Supplementary material for: [https://doi.org/10.1039/c5cc04139b]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/1747]Related to accepted  version: [http://cherry.chem.bg.ac.rs/handle/123456789/3424

Blagojević, Jelena P.

Zarić, Snežana D.

Chemical Communications

English

Cherry - Repository of the Faculty of Chemistry;  University of Belgrade

  
 
 
 
 
 
 
 
 
 
 
 
Supplementary data for article:. 
 
         Blagojević, J. P.; Zarić, S. D. Stacking Interactions of Hydrogen-Bridged Rings-Stronger 
than the Stacking of Benzene Molecules. Chemical Communications 2015, 51 (65), 12989–
12991. https://doi.org/10.1039/c5cc04139b 
 
 
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Cite this: DOI: 10.1039/c0xx00000x
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This journal is © The Royal Society of Chemistry [year] [journal], [year], [vol], 00–00  |  1
-Supplementary material- 
Full Name,*a Full Namea,b and Full Nameb
Received (in XXX, XXX) Xth XXXXXXXXX 20XX, Accepted Xth XXXXXXXXX 20XX
DOI: 10.1039/b000000x
5 Distribution of interplanar angle and absolute of torsion angles H1Ω1Ω2H2 (θ1) and A1Ω1Ω2A2 (θ2)
Interplanar angle and absolute torsion angle H1Ω1Ω2H2 (θ1) and A1Ω1Ω2A2 (θ2) distributions, indicating the preferred antiparallel 
orientation of the middle planes of saturated five-membered hydrogen-bridged rings with planar surroundings of all atoms in the ring, are 
given in Fig. S1 and S2, respectively.
0-10 10-20 20-30 30-40 40-50 50-60 60-70 70-80 80-90
0
100
200
300
N
10 Fig. S1. Interplanar angle distributions 
0-2
0
20
-40
40
-60
60
-80
80
-10
0
10
0-1
20
12
0-1
40
14
0-1
60
16
0-1
80
0
100
200
300 |θ1| |θ2|
|θ|
(°)
N
Fig. S2. Distributions of absolute values of torsion angles H1Ω1Ω2H2 (|θ1|) and A1Ω1Ω2A2 (|θ2|). Centroid and atom labelling is consistent with the scheme 
given in Fig 1.
Evaluation of methods for calculating potential curves
15
(a) (b)  (c) (d) (e)
Figure S3. Model systems of 2-methylidenehydrazinecarbothioamide, used for the evaluation of different methods: a) orientation 1; b) orientation 2;
c) orientation 3; d) orientation 4; e) orientation 5
Electronic Supplementary Material (ESI) for ChemComm.
This journal is © The Royal Society of Chemistry 2015
2  |  Journal Name, [year], [vol], 00–00 This journal is © The Royal Society of Chemistry [year]
(a) (b)  (c) (d) (e)
Figure S4. Model systems of 2-methylidenehydrazinecarboxamide, used for the evaluation of different methods: a) orientation 1; b) orientation 2;
c) orientation 3; d) orientation 4; e) orientation 5
5
Several model systems (Figures S3 and S4) were chosen for the estimation of interaction energies at CCSD(T) level at complete basis 
set, by performing the method of Mackie and DiLabio1. Model systems are composed of dimers, having antiparallel middle molecular 
planes and offset values of -2.5 Å and 2.5 Å along Ω-C direction (orientations 1 and 2, respectively- Figures S3 and S4), 0.0 Å 
(orientation 3- Figures S3 and S4), -2.5 Å and 2.5 Å along the direction orthogonal to Ω-C direction (orientations 4 and 5, respectively- 
10 Figures S3 and S4). Distances between middle molecular planes in all model systems are 3.0 Å. Calculated interaction energies at 
CCSD(T)/CBS level are given in Tables S1-S5. Møller-Plesett perturbation theory of the second order (MP2)2 and several D3 corrected3 
DFT functionals were tested in order to find less time-consuming methods for the calculation of potential curves, which approximately 
reproduce CCSD(T)/CBS interaction energies. Basis set effect was also tested by applying several basis sets: cc-pVDZ4, cc-pVTZ5, aug-
cc-pVDZ4-6and 6-31++G**7. The results are given in Tables S1-S5 for all five orientations. with the values obtained by methods that 
15 were chosen for calculation of potential curves pointed out within a box. The selected method for calculating potential curves in the Ω-C 
direction is BLYP-d3/cc-pVDZ, since this method gives good results in orientations 2 (Table S1) and 3 (Table S3), while M06HF-d3/cc-
pVDZ and M052X-d3/6-31++G** methods were chosen for calculating potential curves for 2-methylidenehydrazinecarbothioamide and 
2-methylidenehydrazinecarboxamide, respectively, in the orthogonal direction, since they give good results in orientations 3 (Table S3), 
4 (Table S4), and 5 (Table S5). Neither of the selected methods gives particulary good results for orientations 1, but this is of no great 
20 importance, since energies are not high. 
Table S1. Interaction energies in kcal/mol, obtained by MP2 method and different D3 corrected DFT functionals, by using several basis sets and energies 
at CCSD(T)/CBS level, calculated on model systems corresponding to orientation 1 in Figures S3 and S4 
25
2-methylidenehydrazinecarbothioamide 2-methylidenehydrazinecarboxamide
orientation 1 cc-pVDZ cc-pVTZ aug-cc-pVDZ 6-31++G** cc-pVDZ cc-pVTZ aug-cc-pVDZ 6-31++G**
MP2 4.99 0.22 -0.58 3.63 1.63 -0.48 -1.13 0.58
TPSS-D3 1.77 1.65 0.96 1.18 -0.48 -0.77 -0.95 -0.74
BLYP-D3 2.62 2.04 1.90 2.12 -1.17 -1.36 -1.39 -1.07
BP86-D3 0.60 -0.15 -0.49 -0.21 -0.85 -1.43 -1.54 -1.21
PBE1PBE-D3 2.01 1.66 1.20 1.36 -0.37 -0.87 -1.01 -0.80
M05-D3 3.51 3.45 2.75 3.00 -0.68 -1.02 -1.45 -1.29
M06-D3 1.18 0.29 -0.22 0.05 -1.13 -1.98 -2.21 -2.11
M052X-D3 2.05 1.06 0.56 0.79 -0.63 -1.47 -1.67 -1.55
M06HF-D3 -0.36 -0.96 -2.43 -1.61 -1.10 -1.68 -2.34 -2.56
CCSD(T)/CBS -0.72 -1.92
Table S2. Interaction energies in kcal/mol, obtained by MP2 method and different D3 corrected DFT functionals, by using several basis sets and energies 
at CCSD(T)/CBS level, calculated on model systems corresponding to orientation 2 in Figures S3 and S4
2-methylidenehydrazinecarbothioamide 2-methylidenehydrazinecarboxamide
orientation 2 cc-pVDZ cc-pVTZ aug-cc-pVDZ 6-31++G** cc-pVDZ cc-pVTZ aug-cc-pVDZ 6-31++G**
MP2 -0.27 -1.59 -1.90 -0.70 0.55 -0.72 -1.03 0.08
TPSS-D3 -2.16 -2.19 -2.23 -2.13 -1.48 -1.54 -1.60 -1.50
BLYP-D3 -2.28 -2.24 -2.13 -2.03 -1.60 -1.58 -1.51 -1.41
BP86-D3 -2.03 -2.26 -2.25 -2.12 -1.36 -1.62 -1.64 -1.50
PBE1PBE-D3 -2.04 -2.21 -2.25 -2.16 -1.37 -1.57 -1.63 -1.54
M05-D3 -2.15 -2.22 -2.40 -2.38 -1.55 -1.65 -1.85 -1.83
M06-D3 -1.60 -2.03 -2.25 -2.34 -1.02 -1.52 -1.74 -1.78
This journal is © The Royal Society of Chemistry [year] Journal Name, [year], [vol], 00–00  |  3
5
Table S3. Interaction energies in kcal/mol, obtained by MP2 method and different D3 corrected DFT functionals, by using several basis sets and energies 
at CCSD(T)/CBS level, calculated on model systems corresponding to orientation 3 in Figures S3 and S4
10
15
20
25
Table S4. Interaction energies in kcal/mol, obtained by MP2 method and different D3 corrected DFT functionals, by using several basis sets and energies 
at CCSD(T)/CBS level, calculated on model systems corresponding to orientation 4 in Figures S3 and S4
30
35
40
Table S5. Interaction energies in kcal/mol, obtained by MP2 method and different D3 corrected DFT functionals, by using several basis sets and energies 
45 at CCSD(T)/CBS level, calculated on model systems corresponding to orientation 5 in Figures S3 and S4
50
55
M052X-D3 -1.69 -2.12 -2.20 -2.18 -1.06 -1.50 -1.60 -1.56
M06HF-D3 -1.36 -1.73 -2.02 -2.22 -0.68 -1.07 -1.37 -1.60
CCSD(T)/CBS -2.23 -1.54
2-methylidenehydrazinecarbothioamide 2-methylidenehydrazinecarboxamide
orientation 3 cc-pVDZ cc-pVTZ aug-cc-pVDZ 6-31++G** cc-pVDZ cc-pVTZ aug-cc-pVDZ 6-31++G**
MP2 0.74 -2.76 -3.49 -0.58 2.53 -0.25 -0.83 1.28
TPSS-D3 -2.29 -2.36 -2.72 -2.86 -0.41 -0.58 -0.93 -0.99
BLYP-D3 -2.89 -3.37 -3.14 -3.18 -1.16 -1.53 -1.42 -1.38
BP86-D3 -3.64 -4.24 -4.35 -4.40 -1.41 -1.96 -2.10 -2.03
PBE1PBE-D3 -2.07 -2.34 -2.59 -2.75 -0.31 -0.65 -0.89 -0.97
M05-D3 -1.67 -1.73 -2.14 -2.19 -0.23 -0.46 -0.86 -0.92
M06-D3 -3.33 -3.94 -4.54 -4.71 -1.23 -2.00 -2.33 -2.42
M052X-D3 -2.07 -2.68 -3.22 -3.45 -0.30 -0.99 -1.40 -1.50
M06HF-D3 -3.58 -3.73 -5.20 -5.53 -1.25 -1.65 -2.77 -3.28
CCSD(T)/CBS -3.64 -1.54
2-methylidenehydrazinecarbothioamide 2-methylidenehydrazinecarboxamide
orientation 4 cc-pVDZ cc-pVTZ aug-cc-pVDZ 6-31++G** cc-pVDZ cc-pVTZ aug-cc-pVDZ 6-31++G**
MP2 -1.57 -2.74 -3.07 -2.03 0.35 -0.75 -1.01 -0.24
TPSS-D3 -3.39 -3.29 -3.37 -3.45 -1.70 -1.72 -1.85 -1.94
BLYP-D3 -3.37 -3.26 -3.14 -3.19 -1.73 -1.74 -1.69 -1.75
BP86-D3 -3.29 -3.35 -3.33 -3.41 -1.63 -1.79 -1.83 -1.89
PBE1PBE-D3 -3.27 -3.32 -3.40 -3.48 -1.57 -1.72 -1.83 -1.92
M05-D3 -3.12 -3.18 -3.41 -3.48 -1.50 -1.64 -1.85 -1.95
M06-D3 -3.03 -3.50 -3.68 -3.86 -1.21 -1.68 -1.81 -1.96
M052X-D3 -2.83 -3.23 -3.32 -3.50 -1.17 -1.59 -1.69 -1.80
M06HF-D3 -3.28 -3.69 -4.16 -4.36 -1.34 -1.78 -2.22 -2.47
CCSD(T)/CBS -3.27 -1.57
2-methylidenehydrazinecarbothioamide 2-methylidenehydrazinecarboxamide
orientation 5 cc-pVDZ cc-pVTZ aug-cc-pVDZ 6-31++G** cc-pVDZ cc-pVTZ aug-cc-pVDZ 6-31++G**
MP2 0.20 -4.37 -5.05 -1.19 -0.14 -3.50 -4.27 -2.02
TPSS-D3 -2.95 -3.29 -3.71 -3.79 -2.60 -3.02 -3.39 -3.51
BLYP-D3 -2.71 -3.34 -3.43 -3.35 -3.15 -3.74 -3.83 -3.79
BP86-D3 -4.37 -5.15 -5.42 -5.38 -3.60 -4.42 -4.69 -4.67
PBE1PBE-D3 -3.08 -3.56 -3.90 -4.01 -2.80 -3.41 -3.72 -3.86
M05-D3 -2.03 -2.16 -2.87 -2.92 -2.70 -3.05 -3.71 -3.88
M06-D3 -4.08 -4.91 -5.77 -6.05 -3.56 -4.60 -5.23 -5.52
M052X-D3 -3.14 -4.35 -4.63 -4.82 -3.14 -4.38 -4.66 -4.87
M06HF-D3 -5.30 -6.45 -7.32 -7.33 -4.56 -5.64 -6.49 -7.07
CCSD(T)/CBS -5.31 -4.89
4  |  Journal Name, [year], [vol], 00–00 This journal is © The Royal Society of Chemistry [year]
Potential curves 
Potential curves obtained by moving molecules along Ω-C direction and along the orthogonal direction are shown in Fig S5.
           
-3 -2 -1 0 1 2 3
-5
-4.5
-4
-3.5
-3
-2.5
-2
-1.5
-1
-0.5
0
1    BLYP-d3/cc-pVDZ method
2    BLYP-d3/cc-pVDZ method
E (kcal/mol)
r (Å)
          
-3 -2.
5
-2 -1.
5
-1 -0.
5 0 0.5 1 1.5 2 2.5 3
-7
-6
-5
-4
-3
-2
-1
0
1    M06HF-d3/cc-pVDZ method
2    М052X-d3/6-31++G** method
r (Å)
E (kcal/mol)
                                                       (a)                                                                                                                 (b)
5 Fig S5. (a) Potential curves for offset values varied in the Ω-C direction; (b) Potential curves for offset values varied orthogonal to Ω-C direction
Normal distances 
Figure S6 shows normal distance dependencies on offset values.
-3 -2.5 -2 -1.5 -1 -0.5 0 0.5 1 1.5 2 2.5 3
0
1
2
3
4
2-methylidenehydrazinecarbothioamide
BLYP-d3/cc-pVDZ method
2-methylidenehydrazinecarboxamide
BLYP-d3/cc-pVDZ method
r (Å)
R (Å)
-3 -2.5 -2 -1.5 -1 -0.5 0 0.5 1 1.5 2 2.5 3
0
1
2
3
4
2-methylidenehydrazinecarbothioamide
M06HF-d3/cc-pVDZ method
2-methylidenehydrazinecarboxamide
M052X-d3/6-31++G**  method
r
(Å)
R (Å)
a)                                                                                                b)
10 Figure S6. Normal distance dependencies on offset values; a) Ω-C direction; b) orthogonal to Ω-C direction
Normal distances are approximately constant, in the range between 3.0 and 3.5 Å, which is in accord with the results of crystal structure 
analysis (Fig. 2).
Electrostatic potentials
Maps of electrostatic potentials for 2-methylidenehydrazinecarbothioamide and 2-methylidenehydrazinecarboxamide molecules, 
15 calculated and visualized from wavefunction files using the Wavefunction Analysis Program (WFA-SAS)8.9 are shown in Figure S7. The 
wavefunctions were calculated on mp2/cc-pVTZ level of theory using Gaussian09 series of programs10. Electronic density is more 
localized on oxygen atom in case of 2-methylidenehydrazinecarboxamide than it is localized on sulphur atom in case of 2-
methylidenehydrazinecarbothioamide.
20
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This journal is © The Royal Society of Chemistry [year] Journal Name, [year], [vol], 00–00  |  5
                
(a)                                                                                          (b)
Figure S7. Side and top views of electrostatic potential maps for (a) 2-methylidenehydrazinecarbothioamide and (b) 2-methylidenehydrazinecarboxamide 
5 molecule; Values of some important ESP maxima (empty circles) and minima (filled circles) in hartrees (Ha) are indicated onto the surfaces of the maps. 
Notes and references
a Address, Address, Town, Country. Fax: XX XXXX XXXX; Tel: XX XXXX XXXX; E-mail: xxxx@aaa.bbb.ccc
b Address, Address, Town, Country. Fax: XX XXXX XXXX; Tel: XX XXXX XXXX; E-mail: xxxx@aaa.bbb.ccc
1 I. D. Mackie, G. A. DiLabio, J. Chem. Phys, 2011, 135, 1343181.
10 2 C. Møller, M. S. Plesset, Phys. Rev, 1934, 46, 618–622.
3 S. Grimme, J. Antony, S. Ehrlich, H. Krieg, J. Chem. Phys, 2010, 132, 154104.
4 T. H. Dunning Jr, J. Chem. Phys, 1989, 90, 1007–1023.
5 R. A. Kendall, T. H. Dunning Jr, R. J. Harrison, J. Chem. Phys, 1992, 96, 6796–6806.
6 D. E. Woon, T. H. Dunning Jr, J. Chem. Phys, 1993, 98, 1358–1371.
15 7 R. Krishnan, J. S. Binkley, R. Seeger, J. A. Pople, J. Chem. Phys, 1980, 72, 650-654.
8 F. A. Bulat, A. Toro-Labbe, WFA: A suite of programs to analyse wavefunctions, unpublished.
9 F. A. Bulat, A. Toro-Labbe, T. Brinck, J. S. Murray, P. Politzer, J. Mol. Model, 2010, 16, 1679–1691.
10 Gaussian 09 (Revision D.01), M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. 
Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. 
20 Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery, Jr., J. E. Peralta, F. 
Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, 
S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. 
Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, 
J. J. Dannenberg, S. Dapprich, A. D. Daniels, Ö. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, D. J. Fox, Gaussian, Inc., Wallingford CT, 2013.
25


Supplementary data for article: Blagojević, J. P.; Zarić, S. D. Stacking Interactions of Hydrogen-Bridged Rings-Stronger than the Stacking of Benzene Molecules. Chemical Communications 2015, 51 (65), 12989–12991. https://doi.org/10.1039/c5cc04139b

http://cherry.chem.bg.ac.rs/bitstream/handle/123456789/3425/Stacking_interactions_of_sup_2015.pdf?sequence=1&isAllowed=y

Supplementary data for article: Blagojević, J. P.; Zarić, S. D. Stacking Interactions of Hydrogen-Bridged Rings-Stronger than the Stacking of Benzene Molecules. Chemical Communications 2015, 51 (65), 12989–12991. https://doi.org/10.1039/c5cc04139b

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