Chirality control of a single carbene molecule by tip-induced van der Waals interactions.

Non-covalent interactions such as van der Waals interactions and hydrogen bonds are crucial for the chiral induction and control of molecules, but it remains difficult to study them at the single-molecule level. Here, we report a carbene molecule on a copper surface as a prototype of an anchored molecule with a facile chirality change. We examine the influence of the attractive van der Waals interactions on the chirality change by regulating the tip-molecule distance, resulting in an excess of a carbene enantiomer.

Multivalent Molecular Tweezers Disrupt the Essential NDC80 Interaction with Microtubules.

Binding of microtubule filaments by the conserved Ndc80 protein is required for kinetochore-microtubule attachments in cells and the successful distribution of the genetic material during cell division. The reversible inhibition of microtubule binding is an important aspect of the physiological error correction process. Small molecule inhibitors of protein-protein interactions involving Ndc80 are therefore highly desirable, both for mechanistic studies of chromosome segregation and also for their potential therapeutic value.

C-C Coupling of Carbene Molecules on a Metal Surface in the Presence of Water.

A novel surface-confined C-C coupling reaction involving two carbene molecules and a water molecule was studied by scanning tunneling microscopy in real space. Carbene fluorenylidene was generated from diazofluorene in the presence of water on a silver surface. While in the absence of water, fluorenylidene covalently binds to the surface to form a surface metal carbene, and water can effectively compete with the silver surface in reacting with the carbene.

The C-terminal 32-mer fragment of hemoglobin alpha is an amyloidogenic peptide with antimicrobial properties.

Antimicrobial peptides (AMPs) are major components of the innate immune defense. Accumulating evidence suggests that the antibacterial activity of many AMPs is dependent on the formation of amyloid-like fibrils. To identify novel fibril forming AMPs, we generated a spleen-derived peptide library and screened it for the presence of amyloidogenic peptides.

Surface Diffusion Aided by a Chirality Change of Self-Assembled Oligomers under 2D Confinement.

Chirality switching of self-assembled molecular structures is of potential interest for designing functional materials but is restricted by the strong interaction between the embedded molecules. Here, we report on an unusual approach based on reversible chirality changes of self-assembled oligomers using variable-temperature scanning tunneling microscopy supported by quantum mechanical calculations. Six functionalized diazomethanes each self-assemble into chiral wheel-shaped oligomers on Ag(111).

PPI-Affinity: A Web Tool for the Prediction and Optimization of Protein-Peptide and Protein-Protein Binding Affinity.

Virtual screening of protein-protein and protein-peptide interactions is a challenging task that directly impacts the processes of hit identification and hit-to-lead optimization in drug design projects involving peptide-based pharmaceuticals. Although several screening tools designed to predict the binding affinity of protein-protein complexes have been proposed, methods specifically developed to predict protein-peptide binding affinity are comparatively scarce. Frequently, predictors trained to score the affinity of small molecules are used for peptides indistinctively, despite the larger complexity and heterogeneity of interactions rendered by peptide binders.

An allosteric HTRA1-calpain 2 complex with restricted activation profile.

SignificanceClassic serine proteases are synthesized as inactive precursors that are proteolytically processed, resulting in irreversible activation. We report an alternative and reversible mechanism of activation that is executed by an inactive protease. This mechanism involves a protein complex between the serine protease HTRA1 and the cysteine protease calpain 2.

The role of DNA nanostructures in the catalytic properties of an allosterically regulated protease.

DNA-scaffolded enzymes typically show altered kinetic properties; however, the mechanism behind this phenomenon is still poorly understood. We address this question using thrombin, a model of allosterically regulated serine proteases, encaged into DNA origami cavities with distinct structural and electrostatic features. We compare the hydrolysis of substrates that differ only in their net charge due to a terminal residue far from the cleavage site and presumably involved in the allosteric activation of thrombin.

Inhibition of Staphylococcus aureus biofilm-forming functional amyloid by molecular tweezers.

Biofilms are rigid and largely impenetrable three-dimensional matrices constituting virulence determinants of various pathogenic bacteria. Here, we demonstrate that molecular tweezers, unique supramolecular artificial receptors, modulate biofilm formation of Staphylococcus aureus. In particular, the tweezers affect the structural and assembly properties of phenol-soluble modulin α1 (PSMα1), a biofilm-scaffolding functional amyloid peptide secreted by S.

Specific inhibition of the Survivin-CRM1 interaction by peptide-modified molecular tweezers.

Survivin's dual function as apoptosis inhibitor and regulator of cell proliferation is mediated via its interaction with the export receptor CRM1. This protein-protein interaction represents an attractive target in cancer research and therapy. Here, we report a sophisticated strategy addressing Survivin's nuclear export signal (NES), the binding site of CRM1, with advanced supramolecular tweezers for lysine and arginine.

Controlling Reactivity-Real-Space Imaging of a Surface Metal Carbene.

Metal carbenes are key intermediates in a plethora of homogeneous and heterogeneous catalytic processes. However, despite their importance to heterogeneous catalysis, the influence of surface attachment on carbene reactivity has not yet been explored. Here, we reveal the interactions of fluorenylidene (FY), an archetypical aromatic carbene of extreme reactivity, with a Ag(111) surface.

Conformer-Specific Heavy-Atom Tunneling in the Rearrangement of Benzazirines to Ketenimines.

5-Methoxy-2-benzazirine was prepared via irradiation of the corresponding phenyl azide, isolated in an argon matrix at cryogenic temperatures. It undergoes ring expansion to the corresponding ketenimine in the dark at < 30 K despite a calculated activation barrier of 4.9 kcal mol [B3LYP/6-311++G(d,p)].

Persistent Organic High-Spin Trinitrenes.

The septet ground state trinitrenes 1,3,5-trichloro-2,4,6-trinitrenobenzene and 1,3,5-tribromo-2,4,6-trinitrenobenzene were isolated in inert (Ar, Ne, and Xe) as well as reactive matrices (H , O , and H O) at cryogenic temperatures. These trinitrenes were obtained in high yields by UV photolysis of the corresponding triazides and characterized by IR and UV/Vis spectroscopy. The trinitrenes, despite bearing six unpaired electrons, are remarkably unreactive towards molecular oxygen and hydrogen and are persistent in water ice up to 160 K where the water matrix starts to sublime off.

Solvent-Enhanced Conformational Flexibility of Cyclic Tetrapeptides.

Solvent and temperature can affect the structural properties of cyclic peptides by controlling their flexibility. Here, we investigate two cyclic peptides, featuring beta turns. Using temperature-dependent NMR and FT-IR, we observed a pronounced temperature effect on the conformation of the cyclic peptide D-1 in CHCl but a much smaller effect in CH CN.

Gas-Phase Deprotonation of Benzhydryl Cations: Carbene Basicity, Multiplicity, and Rearrangements.

Many fundamental properties of carbenes, particularly basicity, remain poorly understood. Herein, an experimental and computational examination of the deprotonation of a series of benzhydryl cations has been undertaken. These studies represent the first attempt at providing experimental values for diarylcarbene basicities.

Switching the Spin State of Pentafluorophenylnitrene: Isolation of a Singlet Arylnitrene Complex.

The chemistry of arylnitrenes is dominated by their triplet ground states and excited open-shell singlet states. This results in radical-type reactions and unwanted rearrangements, which diminish the use of arylnitrenes as intermediates in organic synthesis. While the closed-shell singlet states of arylnitrenes are expected to undergo useful chemical transformations (comparable to the closed-shell singlet states of carbenes), these states are too high in energy to be chemically accessible.

Activation of Molecular Hydrogen by Arylcarbenes.

The hydrogenation reactions of diphenylcarbene 1, fluorenylidene 2, and dibenzocycloheptadienylidene 3 were investigated in solid H and D matrices and in H - and D -doped argon matrices at cryogenic temperatures. The reactivity of the carbenes towards H increases in the order 1<3<2. Whereas 1 is stable in solid H , 2 and 3 react fast under the same conditions via quantum chemical tunneling.

Reactions of Cyclopentadienylidenes with CFI: Electron Bond Donation versus Halogen Bond Donation of the Iodine Atom.

The interaction of cyclopentadienylidene and tetrachlorocyclopentadienylidene with the halogen bond donor CFI has been studied by matrix isolation spectroscopy. The carbenes were produced by photolysis of the corresponding diazo compounds, matrix-isolated in argon doped with 1% CFI at 3 K. Bimolecular reactions between the carbenes and CFI were induced by annealing these matrices to 25-30 K to allow for the diffusion of trapped species.

Isolation of an Antiaromatic Singlet Cyclopentadienyl Zwitterion.

The reaction of triplet tetrachlorocyclopentadienylidene with BF in rare gas matrices yields a zwitterion consisting of a cyclopentadienyl cation bearing a positive charge and a negatively charged BF unit. IR and UV-vis spectra as well as the absence of EPR signals demonstrate a singlet ground state of the zwitterion, and its calculated geometry and magnetic properties clearly reveal a strong antiaromatic character. The zwitterion is highly labile and by visible or IR irradiation rearranges via a 1,2-fluorine migration from boron to carbon.

Photoinduced Reversible Electron Transfer Between the Benzhydryl Radical and Benzhydryl Cation in Amorphous Water-Ice.

The benzhydryl radical is generated in high yields by flash-vacuum thermolysis of 1,1,2,2-tetraphenylethane with subsequent trapping of the product in argon or amorphous water at 3-4 K. Photoionization of the radical with various UV lights and electron sources produces the benzhydryl cation, which was identified by IR and UV-vis spectroscopy. In solid argon, the formation of the benzhydryl cation is irreversible, whereas in amorphous water-ice the electron transfer is reversible, and irradiation into the major absorption band at 443 nm of the cation leads back to the radical by electron attachment.

The Cope Rearrangement of 1,5-Dimethylsemibullvalene-2(4)-d : Experimental Evidence for Heavy-Atom Tunneling.

As an experimental test of the theoretical prediction that heavy-atom tunneling is involved in the degenerate Cope rearrangement of semibullvalenes at cryogenic temperatures, monodeuterated 1,5-dimethylsemibullvalene isotopomers were prepared and investigated by IR spectroscopy using the matrix isolation technique. As predicted, the less thermodynamically stable isotopomer rearranges at cryogenic temperatures in the dark to the more stable one, while broadband IR irradiation above 2000 cm results in an equilibration of the isotopomeric ratio. Since this reaction proceeds with a rate constant in the order of 10  s despite an experimental barrier of E =4.

Activation of the B-F Bond by Diphenylcarbene: A Reversible 1,2-Fluorine Migration between Boron and Carbon.

Experiments in low-temperature matrices reveal that triplet diphenylcarbene inserts into the very strong B-F bond of BF in a two-step reaction. The first step is the formation of a strongly bound Lewis acid-base complex between the singlet state of diphenylcarbene and BF . This step involves an inversion of the spin state of the carbene from triplet to singlet.

Reaction of Triplet Phenylnitrene with Molecular Oxygen.

Triplet carbenes react with molecular oxygen with rates that approach diffusion control to carbonyl O-oxides, whereas triplet nitrenes react much slower. For investigating the reaction of phenylnitrene with O2, the nitrene was generated by flash vacuum thermolysis (FVT) of phenylazide and subsequently isolated in O2-doped matrices. FVT of the azide produces the nitrene in high yield and with only minor contaminations of the rearranged products that are frequently observed if the nitrene is produced by photolysis.