Cluster-model DFT simulations of the infrared spectra of ... file16-molecule cluster 352 1 5 8 12.2...
Transcript of Cluster-model DFT simulations of the infrared spectra of ... file16-molecule cluster 352 1 5 8 12.2...
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Electronic Supplementary Information:
Cluster-model DFT simulations of the infrared spectra of triazine-based
molecular crystals
Xiaohong Yuan,a Kun Luo,
ab Nan Liu,
a Xueqiang Ji,
a Chao Liu,
a Julong He,
a Guangjun Tian,
b
Yuanchun Zhao*a and Dongli Yu*
a
aState Key Laboratory of Metastable Materials Science and Technology, Yanshan University,
Qinhuangdao 066004, China.
bHebei Key Laboratory of Microstructural Material Physics, School of Science, Yanshan University,
Qinhuangdao 066004, China
*E-mail: [email protected] (Y.C.Z.); [email protected] (D.L.Y.)
Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics.This journal is © the Owner Societies 2018
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Fig. S1 Crystal structures of (a) melam reported by Lotsch and Schnick in ref. S1 (lattice parameters:
C2/c, a = 18.11 Å, b = 10.87 Å, c = 13.98 Å, and β = 96.31°) and (b) melem reported by Jürgens et al.
in ref. S2 (lattice parameters: P21/c, a = 7.40 Å, b = 8.65 Å, c = 13.38 Å, and β = 99.91°). The C, N, and
H atoms are distinguished with dark grey, blue, and light grey colors, respectively.
Note: The crystal structure and X-ray diffraction pattern of melamine can be found in our previous
work.S3
a
cb
a
cb
(a)
(b)
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10 20 30 40 50
Inte
nsity (
a.u
.)
2 (degree)
Melem(b)
Experimental
Theoretical
10 20 30 40 50
Experimental
Inte
nsity (
a.u
.)
2 (degree)
Theoretical
Melam(a)
Fig. S2 Experimental and theoretically generated XRD patterns of (a) melam, and (b) melem.
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Fig. S3 Comparison between molecular geometries before and after geometry optimization of (a) the
32-molecule cluster, and (b) the 13-molecule cluster of melamine. The bule(N)-grey(C)-white(H)
colored structures represent the models directly extracted from the crystal structure of melamine, and
the green(N)-grey(C)-white(H) colored structures are those optimized by Gaussian 16 software
package for further IR calculations.
(a)
(b)
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Fig. S4 Comparison between molecular geometries before and after geometry optimization of (a) a
single molecule, and (b) the built 16-molecule cluster of melem. The bule(N)-grey(C)-white(H) colored
structures represent the models directly extracted from the crystal structure of melem, and the
green(N)-grey(C)-white(H) colored structures are those optimized by Gaussian 16 software package
for further IR calculations.
(a) 119.6°
127.9°
121.7°121.7°119.3°120.5°
134.8°
121.7°
(b)
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Fig. S5 Comparison between molecular geometries before and after geometry optimization of (a) a
single molecule and (b) the 2-molecule cluster, (c) the 17-molecule cluster A, (d) the 16-molecule
cluster B, and (e) the finally built 25-molecule cluster of melam. The bule(N)-grey(C)-white(H) colored
structures represent the models directly extracted from the crystal structure of melam, and the
green(N)-grey(C)-white(H) colored structures are those optimized by Gaussian 16 software package
for further IR calculations.
2.09Å
2.38Å 1.97Å
1.91Å
1.97Å
A B
121.0°
128.9°
118.7°
133.3°
119.9°119.9°116.6°119.5°
120.3°120.4°
(e)
(c)
(b)
(a)
17-molecule cluster A
(d)
16-molecule cluster B
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Table S1 Details of the molecules and cluster models designed for IR calculations in this work, which
were directly extracted from the corresponding crystal structures and the geometry optimizations were
performed by the Gaussian 16 software package.
models total atom
numbers
Representative
molecules
numbers of the
surrounding
molecules hydrogen-
bonded with the
representative ones
numbers of the
formed hydrogen
bonds with the
representative
molecules
computational
costsa
melamine 32-molecule cluster 480 4 12 30 31 h
13-molecule cluster 195 1 4 8 4.5 h
melem single molecule 22 1 0 0 0.5 h
16-molecule cluster 352 1 5 8 12.2 h
melam
single molecule 26 1 0 0 0.6 h
2-molecule cluster 52 2 0
from 2 to 3 (before
and after geometry
optimization)
3 h
17-molecule cluster A 442 1 6 10 24 h
16-molecule cluster B 416 1 6 11 19 h
25-molecule cluster 650 2 10 19 65.5 h
aComputer server: Super Sever X10QBL-4, 4 x 2.10 GHz Xeon® Procssor E7-8870 v3/18 Core, 16 x 16 GB ECC DDR3/2133 MHz; the
single-molecule models (melem and melam) and the 2-molecule model of melam were calculated using 20 cores with a memory of 45 GB;
the rest of 6 cluster models were calculated using 60 cores with a memory of 230 GB.
Note: As summarized in Table S1, totally 9 models have been designed for the IR simulations in this
work. By considering the crystallographic equivalence of the corresponding crystal structures, only one
representative molecule has been determined for melamine and melem, respectively; while for melam
two crystallographically independent molecules need to be considered. We have further built specific
cluster models based on the two different molecules of melam A and B (Fig. S5), which present
different molecule numbers as well as distinct hydrogen-bonding environments. For the 2-molecule
cluster of melam, two hydrogen bonds are formed between the considered molecules, whereas after
geometry optimization an additional hydrogen bond is formed with the bridging N−H bond of melam B
(Fig. S5b). The computational costs of all the listed models have also been combined into Table S1 as a
reference.
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2600 2800 3000 3200 3400 3600
Experimental
13-molecule cluster
3442
3406
3301
3228
3141
3468
3420
3331
3188
Tra
nsm
itta
nce
(a
.u.)
Wavenumber (cm-1)
3129
H1
H4
H3
H2
H5
H6
Fig. S6 Zoomed FTIR spectra of melamine showing the characteristic NH2 stretching region. The inset
shows the representative molecule and the formed hydrogen bonds, N−H4 and N−H6 are free from
hydrogen bonding and thus show remarkably small intensities at 3406 and 3442 cm-1
in the simulated
spectra.
Table S2 Comparison between the experimental IR absorption peaks and those in the stimulated 13-
molecule-cluster spectrum of melamine related to the characteristic NH2 stretching modes. The
dominant components of each vibration mode have been highlighted, respectively.
wavenumber (cm-1) assignmentsa detailed vibrational componentsb
experimental calculated
3129 3141 νs NH1(m)+NH2(s)+NH3(w)+NH4(w)+NH5(s)+NH6(m)
3188 3228 νs NH1(w)+NH2(w)+NH3(s)+NH4(m)+NH5(w)+NH6(w)
3331 3301 νas NH1(s)+NH2(s)
3420 3406 νas NH3(m)+NH4(s)
3468 3442 νas NH5(m)+NH6(s)
aνs: symmetrical stretching vibration, νas: asymmetrical stretching vibration. bs: strong, m: medium, w: weak.
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3141 cm-1 3228 cm-1 3301 cm-1
3406 cm-1 3442 cm-1
H1
H4
H3
H2
H5
H6
Fig. S7 Calculated eigenvectors of the characteristic NH2 stretching modes of melamine at 3141, 3228,
3301, 3406 and 3442 cm-1
. The latter two modes are dominated by the stretching vibrations of N−H4
and N−H6 bonds, which are free from hydrogen bonding. The C, N and H atoms are distinguished by
dark grey, blue, and light grey colors, respectively.
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500 1000 1500 2000 2500 3000 3500 4000
Tra
nsm
itta
nce
(a
.u.)
Wavenumber (cm-1)
3325
3424
3487
3119
1612
14701
306
1097
804
16-molecule cluster
Single melem molecule
1640
1612
1555
1518
3426
3462
1167
599
694
771
1060
1480 3
128
3251 3
287493
3534
3401
1646
1581
1522
14501
266
804
1042
Experimental
Fig. S8 Detailed IR peak positions in the experimental and simulated spectra of melem based on
different models.
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Table S3 Comparison between the experimental IR absorption peaks and the calculated wavenumbers
of melem based on a single molecule and the built 16-molecule cluster and the corresponding
combinatorial vibration-mode assignments.
calculated experimental
wavenumbers (cm-1) combinatorial vibration-mode
assignmentsa
wavenumbers (cm-1) assignmentsS2 single melem
molecule 16-melem cluster
493,599,694 γ(NH) 478,597,740b
804 771 γ(CN) + γ(NH)
804 the ring-sextant out-of-plane
bending
1042 1060,1090 ρ(NH2) + ν(CN) 1097 NH stretching
1266 1167 ρ(NH2) + ν(CN1)c
1306 CNC bending
1450 1465,1480 ρ(NH2) + δ(NH2) + ν(CN) 1470 side-chain CN breathing
1521 1518 δ(NH2) + ν(CN)OR + ν(CN4,5)
1580 1555 Ring breathing + δ(NH2)
1645 1595,1612,1640 ν(CN2-7) + δ(NH2)
1612 NH2 bending
3401 3128 νs (N8H2) 3119
NH stretching 3251 νas (N8H2) + νs (N9H2) 3325
3534 3287,3426,3462 νas (NH2) 3424,3487
aνs: symmetrical stretching vibration, νas: asymmetrical stretching vibration, ν: stretching vibration, β: in-plane bending vibration, δ:
shearing vibration, ρ: in-plane rocking vibration, γ: out-of-plane bending vibration, R: mode on the ring atoms, OR: mode out of the ring. bThese three peaks are observed in the experimental spectrum in ref. S2 but absent from the spectrum in this study. cN atoms are numbered
in the top panel of Fig. S9.
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493 cm-1
599 cm-1
1518 cm-1 1555 cm-1 1612 cm-1
694 cm-1
771 cm-1
1060 cm-1 1090 cm-1
1480 cm-11167 cm-1 1465 cm-1
3128 cm-1 3251 cm-11640 cm-1 3426 cm-1 3462 cm-13287 cm-1
N7
N1
N2
N3
N4N5
N6
N8
N10 N9
Fig. S9 Calculated eigenvectors of the characteristic vibrational modes of melem based on the built 16-
molecule cluster. The C, N and H atoms are distinguished by dark grey, blue, and light grey colors,
respectively.
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500 1000 1500 2000 2500 3000 3500 4000
1687
1688
1639
1006
673
566
516
576
Tra
nsm
itta
nce
(a
.u.)
Wavenumber (cm-1)
Single molecule
2-molecule cluster
16-molecule cluster B
17-molecule cluster A
25-molecule cluster
Experimental
3493
15551
429
1491
1339
1252
1452
1516
1614
3074
3180
3321
34161103
3458
808
1589
1245
14181362
1538 1
502
3463
3394
31752955 3522
1330
915
808
1540
984
1241
1327
1498
1593 3
395
3521
1413
674
808
1454
792
1024
1260
1352
1415
1512
1582 1646
3214 3
286
3390
3474
727
3269
3479
3348
32933170
1349
15671
505
1418 1629
1680
1017
1254
787
680
562
692
789
1024
1253
1353
1511
1566 1630
1417
3259
3210
3136
3347
3474
Fig. S10 Detailed IR peak positions in the experimental and simulated spectra of melam based on
different models.
Note: The absorption bands in range of 1200−1700 cm-1
correspond to the vibrational modes of
C−N/C=N stretching and NH/NH2 shearing. As shown in Fig. S10, the peaks at 1253, 1353, 1417, and
1566 cm-1
observed in the 25-molecule-cluster spectrum are dominated by the intramolecular C−N/C=N
stretching (Table S5 and Fig. S11), and the corresponding peaks can be identified in other simulated
spectra, even the one based on a single molecule. However, the vibrational peaks at 1454, 1511, 1630,
and 1687 cm-1
in the 25-molecule-cluster spectrum are mainly related to the NH/NH2 shearing and NH
in-plane rocking, significant differences have been observed in other simulated spectra including those
based on the 17-molecule cluster with melam A and 16-molecule cluster with melam B, indicating these
vibrational modes are more sensitive to the surrounding crystallographic environments.
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Table S4 Comparison of the experimental IR absorption peaks and the calculated wavenumbers of
melam based on different models.
experimental absorption
peak
(cm-1)
calculated wavenumbers (cm-1)
25-molecule
cluster
17-molecule cluster
A
16-molecule cluster
B
2-molecule
cluster
single
molecule
562,692 566, 680 516, 576, 727,751 673 674
808 789 787 792 808 808
1103 1024,1060 1017 1024 915,1006 984
1252 1253 1254 1260 1245 1241
1339 1353 1349 1352 1330, 1362 1327
1429 1417 1418 1415 1418 1413
1452 1454 1456 1454 1442 1439
1491,1516 1511 1505 1512 1502,1538 1498,1540
1555 1566 1567 1582 1589 1593
1614 1608 1598 1601 1617
1639 1630 1629 1646 1649
1688 1687 1680
2955
3074 3136,3159 3170 3214 3175
3395
3180 3210
3321
3259 3269
3294 3293 3286
3347 3348
3416 3396,3427 3390,3426 3394,3463 3521
3458 3453,3474 3479 3454,3474 3493,3522
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Table S5 Comparison between the experimental IR absorption peaks and calculated wavenumbers of
melam based on the finally built 25-molecule cluster and the corresponding combinatorial vibration-
mode assignments.
calculated (25-molecule cluster) experimental
wavenumbers (cm-1) combinatorial vibration-mode assignmentsa wavenumbers (cm-1) assignmentS1,S4
562,692 γ(NH)
789 γ(CN) + γ(NH)
808 the characteristic sextant ring
bending
1024 (molecule B) ρ(N2H)b
1060 (molecule A)
1253 ρ(NH) + ν(CN)R 1252
C−N/C=N stretching and NH/NH2
shearing
1353 ρ(NH) + ν(CN)OR 1339
1417 δ(NH) + ν(CN)OR 1429
1454 δ(NH) + ν(CN)OR + β(CN2C) 1452
1511 δ(NH) + β(CNH) 1491,1516
1566 δ(N1H) + ρ(N3H) + ν(CN)R 1555
1608 ρ(NH)
1614
1630,1687
3136,3159,3210 νs(NH2) 3074,3180
characteristic N−H stretching
3249,3259 νas(NH2) + ν(N2H) 3321
3294 νs(NH2)
3347 ν(N2H) 3416
3396,3427 νas(NH2)
3458
3453,3474 3562 aνs: symmetrical stretching vibration, νas: asymmetrical stretching vibration, ν: stretching vibration, β: in-plane bending vibration, δ:
shearing vibration, ρ: in-plane rocking vibration, γ: out-of-plane bending vibration, R: mode on the ring atoms, OR: mode out of the ring. bN atoms are numbered in the top panel of Fig. S11.
(to be continued)
562 cm-1
692 cm-1
789 cm-1
1024 cm-1 1253 cm-1 1353 cm-1
1417 cm-1 1454 cm-1 1511 cm-1
1566 cm-1 1608 cm-1 1630 cm-1
N1 N1
N3N3
A B
N2
S16
(continued)
562 cm-1
692 cm-1
789 cm-1
1024, 1060 cm-1 1253 cm-1 1353 cm-1
1417 cm-1 1454 cm-1 1511 cm-1
1566 cm-1 1608 cm-1 1630 cm-1
N1 N1
N3N3
A B
N2
1687 cm-1 3136 cm-1 3159 cm-1
3294 cm-13210 cm-1 3259 cm-1
3347 cm-1 3396 cm-1 3474 cm-1
Fig. S11 Calculated eigenvectors of the characteristic vibrational modes of melam based on the finally
built 25-molecule cluster. The C, N and H atoms are distinguished by dark grey, blue, and light grey
colors, respectively.
S17
References
S1 B. V. Lotsch and W. Schnick, Chem. Eur. J., 2007, 13, 4956−4968.
S2 B. Jürgens, E. Irran, J. Senker, P. Kroll, H. Müller and W. Schnick, J. Am. Chem. Soc., 2003, 125,
10288−10300.
S3 X. Yuan, K. Luo, K. Zhang, J. He, Y. Zhao and D. Yu, J. Phys. Chem. A, 2016, 120, 7427−7433.
S4 E. Wirnhier, M. B. Mesch, J. Senker and W. Schnick, Chem. Eur. J., 2013, 19, 2041−2049.