CHORUS quantification 2: Experimental data, analysis tools and simulation code for CHORUS broadband excitation in NMR, part 2

Experimental data, analysis tools and simulation code for CHORUS broadband excitation in NMR, part 2 Quantification using CHORUS Files are split across two archives CHORUSquantification1.zip and CHORUSquantification2.zip Experimental data for the tests of robustness with respect to offset (files 20150812_rob_dec1, 20150812_rob_dec2 and 20150815_rob_dec3 below) are in CHORUSquantification2, all others in CHORUSquantification1. ===================================================================================================== Pulse sequences [Pulse_sequences]: 1. CHORUSdec.mfjp 2. zg_zgrec_interleav.mfjp. Data were acquired to show the effects of receiver signal filtration on signal amplitude, where hard pulses were interleaved (a) on resonance and (b) with the frequency of the receiver varied in steps. =================================================================================================================================================================================================================================== Chirp Pulses [Chirp_pulses]: The chirp pulses, used in CHORUS, to acquire data for Figures 1b and 2 (main text) and for Figures 7b, 8a and 8b (Supplementary Information) were: 1st 90 degree chirp & 1st 180 degree chirp element: ChirpLinPh300kHz2m5s10000.txt 2nd 180 degree chirp element: ChirpLin300kHz1m5s10000.txt For quantitative integral analysis, the chirp pulses used were: 1st 90 degree chirp & 1st 180 degree chirp element: ChirpLinPh300kHz2m5s2000.txt 2nd 180 degree chirp element: ChirpLin300kHz1m5s1000.txt ======================================================================================================================== Matlab Notebook (see Supplementary Information, pp. S2 and S18) [Matlab], to generate chirp pulses in the Bruker format: CHORUS_Bloch.m ======================================================================================================================== Mathematica Notebooks (see Supplementary Information, p. S4)[Mathematica]: (A) Simulation_19Fexc_profile_CHORUS_Hard_Pulse.nb Associated text files: JPpeak 20150817_zg.txt 20150817_sp.txt (B) CHORUS_robustness_reproducibility.nb Associated text files, see section below, "Experimental Data (Quantitative Analysis)" ================================================================================================================================================================================================================================== Experimental Data (main text): 1. Figure 1b [20141211_zgarrayfig1b]. Data were acquired using simple 90-degree excitation, the frequency of the excitation was varied in steps over 300 kHz with the receiver kept on resonance. 2. Figure 1b [20150817_sparrayfig1b]. Data were acquired using CHORUS excitation, the frequency of the excitation was varied in steps over 300 kHz with the receiver kept on resonance. The interleaved experiment was set up and executed using an AU_program, array_spoffs [AU_programs] 3. Figure 2 [20150910_paperfig2]. Data were acquired using CHORUS and a hard pulse. Experimental Data (Supplementary Information): 1. Figure 7b, p. S15 [20141224_NaPFO]. Data were acquired to show the effects of J-modulation, using CHORUS in comparison to a hard pulse, using a sample of NaPFO. 2. Figures 8a and 8b, p.S16 [20141211_rec_interarry2]. Data were acquired to show the effects of receiver signal filtration on signal amplitude using pulse sequence zg_zgrec_interleav.mfjp. =================================================================================================================================================================================================================================== Experimental Data (Quantitative Analysis)[Integral_analysis]: CHORUS was interleaved with a hard pulse on resonance, for (A) Robustness and (B) Reproducibility. The experiments were set up and executed using AU_programs, Make_Array and Run_Array [AU_programs]. (A) Robustness (x 3 repeats) (Table 1(main text) and Tables S3a, S3b, S3c (Supplementary Information)): 1. 20150812_rob_dec1 2. 20150812_rob_dec2 3. 20150815_rob_dec3 Processed Data: The data were processed in VnmrJ format(see Supplementary Information p. S6) using the macros [Integral_analysisRobust]: GMJProbass 1, 2 and 3 GMJProbassproc and GMJProbassproczg GMJPsetints GMJPints Hard pulse output text files: rep1hl5w0.5pf0.5p rep2hl5w0.5pf0.5p rep3hl5w0.5pf0.5p CHORUS output text files: rep1cl5w0.5pf0.5p rep2cl5w0.5pf0.5p rep3cl5w0.5pf0.5p (B) Reproducibility (Table 1(main text) and Tables S2a and S2b (Supplementary Information)): 1. 20150816_rep_minus100_dec Processed Data: The data were processed in VnmrJ format (see Supplementary Information p. S6) using the macro [Integral_analysisReprod]: GMJPreprodproc Hard pulse output text files: reprodh CHORUS output text files: reprodc Receiver filter text file used for (A) Robustness and (B) Reproducibility [Integral_analysisRobust]: receiveramp.inp was produced with the macro analyze_amp [Integral_analysis] ===================================================================================================================================================================================================================================

PureShift_2DJ: Experimental data, parameters, pulse sequence and macros for PSYCHE pure shift 2D J spectroscopy

Experimental data, parameters, pulse sequence and macros for PSYCHE pure shift 2D J spectroscopy Pulse sequence [\psglib]: kp_2dj_ifPSYCHE_27_published.c ===================================================================================================== VnmrJ macros [\maclib]: kp_if2djproc_v6: macro to reconstruct pure shift data set from raw data (for manual post-acquisition processing) kp_if2djproc_v6au: macro to reconstruct pure shift data set from raw data (this version can be executed in a queue of experiments using wexp or wdone parameters when acquisitions have been started by au('wait') ) kp2_psyche2: creates the psyche shapes for experiments that use the 2nd ZQS filter (Gzqfilt='yy') kp2_zqf1: creates the wurst shape for the 1st ZQS element kp2_zqf2: creates the wurst shapes for the 2nd ZQS element ===================================================================================================== VnmrJ wave definitions [\wavelib\inversion]: psyche Wave definition file, which needs to be copied to /vnmr/wavelib/inversion. ===================================================================================================== Experimental Data [\data]: Each *.fid directory contains standard Varian/Agilent data, which were collected using VNMRS console and VnmrJ4.0A. Additionally, there are subfolders \psglib and \shapelib which contains the pulse sequence and all shape files which were used when data was collected. A) estradiol in dmso-d6 1) standard proton: 01_estradiol_2015-08-01_v500_s2pul_dmso_25C_3ax2_01.fid 2) classic 2DJ data: 11_estradiol_OVERNIGHT_ref-2dj_new-sw2_ni2-128_2015-08-09_v500_kp_2dj_ifPSYCHE_16_dmso_25C_3ax2_01.fid 3) pure absorption, pure shift 2DJ raw data: 08_estradiol_2dj-PSYCHE-3D_ZQF-yy-raw_2016-12-02_v500_kp_2dj_ifPSYCHE_27_dmso_25C_3ax2_01.fid 4) pure absorption, pure shift 2DJ reconstructed pure shift data: 09_estradiol_2dj-PSYCHE-3D_ZQF-yy-proc_2016-12-02_v500_kp_2dj_ifPSYCHE_27_dmso_25C_3ax2_01.fid B) amikacin in d2o 1) standard proton: 01_amikacin_H1_2015-08-13_v500_s2pul_d2o_25C_3ax2_01.fid 2) classic 2DJ data: 05_amikacin_ref-2dj_high-res_2015-08-15_v500_kp_2dj_ifPSYCHE_16_d2o_25C_3ax2_01.fid 3) pure absorption, pure shift 2DJ raw data: 11_amikacin_2dj-PSYCHE-3D_ZQF-yy-raw_2016-12-04_v500_kp_2dj_ifPSYCHE_27_d2o_25C_3ax2_01.fid 4) pure absorption, pure shift 2DJ reconstructed pure shift data: 12_amikacin_2dj-PSYCHE-3D_ZQF-yy-proc_2016-12-04_v500_kp_2dj_ifPSYCHE_27_d2o_25C_3ax2_01.fid C) methanol (and 2-bromo-thiophene which is not shown in the paper) in dmso-d6 1) raw data without any of the ZQS elements ("nn"): 04_AX3_AMX_CH3OH_2Br-thiophene_PS-2DJ-3D_ZQF-nn_single-sweep-raw_2016-11-28_v500_kp_2dj_ifPSYCHE_27_dmso_25C_3ax2_01.fid 2) reconstructed pure shift data without any of the ZQS elements ("nn"): 05_AX3_AMX_CH3OH_2Br-thiophene_PS-2DJ-3D_ZQF-nn_single-sweep-proc_2016-11-28_v500_kp_2dj_ifPSYCHE_27_dmso_25C_3ax2_01.fid 3) raw data without any of the ZQS elements ("ny"): 10_AX3_AMX_CH3OH_2Br-thiophene_PS-2DJ-3D_ZQF-ny_single-sweep-raw_2016-11-29_v500_kp_2dj_ifPSYCHE_27_dmso_25C_3ax2_01.fid 4) reconstructed pure shift data without any of the ZQS elements ("ny"): 11_AX3_AMX_CH3OH_2Br-thiophene_PS-2DJ-3D_ZQF-ny_single-sweep-proc_2016-11-29_v500_kp_2dj_ifPSYCHE_27_dmso_25C_3ax2_01.fid 5) raw data without any of the ZQS elements ("yn"): 08_AX3_AMX_CH3OH_2Br-thiophene_PS-2DJ-3D_ZQF-yn_single-sweep-raw_2016-11-28_v500_kp_2dj_ifPSYCHE_27_dmso_25C_3ax2_01.fid 6) reconstructed pure shift data without any of the ZQS elements ("yn"): 09_AX3_AMX_CH3OH_2Br-thiophene_PS-2DJ-3D_ZQF-yn_single-sweep-proc_2016-11-28_v500_kp_2dj_ifPSYCHE_27_dmso_25C_3ax2_01.fid 7) raw data without any of the ZQS elements ("yy"): 02_AX3_AMX_CH3OH_2Br-thiophene_PS-2DJ-3D_ZQF-yy_single-sweep-raw_2016-11-27_v500_kp_2dj_ifPSYCHE_27_dmso_25C_3ax2_01.fid 8) reconstructed pure shift data without any of the ZQS elements ("yy"): 03_AX3_AMX_CH3OH_2Br-thiophene_PS-2DJ-3D_ZQF-yy_single-sweep-proc_2016-11-27_v500_kp_2dj_ifPSYCHE_27_dmso_25C_3ax2_01.fid ===================================================================================================== Pulse sequence [\psglib]: kp_2dj_ifPSYCHE_27_published.c ===================================================================================================== VnmrJ macros [\maclib]: kp_if2djproc_v6: macro to reconstruct pure shift data set from raw data (for manual post-acquisition processing) kp_if2djproc_v6au: macro to reconstruct pure shift data set from raw data (this version can be executed in a queue of experiments using wexp or wdone parameters when acquisitions have been started by au('wait') ) kp2_psyche2: creates the psyche shapes for experiments that use the 2nd ZQS filter (Gzqfilt='yy') kp2_zqf1: creates the wurst shape for the 1st ZQS element kp2_zqf2: creates the wurst shapes for the 2nd ZQS element ===================================================================================================== VnmrJ wave definitions [\wavelib\inversion]: psyche Wave definition file, which needs to be copied to /vnmr/wavelib/inversion. ===================================================================================================== Experimental Data [\data]: Each *.fid directory contains standard Varian/Agilent data, which were collected using VNMRS console and VnmrJ4.0A. Additionally, there are subfolders \psglib and \shapelib which contains the pulse sequence and all shape files which were used when data was collected. A) estradiol in dmso-d6 1) standard proton: 01_estradiol_2015-08-01_v500_s2pul_dmso_25C_3ax2_01.fid 2) classic 2DJ data: 11_estradiol_OVERNIGHT_ref-2dj_new-sw2_ni2-128_2015-08-09_v500_kp_2dj_ifPSYCHE_16_dmso_25C_3ax2_01.fid 3) pure absorption, pure shift 2DJ raw data: 08_estradiol_2dj-PSYCHE-3D_ZQF-yy-raw_2016-12-02_v500_kp_2dj_ifPSYCHE_27_dmso_25C_3ax2_01.fid 4) pure absorption, pure shift 2DJ reconstructed pure shift data: 09_estradiol_2dj-PSYCHE-3D_ZQF-yy-proc_2016-12-02_v500_kp_2dj_ifPSYCHE_27_dmso_25C_3ax2_01.fid B) amikacin in d2o 1) standard proton: 01_amikacin_H1_2015-08-13_v500_s2pul_d2o_25C_3ax2_01.fid 2) classic 2DJ data: 05_amikacin_ref-2dj_high-res_2015-08-15_v500_kp_2dj_ifPSYCHE_16_d2o_25C_3ax2_01.fid 3) pure absorption, pure shift 2DJ raw data: 11_amikacin_2dj-PSYCHE-3D_ZQF-yy-raw_2016-12-04_v500_kp_2dj_ifPSYCHE_27_d2o_25C_3ax2_01.fid 4) pure absorption, pure shift 2DJ reconstructed pure shift data: 12_amikacin_2dj-PSYCHE-3D_ZQF-yy-proc_2016-12-04_v500_kp_2dj_ifPSYCHE_27_d2o_25C_3ax2_01.fid C) methanol (and 2-bromo-thiophene which is not shown in the paper) in dmso-d6 1) raw data without any of the ZQS elements ("nn"): 04_AX3_AMX_CH3OH_2Br-thiophene_PS-2DJ-3D_ZQF-nn_single-sweep-raw_2016-11-28_v500_kp_2dj_ifPSYCHE_27_dmso_25C_3ax2_01.fid 2) reconstructed pure shift data without any of the ZQS elements ("nn"): 05_AX3_AMX_CH3OH_2Br-thiophene_PS-2DJ-3D_ZQF-nn_single-sweep-proc_2016-11-28_v500_kp_2dj_ifPSYCHE_27_dmso_25C_3ax2_01.fid 3) raw data without any of the ZQS elements ("ny"): 10_AX3_AMX_CH3OH_2Br-thiophene_PS-2DJ-3D_ZQF-ny_single-sweep-raw_2016-11-29_v500_kp_2dj_ifPSYCHE_27_dmso_25C_3ax2_01.fid 4) reconstructed pure shift data without any of the ZQS elements ("ny"): 11_AX3_AMX_CH3OH_2Br-thiophene_PS-2DJ-3D_ZQF-ny_single-sweep-proc_2016-11-29_v500_kp_2dj_ifPSYCHE_27_dmso_25C_3ax2_01.fid 5) raw data without any of the ZQS elements ("yn"): 08_AX3_AMX_CH3OH_2Br-thiophene_PS-2DJ-3D_ZQF-yn_single-sweep-raw_2016-11-28_v500_kp_2dj_ifPSYCHE_27_dmso_25C_3ax2_01.fid 6) reconstructed pure shift data without any of the ZQS elements ("yn"): 09_AX3_AMX_CH3OH_2Br-thiophene_PS-2DJ-3D_ZQF-yn_single-sweep-proc_2016-11-28_v500_kp_2dj_ifPSYCHE_27_dmso_25C_3ax2_01.fid 7) raw data without any of the ZQS elements ("yy"): 02_AX3_AMX_CH3OH_2Br-thiophene_PS-2DJ-3D_ZQF-yy_single-sweep-raw_2016-11-27_v500_kp_2dj_ifPSYCHE_27_dmso_25C_3ax2_01.fid 8) reconstructed pure shift data without any of the ZQS elements ("yy"): 03_AX3_AMX_CH3OH_2Br-thiophene_PS-2DJ-3D_ZQF-yy_single-sweep-proc_2016-11-27_v500_kp_2dj_ifPSYCHE_27_dmso_25C_3ax2_01.fid ====================================================================================================

Spectral aliasing: a super zoom for 2D-NMR spectra. principles and applications

The NMR methodology based on spectral aliasing developed at the University of Geneva is reviewed. Different approaches aimed at increasing the resolution in the indirect carbon dimension of 2D heteronuclear experiments are presented with their respective advantages. Applications to HSQC, HMBC and other 2D heteronuclear experiments to the study of natural products and synthesis intermediates are shown. HSQC-based experiments for diffusion measurements, kinetics studies and titrations experiments all take advantage of spectral aliasing to reduce the experimental time from unrealistically long acquisition times to overnight experiments. The roles of computational methods such as DFT/GIAO and Logic for Structure Determination (LSD) in structure determination are discussed