Supplementary Material
Mimicking trimeric interactions in the aromatic side chains of the
proteins: A gas phase study of indole...(pyrrole)2 heterotrimer
Sumit Kumar and Aloke Das*
Department of Chemistry
Indian Institute of Science Education and Research (IISER)
900 NCL Innovation Park, Dr. Homi Bhabha Road
Pune-411008, Maharashtra, India
Email: a.das@iiserpune.ac.in, aloke.das73@gmail.com
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Contents
1. One-color R2PI (1C-R2PI) spectra recorded at (a) indole...(pyrrole)2 trimer mass channel (b)
indole...pyrrole dimer mass channel. Two-color R2PI (2C-R2PI) spectra recorded at (c)
indole...(pyrrole)2 trimer mass channel (d) indole...pyrrole dimer mass channel.
2. RIDIR spectra in the N-H stretching region by probing (a) 0 00 (b) 0 00 + 23 cm-1 and (b) 0 00 + 40
cm-1 (c) 0 00 + 51 cm-1, and (d) 0 00 + 85 cm-1 bands of indole…(pyrrole)2 trimer.
3. Structures of (phenol)3, (CH3OH)3, and (H2O)3 optimized at the M05-2X/cc-pVTZ level of
theory.
4. A few selected geometrical parameters of (phenol)3, (CH3OH)3, and (H2O)3 calculated at the
M05-2X/cc-pVTZ level of theory.
5. Theoretical frequencies, their assignments as well as IR and Raman intensity (km/mol) of the NH stretching modes of (pyrrole)3 and IP2-1, IP2-2 structures of the indole...(pyrrole)2 trimer
calculated at various level of DFT.
6. Natural bond orbitals of the cyclic structure of pyrrole trimer showing multiple N-H…π
hydrogen bonding interactions calculated at the M05-2X/cc-pVTZ level of theory.
7. Completed reference 53.
2
-1
(35104 cm )
(a)
0
00
23
40
28 36
64
51
85
(b)
(c)
(d)
35080
35120
35160
35200
-1
Wavenumber (cm )
Figure S1: One-color R2PI (1C-R2PI) spectra recorded at (a) indole...(pyrrole)2
trimer mass channel (b) indole...pyrrole dimer mass channel. Two-color R2PI (2CR2PI) spectra recorded at (c) indole...(pyrrole)2 trimer mass channel (d)
indole...pyrrole dimer mass channel.
3
(a)
3376
3408
3389
(b)
(c)
(d)
(e)
3340 3360 3380 3400 3420 3440
-1
Wavenumber (cm )
Figure S2. RIDIR spectra in the N-H stretching region by probing (a) 0 00 , (b) 0 00 +
23 cm-1, (c) 0 00 + 40 cm-1, (d) 0 00 + 51 cm-1, and (e) 0 00 + 85 cm-1 bands of
indole...(pyrrole)2 trimer.
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(H2O)3
(CH3OH)3
(phenol)3
Figure S3. Structures of (H2O)3, (CH3OH)3, and (phenol)3 optimized at the M052X/cc-pVTZ level of theory.
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Table S1.
A few selected geometrical parameters of the cyclic structures of
(phenol)3, (CH3OH)3, and (H2O)3 calculated at the M05-2X/cc-pVTZ level of theory
Geometrical
parameters
(phenol)3
(CH3OH)3
(H2O)3
rO1-H2 (Å)
0.0100
0.0143
0.0139
rO3-H4 (Å)
0.0101
0.0136
0.0145
rO5-H6 (Å)
0.0101
0.0127
0.0143
O1-H2-O3
144.2
151.3
150.3
O3-H4-O5
144.2
149.5
152.2
O5-H6-O1
144.2
150.0
152.0
dO3…H2 (Å)
1.91
1.89
1.90
dO5…H4 (Å)
1.91
1.90
1.88
dO1…H6 (Å)
1.91
1.88
1.88
Dipole Moment
(Debye)
0.00
1.22
1.18
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Table S2. Theoretical frequencies, their assignments as well as IR and Raman intensity
(km/mol) of the N-H stretching modes of (pyrrole)3 and IP2-1, IP2-2 structures of the
indole...(pyrrole)2 trimer calculated at various level of DFT
IP2-1
M05-2X/aVDZ
M06-2X/cc-pVTZ
M06-2X/aVDZ
B97-D/cc-pVTZ
B97-D/aVDZ
B97x-D/cc-pVTZ
B97x-D/aVDZ
IP2-2
IR
Intensity
Raman
Intensity
494
101
N-H
3456
3410
657
87
3397
74
3420
(pyrrole)3
IR
Intensity
Raman
Intensity
327
91
N-H
3416
IR
Intensity
Raman
Intensity
645
90
3411
614
86
3413
645
88
257
3400
191
221
3399
9
271
513
85
3454
304
93
3426
622
92
3416
591
87
3421
593
81
3425
622
92
3402
32
268
3410
141
229
3409
3
285
3427
585
82
3463
314
86
3436
642
95
3424
566
93
3428
593
82
3435
641
95
3410
14
279
3418
150
229
3419
2
293
3422
504
124
3479
279
131
3431
607
133
3420
605
127
3420
595
128
3431
608
132
3406
20
402
3410
167
337
3415
1
418
3423
615
124
3484
272
142
3434
627
143
3419
527
150
3423
593
140
3433
624
144
3406
10
390
3411
195
328
3418
3
435
3422
432
106
3463
247
110
3418
590
92
3410
584
91
3398
493
132
3418
591
92
3397
71
276
3413
249
245
3403
0.03
293
3423
456
105
3474
254
88
3425
618
93
3414
598
92
3417
592
107
3424
621
92
3401
83
254
3405
184
262
3408
2
278
N-H
3422
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 C 1-C 2   *N25-H30
 C 3-C 4   *N25-H30
2 
2 
E i j * = 1.49 kcal/mol
E i j * = 1.54 kcal/mol
 C 11-C 12   *N5-H10
 C 13-C 14   *N5-H10
E i j * = 1.50 kcal/mol
E i j * = 1.54 kcal/mol
 C 21-C 22   *N15-H20
 C 23-C 24   *N15-H20
E i j * = 1.50 kcal/mol
E i j * = 1.54 kcal/mol
2 
2 
2 
2 
Figure S4. Natural bond orbitals of the cyclic structure of pyrrole trimer showing
multiple N-H…π hydrogen bonding interactions calculated at the M05-2X/cc-pVTZ
level of theory. For atom numbering, refer to Figure 4 in the text.
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Completed reference 53:
(53)
Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman,
J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X. H.,
H. P.; Izmaylov, A. F. B., J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda,
R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery,
J., J. A.; Peralta, J. E.; Ogliaro, F.; Bearpark, M.; Heyd, J. J.; Brothers, E.; Kudin, K. N.; Staroverov, V.
N.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.;
Cossi, M.; Rega, N.; Millam, N. J.; Klene, M.; Knox, J. E.; Cross, J. B.; Bakken, V.; Adamo, C.;
Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.;
Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.; Voth, G. A.; Salvador, P.;
Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas, Ö.; Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.;
Fox, D. J. GAUSSIAN 09, Revision B.01, Gaussian, Inc., Wallingford CT, 2009.
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