Proton-Driven Spin Diffusion (PDSD/RAD/DARR)

****** The System ***********************************
spectrometer(MHz)  500
spinning_freq(kHz) 10.0
channels           C13 H1
nuclei             *
atomic_coords      {mol}.cor
cs_isotropic       {mol}.cs
csa_parameters     {mol}.csa ppm
j_coupling         *
quadrupole         *
dip_switchboard    *
csa_switchboard    *
exchange_nuclei    {mol}-exch.dat
bond_len_nuclei    {mol}-bond.dat
bond_ang_nuclei    *
tors_ang_nuclei    *
groups_nuclei      {mol}-groups.dat
******* Pulse Sequence ******************************
CHN 1
timing(usec)     (100)x64
power(kHz)        0
phase(deg)        0
freq_offs(kHz)    0
CHN 2
timing(usec)     100
power(kHz)       10
phase(deg)        0
freq_offs(kHz)    0
**************************VARIABLES***************************************
* {i}, {j}, {m}, {n}, and {M} macros must be specified at the command line
* {i} and {j} are the two C13 spins (in the extended molecule)
* {m} is the number of protons to use in the spin system
* {M} is the number of protons in the extended molecule (ggv.cor file)
* {n} is the number of the non-proton nuclei in the extended molecule
**************************************************************************
N=2+{m}   // the total number of spins in the spin system

* Each ({i},{j}) 13C pair has its own nearest environment of protons
* In the files c{i}c{j}h{M}.s2e all protons in the extended molecule are
* sorted according to their closeness to the ({i},{j}) pair of carbons.
* The line below selects N nearest protons from the extended molecule
sys2ext_map=((load("{mol}-s2e/c{i}c{j}h{M}.s2e"))')(["1:N"],1)

**** Molecular orientation ****

** Use orientations from the rep100 set
rep100=load("rep100.dat")
scan_par1d i/4:5/
alpha_CR=rep100(i,1)
beta_CR=rep100(i,2)
ID="cry"&num2str(i)

** Alternatively: rotate the molecule to put the C-C axis at an angle
** theta with the rotor axis
*group_23_R=load("{mol}-c{i}c{j}-euler.dat")
*theta=360-45
*group_24_R=["0; theta; 0"]
*ID="rot"&num2str(360-theta)

********************************

** Specify local CSA axes, 1H chem. shifts, and directly bonded CH dist.
load_vars {mol}.par

** Calculate the distance between spins 1 and 2 ({i} and {j})
r12vec=XYZ_ext(:,sys2ext_map(1))-XYZ_ext(:,sys2ext_map(2))
r12=sqrt(r12vec'*r12vec)

** Vibrational averaging correction for directly bonded carbons 
ccsc0=(r12<2)?(1.525/1.550)^3:1

power_2_1_1=10

** File naming prefix
name="{mol}-c{i}c{j}h{m}-"&ID

*** Direct-method-specific settings ***

** Scale CC coupling and set gsize_1
dip_swb_1_1_2=ccsc0
gsize_1=(r12<2)?16:64

** Compute the spin diffusion constant
dw=1/spinning_freq
x=2*data_re
w=-(x>0.0005? ln(1-x) : -x)/(2*dw*gsize_1)

*** OUTPUT ***

disp("ID "&ID)
disp(w)

*save(w,name&"-w.dat")

******* Options etc *************************************
rho0               I1z
observables        I2z
EulerAngles        *
n_gamma   	   *
line_broaden(Hz)   *
zerofill           *
FFT_dimensions     *
options            -dt2 -o0 -v0 -vclk -sysc2h{m} -xsysc{n}h{M}

*** Macros {mol}, {i}, {j}, {n}, {m}, and {M} must be supplied at the command line, for example:

spinev pdsd -macro'{i}'=1 -macro'{j}'=2 -macro'{mol}'=ggv -macro'{n}'=16 -macro'{m}'=9 -macro'{M}'=82
ggv-bond.dat
****************************************************************
** Directly bonded CH pairs in G1 and G2 of GGV
** The indices of the nuclei are defined by the ggv.cor file
****************************************************************
1 (3 35)
2 (3 39)
3 (4 26)
4 (4 28)
ggv-exch.dat
****************************************************************
** Goups in fast exchange in GGV (CH3, NH3, and water molecules)
** The indices of the nuclei are defined by the ggv.cor file
****************************************************************
1  (18 22 23)  -NH3
2  (19 21 24)  G1-NH3
3  (54 57 61)  CH3
4  (55 59 62)
5  (66 70 76)
6  (52 56 64)
7  (69 74 78)
8  (79 84)
9  (80 85)
10 (81 87)
11 (82 88)
12 (83 89)
13 (91 95)
14 (90 96)
15 (93 97)
16 (94 98)
ggv-groups.dat
****************************************************************
** Goups defining local axes of the 13C and 1H CSA tensors in GGV
** The indices of the nuclei are defined by the ggv.cor file
****************************************************************
1  (6 1 15)   V-CO   CA-CO-Oa
2  (13 2 11)  G1-CO  O-CO-N
3  (5 3 11)   G2-CA  CO-CA-N
4  (2 4 10)   G1-CA  CO-CA-N
5  (14 5 12)  G2-CO  O-CO-N
6  (1 6 12)   V-CA   CO-CA-N 
7  (6 7 49)   V-CB   CA-CB-H
8  (7 8 52)   V-CGa  CB-CGa-H
9  (7 9 69)   V-CGb  CB-CGb-H
10 (10 4 2)   G1-NH3 
11 (10 4 2)   G1-NH3 
12 (26 4 28)  G1-CH2 
13 (26 4 28)  CH2  arbitrary
14 (28 4 26)  G1-CH2 
15 (31 11 3)  G2-NH  
16 (35 3 39)  G2-CH2 
17 (39 3 35)  G2-CH2 
18 (42 12 6)  V-NH  
19 (46 6 7)   V-CAH 
20 (46 6 7)   CH   arbitrary
21 (49 7 6)   V-CBH 
22 (9 7 8)    V-bCH3 
23 (1:98)     The whole molecule
24 (1:98)     The whole molecule
c1c2h82.s2e (should be placed into subdirectory named ggv-s2e)
1 2 31 46 28 26 27 42 98 93 74 39 24 49 21 89 81 97 23 35 43 32 19 69 29 18 22 25 20 65 64 50 78 40 94 83 87 84 56 79 90 66 76 54 96 52 45 86 53 36 80 95 57 38 88 48 77 71 72 91 17 82 37 33 58 85 60 73 92 61 70 75 68 44 62 34 51 59 63 47 67 55 30 41
ggv-c1c2-euler.dat
** P2C_Euler_angles of the C-C dipolar tensor as shown by the -s option
0
66.42
39.96
ggv.par
*** local CSA axes
csa_group_[1:9]=[1:9]                                       // carbons
csa_group_[21 24 26 27 28 31 35 39 42 46 48 49 74]=[10:22]  // protons

*** proton isotropic shifts at 500 MHz ***
***     G1  G1  G1  ??  G1  G2  G2  G2   V   V  ??   V   V
***    NH3 NH3 CH2 CH2 CH2  NH CH2 CH2  NH CAH CBH CBH CH3    W    W    W
cs_iso_[21  24  26  27  28  31  35  39  42  46  48  49  74   81   93   98]= -1.2+([ -1  -1 1.2 1.2 1.2   0 1.2 1.2   0 0.8 0.8 0.8 1.3 -0.7 -0.7 -0.7])

*** set directly bonded CH distances
rCH2=1.12
r_[1:4]=rCH2
ggv.cs
-8.53  C1 (V-CO)
-7.44  C2 (G1-CO)
 8.54  C3 (G2-CA)
 8.86  C4 (G1-CA)
-7.44  C5 (G2-CO)
 5.89  C6 (V-CA)
 10.48 C7 (V-CB)
 11.27 C8 (V-CGa)
 11.52 C9 (V-CGb)
ggv.csa
****************************************************************
** The indices of the nuclei are defined by the ggv.cor file
****************************************************************
1 -75 0.66   0  0  0  V-CO   CA-CO-Oa  242 192 104  (EV in Gu JACS 94)
2 -76 0.83  98  0  0  G1-CO  O-CO-N    240 177  94  (AGG in Wei JACS 01)
3  26 0.77  35  0  0  G2-CA  CO-CA-N    71  42  22  (Chekmenev JACS 02)
4 -17 0.29   0 90 35  G1-CA  CO-CA-N    51  46  23  (GA in Wei JACS 01)
5 -76 0.83  98  0  0  G2-CO  O-CO-N    240 177  94  (AGG in Wei JACS 01)
6 -11 0.94   0 90 35  V-CA   CO-CA-N    72  62  51  (V in Ye MagResChem 93)
7  11 0.88   0  0  0  V-CB   CA-CB-H    43  31  21  (V in Ye MagResChem 93)
8 -15 0.00   0 90  0  V-CGa  CB-CGa-H   30  30   7  (V in Ye MagResChem 93)
9 -15 0.00   0 90  0  V-CGb  CB-CGb-H   30  30   7  (V in Ye MagResChem 93)

** Notes:
** G1-CO and G2-CO have the same isotropic shift as G2-CO in AGG
** CA's CSA orient. are from a.a. Gly: (35,0,0) if >0; (0,90,35) if <0
** carbonyl CSA orientation: 8 degrees away from CO (Oas JACS 87)
** carboxyl CSA orientation: standard (Haberkorn JACS 81)

** Protons
21 -3 0.0  0 90 0  G1-NH3 (10 4 2)
24 -3 0.0  0 90 0  G1-NH3 (10 4 2)
26 -5 0.5  0 90 0  G1-CH2 (26 4 28)
27 -5 0.5  0 90 0  CH2    (26 4 28) arbitrary
28 -5 0.5  0 90 0  G1-CH2 (28 4 26)
31 -8 0.0  0 90 0  G2-NH  (31 11 3)
35 -5 0.5  0 90 0  G2-CH2 (35 3 39)
39 -5 0.5  0 90 0  G2-CH2 (39 3 35)
42 -8 0.0  0 90 0  V-NH   (42 12 6)
46 -5 0.5  0 90 0  V-CAH  (46 6 7)
48 -5 0.5  0 90 0  CH     (46 6 7) arbitrary
49 -5 0.5  0 90 0  V-CBH  (49 7 6)
74 -2 0.0  0 90 0  V-bCH3 (9 7 8)
81 -15  0  0 90 0  W
93 -15  0  0 90 0  W
98 -15  0  0 90 0  W
ggv.cor
*** GGV molecule with its nearest protons ****
-14.779  17.388 -16.773 C ID1  V-CO
-11.332  14.500 -18.736 C ID2  G1-CO
-12.277  13.612 -16.706 C ID3  G2-CA
-10.079  14.960 -19.452 C ID4  G1-CA
-13.279  14.658 -16.237 C ID5  G2-CO
-13.815  16.947 -15.652 C ID6  V-CA
-13.056  18.152 -15.071 C ID7  V-CB
-12.127  17.722 -13.932 C ID8  V-CGa
-14.058  19.194 -14.572 C ID9  V-CGb
-10.442  15.845 -20.581 N ID10 G1-N
-11.161  14.140 -17.461 N ID11 G2-N
-12.881  15.932 -16.140 N ID12 V-N
-12.426  14.434 -19.317 O ID13 G1-O
-14.421  14.288 -15.921 O ID14 G2-O
-16.009  17.368 -16.520 O ID15 V-Oa
-14.279  17.743 -17.880 O ID16 V-Ob
-7.618  12.188 -20.667 H ID17
-13.362  12.188 -20.317 H ID18 1-NH3
-9.617  16.155 -21.079 H ID19  G1-NH3a
-15.361  16.155 -20.729 H ID20
-10.990  15.338 -21.263 H ID21 G1-NH3b
-11.989  11.371 -20.133 H ID22 1-NH3
-12.070  12.688 -21.202 H ID23 1-NH3
-10.909  16.655 -20.194 H ID24 G1-NH3c
-16.654  16.655 -19.844 H ID25
-9.393  15.481 -18.767 H ID26  G1-CH2a
-15.137  15.481 -18.417 H ID27 CH2
-9.485  14.100 -19.786 H ID28  G1-CH2b
-15.229  14.100 -19.436 H ID29
-12.719  18.147 -10.125 H ID30
-10.260  14.180 -17.005 H ID31 G2-NH
-16.005  14.180 -16.655 H ID32
-16.005  22.115 -16.655 H ID33
-11.082  17.092 -11.336 H ID34
-11.897  13.124 -15.794 H ID35 G2-CH2a
-11.897  21.059 -15.794 H ID36
-17.642  21.059 -15.444 H ID37
-7.106  12.902 -17.668 H ID38
-12.851  12.902 -17.318 H ID39 G2-CH2b
-12.851  20.837 -17.318 H ID40
-11.064  20.091 -10.752 H ID41
-11.915  16.124 -16.378 H ID42 V-NH
-17.659  16.124 -16.028 H ID43
-14.270  20.448 -11.908 H ID44
-8.709  16.481 -15.223 H ID45
-14.454  16.481 -14.872 H ID46 V-CAH
-10.507  14.624 -11.223 H ID47
-12.472  10.657 -15.908 H ID48 other_V-CBH
-12.472  18.591 -15.908 H ID49 V-CBH
-18.217  18.591 -15.557 H ID50
-11.576  10.633 -13.531 H ID51
-11.576  18.568 -13.531 H ID52 V-CGaH3a
-17.320  18.568 -13.181 H ID53
-11.403  14.600 -13.599 H ID54 2-CH3
-11.403  22.535 -13.599 H ID55 3-CH3
-12.673  17.258 -13.114 H ID56 V-CGaH3b
-10.306  13.291 -14.017 H ID57 2-CH3
-16.051  13.291 -13.667 H ID58
-10.306  21.226 -14.017 H ID59 3-CH3
-16.051  21.226 -13.667 H ID60
-11.593  13.037 -12.843 H ID61 2-CH3
-11.593  20.972 -12.843 H ID62 3-CH3
-17.338  20.972 -12.493 H ID63
-11.386  17.004 -14.288 H ID64 V-CGaH3c
-17.131  17.004 -13.937 H ID65
-14.040  14.838 -13.013 H ID66 4-CH3
-14.040  22.773 -13.013 H ID67
-8.939  18.806 -14.117 H ID68
-14.684  18.806 -13.767 H ID69 V-CGbH3a
-13.994  15.521 -11.404 H ID70 4-CH3
-8.985  11.553 -15.726 H ID71
-14.730  11.553 -15.376 H ID72
-8.985  19.488 -15.726 H ID73
-14.730  19.488 -15.376 H ID74 V-CGbH3b
-9.416  16.148 -12.866 H ID75
-15.160  16.148 -12.515 H ID76 4-CH3
-13.563  12.180 -14.265 H ID77
-13.563  20.115 -14.265 H ID78 V-CGbH3c
-9.778  11.323 -20.667 H ID79 W1b
-7.457  15.291 -21.079 H ID80 W2b
-13.201  15.291 -20.729 H ID81 W3b
-9.778  19.258 -20.667 H ID82 W4b
-15.522  19.258 -20.317 H ID83 W5b
-9.203  11.196 -19.231 H ID84 W1a
-8.031  15.164 -22.515 H ID85 W2a
-14.948  11.196 -18.881 H ID86
-13.776  15.164 -22.165 H ID87 W3a
-9.203  19.131 -19.231 H ID88 W4a
-14.948  19.131 -18.881 H ID89 W5a
-10.295  13.735 -22.806 H ID90 W7b
-12.684   9.768 -18.589 H ID91 W6b
-6.940  17.703 -18.940 H ID92
-12.684  17.703 -18.589 H ID93 W8b
-18.429  17.703 -18.239 H ID94 W9b
-11.174   9.871 -18.259 H ID95 W6a
-11.805  13.838 -23.137 H ID96 W7a
-11.174  17.806 -18.259 H ID97 W8a
-16.918  17.806 -17.909 H ID98 W9a
rep100.dat file is not given here, as it can be generated by placing the statement
save(euler_CR',"rep100.dat")
into the Variables section of any main input file that specifies rep100 for powder averaging (at the EulerAngles line)