Molecular Structures and Intermolecular Hydrogen Bonding of Silylated 2-Aminopyrimidines

Abstract

A series of silylated 2-aminopyrimidines Me_(4−n)Si(NHpyr)_n (Me = methyl, NHpyr = pyrimid-2-ylamino, n = 1, 2, 3, 4), i.e., compounds 1, 2, 3, and 4, respectively, was prepared from a series of the respective chlorosilanes Me_(4−n)SiCl_n and 2-aminopyrimidine. Triethylamine was used as a sacrificial base. Compounds 1, 2, 3, and 4 are solid at room temperature. They were analyzed using ¹H, ¹³C, ²⁹Si NMR, and Raman spectroscopy, and their molecular structures were confirmed by single-crystal X-ray diffraction analyses. All structures exhibit intramolecular van der Waals contacts between the silicon atom and one nitrogen atom of the pyrimidine moiety. Thus, their Si coordination spheres can be interpreted as [4+n] coordinated capped tetrahedra. Intermolecular hydrogen bonds (N–H···N bridges between the Si-bound amino groups and the non-Si-capping pyrimidine N atoms) are a constant contributor to the solid-state structures of these compounds. Furthermore, compounds 2 and 4 exhibit N–H···N bridges which involve 50% of their Si-capping N atoms as hydrogen bridge acceptors. Consequently, 50% of the non-Si-capping pyrimidine N atoms are stabilized by C–H···N contacts. As a result of a particularly dense network of intermolecular hydrogen bridges, the melting point of Si(NHpyr)₄ (compound 4) is higher than 300 °C.

1. Introduction

Silylated amines, also known as aminosilanes, are compounds with at least one Si–N bond. Because of the trifunctionality of the nitrogen atom, this generic class of compounds involves silylated amines with one N-bound silyl group (I in Figure 1, aminosilanes with terminal amino groups), two (II, referred to as silazanes), or even three Si–N bonds per N atom (III, trisilylamines). They have been the focus of many research projects for several decades, driven, e.g., by some of their inherent properties. Their elemental composition (Si, C, N in particular) is speaking for their investigation as precursors for SiNC or SiONC ceramic materials, e.g., [1,2]. Further aspects of their materials chemistry involve the use of silazanes in coatings [3]. Their mutual feature, the Si–N bond, also offers entry into further fields of silicon chemistry which make use of this synthon. For example, CO₂ can insert into the Si–N bond with the formation of carbamoyloxysilanes (e.g., IV) [4,5,6]. The latter are interesting starting materials for the synthesis of isocyanates and silicones in a CO₂-consuming process [5,7,8]. The insertion of isocyanates in Si–N bonds may afford silylated urea derivatives (e.g., V) [9]. The insertion of heteroallenes into Si–N bonds may also serve as an entry into silicon coordination chemistry (i.e., the syntheses of Si compounds with hexa- or pentacoordinate Si atom, VI [10] and VII [11], respectively). As part of those studies and of related investigations in our group, we synthesized a portfolio of aminosilanes and other compounds with Si–N bond(s), including silylated amines [6,9,12], imines [13], and cyclic aminosilanes [14], and explored their reactions with CO₂ or isocyanates. In addition, we have already investigated the reactivity of silyl morpholine towards a variety of heteroallenes [15].

Guanidinosilanes (or silicon guanidinates) represent another class of Si–N compounds with interesting properties. Guanidinates (the mono-anionic forms of guanidine derivatives) may form simple silylguanidines (VIII [16], IX [17], X [18], XI [19], XII [20], Figure 2), some are capable of acting as chelating ligands in hypercoordinate Si complexes (XIII [21], XIV [22]), and some are capable of stabilizing low-coordinate Si compounds (e.g., XV [23], XVI [24]).

Furthermore, some guanidinates are also capable of bridging Si atoms with other metal atoms in heteronuclear complexes (e.g., XVII [25], XVIII [20], XIX [26], Figure 3). For some representatives of Si-guanidinates, it has also been shown that their Si–N bond may be prone to CO₂ insertion [22,27]. The silicon compounds of aromatic guanidines (2-aminopyrimidine derivatives), however, are scarcely explored. Compounds XX [28], XXI [29], and XXII [30] are some isolated examples of compounds which feature the silylated 2-aminopyrimidine motif. This served as motivation for us to explore the first systematic series of 2-aminopyrimidine-derived silanes Me_(4−n)Si(NHpyr)_n (Me = methyl, NHpyr = pyrimid-2-ylamino, n = 1, 2, 3, 4), i.e., compounds 1, 2, 3, and 4, respectively.

2. Materials and Methods

2.1. General Considerations

All reactions were carried out under dry argon atmosphere using standard Schlenk techniques [31,32]. Details of the chemicals used and purification methods applied can be found in the supporting information (cf. Table S1). NMR spectra (of CDCl₃ solutions with tetramethylsilane, TMS, as an internal standard) were recorded either on a BRUKER DPX 400 spectrometer (Bruker Biospin, Rheinstetten/Karlsruhe, Germany) at 400.13 MHz, 100.61 MHz, and 79.49 MHz or on a BRUKER AVANCE III 500 MHz spectrometer (Bruker Biospin, Rheinstetten/Karlsruhe, Germany) at 500.13 MHz, 125.76 MHz, and 99.36 MHz for ¹H, ¹³C, and ²⁹Si, respectively. The spectra are shown in the supporting information (Figures S1–S15). Raman spectra (cf. Figure S16 in the supporting information) were measured with a Bruker FT-Raman spectrometer RFS 100/S (Bruker Optics, Ettlingen, Germany). The device works with an air-cooled Nd:YAG-Laser with a wavelength of 1064 nm and a nitrogen-cooled detector. The samples (dried in vacuo; according to ¹H and ¹³C NMR, they were devoid of solvent of crystallization) were filled in glass tubes and sealed with PTFE-paste. The intensity is listed as follows: vs (very strong) 80–100% of the highest signal, followed by s (strong), m (medium), w (weak), and vw (very weak), descending further in intensity in 20% increments with respect to the strongest signal. The boiling points of liquid samples were measured as described in [33]. Melting points were measured using a Polytherm A hot stage microscope (Wagner & Munz, München, Germany) with an attached 52II thermometer from Fluke. For single-crystal X-ray diffraction studies, data collection was performed on a STOE IPDS2 image plate diffractometer (STOE & Cie, Darmstadt, Germany) equipped with a low-temperature device with Mo-Kα radiation (λ = 0.71073 Å) using ω scans. Software for data collection: X-AREA, cell refinement: X-AREA, and data reduction: X-RED [34]. Preliminary structure models were derived by direct methods [35]. Non-hydrogen atoms were refined anisotropically in full-matrix least-squares cycles based on F² for all reflections using SHELXL 2019/3 [36]. C-bound hydrogen atoms were included isotropically in the models in idealized positions constrained to the pivot atoms (riding model). N-bound hydrogen atoms were located as residual electron density peaks and were refined isotropically without restraints. Graphics of the molecular structures were generated with ORTEP-3 (version 2014.1) [37,38] and POV-RAY (version 3.7) [39].

2.2. Syntheses and Characterization

Compound 1 (pyrimid-2-ylaminotrimethylsilane). 2-Aminopyrimidine (4.44 g, 47 mmol) and triethylamine (4.89 g, 48 mmol) were dissolved in 50 mL of THF, whereupon chlorotrimethylsilane (4.99 g, 46 mmol) was added with stirring, and the mixture was heated to reflux for 4 h. After stirring at room temperature overnight, the resultant suspension was filtered, and from the filtrate all volatiles were removed under reduced pressure (condensation into a cold trap) to afford 4.03 g (24 mmol, 52%) of crude product 1, which was contaminated with small amounts of 2-aminopyrimidine. To this crude product, 2 mL of CDCl₃ was added to obtain a saturated solution for an initial NMR analysis (general reaction control). In the presence of this solvent, suitable crystals for single-crystal X-ray diffraction were obtained after standing for several days at room temperature. The crystals were washed with n-pentane and dried under reduced pressure. To remove traces of THF and 2-aminopyrimidine, the product was recrystallized from CHCl₃. A product of sufficient purity (according to NMR spectroscopy) was obtained along an analogous route using excess triethylamine and chlorotrimethylsilane: 4.38 g (46 mmol) 2-aminopyrimidine, 7.35 g (72 mmol) triethylamine, and 7.75 g (71 mmol) chlorotrimethylsilane yielded 5.25 g (31 mmol, 68%,) of 1. Melting point: 58 °C; boiling point: 88 °C/0.9 Torr; Raman: ν (cm⁻¹) 3086 (w), 3032 (w), 2959 (s), 2901 (vs), 1584 (w), 1087 (m), 992 (w), 925 (w), 871 (vw), 855 (vw), 788 (vw), 641 (vw), 626 (w), 392 (vw), 296 (vw), 250 (vw), 230 (vw), 219 (vw), 203 (vw), 182 (vw), and 103 (m); ¹H NMR (CDCl₃, 400 MHz): δ (ppm) 0.29 (s, 9 H, SiMe₃), 4.88 (s (br), 1 H, NH), 6.55 (t, 4.8 Hz, 1 H, H⁵), and 8.26 (d, 4.8 Hz, 2 H, H^4,6); ¹³C NMR (CDCl₃, 100 MHz): δ (ppm) −0.4 (SiMe₃), 111.1 (C⁵), 157.9 (C^4,6), and 164.5 (C²); and ²⁹Si NMR (CDCl₃, 79 MHz): δ (ppm) 4.7.

Compound 2 (bis(pyrimid-2-ylamino)dimethylsilane). 2-Aminopyrimidine (7.38 g, 78 mmol) and triethylamine (7.96 g, 79 mmol) were dissolved in 80 mL of THF, whereupon dichlorodimethylsilane (5.04 g, 39 mmol) was added with stirring, and the mixture was heated to reflux for 6 h. After stirring at room temperature overnight, the suspension was filtered, and all volatiles were removed from the filtrate under reduced pressure to afford 6.94 g (28 mmol, 72%) of crude product 2. To this crude product, 2 mL of CDCl₃ was added to obtain a saturated solution for an initial NMR analysis (general reaction control). In the presence of this solvent, suitable crystals for single-crystal X-ray diffraction were obtained after standing for several days at room temperature. The crystals were washed with n-pentane. To remove traces of THF, the product was recrystallized from CHCl₃. Melting point: 134 °C; Raman: ν (cm⁻¹) 3121 (vw), 3088 (w), 3052 (w), 3027 (w), 3001 (vw), 2965 (vw), 2905 (vw), 1580 (w), 1133 (vw), 1079 (w), 986 (vw), 871 (vs), 780 (vw), 707 (vw), 651 (vw), 587 (vw), 458 (vw), 410 (vw), 194 (w), 120 (vs), and 78 (vw); ¹H NMR (CDCl₃, 400 MHz): δ (ppm) 0.56 (s, 6 H, SiMe₂), 5.74 (s (br), 2 H, NH), 6.55 (t, 4.8 Hz, 2 H, H⁵), and 8.25 (d, 4.8 Hz, 4 H, H^4,6); ¹³C NMR (CDCl₃, 100 MHz) δ (ppm) −1.0 (SiMe₂), 111.4 (C⁵), 157.9 (C^4,6), and 164.1 (C²); and ²⁹Si NMR (CDCl₃, 79 MHz): δ (ppm) −5.6.

Compound 3 (tris(pyrimid-2-ylamino)methylsilane). 2-Aminopyrimidine (5.77 g, 61 mmol) and triethylamine (6.17 g, 61 mmol) were dissolved in 80 mL of THF, whereupon trichloromethylsilane (2.99 g, 20 mmol) was added with stirring, and the mixture was heated to reflux for 1 h. After stirring at room temperature overnight, the suspension was filtered, and half of the solvent was removed from the filtrate under reduced pressure. Crystals, suitable for single-crystal X-ray diffraction, were obtained after standing one night at room temperature. The crystals were isolated by decantation, washed with n-pentane, and briefly dried in vacuo. Yield: 2.60 g (3.6 mmol, 36%) of the THF solvate (3)₂ · (THF). Melting point: 134 °C (decomp.); Raman: ν (cm⁻¹) 3156 (vw), 3121 (vw), 3088 (w), 3052 (w), 3027 (w), 3000 (vw), 2913 (vw), 1580 (w), 1133 (vw), 1079 (w), 986 (vw), 871 (vs), 815 (vw), 780 (vw), 763 (vw), 651 (vw), 587 (vw), 458 (w), 410 (w), 194 (w), 120 (vs), and 78 (vw); and for NMR characterization, the compound was recrystallized from CHCl₃. ¹H NMR (CDCl₃, 400 MHz): δ (ppm) 0.81 (s, 3 H, SiMe), 6.26 (s (br), 3 H, NH), 6.62 (t, 4.8 Hz, 3 H, H⁵), and 8.30 (d, 4.8 Hz, 6 H, H^4,6); ¹³C NMR (CDCl₃, 100 MHz): δ (ppm) −1.3(SiMe₂), 111.9 (C⁵), 158.1 (C^4,6), and 163.6 (C²); ²⁹Si NMR (CDCl₃, 79 MHz): δ (ppm) −24.2.

Compound 4 (tetrakis(pyrimid-2-ylamino)silane). 2-Aminopyrimidine (6.72 g, 71 mmol) and triethylamine (7.28 g, 72 mmol) were dissolved in 80 mL of THF, whereupon tetrachlorosilane (3.06 g, 18 mmol) was added with stirring, and the mixture was heated to reflux for 1 h (and 40 mL of additional THF was added). After stirring at room temperature overnight, the suspension was filtered, and all volatiles were removed from the filtrate under reduced pressure (50 °C water bath, ≤1 mbar). First, a slightly yellowish solution was obtained. According to NMR spectroscopy, this liquid still contained THF, which was not removed under the conditions applied. Upon storing this solution at room temperature for two days, slightly yellow crystals and a colorless liquid (THF) formed. The solid was isolated by decantation and dried in vacuum to afford 2.22 g (5 mmol, 28%) of a white solid. Whereas NMR and Raman spectroscopy were carried out with this product obtained from THF, crystals for the X-ray diffraction analysis of 4 were obtained along a transsilylation route: Heating of 1 (2.05 g, 12 mmol) with tetrachlorosilane (0.52 g, 3 mmol) in 100 mL anisole for 4 h and slowly cooling to room temperature afforded a few crystals of the anisole solvate of 4. Melting point: >300 °C; Raman: ν (cm⁻¹) 3158 (vw), 3121 (vw), 3088 (w), 3052 (w), 3027 (w), 3000 (vw), 1580 (w), 1133 (vw), 1079 (w), 986 (vw), 871 (vs), 651 (vw), 521 (vw), 458 (w), 410 (w), 194 (w), and 120 (vs); ¹H NMR (CDCl₃, 400 MHz): δ (ppm) 5.48 (s (br), 4 H, NH), 6.59 (t, 4.8 Hz, 4 H, H⁵), and 8.29 (d, 4.8 Hz, 8 H, H^4,6); ¹³C NMR (CDCl₃, 100 MHz): δ (ppm) 111.5 (C⁵), 158.3 (C^4,6), and 163.2 (C²); and ²⁹Si NMR (CDCl₃, 79 MHz): δ (ppm) −52.5.

Attempt of the reaction of 1 with CO₂. A sample of 1 (ca. 20 mg) was dissolved in about 1 mL of THF-d8 in an NMR tube. With a long cannula, CO₂ was introduced into this solution (slow bubbling) for 20 min and NMR spectra were recorded afterwards (cf. Figures S13–S15). The three NMR spectra show the signals of the starting material 1. According to the ²⁹Si NMR spectrum, besides SiMe₄, this is still the sole Si compound in this sample. In the ¹H and ¹³C spectra, some additional signals are present which can be assigned to free 2-aminopyrimidine and CO₂ (the latter is assigned to the ¹³C NMR signal at 126 ppm). No signal for any new carbonyl moiety (such as a carbamate) could be found.

3. Results and Discussion

3.1. Syntheses

The herein reported silylated derivatives of 2-aminopyrimidine (H₂Npyr), i.e., compounds 1, 2, 3, and 4, could be synthesized, starting from the respective chlorosilanes and triethylamine (as HCl scavenger) in THF as the solvent with good yields (Scheme 1). The recrystallization of compounds 1 and 2 (from chloroform) and compound 3 (from THF) afforded crystals suitable for single-crystal X-ray diffraction analyses. As compound 4 exhibits very poor solubility in these solvents, an alternative synthesis path (a transsilylation of 1 and SiCl₄ in anisole as the solvent) was pursued to obtain crystals suitable for X-ray diffraction (Scheme 1, bottom).

3.2. Raman Spectroscopy

In the Raman spectra, besides the typical ν(C-H_arom) slightly above 3000 cm⁻¹ and ν(C-H_aliph.) slightly below 3000 cm⁻¹, specific bands for the pyrimidine units are present (see

Table 1. Specific Raman bands for the pyrimidine unit in all compounds in cm⁻¹.

Vibration	1	2	3	4
1590-1520 (aromatic CC, CN str.)	1584	1580	1580	1580
1005-960 (aromatic CC, CN str.)	992	986	986	986
650-630	641	651	651	651

, assignment of bands taken from [40]). Whereas corresponding vibrations are found at the same wavenumbers for compounds 2, 3, and 4, the respective data of 1 are slightly different. We attribute this to the pronounced flexibility of the molecules of compound 1. Whereas the former three are bound to more than just one neighbor molecules via N–H···N hydrogen bridges and their Si atom represents a bridge/node in this network, in compound 1, only two molecules are combined into dimers via N–H···N hydrogen bridges, and their Si atoms are part of terminal groups (vide infra).

3.3. Molecular Structures

The molecular structures of compounds 1–4 in their solid forms exhibit common features of the Si coordination spheres, which are based on formally covalent Si–N bonds (involving the amino group of the 2-aminopyrimidine building block) and additional remote Si···N interactions with pyrimidine N atoms. The typical bond length of Si–N bonds in silylated guanidines is 1.76(2) Å for 40 examples of compounds with tetracoordinate Si at the tricoordinate guanidine N and 1.66(2) Å for 73 examples of compounds with tetracoordinate Si at the dicoordinate guanidine N (a search in CSD 2023 version 5.44). Because of the latter group, the average Si–N bond length in silylated guanidines is shorter than Si–N bonds in general (1.739 ± 0.030 Å [41]), but the former is more representative for the herein presented compounds. With reference to the van der Waals radii of silicon and nitrogen (2.10 and 1.55 Å, respectively), any Si-N distance below 3.65 Å is an indication of atomic interaction [42]. Particular individual features of the molecular structures of compounds 1, 2, 3, and 4 (

Table 2. Selected bond lengths [Å] and angles [deg] in the Si coordination spheres of compounds 1, 2, 3, and 4. Prominent values within groups of corresponding angles are shaded in grey.

Compound	Atoms	Bond Length [Å]	Atoms	Bond Angle [°]
1	Si1–N1	1.7490(13)	N1-Si1-C5	112.66(7)
	Si1–C5	1.8501(17)	N1-Si1-C6	110.28(7)
	Si1–C6	1.8499(18)	N1-Si1-C7	102.94(8)
	Si1–C7	1.8565(19)	C5-Si1-C6	109.77(10)
			C6-Si1-C7	111.10(10)
			C5-Si1-C7	109.94(9)
	Si2–N4	1.7485(13)	N4-Si2-C12	104.00(8)
	Si2–C12	1.8562(18)	N4-Si2-C13	111.12(7)
	Si2–C13	1.8544(16)	N4-Si2-C14	111.27(8)
	Si2–C14	1.8556(19)	C12-Si2-C13	108.99(9)
			C13-Si2-C14	111.19(8)
			C12-Si2-C14	110.01(10)
2	Si1–N1	1.7377(10)	N1-Si1-N4	111.66(5)
	Si1–N4	1.7439(10)	N1-Si1-C9	105.37(5)
	Si1–C9	1.8521(13)	N1-Si1-C10	112.33(5)
	Si1–C10	1.8481(12)	N4-Si1-C9	111.76(6)
			N4-Si1-C10	104.54(5)
			C9-Si1-C10	111.35(6)
3	Si1–N1	1.7369(12)	N1-Si1-N4	104.81(6)
	Si1–N4	1.7369(12)	N1-Si1-N7	105.72(6)
	Si1–N7	1.7338(11)	N4-Si1-N7	104.73(5)
	Si1–C13	1.8451(14)	N1-Si1-C13	112.00(6)
			N4-Si1-C13	115.55(6)
			N7-Si1-C13	113.14(6)
	Si2–N10	1.7332(11)	N10-Si2-N13	105.81(6)
	Si2–N13	1.7336(12)	N10-Si2-N16	104.46(5)
	Si2–N16	1.7438(12)	N13-Si2-N16	104.11(6)
	Si2–C26	1.8400(14)	N10-Si2-C26	113.22(6)
			N13-Si2-C26	112.49(6)
			N16-Si2-C26	115.77(6)
4	Si1–N1	1.7218(13)	N1-Si1-N4	107.83(6)
	Si1–N4	1.7180(12)	N1-Si1-N7	112.77(7)
	Si1–N7	1.7153(14)	N1-Si1-N10	107.28(6)
	Si1–N10	1.7189(13)	N4-Si1-N7	107.43(6)
			N4-Si1-N10	113.07(6)
			N7-Si1-N10	108.57(6)
	Si2–N13	1.7192(13)	N13-Si2-N16	109.10(6)
	Si2–N16	1.7181(12)	N13-Si2-N19	108.96(6)
	Si2–N19	1.7272(13)	N13-Si2-N22	108.53(6)
	Si2–N22	1.7196(12)	N16-Si2-N19	109.11(6)
			N16-Si2-N22	112.34(6)
			N19-Si2-N22	108.75(6)
	Si3–N25	1.7166(13)	N25-Si3-N28	107.78(6)
	Si3–N28	1.7158(13)	N25-Si3-N31	111.48(6)
	Si3–N31	1.7202(13)	N25-Si3-N34	107.66(6)
	Si3–N34	1.7200(13)	N28-Si3-N31	108.10(6)
			N28-Si3-N34	113.35(6)
			N31-Si3-N34	108.52(6)

and

Table 3. Selected interatomic distances [Å] of the remote N···Si coordination in compounds 1, 2, 3, and 4.

Compound	Atoms	Distance [Å]	Atoms	Distance [Å]
1	Si1···N2	3.0464(13)	Si2···N6	3.0035(12)
2	Si1···N2	3.0609(11)	Si1···N5	3.0450(11)
3	Si1···N3	2.9826(13)	Si2···N12	2.9990(12)
	Si1···N6	3.1337(13)	Si2···N15	2.9773(18)
	Si1···N9	2.9452(12)	Si2···N18	3.1320(13)
4	Si1···N2	3.0442(13)	Si2···N20	3.0120(13)
	Si1···N5	3.0098(13)	Si2···N23	3.0494(14)
	Si1···N8	3.0792(13)	Si3···N26	3.0269(13)
	Si1···N11	3.0165(14)	Si3···N29	3.0718(15)
	Si2···N14	3.0453(13)	Si3···N32	3.0610(13)
	Si2···N17	2.9621(13)	Si3···N35	3.0307(14)

) will be discussed in the following.

Compound 1 (monoclinic, P2₁/c) crystallizes with two independent molecules in the asymmetric unit (Figure 4, Table 2, Table 3 and

Table A1. Crystallographic data from data collection and refinement for compounds 1, 2, 3 (THF solvate), and 4 (anisole solvate).

Parameter	1	2 1	(3)2 · (THF) 2	4 · (Anisole) 3
Formula	C7H13N3Si	C10H14N6Si	C30H38N18OSi2	C23H24N12OSi
Moiety formula	C7H13N3Si	C10H14N6Si	2 (C13H15N9Si), C4H8O	C16H16N12Si, C7H8O
Mr	167.29	246.36	722.96	512.63
T (K)	180(2)	180(2)	180(2)	180(2)
λ (Å)	0.71073	0.71073	0.71073	0.71073
Crystal system	monoclinic	triclinic	triclinic	monoclinic
Space group	P21/c	P$\overline{1}$	P$\overline{1}$	P21/c
a (Å)	9.4337(3)	8.6757(4)	10.0640(3)	15.9611(2)
b (Å)	19.5412(6)	8.8740(4)	11.1921(3)	21.1674(3)
c (Å)	10.7349(3)	9.0989(4)	18.6757(5)	22.6832(3)
α (°)	90	64.211(3)	72.898(2)	90
β (°)	100.794(3)	75.463(3)	89.000(2)	97.740(1)
γ (°)	90	79.194(3)	63.346(2)	90
V (Å3)	1943.92(10)	608.08(5)	1780.70(9)	7593.81(18)
Z	8	2	2	12
ρcalc (g·cm−1)	1.14	1.35	1.35	1.35
μMoKα (mm−1)	0.2	0.2	0.2	0.1
F (000)	720	260	760	3216
θmax (°), Rint	28.0, 0.0377	28.0, 0.0232	28.0, 0.0319	27.0, 0.0428
Completeness	100%	99.8%	99.9%	99.9%
Reflns collected	17,865	9797	33,018	130,089
Reflns unique	4699	2937	8598	16,561
Restraints	0	0	24	0
Parameters	214	165	527	1150
GoF	1.097	1.080	1.063	1.108
R1, wR2 [I > 2σ(I)]	0.0367, 0.0876	0.0308, 0.0770	0.0385, 0.0959	0.0407, 0.0939
R1, wR2 (all data)	0.0495, 0.0957	0.0336, 0.0792	0.0462, 0.1019	0.0506, 0.1010
Largest peak/hole (e·Å−3)	0.24, −0.23	0.25, −0.25	0.28, −0.31	0.27, −0.35

¹ One of the two methyl groups was refined disordered (rotational disorder about the Si–C bond) with site occupancies of 0.40(2) and 0.60(2). ² This structure features two disordered moieties. The solvent of crystallization (a THF molecule) was refined disordered over two sites with site occupancies of 0.771(4) and 0.229(4). Furthermore, the pyrimidino group of one of the two crystallographically independent molecules of 3 was refined disordered over two sites with site occupancies of 0.914(2) and 0.086(2). ³ The asymmetric unit of this structure comprises three molecules of 4 and three molecules of the solvent of crystallization (anisole). The latter consist of (i) a couple of two anisole molecules connected by C–H···C(π) stacking (with site occupancy of 0.5), which is located near a center of inversion and thus disordered by symmetry (thus furnishing full site occupancy); (ii) an adjacent anisole molecule, which is slightly disordered over two sites (site occupancy factors refined to 0.407(13) and 0.593(13); for stable refinement of this less pronounced disorder, the benzene rings of this molecule were treated as idealized hexagons); and (iii) an additional (remote) anisole molecule which did not show disorder.

). The silicon atoms are situated in slightly distorted tetrahedral coordination spheres with bond angles in the ranges 102.94(8)–111.10(10)° and 104.00(8)–111.27(8)° around Si1 and Si2, respectively. The Si–N bond lengths of the two independent molecules are essentially equal (1.749(1) Å, Table 2). They are in the expected range for Si–N bonds in general and for those in guanidines with silylated tricoordinate N atom. For each Si atom, the Si···N distance to one of the pyrimidine nitrogen atoms is markedly below the sum of van der Waals radii (3.064 Å for Si1···N2 and 3.004 Å for Si2···N6, Table 3). These N atoms are capping a tetrahedral face of the Si coordination sphere, thus creating a remote [4+1]-coordination. This affects the angles between the four covalently Si-bound substituents: The sum of C-Si-C and C-Si-N angles of the capped tetrahedral face (332.7 and 333.6° at Si1 and Si2, respectively) exceeds the 3-fold tetrahedral angle (328.5°), and the noticeably smallest angle in the Si coordination sphere (highlighted in Table 2) is spanned by the Si–N bond and the Si–C bond trans to the N-capped tetrahedral face. The other pyrimidine N atoms, which are not involved in remote Si···N coordination, are involved in intermolecular N–H···N hydrogen bridges (vide infra).

The crystal structure of compound 2 (triclinic, P$\overline{1}$) comprises one molecule in the asymmetric unit (Figure 5, Table 2, Table 3 and Table A1). This structure has recently been reported by Merzweiler and Lechner [43]. As our own structure determination afforded a model with the enhanced precision of bond lengths and angles, we refer to our data in the discussion. As found for compound 1, the Si–N bonds in 2 (1.738(1) Å and 1.744(1) Å) are in the expected range for Si–N bonds. The silicon atom is in a tetrahedral coordination sphere with angles between 104.54(5) and 112.33(5)°. As a result of the presence of two pyrimidylamino groups, the molecule of 2 features two Si···N contacts below the sum of the van der Waals radii (Si1···N2 3.061 Å, Si1···N5 3.045 Å). As a common feature of 1 and 2, the smallest angles in the silicon coordination sphere (highlighted in Table 2) are also the Me-Si-N angles which involve the methyl group trans to the tetrahedral face capped by a pyrimidine N atom of this entity.

Compound 3 (triclinic, P$\overline{1}$) crystallizes with two independent aminosilane molecules and one THF molecule in the asymmetric unit (Figure 6, Table 2, Table 3 and Table A1). For both molecules, the Si–N bond lengths are in the range from 1.733(1) Å to 1.744(1) Å, which is within the expected range for general Si–N bonds. The silicon atoms in both molecules have a markedly distorted tetrahedral coordination sphere with angles ranging between 104.11(6) and 115.77(6)°, with the N-Si-N angles at the lower end (around 105°) and the N-Si-C angles at the upper end, which is essentially in accordance with VSEPR. Furthermore, this rather pronounced difference between these groups of angles is a result of the molecular conformation in which each molecule of 3 features three Si···N contacts below the sum of the van der Waals radii between its Si atom and one pyrimidine nitrogen atom of each pyrimidine moiety. All of these Si···N contacts are established by capping the tetrahedral faces trans to the Si–N bonds, which results in mutual widening of the C-Si-N and compressing of the N-Si-N angles. Interestingly, for each molecule of 3, one of these Si···N contacts is markedly longer than the other two (Table 3). While the pyrimidine moieties involved in this remote coordination are all involved in the same type of N–H···N hydrogen bonding in the crystal packing (vide infra), the remote N···Si coordination of one out of three N···Si interactions per molecule is markedly off from capping the center of a tetrahedral face. This is best reflected by the different N-Si-N angles spanned by the capping N atom and the Si–N bond trans to the capped face (molecule 1: N9-Si1-N1 157.04(5)°, N3-Si1-N4 154.85(5)°, N6-Si1-N7 147.92(5)°; molecule 2: N15-Si2-N16 154.15(5)°, N12-Si2-N13 154.61(5)°, N18-Si2-N10 144.36(5)°).

Compound 4 (monoclinic, P2₁/c) crystallizes with three aminosilane molecules and three anisole molecules in the asymmetric unit (Figure 7, Table 2, Table 3 and Table A1). All Si–N bond lengths are in the narrow range of 1.7153(14) Å to 1.7272(13) Å (in accordance with the expected range of Si–N bond lengths in general). In the order 1 > 2 > 3 > 4, systematic shortening of the Si–N bonds is observed, which causes slight but increasing deviations of the Si–N bond lengths from the expected values for compounds with tetracoordinate Si at the tricoordinate guanidine N (for compound 4 in particular). We attribute this to the Si–N bond shortening as a result of a greater number of electronegative substituents at Si (especially in compound 4), whereas many silylated guanidines with Si–C bonds (such as compounds VIII, XII, and XX) contribute to the average Si–N bond length. The silicon atoms are situated in distorted tetrahedral coordination spheres with angles ranging from 107.28(6)° to 113.35(6)°. This distortion is less pronounced than in compound 3 as the Si coordination sphere is more symmetric (SiN₄), and this is true for the wider coordination sphere as well. Each of the three crystallographically independent molecules of 4 features four intramolecular Si···N contacts with interatomic distances around 3 Å, thus each of the tetrahedral faces is capped similarly. Nonetheless, a systematic feature of distortion of the tetrahedral coordination sphere is encountered, which is particularly pronounced for molecules 1 and 3 of the asymmetric unit: Two out of six N-Si-N angles are markedly wider than the other four (highlighted in Table 2). These wider angles are those of the tetrahedron which do not feature an N–H bond pointing along the tetrahedral edge. Even though there are no intramolecular N–H···N hydrogen bonds, intramolecular N–H → N orientation systematically supports N-Si-N bond angles < 109.5° in the otherwise tetrahedral SiN₄ coordination sphere. These attractive interactions may also contribute to the shorter Si–N bonds in compound 4 in particular.

3.4. Intermolecular N–H···N Hydrogen Bonding

In addition to the Si···N contacts (cf. Section 3.3), the pyrimid-2-ylamino groups of compounds 1–4 establish intermolecular N–H···N bridges in these solid-state structures. Comparison of the four silanes reveals that intermolecular contacts via N–H···N bridges are always established by sets of two of such interactions (each silane molecule acting as a hydrogen bridge donor and as a hydrogen bridge acceptor in the one and the other case). The structures under investigation exhibit three different motifs of that dimeric N–H···N bridging (we call them types A, B, C, Figure 8). Type A: the NH group and pyrimidine N atom of one pyrimidylamino group of molecule 1 interact with the pyrimidine N atom and NH group, respectively, of one pyrimidylamino group of molecule 2. This interaction pattern results in the formation of an NHNCNHNC eight-membered ring (R${}_2{}^2\left(8\right)$ motif [44]). Type B: the NH group and pyrimidine N atom of two individual pyrimidylamino groups of molecule 1 interact with the pyrimidine N atom and NH group, respectively, of two individual pyrimidylamino groups of molecule 2. This interaction pattern results in the formation of an NHNCNSiNHNCNSi twelve-membered ring (R${}_2{}^2\left(12\right)$ motif). Type C: This represents an arrangement intermediate between types A and B. The NH group and pyrimidine N atom of two individual pyrimidylamino groups of molecule 1 interact with the pyrimidine N atom and NH group, respectively, of one pyrimidylamino group of molecule 2. This interaction pattern results in the formation of an R${}_2{}^2\left(10\right)$ motif with an NHNCNSiNHNC ten-membered ring.

Within the group of compounds under investigation, hydrogen bond systems of type A were encountered with different compounds (1, 2, and 3, cf. Figure 9, Figure 10 and Figure 11, respectively), whereas the other two types were observed in one case each (type B in compound 2, Figure 10, and type C in compound 4, Figure 12).

The packing in favor of the formation of interactions of type A can be reasoned by the possibility of the formation of a pair of N–H···N bridges in which the H-bond donor meets the acceptor at the ideal angle with respect to the orientation of the H-bond acceptor’s lone pair. In principle, this should lead to near linear arrangements of the atom sequence N–H···N…C(γ) (C(γ) being the pyrimidine C atom in γ position with respect to the hydrogen bond acceptor pyrimidine N atom). The variability in the N-N-C angles of these arrays (see

Table 4. Selected interatomic distances [Å] and angles [deg] associated with N–H···N hydrogen bridges in compounds 1, 2, 3, and 4. The symmetry codes (asterisks * at the atom labels) used with compounds 2, 3, and 4 are the same as those listed in the caption of the figure which depicts that particular compound (Figure 10, Figure 11 and Figure 12, respectively).

Compound	Atoms	Distance [Å]	Atoms	Angle [°]
1	N1–N5	3.1279(17)	N1-N5-C11	156.45(6)
	N3–N4	3.0702(17)	C2-N3-N4	151.03(7)
2	N1–N5 *	3.2573(14)
	N4–N6 **	3.3115(14)	N4-N6**-C6 **	157.88(6)
3	N1–N2 *	3.0607(17)	N1-N2 *-C4 *	172.20(6)
	N4–N14	3.0292(17)	N4-N14-C21	161.63(8)
	N5–N13	3.1112(16)	N13-N5-C8	170.77(6)
	N7–N17 **	3.1330(16)	N7-N17 **-C25 **	172.30(6)
	N8–N16 **	3.1037(16)	N16 **-N8-C12	172.39(6)
	N10–N11 ***	3.0532(16)	N10-N11 ***-C17 ***	177.81(6)
4	N1–N18	3.0625(19)
	N8–N16	3.1051(18)
	N4–N32 *	3.0728(17)
	N6–N25 *	3.0227(18)
	N7–N36 *	2.9871(19)
	N2–N34 *	3.0881(18)
	N10–N14	3.0374(17)
	N12–N19	3.1256(18)

) indicates that this hydrogen bonding motif offers some flexibility to adapt to further packing requirements.

Intermolecular packing types B and C provide some interesting insights into these and related silanes with this kind of remote Si coordination in which the tetrahedral Si coordination sphere is capped by pyridine (or related) N atom(s). Even though pyrimid-2-ylamino groups always offer an N-located lone pair for Si-coordination and a second N-located lone pair for other interactions such as N–H···N hydrogen bridges, the latter proved capable of competing with the remote N···Si-coordination by interacting with the same N atom and thus leaving the other pyrimidine N atom available for further packing interactions. This finding complements the insight that 2-pyridylaminosilanes of the type R₂Si(NH-pyridyl)₂ may sacrifice their possibility of N···Si-coordination in favor of using the pyridine N atom for establishing intermolecular packing interactions. In detail, Me₂Si(NH-pyridyl)₂ features remote coordination, whereas Ph₂Si(NH-pyridyl)₂ utilizes pyridine N atoms for other interactions [45].

3.5. Reaction with CO₂

CO₂ can insert into Si–N bonds with the formation of carbamoyloxysilanes in certain cases (e.g., IV) [1,5,6]. Even though CO₂ insertion into the Si–N bonds of arylamines is not as facile as the insertion into the Si–N bonds of alkylamines [8], additional N-donor bases may support the reaction of Si–N bonds and CO₂ [8] by increasing the CO₂ concentration in the solution [46] or because N-donor bases are assumed to catalyze the reaction [47,48]. Therefore, we investigated the reaction of 1 with CO₂. Introducing gaseous CO₂ into a solution of 1 in THF-d8 for 20 min did not show any formation of carbamoyloxysilanes according to the NMR spectra which only show 1, free 2-aminopyrimidine, and CO₂ (at δ 126 ppm in the ¹³C NMR spectrum). This result indicates that CO₂ insertion into the Si–N bonds of this arylamine is hampered, and the additional N-donor sites (of the Si-bound and of the free 2-aminopyrimidine) do not drive this reaction to a facile level under ambient conditions (room temperature, CO₂ bubbling into a THF solution of the aminosilane). The exploration of the reaction conditions required for utilizing CO₂ insertion into the Si–N bonds of pyrimidylaminosilanes will thus be subject to future studies.

4. Conclusions

Four silylated 2-aminopyrimidines were synthesized, crystallized, and analyzed using X-ray diffraction. Silanes with related pyridine motifs (such as pyridine-2-olate and pyridine-2-thiolate) involve their pyridine N atoms in remote N···Si coordination [49,50,51,52]. In the case of some representatives with pyridine-2-thiolate, rather strong N-Si-bonding with the formation of hexacoordinate Si complexes was found [51,53,54]. With the pyridine-2-amino group at the Si atom, both the presence and absence of remote N···Si coordination were encountered [45]. The series of silanes 1–4 with the related pyrimidine-2-amino motif exhibits remote N···Si coordination for all representatives, but the additional interactions possible because of the second lone pair donor N atom in the aromatic ring open a portfolio of intermolecular packing interactions via N–H···N hydrogen bridges. Interestingly, in some cases, the remotely N···Si coordinating pyrimidine N atom serves as the hydrogen bridge acceptor. With more than one pyrimidylamino group bound per Si atom, these compounds may form highly linked networks through hydrogen bonds. In this regard, the compound Si(NHPyr)₄ (compound 4) may become interesting for high-temperature applications as the melting point is higher than 300 °C. Moreover, functional groups with hydrogen bridge donor or acceptor qualities may be adsorbed in silica aerogels (e.g., the sorption of mefenamic acid [55]), a feature which is of importance for drug delivery investigations. Vice versa, functional groups with hydrogen bridge donor or acceptor qualities may alter the sorbent properties of porous materials. In this regard, pyrimidylaminosilanes may become interesting starting materials for the tuning of properties in non-hydrolytic Si–N-based sol–gel processes [56,57,58]. For a further exploration of coordination chemistry (such as the use of these silanes as ligands in main group or transition metal chemistry), stronger intermolecular packing may pose an obstacle for providing well-soluble ligands and molecular complexes resulting therefrom. Thus, the preparation of coordination compounds (such as analogs of the Pb and Sn complexes obtained from pyrid-2-ylaminosilanes [45] or Pd and Cu complexes obtained from silicon pyridine-2-olates [49,52]) may pose challenges. The additional functional groups (the second pyrimidine N atom in combination with the still present Si-NH group) may give rise to heteronuclear complexes which may form 3D networks, a group of compounds which is yet to be explored. The 2-aminopyrimidine motif itself has already entered that field of research, e.g., in Cu(II)-containing MOFs [59] and in coordination networks with Ag(I) centers [60].