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Interest in deep eutectic solvents (DESs), particularly for electrochemical applications, has boomed in the past decade because they are more versatile than conventional electrolyte solutions and are low cost, renewable, and non-toxic. The molecular scale lateral nanostructures as a function of potential at the solid–liquid interface—critical design parameters for the use of DESs as electrochemical solvents—are yet to be revealed. In this work, in situ amplitude modulated atomic force microscopy complemented by molecular dynamics simulations is used to probe the Stern and near-surface layers of the archetypal and by far most studied DES, 1:2 choline chloride:urea (reline), at the highly orientated pyrolytic graphite surface as a function of potential, to reveal highly ordered lateral nanostructures with unprecedented molecular resolution. This detail allows identification of choline, chloride, and urea in the Stern layer on graphite, and in some cases their orientations. Images obtained after the potential isswitched from negative to positive show the dynamics of the Stern layer response, revealing that several minutes are required to reach equilibrium. These results provide valuable insight into the nanostructure and dynamics of DESs at the solid–liquid interface, with implications for the rational design of DESs for interfacial applications.

Spectroscopic and computational examination of a homologous series of rhodium(I) pybox carbonyl complexes has revealed a correlation between the conformation of the flanking aryl-substituted oxazoline donors and the carbonyl stretching frequency. This relationship is also observed experimentally for octahedral rhodium(III) and ruthenium(II) variants and cannot be explained through the classical, Dewar-Chatt-Duncanson, interpretation of metal-carbonyl bonding. Instead, these findings are reconciled by local changes in the magnitude of the electric field that is projected along the metal-carbonyl vector: the internal Stark effect. ispartof: CHEMISTRY-A EUROPEAN JOURNAL vol:28 issue:69 ispartof: location:Germany status: published

A hitherto unexplored class of molecules for molecular force probe applications are expanded porphyrins. This work proves that mechanical force is an effective stimulus to trigger the interconversion between Hückel and Möbius topologies in [28]hexaphyrin, making these expanded porphyrins suitable to act as conformational mechanophores operating at mild (sub‐1 nn) force conditions. A straightforward approach based on distance matrices is proposed for the selection of pulling scenarios that promote either the planar Hückel topology or the three lowest lying Möbius topologies. This approach is supported by quantum mechanochemical calculations. Force distribution analyses reveal that [28]hexaphyrin selectively allocates the external mechanical energy to molecular regions that trigger Hückel–Möbius interconversions, explaining why certain pulling scenarios favor the Hückel two‐sided topology and others favor Möbius single‐sided topologies. The meso‐substitution pattern on [28]hexaphyrin determines whether the energy difference between the different topologies can be overcome by mechanical activation., Use the force: The Hückel and Möbius topology of [28]hexaphyrin can be mechanically locked by applying an external pulling force to different meso positions in a sub‐nano‐Newton force regime. The mechanical energy is distributed to a specific region in the molecule to trigger the interconversion.

Metabolomics is recognized as a crucial scientific domain, promising to advance our understanding of cell biology, physiology and medicine. Tandem mass spectrometry (MS/MS) has strong potential to elucidate the metabolites in complex biological samples and to become a standard tool complementing established techniques. However, despite its potential for answering many key questions, a major challenge in the use of tandem mass spectrometry for characterizing metabolites lies in a lack of computational tools for accurate annotation and structure identification allowing us to turn complex data into molecular knowledge. Chemo-informatics and related machine-learning in silico fragmentation tools have already been established and used for different classes of metabolites. For the classes of metabolites where existing chemo-informatics approaches produce insufficiently accurate predictions a supervised machine learning based strategy can be used to predict possible molecular structures from “unassigned” experimental tandem MS data. Here, we propose a new innovative in silico approach employing quantum mechanical (QM) methods in order to predict ion formation and subsequent fragmentation patterns of arbitrary small molecules and validate putative annotations of tandem mass spectrometry (MS) data. The focus is on the evaluation of a new conceptual density functional theory (CDFT) nuclear reactivity descriptor of the nuclear Fukui function type, that characterizes the forces that the atomic nuclei experience due to proton attachment and captures the onset of the change in the nuclear positions induced by it. A series of test compounds for which high quality experimental data exist and that were investigated before in a more approximate theoretical framework have been examined. The output of these calculations provides a list of the most probable molecular structures predicted to match the experimental tandem MS spectrum (“de novo metabolite identification”).

The bonding in heavier Group 14 zero-valent complexes of a general formula L2 E (E=Si-Pb; L=phosphine, N-heterocyclic and acyclic carbene, cyclic tetrylene and carbon monoxide) is probed by combining valence bond (VB) theory and maximum probability domain (MPD) approaches. All studied complexes are initially evaluated on the basis of the structural parameters and the shape of frontier orbitals revealing a bent structural motif and the presence of two lone pairs at the central E atom. For the VB calculations three resonance structures are suggested, representing the "ylidone", "ylidene" and "bent allene" structures, respectively. The influence of both ligands and central atoms on the bonding situation is clearly expressed in different weights of the resonance structures for the particular complexes. In general, the bonding in the studied E0 compounds, the tetrylones, is best described as a resonating combination of "ylidone" and "ylidene" structures with a minor contribution of the "bent allene" structure. Moreover, the VB calculations allow for a straightforward assessment of the π-backbonding (E→L) stabilization energy. The validity of the suggested resonance model is further confirmed by the complementary MPD calculations focusing on the E lone pair region as well as the E-L bonding region. Likewise, the MPD method reveals a strong influence of the σ-donating and π-accepting properties of the ligand. In particular, either one single domain or two symmetrical domains are found in the lone pair region of the central atom, supporting the predominance of either the "ylidene" or "ylidone" structures having one or two lone pairs at the central atom, respectively. Furthermore, the calculated average populations in the lone pair MPDs correlate very well with the natural bond orbital (NBO) populations, and can be related to the average number of electrons that is backdonated to the ligands.

International audience; G protein-coupled receptors (GPCRs) play an important role in many cellular responses; as such, their mechanism of action is of utmost interest. To gain insight into the active conformation of GPCRs, the X-ray crystal structures of nanobody (Nb)-stabilized β2 -adrenergic receptor (β2 AR) have been reported. Nb80, in particular, is able to bind the intracellular G protein binding site of β2 AR and stabilize the receptor in an active conformation. Within Nb80, the complementarity-determining region 3 (CDR3) is responsible for most of the binding interactions. Hence, we hypothesized that peptidomimetics of the CDR3 loop might be sufficient for binding to the receptor, inhibiting the interaction of β2 AR with intracellular GPCR interacting proteins (e.g., G proteins). Based on previous crystallographic data, a set of peptidomimetics were synthesized that, similar to the Nb80 CDR3 loop, adopt a β-hairpin conformation. Syntheses, conformational analysis, binding and functional in vitro assays, as well as internalization experiments, were performed. We demonstrate that peptidomimetics can structurally mimic the CDR3 loop of a nanobody and its function by inhibiting G protein coupling as measured by partial inhibition of cAMP production.

A set of neutral and ionic ruthenium arene trichlorostannyl complexes are reported herein. The tin(II) compounds L 1SnCl {1; L 1 = [2-(CH 2NEt 2)-4,6-(tBu) 2C 6H 2] –} and [L 2SnCl][SnCl 3] {2; L 2 = 2,6-[(CH 3)C=N(C 6H 3-2,6-iPr 2) 2]C 5H 3N} showed a rather different reactivity towards the ruthenium complex [(η 6-cymene)RuCl] 2(η-Cl) 2. As a consequence, the neutral complex [Ru(η 6-cymene)(L 1SnCl)Cl 2] (4) and the ionic compound [L 2SnCl][Ru(η 6-cymene)(SnCl 3) 2Cl] (8) were isolated. The insertion reaction of 4 with SnCl 2 provided the neutral trimetallic ruthenium complex [Ru(η 6-cymene)(L 1SnCl)(SnCl 3)Cl] (6). Analogous ruthenium complexes [Ru(η 6-cymene)(L 3PPh 2)Cl 2] (5) and [Ru(η 6-cymene)(L 3PPh 2)(SnCl 3)Cl] (7) containing the phosphane ligand L 3PPh 2 {3; L 3 = [2,6-iPr 2-(C 6H 3)NH] –} were also prepared to evaluate the donor–acceptor strength of the tin(II)- and phosphorus-containing ligands. The structural characterization and DFT calculations of the above-mentioned complexes suggest a strong influence of the [SnCl 3] – moiety on the Ru–E interaction (E = Sn, P). The influence of the trichlorostannyl ligand on the Ru–E interaction in the complexes 4–7 was further evaluated by means of a distortion/interaction analysis.

In this work, electrical currents through nanographenes, a class of alternant hydrocarbons also known as polycyclic aromatic hydrocarbons, in molecular junctions under small bias are explored. We illustrate that when the π-current dominates, that is, when no quantum interference takes place, the current prefers the direction of the shortest bond (the bond with the highest double bond character) upon entering the molecule from the contacts. As such, the idea of electrons propagating through double bonds from contact to contact, originating from the curly arrow drawings used in a previously established selection rule for transmission, seems to be more deeply rooted in the actual physical process of electron transport than previously anticipated. Furthermore, this work confirms that the σ-current behaves completely differently than the π-current. When this type of current becomes important, that is, when quantum interference takes place, the current generally prefers the shortest path from contact to contact, irrespective of the length of the bonds constituting this path, in accordance with the strong distance dependency of the σ-current. Finally, it is demonstrated that keto groups (and cross-conjugating groups in general) can be used to seal off parts of the molecule for the current. No current flows through the sealed off part of the molecule under small bias and it does not influence the transmission spectrum of the considered system.

The first structural elucidation of the first group 4 transition metal P2 complex, namely [(nacnac)Ti(OAr)]2(μ2:η2,η2-P2) (1), is reported. Complex 1 is formed via reductive decarbonylation of the phosphaethynolate ion -[OCP], which serves as a P atom source. The rhombic Ti2P2 core is essentially planar with short bond lengths suggesting some degree of multiple bonding character between the Ti-P and P-P sites. Also observed in 1 was the rather downfield shifted 31P NMR spectroscopic signal, appearing as a broadened resonance (Δν1/2 ~ 4034 Hz) at 907 ppm. Computational studies of 1 provide an understanding of the Ti2P2 core as well as the origin of the highly downfield 31P NMR spectroscopic signal.

Our attempts to synthesise N→M intramolecularly coordinated diorganometallic hydrides L2MH2 [M=Si (4), Ge (5), Sn (6)] containing the CH=N imine group (in which L is C,N-chelating ligand {2-[(2,6-iPr2C6H3)N=CH]C6 H4}(-)) yielded 1,1'-bis(2,6-diisopropylphenyl)-2,2'-spriobi[benzo[c][1,2]azasilole] (7), 1,1'-bis(2,6-diisopropylphenyl)-2,2'-spriobi[benzo[c][1,2]azagermole] (8) and C,N-chelated homoleptic stannylene L2Sn (10), respectively. Compounds 7 and 8 are an outcome of a spontaneous double hydrometallation of the two CH=N imine moieties induced by N→M intramolecular coordination (M=Si, Ge) in the absence of any catalyst. In contrast, the diorganotin hydride L2SnH2 (6) is redox-unstable and the reduction of the tin centre with the elimination of H2 provided the C,N-chelated homoleptic stannylene L2Sn (10). Compounds 7 and 8 were characterised by NMR spectroscopy and X-ray diffraction analysis. Because the proposed N→M intramolecularly coordinated diorganometallic hydrides L2MH2 [M=Si (4), Ge (5), Sn (6)] revealed two different types of reduction reactions, DFT calculations were performed to gain an insight into the structures and bonding of the non-isolable diorganometallic hydrides as well as the products of their subsequent reactions. Furthermore, the thermodynamic profiles of the different reaction pathways with respect to the central metal atom were also investigated.

The contributions of covalent and noncovalent interactions to the formation of classical adducts of bulky Lewis acids and bases and frustrated Lewis pairs (FLPs) were scrutinized by using various conceptual quantum chemical techniques. Significantly negative complexation energies were calculated for fourteen investigated Lewis pairs containing bases and acids with substituents of various sizes. A Ziegler–Rauk-type energy decomposition analysis confirmed that two types of Lewis pairs can be distinguished on the basis of the nature of the primary interactions between reactants; dative-bond formation and concomitant charge transfer from the Lewis base to the acid is the dominant and most stabilizing factor in the formation of Lewis acid–base adducts, whereas weak interactions are the main thermodynamic driving force (>50 %) for FLPs. Moreover, the ease and extent of structural deformation of the monomers appears to be a key component in the formation of the former type of Lewis pairs. A Natural Orbital for Chemical Valence (NOCV) analysis, which was used to visualize and quantify the charge transfer between the base and the acid, clearly showed the importance and lack of this type of interaction for adducts and FLPs, respectively. The Noncovalent Interaction (NCI) method revealed several kinds of weak interactions between the acid and base components, such as dispersion, π–π stacking, C[BOND]H⋅⋅⋅π interaction, weak hydrogen bonding, halogen bonding, and weak acid–base interactions, whereas the Quantum Theory of Atoms in Molecules (QTAIM) provided further conceptual insight into strong acid–base interactions.

Theoretical design can be an important aid in the discovery of valuable stable radical systems. In this study, inverse molecular design was applied to thiadiazinyl radicals to maximize two fundamental electronic properties in chemistry, namely electrophilicity and nucleophilicity. We discovered that the thiadiazinyl structure can be made moderately nucleophilic or highly electrophilic, depending on the electronic character of its substituents. The most electrophilic thiadiazinyl radical displays the highest electrophilic character encountered so far for uncharged radical systems. The accumulated data relating to the influence of different substituents at the various sites has allowed us to propose thiadiazinyl radicals that are intrinsically stable and as electrophilic or nucleophilic as possible. Although the nucleophilicity optimum fulfills the additional requirement of being stable, a significant drop from highly to merely moderately electrophilic is observed for the new electrophilicity optimum.

Topology Switching in [32]Heptaphyrins controlled by Solvent, Protonation and meso-Substituents

Recently, hexaphyrins have emerged as a promising class of π-conjugated molecules that display a range of interesting electronic, optical, and conformational properties, including the formation of stable Mobius aromatic systems. Besides the Mobius topology, hexaphyrins can adopt a variety of conformations with Huckel and twisted Huckel topologies, which can be interconverted under certain conditions. To determine the optimum conditions for viable Mobius topologies, the conformational preferences of [26]- and [28]hexaphyrins and the dynamic interconversion between the Mobius and Huckel topologies were investigated by density functional calculations. In the absence of meso substituents, [26]hexaphyrin prefers a planar dumbbell conformation, strongly aromatic and relatively strain free. The Mobius topology is highly improbable: the most stable tautomer is 33 kcal mol(-1) higher in energy than the global minimum. On the other hand, the Mobius conformer of [28]hexaphyrin is only 6.5 kcal mol(-1) higher in energy than the most stable dumbbell conformation. This marked difference is due to aromatic stabilization in the Mobius 4n electron macrocycle as opposed to antiaromatic destabilization in the 4n+2 electron system, as revealed by several energetic, magnetic, structural, and reactivity indices of aromaticity. For [28]hexaphyrins, the computed activation barrier for interconversion between the Mobius aromatic and Huckel antiaromatic conformers ranges from 7.2 to 10.2 kcal mol(-1), in very good agreement with the available experimental data. The conformation of the hexaphyrin macrocycle is strongly dependent on oxidation state and solvent, and this feature creates a promising platform for the development of molecular switches.

We analyse the electronic structure and aromaticity of graphene nanoribbons and carbon nanotubes through a series of delocalisation and geometry analysis methods. In particular, the six-centre index (SCI) is found to be in good agreement with the mean bond length (MBL) and ring bond dispersion (RBD) geometry descriptors. Based on DFT periodic calculations, three distinct classes of aromaticity patterns have been found for armchair graphene nanoribbons, appearing periodically as the width of the ribbon is increased. The periodicity in the band gap is found to be related to these aromaticity patterns. Also, the appearance of such distinct aromaticity distribution is explained within the framework of the Clar’s sextet theory. Both delocalisation and geometry analysis methods are shown to be very fast and reliable tools for easily analysing the aromaticity in carbon nanosystems.

Using DFT in search for support-effects during methanol oxidation on supported molybdenum oxides

Intramolecularly Coordinated Tin (II) Selenide and Triseleneoxostannonic Acid Anhydride

In this work, we will show that the largest values of the local softness and hardness do not necessarily correspond to the softest and hardest regions of the molecule, respectively. Based on our results, we will argue that it is more useful to interpret the local softness and the local hardness as functions that measure the "local abundance" or "concentration" of the corresponding global properties. This new point of view helps reveal how and when these local reactivity indices are most useful.

Understanding the Reactivity and Basicity of Zeolites. A Periodic DFT Study of the N 2 O 4 Disproportionation over Alkaline Cation Exchanged Zeolite Y

Can the Electrophilicity act as a Measure for the Redox Potential of First Row Transition Metal Ions Previous contributions concerning the computational approach to redox chemistry have made use of thermodynamic cycles and Car-Parrinello molecular dynamics simulations to obtain accurate redox potential values, whereas this article adopts a conceptual density functional theory (DFT) approach. Conceptual DFT descriptors have found widespread use in the study of thermodynamic and kinetic aspects of a variety of organic and inorganic reactions. However, redox reactions have not received much attention until now. In this contribution, we prove the usefulness of global and local electrophilicity descriptors for the prediction of the redox characteristics of first row transition metal ions (from Sc3+ jSc2+ to Cu3+ jCu2+) and introduce a scaled definition of the electrophilicity based on the number of electrons an electrophile ideally accepts. This scaled electrophilicityconcept acts as a good quantitative estimate of the redox potential. We also identify the first solvation sphere together with the metal ion as the primary active region during the electron uptake process, whereas the second solvation sphere functions as a non-reactive continuum region.

The reduction of arsenate to arsenite by pI258 arsenate reductase (ArsC) combines a nucleophilic displacement reaction with a unique intramolecular disulfide cascade. Within this reaction mechanism, the oxidative equivalents are translocated from the active site to the surface of ArsC. The first reaction step in the reduction of arsenate by pI258 ArsC consists of a nucleophilic displacement reaction carried out by Cys10 on dianionic arsenate. The second step involves the nucleophilic attack of Cys82 on the Cys10-arseno intermediate formed during the first reaction step. The onset of the second step is studied here by using quantum chemical calculations in a density functional theory context. The optimised geometry of the Cys10-arseno adduct in the ArsC catalytic site (sequence motif: Cys10-Thr11-Gly12-Asn13-Ser14-Cys15-Arg16-Ser17) forms the starting point for all subsequent calculations. Thermodynamic data and a hard and soft acids and bases (HSAB) reactivity analysis show a preferential nucleophilic attack on a monoanionic Cys10-arseno adduct, which is stabilised by Ser17. The P-loop active site of pI258 ArsC activates first a hydroxy group and subsequently arsenite as the leaving group, as is clear from an increase in the calculated nucleofugality of these groups upon going from the gas phase to the solvent phase to the enzymatic environment. Furthermore, the enzymatic environment stabilises the thiolate form of the nucleophile Cys82 by 3.3 pH units through the presence of the eight-residue alpha helix flanked by Cys82 and Cys89 (redox helix) and through a hydrogen bond with Thr11. The importance of Thr11 in the pKa regulation of Cys82 was confirmed by the observed decrease in the kcat value of the Thr11Ala mutant as compared to that of wild-type ArsC. During the final reaction step, Cys89 is activated as a nucleophile by structural alterations of the redox helix that functions as a pKa control switch for Cys89; this final step is necessary to expose a Cys82-Cys89 disulfide.