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To circumvent time-consuming clinical trials, testing whether existing drugs are effective inhibitors of SARS-CoV-2, has led to the discovery of Remdesivir. We decided to follow this path and screened approved medications "off-label" against SARS-CoV-2. Fluoxetine inhibited SARS-CoV-2 at a concentration of 0.8 mu g/ml significantly in these screenings, and the EC50 was determined with 387 ng/ml. Furthermore, Fluoxetine reduced viral infectivity in precision-cut human lung slices showing its activity in relevant human tissue targeted in severe infections. Fluoxetine treatment resulted in a decrease in viral protein expression. Fluoxetine is a racemate consisting of both stereoisomers, while the S-form is the dominant serotonin reuptake inhibitor. We found that both isomers show similar activity on the virus, indicating that the R-form might specifically be used for SARS-CoV-2 treatment. Fluoxetine inhibited neither Rabies virus, human respiratory syncytial virus replication nor the Human Herpesvirus 8 or Herpes simplex virus type 1 gene expression, indicating that it acts virus-specific. Moreover, since it is known that Fluoxetine inhibits cytokine release, we see the role of Fluoxetine in the treatment of SARS-CoV-2 infected patients of risk groups.
In this communication, we demonstrate a novel approach to prepare a discrete dimer of chiral phthalocyanine (Pc) by exploiting the flexible molecular geometry of helicenes, which enables structural interlocking and strong aggregation tendency of Pcs. Synthesized [7]helicene-Pc hybrid molecular structure, zinc-[7]helicenocyanine (Zn-7HPc), exclusively forms a stable dimeric pair consisting of two homochiral molecules. The dimerization constants were estimated to be as high as 8.96×10\(^6\) M\(^{−1}\) and 3.42×107 M\(^{−1}\) in THF and DMSO, respectively, indicating remarkable stability of dimer. In addition, Zn\(^{-7}\)HPc exhibited chiral self-sorting behavior, which resulted in preferential formation of a homochiral dimer also in the racemic sample. Two phthalocyanine subunits in the dimeric form strongly communicate with each other as revealed by a large comproportionation constant and observation of an IV-CT band for the thermodynamically stable mixed-valence state.
Stereospecific Synthesis and Photophysical Properties of Propeller-Shaped C\(_{90}\)H\(_{48}\) PAH
(2019)
Herein, we have synthesized an enantiomerically pure propeller‐shaped PAH, C\(_{90}\)H\(_{48}\), possessing three [7]helicene and three [5]helicene subunits. This compound can be obtained in gram quantities in a straightforward manner. The photophysical and chiroptical properties were investigated using UV/Vis absorption and emission, optical rotation and circular dichroism spectroscopy, supported by DFT calculations. The nonlinear optical properties were investigated by two‐photon absorption measurements using linearly and circularly polarized light. The extremely twisted structure and packing of the homochiral compound were investigated by single‐crystal X‐ray diffraction analysis.
Marine organisms and their associated microbes are rich in diverse chemical leads. With the development of marine biotechnology, a considerable number of research activities are focused on marine bacteria and fungi-derived bioactive compounds. Marine bacteria and fungi are ranked on the top of the hierarchy of all organisms, as they are responsible for producing a wide range of bioactive secondary metabolites with possible pharmaceutical applications. Thus, they have the potential to provide future drugs against challenging diseases, such as cancer, a range of viral diseases, malaria, and inflammation. This review aims at describing the literature on secondary metabolites that have been obtained from Scleractinian-associated organisms including bacteria, fungi, and zooxanthellae, with full coverage of the period from 1982 to 2020, as well as illustrating their biological activities and structure activity relationship (SAR). Moreover, all these compounds were filtered based on ADME analysis to determine their physicochemical properties, and 15 compounds were selected. The selected compounds were virtually investigated for potential inhibition for SARS-CoV-2 targets using molecular docking studies. Promising potential results against SARS-CoV-2 RNA dependent RNA polymerase (RdRp) and methyltransferase (nsp16) are presented.
A Calix[4]arene‐Based Cyclic Dinuclear Ruthenium Complex for Light‐Driven Catalytic Water Oxidation
(2021)
A cyclic dinuclear ruthenium(bda) (bda: 2,2’‐bipyridine‐6,6’‐dicarboxylate) complex equipped with oligo(ethylene glycol)‐functionalized axial calix[4]arene ligands has been synthesized for homogenous catalytic water oxidation. This novel Ru(bda) macrocycle showed significantly increased catalytic activity in chemical and photocatalytic water oxidation compared to the archetype mononuclear reference [Ru(bda)(pic)\(_2\)]. Kinetic investigations, including kinetic isotope effect studies, disclosed a unimolecular water nucleophilic attack mechanism of this novel dinuclear water oxidation catalyst (WOC) under the involvement of the second coordination sphere. Photocatalytic water oxidation with this cyclic dinuclear Ru complex using [Ru(bpy)\(_3\)]Cl\(_2\) as a standard photosensitizer revealed a turnover frequency of 15.5 s\(^{−1}\) and a turnover number of 460. This so far highest photocatalytic performance reported for a Ru(bda) complex underlines the potential of this water‐soluble WOC for artificial photosynthesis.
Photocatalytic water oxidation is a promising process for the production of solar fuels and the elucidation of factors that influence this process is of high significance. Thus, we have studied in detail light‐driven water oxidation with a trinuclear Ru(bda) (bda: 2,2’‐bipyridine‐6,6’‐dicarboxylate) macrocycle MC3 and its highly water soluble derivative m‐CH\(_2\)NMe\(_2\)‐MC3 using a series of ruthenium tris(bipyridine) complexes as photosensitizers under varied reaction conditions. Our investigations showed that the catalytic activities of these Ru macrocycles are significantly affected by the choice of photosensitizer (PS) and reaction media, in addition to buffer concentration, light intensity and concentration of the sensitizer. Our steady‐state and transient spectroscopic studies revealed that the photocatalytic performance of trinuclear Ru(bda) macrocycles is not limited by their intrinsic catalytic activities but rather by the efficiency of photogeneration of oxidant PS\(^+\) and its ability to act as an oxidizing agent to the catalysts as both are strongly dependent on the choice of photosensitizer and the amount of employed organic co‐solvent.
Multimetallic complexes with extended and highly conjugated bis-2,2':6',2''-terpyridyl bridging ligands, which present building blocks for coordination polymers, are investigated with respect to their ability to act as light-harvesting antennae. The investigated species combine Ru(II)- with Os(II)- and Fe(II)-terpyridyl chromophores, the latter acting as energy sinks. Due to the extended conjugated system the ligands are able to prolong the lifetime of the \(^3\)MLCT states compared to unsubstituted terpyridyl species by delocalization and energetic stabilization of the \(^3\)MLCT states. This concept is applied for the first time to Fe(II) terpyridyl species and results in an exceptionally long lifetime of 23 ps for the Fe(II) \(^3\)MLCT state. While partial energy (>80%) transfer is observed between the Ru(II) and Fe(II) centers with a time-constant of 15 ps, excitation energy is transferred completely from the Ru(II) to the Os(II) center within the first 200 fs after excitation.
Boric acid (BA) has been used as a transparent glass matrix for optical materials for over 100 years. However, recently, apparent room-temperature phosphorescence (RTP) from BA (crystalline and powder states) was reported (Zheng et al., Angew. Chem. Int. Ed. 2021, 60, 9500) when irradiated at 280 nm under ambient conditions. We suspected that RTP from their BA sample was induced by an unidentified impurity. Our experimental results show that pure BA synthesized from B(OMe)\(_{3}\) does not luminesce in the solid state when irradiated at 250–400 nm, while commercial BA indeed (faintly) luminesces. Our theoretical calculations show that neither individual BA molecules nor aggregates would absorb light at >175 nm, and we observe no absorption of solid pure BA experimentally at >200 nm. Therefore, it is not possible for pure BA to be excited at >250 nm even in the solid state. Thus, pure BA does not display RTP, whereas trace impurities can induce RTP.
Designing highly efficient purely organic phosphors at room temperature remains a challenge because of fast non-radiative processes and slow intersystem crossing (ISC) rates. The majority of them emit only single component phosphorescence. Herein, we have prepared 3 isomers (o, m, p-bromophenyl)-bis(2,6-dimethylphenyl)boranes. Among the 3 isomers (o-, m- and p-BrTAB) synthesized, the ortho-one is the only one which shows dual phosphorescence, with a short lifetime of 0.8 ms and a long lifetime of 234 ms in the crystalline state at room temperature. Based on theoretical calculations and crystal structure analysis of o-BrTAB, the short lifetime component is ascribed to the T\(^M_1\) state of the monomer which emits the higher energy phosphorescence. The long-lived, lower energy phosphorescence emission is attributed to the T\(^A_1\) state of an aggregate, with multiple intermolecular interactions existing in crystalline o-BrTAB inhibiting nonradiative decay and stabilizing the triplet states efficiently.
The minimum energy path for the reaction O(\(^3\)P\(_g\)) + C\(_2\)H\(_4\)(\(^1\)A\(_g\)) has been calculated by optimizing all relevant geometrical parameters along the approach of oxygen to ethene. A barrier of 4.7 kcal/mol in the \(^3\)A"( ... 9a'\(^2\)- 10a'3a") potential energy surface and an energy difference of 14.4 kcal/mol between the product and the fragments is found at the multireference-configuration interaction level. The corresponding values at the lower-level treatment CASSCF are 9 kcal/mol for the barrier and 9 kcal/mol for the depth of the potential; this shows the importance of inclusion of electron correlation. The barrier for CH\(_2\) rotation for the lowestenergy structure (asymmetric OC\(_2\)H\(_4\)) is around 5 kcal/mol. The energy gap to the first excited state \(^3\)A'( ... 9a'l0a'3a'12) is found tobe 3.6 kcal/mol in MRD-CI calculations at the ground-state minimum. Comparison with \(^3\)CH\(_2\) + C\(_2\)H\(_4\) shows that in this system the lowest-energy surface is \(^3\)A', i.e., the state which is the excited state in 0 + C\(_2\)H\(_4\). This difference in energy ordering of \(^3\)A' and \(^3\)A" states results from the fact that the p\(_x\), p\(_y\), p\(_z\) degeneracy of oxygen orbitals is lifted in \(^3\)CH\(_2\)leading to b\(_1\), b\(_2\). and a\(_1\) MOs whereby the lowest b\(_2\) (a") remains doubly occupied; as a consequence, the reaction pattem between the oxygen and \(^3\)CH\(_2\) approach is different, which is also quite apparent in the calculated charge transfer.
The size-dependent exciton dynamics of one-dimensional aggregates of substituted perylene bisimides are studied by ultrafast transient absorption spectroscopy and kinetic Monte-Carlo simulations as a function of the excitation density and the temperature in the range of 25-90 degrees C. For low temperatures, the aggregates can be treated as infinite chains and the dynamics is dominated by diffusion-driven exciton-exciton annihilation. With increasing temperature the aggregates dissociate into small fragments consisting of very few monomers. This scenario is also supported by the time-dependent anisotropy deduced from polarization-dependent experiments.
The solvatochromic behavior of two donor-π bridge-acceptor (D-π-A) compounds based on the 2-(3-boryl-2-thienyl)thiazole π-linker and indandione acceptor moiety are investigated. DFT/TD-DFT calculations were performed in combination with steady-state absorption and emission measurements, along with electrochemical studies, to elucidate the effect of two different strongly electron-donating hydrazonyl units on the solvatochromic and fluorescence behavior of these compounds. The Lippert–Mataga equation was used to estimate the change in dipole moments (Δµ) between ground and excited states based on the measured spectroscopic properties in solvents of varying polarity with the data being supported by theoretical studies. The two asymmetrical D-π-A molecules feature strong solvatochromic shifts in fluorescence of up to ~4300 cm\(^{−1}\) and a concomitant change of the emission color from yellow to red. These changes were accompanied by an increase in Stokes shift to reach values as large as ~5700–5800 cm\(^{−1}\). Quantum yields of ca. 0.75 could be observed for the N,N-dimethylhydrazonyl derivative in nonpolar solvents, which gradually decreased along with increasing solvent polarity, as opposed to the consistently reduced values obtained for the N,N-diphenylhydrazonyl derivative of up to ca. 0.20 in nonpolar solvents. These two push–pull molecules are contrasted with a structurally similar acceptor-π bridge-acceptor (A-π-A) compound.
Genetic deficiency for acid sphingomyelinase or its pharmacological inhibition has been shown to increase Foxp3\(^+\) regulatory T-cell frequencies among CD4\(^+\) T cells in mice. We now investigated whether pharmacological targeting of the acid sphingomyelinase, which catalyzes the cleavage of sphingomyelin to ceramide and phosphorylcholine, also allows to manipulate relative CD4\(^+\) Foxp3\(^+\) regulatory T-cell frequencies in humans. Pharmacological acid sphingomyelinase inhibition with antidepressants like sertraline, but not those without an inhibitory effect on acid sphingomyelinase activity like citalopram, increased the frequency of Foxp3\(^+\) regulatory T cell among human CD4\(^+\) T cells in vitro. In an observational prospective clinical study with patients suffering from major depression, we observed that acid sphingomyelinase-inhibiting antidepressants induced a stronger relative increase in the frequency of CD4\(^+\) Foxp3\(^+\) regulatory T cells in peripheral blood than acid sphingomyelinase-non- or weakly inhibiting antidepressants. This was particularly true for CD45RA\(^-\) CD25\(^{high}\) effector CD4\(^+\) Foxp3\(^+\) regulatory T cells. Mechanistically, our data indicate that the positive effect of acid sphingomyelinase inhibition on CD4\(^+\) Foxp3\(^+\) regulatory T cells required CD28 co-stimulation, suggesting that enhanced CD28 co-stimulation was the driver of the observed increase in the frequency of Foxp3+ regulatory T cells among human CD4\(^+\) T cells. In summary, the widely induced pharmacological inhibition of acid sphingomyelinase activity in patients leads to an increase in Foxp3+ regulatory T-cell frequencies among CD4\(^+\) T cells in humans both in vivo and in vitro.
By introduction of four hydroxy (HO) groups into the two perylene bisimide (PBI) bay areas, new HO‐PBI ligands were obtained which upon deprotonation can complex ZnII ions and photosensitize semiconductive zinc oxide thin films. Such coordination is beneficial for dispersing PBI photosensitizer molecules evenly into metal oxide films to fabricate organic–inorganic hybrid interlayers for organic solar cells. Supported by the photoconductive effect of the ZnO:HO‐PBI hybrid interlayers, improved electron collection and transportation is achieved in fullerene and non‐fullerene polymer solar cell devices, leading to remarkable power conversion efficiencies of up to 15.95 % for a non‐fullerene based organic solar cell.
Homo- and heterochiral aggregation during crystallization of organic molecules has significance both for fundamental questions related to the origin of life as well as for the separation of homochiral compounds from their racemates in industrial processes. Herein, we analyse these phenomena at the lowest level of hierarchy - that is the self-assembly of a racemic mixture of (R,R)- and (S,S)-PBI into 1D supramolecular polymers. By a combination of UV/vis and NMR spectroscopy as well as atomic force microscopy, we demonstrate that homochiral aggregation of the racemic mixture leads to the formation of two types of supramolecular conglomerates under kinetic control, while under thermodynamic control heterochiral aggregation is preferred, affording a racemic supramolecular polymer. FT-IR spectroscopy and quantum-chemical calculations reveal unique packing arrangements and hydrogen-bonding patterns within these supramolecular polymers. Time-, concentration- and temperature-dependent UV/vis experiments provide further insights into the kinetic and thermodynamic control of the conglomerate and racemic supramolecular polymer formation. Homo- and heterochiral aggregation is a process of interest to prebiotic and chiral separation chemistry. Here, the authors analyze the self-assembly of a racemic mixture into 1D supramolecular polymers and find homochiral aggregation into conglomerates under kinetic control, while under thermodynamic control a racemic polymer is formed.
The discrimination of enantiomers by natural receptors is a well-established phenomenon. In contrast the number of synthetic receptors with the capability for enantioselective molecular recognition of chiral substrates is scarce and for chiral cyclophanes indicative for a preferential binding of homochiral guests. Here we introduce a cyclophane composed of two homochiral core-twisted perylene bisimide (PBI) units connected by p-xylylene spacers and demonstrate its preference for the complexation of [5]helicene of opposite helicity compared to the PBI units of the host. The pronounced enantio-differentiation of this molecular receptor for heterochiral guests can be utilized for the enrichment of the P-PBI-M-helicene-P-PBI epimeric bimolecular complex. Our experimental results are supported by DFT calculations, which reveal that the sterically demanding bay substituents attached to the PBI chromophores disturb the helical shape match of the perylene core and homochiral substrates and thereby enforce the formation of syndiotactic host-guest complex structures. Hence, the most efficient substrate binding is observed for those aromatic guests, e. g. perylene, [4]helicene, phenanthrene and biphenyl, that can easily adapt in non-planar axially chiral conformations due to their inherent conformational flexibility. In all cases the induced chirality for the guest is opposed to those of the embedding PBI units, leading to heterochiral host-guest structures.
Deracemization describes the conversion of a racemic mixture of a chiral molecule into an enantioenriched mixture or an enantiopure compound without structural modifications. Herein, we report an inherently chiral perylene bisimide (PBI) cyclophane whose chiral pocket is capable of transforming a racemic mixture of [5]‐helicene into an enantioenriched mixture with an enantiomeric excess of 66 %. UV/Vis and fluorescence titration studies reveal this cyclophane host composed of two helically twisted PBI dyes has high binding affinities for the respective homochiral carbohelicene guests, with outstanding binding constants of up to 3.9×10\(^{10}\) m\(^{-1}\) for [4]‐helicene. 2D NMR studies and single‐crystal X‐ray analysis demonstrate that the observed strong and enantioselective binding of homochiral carbohelicenes and the successful template‐catalyzed deracemization of [5]‐helicene can be explained by the enzyme‐like perfect shape complementarity of the macrocyclic supramolecular host.
β-glucans are well-known modulators of the immune system in mammals but little is known about β-glucan triggered immunity in planta. Here we show by isothermal titration calorimetry, circular dichroism spectroscopy and nuclear magnetic resonance spectroscopy that the FGB1 gene from the root endophyte Piriformospora indica encodes for a secreted fungal-specific β-glucan-binding lectin with dual function. This lectin has the potential to both alter fungal cell wall composition and properties, and to efficiently suppress β-glucan-triggered immunity in different plant hosts, such as Arabidopsis, barley and Nicotiana benthamiana. Our results hint at the existence of fungal effectors that deregulate innate sensing of β-glucan in plants.
Decandrinin (1), an unprecedented \(C_9\)-spiro-fused 7,8-\(seco-ent\)-abietane, was obtained from the bark of an Indian mangrove, \(Ceriops\ decandra\), collected in the estuary of Godavari, Andhra Pradesh. The constitution and the relative configuration of 1 were determined by HRMS (ESI) and extensive NMR investigations, and the absolute configuration by circular dichroism (CD) and optical-rotatory dispersion (ORD) spectroscopy in combination with quantum-chemical calculations. Decandrinin is the first 7,8-\(seco-ent\)-abietane.
A protecting group strategy was employed to synthesise a series of indolenine squaraine dye oligomers up to the nonamer. The longer oligomers show a distinct solvent dependence of the absorption spectra, that is, either a strong blue shift or a strong red shift of the lowest energy bands in the near infrared spectral region. This behaviour is explained by exciton coupling theory as being due to H- or J-type coupling of transition moments. The H-type coupling is a consequence of a helix folding in solvents with a small Hansen dispersity index. DOSY NMR, small angle neutron scattering (SANS), quantum chemical and force field calculations agree upon a helix structure with an unusually large pitch and open voids that are filled with solvent molecules, thereby forming a kind of clathrate. The thermodynamic parameters of the folding process were determined by temperature dependent optical absorption spectra.
A series of seven unusual dimeric naphthylisoquinoline alkaloids was isolated from the leaves of the tropical liana Ancistrocladus ealaensis J. Léonard, named cyclombandakamine A (1), 1-epi-cyclombandakamine A (2), and cyclombandakamines A3–7 (3–7). These alkaloids have a chemically thrilling structural array consisting of a twisted dihydrofuran-cyclohexenone-isochromene system. The 1′″-epimer of 4, cyclombandakamine A1 (8), had previously been discovered in an unidentified Ancistrocladus species related to A. ealaensis. Both lianas produce the potential parent precursor, mbandakamine A (9), but only A. ealaensis synthesizes the corresponding cyclized form, along with a broad series of slightly modified analogs. The challenging isolation required, besides multi-dimensional chromatography, the use of a pentafluorophenyl stationary phase. Featuring up to six stereocenters and two types of chiral axes, their structures were elucidated by means of 1D and 2D NMR, HRESIMS, in combination with oxidative chemical degradation experiments as well as chiroptical (electronic circular dichroism spectroscopy) and quantum chemical calculations. Compared to the ‘open-chain’ parent compound 9, these dimers displayed rather moderate antiplasmodial activities.
Three unusual heterodimeric naphthylisoquinoline alkaloids, named ealapasamines A-C (1–3), were isolated from the leaves of the tropical plant Ancistrocladus ealaensis J. Léonard. These ‘mixed’, constitutionally unsymmetric dimers are the first stereochemically fully assigned cross-coupling products of a 5,8′- and a 7,8′-coupled naphthylisoquinoline linked via C-6′ in both naphthalene portions. So far, only two other West and Central Ancistrocladus species were known to produce dimers with a central 6,6″-axis, yet, in contrast to the ealapasamines, usually consisting of two 5,8′-coupled monomers, like e.g., in michellamine B. The new dimers 1–3 contain six elements of chirality, four stereogenic centers and the two outer axes, while the central biaryl axis is configurationally unstable. The elucidation of the complete stereostructures of the ealapasamines was achieved by the interplay of spectroscopic methods including HRESIMS, 1D and 2D NMR (in particular ROESY measurements), in combination with chemical (oxidative degradation) and chiroptical (electronic circular dichroism) investigations. The ealapasamines A-C display high antiplasmodial activities with excellent half-maximum inhibition concentration values in the low nanomolar range.
Depending on the connectivity of solubilizing oligoethylene glycol (OEG) side chains to the π‐cores of amphiphilic naphthalene and perylene bisimide dyes, self‐assembly in water occurs either upon heating or cooling. Herein, we show that this effect originates from differences in the enwrapping capability of the π‐cores by the OEG chains. Rylene bisimides bearing phenyl substituents with three OEG chains attached directly to the hydrophobic π‐cores are strongly sequestered by the OEG chains. These molecules self‐assemble at elevated temperatures in an entropy‐driven process according to temperature‐ and concentration‐dependent UV/Vis spectroscopy and calorimetric dilution studies. In contrast, for rylene bisimides in which phenyl substituents with three OEG chains are attached via a methylene spacer, leading to much weaker sequestration, self‐assembly originates upon cooling in an enthalpy‐driven process. Our explanation for this controversial behavior is that the aggregation in the latter case is dictated by the release of “high energy water” from the hydrophobic π‐surfaces as well as dispersion interactions between the π‐scaffolds which drive the self‐assembly in an enthalpically driven process. In contrast, for the former case we suggest that in addition to the conventional explanation of a dehydration of hydrogen‐bonded water molecules from OEG units it is in particular the increase in conformational entropy of back‐folded OEG side chains upon aggregation that provides the pronounced gain in entropy that drives the aggregation process. Thus, our studies revealed that a subtle change in the attachment of solubilizing substituents can switch the thermodynamic signature for the self‐assembly of amphiphilic dyes in water from enthalpy‐ to entropy‐driven.
Density functional theory is applied to the calculation ofthe isotropic byperfine coupJing constants in some small molecules. Various functionals are tested. The agreement of the calculated values to experimental data and values obtained from sophisticated ab initio methods depends on the functionals used and the system under consideration. With respect to spin density calculations the functional of Lee, Yang and Parr with Becke's excbange functional (BLYP) is found to give good results for tbe heavier center of the CH and the NH molecule, while the spin densities of other molecules such as OH, H\(_2\)CN, H\(_2\)CO\(^+\), NO and O\(_2\) deviate considerably from experimental and/or other theoretical results (30%-60%). In cases where the singly occupied orbital can contribute to the isotropic hyperfine coupling constants, accurate results are obtained. The reason fortbis is analyzed.
The hyperfine structures of the isoelectronic molecules CCO. CNN, and NCN in their triplet ground states (X\(^3 \sum ^-\)) are investigated by means of ab initio methods. The infrared frequencies and geometries are detennined and compared with experiment. Configuration selected multireference configuration interaction calculations in combination with perturbation theory to correct the wave function (MRD-CI/B\(_K\)) employing extended atomic orbital (AO) basis sets yielded very accurate hyperfine properties. The theoretical values for CCO are in excellent agreement with the experimental values determined by Smith and Weltner [J. Chem. Phys. 62,4592 (1975)]. For CNN, the first assignment of Smith and Weltner for the two nitrogen atoms has to be changed. A qualitative discussion of the electronic structure discloses no simple relation between the structure of the singly occupied orbitals and the measured hyperfine coupling constants. Vibrational effects were found to be of little importance.
The hyperfine structure of the two isoelectronic molecules H\(_2\)CN and H\(_2\)CO\(^+\) in their electronic ground state (X\(^2\)B\(_2\)) is studied. The influence of the atomic orbital (AO), basis sets, of the correlation treatment, and of the. equilibrium geometry on the obtained hyperfine propertles 1s - investigated. It is found that the multireference double excitation-configuration interaction (MRD-CI)/ BK treatment in which an MRD-CI wave function is corrected by a modified B\(_K\) method yields equivalent results to quadratic CI [QCISD(T)], coupled cluster single doubles [CCSD(T)), or Brueckner doubled [BD(T)]. Uncertainties in the equilibrium geometries are found to be the major source for discrepancies between theoretically and experimentally determined isotropic hyperfine coupling constants (hfccs). For the heavier centers, the calculated values of the isotropic hfccs agrees nearly perfectly with experimental values (\(\approx\) 1%-2%). The calculated values for the hydrogens are too low, but using the equilibrium structure suggested by Yamamoto and Sato [J. Chem. Phys. 96, 4157 ( 1992)], the best estimate deviates by less than 3%.
Ever since the discovery of dye self-assemblies in nature, there have been tremendous efforts to exploit biomimetic supramolecular assemblies for tailored artificial photon processing materials. This feature necessarily has resulted in an increasing demand for understanding exciton dynamics in the dye self-assemblies. In a sharp contrast with pi-type aggregates, however, the detailed observation of exciton dynamics in H-type aggregates has remained challenging. In this study, as we succeed in measuring transient fluorescence from Frenkel state of π-stacked perylene tetracarboxylic acid bisimide dimer and oligomer aggregates, we present an experimental demonstration on Frenkel exciton dynamics of archetypal columnar π-π stacks of dyes. The analysis of the vibronic peak ratio of the transient fluorescence spectra reveals that unlike the simple π-stacked dimer, the photoexcitation energy in the columnar π-stacked oligomer aggregates is initially delocalized over at least three molecular units and moves coherently along the chain in tens of femtoseconds, preceding excimer formation process.
Activating Organic Phosphorescence via Heavy Metal–π Interaction Induced Intersystem Crossing
(2022)
Heavy‐atom‐containing clusters, nanocrystals, and other semiconductors can sensitize the triplet states of their surface‐bonded chromophores, but the energy loss, such as nonradiative deactivation, often prevents the synergistic light emission in their solid‐state coassemblies. Cocrystallization allows new combinations of molecules with complementary properties for achieving functionalities not available in single components. Here, the cocrystal formation that employs platinum(II) acetylacetonate (Pt(acac)\(_{2}\)) as a triplet sensitizer and electron‐deficient 1,4,5,8‐naphthalene diimides (NDIs) as organic phosphors is reported. The hybrid cocrystals exhibit room‐temperature phosphorescence confined in the low‐lying, long‐lived triplet state of NDIs with photoluminescence (PL) quantum yield (Φ\(_{PL}\)) exceeding 25% and a phosphorescence lifetime (τ\(_{Ph}\)) of 156 µs. This remarkable PL property benefits from the noncovalent electronic and spin–orbital coupling between the constituents.
The aim is to evaluate the effect of modifying poly[(L-lactide)-co-(epsilon-caprolactone)] scaffolds (PLCL) with nanodiamonds (nDP) or with nDP+physisorbed BMP-2 (nDP+BMP-2) on in vivo host tissue response and degradation. The scaffolds are implanted subcutaneously in Balb/c mice and retrieved after 1, 8, and 27 weeks. Molecular weight analysis shows that modified scaffolds degrade faster than the unmodified. Gene analysis at week 1 shows highest expression of proinflammatory markers around nDP scaffolds; although the presence of inflammatory cells and foreign body giant cells is more prominent around the PLCL. Tissue regeneration markers are highly expressed in the nDP+BMP-2 scaffolds at week 8. A fibrous capsule is detectable by week 8, thinnest around nDP scaffolds and at week 27 thickest around PLCL scaffolds. mRNA levels of ALP, COL1 alpha 2, and ANGPT1 are signifi cantly upregulating in the nDP+BMP-2 scaffolds at week 1 with ectopic bone seen at week 8. Even when almost 90% of the scaffold is degraded at week 27, nDP are observable at implantation areas without adverse effects. In conclusion, modifying PLCL scaffolds with nDP does not aggravate the host response and physisorbed BMP-2 delivery attenuates infl ammation while lowering the dose of BMP-2 to a relatively safe and economical level.
This study aimed to evaluate the tumorigenic potential of functionalising poly(LLA-co-CL) scaffolds. The copolymer scaffolds were functionalised with nanodiamonds (nDP) or with nDP and physisorbed BMP-2 (nDP-PHY) to enhance osteoinductivity. Culturing early neoplastic dysplastic keratinocytes (DOK\(^{Luc}\)) on nDP modified scaffolds reduced significantly their subsequent sphere formation ability and decreased significantly the cells' proliferation in the supra-basal layers of in vitro 3D oral neoplastic mucosa (3D-OT) when compared to DOK\(^{Luc}\) previously cultured on nDP-PHY scaffolds. Using an in vivo non-invasive environmentally-induced oral carcinogenesis model, nDP scaffolds were observed to reduce bioluminescence intensity of tumours formed by DOK\(^{Luc}\) + carcinoma associated fibroblasts (CAF). nDP modification was also found to promote differentiation of DOK\(^{Luc}\) both in vitro in 3D-OT and in vivo in xenografts formed by DOKLuc alone. The nDP-PHY scaffold had the highest number of invasive tumours formed by DOK\(^{Luc}\) + CAF outside the scaffold area compared to the nDP and control scaffolds. In conclusion, in vitro and in vivo results presented here demonstrate that nDP modified copolymer scaffolds are able to decrease the tumorigenic potential of DOK\(^{Luc}\), while confirming concerns for the therapeutic use of BMP-2 for reconstruction of bone defects in oral cancer patients due to its tumour promoting capabilities.
Single crystals of three at bay area tetraphenoxy‐substituted perylene bisimide dyes are grown by vacuum sublimation. X‐ray analysis reveals the self‐assembly of these highly twisted perylene bisimides (PBIs) in the solid state via imide–imide hydrogen bonding into hydrogen‐bonded PBI chains. The crystallographic insights disclose that the conformation and sterical congestion imparted by the phenoxy substituents can be controlled by ortho‐substituents. Accordingly, whilst sterically less demanding methyl and isopropyl substituents afford double‐stranded PBI chains of complementary P and M atropo‐enantiomers, single hydrogen‐bonded chains of homochiral PBIs are observed for the sterically more demanding ortho‐phenyl substituents. Investigation of the absorption and fluorescence properties of microcrystals and thin films of these PBIs allow for an unambiguous interpretation of these exciton systems. Thus, the J‐aggregates of the double‐stranded crystals exhibit a much larger (negative) exciton coupling than the single‐stranded one, which in contrast has the higher solid‐state fluorescence quantum yield.
RNA aptamers form compact tertiary structures and bind their ligands in specific binding sites. Fluorescence-based strategies reveal information on structure and dynamics of RNA aptamers. Here we report the incorporation of the universal emissive nucleobase analog 4-cyanoindole into the fluorogenic RNA aptamer Chili, and its application as a donor for supramolecular FRET to bound ligands DMHBI+ or DMHBO+. The photophysical properties of the new nucleobase-ligand-FRET pair revealed structural restraints for the overall RNA aptamer organization and identified nucleotide positions suitable for FRET-based readout of ligand binding. This strategy is generally suitable for binding site mapping and may also be applied for responsive aptamer devices.
Structure-fluorescence activation relationships of a large Stokes shift fluorogenic RNA aptamer
(2019)
The Chili RNA aptamer is a 52 nt long fluorogen-activating RNA aptamer (FLAP) that confers fluorescence to structurally diverse derivatives of fluorescent protein chromophores. A key feature of Chili is the formation of highly stable complexes with different ligands, which exhibit bright, highly Stokes-shifted fluorescence emission. In this work, we have analyzed the interactions between the Chili RNA and a family of conditionally fluorescent ligands using a variety of spectroscopic, calorimetric and biochemical techniques to reveal key structure - fluorescence activation relationships (SFARs). The ligands under investigation form two categories with emission maxima of ~540 nm or ~590 nm, respectively, and bind with affinities in the nanomolar to low-micromolar range. Isothermal titration calorimetry was used to elucidate the enthalpic and entropic contributions to binding affinity for a cationic ligand that is unique to the Chili aptamer. In addition to fluorescence activation, ligand binding was also observed by NMR spectroscopy, revealing characteristic signals for the formation of a G-quadruplex only upon ligand binding. These data shed light on the molecular features required and responsible for the large Stokes shift and the strong fluorescence enhancement of red and green emitting RNA-chromophore complexes.
No abstract available
Results ofan ab initio study ofthe hyperfine structure of the X\(^2\)A', A\(^2\) A" ( 1\(^2 \Pi\)) system ofthe formyl radical are presented. Special attention is paid to the analysis of the interplay between the vibronic and magnetic hyperfine etfects. The results of computations are in very good agreement with the available experimental findings. The values for the hyperfine coupling constants in lower bending Ievels of both electronic species are predicted.
Cofacial positioning of two perylene bisimide (PBI) chromophores at a distance of 6.5 angstrom in a cyclophane structure prohibits the otherwise common excimer formation and directs photoexcited singlet state relaxation towards intramolecular symmetry-breaking charge separation (τ\(_{CS}\) = 161 +/- 4 ps) in polar CH\(_2\)Cl\(_2\), which is thermodynamically favored with a Gibbs free energy of ΔG\(_{CS}\) = -0.32 eV. The charges then recombine slowly in τ\(_{CR}\) = 8.90 +/- 0.06 ns to form the PBI triplet excited state, which can be used subsequently to generate singlet oxygen in 27% quantum yield. This sequence of events is eliminated by dissolving the PBI cyclophane in non-polar toluene, where only excited singlet state decay occurs. In contrast, complexation of electron-rich aromatic hydrocarbons by the host PBI cyclophane followed by photoexcitation of PBI results in ultrafast electron transfer (<10 ps) from the guest to the PBI in CH\(_2\)Cl\(_2\). The rate constants for charge separation and recombination increase as the guest molecules become easier to oxidize, demonstrating that charge separation occurs close to the peak of the Marcus curve and the recombination lies far into the Marcus inverted region.
Obligate human pathogenic Neisseria gonorrhoeae are the second most frequent bacterial cause of sexually transmitted diseases. These bacteria invade different mucosal tissues and occasionally disseminate into the bloodstream. Invasion into epithelial cells requires the activation of host cell receptors by the formation of ceramide-rich platforms. Here, we investigated the role of sphingosine in the invasion and intracellular survival of gonococci. Sphingosine exhibited an anti-gonococcal activity in vitro. We used specific sphingosine analogs and click chemistry to visualize sphingosine in infected cells. Sphingosine localized to the membrane of intracellular gonococci. Inhibitor studies and the application of a sphingosine derivative indicated that increased sphingosine levels reduced the intracellular survival of gonococci. We demonstrate here, that sphingosine can target intracellular bacteria and may therefore exert a direct bactericidal effect inside cells.
A bis(squaraine) dye equipped with alkyl and oligoethyleneglycol chains was synthesized by connecting two dicyanomethylene substituted squaraine dyes with a phenylene spacer unit. The aggregation behavior of this bis(squaraine) was investigated in non-polar toluene/tetrachloroethane (98:2) solvent mixture, which revealed competing cooperative self-assembly pathways into two supramolecular polymorphs with entirely different packing structures and UV/Vis/NIR absorption properties. The self-assembly pathway can be controlled by the cooling rate from a heated solution of the monomers. For both polymorphs, quasi-equilibrium conditions between monomers and the respective aggregates can be established to derive thermodynamic parameters and insights into the self-assembly mechanisms. AFM measurements revealed a nanosheet structure with a height of 2 nm for the thermodynamically more stable polymorph and a tubular nanorod structure with a helical pitch of 13 nm and a diameter of 5 nm for the kinetically favored polymorph. Together with wide angle X-ray scattering measurements, packing models were derived: the thermodynamic polymorph consists of brick-work type nanosheets that exhibit red-shifted absorption bands as typical for J-aggregates, while the nanorod polymorph consists of eight supramolecular polymer strands of the bis(squaraine) intertwined to form a chimney-type tubular structure. The absorption of this aggregate covers a large spectral range from 550 to 875 nm, which cannot be rationalized by the conventional exciton theory. By applying the Essential States Model and considering intermolecular charge transfer, the aggregate spectrum was adequately reproduced, revealing that the broad absorption spectrum is due to pronounced donor-acceptor overlap within the bis(squaraine) nanorods. The latter is also responsible for the pronounced bathochromic shift observed for the nanosheet structure as a result of the slip-stacked arranged squaraine chromophores.
Herein, we report the one-pot synthesis of an electron-poor nanographene containing dicarboximide groups at the corners. We efficiently combined palladium-catalyzed Suzuki-Miyaura cross-coupling and dehydrohalogenation to synthesize an extended two-dimensional pi-scaffold of defined size in a single chemical operation starting from N-(2,6-diisopropylphenyl)-4,5-dibromo-1,8-naphthalimide and a tetrasubstituted pyrene boronic acid ester as readily accessible starting materials. The reaction of these precursors under the conditions commonly used for Suzuki-Miyaura cross-coupling afforded a C\(_{64}\) nanographene through the formation of ten C-C bonds in a one-pot process. Single-crystal X-ray analysis unequivocally confirmed the structure of this unique extended aromatic molecule with a planar geometry. The optical and electrochemical properties of this largest ever synthesized planar electron-poor nanographene skeleton were also analyzed.
A highly strained covalent organic cage compound was synthesized from hexahydroxy tribenzotriquinacene (TBTQ) and a meta-terphenyl-based diboronic acid with an additional benzoic acid substituent in 2’-position. Usually, a 120° bite angle in the unsubstituted ditopic linker favors the formation of a [4+6] cage assembly. Here, the introduction of the benzoic acid group is shown to lead to a perfectly preorganized circular hydrogen-bonding array in the cavity of a trigonal-bipyramidal [2+3] cage, which energetically overcompensates the additional strain energy caused by the larger mismatch in bite angles for the smaller assembly. The strained cage compound was analyzed by mass spectrometry and \(^{1}\)H, \(^{13}\)C and DOSY NMR spectroscopy. DFT calculations revealed the energetic contribution of the hydrogen-bonding template to the cage stability. Furthermore, molecular dynamics simulations on early intermediates indicate an additional kinetic effect, as hydrogen bonding also preorganizes and rigidifies small oligomers to facilitate the exclusive formation of smaller and more strained macrocycles and cages.
Many dyes suffer from fast non-radiative decay pathways, thereby showing only short-lived excited states and weak photoluminescence. Here we show a pronounced fluorescence enhancement for a weakly fluorescent merocyanine (MC) dye by being co-facially stacked to other dyes in hetero-folda-trimer architectures. By means of fluorescence spectroscopy (lifetime, quantum yield) the fluorescence enhancement was explained by the rigidification of the emitting chromophore in the defined foldamer architecture and the presence of a non-forbidden lowest exciton state in H-coupled hetero-aggregates. This folding-induced fluorescence enhancement (FIFE) for specific sequences of π-stacked dyes points at a viable strategy toward improved fluorophores that relates to the approach used by nature in the green fluorescent protein (GFP).
The ongoing transition from fossil to renewable feedstocks demands new efficient processes for an economically viable production of biomass‐derived commodities and fine chemicals. Novel energy‐ and material‐efficient product purification and separation will play a crucial role due to altered product and feed composition. The present study comprises the synthesis and tests of cross‐linked p‐vinylphenylboronate polymers for the separation of 18 diols, sugar alcohols, and saccharides, which can be obtained during biomass processing. The separation was based on molecular recognition, that is, esterification of the phenylboronate with vicinal diols. A correlation of the molecular complexation constant, the polymer swelling, and the maximum adsorption capacity was found. The adsorption curves over time were recorded. Preliminary results on competitive adsorption of binary mixtures showed a high potential for the separation of substrates with significantly different complexation constants. Desorption tests implied easier desorption of substrates that only adsorb on the outer polymer shell.
No abstract available
Palladium‐catalyzed [5+2] annulation of 1‐boraphenalenes with ortho‐dihaloarenes afforded negatively curved π‐extended pleiadienes. Two benzo[1,2‐i:4,5‐i’]dipleiadienes (BDPs) featuring a seven‐six‐seven‐membered ring arrangement were synthesized and investigated. Their crystal structure revealed a unique packing arrangement and theoretical calculations were employed to shed light onto the dynamic behavior of the BDP moiety and its aromaticity. Further, a naphthalene‐fused pleiadiene was stitched together by oxidative cyclodehydrogenation to yield an additional five‐membered ring. This formal azulene moiety led to distinct changes in optical and redox properties and increased perturbation of the aromatic system.
Utilizing Pd‐catalyzed [5+2] annulation a series of heptagon‐extended corannulenes could be synthesized from a borinic acid precursor furnished by C−H borylation strategy. Single‐crystal X‐ray analysis revealed the presence of two conformational enantiomers crystallizing in a racemic mixture. Through their embedded five‐ and seven‐membered rings these polycyclic aromatic hydrocarbons (PAHs) exhibit both negative and positive curvature and UV/Vis/NIR absorption spectroscopy as well as cyclic voltammetry experiments provided insights into the influence of larger flanking aromatic systems and electron‐donating substituents encompassing the heptagonal ring. Through [5+2] annulation of acenaphthylene an azulene‐containing PAH with intriguing optoelectronical properties including a very small bandgap and absorption over the whole visible spectrum could be obtained. Theoretical calculations were employed to elucidate the long‐wavelength absorption and aromaticity.
As viruses are obligatory intracellular parasites, any step during their life cycle strictly depends on successful interaction with their particular host cells. In particular, their interaction with cellular membranes is of crucial importance for most steps in the viral replication cycle. Such interactions are initiated by uptake of viral particles and subsequent trafficking to intracellular compartments to access their replication compartments which provide a spatially confined environment concentrating viral and cellular components, and subsequently, employ cellular membranes for assembly and exit of viral progeny. The ability of viruses to actively modulate lipid composition such as sphingolipids (SLs) is essential for successful completion of the viral life cycle. In addition to their structural and biophysical properties of cellular membranes, some sphingolipid (SL) species are bioactive and as such, take part in cellular signaling processes involved in regulating viral replication. It is especially due to the progress made in tools to study accumulation and dynamics of SLs, which visualize their compartmentalization and identify interaction partners at a cellular level, as well as the availability of genetic knockout systems, that the role of particular SL species in the viral replication process can be analyzed and, most importantly, be explored as targets for therapeutic intervention.
Protein-like enwrapped perylene bisimide chromophore as bright microcrystalline emitter material
(2019)
Strongly emissive solid‐state materials are mandatory components for many emerging optoelectronic technologies, but fluorescence is often quenched in the solid state owing to strong intermolecular interactions. The design of new organic pigments, which retain their optical properties despite their high tendency to crystallize, could overcome such limitations. Herein, we show a new material with monomer‐like absorption and emission profiles as well as fluorescence quantum yields over 90 % in its crystalline solid state. The material was synthesized by attaching two bulky tris(4‐tert‐butylphenyl)phenoxy substituents at the perylene bisimide bay positions. These substituents direct a packing arrangement with full enwrapping of the chromophore and unidirectional chromophore alignment within the crystal lattice to afford optical properties that resemble those of their natural pigment counterparts, in which chromophores are rigidly embedded in protein environments.
It is demonstrated that the di‐\(\pi\)‐methane (DPM) rearrangement of carbonyl‐substituted dibenzobarrelene (9,10‐dihydro‐9,10‐ethenoanthracene) derivatives is induced by visible‐light‐induced triplet photosensitization with Ir(ppy)\(_{3}\), Ir(dFppy)\(_{3}\) or 1‐butyl‐7,8‐dimethoxy‐3‐methylalloxazine as catalysts, whereas derivatives that lack carbonyl substituents are photoinert under these conditions. Notably, the products are formed almost quantitatively.
Water‐soluble multinuclear complexes based on ruthenium 2,2′‐bipyridine‐6,6′‐dicarboxylate (bda) and ditopic bipyridine linker units are investigated in three‐component visible light‐driven water oxidation catalysis. Systematic studies revealed a strong enhancement of the catalytic efficiency in the absence of organic co‐solvents and with increasing oligomer length. In‐depth kinetic and morphological investigations suggest that the enhanced performance is induced by the self‐assembly of linear Ru(bda) oligomers into aggregated superstructures. The obtained turnover frequencies (up to 14.9 s\(^{−1}\)) and turnover numbers (more than 1000) per ruthenium center are the highest reported so far for Ru(bda)‐based photocatalytic water oxidation systems.
Poorly water-soluble drugs frequently solubilize into bile colloids and this natural mechanism is key for efficient bioavailability. We tested the impact of pharmaceutical polymers on this solubilization interplay using proton nuclear magnetic resonance spectroscopy, dynamic light scattering, and by assessing the flux across model membranes. Eudragit E, Soluplus, and a therapeutically used model polymer, Colesevelam, impacted the bile-colloidal geometry and molecular interaction. These polymer-induced changes reduced the flux of poorly water-soluble and bile interacting drugs (Perphenazine, Imatinib) but did not impact the flux of bile non-interacting Metoprolol. Non-bile interacting polymers (Kollidon VA 64, HPMC-AS) neither impacted the flux of colloid-interacting nor colloid-non-interacting drugs. These insights into the drug substance/polymer/bile colloid interplay potentially point towards a practical optimization parameter steering formulations to efficient bile-solubilization by rational polymer selection.
Two di- and tetranuclear Ru(bda) (bda: 2,2′-bipyridine-6,6′-dicarboxylate) macrocyclic complexes were synthesized and their catalytic activities in chemical and photochemical water oxidation investigated in a comparative manner to our previously reported trinuclear congener. Our studies have shown that the catalytic activities of this homologous series of multinuclear Ru(bda) macrocycles in homogeneous water oxidation are dependent on their size, exhibiting highest efficiencies for the largest tetranuclear catalyst. The turnover frequencies (TOFs) have increased from di- to tetranuclear macrocycles not only per catalyst molecule but more importantly also per Ru unit with TOF of 6 \(^{-1}\) to 8.7 \(^{-1}\) and 10.5 s\(^{-1}\) in chemical and 0.6 s\(^{-1}\) to 3.3 \(^{-1}\) and 5.8 \(^{-1}\) in photochemical water oxidation per Ru unit, respectively. Thus, for the first time, a clear structure–activity relationship could be established for this novel class of macrocyclic water oxidation catalysts.
Catalytic water splitting is a viable process for the generation of renewable fuels. Here it is reported for the first time that a trinuclear supramolecular Ru(bda) (bda: 2,2′‐bipyridine‐6,6′‐dicarboxylate) catalyst, anchored on multi‐walled carbon nanotubes and subsequently immobilized on glassy carbon electrodes, shows outstanding performance in heterogeneous water oxidation. Activation of the catalyst on anodes by repetitive cyclic voltammetry (CV) scans results in a catalytic current density of 186 mA cm\(^{−2}\) at a potential of 1.45 V versus NHE. The activated catalyst performs water oxidation at an onset overpotential of 330 mV. The remarkably high stability of the hybrid anode is demonstrated by X‐ray absorption spectroscopy and electrochemically, revealing the absence of any degradation after 1.8 million turnovers. Foot of the wave analysis of CV data of activated electrodes with different concentrations of catalyst indicates a monomolecular water nucleophilic attack mechanism with an apparent rate constant of TOFmax (turnover frequency) of 3200 s\(^{−1}\).
Two dipolar merocyanines consisting of the same π‐conjugated chromophore but different alkyl substituents adopt very different packing arrangements in their respective solid state with either H‐ or J‐type exciton coupling, leading to ultranarrow absorption bands at 477 and 750 nm, respectively, due to exchange narrowing. The social self‐sorting behavior of these push‐pull chromophores in their mixed thin films is evaluated and the impact on morphology as well as opto‐electronical properties is determined. The implementation of this well‐tuned two‐component material with tailored optical features allows to optimize planar heterojunction organic photodiodes with fullerene (C\(_{60}\)) with either dual or single wavelength selectivity in the blue and NIR spectral range with ultranarrow bandwidths of only 11 nm (200 cm\(^{-1}\)) and an external quantum efficiency of up to 18% at 754 nm under 0 V bias. The application of these photodiodes as low‐power consuming heart rate monitors is demonstrated by a reflectance‐mode photoplethysmography (PPG) sensor.
Site-specific introduction of biorthogonal handles into RNAs is in high demand for decorating RNAs with fluorophores, affinity labels or other modifications. Aldehydes represent attractive functional groups for post-synthetic bioconjugation reactions. Here, we report a ribozyme-based method for the synthesis of aldehyde-functionalized RNA by directly converting a purine nucleobase. Using the methyltransferase ribozyme MTR1 as an alkyltransferase, the reaction is initiated by site-specific N1 benzylation of purine, followed by nucleophilic ring opening and spontaneous hydrolysis under mild conditions to yield a 5-amino-4-formylimidazole residue in good yields. The modified nucleotide is accessible to aldehyde-reactive probes, as demonstrated by the conjugation of biotin or fluorescent dyes to short synthetic RNAs and tRNA transcripts. Upon fluorogenic condensation with a 2,3,3-trimethylindole, a novel hemicyanine chromophore was generated directly on the RNA. This work expands the MTR1 ribozyme’s area of application from a methyltransferase to a tool for site-specific late-stage functionalization of RNA.
Deoxyribozymes (DNAzymes) are small, synthetic, single-stranded DNAs capable of catalysing chemical reactions, including RNA ligation. Herein, we report a novel class of RNA ligase deoxyribozymes that utilize 5’-adenylated RNA (5’-AppRNA) as the donor substrate, mimicking the activated intermediates of protein-catalyzed RNA ligation. Four new DNAzymes were identified by in vitro selection from an N40 random DNA library and were shown to catalyze the intermolecular linear RNA-RNA ligation via the formation of a native 3’-5’-phosphodiester linkage. The catalytic activity is distinct from previously described RNA-ligating deoxyribozymes. Kinetic analyses revealed the optimal incubation conditions for high ligation yields and demonstrated a broad RNA substrate scope. Together with the smooth synthetic accessibility of 5’-adenylated RNAs, the new DNA enzymes are promising tools for the protein-free synthesis of long RNAs, for example containing precious modified nucleotides or fluorescent labels for biochemical and biophysical investigations.
Although solid-state nuclear magnetic resonance (NMR) is a versatile analytical tool to study polymorphs and phase transitions of pharmaceutical molecules and products, this work summarizes examples of spontaneous and unexpected (and unwanted) structural rearrangements and phase transitions (amorphous-to-crystalline and crystalline-to-crystalline) under magic angle spinning (MAS) conditions, some of them clearly being due to the pressure experienced by the samples. It is widely known that such changes can often be detected by X-ray powder diffraction (XRPD); here, the capability of solid-state NMR experiments with a special focus on \(^{1}\)H-\(^{13}\)C frequency-switched Lee–Goldburg heteronuclear correlation (FSLG HETCOR)/MAS NMR experiments to detect even subtle changes on a molecular level not observable by conventional 1D NMR experiments or XRPD is presented. Furthermore, it is shown that a polymorphic impurity combined with MAS can induce a crystalline-to-crystalline phase transition. This showcases that solid-state NMR is not always noninvasive and such changes upon MAS should be considered in particular when compounds are studied over longer time spans.
Two series of organic–inorganic composite materials were synthesized through solvothermal imine condensation between diketopyrrolopyrrole dialdehyde DPP-1 and 5,10,15,20-tetrakis(4-aminophenyl)porphyrin (TAPP) in the presence of varying amounts of either amino- or carboxy-functionalized superparamagnetic iron oxide nanoparticles (FeO). Whereas high FeO loading induced cross-linking of the inorganic nanoparticles by amorphous imine polymers, a lower FeO content resulted in the formation of crystalline covalent organic framework domains. All hybrid materials were analyzed by magnetization measurements, powder X-ray diffraction, electron microscopy, IR, and UV/Vis absorption spectroscopy. Crystallinity, chromophore stacking, and visible absorption features are directly correlated to the mass fraction of the components, thus allowing for a fine-tuning of materials properties.
Molecular functionality can be often directly attributed to given properties of the electronic wavefunction. Analogous to the potential energy surface, these properties can be represented as a function of the nuclear coordinates, giving rise to molecular “functional landscapes.” However, so far there has been no possibility for their systematic investigation. This perspective aims to discuss the development of new theoretical methods based on the multistate extension of the metadynamics approach, employing electronic collective variables. This emerging methodology allows to explore functional landscapes and to gain a deeper understanding of the structure–function relation in molecules and complex molecular systems in the ground and excited electronic state.
Although a broad variety of classes of bioactive compounds have already been isolated from seaweeds of the genus Dictyota, most different species are still chemically and biologically unexplored. Dictyota species are well-known brown seaweeds belonging to the Dictyotaceae (Phaeophyta). The phytochemical composition within the genus Dictyota has recently received considerable interest, and a vast array of components, including diterpenes, sesquiterepenes, sterols, amino acids, as well as saturated and polyunsaturated fatty acids, have been characterized. The contribution of these valued metabolites to the biological potential, which includes anti-proliferative, anti-microbial, antiviral, antioxidant, anti-inflammatory, and anti-hyperpigmentation activities, of the genus Dictyota has also been explored. Therefore, this is the most comprehensive review, focusing on the published literature relevant to the chemically and pharmacologically diverse biopharmaceuticals isolated from different species of the genus Dictyota during the period from 1976 to now.
Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes
(2020)
This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression–regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule – glucosamine-6-phosphate – to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
Tristriazolotriazines (TTTs) with a threefold alkoxyphenyl substitution were prepared and studied by DSC, polarized optical microscopy (POM) and X-ray scattering. Six pentyloxy chains are sufficient to induce liquid-crystalline behavior in these star-shaped compounds. Thermotropic properties of TTTs with varying substitution patterns and a periphery of linear chains of different lengths, branching in the chain and swallow-tails, are compared. Generally, these disks display broad and stable thermotropic mesophases, with the tangential TTT being superior to the radial isomer. The structure–property relationships of the number of alkyl chains, their position, length and structure were studied.
Large-scale multireference configuration interaction (MRD-CI) calculations in a flexible atomic orbital (AO) basis are employed to study the reaction of C\(_2\)H\(_4\) with CH\(_2\) in its firSt triplet and singlet state. The minimum energy path (MEP) of both reactions is calculated, and different mechanisms are discussed. To examine the possible participation of the singlet state in the overall reaction starting from the triplet channel and terminating in the singlet-state c-C\(_3\)H\(_6\), various cuts through both hypersurfaces are calculated. lt is found that favorable interconversion from the trip1et to the singlet surface can only occur at !arge separations of the two fragments of CH2 and C\(_2\)H\(_4\). Experimental data considering the vibrational motion of CH\(_2\) in connection with the relative position of both surfaces are used to obtain an estimate for the overall barrier of the reaction. The height of the barrier is about 6 kcal/mol, while the barrier of the pure triplet reaction is calculated to be 7-9 kcal/mol.
No abstract available
Self-organization and self-sorting processes are responsible for the regulation and control of the vast majority of biological processes that eventually sustain life on our planet. Attempts to unveil the complexity of these systems have been devoted to the investigation of the binding processes between artificial molecules, complexes or aggregates within multicomponent mixtures, which has facilitated the emergence of the field of self-sorting in the last decade. Since, artificial systems involving discrete supramolecular structures, extended supramolecular aggregates or gel-phase materials in organic solvents or—to a lesser extent—in water have been investigated. In this review, we have collected diverse strategies employed in recent years to construct extended supramolecular aggregates in water upon self-sorting of small synthetic molecules. We have made particular emphasis on co-assembly processes in binary mixtures leading to supramolecular structures of remarkable complexity and the influence of different external variables such as solvent and concentration to direct recognition or discrimination processes between these species. The comprehension of such recognition phenomena will be crucial for the organization and evolution of complex matter.
The self-assembly of a bowl-shaped naphthalimide-annulated corannulene of high solubility has been studied in a variety of solvents by NMR and UV/Vis spectroscopy. Evaluation by the anti-cooperative K\(_2\)-K model revealed the formation of supramolecular dimers of outstanding thermodynamic stability. Further structural proof for the almost exclusive formation of dimers over extended aggregates is demonstrated by atomic force microscopy (AFM) and diffusion ordered spectroscopy (DOSY) measurements as well as by theoretical calculations. Thus, herein we present the first report of a supramolecular dimer of an annulated corannulene derivative in solution and discuss its extraordinarily high thermodynamic stability with association constants up to > 10\(^6\)M\(^-\) \(^1\) in methylcyclohexane, which is comparable to the association constants given for planar phthalocyanine and perylene bisimide dyes.
A series of perylene bisimide (PBI) dyes bearing various aryl substituents in 1,6,7,12 bay positions has been synthesized by Suzuki cross-coupling reaction. These molecules exhibit an exceptionally large and conformationally fixed twist angle of the PBI π-core due to the high steric congestion imparted by the aryl substituents in bay positions. Single crystal X-ray analyses of phenyl-, naphthyl- and pyrenyl-functionalized PBIs reveal interlocked π-π-stacking motifs, leading to conformational chirality and the possibility for the isolation of enantiopure atropoisomers by semipreparative HPLC. The interlocked arrangement endows these molecules with substantial racemization barriers of about 120 kJ mol\(^{−1}\) for the tetraphenyl- and tetra-2-naphthyl-substituted derivatives, which is among the highest racemization barriers for axially chiral PBIs. Variable temperature NMR studies reveal the presence of a multitude of up to fourteen conformational isomers in solution that are interconverted via smaller activation barriers of about 65 kJ mol\(^{−1}\). The redox and optical properties of these core-twisted PBIs have been characterized by cyclic voltammetry, UV/Vis/NIR and fluorescence spectroscopy and their respective atropo-enantiomers were further characterized by circular dichroism (CD) and circular polarized luminescence (CPL) spectroscopy.
The most important stereodynamic feature of carbo[n]helicenes is the interconversion of their enantiomers. The Gibbs activation energy (ΔG≠(T)) of this process, which determines the rate of enantiomerization, dictates the configurational stability of [n]helicenes. High values of ΔG≠(T) are required for applications of functional chiral molecules incorporating [n]helicenes or helicene substructures. This minireview provides an overview of the mechanism, recent developments, and factors affecting the enantiomerization of [n]helicenes, which will accelerate the design process of configurationally stable functional chiral molecules based on helicene substructures. Additionally, this minireview addresses the misconception and irregularities in the recent literature on how the terms “racemization” and “enantiomerization” are used as well as how the activation parameters are calculated for [n]helicenes and related compounds.
In recent years, covalent organic frameworks (COFs) have attracted considerable attention due to their crystalline and porous nature, which positions them as intriguing candidates for diverse applications such as catalysis, sensing, or optoelectronics. The incorporation of dyes or semiconducting moieties into a rigid two-dimensional COF can offer emergent features such as enhanced light harvesting or charge transport. However, this approach can be challenging when dealing with dye molecules that exhibit a large aromatic backbone, since the steric demand of solubilizing side chains also needs to be integrated into the framework. Here, we report the successful synthesis of DPP2-HHTP-COF consisting of diketopyrrolopyrrole (DPP) diboronic acid and hexahydroxytriphenylene (HHTP) building blocks. The well-known boronate ester coupling motif guides the formation of a planar and rigid backbone and long-range molecular DPP stacks, resulting in a highly crystalline and porous material. DPP2-HHTP-COF exhibits excellent optical properties including strong absorption over the visible spectral range, broad emission into the NIR and a singlet lifetime of over 5 ns attributed to the formation of molecular stacks with J-type interactions between the DPP subcomponents in the COF. Electrical measurements of crystalline DPP2-HHTP-COF pellets revealed conductivity values of up to 10(-6) S cm(-1).
Chemical processes mostly happen in fluid environments where reaction partners encounter via diffusion. The bimolecular encounters take place at a nanosecond time scale. The chemical environment (e.g., solvent molecules, (counter)ions) has a decisive influence on the reactivity as it determines the contact time between two molecules and affects the energetics. For understanding reactivity at an atomic level and at the appropriate dynamic time scale, it is crucial to combine matching experimental and theoretical data. Here, we have utilized all-atom molecular-dynamics simulations for accessing the key time scale (nanoseconds) using a QM/MM-Hamiltonian. Ion pairs consisting of a radical ion and its counterion are ideal systems to assess the theoretical predictions because they reflect dynamics at an appropriate time scale when studied by temperature-dependent EPR spectroscopy. We have investigated a diketone radical anion with its tetra-ethylammonium counterion. We have established a funnel-like transition path connecting two (equivalent) complexation sites. The agreement between the molecular-dynamics simulation and the experimental data presents a new paradigm for ion–ion interactions. This study exemplarily demonstrates the impact of the molecular environment on the topological states of reaction intermediates and how these states can be consistently elucidated through the combination of theory and experiment. We anticipate that our findings will contribute to the prediction of bimolecular transformations in the condensed phase with relevance to chemical synthesis, polymers, and biological activity.
Detaillierte Einblicke in die Struktur von mit Wirkstoffen beladenen Polymermizellen sind rar, aber wichtig um gezielt optimierte Transportsysteme entwickeln zu können. Wir konnten beobachten, dass eine Erhöhung der Curcumin‐Beladung von Triblockcopolymeren auf Basis von Poly(2‐oxazolinen) und Poly(2‐oxazinen) schlechtere Auflösungseigenschaften nach sich zieht. Mitthilfe von Festkörper‐NMR‐Spektroskopie und komplementären Techniken ist es möglich, ein ladungsabhängiges Strukturmodell auf molekularer Ebene zu erstellen, das eine Erklärung für die beobachteten Unterschiede liefert. Dabei belegen die Änderungen der chemischen Verschiebungen und Kreuzsignale in 2D‐NMR‐Experimenten die Beteiligung des hydrophoben Polymerblocks an der Koordination der Curcumin‐Moleküle, während bei höherer Beladung auch eine zunehmende Wechselwirkung mit dem hydrophilen Polymerblock beobachtet wird. Letztere könnte elementar für die Stabilisierung von ultrahochbeladenen Polymermizellen sowie das Design von verbesserten Wirkstofftransportsystemen sein.
Detailed insight into the internal structure of drug‐loaded polymeric micelles is scarce, but important for developing optimized delivery systems. We observed that an increase in the curcumin loading of triblock copolymers based on poly(2‐oxazolines) and poly(2‐oxazines) results in poorer dissolution properties. Using solid‐state NMR spectroscopy and complementary tools we propose a loading‐dependent structural model on the molecular level that provides an explanation for these pronounced differences. Changes in the chemical shifts and cross‐peaks in 2D NMR experiments give evidence for the involvement of the hydrophobic polymer block in the curcumin coordination at low loadings, while at higher loadings an increase in the interaction with the hydrophilic polymer blocks is observed. The involvement of the hydrophilic compartment may be critical for ultrahigh‐loaded polymer micelles and can help to rationalize specific polymer modifications to improve the performance of similar drug delivery systems.
A bis(trialkoxybenzamide)-functionalized quaterthiophene derivative was synthesized and its self-assembly properties in solution were studied. In non-polar solvents such as cyclohexane, this quaterthiophene π-system formed fibril aggregates with an H-type molecular arrangement due to synergistic effect of hydrogen bonding and π-stacking. The self-assembled fibres were found to gelate numerous organic solvents of diverse polarity. The charge transport ability of such elongated fibres of quaterthiophene π-system was explored by the pulse radiolysis time resolved microwave conductivity (PR-TRMC) technique and moderate mobility values were obtained. Furthermore, initial AFM and UV-vis spectroscopic studies of a mixture of our electron-rich quaterthiophene derivative with the electron acceptor [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) revealed a nanoscale segregated assembly of the individual building blocks in the blend.
The quantum efficiency of light emission is a crucial parameter of supramolecular aggregates that can be tuned by the molecular design of the monomeric species. Here, we report on a strong variation of the fluorescence quantum yield due to different phases of aggregation for the case of a perylene bisimide dye. In particular, a change of the dominant aggregation character from H- to J-type within the first aggregation steps is found, explaining the observed dramatic change in quantum yield. This behaviour is rationalised by means of a systematic study of the intermolecular potential energy surfaces using the time-dependent density functional based tight-binding (TD-DFTB) method. This provides a correlation between structural changes and a coupling strength and supports the notion of H- type stacked dimers and J-type stack-slipped dimers. The exciton-vibrational level structure is modelled by means of an excitonic dimer model including two effective vibrational modes per monomer. Calculated absorption and fluorescence spectra are found to be in reasonable agreement with experimental ones, thus supporting the conclusion on the aggregation behaviour.
The energy difference between the three lowest-lying isomers of C\(_6\) the linear \(^3 \sum ^-\) state and the two ring forms,the benzene structure (\(^1\)A\(_{18}\)) possessing D\(_{6h}\) symmetry and a distorted cyclic form ( \(^1\)A'\(_1\), D\(_{3h}\) symmetry) have been calculated using various ab initio methods. Variational methods such as multireference configuration interaction (MR-CI) and complete active space second order perturbatiOn treatment (CASPT2) have been applied, as weil as perturbational treatments and coupled cluster calculations (CCD). The correlation of all valence shell electrons is found to be important for a balanced description of the isomers of C\(_6\) . Methods which do not account for higher-order effects appropriately proved to be unsuitable for calculating the energy difference correctly. The results from multireference configuration interaction methods show that the isomers are close in energy with the cyclic forms somewhat lower than the linear form. The ring form possessing D\(_{3h}\) symmetry (\(^1\)A'\(_1\)} is found tobe the lowest-lying structure.
Interactions between proteins and carbohydrates with larger biomacromolecules, e.g., lectins, are usually examined using self-assembled monolayers on target gold surfaces as a simplified model measuring setup. However, most of those measuring setups are either limited to a single substrate or do not allow for control over ligand distance and spacing. Here, we develop a synthetic strategy, consisting of a cascade of a thioesterification, native chemical ligation (NCL) and thiol-ene reaction, in order to create three-component polymer conjugates with a defined double bioactivation at the chain end. The target architecture is the vicinal attachment of two biomolecule residues to the α telechelic end point of a polymer and a thioether group at the ω chain end for fixating the conjugate to a gold sensor chip surface. As proof-of-principle studies for affinity measurements, we demonstrate the interaction between covalently bound mannose and ConA in surface acoustic wave (SAW) and surface plasmon resonance (SPR) experiments.
Four new tetromycin derivatives, tetromycins 1-4 and a previously known one, tetromycin B (5) were isolated from Streptomyces axinellae Pol001(T) cultivated from the Mediterranean sponge Axinella polypoides. Structures were assigned using extensive 1D and 2D NMR spectroscopy as well as HRESIMS analysis. The compounds were tested for antiparasitic activities against Leishmania major and Trypanosoma brucei, and for protease inhibition against several cysteine proteases such as falcipain, rhodesain, cathepsin L, cathepsin B, and viral proteases SARS-CoV M(pro), and PL(pro). The compounds showed antiparasitic activities against T. brucei and time-dependent inhibition of cathepsin L-like proteases with K(i) values in the low micromolar range.
Sphingolipids, including ceramides, are a diverse group of structurally related lipids composed of a sphingoid base backbone coupled to a fatty acid side chain and modified terminal hydroxyl group. Recently, it has been shown that sphingolipids show antimicrobial activity against a broad range of pathogenic microorganisms. The antimicrobial mechanism, however, remains so far elusive. Here, we introduce 'click-AT-CLEM', a labeling technique for correlated light and electron microscopy (CLEM) based on the super-resolution array tomography (srAT) approach and bio-orthogonal click chemistry for imaging of azido-tagged sphingolipids to directly visualize their interaction with the model Gram-negative bacterium Neisseria meningitidis at subcellular level. We observed ultrastructural damage of bacteria and disruption of the bacterial outer membrane induced by two azido-modified sphingolipids by scanning electron microscopy and transmission electron microscopy. Click-AT-CLEM imaging and mass spectrometry clearly revealed efficient incorporation of azido-tagged sphingolipids into the outer membrane of Gram-negative bacteria as underlying cause of their antimicrobial activity.
The hyperfine coupling constants (isotropic hfcc and four Cartesian components of the ani~ tropic tensor) are calculated for all three atoms of C\(_2\)H in its three lowest-lying electronic states at various molecu)ar geometries by means of the ab initio configuration interaction ( MRO.CI) method. The off-diagonal electronic matrix elements involving the two species ofthe A' symmetry are also computed. A diabatic transforrnation is perforrned Jeading to simple geometrical depen· dences of the hyperline coupling constants.
The vibronically averaged values for tbe hyperfine coupling constants in the X\(^2 \sum\)-A\(^2 \Pi\) system of the ethynyl radical are computed by means of tbe ab initio metbod calculations. The results point at tbe importance of taking into account the coupling of a1l tbree electronic states in question ( I\(^2\)A', 2\(^2\)A', and 1\(^2\)A") for a reliable explanation of the available experimental findings. The mean values of the hfcc's for K = 0 and 1 levels in \(^{13}\)C\(_2\)H and \(^{13}\)C\(_2\)D in the energy range up to 6000 cm\(^{-1}\) are predicted.
Vibronically averaged values for K =0 and K = 1 bending levels in the energy range between 0 and 25 000 cm\(^{-1}\) are computed for the \(^{14}\)N, H, and D atoms in NH\(_2\), NHD, and ND\(_2\) The pure ab initio electronic potentials, as well as those derived by fitting of experimentally observed band positions are employed. Effects of vibronic coupling and local perturbations of close-lying levels belanging to different electronic states are discussed.
Multichromophoric macrocycles and cyclophanes are important supramolecular architectures for the elucidation of interchromophoric interactions originating from precise spatial organization. Herein, by combining an axially chiral binaphthol bisimide (BBI) and a bay-substituted conformationally labile twisted perylene bisimide (PBI) within a cyclophane of well-defined geometry, we report a chiral PBI hetero-cyclophane (BBI-PBI) that shows intramolecular energy and solvent-regulated chirality transfer from the BBI to the PBI subunit. Excellent spectral overlap and spatial arrangement of BBI and PBI lead to efficient excitation energy transfer and subsequent PBI emission with high quantum yield (80–98 %) in various solvents. In contrast, chirality transfer is strongly dependent on the respective solvent as revealed by circular dichroism (CD) spectroscopy. The combination of energy and chirality transfer affords a bright red circularly polarized luminescence (CPL) from the PBI chromophore by excitation of BBI.
Sialyltransferases (STs) are disulfide-containing, type II transmembrane glycoproteins that catalyze the transfer of sialic acid to proteins and lipids and participate in the synthesis of the core structure oligosaccharides of human milk. Sialic acids are found at the outermost position of glycostructures, playing a key role in health and disease. Sialylation is also essential for the production of recombinant therapeutic proteins (RTPs). Despite their importance, availability of sialyltransferases is limited due to the low levels of stable, soluble and active protein produced in bacterial expression systems, which hampers biochemical and structural studies on these enzymes and restricts biotechnological applications. We report the successful expression of active human sialyltransferases ST3Gal1 and ST6Gal1 in commercial Escherichia coli strains designed for production of disulfide-containing proteins. Fusion of hST3Gal1 with different solubility enhancers and substitution of exposed hydrophobic amino acids by negatively charged residues (supercharging-like approach) were performed to promote solubility and folding. Co-expression of sialyltransferases with the chaperon/foldases sulfhydryl oxidase, protein disulfide isomerase and disulfide isomerase C was explored to improve the formation of native disulfide bonds. Active sialyltransferases fused with maltose binding protein (MBP) were obtained in sufficient amounts for biochemical and structural studies when expressed under oxidative conditions and co-expression of folding factors increased the yields of active and properly folded sialyltransferases by 20%. Mutation of exposed hydrophobic amino acids increased recovery of active enzyme by 2.5-fold, yielding about 7 mg of purified protein per liter culture. Functionality of recombinant enzymes was evaluated in the synthesis of sialosides from the β-d-galactoside substrates lactose, N-acetyllactosamine and benzyl 2-acetamido-2-deoxy-3-O-(β-d-galactopyranosyl)-α-d-galactopyranoside.
Post-transcriptional RNA modification methods are in high demand for site-specific RNA labelling and analysis of RNA functions. In vitro-selected ribozymes are attractive tools for RNA research and have the potential to overcome some of the limitations of chemoenzymatic approaches with repurposed methyltransferases. Here we report an alkyltransferase ribozyme that uses a synthetic, stabilized S-adenosylmethionine (SAM) analogue and catalyses the transfer of a propargyl group to a specific adenosine in the target RNA. Almost quantitative conversion was achieved within 1 h under a wide range of reaction conditions in vitro, including physiological magnesium ion concentrations. A genetically encoded version of the SAM analogue-utilizing ribozyme (SAMURI) was expressed in HEK293T cells, and intracellular propargylation of the target adenosine was confirmed by specific fluorescent labelling. SAMURI is a general tool for the site-specific installation of the smallest tag for azide-alkyne click chemistry, which can be further functionalized with fluorophores, affinity tags or other functional probes.
Inspired by the proficiency of natural enzymes, mimicking of nanoenvironments for precise substrate preorganisation is a promising strategy in catalyst design. However, artificial examples of enzyme-like activation of H\(_2\)O molecules for the challenging oxidative water splitting reaction are hardly explored. Here, we introduce a mononuclear Ru(bda) complex (M1, bda: 2,2’-bipyridine-6,6’-dicarboxylate) equipped with a bipyridine-functionalized ligand to preorganize H\(_2\)O molecules in front of the metal center as in enzymatic clefts. The confined pocket of M1 accelerates chemically driven water oxidation at pH 1 by facilitating a water nucleophilic attack pathway with a remarkable turnover frequency of 140 s\(^{−1}\) that is comparable to the oxygen-evolving complex of photosystem II. Single crystal X-ray analysis of M1 under catalytic conditions allowed the observation of a 7th H\(_2\)O ligand directly coordinated to a RuIII center. Via a well-defined hydrogen-bonding network, another H\(_2\)O substrate is preorganized for the crucial O–O bond formation via nucleophilic attack.
Proton‐coupled electron‐transfer (PCET) processes play a key role in biocatalytic energy conversion and storage, for example, photosynthesis or nitrogen fixation. Here, we report a series of bipyridine‐containing di‐ to tetranuclear Ru(bda) macrocycles 2 C–4 C (bda: 2,2′‐bipyridine‐6,6′‐dicarboxylate) to promote O−O bond formation. In photocatalytic water oxidation under neutral conditions, all complexes 2 C–4 C prevail in a folded conformation that support the water nucleophilic attack (WNA) pathway with remarkable turnover frequencies of up to 15.5 s\(^{−1}\) per Ru unit respectively. Single‐crystal X‐ray analysis revealed an increased tendency for intramolecular π‐π stacking and preorganization of the proximal bases close to the active centers for the larger macrocycles. H/D kinetic isotope effect studies and electrochemical data demonstrate the key role of the proximal bipyridines as proton acceptors in lowering the activation barrier for the crucial nucleophilic attack of H\(_{2}\)O in the WNA mechanism.
Arene‐fluoroarene interactions offer outstanding possibilities for engineering of supramolecular systems, including nucleic acids. Here, we implement the tolane‐perfluorotolane interaction as base pair replacement in DNA. Tolane (THH) and perfluorotolane (TFF) moieties were connected to acyclic backbone units, comprising glycol nucleic acid (GNA) or butyl nucleic acid (BuNA) building blocks, that were incorporated via phosphoramidite chemistry at opposite positions in a DNA duplex. Thermodynamic analyses by UV thermal melting revealed a compelling stabilization by THH/TFF heteropairs only when connected to the BuNA backbone, but not with the shorter GNA linker. Detailed NMR studies confirmed the preference of the BuNA backbone for enhanced polar π‐stacking. This work defines how orthogonal supramolecular interactions can be tailored by small constitutional changes in the DNA backbone, and it inspires future studies of arene‐fluoroarene‐programmed assembly of DNA.
Herein we devise and execute a new synthesis of a pristine boron-doped nanographene. Our target boron-doped nanographene was designed based on DFT calculations to possess a low LUMO energy level and a narrow band gap derived from its precise geometry and B-doping arrangement. Our synthesis of this target, a doubly B-doped hexabenzopentacene (B\(_{2}\)-HBP), employs six net C−H borylations of an alkene, comprising consecutive hydroboration/electrophilic borylation/dehydrogenation and BBr\(_{3}\)/AlCl\(_{3}\)/2,6-dichloropyridine-mediated C−H borylation steps. As predicted by our calculations, B\(_{2}\)-HBP absorbs strongly in the visible region and emits in the NIR up to 1150 nm in o-dichlorobenzene solutions. Furthermore, B\(_{2}\)-HBP possesses a very low LUMO level, showing two reversible reductions at −1.00 V and −1.17 V vs. Fc\(^{+}\)/Fc. Our methodology is surprisingly selective despite its implementation of unfunctionalized precursors and offers a new approach to the synthesis of pristine B-doped polycyclic aromatic hydrocarbons.
We investigated the folding kinetics of G‐quadruplex (G4) structures by comparing the K\(^{+}\)‐induced folding of an RNA G4 derived from the human telomeric repeat‐containing RNA (TERRA25) with a sequence homologous DNA G4 (wtTel25) using CD spectroscopy and real‐time NMR spectroscopy. While DNA G4 folding is biphasic, reveals kinetic partitioning and involves kinetically favoured off‐pathway intermediates, RNA G4 folding is faster and monophasic. The differences in kinetics are correlated to the differences in the folded conformations of RNA vs. DNA G4s, in particular with regard to the conformation around the glycosidic torsion angle χ that uniformly adopts anti conformations for RNA G4s and both, syn and anti conformation for DNA G4s. Modified DNA G4s with \(^{19}\)F bound to C2′ in arabino configuration adopt exclusively anti conformations for χ. These fluoro‐modified DNA (antiTel25) reveal faster folding kinetics and monomorphic conformations similar to RNA G4s, suggesting the correlation between folding kinetics and pathways with differences in χ angle preferences in DNA and RNA, respectively.
Various structural possibilities for Si\(_3\)C\(_3\) clusters are investigated by ab initio calculations employing basis sets of double- and triple-zeta quality augmented by d polarization functions. Correlation effects are included by a second-order Moeller Piesset perturbation treatment. For the two lowest-lying structures higher-order correlation corrections and multi-reference effects are also included. Bonding features are investigated by two different types of population analyses to obtain insight into the nature of chemical bonding. A total of 17 stationary points were investigated, 14 of which correspond to local minima and three being transition states. The energetically lowest-lying structures are: A "pyramidlike" structure with various multicenter bonds, followed by a es symmetric isomer closely related to the ground state Si6 structure. Planar structures, favoured in small carbon clusters, lie higher in energy and are transition states. The lowest-lying triplet system is found to be the linear nonsymmetric Si - C-C-C-Si -Si structure, which is calculated to lie about 38 kcalfmole above the singlet ground state. A building-up principle based on bonding criteria is suggested for the occurence of the various structural possibilities.
No abstract available
From the leaves of a botanically and phytochemically as yet unexplored Ancistrocladus liana discovered in the rainforests of the Central region of the Democratic Republic of the Congo in the vicinity of the town of Ikela, six new naphthylisoquinoline alkaloids were isolated, viz., two constitutionally unsymmetric dimers, the mbandakamines B\(_3\) (3) and B\(_4\) (4), and four related 5,8′-linked monomeric alkaloids, named ikelacongolines A–D (5a, 5b, 6, and 7). The dimers 3 and 4 are structurally unusual quateraryls comprising two 5,8′-coupled monomers linked via a sterically strongly constrained 6′,1′′-connection between their naphthalene units. These compounds contain seven elements of chirality, four stereogenic centers and three consecutive chiral axes. They were identified along with two known related compounds, the mbandakamines A (1) and B\(_2\) (2), which had so far only been detected in two Ancistrocladus species indigenous to the Northwestern Congo Basin. In addition, five known monomeric alkaloids, previously found in related Central African Ancistrocladus species, were isolated from the here investigated Congolese liana, three of them belonging to the subclass of 5,8′-coupled naphthylisoquinoline alkaloids, whereas two compounds exhibited a less frequently occurring 7,8′-biaryl linkage. The stereostructures of the new alkaloids were established by spectroscopic (in particular HRESIMS, 1D and 2D NMR), chemical (oxidative degradation), and chiroptical (electronic circular dichroism) methods. The mbandakamines B\(_3\) (3) and B\(_4\) (4) displayed pronounced activities in vitro against the malaria parasite Plasmodium falciparum and the pathogen of African sleeping sickness, Trypanosoma brucei rhodesiense.
Rapid multiple-quantum three-dimensional fluorescence spectroscopy disentangles quantum pathways
(2019)
Coherent two-dimensional spectroscopy is a powerful tool for probing ultrafast quantum dynamics in complex systems. Several variants offer different types of information but typically require distinct beam geometries. Here we introduce population-based three-dimensional (3D) electronic spectroscopy and demonstrate the extraction of all fourth- and multiple sixth-order nonlinear signal contributions by employing 125-fold (1⨯5⨯5⨯5) phase cycling of a four-pulse sequence. Utilizing fluorescence detection and shot-to-shot pulse shaping in single-beam geometry, we obtain various 3D spectra of the dianion of TIPS-tetraazapentacene, a fluorophore with limited stability at ambient conditions. From this, we recover previously unknown characteristics of its electronic two-photon state. Rephasing and nonrephasing sixth-order contributions are measured without additional phasing that hampered previous attempts using noncollinear geometries. We systematically resolve all nonlinear signals from the same dataset that can be acquired in 8 min. The approach is generalizable to other incoherent observables such as external photoelectrons, photocurrents, or photoions.
Fluorogenic RNA aptamers are synthetic functional RNAs that specifically bind and activate conditional fluorophores. The Chili RNA aptamer mimics large Stokes shift fluorescent proteins and exhibits high affinity for 3,5-dimethoxy-4-hydroxybenzylidene imidazolone (DMHBI) derivatives to elicit green or red fluorescence emission. Here, we elucidate the structural and mechanistic basis of fluorescence activation by crystallography and time-resolved optical spectroscopy. Two co-crystal structures of the Chili RNA with positively charged DMHBO+ and DMHBI+ ligands revealed a G-quadruplex and a trans-sugar-sugar edge G:G base pair that immobilize the ligand by π-π stacking. A Watson-Crick G:C base pair in the fluorophore binding site establishes a short hydrogen bond between the N7 of guanine and the phenolic OH of the ligand. Ultrafast excited state proton transfer (ESPT) from the neutral chromophore to the RNA was found with a time constant of 130 fs and revealed the mode of action of the large Stokes shift fluorogenic RNA aptamer.