Si-E (E = N, O, F) bonding in a hexacoordinated silicon complex: new facts from experimental and theoretical charge density studies

Structural and Electronic Effects on Phosphine Chalcogenide Stabilized Silicon Centers in Four-Membered Heterocyclic Cations

Understanding the interplay of structural and electronic parameters in the stabilization of Lewis acidic silicon centers is crucial for stereochemical questions and applications in bond activation and catalytic transformations. Phosphine chalcogenide functionalized (Ch = O, S, and Se) hydrosilanes having tert-butyl and 2,4,6-trimethoxyphenyl (TMP) substituents on the silicon atom were synthesized, and the ring-closing reactions to afford the heterocyclic four-membered CPChSi cations were investigated. Synthetic access was only achieved for the sulfur- and selenium-based cations. A thorough study by means of single-crystal X-ray structure determination, NMR spectroscopic data, and density functional theory (DFT) calculations provided insight into important electronic and structural parameters affecting the stability of the intramolecularly stabilized cations. Detailed structural considerations were made on the contributions to the ring strain (angular strain and steric repulsion). Thermochemical investigations showed that the substituents on the silicon and phosphorus atoms play an important role for the stability of the cationic heterocycles. In the absence of large steric repulsions through bulky substituents (methyl groups on silicon and tert-butyl groups on phosphorus), an intrinsic stability sequence of the intramolecular Ch-Si coordination depending on the chalcogen atom in the direction Se ≤ S < O can be observed. However, the order is reversed (O < S < Se) in the case of strong repulsions between sterically demanding substituents (tert-butyl groups on both silicon and phosphorus atoms). Natural bond orbital (NBO) analysis supported the explanations for the observed deshielding trends in ³¹P NMR spectroscopy and revealed that the O-Si bond is more ionic in nature compared to the S-Si and Se-Si bonds, with the latter exhibiting higher covalent character due to a more efficient charge transfer through a σ-type n_Ch → p_Si interaction.

Synthesis and Characterization of Hypercoordinated Silicon Anions: Catching Intermediates of Lewis Base Catalysis

Anionic hypercoordinated silicates with weak donors were proposed as key intermediates in numerous silicon‐based reactions. However, their short‐lived nature rendered even spectroscopic observations highly challenging. Here, we characterize hypercoordinated silicon anions, including the first bromido‐, iodido‐, formato‐, acetato‐, triflato‐ and sulfato‐silicates. This is enabled by a new, donor‐free polymeric form of Lewis superacidic bis(perchlorocatecholato)silane 1. Spectroscopic, structural, and computational insights allow a reassessment of Gutmann's empirical rules for the role of silicon hypercoordination in synthesis and catalysis. The electronic perturbations of 1 exerted on the bound anions indicate pronounced substrate activation.

Si-H···Se Chalcogen-Hydride Bond Quantified by Diffraction and Topological Analyses

The Si-H···Se contact in 1-mesitylselanyl-8-(dimethylsilyl)naphthalene (1), which exhibits the spatial arrangement of a δ-agostic interaction from geometric considerations, was investigated. Is this just enforced by close 1,8-proximity or is this a favorable interaction? Charge density studies are best suited to investigate the exact origin of the interaction and to quantify the properties. Hence, they are most elucidating. High-resolution X-ray diffraction data of 1 were collected, and a multipole refinement followed by a topological analysis using Bader's quantum theory of atoms in molecules was employed. The resulting bond properties were set in relation to high-level computational parameters. The comparison to Si-H···[M] agostics, hydride bonding, chalcogen bonds, and charge-inverted hydrogen bonds qualified the Si-H···Se noncovalent interaction to be best classified as a chalcogen-hydride bond.

Similarities and Differences between Crystal and Enzyme Environmental Effects on the Electron Density of Drug Molecules

The crystal interaction density is generally assumed to be a suitable measure of the polarization of a low-molecular weight ligand inside an enzyme, but this approximation has seldomly been tested and has never been quantified before. In this study, we compare the crystal interaction density and the interaction electrostatic potential for a model compound of loxistatin acid (E64c) with those inside cathepsin B, in solution, and in vacuum. We apply QM/MM calculations and experimental quantum crystallography to show that the crystal interaction density is indeed very similar to the enzyme interaction density. Less than 0.1 e are shifted between these two environments in total. However, this difference has non-negligible consequences for derived properties.

The synthesis, characterization, and theoretical analysis of novel Si-substituted silylethyl derivatives of 2-mercaptobenzoxazole and 2-mercaptobenzothiazole

Trifluorosilylethyl derivatives of 2-mercaptobenzoxazole and 2-mercaptobenzothiazole C₆H₄NYCS(CH₂)₂SiF₃ (Y = O, S) have been synthesized in order to study the intramolecular N → Si interaction in compounds with the SiCCSCN fragment.

Intercalating Anions between Terminated Anion Layers: Unusual Ionic S-Se Bonds and Hole-Doping Induced Superconductivity in S0.24(NH3)0.26Fe2Se2

The pairing of ions of opposite charge is a central principle of chemistry. Even though the ability to intercalate anions is desirable for many applications, it remains a key challenge for numerous host materials with their outmost layers beingn anions. In this work, we introduce a hydrothermal ion-exchange synthesis to intercalate oxidative S and Se anions between the Se layers of FeSe, which leads to single crystals of novel compounds (Se/S)x(NH3)yFe2Se2. In particular, the unusual anion-anion bonding between the intercalated S (or Se) and Se layers exhibits strong ionic characteristics. The charge transfer through the Se layer to S (or Se) intercalants is further confirmed by the elevated oxidation state of Fe ions and the dominant hole carriers in the intercalated compounds. By intercalating S, for the first time superconductivity emerged in hole-doped iron chalcogenides. The generality of this chemical approach was further demonstrated with layered FeS and NiSe. Our findings thus open an avenue to exploring diverse aspects of anionic intercalation in similar materials.

Synthesis and Reactivity of a Hypersilylsilylene

Stabilization of an amidinatosilylene with a bulky tris(trimethylsilyl)silyl substituent was realized with the preparation of PhC(NtBu)₂Si{Si(SiMe₃)₃} (1) from PhC(NtBu)₂SiHCl₂ with K{Si(SiMe₃)₃} in more than 90% yield. The highly deshielded ²⁹Si NMR resonance (δ = 76.91 ppm) can be attributed to the absence of a π-donating substituent. The molecular structure of 1 shows a trigonal-planar geometry around the Si^II center with a Si^II-Si^IV bond length of 2.4339(13) Å. A series of reactions of 1 with Me₃NO, S, Se, and Te were performed. While siloxane derivatives (2 and 3) are obtained from reactions with Me₃NO, silachalcogenones (4-6) are formed with other chalcogens. The presence of Si═E (E = S, Se, and Te) bonds in 4-6 have been confirmed by single-crystal X-ray studies. Silaoxirane (7) formation was observed when 1 was treated with acetone, demonstrating the importance of the tris(trimethylsilyl)silyl group to kinetically and thermodynamically protect the silaoxirane derivative with less bulky substituents on the C atom.

Revisiting a Historical Concept by Using Quantum Crystallography: Are Phosphate, Sulfate and Perchlorate Anions Hypervalent?

There are many examples of atoms in molecules that violate Lewis' octet rule, because they have more than four electron pairs assigned to their valence. These atoms are referred to as hypervalent. However, hypervalency may be regarded as an artifact arising from Lewis' description of molecules, which is based on the assumption that electrons are localized in two-center two-electron bonds and lone pairs. In the present paper, the isoelectronic phosphate (PO₄ ^3- ), sulfate (SO₄ ^2- ) and perchlorate (ClO₄ ^- ) anions were examined with respect to the concept of hypervalency. Lewis formulas containing a hypervalent central atom exist for all three anions. Based on X-ray wavefunction refinements of high-resolution X-ray diffraction data of representative crystal structures (MgNH₄ PO₄ ⋅6 H₂ O, Li₂ SO₄ ⋅H₂ O, and KClO₄ ), complementary bonding analyses were performed. In this way, experimental information from the new field of quantum crystallography validate long-known facts, or refute long-standing misunderstandings. It is shown that the P-O and S-O bonds are highly polarized covalent bonds and, thus, the increase in the valence population following three-center four-electron bonding is not sufficient to yield hypervalent phosphorus or sulfur atoms, respectively. However, for the highly covalent Cl-O bond, most bonding indicators imply a hypervalent chlorine atom.

Complementary bonding analysis of the N–Si interaction in pentacoordinated silicon compounds using quantum crystallography

The unique combination of quantum crystallography and complementary bonding analysis is used to investigate the bonding of pentacoordinated silicon atoms.

Yttrium dialkyl supported by a silaamidinate ligand: synthesis, structure and catalysis on cyclotrimerization of isocyanates

A four-coordinate yttrium dialkyl complex with a sterically demanding silaamidinate ligand exhibited high activity and excellent functional group tolerance for the catalysis of isocyanate cyclotrimerization.

Experimental charge density study on FLPs and a FLP reaction product

The charge density distribution of the intramolecular frustrated Lewis pair (FLP) Mes2PCH2CH2B(C6F5)2 (1), the phosphinimine HNPMes2CH2CH2B(C6F5)2 (2), as well as a FLP homologue with nitrogen NEt2CHPhCH2B(C6F5)2 (3) were investigated with Bader’s quantum theory of atoms in molecules (QTAIM). The charge densities were derived from both experimental high-resolution X-ray diffraction data (2, 3) and theoretical calculations (1, 3). The QTAIM analysis for the FLPs 1 and 3 showed the prominent B-pnictogen interaction to be weak dative bonds without significant charge-transfer. This holds also true for the B–N–bond of 2. The nitrogen atom is negatively charged, due to a charge transfer from phosphorous and shows features of a sp2-hybridization. The bond is therefore best described as a non-hypervalent Pδ+–Nδ− moiety.

Assignment of photoelectron spectra of intramolecular silicon complexes: 1-vinyl- and 1-phenylsilatranes

The problematic photoelectron spectra of 1-vinyl- and 1-phenylsilatranes were theoretically studied and the correlation between the VIE and thed_SiNwas proposed to be used for the identification of orbitals in the Si←N coordination bond in XSi[OCH₂CH₂]₃N.

Assignment of photoelectron spectra of silatranes: first ionization energies and the nature of the dative Si←N contact

The problematic experimental (8–12 eV) photoelectron spectra of silatranes were theoretically studied and the correlation was found between the first vertical ionization energies, VIEs₁, and the various characteristics of the coordination Si←N contact.

Invariom based electron density studies on the C/Si analogues haloperidol/sila-haloperidol and venlafaxine/sila-venlafaxine

Hirshfeld surfaces of haloperidol hydropicrate (left) and sila-haloperidol hydrochloride (right) show comparable sites of ED concentrations due to comparable intermolecular environments.

Base-stabilized silaimine and its donor-free dimer derived from the reaction of NHC-supported silylene with SiCl4

Reaction of the N-heterocyclic carbene (NHC)-stabilized silylene ArN(SiMe₃)Si(IiPr)Cl (1, Ar = 2,6-iPr₂C₆H₃, IiPr = 1,3-diisopropyl-4,5-dimethyl-imidazol-2-ylidene) with SiCl₄ resulted in the formation of three different products ArNSi(IiPr)Cl₂ (2), ArN(SiMe₃)SiCl₃ (3) and (ArNSiCl₂)₂ (4) under different conditions.

A density function theory study on the NO reduction on nitrogen doped graphene

The nitrogen doped graphene is an efficient metal-free catalyst for NO reduction by the dimer mechanism.

Reaction of N-heterocyclic silylenes with thioketone: formation of silicon-sulfur three (Si-C-S)- and five (Si-C-C-C-S)-membered ring systems

Three- and five-membered rings that bear the (Si-C-S) and (Si-C-C-C-S) unit have been synthesized by the reactions of LSiCl (1; L=PhC(NtBu)2 ) and L'Si (2; L'=CH{(CCH2 )(CMe)(2,6-iPr2 C6 H3 N)2 }) with the thioketone 4,4'-bis(dimethylamino)thiobenzophenone. Treatment of 4,4'-bis(dimethylamino)thiobenzophenone with LSiCl at room temperature furnished the [1+2]-cycloaddition product silathiacyclopropane 3. However, reaction of 4,4'-bis(dimethylamino)thiobenzophenone with L'Si at low temperature afforded a [1+4]-cycloaddition to yield the five-membered ring product 4. Compounds 3 and 4 were characterized by NMR spectroscopy, EIMS, and elemental analysis. The molecular structures of 3 and 4 were unambiguously established by single-crystal X-ray structural analysis. The room-temperature reaction of 4,4'-bis(dimethylamino)thiobenzophenone with L'Si resulted in products 4 and 5, in which 4 is the dearomatized product and 5 is formed under the 1,3-migration of a hydrogen atom from the aromatic phenyl ring to the carbon atom of the CS unit. Furthermore, the optimized structures of probable products were investigated by using DFT calculations.

Sequence selectivity of azinomycin B in DNA alkylation and cross-linking: a QM/MM study

Azinomycin B--a well-known antitumor drug--forms cross-links with DNA through alkylation of purine bases and blocks tumor cell growth. This reaction has been modeled using the ONIOM (B3LYP/6-31+g(d):UFF) method to understand the mechanism and sequence selectivity. ONIOM results have been checked for reliability by comparing them with full quantum mechanics calculations for selected paths. Calculations reveal that, among the purine bases, guanine is more reactive and is alkylated by aziridine ring through the C10 position, followed by alkylation of the epoxide ring through the C21 position of Azinomycin B. While the mono alkylation is controlled kinetically, bis-alkylation is controlled thermodynamically. Solvent effects were included using polarized-continuum-model calculations and no significant change from gas phase results was observed.