Interaction of OH- with Xylan and Its Hydrated Complexes:
Structures and Molecular Dynamics Study Using Elongation
Method
Lin Jin1, Kai Liu1, Yuriko Aoki 1,2,*
1. Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 61 Kasuga-Park, Fukuoka 816-8580, Japan
2. Japan Science and Technology Agency, CREST, 4-1-8 Hon-chou, Kawaguchi, Saitama
332-0012, Japan E-mail address: aoki.yuriko.397@m.kyushu-u.ac.jp
Supplemental Information
S1. The bond length changes, dihedral changes and representative snapshots of complex
(Xylan)12-–H2O (R11 and R12 only) at 300K.
S2. The bond length changes and representative snapshots of (Xylan)6-–H2O (two the end rings)
at 700K obtained at HF/STO-3G (a) and HF/6-31G (b) levels.
Fig. S2(a) and S2(b) described 4 similar motions. The details were shown in the table below.
Motion
The formation of O3…H2’
The formation of O2’…H3’
The break of O3…H2
Proton transfer (the formation of
O3-H3 and the break of Ow-H3)
Method
HF/STO-3G
HF/6-31G
HF/STO-3G
HF/6-31G
HF/STO-3G
HF/6-31G
HF/STO-3G
HF/6-31G
Time of occurrence
2.44ps
2.00ps
2.83ps
1.58ps
5.96ps
Extremely shortly formed at 0.53ps, and
then vibrated.
Extremely shortly formed at 5.96ps
Extremely shortly formed at 1.58ps
There was a short phenomenon in the simulation using 6-31G basis set, and it was not found in the
simulation using STO-3G in 10ps. On the Fig S2(b) there were two big peaks on the trajectory of
bond length of O3-H3. At about 6.86ps, H3 broke away from O3, and O3 attracted H2’ to form a
new covalent bond. However at about 8ps, H3-O3 hydrogen bond re-formed. Generally speaking,
10ps simulation is rather limited for such a big system, and we can’t know whether this
phenomenon could be found or not in a long time simulation when using STO-3G basis set.
Considering the all of the above, we think that the simulation using STO-3G basis set could get
similar result as using 6-31G.
S3. The bond length changes and representative snapshots of (Xylan)12-–2H2O (R11 and R12
only) at 500K and 700K.
S4. The bond length changes of (Xylan)12-–3H2O at 300K, 500K and 700K.
S5: Computational method of solvent effect
The effect of solvent was calculated using Gamess package. Conductor Polarizable
Continuum Model (C-PCM) was selected, [1,2] and solvent was water. The molecular cavity was
centered on each nucleus in the solute and every atom in effective fragment potential. No
induced charge was considered. The cavition energy, dispersion free energy and repulsion free
energy calculations were ignored.
References
1. Barone V, Cossi M (1998) Quantum Calculation of Molecular Energies and Energy Gradients
in Solution by a Conductor Solvent Model J Phys Chem A 102: 1995-2001
2. Cossi M, Rega N, Scalmani G, Barone V (2003) Energies, structures, and electronic properties
of molecules in solution with the C-PCM solvation model JComput Chem 24: 669-681
S6. Coordinates of (Xylan)12 obtained at elongation-HF/STO-3G level.
C
O
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C
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C
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C
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H
C
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O
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C
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C
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C
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O
C
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C
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C
H
H
O
C
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C
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H
C
O
H
H
C
O
H
O
-0.3096406948
-0.9730603678
0.5958110085
-1.3351458038
-1.6745141093
-2.0629581727
-2.2217199303
-0.7089619195
-1.6480010003
-1.9542224370
0.1545181905
-0.2147549952
0.5421133797
-0.0732173115
-1.0964822231
0.7071053986
0.9855087022
1.6243227183
0.0450895263
-0.0888261881
0.8442573093
0.2653113398
1.2467566416
0.8408285980
-0.6706983345
0.8577888854
0.9353034961
1.3713454150
1.8492737206
-0.0252894861
0.6682177879
-1.0224625330
-0.1648584198
-0.8679659751
-1.0083055424
-1.8582610392
-0.0067794631
-0.6458796153
1.0555638993
-0.7781163209
-0.6216185968
-1.0246142760
-1.8327206598
-0.2442460605
-1.1414200370
-0.7828261320
0.7735998770
-0.1517653651
-1.1673745926
0.5381269271
0.4943686356
1.5934200301
-0.1064958412
0.1481080837
1.2092548209
0.0023734503
0.7539277898
0.4020665976
-1.0691929179
0.5362460182
0.1699092444
0.5854790638
1.6260382919
-0.0526987567
0.5816404343
-1.1482467523
0.2574889449
5.3161916419 -20.3788384699
5.3238839718 -19.1187289426
4.6825602469 -20.3544203817
4.7272071672 -21.4056732790
3.3726195645 -21.0918499736
3.4308190247 -20.1831178236
5.3743171702 -21.3961971992
4.7452429087 -22.8284691267
4.3770199422 -23.8448993531
3.4763018873 -23.5716382633
4.0661822076 -22.8303351962
6.1859374617 -23.1524957058
6.2298357038 -24.3672713622
5.8339168723 -25.0350385127
6.8380360609 -23.2099066219
6.6956018644 -22.0071003956
7.7355525706 -22.1942830004
6.0954584005 -21.9859874255
6.6674763040 -20.7299884581
5.4431567611 -17.9852343346
4.8930767105 -18.1556896138
6.9348684385 -17.6375713688
7.4871642177 -18.5125991304
7.3961116988 -19.4126771489
7.5110315433 -17.6566472461
7.0126821918 -16.2001989127
8.3922414454 -15.8240878682
8.3623142825 -14.9343292211
6.5419402213 -16.2092805638
6.2252558837 -15.1743028708
6.2809629289 -13.9318780487
6.6959856467 -15.1015972956
4.8463773559 -15.5665269734
4.7702855273 -16.8142671852
3.7087740875 -17.0335574150
5.2344609082 -16.7356636983
5.1209740909 -9.9996024552
4.9134155948 -8.7440022946
4.8184686233 -9.9665023998
4.2301181343 -11.0307648890
2.8460202057 -10.6985435789
2.7813392794 -9.7952270948
4.5331353075 -11.0023075803
4.4462412696 -12.4766711139
3.7624943862 -13.3497909564
3.9530143989 -14.2543888400
4.0350046967 -12.5336920044
5.9853437423 -12.7828858366
6.3774762312 -12.9128789104
6.7434776713 -11.6080782900
7.8194555121 -11.7951141206
6.4485173640 -11.5684901043
6.5149933806 -10.3470864430
5.3021991509 -7.6046010309
5.0822499337 -7.7710603567
6.8261347947 -7.2478926010
7.6707556762 -8.1175949715
7.4558982843 -9.0192809625
7.0703886487 -7.2668439830
7.0811769384 -5.8083066503
8.4113677515 -5.4247888176
8.5135629578 -4.5306666179
6.9506919204 -5.8153144853
6.0471526066 -4.7904254239
6.3159731175 -3.5441033713
6.1744177418 -4.7212229987
4.6983050011 -5.1884251002
C
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C
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H
C
O
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O
C
H
-0.3786097925
-0.1697832956
-1.4658019502
-0.1073785988
-1.1944204514
0.2771589255
-0.3647428347
-0.0728132078
1.3722160663
-0.1682083868
0.4037495381
0.0361799778
-1.2649960570
0.2912149899
-0.2566139769
1.3951491071
-0.2290181385
0.3160041169
1.4108661333
-0.0549439158
0.3784189848
1.4564593691
-0.2264466193
0.2322004193
-0.0350081554
-1.3214048012
0.2018836345
-0.5530803491
-0.1898703151
1.2796196869
-0.0454692463
0.4742512543
-1.1277534396
0.6622045913
0.1474092868
-0.9250501195
0.6669158752
-0.0172495008
-1.0699974004
0.8086483363
0.4845751043
0.6719689320
1.8746845365
0.4974486882
1.4333345709
1.1393062950
-0.5351439742
0.5980946019
0.1951520361
1.6368286474
-0.2958449909
0.0968641150
1.1255972310
-0.5668366562
0.6072901164
1.5977429530
-0.4029854079
-0.2833051290
-0.4376968415
-1.4151698944
-0.1247938504
-1.2002508633
-0.9261559796
0.8363686682
-0.0040852727
0.3475214420
-0.9680730367
1.0373898248
0.6968293271
-0.2565656169
4.4080621075
3.3590942580
4.5291576315
5.7719215240
5.8340734061
4.2763838497
3.3573272040
3.6509505771
4.1982870305
3.8951805639
2.6227062189
2.4293051949
3.8609241638
4.9705570431
4.5666211138
5.0069653781
6.2703833533
6.6953933317
6.7374485931
7.7078019348
5.1690512632
5.2851537466
6.5723963597
7.6137554325
7.3088444592
6.4777047981
6.9652931464
8.1170156090
8.3328147760
7.1733305212
5.7917450205
6.2295112418
5.5781900788
4.6054222196
4.1462616632
3.9292186567
3.2131401420
5.4891051276
5.2142134125
4.1822212849
3.1181148335
3.4964561699
4.4460096868
3.6688102078
2.6322550793
2.3258465131
3.2970982177
4.8233660533
4.2578553677
5.1978225300
5.9028863004
6.4869104770
6.8632136587
7.3377324375
5.0149788108
5.4595350732
6.1595657692
7.3002651816
6.9369022550
5.7319300422
6.6507014940
7.5096060811
7.8178841607
7.1807163376
5.4478290092
6.0115790709
4.9101589526
4.5417210040
3.9591224780
3.4208755217
-6.4410088055
-6.6659376371
-6.3662930217
-2.3999641042
-2.5294895703
-2.1056737682
-2.9875312880
-3.8884854910
-2.1606323660
-0.6640214797
-0.3409248039
0.5590985435
-0.6382688255
0.3773143005
1.6282459230
0.4131877980
0.0400426444
-1.2171318284
-1.1759801022
-1.3960839516
2.7742909135
2.6113114907
3.1424847043
2.2823684381
1.3774769186
3.1212829975
4.5863509998
4.9791083819
5.8758838418
4.5829114934
5.5933140039
6.8449062485
5.6583639624
5.1859550346
3.9281548995
3.9989453509
3.6958684346
7.9807380645
7.8452726248
8.2656631817
7.3729663717
6.4758158254
8.2170073316
9.7015244690
10.0185682282
10.9142450783
9.7195547036
10.7544436195
11.9978260404
10.7994208843
10.4235948640
9.1734044606
9.2224114979
8.9998646945
13.1538183952
13.0004755188
13.5279646677
12.6800290398
11.7704480889
13.4968803788
14.9784710594
15.3740107592
16.2753520645
14.9859724474
15.9738596054
17.2335547835
16.0276206480
15.5634033261
14.2974751641
14.3571314317
H
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C
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C
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H
C
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O
C
H
H
C
H
C
O
H
H
C
O
H
H
C
H
O
C
H
H
O
H
1.4803638340
0.1018882611
-0.8126426808
1.2907174450
1.3179173562
1.3831213882
2.2224809250
1.1462366061
2.3562812081
2.1671758391
0.2803993650
0.8763602934
0.6623531826
1.7465534923
-0.3073089676
-0.1078542120
0.7522659631
-1.0022922366
0.8089605097
1.6104338870
-0.5121256282
-0.7509049384
-0.7761048825
-1.3386284811
-0.4121585563
-1.7054644924
-1.5479301145
0.3339126433
0.0733237408
0.2193686339
-0.6727378179
1.3501616477
1.2191552999
2.1927686601
0.4837081680
0.2508766863
-0.4287980566
1.6892125465
2.0725203063
2.0079032830
2.3886873079
1.7285023584
3.0937192469
3.0302105369
1.1210584172
1.1083649976
1.1109361111
1.7152483450
-0.2501792892
-0.2686381286
0.3310251775
-1.3067510805
0.9590780067
1.4822400803
-0.5394622525
-1.1844699489
-1.0381164943
-1.0684280391
-0.6018261653
-1.9477912522
-2.4015091414
-0.1031126467
0.1613511250
-0.3233795980
1.5415571519
1.6325434400
1.1841806090
2.6970207748
0.1823035422
-0.7643168339
3.2343423615
5.1438727479
4.5573087618
4.1550327506
3.0516177385
3.4780719408
4.7370385044
3.5567252383
2.8597463829
2.4685552872
2.8821492888
4.6754747134
4.0016216714
5.3543496826
5.4259828280
6.1157514852
6.7930438894
6.7195143662
4.8401326718
5.5746913414
5.6063020059
6.7349177798
6.3502065176
4.8828637712
6.1463023289
6.6206855859
6.9894720253
6.9511406821
5.0327540939
5.6663394163
4.2184775287
4.5049960518
3.8562785434
3.4175722805
3.0443982860
4.7546616668
3.9097804547
4.1912008742
3.1615098302
3.5947937677
5.0388240652
3.5657343930
3.2852014895
2.8655084148
2.6514399046
4.5315144389
3.8153604758
5.4527063421
4.8694944407
5.5983094255
6.5132185897
5.8882953126
4.6487375851
5.6034456842
4.9350794133
5.8854410816
5.5366405234
3.9713770861
5.5297231755
5.6503178561
6.1584776527
6.5078335764
4.6153973670
3.6197648311
4.4970468706
3.8452455522
2.8448961514
3.7297680110
5.1843547766
5.4384614757
14.0622245377
18.3589434251
18.2111599839
18.6417661200
17.7383751328
16.8455908342
18.6038413819
20.0712377725
20.3886955902
21.2796486601
20.0779317352
21.1331282201
22.3693482923
21.1891900483
20.8019553633
19.5599676594
19.6211303936
19.3867102255
23.5334195578
23.3910576611
23.9058886037
23.0669830537
22.1534416651
23.8621736397
25.3621694883
25.7536398190
26.6601691970
25.3823077667
26.3503183554
27.6173365105
26.3902656384
25.9440939857
24.6713147374
24.4385416481
24.7186687706
28.7344045283
28.5717244557
29.0258554572
28.1162143154
27.2267693230
29.0015252200
30.4505072272
30.7790525321
31.6748689670
30.4437550291
31.5154543789
32.7450809603
31.5821757222
31.1735986403
29.9383315627
30.0136135972
29.7569922908
33.9127601462
33.7832171965
34.2716317178
33.4250158407
32.5089025842
34.2662997086
35.7078104666
36.1822770030
35.4645696141
35.6935622205
36.7200461755
36.7294592185
36.3454001095
35.0718216458
35.1013199695
34.8526877285
38.0292797851
38.1756449711
S7. Coordinates of (Xylan)12-–H2O obtained at elongation-HF/STO-3G level.
C
O
H
H
C
O
H
H
C
O
H
H
C
O
H
O
C
H
H
C
H
C
O
H
H
C
O
H
H
C
O
H
O
C
H
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C
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C
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C
O
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H
C
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O
C
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C
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C
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H
H
C
O
H
O
-2.0324094458
-2.8776478618
-2.2908494278
-1.1973669662
-1.4316371575
-0.5497178579
-0.1717744612
-2.2513163665
-0.7024211340
-0.2614006672
0.1888696665
0.1426747532
-1.6826798114
-0.9295421291
-2.5446228756
-2.1419392770
-2.8964386205
-3.2489648295
-3.7725010271
-1.7330687032
-2.6389966488
-2.1553172567
-3.2311838844
-2.8860009696
-1.2619230130
-2.6451641113
-2.7845908554
-3.1508207157
-3.6019772617
-1.6402865404
-2.2441533403
-0.6734652955
-1.4397346319
-0.8275146420
0.1337285628
-0.6352029951
-1.3247969669
-0.3527774787
-1.0968160132
-0.2166054579
-0.6560877518
-2.0827818646
-0.4459538472
-0.4737006357
-0.0043525169
0.5821054992
-1.2067583845
-0.4673195707
-2.2387443230
-1.2355337645
-1.9834107642
-2.0325121805
-3.0086088884
-1.2059392876
-2.2573521990
-1.1467879777
-2.0164024527
-1.7146674193
-0.0996671350
-1.5961061992
-1.3004517577
-1.6597825324
-2.6716054752
-0.8653768956
-1.4307607974
0.2202803267
-1.1036003406
3.6062161585 -38.5574775628
3.6028992644 -39.7133599376
3.9594396221 -40.4273800896
2.9025318335 -38.6738987074
5.0162289941 -38.2821314866
5.3243442192 -39.3674632609
6.2062988884 -39.1245622097
5.7454779301 -38.2260716996
5.0019875276 -36.9092361056
6.3351483829 -36.6318744845
6.2571170814 -35.7536807953
4.3033103306 -36.9596269831
4.4790025546 -35.8052817236
4.4358948017 -34.5973465669
5.1657296701 -35.7193606983
3.1500117754 -36.1186445677
3.1567628155 -37.3437533215
2.1345483899 -37.5017328096
3.8106814892 -37.2605600549
4.3767669100 -33.4008282374
4.9854764133 -33.5060011898
2.9121301802 -33.0163571617
2.4210734914 -33.8134333227
2.4806684882 -34.7410908577
2.2769568000 -33.0985037183
2.8781961799 -31.5392377973
1.5079992497 -31.1470542520
1.5696463316 -30.2279905598
3.4127543867 -31.4800856275
3.6095636152 -30.5865645890
3.6036327852 -29.2969313926
3.0743512236 -30.5822257784
4.9750872216 -30.9988615134
5.0009637586 -32.2957000655
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-0.4874918662 1.8009749012 15.2302721344
-0.0055266065 0.9448928178 15.3509201000
S8. Coordinates of (Xylan)12-–2H2O obtained at elongation-HF/STO-3G level.
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0.6397091464
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16.0938074318
16.8715035248
16.5259170472
S9. Coordinates of (Xylan)12-–3H2O obtained at elongation-HF/STO-3G level.
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4.2477371442 -30.5507658688
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7.2286867799 -20.6353986689
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0.9133669168
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-1.5687660101
-1.0740636805
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