OsB : An Aromatic Osmium-Centered Monocyclic Boron Ring.

Transition-metal-centered monocyclic boron wheels are important candidates in the family of planar hypercoordinate species that show intriguing structure, stability and bonding situation. Through the detailed potential energy surface explorations of MB (M = Fe, Ru, Os) clusters, we introduce herein OsB to be a new member in the transition-metal-centered borometallic molecular wheel gallery. Previously, FeB and RuB clusters were detected by photoelectron spectroscopy and the structures were reported to have singlet symmetry.

A Two-Step Baromechanical Cycle for Repeated Activation and Deactivation of Mechanophores.

Mechanophores that are embedded in a polymer backbone respond to the application of mechanical stretching forces by geometric changes such as bond rupture. Typically, these structural changes are irreversible, which limits the applicability of functional materials incorporating mechanophores. Using computational methods, we, here, present a general method of restoring a force-activated mechanophore to its deactivated form by using hydrostatic pressure.

Assessing Density Functional Theory for Chemically Relevant Open-Shell Transition Metal Reactions.

Due to the principle lack of systematic improvement possibilities of density functional theory, careful assessment of the performance of density functional approximations (DFAs) on well-designed benchmark sets, for example, for reaction energies and barrier heights, is crucial. While main-group chemistry is well covered by several available sets, benchmark data for transition metal chemistry is sparse. This is especially the case for larger, chemically relevant molecules.

Diphosphino-Functionalized 1,8-Naphthyridines: a Multifaceted Ligand Platform for Boranes and Diboranes.

A 1,8-naphthyridine diphosphine (NDP) reacts with boron-containing Lewis acids to generate complexes featuring a number of different naphthyridine bonding modes. When exposed to diborane B Br , NDP underwent self-deprotonation to afford [NDP-B Br ]Br, an unsymmetrical diborane comprised of four fused rings. The reaction of two equivalents of monoborane BBr and NDP in a non-polar solvent provided the simple phosphine-borane adduct [NDP(BBr ) ], which then underwent intramolecular halide abstraction to furnish the salt [NDP-BBr ][BBr ], featuring a different coordination mode from that of [NDP-B Br ]Br.

KAHRP dynamically relocalizes to remodeled actin junctions and associates with knob spirals in Plasmodium falciparum-infected erythrocytes.

The knob-associated histidine-rich protein (KAHRP) plays a pivotal role in the pathophysiology of Plasmodium falciparum malaria by forming membrane protrusions in infected erythrocytes, which anchor parasite-encoded adhesins to the membrane skeleton. The resulting sequestration of parasitized erythrocytes in the microvasculature leads to severe disease. Despite KAHRP being an important virulence factor, its physical location within the membrane skeleton is still debated, as is its function in knob formation.

Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package.

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods.

Insights from Adsorption and Electron Modification Studies of Polyoxometalates on Surfaces for Molecular Memory Applications.

This Account highlights recent experimental and theoretical work focusing on the development of polyoxometalates (POMs) as possible active switching units in what may be called "molecule-based memory cells". Herein, we critically discuss how multiply charged vanadium-containing POMs, which exhibit stable metal-oxo bonds and are characterized by the excellent ability to change their redox states without significant structural distortions of the central polyoxoanion core, can be immobilized best and how they may work optimally at appropriate surfaces. Furthermore, we critically discuss important issues and challenges on the long way toward POM-based nanoelectronics.

High-Throughput Non-targeted Chemical Structure Identification Using Gas-Phase Infrared Spectra.

The high-throughput identification of unknown metabolites in biological samples remains challenging. Most current non-targeted metabolomics studies rely on mass spectrometry, followed by computational methods that rank thousands of candidate structures based on how closely their predicted mass spectra match the experimental mass spectrum of an unknown. We reasoned that the infrared (IR) spectra could be used in an analogous manner and could add orthologous structure discrimination; however, this has never been evaluated on large data sets.

Serine-ubiquitination regulates Golgi morphology and the secretory pathway upon Legionella infection.

SidE family of Legionella effectors catalyze non-canonical phosphoribosyl-linked ubiquitination (PR-ubiquitination) of host proteins during bacterial infection. SdeA localizes predominantly to ER and partially to the Golgi apparatus, and mediates serine ubiquitination of multiple ER and Golgi proteins. Here we show that SdeA causes disruption of Golgi integrity due to its ubiquitin ligase activity.

Synthesis, Structure, and Surface Adsorption Characteristics of a Polynuclear Mn-Yb Complex.

The controlled adsorption of polynuclear coordination compounds with specific structural and electronic characteristics on surfaces is crucial for the prospective implementation of molecule-surface interfaces into practical electronic devices. From this perspective, a neutral 3d,4f-coordination cluster [MnMnYbO(OH)(L·SMe)(OOCMe)]·2MeCN·3EtOH (·2MeCN·3EtOH), where L·SMe is a Schiff base, has been synthesized and fully characterized and its adsorption on two different solid substrates, gold and graphite, has been studied. The mixed-valence compound with a bilayered metal core structure and the structurally exposed thioether groups exhibits a substantially different surface bonding to metallic gold and semimetallic graphite substrates.

Universal quenching of common fluorescent probes by water and alcohols.

Although biological imaging is mostly performed in aqueous media, it is hardly ever considered that water acts as a classic fluorescence quencher for organic fluorophores. By investigating the fluorescence properties of 42 common organic fluorophores recommended for biological labelling, we demonstrate that HO reduces their fluorescence quantum yield and lifetime by up to threefold and uncover the underlying fluorescence quenching mechanism. We show that the quenching efficiency is significantly larger for red-emitting probes and follows an energy gap law.

Efficient Quantum-Chemical Calculations of Acid Dissociation Constants from Free-Energy Relationships.

The calculation of acid dissociation constants (p) is an important task in computational chemistry and chemoinformatics. Theoretically and with minimal empiricism, this is possible from computed acid dissociation free energies via so-called linear free-energy relationships. In this study some modifications are introduced to the latter, providing a straightforward, broadly applicable protocol with an adjustable degree of sophistication for quantum chemistry-based calculations of p in water.

π-Conjugated stannole copolymers synthesised by a tin-selective Stille cross-coupling reaction.

The synthesis of four well-defined conjugated polymers containing unusual heterocycle units in the main chain, namely stannole units as building blocks, is reported. The stannole-thiophenyl copolymers were generated by tin-selective Stille coupling reactions in nearly quantitative yields of 94% to 98%. NMR data show that the tin atoms in the rings remain unaffected.

The rupture mechanism of rubredoxin is more complex than previously thought.

The surprisingly low rupture force and remarkable mechanical anisotropy of rubredoxin have been known for several years. Exploiting the first combination of steered molecular dynamics and the quantum chemical Judgement of Energy DIstribution (JEDI) analysis, the common belief that hydrogen bonds between neighboring amino acid backbones and the sulfur atoms of the central FeS unit in rubredoxin determine the low mechanical resistance of the protein is invalidated. The distribution of strain energy in the central part of rubredoxin is elucidated in real-time with unprecedented detail, giving important insights into the mechanical unfolding pathway of rubredoxin.

From QCEIMS to QCxMS: A Tool to Routinely Calculate CID Mass Spectra Using Molecular Dynamics.

Mass spectrometry (MS) is a powerful tool in chemical research and substance identification. For the computational modeling of electron ionization MS, we have developed the quantum-chemical electron ionization mass spectra (QCEIMS) program. Here, we present an extension of QCEIMS to calculate collision-induced dissociation (CID) spectra.

Calculation of absolute molecular entropies and heat capacities made simple.

We propose a fully-automated composite scheme for the accurate and numerically stable calculation of molecular entropies by efficiently combining density-functional theory (DFT), semi-empirical methods (SQM), and force-field (FF) approximations. The scheme is systematically expandable and can be integrated seamlessly with continuum-solvation models. Anharmonic effects are included through the modified rigid-rotor-harmonic-oscillator (msRRHO) approximation and the Gibbs-Shannon formula for extensive conformer ensembles (CEs), which are generated by a metadynamics search algorithm and are extrapolated to completeness.

Proton-Transfer Dynamics of Photoacidic Merocyanines in Aqueous Solution.

Photoacids attract increasing scientific attention, as they are valuable tools to spatiotemporally control proton-release reactions and pH values of solutions. We present the first time-resolved spectroscopic study of the excited state and proton-release dynamics of prominent merocyanine representatives. Femtosecond transient absorption measurements of a pyridine merocyanine with two distinct protonation sites revealed dissimilar proton-release mechanisms: one site acts as a photoacid generator as its pK value is modulated in the ground state after photoisomerization, while the other functions as an excited state photoacid which releases its proton within 1.

Two-photon absorption and excitation spectroscopy of carotenoids, chlorophylls and pigment-protein complexes.

In addition to (bacterio)chlorophylls, (B)Chls, photosynthetic pigment-protein complexes bind carotenoids (Cars) that fulfil various important functions which are not fully understood, yet. However, certain excited states of Cars are optically one-photon forbidden ("dark") and can potentially undergo excitation energy transfer (EET) to (B)Chls following two-photon absorption (TPA). The amount of EET is reflected by the differences in TPA and two-photon excitation (TPE) spectra of a complex (multi-pigment) system.

Isolation of Neutral, Mono-, and Dicationic B P Rings by Diphosphorus Addition to a Boron-Boron Triple Bond.

The NHC-stabilised diboryne (B (SIDep) ; SIDep=1,3-bis(2,6-diethylphenyl)imidazolin-2-ylidene) undergoes a high-yielding P-P bond activation with tetraethyldiphosphine at room temperature to form a B P heterocycle via a diphosphoryldiborene by 1,2-diphosphination. The heterocycle can be oxidised to a radical cation and a dication, respectively, depending on the oxidant used and its counterion. Starting from the planar, neutral 1,3-bis(alkylidene)-1,3-diborata-2,4-diphosphoniocyclobutane, each oxidation step leads to decreased B-B distances and loss of planarity by cationisation.

Adducts of the Parent Boraphosphaketene H BPCO and their Decarbonylative Insertion Chemistry.

The first examples of Lewis base adducts of the parent boraphosphaketene (H B-PCO) and their cyclodimers are prepared. One of these adducts is shown to undergo mild decarbonylation and phosphinidene insertion into a B-C bond of a borole, forming very rare examples of 1,2-phosphaborinines, B/P isosteres of benzene. The strong donor properties of these 1,2-phosphaborinines are confirmed by the synthesis of their π complexes with the Group 6 metals.

Selected tools to visualize membrane interactions.

In the past decade, we developed various fluorescence-based methods for monitoring membrane fusion, membrane docking, distances between membranes, and membrane curvature. These tools were mainly developed using liposomes as model systems, which allows for the dissection of specific interactions mediated by, for example, fusion proteins. Here, we provide an overview of these methods, including two-photon fluorescence cross-correlation spectroscopy and intramembrane Förster energy transfer, with asymmetric labelling of inner and outer membrane leaflets and the calibrated use of transmembrane energy transfer to determine membrane distances below 10 nm.

What defines a synthetic riboswitch? - Conformational dynamics of ciprofloxacin aptamers with similar binding affinities but varying regulatory potentials.

Among the many in vitro-selected aptamers derived from SELEX protocols, only a small fraction has the potential to be applied for synthetic riboswitch engineering. Here, we present a comparative study of the binding properties of three different aptamers that bind to ciprofloxacin with similar KD values, yet only two of them can be applied as riboswitches. We used the inherent ligand fluorescence that is quenched upon binding as the reporter signal in fluorescence titration and in time-resolved stopped-flow experiments.

Efficient Quantum Chemical Calculation of Structure Ensembles and Free Energies for Nonrigid Molecules.

The application of quantum chemical, automatic multilevel modeling workflows for the determination of thermodynamic (e.g., conformation equilibria, partition coefficients, p values) and spectroscopic properties of relatively large, nonrigid molecules in solution is described.

Quantum Dynamics of Exciton Transport and Dissociation in Multichromophoric Systems.

Due to the subtle interplay of site-to-site electronic couplings, exciton delocalization, nonadiabatic effects, and vibronic couplings, quantum dynamical studies are needed to elucidate the details of ultrafast photoinduced energy and charge transfer events in organic multichromophoric systems. In this vein, we review an approach that combines first-principles parameterized lattice Hamiltonians with accurate quantum dynamical simulations using advanced multiconfigurational methods. Focusing on the elementary transfer steps in organic functional materials, we address coherent exciton migration and creation of charge transfer excitons in homopolymers, notably representative of the poly(3-hexylthiophene) material, as well as exciton dissociation at polymer:fullerene heterojunctions.