Crystal Structure and Optical Behavior of Diamino-Substituted 1,4-Benzoquinones

Abstract

Reactions of benzoquinone with amines can potentially lead to the formation of coupled merocyanine or merocyanine/polymethine systems. In this study, several diamino-substituted 1,4-benzoquinones were synthesized. The crystal structures for three derivatives bearing 2-hydroxyethylamino or 2-(2-hydroxyethoxy)ethyl)amino substituents were determined using single-crystal X-ray crystallographic analysis. A characteristic feature of all molecular structures is the presence of an extensive network of intermolecular interactions, significantly stabilized by hydrogen bonding. Additionally, changes in the optical behavior of the synthesized compounds were monitored by UV-Vis spectroscopy in the presence of Cu²⁺ and Zn²⁺ ions, followed by the addition of primary, secondary or biogenic (butane-1,4-diamine) amines.

1. Introduction

Quinones are small molecules found widespread in nature and known due to involvement into numerous biological processes such as photosynthesis [1] and respiratory chains [2] as well as their derivatives have a deep impact on the composition and function of bacterial ecosystems [3]. Moreover, quinone motifs are found in the structure of some co-factors, e.g., Pyrroloquinoline Quinone (PQQ) [4] and 2,4,5-trihydroxyphenylalanine quinone (TPQ). TPQ serves as a part of the copper-containing amine oxidases (CuAOs) where both (copper ion and quinone) are involved in a catalytic cycle [5]. Quinones have shown promise in antimalarial drug design [6]. Interaction between quinones and amino acids can lead to enzymatic browning of foods, the formation of humic substances, and the discoloration of various plants during processing [7]. Also, benzoquinones with replaceable halide or pseudohalide substituents were tested for optical chirality sensing of chiral amines, amino alcohols, and amino acids [8]. Additionally, naturally occurring quinone derivatives can potentially replace synthetic azodyes due to the latter’s known toxicity [9].

During the last decade, quinone derivatives have been intensively studied for application as electroactive materials in advanced electrochemical energy storage devices [10]. Quinones have been investigated for the creation of all-organic aqueous redox systems [11] and to serve as both cathodes [12] and anodes [13] in Li, Na or Zn [14] ion batteries.

It is known that derivatives of 2,5-dihydroxy-1,4-benzoquinone or 2,5-diamino-1,4-benzoquinone are extensively studied as ligands for metal complexes and MOFs [15] which have been investigated for spin–spin coupling, redox isomerism and sensors based on supramolecular assemblies [16].

2,5-Diaminosubstituted 1,4-benzoquinones represent a class of coupled polymethines that possess a unique electronic structure. The simplest derivative-2,5-diamino-3,6-dichloro-1,4-benzoquinone-consist of two nearly independent merocyanine fragments connected by two long single bonds (approximately 1.52 Å). Each merocyanine fragment contains 6π electrons delocalized over the fragment [17]. Such coupled polymethines show a bathochromic shift in their UV-Vis spectra in comparison to the absorption of a single polymethine [18]. Incorporation of substituents that do not affect the merocyanines fragments but can form different types intra- and intermolecular interactions can be beneficial.

In this paper, we report on the results received from the study of 1,4-benzoquinones bearing 2-hydroxyethylamino or 2-(2-hydroxyethoxy)ethyl)amino groups along to halide or pseudohalide (CN) substituents. Molecular structures of quinones 3–5 have been determined by single-crystal X-ray diffraction to investigate the effects of substituents on the formed intra- and intermolecular interactions. Furthermore, considering the potential synergistic effects of quinones and metal ions, we investigated the optical behavior of the synthesized compounds 3–6 in the presence of various amines (sec-butylamine, diethylamine and butane-1,4-diamine) and Cu²⁺ or Zn²⁺ ions. Butane-1,4-diamine is a representative of biogenic amines, which are compounds formed during the food spoilage process [19].

2. Materials and Methods

2.1. Materials and Instrumentation

Reagents and solvents were purified by standard means or used without further purification. Melting points were measured on KSPII Melting Point Analyzer (A.Krüss Optronic, Hamburg, Germany). ¹H and ¹³C NMR spectra were recorded on a Bruker Avance Neo 500 spectrometer (Bruker BioSpin AG BBIO, Rheinstetten, Germany) at 500 Hz in DMSO-d₆ solutions. Chemical shifts were expressed in parts per million (δ, ppm) relative to solvent signal (DMSO-d₆: 2.50 ppm for ¹H and 39.52 ppm for ¹³C) [20]. Elemental CHN analysis was carried on Euro Vector EA 3000 analyzer (EuroVector, Milan, Italy). IR spectra were recorded on a Spectrum 100 FTIR spectrometer (PerkinElmer instruments, Waltham, MA, USA). The UV-Vis absorption spectra were acquired with Lambda 35 35 UV/Vis spectrometer (PerkinElmer instruments, Shelton, CT, USA) using 1 cm length quartz cuvettes with a concentration c = 5 × 10⁻⁵ M of compounds 3–6 in DMF/MeOH (3/2) solutions. Cu²⁺ and Zn²⁺ ions were added as chloride salts (10 eq.) and selected amines were added in excess. Low resolution mass spectra were acquired on a Waters EMD 1000MS mass detector (Waters, Milford, MA, USA) (ESI + mode, voltage 30 V) with Xterra MS C18 5 μm 2.1 100 mm column and gradient eluent mode using 0.1% HCOOH in deionized water and MeCN or MeOH.

2.2. Synthesis of Compounds 3–6

2.2.1. Synthesis Method for Compounds 3, 4 and 6

Chloranil (1a) (0.5 g, 2.03 mmol) or bromanil (1c) (0.86 g, 2.03 mmol) was dissolved in toluene (50 mL) and aminoethanol (2a, 8.13 mmol) or 2-(2-aminoethoxy)ethanol (2b, 8.13 mmol) was added to a stirring solution dropwise at room temperature. The solution was stirred for 8 h. Formed precipitate was filtered and washed with toluene and n-hexane. The precipitate can be recrystallized from MeOH or MeCN.

2.2.2. 2,5-Dichloro-3,6-bis((2-hydroxyethyl)amino)cyclohexa-2,5-diene-1,4-dione (3)

Yield: 0.21 g (35%), dark red solid. M.P.: 187–188 °C (toluene). MS: C₁₀H₁₂Cl₂N₂O₄ requires [M + H]⁺ 297.02; found [M + H]⁺ 297.2. ¹H NMR (500 MHz, DMSO-d₆): δ 7.93 (br.s, 2H, exchange with D₂O, NH), 4.97 (s, 2H, exchange with D₂O, OH), 3.84 (m, 4H, CH₂), 3.58 (m, 4H, CH₂). ¹³C{¹H} NMR could not be acquired due to poor solubility of a compound. IR (KBr pellet, cm⁻¹): 3401, 3314, 3179, 2968, 2926, 1655, 1583, 1503, 1430, 1325, 1082. Anal. Calcd. for C₁₀H₁₂Cl₂N₂O₄ + H₂O (a water molecule is presented in a crystal structure of the compound): C, 38.36; H, 4.51; N, 8.95; found C, 38.75; H, 4.51; N, 9.08.

2.2.3. 2,5-Dichloro-3,6-bis((2-(2-hydroxyethoxy)ethyl)amino)cyclohexa-2,5-diene-1,4-dione (4)

Yield: 0.37 g (48%), dark red solid. M.P.: 137–138 °C (4-I, MeOH). MS: C₁₄H₂₀Cl₂N₂O₆ requires [M + H]⁺ 383.07; found [M + H]⁺ 383.2. ¹H NMR (500 MHz, DMSO-d₆): δ 7.91 (br.s, 2H, exchange with D₂O, NH), 4.62 (t, J = 5.2 Hz, 2H, exchange with D₂O, OH), 3.93 (t, J = 5.2 Hz, 4H, CH₂), 3.62 (t, J = 5.7 Hz, 4H, CH₂), 3.50 (dd, J = 9.9, 4.9 Hz, 4H, CH₂), 3.45 (m, 4H, CH₂). ¹³C{¹H} NMR could not be acquired due to poor solubility of a compound. IR (KBr pellet, cm⁻¹): 3468, 3246, 2960, 2925, 2882, 1659, 1606, 1508, 1479. Anal. Calcd. for C₁₄H₂₀Cl₂N₂O₆: C, 43.88; H, 5.26; N, 7.31; found C, 43.99; H, 5.33; N, 7.45.

2.2.4. 4-Chloro-2,5-bis((2-hydroxyethyl)amino)-3,6-dioxocyclohexa-1,4-dienecarbonitrile (5)

DDQ (1b) (0.5 g, 2.20 mmol) was dissolved in THF (50 mL) and aminoethanol (2a, 0.53 mL, 8.81 mmol) was added to a stirring solution dropwise at room temperature. Solution was stirred for 8 h. Formed precipitate was filtered and recrystallized from MeCN. Yield: 0.25 g (40%), red solid. M.P.: 223–225 °C. MS: C₁₁H₁₂ClN₃O₄ requires [M − H]⁻ 284.05; found [M − H]⁻ 284.2. ¹H NMR (500 MHz, DMSO-d₆): δ 9.12 (br.s, 1H, exchange with D₂O, NH), 8.07 (br.s, 1H, exchange with D₂O, NH), 5.05 (t, J = 5.2 Hz, 1H, exchange with D₂O, OH), 4.99 (s, 1H, exchange with D₂O, OH), 3.86 (m, 2H, CH₂), 3.82 (t, J = 4.5 Hz, 2H, CH₂), 3.66 (q, J = 5.2 Hz, 2H, CH₂), 3.59 (d, J = 5.1 Hz, 2H, CH₂). ¹³C{¹H} NMR (126 MHz, DMSO-d₆): δ 175.6 (C=O), 170.22 (C=O), 152.37 (C-NH), 146.24 (C-NH), 131.01 (C-Cl), 116.3 (CN), 109.2 (C-CN), 60.6 (CH₂), 59.5(CH₂), 46.6(CH₂), 46.3(CH₂). IR (KBr pellet, cm⁻¹): 3370, 3268, 3219, 2958, 2892, 2212, 1662, 1558, 1504, 1450. Anal. Calcd. for C₁₁H₁₂ClN₃O₄: C, 46.25; H, 4.23; N, 14.71; found: C, 46.40; H, 4.31; N, 14.73

2.2.5. 2,5-Dibromo-3,6-bis((2-(2-hydroxyethoxy)ethyl)amino)cyclohexa-2,5-diene-1,4-dione (6)

Yield: 0.13 g (24%), dark red solid. M.P.: 136–137 °C (MeOH). MS: C₁₄H₂₀Br₂N₂O₆ requires [M + H]⁺ 473.13; found [M + H]⁺ 473.3. ¹H NMR (500 MHz, DMSO-d₆): δ 7.98 (br.s, 2H, exchange with D₂O, NH), 4.64 (s, 2H, exchange with D₂O, OH), 3.98 (t, J = 5.4 Hz, 4H, CH₂), 3.63 (t, J = 5.4 Hz, 4H, CH₂), 3.49 (s, 4H, CH₂), 3.46 (m, 4H, CH₂). ¹³C{¹H} NMR could not be acquired due to poor solubility of a compound. IR (KBr pellet, cm⁻¹): 3449, 3257, 3008, 2949, 2919, 2880, 2815, 1651, 1611, 1505, 1478, 1317, 1108, 1077, 1062.

2.3. X-Ray Crystallography Analysis

Crystals of compound 3 were obtained from a reaction mixture solution of toluene and were washed several times with toluene and n-hexane. Single crystals of compounds 3 were investigated on a Bruker Nonius KappaCCD diffractometer. The structures of compounds have been deposited to the Cambridge Crystallographic Data Centre (CCDC), with deposition number CCDC 2247575.

Crystals of compound 4 were obtained by slow solvent evaporation from a hot saturated solution of the compound in MeOH (crystalline forms 4-I) or acetonitrile (MeCN) (crystalline form 4-II). Experimental Diffraction data of 4-I and 4-II were collected at 150 K on a Rigaku, XtaLAB Synergy, Dualflex, HyPix diffractometer using Cu Kα radiation (λ = 1.54184 Å). The crystal structure was solved by direct methods and refined by full-matrix least squares. For further details, see crystallographic data for 4-I and 4-II deposited at the Cambridge Crystallographic Data Centre as Supplementary Publication Numbers CCDC 2487932 (for 4-I) and CCDC 2487933 (for 4-II). Copies of the data can be obtained, free of charge, on application to CCDC, 12 Union Road, Cambridge CB2 1EZ, UK.

Crystals of compound 5 were obtained by slow solvent evaporation from a hot saturated solution of the compound in acetonitrile (MeCN). Diffraction data were collected at 150.0 (1) K on a Rigaku, XtaLAB Synergy, Dualflex, HyPix diffractometer diffractometer. The structures were solved with the help of the Superflip [21,22,23] structure solution program using Charge Flipping and refined with the olex2.refine [24] refinement package using Levenberg-Marquardt minimisation. For further details, see crystallographic data for compound 5 deposited at the Cambridge Crystallographic Data Centre as Supplementary Publication Numbers CCDC 2455226.

For crystal packing visualization program Mercury [25] was used.

3. Results and Discussion

3.1. Synthesis

Synthesis of substituted 1,4-benzoquinones 3–6 starts from commercially available chloranil (1a), 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (1b) or bromanil (1c). Reaction with aminoethanol (2a) or 2-(2-aminoethoxy)ethanol (2b) proceeds at room temperature during a few hours with precipitation of the final product. It should be noted that only disubstituted products were isolated that can be explained by a greater stability of the formed coupled polymethine. It is known [8] that synthesis of monosubstituted product requires more complex approach.

3.2. X-Ray Crystallography

Crystals of compounds 3–5 suitable for X-ray analysis were obtained either directly from the reaction mixture (compound 3) or by recrystallization followed by solvent evaporation from a saturated solution of the respective compound in MeOH or MeCN (compounds 4 and 5). The crystal structure of compound 3 contains a water molecule. For compound 4, two different crystals were obtained for X-ray crystallography analysis—one form from MeOH (4-I) and the other from MeCN (4-II).

Table 1. Crystal data and structure refinement for crystals of compounds 3–5.

Parameter	Compound 3	Compound 4-I	Compound 4-II	Compound 5
CCDC number	2247575	2487932	2487933	2455226
Empirical formula	C10H14Cl2N2O5	C14H20Cl2N2O6	C14H20Cl2N2O6	4(C11H12ClN3O4)
Formula weight	313.137	383.21	383.21	1142.75
Temperature/K	193.0 (2)	150.0 (2)	150 (2)	150.0 (1)
Crystal system	monoclinic	monoclinic	monoclinic	monoclinic
Space group	C2/c	C2/c	P21/c	P21
a/Å	18.2431 (11)	24.3813 (3)	13.0548 (2)	13.07156 (7)
b/Å	4.7286 (2)	4.6755 (1)	4.76760 (10)	12.86560 (7)
c/Å	16.0608 (12)	14.7186 (2)	14.2266 (3)	14.89482 (10)
α/°	90.00	90.00	90.00	90
β/°	111.822 (2)	101.655 (1)	113.292 (2)	105.3941 (6)
γ/°	90.00	90.00	90.00	90
Volume/Å3	1286.2 (1)	1643.25 (5)	813.30 (3)	2415.04 (3)
Z	4	4	2	2
ρcalcg/cm3	1.617	1.549	1.565	1.5713
Absorption coefficient/mm−1	0.523	3.876	3.915	2.972
F(000)	648	800	400	1184
Crystal size/mm3	0.33 × 0.19 × 0.04	0.21 × 0.04 × 0.03	0.17 × 0.07 × 0.04	0.14 × 0.11 × 0.02
Radiation	Mo Kα (λ = 0.71073 Å)	Cu Kα (λ = 1.54184 Å)	Cu Kα (λ = 1.54184 Å)	Cu Kα (λ = 1.54184 Å)
2Θ max. for data collection/°	55	160	160	160
Index ranges	−23 ≤ h ≤ 23, −5 ≤ k ≤ 6, −21 ≤ l ≤ 20	−24 ≤ h ≤ 30, −5 ≤ k ≤ 5, −18 ≤ l ≤ 18	−16 ≤ h ≤ 16, −6 ≤ k ≤ 5, −18 ≤ l ≤ 17	−16 ≤ h ≤ 16, −16 ≤ k ≤ 16, −19 ≤ l ≤ 18
Reflections collected	2800	8190	7382	58,128
Independent reflections	1280	1782	1763	10,490
Data/restraints/parameters	1280/0/99	1782/0/117	1763/0/117	10,490/1/753
Goodness-of-fit on F2	1.028	1.080	1.054	1.043
Final R indexes [I > 2σ(I)]	R1 = 0.037, wR2 = 0.095	R1 = 0.0275, wR2 = 0.0753	R1 = 0.0269, wR2 = 0.0722	R1 = 0.0432, wR2 = 0.1138
Final R indexes [all data]	R1 = 0.050, wR2 = 0.090	R1 = 0.0278, wR2 = 0.0756	R1 = 0.0277, wR2 = 0.0727	R1 = 0.0439, wR2 = 0.1144
Largest diff. peak/hole/e Å−3	0.24/−0.35	0.330/−0.291	0.245/−0.261	0.74/−0.34

lists the main crystallographic data for compounds 3, 4-I, 4-II and 5.

Compound 3 (Figure 1) was isolated from the reaction of chloranil (1a) with aminoethanol (2a) (Scheme 1). Compound 3 can be described as quadrupole meropolymethine [17] that consists of two polymethine fragments coupled by two long C-C single bonds with electronic delocalization between polarized amino and carbonyl groups. In ¹H NMR spectrum of compound 3 NH group appeared at 7.93 ppm but signals of both methylene groups appeared at 3.58 (CH₂-OH) and 3.84 (HN-CH₂) ppm and were assigned from 2D ¹H-¹H-COSY spectrum (Figure S2).

In the crystal structure of compound 3 formed H-bond network was assisted by water molecules (Figure 2). The crystalline structure has the following elements: twofold symmetry axes and symmetry centers. Molecules of compound 3 are located at the symmetry centers, while the water molecules are located at the twofold axes of symmetry. Each hydrogen atom of a water molecule forms H-bonds with carbonyl group. At the same time, each oxygen atom of water molecule (as an acceptor) forms two hydrogen bonds with OH groups of substituents (R = (CH₂)₂OH). Additionally, H-bonds were found between sidechains leading to the formation of centrosymmetric $R_2^2\left(10\right)$ dimers.

Compound 4 gives different crystalline forms when crystallized from different solvents. We obtained crystalline modifications of 4-I and 4-II. In accordance with single-crystal X-ray diffraction data the title compound gives monoclinic centrosymmetric molecular crystals. Figure 3A shows a perspective view of molecule 4-I with thermal ellipsoids and the atom-numbering scheme followed in the text.

Molecules of compound 4 are stabilized by intramolecular hydrogen bonds of the NH···O type between the amino group and the carbonyl oxygen atom. The conformations of molecules in 4-I and 4-II differ very slightly.

Table 2. Values of selected torsion angles in 4-I and 4-II (in °).

Torsion Angle	4-I	4-II
C1-C2-C3-N7	−177.6 (1)	−179.9 (1)
C2-C3-N7-C8	3.8 (2)	3.5 (2)
C3-N7-C8-C9	−86.7 (2)	−83.1 (2)
N7-C8-C9-O10	−67.1 (1)	−71.5 (1)
C8-C9-O10-C11	−178.0 (1)	−178.8 (1)
C9-O10-C11-C12	−175.9 (1)	−176.7 (1)
O10-C11-C12-O13	−68.7 (2)	−70.4 (1)

gives the values of torsion angles characterizing the conformation of molecules in compound 4.

In both crystal structures, the gravity center of the molecule of compound 4 is on the inversion center, which results in the symmetry equivalency of its components, so the asymmetric unit in 4-I and 4-II contains only half a molecule (Figure 3B). Based on the coupling principles used in organic dyes, this half of the molecule corresponds to one of the two polymethine units of the quinone derivative [17]. The merocyanine unit is determined in O1-C1-C2-C3-N7 fragment as C-C bonds are equivalized (d(C1-C2) = 1.43 Å, d(C2-C3) = 1.38 Å), C1=O bond is elongated (1.23 Å) and C3-N7 bond is shortened (1.33 Å).

Both crystal structures are stabilized by intermolecular hydrogen bonds of NH···O and OH···O types.

Table 3. Parameters of hydrogen bonds in 4-I and 4-II.

Hydrogen Bond D-H···O	Distances in Å			Angle D-H···O (°)	Symmetry of Atom A
	D···O	H···O	D-H
4-I
N7-H7···O1	2.574 (2)	2.09 (2)	0.89 (2)	113 (2)	−x + 1/2, −y + 1/2, −z + 1
N7-H7···O13	2.888 (2)	2.18 (2)	0.89 (2)	136 (2)	−x + 1, y, −z + 3/2
O13-H13···O10	2.783 (1)	2.03 (1)	0.80 (1)	156 (2)	−x + 1, y, −z + 3/2
4-II
N7-H7···O1	2.560 (2)	2.08 (2)	0.85 (2)	115 (2)	−x + 1, −y + 1, −z + 1
N7-H7···O13	3.004 (2)	2.35 (2)	0.85 (2)	134 (2)	−x, y + 1, −z + 1
O13-H13···O10	2.783 (1)	1.98 (1)	0.82 (2)	166 (2)	−x, y + 1, −z + 1

gives the main parameters of hydrogen bonds in 4-I and 4-II.

In the crystal structure of 4-I, that was crystallized from MeOH, the amino group forms a bifurcated hydrogen bond: N7-H7···O1 and N7-H7···O13; the first bond is intramolecular, and the second is intermolecular. In addition, the crystal structure is stabilized by the intermolecular hydrogen bond O13-H13···O10. Due to these intermolecular bonds, the molecule is linked to its first neighbor via a two-fold symmetry axis; a second 2-(2-hydroxyethoxy)ethylamino group allows the molecule to bind to an additional neighbor, thus forming molecular chains along the crystallographic direction [1 0 1]. Figure 4 shows a projection of the crystal structure of 4-I along the monoclinic axis.

The molecular chains (see Figure 5) are formed along the hydrogen-bonded motifs, where quinone rings are located almost perpendicular to each other (interplanar angle is 87.96°).

In the crystal structure of 4-II (crystallized from MeCN) there are similar hydrogen bonds, by means of which the molecule is united with neighboring ones. The resulting centrosymmetric molecular chains are extended along the crystallographic direction of [1 0 0] (see Figure 6). The crystal structure of 4-II denser, and therefore it can be expected that at lower temperatures this modification should predominantly crystallize.

The molecular chains (Figure 7) of crystalline from 4-II are formed along the hydrogen-bonded motifs, where quinone rings are located parallel to each other.

Figure 8 shows a perspective view of the content of the asymmetric unit for compound 5. The asymmetric unit consists of four molecules, one of which (molecule D) is disordered.

The large number of crystallographically independent molecules in the asymmetric unit is a consequence of the fact that the compound belongs to a conformationally rich class due to the presence of (2-hydroxyethyl)amino groups. All four of these molecules differ in conformation.

Table 4. Values of selected torsion angles in molecules 5 (in °).

Angle	Molecule A	Molecule B	Molecule C	Molecule D 1
C1-C2-N9-C10	−3.2 (4)	5.1 (4)	−2.8 (5)	4.7 (5)
C2-N9-C10-C11	169.8 (2)	−171.0 (3)	176.7 (3)	179.2 (4) [161.4 (5)]
N9-C10-C11-O12	52.9 (3)	−53.0 (3)	48.2 (3)	−49.8 (5) [53.9 (8)]
C4-C5-N15-C16	2.7 (5)	−5.7 (5)	−8.4 (4)	7.9 (5)
C5-N15-C16-C17	−178.2 (2)	90.7 (3)	172.3 (2)	−91.8 (4)

¹ Torsion angles C2-N9-C10-C11 and N9-C10-C11-O12 are given for both disordered molecules D.

shows the values of selected torsion angles characterizing the molecular conformation.

Despite sharing the same short sidechain with compound 3, compound 5 does not form centrosymmetric dimers. Instead, crystal structure of compound 5 is characterized by layers formed through the inclusion of sidechains in an extensive system of intermolecular hydrogen bonds of OH···O, OH···Cl and NH···N types (Figure 9).

Table 5. Hydrogen-bond geometry for 5.

Hydrogen Bond DH···A	D···A (Å)	H···A (Å)	D-H···A (°)	Symmetry of Atom A
O12(A 1)-H···O18(A)	2.685 (3)	1.98 (4)	170 (3)	x + 1, y, z
N15(B)-H···N8(B)	3.075 (4)	2.29 (4)	142 (3)	x, y − 1, z
O18(A)-H···O13(B)	2.775 (3)	2.09 (4)	173 (4)	x, y, z
O12(B)-H···O18(B)	2.687 (3)	1.74 (3)	166 (3)	x + 1, y, z
N15(B)-H···N8(A)	2.997 (4)	2.33 (4)	136 (4)	x − 1, y + 1, z
O18(B)-H···O13(A)	2.791 (3)	1.95 (4)	175 (4)	x − 1, y, z
O12(C)-H···O18(C)	2.703 (3)	1.73 (3)	176 (3)	x, y + 1, z
N15(C)-H···N8(C)	3.021 (4)	2.24 (4)	146 (4)	x − 1, y − 1, z
O18(C)-H···O13(D)	2.764 (4)	1.99 (4)	170 (4)	x, y − 1, z
O18(C)-H···Cl14(D)	3.302 (3)	2.85 (3)	119 (3)	x, y − 1, z
O12(D)-H···O18(D)	2.687 (5)	1.83 (5)	169 (5)	x, y + 1, z
N15(D)-H···N8(C)	3.038 (4)	2.24 (5)	142 (4)	x + 1, y, z
O18(D)-H···O13(C)	2.714 (4)	1.89 (4)	167 (4)	x, y, z

¹ Molecule A of compound 5.

lists the main geometrical parameters of these bonds. By means of these hydrogen bonds, double molecular layers (Figure S11) are formed in the crystal structure, perpendicular to the monoclinic axis. All molecular layers in the crystal are related by symmetry operations, which are generated by the screw axis of symmetry 2₁.

To compare the intermolecular interactions in crystal structures, CrystalExplorer [26] software (version 21.5) was utilized and normalized contact distances (d_norm), which are calculated relative to van der Waals radii, are mapped onto the Hirshfeld surfaces (Figures S12–S18). The quantitative analysis utilizes fingerprint plots that are created as two-dimensional histograms by collecting data points from every surface spot, using the internal distance (d_i) and external distance (d_e) as coordinates [27].

Two-dimensional fingerprint plots in crystal of compounds 3–5 are shown in Figure 10. In all cases the fingerprint plots exhibit two pronounced spikes, which indicate strong O···H bonding. An additional spike, corresponding to H···H interactions, is observed in the case of compound 4-I and all molecules of compound 5.

Figure 11 represents the contribution (in %) of each contact type to the crystal packing of compounds 3–5. Overall, H···H and strong O···H interactions collectively constitute more than 50% of all intermolecular contacts. There is higher proportion of H···H interactions in compounds 4-I and 4-II which can be attributed to the long sidechains and additional methylene groups.

Compound 5 exhibits fewer O···H contacts (26.7–28.5%) compared to compounds 3 and 4 (32.3–33.4%). Conversely, strong N···H contacts were found in all four molecules of compound 5 (12.9–15.5%) due to the presence of the CN substituent; however, N···H contacts in compounds 3 and 4 were negligible (less than 1%). Interestingly, compound 3 showed Cl···H interactions (20%), a percentage higher than that observed for the other compounds, although Cl-Cl interaction (around 3%) was found in the crystal packing of compounds 4-I and 4-II.

Approximately 5% of C···C contacts and minimal C···O interactions were detected for all molecules of compound 5. These contacts are associated with π-π stacking interactions, which result from the layered crystal structure. For example, the distance between the quinone rings of molecules B and C is 3.262 Å.

Compounds 3–5 are assessed by comparing their crystal data and supramolecular architecture with six related, symmetrically diaminosubstituted 1,4-benzoquinones (7a–f) (Figure 12): 2,5-bis(2-propylamino)-1,4-benzoquinone (7a) [28], 2,5-bis(cyclohexylamino)-1,4-benzoquinone (7b) [28], 2,5-bis(3-methylanilino)-1,4-benzoquinone (7c) [28], (S,S)-2,5-difluoro-3,6-bis((1-phenylethyl)amino)-1,4-benzoquinone (7d) [8], (S,S)-2-chloro-5-cyano-3,6-bis((1-phenylethyl)amino)-1,4-benzoquinone (7e) [8], and 2,5-diamino-3,6-dichloro-1,4-benzoquinone (7f) [29].

Compounds 3–5 feature a 2-hydroxyethylamino or 2-(2-hydroxyethoxy)ethylamino substituents, while compounds 7a–e contain simple alkyl or aryl amino groups. Both series of compounds (3–5 and 7a–f) exist in the solid state as coupled polymethines. This is evidenced by the equalization of bonds within the O=C1-C2=C3-N fragment. The two single carbon-carbon bonds (C3-C4 and C1-C6) connecting the polymethine fragments exhibit similar lengths in both series of compounds: 1.52(8)–1.53(9) Å for compounds 3–5 and 1.50(9)–1.52(3) Å for 7a–f. Analysis of the torsion angles in the O=C1-C6-N and O=C4-C3-N fragments of compounds 3–5 (0.07–6.71°) and 7a–f (0.42–3.68°) revealed slight deviations from planarity for the benzoquinone core in both series. These structural similarities confirm that the core electronic structure is maintained across both sets of compounds, regardless of the substituents’ structure.

The dominant structural motif for compounds 7a–f is the formation of dimeric supramolecular synthons, $R_2^2\left(10\right)$, achieved via intermolecular N-H…O=C hydrogen bonding between the amino and carbonyl groups of two molecules. Despite the similar core molecular structures, the intermolecular interactions and resulting supramolecular architecture of compounds 3–5 are different. This distinction arises due to the presence of the 2-hydroxyethylamino or 2-(2-hydroxyethoxy)ethylamino groups, which contain hydrogen bond donor and acceptor sites. Consequently, intermolecular interactions among the side chains of compounds 3–5 led to the formation of molecular chains.

3.3. UV-Vis Studies

We first investigated the UV-Vis spectra of compounds 3–6 in polar solvent (DMF), revealing a weak absorption band in the region of 450–650 nm (

Table 6. Data from UV-Vis spectra of compounds 3–6 in DMF/MeOH solutions with or without additives.

Added M2+/Amine	λmax (log ε)
	Compound 3	Compound 4	Compound 5	Compound 6
Without additives	535 (2.25)	532 (2.43)	508 (2.92)	523 (2.15)
Zn2+/sec-butylamine	473 (3.04)	481 (3.50)	516 (3.15)	506 (2.47)
Zn2+/diethylamine	503 (2.75)	474 (3.42)	507 (sh)	552 (sh)
Zn2+/butane-1,4-diamine	503 (2.73)	484 (3.55)	486 (3.26)	511 (2.48)
Cu2+/sec-butylamine	579 (sh *)	595 (sh)	524 (sh)	582 (sh)
Cu2+/diethylamine	581 (sh)	596 (sh)	520 (sh)	610 (sh)
Cu2+/butane-1,4-diamine	557 (3.18)	565 (3.13)	502 (3.36)	563 (3.11)

* sh = shoulder.

). The addition of various amines (sec-butylamine, diethylamine, and butane-1,4-diamine) had practically no effect on the absorption of compounds 3–6 in this region (Figures S19–S22). Next, we tested the effect on the absorption band produced by the addition of Cu²⁺ or Zn²⁺ ions (added as their chloride salts) to the solutions of compounds 3–6. Despite the presence of flexible side chains in the structure of quinones 3–6 with potential metal coordination sites, no pronounced effect on absorption was observed. This can be explained by the stability of the coupled polymethine structure that is responsible for the absorption in the 450–600 nm region. Finally, metal ion and amine were added to the solution of compound of interest (3–6).

Analysis of the obtained data revealed a universal increase in absorbance intensity across the 450–600 nm region upon the addition of M²⁺ (Cu²⁺ or Zn²⁺) ions and amine to the solution of compounds 3–6 (Figure 13). For compounds 4 and 6 (possessing long side chains (R = (CH₂)₂O(CH₂)₂OH)), the addition of Cu²⁺ ions and butane-1,4-diamine resulted in a bathochromic shift in the UV-Vis spectra relative to the initial quinone. The addition of Zn²⁺ ions and amines induced a pronounced increase in absorption intensity as well as a hypsochromic shift relative to compound 4 solution. At the same time, absorption intensity of quinone 6 was low upon addition of Zn²⁺ ions and amines. Quinones 3 and 5 with short sidechains (R = (CH₂)₂OH) differ in the halide/pseudohalide at the 2-position (Cl or CN). In the case of quinone 3, hypsochromic shift (62 nm) was observed upon addition of Zn²⁺/sec-butylamine, and bathochromic shift (22 nm) after the addition of Cu²⁺/butane-1,4-diamine. The addition of Zn²⁺ and butane-1,4-diamine to the solution of compound 5 resulted in a hypsochromic shift of 22 nm.

It should be noted that fast precipitation (within a few minutes) occurs upon addition of Cu²⁺ ions and amine to solutions of all compounds, whereas addition of Zn²⁺ ions and amines leads to precipitate formation over a few hours.

4. Conclusions

Single crystal X-ray diffraction data for three 1,4-benzoquinone derivatives 3–5 with flexible side chains were obtained. Compounds exist as quadrupole meropolymethines and consist of two fragments with equalized bonds, which are connected by two long single bonds. Additionally, the solid-state structure is characterized by an extensive network of intra- and intermolecular interactions. Compounds 3–6 were tested on optical response towards amines including representative of biogenic amines (butane-1,4-diamine). Analysis of UV-Vis data revealed that the optical response can be obtained from a combination of the amine and the metal ion, which is a promising result for further investigations.