Influence of the Z/E Isomerism on the Pathway Complexity of a Squaramide-Based Macrocycle.

The rising interest on pathway complexity in supramolecular polymerization has prompted the finding of novel monomer designs able to stabilize kinetically trapped species and generate supramolecular polymorphs. In the present work, the exploitation of the Z/E (geometrical) isomerism of squaramide (SQ) units to produce various self-assembled isoforms and complex supramolecular polymerization pathways in methylcyclohexane/CHCl3 mixtures is reported for the first time. This is achieved by using a new bissquaramidic macrocycle (MSq) that self-assembles into two markedly different thermodynamic aggregates, AggA (discrete cyclic structures) and AggB (fibrillar structures), depending on the solvent composition and concentration. Remarkably, UV-vis, 1 H NMR, and FT-IR experiments together with quantum-chemical calculations indicate that these two distinct aggregates are formed via two different hydrogen bonding patterns (side-to-side in AggA and head-to-tail in AggB) due to different conformations in the SQ units (Z,E in AggA and Z,Z in AggB). The ability of MSq to supramolecularly polymerize into two distinct aggregates is utilized to induce the kinetic-to-thermodynamic transformation from AggA to AggB, which occurs via an on-pathway mechanism. It is believed that this system provides new insights for the design of potential supramolecular polymorphic materials by using squaramide units.

Gold(I) Complexation of Phosphanoxy-Substituted Phosphaalkenes for Activation-Free LAuCl Catalysis.

The phosphanoxy-substituted phosphaalkene bearing the P=C-O-P skeleton can be prepared from diphosphene Mes*P=PMes* (Mes*=2,4,6-tBu3 C6 H2 ), and their use for catalysis is of interest. In this paper, complexation of the phosphanoxy-substituted phosphaalkenes with gold are investigated, and the catalytic activity of the mono- and bis(chlorogold) complexes are subsequently evaluated. Reaction of the P=C-O-P compound with (tht)AuCl (tht=tetrahydrothiophene) showed dominant coordination on the sp3 phosphorus, and complete coordination on the sp2 phosphorus required removal of tetrahydrothiophene. Atoms In Molecules (AIM) analysis based on the X-ray structure of the mono(chlorogold) complex indicated a pseudo coordinating interaction between the gold center and the P=C unit. The bis(chlorogold) complexes displayed conformational isomerism, and catalyzed the cycloisomerization/alkoxycyclization of 1,6-enyne and for hydration of terminal alkyne without activation treatment. Even the mono(chlorogold) complexes catalyzed the alkoxycyclization reactions without a silver co-catalyst, indicating that the alcohols were effective in activating the AuCl unit.

Quantifying Conformational Isomerism in Chain Molecules by Linear Raman Spectroscopy: The Case of Methyl Esters.

The conformational preferences of the ester group have the potential to facilitate the large amplitude folding of long alkyl chains in the gas phase. They are monitored by Raman spectroscopy in supersonic jet expansions for the model system methyl butanoate, after establishing a quantitative relationship with quantum-chemical predictions for methyl methanoate. This requires a careful analysis of experimental details, and a simulation of the rovibrational contours for near-symmetric top molecules. The technique is shown to be complementary to microwave spectroscopy in quantifying coexisting conformations. It confirms that a C-O-C(=O)-C-C chain segment can be collapsed into a single all-trans conformation by collisional cooling, whereas alkyl chain isomerism beyond this five-membered chain largely survives the jet expansion. This sets the stage for the investigation of linear alkyl alkanoates in terms of dispersion-induced stretched-chain to hairpin transitions by Raman spectroscopy.

Alpha-Carbonic Acid Revisited: Carbonic Acid Monomethyl Ester as a Solid and its Conformational Isomerism in the Gas Phase.

In this work, earlier studies reporting α-H2 CO3 are revised. The cryo-technique pioneered by Hage, Hallbrucker, and Mayer (HHM) is adapted to supposedly prepare carbonic acid from KHCO3 . In methanolic solution, methylation of the salt is found, which upon acidification transforms to the monomethyl ester of carbonic acid (CAME, HO-CO-OCH3 ). Infrared spectroscopy data both of the solid at 210 K and of the evaporated molecules trapped and isolated in argon matrix at 10 K are presented. The interpretation of the observed bands on the basis of carbonic acid [as suggested originally by HHM in their publications from 1993-1997 and taken over by Winkel et al., J. Am. Chem. Soc. 2007 and Bernard et al., Angew. Chem. Int. Ed. 2011] is inferior compared with the interpretation on the basis of CAME. The assignment relies on isotope substitution experiments, including deuteration of the OH- and CH3 - groups as well as 12 C and 13 C isotope exchange and on variation of the solvents in both preparation steps. The interpretation of the single molecule spectroscopy experiments is aided by a comprehensive calculation of high-level ab initio frequencies for gas-phase molecules and clusters in the harmonic approximation. This analysis provides evidence for the existence of not only single CAME molecules but also CAME dimers and water complexes in the argon matrix. Furthermore, different conformational CAME isomers are identified, where conformational isomerism is triggered in experiments through UV irradiation. In contrast to earlier studies, this analysis allows explanation of almost every single band of the complex spectra in the range between 4000 and 600 cm-1 .

Structural and Optical Properties of Metal-Nitrosyl Complexes.

The electronic, structural and optical properties (including Spin-Orbit Coupling) of metal nitrosyl complexes [M(CN)5(NO)]2- (M = Fe, Ru or Os) are investigated by means of Density Functional Theory, TD-DFT and MS-CASPT2 based on an RASSCF wavefunction. The energy profiles connecting the N-bound (η1-N), O-bound (η1-O) and side-on (η2-NO) conformations have been computed at DFT level for the closed shell singlet electronic state. For each structure, the lowest singlet and triplet states have been optimized in order to gain insight into the energy profiles describing the conformational isomerism in excited states. The energetics of the three complexes are similar-with the N-bound structure being the most stable-with one exception, namely the triplet ground state of the O-bound isomer for the iron complex. The conformation isomerism is highly unfavorable in the S0 electronic state with the occurrence of two energy barriers higher than 2 eV. The lowest bands of the spectra are assigned to MLCTNO/LLCTNO transitions, with an increasing MLCT character going from iron to osmium. Two low-lying triplet states, T1 (MLCTNO/LLCTNO) and T2 (MLCTNO/ILNO), seem to control the lowest energy profile of the excited-state conformational isomerism.

Cyclic Octamer Peptoids: Simplified Isosters of Bioactive Fungal Cyclodepsipeptides.

Cyclic peptoids have recently emerged as an important class of bioactive scaffolds with unique conformational properties and excellent metabolic stabilities. In this paper, we describe the design and synthesis of novel cyclic octamer peptoids as simplified isosters of mycotoxin depsipeptides bassianolide, verticilide A1, PF1022A and PF1022B. We also examine their complexing abilities in the presence of sodium tetrakis[3,5-bis(trifluoromethyl)phenyl]borate (TFPB) salt and explore their general insecticidal activity. Finally, we discuss the possible relationship between structural features of free and Na⁺-complexed cyclic octamer peptoids and bioactivities in light of conformational isomerism, a crucial factor affecting cyclic peptoids' biomimetic potentials.

Coarse-grained, foldable, physical model of the polypeptide chain.

Although nonflexible, scaled molecular models like Pauling-Corey's and its descendants have made significant contributions in structural biology research and pedagogy, recent technical advances in 3D printing and electronics make it possible to go one step further in designing physical models of biomacromolecules: to make them conformationally dynamic. We report here the design, construction, and validation of a flexible, scaled, physical model of the polypeptide chain, which accurately reproduces the bond rotational degrees of freedom in the peptide backbone. The coarse-grained backbone model consists of repeating amide and α-carbon units, connected by mechanical bonds (corresponding to ϕ and ψ) that include realistic barriers to rotation that closely approximate those found at the molecular scale. Longer-range hydrogen-bonding interactions are also incorporated, allowing the chain to readily fold into stable secondary structures. The model is easily constructed with readily obtainable parts and promises to be a tremendous educational aid to the intuitive understanding of chain folding as the basis for macromolecular structure. Furthermore, this physical model can serve as the basis for linking tangible biomacromolecular models directly to the vast array of existing computational tools to provide an enhanced and interactive human-computer interface.

Conformational isomerism in trans-3-methoxycinnamic acid: From solid to gas phase.

The rotational spectrum of laser ablated trans-3-methoxycinnamic acid has been observed in the 2-8 GHz range using chirped-pulse Fourier transform microwave spectroscopy coupled to a supersonic jet and adapted to support a laser ablation vaporization system (LA-CP-FTMW). Eight stable conformers were theoretically predicted to exist at B3LYP-D3BJ/6-311++(2d,p) level, all of which were experimentally detected. The experimental rotational parameters data evidence the essentially planar structures for all the conformers. The relative population distribution of conformers in the supersonic jet was investigated from relative intensity measurements. Cooling in the jet brings rotational temperatures close to 1 K for all the conformers. The theoretical predictions for the rotational constants and electric dipole moments show good agreement with the experimental constants and selection rules observed. The population distribution of conformers in the supersonic jet was found to be close to the equilibrium distribution calculated at temperatures lower than the stagnation temperature. Finally, the correlation of the observed conformers structures with those found in condensed phases was investigated.

Conformational Isomerism of trans-[Pt(NH2C6H11)2I2] and the Classical Wernerian Chemistry of [Pt(NH2C6H11)4]X2 (X = Cl, Br, I).

X-ray crystallographic analysis of the compound trans-[Pt(NH2C6H11)2I2] revealed the presence of two distinct conformers within one crystal lattice. This compound was studied by variable temperature NMR spectroscopy to investigate the dynamic interconversion between these isomers. The results of this investigation were interpreted using physical (CPK) and computational (molecular mechanics and density functional theory) models. The conversion of the salts [Pt(NH2C6H11)4]X2 into trans-[Pt(NH2C6H11)2X2] (X = Cl, Br, I) was also studied and is discussed here with an emphasis on parallels to the work of Alfred Werner.

Ab initio study on the six lowest energy conformers of iso-octane: conformational stability, barriers to internal rotation, natural bond orbital and first-order hyperpolarizability analyses, UV and NMR predictions, spectral temperature sensitivity, and scaled vibrational assignment.

In this paper, we present the quantum electronic study of iso-octane, based on MP2 and B3LYP methods using the 6-311++G(d,p) basis set. In addition to conformational stability and internal rotation barriers studies, the delocalization energies associated with the internal charge transfer (ICT) within each of the six lowest energy conformers were evaluated using NBO analysis. With the aim to differentiate even more between these conformers, the energy gap between HOMO and LUMO orbitals, chemical softness, and first-order hyperpolarizability (nonlinear optics property) were evaluated. Similarly, their spectral behavior was investigated at different levels; the ultraviolet (UV) absorption bands were assigned using molecular orbitals data obtained by TD-B3LYP calculations with 6-311++G(d,p) basis set, while carbon 13C NMR and proton 1H signal peaks were assigned using the GIAO-B3LYP/6-311++G(d,p) method. In addition, the normal mode calculations of the most and least stable conformers using a scaled force field in terms of nonredundant local symmetry coordinates were carried out to approach the vibrational spectra temperature dependency.

Involvement of conformational isomerism in the complexity of the crystal network of 1-(4-nitrophenyl)-1H-1,3-benzimidazole derivatives driven by C-H...A (A = NO2, Npy and π) and orthogonal Npy...NO2 and ONO...Csp2 interactions.

A detailed structural analysis of the benzimidazole nitroarenes 1-(4-nitrophenyl)-1H-1,3-benzimidazole, C13H9N3O2, (I), 1-(4-nitrophenyl)-2-phenyl-1H-1,3-benzimidazole, C19H13N3O2, (II), and 2-(3-methylphenyl)-1-(4-nitrophenyl)-1H-1,3-benzimidazole, C20H15N3O2, (III), has been performed. They are nonplanar structures whose crystal arrangement is governed by Csp2-H...A (A = NO2, Npy and π) hydrogen bonding. The inherent complexity of the supramolecular arrangements of compounds (I) (Z' = 2) and (II) (Z' = 4) into tapes, helices and sheets is the result of the additional participation of π-πNO2 and n-π* (n = O and Npy; π* = Csp2 and NNO2) interactions that contribute to the stabilization of the equi-energetic conformations adopted by each of the independent molecules in the asymmetric unit. In contrast, compound (III) (Z' = 1) is self-paired, probably due to the effect of the steric demand of the methyl group on the crystal packing. Theoretical ab initio calculations confirmed that the presence of the arene ring at the benzimidazole 2-position increases the rotational barrier of the nitrobenzene ring and also supports the electrostatic nature of the orthogonal ONO...Csp2 and Npy...NO2 interactions.

Structural and spectroscopic characterisation of C4 oxygenates relevant to structure/activity relationships of the hydrogenation of α,ß-unsaturated carbonyls.

In the present work, we have investigated the conformational isomerism and calculated the vibrational spectra of the C4 oxygenates: 3-butyne-2-one, 3-butene-2-one, 2-butanone and 2-butanol using density functional theory. The calculations are validated by comparison to structural data where available and new, experimental inelastic neutron scattering and infrared spectra of the compounds. We find that for 3-butene-2-one and 2-butanol the spectra show clear evidence for the presence of conformational isomerism and this is supported by the calculations. Complete vibrational assignments for all four molecules are provided and this provides the essential information needed to generate structure/activity relationships for the sequential catalytic hydrogenation of 3-butyne-2-one to 2-butanol.

Conformational isomerism of pyridoxal. Infrared matrix isolation and theoretical studies.

A combined matrix isolation FTIR and theoretical DFT/B3LYP/6-311++G(2p,2d) study of pyridoxal was performed. The calculations resulted in five stable PLHB conformers stabilized by intramolecular O-H⋯O bonding between phenolic OH and carbonyl C=O groups and another thirteen conformers in which OH or/and aldehyde groups are rotated by 180° around CO or/and CC bonds leading, respectively, to formation of PLO, PLA and PLOA conformers. The analysis of the spectra of the as-deposited matrix indicated that two most stable PLHB1 and PLHB2 conformers with intramolecular hydrogen bond are present in the matrix. The exposure of the PL/Ar matrix to mercury lamp radiation (λ>345 nm) induced conformational change of PLHB isomers to PLOA ones.

Conformational state of ß-hydroxynaphthylamides: Barriers for the rotation of the amide group around CN bond and dynamics of the morpholine ring.

Three ß-hydroxynaphthylamides (morpholine, pyrrolidine and dimethylamine derivatives) have been synthesized and their conformational state was analyzed by NMR, X-ray and DFT calculations. In aprotic solution the molecules contain intramolecular OHO hydrogen bonds, which change into intermolecular ones in solid state. The energy barriers for the amide group rotation around the CN bond were estimated from the line shape analysis of (1)H and (13)C NMR signals. A tentative correlation between the barrier height and the strength of OHO bond was proposed. Calculations of the potential energy profiles for the rotations around CC and CN bonds were done. In case of morpholine derivative experimental indications of additional dynamics: chair-chair 'ring flip' in combination with the twisting around CC bond were obtained and confirmed by quantum chemistry calculations.

Supramolecular self-organisation and conformational isomerism of a binuclear O,O'-dipropyl dithiophosphate gold(I) complex, [Au2{S2P(OC3H7)2}2]: Synthesis, (13)C and (31)P CP/MAS NMR spectroscopy, single-crystal X-ray diffraction study and thermal behaviour.

Crystalline one-dimensional polymeric catena-poly[bis(µ2-O,O'-dipropyldithiophosphato-S,S')digold(I)] (Au-Au) (1) was prepared and studied using (13)C and (31)P CP/MAS NMR spectroscopy and single-crystal X-ray diffraction. To elucidate the structural function of Dtph ligands in crystalline gold(I) O,O'-dipropyl dithiophosphate, the chemical shift anisotropy parameters (δaniso and η) were calculated from spinning sideband manifolds in (31)P MAS NMR spectra. A novel structure of the gold(I) compound comprises two isomeric, non-centrosymmetric binuclear molecules of [Au2{S2P(OC3H7)2}2] (isomers 'A' and 'B'), whose four Dtph groups display structural inequivalence. In each isomeric binuclear molecule of 1, a pair of µ2-bridging dipropyl Dtph ligands almost symmetrically links two neighbouring gold atoms, forming an extensive eight-membered metallocycle [Au2S4P2], while the intramolecular aurophilic Au⋯Au bond additionally stabilises this central cyclic moiety. At the supramolecular level of complex 1, intermolecular aurophilic Au⋯Au bonds yield almost linear infinite polymeric chains (⋯'A'⋯'B'⋯'A'⋯'B'⋯)n. The thermal behaviour of this compound was studied by the simultaneous thermal analysis (STA) technique (a combination of TG and DSC) under an argon atmosphere.

Development of a carbohydrate silylation method in ionic liquids for their gas chromatographic analysis.

This paper reports on the feasibility of silylation of low molecular weight carbohydrates dissolved in different ionic liquids (ILs) for their further analysis by gas chromatography (GC). Derivatization reagents (nature and amounts), temperature and time of reaction and stirring conditions were evaluated for different carbohydrates (i.e., glucose, mannose, fructose and lactose) dissolved in 1-ethyl-3-methylimidazolium dicyanamide [EMIM][DCA]. Evaluation of conformational isomerism of glucose dissolved in [EMIM][DCA] revealed the effect of the time of dissolution in the equilibration of α- and ß-furanoses (up to 3% and 6%, respectively, after 70 h of incubation) and that 21 h sufficed to obtain results similar to those provided by the reference method involving pyridine. Once optimized, the proposed derivatization procedure provided satisfactory yields (i.e., close to 100%) using 100 µL of trimethylsilylimidazole (TMSI) at mild conditions (25°C) for a relatively short time (1h) for most of the investigated carbohydrates. Under these experimental conditions, linear responses (i.e., R(2) better than 0.974) were obtained in the tested range of 0.25-1mg of the derivatized target compounds. Other reagents, such as N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA)+1% trimethylchlorosilane (TMCS), were successfully used under ultrasonic conditions for aldose monosaccharides and disaccharides derivatization, while BSTFA was useful for ketose monosaccharides. The possibility of using the proposed method for the derivatization of selected carbohydrates dissolved in different ILs and the efficiency of the method applied to the analysis of carbohydrates present in real samples (fruit juices) have also been investigated.

Five Stereoactive Orbitals on Silicon: Charge and Spin Localization in the n-Si4Me10(-•) Radical Anion by Trigonal Bipyramidalization.

RIUMP2/def2-TZVPPD calculations show that in addition to its usual conformation with charge and spin delocalized over the Si backbone, the isolated Si4Me10(-•) radical anion also has isomeric conformations with localized charge and spin. A structure with localization on a terminal Si atom has been examined in detail. In vacuum, it is calculated to lie 11.5 kcal/mol higher in energy than the charge-and-spin delocalized conformation, and in water the difference is as little as 1.6 kcal/mol. According to natural orbital and localized orbital analyses, the charge-and-spin-carrying terminal Si atom uses five stereoactive hybrid orbitals in a trigonal bipyramidal geometry. Four are built mostly from 3s and 3p atomic orbitals (AOs) and are used to attach a Si3(CH3)7 and three CH3 groups, whereas the larger equatorial fifth orbital is constructed from 4s and 4p AOs and acts as a nonbonding (radical) hybrid orbital with an occupancy of about 0.65 e.

Cytokinergic IgE Action in Mast Cell Activation.

Some 10 years ago it emerged that at sufficiently high concentrations certain monoclonal mouse IgEs exert previously unsuspected effects on mast cells. Thus they can both promote survival and induce activation of mast cells without the requirement for antigens. This was a wake up call that appears to have been missed (or dismissed) by the majority of immunologists. The structural attributes responsible for the potency of the so-called "highly cytokinergic" or HC IgEs have not yet been determined, but the events that ensue when such IgEs bind to the high-affinity receptor, FcεRI, on mast cells have been thoroughly studied, and are strikingly similar to those engendered by antigens when they form cross-linked complexes with the receptors. We review the evidence for the cytokinergic activity of IgE, and the structural features and known properties of immunoglobulins, and of IgE in particular, most likely to be implicated in the phenomenon. We suggest that IgEs with cytokinergic activity may be generated by local germinal center reactions in the target organs of allergy. We consider also the important implications that the existence of cytokinergic IgE may have for a fuller understanding of adaptive immunity and of the action of IgE in asthma and other diseases.