NMR SOS-filter Web page

Welcome to the Singlet-Order-Selection (SOS)-filter home page.

The SOS-filter is a simple sequence of two shaped pulses designed to populate and to store singlet spin order in coupled spin systems. The SOS-filter can be introduced as a block of an arbitrary NMR pulse sequence when one needs to detect only the spins that have passed through a long-lived singlet state. The SOS-filter consist of two APSOC (Adiabatic Passage Singlet Order Conversion) steps with (optional) spin-locking step introduced for singlet-state maintenance.

A detailed description is available in our recent papers:

APSOC: DOI: 10.1016/j.jmr.2016.10.003

SOS-filter: DOI: 10.1021/acs.jpcb.6b08879

Pulse programs for Bruker NMR spectrometers (operating with TOPSPIN 3 and higher) are available by links below:

Simple SOS-filter		SOS
SOS-filter with presaturation		SOSpr
SOS-filter with CW spin-locking		slSOS
Determination of TS		slSOSvd
Determination of T1 with SOS-filtering		t1irSOS
Determination of T2 with SOS-filtering (CPMG-SOS)		cpmgSOS
Determination of T2 with SOS-filtering (PROJECT-SOS)		projectSOS

Switching (on and off) of an RF-field is done by shaped pulses sp1, sp2, sp3 and sp4. Before starting the pulse programs one needs to introduce two shaped pulses: Ramp from 0% to 100% (line_up) and Ramp from 100% to 0% (line_down). To create a new shaped pulse one should use stdisp command in the TOPSPIN command line. Choose Basic shapes and then Ramp. Create two shaped pulses with names, for example, line_up and line_down. It is also possible to export a shaped pulse from the APSOC program, see below. Each shaped pulse (e.g. sp1) has its own parameters: SPOFFS1 is the frequency offset from the main frequency SFO2 in Hz, SPdB1 or SPW1 is the maximal amplitude of the RF-field, SPOAL1 is the phase alignment, and p11 is duration of shaped pulses in microseconds.

To find optimal parameters (p11, SPW1, SPOFFS1) for the desired two-spin 1/2 system we recommend to use executable program APSOC written in Matlab or script file (.m) with GUI interface (.fig).

Executable file	URL link to Matlab Compiler Runtime (MCR)
APSOC_win64	MCR for windows 64 bit
APSOC_linux64	MCR for linux 64 bit

Running executable file APSOC on Windows 64bit systems:

- Install MCR Matlab

- Extract file APSOC.exe from the archive APSOC_win64.zip

- Run the application

Running executable file APSOC on linux 64bit systems:

To run APSOC program in linux system:

- Install MCR Matlab to the directory /home/<user>/MATLAB/MCR/ (please follow instructions from Mathworks)

- Copy files from zip-archive APSOC_linux64.zip to your home directory /home/<user>/APSOC/

- Run program with MCR environment by following command in terminal:

/home/<user>/APSOC/run_APSOC.sh      /home/<user>/MATLAB/MCR/v81/

Running matlab-script file APSOC in Matlab environment:

- Download .m file and .fig file      APSOC.m     APSOC.fig

- Copy both files to the one working directory

- Run APSOC.m file from the Matlab program

Description of  the APSOC program

The main window of our APSOC program is shown below. It contains several fields and buttons.

1.       Define your spin system by filling chemical shift difference (Chem.sh.diff./Hz) and scalar coupling constant (J/Hz) in Hz. It is possible to type individual chemical shifts: the program will calculate the differenece and mean value of them.

2.       Define number of points in the profile (Num. steps). This parameter influences the calculation time. 500-1000 points is usually sufficient.

3.      Choose the linear profile from the list (RF-profile). Linear ramp is the simplest option to make adiabatic switching. Later on, you can try other profiles. Mathematical expressions are written in the Help tab.

4.       Type in the starting parameters in the (RF-parameters), for example, Bmax=1000 Hz, Vrf-V0=10 Hz, Tfs=0.2 s.

5.       Press button (GO) to see the result of Singlet Order Conversion ratio. The goal is to find the parameters that provide maximal (almost 100%) value of singlet order conversion.

6.       Press button (BBEST). Program will find the Bmax for local maximum of Singlet Order Conversion at current Tfs and Vrf-V0.

7.       If you want to see how Singlet Order Conversion depends on Bmax, Vrf or Tfs, fill in the corresponding fields and press button Bmax vary, Vrf vary, or Tfs vary. It helps to understand how far you are from the opimal conditions.

8.       3D plots show you how the Singlet Order Conversion dependends on two parameters.

Once you found the optimal parameters

- Export shaped pulses from the Menu tab or by button "Export shape"  to the folder <TOPSPIN>/exp/stan/nmr/list/wave/user/ 

- Use AU program SOS_au to set optimal parameters into current dataset

Overview of TOPSPIN parameters used in pulse programs (SOS, SOSpr, slSOS, slSOSvd, t1irSOS, cpmgSOS, projectSOS):

O2 - center of the chemical shifts of the spin system under study (mean value from APSOC program or defined manually from a 1D NMR spectrum. Be sure that the SR parameter is set to 0)

SPNAM1=line_up, SPNAM2=line_down, SPNAM3=line_up, SPNAM4=line_down - names of the shaped pulses

SPOFFS1=Vrf-V0, SPOFFS2=Vrf-V0, SPOFFS3=-(Vrf-V0), SPOFFS4=-(Vrf-V0) - offsets for the shaped pulses in Hz

SPOAL1=1, SPOAL2=0, SPOAL3=1, SPOAL4=0 - phase allignments for the shaped pulses

p11 - duration of sp1, sp2, sp3 and sp4 (Tsw), try to use as short as possible, because of realaxtion

SPW1, SPW2, SPW3, SPW4 - power values of shaped pulses (Bmax in Watt)

PLW2 or PLdB2 - amplitude of a CW spin-locking field

d2 - duration of a CW spin-locking

d20 - echo time delay

                                                                                                                                   last update 30.01.2019