Crystal Structure, Thermodynamic Properties and DFT Studies of 5,6-dimethyl-1H-benzo[d]imidazol-3-ium 3-((2,4-dioxo-1,5-dioxaspiro[5.5]undecan-3-ylidene)methyl) -2,4-dioxo-1,5-dioxaspiro[5.5]undecane Hydrate

Abstract

A new 1,5-dioxaspiro[5.5] derivative coupled with a benzimidazole moiety: 5,6-dimethyl-1H-benzo[d]imidazol-3-ium 3-((2,4-dioxo-1,5-dioxaspiro[5.5]undecan-3-ylidene) methyl) -2,4-dioxo-1,5-dioxaspiro[5.5]undecane hydrate (DBH) was prepared. The crystal structure confirmed that it belongs to triclinic, P-1 space group. The title compound includes one (C₁₉H₂₁O₈)⁻ anion, one (C₉H₁₁N₂)⁺ cation and one water molecule, which assembled into a 2D-net framework by O–H···O and N–H···O hydrogen bonds. The quantum chemical computations using the B3LYP/6-311G (d, p) basis level of theory reveal that the optimized geometric structure is suitable to study the molecule. The theoretically simulated FT-IR spectra and electronic spectra of DBH are compared with experimental data. The results show that the B3LYP/6-311g (d, p) method fits well with the molecular structure. In addition, the thermodynamic properties have also been studied to determine the nature of the DBH.

1. Introduction

Heterocyclic compounds play an important role in biochemistry, medicinal chemistry, organic chemistry and agrochemical industries. In recent years, attention has been given to the benzimidazole class of compounds due to their diverse biological activities, such as anticancer [1,2], antifungal [3], antioxidant [4], cytotoxic [5], antiprotozoal [6], anti-T. cruzi (Trypanosoma cruzi) [7], antiproliferative [8], antihistaminic [9], anti-inflammatory [10], analgesics [11], antibacterial [12], anticonvulsant [13] and acetylcholinesterase [14]. In addition, benzimidazole has been used as corrosion inhibition for mild steel [15], catalytic activity [16], fluorescence chemosensors [17] and chiroptical sensors [18]. As other heterocyclic compounds, spiro compounds containing O heteroatom have also attracted much attention due to its special structure in recent years. All kinds of spirocyclic compounds were designed and synthesized [19,20,21]. Based on the above reasons, our group has prepared several spirocyclic compounds derived from the 1,5-dioxaspiro group or the 6,10-dioxaspiro group in ten years [22,23,24,25]. However, to the best of our knowledge, among so many reported oxaspirocyclic compounds, neither theory studies nor comparison between the experimental and calculational results for derivatives from a benzodimidazole moiety are available. Herein, we have prepared a new 1,5-dioxaspiro[5.5] derivative coupled with benzodimidazole moiety: 5,6-dimethyl-1H-benzo[d]imidazol-3-ium 3-((2,4-dioxo-1,5-dioxaspiro[5.5]undecane-3-ylidene)methyl)-2,4-dioxo-1,5-dioxaspiro[5.5] undecane hydrate (DBH), seen as Scheme 1. In addition, its crystal structure, FT-IR spectra and electronic spectra have been compared with DFT or TD-DFT calculational results.

2. Materials and Methods

2.1. Physical Measurements

The infrared (IR) spectra were recorded using a Nicolet 6700 spectrometer (Nicolet Instrument Inc., Madison, WI, USA). The C, H, and N elemental analyses were performed on an Elementar Vario EL III elemental analyzer (Elementar, Hanau, Germany). The UV–Vis spectra were measured on a TU-1901 spectrometer (Persee, Beijing, China). ¹H NMR and ¹³C NMR spectra were obtained with a Bruker AVANCE III HD NMR (400 MHz) spectrometer (Bruker, Elisabethhof, The Netherlands) in CDCl₃.

2.2. Preparation of DBH

The trimethyl orthoformate (1.27 g, 12 mmol) was refluxed with 1,5-dioxaspiro[5.5]undecane-2,4-dione (1.84 g, 10 mmol) in ethanol (30 mL) for 3 h at 60 ℃. After adding 5,6-dimethyl-1H-benzene (1.46 g, 10mmol), the mixture lasted for a further 4 h. Then, the above mixture was cooled, and the yellow powder (DBH) was isolated by filtration. Yield 17.8 %. m. p.: 175.2–175.3 °C. Anal. Calcd. for C₂₈ H₃₄ N₂ O₉: C, 61.98; H, 6.32; N, 5.16. Found: C, 61.83; H, 6.27; N, 5.25. ¹H NMR (400 MHz, CDCl₃, δ_ppm) 9.55 (s, 1H), 8.80 (s, 1H), 7.53 (s, 1H), 4.37 (m, 3H), 2.36 (s, 6H), 2.01 (t, J = 8.0 Hz, 8H), 1.56 (s, 2H), 1.44 (m, 6H), 1.34 (m, 6H). ¹³C NMR (125 MHz, CDCl₃, δ_ppm) 151, 138, 134, 132, 114,103, 95, 34, 24, 23, 20. Yellow block crystals are obtained using ethanol solvents.

2.3. X-ray Diffraction Analysis of DBH

The crystal of DBH was mounted on a Spider Rapid IP (Rigaku, Japan) area detector at 293 K. Reflection data were obtained using MoKα (λ = 0.71073 Å) radiation. Its structure was solved using SHELXL-2015 and SHELXT-2015 [26,27], respectively. The H atoms of DBH were refined using the riding model. The final R indices: R₁ = 0.045, wR₂ = 0.1099 for 4741 reflections with I > 2σ(I) using the weighting scheme, w = 1/[σ²(Fo²) + (0.645 P)² + 0.1579P], where P = (Fo² + 2Fc²)/3.

2.4. Computational Methods

The Gaussian 09 [28] software is used to execute the quantum chemical computations by the DFT/B3LYP method with a 6-311G (d, p) basis set [29]. Gauss view is used to inspect the output graphically obtained by the Gaussian 09 software. The geometric optimization of DBH is accomplished by DFT/B3LYP/6-311G (d, p) level of theory [30]. The FT-IR infrared and electronic spectra are calculated by the same method. The calculated wavenumbers are scaled by 0.96 at the B3LYP/6-311G (d, p) level.

3. Results and Discussion

3.1. Crystal Structure of DBH

The crystal data and structure refinement for DBH are list in

Table 1. Crystal Data and Structure Refinement for DBH.

Formula	C28H34N2O9
CCDC	1948628
Mr	380.35
Color/shape	yellow/block
Temperature	293(2) K
Crystal system, space group	Triclinic, P-1
Unit cell dimensions	a = 10.5431(3) Å α = 73.9160(10)° b = 11.3397(4) Å β = 70.7600(10)° c = 12.4926(4) Å γ =89.8030(10)°
V	1348.57(8) Å3
Z, Density	2, 1.336 Mg/m3
μ	0.100 mm−1
F(000)	576
θ	3.117 to 27.484°
Limiting indices	−13 ≤ h ≤ 12, −14 ≤ k ≤ 14, −16 ≤ l ≤ 16
No. of reflections collected/unique	13,425/6145 (Rint = 0.0188)
No. of parameters	357
GOF	1.132
R1 (I > 2σ (I))	0.0450
wR2 (I > 2σ (I))	0.1099
R1 (all data)	0.0595
wR2 (all data)	0.1284
Largest diff. peak and hole	0.372 and −0.224 e. Å−3

. Its molecular structure, which includes no H atoms, and its optimized geometric structure are both shown in Figure 1.

As shown in Figure 1 and

Table 2. Experimental and Computational Bond Distances (Å), Bond Angles (°) and Torsion Angles for DBH.

Bond Lengths	Exp. (Å)	Calc. (Å)	Bond	Exp. (Å)	Calc. (Å)
C8–C10	1.389(2)	1.395	O1–C1	1.436(16)	1.419
C10–C11	1.382(2)	1.388	O1–C7	1.365(18)	1.385
O8–C14	1.213(16)	1.201	C1–O4	1.441(15)	1.449
O5–C12	1.212(16)	1.231	O2–C7	1.218(17)	1.201
O6–C12	1.361(17)	1.351	O3–C9	1.221(16)	1.231
O6–C13	1.438 (15)	1.456	O4–C9	1.356(16)	1.352
O7–C14	1.363(18)	1.382	N1–C20	1.318(2)	1.329
N2–C20	1.322(19)	1.333	N2–C21	1.389(17)	1.391
Bond angle	Exp (°)	Calc. (°)	Bond angle	Exp (°)	Calc. (°)
C11–C10–C8	130.62(13)	132.30	C10–C8–C7	118.45(13)	117.36
C10–C11–C12	117.58(12)	117.45	C10–C8–C9	123.96(12)	123.18
C10–C11–C14	123.67(12)	122.91	C7–C8–C9	117.00(13)	118.61
C12–C11–C14	118.17(13)	118.41	N1–C20–N2	110.32(12)	110.43
Torsion angle	Exp (°)	Calc. (°)	Torsion angle	Exp (°)	Calc. (°)
C7–C8–C10–C11	167.64(14)	168.64	O1–C7–C8–C9	19.52(18)	18.90
C8–C10–C11–C12	168.36(13)	166.71	O2–C7–C8–C9	−158.30(15)	−160.69
C8–C10–C11–C14	−20.6(2)	−24.00	C9–C8–C10–C11	−21.4(2)	−24.28

, DBH is composed of one (C₁₉H₂₁O₈)⁻ anion, one (C₉H₁₁N₂)⁺ cation and one water molecule. The central C(10) atom is used to join two 1,5-dioxaspiro[5.5] undecane-2,4-dione moieties. The bond lengths reported for C8–C10 and C10–C11 are 1.389(2) Å and 1.382(2) Å, respectively, which resemble related published compounds (1.386(2) Å, 1.380(2) Å) [24]. Their corresponding calculated results are 1.395 Å and 1.388 Å. On the other hand, the bond angle of C8–C10–C11 in predicted values with the experimental ones is 132.30° and 130.62(13)°, respectively, which is also similar to related structures reported(C15–C17–C9 131.19(1)°) [24]. The experimental torsion angles for C7–C8–C10–C11, C8–C10–C11–C12, C8–C10–C11–C14 and C9–C8–C10–C11 are 167.64(14)°, 168.36(13)°, −20.60(2)° and −21.40(2)°, respectively. Their corresponding calculated torsion angles are 168.64°, 166.71°, −24.00°, and −24.28°, respectively. The two 1.3-dioxane rings R1 (O1, C1, O4, C9, C8, C7) and R2 (O6, C12, C11, C14, O7, C13) display distorted envelope conformation, with puckering parameters (Q, ϑ, ϕ) of (0.5052 Å, 105.63°, 234.40°) and (0.4781 Å, 70.33°, 304.46°), respectively. The maximum difference of bond lengths, bond angles and torsion angles between experimental values and calculated ones is 0.019 Å, 1.68° and 3.4°, respectively, which hereby certifies that the B3LYP/6-311G (d, p) level can simulate the crystal structure.

In DBH, the H₂O molecule connects the two (C₁₉H₂₁O₈)⁻ anions with the (C₉H₁₁N₂)⁺ cation via O9–H9A···O2, O9–H9B···O5 hydrogen bonds and N2–H2···O9 hydrogen bonds, respectively. The distance of O9···O2, O9···O5 and N2···O9 is 2.792(18) Å, 2.728(16) Å and 2.650(18) Å, respectively (

Table 3. N–H···O and O–H···O Molecular Interactions for DBH.

D–H···A	Symmetry	D–H (Å)	H···A (Å)	D···A (Å)	∠D–H···A (°)
N1–H1···O3	x, y − 1, z	0.86	1.94	2.777 (15)	165.0
N2−H2···O9	intra	0.86	1.79	2.650(18)	172.3
O9–H9A···O2	−x + 2, −y + 1, z + 1	0.86	1.97	2.792(18)	161.6
O9–H9B···O5	intra	0.86	1.90	2.728(16)	165.5

). The (C₉H₁₁N₂)⁺ cation and the (C₁₉H₂₁O₈)⁻ anion were linked by N1–H1···O3 intermolecular hydrogen bonds, and donor and acceptor distances are 2.777(15) Å, symmetry code: x, y − 1, z. DBH displays a 2D-net structure by O–H···O and N–H···O hydrogen bonds (Figure 2). A three-dimensional network was further generated by the above hydrogen bonds, as shown in Figure 3.

3.2. Vibrational Analysis

As shown in Figure 4, the ν_O−H vibration appeared at 3383 cm⁻¹ in the infrared spectra and at 3388 cm⁻¹ in DFT calculations, which is due to the water of DBH. The ν_C−H vibration of the 5,6-dimethyl-1H-benzo[d]imidazole ring appeared at 3106 cm⁻¹, and the corresponding calculated band was observed at 3126 cm⁻¹. The calculated and experimental ν_C=O vibrations of the 1,3-dioxane ring were observed at 1737 cm⁻¹ and 1629 cm⁻¹ and at 1691 cm⁻¹ and 1652 cm⁻¹, respectively. The ν_C–O bands of 1,3-dioxane ring were seen at 1261 cm⁻¹ and 1225 cm⁻¹ in DFT and at 1255 cm⁻¹ and 1215 cm⁻¹ in the IR spectra, respectively. These values agree well with literature reports [22,23,24]. The ν_C=N and ν_C–N vibrations occurred at 1490 cm⁻¹ and 1347 cm⁻¹ in DFT, respectively. The corresponding bands were seen at 1489 cm⁻¹ and 1366 cm⁻¹ in the IR spectra. In a word, the IR spectra for DBH agree very well with the calculated values.

3.3. Thermodynamic Properties

Thermodynamic parameters for different temperatures were calculated at the B3LYP/6-311G (d, p) level and scaled by 0.96. Three main thermodynamic properties—capacity (C⁰_p,m), entropy (S⁰_m) and enthalpy (H⁰_m)—are listed in

Table 4. C⁰_p,m, S⁰_m and H⁰_m from 100.0 to 1000.0 K at the B3LYP/6-311G (d, p) level.

T (K)	C0p,m (J·mol−1·K−1)	S0m (J·mol−1·K−1)	H0m (kJ·mol−1)
100.0	245.91	520.42	14.32
200.0	423.94	745.99	47.88
298.1	601.87	948.26	98.18
300.0	605.24	951.99	99.29
400.0	780.04	1150.47	168.70
500.0	930.87	1341.24	254.48
600.0	1054.72	1522.29	353.97
700.0	1155.81	1692.73	464.66
800.0	1239.14	1852.68	584.54
900.0	1308.68	2002.76	712.03
1000.0	1367.29	2143.76	845.91

. As shown in Table 4, all the values increase when the temperature rises in the range of 100.0–1000.0 K, which is mainly because a higher temperature can strengthen the vibration of molecules [31].

The correlation equations of C⁰_p,m, S⁰_m, H⁰_m and temperature T are as follows:

C⁰_p,m = 15.072 + 2.275 T − 9.247∗10⁻⁴ T ² (R² = 0.99947)

S⁰_m = 293.009 + 2.345 T − 4.947∗10⁻⁴ T ² (R² = 0.99999)

H⁰_m = −26.153 + 0.249 T +6.323∗10⁻⁴ T ² (R² = 0.9994)

3.4. Electronic Analysis

To compare with the experimental spectra, the calculated spectra of DBH are performed with the TD-DFT/B3LYP/6-311G (d, p) basis level and shown in Figure 5. As seen in Figure 5, two peaks arise at 245 nm and 378 nm in the experimental spectra and 252 nm and 339 nm in the calculated spectra, respectively. Figure 6 depicts eight frontier molecular orbitals of DBH, which is in agreement with the electron transitions shown in

Table 5. Experimental and calculated electronic absorption spectra values.

Exp.	Calc. (TD-DFT)
Wavelength (nm)	Wavelength (nm)	Oscillator Strength(f)	Electronic Transition Modes
245	252	0.2079	139HOMO − 5→147LUMO + 2
			140HOMO − 4→145LUMO
			141HOMO − 3→145LUMO
378	339	0.4089	144HOMO→146LUMO + 1

. As shown in Figure 6, the electron clouds of DBH are mainly localized on 5,6-dimethyl-1H-benzo[d]imidazole ring, two 1,3-dioxane rings and C8–C10=C11 bands, which indicate that the electronic transitions in UV–Vis spectra are in accordance with π → π* and n → π* transitions. For example, the first peak at 252 nm is mainly assigned to three electronic transition modes HOMO-5→LUMO+2, HOMO-4→LUMO and HOMO-3→LUMO. In HOMO-5, HOMO-4 and HOMO-3, electrons are distributed on the 5, 6-dimethyl-1H-benzo[d]imidazole ring, two 1,3-dioxane rings and C8–C10=C11 bonds, while in LUMO and LUMO+2, electrons are distributed on the 5, 6-dimethyl-1H-benzo[d]imidazole ring. The second peak at 339 nm is only one electronic transition mode HOMO→LUMO+1. In HOMO and LUMO+1, electrons are distributed on both two 1,3-dioxane rings and C8–C10=C11 bonds. Then, electronic transitions related with the peak at 339 nm are mainly from C8–C10=C11 bonds and oxygen atoms of 1,3-dioxane rings to C8–C10=C11 bonds, which are consistent with π → π* and n → π* transitions [32].

4. Conclusions

5,6-dimethyl-1H-benzo[d]imidazol-3-ium,3-((2,4-dioxo-1,5-dioxaspiro[5.5]undecan-3-ylidene)methyl)-2,4-dioxo-1,5-dioxaspiro[5.5]undecane hydrate (DBH) has been prepared, and its structure has been confirmed by single-crystal X-ray diffraction. DBH includes one (C₁₉H₂₁O₈)⁻ anion, one (C₉H₁₁N₂)⁺ cation and one water molecule, which assembled into a 2D-net framework by O–H···O and N–H···O hydrogen bonds. By comparing with experimental values, the calculated vibration frequencies and electronic spectra of DBH using the DFT/B3LYP/6-311g (d, p) level of theory fit well with the molecule.