Ring Inversion Research Articles

Acenaphthylene‐Fused Cyclo[8]pyrroles with Intense Near‐IR‐Region Absorption Bands

An acenaphthylene-fused cyclo[8]pyrrole was synthesized by using an oxidative coupling reaction of the corresponding 2,2'-bipyrrole. Two conformational isomers 1 a and 1 b were isolated, and their molecular structures were elucidated by X-ray crystallographic studies. The less-polar and lower-symmetry 1 b isomer can be converted into the 1 a isomer through a thermal ring flip. Application of the perimeter model developed by Michl to magnetic circular dichroism spectroscopic data and theoretical calculations demonstrate that there is a marked redshift of the near-IR absorption maxima relative to cyclo[8]isoindole because there is a significant stabilization of the LUMO due to the differing effects of a fused ring expansion with acenaphthylene and benzene moieties on the frontier π molecular orbitals.

Outer generalized inverses with prescribed ideals

The outer inverse of a bounded linear operator on a Banach space is unique if we fix its range and nullspace. In this note we review several approaches to the uniqueness of the outer inverse in rings and explore the underlying idea of prescribing certain ideals in a way that mimics the operators case. Starting with Djordjevic and Wei -inverses, we show some connections with Mary’s inverse along an element and give a characterization of Drazin’s annihilator -inverse.

Synthesis, Characterization, and Photophysical Properties of Heteroleptic Copper(I) Complexes with Functionalized 3-(2′-Pyridyl)-1,2,4-triazole Chelating Ligands

A new series of mononuclear copper(I) complexes (1-9) with functionalized 3-(2'-pyridyl)-1,2,4-triazole chelating ligands, as well as the halide and/or phosphine ancillary ligands, have been synthesized. Complexes 1-9 were fully characterized by elemental analysis, NMR spectroscopy, mass spectroscopy, electronic absorption spectroscopy, fluorescence spectroscopy, cyclic voltammetry, and X-ray crystallography (1-8). They adopt a distorted tetrahedral configuration, and are considerably air-stable in solid state and in solution. All these Cu(I) complexes display a comparatively weak low-energy absorption in CH2Cl2 solution, assigned to charge-transfer transitions with appreciable MLCT character, as supported by TD-DFT studies. Cu(I) halide complexes 1-4 each shows bright solid-state emission at room temperature, although they are nonemissive in fluid solutions, in which the emission markedly depends on the halide and the substituent on the 2-pyridyl ring. Complexes 5-9 bearing 2-pyridyl functionalized 1,2,4-triazole and phosphine exhibit good photoluminescence properties in solution and solid states at ambient temperature, which are well-modulated via the alteration of the auxiliary phosphine ligand and the structural modification of 3-(2'-pyridyl)-1,2,4-triazole. Interestingly, cationic complex 6 and neutral derivative 7 can readily be interconverted through the ring inversion of the 1,2,4-triazolyl regulated by the NH ↔ N(-) transformation.

Slow Aromatic Ring Flips Detected Despite Near-Degenerate NMR Frequencies of the Exchanging Nuclei

Aromatic ring flips of Phe and Tyr residues are a hallmark of protein dynamics with a long history in molecular biophysics. Ring flips lead to symmetric exchange of nuclei between sites with distinct magnetic environments, which can be probed by NMR spectroscopy. Current knowledge of ring-flip rates originates from rare cases in which the chemical shift difference between the two sites is sufficiently large and the ring-flip rate sufficiently slow, typically kflip < 10(3) s(-1), so that separate peaks are observed in the NMR spectrum for the two nuclei, enabling direct measurement of the flip rate. By contrast, a great majority of aromatic rings show single peaks for each of the pairs of δ or ε nuclei, which commonly are taken as inferential evidence that the flip rate is fast, kflip < 10(3) s(-1), even though rate measurements have not been achieved. Here we report a novel approach that makes it possible to identify slow ring flips in previously inaccessible cases where only single peaks are observed. We demonstrate that Y21 in the bovine pancreatic trypsin inhibitor (BPTI) has a slow ring-flip rate, kflip < 100 s(-1), a result that contrasts with previous estimates of 10(4)-10(6) s(-1) inferred from the single-peak spectrum of Y21. Comparison with a recent 1 ms molecular dynamics trajectory of BPTI shows qualitative agreement and highlights the value of accurate aromatic ring flip data as an important benchmark for molecular dynamics simulations of proteins across wide time scales.

A theoretical study of the conformation and dynamic properties of 1,5-benzodiazepines and their derivatives

The geometries of eighteen 1,5-benzodiazepines including their oxo and thioxo derivatives have been calculated and compared with experimental geometries determined by X-ray crystallography using as property the methylene flip angle. Protonation of 3H-1,5-benzodiazepine lead to a planar quasi-aromatic cation. For the non-planar structures we have calculated ring inversion barriers that are well correlated with ten experimental values determined by Dynamic NMR allowing the establishment of an empirical equation for predicting new values.

The Archaeal Exosome: Identification and Quantification of Site-Specific Motions That Correlate with Cap and RNA Binding

The Archaeal Exosome: Identification and Quantification of Site-Specific Motions That Correlate with Cap and RNA Binding

Mechanistic Insights into the Bifunctional Non-Heme Iron Oxygenase Carbapenem Synthase by Active Site Saturation Mutagenesis

The carbapenem class of β-lactam antibiotics is known for its remarkable potency, antibacterial spectrum, and resistance to β-lactamase-mediated inactivation. While the biosynthesis of structurally "complex" carbapenems, such as thienamycin, share initial biochemical steps with carbapenem-3-carboxylate ("simple" carbapenem), the requisite inversion at C5 and formation of the characteristic α,β-unsaturated carboxylate are different in origin between the two groups. Here, we consider carbapenem synthase, a mechanistically distinct bifunctional non-heme iron α-ketoglutarate-dependent enzyme responsible for the terminal reactions, C5 epimerization and desaturation, in simple carbapenem production. Interestingly, this enzyme accepts two stereoisomeric substrates and transforms each to a common active antibiotic. Owing both to enzyme and product instability, resorting to saturation mutagenesis of active site and selected second-sphere residues gave clearly differing profiles of CarC tolerance to structural modification. Guided by a crystal structure and the mutational data, in silico docking was used to suggest the positioning of each disastereomeric substrate in the active site. The two orientations relative to the reactive iron-oxo center are manifest in the two distinct reactions, C5-epimerization and C2/3-desaturation. These observations favor a two-step reaction scheme involving two complete oxidative cycles as opposed to a single catalytic cycle in which an active site tyrosine, Tyr67, after hydrogen donation to achieve bicyclic ring inversion, is further hypothesized to serve as a radical carrier.

Silacyclohexanes and silaheterocyclohexanes—why are they so different from other heterocyclohexanes?

Stereochemical studies on silaheterocyclohexanes is a ‘hot topic’ as evidenced by the growing number of publications. During last 10 years a substantial number of substituted silacyclohexanes and heterocyclohexanes containing sulfur, oxygen or nitrogen as the second (or third) heteroatom have been synthesized and studied by variable temperature dynamic NMR spectroscopy, gas-phase electron diffraction, variable temperature IR, Raman, microwave spectroscopy with respect to thermodynamic (frozen conformational equilibria) and kinetic (barrier to ring inversion) information. As the stereochemistry of cyclohexane and its N-, O-, P-, S-hetero analogues is one of keystones of modern theoretical and synthetic organic and heterocyclic chemistry, the stereochemistry of silacyclohexane and its hetero analogs is an important element of theoretical and synthetic organosilicon chemistry. The various classes of saturated six-membered rings were critically compared and studied in detail with respect to differences in their stereochemistry and dynamic behavior.

Coordination Programming of Photofunctional Molecules

Our recent achievements relating to photofunctional molecules are addressed. Section 1 discloses a new concept of photoisomerization. Pyridylpyrimidine-copper complexes undergo a ring inversion that can be modulated by the redox state of the copper center. In combination with an intermolecular photoelectron transfer (PET) initiated by the metal-to-ligand charge transfer (MLCT) transition of the Cu(I) state, we realize photonic regulation of the ring inversion. Section 2 reports on the first examples of heteroleptic bis(dipyrrinato)zinc(II) complexes. Conventional homoleptic bis(dipyrrinato)zinc(II) complexes suffered from low fluorescence quantum yields, whereas the heteroleptic ones feature bright fluorescence even in polar solvents. Section 3 describes our new findings on Pechmann dye, which was first synthesized in 1882. New synthetic procedures for Pechmann dye using dimethyl bis(arylethynyl)fumarate as a starting material gives rise to its new structural isomer. We also demonstrate potentiality of a donor-acceptor-donor type of Pechmann dye in organic electronics.

Mixed-type reverse order laws for generalized inverses in rings with involution

Mixed-type reverse order laws for generalized inverses in rings with involution

DFT study of 1-, 4-, and 5-substituted 2-oxo-1,2,3,4-tetrahydropyrimidines: substituent steric and electronic effects, and ring flipping

Steric and the electronic effects caused by the substituents in the 1-, 4-, and 5-positions of substituted 2-oxo-1,2,3,4-tetrahydropyrimidines were investigated using density functional theory at the B3LYP/6-31++G(d,p) level. Results of this study show that the heterocyclic ring adopts a pseudo-boat conformation, in which the C4 and N1 atoms are deviated from ring planarity. The C4-substituent occupies a pseudo-axial position and the space orientation of the substituent depends on the type and position of the additional substituent in this aryl group. The heights of the C4 and N1 atoms from the boat plane and the orientation of 5-CO moiety toward the heterocyclic ring depend on the electronic and steric effects of the substituents in the various positions. Ring flip calculations for 4-phenyl substituent explain the extreme steric effect caused by the substituent in the 1-position. These calculations indicate the more favored pseudo-axial orientation of the phenyl group over the equatorial orientation.

1,3-Dimethyl-3-silapiperidine: Synthesis, Molecular Structure, and Conformational Analysis by Gas-Phase Electron Diffraction, Low Temperature NMR, IR and Raman Spectroscopy, and Quantum Chemical Calculations

The first Si-H-containing azasilaheterocycle, 1,3-dimethyl-3-silapiperidine 1, was synthesized, and its molecular structure and conformational properties were studied by gas-phase electron diffraction (GED), low temperature NMR, IR and Raman spectroscopy and quantum chemical calculations. The compound exists as a mixture of two conformers possessing the chair conformation with the equatorial NMe group and differing by axial or equatorial position of the SiMe group. In the gas phase, the SiMe(ax) conformer predominates (GED: ax/eq = 65(7):35(7)%, ΔG = 0.36(18) kcal/mol; IR: ax/eq = 62(5):38(5)%, ΔG = 0.16(7) kcal/mol). In solution, at 143 K the SiMe(eq) conformer predominates in the frozen equilibrium (NMR: ax/eq = 31.5(1.5):68.5(1.5)%, ΔG = -0.22(2) kcal/mol). Thermodynamic parameters of the ring inversion are determined (ΔG(‡) = 8.9-9.0 kcal/mol, ΔH(‡) = 9.6 kcal/mol, ΔS(‡) = 2.1 eu). High-level quantum chemical calculations (MP2, G2, CCSD(T)) nicely reproduce the experimental geometry and the predominance of the axial conformer in the gas phase.

Multireference calculations for ring inversion and double bond shifting in cyclooctatetraene

We present multireference calculations for the characterization of ring inversion and double bond shifting in cyclooctatetraene. The results show that it is necessary to treat the dynamical correlation very accurately to obtain correct values for the barrier heights. This can be done, for example, with multireference configuration interaction or with perturbation theory of third order. However, detailed analysis also shows that already a complete active space self-consistent field treatment describes the processes surprisingly well. Thus, this method could be used as a computationally cheap method, for example, for dynamics simulations.

Synthesis, characterization and dynamic NMR studies of a novel chalcone based N-substituted morpholine derivative

The synthesis of a novel chalcone based N-substituted morpholine derivative namely, (E)-1-(biphenyl-4-yl)-3-(4-(5-morpholinopentyloxy) phenyl) prop-2-en-1-one (BMPP), using a two step protocol is reported. The compound is characterized by FTIR, GC–MS and FTNMR spectroscopy techniques. Advanced 2D NMR techniques such as gradient enhanced COSY, HSQC, HMBC and NOESY were employed to establish through-bond and through-space correlations. Dynamic NMR measurements were carried out to obtain the energy barrier to ring inversion of the morpholine moiety.

Local chain mobility dependence on molecular structure in polyimides with bulky side groups: Correlation with gas separation properties

The effect of bulky side groups on the molecular mobility and chain packing of three polyimides derived from dianhydrides with m-terphenyl moieties and 2,4,6-trimethyl-m-phenylenediamine has been studied. Moreover, structure–properties relationships in terms of gas transport have been established. One of the polyimides has no side groups, while the other two have a t-butyl group in 5′ (meta) position on the central ring of the m-terphenyl moiety and one of them has also a pivaloylimino group placed in the 2′ (ortho) position. The changes in chain packing of the membranes were evidenced by wide angle X-ray diffraction (WAXS), whilst the molecular mobility was evaluated from the dielectric sub-ambient secondary relaxation, γ relaxation. The WAXS pattern of the polyimide containing both t-butyl and pivaloylimino side groups evidenced a greater degree of packing regularity than in the other two polyimides. Moreover, the additional pivaloylimino group strongly restricted the local molecular mobility associated with the phenylene-imide ring flips. On the other hand, the gas permeability of the polyimides strongly increased with the introduction of side groups. This increase was mainly related to the increase in the gas diffusivity, which could not be explained by an increase in fractional free volume (FFV). The results presented in this work indicate that the difference in gas diffusivity of the substituted polyimides is consistent with a difference in size distribution of free volume elements.

Equilibrium 2H/1H fractionation in organic molecules: III. Cyclic ketones and hydrocarbons

Quantitative interpretation of stable hydrogen isotope ratios (2H/1H) in organic compounds is greatly aided by knowledge of the relevant equilibrium fractionation factors (εeq). Previous efforts have combined experimental measurements and hybrid Density Functional Theory (DFT) calculations to accurately predict equilibrium fractionations in linear (acyclic) organic molecules (Wang et al., 2009a,b), but the calibration produced by that study is not applicable to cyclic compounds. Here we report experimental measurements of equilibrium 2H/1H fractionation in six cyclic ketones, and use those data to evaluate DFT calculations of fractionation in diverse monocyclic and polycyclic compounds commonly found in sedimentary organic matter and petroleum. At 25, 50, and 75°C, the experimentally measured εeq values for secondary and tertiary Hα in isotopic equilibrium with water are in the ranges of −130‰ to −150‰ and +10‰ to −40‰ respectively. Measured data are similar to DFT calculations of εeq for axial Hα but not equatorial Hα. In tertiary Cα positions with methyl substituents, this can be understood as a result of the methyl group forcing Hα atoms into a dominantly axial position. For secondary Cα positions containing both axial and equatorial Hα atoms, we propose that axial Hα exchanges with water significantly faster than the equatorial Hα does, due to the hyperconjugation-stabilized transition state. Interconversion of axial and equatorial positions via ring flipping is much faster than isotopic exchange at either position, and as a result the steady-state isotopic composition of both H’s is strongly weighted toward that of axial Hα. Based on comparison with measured εeq values, a total uncertainty of 10–30‰ remains for theoretical εeq values.Using DFT, we systematically estimated the εeq values for individual H positions in various cyclic structures. By summing over all individual H positions, the molecular equilibrium fractionation was estimated to be −75‰ to −95‰ for steroids, −90‰ to −105‰ for hopanoids, and −65‰ to −100‰ for typical cycloparaffins between 0 and 100°C relative to water. These are distinct from the typical biosynthetic fractionations of −150‰ to −300‰, but are similar to equilibrium fractionations for linear hydrocarbons (Wang et al., 2009b). Thus post-burial H exchange will generally remove the ∼50–100‰ biosynthetic fractionations between cyclic isoprenoid and n-alkyl lipid molecules, which can be used to evaluate the extent of H exchange in sedimentary organic matter and oils.

Detection of slow dynamics by solid‐state NMR: Application to L‐phenylalanine hydrochloride

AbstractNew methods for probing dynamical properties of biological macromolecules on the millisecond timescale will enable a better understanding of the structure–function relationship. In this article, three solid‐state NMR detection methods, line‐shape analysis, two‐dimensional exchange experiments, and a variant of the center‐band only detection of exchange (CODEX) experiment called R‐CODEX, are used to characterize a crystalline amino acid that serves as a model for motions in solid proteins, L‐phenylalanine hydrochloride. The millisecond ring flip motion of the aromatic ring in L‐phenylalanine hydrochloride is characterized in detail for the first time. Limitations of these experiments for processes involving submillisecond timescales are also discussed. © 2013 Wiley Periodicals, Inc. Concepts Magn Reson Part A 42A: 14–22, 2013.

Highly selective and efficient extraction of two Pb2+ ions with a p-tert-butylcalix[6]arene hexacarboxylic acid ligand: an allosteric effect in extraction

Solvent extraction behavior of p-tert-butylcalix[6]arene hexacarboxylic acid towards Pb2+ and other divalent transition metal ions has been studied to investigate the selectivity, extraction mechanism, stoichiometry of complexation and composition of the complex in the organic phase. Extractability and selectivity of the cyclic ligand were analyzed in comparison with the acyclic analog. The macrocyclic effect was genuinely operative and the size-match effect was the governing factor for cation selectivity. Accordingly, the cyclic ligand selectively extracted the Pb2+ ion in a pH range fairly more acidic than the acyclic ligand. The cations were extracted by ion exchange mechanism, and the electroneutral complexes were resulted by the exchange of two protons for a divalent cation. A molecule of p-tert-butyl calix[6]arene hexacarboxylic acid ligand extracted two Pb2+ ions. One Pb2+ was extracted due to the size-fit effect inside the hydrophilic cavity of calix[6]arene composed by phenoxy and carbonyl oxygen atoms. The macrocyclic ring inversion was obstructed due to guest encapsulation, and the encapsulated Pb2+ ion acted as a template for aggregation of the carboxyl groups. This binding event caused a positive allosteric effect and led to the extraction of the second Pb2+ ion at the aggregated functional group site.

Fluxional interconversion of divalent palladium complexes having NSNSN ligands between flexible SNS and rigid NNN-coordinated structures

Mono- and dicationic divalent palladium complexes having 2,6-bis(N-heteroarylsulfanylmethyl)pyridine ligands (NSNSN ligands) were synthesized and characterized. The NSNSN ligands were fixed in a rac-SNS tridentate coordination mode in the solid state, while the equilibria among meso-SNS, rac-SNS, and NNN isomers were observed in solution. The equilibrium between the SNS and NNN isomers could be modulated by temperature, as well as by the steric and electronic factors of the NSNSN and monodentate ligands. Lowering the temperature tended to make NNN isomers more predominant compared with SNS isomers. On the other hand, the steric demand between the ligands in the complexes shifted the equilibrium from NNN to SNS isomers. Introduction of pyridyl groups instead of pyrimidyl groups as N-heteroarenes also shifted the equilibrium to SNS isomers. DFT calculation indicated rapid ring inversion of the metallacycle moieties and relatively slow S-inversion in the SNS isomers, a result that was in good agreement with the experimentally observed dynamic behaviors. Both the experimental and theoretical results revealed that the SNS isomers had flexible structures in solution, whereas the NNN isomers were rigid and less dynamic. The mechanistic pathways for interconversion between SNS and NNN isomers were also calculated. Such calculations indicated that a pathway featuring a relatively unstable, distorted ax-SNN intermediate was plausible. The intermediate had an N-heteroarene on the coordinated sulfur atom at an axial position.

Conformational analysis of 2-acetylcyclopentanone by the density functional and MP2 methods

Two-dimensional potential energy surfaces for internal rotation of the acetyl substituent and inversion of the five-membered ring in the gas phase and in acetonitrile were constructed by the B3LYP/6-31G(d) method for the diketo form of the 2-acetylcyclopentanone (2-ACPN) molecule. The diketo form of 2-ACPN exists in the gas phase and in low-polarity cyclohexane as a mixture of four rotamers K1, K2, K3, and K4. The fifth isomeric form K3a exists in polar acetonitrile. The estimation of the tautomeric composition of 2-ACPN taking into account the influence of the cyclohexane medium in the framework of the polarizable continuum model (PCM) using the MP 2/cc-pVTZ method agrees better with experimental data than the estimate obtained by the B3LYP/cc-pVTZ method. The constants of the enol-enol and keto-enol tautomeric equilibria of the 2-ACPN tautomers in solutions of aprotic solvents were estimated.