SUPPORTING INFORMATION
QM/MM calculations
In this section we provide a detailed description of the methods used and justify our
confidence in the best results, reported in the main text. Table S1 displays the results.
All calculation codes m1–10 in this section refer to this table.
Choice of functional:
The mPWPW functional underestimates the energy barrier, as can be seen in m1.
Optimisation with its hybrid version, mPW1PW, gives geometries that are very close
(see table S2) and an energy difference that is very similar to the one obtained using the
mPWPW geometry (cf. m2 with m3).
Choice of basis set:
Expansion of the basis set from b1 to b2 with DFT methods does not change
considerably the energy barrier (Compare m2 with m4). It is also well known that
geometries are less sensitive to basis sets than energies. Ab initio correlated methods,
such as MP2, do need larger basis sets, and the b1 result shows a significant discrepancy
with the b2 result, justifying the use of the larger basis set for these calculations. m6
therefore is much more reliable than m5, the latter being displayed for the sake of
coherence.
Comparison of m2 and m4 shows that a larger basis set does not render the
pentacoordinated structure stable enough to become an intermediate, and thus, that the
inability to locate a phosphorane is not a limitation of the basis set. In our previous
work, we showed that a split-valence basis set with polarisation functions on oxygens
and phosphorus gave correct geometries for stable phosphoranes and transition states1.
Choice of QM region:
Expanding the QM region to include further residues will improve the result, but the
numbers do not change significantly. Compare m4 with m7, and m6 with m8.
Overall:
Our best methods are m7 and m8. We have shown that the error for each method
arising from the basis set and the QM region is around 1-2 kJ/mol. The barriers for m7
and m8 also differ by a similar amount (1.4 kJ/mol difference). The exothermicity is
slightly larger for SCS-MP2 (-29.7 vs -35.0 kJ/mol). SCS-MP2 is considered a more
reliable method but we have no benchmarks to compare with. A difference of 5.3
kJ/mol, however, should be considered small when all the approximations of the
computational setup are taken into account.
Table S1. Relative energies of reactants, TS and products in kJ mol-1.
Method[a]
Reactants
TS[b]
Products
m1
mPWPW/b1/q1
0.0
7.2
–31.1
m2
mPW1PW/b1/q1
0.0
24.2
–31.2
m3
mPW1PW/b1/q1[c]
0.0
-
–32.4
m4
mPW1PW/b2/q1
0.0
25.0
–30.6
m5[d]
SCS-MP2/b1/q1
0.0
17.3
–36.4
m6
SCS-MP2/b2/q1
0.0
26.0
–36.6
m7[e]
mPW1PW/b2/q2
0.0
25.5
–29.7
m8[e]
SCS-MP2/b2/q2
0.0
24.9
–35.0
[d]
[a] The QM method, the basis set and the QM region used for single-point calculations
at the geometries optimized with the mPWPW/b1/q1 scheme are indicated. [b] The
energy of structure 10 of the reaction path. [c] Geometry of the reactants and products
optimized with the mPW1PW/b1/q1 scheme. [d] These are results of limited value. See
text. [e] These are the most reliable results. See main text.
Table S2. Relevant distances in the optimized reactant and product structures in Angstroms.
Method [a]
d (glucose-P)
R[b]
P[c]
mPWPW/b1/q1
2.73
1.76
1.86
mPW1PW/b1/q1
2.79
1.73
1.81
d (Asp10-H [d])
R
P
d (H[d]-glucose)
R
P
2.90
1.64
1.05
1.02
1.52
2.89
1.67
1.02
1.00
1.54
d (P-Asp8)
R
P
[a] The QM method, the basis set and the QM region used is shown. [b] Reactants. [c] Products.
[d] The hydrogen atom that is transferred from Glucose to Asp10 along the reaction path.
NMR chemical Shifts
We have calculated the NMR chemical shifts with the IGLO method2,3. We used
the B3LYP functional, and the IGLOIII basis set for all atoms except for Mg, for which
it is not defined. Instead we substituted the TVZP basis set. The calculation was done
with the q2 definition of the QM/MM region. The reference was CFCl3, which was
optimized with the SVP basis set and a COSMO solvation model4,5 and the fluorine
chemical displacement was calculated with B3LYP/IGLOIII.
Figure S1. Representation of the first 14 molecules surrounding a given -PGM molecule (in green) in the crystal
under study. This first shell of proteins was generated with Pymol. For these molecules the OPLS-AA MM charges of
all atoms were included. A homogeneous background charge was added to make the system neutral. For additional
images, 6 cells in each of the (i,j,k) directions were considered. To reduce the computational cost, the dipole moment
of each chain was calculated and represented by two equivalent point charges. The unit cell contains 4 molecules and
so the total number of dipoles added was (6x2)3x4-15=6897. Because the energy changes introduced by this shell
were negligible, we did not consider any more distant crystallographic images.
Figure S2. Representation of the the calculated structures for the transition state of the phosphoryl transfer and the
MgF3- complex. Striking similarities are observed in the position of active site residues, thus supporting the efficiency
of the MgF3- ion as a transition state analogue.
Figure S3. 2Fo-Fc electron density map fitting of the MgF3- region.
Structural data
Atomic coordinates of the reactant, transition state, product and the MgF3- complex are
provided below. The Löwdin atomic charges6 for each structure are also given. Both the
geometries and the atomic charges have been calculated with m1 method.
H
C
C
O
O
H
H
H
C
C
O
O
H
H
H
H
C
N
H
H
H
H
H
H
C
C
O
O
H
H
H
C
C
O
O
H
H
C
C
H
H
O
O
O
P
O
O
O
H
H
H
Mg
O
H
H
O
H
H
x
10.848064
9.866140
9.764049
10.726871
8.840747
9.717426
9.086160
10.492049
10.827878
12.327041
12.800192
13.003004
10.601553
10.228668
12.858448
11.542916
12.153531
11.684507
12.121975
13.200960
10.670316
12.248498
11.804684
6.328456
7.314038
7.868321
7.068171
9.074442
8.036620
7.256767
3.952904
4.277055
5.357475
6.351133
5.202396
3.385154
4.673759
12.563520
11.401199
11.306923
13.767728
12.811862
10.161702
13.777629
11.449871
12.362217
10.189870
11.986154
12.250642
11.600692
10.302741
8.209541
7.280337
6.475391
7.652685
8.282670
9.183232
7.842017
REACTANT
y
29.000991
28.612320
27.099864
26.528822
26.505299
28.969629
29.057516
23.714909
22.813793
22.483707
22.494368
22.146045
22.956584
21.955731
22.287667
25.929503
26.646774
26.818883
27.629470
26.285381
27.112956
27.577056
25.919248
29.519881
29.337937
27.933247
27.025640
27.732882
30.085343
29.493555
26.539704
26.019925
24.950435
25.276251
23.806111
25.584419
26.809042
21.327745
20.498300
19.557680
19.764850
22.478444
21.227804
20.584139
24.837308
25.221838
23.971749
24.716334
21.679551
20.282271
22.190279
24.502429
22.707283
22.936538
21.809513
24.866341
24.810183
25.743498
z
11.222942
11.530228
11.532749
12.207901
10.958264
12.571340
10.889801
7.779268
8.314644
8.102439
6.930668
9.128071
9.388464
7.940933
10.757927
16.882075
16.329972
14.934380
16.838569
16.311352
14.877154
14.479066
14.310515
14.347607
14.783002
14.544503
14.106180
14.854779
14.398710
15.879718
11.019565
10.102732
10.322377
11.050440
9.788747
9.619865
9.432351
12.510593
11.939896
12.486485
13.077592
11.760160
12.105265
12.567320
11.918047
10.749641
11.596519
13.365149
13.521261
10.872171
11.864620
11.457959
11.046652
10.464859
10.774883
13.443018
13.817194
13.769977
Atomic Charge
0.107438
-0.266176
0.292574
-0.544302
-0.452730
0.181957
0.155644
0.084123
-0.292038
0.253395
-0.623735
-0.610790
0.182169
0.133864
0.401736
0.160692
-0.256373
-0.201844
0.124689
0.139229
0.310981
0.307146
0.336699
0.140195
-0.301775
0.261183
-0.631744
-0.618957
0.147818
0.154264
0.096185
-0.270201
0.276353
-0.599463
-0.589436
0.140837
0.164884
0.195715
0.006355
0.183212
0.374694
-0.616744
-0.740036
-0.573461
1.083111
-0.768628
-0.823199
-0.787504
0.150746
0.167763
0.391087
1.447406
-0.815164
0.399365
0.435937
-0.790245
0.386185
0.398913
H
C
C
O
O
H
H
H
C
C
O
O
H
H
H
H
C
N
H
H
H
H
H
H
C
C
O
O
H
H
H
C
C
O
O
H
H
C
C
H
H
O
O
O
P
O
O
O
H
H
H
Mg
O
H
H
O
H
H
TRANSITION STATE
x
y
z
10.876635 28.960715 11.228342
9.902948
28.549047 11.530244
9.843821
27.022762 11.557157
10.755944 26.453680 12.250013
8.921429
26.436383 10.933379
9.734066
28.918702 12.563515
9.120675
28.968551 10.873592
10.489080 23.670441
7.792317
10.823918 22.769778
8.329088
12.324265 22.457267
8.140527
12.811444 22.437311
6.978307
13.006705 22.156560
9.181478
10.570990 22.905457
9.397427
10.238672 21.909258
7.940329
12.739824 22.339502 10.619668
11.522918 25.892923 16.851706
12.133467 26.594931 16.280007
11.662581 26.728590 14.878818
12.099439 27.592402 16.758609
13.182002 26.236550 16.271742
10.645946 27.024479 14.816842
12.214677 27.481290 14.405361
11.786461 25.829174 14.280686
6.347707
29.515288 14.352399
7.334904
29.332321 14.784222
7.885285
27.924134 14.549961
7.087580
27.022218 14.097123
9.085266
27.718834 14.882891
8.056978
30.076183 14.391608
7.284159
29.493708 15.880545
3.967561
26.543768 11.023078
4.296426
26.023672 10.108280
5.374397
24.952762 10.337924
6.372585
25.281595 11.055467
5.207655
23.800977
9.821117
3.406509
25.589084
9.620530
4.698796
26.812734
9.440999
12.425265 21.387069 12.466388
11.306522 20.492518 11.905753
11.260391 19.555305 12.462196
13.709473 19.891146 13.039371
12.621736 22.543760 11.661993
10.031242 21.144229 12.066529
13.677661 20.717616 12.534212
11.593218 24.453222 11.895985
12.395710 25.040096 10.731209
10.202479 23.797579 11.605120
12.042831 24.520403 13.373678
12.099251 21.773746 13.458909
11.523323 20.269161 10.841414
10.118768 22.120616 11.832269
8.255154
24.521687 11.458970
7.279480
22.713950 11.104200
6.475238
22.959478 10.526473
7.624419
21.818629 10.798398
8.368657
24.876913 13.453820
9.311655
24.965229 13.700583
7.890550
25.738012 13.760248
Atomic Charge
0.095341
-0.273815
0.272907
-0.596517
-0.521700
0.172557
0.148236
0.090191
-0.287814
0.261112
-0.606690
-0.591054
0.184991
0.138128
0.421261
0.160420
-0.255616
-0.188146
0.126934
0.137822
0.314320
0.307214
0.333400
0.138801
-0.302193
0.262393
-0.633729
-0.620359
0.148223
0.152518
0.096203
-0.270717
0.273569
-0.595212
-0.593953
0.139055
0.163926
0.213273
0.011119
0.186900
0.382296
-0.622243
-0.736828
-0.559039
1.124428
-0.764027
-0.829271
-0.793612
0.168359
0.168290
0.389952
1.446640
-0.813710
0.398322
0.431200
-0.786915
0.386417
0.396444
H
C
C
O
O
H
H
H
C
C
O
O
H
H
H
H
C
N
H
H
H
H
H
H
C
C
O
O
H
H
H
C
C
O
O
H
H
C
C
H
H
O
O
O
P
O
O
O
H
H
H
Mg
O
H
H
O
H
H
x
10.834326
9.833022
9.758588
10.478993
8.964600
9.585259
9.122278
10.507949
10.864279
12.340446
12.810971
13.144118
10.641598
10.281568
12.797945
11.499318
12.113969
11.617059
12.098096
13.158025
10.599848
12.143658
11.727720
6.349769
7.334598
7.872650
7.074716
9.053359
8.064769
7.284320
3.998976
4.335333
5.408715
6.416542
5.221160
3.447392
4.744077
12.347677
11.241430
11.230795
13.675628
12.522028
9.952275
13.616734
11.729112
12.362578
10.223865
12.074063
12.035642
11.463339
10.012605
8.334501
7.288284
6.485998
7.625016
8.524113
9.429277
7.931609
PRODUCT
y
28.976883
28.596374
27.075434
26.583432
26.420348
29.040409
28.980508
23.621167
22.732358
22.452443
22.391607
22.199128
22.890406
21.854950
22.308661
25.835725
26.513807
26.620341
27.523448
26.142405
26.921377
27.368838
25.723313
29.528604
29.343340
27.923184
27.031897
27.709323
30.074325
29.520636
26.542651
26.019918
24.944456
25.274701
23.783102
25.587096
26.808082
21.368241
20.446883
19.508428
19.920277
22.497596
21.057042
20.737394
24.047712
24.889045
23.638473
24.382746
21.766248
20.220797
22.050347
24.518089
22.704414
22.965931
21.826613
24.943648
25.360070
25.706287
z
11.177716
11.420973
11.577309
12.489439
10.829896
12.407649
10.668899
7.823761
8.367577
8.099634
6.955934
9.114550
9.441629
8.015290
10.096624
16.826065
16.231224
14.838516
16.685074
16.217611
14.790822
14.338612
14.242973
14.363296
14.799358
14.593147
14.116447
14.981470
14.396549
15.893224
11.030261
10.119777
10.360780
11.058841
9.867060
9.625966
9.455303
12.448363
11.904423
12.459941
13.009860
11.577688
12.069425
12.491086
11.840630
10.708661
11.567956
13.312545
13.441953
10.838729
11.845077
11.466696
11.180179
10.606707
10.828553
13.446903
13.388882
13.769603
Atomic Charge
0.088332
-0.282525
0.254716
-0.621125
-0.564373
0.166265
0.139394
0.109566
-0.278662
0.290530
-0.508034
-0.475620
0.205041
0.154108
0.416837
0.159273
-0.255380
-0.175716
0.126662
0.133953
0.320275
0.303582
0.335124
0.134582
-0.304676
0.260488
-0.649747
-0.607752
0.145551
0.149966
0.096536
-0.271583
0.269419
-0.587943
-0.603910
0.136270
0.161613
0.220580
0.016364
0.188237
0.385095
-0.625104
-0.741346
-0.550165
1.053271
-0.819432
-0.852103
-0.811267
0.178584
0.158091
0.392494
1.445957
-0.811335
0.396905
0.424113
-0.800731
0.390609
0.390145
H
C
C
O
O
H
H
H
C
C
O
O
H
H
H
H
C
N
H
H
H
H
H
H
C
C
O
O
H
H
H
C
C
O
O
H
H
C
C
H
H
O
O
O
H
H
H
Mg
O
H
H
O
H
H
Mg
F
F
F
x
10.943436
9.996216
9.894598
10.757631
8.940918
9.888769
9.175414
10.452264
10.785735
12.288806
12.752743
12.980289
10.534071
10.188790
12.682652
11.499180
12.078055
11.627338
11.985581
13.142608
10.609490
12.196877
11.765980
6.325185
7.314231
7.881759
7.077958
9.099617
8.027122
7.262820
3.914109
4.242035
5.330970
6.319264
5.157807
3.358769
4.635282
12.367388
11.251737
11.225171
13.671505
12.511618
9.965276
13.627296
12.047739
11.493533
10.014267
8.113615
7.085217
6.333491
7.482411
8.460623
9.387571
7.908707
11.636674
12.685701
9.878609
12.056414
MgF3- complex
y
28.887840
28.444260
26.912732
26.280805
26.384707
28.770582
28.888674
23.662439
22.779165
22.448801
22.400939
22.170447
22.944744
21.909593
22.293471
25.960585
26.702316
26.786025
27.696744
26.394766
27.075129
27.500328
25.828122
29.520591
29.337926
27.935633
27.029724
27.774510
30.096198
29.479745
26.592410
26.093858
25.026032
25.370152
23.883934
25.652551
26.899479
21.323545
20.423555
19.482108
19.859813
22.494854
21.041798
20.674877
21.671814
20.206153
21.986891
24.518424
22.758700
23.028339
21.901050
24.964579
25.307538
25.769791
24.363190
25.187301
23.608364
24.542148
z
11.208894
11.551753
11.545305
12.244828
10.915574
12.608388
10.961009
7.830561
8.398637
8.200744
7.038706
9.245060
9.463117
8.045276
10.619488
16.910450
16.357044
14.950016
16.833800
16.367896
14.856752
14.441338
14.436711
14.342388
14.769265
14.499874
14.082651
14.776923
14.388174
15.868648
11.019425
10.092123
10.312007
11.035619
9.790917
9.598761
9.438902
12.459904
11.892661
12.444386
13.003561
11.681115
12.052162
12.481952
13.474812
10.830330
11.737533
11.469529
11.163738
10.518616
10.825896
13.424136
13.395525
13.764670
11.910163
10.545379
11.475450
13.790724
Atomic Charge
0.077562
-0.364443
0.021783
-0.283214
-0.262573
0.145478
0.129697
0.071860
-0.375783
-0.016132
-0.374347
-0.329181
0.157759
0.122935
0.311272
0.158451
-0.260068
-0.227111
0.119855
0.133708
0.245789
0.288255
0.328405
0.117897
-0.381241
0.000898
-0.372815
-0.312174
0.132831
0.135722
0.079885
-0.343830
0.017822
-0.331050
-0.341413
0.118206
0.150943
0.004916
-0.143316
0.142082
0.308930
-0.354652
-0.438047
-0.336012
0.087460
0.113137
0.324519
1.154920
-0.575669
0.283967
0.347095
-0.556585
0.289512
0.272524
1.316527
-0.923473
-0.943766
-0.865707
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