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=EulerAngles("rep100")
scan_par1d i/4:5/
alpha_CR=rep100(1,i)
beta_CR=rep100(2,i)
ID="cry"&str(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