The raspberry model for protein-like particles: Ellipsoids and confinement in cylindrical pores

The study of protein mass transport via atomistic simulation requires time and length scales beyond the computational capabilities of modern computer systems. The raspberry model for colloidal particles in combination with the mesoscopic hydrodynamic method of lattice Boltzmann facilitates coarse-grained simulations that are on the order of microseconds and hundreds of nanometers for the study of diffusive transport of protein-like colloid particles. The raspberry model reproduces linearity in resistance to motion versus particle size and correct enhanced drag within cylindrical pores at off-center coordinates for spherical particles. Owing to the high aspect ratio of many proteins, ellipsoidal raspberry colloid particles were constructed and reproduced the geometric resistance factors of Perrin and of Happel and Brenner in the laboratory-frame and in the moving body-frame. Accurate body-frame rotations during diffusive motion have been captured for the first time using projections of displacements. The spatial discretization of the fluid leads to a renormalization of the hydrodynamic radius, however, the data describes a self-consistent hydrodynamic frame within this renormalized system.     

Model for self-propulsive helical filaments: kink-pair propagation

Spiroplasma bacteria propel through viscous fluids by sending kinks or domain walls between regions of opposite handedness down their helical body. A simple elastic model for the domain-wall propagation is formulated and studied using hydrodynamic simulations and scaling arguments, giving good agreement with recent video-microscopy observations. It is shown that the observed helical bacterial pitch angle psi approximately 35 degrees is optimized for maximal speed and efficiency.     

Anomalous polymer sedimentation far from equilibrium

A single flexible polymer in strong sedimentation fields is investigated using hydrodynamic simulations and scaling arguments. For short chains and small fields compaction is observed. For elevated fields or long chains the chain stretches and the sedimentation coefficient decreases, in agreement with ultracentrifuge experiments on linear as well as circular DNA. For very large fields a tadpole forms consisting of a compact leading head and a trailing stretched tail.     

Fundamental Characterization,Photophysics and Photocatalysis of a Base Metal Iron(II)-Cobalt(III) Dyad

A new base metal iron-cobalt dyad has been obtained by connection between a heteroleptic tetra-NHC iron(II) photosensitizer combining a 2,6-bis[3-(2,6-diisopropylphenyl)imidazol-2-ylidene]pyridine with 2,6-bis(3-methyl-imidazol-2-ylidene)-4,4′-bipyridine ligand, and a cobaloxime catalyst. This novel iron(II)-cobalt(III) assembly has been extensively characterized by ground- and excited-state methods like X-ray crystallography, X-ray absorption spectroscopy, (spectro-)electrochemistry, and steady-state and time-resolved optical absorption spectroscopy, with a particular focus on the stability of the molecular assembly in solution and determination of the excited-state landscape. NMR and UV/Vis spectroscopy reveal dissociation of the dyad in acetonitrile at concentrations below 1 mM and high photostability. Transient absorption spectroscopy after excitation into the metal-to-ligand charge transfer absorption band suggests a relaxation cascade originating from hot singlet and triplet MLCT states, leading to the population of the ³MLCT state that exhibits the longest lifetime. Finally, decay into the ground state involves a ³MC state. Attachment of cobaloxime to the iron photosensitizer increases the ³MLCT lifetime at the iron centre. Together with the directing effect of the linker, this potentially makes the dyad more active in photocatalytic proton reduction experiments than the analogous two-component system, consisting of the iron photosensitizer and Co(dmgH)₂(py)Cl. This work thus sheds new light on the functionality of base metal dyads, which are important for more efficient and sustainable future proton reduction systems.     

On-Surface Synthesis of Cumulene-Containing Polymers via Two-Step Dehalogenative Homocoupling of Dibromomethylene-Functionalized Tribenzoazulene

Cumulene compounds are notoriously difficult to prepare and study because their reactivity increases dramatically with the increasing number of consecutive double bonds. In this respect, the emerging field of on-surface synthesis provides exceptional opportunities because it relies on reactions on clean metal substrates under well-controlled ultrahigh-vacuum conditions. Here we report the on-surface synthesis of a polymer linked by cumulene-like bonds on a Au(111) surface via sequential thermally activated dehalogenative C−C coupling of a tribenzoazulene precursor equipped with two dibromomethylene groups. The structure and electronic properties of the resulting polymer with cumulene-like pentagon–pentagon and heptagon–heptagon connections have been investigated by means of scanning probe microscopy and spectroscopy methods and X-ray photoelectron spectroscopy, complemented by density functional theory calculations. Our results provide perspectives for the on-surface synthesis of cumulene-containing compounds, as well as protocols relevant to the stepwise fabrication of carbon–carbon bonds on surfaces.     

Near-Enantiopure Trimerization of 9-Ethynylphenanthrene on a Chiral Metal Surface

Enantioselectivity in heterogeneous catalysis strongly depends on the chirality transfer between catalyst surface and all reactants, intermediates, and the product along the reaction pathway. Herein we report the first enantioselective on-surface synthesis of molecular structures from an initial racemic mixture and without the need of enantiopure modifier molecules. The reaction consists of a trimerization via an unidentified bonding motif of prochiral 9-ethynylphenanthrene (9-EP) upon annealing to 500 K on the chiral Pd₃-terminated PdGa{111} surfaces into essentially enantiopure, homochiral 9-EP propellers. The observed behavior strongly contrasts the reaction of 9-EP on the chiral Pd₁-terminated PdGa{111} surfaces, where 9-EP monomers that are in nearly enantiopure configuration, dimerize without enantiomeric excess. Our findings demonstrate strong chiral recognition and a significant ensemble effect in the PdGa system, hence highlighting the huge potential of chiral intermetallic compounds for enantioselective synthesis and underlining the importance to control the catalytically active sites at the atomic level.     

TEAD–YAP Interaction Inhibitors and MDM2 Binders from DNA-Encoded Indole-Focused Ugi Peptidomimetics

DNA-encoded combinatorial synthesis provides efficient and dense coverage of chemical space around privileged molecular structures. The indole side chain of tryptophan plays a prominent role in key, or “hot spot”, regions of protein–protein interactions. A DNA-encoded combinatorial peptoid library was designed based on the Ugi four-component reaction by employing tryptophan-mimetic indole side chains to probe the surface of target proteins. Several peptoids were synthesized on a chemically stable hexathymidine adapter oligonucleotide “hexT”, encoded by DNA sequences, and substituted by azide-alkyne cycloaddition to yield a library of 8112 molecules. Selection experiments for the tumor-relevant proteins MDM2 and TEAD4 yielded MDM2 binders and a novel class of TEAD-YAP interaction inhibitors that perturbed the expression of a gene under the control of these Hippo pathway effectors.     

Protein Allostery at Atomic Resolution

Protein allostery is a phenomenon involving the long range coupling between two distal sites in a protein. In order to elucidate allostery at atomic resoluion on the ligand-binding WW domain of the enzyme Pin1, multistate structures were calculated from exact nuclear Overhauser effect (eNOE). In its free form, the protein undergoes a microsecond exchange between two states, one of which is predisposed to interact with its parent catalytic domain. In presence of the positive allosteric ligand, the equilibrium between the two states is shifted towards domain–domain interaction, suggesting a population shift model. In contrast, the allostery-suppressing ligand decouples the side-chain arrangement at the inter-domain interface thereby reducing the inter-domain interaction. As such, this mechanism is an example of dynamic allostery. The presented distinct modes of action highlight the power of the interplay between dynamics and function in the biological activity of proteins.     

Rare-earth Metal Borosilicides R9Si15–xB3 (R = Tb,Yb): New Ordered Structures Derived from the AlB2 Structure Type

Two novel ternary borosilicides R₉Si_15–xB₃ (R = Tb, x = 1.80, R = Yb, x = 1.17) were synthesized from the initial elements using tin flux method. Their crystal structures were determined by means of X-ray single crystal diffraction. Both refer to space group R32, Z = 1: a = 6.668(2) Å, c = 12.405(4) Å [R₁ = 0.027, wR₂ = 0.031 for 1832 reflections with I_o > 2σ (I_o)] for Tb₉Si_15–xB₃, and a = 6.5796(3) Å, c = 12.2599(5) Å [R_F = 0.052, wR = 0.090 for 1369 reflections with I_o > 2σ (I_o)] for Yb₉Si_15–xB₃. The structures represent a new structure type, derived from that of AlB₂, with ordering in the metalloid sublattice resulting in distorted [Si₅B] hexagons. The presence or absence of boron in this ordered structure is discussed on the basis of difference Fourier syntheses, interatomic distances, structural analysis, and theoretical calculations in relation with the parent structures of the binaries AlB₂ and Yb₃Si₅ (Th₃Pd₅ type of structure). Theoretical calculations show substantial covalent interactions between the metal and nonmetal elements. The small percentage of silicon atoms, which are missing in these nonstoichiometric compounds, probably allows strengthening boron-metal and boron-silicon bonding.     

Capturing the Monomeric (L)CuH in NHC‐Capped Cyclodextrin: Cavity‐Controlled Chemoselective Hydrosilylation of α,β‐Unsaturated Ketones

The encapsulation of copper inside a cyclodextrin capped with an N‐heterocyclic carbene (ICyD) allowed both to catch the elusive monomeric (L)CuH and a cavity‐controlled chemoselective copper‐catalyzed hydrosilylation of α,β‐unsaturated ketones. Remarkably, (α‐ICyD)CuCl promoted the 1,2‐addition exclusively, while (β‐ICyD)CuCl produced the fully reduced product. The chemoselectivity is controlled by the size of the cavity and weak interactions between the substrate and internal C?H bonds of the cyclodextrin.