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Competition between halogen and hydrogen bonds in triiodoimidazole polymorphs Kacper W. Rajewski, Micha# Andrzejewski, and Andrzej Katrusiak Cryst. Growth Des., Just Accepted Manuscript • DOI: 10.1021/acs.cgd.6b00436 • Publication Date (Web): 26 Apr 2016 Downloaded from http://pubs.acs.org on May 26, 2016
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Competition between halogen and hydrogen bonds in triiodoimidazole polymorphs Kacper W. Rajewski, Michał Andrzejewski, Andrzej Katrusiak*
Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland *Corresponding author:
[email protected] Keywords: polymorphs, disappearing polymorphs, halogen bonds, synthon X3, hydrogen bonds, high pressure, phase transition, isostructurality
Abstract
Three polymorphs of 2,4,5-triiodo-1H-imidazole (tIIm), all of exceptionally low symmetry (with 3 and 4 independent molecules), differ in the contributions of halogen bonds to their cohesion forces. The crystals of phase α, of monoclinic space group P21/c and Z’=3, were obtained after the first synthesis of the compound and several of its crystallizations. Above 1.9 GPa phase α isostructurally transformed to phase β. The transition, marked by a huge strain visibly changing the crystal shape, could be reversibly repeated on increasing and releasing pressure. Repeated syntheses of tIIm, by using the same recipe as well as the same
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and varied conditions, resulted exclusively in a new γ phase, of monoclinic space group P21/c and Z’=4, while phase α disappeared. Each of phases α, β, γ is built of Z’ independent molecules and linked by Z’ independent NH···N bonds into chains. In phases β and γ new I···I bonds are formed when one of the NH···N bonds is bent to about 130°.
Introduction Polymorphism is usually associated with different molecular arrangements in crystals,1-5 but there are relatively few studies on the differences in the cohesion forces between polymorphs.6,7 It was recently established that the transformations between polymorphs affect mainly the weaker intermolecular forces, while the strongest interactions are retained.8 The formation of polymorphs and structural phase transitions can be considered as competitions between intermolecular interactions involving different parts of molecules. Pressure-induced polymorphism of NH···N hydrogen bonded compounds has been extensively studied, for example by single-crystal X-ray diffraction in benzimidazole9, 2-methylbenzimidazole10 and by Raman spectroscopy in oxalyl dihydrazide11. The phase transition in bromomethyl CH3Br at 1.5 GPa eliminates Br···Br halogen bridges, and the high-pressure structure is dominated by CH···Br contacts.7 Recently described crystals of trihaloimidazoles C3HN2X3 (tXIm, X=Cl, Br) are isostructural, built of NH···N bonded chains with many X···X contacts within and between the chains.12 However, these structures contrast with the crystal of triiodoimidazole, denoted tIIm (Fig. 1), where only one I···I contact between NH···N bonded chains is formed per each C3HN2I3 interval of three symmetry-independent molecules. Our present study was aimed at obtaining a new form of tIIm similar to those of isostructural tClIm and tBrIm, as well as at exploring the surprisingly small contribution of I···I interactions to the cohesion forces in tIIm, contrasting with many X···X interactions in tClIm and in tBrIm. In order to
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obtain new forms of tIIm we have compressed the crystals grown at ambient conditions, as well as recrystallizations were attempted in situ at high pressure in a diamond-anvil cell.
Figure 1. Molecule of 2,4,5-triiodo-(1H)-imidazole (tIIm), and its atomic labels.
Figure 2. Giant compression of a tIIm single crystal between phases α at 0.1 MPa and β at 1.90 GPa in the diamond-anvil cell, apart from the sample lying along the left edge of the chamber there are two ruby chips (marked by letter R). The sample length in phases α and β is given in mm. Polymorph γ is shown in Fig. S3 in Supporting Information.
Experimental The batch of tIIm crystals synthesized two years earlier12 was used for these experiments. We either used the old crystals of previously described phase α (Table 1) or we recrystallized this phase readily by dissolving the sample in ethanol and then evaporating the solvent. Highpressure experiments were initially performed in a membrane diamond-anvil cell (DAC)13 in 3 ACS Paragon Plus Environment
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order to observe the effect of pressure on the single crystal of tIIm under an optical microscope and a movie was recorded (Movie S1 in SI). At approximately 1.90 GPa a clearly visible giant abrupt change of the crystal shape marked a phase transition to phase β (Fig. 2). The experiment was repeated several times for three samples. This phase transition was reversibly repeated by decreasing and increasing pressure without any noticeable deteriorations of the single-crystal quality. In order to perform structural studies of phase β, a crystal of phase α was mounted in a Merrill-Bassett DAC, modified by mounting the anvils directly on steel supports with conical windows. Isopropanol was used as the hydrostatic medium.14 Pressure was isothermally gradually increased till the phase transition occurred and then X-ray diffraction data were recorded for phase β at 1.94 GPa. We also attempted recrystallizations of tIIm in the DAC in isochoric conditions. About 15 tries were made, using different solvents (e.g. methanol, acetone, isopropanol), concentrations and p/T ranges, but no good quality single-crystal could be obtained. Because we ran off the old tIIm sample, the synthesis was repeated exactly as it had been done before.12 However, this time a new form of crystals, hereafter denoted as phase γ (Table 1), was obtained and no crystals of phase α could be found in this new batch and in any of several samples synthesized later. We measured the crystal compressibility and structural changes of phase γ up to 2 GPa, but no phase transitions were detected (Fig. 3). The stability of phase γ-tIIm can be due to formation of numerous I···I interactions in its structure, similarly like halogen bonds Cl···Cl postulated for 2,4,6-trichloro1,3,5-triazine stable at high-pressure conditions up to 30 GPa.15 The ruby fluorescence method was used for calibrating pressure inside the DAC.16,17 High-pressure single crystal Xray diffraction studies were performed on a 4-circle Agilent diffractometer with a MoKα Xrays source.18 The shadow method was used for centering the crystals.19 Data were collected and reduced by program CrysAlisPro.18 Structures were solved by direct methods using SHELXS and refined by full-matrix least squares on F2 using SHELXL in OLEX2.20,21 Due to
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very strong scattering of iodine atoms and incomplete high-pressure data for β-tIIm and low quality crystal for ambient-pressure γ-tIIm, constrains idealizing the ring geometry (AFIX 56) were applied in the structural models. The diffraction data for high-pressure γ-tIIm allowed the determination of unit-cell parameters only. Azole H-atoms were added from molecular geometry, their Uiso were constrained to 1.2Ueq of their carriers and N-H distances were fixed to 0.86 Å (AFIX 43). The ordered azole H sites were assumed and chosen according to C···N angles closer to the bisecting C-N-C angle22 and the protonated azole nitrogen atom has been labelled N1. Previously, the α-tIIm structure was described in space group P21/a, but presently the conventional setting of space group P21/c has been chosen for all studied polymorphs. The crystallographic data and experimental details are summarized in Table 1 (cf. Table S1 in Supporting Information).
Figure 3. Compression of molecular volume (V/Z’) in tIIm phase γ (green solid line fitted to experimental points determined by X-ray diffraction marked by green squares) as well as the molecular volume of phases α and β (red squares), measured before they disappeared. Hence their compression (dashed red lines) has been assessed from the sample length (as its volume mainly depend on the compression of b, cf. Fig. 2 and Table 1) and it includes the clearly visible strain at 1.9 GPa. 5 ACS Paragon Plus Environment
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Table 1. Selected structural data of tIIm polymorphs, all measured at 296 K. phase
α
β
γ
γ
pressure (GPa)
0.0001
1.94
0.0001
1.96
space group
P21/c
P21/c
P21/c
P21/c
a (Å)
14.0808(5)
13.755(12)
19.6205(10)
18.84(3)
b (Å)
22.0803(7)
18.530(4)
9.0209(3)
8.9295(7)
c (Å)
9.4591(4)
9.262(5)
21.7969(11)
19.238(12)
β (°)
108.219(4)
108.91(8)
116.295(6)
114.28(14) 2950(6)
3
V (Å )
2793.50(18)
2233(3)
3458.7(3)
Z/Z’
12/3
12/3
16/4
16/4
Dx (g·cm-3)
3.180
3.977
3.424
4.014
Discussion The structures of trihaloimidazoles tClIm and tBrIm are very similar, however no similar tIIm form could be obtained. Instead in tIIm the α-to-β phase transition was observed. It is isostructural in character, i.e. it retains the unit-cell translations and the space group symmetry (Table 1).23,24,25 In the least dense phase α, NH···N hydrogen bonds bind the molecules into chains (Fig. 4). Surprisingly, only one of three independent molecules (Z’=3) forms an I···I contact between two Ci-symmetry related molecules B (Figs. 4 and 5). In phase α, there are also contacts I···π involving atoms I1A and I1C interacting with imidazole rings of molecules A and C (Fig. 6 and Table 5). At 1.90 GPa a giant strain marks the transition to phase β-tIIm (Fig. 4, Movie 1 in SI). The monotonic compression and the transition shortens parameter b by over 3.5 Å, i.e. to less than 84% of its ambient-pressure length. In this pressure range, the crystal volume change to 79%, which shows that it is mainly caused by the linear compression of parameter b. The crystal structure considerably reconstructs at the phase transition: the neighboring pairs of chains (Fig. 4) are shifted by approximately a/3 and molecules A, B and C rotate by about 55°, 125° and 60°, respectively (Fig. S1 in Supporting Information). The transition eliminates the large voids present in phase α and the new structural arrangement in β-tIIm is stabilized by numerous additional I···I and I···π interactions (Figs. 5 and 6). High pressure also affects the NH···N bonds, one of which is significantly 6 ACS Paragon Plus Environment
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bent to the N-H···N angle close to 130° in β–tIIm (Table 2). Such a bending of angle NH···N would result in the hydrogen bond breaking, however at high-pressure conditions the close distance between the molecules is preserved. In β-tIIm all iodide atoms are involved in I···I interactions and independent molecules A, B and C form 7, 8 and 5 I···I contacts, respectively (shorter than 3.96Å, i.e. the doubled van der Waals radius of I, according to Bondi26). Noteworthy, each molecule A, B and C is involved in a trifurcated contact scheme of I···I interactions. Molecules A and C are I···I bonded to their Ci-related neighbors. These I···I contacts can be classified according to the location of iodine atoms involved (Fig. 7, Table S4). For example the Ci-symmetric I···I bonds present only at high-pressure in phase β, are described as I2-I3’/I3-I2’, I1-I1’.
Figure 4. Crystal structures of tIIm polymorphs, with the chains of molecules linked by NH···N bonds indicated by dotted blue lines. Shift δ between neighboring pairs of chains in
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phases α and β along their [x] axis has been indicated. Capital letters A, B, C and D label the symmetry-independent molecules; hydrogen bonds NH···N are indicated by blue dotted lines. The H-bonded chains run along directions [2 0 1] in all tIIm phases.
Table 2. Geometry of hydrogen bonds NH···N in tIIm polymorphs α (0.1 MPa), β (1.94 GPa) and γ (0.1 MPa). The H-atoms are ideally located at atom N1 (distances N-H where fixed at 0.86 Å). The symmetry codes are (i) 1+x, 0.5-y, 0.5+z (for phases α and β); and (ii) 1+x, 1.5y, 0.5+z (for phase γ). NH···N bond
H···A (Å)
D···A (Å)
DH···A (°)
1.86
2.72(2)
175.6
1.95
2.81(2)
172.6
1.95
2.806(19)
179.3
1.72
2.556(2)
163.7
N(1B)H···N3C
2.03
2.66(5)
129.9
N(1C)H···N3Ai
2.05
2.87(7)
161.0
N(1A)H···N3B
1.99
2.831(11)
165.5
N(1B)H···N3C
1.98
2.822(11)
165.8
N(1C)H···N3D
1.93
2.786(11)
171.4
N(1D)H···N3Aii
2.36
3.001(12)
131.7
α-tIIm, 0.1 MPa N(1A)H···N3B N(1B)H···N3C N(1C)H···N3A
i
β-tIIm, 1.94 GPa N(1A)H···N3B
γ-tIIm, 0.1 MPa
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Figure 5. Iodine···iodine contacts in the tIIm polymorphs to their independent molecules, shown in red (molecule A), green (B), blue (C) and black (D in phase γ). Hydrogen bonds NH···N are indicated by blue dotted lines, I···I bonds in red and these in synthons I3 present in β-tIIm are marked in pink.
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Figure 6. Contacts I···π, both on the e-donor and acceptor sites to independent molecules A (marked red), B (green), C (blue) and D ( black – for phase γ only) in tIIm phases α, β and γ.
Despite the considerably more compact structure of phase β compared to phase α and the significantly increased number of I···I and I···π contacts, 10 versus 1 and 5 versus 2, respectively, the β phase is unstable below 1.9 GPa. It can be seen in Table 3 that C-I···I angles in phase β considerably deviate from the ideal values for I···I contacts of type I (145° and 145°) and of type II (90° and 180°). The shortest I···I contact in phase β is of type II and distorted from the ideal angles by just 11°, but other contacts are distorted by more than 20° and even over 30°. Thus in phase β most of the I···I contacts (except for one) as well as the 10 ACS Paragon Plus Environment
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bent NH···N bond are strongly strained and therefore the structure returned to phase α when pressure was released. In phase γ the angles involving I···I bonds are much less distorted than in phase β.
Table 3. Dimensions of I···I halogen contacts in tIIm polymorphs α (at 0.1 MPa), β (1.94 GPa) and γ (0.1 MPa): I···I distance, angles C-I···I (θ1), I···I-C (θ2)27,28 as well as their difference |θ1- θ2|,26 used for distinguishing types I and II of halogen bonds. Letters A, B, C and D (the latter needed for polymorph γ) label the independent molecules (cf. Fig. 4); the primes indicate the symmetry-transformed atoms. atom names
I···I (Å)
θ1 (°)
θ2 (°)
|θ1- θ2| (°)
3.811
140.95
140.95
0
I1A···I3A’
3.616
154.61
58.32
96.29
I1A···I2B’
3.463
87.98
168.91
80.93
α-tIIm I2B···I2B’
β-tIIm
I1A···I1B’
3.897
129.10
106.50
22.6
I2A···I3A’
3.526
113.09
163.42
50.33
I2A···I3B’
3.518
161.02
121.91
39.11
I1B···I2B’
3.764
159.44
125.98
33.46
I1B···I1C’
3.908
109.06
153.46
44.4
I2B···I2C’
3.657
64.43
167.75
103.32
I3B···I2C’
3.857
117.18
161.02
43.84
I3C···I2C’
3.736
163.58
113.54
50.4
I3A···I3D’
3.753
170.97
87.72
83.25
I3B···I1C’
3.957
169.13
101.31
67.82
I1C···I2D’
3.787
174.74
95.52
79.22
I2C···I2D’
3.950
73.33
163.08
89.75
I1D···I3D’
3.677
148.06
120.37
27.69
γ-tIIm
When iodine atoms I2 and I3 are assumed equivalent in tIIm molecules, due to undetected or disordered H-atom sites between N1 and N3
(see Experimental), the number of
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I1···I1’, I1···I2’ (equivalent to I1···I3’), I2···I2’ (equivalent to I2···I3’ and I3···I3’) and ‘tandem’ bonds I2···I3’/I3···I2’ (Fig. 7). In polymorphs α, β and γ these configurations of I···I bonds occur 2, 6, 6 and 2 times, respectively (see Table S2 in Supporting Information), which exactly or approximately correspond to the required number of I-atoms involved (two in I1···I2 versus four in I2···I3’/I3···I2’) as well as to the number of possible configurations: one of I1···I1’ and tandem I2···I3’/I3···I2’, two of I1···I2’ and I1···I3’, and three of I2···I2’, I2···I3’ and I3···I3’. According to these numbers, the least frequent should be the double contact I2···I3’/I3···I2’ twice more frequent contact I1···I1’, four times more frequent contact I1···I2’ and six times more frequent contacts I2···I3’. These frequencies are nearly exactly repeated in the tIIm phases (2:6:6:2, respectively), which indicates no preference to form I···I bonds for any of the I-atoms in the tIIm molecule. It contrast with the tClIm and tBrIm crystals, where no halogen···halogen bonds involved the chlorine and bromine atoms at C2.12
Figure 7. Configurations of intermolecular contacts I···I present in tIIm polymorphs α, β and γ. We have assumed (see the text) that iodine substituents I2 and I3 are equivalent due to the H-atom disorder, so for example only bond I1···I2’ is shown, and treated equivalent to I1···I3’.
Table 4. Iodine···π contacts in tIIm polymorphs α (0.1MPa), β (1.94GPa) and γ (0.1MPa) (cf. Table 3).
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Phase
Centroid···I
distance [Å]
α-tIIm
A···I1A’
3.573
C···I1C’
3.577
I3A···C’
3.711
A···I1A’
3.206
A···I3C’
3.545
B···I2C’
3.797
C···I1C’
3.532
I1A···A’
4.052
I2C···C’
3.602
β-tIIm
γ-tIIm
It is characteristic that the dihedral angles between the NH···N bonded molecules are between 57° and 114° (Table 5), which is due to intermolecular hindrances involving the iodine atoms. In phase α one of the angles, between molecules A and B is smaller than two others, while in phase β the molecules rotate so that the smallest angle is between molecules C and A (Fig. 4).
Table 5. Angles between average planes of tIIm molecules in NH···N bonded chains of polymorphs α, β and γ. Capital letters label the independent molecules. Primed labels refer to the molecules transformed according to symmetry code 1+x, 0.5-y, 0.5+z for phases α and β; and 1+x, 1.5-y, 0.5+z for phase γ. Phase
molecules
angle [°]
α-tIIm
A-B
105.2(9)
B-C
102.5(8)
C - A’
57.0(8)
A-B
113.9(19)
B-C
113.6(18)
C - A’
67.8(19)
A–B
109.9(5)
B–C
69.1(5)
C–D
103.8(5)
β-tIIm
γ-tIIm
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85.6(5)
Conclusions Polymorphs of tIIm exemplify the group of compounds with several types of intermolecular interactions competing as the main cohesion forces. There are NH···N, I···I and I···π bonds in tIIm. The I···I bonds, numerous adequately to the presence of three iodine terminal substituents in this relatively small molecule, can be formed in the high-pressure polymorph β and in the low-pressure polymorph γ only when one of independent NH···N bonds be strongly bent to about 130°. Meanwhile, the originally obtained and described polymorph α, with nearly straight NH···N bonds but only one independent I···I bond, disappeared similarily as the disappearing polymorphs of other compounds.30,31 However, it is exceptionally unique for tIIm, that the phase transition has been revealed for the disappearing polymorphs, and consequently that two polymorphs α and β disappeared, as well as that the number of independent molecules in the more stable polymorph γ (Z’=4) is higher than that in polymorphs and (Z’=3) that disappeared. Thus it appears that 4 independent molecules are required for involving adequately numerous I···I and I···π contacts as the cohesion forces in γtIIm, although additionally one of four independent NH···N bonds has to be bent. This is an indication of structural strains that can lead to other forms of this intriguing compound.
Supporting Information: Crystallographic data in CIF format, selected bond lengths and angles. This material is available free of charge via the Internet, at http://pubs.acs.org. Full crystal data have also been deposited in the Cambridge Crystallographic Database Centre as supplementary publication numbers CCDC: α – 1030314, β – 1456549, γ – 1456556, 1456937-1456941. Their copies can be obtained free of charge from http://www.ccdc.cam.ac.uk.
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Acknowledgements: This study was financed by the Polish Ministry of Science and Higher Education.
References: (1) Bernstein, J. Polymorphism in molecular crystals, Oxford University Press, 2008. (2) Desiraju, G. R., Cryst. Growth Des., 2008, 8, 3-5. (3) Bernstein, J. Cryst. Growth Des., 2011, 11, 632-650. (4) Olejniczak, A.; Katrusiak, A.; Szafrański, M. Cryst. Growth Des., 2010, 10, 3537–3546. (5) López-Mejías, V.; Kampf, J.W.; Matzger, A.J. J. Am. Chem. Soc., 2012, 134, 9872– 9875. (6) Destro, R.; Sartirana, E.; Loconte, L.; Soave, R.; Colombo, P.; Destro, C.; and Lo Presti, L.; Cryst. Growth Des., 2013, 13, 4571–4582. (7) Podsiadło, M.; Olejniczak, A.; Katrusiak, A. CrystEngComm, 2014, 16, 8279-8285. (8) Kaźmierczak, M.; Katrusiak, A. CrystEngComm, 2015, 17, 9423-9430. (9) Zieliński, W.; Katrusiak, A. Cryst. Growth Des., 2013, 13, 696-700. (10) Zieliński, W.; Katrusiak, A. Cryst. Growth Des., 2014, 14, 4247-4253. (11) Tan, Z.; Wang, K.; Yan, T.; Li, X.; Liu, J.; Yang, K.; Liu, B.; Zou, G.; Zou, B. J. Phys. Chem. C, 2015, 119, 10178-10188. (12) Andrzejewski, M.; Marciniak, J.; Rajewski, K.W.; Katrusiak, A. Cryst. Growth Des., 2015, 15, 1658–1665.
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(13) Merrill, L., Bassett, W.A. Review of Scientific Instruments, 1974, 45, 290-294. (14) Angel, R. J.; Bujak, M.; Zhao, J.; Gatta, G. D.; Jacobsen, S. D. J. Appl. Crystallogr. 2007, 40, 26–32. (15) Wang, K; Duan, D.; Zhou, M.; Li, S.; Cui, T.; Liu, B.; Liu, J.; Zou, B.; Zou, G. J. Phys Chem B 2011, 115, 4639-4644. (16) Mao, H. K.; Xu, J.; Bell, P.M. J. Geophys. Res., 1986, 91, 4673-4676. (17) Piermarini, G.J.; Block, S.; Barnett, J.D.; Forman, R.A. Journal of Applied Physics, 1975, 46, 2774-2780. (18) Xcalibur CCD System, CrysAlisPro Software System, version 171.37.31; Oxford Diffraction Ltd.: Wrocław, Poland, 2015. (19) Budzianowski A., Katrusiak A. High-Pressure Crystallography. Eds.: A. Katrusiak, P.F. McMillan, Kluwer, Dordrecht 2004, 101-112. (20) Sheldrick, G. M. Acta Crystallogr. A, 2008, 64, 112-122. (21) Dolomanov, O. V.; Bourhis, L. J.; Gildea, R. J.; Howard, J. A. K.; Puschmann, H.J. Appl. Crystallogr. 2009, 42, 339–341. (22) Katrusiak, A. J. Mol. Struct. 1999, 474, 125–133. (23) Boldyreva, E. V. Crystal Engineering, 2003, 6, 235-254. (24) Zhao, J.; Wang, L.; Dong, D.; Liu, Z.; Liu, H.; Chen, G.; Wu, D.; Luo, J.; Wang, N.; Yu, Y.; Jin, C.; Guo, Q. J. Am. Chem. Soc. 2008, 130, 13828–13829.
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Crystal Growth & Design
(25) Liu, Q.; Yu, X.; Wang, X.; Deng, Z.; Lv, Y.; Zhu, J.; Zhang, S.; Liu, H.; Yang, W.; Wang, L.; Mao, H.; Shen, G.; Lu, Z. Y.; Ren, Y.; Chen, Z.; Lin, Z.; Zhao, Y.; Jin, C. J. Am. Chem. Soc. 2011, 133, 7892–7896. (26) Bondi, A. J. Phys. Chem. 1964, 68, 441–451. (27) Desiraju, G. R.; Ho, P. S.; Kloo, L.; Legon, A. C.; Marquardt, R.; Metrangolo, P.; Politzer, P.; Resnati, G.; Rissanen, K. Pure Appl. Chem. 2013, 85, 1711–1713. (28) Metrangolo, P.; Resnati, G. IUCrJ 2013, 1, 5–7. (29) Mukherjee, A.; Tothadi, S.; Desiraju, G. R. Acc. Chem. Res. 2014, 47, 2514–2524. (30) Dunitz, J. D.; Bernstein, J. Acc. Chem. Res. 1995, 28, 193–200. (31) Bučar, D.-K.; Lancaster, R. W.; Bernstein, J. Angew. Chemie Int. Ed. 2015, 54, 6972– 6993.
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For Table of Content Use Only Competition between halogen and hydrogen bonds in triiodoimidazole polymorphs Kacper W. Rajewski, Michał Andrzejewski, Andrzej Katrusiak
The interplay of NH···N hydrogen bonds and I···I halogen interactions has been discussed in three polymorphs of 2,4,5-triiodoimidazole
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