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Are there any modern programs (preferably freeware) that will simulate line broadening in the presence of exchange. Somewhere I have a copy of "DNMR3" (on a 5 1/4 " floppy) and I feel it will be a nightmare trying to get this to work (particularly the graphics output).

asked Sep 18 '09 at 07:16

dstephenson's gravatar image

dstephenson
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updated Sep 20 '09 at 11:53

Evgeny%20Fadeev's gravatar image

Evgeny Fadeev
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These matlab scripts are based on Prof. Alex Bain's MEXICO program... https://docs.google.com/file/d/0B4NAn8pA4nzPQW0zTUhBeUFIYXc/edit?usp=sharing - Jana (Apr 15 '13 at 15:53)

For QM based chemical exchange simulation you can try 'Spinach' by Prof. Ilya Kuprov. http://spindynamics.org/Spinach.php - Jana (Apr 19 '13 at 21:47)


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The two programs I know are lineshapekin by Prof. Evgenii Kovrigin and MEXICO by Prof. Alex Bain.

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answered Sep 18 '09 at 10:02

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Evgeny Fadeev
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updated Sep 18 '09 at 10:02

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Thanks. The MEXICO program looks good, but it only seems to support windows NT (not XP or vista).

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answered Sep 22 '09 at 06:42

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The SpinWorks program has a graphical interface to both DNMR3 and MEXICO. Modified compiled versions of DNMR3 and MEXICO are both included with SpinWorks. It will run on everything from Windows 2000 to Windows 7, and will run on Macs under Parallels or Bootcamp.

-Kirk

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answered Dec 19 '09 at 07:40

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Kirk Marat
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Hi Dstephenson, Mexico is an excellent program for Chemical exchange simulation, likewise, Lineshapekin is very comprehensive with lots of implemented complex mechanisms for line shape analysis. For understanding purpose, here is the matlab version of 1D chemical exchange simulation based on Prof. Alex Bain's work.

The following program requires another m-script "poplig", which is included at the end

% Simulation of 1D NMR with chemical exchange using Bloch-McConnell equations for a two-state

clc; % Parameters

PI=22/7;

% Larmor frequency

W_1 = 7; % ppm

W_2 = 8; % ppm

O_1 = 5; % ppm

%Plot parameter

W_limit=1; % +/- 1ppm

W_resol=0.01;

Wupper=max(W1,W_2)+1;

Wlower=min(W1,W_2)-1;

Wpt=(Wupper-Wlower)/Wresol;

% Relaxation rate

R_1 = 0.05; % ppm

R_2 = 0.05; % ppm

% Kinetic rates

k1 = 1000; %Hz

k_1 = 100; %Hz

dimension=2;

% Scale

S_1=1;

S_2=1;

% Spectrometer field

MHz = 500; % MHz

% Titration parameters

L_T=[0 1 10 30 70 100 200 300 500 700 1000]; % mM

P_T=0.22; % mM

ligcount = size(LT);

% Calculation of free ligand

L=zeros(size(L_T));

P=zeros(size(L_T));

PL1=zeros(size(LT));

pop=zeros(size(L_T),dimension);

for i=1:lig_count(2)

x0=0.5;

Total_L=L_T(i)*0.001; 

Total_P=P_T*0.001;

% Population & Free ligand calculation function

options=optimset('MaxIter',1000,'MaxFunEvals',1000);

S=@(x)poplig(x,Total_L,Total_P,k1,k_1);

[O,fval]=fsolve(S,x0,options);

P(i)=max(O)*Total_P;

PL_1(i)=Total_P-P(i);

L(i)=Total_L-PL_1(i);

pop(i,1)=max(O);

pop(i,2)=1-max(O);

end

% Setting the Larmor, Relax and kinetic matrices

Larmor=[2PIW1*MHz*1i 0; 0 2*PI*W2MHz1i];

Relax=[PIR_1MHz 0; 0 PIR_2MHz];

Comp=zeros(dimension);

V_col=zeros(dimension);

V1row=zeros(dimension);

Pop_col=zeros(dimension);

Intensity=zeros(dimension);

r=size(L_T);

t=round(W_pt);

Spectrum_comp=zeros(t,dimension*r(2));

Spectrum=zeros(t+1,r(2));

for i=1:lig_count(2)

Kinetic=[-k1L(i) k_1; k1L(i) -k_1];

Liouville=(Larmor+Relax-Kinetic);

[V,U]=eig(Liouville);

V_1=inv(V);

% Calculating the individual components

Vcolsum=sum(V(:,1:end),1);

%for j=1:dimension

% V1row(j)=V(j,:);

%end

Pop_col=pop(i,:);

Popcol=Popcol';

for k=1:dimension

Intensity(k)=Vcolsum(k)(V_1(k,:)Pop_col);

end

% Calculation of the line shape from the intensities

for k=1:dimension

a=real(Intensity(k));

b=imag(Intensity(k));

c=real(U(k,k));

d=imag(U(k,k));

for j=1:t

    omegav = (W_lower+(j-1)*W_resol) * MHz * 2 * 22/7;  % PPM to HZ and then to angular freq
   % denom = (c * c) + ((d - omegav) * (d - omegav));

   % num = ((a * c) + b * (d - omegav));            % Juz altering the sign of abs vs dispersive compared to the derivation 

   % Spectrum_comp(j,(i-1)*dimension+k) = (num / denom);

    num=real((a+ b*1i)/(c+(d-omegav)*1i));

    Spectrum_comp(j,(i-1)*dimension+k) = num;

        Spectrum(j,i) = Spectrum(j,i) + Spectrum_comp(j,(i-1)*dimension+k);

end % components

end % dimension

end % lig_count

% Plotting the spectra

figure;

plot(Spectrum(1:Wpt,1:ligcount(2)));


poplig.m

function F=poplig(x,TotalL,TotalP,k1,k_1)

F=-k1(Total_L-Total_P+x(1)TotalP)*x(1)+k1*(1-x(1));


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answered Apr 09 '13 at 22:08

Jana%20Krishna's gravatar image

Jana Krishna
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https://docs.google.com/file/d/0B4NAn8pA4nzPQW0zTUhBeUFIYXc/edit?usp=sharing - Jana (Apr 15 '13 at 15:44)

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