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Ddr nmr spectrometer

Manufactured by Agilent Technologies

The DDR NMR spectrometer is a nuclear magnetic resonance (NMR) instrument designed for the analysis of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) samples. It utilizes a dynamic-decoupling method to enhance the resolution and sensitivity of NMR signals, enabling the study of molecular structures and dynamics in these biomolecules.

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4 protocols using ddr nmr spectrometer

1

Characterization of Cathinone-Cyclodextrin Complexes

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The 1H NMR spectra were recorded at 298 K on a 600 MHz Varian DDR NMR spectrometer equipped with a 5 mm inverse-detection probe fitted with a gradient module (IDPF probe). The stoichiometry of the complex was determined using 20 mM acetate buffer pH 4.5, prepared with D2O. Stock solutions of cathinones, native β-CD, and SBE-β-CD were also prepared at 3 mM, and methanol was added to the solutions as a reference (δ = 3.30 ppm).
Conventional 2D experiments (1H-1H gCOSY, ROESYAD and 1H–13C gHSQCAD, and HMBC) for structural elucidation were acquired on 20 mM acetate buffer pH 4.5 solutions containing 1 mM of the cathinone analogs and 2 mM native β-CD, 1 mM Succ-β-CD 1 mM 6-(SB)7-β-CD or 1 mM SBX (resulting in a 1:2 or 1:1 cathinone–CD molar ratio). ROESY experiments were recorded with a 300 ms mixing time using a 4.2 kHz spin-lock field. For 1D ROESY selective excitation, the selexcit pulse sequence available in the VnmrJ program was used.
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2

NMR Spectroscopy for Compound pKa Determination

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All NMR experiments were recorded at 298 K on a 600 MHz Varian DDR NMR spectrometer equipped with a 5 mm inverse-detection gradient (IDPFG) probe.
For the pH-dependent series of 1H NMR spectra, the solvent mixture was H2O:D2O = 9:1 by volume, the constant ionic strength and the buffer capacity were adjusted using 0.05 M NaCl and 0.05 M H3PO4. An appropriate amount of the corresponding CD was weighed to obtain a 1 mM solution and finally, methanol was added (0.05 mM) as a chemical shift reference (3.31 ppm). The pH was adjusted by using 1 M NaOH. The water resonance was diminished by the dpfgse pulse sequence [25 (link)]. The pH measurements were performed in 25 mL vessels with proper stirring, before transferring 600 μL solutions into the NMR tubes. The pH meter readings were recorded using a Metrohm pH meter, equipped with a Metrohm 6.0234.110 combined glass electrode.
The pKa values were calculated using the equation (1) for compounds 2, 3, 4 and equation (2) for compound 5, where δobs is the observed chemical shift of a given nucleus, appearing at the frequency of the weighted average of δL , δHL and δH2L , the limiting chemical shifts of the species simultaneously present [26 (link)].
δobs=δL+δHL×KH+1+KH+=δL+δHL ×10pKapH1+10pKa pH
δobs=δL+δHL×10pKa1pH+δH2L×10pKa1pH×10pKa2pH1+10pKapH+10pKa1pH×10pKa2pH
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3

NMR Characterization of CD Derivatives

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For structural characterizations of CD derivatives in D2O, a 600 MHz Varian DDR NMR spectrometer equipped with a 5 mm inverse-detection gradient probe or a 400 MHz Varian Mercury Plus spectrometer equipped with a 5mm Varian 400 Automation Triple Resonance Broadband Pulsed Field Gradient probe was used. For NMR-pH titrations, the same instruments were used. The pH-dependent series of 1H NMR spectra were recorded in a solvent mixture of H2O:D2O = 9:1 by volume, where the constant ionic strength and the buffer capacity were adjusted using 0.05 M sodium chloride and 0.05 M acetic acid-d4. An appropriate amount of CD was weighed to obtain a 1 mM solution and finally one drop of methanol was added as a chemical shift reference (3.310 ppm). The water resonance was diminished by the dpfgse pulse sequence [55 (link)] or presaturation. All the spectra were processed using the MestReNova v9.0.1-13254 (Mestralab Research, S.L., Santiago de Compostela, Spain) software.
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4

NMR Analysis of Compounds

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All NMR experiments were carried out on a 600 MHz Varian DDR NMR spectrometer equipped with a 5 mm inverse-detection gradient (IDPFG) probehead. Standard pulse sequences and processing routines available in VnmrJ 3.2 C/Chempack 5.1 were used for structure identifications. The complete resonance assignments were established from direct 1 H-13 C, long-range 1 H- 13 C, and scalar spin-spin connectivities using 1D 1 H, 13 C, 1 H-1 H gCOSY, 1 H-1 H NOESY, 1 H- 13 C gHSQCAD (J = 140 Hz), 1 H- 13 C gHMBCAD (J = 8 Hz) experiments, respectively. The probe temperature was maintained at 298 K and standard 5 mm NMR tubes were used. The 1 H chemical shifts were referenced to the applied NMR solvent CD3OD (δ (CD2HOD) = 3.310 ppm) and 13 C chemical shifts were referenced to 49.00 ppm.
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