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Halogen···halogen contacts in triiodide salts of pyridinium-derived cations: Theoretical and spectroscopic studies
Journal Pre-proof Halogen···halogen contacts in triiodide salts of pyridinium-derived cations: Theoretical and spectroscopic studies Andrey N. Usoltsev, Alexander S. Novikov, Boris A. Kolesov, Katerina V. Chernova, Pavel E. Plyusnin, Vladimir P. Fedin, Maxim N. Sokolov, Sergey A. Adonin PII:
S0022-2860(20)30274-X
DOI:
https://doi.org/10.1016/j.molstruc.2020.127949
Reference:
MOLSTR 127949
To appear in:
Journal of Molecular Structure
Received Date: 12 November 2019 Revised Date:
20 January 2020
Accepted Date: 20 February 2020
Please cite this article as: A.N. Usoltsev, A.S. Novikov, B.A. Kolesov, K.V. Chernova, P.E. Plyusnin, V.P. Fedin, M.N. Sokolov, S.A. Adonin, Halogen···halogen contacts in triiodide salts of pyridinium-derived cations: Theoretical and spectroscopic studies, Journal of Molecular Structure (2020), doi: https:// doi.org/10.1016/j.molstruc.2020.127949. This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. © 2020 Published by Elsevier B.V.
Halogen···halogen contacts in triiodide salts of pyridinium-derived cations: theoretical and spectroscopic studies Andrey N. Usoltsev,a Alexander S. Novikovb, Boris A. Kolesov,a,c Katerina V. Chernova,d Pavel E. Plyusnin,a,c Vladimir P. Fedina,c, Maxim N. Sokolova,c,e and Sergey A. Adonina,c,f* a
Nikolaev Institute of Inorganic Chemistry SB RAS, 630090, 3 Lavrentiev av., Novosibirsk, Russia
b
Saint Petersburg State University, Institute of Chemistry, 199034 Universitetskaya Nab. 7-9, Saint Petersburg, Russia
c
Novosibirsk State University, 630090 Pirogova St. 2, Novosibirsk, Russia
d
Irkutsk National Research Technical University, 664074 Lermontov St. 83, Irkutsk, Russia
e
Kazan Federal University, Alexander Butlerov Institute of Chemistry, Lobachevskogo St. 1/29, 420008, Kazan, Russia
f
South Ural State University, Chelyabinsk, 454080, Russia
Abstract: Triiodide salts of pyridinium-type cations CatI3 (cat = 1,2-MePy (1), 1,2,6-MePy (2) and 1,2,4,6-MePy (3) were prepared and characterized by X-ray diffractometry. In the cases of 1 and 2, formation of supramolecular anionic dimers {(I3)2}2- was observed in solid state (I···I = 3.685 and 3.912 Å, respectively), while in 3 triiodides remain isolated. The features of I···I contacts were studied by theoretical methods and Raman spectroscopy. Keywords: polyhalogens / non-covalent interactions / Raman spectroscopy / DFT calculations contacts / halogen bonding
Introduction Polyhalides, sometimes referred to as polyhalogens, constitute a great class of inorganic compounds which demonstrates fascinating structural diversity.1 Although first representatives of this family were reported 200 years ago,1 this area of chemistry continues its development: within the last decade, many interesting results were presented, such as structurally characterized polychlorides,2,3 polybromides with very high Br content,4 previously unknown structural types,5,6 halometalate-polyhalide hybrids7–15 etc. From the point of view of chemical bonding, there are two types of interatomic interactions in polyhalide structures. First, it is trivial covalent bond (for example, in structurally simplest trihalides16–18). Second, there might appear a system of non-covalent halogen···halogen contacts, sometimes resulting in formation of sophisticated supramolecular architectures.1 While analyzing the structures of triiodide salts (CatI3, where Cat = organic cation), we made the following observation: in some cases, I···I distances in solid state are noticeably shorter than the sum of corresponding van der Waals radii (3.98 Å, according to Bondi19,20), so that the presence of specific contacts (which can be explained in terms of halogen bonding (XB) concept21,22) can be proposed. As a result, there can form dimers {(I3)}2-. Considering that
Raman spectroscopy is widely applied in characterization of polyhalides,23,24 we decided to check whether such dimerization can be detected in Raman spectra as well. In this work, we present three triiodide salts CatI3 (cat = 1,2-MePy (1), 1,2,6-MePy (2) and 1,2,4,6-MePy (3) revealing different I···I distances in solid state. The energies of such contacts were estimated by theoretical methods; additionally, features of Raman spectra of 1-3 are discussed. Experimental part All experiments were carried out in air. Iodide salts of 1,2-dimethyl, 1,2,6-trimethyl or 1,2,4,6tetramethylpyridinium were prepared by reactions of 2-MePy, 2,6-MePy or 2,4,6-MePy with methyl iodide in CH3CN; the purity was confirmed by 1H NMR and element analysis data. Preparation of CatI3 (1-3). 47 mg of 1,2-MePyI (1), 50 mg of 1,2,6-MePyI (2) or 52 mg of 1,2,4,6MePyI (3) (0.2 mmol in all cases) were dissolved in 3 ml of non-purified concentrated HI. 0.5 ml of CH3CN were added and the mixture was kept for 30 min at 70°C. After slow cooling to r.t., there form black crystals of 1, 2 or 3. Yield: 75% (1), 83% (2), 80% (3). (1): For C7H10NI3 calcd, %: C, 17.2; H, 2.1; N, 2.9; found, %: C, 17.5; H, 2.1; N, 3.0. (2): For C8H12NI3 calcd, %: C, 19.1; H, 2.4; N, 2.8; found, %: C, 19.4; H, 2.5; N, 2.9. (3): For C9H14NI3 calcd, %: C, 20.9; H, 2.7; N, 2.7; found, %: C, 21.1; H, 2.8; N, 2.8. Raman spectra were collected using a LabRAM HR Evolution (Horiba) spectrometer with the excitation by 633 nm line of He-Ne laser. The spectra at room temperature were obtained in the backscattering geometry with a Raman microscope. The laser beam was focused to a diameter of 2 micrometers using a LMPlan FL 50x/0.50 Olympus objective. The spectral resolution was 0.7 cm-1. The laser power on the sample surface was about 0.03 mW. X-ray diffractometry. Data for single crystals of 1-3 were obtained at 140K on the Agilent Xcalibur diffractometer equipped with an area AtlasS2 detector (graphite monochromator, λ(MoKα) = 0.71073 Å, ω-scans). Integration, absorption correction, and determination of unit cell parameters were performed using the CrysAlisPro program package (CrysAlisPro 1.171.38.41. Rigaku Oxford Diffraction: The Woodlands, TX, USA, 2015). The structures were solved by dual space algorithm (SHELXT) and refined by the full-matrix least squares technique (SHELXL)25 in the anisotropic approximation (except hydrogen atoms). Positions of hydrogen atoms of organic ligands were calculated geometrically and refined in the riding model. The crystallographic data and details of the structure refinements are summarized in Table 1. CCDC 1962920-1962922 contain the supplementary crystallographic data for this paper. These data can be obtained free of charge from The Cambridge Crystallographic Data Center at http://www.ccdc.cam.ac.uk/data_request/cif.
Table 1. Crystal data and structure refinement for 1-3 1 C7H10I3N 488.86 Orthorhombic, Cmca
2 C8H12I3N 502.89 Monoclinic, P21/n
3 C9H14I3N 516.91 Monoclinic, P21/n
8.8574 (4), 13.2856 (5), 20.1005 (8)
9.0700 (6), 13.7418 (6), 11.2680 (9)
α,β,γ° V, Å3 Z F(000) No. of reflections for cell measurement
90, 90, 90 2365.34 (17) 8 1744 5337
90, 110.276 (8), 90 1317.40 (16) 4 904 3748
8.0335 (6), 20.6525 (12), 9.2259 (6) 90, 112.710 (9), 90 1412.01 (18) 4 936 3213
θ range (°) for cell measurement
2.3–28.8
2.4–28.7
3.1–28.6
μ (mm-1)
7.88
7.08
6.61
Crystal size (mm)
0.39 × 0.32 × 0.27
0.40 × 0.39 × 0.14
0.40 × 0.17 × 0.14
Tmin, Tmax
0.480, 1.000
0.219, 1.000
0.501, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections
9032, 1507, 1375
9628, 3044, 2561
10528, 3250, 2673
Rint
0.020
0.028
0.029
θ values (°)
θmax = 28.9, θmin = 2.0
θmax = 28.9, θmin = 2.4
(sin θ/λ)max (Å-1)
0.679
0.681
θmax = 28.9, θmin = 2.0 0.681
Range of h, k, l
h = −11→10, k = −16→17, l = −24→27
h = −11→11, k = −17→14, l = −14→11
R[F2 > 2σ(F2)], wR(F2), S
0.017, 0.037, 1.20
0.030, 0.061, 1.05
h = −10→10, k = −23→26, l = −12→10 0.025, 0.039, 1.03
No. of reflections
1507
3044
3250
No. of parameters
55
109
118
Δρmax, Δρmin (e Å-3)
0.44, −0.50
0.82, −1.26
0.56, -0.51
Empirical formula M, g/mol Crystal system, space group a,b,c, Å
Thermogravimetric analyses were carried out on a TG 209 F1 Iris thermobalance (NETZSCH, Germany). The measurements were made in a helium flow in the temperature range of 30– 400°C using the heating rate of 10°C min-1 the gas flow rate of 60 mL min-1 and open Al crucibles.
Computational details. The single point calculations based on the experimental X-ray geometries of 1 and 2 have been carried out at the DFT level of theory using the M06 functional26 with the help of Gaussian-09 (M. J. Frisch et al., Gaussian 09, Revision C.01, Gaussian, Inc., Wallingford, CT, 2010) program package. The Douglas–Kroll–Hess 2nd order scalar relativistic calculations requested relativistic core Hamiltonian were carried out using the DZP-DKH basis sets27 for all atoms. The topological analysis of the electron density distribution with the help of the atoms in molecules (QTAIM) method developed by Bader28 has been performed by using the Multiwfn program (version 3.6).29 The Wiberg bond indices were computed by using the Natural Bond Orbital (NBO) partitioning scheme.30 The Cartesian atomic coordinates of model supramolecular associates 1 and 2 are presented in Table S1 (SI).
Results and discussion Trihalides can be considered as the most common outcome in reactions aiming preparation of polyhalides in general.1 From this point of view, their formation at abovementioned reaction conditions (naturally oxidized hydroiodic acid solution) is rather predictable. As mentioned above, the main difference in the structures of 1-3 is the distances between neighbouring triiodide anions. In 3, those significantly exceed the sum of corresponding van der Waals radii (4.568 vs 3.98 Å), so the absence of I···I interactions becomes evident (crystal packing is shown on Figure 1). Such situation in rather usual for triiodides.31–33 In 3, I3- is asymmetric (I-I = 2.8938(3) and 2.9377(3) Å). In 2, the I···I distances are 3.9127(5) Å, being slightly shorter than 3.98 Å, so it can be considered as a weak contact. As a result, two I3anions form N-shaped dimer (Figure 2); the I-I-I angle is 132.22(1)°. The difference in bond lengths in I3- is slightly greater than in 3 (2.8775(4) and 2.9443(4) Å). Finally, compound 1 features the shortest I···I contacts (3.6858(5) Å) (the overall shape of forming dimer is the same as in 2). In this case, the I-I-I angle is greater (163.11(2)°). The asymmetry of I3- is less prominent than in 2 (I-I = 2.8974(5) and 2.9509(6) Å), so there seems to be no relationship with the strength of I···I contacts. According to the CSD data, appearance of such supramolecular interactions is not uncommon for polyiodides, and those can be even shorter: there are at least five examples34–38 of triiodide structures where I···I distances are less than 3.5 Å (the lowest value is 3.420 Å34). Interestingly, in all these cases there form dimers with linear (or distorted linear) dimers, but not infinite polymers.
Figure 1. Crystal packing in the structure of 3. Cations are shown in wire-and-stick representation.
Figure 2. {(I3)2}2- in the structure of 2 and 3. I···I contacts dashed, I purple
In order to estimate the energies of non-covalent interactions in 1 and 2, we applied the approach which is widely used in supramolecular chemistry39–44: DFT calculations performed on atomic coordinated which were extracted from XRD data followed by topological analysis of electronic density distribution.28 Results are summarized in Table 2, the contour line diagrams of the Laplacian of electron density distribution ∇2ρ(r), bond paths, and selected zero-flux surfaces as well as reduced density gradient (RDG) isosurfaces for intermolecular contacts I···I in 1 and 2 are shown in Figures 3 and 4. According to the data of QTAIM analysis, there are of appropriate bond critical points (BCP’s) (3, –1) for the I···I contacts. The low magnitude of the electron density (0.009–0.012 a.u.), positive values of the Laplacian (0.030–0.035 a.u.), and very close to zero positive energy density (0.001 a.u.) in these BCP’s as well as very small Wiberg bond indices for appropriate contacts (0.01–0.03) are typical for non-covalent interactions involving halogen atoms.45,46 Depending on the procedure used for estimation of energies of
these contacts, those are within the 2.2-3.4 and 1.6-2.5 kcal/mol ranges for 1 and 2, respectively. According to the criterion proppsed by Espinosa et al.,47 it can be stated that covalent contribution in these contacts is negligible. Table 2. Values of the density of all electrons – ρ(r), Laplacian of electron density – ∇2ρ(r) and appropriate λ2 eigenvalues (with promolecular approximation), energy density – Hb, potential energy density – V(r), and Lagrangian kinetic energy – G(r) (a.u.) at the bond critical points (3, – 1), corresponding to intermolecular non-covalent interactions I···I in 1 and 2, bond lengths – l (Å), Wiberg bond indices (WI), as well as energies for these contacts Eint (kcal/mol), defined by different approaches.* Structure
ρ(r)
∇2ρ(r)
λ2
Hb
V(r)
G(r)
Einta
Eintb
Eintc
Eintd
l†
WI
1 2
0.012 0.009
0.035 0.030
–0.013 –0.009
0.001 0.001
–0.007 –0.005
0.008 0.006
2.2 1.6
2.2 1.6
3.0 2.1
3.4 2.5
3.685 3.911
0.03 0.01
*
Two types of halogen···halogen contacts are usually discussed21,48. Type I is believed to depend on the effects of crystal packing, while type II is due to a classic halogen bonding (a halogen atom with a 90° angle provides its lone pair for interaction and the other one provides its σ-hole). The intermolecular non-covalent interactions I···I in 1 and 2 can be classified as type I contacts. a
Eint = –V(r)/249 (general correlation developed for hydrogen bonds). b Eint = 0.429G(r)50 (general correlation developed for hydrogen bonds). c Eint = 0.68(−V(r)) (correlation developed exclusively for non-covalent interactions involving iodine atoms)51. d Eint = 0.67G(r) (correlation developed exclusively for non-covalent interactions involving iodine atoms)51
†
The shortest van der Waals radius for I atom is 1.98 Å19
Figure 3. Contour line diagram of the Laplacian of electron density distribution ∇2ρ(r), bond paths and selected zero-flux surfaces (top) and RDG isosurface (bottom) referring to intermolecular non-covalent interactions I···I in 1. Bond critical points (3, –1) are shown in blue, nuclear critical points (3, –3) – in pale brown. Length units – Å, RDG isosurface values are given in a.u.
Figure 4. Description see Figure 2, for 2. Raman spectra of 1-3 are shown on Figure 5. The modes signed on this figure with wavelength numbers correspond to the valent vibrations of I3- (symmetric (ν1) with lower and asymmetric (ν3) with higher frequencies, respectively52). All other modes are related to diverse anion vibrations. It can be noticed that both ν1 и ν3 in 1 are shifted to the lower wavelength ranges in comparison with those of 2 and 3. This effect can be attributed to the abovementioned dimerization observed in the structure of 1. The overall shape of calculated spectra matches with experimental data (see SI).
Figure 5. Raman spectra of 1-3 at room temperature
Data of thermogravimetric analysis for 1-3 are presented on Figure 6. Melting points for 1-3 are 100, 105 and 135°C, respectively. All compounds are stable up to 175°C; after that, there begins decomposition (or sublimation) which finishes at 280°C for 1 and 2 and 290°C for 3, respectively.
Figure 6. TG- and DTA-curves of compounds 1-3.
Conclusions Analysis of structural data reveals that dimerization of triiodide anions via non-covalent I···I interactions involving terminal iodine atoms is rather common feature. The I···I distances can vary in wide range (the shortest contacts of this type described earlier were 3.420 Å). In the compounds 1 and 2, the energies of these interactions are up to 3.4 kcal/mol; such values are common for Type I or II halogen···halogen contacts42,48. Such dimerization can be detected by Raman spectroscopy as well (characteristic shift of I3- valent vibrations).
Acknowledgements Experimental part of this work was supported by Russian Science Foundation (SAA, ANU, Grant No. 18-73-10040). Theoretical calculations (ASN) were supported by Russian Science Foundation (Grant No. 19-73-00001).
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• • •
Three triiodide salts were prepared Supramolecular contacts I···I may be present in solid state These contacts can be detected by Raman spectroscopy
Sergey A. Adonin: conceptualization, investigation (XRD), methodology, writing – Original Draft Alexander S. Novikov: investigation (quantum chemistry calculations), writing – Original Draft Katerina V. Chernova: investigation (syntheses), Writing - Original Draft Boris A. Kolesov: investigation (Raman), Writing - Original Draft Pavel E. Plyusnin: investigation (thermal stability), Writing - Original Draft Maxim N. Sokolov: supervision, Writing - Review & Editing Vladimir P. Fedin: supervision
Declaration of interests ☒ The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. ☐The authors declare the following financial interests/personal relationships which may be considered as potential competing interests:
S0022-2860(20)30274-X
DOI:
https://doi.org/10.1016/j.molstruc.2020.127949
Reference:
MOLSTR 127949
To appear in:
Journal of Molecular Structure
Received Date: 12 November 2019 Revised Date:
20 January 2020
Accepted Date: 20 February 2020
Please cite this article as: A.N. Usoltsev, A.S. Novikov, B.A. Kolesov, K.V. Chernova, P.E. Plyusnin, V.P. Fedin, M.N. Sokolov, S.A. Adonin, Halogen···halogen contacts in triiodide salts of pyridinium-derived cations: Theoretical and spectroscopic studies, Journal of Molecular Structure (2020), doi: https:// doi.org/10.1016/j.molstruc.2020.127949. This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. © 2020 Published by Elsevier B.V.
Halogen···halogen contacts in triiodide salts of pyridinium-derived cations: theoretical and spectroscopic studies Andrey N. Usoltsev,a Alexander S. Novikovb, Boris A. Kolesov,a,c Katerina V. Chernova,d Pavel E. Plyusnin,a,c Vladimir P. Fedina,c, Maxim N. Sokolova,c,e and Sergey A. Adonina,c,f* a
Nikolaev Institute of Inorganic Chemistry SB RAS, 630090, 3 Lavrentiev av., Novosibirsk, Russia
b
Saint Petersburg State University, Institute of Chemistry, 199034 Universitetskaya Nab. 7-9, Saint Petersburg, Russia
c
Novosibirsk State University, 630090 Pirogova St. 2, Novosibirsk, Russia
d
Irkutsk National Research Technical University, 664074 Lermontov St. 83, Irkutsk, Russia
e
Kazan Federal University, Alexander Butlerov Institute of Chemistry, Lobachevskogo St. 1/29, 420008, Kazan, Russia
f
South Ural State University, Chelyabinsk, 454080, Russia
Abstract: Triiodide salts of pyridinium-type cations CatI3 (cat = 1,2-MePy (1), 1,2,6-MePy (2) and 1,2,4,6-MePy (3) were prepared and characterized by X-ray diffractometry. In the cases of 1 and 2, formation of supramolecular anionic dimers {(I3)2}2- was observed in solid state (I···I = 3.685 and 3.912 Å, respectively), while in 3 triiodides remain isolated. The features of I···I contacts were studied by theoretical methods and Raman spectroscopy. Keywords: polyhalogens / non-covalent interactions / Raman spectroscopy / DFT calculations contacts / halogen bonding
Introduction Polyhalides, sometimes referred to as polyhalogens, constitute a great class of inorganic compounds which demonstrates fascinating structural diversity.1 Although first representatives of this family were reported 200 years ago,1 this area of chemistry continues its development: within the last decade, many interesting results were presented, such as structurally characterized polychlorides,2,3 polybromides with very high Br content,4 previously unknown structural types,5,6 halometalate-polyhalide hybrids7–15 etc. From the point of view of chemical bonding, there are two types of interatomic interactions in polyhalide structures. First, it is trivial covalent bond (for example, in structurally simplest trihalides16–18). Second, there might appear a system of non-covalent halogen···halogen contacts, sometimes resulting in formation of sophisticated supramolecular architectures.1 While analyzing the structures of triiodide salts (CatI3, where Cat = organic cation), we made the following observation: in some cases, I···I distances in solid state are noticeably shorter than the sum of corresponding van der Waals radii (3.98 Å, according to Bondi19,20), so that the presence of specific contacts (which can be explained in terms of halogen bonding (XB) concept21,22) can be proposed. As a result, there can form dimers {(I3)}2-. Considering that
Raman spectroscopy is widely applied in characterization of polyhalides,23,24 we decided to check whether such dimerization can be detected in Raman spectra as well. In this work, we present three triiodide salts CatI3 (cat = 1,2-MePy (1), 1,2,6-MePy (2) and 1,2,4,6-MePy (3) revealing different I···I distances in solid state. The energies of such contacts were estimated by theoretical methods; additionally, features of Raman spectra of 1-3 are discussed. Experimental part All experiments were carried out in air. Iodide salts of 1,2-dimethyl, 1,2,6-trimethyl or 1,2,4,6tetramethylpyridinium were prepared by reactions of 2-MePy, 2,6-MePy or 2,4,6-MePy with methyl iodide in CH3CN; the purity was confirmed by 1H NMR and element analysis data. Preparation of CatI3 (1-3). 47 mg of 1,2-MePyI (1), 50 mg of 1,2,6-MePyI (2) or 52 mg of 1,2,4,6MePyI (3) (0.2 mmol in all cases) were dissolved in 3 ml of non-purified concentrated HI. 0.5 ml of CH3CN were added and the mixture was kept for 30 min at 70°C. After slow cooling to r.t., there form black crystals of 1, 2 or 3. Yield: 75% (1), 83% (2), 80% (3). (1): For C7H10NI3 calcd, %: C, 17.2; H, 2.1; N, 2.9; found, %: C, 17.5; H, 2.1; N, 3.0. (2): For C8H12NI3 calcd, %: C, 19.1; H, 2.4; N, 2.8; found, %: C, 19.4; H, 2.5; N, 2.9. (3): For C9H14NI3 calcd, %: C, 20.9; H, 2.7; N, 2.7; found, %: C, 21.1; H, 2.8; N, 2.8. Raman spectra were collected using a LabRAM HR Evolution (Horiba) spectrometer with the excitation by 633 nm line of He-Ne laser. The spectra at room temperature were obtained in the backscattering geometry with a Raman microscope. The laser beam was focused to a diameter of 2 micrometers using a LMPlan FL 50x/0.50 Olympus objective. The spectral resolution was 0.7 cm-1. The laser power on the sample surface was about 0.03 mW. X-ray diffractometry. Data for single crystals of 1-3 were obtained at 140K on the Agilent Xcalibur diffractometer equipped with an area AtlasS2 detector (graphite monochromator, λ(MoKα) = 0.71073 Å, ω-scans). Integration, absorption correction, and determination of unit cell parameters were performed using the CrysAlisPro program package (CrysAlisPro 1.171.38.41. Rigaku Oxford Diffraction: The Woodlands, TX, USA, 2015). The structures were solved by dual space algorithm (SHELXT) and refined by the full-matrix least squares technique (SHELXL)25 in the anisotropic approximation (except hydrogen atoms). Positions of hydrogen atoms of organic ligands were calculated geometrically and refined in the riding model. The crystallographic data and details of the structure refinements are summarized in Table 1. CCDC 1962920-1962922 contain the supplementary crystallographic data for this paper. These data can be obtained free of charge from The Cambridge Crystallographic Data Center at http://www.ccdc.cam.ac.uk/data_request/cif.
Table 1. Crystal data and structure refinement for 1-3 1 C7H10I3N 488.86 Orthorhombic, Cmca
2 C8H12I3N 502.89 Monoclinic, P21/n
3 C9H14I3N 516.91 Monoclinic, P21/n
8.8574 (4), 13.2856 (5), 20.1005 (8)
9.0700 (6), 13.7418 (6), 11.2680 (9)
α,β,γ° V, Å3 Z F(000) No. of reflections for cell measurement
90, 90, 90 2365.34 (17) 8 1744 5337
90, 110.276 (8), 90 1317.40 (16) 4 904 3748
8.0335 (6), 20.6525 (12), 9.2259 (6) 90, 112.710 (9), 90 1412.01 (18) 4 936 3213
θ range (°) for cell measurement
2.3–28.8
2.4–28.7
3.1–28.6
μ (mm-1)
7.88
7.08
6.61
Crystal size (mm)
0.39 × 0.32 × 0.27
0.40 × 0.39 × 0.14
0.40 × 0.17 × 0.14
Tmin, Tmax
0.480, 1.000
0.219, 1.000
0.501, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections
9032, 1507, 1375
9628, 3044, 2561
10528, 3250, 2673
Rint
0.020
0.028
0.029
θ values (°)
θmax = 28.9, θmin = 2.0
θmax = 28.9, θmin = 2.4
(sin θ/λ)max (Å-1)
0.679
0.681
θmax = 28.9, θmin = 2.0 0.681
Range of h, k, l
h = −11→10, k = −16→17, l = −24→27
h = −11→11, k = −17→14, l = −14→11
R[F2 > 2σ(F2)], wR(F2), S
0.017, 0.037, 1.20
0.030, 0.061, 1.05
h = −10→10, k = −23→26, l = −12→10 0.025, 0.039, 1.03
No. of reflections
1507
3044
3250
No. of parameters
55
109
118
Δρmax, Δρmin (e Å-3)
0.44, −0.50
0.82, −1.26
0.56, -0.51
Empirical formula M, g/mol Crystal system, space group a,b,c, Å
Thermogravimetric analyses were carried out on a TG 209 F1 Iris thermobalance (NETZSCH, Germany). The measurements were made in a helium flow in the temperature range of 30– 400°C using the heating rate of 10°C min-1 the gas flow rate of 60 mL min-1 and open Al crucibles.
Computational details. The single point calculations based on the experimental X-ray geometries of 1 and 2 have been carried out at the DFT level of theory using the M06 functional26 with the help of Gaussian-09 (M. J. Frisch et al., Gaussian 09, Revision C.01, Gaussian, Inc., Wallingford, CT, 2010) program package. The Douglas–Kroll–Hess 2nd order scalar relativistic calculations requested relativistic core Hamiltonian were carried out using the DZP-DKH basis sets27 for all atoms. The topological analysis of the electron density distribution with the help of the atoms in molecules (QTAIM) method developed by Bader28 has been performed by using the Multiwfn program (version 3.6).29 The Wiberg bond indices were computed by using the Natural Bond Orbital (NBO) partitioning scheme.30 The Cartesian atomic coordinates of model supramolecular associates 1 and 2 are presented in Table S1 (SI).
Results and discussion Trihalides can be considered as the most common outcome in reactions aiming preparation of polyhalides in general.1 From this point of view, their formation at abovementioned reaction conditions (naturally oxidized hydroiodic acid solution) is rather predictable. As mentioned above, the main difference in the structures of 1-3 is the distances between neighbouring triiodide anions. In 3, those significantly exceed the sum of corresponding van der Waals radii (4.568 vs 3.98 Å), so the absence of I···I interactions becomes evident (crystal packing is shown on Figure 1). Such situation in rather usual for triiodides.31–33 In 3, I3- is asymmetric (I-I = 2.8938(3) and 2.9377(3) Å). In 2, the I···I distances are 3.9127(5) Å, being slightly shorter than 3.98 Å, so it can be considered as a weak contact. As a result, two I3anions form N-shaped dimer (Figure 2); the I-I-I angle is 132.22(1)°. The difference in bond lengths in I3- is slightly greater than in 3 (2.8775(4) and 2.9443(4) Å). Finally, compound 1 features the shortest I···I contacts (3.6858(5) Å) (the overall shape of forming dimer is the same as in 2). In this case, the I-I-I angle is greater (163.11(2)°). The asymmetry of I3- is less prominent than in 2 (I-I = 2.8974(5) and 2.9509(6) Å), so there seems to be no relationship with the strength of I···I contacts. According to the CSD data, appearance of such supramolecular interactions is not uncommon for polyiodides, and those can be even shorter: there are at least five examples34–38 of triiodide structures where I···I distances are less than 3.5 Å (the lowest value is 3.420 Å34). Interestingly, in all these cases there form dimers with linear (or distorted linear) dimers, but not infinite polymers.
Figure 1. Crystal packing in the structure of 3. Cations are shown in wire-and-stick representation.
Figure 2. {(I3)2}2- in the structure of 2 and 3. I···I contacts dashed, I purple
In order to estimate the energies of non-covalent interactions in 1 and 2, we applied the approach which is widely used in supramolecular chemistry39–44: DFT calculations performed on atomic coordinated which were extracted from XRD data followed by topological analysis of electronic density distribution.28 Results are summarized in Table 2, the contour line diagrams of the Laplacian of electron density distribution ∇2ρ(r), bond paths, and selected zero-flux surfaces as well as reduced density gradient (RDG) isosurfaces for intermolecular contacts I···I in 1 and 2 are shown in Figures 3 and 4. According to the data of QTAIM analysis, there are of appropriate bond critical points (BCP’s) (3, –1) for the I···I contacts. The low magnitude of the electron density (0.009–0.012 a.u.), positive values of the Laplacian (0.030–0.035 a.u.), and very close to zero positive energy density (0.001 a.u.) in these BCP’s as well as very small Wiberg bond indices for appropriate contacts (0.01–0.03) are typical for non-covalent interactions involving halogen atoms.45,46 Depending on the procedure used for estimation of energies of
these contacts, those are within the 2.2-3.4 and 1.6-2.5 kcal/mol ranges for 1 and 2, respectively. According to the criterion proppsed by Espinosa et al.,47 it can be stated that covalent contribution in these contacts is negligible. Table 2. Values of the density of all electrons – ρ(r), Laplacian of electron density – ∇2ρ(r) and appropriate λ2 eigenvalues (with promolecular approximation), energy density – Hb, potential energy density – V(r), and Lagrangian kinetic energy – G(r) (a.u.) at the bond critical points (3, – 1), corresponding to intermolecular non-covalent interactions I···I in 1 and 2, bond lengths – l (Å), Wiberg bond indices (WI), as well as energies for these contacts Eint (kcal/mol), defined by different approaches.* Structure
ρ(r)
∇2ρ(r)
λ2
Hb
V(r)
G(r)
Einta
Eintb
Eintc
Eintd
l†
WI
1 2
0.012 0.009
0.035 0.030
–0.013 –0.009
0.001 0.001
–0.007 –0.005
0.008 0.006
2.2 1.6
2.2 1.6
3.0 2.1
3.4 2.5
3.685 3.911
0.03 0.01
*
Two types of halogen···halogen contacts are usually discussed21,48. Type I is believed to depend on the effects of crystal packing, while type II is due to a classic halogen bonding (a halogen atom with a 90° angle provides its lone pair for interaction and the other one provides its σ-hole). The intermolecular non-covalent interactions I···I in 1 and 2 can be classified as type I contacts. a
Eint = –V(r)/249 (general correlation developed for hydrogen bonds). b Eint = 0.429G(r)50 (general correlation developed for hydrogen bonds). c Eint = 0.68(−V(r)) (correlation developed exclusively for non-covalent interactions involving iodine atoms)51. d Eint = 0.67G(r) (correlation developed exclusively for non-covalent interactions involving iodine atoms)51
†
The shortest van der Waals radius for I atom is 1.98 Å19
Figure 3. Contour line diagram of the Laplacian of electron density distribution ∇2ρ(r), bond paths and selected zero-flux surfaces (top) and RDG isosurface (bottom) referring to intermolecular non-covalent interactions I···I in 1. Bond critical points (3, –1) are shown in blue, nuclear critical points (3, –3) – in pale brown. Length units – Å, RDG isosurface values are given in a.u.
Figure 4. Description see Figure 2, for 2. Raman spectra of 1-3 are shown on Figure 5. The modes signed on this figure with wavelength numbers correspond to the valent vibrations of I3- (symmetric (ν1) with lower and asymmetric (ν3) with higher frequencies, respectively52). All other modes are related to diverse anion vibrations. It can be noticed that both ν1 и ν3 in 1 are shifted to the lower wavelength ranges in comparison with those of 2 and 3. This effect can be attributed to the abovementioned dimerization observed in the structure of 1. The overall shape of calculated spectra matches with experimental data (see SI).
Figure 5. Raman spectra of 1-3 at room temperature
Data of thermogravimetric analysis for 1-3 are presented on Figure 6. Melting points for 1-3 are 100, 105 and 135°C, respectively. All compounds are stable up to 175°C; after that, there begins decomposition (or sublimation) which finishes at 280°C for 1 and 2 and 290°C for 3, respectively.
Figure 6. TG- and DTA-curves of compounds 1-3.
Conclusions Analysis of structural data reveals that dimerization of triiodide anions via non-covalent I···I interactions involving terminal iodine atoms is rather common feature. The I···I distances can vary in wide range (the shortest contacts of this type described earlier were 3.420 Å). In the compounds 1 and 2, the energies of these interactions are up to 3.4 kcal/mol; such values are common for Type I or II halogen···halogen contacts42,48. Such dimerization can be detected by Raman spectroscopy as well (characteristic shift of I3- valent vibrations).
Acknowledgements Experimental part of this work was supported by Russian Science Foundation (SAA, ANU, Grant No. 18-73-10040). Theoretical calculations (ASN) were supported by Russian Science Foundation (Grant No. 19-73-00001).
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• • •
Three triiodide salts were prepared Supramolecular contacts I···I may be present in solid state These contacts can be detected by Raman spectroscopy
Sergey A. Adonin: conceptualization, investigation (XRD), methodology, writing – Original Draft Alexander S. Novikov: investigation (quantum chemistry calculations), writing – Original Draft Katerina V. Chernova: investigation (syntheses), Writing - Original Draft Boris A. Kolesov: investigation (Raman), Writing - Original Draft Pavel E. Plyusnin: investigation (thermal stability), Writing - Original Draft Maxim N. Sokolov: supervision, Writing - Review & Editing Vladimir P. Fedin: supervision
Declaration of interests ☒ The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. ☐The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: