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Article

α-Amino Isobutyric Acid-Derived Silacyclopentane Complexes with Penta- and Hexacoordinate Si Atoms

by
Anne Seidel
,
Steven Knerr
and
Jörg Wagler
*
Institut für Anorganische Chemie, Technische Universität Bergakademie Freiberg, D-09596 Freiberg, Germany
*
Author to whom correspondence should be addressed.
Crystals 2026, 16(6), 389; https://doi.org/10.3390/cryst16060389 (registering DOI)
Submission received: 13 May 2026 / Revised: 9 June 2026 / Accepted: 10 June 2026 / Published: 13 June 2026
(This article belongs to the Section Inorganic Crystalline Materials)
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Abstract

Pyrrolidinyl-substituted silacyclopentane (CH2)4Si(Pyr)2 and α-amino isobutyric acid (H2Aib) react with the release of one equivalent pyrrolidine (HPyr) and the formation of the pentacoordinate silicon bis-chelate (Aib)Si(CH2)4(HPyr), which features the di-anion of the amino acid as an (O,N)-chelator and one equivalent of pyrrolidine as an additional lone-pair donor. Crystallographic analyses of the chloroform solvate (Aib)Si(CH2)4(HPyr)·(CHCl3), which undergoes a phase transition at 200 K, and a solvent-free modification (Aib)Si(CH2)4(HPyr), which features two crystallographically independent molecules of the complex, revealed that the N atom of the HPyr ligand, as well as the carboxylate of Aib, occupy the axial positions in the trigonal bipyramidal Si coordination sphere; the Si–C bonds of the silacyclopentane rest on equatorial sites. For the isolated molecule in a solvent environment, computational analyses revealed that the energy difference between this configuration and the related isomer with an equatorial HPyr and equatorial–axial positioning of the silacyclopentane motif is marginal. In DMSO solution, the adduct (Aib)Si(CH2)4(HPyr) decomposed, forming the hexacoordinate Si complex (HAib)2Si(CH2)4 as one of the decomposition products. In a deliberate manner, this compound was accessible from the diethylamino-substituted silacyclopentane (CH2)4Si(NEt2)2 and H2Aib with the liberation of diethylamine. (HAib)2Si(CH2)4 features two mono-anions of the α-amino acid as (O,N)-chelators, their carboxylate O atoms are trans-disposed to silacyclopentane, and their NH2 groups are mutually trans.

1. Introduction

The chemistry of hypercoordinated silicon compounds is a multi-faceted field that features, e.g., compounds with Si coordination numbers 5 or 6 and spans from the simple textbook example of hexafluorosilicate to a great variety of compounds. Various examples of these have been studied with respect to their molecular dynamics, Si–X bond activation through hypercoordination, ligand exchange equilibria and other properties that can be tuned by altering the Si coordination number and ligand sphere [1,2,3,4,5,6]. In general, the utilization of chelating ligands promotes the binding of additional donor atoms to a particular central atom. Moreover, small chelate rings with rather narrow bite angles are helpful because of their lower steric demand in the first coordination sphere and because of the so-called ring strain-release Lewis acidity [7]. The latter essentially means that the central atom pursues a coordination geometry that is suited to accommodate the small bite angle. For example, a chelate with a bite angle ≤90° in an otherwise tetrahedral coordination sphere reflects the particular strain associated with that angle because of its great deviation from the ideal of 109.5°. In contrast, positioning of the same chelate in axial–equatorial positions of a trigonal bipyramid or in cis-positions of an octahedral coordination sphere (both ideally span a 90° angle) results in a less pronounced angle discrepancy, i.e., less strain.
α-amino acids basically represent a class of compounds that should be suitable as chelators for silicon coordination chemistry as they bear various favorable features: (i) They offer O and N lone-pair donor atoms, which are frequently encountered in Si complexes. (ii) They can form anions (mono- and di-anions), which aid the binding to a Lewis acidic center. (iii) As (O,N)-chelators, they are capable of forming five-membered chelates about Si, which are supportive of Si hypercoordination as a means of achieving ring strain release. Nonetheless, α-amino acids in silicon coordination chemistry appear rather unexplored to date, as concluded from the discrepancy between the availability of a wide range of amino acids (also in the natural chiral pool) and the few structurally characterized silicon complexes with ligands of this type [8]. Figure 1 lists the classes of amino acid-derived Si complexes that have been crystallographically confirmed to date. These are: I: neutral pentacoordinate Si complexes that feature one di-anion (αA)2− and mono-anion (HαA)− of an α-amino acid (H2αA) as (O,N)-chelators and an Si-bound hydrocarbyl substituent [9]; II: zwitterionic pentacoordinate Si complexes that feature two di-anions (αA)2− as (O,N)-chelators and an ammonium-functionalized Si-bound hydrocarbyl substituent [10,11]; III: anionic pentacoordinate Si complexes, which are related to those in class II but feature an isolated counter-cation [12]; IV: neutral pentacoordinate Si complexes that feature one di-anion (αA)2− as an (O,N)-chelator, two Si-bound hydrocarbyl substituents and an additional N-donor ligand [12,13,14]; and V: a neutral hexacoordinate Si complex that features two mono-anions (HαA)− as (O,N)-chelators and two Si-bound isocyanato substituents [9].
In the context of our ongoing studies of amino acid-derived silicon complexes, which have mainly dealt with compounds of class IV [12,13,14], the current study investigates the effect of a silacyclopentane motif on the formation of these kinds of complexes. Such compounds represent a hitherto missing link between the pentacoordinate diorganosilicon complexes of class IV and Si–spirocyclic compounds with a pentacoordinate Si atom (like classes I, II, and III).

2. Materials and Methods

2.1. General Considerations

Starting materials were α-amino isobutyric acid (Roth, Karlsruhe, Germany, ≥97%), TMEDA (Sigma-Aldrich, Hamburg, Germany, ≥99.0%), diethylamine (Honeywell, Seelze, Germany, >99%), pyrrolidine (abcr, Karlsruhe, Germany, 99%), and n-butyllithium (2.5 M in hexane, Thermo Fisher Scientific, Dreieich, Germany). n-Hexane (VWR, Darmstadt, Germany, ≥99%), n-pentane (Honeywell, Seelze, Germany, ≥99.8%), acetonitrile (VWR, Darmstadt, Germany, ≥99%), and chloroform, stabilized with amylenes (Honeywell, Seelze, Germany, ≥99.5%), CDCl3 (Deutero, Kastellaun, Germany, 99.8%), and DMSO-d6 (ARMAR, Leipzig, Germany, 99.8%), were stored over activated molecular sieves (3 Å) for at least 7 days and used without further purification. 1,1-Dichlorosilacyclopentane was prepared according to a published protocol [15].
All the reactions were carried out under an atmosphere of dry argon utilizing standard Schlenk techniques. For syringe filtration, PTFE syringe filters with 15 mm diameter and 0.2 μm pore size (Roth, Karlsruhe, Germany) were used. The solution NMR spectra (1H, 13C, 29Si) (cf. Figures S1–S7 and S11–S14 in the Supporting Information) were recorded on a Bruker Nanobay 400 MHz spectrometer (Bruker, Ettlingen, Germany). The 1H, 13C, and 29Si chemical shifts are reported relative to Me4Si (0 ppm) as an internal reference. The solid-state NMR experiments (cf. Figures S8–S10, S15 and S16 in the Supporting Information) were performed on a Bruker Avance HD 400 MHz WB spectrometer (Bruker, Ettlingen, Germany) using a 4 mm DVT CP/MAS probe with ZrO2 rotors. The chemical shift is reported relative to Me4Si (0 ppm) and was referenced externally for 29Si to octakistrimethylsiloxyoctasilsesquioxane Q8M8 (most upfield signals of Q4 groups at δiso = −109 ppm) and for 13C to adamantane (downfield signal at δiso = 38.5 ppm). The cross-polarization NMR experiments were carried out with a 5 ms contact time for 29Si and 2 ms for 13C, and an 80% ramp was used for 29Si and 13C. The boiling points were determined in duplicate using an in-house method wherein the samples, held in inert gas-flushed NMR tubes, were heated by a resistance furnace, with the temperatures monitored via a J-type thermocouple. For the single-crystal X-ray diffraction analysis, the data were collected on a Stoe IPDS-2/2T diffractometer (STOE, Darmstadt, Germany) using Mo Kα-radiation. Data integration and absorption correction were performed with STOE software XArea (version 2.3) and XShape (version 2.25), respectively. The structures were solved using SHELXT-2018/2 [16] and refined with the full-matrix least-squares methods of F2 against all reflections with SHELXL-2019/3 [17,18,19]. All non-hydrogen atoms were anisotropically refined, the C-bound hydrogen atoms were isotropically refined in idealized positions (riding model), and the N-bound hydrogen atoms were isotropically refined (bond length constraints were applied only when necessary). For details of data collection and refinement, see Appendix A, Table A1 and Table A2. Graphics of molecular structures were generated with ORTEP-3 [20,21] and POV-Ray 3.7 [22]. CCDC 2552360 ((HAib)2Si(CH2)4·(THF)), 2552361 ((HAib)2Si(CH2)4·2(CHCl3)), 2552362 ((Aib)Si(CH2)4(HPyr)·(CHCl3)L), 2552363 ((Aib)Si(CH2)4(HPyr)) and 2552364 ((Aib)Si(CH2)4(HPyr)·(CHCl3)H) contain the supplementary crystal data for this article. These data can be obtained free of charge from the Cambridge Crystallographic Data Centre via https://www.ccdc.cam.ac.uk/structures/ (accessed on 7 May 2026). The quantum chemical optimization of molecular structures (cf. Figures S17–S25, Tables S1–S9 in the Supporting Information) was performed with ORCA 6.0.1 [23]. The atomic coordinates from the crystal structures were used as starting points for the optimization of the corresponding isomer. For the other isomers, the respective structures were drawn using Avogadro2 [24]. The geometry optimizations were performed with PBE0 with the def2-TZVPP [25,26] basis set and D4 correction [27], and the CPCMC solvent model for chloroform was applied [28].

2.2. Syntheses and Characterization

Compound (CH2)4Si(Pyr)2 (C12H24N2Si, M = 224.42 g/mol): To a stirred solution of 1,1-dichlorosilacyclopentane (8.80 g, 56.7 mmol) in n-hexane (250 mL), pyrrolidine (16.9 g, 238 mmol) was added at room temperature, which resulted in the formation of a white suspension. Stirring of the reaction mixture at room temperature was continued for 4 days, whereupon the solid was filtered off and washed with n-hexane (5 × 10 mL). From the filtrate, the solvent was distilled off at atmospheric pressure, and the resulting clear, colorless residue (a liquid) was purified by vacuum distillation (45 °C, 0.04 mbar), with a yield of 9.43 g (42.0 mmol, 74%) and a bp of 277 °C. 1H NMR (400.1 MHz, CDCl3, TMS): δ (ppm) = 0.53 (mult., 4H, Si-CH2-CH2-CH2-CH2-@Si); 1.56 (mult., 4H, Si-CH2-CH2-CH2-CH2-@Si); 1.70 (mult., 8H, pyrrolidine β-CH2); 2.96 (mult., 8H, pyrrolidine α-CH2). 13C NMR (100.6 MHz, CDCl3, TMS): δ (ppm) = 9.4 (Si-CH2-CH2-CH2-CH2-@Si); 26.3 (Si-CH2-CH2-CH2-CH2-@Si); 26.9 (pyrrolidine β-CH2); 47.1 (pyrrolidine α-CH2). 29Si NMR (79.5 MHz, CDCl3, TMS): δ (ppm) = 8.5.
Compound (CH2)4Si(NEt2)2 (C12H28N2Si, M = 228.46 g/mol): A stirred solution of diethylamine (10.2 g, 140 mmol) in n-hexane (300 mL) was cooled to −89 °C (using a cold bath prepared from liquid N2 and n-butanol). To this cold solution, a 2.5 M solution of n-butyllithium in n-hexane (56 mL, 140 mmol n-butyllithium) was added via a dropping funnel. The reaction mixture was allowed to attain room temperature overnight, whereupon TMEDA (0.5 mL) was added, and the mixture was stirred and heated under reflux for 4 h. Then, the suspension was cooled to −89 °C, and 1,1-dichlorosilacyclopentane (10.7 g, 68.9 mmol) was added with stirring at −89 °C. Upon its complete addition, the reaction mixture was heated to reflux and kept under reflux for 2 h. After cooling to room temperature, the resulting white suspension was filtered, and the solid was washed with n-hexane (2 × 10 mL). From the combined filtrate and washings, the solvent was removed under vacuum, and the residue (a liquid) was purified by vacuum distillation (40 °C, 0.002 mbar), with a yield of 12.2 g (53.5 mmol, 78%) and a bp of 242 °C. 1H NMR (400.1 MHz, CDCl3, TMS): δ (ppm) = 0.51 (mult., 4H, Si-CH2-CH2-CH2-CH2-@Si); 0.98 (t, 3JH-H = 7.0 Hz, 12H, N(CH2CH3)2); 1.56 (mult., 4H, Si-CH2-CH2-CH2-CH2-@Si); 2.82 (q, 3JH-H = 7.0 Hz, 8H, N(CH2CH3)2). 13C NMR (100.6 MHz, CDCl3, TMS): δ (ppm) = 11.1 (Si-CH2-CH2-CH2-CH2-@Si); 15.7 (N(CH2CH3)2); 26.3 (Si-CH2-CH2-CH2-CH2-@Si); 40.1 (N(CH2CH3)2). 29Si NMR (79.5 MHz, CDCl3, TMS): δ (ppm) = 10.9.
Compound (Aib)Si(CH2)4(HPyr)·(CHCl3) (C13H25Cl3N2O2Si, M = 375.79 g/mol): In a small Schlenk tube equipped with a magnetic stirring bar, α-amino isobutyric acid (H2Aib, 300 mg, 2.91 mmol) was evacuated and then set under an argon atmosphere. Upon addition of chloroform (2 mL), the mixture was cooled in an ice bath. To the cold mixture, the aminosilane (CH2)4Si(Pyr)2 (752 mg, 3.35 mmol) was added with a syringe, and stirring at 0 °C was continued for 5 h. By the end of that time, the amino acid had dissolved for the most part, and a slightly cloudy solution remained (unreacted H2Aib). The solution was pressed through a syringe filter, and the clear filtrate was placed in a freezer (at −28 °C). The product emerged as a semi-transparent solid in the upper part of the clear solution. After 1 week of storage in the freezer, the Schlenk tube was immediately attached to a flow of dry argon, and the cold supernatant was removed with a syringe. The remaining solid was washed with n-pentane (2 × 0.5 mL). The product was then briefly dried in a vacuum, with a yield of 227 mg (0.60 mmol, 21% with respect to the composition (Aib)Si(CH2)4(HPyr)·(CHCl3)). We attributed the rather poor yield of isolated solid product to its good solubility in chloroform. Whereas the single-crystal X-ray diffraction analyses of crystals obtained from the mother liquor confirmed the composition (Aib)Si(CH2)4(HPyr)·(CHCl3) and one crystallographic Si position, the 29Si solid-state NMR spectroscopic analysis of the briefly dried solid indicated the presence of an additional phase with two crystallographically independent Si positions (cf. Figure S10). Integration of the signal intensities indicated a molar fraction of 20% of the additional phase in the sample. Recrystallization of a sample from acetonitrile afforded some crystals of the solvent-free compound (Aib)Si(CH2)4(HPyr), and the single-crystal X-ray diffraction analysis of that confirmed a structure that featured two crystallographically independent Si sites. 29Si CP/MAS NMR (79.5 MHz, υrot = 5 kHz): δiso (ppm) = −49.3 ((Aib)Si(CH2)4(HPyr)·(CHCl3)), −56.4, and −57.7 ((Aib)Si(CH2)4(HPyr)). For the 13C CP/MAS NMR characterization (100.7 MHz, υrot = 10 kHz), please refer to the spectrum with assignment of groups of signals, shown in Figures S8 and S9.
Compound (HAib)2Si(CH2)4·2(CHCl3) (C14H26Cl6N2O4Si, M = 527.16 g/mol): In a small Schlenk tube equipped with a magnetic stirring bar, α-amino isobutyric acid (H2Aib, 400 mg, 3.88 mmol) was evacuated and then set under an argon atmosphere. Upon addition of chloroform (3 mL), the silane (CH2)4Si(NEt2)2 (459 mg, 2.01 mmol) was added drop-wise with stirring, and stirring of the resulting pastel-pink suspension at room temperature was continued for 3 days. The white solid was filtered off and washed with a small amount of chloroform (1 × 1 mL, 2 × 0.5 mL) and briefly dried in a vacuum, with a yield of 680 mg (1.29 mmol, 66% with respect to the composition (HAib)2Si(CH2)4·2(CHCl3)). 1H NMR (400.1 MHz, DMSO-d6, TMS): δ (ppm) = −0.1 (mult. broad, 4H, Si-CH2-CH2-CH2-CH2-@Si); 0.3 (mult. broad, 4H, Si-CH2-CH2-CH2-CH2-@Si); 1.33 (s, 6H, AibMe2); 1.38 (s, 6H, AibMe2); 4.90 (d, 12.8 Hz, 2H, NH2); 5.57 (d, 12.8 Hz, 2H, NH2). 13C NMR (100.6 MHz, DMSO-d6, TMS): δ (ppm) = 20.3 (Si-CH2-CH2-CH2-CH2-@Si); 24.2 (Si-CH2-CH2-CH2-CH2-@Si); 26.9, 27.2 (AibMe2); 56.2 (Aib αC); 174.9 (COO). 29Si NMR (79.5 MHz, DMSO-d6, TMS): δ (ppm) = −134.8. (Note: In the 1H and 13C NMR spectra, cf. Figures S11 and S13, the chloroform signals are basically absent. We attribute this observation to the loss of chloroform from the powdery solid during NMR sample preparation, which involved the transfer of a small sample of the solid into a new Schlenk tube, followed by brief evacuation and setting under an argon atmosphere prior to adding the NMR solvent.)

3. Results and Discussion

3.1. Synthesis and NMR Spectroscopic Characterization of Compounds (Aib)Si(CH2)4(HPyr) and (HAib)2Si(CH2)4

In one of our previous reports, we showed that pyrrolidinyl-substituted silanes RR’Si(Pyr)2 (R,R’ = Me, Me; Me, Vi; Me, H; Et, Et) and α-amino isobutyric acid (H2Aib) react with the substitution of the two Si-bound pyrrolidinyl groups and liberation of pyrrolidine. However, one equivalent of that amine base is involved in the formation of the respective product, a pentacoordinate Si complex of the type (Aib)SiRR’(HPyr) (Scheme 1a) [12]. In the solid state, the Si coordination spheres of these compounds are distorted trigonal bipyramids with axially bound pyrrolidine trans to the amino acid’s O atom. An analogous reaction of the pyrrolidinyl-substituted silacyclopentane derivative (CH2)4Si(Pyr)2 and H2Aib afforded a corresponding pyrrolidine adduct (Aib)Si(CH2)4(HPyr) (Scheme 1b). As reported for the previous examples of (Aib)SiRR’(HPyr) and related complexes (e.g., (Aib)SiMe2(NMI) [14]), this adduct also undergoes decomposition reactions in DMSO solution, which include the dissociation of the Si-bound N-donor ligand pyrrolidine [12]. Moreover, in the 29Si NMR spectrum, a peak at δ −134.9 ppm (cf. Figure S7) indicates the occurance of reactions that eventually furnish a hexacoordinate Si complex, (HAib)2Si(CH2)4. The latter was accessible in a deliberate manner through the reaction of the diethylamino-substituted silacyclopentane derivative (CH2)4Si(NEt2)2 and H2Aib (Scheme 1c).
Due to the abovementioned reason of dissociation in solution, the compound (Aib)Si(CH2)4(HPyr) was NMR-spectroscopically characterized in the solid state only. The 29Si CP/MAS NMR spectrum (CP/MAS = cross polarization, magic angle spinning), cf. Figure 2a and Figure S10, exhibits a signal at δiso = −49.3 ppm with an asymmetrical line shape that results from residual dipolar coupling with an Si-bound N atom, which is well in accordance with the signals observed with the previously reported adducts (Aib)SiRR’(HPyr) [12]. With respect to the related dialkyl silicon compounds (Aib)SiMe2(HPyr) and (Aib)SiEt2(HPyr), which produce 29Si CP/MAS NMR signals at δiso = −71.6 and −62.9 ppm, respectively [12], the signal of (Aib)Si(CH2)4(HPyr) is markedly low-field shifted. This can be attributed to the silacyclopentane motif, which causes a low-field shift of the 29Si resonance relative to, e.g., the dimethyl derivative. A pair of mutually related pentacoordinate Si complexes with (O,N,O’)Si(CH2)4 and (O,N,O’)Si(CH3)2 motifs (O,N,O’ = a di-anionic ligand with N(2-oxyethyl)salicylaldiminate motif) exhibit the same trend (δ(CDCl3) = −53.0 ppm [29] and −66.2 ppm [30], respectively), and this trend is also evident for simple examples, such as 1,1-dichlorosilacyclopentane and dimethyldichlorosilane (δ = 45.5 [15] and 32.0 ppm [31], respectively). While the major signal at δiso = −49.3 is in accordance with the structure of the chloroform solvate, which features one Si site in the asymmetric unit, the 29Si CP/MAS NMR spectrum of (Aib)Si(CH2)4(HPyr) features two additional signals of essentially equal intensity (at δiso = −56.4 and −57.7 ppm). We attribute these signals to the presence of solvent-free (Aib)Si(CH2)4(HPyr) in the sample, which may have originated from loss of solvent upon brief drying after synthesis. The presence of the two signals and the deviation in the chemical shift is well in accordance with the crystal structure obtained from a crystal of solvent-free (Aib)Si(CH2)4(HPyr), which features two independent molecules in the asymmetric unit and different intermolecular hydrogen-bonding patterns (vide infra). The 13C CP/MAS NMR spectrum of (Aib)Si(CH2)4(HPyr) (cf. Figure 2b as well as Figures S8 and S9) features the set of signals expected for the different C sites of this compound, e.g., two signals for the crystallographically independent Si-bound CH2 groups in (Aib)Si(CH2)4(HPyr)·(CHCl3) at δ = 10.9 and 13.4 ppm. Again, additional signals of markedly lower intensity are present, which correspond to the same structural motifs and are in accordance with the number of sites in the asymmetric unit of solvent-free (Aib)Si(CH2)4(HPyr), e.g., four signals for the crystallographically independent Si-bound CH2 groups at δ = 15.6, 16.2, 16.7 and 17.7 ppm. In addition to the positions of the expected groups of signals in the 13C spectrum (Figures S8 and S9), which are in general accordance with the corresponding signals of adduct (Aib)SiMe2(HPyr) [12], the presence of signals in the range 79–80 ppm points at the presence of different chloroform sites in the sample, which is in accordance with the disordered solvent of crystallization in (Aib)Si(CH2)4(HPyr)·(CHCl3).
Compound (HAib)2Si(CH2)4·2(CHCl3) exhibits similar 29Si NMR shifts in the DMSO-d6 solution (−134.8 ppm) and in the solid state (a predominant signal at −130.0 ppm with additional signals of lower intensity at −131.6 and −133.1 ppm, cf. Figure S16). As the solid-state structure features disordered chloroform molecules (vide infra), we attribute the occurrence of the set of signals to the different molecular environments that originated from the different alternative chloroform positions or from the loss of solvent of crystallization. The presence of additional signals of lower intensity for each characteristic group of signals is also found in the 13C solid-state NMR spectrum. Moreover, in the 13C solid-state NMR spectrum (cf. Figure S15), the signals in the range 78–80 ppm point at the presence of different chloroform sites in the sample, which is in accordance with disordered solvent of crystallization. In the case of compound (HAib)2Si(CH2)4, recrystallization from a different solvent (THF) also afforded crystals of a chloroform-free composition, but with the inclusion of the new solvent of crystallization (vide infra). In the DMSO-d6 solution, the rather simple 13C NMR spectra indicate that this hexacoordinate Si complex features two chemically equivalent (Aib) ligands (it features one signal of the COO group at 174.9 ppm and one signal of the Aib-α-C atom at 56.2 ppm) and pairs of chemically equivalent α- and β-CH2 groups of the silacyclopentane ring (δ = 20.3 and 24.2 ppm, respectively). The presence of two Aib-CH3 signals in the 13C spectrum (δ = 26.9 and 27.2 ppm), as well as the presence of two singlet Aib-CH3 signals and two Aib-NH2 doublets in the 1H NMR spectrum, reveal diastereotopicity of the sides of the otherwise mirror-symmetric Aib ligands. These NMR spectroscopic data are in accordance with the molecular configuration found in the crystal structures of both solvates (HAib)2Si(CH2)4·2(CHCl3) and (HAib)2Si(CH2)4·(THF) (vide infra).

3.2. Crystallographic Analysis of the Molecular Structure of Compound (Aib)Si(CH2)4(HPyr)

Crystals of the pentacoordinate Si complex (Aib)Si(CH2)4(HPyr) were obtained from the synthesis in chloroform (solvate (Aib)Si(CH2)4(HPyr)·(CHCl3)) and upon recrystallization from acetonitrile ((Aib)Si(CH2)4(HPyr)).
A crystal of (Aib)Si(CH2)4(HPyr)·(CHCl3), which was freshly taken from the mother liquor and immediately mounted on the goniometer under a cold nitrogen flow at 180 K, produced a rather diffuse diffraction pattern. As this could indicate both effects of heavy disorders and shattering of the crystal upon cooling, a new crystal was mounted at 230 K and cooled to 180 K in increments of 10 K, with intermittent recording of corresponding diffraction patterns for unit cell determination. At 200 K, a general change in the diffraction pattern was observed, in combination with a more diffuse appearance of images. Upon warming to above 200 K, the initial diffraction pattern was observed, with principle retention of the diffuse appearance of the data. Hence, at ca. 200 K, an in-principle reversible phase transition occurred, which resulted in partial shattering of the crystal and loss of diffraction power. Therefore, the full data sets of the two modifications, (Aib)Si(CH2)4(HPyr)·(CHCl3)H and (Aib)Si(CH2)4(HPyr)·(CHCl3)L, were collected at 210 K and 180 K, respectively, as the further cooling of the lower-temperature modification (Aib)Si(CH2)4(HPyr)·(CHCl3)L essentially caused the loss of crystal quality. Selected views of the molecular structures and selected bond lengths and angles of (Aib)Si(CH2)4(HPyr) in the higher- and lower-temperature modifications, (Aib)Si(CH2)4(HPyr)·(CHCl3)H and (Aib)Si(CH2)4(HPyr)·(CHCl3)L, respectively, and in the solvent-free crystal of (Aib)Si(CH2)4(HPyr), are presented in Figure 3 and Table 1.
The phase transition of (Aib)Si(CH2)4(HPyr)·(CHCl3) at 200 K is accompanied by noticeable alterations in the orientation of the solvent of crystallization and of the conformation of the silacyclopentane ring as demonstrated by the comparative view along the Si1–N1 bond (Figure 4). Regarding the chloroform molecule, in the higher-temperature modification (Aib)Si(CH2)4(HPyr)·(CHCl3)H, one Cl atom (Cl2 and the corresponding sites of the disorder positions) is involved in a bifurcated van der Waals contact with both methyl groups (C3 and C4) of the Aib backbone. In the lower-temperature modification, two Cl atoms (Cl2 and Cl3, as well as their corresponding sites of the disorder positions) are involved in individual van der Waals contacts with these methyl groups. The silacyclopentane ring in (Aib)Si(CH2)4(HPyr)·(CHCl3)H is disordered across the C6–C7 bond, and the orientation of minor occupancy (20%) in the higher-temperature modification becomes the exclusive orientation in (Aib)Si(CH2)4(HPyr)·(CHCl3)L. In contrast, the orientation of the third rather flexible moiety of (Aib)Si(CH2)4(HPyr)·(CHCl3), the pyrrolidine ligand, rests in an essentially identical orientation in both modifications. This may result from its involvement in similar N–H···O hydrogen bonds. Apart from a relative shift of the molecules, which alters the lengths of the hydrogen bonds, the set of hydrogen bonds is essentially retained upon the phase transition at 200 K (vide infra). Both the abovementioned changes in molecular conformation and the relative shift of the molecules result in a more compact molecular packing in the lower-temperature modification. This is reflected by the pronounced decrease in the unit cell volume upon phase transition, which, for (Aib)Si(CH2)4(HPyr)·(CHCl3)H, is 1851.43(9) Å3 at 230 K and 1841.96(8) Å3 at 210 K, and shrinks to 1818.42(9) Å3 at 200 K and 1809.64(9) Å3 at 180 K for (Aib)Si(CH2)4(HPyr)·(CHCl3)L. (For the changes in all unit cell parameters, a, b, c, β, and V in the same temperature range, cf. Figure S26).
A noticeable difference in the molecular conformation of (Aib)Si(CH2)4(HPyr) between the modifications of the solvate (Aib)Si(CH2)4(HPyr)·(CHCl3) and the two crystallographically independent molecules in the solvent-free crystal structure is manifest in the torsion of the pyrrolidine ligand about the N2–Si1 bond axis (Figure 3). Whereas in the former the dihedral angle of the sequence N(Aib)-Si-N-H(HPyr) is close to 60°, it is close to 180° in the latter, corresponding to a 120° rotation of the essentially staggered arrangement about the N2–Si1 bond. This conformational difference, in combination with the presence vs. absence of chloroform as an additional H-bond donor, results in completely different H-bond systems in the crystal structures (Figure 5, Table 2). The conformation in the solvate (Aib)Si(CH2)4(HPyr)·(CHCl3) allows for the formation of bifurcated H bonds (a combination of an R ( 6 ) 2 1 and an R ( 4 ) 1 2 motif that have one H···O contact in common, which fuses them to an R ( 8 ) 2 2 motif [33]), involving both NH functions of one molecule in combination with both O atoms of the carboxylate group of an adjacent molecule. Moreover, the carbonyl O atom (O2) serves as a H-bond acceptor in a Cl3C–H···O interaction with the solvent of crystallization. This hydrogen-bond ensemble in the structures of (Aib)Si(CH2)4(HPyr)·(CHCl3), and in the higher-temperature modification (Aib)Si(CH2)4(HPyr)·(CHCl3)H in particular, is related to the situation encountered in the structure of the previously reported derivative 2(Aib)SiMe2(HPyr)·3(CHCl3) [12]. In the solvent-free form, each molecule establishes one H bond only, in which the pyrrolidine NH moiety (at N2 and N4, respectively) is the H-bond donor and the carbonyl O atom of an adjacent molecule (O2 and O4, respectively) serves as the corresponding acceptor.
With respect to the individual molecular structures of (Aib)Si(CH2)4(HPyr) in the crystal structures of the chloroform solvate (Aib)Si(CH2)4(HPyr)·(CHCl3) and the solvent-free form (Aib)Si(CH2)4(HPyr), the Si–O and Si–NPyrrolidine bonds are markedly shorter in the latter (Table 1). We attribute the markedly different 29Si NMR shifts of these solids (vide supra) to their different H-bond patterns and to the particularly pronounced difference in their Si coordination spheres. Apart from the differences in their axial bond lengths, the conformations of the Si coordination spheres (distorted trigonal bipyramids with an O–-Si–NPyrrolidine axis) are very similar with respect to the geometry parameter τ5, which may range from 1 (for trigonal bipyramidal) to 0 (for square-based pyramidal coordination polyhedra) [32]. Even though the deviation of the axial angle from linearity ranges between 6.7 and 10.3°, the deviation of τ5 from one is mainly caused by the widest equatorial N–Si–C angles that exceed the ideal 120° by 11.7–14.2°. This deviation originates in the equatorial silacyclopentane motif, which itself spans a rather small equatorial angle (C–Si–C in the range of 96 to 98°). These C–Si–C angles in (Aib)Si(CH2)4(HPyr) are similar to those encountered with 1,1-dichlorosilacyclopentane (98.40(11) and 98.72(11) [34]). Whereas in the latter there is a clear discrepancy between the actual angle and the ideal value for a tetrahedral Si coordination sphere, the deviation of the C–Si–C angle in (Aib)Si(CH2)4(HPyr) from a certain “ideal angle” must be discussed with care. While a deviation from the “ideal 120° angle” refers to an all-equatorial arrangement in a perfect trigonal bipyramid, a distortion of the Si coordination sphere toward a square-based pyramidal shifts the C–Si–C motif toward apical–basal positions, where markedly smaller angles can be accommodated without implying strain. For comparison, in an acetone solvate of compound K[SiPh(cat)2] (cat = benzene-1,2-diolate) [35], a square-based Si coordination sphere with basal Si–O bonds and an apical Si–C bond was encountered, and the apical–basal angles therein ranged from 103.5 to 105.9°. Thus, it is not surprising that silacyclopentane motifs may be located in all-equatorial positions of trigonal bipyramidal Si coordination spheres, with some distortion toward a square-based pyramid. Figure 6 shows sketches of the hitherto crystallographically characterized silacyclopentane complexes with a pentacoordinate Si atom and selected geometry data of their Si coordination spheres. Whereas compound VI (in two modifications [29]) features an axial–equatorial silacyclopentane motif with a geometry index close to one and a C–Si–C angle close to the (in this setting) ideal 90°, compounds VII [36] and VIII [37] feature all-equatorial silacyclopentane motifs with respect to strongly distorted trigonal bipyramidal Si coordination, and more pronounced distortion (more pronounced deviation of τ5 from 1) is accompanied by a widening of the C–Si–C angle. In this context, the geometric parameters encountered in the crystal structures of (Aib)Si(CH2)4(HPyr) (cf. Table 1) align very well with those of the anionic complex VII [36] (Figure 6). For an energetic evaluation of the relative stability of the experimentally encountered conformation of (Aib)Si(CH2)4(HPyr) with respect to alternative configurations, computational analyses were applied (vide infra).

3.3. Crystallographic Analysis of the Molecular Structure of Compound (HAib)2Si(CH2)4

Crystals of the hexacoordinate Si complex (HAib)2Si(CH2)4 were obtained from the synthesis in chloroform (solvate (HAib)2Si(CH2)4·2(CHCl3)) and upon recrystallization from THF (solvate (HAib)2Si(CH2)4·(THF)). X-ray diffraction analyses revealed the same molecular configuration of this complex in both solvates (Figure 7). That is, the O atoms of the mono-anionic (O,N)-chelators were trans-disposed to the Si–C bonds, and the Si–N bonds were mutually trans. Selected bond lengths and angles of the Si coordination spheres are listed in Table 3.
In principle, compound (HAib)2Si(CH2)4 is the first crystallographically characterized hexacoordinate diorganosilicon complex that is (O,N)-ligated by α-amino acid-derived mono-anions. Apart from this particular trait, it combines a set of structural features that are still scarcely encountered in crystal structures of hexacoordinate Si complexes. The one closest relative, which exhibits a (HαA)2SiX1X2 motif (HαA = mono-anion of an α-amino acid; X = any additional Si-bound substituents), is the complex (HAla)2Si(NCO)2 (compound V in Figure 1 and Figure 8) [9]. Even with other amine ligand functions of the type CNH2 (C = any N-bound substituted or unsubstituted hydrocarbyl residue), the portfolio of crystallographically characterized hexacoordinate Si complexes of the type Si(X1,X2,X3,X4)(RNH2)2 is rather scarce, with the complex SiF4(EtNH2)2 (IX) being the sole additional example (Figure 8) [38]. The presence of Si-coordinated NH2 groups, which may give rise to side reactions, such as substitution of Si-bound reactive groups with the formation of silazanes [39] and, in case of amino acid-derived ligands, reactions such as peptide formation [9,13], are among the reasons for this. In contrast, amine-derived ligands devoid of NH functions are more frequently encountered, e.g., in compounds X [40], XI [41], XII [42], XIII [43], XIV [44], XV [45], XVI [46] and, with a hydrazine type ligand, in XVII [47] (Figure 8). In this context, because of the ligands’ structural relationship to the amino acid mono-anions, the great variety of structurally characterized silicon bis- and tris-chelates with two hydrazide-derived mono-anionic (O,N)-chelators in XVIII [3] (for example, compounds XVIII-1-XVIII-12 [48,49,50,51,52,53] (Figure 8)) is noteworthy. In addition to the two mono-anionic (O,N)-chelators, which form five-membered chelates about the Si atom, their Si–N bonds are mutually trans. Table 4 gives an impression of the variability in the Si–N bond lengths in this class of complexes, which mainly depends on the further two Si-bound substituents X and, to a lesser extent, on the ligand backbone (substituent R). Whereas the presence of rather electronegative substituents X is accompanied by shorter Si–N bonds (e.g., compounds XVIII-6 and XVIII-7, with Si–N bond lengths of ca. 1.96 and 2.01 Å, respectively), Si-bound alkyl groups or silacycloalkane motifs may cause markedly longer Si–N bonds (e.g., compounds XVIII-8-XVIII-12, with Si–N bond lengths in the range 2.08–2.10 Å). In this regard, the Si–N bonds in the hexacoordinate amino acid chelated complexes (HAla)2Si(NCO)2 (1.8857(11) Å) [9] and (HAib)2Si(CH2)4 (1.9547(12) Å in the chloroform solvate; Si1–N2 1.933(3) and Si1–N1 1.966(3) Å in the THF solvate) reflect the same trend, but their Si–N bonds are always noticeably shorter than those of the respective groups of hydrazide complexes in XVIII. One reason may be found in the lower steric demand of the NH2 group (vs. NMe2), which is supportive of the pyramidalization of the N coordination sphere and exposure of the N-located lone pair towards a Lewis acid.
For the two different solvates of (HAib)2Si(CH2)4, the effect of the crystal environment on the individual Si–N bonds must be noted. This is particularly obvious for the THF solvate, which features two crystallographically independent Si–N bonds per molecule. The different H-bond systems in the crystals of the solvates of (HAib)2Si(CH2)4 provide an explanation (Figure 9, Table 5).
In the chloroform solvate (HAib)2Si(CH2)4·2(CHCl3), only one H atom per NH2 group is involved in N–H···O hydrogen bonding. In accordance with the H-bond situations encountered with the structures of the pyrrolidine adduct (Aib)Si(CH2)4(HPyr) (vide supra), the carbonyl O atom of the amino acid-derived anion is the preferred H-bond acceptor in the hexacoordinate Si complex (HAib)2Si(CH2)4 as well. Moreover, in the chloroform solvate (Figure 9a), the carbonyl O is involved in a combination of a Cl3C–H···O and an N–H···O contact, whereas each carbonyl group is involved in a single N–H···O contact in the THF solvate (Figure 9b). The latter’s solvent of crystallization contributes to a further N–H···O contact. Resulting from this, the two crystallographically independent NH2 groups in the structure of the THF solvate are involved in one (N1) and two (N2) N–H···O hydrogen bonds. Moreover, the latter N atom, N2, is involved in the shortest Si–N bond encountered in (HAib)2Si(CH2)4, and the different H-bond situation serves as an explanation. Enhanced polarization of the amino group by an additional intermolecular H-bond acceptor can be expected to enhance the negative partial charge at the N atom, thus enhancing its lone-pair donor quality with respect to the formation of the Si–N bond.
Regarding the silacyclopentane motif, the structures of compound (HAib)2Si(CH2)4 are accompanied by three other crystallographically characterized hexacoordinate Si complexes that feature this motif (Figure 10). In addition to XIX, the cationic complex with monodentate N-methylimidazole donor molecules [54], the portfolio features two complexes, XX [55] and XXI [56], with mono-anionic ambidentate chelating ligands. Whereas in XX [55] the formally dative bonds (Si–N) are trans to the silacyclopentane Si–C bonds and the two formally covalent bonds (Si–O) are mutually trans, the complex XXI [56] has an all-cis configuration. Thus, the complex (HAib)2Si(CH2)4, with its mutually trans dative bonds, complements the series with the third principle orientation of two mono-anionic ambidentate chelators at the Si-hexacoordinate silacyclopentane. In accordance with the distorted octahedral Si coordination, the C–Si–C angles in these compounds, as well as in (HAib)2Si(CH2)4 (Table 3), approach the ideal angle of 90°.

3.4. Computational Analysis of Isomers of Compound (Aib)Si(CH2)4(HPyr)

The crystallographically determined molecular structures of (Aib)Si(CH2)4(HPyr) and (HAib)2Si(CH2)4 gave rise to questions about the relative stability of other configurational isomers of (Aib)Si(CH2)4(HPyr) and, because (HAib)2Si(CH2)4 demonstrated the chelate bonding of the mono-anionic ligand (HAib)−, the stability of isomers of the type (HAib)Si(CH2)4(Pyr). To address these questions, the isomers shown in Figure 11 were used as starting geometries for optimization of their molecular conformations.
In principle, the crystallographically confirmed isomer of (Aib)Si(CH2)4(HPyr) with an O–Si–N axis of the Si coordination sphere (isomer ON) was confirmed as an energetic minimum, and the isomers (HAib)Si(CH2)4(Pyr) with mono-anionic (HAib)− chelating ligand and an amidic pyrrolidine substituent (bottom row in Figure 11) are markedly less stable. Out of the alternative isomers with the composition (Aib)Si(CH2)4(HPyr), the “strain-release isomer” OC, which features axial–equatorial situations of both five-membered chelates, is only slightly higher in energy. The other two isomers (NN and NC), with an amidic Si–N bond in the axial position, are less stable and converge to other configurations. The relative stabilities of the configurational isomers of (Aib)Si(CH2)4(HPyr) can be interpreted with reference to the apicophilicity of donor sites in trigonal bipyramidal Si complexes. That is, the axial positions are preferentially occupied by substituents that are particularly electronegative or stabilize anionic charges in other ways (which is the carboxylate O atom), by ligands that establish formally dative bonds (which are amine moieties) and atoms of small rings that may achieve strain release upon occupying one axial position. In isomers ON and OC, two of the abovementioned groups occupy the axial positions, whereas in isomers NN and NC only one axial position accommodates such a group. Within the configurational isomers of (HAib)Si(CH2)4(Pyr), the relatively stable isomer NC’ features two of those groups in axial positions as well. The slightly higher stability of NN’ over OC’, however, appears counter-intuitive. The weakly pronounced ring strain apicophilicity of the silacyclopentane ring (lower strain upon partial distortion toward square-based pyramidal Si coordination, cf. Section 3.2.) and pronounced apicophilicity of NH2 over carboxylate O within the (HAib)− mono-anion may be considered as reasons. (Out of three previously reported examples of Si-pentacoordinate silacyclopentanes, cf. Figure 6, only one features a silacyclopentane C in an axial position; out of five examples of pentacoordinate Si complexes with an (O,NH2)-functionalized chelating ligand, four examples feature axial NH2 coordination [9].) Last but not least, optimization of both NC and ON’ resulted in the transformation of the complex into an isomer with a different axial donor atom in the amino acid-derived anion (OC and NC’, respectively). As in both series the donor sites swapped axial vs. equatorial positions rather than converging into a local minimum with all-equatorial positioning for this respective chelator, (Aib)2− or (HAib)−, we did not consider further isomers, which would be based on such an arrangement. Moreover, apart from the two silacyclopentane derivatives VII and VIII (Figure 6), there are no precedents in the literature of crystallographically proven pentacoordinate Si complexes with all-equatorial positioning of any other five-membered chelates.

3.5. Computational Analysis of the Influence of External H-Bond Donors and Acceptors on the Axial Si–O and Si–N Bond Lengths of Compound (Aib)Si(CH2)4(HPyr)

In a previous study, we showed that the hydrogen bonding of a chloroform molecule to the carbonyl group of (Aib)SiMe2(NMI) and related complexes causes lengthening of the axial Si–O and shortening of the axial Si–N bonds [14]. As in the solvent-free crystal structure of (Aib)Si(CH2)4(HPyr) the Si–O and Si–N bonds are shorter than in the chloroform solvate (Table 1), and the structures exhibit markedly different hydrogen-bonding situations of the axial donor groups (Figure 5), we optimized the molecular conformations of ensembles of (Aib)Si(CH2)4(HPyr) with chloroform and/or methylformate as hydrogen-bond donors and/or acceptors, respectively, as shown in Figure 12. The calculated axial Si–O and Si–N bond lengths (Å) are listed below the respective molecules.
As found with (Aib)SiMe2(NMI) [14], the interaction of the (O,N)-chelator’s carbonyl O atom with a chloroform molecule results in lengthening of the Si–O and shortening of the trans-disposed Si–N bonds (from ON-1 to ON-2). In the case of (Aib)Si(CH2)4(HPyr), this effect is markedly enhanced by the addition of a carbonyl O atom as a hydrogen-bond acceptor to the pyrrolidine NH group (from ON-2 to ON-3), and ON-2 vs. ON-4 indicate that the effect of the N–H···O hydrogen bond is more expressed than the effect of the Cl3C–H···O contact. Whereas the orientation of the pyrrolidine moiety in the ensembles ON-1-ON-4 is related to those encountered in the crystal structures of the chloroform solvate, which gives rise to bifurcated (N–H)2···O hydrogen bonds, the orientation in ON-5 resembles that in the solvent-free form. Comparison of ON-4 and ON-5 indicates that the hydrogen bonding in the latter causes shortening of the axial Si–O and Si–N bonds. Thus, this series of ensembles, ON-1-ON-5, indicates that the markedly different axial bond lengths of (Aib)Si(CH2)4(HPyr) encountered in its different crystal structures mainly originate from the different hydrogen-bonding situations therein. Moreover, the ensembles ON-3-ON-5 vs. ON-1 and ON-2 demonstrate that the addition of a H-bond acceptor to an NH moiety of an Si-coordinated amine ligand causes pronounced shortening of the Si–N bond, which is also relevant to the different crystal structures of (HAib)2Si(CH2)4, where one of the NH2 groups in the solvate (HAib)2Si(CH2)4·(THF) (the one with THF as an additional H-bond acceptor) forms a particularly shorter Si–N bond.

4. Conclusions

Our investigation of reactions of α-amino isobutyric acid and 1,1-diamino-functionalized silacyclopentanes ((CH2)4Si(Pyr)2 and (CH2)4Si(NEt2)2) gave rise to the structural characterization of two new silicon complexes with α-amino acid-derived chelating ligands, i.e., (Aib)Si(CH2)4(HPyr) and (HAib)2Si(CH2)4. Whereas the former features a di-anionic (O,N)-chelating ligand and a pentacoordinate Si atom, the latter features two mono-anionic (O,N)-chelators and a hexacoordinate Si atom. Even though the solvates of the complexes obtained are unstable (partial loss of solvent upon drying; decomposition of (Aib)Si(CH2)4(HPyr) in DMSO solution), and thus hampered some means of characterization, sets of different crystal structures were obtained for each of the two compounds, which demonstrated the dependence of the Si coordination sphere on the hydrogen-bonding system in the crystal. For example, different Si–N bond lengths were encountered for the formally dative Si–N bonds in (Aib)Si(CH2)4(HPyr)·(CHCl3) vs. (Aib)Si(CH2)4(HPyr) and in (HAib)2Si(CH2)4·2(CHCl3) vs. (HAib)2Si(CH2)4·(THF). They indicate that the involvement of Si-coordinated NH-featuring amines in intermolecular N–H···O hydrogen bonds strengthen (i.e., shorten) the Si–N bond. Moreover, the herein reported crystal structures add to the portfolio of the still scarcely crystallographically characterized hypercoordinate silacyclopentanes. The characterization of (Aib)Si(CH2)4(HPyr), supported by computational analyses, indicate that silacyclopentane motifs in distorted trigonal bipyramidal Si coordination spheres may cope with an all-equatorial arrangement. The complex (HAib)2Si(CH2)4, which represents the hitherto first crystallographically characterized hexacoordinate diorganosilicon complex of α-amino acid-derived (O,N)-chelators, completes the series of principle configurations of bis-chelated silacyclopentanes with different orientations of dative bonds with respect to the silacyclopentane Si–C bonds. While complexes with two [55] and one [56] dative bond(s) trans to the silacyclopentane Si–C bond(s) have already been reported, the dative Si–N bonds in compound (HAib)2Si(CH2)4 are mutually trans, thus none are trans-disposed to Si–C.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/cryst16060389/s1, Figure S1: 1H NMR spectrum (CDCl3) of (CH2)4Si(Pyr)2 (full spectrum and magnified inset with signal assignment); Figure S2: 13C{1H} NMR spectrum (CDCl3) of (CH2)4Si(Pyr)2 (full spectrum and magnified inset with signal assignment); Figure S3: 29Si{1H} NMR spectrum (CDCl3) of (CH2)4Si(Pyr)2 (full spectrum and magnified inset); Figure S4: 1H NMR spectrum (CDCl3) of (CH2)4Si(NEt2)2 (full spectrum and magnified inset with signal assignment); Figure S5: 13C{1H} NMR spectrum (CDCl3) of (CH2)4Si(NEt2)2 (full spectrum and magnified inset with signal assignment); Figure S6: 29Si{1H} NMR spectrum (CDCl3) of (CH2)4Si(NEt2)2 (full spectrum and magnified inset); Figure S7: 29Si{1H} NMR spectrum (DMSO-d6) of (Aib)Si(CH2)4(HPyr) (full spectrum and magnified insets with signal assignment); Figure S8: 13C{1H} CP/MAS NMR spectrum of (Aib)Si(CH2)4(HPyr)·CHCl3 (νrot = 10 kHz) with assignment of (groups of) signals; Figure S9: Alkyl section of the 13C{1H} CP/MAS NMR spectrum of (Aib)Si(CH2)4(HPyr)·CHCl3 (νrot = 10 kHz) with assignment of (groups of) signals; Figure S10: 29Si{1H} CP/MAS NMR spectrum of (Aib)Si(CH2)4(HPyr)·CHCl3 (νrot = 5 kHz, spinning side bands are asterisked *) with a magnification of the isotropic shift signals in the inset; Figure S11: 1H NMR spectrum (DMSO-d6) of (HAib)2Si(CH2)4 (with signal assignment); Figure S12: Magnified section of the 1H NMR spectrum (DMSO-d6) of (HAib)2Si(CH2)4 (with signal assignment); Figure S13: 13C{1H} NMR spectrum (DMSO-d6) of (HAib)2Si(CH2)4 with an inset of the magnified section of the 13C(sp3) signals (with signal assignment); Figure S14: 29Si{1H} NMR spectrum (DMSO-d6) of (HAib)2Si(CH2)4; Figure S15: 13C{1H} CP/MAS NMR spectrum of (HAib)2Si(CH2)4·2(CHCl3) (νrot = 10 kHz) with assignment of (groups of) signals; Figure S16: 29Si{1H} CP/MAS NMR spectrum of (HAib)2Si(CH2)4·2(CHCl3) (νrot = 5 kHz) with a magnification of the isotropic shift signals in the inset. The emergence of that group of signals, instead of a single signal, is attributed to effects of disorder and loss of solvent of crystallization; Figure S17: Optimized molecular structure of (Aib)Si(CH2)4(HPyr) configurational isomer ON (= ON-1); Table S1: Atomic coordinates for optimized structure of (Aib)Si(CH2)4(HPyr) configurational isomer ON (= ON-1); Figure S18: Optimized molecular structure of (Aib)Si(CH2)4(HPyr) configurational isomer OC; Table S2: Atomic coordinates for optimized structure of (Aib)Si(CH2)4(HPyr) configurational isomer OC; Figure S19: Optimized molecular structure of (HAib)Si(CH2)4(Pyr) configurational isomer OC’; Table S3: Atomic coordinates for optimized structure of (HAib)Si(CH2)4(Pyr) configurational isomer OC’; Figure S20: Optimized molecular structure of (HAib)Si(CH2)4(Pyr) configurational isomer NN’; Table S4: Atomic coordinates for optimized structure of (HAib)Si(CH2)4(Pyr) configurational isomer NN’; Figure S21: Optimized molecular structure of (HAib)Si(CH2)4(Pyr) configurational isomer NC’; Table S5: Atomic coordinates for optimized structure of (HAib)Si(CH2)4(Pyr) configurational isomer NC’; Figure S22: Optimized molecular structure of solvate (Aib)Si(CH2)4(HPyr)·(CHCl3), ON-2; Table S6: Atomic coordinates for optimized structure of solvate (Aib)Si(CH2)4(HPyr)·(CHCl3), ON-2; Figure S23: Optimized molecular structure of solvate (Aib)Si(CH2)4(HPyr)·(CHCl3)·(O=CHOMe), ON-3; Table S7: Atomic coordinates for optimized structure of solvate (Aib)Si(CH2)4(HPyr)·(CHCl3)·(O=CHOMe), ON-3; Figure S24: Optimized molecular structure of solvate (Aib)Si(CH2)4(HPyr)·(O=CHOMe), ON-4; Table S8: Atomic coordinates for optimized structure of solvate (Aib)Si(CH2)4(HPyr)·(O=CHOMe), ON-4; Figure S25: Optimized molecular structure of solvate (Aib)Si(CH2)4(HPyr)·(O=CHOMe), ON-5; Table S9: Atomic coordinates for optimized structure of solvate (Aib)Si(CH2)4(HPyr)·(O=CHOMe), ON-5; Figure S26: Unit cell parameters of (Aib)Si(CH2)4(HPyr)·(CHCl3) at different temperatures.

Author Contributions

Conceptualization, J.W.; investigation, A.S., S.K. and J.W.; writing—original draft preparation, J.W.; writing—review and editing, A.S., S.K. and J.W.; visualization, J.W.; supervision, J.W. All authors have read and agreed to the published version of the manuscript.

Funding

Parts of this work were carried out with financial support from the European Union (European Social Fund, ESF); the federal state of Saxony (Sächsische Aufbaubank, SAB, Dresden, Germany) via a Ph.D. scholarship to A.S. under Project 100670490-AP2; and with financial support to S.K. from the German Science Foundation (DFG) under Project 509900844 (Neue Si-O-P-N Verbindungen und Materialien: Synthesen, Strukturen und Materialeigenschaften).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

CCDC 2552360 ((HAib)2Si(CH2)4·(THF)), 2552361 ((HAib)2Si(CH2)4·2(CHCl3)), 2552362 ((Aib)Si(CH2)4(HPyr)·(CHCl3)L), 2552363 ((Aib)Si(CH2)4(HPyr)) and 2552364 ((Aib)Si(CH2)4(HPyr)·(CHCl3)H) contain the supplementary crystal data for this article. These data can be obtained free of charge from the Cambridge Crystallographic Data Centre via https://www.ccdc.cam.ac.uk/structures/ (accessed on 7 May 2026). The original contributions presented in this study are included in the article/Supplementary Materials. Further inquiries can be directed to the corresponding author.

Acknowledgments

The authors are grateful to Beate Kutzner (TU Bergakademie Freiberg, Institut für Anorganische Chemie) for solution NMR service, and Julius Zimmermann (TU Bergakademie Freiberg, Institut für Anorganische Chemie) for boiling point determination.

Conflicts of Interest

The authors declare no conflicts of interest.

Appendix A

Table A1. Crystallographic data from data collection and refinement of the pyrrolidine adducts (Aib)Si(CH2)4(HPyr)·(CHCl3)H, (Aib)Si(CH2)4(HPyr)·(CHCl3)L and (Aib)Si(CH2)4(HPyr).
Table A1. Crystallographic data from data collection and refinement of the pyrrolidine adducts (Aib)Si(CH2)4(HPyr)·(CHCl3)H, (Aib)Si(CH2)4(HPyr)·(CHCl3)L and (Aib)Si(CH2)4(HPyr).
Parameter(Aib)Si(CH2)4(HPyr)·(CHCl3)H 1(Aib)Si(CH2)4(HPyr)·(CHCl3)L 1(Aib)Si(CH2)4(HPyr)
FormulaC13H25Cl3N2O2SiC13H25Cl3N2O2SiC12H24N2O2Si
Mr375.79375.79256.42
T(K)210(2) 1180(2) 1180(2)
λ(Å)0.710730.710730.71073
Crystal systemmonoclinicmonoclinicmonoclinic
Space groupP21/cP21/cP21/c
a(Å)10.3066(3)10.8292(3)14.7139(5)
b(Å)15.5880(3)14.6414(5)15.3923(5)
c(Å)11.4717(3)11.4137(3)14.2576(5)
γ(°)91.954(2)89.534(2) 2118.561(2)
V(Å3)1841.96(8)1809.64(9)2836.12(17)
Z448
ρcalc(g·cm−1)1.361.381.20
μMoKα (mm−1)0.60.60.2
F(000)7927921120
θmax(°), Rint27.0, 0.032627.0, 0.035626.0, 0.0638
Completeness100%100%99.9%
Reflns collected353352846538638
Reflns unique402239595565
Restraints76 36 434 5
Parameters270213378
GoF1.0371.0581.052
R1, wR2 [I > 2σ(I)]0.0309, 0.08220.0284, 0.07150.0355, 0.0802
R1, wR2 (all data)0.0376, 0.08560.0331, 0.07450.0568, 0.0866
Largest peak/hole (e·Å−3)0.28, −0.190.35, −0.200.27, −0.23
1 The superscript H relates to the “higher temperature modification”. Upon cooling to a temperature of around 200 K and below, the crystals undergo a phase transition into the “lower temperature modification”, indicated by a superscript L. This phase transition is, in principle, reversible; i.e., upon warming to above 200 K, the crystal system reverts the modification H. However, this phase transition is accompanied by a decay of crystal quality (enhanced mosaicity; decrease in diffraction power). 2 For this “lower temperature modification”, the non-standard unit cell setting with a monoclinic angle β < 90° was chosen on purpose for the principle retention of the atomic coordinates of the asymmetric unit and to relate the changes in unit cell geometry to the actual phase transition. 3 The restraints were applied for the refinement of disorders (chloroform molecule disordered over three sites with site occupancies of 0.406(3), 0.313(3), and 0.281(3); silacyclopentane section C6–C7 disordered in a cross-wise manner over two positions with site occupancies of 0.802(5) and 0.198(5)). 4 The restraints were applied for the refinement of the disorder of the chloroform molecule over two sites with site occupancies of 0.896(13) and 0.104(13). 5 The restraints were applied for the refinement of disorders (silacyclopentane section C6–C7 disordered in a cross-wise manner over two positions with site occupancies of 0.910(5) and 0.090(5); similar disorder of silacyclopentane section C18–C19 with site occupancies of 0.618(7) and 0.382(7); similar disorder of pyrrolidine section C22–C23 with site occupancies of 0.854(8) and 0.146(8)).
Table A2. Crystallographic data from data collection and refinement of solvates of the hexacoordinate Si compounds (HAib)2Si(CH2)4·2(CHCl3) and (HAib)2Si(CH2)4·(THF).
Table A2. Crystallographic data from data collection and refinement of solvates of the hexacoordinate Si compounds (HAib)2Si(CH2)4·2(CHCl3) and (HAib)2Si(CH2)4·(THF).
Parameter(HAib)2Si(CH2)4·2(CHCl3)(HAib)2Si(CH2)4·(THF) 2
FormulaC14H26Cl6N2O4SiC16H32N2O5Si
Mr527.16360.52
T(K)160(2)160(2)
λ(Å)0.710730.71073
Crystal systemmonoclinicmonoclinic
Space groupC2/cP21/n
a(Å)26.9002(11)13.9769(7)
b(Å)8.2978(4)8.9978(5)
c(Å)11.1868(4)15.4565(9)
γ(°)112.740(3)92.777(4)
V(Å3)2302.93(17)1941.55(18)
Z44
ρcalc (g·cm−1)1.521.23
μMoKα (mm−1)0.80.1
F(000)1088784
θmax(°), Rint26.0, 0.038323.5, 0.1330 2
Completeness100%99.9%
Reflns collected1487313732 2
Reflns unique22722857
Restraints32 10
Parameters168234
GoF1.0540.964
R1, wR2 [I > 2σ(I)]0.0245, 0.06000.0485, 0.0978
R1, wR2 (all data)0.0346, 0.06270.1106, 0.1169
Largest peak/hole (e·Å−3)0.26, −0.200.19, −0.22
1 The restraints were applied for the refinement of disorders (chloroform molecule disordered over two sites with site occupancies of 0.50(2) and 0.50(2); silacyclopentane Cβ–Cβ bond disordered in a cross-wise manner over two positions with site occupancies of 0.922(6) and 0.078(6)). 2 The data set was collected from a small crystal with poor diffraction power, which comprised minor contributions of a twin (twin law: 0.105 0.000 −0.895, 0.000 −1.000 0.000, −1.105 0.000 −0.105). Therefore, data collection and integration were performed for the predominant domain, and the twin contribution was accounted for by subsequent detwinning using TwinRotMat as implemented in PLATON [57]. The latter procedure produced a merged HKLF5 format data set for the final refinement. Therefore, the entries for Rint and Reflns collected from the parent HKLF4 data set are reported here. The twin contribution (batch scale factor, BASF) was refined to 0.089(3).

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Crystals 16 00389 g001
Figure 1. Generic representations of the classes of crystallographically confirmed hypercoordinate Si complexes with α-amino acid-derived (O,N)-bidentate chelating ligands (R, R′, R″, and R‴ are H or variable hydrocarbyl substituents; L is a neutral N-donor ligand). The sketches indicate the molecular configuration encountered in a solid state. (Of note: In class I, one compound with R = H, R′ = tBu, and R″ = Ph exhibits a different configuration, i.e., with an O–Si–O axis as encountered in classes II and III. In class II, an example with proline-derived ligands has been reported as well. In that case, R′ and the (O,N)-chelator’s N atom are part of the amino acid’s pyrrolidine ring. To date, classes III and V are represented by the explicitly depicted respective single example).
Figure 1. Generic representations of the classes of crystallographically confirmed hypercoordinate Si complexes with α-amino acid-derived (O,N)-bidentate chelating ligands (R, R′, R″, and R‴ are H or variable hydrocarbyl substituents; L is a neutral N-donor ligand). The sketches indicate the molecular configuration encountered in a solid state. (Of note: In class I, one compound with R = H, R′ = tBu, and R″ = Ph exhibits a different configuration, i.e., with an O–Si–O axis as encountered in classes II and III. In class II, an example with proline-derived ligands has been reported as well. In that case, R′ and the (O,N)-chelator’s N atom are part of the amino acid’s pyrrolidine ring. To date, classes III and V are represented by the explicitly depicted respective single example).
Crystals 16 00389 g001
Crystals 16 00389 sch001
Scheme 1. Synthesis of silicon complexes from aminosilanes and α-amino isobutyric acid: (a) synthesis of various pyrrolidine adducts (Aib)SiRR’(HPyr) [12], (b) a related reaction with a silacyclopentane starting material to afford (Aib)Si(CH2)4(HPyr), and (c) synthesis of a silacyclopentane derivative (HAib)2Si(CH2)4 with a hexacoordinate Si atom and mono-anionic chelating ligands (HAib).
Scheme 1. Synthesis of silicon complexes from aminosilanes and α-amino isobutyric acid: (a) synthesis of various pyrrolidine adducts (Aib)SiRR’(HPyr) [12], (b) a related reaction with a silacyclopentane starting material to afford (Aib)Si(CH2)4(HPyr), and (c) synthesis of a silacyclopentane derivative (HAib)2Si(CH2)4 with a hexacoordinate Si atom and mono-anionic chelating ligands (HAib).
Crystals 16 00389 sch001
Crystals 16 00389 g002
Figure 2. Selected parts of the (a) 29Si CP/MAS and (b) 13C CP/MAS NMR spectra of (Aib)Si(CH2)4(HPyr), which indicate the presence of molecular sites in accordance with the structures of the chloroform solvate (Aib)Si(CH2)4(HPyr)·(CHCl3) (major component, one molecule per asymmetric unit) and the solvent-free compound (Aib)Si(CH2)4(HPyr) (minor component, two independent molecules in the asymmetric unit).
Figure 2. Selected parts of the (a) 29Si CP/MAS and (b) 13C CP/MAS NMR spectra of (Aib)Si(CH2)4(HPyr), which indicate the presence of molecular sites in accordance with the structures of the chloroform solvate (Aib)Si(CH2)4(HPyr)·(CHCl3) (major component, one molecule per asymmetric unit) and the solvent-free compound (Aib)Si(CH2)4(HPyr) (minor component, two independent molecules in the asymmetric unit).
Crystals 16 00389 g002
Crystals 16 00389 g003
Figure 3. Molecular structures of (Aib)Si(CH2)4(HPyr) in the crystal structures (a) (Aib)Si(CH2)4(HPyr)·(CHCl3)H, (b) (Aib)Si(CH2)4(HPyr)·(CHCl3)L, and (c,d) the two crystallographically independent molecules in (Aib)Si(CH2)4(HPyr), with displacement ellipsoids at the 50% probability level. From disordered moieties, the orientation of predominant site occupancy is depicted.
Figure 3. Molecular structures of (Aib)Si(CH2)4(HPyr) in the crystal structures (a) (Aib)Si(CH2)4(HPyr)·(CHCl3)H, (b) (Aib)Si(CH2)4(HPyr)·(CHCl3)L, and (c,d) the two crystallographically independent molecules in (Aib)Si(CH2)4(HPyr), with displacement ellipsoids at the 50% probability level. From disordered moieties, the orientation of predominant site occupancy is depicted.
Crystals 16 00389 g003
Crystals 16 00389 g004
Figure 4. View along the Si1–N1 bond of (Aib)Si(CH2)4(HPyr) in the crystal structures (a) (Aib)Si(CH2)4(HPyr)·(CHCl3)H and (b) (Aib)Si(CH2)4(HPyr)·(CHCl3)L, with displacement ellipsoids at the 50% probability level. From disordered moieties, the orientation of predominant site occupancy is depicted. The blue lines indicate Cl···H–C van der Waals contacts.
Figure 4. View along the Si1–N1 bond of (Aib)Si(CH2)4(HPyr) in the crystal structures (a) (Aib)Si(CH2)4(HPyr)·(CHCl3)H and (b) (Aib)Si(CH2)4(HPyr)·(CHCl3)L, with displacement ellipsoids at the 50% probability level. From disordered moieties, the orientation of predominant site occupancy is depicted. The blue lines indicate Cl···H–C van der Waals contacts.
Crystals 16 00389 g004
Crystals 16 00389 g005
Figure 5. Ball-and-stick representations of the intermolecular N–H⋯O and Cl3C–H⋯O contacts at the carbonyl groups encountered in the crystal structures of (Aib)Si(CH2)4(HPyr) with (a) (Aib)Si(CH2)4(HPyr)·(CHCl3)H, (b) (Aib)Si(CH2)4(HPyr)·(CHCl3)L, and (c,d) the two crystallographically independent molecules in (Aib)Si(CH2)4(HPyr). The superscripts next to some atom labels indicate the symmetry relation of the respective moiety to the asymmetric unit by symmetry operations (if applicable): a = x, 1.5−y, 0.5+z; b = 2−x, 0.5+y, 1.5–z; c = 1−x, 0.5+y, 1.5–z.
Figure 5. Ball-and-stick representations of the intermolecular N–H⋯O and Cl3C–H⋯O contacts at the carbonyl groups encountered in the crystal structures of (Aib)Si(CH2)4(HPyr) with (a) (Aib)Si(CH2)4(HPyr)·(CHCl3)H, (b) (Aib)Si(CH2)4(HPyr)·(CHCl3)L, and (c,d) the two crystallographically independent molecules in (Aib)Si(CH2)4(HPyr). The superscripts next to some atom labels indicate the symmetry relation of the respective moiety to the asymmetric unit by symmetry operations (if applicable): a = x, 1.5−y, 0.5+z; b = 2−x, 0.5+y, 1.5–z; c = 1−x, 0.5+y, 1.5–z.
Crystals 16 00389 g005
Crystals 16 00389 g006
Figure 6. Sketches of the hitherto crystallographically characterized pentacoordinate Si complexes VI [29], VII [36] and VIII [37] that feature a silacyclopentane motif with selected parameters of their Si coordination spheres: angles 1, 2 and C–Si–C (°), where angles 1 and 2 are the widest angles of the respective coordination sphere; and the geometry index τ5 [32]. (For compound VI [29], two modifications are reported).
Figure 6. Sketches of the hitherto crystallographically characterized pentacoordinate Si complexes VI [29], VII [36] and VIII [37] that feature a silacyclopentane motif with selected parameters of their Si coordination spheres: angles 1, 2 and C–Si–C (°), where angles 1 and 2 are the widest angles of the respective coordination sphere; and the geometry index τ5 [32]. (For compound VI [29], two modifications are reported).
Crystals 16 00389 g006
Crystals 16 00389 g007
Figure 7. Molecular structures of (HAib)2Si(CH2)4 in the crystal structures (a) (HAib)2Si(CH2)4·2(CHCl3), and (b) (HAib)2Si(CH2)4·(THF), with displacement ellipsoids at the 50% and 30% probability levels, respectively. In the solvate (HAib)2Si(CH2)4·2(CHCl3) (a), the atom Si1 is situated on a two-fold axis. Labels of selected symmetry-equivalent atoms carry the superscript suffix e for the symmetry operation 1−x, y, 0.5−z. The silacyclopentane ring in this structure is disordered over two sites, across the bond C6–C6e in a cross-wise manner. Only the atom positions of predominant site occupancy (s.o.f. 0.922(6)) are shown.
Figure 7. Molecular structures of (HAib)2Si(CH2)4 in the crystal structures (a) (HAib)2Si(CH2)4·2(CHCl3), and (b) (HAib)2Si(CH2)4·(THF), with displacement ellipsoids at the 50% and 30% probability levels, respectively. In the solvate (HAib)2Si(CH2)4·2(CHCl3) (a), the atom Si1 is situated on a two-fold axis. Labels of selected symmetry-equivalent atoms carry the superscript suffix e for the symmetry operation 1−x, y, 0.5−z. The silacyclopentane ring in this structure is disordered over two sites, across the bond C6–C6e in a cross-wise manner. Only the atom positions of predominant site occupancy (s.o.f. 0.922(6)) are shown.
Crystals 16 00389 g007
Crystals 16 00389 g008
Figure 8. Examples of crystallographically characterized hexacoordinate Si complexes (V, IX–XVIII) that feature two or more amine- or hydrazine-derived formal N(sp3)-lone-pair donors.
Figure 8. Examples of crystallographically characterized hexacoordinate Si complexes (V, IX–XVIII) that feature two or more amine- or hydrazine-derived formal N(sp3)-lone-pair donors.
Crystals 16 00389 g008
Crystals 16 00389 g009
Figure 9. Ball-and-stick representations of the intermolecular N–H⋯O and Cl3C–H⋯O contacts encountered in the crystal structures of (a) (HAib)2Si(CH2)4·2(CHCl3) and (b) (HAib)2Si(CH2)4·(THF). The superscripts next to some atom labels indicate the symmetry relation of the respective moiety to the asymmetric unit by a symmetry operation (if applicable): d = x, 1−y, 0.5+z; e = 1−x, y, 0.5–z; f = 1−x, 1−y, 1–z; g = 1.5−x, 0.5+y, 0.5–z; h = 1−x, 1−y, 1−z.
Figure 9. Ball-and-stick representations of the intermolecular N–H⋯O and Cl3C–H⋯O contacts encountered in the crystal structures of (a) (HAib)2Si(CH2)4·2(CHCl3) and (b) (HAib)2Si(CH2)4·(THF). The superscripts next to some atom labels indicate the symmetry relation of the respective moiety to the asymmetric unit by a symmetry operation (if applicable): d = x, 1−y, 0.5+z; e = 1−x, y, 0.5–z; f = 1−x, 1−y, 1–z; g = 1.5−x, 0.5+y, 0.5–z; h = 1−x, 1−y, 1−z.
Crystals 16 00389 g009
Crystals 16 00389 g010
Figure 10. Sketches of the hitherto crystallographically characterized hexacoordinate Si complexes XIX [54], XX [55] and XXI [56] that feature a silacyclopentane motif, and the C–Si–C angles therein. (The latter features two independent molecules in the crystallographic asymmetric unit).
Figure 10. Sketches of the hitherto crystallographically characterized hexacoordinate Si complexes XIX [54], XX [55] and XXI [56] that feature a silacyclopentane motif, and the C–Si–C angles therein. (The latter features two independent molecules in the crystallographic asymmetric unit).
Crystals 16 00389 g010
Crystals 16 00389 g011
Figure 11. Configurational isomers of (Aib)Si(CH2)4(HPyr) (top row) and of their potential H-exchanged tautomers (HAib)Si(CH2)4(Pyr) (bottom row). The individual isomer compound code indicates the axially bound atoms with respect to the trigonal bipyramidal Si coordination sphere, and the relative energy (in kJ mol−1) is listed below the compound code. (In case of unstable configuration during the optimization process, the resultant local minimum configuration is listed. In case of isomer NN, decomposition with cleavage of the Si–NPyrrolidine bond occurs, resulting in a compound with N–H···O hydrogen-bonded pyrrolidine).
Figure 11. Configurational isomers of (Aib)Si(CH2)4(HPyr) (top row) and of their potential H-exchanged tautomers (HAib)Si(CH2)4(Pyr) (bottom row). The individual isomer compound code indicates the axially bound atoms with respect to the trigonal bipyramidal Si coordination sphere, and the relative energy (in kJ mol−1) is listed below the compound code. (In case of unstable configuration during the optimization process, the resultant local minimum configuration is listed. In case of isomer NN, decomposition with cleavage of the Si–NPyrrolidine bond occurs, resulting in a compound with N–H···O hydrogen-bonded pyrrolidine).
Crystals 16 00389 g011
Crystals 16 00389 g012
Figure 12. Ensembles of (Aib)Si(CH2)4(HPyr) and hydrogen-bond donor (chloroform) and/or acceptor (methylformate) moieties and their calculated axial Si–O and Si–N bond lengths.
Figure 12. Ensembles of (Aib)Si(CH2)4(HPyr) and hydrogen-bond donor (chloroform) and/or acceptor (methylformate) moieties and their calculated axial Si–O and Si–N bond lengths.
Crystals 16 00389 g012
Table 1. Selected bond lengths (Å), angles (°), and geometry index τ5 [32] of the Si coordination spheres of the molecules of (Aib)Si(CH2)4(HPyr) in the crystal structures (Aib)Si(CH2)4(HPyr)·(CHCl3)H, (Aib)Si(CH2)4(HPyr)·(CHCl3)L, and (Aib)Si(CH2)4(HPyr). The atomic labels refer to Figure 3a–c. The corresponding parameters of the molecule shown in Figure 3d are listed in italics.
Table 1. Selected bond lengths (Å), angles (°), and geometry index τ5 [32] of the Si coordination spheres of the molecules of (Aib)Si(CH2)4(HPyr) in the crystal structures (Aib)Si(CH2)4(HPyr)·(CHCl3)H, (Aib)Si(CH2)4(HPyr)·(CHCl3)L, and (Aib)Si(CH2)4(HPyr). The atomic labels refer to Figure 3a–c. The corresponding parameters of the molecule shown in Figure 3d are listed in italics.
Bond(Aib)Si(CH2)4(HPyr)
·(CHCl3)H		(Aib)Si(CH2)4(HPyr)
·(CHCl3)L		(Aib)Si(CH2)4(HPyr)
Si1–O11.8932(9)1.8968(9)1.8573(12), 1.8603(12)
Si1–N11.7151(12)1.7183(11)1.7143(15), 1.7153(15)
Si1–N22.0507(11)2.0560(11)2.0184(14), 2.0309(14)
Si1–C51.8811(14)1.8862(13)1.8857(18), 1.8874(18)
Si1–C81.8789(14)1.8788(14)1.8851(17), 1.8842(19)
O1–C11.2866(15)1.2893(15)1.297(2), 1.291(2)
O2–C11.2332(15)1.2308(16)1.224(2), 1.226(2)
O1–Si1–N2170.05(4)169.73(4)173.07(6), 173.01(6)
N1–Si1–C5131.69(7)133.00(6)129.33(9), 129.45(14)
N1–Si1–C8130.31(7)129.11(6)133.74(8), 134.18(13)
C5–Si1–C897.74(7)97.67(6)96.85(9), 96.34(16)
τ50.640.610.66, 0.65
Table 2. D···O distances d(D···O) (Å) and D–H···O angles (°) of the H-bond donor atom (D) and the H-bond acceptor O atom in hydrogen bonds of the carboxylate groups of the herein investigated structures of (Aib)Si(CH2)4(HPyr). Note: These D–H···O angles should be interpreted with care. As the H sites in X-ray diffraction analyses represent the location of the H-associated electron density peak (not the site of the H atom), the D–H···O angles are reported without decimal places and without s.u.s, and just serve as a rough estimate of that angle.
Table 2. D···O distances d(D···O) (Å) and D–H···O angles (°) of the H-bond donor atom (D) and the H-bond acceptor O atom in hydrogen bonds of the carboxylate groups of the herein investigated structures of (Aib)Si(CH2)4(HPyr). Note: These D–H···O angles should be interpreted with care. As the H sites in X-ray diffraction analyses represent the location of the H-associated electron density peak (not the site of the H atom), the D–H···O angles are reported without decimal places and without s.u.s, and just serve as a rough estimate of that angle.
CompoundC···Ocarbonyld(D···O)
D–H···O		N···Ocarbonyld(D···O)
D–H···O		N···Ocarboxylatod(D···O)
D–H···O		Symmetry Operations
(Aib)Si(CH2)4(HPyr)
·(CHCl3)H		C13···O2 13.142(14)
167		N1a···O2
 
N2a···O2		3.327(2)
137
2.920(2)
174		N2a···O13.598(2)
137		a x, 1.5−y, 0.5+z
(Aib)Si(CH2)4(HPyr)
·(CHCl3)L		C13···O2 23.140(3)
164		N1a···O2
 
N2a···O2		3.188(2)
154
3.006(2)
150		N2a···O13.379(2)
155		a x, 1.5−y, 0.5+z
(Aib)Si(CH2)4(HPyr) molecule 1 N2b···O22.810(2)
154		 b 2−x, 0.5+y, 1.5–z
(Aib)Si(CH2)4(HPyr) molecule 2 N4c···O42.859(2)
161		 c 1−x, 0.5+y, 1.5–z
1 The chloroform molecule is refined disordered over 3 positions; the C atom coordinates of the site with predominant occupancy, s.o.f. 0.406(3), are employed. 2 The chloroform molecule is refined disordered over 2 positions; the C atom coordinates of the site with predominant occupancy, s.o.f. 0.896(13), are employed.
Table 3. Selected bond lengths (Å) and angles (°) of the Si coordination spheres of the molecules of (HAib)2Si(CH2)4 in the crystal structures (HAib)2Si(CH2)4·2(CHCl3) and (HAib)2Si(CH2)4·(THF). For (HAib)2Si(CH2)4·(THF), the italicized values correspond to the moiety with the first higher label.
Table 3. Selected bond lengths (Å) and angles (°) of the Si coordination spheres of the molecules of (HAib)2Si(CH2)4 in the crystal structures (HAib)2Si(CH2)4·2(CHCl3) and (HAib)2Si(CH2)4·(THF). For (HAib)2Si(CH2)4·(THF), the italicized values correspond to the moiety with the first higher label.
Bond(HAib)2Si(CH2)4·2(CHCl3)(HAib)2Si(CH2)4·(THF)
Si1–O1, Si1–O31.8425(10)1.833(2), 1.859(2)
Si1–N1, Si1–N21.9547(12)1.966(3), 1.933(3)
Si1–C51.9202(14)
Si1–C9, Si1–C14 1.921(3), 1.920(3)
O1–C1, O3–C51.2821(16)1.291(4), 1.295(4)
O2–C1, O4–C51.2286(16)1.224(4), 1.228(4)
N–Si–N164.07(8)163.49(13)
O–Si–C(trans)177.49(6)176.13(14), 176.81(14)
Table 4. Bond lengths d [Å] of the N–Si bonds in complexes of type XVIII (cf. Figure 8).
Table 4. Bond lengths d [Å] of the N–Si bonds in complexes of type XVIII (cf. Figure 8).
EntryRef.RX1X2d(Si–N)
XVIII-1[48]CF3PhH2.023(2), 2.026(2) 1
XVIII-2[48]PhPhH2.014(2), 2.032(2) 1
XVIII-3[49]CF3PhOTf2.029(4), 2.037(4)
XVIII-4[50]CF3PhF2.021(3), 2.029(3)
XVIII-5[51]CF3PhCl2.042(4), 2.046(4) 2
XVIII-6[50]CF3FF1.962(2) 3
XVIII-7[51]CF3ClCl2.011(2), 2.013(2) 2
XVIII-8[52]CF3ClCy2.097(2), 2.102(2) 1
XVIII-9[53]CF3(CH2)3 2.094(2), 2.100(2) 1
XVIII-10[53]Ph(CH2)3 2.0852(10) 3
XVIII-11[53]tBu(CH2)3 2.098(2) 1,3
XVIII-12[53]NMe2(CH2)3 2.085(2), 2.089(2) 1
1 The data are rounded to the 3rd decimal place; the respective s.u.s before rounding are (2) > s.u. > (1). 2 Out of two crystallographically independent molecules, the bond lengths of one representative example molecule are reported. 3 The molecule is situated at a special position; only one Si–N bond is encountered in the asymmetric unit.
Table 5. D···O distances d(D···O) (Å) and D–H···O angles (°) of the H-bond donor atom (D) and the H-bond acceptor O atom in hydrogen bonds of the herein investigated structures of (HAib)2Si(CH2)4. Note: These D–H···O angles should be interpreted with care. As the H sites in X-ray diffraction analyses represent the location of the H-associated electron density peak (not the site of the H atom), the D–H···O angles are reported without decimal places and without s.u.s and just serve as a rough estimate of that angle.
Table 5. D···O distances d(D···O) (Å) and D–H···O angles (°) of the H-bond donor atom (D) and the H-bond acceptor O atom in hydrogen bonds of the herein investigated structures of (HAib)2Si(CH2)4. Note: These D–H···O angles should be interpreted with care. As the H sites in X-ray diffraction analyses represent the location of the H-associated electron density peak (not the site of the H atom), the D–H···O angles are reported without decimal places and without s.u.s and just serve as a rough estimate of that angle.
CompoundC···Ocarbonyld(D···O)
D–H···O		N···Ocarbonyld(D···O)
D–H···O		N···Ootherd(D···O)
D–H···O		Symmetry Operations
(HAib)2Si(CH2)4·2(CHCl3)C7···O2 13.092(6)
155		N1d···O22.942(2)
157		--d x, 1−y, 0.5+z
(HAib)2Si(CH2)4·(THF)--N1g···O4
 
N2h···O2		2.915(4)
165
2.970(4)
158		N2···O52.882(4)
169		g 1.5−x, 0.5+y, 0.5−z
h 1−x, 1−y, 1−z
1 The chloroform molecule is refined disordered over 2 positions with essentially equal site occupancy (s.o.f. 0.50(2)). The C atom coordinates of site C7 are employed.
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Seidel, A.; Knerr, S.; Wagler, J. α-Amino Isobutyric Acid-Derived Silacyclopentane Complexes with Penta- and Hexacoordinate Si Atoms. Crystals 2026, 16, 389. https://doi.org/10.3390/cryst16060389

AMA Style

Seidel A, Knerr S, Wagler J. α-Amino Isobutyric Acid-Derived Silacyclopentane Complexes with Penta- and Hexacoordinate Si Atoms. Crystals. 2026; 16(6):389. https://doi.org/10.3390/cryst16060389

Chicago/Turabian Style

Seidel, Anne, Steven Knerr, and Jörg Wagler. 2026. "α-Amino Isobutyric Acid-Derived Silacyclopentane Complexes with Penta- and Hexacoordinate Si Atoms" Crystals 16, no. 6: 389. https://doi.org/10.3390/cryst16060389

APA Style

Seidel, A., Knerr, S., & Wagler, J. (2026). α-Amino Isobutyric Acid-Derived Silacyclopentane Complexes with Penta- and Hexacoordinate Si Atoms. Crystals, 16(6), 389. https://doi.org/10.3390/cryst16060389

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