Theoretical study of water-assisted hydrolytic deamination mechanism of adenine
Hongyan Zhenga, Fancui Mengb,*
a ChineseAcademy of Inspection and Quarantine, Beijing 100123, P.R. China
b Institute of Crystal Materials, ShandongUniversity, Jinan 250100, P.R. China
Supporting Information:
The cartesian coordinates of stationary points for the hydrolytic deamination reaction of adenine at B3LYP/6-311G(d,p) level.
Table S1: The energy properties of stationary points in different systems (in kcal/mol)
Figure S1 and S2: optimized geometries of reaction pathway of (A+3H2O)
wInt1 optimized at B33LYP/6-311G(d,p) level
------
7 0 3.186195 0.306187 -0.011815
6 0 3.211658 -1.071132 0.072560
7 0 2.018839 -1.606772 0.097622
6 0 1.160448 -0.525850 0.027407
6 0 -0.251539 -0.442808 0.010055
7 0 -1.030839 -1.529542 0.067985
7 0 -0.796769 0.794276 -0.065380
6 0 0.013083 1.867375 -0.129574
7 0 1.340082 1.907249 -0.124451
6 0 1.862100 0.676100 -0.042365
1 0 3.973436 0.934680 -0.047171
1 0 4.141824 -1.618179 0.111814
1 0 -0.578379 -2.427716 0.118536
1 0 -2.582337 1.151285 0.061525
1 0 -0.496386 2.824524 -0.194061
1 0 -2.053068 -1.482310 -0.004952
8 0 -3.895183 -1.404650 -0.146077
1 0 -4.208022 -1.515722 -1.049092
8 0 -3.553928 1.265832 0.206769
1 0 -3.967660 -0.438070 0.022276
1 0 -3.633578 1.560161 1.119368
------
wTS12 optimized at B33LYP/6-311G(d,p) level
------
7 0 -2.780896 0.323456 0.260809
6 0 -2.809490 -1.049588 0.135245
7 0 -1.633706 -1.557425 -0.139510
6 0 -0.797239 -0.470444 -0.194554
6 0 0.603941 -0.390208 -0.447349
7 0 1.299382 -1.362955 -1.079482
7 0 1.050739 0.920695 -0.552987
6 0 0.286797 1.998075 -0.228935
7 0 -0.984578 1.972913 0.058612
6 0 -1.483245 0.710059 0.046460
1 0 -3.552505 0.940372 0.462554
1 0 -3.722179 -1.612978 0.255309
1 0 0.963906 -2.286934 -0.840251
1 0 2.086437 0.997451 -0.529033
1 0 0.807401 2.948983 -0.240762
1 0 2.309173 -1.250939 -0.964643
8 0 1.532698 -0.788378 1.448125
1 0 1.237629 -0.173541 2.129383
8 0 3.399058 0.021904 0.133362
1 0 2.664459 -0.355775 0.893726
1 0 4.290453 0.061006 0.484523
------
wInt2 optimized at B33LYP/6-311G(d,p) level
------
7 0 2.828909 0.281443 -0.121402
6 0 2.812136 -1.092497 -0.094734
7 0 1.592053 -1.571819 -0.008056
6 0 0.783905 -0.461995 0.023512
6 0 -0.697684 -0.417619 0.133847
7 0 -1.208849 -1.138089 1.264782
7 0 -1.057387 1.002400 0.224752
6 0 -0.205855 2.056561 0.135545
7 0 1.084681 1.998078 0.000546
6 0 1.520288 0.698421 -0.039754
1 0 3.631397 0.888965 -0.172965
1 0 3.716144 -1.679613 -0.144008
1 0 -0.851016 -2.087778 1.228453
1 0 -2.051001 1.180797 0.320967
1 0 -0.684515 3.030293 0.186641
1 0 -2.224502 -1.167325 1.214006
8 0 -1.345462 -0.972222 -1.066696
1 0 -0.860837 -0.645653 -1.834829
8 0 -3.759250 0.046655 -0.208892
1 0 -3.163381 -0.457551 -0.790985
1 0 -4.627184 -0.358905 -0.277439
------
wTS01foptimized at B33LYP/6-311G(d,p) level
------
7 0 2.807644 0.410405 -0.153122
6 0 2.871335 -0.962922 -0.139751
7 0 1.683617 -1.513562 -0.043154
6 0 0.809841 -0.452496 0.005751
6 0 -0.668229 -0.504357 0.134708
7 0 -1.132674 -1.341278 1.218268
7 0 -1.094485 0.895011 0.318165
6 0 -0.314725 1.997601 0.216890
7 0 0.974115 2.019940 0.031358
6 0 1.478969 0.751308 -0.048042
1 0 3.573447 1.064229 -0.198326
1 0 3.807551 -1.495517 -0.205261
1 0 -0.379558 -1.961381 1.495456
1 0 -2.099731 1.007617 0.427680
1 0 -0.844890 2.940342 0.316582
1 0 -1.897737 -1.922349 0.893326
8 0 -1.335994 -1.016187 -1.059579
1 0 -0.916281 -0.604653 -1.824445
8 0 -3.840880 0.199936 -0.311836
1 0 -3.217936 -0.364355 -0.799254
1 0 -4.340546 -0.402355 0.247631
------
wTS12f-fInt optimized at B33LYP/6-311G(d,p) level
------
7 0 -2.803002 0.437128 -0.193342
6 0 -2.877423 -0.934190 -0.246253
7 0 -1.699066 -1.501423 -0.129064
6 0 -0.817987 -0.452762 0.005508
6 0 0.659097 -0.517903 0.196054
7 0 1.422261 -1.296349 -0.789320
7 0 1.124694 0.875593 0.132011
6 0 0.347221 1.987881 0.106475
7 0 -0.950982 2.022492 0.031000
6 0 -1.474145 0.759171 -0.035168
1 0 -3.558024 1.100768 -0.267477
1 0 -3.815319 -1.453839 -0.369378
1 0 1.259327 -2.280745 -0.596557
1 0 2.141640 0.971376 0.141087
1 0 0.894699 2.925522 0.141692
1 0 1.060925 -1.100156 -1.717657
8 0 1.044888 -1.128689 1.419968
1 0 0.419825 -0.839212 2.092743
8 0 3.882886 0.136559 -0.324741
1 0 4.236116 0.391630 -1.182660
1 0 3.260713 -0.593567 -0.522298
------
wTS12foptimized at B33LYP/6-311G(d,p) level
------
7 0 -2.811360 0.408626 -0.178928
6 0 -2.867881 -0.961974 -0.240994
7 0 -1.680282 -1.514687 -0.131294
6 0 -0.816227 -0.457655 0.011135
6 0 0.660693 -0.495643 0.213443
7 0 1.412921 -1.336734 -0.736777
7 0 1.120946 0.885778 0.082382
6 0 0.326571 1.996125 0.054800
7 0 -0.969051 2.013804 0.022136
6 0 -1.485212 0.743790 -0.024151
1 0 -3.574513 1.062706 -0.252582
1 0 -3.798784 -1.493580 -0.364932
1 0 1.332069 -2.297032 -0.414307
1 0 2.132799 0.986315 -0.022264
1 0 0.868272 2.937527 0.042461
1 0 0.975955 -1.286355 -1.653293
8 0 0.995820 -1.028861 1.498132
1 0 1.484196 -0.349719 1.973173
8 0 3.836323 0.103869 -0.373294
1 0 4.297041 0.308482 -1.192489
1 0 3.205948 -0.613784 -0.602498
------
wInt3aoptimized at B33LYP/6-311G(d,p) level
------
7 0 -2.845070 0.181899 0.017654
6 0 -2.763149 -1.189063 -0.006290
7 0 -1.518367 -1.611841 -0.010900
6 0 -0.762560 -0.467053 0.014751
6 0 0.722197 -0.351734 0.039493
7 0 1.433254 -1.121211 -1.010471
7 0 1.012265 1.073058 -0.193852
6 0 0.113928 2.094208 -0.086251
7 0 -1.172975 1.975606 0.013851
6 0 -1.553442 0.657157 0.025435
1 0 -3.676378 0.751538 0.020106
1 0 -3.640406 -1.817204 -0.020817
1 0 1.220640 -2.103320 -0.848721
1 0 2.000537 1.299476 -0.190312
1 0 0.550017 3.088457 -0.122853
1 0 1.048110 -0.878617 -1.919529
8 0 1.223116 -0.793756 1.278107
1 0 2.187313 -0.669316 1.249477
8 0 3.722229 -0.042818 0.064946
1 0 4.637180 -0.332626 0.019667
1 0 3.204630 -0.589457 -0.568245
------
wTS34aoptimized at B33LYP/6-311G(d,p) level
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7 0 2.817547 0.096246 0.017012
6 0 2.682412 -1.270236 -0.042879
7 0 1.424526 -1.643428 -0.103095
6 0 0.713672 -0.468778 -0.088075
6 0 -0.749738 -0.280478 -0.151183
7 0 -1.440442 -0.948356 1.193470
7 0 -1.004492 1.154562 0.016326
6 0 -0.060898 2.133105 0.043288
7 0 1.225719 1.955664 0.050448
6 0 1.548046 0.624672 -0.002838
1 0 3.670464 0.632211 0.053504
1 0 3.534333 -1.932476 -0.034762
1 0 -1.232968 -1.944648 1.168406
1 0 -1.993507 1.382978 -0.078411
1 0 -0.453681 3.145429 0.065591
1 0 -1.108308 -0.538159 2.062407
8 0 -1.429265 -0.843864 -1.145778
1 0 -2.499767 -0.582310 -0.876399
8 0 -3.450316 -0.127645 -0.080749
1 0 -4.351191 -0.379721 -0.291981
1 0 -2.489696 -0.743754 0.974866
------
wInt4aoptimized at B33LYP/6-311G(d,p) level
------
7 0 -3.185941 0.268957 0.028789
6 0 -3.209647 -1.110749 0.009786
7 0 -2.015084 -1.640262 -0.015111
6 0 -1.156605 -0.561966 -0.013019
6 0 0.282714 -0.515433 -0.035459
7 0 3.562957 1.325671 -0.013078
7 0 0.730763 0.825857 -0.021119
6 0 -0.075131 1.918071 0.006959
7 0 -1.379856 1.902454 0.025485
6 0 -1.866395 0.637309 0.014581
1 0 -3.970473 0.901940 0.048034
1 0 -4.138311 -1.661607 0.015700
1 0 3.964722 1.739974 -0.849051
1 0 1.765013 0.995640 -0.027359
1 0 0.440936 2.872855 0.013790
1 0 3.952472 1.822919 0.782377
8 0 1.070866 -1.454010 -0.064214
1 0 2.879050 -1.622179 -0.124893
8 0 3.849710 -1.583624 -0.012883
1 0 4.013396 -2.082659 0.792695
1 0 3.889103 0.352048 0.033636
------
wTS01goptimized at B33LYP/6-311G(d,p) level
------
7 0 2.814029 0.386288 -0.169020
6 0 2.862435 -0.986636 -0.189632
7 0 1.672978 -1.529076 -0.071340
6 0 0.810884 -0.463311 0.030960
6 0 -0.670927 -0.497047 0.203944
7 0 -1.132278 -1.218943 1.375535
7 0 -1.093320 0.909747 0.265154
6 0 -0.295624 2.008616 0.149794
7 0 0.994778 2.010698 0.020462
6 0 1.489920 0.734031 -0.031545
1 0 3.582457 1.034918 -0.235357
1 0 3.790943 -1.526829 -0.293954
1 0 -1.714557 -2.002814 1.114354
1 0 -2.104331 1.032131 0.238067
1 0 -0.824793 2.956518 0.185816
1 0 -1.603885 -0.611771 2.031120
8 0 -1.323321 -1.157975 -0.911883
1 0 -0.741186 -1.075623 -1.676664
8 0 -3.781966 0.194114 -0.513063
1 0 -3.135088 -0.425509 -0.892230
1 0 -4.380693 -0.355054 0.001764
------
wTS01g-rIntoptimized at B33LYP/6-311G(d,p) level
------
7 0 2.833345 0.279661 -0.115116
6 0 2.823579 -1.095451 -0.103102
7 0 1.609888 -1.583924 -0.017056
6 0 0.788835 -0.480747 0.030496
6 0 -0.698246 -0.446617 0.119852
7 0 -1.238912 -1.208882 1.211083
7 0 -1.047307 1.005054 0.182768
6 0 -0.196264 2.058369 0.103311
7 0 1.097375 1.989599 -0.000950
6 0 1.523491 0.687898 -0.029337
1 0 3.629972 0.894871 -0.166180
1 0 3.731333 -1.676389 -0.161573
1 0 -2.248802 -1.096747 1.239811
1 0 -2.044396 1.184158 0.239650
1 0 -0.669012 3.036060 0.142627
1 0 -0.842275 -0.889298 2.086182
8 0 -1.354949 -1.000952 -1.040597
1 0 -0.868306 -0.693034 -1.813079
8 0 -3.781205 0.051164 -0.223637
1 0 -3.191416 -0.487090 -0.779699
1 0 -4.636949 -0.385505 -0.226287
------
wInt3b optimized at B33LYP/6-311G(d,p) level
------
7 0 2.827837 0.314346 -0.129585
6 0 2.831446 -1.059718 -0.121110
7 0 1.620690 -1.558442 -0.017405
6 0 0.795772 -0.461832 0.047443
6 0 -0.690757 -0.439711 0.119395
7 0 -1.219892 -1.284967 1.163318
7 0 -1.065794 0.978078 0.226518
6 0 -0.230762 2.044925 0.113671
7 0 1.061102 2.003335 -0.003651
6 0 1.514703 0.709904 -0.025479
8 0 -1.319418 -0.899423 -1.110676
1 0 3.618903 0.935075 -0.196704
1 0 3.743070 -1.632664 -0.193009
1 0 -1.151615 -1.851325 -1.130753
1 0 -2.219672 -1.133158 1.269260
1 0 -0.751834 -1.109876 2.044558
1 0 -2.068442 1.139663 0.249571
1 0 -0.723386 3.012485 0.153507
8 0 -3.756442 0.018265 -0.168740
1 0 -3.150686 -0.412133 -0.799382
1 0 -4.579472 0.173346 -0.639609
------
wTS34b optimized at B33LYP/6-311G(d,p) level
------
7 0 2.785567 0.466159 -0.233828
6 0 2.853688 -0.894749 -0.409344
7 0 1.674615 -1.467724 -0.323710
6 0 0.800428 -0.433777 -0.093072
6 0 -0.663229 -0.497760 0.114463
7 0 -1.014523 -1.444162 1.404484
7 0 -1.125181 0.864450 0.339536
6 0 -0.343216 1.983529 0.339812
7 0 0.945580 2.022766 0.198162
6 0 1.461886 0.772657 -0.020509
8 0 -1.459149 -1.230285 -0.715427
1 0 3.540200 1.133312 -0.271872
1 0 3.787625 -1.404251 -0.590353
1 0 -1.616715 -1.876290 0.431093
1 0 -1.491076 -0.973478 2.170079
1 0 -0.210083 -1.968374 1.741514
1 0 -2.132745 0.978923 0.196291
1 0 -0.887546 2.915127 0.465817
8 0 -3.727244 0.263019 -0.663271
1 0 -3.041391 -0.404992 -0.894513
1 0 -3.976875 0.668323 -1.499087
------
wInt4b optimized at B33LYP/6-311G(d,p) level
------
7 0 2.659966 -0.899502 0.009745
6 0 2.780959 0.472989 -0.008727
7 0 1.624627 1.083159 -0.019377
6 0 0.692076 0.068967 -0.008917
6 0 -0.745922 0.116045 -0.019508
7 0 0.023282 4.047044 -0.052697
7 0 -1.276325 -1.199197 0.001354
6 0 -0.549615 -2.347858 0.017966
7 0 0.751752 -2.407973 0.023590
6 0 1.318870 -1.176755 0.009901
8 0 -1.497154 1.085522 -0.046224
1 0 3.399464 -1.585322 0.017506
1 0 3.744477 0.959627 -0.013954
1 0 -0.780547 3.436256 -0.181116
1 0 -0.019724 4.351712 0.916996
1 0 0.816053 3.410316 -0.104623
1 0 -2.304336 -1.233565 -0.000845
1 0 -1.124007 -3.268017 0.026435
8 0 -3.931965 -0.283926 -0.070893
1 0 -3.333694 0.483712 -0.146984
1 0 -4.426051 -0.132533 0.740921
------
Table S1 The energy properties of stationary points in different systems (in kcal/mol)
System / A+2H2O / (A+3H2O)-1 / (A+3H2O)-2Int1 / -27.31a / -21.73b / -34.63 / -27.15 / -40.21 / -32.25
TS12 / 16.88 / 20.68 / 2.90 / 9.32 / 2.95 / 9.40
Int2 / 2.15 / 8.47 / -13.81 / -4.45 / -10.79 / -2.02
Int3a / -1.12 / 6.05 / -17.01 / -6.80 / -14.70 / -4.95
TS34a / 19.16 / 23.40 / -0.23 / 7.62 / 5.54 / 12.36
Int4a / -27.89 / -22.39 / -33.13 / -25.47 / -40.87 / -32.95
Int3b / 1.50 / 8.09 / -10.10 / -1.17 / -12.05 / -2.94
TS34b / 33.94 / 37.17 / 18.40 / 24.76 / 20.52 / 26.26
Int4b / -19.99 / -15.18 / -33.13 / -25.47 / -42.08 / -33.96
a Relative energies at B3LYP/6-311G(d,p) level
b ZPVE-corrected relative energies at B3LYP/6-311G(d,p) level
Figure S1: optimized geometries of reaction pathway of (A+3H2O)-1
Figure S2: optimized geometries of reaction pathway of (A+3H2O)-2
1