X-ray Structure of Eleven New N,N′-Substituted Guanidines: Effect of Substituents on Tautomer Structure in the Solid State

Abstract

Guanidine-containing molecules are an interesting class of compounds within both medicinal and material sciences. Having knowledge of their tautomerism is key in designing guanidines that interact with biological and chemical receptors. However, there are limited data on the solid-phase structure of N,N′-substituted guanidines. Thus, eleven guanidines bearing a 4,6-dimethylpyrimidyl at one end and substituents of varying sizes and electronic properties at the other side, were synthesised, crystallised, and analysed by X-ray crystallography. Calculations of isolated molecules of tautomer energies and bond lengths were performed for comparison. One class of guanidines crystallised as a cis–trans tautomer with the shorter bond directed towards the pyrimidyl unit. When more electron-deficient aniline substituents were inserted, the crystallised tautomer changed to a cis–cis form where the shorter bond was directed towards the aniline. The switch in the tautomer structure is concluded to be due to both the electronic properties of the substituents and the intermolecular hydrogen bonding in the crystal lattice.

1. Introduction

Guanidines are of interest as sweeteners [1], organo-catalysts [2], catalysts for asymmetric synthesis [3], bases [4], metal ligands [5], sensor devices [6], drug candidates [7], and polyelectrolyte materials [8]. In all of these applications, intra- and intermolecular hydrogen bonding involving guanidines are crucial for the performance of the molecule or material. In this respect, having knowledge of the preferred tautomer structure is of importance. Generally, the most stable tautomer can be deduced from the relative acidity of the protonated version of the molecule [9]. While guanidine itself is highly basic (pK_a = 13.6), N-substitution with aromatic groups lowers the pK_a [10,11]. For instance 1,3-diphenyl guanidine has a pK_a of 9.1 in dimethylformamide [12]. Very few X-ray structures have been reported for N,N′-substituted guanidines, but some are shown in Figure 1. Paixao et al. reported an X-ray structure of 1,3-diphenylguanidine (I) [13], Zheng et al. analysed structures II and III [14], while Carpy et al. [15] provided structure IV. These four structures were found to have one short bond (1.271–1.308 Å) corresponding to that typical for C=N bonds [14]. The tautomer structures of I–IV follow that expected from the pK_a. In contrast, Brown et al. [16], for structure V, reasoned that all three hydrogens were located at the central nitrogen atom.

Hydrogen bonding can also increase the stability of a specific tautomer form [17,18,19]. Some of these intramolecular hydrogen-bonded structures can be regarded as a semi-aromatic six-membered ring with a bond length deviating from that of a classical-type tautomer [20]. This type of bonding has been termed resonance-assisted hydrogen bonding. Additionally, in the solid state, intermolecular interactions are also factors strongly affecting the structure. We have previously published the X-ray structure of 1-(3-chlorophenyl)-2-(4,6-dimethylpyrimidin-2-yl)guanidine [21]. Herein, we have included data for eleven additional guanidine X-ray crystals. These contain the same 4,6-dimethylpyrimidyl unit at one side, which are decorated with amines with variance in basicity, and steric bulk at the other side. We show that the guanidine tautomer structure is dictated by the electronic properties of the guanidine substituents and by intermolecular hydrogen bonding. Hopefully, information on guanidine tautomerism will be useful in the design of biologically active molecules.

2. Materials and Methods

2.1. Chemicals, Equipment, and Analysis

N-(4,6-Dimethylpyrimidin-2-yl)cyanamide was prepared as previously described [21]. All other reagents and solvents were purchased from Merck and used directly without any further purification. NMR spectra were recorded at an ambient temperature at a frequency of 400 and 600 MHz for ¹H and 101 and 151 MHz for ¹³C, respectively. The chemical shift values are reported in ppm from tetramethylsilane as the internal standard, calibrated with a residual signal of DMSO-d₅ for proton (δ = 2.50 ppm), with a signal from DMSO-d₆ for carbon (δ = 39.52 ppm), or with a signal from AcOH-d₃ for proton (δ = 2.04 and 11.65 ppm), with a signal from AcOH-d₄ for carbon (δ = 20 and 178.99 ppm).

¹⁹F NMR was recorded with hexafluorobenzene as the internal standard. The splitting patterns are reported as singlet (s), broad singlet (br s), doublet (d), triplet (t), quartet (q), doublet of doublet (dd), doublet of triplet (dt), triplet of doublet (td), doublet of doublet of doublets (ddd), and multiplet (m). The coupling constants (J) are reported in Hertz (Hz). High-resolution mass spectra (HRMS) were recorded on a water ‘Synapt G2-S’ Q-TOF instrument with electrospray (ES) positive mode ionisation. The IR spectra were obtained using a Bruker Alpha Eco-ATR FTIR spectrometer (Bruker, Billerica, MA, USA). The microwave reactions were performed using a Biotage initiator⁺ Microwave system (Biotage, Uppsala, Sweeden).

2.2. General Procedure A: Classical Heating

N-(4,6-Dimethylpyrimidin-2-yl)cyanamide (1 equiv.) and the amine derivative (1 equiv.) in dioxane (20 mL) were refluxed for 24 h and then cooled to 22 °C. The reaction mixture was then added to a basic solution (2% NH₃ in 50 mL distilled water). The precipitate that formed (pH: 11) was isolated by filtration, washed with water, and dried under vacuum to obtain the target molecules. The attained solid was further purified by recrystallisation from 2-PrOH, and the obtained crystals were used for X-ray crystallographic analysis.

2.3. General Procedure B: Microwave

In a microwave vial (20 mL), N-(4,6-dimethylpyrimidin-2-yl)cyanamide (1 equiv.) and an amine derivative (1 equiv.) in dioxane (15 mL) were mixed and heated under microwave irradiation at 150 °C for 1 h. The reaction mixture was cooled to 22 °C and added to a basic solution (2% NH₃ in 50 mL water). The precipitate that formed (pH: 11) was isolated by filtration, washed with water, and dried under vacuum to obtain the target compounds. For some compounds, the attained solid was further purified by recrystallisation from 2-PrOH, and the obtained crystals were used for X-ray crystallographic analysis.

2.4. Synthesised Guanidines

2.4.1. 1-Benzyl-2-(4,6-dimethylpyrimidin-2-yl)guanidine (5)

N-(4,6-Dimethylpyrimidin-2-yl)cyanamide (578 mg, 3.90 mmol) and benzylamine (0.42 mL, 3.89 mmol) were reacted following General Procedure A. The resulting precipitate was isolated as an off-white solid (0.565 g, 57%). This material was further purified by recrystallisation using 2-PrOH (13 mL) giving 301 mg (1.18 mmol, 30%) of an off-white crystalline solid, as follows: mp. 207–208 °C; ¹H NMR (400 MHz, DMSO-d₆) δ 7.68 (s, 2H, br, NH₂), 7.34 (m, 4H), 7.30–7.19 (m, 1H), 6.48 (s, 1H), 4.50 (s, 2H), 2.22 (s, 6H); ¹³C NMR (101 MHz, DMSO-d₆) δ 166.5, 166.2 (2C), 158.2, 140.7, 128.7 (2C), 127.5 (2C), 127.1, 110.6, 44.0, 24.0 (2C); HRMS (TOF, ES+): found 256.1565, calcd for C₁₄H₁₈N₅ (M + H)⁺, 256.1562; IR (neat, cm-1): 3272, 3109, 3024, 2980, 2918, 1566, 1520, 1411, 1373, 1328, 1173, 805, 732.

2.4.2. 1-Benzyl-2-(4,6-dimethylpyrimidin-2-yl)guanidine hydrochloride (5-HCl)

Compound 5 was mixed with an EtOH solution of HCl and stirred for 1 h. Upon evaporation and drying, a solid formed, as follows: ¹H NMR (400 MHz, DMSO-d₆) δ 11.13 (br s, 1H), 10.16 (br s, 1H), 9.16 (br s, 2H), 7.46–7.34 (m, 4H), 7.32 (m, 1H), 7.05 (s, 1H), 4.69 (d, J = 6.0 Hz, 2H), 2.38 (s, 6H).

2.4.3. 2-(4,6-Dimethylpyrimidin-2-yl)-1-(2-methylbenzyl)guanidine (6)

N-(4,6-Dimethylpyrimidin-2-yl)cyanamide (0.578 g, 3.90 mmol) and 2-methylbenzylamine (0.47 g, 0.48 mL, 3.89 mmol) were reacted following General Procedure A. The resulting precipitate was isolated as an off-white solid (0.60 g, 57%). The material was further purified by recrystallisation using refluxing 2-PrOH (200 mL) to give 210 mg (0.78 mmol, 20%) of an off-white crystalline solid, as follows: mp. 184–185 °C; ¹H NMR (400 MHz, DMSO-d₆) δ 7.58 (br s, 2H), 7.31–7.22 (m, 1H), 7.22–7.11 (m, 2H), 6.47 (s, 1H), 4.43 (s, 2H), 2.31 (s, 2H), 2.21 (s, 5H). The proton spectrum matched well that reported in [22], as follows: ¹H NMR (400 MHz, CD₃CO₂D) δ 7.47–7.33 (m, 1H), 7.36–7.15 (m, 3H), 6.98 (s, 1H), 4.69 (s, 2H), 2.42 (s, 6H), 2.41 (s, 3H); ¹³C NMR (101 MHz, CD₃CO₂D) δ 170.6 (2C), 158.7, 155.8, 138.0, 134.9, 132.4, 130.0, 129.0, 128.1, 117.8, 45.2, 24.1 (2C), 19.8; HRMS (TOF, ES+): found 270.1723, calcd for C₁₅H₂₀N₅ (M + H)⁺, 270.1719; IR (neat, cm⁻¹): 3266, 3097, 2956, 1519, 1407, 1373, 1331, 1150, 805, 735, 557, 472.

2.4.4. (S)-1-(4,6-Dimethylpyrimidin-2-yl)-3-(1-phenylethyl)guanidine (7)

N-(4,6-Dimethylpyrimidin-2-yl)cyanamide (576 mg, 3.89 mmol) and (S)-1-phenylethan-1-amine (565 mg, 4.67 mmol) were reacted following General Procedure B. After cooling to rt (22 °C), the mixture was quenched in an aqueous solution of ammonia (50 mL, 2%). The resulting solid was isolated by filtration and washed with water. This gave, after drying, 344 mg (1.28 mmol, 33%) of a light beige solid, as follows: mp. 154.6–157.5 °C, [α${]}_{20}^{\mathrm{D}}$ = 56.0 (c 1.00, MeOH); ¹H NMR (400 MHz, DMSO-d₆) δ 7.54 (br s, 2H), 7.41–7.30 (m, 4H), 7.28–7.19 (m, 1H), 6.48 (s, 1H), 5.14 (s, 1H), 2.22 (s, 6H), 1.41 (d, J = 6.9 Hz, 3H); ¹H NMR (600 MHz, CD₃CO₂D) δ 7.51–7.47 (m, 2H), 7.44 (t, J = 7.7 Hz, 2H), 7.39–7.34 (m, 1H), 6.99 (s, 1H), 5.06 (d, J = 9.0 Hz, 1H), 2.47 (s, 6H), 1.70 (d, J = 6.7 Hz, 3H); ¹³C NMR (151 MHz, CD₃CO₂D) δ 168.8 (2C), 157.0, 153.3, 141.1, 129.0 (2C), 128.1, 125.7 (2C), 116.0, 51.9, 22.5 (2C), 22.4; HR-MS (TOF MS ES+): found 270.1716, calcd for C₁₅H₂₀N₅, (M + H)⁺, 270.1719; IR (neat, cm⁻¹): 3269, 3112, 2960, 2923, 2852, 1611, 1572, 1519, 1410, 1376, 1335, 1254, 1211, 1120, 806, 700, 559.

2.4.5. (1-(4,6-Dimethylpyrimidin-2-yl)-3-(2,2,2-trifluoro-1-phenylethyl)guanidine (8)

To a solution of N-(4,6-dimethylpyrimidin-2-yl)cyanamide (230 mg, 1.55 mmol) in dioxane (10 mL), 2,2,2-trifluoro-1-phenylethan-1-amine (326 mg, 1.86 mmol) and HCl (0.13 mL, 1.2 equiv.) were added. The mixture was treated by microwave irradiation for 1 h at 150 °C (6 bar), before quenching it with NaOH (2M, 0.5 mL) until reaching pH = 8. Upon the addition of water (5 mL), a precipitate was formed, which was isolated by filtration and washed with MeCN (5 mL) to afford 224 mg (0.69 mmol, 45%) of white powder. A sample (129 mg) was recrystallised from 2-PrOH (10 mL) to yield 47 mg (0.15 mmol, 36%) of translucent starshaped crystals, as follows: mp. 186.7–188.8 °C; ¹H NMR (400 MHz, DMSO-d₆): 8.10-7.30 (m, 8H), 6.57 (s, 1H), 6.15 (br s, 1H), 2.26 (s, 6H); ¹H NMR (400 MHz, CD₃CO₂D) δ 7.67–7.60 (m, 2H), 7.53 (dd, J = 5.1, 2.0 Hz, 3H), 7.04 (d, J = 2.1 Hz, 1H), 5.94 (q, J = 6.9 Hz, 1H), 2.52 (s, 6H). ¹³C NMR (101 MHz, CD₃CO₂D) δ 168.8 (2C), 156.9, 154.7, 130.5, 130.1, 129.2 (2C), 128.4–112.0 (q, J = 282.8 Hz), 128.0 (2C), 116.3, 57.3–56.3 (q, J = 32.3 Hz), 22.5 (2C); ¹⁹F NMR (565 MHz, DMSO-d₆) δ −72.9; HRMS (TOF MS ES+): found 324.1440, calcd for C₁₅H₁₇N₅F₃, (M + H)⁺, 324.1436; IR (neat, cm⁻¹): 3269, 3109, 2974, 2927, 1612, 1576, 1514, 1407, 1377, 1337 1252, 1210, 1166, 1118, 700, 637.

2.4.6. (1-(4,6-Dimethylpyrimidin-2-yl)-3-(2,2,2-trifluoro-1-phenylethyl)guanidine hydrochloride (8-HCl)

A small sample of compound 8 was treated with an EtOH solution of HCl and evaporated to dryness. ¹H NMR (400 MHz, DMSO-d₆): 11.14 (br s, 1H), 10.12 (br s, 1H), 9.95 (br s, 1H), 7.73–7.70 (m, 2H), 7.53–7.45 (m, 3H); 7.09 (s, 1H), 6.67 (br s, 1H), 2.42 (s, 6H).

2.4.7. 1-(Cyclohexylmethyl)-2-(4,6-dimethylpyrimidin-2-yl)guanidine (9)

N-(4,6-Dimethylpyrimidin-2-yl)cyanamide (576 mg, 3.89 mmol) and cyclohexyl methylamine (528 mg, 4.67 mmol) were reacted following General Procedure B. The precipitate was isolated and recrystallised from 2-PrOH (56 mL) to give 676 mg (2.59 mmol, 67%) as a white solid, as follows: mp. 231.6–232.4 °C (lit. [23] 236–238 °C; ¹H NMR (400 MHz, DMSO-d₆) δ 7.36 (s, 2H), 6.45 (s, 1H), 3.06 (d, J = 6.7 Hz, 2H), 2.22 (s, 6H), 1.74–1.60 (m, 5H), 1.25–1.10 (m, 3H), 0.94 (m, 2H); ¹H NMR (400 MHz, CD₃CO₂D) δ 7.00 (s, 1H), 3.32 (d, J = 6.7 Hz, 2H), 2.48 (s, 6H), 1.93–1.70 (m, 6H), 1.43–1.05 (m, 5H); ¹³C NMR (101 MHz, CD₃CO₂D) δ 168.79 (2C), 156.97, 153.98, 115.92, 47.52, 36.87, 30.28 (2C), 25.97, 25.44 (2C), 22.48 (2C); HRMS (TOF MS ES+): found 262.2036, calcd for C₁₄H₂₄N₅, (M + H)⁺, 262.2032; IR (neat, cm⁻¹): 3259, 3098, 2920, 2848, 1519, 1412, 1370, 1331, 1176, 806.

2.4.8. 1-Butyl-2-(4,6-dimethylpyrimidin-2-yl)guanidine (10)

N-(4,6-Dimethylpyrimidin-2-yl)cyanamide (0.578 g, 3.90 mmol) and butylamine (0.38 mL, 3.89 mmol) were reacted following General Procedure A. The resulting precipitate was isolated as an off-white solid (0.657 g, 76%). The material was further purified by recrystallisation from 2-PrOH (45 mL, at 82 °C), giving 495 mg (2.24 mmol, 57%) of tiny off-white crystals, as follows: mp. 188–189 °C; ¹H NMR (600 MHz, DMSO-d₆) δ 7.47 (s, 2H, br, NH₂), 6.44 (s, 1H), 3.19 (t, J = 7.0 Hz, 2H), 2.21 (s, 6H), 1.50–1.42 (m, 2H), 1.38–1.29 (m, 2H), 0.90 (t, J = 7.4 Hz, 3H); ¹³C NMR (151 MHz, DMSO-d₆) δ 166.1, 165.5 (2C), 157.9, 109.7, 40.1, 31.4, 23.6 (2C), 19.6, 13.7; HRMS (TOF, ES+): found 222.1723, calcd for C₁₁H₂₀N₅, (M + H)⁺, 222.1719; IR (neat, cm⁻¹): 3264, 3099, 2957, 2923, 2870, 1525, 1410, 1374, 1330, 1176, 806, 733.

2.4.9. N′-(4,6-Dimethylpyrimidin-2-yl) pyrrolidine-1-carboximidamide (11)

N-(4,6-Dimethylpyrimidin-2-yl)cyanamide (0.578 g, 3.90 mmol) and pyrrolidine (0.44 mL, 3.89 mmol) were reacted following General Procedure B. The resulting homogeneous solution was kept at 22 °C overnight, and the desired product was crystallised slowly. The crystals were isolated by filtration, washed with water, and then dried under vacuum to give 715 mg (3.26 mmol, 84%) of an off-white crystalline solid, as follows: mp. 210–211 °C; ¹H NMR (400 MHz, DMSO-d₆) δ 8.06 (s, 2H, br, NH₂), 6.43 (s, 1H), 3.38 (m, 4H), 2.21 (s, 6H), 1.91–1.79 (m, 4H); ¹³C NMR (101 MHz, DMSO-d₆) δ 166.0, 165.7 (2C), 156.3, 109.8, 46.2 (2C), 25.1 (2C), 23.8 (2C); HRMS (TOF, ES+): found 220.1565, calcd for C₁₁H₁₈N₅, (M + H)⁺, 220.1562; IR (neat, cm⁻¹): 3316, 3153, 2947, 2880, 1616, 1531, 1411, 1334, 1112, 802.

2.4.10. N′-(4,6-Dimethylpyrimidin-2-yl)-1,3,4,5-tetrahydro-2H-pyrido[4,3-b]indole-2-carboximidamide (12)

N-(4,6-Dimethylpyrimidin-2-yl)cyanamide (578 mg, 3.90 mmol) and 1,2,3,4-tetrahydro-9H-pyrido[3,4-b]indole (670 mg, 3.89 mmol) were reacted following General Procedure B. The resulting homogeneous solution was kept at 22 °C, and the product was precipitated slowly. The precipitate was isolated by filtration, washed with water, and dried under vacuum to give a yellow solid (1.03 g, 82%). The obtained solid was crystallised from 2-PrOH (50 mL) to give 880 mg (2.75 mmol, 71%) of a yellow crystalline solid, as follows: mp. 210–211 °C, ¹H NMR (400 MHz, DMSO-d₆) δ 10.91 (s, 1H, NH-indole), 8.53 (s, 2H, NH₂), 7.41 (d, J = 7.7 Hz, 1H), 7.32 (d, J = 8.1 Hz, 1H), 7.04 (ddd, J = 8.2, 7.0, 1.3 Hz, 1H), 6.97 (td, J = 7.5, 1.1 Hz, 1H), 6.51 (s, 1H), 4.87 (s, 2H), 3.88 (t, J = 5.6 Hz, 2H), 2.76 (t, J = 5.7 Hz, 2H), 2.25 (s, 6H); ¹³C NMR (151 MHz, DMSO-d₆) δ 166.2 (2C), 166.1, 157.9, 136.5, 132.7, 127.1, 121.1, 118.9, 117.9, 111.5, 110.8, 107.4, 42.8, 42.8, 24.0 (2C), 21.4; HRMS (ES): found 321.1831, calcd for C₁₈H₂₁N₆, (M + H)⁺, 321.1828; IR (neat, cm⁻¹): 3349, 3254, 3162, 2998, 2957, 2916, 2847, 1618, 1577, 1520, 1490, 1431, 1412, 1335, 1109, 1010, 893, 736.

2.5. X-ray Crystal Determination

The crystalline material was mounted on glass fibre and measured using either Rigaku OD Gemini, utilising an Atlas S2 CCD camera and mirror-collimated Cu-Kα radiation from a sealed X-ray tube (comp. 5, 6, and 11), or Rigaku OD Supernova, utilising an Atlas S2 CCD camera and Cu-Kα radiation from a micro-focused sealed X-ray tube (1, 2, 3, 4, 7, 8, 9, 10, and 12). Both diffractometers and their detectors were supplied by Rigaku Europe SE, Neu-Isenburg, Germany In both cases, the samples were cooled during measurement using an open flow N₂ system Cryojet 5 from Oxford Cryosystems to 180 K for 5, 6, and 7 and Cryostream 800 from Oxford Cryosystems (Oxford, United Kingdom) to 95 K for compounds 1, 2, 3, 4, 7, 8, 9, 10, and 12. The data integration, reduction, scaling, and absorption correction were handled in CrysAlis PRO [24]. The phase problem was solved using charge flipping methods in Superflip [25]. The structure models were refined using Crystals [26], except for 10, which was solved in Jana2020 [27]. Samples 9 and 10 were found to be twinned with twin volume ratios [28] of 764(4):236(4) and 5592(12):4408(12), respectively. Structure 10 had a significant number of overlapping reflections and benefited significantly from hklf5 refinement. The aromatic substituent in 4 was found to be disordered over two positions and refined with restrained geometry and a constrained sum of occupancies to 1, resulting in an occupancy ratio of 917(3):83(3). The hydrogen atoms bonded to heteroatoms were refined with restrained geometry, while the hydrogen atoms bonded to carbon atoms were placed in calculated positions and refined with riding constraints. The residual electron density maps were visualised using MCE 4.2.00 [29]. The crystal structures were visualised using Diamond 3.0c [30]. For further information on data collection, data reduction, and refinement, see Supplementary Materials, Tables S1–S3.

3. Results and Discussion

3.1. Synthesis

We selected 4,6-dimethylpyrimidine for one side of the guanidines, while the other side was varied with amine substituents having differences in basicity and steric bulk (see Scheme 1). Details on the synthesis of the aryl-containing guanidines 1–4 using HCl in 2-PrOH have recently been reported [21]. Due to its low basicity, trifluoro-containing guanidine 8 was also prepared by this method. In contrast, the guanidines containing aliphatic and benzylic amines (5–7 and 9–12) were more efficiently prepared from N-(4,6-dimethylpyrimidin-2-yl)cyanamide without acid by thermal or microwave heating in 1,4-dioxane. After the reaction, the mixture was quenched with aqueous ammonia to ensure that the guanidines were in the neutral form. Most of the compounds were recrystallised from 2-PrOH, giving yields in the range of 20–84%.

Guanidines 7–8 and 11–12 are new chemical entities, while NMR spectroscopic data were lacking for benzyl derivative 5 and n-butyl analogue 10. Compounds 6 and 9 were previously well characterised and have been investigated for their biological activity as inhibitors of FOXO3-induced gene transcription [22] and Rho GTPase Rac1 inhibitors [23], respectively.

¹H NMR spectroscopy in DMSO-d₆ of compounds 5–12 showed a broad two-proton singlet from the guanidine residing at 7.35–8.35 ppm, while one of the guanidine protons underwent rapid exchange and was not observed. A diagnostic shift confirming that the guanidines are in neutral form is the one proton singlet at C-5 of the pyrimidine moiety, which resonates at 6.43–6.57 ppm, depending on the structure. For the protonated version of the molecule, and when analysed in deuterated acetic acid, these signals shifted 0.5 ppm towards the lower field. ¹H NMR of the hydrochloride salt of 5 (5-HCl) in DMSO-d₆ showed that proton exchange in the guanidine unit is slower than that observed in the case of neutral 5. Thus, all four N-H protons could be observed by ¹H NMR and coupling between the benzylic protons, and the nearby N-H group was detected. Not all of these neutral guanidines have sufficient solubility in DMSO-d₆ to be analysed by ¹³C NMR spectroscopy. However, their protonated versions have good solubility, and deuterated acetic acid was, therefore, applied as a solvent for some ¹³C NMR spectra. The NMR spectra are shown in Supplementary Materials, Figures S20–S40. The IR spectra of compounds 1–12 are presented in Tables S13 and S14 and in Figures S41–S52. Compounds 2–4, which crystallised in a T2 cis–cis tautomer form, have strong NH stretching in the range of 3420–3504 cm⁻¹. In contrast, structures 1 and 5–12 have broader bands in the range of 3220–3282 cm⁻¹, indicative of the other form of hydrogen bonding. The region 1700–1500 cm⁻¹ is crowded with bands from C=N and aromatic bonds. Compounds 1–4 appear to have C=N stretching in the range of 1650–1656 cm⁻¹, while the corresponding absorbance for 5–12 lies in the range of 1610–1621 cm⁻¹.

3.2. X-ray Crystal Structures

Table 1. Overview of the guanidines analysed by X-ray, the number of molecules in the asymmetric unit (AS), and their space group.

Comp.	Structure	AS 1	Space Group
1		1	P21/c
2		1	P1
3		2	P21/n
4		1	P1
5		1	P21/c
6		1	P21/c
7		3	P21
8		3	Cc
9		2	P21/c
10		2	P21/c
11		3	P1
12		3	P21/c

¹ Number of molecules in asymmetric unit.

provides an overview of the X-ray structures, their space group, and the number of molecules in the asymmetric unit. The aniline-substituted structures 1, 2, and 4, alongside benzylic compounds 5 and 6, all have one molecule in the asymmetric unit.

Two molecules in the asymmetric units are seen for the pentafluoro derivative 3, and the guanidines have aliphatic primary amines as substituents (comp. 9 and 10). The presence of two molecules in the asymmetric unit allows for better adaption for steric demands in the structure. The main part of the scaffold remains almost planar; however, the twisting is more pronounced than that observed in the former compounds. In the case of guanidines substituted with chiral (7 and 8) and secondary amines (11 and 12), the added steric bulk leads to three molecules in the asymmetric unit and significant twisting in the main part of the molecule.

3.3. Calculations

We performed gas-phase calculations (B3LYP [31]/cc-pVDZ [32,33]) with the PySCF software [34,35] of the stability of the different tautomers and their bond lengths (see Figure 2 and Table S3). Obviously, gas-phase calculation will not be able to predict the solid-phase structure but is otherwise a useful reference point for bond lengths. Tautomer T1 has a shorter bond (double-bond character) between atoms N7 and C8, tautomer T3 has double bond to the central amine, and tautomer T2 has double-bond character between atoms C8 and N10. The guanidines can also be in a different conformation, with respect to the position of the R-group (cis or trans in relation to the central nitrogen atom).

Overall, gas-phase calculation indicated tautomer T2 with a cis–cis geometry to be most stable for compounds 1–9, while n-butyl derivative 10 appeared most stable as tautomer T1-cis–trans with a low margin. Derivatives 11–12, having cyclic secondary amine substituents, are also indicated to be most stable as tautomer T1. Note that the T2 structure is prohibited by the lack of a proton at this side. Tautomer T3 was found to be 15–17 KJ/mol higher in energy. Tautomer T1-cis–trans was relatively stable for the non-aniline structures 5–12 (see Supplementary Materials, Table S7), but high in energy for the aniline structures. Additionally, the tautomer stability of five guanidines (comp. 1, 3, 4, 5, and 8) was also computationally evaluated, with other basis sets and density functionals showing similar trends (Supplementary Materials, Table S8). The average of the calculated bond lengths is shown in Figure 2. No significant difference in bond length was seen between the cis–cis and cis–trans forms of the tautomers (Supplementary Materials, Table S9). Pyrimidines are potential hydrogen bond acceptors. The distance between the pyrimidine atom N3 (hydrogen bond acceptor) and N9 (hydrogen bond donor) was indicated to be within distance for medium strength hydrogen bonding (Supplementary Materials, Table S9). The average distance between N3 and N9 was 2.67 Å, 2.76 Å, and 2.91 Å for T1, T2, and T3 structures, respectively. This could indicate stronger hydrogen bonds for the T1 tautomers, as compared to the others. The Moltaut program [36] predicted tautomer T1 to be most stable in 10 of the 11 cases tested (Supplementary Materials, Table S10). The program was not able to handle the larger molecule 12. Furthermore, to indicate the effect of electronic properties of the different amine substituents, the proton affinities of the guanidines were calculated using B3LYP/cc-pVDZ (Table S11). The correlation with the experimental pK_a values was reasonably good (R₂ = 0.952, Figure S19).

3.4. Description of the Solid-Phase Guanidine Structures

The solid-phase structures of guanidines 1–12 depend on the amine substituents and can broadly be classified in two groups. The bond length data are shown in

Table 2. Bond length (Å) for the central part of the guanidine structures. The values are averaged for all of the molecules in the asymmetric unit.

Comp.	N3-C2	C2-N1	C2-N7	N7-C8	C8-N9	C8-N10	N10-C11
1	1.346	1.358	1.375	1.328	1.340	1.368	1.407
2	1.341	1.339	1.384	1.386	1.343	1.301	1.400
3	1.342	1.339	1.387	1.380	1.335	1.313	1.402
4	1.334	1.342	1.379	1.386	1.336	1.294	1.412
5	1.352	1.359	1.367	1.334	1.341	1.339	1.457
6	1.349	1.360	1.369	1.332	1.342	1.346	1.459
7	1.352	1.362	1.367	1.333	1.347	1.346	1.455
8	1.351	1.360	1.368	1.333	1.343	1.344	1.457
9	1.353	1.362	1.368	1.333	1.347	1.346	1.453
10	1.349	1.361	1.362	1.339	1.355	1.343	1.456
11	1.352	1.359	1.371	1.343	1.341	1.344	1.467; 1.462
12	1.352	1.357	1.372	1.328	1.346	1.368	1.470; 1.471

, while representative X-ray structures are displayed in Figure 3 and in Supplementary Materials, Figures S1–S19.

For meta-chloroaniline-substituted 1 and benzylic/aliphatic-substituted 5–10, the bond lengths from the central carbon (C8) to the three connected nitrogen atoms are very similar, with average values of N7-C8: 1.333 ± 0.003 Å, C8-N9: 1.345 ± 0.005 Å, and C8-N10: 1.347 ± 0.008 Å. The N7-C8 bond is longer than that seen in the analogues I–IV [13,14,15] (1.294 ± 0.0148 Å, structures in Figure 1) and that calculated in the gas phase. As a note, the N10-C11 bond in compound 1 is shorter than that observed for the aliphatic and benzylic amines, which is typical for anilines [37]. The measured bond lengths of guanidines 1 and 5–10 are consistent with a T1 tautomer structure, and they all are substituted with amines with a pK_a > 3.8. The solid-phase structure of pyrrolidine-substituted 11 has N7-C8, C8-N9, and C8-N10 bonds, which are even more equal (1.341–1.344 Å). The lengths for the corresponding bonds in compound 12, however, mimic those seen for compound 1. A larger variance in bond length between the central atoms was seen for compounds 2–4. The average values were N7-C8: 1.384 ± 0.003 Å, C8-N9: 1.338 ± 0.003 Å, and C8-N10 1.303 ± 0.007 Å. Thus, the N7-C8 bond and the C8-N10 bonds are more in line with that estimated by DFT calculations in the gas phase (Supplementary Materials, Table S9).

These bonds are approaching single- and double-bond character, respectively, and the visualisation of tautomer T2 with a cis–cis geometry, as shown in Figure 2, is descriptive. The anilines used in the preparation of these three molecules have pK_a < 3.2. Thus, the electronic properties of the substituents appear to play a major role in determining the tautomer type. The bond and torsion angels for the central part of the molecules are visualised in Figure 4 and in Supplementary Materials, Tables S5 and S6. For compounds 1 and 5–12, the following average bond angles were observed: N7-C8-N9: 126.1 ± 0.6°, N7-C8-N10: 118.2 ± 0.8°, and N9-C8-N10: 115.7 ± 1.3°. The bond angles for guanidines 2–4 are very similar, but they are arranged in an opposite way, being N7-C8-N9: 118.0 ± 0.2°, N7-C8-N10: 115.6 ± 0.4°, and N9-C8-N10: 126.4 ± 0.3°.

Guanidines 1 and 5–12 have N7-C8-N10-C11 torsion angle between 28.1° and −16.9°, with an average absolute value of 8.6°. The N9-C8-N10-C11 torsion angle has an average absolute value of 173.1°. Thus, in these compounds, the substituent on N10 is trans in relation to N9. An outlier in this series is m-chloroaniline derivative 1, which, due to its bulk and shorter C-N bond, requires some reorientation of the structure. For guanidines 2–4, the situation is reversed, with the N7-C8-N10-C11 torsion angle being close to 180°, with an average absolute value of 176.6° and an average N9-C8-N10-C11 torsion angle of 3.9°. Thus, these structures are crystallised with a cis–cis structure. The deviation from planarity within the central part of the molecules defined by atoms N3-N7-C8-N9-N10 is only minor. For the cis–cis tautomer structures, atomN7 shifts out of this plane by an average value of 0.105 Å, while the value for cis–trans is 0.051 Å.

3.5. Hydrogen Bonding and the Effect on Solid-Phase Structure

One possible explanation for the bond length averaging especially seen for compounds 1 and 5–12 could be intramolecular hydrogen bonding leading to semi-aromatic substructures. Such a phenomenon has been explained by resonance-assisted hydrogen bonding [17,18,19]. In all of the X-ray structures, intramolecular hydrogen bonding involving the central N9 atom as a donor and pyrimidine N3 as an acceptor is indicated. The distance between N3 and N9 is in the range expected for hydrogen bonds (average value for all compounds, 2.68 Å), but the interatomic distances (2.66–2.71 Å) are not shorter for these molecules in comparison with guanidines 2–4. Thus, resonance-assisted hydrogen bonding is not likely to explain the X-ray tautomer forms for 1 and 5–12. However, the intermolecular hydrogen bonding in the crystals differ. The cis–trans geometry of guanidines 1 and 5–10 dictate that two hydrogens (on N9 and N10) are heading in the same direction, providing two interaction sites. Atoms N1 and N7 in a neighbouring molecule are in perfect distance to be acceptors of these hydrogen bonds. This leads to the formation of infinite chains in the structure connected by hydrogen bonds (see Figure 5).

For guanidines 2–4, the two hydrogens are on opposite sides, thus not allowing for the same intermolecular hydrogen bonding. However, another preorganised block emerges, allowing for the formation of dimers via N7-H···N1 and N7-H ···N10 hydrogen bonds. This is probably the distinct IR absorptions seen for 2–4 in the range of 3400–3500 cm⁻¹ (Supplementary Materials, Table S13). Fluorine can also engage in weak hydrogen bonds, with bond distances and angles deviating from those of more classical hydrogen bonds [38]. Pentafluoro derivative 3 has a N9-F distance of 2.98 Å at an angle of 101.5°, while trifluoromethyl analogue 8 has a N10-F distance of 2.80 Å at 95°. Both are within length–angle boundaries expected for a weak N-H···F interaction [38]; however, they are not expected to significantly affect the structure in the solid state. For 2,5-dimethoxy derivative 4, the N9-O distance is 3.33 Å at an angle of 95°. Thus, hydrogen bonding for this pair is not likely. Compounds 11 and 12 have disubstituted N10, which does not allow for the pair of intermolecular hydrogen bonds seen in other structures. For 11, a water molecule donates a hydrogen bond to N7 (3.0 Å at 166.6°). This same water molecule might also interact weakly with the pyrimidine N1 (3.4 Å, 126.8°). Compound 12 instead forms a supramolecular block consisting of two molecules of 12 and one 1,4-dioxane molecule. The pyrrole unit of the N10 substituent is indicated to be an acceptor of a T-shaped hydrogen bond from the CH unit of the 1,4-dioxane, in addition to other van der Waal contacts. To summarise, the solid-phase structure of the guanidines investigated is in part dictated by the electronic properties of the amine substituent and in part by intermolecular hydrogen bonding. The guanidines substituted with amines with a pK_a > 3.8 crystallised in a cis–trans T1 form, while those substituted with anilines with pK_a < 3.2 had a cis–cis T2 solid-phase structure.

4. Conclusions

This series of N,N′-substituted guanidines was prepared from N-(4,6-dimethylpyrimidin-2-yl)cyanamide. The conditions used depend on the pK_a of the amine nucleophile. The compounds were crystallised and analysed by X-ray crystallography. Two main types of structures were obtained. Guanidines substituted with amines with pK_a > 3.8 had a cis–trans geometry, with the shortest bond between atoms N7 and C8. When the amine used to form the guanidines had pK_a below 3.2, the solid-phase structure had cis–cis geometry with a short bond on the opposite side of the guanidine. The bond lengths differ from that expected from single and double bonds, due to the conjugate nature of these guanidines alongside the effects from inter- and intramolecular hydrogen bonding.