Fluoride binding to an organoboron wire controls photoinduced electron transfer

We demonstrate that the rates for long-range electron transfer can be controlled actively by tight anion binding to a rigid rod-like molecular bridge. Electron transfer from a triarylamine donor to a photoexcited Ru(bpy)₃²⁺ acceptor (bpy = 2,2′-bipyridine) across a 2,5-diboryl-1,4-phenylene bridge occurs within less than 10 ns in CH₂Cl₂ at 22 °C. Fluoride anions bind with high affinity to the organoboron bridge due to strong Lewis base/Lewis acid interactions, and this alters the electronic structure of the bridge drastically. Consequently, a large tunneling barrier is imposed on photoinduced electron transfer from the triarylamine to the Ru(bpy)₃²⁺ complex and hence this process occurs more than two orders of magnitude more slowly, despite the fact that its driving force is essentially unaffected by fluoride addition. Electron transfer rates in proteins could potentially be regulated via a similar fundamental principle, because interactions between charged amino acid side chains and counter-ions can modulate electronic couplings between distant redox partners. In artificial donor-bridge-acceptor compounds, external stimuli have been employed frequently to control electron transfer rates, but the approach of exploiting strong Lewis acid/Lewis base interactions to regulate the tunneling barrier height imposed by a rigid rod-like molecular bridge is conceptually novel and broadly applicable, because it is largely independent of the donor and the acceptor, and because the effect is not based on a change of the driving-force for electron transfer. The principle demonstrated here can potentially be used to switch between conducting and insulating states of molecular wires between electrodes.     

Folding Dynamics of 10‐Residue β‐Hairpin Peptide Chignolin

Short peptides that fold into β‐hairpins are ideal model systems for investigating the mechanism of protein folding because their folding process shows dynamics typical of proteins. We performed folding, unfolding, and refolding molecular dynamics simulations (total of 2.7 μs) of the 10‐residue β‐hairpin peptide chignolin, which is the smallest β‐hairpin structure known to be stable in solution. Our results revealed the folding mechanism of chignolin, which comprises three steps. First, the folding begins with hydrophobic assembly. It brings the main chain together; subsequently, a nascent turn structure is formed. The second step is the conversion of the nascent turn into a tight turn structure along with interconversion of the hydrophobic packing and interstrand hydrogen bonds. Finally, the formation of the hydrogen‐bond network and the complete hydrophobic core as well as the arrangement of side‐chain–side‐chain interactions occur at approximately the same time. This three‐step mechanism appropriately interprets the folding process as involving a combination of previous inconsistent explanations of the folding mechanism of the β‐hairpin, that the first event of the folding is formation of hydrogen bonds and the second is that of the hydrophobic core, or vice versa.     

In vivo visible light-triggered drug release from an implanted depot

Controlling chemistry in space and time has offered scientists and engineers powerful tools for research and technology. For example, on-demand photo-triggered activation of neurotransmitters has revolutionized neuroscience. Non-invasive control of the availability of bioactive molecules in living organisms will undoubtedly lead to major advances; however, this requires the development of photosystems that efficiently respond to regions of the electromagnetic spectrum that innocuously penetrate tissue. To this end, we have developed a polymer that photochemically degrades upon absorption of one photon of visible light and demonstrated its potential for medical applications. Particles formulated from this polymer release molecular cargo in vitro and in vivo upon irradiation with blue visible light through a photoexpansile swelling mechanism.     

Profiling the reactivity of cyclic C-nucleophiles towards electrophilic sulfur in cysteine sulfenic acid

Oxidation of a protein cysteine thiol to sulfenic acid, termed S-sulfenylation, is a reversible post-translational modification that plays a crucial role in regulating protein function and is correlated with disease states. The majority of reaction-based small molecule and immunochemical probes used for detecting sulfenic acids are based on the 5,5-dimethyl-1,3-cyclohexanedione (dimedone) scaffold, which is selective, but suffers from low reactivity. In addition, mechanistic details and features that diminish or enhance nucleophile reactivity remain largely unknown. A significant hurdle to resolving the aforementioned issues has been the chemically unstable nature of small-molecule sulfenic acid models. Herein, we report a facile mass spectrometry-based assay and repurposed dipeptide-based model to screen a library of cyclic C-nucleophiles for reactivity with sulfenic acid under aqueous conditions. Observed rate constants for ∼100 cyclic C-nucleophiles were obtained and, from this collection, we have identified novel compounds with more than 200-fold enhanced reactivity, as compared to dimedone. The increase in reactivity and retention of selectivity of these C-nucleophiles were validated in secondary assays, including a protein model for sulfenic acid. Together, this work represents a significant step toward developing new chemical reporters for detecting protein S-sulfenylation with superior kinetic resolution. The enhanced rates and varied composition of the C-nucleophiles should enable more comprehensive analyses of the sulfenome and serve as the foundation for reversible or irreversible nucleophilic covalent inhibitors that target oxidized cysteine residues in therapeutically important proteins.     

Folding and fluorescence enhancement with strong odd–even effect for a series of merocyanine dye oligomers

A series of merocyanine (MC) oligomers with a varying number of chromophores from two to six has been synthesized via a peptide synthesis strategy. Solvent-dependent UV/vis spectroscopic studies reveal folding processes for the MC oligomers driven by strong dipole–dipole interactions resulting in well-defined π-stacks with antiparallel orientation of the dyes. Whilst even-numbered tetramer 4 and hexamer 6 only show partial folding into dimeric units, odd-numbered trimer 3 and pentamer 5 fold into π-stacks of three and five MC units upon decreasing solvent polarity. In-depth 2D NMR studies provided insight into the supramolecular structure. For trimer 3, an NMR structure could be generated revealing the presence of a well-defined triple π-stack in the folded state. Concomitant with folding, the fluorescence quantum yield is increased for all MC oligomers in comparison to the single chromophore. Based on radiative and non-radiative decay rates, this fluorescence enhancement can be attributed to the rigidification of the chromophores within the π-stacks that affords a pronounced decrease of the non-radiative decay rates. Theoretical investigations for the double and triple dye stacks based on time-dependent density functional theory (TD-DFT) calculations indicate for trimer 3 a pronounced mixing of Frenkel and charge transfer (CT) states. This leads to significant deviations from the predictions obtained by the molecular exciton theory which only accounts for the Coulomb interaction between the transition dipole moments of the chromophores.

A series of merocyanine (MC) oligomers with a varying number of chromophores from two to six has been synthesized via a peptide synthesis strategy.     

Regioselective thioacetylation of chitosan end-groups for nanoparticle gene delivery systems

Chitosan (CS) end-group chemistry is a conjugation strategy that has been minimally exploited in the literature to date. Although the open-chain form of the CS reducing extremity bears a reactive aldehyde moiety, the most common method to generate a reactive end-group on CS is nitrous acid depolymerization, which produces a 2,5-anhydro-d-mannose unit (M-Unit) bearing also an aldehyde moiety. However, the availability of the latter might be low, since previous literature suggests that its hydrated and non-reactive form, namely the gem-diol form, is predominant in acidic aqueous conditions. Oxime-click chemistry has been used to react on such aldehydes with various degrees of success, but the use of a co-solvent and additional chemical reagents remain necessary to obtain the desired and stable covalent linkage. In this study, we have assessed the availability of the aldehyde reactive form on chitosan treated with nitrous acid. We have also assessed its reactivity towards thiol-bearing molecules in acidic conditions where CS amino groups are fully protonated and thus unreactive towards aldehyde. LC-MS and NMR spectroscopy methods (¹H and DOSY, respectively) confirmed the regioselective thioacetylation of the reactive aldehyde with conversion rates between 55 and 70% depending on the thiol molecule engaged. The stabilization of the hemithioacetal intermediates into the corresponding thioacetals was also found to be facilitated upon freeze-drying of the reaction medium. The PEGylation of the CS M-Unit aldehyde by thioacetylation was also performed as a direct application of the proposed conjugation approach. CS-b-PEG₂ block copolymers were successfully synthesized and were used to prepare block ionomer complexes with plasmid DNA, as revealed by their spherical morphology vs. the rod-like/globular/toroidal morphology observed for polyplexes prepared using native unmodified chitosan. This novel aqueous thiol-based conjugation strategy constitutes an alternative to the oxime-click pathway; it could be applicable to other polymers.     

N 6-Hydroperoxymethyladenosine: a new intermediate of chemical oxidation of N6-methyladenosine mediated by bicarbonate-activated hydrogen peroxide

N ⁶-Methyladenosine (m⁶A) represents a relatively abundant modification in eukaryotic RNA. Because m⁶A has similar properties to adenosine and a low reactivity, limited research has been focused on this nucleoside. In this study, we revealed an important intermediate in the oxidation of m⁶A through the bicarbonate-activated peroxide system. Over the course of oxidation, we found a new mechanism in which N⁶-hydroxymethyladenosine (hm⁶A), N⁶-formyladenosine (f⁶A) and N⁶-hydroperoxymethyladenosine (oxm⁶A) were intermediate products, and adenosine was the final product. In this study, oxm⁶A was isolated using HPLC and characterized by mass spectrometry, NMR and diphenyl-1-pyrenylphosphine (DPPP) fluorescence detection. This study provides a new modified nucleoside and demonstrates oxidative demethylation of m⁶A by reactive oxygen species at the nucleobase level and in RNA strands.     

Elucidating organ-specific metabolic toxicity chemistry from electrochemiluminescent enzyme/DNA arrays and bioreactor bead-LC-MS/MS

Human toxic responses are very often related to metabolism. Liver metabolism is traditionally studied, but other organs also convert chemicals and drugs to reactive metabolites leading to toxicity. When DNA damage is found, the effects are termed genotoxic. Here we describe a comprehensive new approach to evaluate chemical genotoxicity pathways from metabolites formed in situ by a broad spectrum of liver, lung, kidney and intestinal enzymes. DNA damage rates are measured with a microfluidic array featuring a 64-nanowell chip to facilitate fabrication of films of DNA, electrochemiluminescent (ECL) detection polymer [Ru(bpy)₂(PVP)₁₀]²⁺ {(PVP = poly(4-vinylpyridine))} and metabolic enzymes. First, multiple enzyme reactions are run on test compounds using the array, then ECL light related to the resulting DNA damage is measured. A companion method next facilitates reaction of target compounds with DNA/enzyme-coated magnetic beads in 96 well plates, after which DNA is hydrolyzed and nucleobase-metabolite adducts are detected by LC-MS/MS. The same organ enzymes are used as in the arrays. Outcomes revealed nucleobase adducts from DNA damage, enzymes responsible for reactive metabolites (e.g. cyt P450s), influence of bioconjugation, relative dynamics of enzymes suites from different organs, and pathways of possible genotoxic chemistry. Correlations between DNA damage rates from the cell-free array and organ-specific cell-based DNA damage were found. Results illustrate the power of the combined DNA/enzyme microarray/LC-MS/MS approach to efficiently explore a broad spectrum of organ-specific metabolic genotoxic pathways for drugs and environmental chemicals.     

A statistical model for predicting protein folding rates from amino acid sequence with structural class information

Prediction of protein folding rates from amino acid sequences is one of the most important challenges in molecular biology. In this work, I have related the protein folding rates with physical-chemical, energetic and conformational properties of amino acid residues. I found that the classification of proteins into different structural classes shows an excellent correlation between amino acid properties and folding rates of two- and three-state proteins, indicating the importance of native state topology in determining the protein folding rates. I have formulated a simple linear regression model for predicting the protein folding rates from amino acid sequences along with structural class information and obtained an excellent agreement between predicted and experimentally observed folding rates of proteins; the correlation coefficients are 0.99, 0.96 and 0.95, respectively, for all-alpha, all-beta and mixed class proteins. This is the first available method, which is capable of predicting the protein folding rates just from the amino acid sequence with the aid of generic amino acid properties and structural class information.     

Cobalt-catalysed asymmetric hydrovinylation of 1,3-dienes

In the presence of bidentate 1,n-bis-diphenylphosphinoalkane-CoCl₂ complexes {Cl₂Co[P ∼ P]} and Me₃Al or methylaluminoxane, acyclic (E)-1,3-dienes react with ethylene (1 atmosphere) to give excellent yields of hydrovinylation products. The regioselectivity (1,4- or 1,2-addition) and the alkene configuration (E- or Z-) of the resulting product depend on the nature of the ligand and temperature at which the reaction is carried out. Cobalt(ii)-complexes of 1,1-diphenylphosphinomethane and similar ligands with narrow bite angles give mostly 1,2-addition, retaining the E-geometry of the original diene. Complexes of most other ligands at low temperature (–40 °C) give almost exclusively a single branched product, (Z)-3-alkylhexa-1,4-diene, which arises from a 1,4-hydrovinylation reaction. A minor product is the linear adduct, a 6-alkyl-hexa-1,4-diene, also arising from a 1,4-addition of ethylene. As the temperature is increased, a higher proportion of the major branched-1,4-adduct appears as the (E)-isomer. The unexpectedly high selectivity seen in the Co-catalysed reaction as compared to the corresponding Ni-catalysed reaction can be rationalized by invoking the intermediacy of an η⁴-[(diene)[P ∼ P]CoH]⁺-complex and its subsequent reactions. The enhanced reactivity of terminal E-1,3-dienes over the corresponding Z-dienes can also be explained on the basis of the ease of formation of this η⁴-complex in the former case. The lack of reactivity of the X₂Co(dppb) (X = Cl, Br) complexes in the presence of Zn/ZnI₂ makes the Me₃Al-mediated reaction different from the previously reported hydroalkenylation of dienes. Electron-rich phospholanes, bis-oxazolines and N-heterocyclic carbenes appear to be poor ligands for the Co(ii)-catalysed hydrovinylation of 1,3-dienes. An extensive survey of chiral ligands reveals that complexes of DIOP, BDPP and Josiphos ligands are quite effective for these reactions even at –45 °C and enantioselectivities in the range of 90–99% ee can be realized for a variety of 1,3-dienes. Cobalt(ii)-complex of an electron-deficient Josiphos ligand is especially active, requiring only <1 mol% catalyst to effect the reactions.     

Chemoselective palladium-catalyzed deprotonative arylation/[1,2]-Wittig rearrangement of pyridylmethyl ethers

Control of chemoselectivity is one of the most challenging problems facing chemists and is particularly important in the synthesis of bioactive compounds and medications. Herein, the first highly chemoselective tandem C(sp³)–H arylation/[1,2]-Wittig rearrangement of pyridylmethyl ethers is presented. The efficient and operationally simple protocols enable generation of either arylation products or tandem arylation/[1,2]-Wittig rearrangement products with remarkable selectivity and good to excellent yields (60–99%). Choice of base, solvent, and reaction temperature play a pivotal role in tuning the reactivity of intermediates and controlling the relative rates of competing processes. The novel arylation step is catalyzed by a Pd(OAc)₂/NIXANTPHOS-based system via a deprotonative cross-coupling process. The method provides rapid access to skeletally diverse aryl(pyridyl)methanol core structures, which are central components of several medications.     

Controlling the activity of quorum sensing autoinducers with light

Bacteria use a communication system, called quorum sensing (QS), to organize into communities and synchronize gene expression to promote virulence and secure survival. Here we report on a proof-of-principle for externally interfering with this bacterial communication system, using light. By employing photoswitchable small molecules, we were able to photocontrol the QS-related bioluminescence in an Escherichia coli reporter strain, and the expression of target QS genes and pyocyanin production in Pseudomonas aeruginosa.     

Importance of native-state topology for determining the folding rate of two-state proteins

Understanding the relationship between amino acid sequences and folding rate of proteins is a challenging task similar to protein folding problem. In this work, we have analyzed the relative importance of protein sequence and structure for predicting the protein folding rates in terms of amino acid properties and contact distances, respectively. We found that the parameters derived with protein sequence (physical-chemical, energetic, and conformational properties of amino acid residues) show very weak correlation (|r| < 0.39) with folding rates of 28 two-state proteins, indicating that the sequence information alone is not sufficient to understand the folding rates of two-state proteins. However, the maximum positive correlation obtained for the properties, number of medium-range contacts, and alpha-helical tendency reveals the importance of local interactions to initiate protein folding. On the other hand, a remarkable correlation (r varies from -0.74 to -0.88) has been obtained between structural parameters (contact order, long-range order, and total contact distance) and protein folding rates. Further, we found that the secondary structure content and solvent accessibility play a marginal role in determining the folding rates of two-state proteins. Multiple regression analysis carried out with the combination of three properties, beta-strand tendency, enthalpy change, and total contact distance improved the correlation to 0.92 with protein folding rates. The relative importance of existing methods along with multiple-regression model proposed in this work will be discussed. Our results demonstrate that the native-state topology is the major determinant for the folding rates of two-state proteins.     

A hexanuclear gold carbonyl cluster

The hexanuclear gold carbonyl cluster [PPh₄]₂[Au₆(CF₃)₆Br₂(CO)₂] (4) has been obtained by spontaneous self-assembly of the following independent units: CF₃AuCO (1) and [PPh₄][Br(AuCF₃)₂] (3). The cyclo-Au₆ aggregate 4, in which the components are held together by unassisted, fairly strong aurophilic interactions (Au···Au ∼310 pm), exhibits a cyclohexane-like arrangement with chair conformation. These aurophilic interactions also result in significant ν(CO) lowering: from 2194 cm^–1 in the separate component 1 to 2171 cm^–1 in the mixed aggregate 4. Procedures to prepare the single-bridged dinuclear component 3 as well as the mononuclear derivative [PPh₄][CF₃AuBr] (2) are also reported.     

Exploiting parameter space in MOFs: a 20-fold enhancement of phosphate-ester hydrolysis with UiO-66-NH2

The hydrolysis of nerve agents is of primary concern due to the severe toxicity of these agents. Using a MOF-based catalyst (UiO-66), we have previously demonstrated that the hydrolysis can occur with relatively fast half-lives of 50 minutes. However, these rates are still prohibitively slow to be efficiently utilized for some practical applications (e.g., decontamination wipes used to clean exposed clothing/skin/vehicles). We thus turned our attention to derivatives of UiO-66 in order to probe the importance of functional groups on the hydrolysis rate. Three UiO-66 derivatives were explored; UiO-66-NO₂ and UiO-66-(OH)₂ showed little to no change in hydrolysis rate. However, UiO-66-NH₂ showed a 20 fold increase in hydrolysis rate over the parent UiO-66 MOF. Half-lives of 1 minute were observed with this MOF. In order to probe the role of the amino moiety, we turned our attention to UiO-67, UiO-67-NMe₂ and UiO-67-NH₂. In these MOFs, the amino moiety is in close proximity to the zirconium node. We observed that UiO-67-NH₂ is a faster catalyst than UiO-67 and UiO-67-NMe₂. We conclude that the role of the amino moiety is to act as a proton-transfer agent during the catalytic cycle and not to hydrogen bond or to form a phosphorane intermediate.     

Vermicious thermo-responsive Pickering emulsifiers

Thermo-responsive vermicious (or worm-like) diblock copolymer nanoparticles prepared directly in n-dodecane via polymerisation-induced self-assembly (PISA) were used to stabilise water-in-oil Pickering emulsions. Mean droplet diameters could be tuned from 8 to 117 μm by varying the worm copolymer concentration and the water volume fraction and very high worm adsorption efficiencies (∼100%) could be obtained below a certain critical copolymer concentration (∼0.50%). Heating a worm dispersion up to 150 °C led to a worm-to-sphere transition, which proved to be irreversible if conducted at sufficiently low copolymer concentration. This affords a rare opportunity to directly compare the Pickering emulsifier performance of chemically identical worms and spheres. It is found that the former nanoparticles are markedly more efficient, since worm-stabilised water droplets are always smaller than the equivalent sphere-stabilised droplets prepared under identical conditions. Moreover, the latter emulsions are appreciably flocculated, whereas the former emulsions proved to be stable. SAXS studies indicate that the mean thickness of the adsorbed worm layer surrounding the water droplets is comparable to that of the worm cross-section diameter determined for non-adsorbed worms dispersed in the continuous phase. Thus the adsorbed worms form a monolayer shell around the water droplets, rather than ill-defined multilayers. Under certain conditions, demulsification occurs on heating as a result of a partial worm-to-sphere morphological transition.     

Extending N-heterocyclic carbene ligands into the third dimension: a new type of hybrid phosphazane/NHC system

A simple, “click” synthetic approach to a new type of hybrid phosph(III)azane/NHC system is described. The presence of the phosphazane P₂N₂ ring unit, with P atoms flanking the NCN fragment and with this ring perpendicular to the binding site of the NHC, provides unique opportunities for modifying the electronic and steric character of these carbenes.     

Biphen[n]arenes

To design and exploit novel macrocyclic synthetic receptors is a permanent and challenging topic in supramolecular chemistry. Here we describe the one-pot synthesis, unique geometries and intriguing host–guest properties of a new class of supramolecular macrocycles – biphen[n]arenes (n = 3, 4), which are made up of 4,4′-biphenol or 4,4′-biphenol ether units linked by methylene bridges at the 3- and 3′- positions. The biphenarene macrocycles are conveniently accessible/modifiable and extremely guest-friendly. Particularly, biphen[4]arene is capable of forming inclusion complexes with not only organic cationic guests but also neutral π-electron deficient molecules. Compared with calixarenes, resorcinarenes, cyclotriveratrylenes and pillararenes with substituted mono-benzene units, the biphen[n]arenes reported here possess significantly different characteristics in both their topologic structures and their recognition properties, and thus can find broad applications in supramolecular chemistry and other areas.     

Redox-induced umpolung of transition metal carbenes

Metal carbene complexes have been at the forefront of organic and organometallic synthesis and are instrumental in guiding future sustainable chemistry efforts. While classical Fischer and Schrock type carbenes have been intensely studied, compounds that do not fall within one of these categories have attracted attention only recently. In addition, applications of carbene complexes rarely take advantage of redox processes, which could open up a new dimension for their use in practical processes. Herein, we report an umpolung of a nucleophilic palladium carbene complex, [{PC(sp²)P}^tBuPd(PMe₃)] ({PC(sp²)P}^tBu = bis[2-(di-iso-propylphosphino)-4-tert-butylphenyl]methylene), realized by successive one-electron oxidations that generated a cationic carbene complex, [{PC(sp²)P}^tBuPdI]⁺, via a carbene radical, [{PC˙(sp²)P}^tBuPdI]. An EPR spectroscopic study of [{PC˙(sp²)P}^tBuPdI] indicated the presence of a ligand-centered radical, also supported by the results of reactions with 9,10-dihydroanthracene and PhSSPh. The cationic carbene complex shows electrophilic behavior toward nucleophiles such as NaH, ^pTolNHLi, PhONa, and PMe₃, resulting from an inversion of the electronic character of the Pd–C_carbene bond in [{PC(sp²)P}^tBuPd(PMe₃)]. The redox induced umpolung is reversible and unprecedented.