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Article

Intra-/Intermolecular Bifurcated Chalcogen Bonding in Crystal Structure of Thiazole/Thiadiazole Derived Binuclear (Diaminocarbene)PdII Complexes

by
Alexander S. Mikherdov
,
Alexander S. Novikov
,
Mikhail A. Kinzhalov
,
Andrey A. Zolotarev
and
Vadim P. Boyarskiy
*
Saint Petersburg State University, 7/9 Universitetskaya Nab., Saint Petersburg 199034, Russia
*
Author to whom correspondence should be addressed.
Crystals 2018, 8(3), 112; https://doi.org/10.3390/cryst8030112
Submission received: 26 January 2018 / Revised: 14 February 2018 / Accepted: 24 February 2018 / Published: 27 February 2018
(This article belongs to the Special Issue Chalcogen Bonding in Crystalline and Catalyst Materials)
Browse Figures
Versions Notes

Abstract

:
The coupling of cis-[PdCl2(CNXyl)2] (Xyl = 2,6-Me2C6H3) with 4-phenylthiazol-2-amine in molar ratio 2:3 at RT in CH2Cl2 leads to binuclear (diaminocarbene)PdII complex 3c. The complex was characterized by HRESI+-MS, 1H NMR spectroscopy, and its structure was elucidated by single-crystal XRD. Inspection of the XRD data for 3c and for three relevant earlier obtained thiazole/thiadiazole derived binuclear diaminocarbene complexes (3a EYOVIZ; 3b: EYOWAS; 3d: EYOVOF) suggests that the structures of all these species exhibit intra-/intermolecular bifurcated chalcogen bonding (BCB). The obtained data indicate the presence of intramolecular S•••Cl chalcogen bonds in all of the structures, whereas varying of substituent in the 4th and 5th positions of the thiazaheterocyclic fragment leads to changes of the intermolecular chalcogen bonding type, viz. S•••π in 3a,b, S•••S in 3c, and S•••O in 3d. At the same time, the change of heterocyclic system (from 1,3-thiazole to 1,3,4-thiadiazole) does not affect the pattern of non-covalent interactions. Presence of such intermolecular chalcogen bonding leads to the formation of one-dimensional (1D) polymeric chains (for 3a,b), dimeric associates (for 3c), or the fixation of an acetone molecule in the hollow between two diaminocarbene complexes (for 3d) in the solid state. The Hirshfeld surface analysis for the studied X-ray structures estimated the contributions of intermolecular chalcogen bonds in crystal packing of 3a–d: S•••π (3a: 2.4%; 3b: 2.4%), S•••S (3c: less 1%), S•••O (3d: less 1%). The additionally performed DFT calculations, followed by the topological analysis of the electron density distribution within the framework of Bader’s theory (AIM method), confirm the presence of intra-/intermolecular BCB S•••Cl/S•••S in dimer of 3c taken as a model system (solid state geometry). The AIM analysis demonstrates the presence of appropriate bond critical points for these interactions and defines their strength from 0.9 to 2.8 kcal/mol indicating their attractive nature.

Graphical Abstract

1. Introduction

The field of non-covalent interactions has grown explosively in the past decade. The hydrogen [1,2], halogen [3,4,5,6,7,8,9,10], chalcogen [11,12,13,14,15,16,17,18,19,20,21,22,23,24], pnictogen [25,26,27,28,29,30,31], tetrel [32] bonding, stacking [33,34,35,36,37], cation/anion-π [38,39,40,41,42], and metallophilic interactions [43,44,45] play key roles in many chemical, physical, and biochemical processes, due to their ability to control structures and properties of associates and supramolecular systems.
Nowadays, one of the vigorously investigating types of such interactions is chalcogen bonding (CB). CB is usually defined as non-covalent interactions between localized positive regions on a chalcogen atom in the extension of the covalent bonds (σ-holes) and electron donor species serving as CB acceptors [11,12,13,14,15,46,47,48,49,50]. Unlike halogens a chalcogen atom possess two σ-holes at the same time and is prone to the formation of bifurcated chalcogen bonding (BCB) (Figure 1) [51,52,53,54,55,56,57].
In the continuation of our projects focused on metal-mediated reactions of isocyanides [15,58,59,60,61,62,63,64,65,66,67,68] and on non-covalent interactions [15,58,69,70,71,72,73,74,75,76,77], we recently reported on the coupling between cis-[PdCl2(CNXyl)2] (Xyl = 2,6-Me2C6H4) and various thiazol- and thiadiazol-2-amines that leads to a mixture of two regioisomeric binuclear diaminocarbene complexes corresponding to kinetically (3a–d) or thermodynamically (4a–d) controlled regioisomers (Scheme 1). There is an equilibrium between these two species in CHCl3 solutions that depends on the energy difference between two types of intramolecular CBs, viz. S•••Cl and S•••N [58].
In this work, we would like to focus on the ability of the sulfur atom in species 3a–d to participate not only in intramolecular CB, but also in intermolecular contacts as a donor of bifurcated chalcogen bonding (BCB). We synthesized and characterized by single-crystal X-ray diffraction (XRD) binuclear (diaminocarbene)PdII complex 3c, bearing 4-phenyl-thiazole moiety. Also we analyzed the earlier obtained single-crystal XRD data for binuclear diaminocarbene species with unsubstituted 1,3-thiazole (3a: CCDC code—EYOVIZ), unsubstituted 1,3,4-thiadiazole (3b: CCDC code—EYOWAS), and 5-phenyl-1,3,4-thiadiazole fragment (3d: CCDC code—EYOVOF). That allowed us to define the relationship between the nature and the position of the substituents in the ligands and the type of the non-covalent interaction. Additionally, we carried out the Hirshfeld surface analysis (for 3a–d) and DFT calculations followed by the topological analysis of the electron density distribution within the framework of Bader’s theory (AIM method; for 3c) to study the nature and energies of these non-covalent interactions and determine their contributions in the crystal packing. These results are accordingly discussed in the sections that follow.

2. Materials and Methods

2.1. Materials and Instrumentation

Solvents, PdCl2, 4-phenyl-1,3-thiazol-2-amine, and xylyl isocyanide were obtained from commercial sources and used as received. Complex cis-[PdCl2(CNXyl)2] was synthesized by the literature procedure [58]. Mass-spectra were obtained on a Bruker micrOTOF spectrometer (Billerica, Massachusetts, MA, USA) equipped with electrospray ionization (ESI) source; a mixture of MeOH and CH2Cl2 was used for samples dissolution. The instrument was operated at a positive ion mode using m/z range of 50–3000. The capillary voltage of the ion source was set at −4500 V and the capillary exit at 50–150 V. The nebulizer gas pressure was 0.4 bar and the drying gas flow 4.0 L/min. All NMR spectra were acquired on a Bruker Avance 400 spectrometer (Billerica, Massachusetts, MA, USA) in CDCl3 at ambient temperature.

2.2. Synthesis and Characterization

Complex 3c were synthesized by reported procedure [58]. A solution of 4-phenyl-1,3-thiazol-2-amine (12 mg, 0.068 mmol) in CH2Cl2 (3 mL) was added to solid cis-[PdCl2(CNXyl)2] (20 mg, 0.045 mmol) placed in a 10-mL round-bottom flask. The reaction mixture was stirred in air at RT for 24 h. The color of the reaction mixture gradually turned from pale yellow to intense lemon yellow and solid cis-[PdCl2(CNXyl)2] was dissolved. The formed solution was filtered from some insoluble material and evaporated to dryness. Then, the solid residue was redissolved in an acetone (1.5 mL)/CH2Cl2 (2 mL) mixture and left to evaporate at 20–25 °C to ca. 1 mL till the crystalline product formation.
3c. Yield: 49% (11 mg). HRESI+-MS: calcd for C45H42ClN6SPd2+ 947.0949, found m/z 947.0973 [M-Cl]+. 1H NMR (δ, ppm, J/Hz): 2.08 (s, 6H, CH3, Xyl), 2.22 (s, 6H, CH3, Xyl), 2.26 (s, 6H, CH3, Xyl), 2.48 (s, 6H, CH3, Xyl), 6.19 (t, 1H, para-H, Xyl, J = 7.5), 6.56 (t, 1H, para-H, Xyl, J = 7.6), 6.67 (d, 2H, meta-H, Xyl, J = 7.5), 6.71 (s, 1H, thiazole), 6.88 (d, 2H, meta-H, Xyl, J = 7.6), 6.98 (d, 2H, meta-H, Xyl, J = 7.6), 7.01 (d, 2H, meta-H, Xyl, J = 7.3), 7.11–7.19 (m, 2H, para-H, Xyl), 7.35–7.39 (m, 3H, meta- and para- H, Ph) 7.47–7.52 (m, 2H, orto-H, Ph).

2.3. X-ray Structure Determination

Single crystal of 3c was grown from an acetone/CH2Cl2 mixture. The crystal was measured at Agilent Technologies SuperNova diffractometer at a temperature of 100 K using monochromated CuKα radiation (Yarnton, Oxfordshire, UK). The structures have been solved by the direct methods and refined by means of the SHELX program [78] incorporated in the OLEX2 program package [79]. The crystallographic data and some parameters of refinement are placed in Table 1. The carbon-bound H atoms were placed in calculated positions and were included in the refinement in the ‘riding’ model approximation, with Uiso(H) set to 1.5 Ueq(C) and C–H 0.96 Å for CH3 groups and with Uiso(H) set to 1.2 Ueq(C), C–H 0.93 Å for CH groups. Empirical absorption correction was applied in CrysAlisPro program complex using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm [80]. The unit cell of 3c also contains disordered dichloromethane molecules, which have been treated as a diffuse contribution to the overall scattering without specific atom positions by SQUEEZE/PLATON [81]. Supplementary crystallographic data for this paper have been deposited at Cambridge Crystallographic Data Centre (1815713) and can be obtained free of charge via www.ccdc.cam.ac.uk/data_request/cif.

2.4. Details of Hirshfeld Surface Analysis

The Hirshfeld molecular surfaces were generated by CrystalExplorer 3.1 program [82,83]. The normalized contact distances, dnorm [84], based on Bondi’s van der Waals radii [85], were mapped into the Hirshfeld surface. In the color scale, negative values of dnorm are visualized by the red color indicating contacts shorter than the sum of van der Waals radii. The white color denotes intermolecular distances that are close to van der Waals contacts with dnorm equal to zero. In turn, contacts longer than the sum of van der Waals radii with positive dnorm values are colored with blue.

2.5. Computational Details.

The single point DFT calculations with relativistic core Hamiltonian [86,87] based on the experimental X-ray data for 3c have been carried out at the M06/DZP-DKH level of theory in Gaussian-09 [88] program package. The topological analysis of the electron density distribution with the help of the “atoms in molecules” (AIM) method developed by R. Bader [89] has been performed by using the Multiwfn program [90]. The Wiberg bond indices were computed by using the Natural Bond Orbital (NBO) partitioning scheme [91].

3. Results and Discussion

3.1. Synthesis and Crystallization

In accordance with our recently reported procedure [58], binuclear (diaminocarbene)PdII complex 3c was synthesized by coupling of cis-[PdCl2(CNXyl)2] (Xyl = Me2C6H3) with 4-phenyl-1,3-thiazol-2-amine in molar ratio 2:3 at RT in CH2Cl2 (Scheme 1) followed by purification of the formed species by fractional crystallization from an acetone/CH2Cl2 mixture. Crystals of 3c for XRD were grown also from an acetone/CH2Cl2 mixture. The complex was characterized by HRESI+-MS, 1H NMR spectroscopy (Section 2.2), and its structure was elucidated by single-crystal X-ray diffraction (Section 3.2.2).

3.2. Non-Covalent Interactions in the Crystal Structures of 3a–d

3.2.1. Recognition of S•••Cl/S•••π BCBs in 3a,b

In both the structures of 3a (EYOVIZ) and 3b (EYOWAS) with unsubstituted thiazole/thiadiazole moieties, intra-/intermolecular BCB S•••Cl/S•••πXyl are present (Figure 2). Remarkably the change of heterocyclic system (from thiazole in 3a to thiadiazole to 3b) does not affect the pattern of non-covalent interactions and structures of 3a and 3b are isomorphic. The corresponding distances S•••Cl and the distances between the sulfur and both the center of π-system of Xyl ring (Xylcenter) and the closest C atom in this π-system are less than the sum of Rowland’s [92] and Bondi’s [85] vdW radii of these atoms, whereas the corresponding angles C–S•••Cl and C–S•••Xylcenter are close to 180° (Table 2) and these contacts could be defined as CBs [93,94].
Intermolecular S•••π CBs in crystal structures of 3a and 3b lead to the formation of one-dimensional (1D) chains (Figure 3). These interactions in both structures are also supported by the intermolecular C–H•••N hydrogen bonds (HBs) and their parameters (Table 2) are consistent with the IUPAC criterion [95].

3.2.2. Recognition of S•••Cl/S•••S BCB in 3c

The sulfur atom in 3c possesses one intramolecular CB with the PdII-bound chloride (as in the previous cases) and one intermolecular CB with the symmetrically located S atom in the neighboring molecule (Type I [96]; Figure 4). In contrast to 3a,b steric hindrance of the bulky phenyl substituent in the 4th position of the thiazole ring prevents formation of S•••πXyl CB and leads to the formation of different intermolecular CB. The intermolecular S•••S CB connects two symmetrically located molecules of 3c providing the dimeric structure in the solid state. The distances between the S and the Cl (3.1419(18) Å) and between two S atoms (3.459(2) Å) are less than the sum of their Rowland’s [92] or even Bondi’s [85] vdW radii (S•••S 3.62 and 3.60 Å). The corresponding angle C1–S•••Cl is 177.65(17) being appropriate for the classic CB (Type II) [93,94], whereas C2–S•••S’ angle is 153.99(16) in the case of both symmetrically located molecules of 3c revealing that it is Type I interaction [96]. The S•••Cl/S•••S BCB in 3c were theoretically studied by AIM analysis (see Section 3.3.2), and estimated energies of these non-covalent contacts are 2.7–2.8 (S•••Cl) and 0.9–1.3 (S•••S) kcal/mol.

3.2.3. Recognition of S•••Cl/S•••O BCB in 3d

Introduction of the Ph-group in the 5th position of the thiadiazole fragment in case of 3d (EYOVOF) does not affect intramolecular S•••Cl CB (Table 1), but prevents the convergence of two molecules of 3d with formation of intermolecular CBs between them (unlike above discussed structures). It leads to formation of hollows in the crystal structure between symmetrically located moieties of 3d in which solvated species can be placed and fixed by non-covalent interactions. In EYOVOF structure, two molecules of 3d co-crystallized with one molecule of acetone placed in the hollow between the complexes. This acetone molecule is disordered and exists in two positions with 0.5 occupancy each (Figure 5). The solvated acetone in each position is bonded by simultaneous CB and HB with the closest moiety of the complex forming six-membered cycle. The distance between the O and H (2.46(5) Å) is less than the sum of their Rowland’s [92] (2.68 Å) whereas the distance between the O and C (3.373(6) Å) atoms is just on border of the sum of Rowland’s [92] vdW radii (O•••C 3.35 Å), but shorter than the sum of Allinger’s vdW radii (O•••C 3.64 Å [97]), and the corresponding angle C–H•••O is close to 180°, indicating that this contact could be interpreted as HB. The S•••O distance (3.334(5) Å) is less than the sum of their Rowland’s [92] (3.39 Å) and on the border of Bondi’s [85] vdW radii (3.32 Å) and the angle C–S•••O is in range 150°–180° so this contact could be defined as CB [93,94].
Additionally, there is the contact between the C atom of the C=O group in acetone and the Pd-bound chloride (Figure 6). The distances between the C and Cl atoms (3.307(7) Å) are substantially less than the sums of Rowland’s [92], or even Bondi’s [85], vdW radii (3.53 and 3.45 Å). In this case the acyl C atom should acts as an electron density acceptor due to the π-hole on it [32,98,99,100], whereas the lone pair of the chloride ligand is an electron density donor.

3.3. Theoretical Consideration of Intra-/Intermolecular Bifurcated Chalcogen Bonding in Thiazole/Thiadiazole Derived Binuclear (Diaminocarbene)Pdii Complexes

3.3.1. Hirshfeld Surface Analysis for the X-ray Structures of 3a–d

The molecular Hirshfeld surface represents an area where molecules come into contacts, and its analysis gives the possibility of an additional insight into the nature of intermolecular interactions in the crystal state. We carried out the Hirshfeld surface analysis for the X-ray structures of 3a–d to understand what kind of intermolecular contacts gives the largest contributions in crystal packing (Table 3).
For the visualization, we have used a mapping of the normalized contact distance (dnorm); its negative value enables identification of molecular regions of substantial importance for detection of short contacts. The Figure 7 depicts the Hirshfeld surfaces for 3b–d. In these Hirshfeld surfaces, the regions of shortest intermolecular contacts visualized by red circle areas.
The Hirshfeld surface analysis for the X-ray structures of 3a–d reveals that in all cases crystal packing is determined primarily by intermolecular contacts H–H, Cl–H, and C–H and contributions of studied intermolecular CBs are low but still take a place: S•••π (3a 2.4%; 3b: 2.5%), S•••S (3c: less 1%), S•••O (3d: less 1%). However, this analysis does not answer the question about the nature (attractive or repulsive) and energies of these contacts, and, therefore, the DFT calculations should be further performed.

3.3.2. The QTAIM and NBO Analyses of Intra-/Intermolecular Bifurcated Chalcogen Bonding S•••Cl/S•••S in Model Dimeric Associate 3c

In order to confirm or disprove the hypothesis on the existence of intra-/intermolecular bifurcated chalcogen bonding (BCB) in the studied species we carried out DFT calculations and performed topological analysis of the electron density distribution within the framework of Bader’s theory (AIM method) [89] for model dimeric associate 3c featuring intra-/intermolecular BCB S•••Cl/S•••S to quantify energies of appropriate contacts from theoretical viewpoint. This model dimeric associate was obtained from the corresponding X-ray structure. Results are summarized in Table 4, the contour line diagram of the Laplacian distribution ∇2ρ(r), bond paths, and selected zero-flux surfaces for intra-/intermolecular bifurcated chalcogen bonding S•••Cl/S•••S are shown in Figure 8. To visualize studied non-covalent interactions, reduced density gradient (RDG) analysis [101] was carried out, and RDG isosurface for intra-/intermolecular BCB S•••Cl/S•••S was plotted (Figure 8). The Poincare-Hopf relationship was satisfied, and all of the critical points have been found.
The AIM analysis demonstrates the presence of appropriate bond critical points (BCPs) for the intra-/intermolecular bifurcated chalcogen bonding S•••Cl/S•••S in model dimeric associate 3c (Table 4). The low magnitude of the electron density (0.007–0.015 Hartree), positive values of the Laplacian (0.024–0.049 Hartree), and close to zero positive energy density (0.001–0.002 Hartree) in these BCPs are typical for non-covalent interactions. We have defined energies for these contacts according to the procedures proposed by Espinosa et al. [102] and Vener et al. [103] (Table 4). The strength of intramolecular S•••Cl CB is in the range of 2.8–2.9 kcal/mol, which is comparable with contacts in previously studied thiazole/thiadiazole derived binuclear (diaminocarbene)PdII complexes 3a,b (3.1–3.2 kcal/mol) [58]. In the same time, the intermolecular S•••S CB is much weaker (0.9–1.3 kcal/mol) than intramolecular contact in 3c, but its energy is comparable with I type CB contacts in the X2C=S•••S=CX2 (X = H, Cl, F) systems (0.7–1.1 kcal/mol) [96]. The balance between the Lagrangian kinetic energy G(r) and potential energy density V(r) at the BCPs reveals the nature of these interactions, if the ratio −G(r)/V(r) > 1 is satisfied, than the nature of appropriate interaction is purely non-covalent, in case the −G(r)/V(r) < 1 some covalent component takes place [104]. Based on this criterion one can state that a covalent contribution in both discussed above contacts is absent, and negligible values of Wiberg bond indices additionally confirm this observation.

4. Conclusions

In summary, we have synthesized and characterized by single-crystal XRD binuclear (diaminocarbene)PdII complex 3c bearing 4-phenyl-1,3-thiazole moiety, and, additionally, analyzed the CCDC data for three relevant earlier obtained binuclear diaminocarbene species with unsubstituted and 5-phenyl-substituted thiazole/thiadiazole moieties (3a: EYOVIZ; 3b: EYOWAS; 3d: EYOVOF). Inspection of the single-crystal XRD data for 3a–d reveals that the structure of all these species exhibits the intra-/intermolecular bifurcated chalcogen bonding (BCB) (Section 3.2). The XRD data for 3a,b (EYOVIZ, EYOWAS) indicate the presence of the intramolecular S•••Cl CB in both cases, and, additionally, of the intermolecular contacts of σ-hole on the S atom with the Xyl ring π-system of the neighboring molecule (Section 3.2.1). In the same time, introduction of the phenyl substituent in the 4th and 5th positions of the cyclic fragment does not affect intramolecular S•••Cl CB, but leads to dramatic changes of intermolecular CB’s type. Substitution of the thiazole fragment in the 4th position (3c) leads to change of the intermolecular CB’s type from the S•••π CB to the symmetrical S•••S contact (Type I CB) (Section 3.2.2). In case 3d (EYOVOF), the Ph-group in the 5th position of the thiadiazole fragment prevents the formation of any intramolecular CBs with the neighboring molecule of complex due to steric hindrance of the bulky phenyl substituent but leads to the S•••O CB with co-crystallized molecule of acetone (Section 3.2.3). The presence of the intermolecular CB leads to formation of 1D polymeric chains (for 3a,b), dimeric associates (for 3c), or fixation of the acetone molecules in the hollows between two diaminocarbene complexes (for 3d) in the solid state. The preformed Hirshfeld surface analysis for the studied X-ray structures estimated the contributions of intermolecular CBs in crystal packing of 3a–d: S•••π (3a 2.4%; 3b: 2.4%), S•••S (3c: less 1%), S•••O (3d: less 1%) (Section 3.3.1).
The additionally performed DFT calculations, followed by the topological analysis of the electron density distribution within the framework of Bader’s theory (AIM method), confirm the presence of intra-/intermolecular BCB S•••Cl/S•••S in dimer of 3c taken as a model system (solid state geometry). The AIM analysis demonstrates the presence of appropriate bond critical points for these interactions and defines their strength from 0.9 to 2.8 kcal/mol, indicating their attractive nature (Section 3.3.2.).
Thus, the obtained data indicates that the sulfur atoms in these binuclear diaminocarbene species are able to act as donors of the intra/intermolecular bifurcated chalcogen bonding (BCB) and its type depends on the nature and the position of the substituents in the heterocyclic fragment. These results are useful for understanding the relationship between the molecular structure and the crystal packing of systems with CBs donors and offer new opportunities in the crystal design of functional materials.

Acknowledgments

Support of the synthetic work and compound characterization from the Russian Science Foundation (grant 14-43-00017P) is gratefully acknowledged. Theoretical part of this work was conducted under the Russian Foundation for Basic Research project (16-33-60063). Physicochemical studies were performed at the Center for Magnetic Resonance, Center for X-ray Diffraction Studies, and Center for Chemical Analysis and Materials Research (all belong to Saint Petersburg State University).

Author Contributions

Alexander S. Mikherdov performed synthetic work and crystallization and analyzed data. Andrey A. Zolotarev performed X-ray experiment and structure determinations. Alexander S. Novikov, performed the Hirshfeld surface analysis and AIM analysis. Vadim P. Boyarskiy and Mikhail A. Kinzhalov supervised the research. All author made equal contributions in writing of manuscript.

Conflicts of Interest

The authors declare no conflict of interest.

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Crystals 08 00112 g001 550
Figure 1. Patterns of halogen bonding (XB) and bifurcated chalcogen bonding (BCB).
Figure 1. Patterns of halogen bonding (XB) and bifurcated chalcogen bonding (BCB).
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Crystals 08 00112 sch001 550
Scheme 1. Coupling of cis-[PdCl2(CNXyl)2] with thiazol- and thiadiazol-2-amines.
Scheme 1. Coupling of cis-[PdCl2(CNXyl)2] with thiazol- and thiadiazol-2-amines.
Crystals 08 00112 sch001
Crystals 08 00112 g002 550
Figure 2. Views of 3a and 3b. Thermal ellipsoids are drawn at the 50% probability level. Dotted lines indicate the S•••Cl, S•••π, and H•••N contacts.
Figure 2. Views of 3a and 3b. Thermal ellipsoids are drawn at the 50% probability level. Dotted lines indicate the S•••Cl, S•••π, and H•••N contacts.
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Crystals 08 00112 g003 550
Figure 3. Fragment of one-dimensional (1D) chain of 3a. Thermal ellipsoids are drawn at the 50% probability level. Dotted lines indicate the S···Cl, S···π, and H···N contacts.
Figure 3. Fragment of one-dimensional (1D) chain of 3a. Thermal ellipsoids are drawn at the 50% probability level. Dotted lines indicate the S···Cl, S···π, and H···N contacts.
Crystals 08 00112 g003
Crystals 08 00112 g004 550
Figure 4. View of dimer of 3c. Thermal ellipsoids are drawn at the 50% probability level. Dotted lines indicate the S•••Cl and S•••S contacts.
Figure 4. View of dimer of 3c. Thermal ellipsoids are drawn at the 50% probability level. Dotted lines indicate the S•••Cl and S•••S contacts.
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Crystals 08 00112 g005 550
Figure 5. View of solvate of 3d with acetone. Thermal ellipsoids are drawn at the 50% probability level. Dotted lines indicate the S•••Cl, S•••O, and H•••O contacts.
Figure 5. View of solvate of 3d with acetone. Thermal ellipsoids are drawn at the 50% probability level. Dotted lines indicate the S•••Cl, S•••O, and H•••O contacts.
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Crystals 08 00112 g006 550
Figure 6. View of solvate of 3d with acetone. Thermal ellipsoids are drawn at the 50% probability level. Dotted lines indicate the C···Cl contact.
Figure 6. View of solvate of 3d with acetone. Thermal ellipsoids are drawn at the 50% probability level. Dotted lines indicate the C···Cl contact.
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Crystals 08 00112 g007 550
Figure 7. Hirshfeld surfaces for 3b (left), dimer of 3c (middle), solvate of 3d with acetone (right). Thermal ellipsoids are drawn at the 50% probability level; all of the hydrogen atoms are omitted for clarity.
Figure 7. Hirshfeld surfaces for 3b (left), dimer of 3c (middle), solvate of 3d with acetone (right). Thermal ellipsoids are drawn at the 50% probability level; all of the hydrogen atoms are omitted for clarity.
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Crystals 08 00112 g008 550
Figure 8. Contour line diagram of the Laplacian distribution ∇2ρ(r), bond paths and selected zero-flux surfaces (left) and RDG isosurface (right) referring to the intra-/intermolecular bifurcated chalcogen bonding S•••Cl/S•••S in model dimeric associate 3c. Bond critical points are shown in blue, nuclear critical points– in pale brown, ring critical points—in orange. Length units—Å, RDG isosurface values are given in Hartree.
Figure 8. Contour line diagram of the Laplacian distribution ∇2ρ(r), bond paths and selected zero-flux surfaces (left) and RDG isosurface (right) referring to the intra-/intermolecular bifurcated chalcogen bonding S•••Cl/S•••S in model dimeric associate 3c. Bond critical points are shown in blue, nuclear critical points– in pale brown, ring critical points—in orange. Length units—Å, RDG isosurface values are given in Hartree.
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Table
Table 1. Crystal data and structure refinement for 3c.
Table 1. Crystal data and structure refinement for 3c.
Empirical FormulaC45H42N6SCl2Pd2
Formula weight982.61
Temperature/K100(2)
Crystal systemtriclinic
Space groupP-1
a/Å8.2666(4)
b/Å14.3733(8)
c/Å19.2538(9)
α/°99.238(4)
β/°97.705(4)
γ/°97.182(4)
Volume/Å32212.40(19)
Z2
ρcalcg/cm31.473
μ/mm−18.390
F(000)992.0
Crystal size/mm30.22 × 0.16 × 0.09
RadiationCuKα (λ = 1.54184)
2Θ range for data collection/°6.3–139.9
Index ranges−10 ≤ h ≤ 10, −17 ≤ k ≤ 17, −19 ≤ l ≤ 23
Reflections collected24325
Independent reflections8247 [Rint = 0.0764, Rsigma = 0.0679]
Data/restraints/parameters8247/0/495
Goodness-of-fit on F21.019
Final R indexes [I >= 2σ (I)]R1 = 0.0523, wR2 = 0.1422
Final R indexes [all data]R1 = 0.0623, wR2 = 0.1592
Largest diff. peak/hole/e Å−32.25/−1.64
Table
Table 2. Distances (Å) and angles (°) for chalcogen bonding (CBs) and hydrogen bonds (HBs) in the structures of 3a and 3b.
Table 2. Distances (Å) and angles (°) for chalcogen bonding (CBs) and hydrogen bonds (HBs) in the structures of 3a and 3b.
ContactParameter3a3bRowland wdV [92]Bondi wdV [85]
Intramolecular CBd(S•••Cl)3.097(2)3.0927(9)3.573.55
∠(Y–S•••Cl)172.0(3)172.79(12)
Intermolecular CBd(S•••C)3.445(7)3.425(3)3.583.50
d(S•••Xylcentr)3.351(3)3.2906(13)
∠(Y–S•••Xyl)172.0(3)172.79(12)
∠(S•••Xylplane)88.6(3)91.45(11)
Intermolecular HBd(H•••N)2.51(5)2.50(5)2.742.75
d(C•••N)3.361(9)3.349(4)3.413.25
∠(C–H•••N)151(1)151(1)
Table
Table 3. Results of the Hirshfeld surface analysis for the X-ray structures of 3a–d.
Table 3. Results of the Hirshfeld surface analysis for the X-ray structures of 3a–d.
X-ray structureContributions of Different Intermolecular Contacts to the Molecular Hirshfeld Surface *
3aH–H 52.8%, Cl–H 15.3%, C–H 13.8%, N–H 5.7%, Pd–H 3.6%, S–H 3.4%, C–C 2.5%, S–C 2.4%
3bH–H 49.3%, Cl–H 16.0%, C–H 11.9%, N–H 9.2%, Pd–H 3.7%, S–H 3.3%, C–C 2.6%, S–C 2.5%, N–C 1.1%
3cH–H 53.1%, C–H 20.4%, Cl–H 11.3%, N–H 2.9%, S–H 2.2%, Pd–H 2.1%, C–C 1.2%
3dH–H 45.9%, C–H 23.9%, Cl–H 11.9%, N–H 6.2%, Pd–H 3.2%, S–H 2.9%, O–H 2.6%, C–C 1.9%, Cl–C 1.0%,
* The contributions of all other intermolecular contacts do not exceed 1%.
Table
Table 4. Values of the density of all electrons—ρ(r), Laplacian of electron density—∇2ρ(r), energy density—Hb, potential energy density—V(r), and Lagrangian kinetic energy—G(r) (Hartree) at the bond critical points, corresponding to intra-/intermolecular bifurcated chalcogen bonding S•••Cl/S•••S in model dimeric associate 3c, Wiberg bond indices (WI), as well as energies for appropriate contacts Eint (kcal/mol), defined by two approaches.
Table 4. Values of the density of all electrons—ρ(r), Laplacian of electron density—∇2ρ(r), energy density—Hb, potential energy density—V(r), and Lagrangian kinetic energy—G(r) (Hartree) at the bond critical points, corresponding to intra-/intermolecular bifurcated chalcogen bonding S•••Cl/S•••S in model dimeric associate 3c, Wiberg bond indices (WI), as well as energies for appropriate contacts Eint (kcal/mol), defined by two approaches.
Contactρ(r)∇2ρ(r)HbV(r)G(r)Eint aEint bWI
S•••Cl0.0150.0490.002−0.0090.0102.82.70.02
S•••S0.0070.0240.001−0.0030.0050.91.30.01
a Eint = –V(r)/2. b Eint = 0.429G(r).

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Mikherdov, A.S.; Novikov, A.S.; Kinzhalov, M.A.; Zolotarev, A.A.; Boyarskiy, V.P. Intra-/Intermolecular Bifurcated Chalcogen Bonding in Crystal Structure of Thiazole/Thiadiazole Derived Binuclear (Diaminocarbene)PdII Complexes. Crystals 2018, 8, 112. https://doi.org/10.3390/cryst8030112

AMA Style

Mikherdov AS, Novikov AS, Kinzhalov MA, Zolotarev AA, Boyarskiy VP. Intra-/Intermolecular Bifurcated Chalcogen Bonding in Crystal Structure of Thiazole/Thiadiazole Derived Binuclear (Diaminocarbene)PdII Complexes. Crystals. 2018; 8(3):112. https://doi.org/10.3390/cryst8030112

Chicago/Turabian Style

Mikherdov, Alexander S., Alexander S. Novikov, Mikhail A. Kinzhalov, Andrey A. Zolotarev, and Vadim P. Boyarskiy. 2018. "Intra-/Intermolecular Bifurcated Chalcogen Bonding in Crystal Structure of Thiazole/Thiadiazole Derived Binuclear (Diaminocarbene)PdII Complexes" Crystals 8, no. 3: 112. https://doi.org/10.3390/cryst8030112

APA Style

Mikherdov, A. S., Novikov, A. S., Kinzhalov, M. A., Zolotarev, A. A., & Boyarskiy, V. P. (2018). Intra-/Intermolecular Bifurcated Chalcogen Bonding in Crystal Structure of Thiazole/Thiadiazole Derived Binuclear (Diaminocarbene)PdII Complexes. Crystals, 8(3), 112. https://doi.org/10.3390/cryst8030112

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