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Short Note

Crystal Structure of 9-Dibenzylsulfide-7,8-dicarba-nido-undecaborane 9-Bn2S-7,8-C2B9H11

by
Sergey A. Anufriev
1,
Alexei A. Anisimov
1,2,
Igor B. Sivaev
1,3,* and
Vladimir I. Bregadze
1
1
A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 Vavilov Str., 119991 Moscow, Russia
2
Higher Chemical College at the Russian Academy of Sciences, D.I. Mendeleev Russian Chemical Technological University, 9 Miusskaya Sq., 125047 Moscow, Russia
3
Basic Department of Chemistry of Innovative Materials and Technologies, G.V. Plekhanov Russian University of Economics, 36 Stremyannyi Line, 117997 Moscow, Russia
*
Author to whom correspondence should be addressed.
Molbank 2021, 2021(2), M1230; https://doi.org/10.3390/M1230
Submission received: 15 May 2021 / Revised: 28 May 2021 / Accepted: 2 June 2021 / Published: 7 June 2021
(This article belongs to the Section Structure Determination)
Browse Figures
Versions Notes

Abstract

:
The crystal structure of 9-dibenzylsulfide-7,8-dicarba-nido-undecaborane 9-Bn2S-7,8-C2B9H11 was determined by a single-crystal X-ray diffraction. One of the benzyl groups is located above the open face of the carborane cage with a short H···H distance (2.29 and 2.71 Å for two symmetrically independent molecules) between the BHB-bridging hydrogen atom of the carborane fragment and the ortho-CH group of the aromatic ring. Topological analysis has revealed the existence of a critical bond point with a calculated energy of −0.8 kcal/mol in accordance with an X-ray diffraction molecular geometry. The crystal packing analysis revealed that this benzyl group is also involved in π-stacking interactions, while another benzyl group participates in numerous weak H···π, H···H and van der Waals interactions.

1. Introduction

nido-Carborane derivatives bearing sulfonium and ammonium substituents are widely used for the synthesis of π-complexes of transition metals or metallacarboranes [1,2,3,4,5,6], as well as various neutral functional derivatives of nido-carboranes [7,8,9,10,11,12,13]. A single-crystal X-ray diffraction study of asymmetrically substituted dialkylsulfonium derivatives of nido-carborane 9-R2S-7,8-C2B9H11 [8,9,14] as well as their C- and B-substituted analogues [15,16,17,18,19,20], revealed that the SR2 group in all cases is turned in such way, that the lone pair of the sulfur atom is antiperiplanar to the B(9)–B(10) bond, while their 1H and 13C-NMR spectra indicate the absence of free rotation around the B(9)–S bond.
Analysis of the 1H-NMR spectrum of the previously synthesized 9-dibenzylsulfonium derivative of nido-carborane 9-Bn2S-7,8-C2B9H11 [21] revealed the nonequivalence of the benzyl groups: the signal of the CH2 protons of one benzyl group appears as a singlet, while the signal of the CH2 protons of the other group appears as two doublets. Taking into account the achirality of the sulfur atom in this compound, it can be assumed that there is an interaction between the carborane cage and one of the benzyl groups, which hinders its rotation resulting in non-equivalence of the benzyl protons. To shed light on this issue, we carried out a detailed study of the structure of 9-Bn2S-7,8-C2B9H11 using a single-crystal X-ray diffraction and quantum-chemical calculations.

2. Results and Discussion

The molecular crystal structure of 9-Bn2S-7,8-C2B9H11 was determined by a single-crystal X-ray diffraction study. An asymmetric unit cell contains two molecules (A and A′) which differ slightly in the orientation of the SBn2 substituent. As mentioned in the introduction, in the nido-carboranes substituted with the S(CH2R′)CH2R″ groups at position B(9), the orientation of the substituent is such that one C(8)-B(9)-S-C angle is in the range of 85–115° and the other in the range of 170–140°. In 9-Bn2S-7,8-C2B9H11, the corresponding torsion angles for both symmetrically independent molecules are characterized by expected values (Table 1).
At the same time, according to the literature data, no regularities in the orientation of the R′ and R″ groups were observed. For example, in recently studied 9-ClCH2(Me)S-7,8-C2B9H11 [9], three conformers with respect to rotation around the S–C bond were found by quantum-chemical calculations and intramolecular noncovalent attractive H···Cl contacts were observed in two of them. Due to the relatively low rotation barrier, all three conformers can exist in solution; however, no conformer with intramolecular noncovalent contacts was observed in the crystal structure.
In the case of 9-Bn2S-7,8-C2B9H11, the benzyl group directed downwards relatively to the open pentagonal face of the nido-carborane ligand does not form any intramolecular contacts, while the aromatic ring of the other benzyl group is located above the open face, which might imply intramolecular interactions. We found that the H(9A)···H(12) distance (shown by a dashed line in Figure 1) is 2.29 and 2.71 Å in two symmetrically independent molecules. It is interesting to note here that, in the recently studied 9-Bn(Me)S-7,8-C2B9H11 [8], no intramolecular shortened contacts were observed between the benzyl group and the carborane cage; as a consequence, the aryl ring is involved in extensive intermolecular bonding.
To find the preferred conformation of the isolated molecule of 9-Bn2S-7,8-C2B9H11 for a better understanding of both intra- and intermolecular contacts, we carried out quantum-chemical calculation using the Gaussian program [22] and PBE0 functional with a triple-zeta basis set, which proved to be reliable for studying of molecular geometry [23,24,25,26]. To search for noncovalent intramolecular interactions, the AIM topological theory [27] was utilized. The search for bond critical points was carried out using the AIMAll program [28]. The estimation of the interacting atoms’ energy was based on its correlation with the potential energy density at the bond critical point E = 1/2V(r) [29,30]. Such correlation is often utilized for energetic analysis of a variety of organic compounds [24,31,32,33].
The calculated geometry (Table 1) is close to the geometry of the A′ molecule. Topological analysis revealed the presence of the bond critical point between the H(9A) and H(12) atoms in accordance with our suggestion based on the X-ray geometry of the molecule (Figure 1). The calculated energy of this contact is −0.8 kcal/mol. The crystal packing analysis demonstrates that the upwards-directed benzyl group is involved in the π-stacking interactions (Figure 2), while the other benzyl group participates in numerical weak H···π, H···H and van-der-Waals interactions.
In conclusion, the molecular crystal structure of compound 9-Bn2S-7,8-C2B9H11 was determined. The observed relative orientation of the benzyl groups allowed the formation of both intramolecular noncovalent interactions, intermolecular π–π stacking and H···π interactions in addition to the ordinary van der Waals contacts.

3. Materials and Methods

Synthesis of the 9-dibenzylsulfonium derivative of nido-carborane 9-Bn2S-7,8-C2B9H11 was described in the literature [21]. Its NMR spectral data are as follows: 1H-NMR (400 MHz, CDCl3), δ: 7.38 (10H, m, Ph), 4.43 (1H, d, CHHPh, J = 13.3 Hz), 4.17 (2H, s, CH2Ph), 4.13 (1 H, d, CHHPh, J = 13.3 Hz), 1.93 (2H, br.s, CHcarb), −3.31 (1H, br.s, BHB bridge), 13C{1H}-NMR (100 MHz, CDCl3), δ: 130.34 (Ph), 130.05 (Ph), 129.97 (Ph), 129.76 (Ph), 129.61 (Ph), 129.57 (Ph), 129.52 (Ph), 129.43 (Ph), 52.01 (Ccarb), 47.98 (CH2), 46.10 (CH2), 38.52 (Ccarb), 11B-NMR (128 MHz, CDCl3), δ: −4.0 (1B, d, J = 130 Hz), −8.1 (1B, s), −11.5 (1B, d, J = 130 Hz), −16.7 (1B, d, J = 116 Hz), −17.8 (1B, d, J = 165 Hz), −23.3 (1B, d, J = 149 Hz), −26.0 (1B, d, J = 144 Hz), −29.5 (1B, d, J = 109 Hz), −36.5 (1B, d, J = 144 Hz). MS (EI): found; m/z: 347 (M)−; calculated for C16H25B9S (M)− = 347.
A single-crystal X-ray diffraction experiment was carried out using the SMART APEX2 CCD diffractometer (λ(Mo-Kα) = 0.71073 Å, graphite monochromator, ω-scans) at 120 K. Collected data were processed by the SAINT and SADABS programs incorporated into the APEX2 program package [34]. The structure was solved by direct methods and refined by the full-matrix least-squares procedure against F2 in anisotropic approximation. The refinement was carried out with the SHELXTL program [35]. The CCDC number 2083954 contains the supplementary crystallographic data for this paper. These data can be obtained free of charge via www.ccdc.cam.ac.uk/data_request/cif.
Crystallographic data for 9-Bn2S-7,8-C2B9H11: C16H25B9S are monoclinic, the space group P21/n: a = 11.4570(6) Å, b = 25.5132(14) Å, c = 13.5873(7) Å, β = 102.813(3)°, V = 3872.7(4) Å3, Z = 8, M = 346.71, dcryst = 1.189 g·cm−3, wR2 = 0.0911 calculated on F2hkl for all 7507 independent reflections with 2θ < 52.0°, (GOF = 0.990, R = 0.0416 calculated on Fhkl for 6230 reflections with I > 2σ(I)).

Supplementary Materials

The following are available online, the NMR spectra X-ray diffraction data for 9-Bn2S-7,8-C2B9H11.

Author Contributions

Conceptualization, I.B.S.; investigation, S.A.A. and A.A.A.; project administration, V.I.B. All authors have read and agreed to the published version of the manuscript.

Funding

This research received no external funding.

Institutional Review Board Statement

Not applicable.

Data Availability Statement

The Supplementary Materials for this paper are available.

Acknowledgments

The single-crystal X-ray diffraction data were obtained by using equipment from the Center for Molecular Structure Studies at the A.N. Nesmeyanov Institute of Organoelement Compounds, operating with support from the Ministry of Science and Higher Education of the Russian Federation.

Conflicts of Interest

The authors declare no conflict of interest.

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Molbank 2021 m1230 g001 550
Figure 1. A general view of 9-Bn2S-7,8-C2B9H11 showing atomic numbering. Only the first independent molecule (A) is presented. Thermal ellipsoids are drawn at a 50% probability level. Noncovalent C-H···H-B interaction is shown by a dashed line.
Figure 1. A general view of 9-Bn2S-7,8-C2B9H11 showing atomic numbering. Only the first independent molecule (A) is presented. Thermal ellipsoids are drawn at a 50% probability level. Noncovalent C-H···H-B interaction is shown by a dashed line.
Molbank 2021 m1230 g001
Molbank 2021 m1230 g002 550
Figure 2. Crystal packing fragment of the titled compound showing stacking aggregates. The shortest intermolecular contacts are denoted by dashed lines. Distances C(3)···C(2′) and C(5′)···C(4′A) are equal to 3.383(3) and 3.364(3) Å, respectively.
Figure 2. Crystal packing fragment of the titled compound showing stacking aggregates. The shortest intermolecular contacts are denoted by dashed lines. Distances C(3)···C(2′) and C(5′)···C(4′A) are equal to 3.383(3) and 3.364(3) Å, respectively.
Molbank 2021 m1230 g002
Table
Table 1. Selected torsion angles which define molecular conformation of the titled compound.
Table 1. Selected torsion angles which define molecular conformation of the titled compound.
Torsion AngleMolecule AMolecule A′Calculation
C(8)-B(9)-S(1)-C(1)91.2(2)113.4(2)112.9
C(8)-B(9)-S(1)-C(10)−163.5(2)−140.7(2)−141.0
B(9)-S(1)-C(1)-C(2)−65.8(2)−84.2(2)−77.8
B(9)-S(1)-C(10)-C(11)−165.0(2)179.7(2)−177.2
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Anufriev, S.A.; Anisimov, A.A.; Sivaev, I.B.; Bregadze, V.I. Crystal Structure of 9-Dibenzylsulfide-7,8-dicarba-nido-undecaborane 9-Bn2S-7,8-C2B9H11. Molbank 2021, 2021, M1230. https://doi.org/10.3390/M1230

AMA Style

Anufriev SA, Anisimov AA, Sivaev IB, Bregadze VI. Crystal Structure of 9-Dibenzylsulfide-7,8-dicarba-nido-undecaborane 9-Bn2S-7,8-C2B9H11. Molbank. 2021; 2021(2):M1230. https://doi.org/10.3390/M1230

Chicago/Turabian Style

Anufriev, Sergey A., Alexei A. Anisimov, Igor B. Sivaev, and Vladimir I. Bregadze. 2021. "Crystal Structure of 9-Dibenzylsulfide-7,8-dicarba-nido-undecaborane 9-Bn2S-7,8-C2B9H11" Molbank 2021, no. 2: M1230. https://doi.org/10.3390/M1230

APA Style

Anufriev, S. A., Anisimov, A. A., Sivaev, I. B., & Bregadze, V. I. (2021). Crystal Structure of 9-Dibenzylsulfide-7,8-dicarba-nido-undecaborane 9-Bn2S-7,8-C2B9H11. Molbank, 2021(2), M1230. https://doi.org/10.3390/M1230

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