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Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 80| Part 9| September 2024| Pages 956-960
https://doi.org/10.1107/S2056989024007801

Crystal structure and Hirshfeld surface analysis of di­chlorido­[2-(3-cyclo­pentyl-1,2,4-triazol-5-yl-κN4)pyridine-κN]palladium(II) di­methyl­formamide monosolvate

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Viktoriya V. Dyakonenko,a,b* Dmytro M. Khomenko,c,d Roman O. Doroshchuk,c,d Ganna V. Ivanovac and Rostyslav D. Lampekac

aSSI "Institute for Single Crystals" of National Academy of Sciences of Ukraine, Nauki Ave 60, Kharkiv 61001, Ukraine, bV. I. Vernadskii Institute of General and Inorganic Chemistry of National, Academy of Sciences of Ukraine, Prospect Palladina 32/34, 03680 Kyiv, Ukraine, cDepartment of Chemistry, Taras Shevchenko National University of Kyiv, 12, Hetman Pavlo Skoropadskyi st.,01033 Kyiv, Ukraine, and dEnamine Ltd. (www.enamine.net), Winston Churchill str. 78, 02094 Kyiv, Ukraine
*Correspondence e-mail: dyakvik@gmail.com

Edited by J. Ellena, Universidade de Sâo Paulo, Brazil (Received 30 July 2024; accepted 7 August 2024; online 16 August 2024)

This study presents the synthesis, characterization and Hirshfeld surface analysis of the title mononuclear complex, [PdCl2(C12H14N4)]·C3H7NO. The compound crystalizes in the P21/c space group of the monoclinic system. The asymmetric unit contains one neutral complex Pd(HLc-Pe)Cl2 [HLc-Pe is 2-(3-cyclo­pentyl-1,2,4-triazol-5-yl)pyridine] and one mol­ecule of DMF as a solvate. The Pd atom has a square-planar coordination. In the crystal, mol­ecules are linked by inter­molecular N—H⋯O and C—H⋯N hydrogen bonds, forming layers parallel to the bc plane. A Hirshfeld surface analysis showed that the H⋯H contacts dominate the crystal packing with a contribution of 41.4%. The contribution of the N⋯H/H⋯N and H⋯O/O⋯H inter­actions is somewhat smaller, amounting to 12.4% and 5%, respectively.

CCDC reference: 2376338

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1. Chemical context

In recent years, square-planar coordination compounds of d8 metals with N-containing ligands have been widely investigated as effective catalysts and pre-catalysts in organic transformations (Kumbhar, 2017[Kumbhar, A. (2017). J. Organomet. Chem. 848, 22-88.]; Zakharchenko et al., 2019[Zakharchenko, B. V., Khomenko, D. M., Doroshchuk, R. O., Raspertova, I. V., Starova, V. S., Trachevsky, V. V., Shova, S., Severynovska, O. V., Martins, L. M. D. R. S., Pombeiro, A. J. L., Arion, V. B. & Lampeka, R. D. (2019). New J. Chem. 43, 10973-10984.]; Jindabot et al., 2014[Jindabot, S., Teerachanan, K., Thongkam, P., Kiatisevi, S., Khamnaen, T., Phiriyawirut, P., Charoenchaidet, S., Sooksimuang, T., Kongsaeree, P. & Sangtrirutnugul, P. (2014). J. Organomet. Chem. 750, 35-40.]; Jiao et al., 2020[Jiao, L.-Y., Yin, X.-M., Liu, S., Zhang, Z., Sun, M. & Ma, X.-X. (2020). Catal. Commun. 135, 105889.]), components for optoelectronic devices (Cuerva et al., 2014[Cuerva, C., Campo, J. A., Ovejero, P., Torres, M. R. & Cano, M. (2014). Dalton Trans. 43, 8849-8860.], 2018[Cuerva, C., Campo, J. A., Cano, M., Schmidt, R. & Lodeiro, C. (2018). J. Mater. Chem. C. 6, 9723-9733.], 2023[Cuerva, C., Cano, M. & Schmidt, R. (2023). Dalton Trans. 52, 4684-4691.]; Cuerva, Campo, Cano & Schmidt, 2019[Cuerva, C., Campo, J. A., Cano, M. & Schmidt, R. (2019). J. Mater. Chem. C. 7, 10318-10330.]; Cuerva, Campo, Cano & Lodeiro, 2019[Cuerva, C., Campo, J. A., Cano, M. & Lodeiro, C. (2019). Chem. Eur. J. 25, 12046-12051.]), and analogs of anti­cancer drugs (Abu-Surrah & Kettunen, 2006[Abu-Surrah, A. & Kettunen, M. (2006). Curr. Med. Chem. 13, 1337-1357.]; Ouellette et al., 2019[Ouellette, V., Côté, M.-F., Gaudreault, R. C., Tajmir-Riahi, H.-A. & Bérubé, G. (2019). Eur. J. Med. Chem. 179, 660-666.]; Jakubowski et al., 2020[Jakubowski, M., Łakomska, I., Sitkowski, J., Pokrywczyńska, M., Dąbrowski, P., Framski, G. & Ostrowski, T. (2020). Polyhedron, 180, 114428.]; Zakharchenko et al., 2021[Zakharchenko, B. V., Khomenko, D. M., Doroschuk, R. O., Raspertova, I. V., Shova, S., Grebinyk, A. G., Grynyuk, I. I., Prylutska, S. V., Matyshevska, O. P., Slobodyanik, M. S., Frohme, M. & Lampeka, R. D. (2021). Chem. Pap. 75, 4899-4906.]; Ohorodnik et al., 2023[Ohorodnik, Y. M., Khomenko, D. M., Doroshchuk, R. O., Raspertova, I. V., Shova, S., Babak, M. V., Milunovic, M. N. M. & Lampeka, R. D. (2023). Inorg. Chim. Acta, 556, 121646.]). Concurrently, functionalized pyridyl-azole-based ligands have been used in coordination chemistry as chelating polydentate ligands for obtaining various types of metal complexes with potential applications in similar fields. Complexes of di­chloro­palladium with functionalized pyridyl-1,2,3-triazole ligands were shown to be effective pre-catalysts with a broad functional group tolerance for cross-coupling reactions (Jindabot et al., 2014[Jindabot, S., Teerachanan, K., Thongkam, P., Kiatisevi, S., Khamnaen, T., Phiriyawirut, P., Charoenchaidet, S., Sooksimuang, T., Kongsaeree, P. & Sangtrirutnugul, P. (2014). J. Organomet. Chem. 750, 35-40.]; Jiao et al., 2020[Jiao, L.-Y., Yin, X.-M., Liu, S., Zhang, Z., Sun, M. & Ma, X.-X. (2020). Catal. Commun. 135, 105889.]). A series of metallomesogens of dihalide PdII and PtII compounds containing pyridyl-pyrazole ligands have been obtained in the context of the investigation of these complexes as 2D proton-conducting materials under anhydrous conditions (Cuerva et al., 2014[Cuerva, C., Campo, J. A., Ovejero, P., Torres, M. R. & Cano, M. (2014). Dalton Trans. 43, 8849-8860.], 2018[Cuerva, C., Campo, J. A., Cano, M., Schmidt, R. & Lodeiro, C. (2018). J. Mater. Chem. C. 6, 9723-9733.]; Cuerva, Campo, Cano, & Schmidt, 2019[Cuerva, C., Campo, J. A., Cano, M. & Schmidt, R. (2019). J. Mater. Chem. C. 7, 10318-10330.]). In subsequent studies, coordination compounds of this type were used as building blocks (precursors) for the synthesis of metallomesogens with structural asymmetry, which extends the known ranges of mesophases (Cuerva et al., 2018[Cuerva, C., Campo, J. A., Cano, M., Schmidt, R. & Lodeiro, C. (2018). J. Mater. Chem. C. 6, 9723-9733.], 2023[Cuerva, C., Cano, M. & Schmidt, R. (2023). Dalton Trans. 52, 4684-4691.]; Cuerva, Campo, Cano, & Lodeiro, 2019[Cuerva, C., Campo, J. A., Cano, M. & Lodeiro, C. (2019). Chem. Eur. J. 25, 12046-12051.]). Furthermore, PtII metallomesogens exhibit photophysical multi-stimuli-responsive properties (Cuerva, Campo, Cano, & Lodeiro, 2019[Cuerva, C., Campo, J. A., Cano, M. & Lodeiro, C. (2019). Chem. Eur. J. 25, 12046-12051.]). The complexes of d8 metals with pyridyl-azole-based ligands have been explored in cancer therapy as analogues of cisplatin; their application is limited by the severe side effects and development of drug resistance. The combination of d8 metals and chelating pyridyl-azole-based ligands should lead to an increase in the stability of the corresponding complexes and to a decrease in hydrolysis in biological media and, as a result, to a decrease in the toxicity of the resulting compounds (Abu-Surrah & Kettunen, 2006[Abu-Surrah, A. & Kettunen, M. (2006). Curr. Med. Chem. 13, 1337-1357.]). Previous studies demonstrated that the complexes of Pd and Pt with hydro­phobic pyridyl-azole-based ligands have certain anti­cancer activity against various types of tumour cells in vitro (Ouellette et al., 2019[Ouellette, V., Côté, M.-F., Gaudreault, R. C., Tajmir-Riahi, H.-A. & Bérubé, G. (2019). Eur. J. Med. Chem. 179, 660-666.]; Jakubowski et al., 2020[Jakubowski, M., Łakomska, I., Sitkowski, J., Pokrywczyńska, M., Dąbrowski, P., Framski, G. & Ostrowski, T. (2020). Polyhedron, 180, 114428.]; Zakharchenko et al., 2021[Zakharchenko, B. V., Khomenko, D. M., Doroschuk, R. O., Raspertova, I. V., Shova, S., Grebinyk, A. G., Grynyuk, I. I., Prylutska, S. V., Matyshevska, O. P., Slobodyanik, M. S., Frohme, M. & Lampeka, R. D. (2021). Chem. Pap. 75, 4899-4906.]; Ohorodnik et al., 2023[Ohorodnik, Y. M., Khomenko, D. M., Doroshchuk, R. O., Raspertova, I. V., Shova, S., Babak, M. V., Milunovic, M. N. M. & Lampeka, R. D. (2023). Inorg. Chim. Acta, 556, 121646.]). Our previous research of six dichloride PdII complexes based on 5-substituted 3-(2-pyrid­yl)-5-alkyl-1,2,4-triazoles was reported. The evaluation of 1H NMR spectroscopic data was focused on three types of proton signals of ligands and complexes located near the coordination centre and discussed in the context of the influence that cyclo­alkyl substituents have on intra­molecular inter­actions, being also supported by X-ray data for PdII complexes (Ivanova et al., 2024[Ivanova, H. V., Khomenko, D. M., Doroshchuk, R. O., Stoica, A.-C., Zakharchenko, B. V., Rusanova, J. A., Raspertova, I. V., Shova, S. & Lampeka, R. D. (2024). ChemistrySelect, https://doi. org/10.1002/slct. 202402258.]). We report herein the crystal structure, including characterization of the inter­molecular contacts by Hirshfeld surface analysis, of a new mononuclear di­chloro­palladium(II) complex with 2-(3-cyclo­pentyl-1,2,4-triazol-5-yl)pyridine.

[Scheme 1]

2. Structural commentary

The title compound crystalizes in the P21/c space group of the monoclinic system. The asymmetric unit contains one neutral complex Pd(HLc-Pe)Cl2 [HLc-Pe is 2-(3-cyclo­pentyl-1,2,4-triazol-5-yl)pyridine] and one mol­ecule of DMF as a solvate. The mol­ecular structure of title compound is shown in Fig. 1[link].

[Figure 1]
Figure 1
The mol­ecular structure of the title compound, showing the atom labelling and displacement ellipsoids drawn at the 50% probability level.

The Pd atom has a square-planar environment formed by the bidentate coordination of two nitro­gen atoms of the HLc-Pe ligand and two chlorine atoms. The deviation of the Pd atom from the mean-square plane defined by through the Cl1/Cl2/N1/N2 atoms (r.m.s.d. = 0.002 Å) is −0.0164 (11) Å. The Pd—N and Pd—Cl bond distances are 2.038 (3) and 2.061 (3) Å and 2.2811 (11) and 2.2837 (10) Å, respectively (Table 1[link]). This structure of the title complex is in very good agreement with previously described Pd complexes with a similar coordination (Khomenko et al., 2009[Khomenko, D. N., Doroschuk, R. A. & Lampeka, R. D. (2009). Ukr. J. Chem. 75, 30-33.]; Zakharchenko et al., 2021[Zakharchenko, B. V., Khomenko, D. M., Doroschuk, R. O., Raspertova, I. V., Shova, S., Grebinyk, A. G., Grynyuk, I. I., Prylutska, S. V., Matyshevska, O. P., Slobodyanik, M. S., Frohme, M. & Lampeka, R. D. (2021). Chem. Pap. 75, 4899-4906.])

Table 1
Selected bond lengths (Å)

Pd1—Cl1 2.2811 (11) Pd1—N1 2.061 (3)
Pd1—Cl2 2.2837 (10) Pd1—N2 2.038 (3)

The five-membered ring is rotated relative to the plane of the pyridine-triazole fragment and is in the ac conformation relative to the C7—N4 bond of the triazole ring [the N4—C7—C8—C12 torsion angle is −91.1 (5)°]. The five-membered ring is in an envelope conformation. Atom C8 deviates by 0.564 (8) Å from the mean square plane through the remaining ring atoms (r.m.s.d. = 0.04Å).

3. Supra­molecular features

In the crystal, Pd(HLc-Pe)Cl2 complex mol­ecules, and also mol­ecules of the complex and mol­ecules of DMF are linked by N—H⋯O and C—H⋯N hydrogen bonds (Table 2[link]), forming layers parallel to the bc plane (Fig. 2[link]).

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N4—H4⋯O1 0.86 1.85 2.679 (4) 161
C3—H3⋯N3i 0.93 2.66 3.471 (6) 146
Symmetry code: (i) [x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}].
[Figure 2]
Figure 2
Crystal packing of the title compound.

4. Hirshfeld surface analysis and finger print plots

The inter­molecular inter­actions in the crystal structure of the title compound have been analysed by means of the dnorm property (Fig. 3[link]) mapped over the Hirshfeld surface (Spackman & Jayatilaka, 2009[Spackman, M. A. & Jayatilaka, D. (2009). CrystEngComm, 11, 19-32.]), which was calculated using the CrystalExplorer21 program (Spackman et al., 2021[Spackman, P. R., Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Jayatilaka, D. & Spackman, M. A. (2021). J. Appl. Cryst. 54, 1006-1011.]). The strongest contacts, which are visualized on the Hirshfeld surface as the dark-red spots, correspond to the N—H⋯O hydrogen bond between the complex mol­ecule and the DMF solvent mol­ecule. The lighter red spots correspond to H⋯N/N⋯H inter­actions. The majority of the inter­molecular inter­actions of the title compound are weak, and are represented in blue on the Hirshfeld surface.

[Figure 3]
Figure 3
Three-dimensional Hirshfeld surface of title compound mapped over dnorm.

For further exploration of the inter­mol­ecular inter­actions, two-dimensional fingerprint plots (McKinnon et al., 2007[McKinnon, J. J., Jayatilaka, D. & Spackman, M. A. (2007). Chem. Commun. pp. 3814-3816.]) were generated, as shown in Fig. 4[link]. The H⋯H inter­actions with a contribution of 41.4% have a significant effect on the consolidation in the solid state. The Cl⋯H/H⋯Cl (18.0%), N⋯H/H⋯N (12.4%), C⋯H/H⋯C (10.7%), O⋯H/H⋯O (5%), Cl⋯C/C⋯Cl (4.5%) and N⋯Cl/Cl⋯N (2.5%) inter­actions are less impactful in comparison.

[Figure 4]
Figure 4
Two-dimensional fingerprint plots for title compound showing (a) all inter­actions, and (b)–(f) delineated into contributions from specific contacts (blue areas) [de and di represent the distances from a point on the Hirshfeld surface to the nearest atoms outside (external) and inside (inter­nal) the surface, respectively].

5. Database survey

A search of the Cambridge Structural Database (CSD, Version 5.45, updated March 2024; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) found only eleven structures containing the Pd atom coordinated to two Cl atoms and a pyridine-triazole fragment. Of these, seven structures contain a 1,2,3-triazol fragment (Ervithayasuporn et al., 2015[Ervithayasuporn, V., Kwanplod, K., Boonmak, J., Youngme, S. & Sangtrirutnugul, P. (2015). J. Catal. 332, 62-69.]; Ervithayasuporn, 2016[Ervithayasuporn, V. (2016). CSD Communication (CCDC 1053096). CCDC, Cambridge, England.]; Schweinfurth et al., 2011[Schweinfurth, D., Strobel, S. & Sarkar, B. (2011). Inorg. Chim. Acta, 374, 253-260.]; Yano et al., 2012[Yano, S., Ohi, H., Ashizaki, M., Obata, M., Mikata, Y., Tanaka, R., Nishioka, T., Kinoshita, I., Sugai, Y., Okura, I., Ogura, S., Czaplewska, J. A., Gottschaldt, M., Schubert, U. S., Funabiki, T., Morimoto, K. & Nakai, M. (2012). Chem. Biodivers. 9, 1903-1915.]; Jindabot et al., 2014[Jindabot, S., Teerachanan, K., Thongkam, P., Kiatisevi, S., Khamnaen, T., Phiriyawirut, P., Charoenchaidet, S., Sooksimuang, T., Kongsaeree, P. & Sangtrirutnugul, P. (2014). J. Organomet. Chem. 750, 35-40.]; Schweinfurth et al., 2009[Schweinfurth, D., Pattacini, R., Strobel, S. & Sarkar, B. (2009). Dalton Trans. pp. 9291-9297.]; Lang et al., 2012[Lang, C., Kiefer, C., Lejeune, E., Goldmann, A. S., Breher, F., Roesky, P. W. & Barner-Kowollik, C. (2012). Polym. Chem. 3, 2413-2420.]) and four structures contain a 1,2,4-triazol fragment (Khomenko et al., 2009[Khomenko, D. N., Doroschuk, R. A. & Lampeka, R. D. (2009). Ukr. J. Chem. 75, 30-33.]; Zakharchenko et al., 2021[Zakharchenko, B. V., Khomenko, D. M., Doroschuk, R. O., Raspertova, I. V., Shova, S., Grebinyk, A. G., Grynyuk, I. I., Prylutska, S. V., Matyshevska, O. P., Slobodyanik, M. S., Frohme, M. & Lampeka, R. D. (2021). Chem. Pap. 75, 4899-4906.]; Ohorodnik et al., 2023[Ohorodnik, Y. M., Khomenko, D. M., Doroshchuk, R. O., Raspertova, I. V., Shova, S., Babak, M. V., Milunovic, M. N. M. & Lampeka, R. D. (2023). Inorg. Chim. Acta, 556, 121646.]). All of the structures have a square-planar coordination of the Pd atom. The Pd—N and Pd—Cl bond distances vary from 1.999 (2)–2.066 (3) Å and 2.264 (2)–2.293 (2)Å, respectively.

6. Synthesis and crystallization

To obtain the complex Pd(HLc-Pe)Cl2·DMF, 0.2 mmol of pre-synthesized Pd(HLc-Pe)Cl2 (Ivanova et al., 2024[Ivanova, H. V., Khomenko, D. M., Doroshchuk, R. O., Stoica, A.-C., Zakharchenko, B. V., Rusanova, J. A., Raspertova, I. V., Shova, S. & Lampeka, R. D. (2024). ChemistrySelect, https://doi. org/10.1002/slct. 202402258.]) was dissolved in 1 ml of DMF and salted out with 1 ml of MTBE (methyl tert-butyl ether) at room temperature for 72 h, affording yellow crystals. The crystals were collected by filtration.

Pd(HLc-Pe)Cl2. Yield 66%. m. p. >523 K decomp. 1H NMR (400 MHz, DMSO-d6) δ: 15.17 (br s, 1H, NH), 9.04 (d, J = 5.6 Hz, 1H, Py-H6), 8.28 (t, J = 7.7 Hz, 1H, Py-H4), 8.15 (d, J = 8.1 Hz, 1H, Py-H3), 7.76 (t, J = 6.0 Hz, 1H, Py-H5), 4.20 (m, 1H, H9), 2.15 (m, 2H, Hc-Pe), 1.78–1.62 (m, 6H, Hc-Pe) ppm (Fig. 5[link]). IR (KBr, cm−1): 3457, 3250, 2945, 2873, 1621, 1543, 1470, 1287, 1090, 788, 723, 467 (Fig. 6[link]). Elemental analysis: Analysis calculated for C12H14Cl2N4Pd (391.58): C, 36.81%; H, 3.60%; N, 14.31%. Found: C: 36.65% H: 3.52% N: 14.43%.

[Figure 5]
Figure 5
1H NMR spectrum of Pd(HLc-Pe)Cl2 in DMSO-d6.
[Figure 6]
Figure 6
IR spectrum for Pd(HLc-Pe)Cl2.

7. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3[link]. The H atoms were placed in calculated positions and refined using a riding model with Uiso(H) = nUeq of the carrier atom (n = 1.5 for methyl groups and n = 1.2 for other hydrogen atoms). The Uij values of the C atoms of the five-membered ring were restrained to be similar to each other (within a standard deviation of 0.02 Å2).

Table 3
Experimental details

Crystal data
Chemical formula [PdCl2(C12H14N4)]·C3H7NO
Mr 464.67
Crystal system, space group Monoclinic, P21/c
Temperature (K) 296
a, b, c (Å) 9.3964 (8), 20.2572 (16), 9.9822 (7)
β (°) 96.358 (2)
V (Å3) 1888.4 (3)
Z 4
Radiation type Mo Kα
μ (mm−1) 1.28
Crystal size (mm) 0.4 × 0.2 × 0.15
 
Data collection
Diffractometer Bruker APEXII CCD
Absorption correction Multi-scan (SADABS; Krause et al., 2015[Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3-10.])
Tmin, Tmax 0.533, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections 13789, 4304, 3345
Rint 0.046
(sin θ/λ)max (Å−1) 0.650
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.051, 0.093, 1.12
No. of reflections 4304
No. of parameters 219
No. of restraints 30
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.64, −0.94
Computer programs: APEX2 and SAINT (Bruker, 2014[Bruker (2014). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT2018/2 (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2019/3 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]) and OLEX2 1.5 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]).

Supporting information

CCDC reference: 2376338

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989024007801/ex2086sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989024007801/ex2086Isup2.hkl

checkCIF report


Computing details top

Dichlorido[2-(3-cyclopentyl-1,2,4-triazol-5-yl-κN4)pyridine-κN]palladium(II) dimethylformamide monosolvate top
Crystal data top
[PdCl2(C12H14N4)]·C3H7NOF(000) = 936
Mr = 464.67Dx = 1.634 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 9.3964 (8) ÅCell parameters from 6028 reflections
b = 20.2572 (16) Åθ = 2.3–30.3°
c = 9.9822 (7) ŵ = 1.28 mm−1
β = 96.358 (2)°T = 296 K
V = 1888.4 (3) Å3Block, orange
Z = 40.4 × 0.2 × 0.15 mm
Data collection top
Bruker APEXII CCD
diffractometer		3345 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.046
φ and ω scansθmax = 27.5°, θmin = 2.0°
Absorption correction: multi-scan
(SADABS; Krause et al., 2015)		h = −12→11
Tmin = 0.533, Tmax = 0.746k = −23→26
13789 measured reflectionsl = −10→12
4304 independent reflections
Refinement top
Refinement on F2Primary atom site location: dual
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.051H-atom parameters constrained
wR(F2) = 0.093 w = 1/[σ2(Fo2) + (0.0356P)2 + 0.2719P]
where P = (Fo2 + 2Fc2)/3
S = 1.12(Δ/σ)max = 0.002
4304 reflectionsΔρmax = 0.64 e Å−3
219 parametersΔρmin = −0.94 e Å−3
30 restraints
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. Using Olex2 (Dolomanov et al., 2009), the structure was solved with the SHELXT (Sheldrick, 2018) structure solution program using Intrinsic Phasing and refined with the SHELXL (Sheldrick, 2015) refinement package. Full-matrix least-squares refinement against F2 in anisotropic approximation was used for non-hydrogen atoms.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Pd10.14161 (3)0.51528 (2)0.63841 (3)0.02837 (10)
Cl10.17109 (12)0.61436 (5)0.53648 (11)0.0457 (3)
Cl20.06163 (12)0.56975 (5)0.81588 (11)0.0475 (3)
N10.1217 (3)0.42381 (15)0.7248 (3)0.0309 (7)
N20.2130 (3)0.45857 (15)0.4909 (3)0.0261 (7)
N30.2590 (4)0.35403 (16)0.4333 (3)0.0399 (8)
N40.2936 (4)0.39792 (16)0.3393 (3)0.0382 (8)
H40.3289390.3869350.2666290.046*
C10.0774 (5)0.4111 (2)0.8460 (4)0.0450 (11)
H10.0499670.4460100.8980620.054*
C20.0718 (5)0.3477 (2)0.8945 (5)0.0596 (14)
H20.0402420.3399940.9781520.072*
C30.1129 (5)0.2958 (2)0.8188 (5)0.0582 (13)
H30.1094210.2527210.8506740.070*
C40.1593 (5)0.3083 (2)0.6954 (4)0.0469 (11)
H4A0.1887240.2739510.6429970.056*
C50.1612 (4)0.37237 (19)0.6510 (4)0.0330 (9)
C60.2103 (4)0.39271 (19)0.5233 (4)0.0312 (9)
C70.2667 (4)0.4598 (2)0.3727 (4)0.0313 (8)
C80.2970 (4)0.5186 (2)0.2913 (4)0.0344 (9)
H80.2256340.5524960.3050200.041*
C90.2950 (5)0.5072 (2)0.1405 (4)0.0501 (11)
H9A0.3451620.4669190.1222900.060*
H9B0.1976560.5047720.0968550.060*
C100.3716 (6)0.5671 (3)0.0933 (5)0.0771 (16)
H10A0.4201080.5562420.0152820.093*
H10B0.3041620.6025250.0691440.093*
C110.4769 (6)0.5871 (3)0.2084 (6)0.0959 (19)
H11A0.4685580.6339990.2256070.115*
H11B0.5735290.5781540.1878750.115*
C120.4455 (5)0.5479 (3)0.3309 (5)0.0609 (13)
H12A0.4452560.5763710.4090770.073*
H12B0.5159950.5133550.3510910.073*
O10.4202 (4)0.33801 (18)0.1446 (3)0.0690 (10)
N50.6183 (4)0.28119 (17)0.1094 (4)0.0473 (9)
C130.5478 (6)0.3255 (2)0.1708 (4)0.0543 (13)
H130.5985120.3494480.2399000.065*
C140.5465 (6)0.2439 (3)−0.0011 (5)0.0778 (18)
H14A0.4475180.256600−0.0147840.117*
H14B0.5534800.1976710.0194150.117*
H14C0.5907230.252728−0.0814240.117*
C150.7682 (6)0.2678 (3)0.1477 (6)0.0799 (18)
H15A0.8037690.2965980.2202130.120*
H15B0.8207440.2752030.0718940.120*
H15C0.7798810.2227320.1765560.120*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Pd10.02677 (15)0.02755 (16)0.03033 (17)−0.00105 (13)0.00115 (11)−0.00292 (13)
Cl10.0606 (7)0.0298 (5)0.0473 (6)−0.0059 (5)0.0080 (5)−0.0003 (5)
Cl20.0589 (7)0.0423 (6)0.0431 (6)−0.0010 (5)0.0144 (5)−0.0117 (5)
N10.0259 (16)0.0341 (18)0.0317 (18)0.0024 (14)−0.0002 (13)−0.0026 (14)
N20.0241 (15)0.0229 (15)0.0306 (17)0.0004 (13)−0.0003 (13)−0.0014 (13)
N30.049 (2)0.0303 (19)0.042 (2)0.0047 (16)0.0135 (17)−0.0008 (16)
N40.046 (2)0.037 (2)0.0342 (19)0.0060 (16)0.0126 (16)−0.0037 (15)
C10.056 (3)0.048 (3)0.033 (2)0.005 (2)0.013 (2)−0.001 (2)
C20.077 (4)0.059 (3)0.046 (3)0.007 (3)0.020 (3)0.019 (2)
C30.075 (4)0.039 (3)0.063 (3)0.007 (3)0.018 (3)0.022 (2)
C40.057 (3)0.033 (2)0.052 (3)0.006 (2)0.012 (2)0.007 (2)
C50.028 (2)0.033 (2)0.037 (2)0.0005 (17)−0.0003 (17)0.0011 (18)
C60.030 (2)0.028 (2)0.035 (2)−0.0012 (17)0.0003 (17)−0.0010 (17)
C70.0252 (19)0.037 (2)0.032 (2)0.0006 (17)0.0019 (16)0.0001 (17)
C80.0318 (19)0.040 (2)0.031 (2)−0.0023 (18)0.0002 (16)−0.0001 (18)
C90.055 (3)0.062 (3)0.033 (2)−0.005 (2)0.002 (2)0.005 (2)
C100.077 (3)0.098 (4)0.056 (3)−0.025 (3)0.008 (3)0.024 (3)
C110.080 (4)0.124 (5)0.080 (4)−0.046 (3)−0.009 (3)0.043 (3)
C120.051 (3)0.072 (3)0.056 (3)−0.024 (3)−0.009 (2)0.016 (3)
O10.085 (3)0.071 (3)0.056 (2)0.029 (2)0.026 (2)−0.0065 (18)
N50.054 (2)0.034 (2)0.055 (2)−0.0022 (18)0.0126 (19)−0.0088 (17)
C130.087 (4)0.043 (3)0.036 (3)0.009 (3)0.019 (3)−0.002 (2)
C140.066 (4)0.071 (4)0.095 (5)0.008 (3)0.000 (3)−0.038 (3)
C150.066 (4)0.059 (4)0.115 (5)−0.006 (3)0.012 (4)−0.028 (3)
Geometric parameters (Å, º) top
Pd1—Cl12.2811 (11)C8—C121.528 (6)
Pd1—Cl22.2837 (10)C9—H9A0.9700
Pd1—N12.061 (3)C9—H9B0.9700
Pd1—N22.038 (3)C9—C101.511 (6)
N1—C11.348 (5)C10—H10A0.9700
N1—C51.352 (5)C10—H10B0.9700
N2—C61.374 (5)C10—C111.487 (7)
N2—C71.334 (4)C11—H11A0.9700
N3—N41.358 (4)C11—H11B0.9700
N3—C61.312 (5)C11—C121.514 (7)
N4—H40.8600C12—H12A0.9700
N4—C71.328 (5)C12—H12B0.9700
C1—H10.9300O1—C131.225 (6)
C1—C21.376 (6)N5—C131.308 (5)
C2—H20.9300N5—C141.440 (6)
C2—C31.376 (6)N5—C151.444 (6)
C3—H30.9300C13—H130.9300
C3—C41.375 (6)C14—H14A0.9600
C4—H4A0.9300C14—H14B0.9600
C4—C51.373 (5)C14—H14C0.9600
C5—C61.462 (5)C15—H15A0.9600
C7—C81.487 (5)C15—H15B0.9600
C8—H80.9800C15—H15C0.9600
C8—C91.522 (5)
Cl1—Pd1—Cl289.29 (4)C8—C9—H9A111.1
N1—Pd1—Cl1177.27 (9)C8—C9—H9B111.1
N1—Pd1—Cl293.27 (9)H9A—C9—H9B109.0
N2—Pd1—Cl196.18 (9)C10—C9—C8103.5 (4)
N2—Pd1—Cl2174.47 (9)C10—C9—H9A111.1
N2—Pd1—N181.25 (12)C10—C9—H9B111.1
C1—N1—Pd1126.8 (3)C9—C10—H10A110.5
C1—N1—C5118.3 (4)C9—C10—H10B110.5
C5—N1—Pd1115.0 (2)H10A—C10—H10B108.7
C6—N2—Pd1111.2 (2)C11—C10—C9106.1 (4)
C7—N2—Pd1144.6 (3)C11—C10—H10A110.5
C7—N2—C6104.2 (3)C11—C10—H10B110.5
C6—N3—N4102.1 (3)C10—C11—H11A110.1
N3—N4—H4123.9C10—C11—H11B110.1
C7—N4—N3112.2 (3)C10—C11—C12108.0 (4)
C7—N4—H4123.9H11A—C11—H11B108.4
N1—C1—H1119.3C12—C11—H11A110.1
N1—C1—C2121.4 (4)C12—C11—H11B110.1
C2—C1—H1119.3C8—C12—H12A110.9
C1—C2—H2120.1C8—C12—H12B110.9
C1—C2—C3119.8 (4)C11—C12—C8104.4 (4)
C3—C2—H2120.1C11—C12—H12A110.9
C2—C3—H3120.4C11—C12—H12B110.9
C4—C3—C2119.2 (4)H12A—C12—H12B108.9
C4—C3—H3120.4C13—N5—C14120.0 (4)
C3—C4—H4A120.7C13—N5—C15122.3 (4)
C5—C4—C3118.7 (4)C14—N5—C15117.7 (4)
C5—C4—H4A120.7O1—C13—N5125.2 (5)
N1—C5—C4122.6 (4)O1—C13—H13117.4
N1—C5—C6113.0 (3)N5—C13—H13117.4
C4—C5—C6124.4 (4)N5—C14—H14A109.5
N2—C6—C5119.6 (3)N5—C14—H14B109.5
N3—C6—N2113.7 (3)N5—C14—H14C109.5
N3—C6—C5126.6 (4)H14A—C14—H14B109.5
N2—C7—C8127.7 (4)H14A—C14—H14C109.5
N4—C7—N2107.8 (3)H14B—C14—H14C109.5
N4—C7—C8124.4 (3)N5—C15—H15A109.5
C7—C8—H8108.1N5—C15—H15B109.5
C7—C8—C9116.0 (4)N5—C15—H15C109.5
C7—C8—C12113.2 (3)H15A—C15—H15B109.5
C9—C8—H8108.1H15A—C15—H15C109.5
C9—C8—C12103.0 (3)H15B—C15—H15C109.5
C12—C8—H8108.1
Pd1—N1—C1—C2−178.4 (3)C2—C3—C4—C5−0.8 (7)
Pd1—N1—C5—C4177.8 (3)C3—C4—C5—N11.2 (7)
Pd1—N1—C5—C6−0.1 (4)C3—C4—C5—C6178.8 (4)
Pd1—N2—C6—N3−178.2 (3)C4—C5—C6—N2−177.5 (4)
Pd1—N2—C6—C5−0.5 (4)C4—C5—C6—N30.0 (6)
Pd1—N2—C7—N4177.4 (3)C5—N1—C1—C2−0.1 (6)
Pd1—N2—C7—C8−1.0 (7)C6—N2—C7—N4−0.1 (4)
N1—C1—C2—C30.4 (8)C6—N2—C7—C8−178.5 (3)
N1—C5—C6—N20.4 (5)C6—N3—N4—C70.1 (4)
N1—C5—C6—N3177.8 (4)C7—N2—C6—N30.2 (4)
N2—C7—C8—C9−154.3 (4)C7—N2—C6—C5178.0 (3)
N2—C7—C8—C1286.9 (5)C7—C8—C9—C10−163.2 (4)
N3—N4—C7—N20.0 (4)C7—C8—C12—C11158.7 (4)
N3—N4—C7—C8178.4 (3)C8—C9—C10—C1130.6 (6)
N4—N3—C6—N2−0.2 (4)C9—C8—C12—C1132.7 (5)
N4—N3—C6—C5−177.7 (4)C9—C10—C11—C12−10.2 (7)
N4—C7—C8—C927.7 (5)C10—C11—C12—C8−14.2 (7)
N4—C7—C8—C12−91.1 (5)C12—C8—C9—C10−39.0 (5)
C1—N1—C5—C4−0.7 (6)C14—N5—C13—O11.9 (8)
C1—N1—C5—C6−178.6 (3)C15—N5—C13—O1−178.4 (5)
C1—C2—C3—C40.0 (8)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N4—H4···O10.861.852.679 (4)161
C3—H3···N3i0.932.663.471 (6)146
Symmetry code: (i) x, −y+1/2, z+1/2.
 

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ISSN: 2056-9890
Volume 80| Part 9| September 2024| Pages 956-960
https://doi.org/10.1107/S2056989024007801
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