Si(001) in the 1s region. For the blue and cyan spectra, the cyclooctyne dose was successively increased; adsorption was performed at 80 K. For the blue spectra, the binding energy stays constant and only the intensity increases; further dosing (cyan spectra) leads both to an increase of intensity and a shift of the spectra towards higher higher binding energies. The grey spectrum was measured for a multilayer of THF on Si(001). The red spectrum was obtained when annealing the sample with the highest coverage (upper most cyan spectrum) to 300 K. All measurements were taken at 80 K. S4

5 III N-TP ADSRPTIN F CYCLCTYNE ETHER N Si(001) In Fig. S2, the lateral extension of cyclooctyne ether and water (H 2 ) adsorbed on Si(001) are compared by height profiles through exemplary adsorption features. Due to the static buckling of the dimers at 50 K and the resulting c(4 2) reconstruction, only every second dimer appears as a maximum in the height profile. For the water defect (black height profile), the bright, two dimer-wide protrusion can be attributed to two half-filled dangling bond orbitals on two neighbored dimers, as H 2 adsorbs dissociatively, forming Si- H and Si-H species on two neighboring silicon dimers [9, 10]. In the case of an end-bridge adsorption of cyclooctyne ether, one would expect a similar signature: Cyclooctyne ether would quench two dangling bond orbitals of two neighboring silicon dimers and the remaining half-filled dangling bond orbitals would appear as a two-dimer wide bright protrusion in the empty state STM image. In contrast, the hight profile of cyclooctyne ether (orange) is only one dimer in width; a localization on-top of one dimer and thus a [2+2] cycloaddition of the strained triple bond with one silicon dimer can be concluded, in agreement with the observation for non-derivatized cyclooctyne. In the latter case, a well-ordered saturation coverage was observed [11]. Height (nm) Cyclooctyne Ether H 2 H 3C H 2C H 2C H C C 2 H 2C CH2 H 2C CH2 C C Si Si Si Si CH H H Si Si Si Si Distance (Number of Si Dimers) Figure S2: Height profiles of cyclooctyne ether (orange) and water (black) adsorbed on Si(001). The profiles are measured along the indicated lines in the empty state STM image (+0.8 V, 1 na, 7 7 nm 2, 0.02 ML cyclooctyne ether). The surface was annealed to room temperature prior to scanning at 50 K. The end-bridge water defect occupies two dimers on the same dimer row (lower sketch) whereas cyclooctyne ether is located on-top of one dimer (upper sketch). S5

6 IV SYNTHESIS F CYCLCTYNE ETHER 1 AND ESTER 2 In Scheme 1, the overall synthesis route of the cyclooctyne derivates 1 and 2 is summarized. In the following, the general methods and materials and the synthesis route are described in more detail. 1) tbuh, C PdCl 2, PPh 3 2) LDA; MeI 1) ThBH 2 THF, rt 2) H 2 2, NaH THF/H 2, rt ref [12] 85%, 2 steps 3) PCC CH 2 Cl 2, rt S1 S2 43%, 2 steps S3 PhN(Tf) 2, KHMDS THF, 78 C KHMDS THF, 0 C 41%, 2 steps Tf S4 2 DIBAH THF/CH 2 Cl 2, 20 C to rt 69%, 2 steps H LDA; Et 3 BF 4 78 C to 0 C 57% Et Tf S5 1 Scheme 1: verall summary of the synthesis route of cyclooctyne ether 1 and cyclooctyne ester 2. S6

7 General Methods and Materials All non-aqueous reactions were carried out using flame-dried glassware under argon atmosphere. All solvents were distilled by rotary evaporation. Solvents for non-aqueous reactions were dried as follows prior to use: THF and Et 2 were dried with KH and subsequently distilled from sodium/benzophenone (THF), respectively from Solvona R (Et 2 ). CH 2 Cl 2 was distilled from CaH 2. All commercially available reagents and reactants were used without purification unless otherwise noted. Reactions were monitored by thin layer chromatography (TLC) using Merck Silica Gel 60 F245-plates and visualized by fluorescence quenching under UV-light. In addition, TLCplates were stained using KMn 4. Chromatographic purification of products was performed on Merck Silica Gel 60 ( mesh) unless otherwise noted using a forced flow of eluents. Concentration under reduced pressure was performed by rotary evaporation at 40 C and appropriate pressure and by exposing to high vacuum at room temperature if necessary. In order to check purity, NMR and GCMS were applied. NMR spectra were recorded on a Bruker AV II 300 MHz, AV III HD 300 MHz, AV III 500 MHz, AV III HD 500 MHz or AV II 600 MHz spectrometer at room temperature. Chemical shifts are reported in ppm with the solvent resonance as internal standard. Data are reported as follows: s = singlet, d = doublet, t = triplet, q = quartet, m = multiplet. Mass spectra were recorded by the mass service department of the Philipps-Universität Marburg. HR-ESI & HR-APCI mass spectra were acquired with a LTQ-FT mass spectrometer (Thermo Fischer Scientific). The resolution was set to HR-EI mass spectra were acquired with a MAT95 double focusing sector field mass spectrometer (Finnigan). IR spectra were recorded on a Bruker IFS 200 spectrometer. The absorption bands are given in wave numbers (cm 1 ), intensities are reported as follows: s = strong, m = medium, w = weak, br = broad band. S7

8 tert-butyl-1-methyl-5-oxocyclooctane-1-carboxylate (S3) tbu 1. ThBH 2 ; H 2 2, NaH, THF, 0 C 2. PCC, CH 2 Cl 2, rt tbu S2 S3 2,3-Dimethyl-2-butene (1.16 ml, 9.81 mmol, 1.10 eq) was dissolved in THF (40 ml) at 0 C. BH 3 Me 2 S (0.93 ml, 9.81 mmol, 1.10 eq) was added and the resulting solution was stirred for 1 h at 0 C. Then a solution of alkene S2 [12] (2.00 g, 8.92 mmol, 1.00 eq) in THF (10 ml) was added dropwise. After stirring for 90 min at 0 C 3 m aq. NaH (10 ml) and 35 w% aq. H 2 2 (10 ml) were added carefully. After 10 min the resulting mixture was warmed to rt and stirred at this temperature for 90 min. Then sat. aq. NaCl (20 ml) was added and the organic layer was separated. The aqueous layer was extracted with EtAc (3 x 40 ml). The combined organic layer was washed with sat. aq. NaCl (20 ml) and dried over MgS 4. Evaporation of the solvents gave crude alcohol (mixture of Isomers) which was used for the next step without further purification. The crude alcohol was dissolved in CH 2 Cl 2 (45 ml) and PCC (3.85 g, 17.8 mmol, 2.00 eq) was added in portions at rt. The resulting mixture was stirred at rt for 1 h. Et 2 (100 ml) was added and then the mixture was filtrated over a short plug of Al 2 3 (neutral, activity 1, 10 g) which was washed with Et 2 (100 ml). The filtrate was concentrated under reduced pressure (r.r. 2:1 of the crude product). Column chromatography on silica (npentane/mtbe 7:1) gave pure ketone S3 (r.r >25:1, 919 mg, 3.82 mmol, 43% over 2 steps) as a colorless oil. TLC (n-hexane/mtbe 5:1): R f = H NMR (500 MHz, CDCl 3 ): δ = 1.10 (s, 3H, CH 3 ), 1.44 (s, 9H, C(C H 3 ) 3 ), 1.50 (ddd, J = 15.2, 9.3, 2.5 Hz, 2H, 2-H a, 8-H a ), (m, 4H, 3-H, 7-H), 2.01 (ddd, J = 15.2, 8.7, 2.5 Hz, 2H, 2-H b, 8-H b ), 2.38 (ddd, J = 12.6, 7.6, 5.1 Hz, 2H, 4-H a, 6-H a ), 2.51 (ddd, J = 12.6, 8.6, 5.2 Hz, 2H, 4-H b, 6- H b ). 13 C NMR (125 MHz, CDCl 3 ): δ = 20.8 (2C, C3 + C7), 26.3 (CH 3 ), 28.2 (C(C H 3 ) 3 ), 34.1 (2C, C2 + C8), 43.8 (2C, C4 + C6), 45.7 (C1), 80.3 (C (CH 3 ) 3 ), (CtBu), (C5). HR-MS (EI): m/z calcd for C 14 H 24 3 [M] + : ; found: FT- S8

9 IR (neat): ν = 2972 (w), 2935 (w), 1716 (s), 1703 (s), 1475 (w), 1392 (m), 1324 (w), 1252 (m), 1158 (s), 1123 (s), 849 (w). tert-butyl carboxylate (S4) (E)-1-methyl-5-(((trifluoromethyl)sulfonyl)oxy)cyclooct-4-ene-1-- tbu KHMDS, PhN(Tf) 2 THF 78 C, 30 min tbu S3 Tf S4 Ketone S3 (3.68 g, 15.3 mmol, 1.00 eq) and PhN(Tf) 2 (5.74 g, 16.1 mmol, 1.05 eq) were dissolved in THF (70 ml) and cooled to 78 C. KHMDS (0.5 m in toluene, 33.7 ml, 16.8 mmol, 1.10 eq) was added over a period of 15 min. The resulting mixture was stirred for additionally 20 min at the same temperature. Then H 2 (50 ml) was added and the solution was warmed to rt. MTBE (150 ml) was added and the organic layer was separated. The organic layer was washed with sat. aq. Na 2 C 3 (2 x 50 ml) and sat. aq. NaCl (50 ml) and then dried over MgS 4. The solvents were removed under reduced pressure to give the triflate S4 (5.93 g, 15.9 mmol, 104%) which contains minor amounts of PhN(Tf) 2. An analytically pure sample was obtained by chromatography on silica (n-pentane/et 2 20:1) of a small amount of the compound. TLC (n-hexane/mtbe 40:1): R f = H NMR (400 MHz, C 6 D 6 ): δ = 0.94 (s, 3H, CH 3 ), 1.07 (ddd, J = 14.9, 9.6, 2.2 Hz, 1H, 2-H a ), 1.30 (s, 9H, C(C H 3 ) 3 ), (m, 1H, 8-H a ), (m, 1H, 7-H a ), (m, 3H, 3-H b, 7-H b, 8-H a ), (m, 1H, 8-H b ), (m, 2H, 2-H b, 6-H a ), 2.41 (ddd, J = 15.9, 9.5, 6.1 Hz, 1H, 6-H b ), 5.47 (t, J = 6.5 Hz, 1H, 4-H). 13 C NMR (100 MHz, C 6 D 6 ): δ = 22.9 (C3), 23.1 (C7), 27.6 (CH 3 ), 27.9 (C(C H 3 ) 3 ), 29.5 (C6), 32.9 (C8), 34.8 (C2), 46.1 (C1), 79.7 (C (CH 3 ) 3 ), (q, J = 320 Hz, CF 3 ), (C4), (C5), (CtBu). 19 F NMR (282 MHz, C 6 D 6 ): δ = HR-MS (APCI): m/z calcd for C 15 H 23 F 3 5 SNa [M+Na] + : ; found: FT-IR (neat): ν = 2976 (w), 2936 (w), 1717 (m), 1413 (m), 1368 (w), 1247 (m), 1203 (s), 1142 (s), 1032 (w), 930 (m), 843 (s), 612 (m), 516 (m). S9

10 (E)-5-(Hydroxymethyl)-5-methylcyclooct-1-en-1-yl (S5) trifluoromethanesulfonate tbu DIBAH CH 2 Cl 2 /THF 7:1 15 C to rt, 16 h H Tf S4 Tf S5 Vinyl triflate S4 (5.41 g, 14.5 mmol, 1.00 eq) was dissolved in CH 2 Cl 2 /THF (7:1, 49 ml) and cooled to 15 C. DIBAH (1.2 m in toluene, 30.3 ml, 36.3 mmol, 2.50 eq) was added. After stirring for 15 min at this temperature the cooling bath was removed and the reaction mixture was stirred at rt for 16 h. A sat. aq. solution of sodium potassium tartrate (40 ml) and CH 2 Cl 2 (40 ml) were added and the resulting mixture was stirred for 1 h. The organic layer was separated and the aqueous layer was extracted with CH 2 Cl 2 (3 x 40 ml). The combined organic layer was dried over MgS 4 and the solvents were removed under reduced pressure. Purification by column chromatography on silica (n-pentane/mtbe 2:1) gave alcohol S5 (3.03 g, 10.0 mmol, 69%) as a colorless liquid. TLC (n-hexane/mtbe 2:1): R f = H NMR (500 MHz, acetone-d 6 ): δ = 0.93 (s, 3H, CH 3 ), 1.42 (ddd, J = 14.9, 7.4, 4.1 Hz, 1H, 6-H a ), (m, 2H, 6-H b, 4-H a ), (m, 3H, 4-H b, 7-H), (m, 2H, 3-H), 2.58 (ddd, J = 16.1, 6.5, 6.5 Hz, 1H, 8-H a ), 2.71 (ddd, J = 15.9, 8.8, 6.7 Hz, 1H, 8-H b ), 3.28 (s, 2H, CH 2 H), 3.67 (bs, 1H, H), 5.90 (t, J = 6.0 Hz, 1H, 2-H). 13 C NMR (125 MHz, acetone-d 6 ): δ = 22.8 (C7), 23.2 (C3), 23.5 (CH 3 ), (C8), 31.4 (C6), 34.1 (C4), 39.3 (C5), 71.5 (CH 2 H), (q, J = 319 Hz, CF 3 ), (C2), (C1). 19 F NMR (282 MHz, acetone-d 6 ): δ = FT-IR (neat): ν = 3351 (w), 2938 (w), 2872 (w), 1686 (w), 1409 (s), 1200 (s), 1138 (s), 1023 (m), 982 (m), 934 (m), 821 (m), 766 (w), 607 (s), 510 (m). 5-(Ethoxymethyl)-5-methylcyclooct-1-yne (1) Alcohol S5 (1.50 g, 14.9 mmol, 1.00 eq) was dissolved in THF (20.0 ml) and cooled to 78 C. The freshly prepared LDA (1.0 m in THF/n-hexane, 14.9 ml, 14.9 mmol, 3.00 eq) was added dropwise and the resulting solution was stirred at this temperature for 90 min. Then Et 3 BF 4 (3.77 g, 19.8 mmol, 4.00 eq) was added and the reaction mixture S10

11 H 1) LDA, THF, 78 C, 90 min 2) Et 3 BF 4 THF, 0 C, 24 h Et Tf S5 1 was slowly warmed to 0 C. After stirring for 23 h at 0 C, additional Et 3 BF 4 (3.77 g, 19.8 mmol, 4.00 eq) was added and the mixture was stirred at rt for further 2 h. The reaction was quenched by addition of H 2 (50 ml) and extracted with MTBE (2 x 200 ml). The combined organic layer was washed with sat. aq. NaCl (100 ml) and dried over MgS 4. After removal of the solvents the remaining crude product was purified on a short plug of silica (25 g, n-pentane/et 2 20:1) to give almost pure cyclooctyne. Final distillation in vacuo (30 32 C, 0.1 mbar) gave product 1 (514 mg, 2.85 mmol, 57%) as a colorless liquid. TLC (n-hexane/mtbe 20:1): R f = H NMR (500 MHz, C 6 D 6 ): δ = 1.03 (s, 3H, CH 3 ), 1.09 (t, J = 7.0 Hz, 3H, CH 2 CH 3 ), 1.53 (dd, J = 14.7, 9.8 Hz, 1H, 6-H a ), (m, 5H, 4-H, 6-H b, 7-H), (m, 4H, 3-H, 8-H), 2.94 (d, J = 8.5 Hz, 1H, CH 2 Et), 2.99 (d, J = 8.5 Hz, 1H, CH 2 Et), 3.27 (q, J = 7.0 Hz, 2H, CH 2 CH 3 ). 13 C NMR (125 MHz, C 6 D 6 ): δ = 15.4 (CH 2 C H 3 ), 17.3 (C3), 21.9 (C7), 22.5 (CH 3 ), 28.1 (C8), 37.7 (C6), 37.8 (C5), 43.2 (C4), 66.7 (C H 2 CH 3 ), 81.2 (CH 2 Et), 96.5 (C2), 96.6 (C1). FT-IR (neat): ν = 2926 (m), 2854 (m), 1706 (w), 1441 (w), 1379 (w), 1106 (s), 1071 (m), 1024 (w), 892 (w), 537 (w), 496 (w). tert-butyl 1-methylcyclooct-4-yne-1-carboxylate (2) tbu KHMDS tbu THF 0 C, 1 h Tf S4 2 Ester S4 (3.20 g, 8.59 mmol, 1.00 eq) was dissolved in THF (40 ml) at 0 C. KHMDS (0.5 m in toluene, 24.1 ml, 12.0 mmol, 1.40 eq) was added dropwise over 20 min. After S11

12 stirring for 1 h at 0 C the reaction was quenched by addition of H 2 (20 ml). The mixture was extracted with MTBE (2 x 50 ml). The combined organic layer was washed with sat. aq. NaCl (30 ml) and dried over MgS 4. The solvents were removed under reduced pressure. Column chromatography on silica (n-pentane/mtbe 30:1) gave cyclooctyne 2 (1.10 g, 4.95 mmol, 58%) as a pale yellow liquid. To remove impurities of solvents the product was destilled (50 C, 0.12 mbar) to give very pure cyclooctyne 2 (777 mg, 3.50 mmol, 41%). TLC (n-hexane/mtbe 20:1): R f = H NMR (300 MHz, C 6 D 6 ): δ = 1.17 (s, 3H, CH 3 ), 1.38 (s, 9H, C(CH 3 ) 3 ), (m, 10H). 13 C NMR (125 MHz, CD 2 Cl 2 ): δ = 17.5, 22.1, 22.3 (CH 3 ), 28.1 (C(CH 3 ) 3 ), 28.5, 37.5, 42.4, 45.9 (C1), 79.9 (C(CH 3 ) 3 ), 96.7, 97.7, (CtBu). FT-IR (neat): ν = 2974 (w), 2929 (m), 1718 (s), 1456 (w), 1366 (m), 1255 (m), 1157 (s), 1103 (s), 849 (m), 752 (w), 548 (m), 529 (w), 471 (w), 455 (w). S12

13 1 H and 13 C NMR spectra tbu S3 500 MHz, CDCl ppm ppm tbu S3 125 MHz, CDCl ppm S13

14 tbu Tf S4 400 MHz, C6D ppm ppm tbu Tf S4 100 MHz, C6D ppm S14

15 H Tf S5 500 MHz, acetone-d ppm ppm H Tf S5 125 MHz, acetone-d ppm S15

16 MHz, C6D ppm ppm MHz, C6D ppm S16

17 MHz, CD2Cl ppm ppm MHz, CD2Cl ppm S17

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