MATLAB code for selective weighting (with comments) a. ... spectrum_1 = csvread('/home/darek/NMR/data.2d_4.csv'); %path to csv file containg 1D FIDs j=1 ...
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Supporting Information � Copyright Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, 2019
Monitoring Hydrogenation Reactions using Benchtop 2D NMR with Extraordinary Sensitivity and Spectral Resolution Dariusz Gołowicz, Krzysztof Kazimierczuk,* Mateusz Urbańczyk, and Tomasz Ratajczyk*© 2019 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
1. Acquisition a.) Pulse sequence
Fig. S1. DQF-COSY pulse sequence used in our interleaved TR-NUS experiment. Black bars are rectangular π/2 pulses. Phase cycle used: a: +x, +y, -x, -y; b: +x, +y, -x, -y; c: +x, +x, +x, +x; receiver: +x, -x, +x, -x. Quadrature detection in indirect dimension was obtaind using the method of States[1]. Acquisition time (t2) was set to 1.23s and relaxation delay (τd) to 0.77s minus mixing time (τm), maximum τm was 0.125s. Rounded bars are spoiling z-gradients generated using z-shim. b.) macro for interleaved acquisition of 0th increment of DQF-COSY and 2D TR-NUS DQF-COSY and required pulse sequence files are uploaded separately: - DQFcosy_States_NUS_interleaved_0incr.mac - DQFcosy_States_NUS_interleaved_0incrDefault.par - DQFcosy_States_NUS_interleaved_0incr_interface.mac - DQFcosy_States_NUS_interleaved_0incr_pp.mac The files are necessary for compilation of a pulse sequence using build-in Pulse Program Editor and Compiler in Spinsolve Expert software. In our work we were using Spinsolve Expert 1.26 (SPA-712).
2. MATLAB code for selective weighting (with comments) a.) Fitting polynomial to the enhancement profile obtained from interleaved 1D spectra. %% read and process interleaved 1D's spectrum_1 = csvread('/home/darek/NMR/data.2d_4.csv'); %path to csv file containg 1D FIDs j=1
for i=1:numel(spectrum_1(1,:))/2 %separating real and imaginary data disp(i); real_part(:,i)=spectrum_1(:,j); imag_part(:,i)=spectrum_1(:,j+1); j=j+2; end fid_F2_complex = real_part + imag_part.*1i; %creating complex FID [indir_pts,dir_pts]=size(fid_F2_complex); PHASE0=200 % 0th order phase for 1D spectrum fid_F2_complex=fid_F2_complex.*exp(-1i.*((PHASE0*(pi/180)))); %phasing 1D's zf=16; %zero filling variable A=fft(fid_F2_complex,dir_pts*zf,2); %Zero filling and Fourier Transform A=fftshift(A,2); A=A([1:2:end],[1:end]); %matrix of 1D spectra from interleaved experiment %% fitting enhancement curve reaction_peaks=real(A(:,[64610:65110])); % select region of enhanced peak/peaks (in points) for i=1:1:128 % number of acquired 1D spectra was 128 reaction_curve(i,1)=sum(-(reaction_peaks(i,:))); %remove minus sign if selected peaks are positive end %fitting x=[1:1:128]; fit=polyfit(x,reaction_curve',7); %fit polynomial to reaction progress curve (here it is 7th order polynomial)
b.) selective weighting of the 2D NUS data. PATH='/home/darek/NMR'; % read path PATH_out='/home/darek/NMR'; % save path name='DQFcosy_states_NUS_weighted'; %name of directory to create fileID=fopen([PATH,'/dataNormal.2d']); %read header header=fread(fileID,[1,8],'int','l'); fclose(fileID); scans_1 scans_2 scans_3 scans_4
= = = =
csvread([PATH,'/data.2d.csv']); %read separate scans of NUS 2D spectra csvread([PATH,'/data.2d_1.csv']); csvread([PATH,'/data.2d_2.csv']); csvread([PATH,'/data.2d_3.csv']);
scans=scans_1+scans_2+scans_3+scans_4; %add scans j=1 for i=1:numel(scans(1,:))/2 %separate real and imaginary data (direct dimension) disp(i) real_part(:,i)=scans(:,j); imag_part(:,i)=scans(:,j+1); j=j+2; end fid_F2_complex = real_part + imag_part.*1i; %create complex NUS 2D data [indir_pts,dir_pts]=size(fid_F2_complex); PHASE0=-67.2; %phasing of NUS increments in direct dimension fid_F2_complex=fid_F2_complex.*exp(-1i.*((PHASE0*(pi/180)))); spectrum=fft(fid_F2_complex,dir_pts,2); dimension (without fftshift)
%Fourier Transform of NUS 2D data in direct
x=linspace(1,128,256); %256 was number of 2D NUS points (including quadrature) y= fit(1).*x.^7+fit(2).*x.^6+fit(3).*x.^5+fit(4).*x.^4+fit(5).*x.^3+fit(6).*x.^2+fit(7).*x+fit(8); %selective weighting vector y = repmat(y,8170-8075+1,1); %make selective weighting matrix (number of columns corresponds to the size of a region for selective weighting) spectrum(:,[8075:8170])=(spectrum(:,[8075:8170])./y').*y(1); %APPLYING SELECTIVE WEIGHTING, select a region scans=ifft(spectrum,dir_pts,2); %Inverse Fourier Transform of NUS 2D data in direct dimension k=1 scans_new=ones(indir_pts,dir_pts); %separate real and imaginary points (for saving in original format) for k=[1:dir_pts] scans_new(:,2*k-1)=real(scans(:,k)); scans_new(:,2*k)=imag(scans(:,k)); end scans_new = scans_new'; scans_new = scans_new(:); scans_new = scans_new'; header_to_attach=header; header_to_attach(6)=header(6); % SAVING 2D NUS data to Magritek’s file format mkdir([PATH_out,'/',name]); %create folder structure copyfile([PATH,'/acqu.par'],[PATH_out,'/',name,'/acqu.par']) copyfile([PATH,'/proc.par'],[PATH_out,'/',name,'/proc.par']) copyfile([PATH,'/extraResults.par'],[PATH_out,'/',name,'/extraResults.par']) fileID = fopen([PATH_out,'/',name,'/data.2d.2d'],'w'); %create binary .2d.2d file with header fwrite(fileID,header_to_attach,'int','l'); fclose(fileID); fileID = fopen([PATH_out,'/',name,'/data.2d.2d'],'a'); fwrite(fileID,scans_new,'single','l'); fclose(fileID);
3. Data preprocessing Prior to the signal reconstruction in qMDD software[2], the dataset was converted to nmrPipe file format[3] using TReNDS software macro[4].
References [1] [2] [3] [4]
D. J. States, R. A. Haberkorn, D. J. Ruben, J. Magn. Reson. (1969). 1982, 48 (2), 286-292 V. Y. Orekhov, V. Jaravine, M. Mayzel, K. Kazimierczuk, mddnmr.spektrino.com, 20042018 F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer, A. Bax, J. Biomol. NMR. 1995, 6, 277-293 M. Urbańczyk, A. Shchukina, D. Gołowicz, K. Kazimierczuk, Magn. Reson. Chem. 2019, 57(1), 4-12
