Di­chlorido­[2-(pyridin-2-yl-κN)-1,5-naphthyridine-κN1]zinc(II)

Tsubokawa, K.; Iida, T.; Tsuge, K.; Ohtsu, H.

doi:10.1107/S2414314625007643

metal-organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 10| Part 9| September 2025| x250764

https://doi.org/10.1107/S2414314625007643

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Dichlorido[2-(pyridin-2-yl-κN)-1,5-naphthyridine-κN¹]zinc(II)

Kodai Tsubokawa,^a Takuro Iida,^a Kiyoshi Tsuge ^a and Hideki Ohtsu ^a ^*

^aGraduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
^*Correspondence e-mail: [email protected]

Edited by M. Bolte, Goethe-Universität Frankfurt, Germany (Received 25 August 2025; accepted 27 August 2025; online 5 September 2025)

The title zinc(II) complex, [ZnCl₂(C₁₃H₉N₃)], crystallizes in the triclinic space group P1. The coordination environment around the zinc(II) ion in the title complex can be described as a distorted tetrahedron formed by the two N atoms of the NAD⁺/NADH model ligand pn [pn = 2-(pyridin-2-yl)[1,5]naphthyridine] and two Cl⁻ ions. There are π–π stacking interactions in the crystal packing of the title compound.

Keywords: crystal structure; zinc(II) complex; NAD⁺/NADH model ligand.

CCDC reference: 2480689

Structure description

Photo-driven carbon dioxide (CO₂) reduction has been one of the most attractive approaches to address global energy and environmental problems because of its capacity to transform CO₂ into value-added chemical compounds, such as formic acid and carbon monoxide, under mild conditions by utilizing solar energy (Wang et al., 2022 ). Transition-metal molecular catalysts are an important tool and play a central role in the roadmap to achieve efficient and novel CO₂ photoreduction into valuable chemicals (Kumagai et al., 2022 ). Our motivation for investigating transition-metal complexes with a coenzyme NAD⁺/NADH model ligand is based on their potential as candidates for photocatalytic CO₂ reduction. The synthesis and use of the NAD⁺/NADH model ligand pbn [pbn = 2-(pyridin-2-yl)benzo[b][1,5]naphthyridine] was first reported by Koizumi & Tanaka (2005 ), and we have previously developed a novel photocatalytic CO₂ reduction process to produce formic acid using a Ru-based pbn complex (Ohtsu & Tanaka, 2012 ; Ohtsu et al., 2015 , 2019 ).

In order to further develop transition-metal NAD⁺/NADH model complexes, substituent tuning of NAD⁺/NADH model ligands offers a potentially powerful means not only to control catalytic activity of the complexes but also to confer new reactivity on the complexes. However, the synthetic pathway to introduce substituents into the benzonaphthyridine skeleton of the pbn ligand is considerably difficult.

As part of our ongoing investigation of transition-metal complexes bearing various substituted NAD⁺/NADH model ligands, we have focused on the non-substituted NAD⁺/NADH model ligand pn [pn = 2-(pyridin-2-yl)[1,5]naphthyridine] synthesized by Singh & Thummel (2009 ), which can possess the potential to facilitate the introduction of substituents through a straightforward synthetic process. A new zinc(II) complex with a pn ligand has been structurally characterized and is reported in this paper.

The molecular structure of the title complex, [ZnCl₂(pn)], is shown in Fig. 1 and selected geometrical data are listed in Table 1. The zinc(II) ion in [ZnCl₂(pn)] has a tetracoordinate structure formed by the two N atoms of pn ligand [Zn1—N2 = 2.0909 (14) Å, Zn1—N3 = 2.0560 (14) Å] and two Cl⁻ ions [Zn1—Cl1 = 2.2137 (6) Å, Zn1—Cl2 = 2.2161 (6) Å]. The quantitative difference in four-coordinate geometry is indicated by an index of τ₄. The value can range from τ₄ = 1 for a perfect tetrahedral geometry to τ₄ = 0 for a perfect square planar geometry (Yang et al., 2007 ). The τ₄ value for the zinc(II) ion of the title complex is obtained as τ₄ = 0.88 by using the equation τ₄ = [360–(α+β)]/141 (Yang et al., 2007), where α = N3—Zn1—Cl2 [120.94 (4)°], β = Cl1—Zn1—Cl2 [114.81 (2)°]. Thus, the coordination environment of the zinc(II) ion in [ZnCl₂(pn)] is a slightly distorted tetrahedron. The pyridine ring and the naphthyridine ring system in the pn ligand are twisted to give a dihedral angle of 10.57 (5)° between the two least-squares planes.

Table 1
Selected geometric parameters (Å, °)

Zn1—N3	2.0560 (14)	Zn1—Cl1	2.2137 (6)
Zn1—N2	2.0909 (14)	Zn1—Cl2	2.2161 (6)

N3—Zn1—N2	79.59 (6)	N3—Zn1—Cl2	120.94 (4)
N3—Zn1—Cl1	113.63 (4)	N2—Zn1—Cl2	108.77 (4)
N2—Zn1—Cl1	113.74 (4)	Cl1—Zn1—Cl2	114.81 (2)

Figure 1
The molecular structure of the title compound with displacement ellipsoids for non-hydrogen atoms at the 50% probability level.

The crystal packing of the title complex is shown in Fig. 2. There are noteworthy π–π stacking interactions between neighboring naphthyridine ring systems of the pn ligand, with a centroid–centroid distance of 3.625 (1) Å. No other significant or interesting intermolecular interactions are observed.

Figure 2
Part of the crystal structure showing a π–π interaction (red dotted line). Zn atoms are represented in yellow, Cl in green, N in blue, and C in gray. Hydrogen atoms are omitted for clarity.

Synthesis and crystallization

The NAD⁺/NADH model ligand, 2-(pyridin-2-yl)[1,5]naphthyridine abbreviated as pn, was prepared according to the literature procedure (Singh & Thummel, 2009).

To a dichloromethane solution (4.0 ml) of pn (36.44 mg, 17.6 mmol) was added dropwise ZnCl₂ (23.95 mg, 17.6 mmol) in acetonitrile (4.0 ml), and the resulting solution was left to stand for a few days at room temperature. Light-yellow crystals of the title compound [ZnCl₂(pn)] were obtained (yield; 44.48 mg, 73.7%). Elemental analysis, found: C 45.32, H 2.69, N 12.18%; calculated for C₁₃H₉Cl₂N₃Zn: C 45.45, H 2.64, N 12.23%.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	[ZnCl₂(C₁₃H₉N₃)]
M_r	343.52
Crystal system, space group	Triclinic, P $[\overline{1}]$
Temperature (K)	173
a, b, c (Å)	8.0634 (15), 8.6146 (17), 10.2087 (19)
α, β, γ (°)	86.492 (6), 78.622 (6), 70.336 (5)
V (Å³)	654.6 (2)
Z	2
Radiation type	Mo Kα
μ (mm⁻¹)	2.27
Crystal size (mm)	0.23 × 0.11 × 0.07

Data collection
Diffractometer	Rigaku R-AXIS RAPID
Absorption correction	Multi-scan (ABSCOR; Rigaku, 1995 )
T_min, T_max	0.630, 0.853
No. of measured, independent and observed [F² > 2.0σ(F²)] reflections	6486, 2992, 2693
R_int	0.034
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.026, 0.069, 1.03
No. of reflections	2992
No. of parameters	172
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.43, −0.28
Computer programs: RAPID-AUTO (Rigaku, 2001 ), SHELXT2018/2 (Sheldrick, 2015a ), SHELXL2019/3 (Sheldrick, 2015b ), CrystalStructure (Rigaku, 2019 ), CrystalMaker (Palmer, 2014 ) and publCIF (Westrip, 2010 ).

Structural data

CCDC reference: 2480689

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2414314625007643/bt4180sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314625007643/bt4180Isup2.hkl

checkCIF report

Computing details top

Dichlorido[2-(pyridin-2-yl-κN)-1,5-naphthyridine-κN¹]zinc(II) top

Crystal data top

[ZnCl₂(C₁₃H₉N₃)]	Z = 2
M_r = 343.52	F(000) = 344.00
Triclinic, P1	D_x = 1.743 Mg m⁻³
a = 8.0634 (15) Å	Mo Kα radiation, λ = 0.71075 Å
b = 8.6146 (17) Å	Cell parameters from 4464 reflections
c = 10.2087 (19) Å	θ = 2.0–27.5°
α = 86.492 (6)°	µ = 2.27 mm⁻¹
β = 78.622 (6)°	T = 173 K
γ = 70.336 (5)°	Block, colorless
V = 654.6 (2) Å³	0.23 × 0.11 × 0.07 mm

Data collection top

Rigaku R-AXIS RAPID diffractometer	2693 reflections with F² > 2.0σ(F²)
Detector resolution: 10.000 pixels mm^-1	R_int = 0.034
ω scans	θ_max = 27.5°, θ_min = 2.5°
Absorption correction: multi-scan (ABSCOR; Rigaku, 1995)	h = −10→10
T_min = 0.630, T_max = 0.853	k = −11→11
6486 measured reflections	l = −13→12
2992 independent reflections

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.026	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.069	H-atom parameters constrained
S = 1.03	w = 1/[σ²(F_o²) + (0.0387P)² + 0.1345P] where P = (F_o² + 2F_c²)/3
2992 reflections	(Δ/σ)_max = 0.001
172 parameters	Δρ_max = 0.43 e Å⁻³
0 restraints	Δρ_min = −0.28 e Å⁻³
Primary atom site location: structure-invariant direct methods

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. Refinement was performed using all reflections. The weighted R-factor (wR) and goodness of fit (S) are based on F². R-factor (gt) are based on F. The threshold expression of F² > 2.0 sigma(F²) is used only for calculating R-factor (gt).

H atoms were located in a difference map and refined as riding on their parent atoms with C–H = 0.95 Å and with U_iso(H) = 1.2 U_eq(C).

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
Zn1	0.52702 (3)	0.80210 (2)	0.18747 (2)	0.02563 (8)
Cl1	0.70577 (6)	0.89381 (6)	0.27656 (5)	0.03363 (12)
Cl2	0.29182 (6)	0.99685 (6)	0.13125 (5)	0.03711 (12)
N1	0.1233 (2)	0.5604 (2)	0.59856 (15)	0.0327 (3)
N2	0.43844 (18)	0.62744 (18)	0.30470 (13)	0.0220 (3)
N3	0.66057 (19)	0.59482 (18)	0.07077 (14)	0.0235 (3)
C1	0.0609 (2)	0.7111 (3)	0.64747 (18)	0.0326 (4)
H1	−0.029364	0.732608	0.725885	0.039*
C2	0.1173 (2)	0.8429 (2)	0.59282 (18)	0.0305 (4)
H2	0.068503	0.948033	0.635055	0.037*
C3	0.2437 (2)	0.8172 (2)	0.47777 (18)	0.0284 (4)
H3	0.284141	0.903886	0.438031	0.034*
C4	0.3122 (2)	0.6578 (2)	0.41992 (16)	0.0227 (3)
C5	0.2495 (2)	0.5333 (2)	0.48381 (16)	0.0250 (3)
C6	0.3234 (2)	0.3738 (2)	0.42718 (18)	0.0287 (4)
H6	0.284985	0.286671	0.468330	0.034*
C7	0.4511 (2)	0.3448 (2)	0.31252 (17)	0.0259 (3)
H7	0.501827	0.237854	0.273490	0.031*
C8	0.5059 (2)	0.4762 (2)	0.25336 (15)	0.0215 (3)
C9	0.6415 (2)	0.4540 (2)	0.12667 (15)	0.0218 (3)
C10	0.7425 (2)	0.3016 (2)	0.06984 (18)	0.0280 (4)
H10	0.728308	0.203757	0.111003	0.034*
C11	0.8650 (2)	0.2936 (2)	−0.04844 (18)	0.0303 (4)
H11	0.937152	0.189843	−0.088050	0.036*
C12	0.8812 (2)	0.4371 (2)	−0.10788 (17)	0.0291 (4)
H12	0.961660	0.434432	−0.190011	0.035*
C13	0.7767 (2)	0.5854 (2)	−0.04455 (17)	0.0280 (4)
H13	0.788006	0.684666	−0.084677	0.034*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Zn1	0.02615 (12)	0.01684 (12)	0.03053 (12)	−0.00643 (9)	0.00227 (9)	−0.00346 (8)
Cl1	0.0383 (2)	0.0267 (2)	0.0385 (2)	−0.01520 (19)	−0.0046 (2)	−0.00282 (18)
Cl2	0.0341 (2)	0.0217 (2)	0.0473 (3)	−0.00115 (18)	−0.0029 (2)	−0.00052 (19)
N1	0.0306 (8)	0.0319 (9)	0.0285 (7)	−0.0073 (7)	0.0053 (7)	0.0006 (6)
N2	0.0207 (6)	0.0200 (7)	0.0236 (6)	−0.0062 (5)	−0.0003 (6)	−0.0030 (5)
N3	0.0251 (7)	0.0181 (7)	0.0247 (6)	−0.0057 (6)	−0.0007 (6)	−0.0010 (5)
C1	0.0269 (9)	0.0360 (11)	0.0263 (8)	−0.0041 (8)	0.0039 (7)	−0.0017 (7)
C2	0.0252 (8)	0.0295 (10)	0.0309 (9)	−0.0023 (7)	−0.0014 (7)	−0.0085 (7)
C3	0.0275 (8)	0.0243 (9)	0.0308 (9)	−0.0075 (7)	−0.0003 (8)	−0.0046 (7)
C4	0.0188 (7)	0.0239 (9)	0.0234 (8)	−0.0049 (6)	−0.0030 (7)	−0.0015 (6)
C5	0.0230 (8)	0.0258 (9)	0.0232 (7)	−0.0058 (7)	−0.0023 (7)	0.0019 (6)
C6	0.0322 (9)	0.0226 (9)	0.0301 (8)	−0.0106 (7)	−0.0015 (8)	0.0038 (7)
C7	0.0292 (8)	0.0187 (8)	0.0268 (8)	−0.0052 (7)	−0.0032 (7)	−0.0004 (6)
C8	0.0211 (7)	0.0198 (8)	0.0221 (7)	−0.0053 (6)	−0.0035 (7)	−0.0001 (6)
C9	0.0220 (7)	0.0205 (8)	0.0219 (7)	−0.0060 (6)	−0.0031 (7)	−0.0011 (6)
C10	0.0322 (9)	0.0195 (9)	0.0295 (8)	−0.0071 (7)	−0.0010 (8)	−0.0019 (7)
C11	0.0299 (9)	0.0236 (9)	0.0318 (9)	−0.0049 (7)	0.0023 (8)	−0.0073 (7)
C12	0.0272 (8)	0.0311 (10)	0.0250 (8)	−0.0081 (7)	0.0024 (7)	−0.0034 (7)
C13	0.0298 (9)	0.0247 (9)	0.0271 (8)	−0.0094 (7)	0.0005 (7)	0.0013 (7)

Geometric parameters (Å, º) top

Zn1—N3	2.0560 (14)	C4—C5	1.408 (2)
Zn1—N2	2.0909 (14)	C5—C6	1.410 (3)
Zn1—Cl1	2.2137 (6)	C6—C7	1.371 (2)
Zn1—Cl2	2.2161 (6)	C6—H6	0.9500
N1—C1	1.314 (3)	C7—C8	1.410 (2)
N1—C5	1.366 (2)	C7—H7	0.9500
N2—C8	1.328 (2)	C8—C9	1.496 (2)
N2—C4	1.369 (2)	C9—C10	1.382 (2)
N3—C13	1.340 (2)	C10—C11	1.390 (2)
N3—C9	1.352 (2)	C10—H10	0.9500
C1—C2	1.406 (3)	C11—C12	1.378 (3)
C1—H1	0.9500	C11—H11	0.9500
C2—C3	1.369 (3)	C12—C13	1.386 (3)
C2—H2	0.9500	C12—H12	0.9500
C3—C4	1.414 (2)	C13—H13	0.9500
C3—H3	0.9500

N3—Zn1—N2	79.59 (6)	N1—C5—C6	119.26 (16)
N3—Zn1—Cl1	113.63 (4)	C4—C5—C6	117.99 (15)
N2—Zn1—Cl1	113.74 (4)	C7—C6—C5	119.77 (16)
N3—Zn1—Cl2	120.94 (4)	C7—C6—H6	120.1
N2—Zn1—Cl2	108.77 (4)	C5—C6—H6	120.1
Cl1—Zn1—Cl2	114.81 (2)	C6—C7—C8	119.04 (16)
C1—N1—C5	116.46 (16)	C6—C7—H7	120.5
C8—N2—C4	119.22 (14)	C8—C7—H7	120.5
C8—N2—Zn1	114.20 (11)	N2—C8—C7	122.39 (15)
C4—N2—Zn1	126.40 (11)	N2—C8—C9	115.80 (14)
C13—N3—C9	118.69 (15)	C7—C8—C9	121.80 (15)
C13—N3—Zn1	126.24 (12)	N3—C9—C10	121.59 (15)
C9—N3—Zn1	114.60 (11)	N3—C9—C8	115.16 (14)
N1—C1—C2	125.12 (17)	C10—C9—C8	123.25 (15)
N1—C1—H1	117.4	C9—C10—C11	119.02 (16)
C2—C1—H1	117.4	C9—C10—H10	120.5
C3—C2—C1	118.96 (17)	C11—C10—H10	120.5
C3—C2—H2	120.5	C12—C11—C10	119.61 (17)
C1—C2—H2	120.5	C12—C11—H11	120.2
C2—C3—C4	117.95 (17)	C10—C11—H11	120.2
C2—C3—H3	121.0	C11—C12—C13	118.17 (16)
C4—C3—H3	121.0	C11—C12—H12	120.9
N2—C4—C5	121.59 (15)	C13—C12—H12	120.9
N2—C4—C3	119.67 (16)	N3—C13—C12	122.88 (17)
C5—C4—C3	118.74 (15)	N3—C13—H13	118.6
N1—C5—C4	122.75 (16)	C12—C13—H13	118.6

C5—N1—C1—C2	−1.7 (3)	C4—N2—C8—C9	179.39 (14)
N1—C1—C2—C3	1.8 (3)	Zn1—N2—C8—C9	3.94 (17)
C1—C2—C3—C4	−0.4 (3)	C6—C7—C8—N2	0.0 (3)
C8—N2—C4—C5	−1.3 (2)	C6—C7—C8—C9	−178.65 (15)
Zn1—N2—C4—C5	173.50 (12)	C13—N3—C9—C10	2.0 (2)
C8—N2—C4—C3	177.99 (15)	Zn1—N3—C9—C10	−170.68 (13)
Zn1—N2—C4—C3	−7.2 (2)	C13—N3—C9—C8	−178.52 (15)
C2—C3—C4—N2	179.83 (15)	Zn1—N3—C9—C8	8.83 (18)
C2—C3—C4—C5	−0.8 (2)	N2—C8—C9—N3	−8.6 (2)
C1—N1—C5—C4	0.3 (3)	C7—C8—C9—N3	170.21 (15)
C1—N1—C5—C6	179.19 (17)	N2—C8—C9—C10	170.93 (15)
N2—C4—C5—N1	−179.78 (16)	C7—C8—C9—C10	−10.3 (2)
C3—C4—C5—N1	0.9 (2)	N3—C9—C10—C11	−0.7 (3)
N2—C4—C5—C6	1.4 (2)	C8—C9—C10—C11	179.82 (16)
C3—C4—C5—C6	−177.98 (16)	C9—C10—C11—C12	−1.2 (3)
N1—C5—C6—C7	−179.57 (16)	C10—C11—C12—C13	1.8 (3)
C4—C5—C6—C7	−0.7 (3)	C9—N3—C13—C12	−1.4 (3)
C5—C6—C7—C8	0.0 (3)	Zn1—N3—C13—C12	170.35 (13)
C4—N2—C8—C7	0.6 (2)	C11—C12—C13—N3	−0.5 (3)
Zn1—N2—C8—C7	−174.83 (13)

Selected geometric parameters (Å, °) top

Zn1–N2	2.0909 (14)	Zn1–Cl1	2.2137 (6)
Zn1–N3	2.0560 (14)	Zn1–Cl2	2.2161 (6)

N2–Zn1–Cl1	113.74 (4)	N3–Zn1–Cl1	113.63 (4)
N2–Zn1–Cl2	108.77 (4)	N3–Zn1–Cl2	120.94 (4)
N2–Zn1–N3	79.59 (6)

Funding information

This work was supported by Grants-in-Aid for Scientific Research (C) (22K05126, to HO) from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) and Japan Society for the Promotion of Science (JSPS).

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