Synthesis of Benzaldehyde‐Functionalized Glycans: A Novel Approach Towards Glyco‐SAMs as a Tool for Surface Plasmon Resonance Studies

In recent years the interest in tools for investigating carbohydrate–protein (CPI) and carbohydrate‐carbohydrate interactions (CCI) has increased significantly. For the investigation of CPI and CCI, several techniques employing different linking methods are available. Surface plasmon resonance (SPR) imaging is a most appropriate tool for analyzing the formation of self‐assembled monolayers (SAM) of carbohydrate derivatives, which can mimic the glycocalyx. In contrast to the SPR imaging methods used previously to analyze CPI and CCI, the novel approach reported herein allows a facile and rapid synthesis of linker spacers and carbohydrate derivatives and enhances the binding event by controlling the amount and orientation of ligand. For immobilization on biorepulsive amino‐functionalized SPR chips by reductive amination, diverse aldehyde‐functionalized glycan structures (glucose, galactose, mannose, glucosamine, cellobiose, lactose, and lactosamine) have been synthesized in several facile steps that include olefin metathesis. Effective immobilization and the first binding studies are presented for the lectin concanavalin A.     

Photoinduced Electron Transfer‐based Halogen‐free Photosensitizers: Covalent meso‐Aryl (Phenyl,Naphthyl, Anthryl,and Pyrenyl) as Electron Donors to Effectively Induce the Formation of the Excited Triplet State and Singlet Oxygen for BODIPY Compounds

Pristine BODIPY compounds have negligible efficiency to generate the excited triplet state and singlet oxygen. In this report, we show that attaching a good electron donor to the BODIPY core can lead to singlet oxygen formation with up to 58 % quantum efficiency. For this purpose, BODIPYs with meso ‐aryl groups (phenyl, naphthyl, anthryl, and pyrenyl) were synthesized and characterized. The fluorescence, excited triplet state, and singlet oxygen formation properties for these compounds were measured in various solvents by UV/Vis absorption, steady‐state and time‐resolved fluorescence methods, as well as laser flash photolysis technique. In particular, the presence of anthryl and pyrenyl showed substantial enhancement on the singlet oxygen formation ability of BODIPY with up to 58 % and 34 % quantum efficiency, respectively, owing to their stronger electron‐donating ability. Upon the increase in singlet oxygen formation, the fluorescence quantum yield and lifetime values of the aryl‐BODIPY showed a concomitant decrease. The increase in solvent polarity enhances the singlet oxygen generation but decreases the fluorescence quantum yield. The results are explained by the presence of intramolecular photoinduced electron transfer from the aryl moiety to BODIPY core. This method of promoting T₁ formation is very different from the traditional heavy atom effect by I, Br, or transition metal atoms. This type of novel photosensitizers may find important applications in organic oxygenation reactions and photodynamic therapy of tumors.     

The Hunt for the Closed Conformation of the Fruit-Ripening Enzyme 1-Aminocyclopropane-1-carboxylic Oxidase: A Combined Electron Paramagnetic Resonance and Molecular Dynamics Study

1-Aminocyclopropane-1-carboxylic oxidase (ACCO) is a non-heme iron(II)-containing enzyme involved in the biosynthesis of the phytohormone ethylene, which regulates fruit ripening and flowering in plants. The active conformation of ACCO, and in particular that of the C-terminal part, remains unclear and open and closed conformations have been proposed. In this work, a combined experimental and computational study to understand the conformation and dynamics of the C-terminal part is reported. Site-directed spin-labeling coupled to electron paramagnetic resonance (SDSL-EPR) spectroscopy was used. Mutagenesis experiments were performed to generate active enzymes bearing two paramagnetic labels (nitroxide radicals) anchored on cysteine residues, one in the main core and one in the C-terminal part. Inter-spin distance distributions were measured by pulsed EPR spectroscopy and compared with the results of molecular dynamics simulations. The results reveal the existence of a flexibility of the C-terminal part. This flexibility generates several conformations of the C-terminal part of ACCO that correspond neither to the existing crystal structures nor to the modelled structures. This highly dynamic region of ACCO raises questions on its exact function during enzymatic activity.     

Haruspex: A Neural Network for the Automatic Identification of Oligonucleotides and Protein Secondary Structure in Cryo‐Electron Microscopy Maps

In recent years, three‐dimensional density maps reconstructed from single particle images obtained by electron cryo‐microscopy (cryo‐EM) have reached unprecedented resolution. However, map interpretation can be challenging, in particular if the constituting structures require de‐novo model building or are very mobile. Herein, we demonstrate the potential of convolutional neural networks for the annotation of cryo‐EM maps: our network Haruspex has been trained on a carefully curated set of 293 experimentally derived reconstruction maps to automatically annotate RNA/DNA as well as protein secondary structure elements. It can be straightforwardly applied to newly reconstructed maps in order to support domain placement or as a starting point for main‐chain placement. Due to its high recall and precision rates of 95.1 % and 80.3 %, respectively, on an independent test set of 122 maps, it can also be used for validation during model building. The trained network will be available as part of the CCP‐EM suite.     

Structure and Bonding Nature of the Strained Lewis Acid 3‐Methyl‐1‐boraadamantane: A Case Study Employing a New Data‐Analysis Procedure in Gas Electron Diffraction

Base‐free 3‐methyl‐1‐boraadamantane was synthesized by starting from its known THF adduct, transforming it to a butylate‐complex with n‐butyllithium, cleaving the cage with acetyl chloride to give 3‐n‐butyl‐5‐methyl‐7‐methylene‐3‐borabicyclo[3.3.1]nonane and closing the cage again by reacting the latter with dicyclohexylborane. The identity of 3‐methyl‐1‐boraadamantane was proven by ¹H, ¹¹B and ¹³C NMR spectroscopy and elemental analysis. The experimental equilibrium structure of the free 3‐methyl‐1‐boraadamantane molecules has been determined at 100 °C by using gas‐phase electron diffraction. For this structure determination, an improved method for data analysis has been introduced and tested: the structural refinement versus gas‐phase electron diffraction data (in terms of Cartesian coordinates) with a set of quantum‐chemically derived regularization constraints for the complete structure under optimization of a regularization constant, which maximizes the contribution of experimental data while retaining a stable refinement. The detailed analysis of parameter errors shows that the new approach allows obtaining more reliable results. The most important structural parameters are: r_e(B‐C)_av=1.556(5) Å, ${\angle }$ _e(C‐B‐C)_av=116.5(2)°. The configuration of the boron atom is pyramidal with ${\sum \angle }$ (C‐B‐C)=349.4(4)°. The nature of bonding was analyzed further by applying the natural bond orbital (NBO) and atoms in molecules (AIM) approaches. The experimentally observed shortening of the B? C bonds and elongation of the adjacent C? C bonds can be explained by the σ(C‐C)→p(B) hyperconjugation model. Both NBO and AIM analyses predict that the B? C bonds are significantly bent in the direction out of the cage.     

Modulation of Electron Injection Dynamics of Ru‐Based Dye/TiO2 System in the Presence of Three Different Organic Solvents: Role of Solvent Dipole Moment and Donor Number

In the present work, femtosecond transient absorption spectroscopy (fs‐TAS) has been employed to investigate the electron injection efficiency (EIE) both from the singlet and triplet excited states of a well‐known ruthenium dye (N719) to the conduction band (CB) of nanostructured TiO₂ in presence of three different organic solvents [γ‐butylactone (GBL), 3‐methoxypropionitrile (MPN), and dimethylformamide (DMF)] with different donor numbers (DNs) and dipole moments (DMs). The DM and DN of a solvent modulates the CB edge energy of TiO₂, and this effect reflects well in the fs‐TAS results, which shows an EIE trend following the order GBL≥MPN?DMF, that is, highest in GBL and lowest in DMF solvent environments. Fs‐TAS results indicate a lower contribution of electron injection from both the singlet and triplet states in DMF, for which the dominant adsorption of DMF molecules on the TiO₂ surface seems to play an important role in the mechanism.     

Density Functional Calculations of 55Mn, 14N and 13C Electron Paramagnetic Resonance Parameters Support an Energetically Feasible Model System for the S2 State of the Oxygen‐Evolving Complex of Photosystem II

Metal and ligand hyperfine couplings of a previously suggested, energetically feasible Mn₄Ca model cluster ( SG2009^?1 ) for the S₂ state of the oxygen‐evolving complex (OEC) of photosystem II (PSII) have been studied by broken‐symmetry density functional methods and compared with other suggested structural and spectroscopic models. This was carried out explicitly for different spin‐coupling patterns of the S=1/2 ground state of the Mn^III(Mn^IV)₃ cluster. By applying spin‐projection techniques and a scaling of the manganese hyperfine couplings, computation of the hyperfine and nuclear quadrupole coupling parameters allows a direct evaluation of the proposed models in comparison with data obtained from the simulation of EPR, ENDOR, and ESEEM spectra. The computation of ⁵⁵Mn hyperfine couplings (HFCs) for SG2009^?1 gives excellent agreement with experiment. However, at the current level of spin projection, the ⁵⁵Mn HFCs do not appear sufficiently accurate to distinguish between different structural models. Yet, of all the models studied, SG2009^?1 is the only one with the Mn^III site at the Mn_C center, which is coordinated by histidine (D1‐His332). The computed histidine ¹⁴N HFC anisotropy for SG2009^?1 gives much better agreement with ESEEM data than the other models, in which Mn_C is an Mn^IV site, thus supporting the validity of the model. The ¹³C HFCs of various carboxylates have been compared with ¹³C ENDOR data for PSII preparations with ¹³C‐labelled alanine.