Chapter 6 Experimental
6.1 General Information
Reactions involving moisture sensitive reagents were carried out under a nitrogen atmosphere using standard vacuum line techniques in addition to dry solvents. All glassware used was flame dried and cooled under vacuum. For moisture sensitive reactions, solvents (THF, CH2Cl2, toluene,
and Et2O) were obtained anhydrous and purified by an alumina column (Mbraun SPS-800). Pet.
ether is defined as petroleum ether 40-60 °C. All other solvents and commercial reagents were used as supplied without further purification unless stated otherwise. Room temperature (rt) refers to 20-25 °C. Temperatures of 0 °C and −78 °C were obtained using ice/water and CO2(s)/acetone
baths respectively. Reflux conditions were obtained using an oil bath or DrySyn® equipped with
a contact thermometer. In vacuo refers to the use of a Büchi Rotavapor R-2000 rotary evaporator with a Vacubrand CVC2 vacuum controller or a Heidolph Laborota 4001 rotary evaporator with a vacuum controller.
Analytical thin layer chromatography was performed on pre-coated aluminium plates (Kieselgel 60 F254 silica). Plates were visualised under UV light (254 nm) or by staining with either phosphomolybdic acid or KMnO4 followed by heating. Flash column chromatography was
performed on Kieselgel 60 silica or Biotage® IsoleraTM 4, using Biotage® Snap Ultra or Biotage® KP Sil columns (CV = column volume) under the solvent system stated.
Melting points were recorded on an Electrothermal 9100 melting point apparatus, dec refers to decomposition.
HPLC analyses were obtained on a Shimadzu HPLC consisting of a DGU-20A5 degasser, LC- 20AT liquid chromatography SIL-20AHT autosampler, CMB-20A communications bus module, SPDM20A diode array detector and a CTO-20A column oven that allows the temperature to be set from 25-40 °C. Separation was achieved using a Chiralcel OJ-H or Chiralpak AD-H column.
GC analyses were obtained on a Shimadzu GC-2025 consisting of an AOC-20i auto injector, SPL1 injection port, column oven and flame ionisation detector (FID). Helium (He) was used as the carrier gas in split injection mode at constant linear velocity. An Agilent DB-5 analytical column was used for analyses (30 m, 0.25 mm ID, 0.5 μm film thickness).
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Infrared spectra (νmax) were recorded on a Shimadzu IRAffinity-1 Fourier transform IR
spectrophotometer using either thin film or solid using Pike MIRacle ATR accessory. Analysis was carried out using Shimadzu IRsolution v1.50 and only characteristic peaks are reported.
1H, 13C{1H}, 19F{1H} 11Band 29Si NMR spectra were acquired on either a Bruker Avance 300
{δH (300 MHz), δC (75 MHz), δF (282 MHz), δSi (60 MHz)}, a Bruker Avance II 400 {δH (400
MHz), δC (100 MHz), δF (376 MHz), δB (128 MHz), δSi (60 MHz)}, Bruker Ultrashield 500 {δH
(500 MHz), δC (126 MHz), δF (471 MHz), δSi (79 MHz)} or a Bruker AVIII-HD 700 {δH (700
MHz), δC (175 MHz)} spectrometer at ambient temperature (unless otherwise stated) in the
deuterated solvent stated. Chemical shifts, δ, are quoted in parts per million (ppm) and are referenced to the residual solvent peak. Coupling constants, J, are quoted in Hertz (Hz) to the nearest 0.1 Hz. The following abbreviations are used: s, singlet; d, doublet; t, triplet; q, quartet; dd, doublet of doublets; ddd, doublet of doublet of doublets; dt, doublet of triplets; ddt, doublet of doublets of triplets; dtt, doublet of triplets of triplets; dq, doublet of quartets; td, triplet of doublets; ttd, triplet of triplets of doublets; tt, triplet of triplets; m, multiplet; and br, broad.
Mass spectrometry (HRMS)
Mass spectrometric (m/z) data was acquired by electrospray ionisation (ESI), electron impact (EI) or chemical ionisation (CI), either at the University of St Andrews Mass Spectrometry facility (quoted [M+H]) or from the EPSRC National Mass Spectrometry Service Centre, Swansea (quoted [M+H]+).
Elemental analysis was carried out by the analytical services at London Metropolitan University and obtained for the determination of carbon, hydrogen and nitrogen analysis (%CHN). All values are quoted in mass percentage (%).
X-Ray photoelectron spectroscopy analysis was performed either at the University of Newcastle (NEXUS at nanoLAB) or at the University of St Andrews. St Andrews X-ray photoelectron spectroscopy spectra wereobtained on a Scienta ESCA 300 instrument; all spectra were obtained using monochromated Al Ka radiation at 1486.6 eV. Survey scans were obtained using a pass energy of 300eV and the detailed scans at 150 eV, giving a resolution of approximately 0.8 eV on the detailed scans. All spectra were collected at normal emission, the operating pressure of the instrument is below 5x10−9 mbar. The XPS spectra were corrected for charging by referencing the aliphatic C 1s peak of hydrocarbons to 284.6 eV. Elemental compositions of the various surfaces were determined from the area under individual elemental peaks using sensitivity factors provided with the software as well as taking the transmission
140 function of the analyser into account. CasaXPS (Casa Software Ltd., UK) was used for the analysis. The spectra were fitted using Gaussian/Lorentzian peak shapes with a ratio of 70%/30%. A Shirley background was subtracted for the quantitative analysis.
Water contact angles (DI water) were measured with a G10 goniometer microscope (KRÜSS GmbH, Hamburg, Germany) under ambient conditions at room temperature. Droplets of ~3 µL were dispensed from a microburette. All reported values are the average of three measurements taken from different places of the surface.
Ellipsometry analysis was measured with an M-2000DITM spectroscopic ellipsometer (J. A.
Woollam Co., Inc., USA). Thickness values were extracted from fits to the data taken from 45 to 70° in steps of 5° over wavelengths from 200 to 1000 nm. The sample surface was modelled as a Si substrate with an oxide layer and a Cauchy layer. The thickness of the silicon oxide after the oxidative cleaning treatment was 16 ± 1 Å (average of three samples). The thickness of the monolayer films was calculated with a refractive index of 1.45. The error based on the observed variation of the thickness of the organic films prepared under identical conditions was ~2 Å.
Atomic Force Microscopy (AFM) images were obtained using Bruker Dimension Icon AFM system. AFM images were collected in the PeakForce TappingTM mode using V-shaped
cantilevers of nominal spring constant 0.58 N/m (Veeco SNL-A) with a peak force set point of around 1-4 nN and scan rate of 1 Hz. The RMS roughness of the surfaces was characterized from 1 × 1 µm2 images of 512 × 512 pixels after appropriate image levelling. Quoted roughness values
were calculated from an average of at least two samples and three images of each sample.
AFM force curve collection. A Bruker Dimension Icon AFM system was used to collect force curves between the thiol SAM coated AFM tip (Au coated Veeco SNL-B or SNL-D) and a modified surface in Millipore filtered deionized water. Force curves were collected at a ramp rate of ~1 Hz with 0.5 s of surface dwell time, with a ramp size of 200-500 nm, and with the maximum deflection minimized on a cantilever by cantilever basis to be as small as possible (typically ~0.5- 8.0 nm). For each tip – sample system 25 force curves were collected in 5 × 5 grids in each of four different 500 × 500 nm2 areas resulting in 100 force curves per surface. The same tip was
used to interrogate multiple samples sequentially without alteration of optical readout positioning. Repeat measurements of samples were executed to check for tip changes. The modified tips were not used for imaging to preserve the thiol coating.
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Section 6.2 contains the synthetic and experimental procedures for bulk reagents and catalysts that were used on multiple occasions throughout this work. Section 6.3 describes all other compounds in the order in which they appear in the text.