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43 protocols using mercury 400

1

Synthesis and Characterization of Organic Compounds

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All the solvents and chemicals were obtained from commercial sources and used without further purification. TLC was performed on silica gel plates (GF254) with visualization of components by UV light (254 nm) or exposure to I2. Column chromatography was carried out on silica gel (300-400 mesh). The structural identities of the prepared compounds were confirmed by 1 H NMR and 13 C NMR spectroscopy and mass spectrometry. 1 H NMR spectra were obtained on Varian Mercury-400 at 400 MHz. 13 C NMR spectra were obtained on Varian Mercury-400 at 100 MHz. Chemical shifts (δ) values were referenced to the residual solvent peak and reported in ppm and all coupling constant (J) values were given in Hz.
CDCl3 or DMSO-d6 were used as the standard NMR solvents. The following multiplicity abbreviations are used: (s) singlet, (d) doublet, (t) triplet, (q) quartet, (m) multiplet, and (brs) broad. The chemical shifts of isomer of 13 C NMR were given in parenthesis. ESI-HRMS data were measured on Thermo Exactive Orbitrap plus spectrometer. Melting points were determined on Yanaco MP-J3 microscope melting point apparatus.
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2

Synthesis of α-Diazoacetamides and Oxindoles

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All commercially available reagents were used without further purification. 1H- and 13C-NMR spectra were recorded using Me4Si as the internal standard with a Varian Mercury 400 instrument (Oxford, United Kingdom). Chemical shifts are reported in ppm downfield (δ) from Me4Si for 1H and 13C-NMR. TLC was carried out on SiO2 (silica gel 60 F254, Merck), and the spots were located with UV light or 1% aqueous KMnO4. Flash chromatography was carried out on SiO2 (silica gel 60, SDS, 230–400 mesh ASTM). Organic extracts were dried over anhydrous Na2SO4 during workup of reactions. Evaporation of solvents was accomplished with a rotatory evaporator (Büchi, Flavill, Switzerland). α-Diazoacetamides 1a1j and oxindoles 2a2j are known compounds previously prepared by us [55 (link)], as are α-diazoacetamides 5a5m and β-lactams 7a7m [56 (link)].
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3

Iridium-Catalyzed C-H Sulfonation of Heterocycles

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All synthetic procedures were performed under nitrogen either in a Vacuum Atmospheres glovebox or in a closed reactor. Acetophenone, 4-toluenesulfonyl chloride, 4-fluorobenzenesulfonyl chloride, 2-picolylamine, [Cp*IrCl2]2, potassium tert-butoxide, formic acid (97%), and NaHCO3 were purchased from common vendors and used without further purification. NMR solvents (CD2Cl2, CDCl3, and C6D6), 2-propanol, and triethylamine were dried and distilled over CaH2. Hexane and CH2Cl2 were dried using a solvent purification system.
1H, 13C, and 19F NMR spectra were acquired on Varian Mercury 400, VNMRS-500, and VNMRS-600 spectrometers and processed using MestReNova 12.0.1. All chemical shifts are reported in ppm and referenced to the residual 1H or 13C solvent peaks. Following abbreviations are used: (s) singlet, (bs s) broad singlet, (d) doublet, (t) triplet, (dd) doublet of doublets, etc. NMR spectra of all metal complexes were taken in 8” J. Young tubes (Wilmad or Norell) with Teflon valve plugs. MALDI-MS spectra were acquired on Bruker Autoflex Speed MALDI Mass Spectrometer. X-ray crystallography data were obtained on a Bruker APEX DUO single-crystal diffractometer equipped with an APEX2 CCD detector, Mo fine-focus and Cu micro-focus X-ray sources. IR spectra were obtained using Jasco FT/IR-4600 FT-IR Spectrometer.
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4

Analytical Characterization of Compounds

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An Agilent Technologies LC/MSD TOF instrument was used to record the high-resolution mass spectra. Varian Mercury 400 and 100 MHz spectrometers were used to record the 1H and 13C NMR spectra. High-performance liquid chromatography (HPLC, Shimadzu LC-20A) with a reverse-phase C18 column (4.6 mm × 150 mm, 5 mm, Shim-pack VP-ODS) was used to determine the purity of the target compounds (all above 95%). The detailed chemical data, the 1H and 13C NMR spectra, and the high-resolution mass spectra are provided in the Supplementary material.
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5

Characterization of DNA-Conjugated Agents

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1 H and 13C NMR spectra were measured with Varian NMR spectrometers (Inova 300, Varian 400, and Mercury 400). For optical spectra, DNA-CAs were prepared as ∼1 μM solutions in water (Molecular Biology grade, Corning). Absorption spectra were measured with a Cary 100 Bio UV–vis spectrometer, fluorescence spectra obtained by a Jobin Yvon-Spex Fluorolog 3 spectrometer, and fluorescence lifetime measurements were made with a PTI EasyLife LS spectrometer. Mass spectra were obtained using ESI or MALDI-TOF ionization modes at the Stanford University Mass Spectrometry Facility. HPLC was performed with a Shimadzu LC-20AD equipped with an SPD-M20A diode array detector and a Phenomenex Jupiter reverse phase C5 column. Dynamic light scattering measurements were made with a Malvern Instruments Nanoseries ZS90 Zetasizer. Epifluorescence microscopy for cell bioimaging and library screening were conducted on a Nikon Eclipse 80i microscope equipped with a Nikon Plan Fluor 4–40× objective and a QIClick digital CCD camera, with a 100 W high-pressure mercury lamp as the excitation source (365 nm mercury plasma emission line), 340–380 nm excitation filter, and >420 nm long-pass emission filter. Photographs of aqueous phase DNA-CAs, DNA-CAs in hydrogel, and flexible DNA-CA display were captured with an iPhone 6S+ camera, with a 365 nm gel transilluminator UV source (VWR LM-20E) as backlight.
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6

GCPN Synthesis via Carbodiimide Chemistry

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GCPN is synthesized according to the previously described method (Kim et al., 2018b (link)). In brief, GCA (300 mg) was dissolved in 3 mL dimethyl formamide. Then 173 mg dicyclohexylcarbodiimide (DCC) and 96 mg N-hydroxysuccinimide (NHS) were added to active the carboxyl group, and 2.1 mL ethylenediamine (EDA) was added and stirred at room temperature overnight. After the reaction, unreacted EDA was removed by vacuum evaporation at 80 °C. The mixture was filtered and precipitated in ethyl acetate. The pellet (GCA-EDA) was dissolved in 10 mL water and lyophilized. CPN (0.1 mL) was dispersed in 2 mL 2-(N-morpholino)ethanesulfonic acid buffer (0.1M, pH= 6.0). Then 5 mg 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide hydrochloride and 5 mg NHS were added and stirred for 0.5 h. The synthesized GCA-EDA (10 mg) was added and stirred overnight in dark. After the reaction, GCPN was collected by ultracentrifugation (Mw = 10 kD) at 3500 rpm for 10 min. The synthesis was confirmed by Nuclear magnetic resonance (NMR, Mercury 400, Varian, Palo Alto, CA, USA). The size and Zeta potential were measured by dynamic laser scattering (DLS) using Malvern Zetasizer Nano-ZS (Malvern, Worcestershire, UK). The morphology of CPN and GCPN was observed by JEOL JEM 2800 Scanning Transmission Electron Microscopes (JEOL, MA, USA).
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7

Proton NMR Spectroscopy Protocol

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Proton nuclear magnetic resonance (1H-NMR) spectra were measured on a Varian Mercury 400 (400 MHz) (Santa Clara, CA, USA) spectrometer. Chemical shifts for protons are reported in parts per million (ppm) downfield from tetramethylsilane (TMS) and referenced to the residual proton signal in the NMR solvent (dmso-d6: δ 2.50). Experimental conditions, delay: 1 s; pulse: 45°; scans: 32.
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8

Synthesis and Characterization of Coumarins

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All starting materials were purchased from Merck and used without purification. NMR spectra were determined with Varian Mercury 400 (400 MHz) spectrometer, in DMSO-d6 using tetramethylsilane (TMS) as an internal standard. Elemental analysis (C, H, N, Cl) was performed at the Perkin–Elmer 2400 CHN analyzer and was within ±0.4% from the theoretical values. The purity of the compounds was checked by thin-layer chromatography performed with Merck Silica Gel 60 F254 aluminum sheets. Coumarins 15 (Nagorichna et al., 2009a ) were synthesized as described previously.
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9

Analytical Characterization of Organic Compounds

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Melting points (m.p.) were determined using a BÜCHI B-540 (Flawil, Switzerland) melting point apparatus and were uncorrected. The elemental analysis (C, H, N) was performed on a CHNS/O Elemental Analyzer 2400 Series II (Perkin-Elmer, Waltham, MA, USA). The IR spectra were measured with a Perkin-Elmer FT-IR 1725X spectrophotometer (Perkin-Elmer, Waltham, MA, USA) (in KBr) in the range of 600–4000 cm−1. The NMR spectra (1H NMR) were recorded in DMSO-d6 using a Mercury 400 (Varian, Palo Alto, CA, USA) or Bruker DRX 500 (Bruker Daltonics, Inc., Billerica, MA, USA). Chemical shifts (δ, ppm) were described in relation to tetramethylsilane (TMS) and coupling constants (J) expressed in Hz. The MS spectra (EI, 70 eV) were recorded using the apparatus AMD-604 (AMD Analysis & Technology AG, Harpstedt, Germany).
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10

Detailed NMR Spectroscopy Analysis Protocol

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NMR spectra were recorded on a Bruker DRX-600 (Bruker Corp., Billerica, MA, USA) (operating at 600 and 150 MHz for 1H and 13C, respectively), on a Varian INOVA-500 (Varian Medical Systems, Inc., Palo Alto, CA, USA) (operating at 500.13 and 125.76 MHz for 1H and 13C, respectively), all equipped with cryo-probe, and on a Varian MERCURY 400 (Varian Medical Systems, Inc., Palo Alta, CA, USA) (operating at 400 and 100 MHz for 1H and 13C, respectively). Samples were dissolved in D2O, and acetone (1H: (CH3)2CO at δ 2.22 ppm; 13C: (CH3)2CO at δ 31.5 ppm) or DMSO-d6 (1H: CHD2SOCD3 at δ 2.49 ppm; 13C: CD3SOCD3 at δ 39.5 ppm) were employed as the internal standard. For gradient-selected COSY and TOCSY experiments we used spectral widths of either 6000 Hz in both dimensions and data sets of 2048 × 256 points. TOCSY experiments were recorded using a mixing time of 120 ms. HSQC-DEPT experiments were recorded using the 1H-detected mode via single quantum coherence with proton decoupling the 13C domain. We used data sets of 2048 × 512 points, with typically 60 increments. Finally, in HSQC-TOCSY and HMBC we employed data sets of 2048 × 256 points, with 120 increments, and the mixing time for HSQC-TOCSY was set to 120 ms.
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