Electrooxidation of Hypercoordinated Derivatives of Silicon and Reactivity of Their Electrogenerated Cation Radicals: 1-Substituted Silatranes.

Electrochemical oxidation of 1-R-substituted silatranes 1 (R = Me, vinyl, (CH2)2CN, CH2Ph, CH2(C10H7), Ph, C6H4Me, p-Cl-C6H4, Cl)-classical representatives of pentacoordinated silicon compounds-and the formation of their short living cation radicals upon reversible or quasi-reversible one-electron withdrawal were studied by means of cyclic and square-wave voltammetry, faradaic impedance spectroscopy and real-time temperature-dependent EPR spectroelectrochemistry supported by DFT B3PW91/6-311++G(d,p) (C-PCM, acetonitrile) calculations. The main reaction responsible for the decay of 1+• is shown to be their deprotonation, and ways of increasing the stability of these species are proposed.

The hierarchy of ab initio and DFT methods for describing an intramolecular non-covalent SiN contact in the silicon compounds using electron diffraction geometries.

In the series of silatranes XSi(OCH2CH2)3N, 1 (X = Me, 1a; H, 1b; F, 1c) with the known gas electron diffraction (GED) structures, the problematic geometry of 1-methylsilatrane 1a has been revised. In particular, the new value of the SiN distance (dSiN) in 1a turned out to be ∼0.06 Å longer than the generally accepted one. This dSiN resolves the long-standing contradiction between the data of the structural and spectral experiments regarding the sensitivity of 1 to the medium effect. We also performed the ab initio and DFT study of the combined series of silatranes 1a-c, silylalkylamines H3Si(CH2)3NMe2 (2a) and F3SiCH2NMe2 (2b), silylhydrazines F3SiN(Me)NMe2 (2c) and F3SiN(SiMe3)NMe2 (2d), and silyloxyamines ClH2SiONMe2 (2e,f), (F3C)F2SiONMe2 (2g,h) and F3SiONMe2 (2i), in which the GED dSiN values are in a wide range of 2-3 Å. None of the involved quantum chemical methods has succeeded in reproducing all the experimental gas-phase dSiN values in 1a-c, 2a-i with an acceptable accuracy (0.01-0.03 Å). The problems of the used methods, primarily CCSD with the Pople basis sets, are caused by four molecules with the geminal SiNN and SiON fragments (2d,f-i) and dSiN < 2.3 Å. A reasonable hierarchy of computationally accessible theory levels for studying the physicochemical manifestation of the non-covalent intramolecular SiN interactions can be constructed only at dSiN > 2.3 Å: MP2 < PBE0 ∼ B3PW91 ∼ SCS-MP2 < CCSD < CCSD(T).

"Outlaw" Dipole-Bound Anions of Intra-Molecular Complexes.

Using the example of silatranes XSi(OCH2CH2)3N (X = Me, H, F, Cl), XS, it was found that the effect of the dipole-bound (DB) electron on the cage intramolecular complexes does not fit into the standard views. Upon the transition from XS to the DB anions XS-, the unusual shortening of the internuclear Si···N distance is always observed. For X = Cl, it is equal to 0.15 Å, which is a record length for all DB anions known from the literature. The formation of DB anions with the cage structure has principal features, controlled not only by the "critical" value of the dipole moment (µ > 2.5 D), but also by a geometric factor, such as the degree of pyramidality of the N(CH2)3 moiety-the positive end of the molecular dipole of XS. It was a surprise that the effect of the substituent X on the extent of the structural rearrangement in the process XS → XS- cannot be explained using the values of the electron detachment energy of XS- or the initial strength of the coordination Si ← N bond in XS. The unique sensitivity of the silatrane geometry to the addition of an excess electron is governed by the rate of increase of their dipole moment with the shortening of the dative Si ← N contact. The conclusions drawn are supported by the high-accuracy CCSD and CCSD(T) calculations and the experimental (RET-PES) data. There is no real reason to doubt that the peculiarities of the formation of DB anions of XS- can also be characteristic of many hundreds of their structural analogues XM(YCH2CH2)3N (M = Si, Ge, Sn, Pb, Ti, Al, Cr, Fe, Ni...; Y = O, NR, CH2, S), i.e., substituted 5-azabicyclo[3.3.3]undecans.

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

The problematic experimental photoelectron spectra of silatranes XSi[OCH2CH2]3N (X = vinyl and Ph) were theoretically studied. The ab initio electron propagator theory, many-body methods, and model vibrational Hamiltonian were employed to establish the nature of bands in the energetically lowest part of the photoelectron spectrum of these intramolecular silicon complexes. The first vertical ionization energy corresponds to a nitrogen atom lone pair, nN, in 1-vinylsilatrane, and the essentially doubly degenerate π-orbitals πPh and πPh' of the aromatic ring in 1-phenylsilatrane. Peaks at 9.6 and 9.9 eV in the spectra of both compounds, previously associated with the removal of an electron from the lone pair level of the equatorial oxygens, should actually be assigned to the bonding orbital HV1 of their 3c-4e axial CSi←N moiety. Taking silatranes with X = H, Me, OEt, F, vinyl, and Ph as examples, it was found that the length of the dative Si←N contact and the ionization energy of HV2 (formally nN) were in a good linear relationship. Regardless of the nature of the X substituent, this relationship could be used for the identification of orbitals that participate in the formation of the coordination Si←N bond in the wide series of XSi[OCH2CH2]3N and their structural analogs.

Dipole-Bound Anions of Intramolecular Complexes.

Dipole-bound molecular anions are often envisioned as unperturbed neutral, polar molecules with single excess electrons. We report the observation of intramolecular structural distortions within silatrane molecules due to the formation of their dipole-bound anions. The combination of Rydberg electron transfer-anion photoelectron spectroscopy (RET-PES) and ab initio computational methodologies (CCSD and MP2) was used to study 1-hydro- (HS) and 1-fluoro- (FS) silatranes and their dipole bound anions, HS- and FS-. The vertical detachment energies (VDEs) of HS- and FS- were measured to be 48 and 93 meV, respectively. Ab initio calculations accurately reproduced these VDE values as well as their photoelectron spectral profiles. This work revealed significant shortening (by ∼0.1 Å) of dative Si ← N bond lengths when HS and FS formed dipole-bound anions, HS- and FS-. Detailed computational (Franck-Condon) analyses explained the absence of vibrational features in the photoelectron spectra of HS- and FS-.

Radical cations of phenyl silatrane.

Electrochemical oxidation of phenylsilatrane (1) in CH3CN/0.1 M Bu4NPF6 has been studied by voltammetry, UV-Vis and EPR-coupled spectroelectrochemistry supported by DFT calculations. One-electron withdrawal from the HOMO of 1, formed with a predominant contribution of the atrane N atom to the 3c-4e system, results in a short lived radical cation, in which the atrane nitrogen atom is almost planar and carries most of the spin density showing strong coupling with the protons of the axially directed C-H bonds of the three adjacent α-methylene groups (g = 2.0037, aαHax = 37.93 G, aαHlat = 0.23 G and aßH = 1.8 G). EPR spectroscopy and DFT calculations attest that the unpaired electron in the radical cation does not reside at the Si atom.

Electrochemical Oxidation and Radical Cations of Structurally Non-rigid Hypervalent Silatranes: Theoretical and Experimental Studies.

Using 18 silatranes XSi(OCH2 CH2 )3 N (1) as examples, the potentials of electrochemical oxidation E0 of the hypervalent compounds of Si were calculated for the first time at the ab initio and DFT levels. The experimental peak potentials Ep (acetonitrile) show an excellent agreement (MAE=0.03) with the MP2//B3PW91 calculated E0 (C-PCM). Radical cations of 1 reveal a stretch isomerism of the N→Si dative bond. Localization of the spin density (SD) on the substituent X and the short (s) coordination contact Si⋅⋅⋅N (dSiN <2.13 Å) along with the high five-coordinate character of Si are typical for the first isomer 1+.(s) , whereas the second one, 1+.(l) , has a longer (l) Si⋅⋅⋅N distance (dSiN >3.0 Å), the four-coordinate Si and the SD localized on the silatrane nitrogen atom Ns . The vertical model of adiabatic ionization (1→1+.(s) or 1→1+.(l) ) was developed. It allows, in accordance with an original experimental test (electrooxidation of 1 in the presence of ferrocene), a reliable prediction of the most probable pathways of the silatrane oxidation. The reliable relationships of E0 (1) with the strength characteristics of the dative contact N→Si were revealed.

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

The problematic experimental photoelectron spectra of fluoro- and ethoxy-silatranes, XSi[OCH2CH2]3N (X = F and OEt), were assigned using theoretical spectra obtained by combining the OVGF//CCSD vertical ionization energies with the vibrational widths of the electronic transitions (linear vibronic coupling formalism, LVC). Taking into account the overlapping of the silatrane bands with the bands of probable impurities, bicyclic amines, (OH)XSi(OCH2CH2)2NCH2CH2OH, allowed us to reliably determine the position of the low-energy bands (at ∼9.7 eV for F- and at ∼9.2 eV for EtO-silatrane) associated with the ionization from a nitrogen lone pair level. For XSi[OCH2CH2]3N (X = F, H, OEt, Me), the correlation between the first vertical ionization energies, VIEs1, and the geometrical, electronic and orbital characteristics of the Si←N bonding was found. Its analysis suggests that the Si←N coordination in silatranes is orbital-controlled rather than charge-controlled.

Radical anions of hypervalent silicon compounds: 1-substituted silatranes.

The first representatives of the radical anions of silatranes XSi(OCH2CH2)3N ­ organic derivatives of the pentacoordinate silicon atom (X = Ph, 1; p-NO2PhO, 2a; m-NO2PhO, 2b; o-NO2PhO, 2c) ­ were obtained and characterized by EPR spectroscopy. The structure of 1(−˙), 2a(−˙), 2b(−˙), and 2c(−˙) in polar solvents (C-PCM and COSMO models) was studied at the UMP2 and UB3PW91 levels of theory. The variation of structural characteristics and pentacoordinate character of the silicon atom in 1, 2 upon the attachment of an additional electron to them is discussed. The experimental hyperfine coupling constants aN, aH and those calculated with the UTPSSh/IGLOIII and UB3LYP/N07D methods using the UB3PW91 geometry (taking into account an effect of the potassium cation in the case of 1(−˙)) are in good mutual agreement.

Helicobacter pylori outer membrane protein HopQ identified as a novel T4SS-associated virulence factor.

Helicobacter pylori is a bacterial pathogen that colonizes the gastric niche of ∼ 50% of the human population worldwide and is known to cause peptic ulceration and gastric cancer. Pathology of infection strongly depends on a cag pathogenicity island (cagPAI)-encoded type IV secretion system (T4SS). Here, we aimed to identify as yet unknown bacterial factors involved in cagPAI effector function and performed a large-scale screen of an H. pylori transposon mutant library using activation of the pro-inflammatory transcription factor NF-κB in human gastric epithelial cells as a measure of T4SS function. Analysis of ∼ 3000 H. pylori mutants revealed three non-cagPAI genes that affected NF-κB nuclear translocation. Of these, the outer membrane protein HopQ from H. pylori strain P12 was essential for CagA translocation and for CagA-mediated host cell responses such as formation of the hummingbird phenotype and cell scattering. Besides that, deletion of hopQ reduced T4SS-dependent activation of NF-κB, induction of MAPK signalling and secretion of interleukin 8 (IL-8) in the host cells, but did not affect motility or the quantity of bacteria attached to host cells. Hence, we identified HopQ as a non-cagPAI-encoded cofactor of T4SS function.

Correlation among the gas-phase, solution, and solid-phase geometrical and NMR parameters of dative bonds in the pentacoordinate silicon compounds. 1-Substituted silatranes.

Silatranes XSi(OCH2CH2)3N exhibit a good linear relationship between their experimental and calculated (IGLO and GIAO) values of the NMR chemical shifts of (15)N, δN, and the lengths of dative bonds Si←N, dSiN, determined in the gas phase (ED, CCSD), solutions (COSMO PBE0, B3PW91), and crystals (X-ray). An aggregate of the obtained data provides strong evidence that the gas-phase value of dSiN in MeSi(OCH2CH2)3N should be greater by ∼0.05 Å than that determined in the electron diffraction (ED) experiment (2.45 Å). Given this condition, a long-standing contradiction between the data of the structural (X-ray, ED) and NMR (15)N experiments for the molecules of 1-methyl- and 1-fluorosilatrane regarding the sensitivity of their coordination contact Si←N to the medium effect is resolved.

A new approach to the design of neutral 10-C-5 trigonal-bipyramidal carbon compounds: a "π-electron cap" effect.

DFT (B3LYP, M06-2X) and MP2 methods are applied to the design of a wide series of the potentially 10-C-5 neutral compounds based on 6-azabicyclotetradecanes: XC(1)(YCH2CH2CH2)3N 1-3, XC(1)(YC6H4CH2)3N 4-6, XC(1)[Y(tBuC6 H3)CH2]3N 7-9 and carbatranophanes C6H3[XC(1)(YC6H3CH2)3N] 10-25 (X = Me, F, Cl; Y = O, NH, CH2, SiH2; Z = O, CH2, (CH2)2, (CH2)3). Carbatranophanes 10-25 are characterized by a sterical compression of their axial 3c-4e XC(1)←N fragment with respect to that in the parent molecules 4-6. A magnitude of the revealed effect depends on a valence surrounding of the central carbon atom C(1), the size and the nature of the side chains (Z) that link the "π-electron cap" with a tetradecane backbone. This circumstance allowed us to obtain 10-C-5 structures with the configuration of the bonds around the C(1) atom, which corresponds to practically an ideal trigonal bipyramid. In these compounds, the values of the covalence ratio χ (C1←N) of approximately 0.6 for the coordination C(1)←N contacts with a covalent contribution (atoms in molecules (AIM) and natural bond orbital (NBO)) are record in magnitude. These values lie close to a low limit of the interval of the χ(Si←D) change (0.6-0.9) being characteristic of the dative and ionic-covalent (by nature) Si←D bond (D = N, O) in the known 10-Si-5 silicon compounds.

Comparative analysis of the interaction of Helicobacter pylori with human dendritic cells, macrophages, and monocytes.

Helicobacter pylori may cause chronic gastritis, gastric cancer, or lymphoma. Myeloid antigen-presenting cells (APCs) are most likely involved in the induction and expression of the underlying inflammatory responses. To study the interaction of human APC subsets with H. pylori, we infected monocytes, monocyte-derived dendritic cells (DCs), and monocyte-derived (classically activated; M1) macrophages with H. pylori and analyzed phenotypic alterations, cytokine secretion, phagocytosis, and immunostimulation. Since we detected CD163(+) (alternatively activated; M2) macrophages in gastric biopsy specimens from H. pylori-positive patients, we also included monocyte-derived M2 macrophages in the study. Upon H. pylori infection, monocytes secreted interleukin-1ß (IL-1ß), IL-6, IL-10, and IL-12p40 (partially secreted as IL-23) but not IL-12p70. Infected DCs became activated, as shown by the enhanced expression of CD25, CD80, CD83, PDL-1, and CCR7, and secreted IL-1ß, IL-6, IL-10, IL-12p40, IL-12p70, and IL-23. However, infection led to significantly downregulated CD209 and suppressed the constitutive secretion of macrophage migration inhibitory factor (MIF). H. pylori-infected M1 macrophages upregulated CD14 and CD32, downregulated CD11b and HLA-DR, and secreted mainly IL-1ß, IL-6, IL-10, IL-12p40, and IL-23. Activation of DCs and M1 macrophages correlated with increased capacity to induce T-cell proliferation and decreased phagocytosis of dextran. M2 macrophages upregulated CD14 and CD206 and secreted IL-10 but produced less of the proinflammatory cytokines than M1 macrophages. Thus, H. pylori affects the functions of human APC subsets differently, which may influence the course and the outcome of H. pylori infection. The suppression of MIF in DCs constitutes a novel immune evasion mechanism exploited by H. pylori.

Modulation of the CD4+ T-cell response by Helicobacter pylori depends on known virulence factors and bacterial cholesterol and cholesterol α-glucoside content.

Helicobacter pylori blocks the proliferation of human CD4(+) T cells, facilitated by vacuolating exotoxin (VacA) and γ-glutamyl transpeptidase (GGT). H. pylori-triggered T-cell reactions in mice correlate with bacterial cholesterol and cholesterol α-glucoside content but their role in human cells is unclear. We characterized the effect of VacA, GGT, and cholesterol on T-helper 1, T-helper 2, T-regulatory and T-helper 17 associated cytokines and T-cell proliferation. VacA, GGT, and bacterial cholesterol content exhibited differential and synergistic inhibitory effects on the expression of activation markers CD25 and CD69 and on interleukin 2, interleukin 4, interleukin 10, and interferon γ production. These factors did not affect the H. pylori-mediated abrogation of transforming growth factor ß secretion or increased interleukin 6 production. Cholesterol α-glucosyltransferase-deficient bacteria exerted strongly reduced antiproliferative effects on primary human CD4(+) T cells. In conclusion, H. pylori shapes rather than suppresses human CD4(+) T-cell responses, and glucosylated cholesterol is a relevant bacterial component involved in this modulation.

Helicobacter pylori induces miR-155 in T cells in a cAMP-Foxp3-dependent manner.

Amongst the most severe clinical outcomes of life-long infections with Helicobacter pylori is the development of peptic ulcers and gastric adenocarcinoma--diseases often associated with an increase of regulatory T cells. Understanding H. pylori-driven regulation of T cells is therefore of crucial clinical importance. Several studies have defined mammalian microRNAs as key regulators of the immune system and of carcinogenic processes. Hence, we aimed here to identify H. pylori-regulated miRNAs, mainly in human T cells. MicroRNA profiling of non-infected and infected human T cells revealed H. pylori infection triggers miR-155 expression in vitro and in vivo. By using single and double H. pylori mutants and the corresponding purified enzymes, the bacterial vacuolating toxin A (VacA) and gamma-glutamyl transpeptidase (GGT) plus lipopolysaccharide (LPS) tested positive for their ability to regulate miR-155 and Foxp3 expression in human lymphocytes; the latter being considered as the master regulator and marker of regulatory T cells. RNAi-mediated knockdown (KD) of the Foxp3 transcription factor in T cells abolished miR-155 expression. Using adenylate cyclase inhibitors, the miR-155 induction cascade was shown to be dependent on the second messenger cyclic adenosine monophosphate (cAMP). Furthermore, we found that miR-155 directly targets the protein kinase A inhibitor alpha (PKIalpha) mRNA in its 3'UTR, indicative of a positive feedback mechanism on the cAMP pathway. Taken together, our study describes, in the context of an H. pylori infection, a direct link between Foxp3 and miR-155 in human T cells and highlights the significance of cAMP in this miR-155 induction cascade.

Effect of the earthworms Lumbricus terrestris and Aporrectodea caliginosa on bacterial diversity in soil.

Earthworms ingest large amounts of soil and have the potential to radically alter the biomass, activity, and structure of the soil microbial community. In this study, the diversity of eight bacterial groups from fresh soil, gut, and casts of the earthworms Lumbricus terrestris and Aporrectodea caliginosa were studied by single-strand conformation polymorphism (SSCP) analysis using both newly designed 16S rRNA gene-specific primer sets targeting Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Bacteroidetes, Verrucomicrobia, Planctomycetes, and Firmicutes and a conventional universal primer set for SSCP, with RNA and DNA as templates. In parallel, the study of the relative abundance of these taxonomic groups in the same samples was performed using fluorescence in situ hybridization. Bacteroidetes, Alphaproteobacteria, and Betaproteobacteria were predominant in communities from the soil and worm cast samples. Representatives of classes Flavobacteria and Sphingobacteria (Bacteroidetes) and Pseudomonas spp. (low-abundant Gammaproteobacteria) were detected in soil and worm cast samples with conventional and taxon-targeting SSCP and through the sequence analysis of 16S rRNA clone libraries. Physiologically active unclassified Sphingomonadaceae (Alphaproteobacteria) and Alcaligenes spp. (Betaproteobacteria) also maintained their diversities during transit through the earthworm intestine and were found on taxon-targeting SSCP profiles from the soil and worm cast samples. In conclusion, our results suggest that some specific bacterial taxonomic groups maintain their diversity and even increase their relative numbers during transit through the gastrointestinal tract of earthworms.

Molecular design of neutral intramolecular complexes bearing two silicon atoms anchored by a carbonyl oxygen atom: N,N'-bis(silylmethyl)propylene ureas.

B3LYP and MP2 computations have been performed on a variety of Si,Si'-substituted N,N'-bis(silylmethyl)propylene ureas. According to electron-density atoms-in-molecules (AIM) and electron localization function (ELF) quantum-topological analyses, a transition from the unstable non-chelate forms of these compounds to mono- and bis-chelate forms results in the successive interaction of one and two tetracoordinate silicon atoms with the carbonyl oxygen and the formation, respectively, of one and two covalent, polar Si...O bonds. This previously unknown X-Si<--O-->Si-X type of bonding in isomers possessing an anchor structure may be classified as a five-center, six-electron (5c-6e) bond. The factors that favor the existence of Si,Si'-substituted N,N'-bis(silylmethyl)propylene ureas exclusively in the form of stable, bridged complexes (the size of equatorial ligands and the electronegativity of axial substituents at the silicon atom, change in the donor capability of the carbonyl group, and effect of the polar solvent) are discussed.