Items 1-20 of 574

• Journal Article

#### Falloff curves and mechanism of thermal decomposition of CF3I in shock waves ﻿

Physical Chemistry Chemical Physics 2019; 21(43) p.23893-23899
The falloff curves of the unimolecular dissociation CF3I (+Ar) → CF3 + I (+Ar) are modelled by combining quantum-chemical characterizations of the potential energy surface for the reaction, standard unimolecular rate theory, and experimental information on the average energy transferred per collision between excited CF3I and Ar. The (essentially) parameter-free theoretical modelling gives results in satisfactory agreement with data deduced from earlier shock wave experiments employing a variety of reactant concentrations (between a few ppm and a few percent in the bath gas Ar). New experiments recording absorption-time signals of CF3I, I2, CF2 and (possibly) IF at 450-500 and 200-300 nm are reported. By analysing the decomposition mechanism, besides the unimolecular dissociation of CF3I, these provide insight into the influence of secondary reactions on the experimental observations.
• Journal Article

#### Using invariom modelling to distinguish correct and incorrect central atoms in duplicate structures' with neighbouring 3 d elements ﻿

Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 2017; 73(5) p.794-804
Modelling coordination compounds has been shown to be feasible using the invariom method; for the best fit to a given set of diffraction data, additional steps other than using lookup tables of scattering factors need to be carried out. Here such procedures are applied to a number of duplicate structures', where structures of two or more supposedly different coordination complexes with identical ligand environments, but with different 3d metal ions, were published. However, only one metal atom can be plausibly correct in these structures, and other spectroscopic data are unavailable. Using aspherical scattering factors, a structure can be identified as correct from the deposited Bragg intensities alone and modelling only the ligand environment often suffices to make this distinction. This is not possible in classical refinements using the independent atom model. Quantum-chemical computations of the better model obtained after aspherical-atom refinement further confirm the assignment of the element in the respective figures of merit.
• Journal Article

#### Efficient phenotypic sex classification of zebrafish using machine learning methods ﻿

Ecology and Evolution p.1-12
Sex determination in zebrafish by manual approaches according to current guidelines relies on human observation. These guidelines for sex recognition have proven to be subjective and highly labor‐intensive. To address this problem, we present a methodology to automatically classify the phenotypic sex using two machine learning methods: Deep Convolutional Neural Networks (DCNNs) based on the whole fish appearance and Support Vector Machine (SVM) based on caudal fin coloration. Machine learning techniques in sex classification provide potential efficiency with the advantage of automatization and robustness in the prediction process. Furthermore, since developmental plasticity can be influenced by environmental conditions, we have investigated the impact of elevated water temperature during embryogenesis on sex and sex‐related differences in color intensity of adult zebrafish. The estimated color intensity based on SVM was then applied to detect the association between coloration and body weight and length. Phenotypic sex classifications using machine learning methods resulted in a high degree of association with the real sex in nontreated animals. In temperature‐induced animals, DCNNs reached a performance of 100%, whereas 20% of males were misclassified using SVM due to a lower color intensity. Furthermore, a positive association between color intensity and body weight and length was observed in males. Our study demonstrates that high ambient temperature leads to a lower color intensity in male animals and a positive association of male caudal fin coloration with body weight and length, which appears to play a significant role in sexual attraction. The software developed for sex classification in this study is readily applicable to other species with sex‐linked visible phenotypic differences.
• Journal Article

#### Hydridoorganostannylene Coordination: Group 4 Metallocene Dichloride Reduction in Reaction with Organodihydridostannate Anions ﻿

Chemistry – A European Journal(25) p.1-8
Organodihydridoelement anions of germanium and tin were reacted with metallocene dichlorides of Group 4 metals Ti, Zr and Hf. The germate anion [Ar*GeH2 ]- reacts with hafnocene dichloride under formation of the substitution product [Cp2 Hf(GeH2 Ar*)2 ]. Reaction of the organodihydridostannate with metallocene dichlorides affords the reduction products [Cp2 M(SnHAr*)2 ] (M=Ti, Zr, Hf). Abstraction of a hydride substituent from the titanium bis(hydridoorganostannylene) complex results in formation of cation [Cp2 M(SnAr*)(SnHAr*)]+ exhibiting a short Ti-Sn interaction. (Ar*=2,6-Trip2 C6 H3 , Trip=2,4,6-triisopropylphenyl).
• Journal Article

#### Measurement of Angstrom to Nanometer Molecular Distances with 19 F Nuclear Spins by EPR/ENDOR Spectroscopy ﻿

Angewandte Chemie International Edition(58) p.2-9
Spectroscopic and biophysical methods for structural determination at atomic resolution are fundamental in studies of biological function. Here we introduce an approach to measure molecular distances in bio-macromolecules using 19 F nuclear spins and nitroxide radicals in combination with high-frequency (94 GHz/3.4 T) electron-nuclear double resonance (ENDOR). The small size and large gyromagnetic ratio of the 19 F label enables to access distances up to about 1.5 nm with an accuracy of 0.1-1 Å. The experiment is not limited by the size of the bio-macromolecule. Performance is illustrated on synthesized fluorinated model compounds as well as spin-labelled RNA duplexes. The results demonstrate that our simple but strategic spin-labelling procedure combined with state-of-the-art spectroscopy accesses a distance range crucial to elucidate active sites of nucleic acids or proteins in the solution state.
• Journal Article

#### Multispectral near infrared absorption imaging for histology of skin cancer ﻿

Journal of Biophotonics
Multispectral imaging combines the spectral resolution of spectroscopy with the spatial resolution of imaging and is therefore very useful for biomedical applications. Currently, histological diagnostics use mainly stainings with standard dyes (eg, hematoxylin + eosin) to identify tumors. This method is not applicable in vivo and provides low amounts of chemical information. Biomolecules absorb near infrared light (NIR, 800-1700 nm) at different wavelengths, which could be used to fingerprint tissue. Here, we built a NIR multispectral absorption imaging setup to study skin tissue samples. NIR light (900-1500 nm) was used for homogenous wide-field transmission illumination and detected by a cooled InGaAs camera. In this setup, images I(x, y, λ) from dermatological samples (melanoma, nodular basal-cell carcinoma, squamous-cell carcinoma) were acquired to distinguish healthy from diseased tissue regions. In summary, we show the potential of multispectral NIR imaging for cancer diagnostics.
• Journal Article

#### Soft experimental constraints for soft interactions: a spectroscopic benchmark data set for weak and strong hydrogen bonds ﻿

Physical Chemistry Chemical Physics 2019; 21(35) p.18799-18810
An experimental benchmark data base on rotational constants, vibrational properties and energy differences for weakly and more strongly hydrogen-bonded complexes and their constituents from the spectroscopic literature is assembled. It is characterized in detail and finally contracted to a more compact, discriminatory set (ENCH-51, for Experimental Non-Covalent Harmonic with 51 entries). The meeting points between theory and experiment consist of equilibrium rotational constants and harmonic frequencies and energies, which are back-corrected from experimental observables and are very easily accessible by quantum chemical calculations. The relative performance of B3LYP-D3, PBE0-D3 and M06-2X density functional theory predictions with a quadruple-zeta basis set is used to illustrate systematic errors, error compensation and selective performance for structural, vibrational and energetical observables. The current focus is on perspectives and different benchmarking methodologies, rather than on a specific theoretical method or a specific class of compounds. Extension of the data base in chemical, observable and quantum chemical method space is encouraged.
• Journal Article

#### New Insights in the Catalytic Activity of Cobalt Orthophosphate Co3 (PO4)2 from Charge Density Analysis ﻿

Chemistry – A European Journal(25)
An extensive characterization of Co3 (PO4 )2 was performed by topological analysis according to Bader's Quantum Theory of Atoms in Molecules from the experimentally and theoretically determined electron density. This study sheds light on the reactivity of cobalt orthophosphate as a solid-state heterogeneous oxidative-dehydration and -dehydrogenation catalyst. Various faces of the bulk catalyst were identified as possible reactive sites given their topological properties. The charge accumulations and depletions around the two independent five- and sixfold-coordinated cobalt atoms, found in the topological analysis, are correlated to the orientation and population of the d-orbitals. It is shown that the (011) face has the best structural features for catalysis. Fivefold-coordinated ions in close proximity to advantageously oriented vacant coordination sites and electron depletions suit the oxygen lone pairs of the reactant, mainly for chemisorption. This is confirmed both from the multipole refinement as well as from density functional theory calculations. Nearby basic phosphate ions are readily available for C-H activation.
• Journal Article

#### Soft experimental constraints for soft interactions: a spectroscopic benchmark data set for weak and strong hydrogen bonds ﻿

Physical Chemistry Chemical Physics 2019; 21(35) p.18799-18810
An experimental benchmark data base on rotational constants, vibrational properties and energy differences for weakly and more strongly hydrogen-bonded complexes and their constituents from the spectroscopic literature is assembled. It is characterized in detail and finally contracted to a more compact, discriminatory set (ENCH-51, for Experimental Non-Covalent Harmonic with 51 entries). The meeting points between theory and experiment consist of equilibrium rotational constants and harmonic frequencies and energies, which are back-corrected from experimental observables and are very easily accessible by quantum chemical calculations. The relative performance of B3LYP-D3, PBE0-D3 and M06-2X density functional theory predictions with a quadruple-zeta basis set is used to illustrate systematic errors, error compensation and selective performance for structural, vibrational and energetical observables. The current focus is on perspectives and different benchmarking methodologies, rather than on a specific theoretical method or a specific class of compounds. Extension of the data base in chemical, observable and quantum chemical method space is encouraged.
• Journal Article

#### Machine learning molecular dynamics for the simulation of infrared spectra ﻿

Chemical Science 2017; 8(10) p.6924-6935
Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for vibrational anharmonic and dynamical effects - typically neglected by conventional quantum chemistry approaches - we base our machine learning strategy on ab initio molecular dynamics simulations. While these simulations are usually extremely time consuming even for small molecules, we overcome these limitations by leveraging the power of a variety of machine learning techniques, not only accelerating simulations by several orders of magnitude, but also greatly extending the size of systems that can be treated. To this end, we develop a molecular dipole moment model based on environment dependent neural network charges and combine it with the neural network potential approach of Behler and Parrinello. Contrary to the prevalent big data philosophy, we are able to obtain very accurate machine learning models for the prediction of infrared spectra based on only a few hundreds of electronic structure reference points. This is made possible through the use of molecular forces during neural network potential training and the introduction of a fully automated sampling scheme. We demonstrate the power of our machine learning approach by applying it to model the infrared spectra of a methanol molecule, n-alkanes containing up to 200 atoms and the protonated alanine tripeptide, which at the same time represents the first application of machine learning techniques to simulate the dynamics of a peptide. In all of these case studies we find an excellent agreement between the infrared spectra predicted via machine learning models and the respective theoretical and experimental spectra.
• Journal Article

#### Dispersion-controlled docking preference: multi-spectroscopic study on complexes of dibenzofuran with alcohols and water ﻿

Physical Chemistry Chemical Physics 2019; 21(29) p.16032-16046
The structural preferences within a series of dibenzofuran-solvent complexes have been investigated by electronic, vibrational, and rotational spectroscopic methods probing supersonic jet expansions. The experimental study is accompanied by a detailed theoretical analysis including dispersion-corrected density functional theory, symmetry adapted perturbation theory, as well as coupled cluster approaches. The complementary, multi-spectroscopic results reveal a preferred OHO structure for the smallest complex of dibenzofuran-water, whereas for the methanol complex an OHπ isomer is simultaneously observed. For the largest complex, dibenzofuran-tert-butyl alcohol, only a π-bound structure is found. These comprehensive investigations show that a completely inverse trend regarding the docking preference is observed by comparing the present results with the ones for analogous diphenyl ether complexes. This can be rationalized on the basis of the planarity/non-planarity and rigidity/flexibility of the different systems, providing valuable insight into the interplay between different non-covalent interactions. This analysis is a further step towards a quantitative description of very delicate energetic balances with the overall goal of yielding reliable structural predictions for non-covalently bound systems.
• Journal Article

#### Shiga toxin binding alters lipid packing and the domain structure of Gb3-containing membranes: a solid-state NMR study ﻿

Physical Chemistry Chemical Physics 2019; 21(28): Art. 15630
We studied the influence of globotriaosylceramide (Gb3) lipid molecules on the properties of phospholipid membranes composed of a liquid ordered (lo)/liquid disordered (ld) phase separated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/N-palmitoyl-d-erythro-sphingosylphosphorylcholine (PSM)/cholesterol mixture (40/35/20, mol/mol/mol) supplemented with 5 mol% of either short acyl chain palmitoyl-Gb3 or long acyl chain lignoceryl-Gb3 using 2H solid-state NMR spectroscopy. To this end, both globotriaosylceramides were chemically synthesized featuring a perdeuterated lipid acyl chain. The solid-state 2H NMR spectra support the phase separation into a POPC-rich ld phase and a PSM/cholesterol-rich lo phase. The long chain lignoceryl-Gb3 showed a rather unusual order parameter profile of the acyl chain, which flattens out for the last ∼6 methylene segments. Such an odd chain conformation can be explained by partial chain interdigitation and/or a very fluid midplane region of the membrane. Possibly, the Gb3 molecules may thus preferentially be localized at the lo/ld phase boundary. In contrast, the short chain palmitoyl-Gb3 was well associated with the PSM/cholesterol-rich lo phase. Gb3 molecules act as membrane receptors for the Shiga toxin (STx) produced by Shigella dysenteriae and by enterohemorrhagic strains of Escherichia coli (EHEC). The B-subunits of STx (STxB) forming a pentameric structure were produced recombinantly and incubated with the membrane mixtures leading to alterations in the lipid packing properties and lateral organization of the membranes. Typically, STxB binding led to a decrease in lipid chain order in agreement with partial immersion of protein segments into the lipid-water interface of the membrane. In the presence of STxB, Gb3 preferentially partitioned into the lo membrane phase. In particular the short acyl chain palmitoyl-Gb3 showed very similar chain order parameters to PSM. In the presence of STxB, all lipid species showed isotropic contributions to the 2H NMR powder spectra; this was most pronounced for the Gb3 molecules. Such isotropic contributions are caused by highly curved membrane structures, which have previously been detected as membrane invaginations in fluorescence microscopy. Our analysis estimated that STxB induced highly curved membrane structures with a curvature radius of less than ∼10 nm likely related to the insertion of STxB segments into the lipid-water interface of the membrane.
• Journal Article

#### Synthetic Lugdunin Analogues Reveal Essential Structural Motifs for Antimicrobial Action and Proton Translocation Capability ﻿

Angewandte Chemie International Edition 2019; 58(27) p.9234-9238
Lugdunin, a novel thiazolidine cyclopeptide, exhibits micromolar activity against methicillin-resistant Staphylococcus aureus (MRSA). For structure-activity relationship (SAR) studies, synthetic analogues obtained from alanine and stereo scanning as well as peptides with modified thiazolidine rings were tested for antimicrobial activity. The thiazolidine ring and the alternating d- and l-amino acid backbone are essential. Notably, the non-natural enantiomer displays equal activity, thus indicating the absence of a chiral target. The antibacterial activity strongly correlates with dissipation of the membrane potential in S. aureus. Lugdunin equalizes pH gradients in artificial membrane vesicles, thereby maintaining membrane integrity, which demonstrates that proton translocation is the mode of action (MoA). The incorporation of extra tryptophan or propargyl moieties further expands the diversity of this class of thiazolidine cyclopeptides.
• Journal Article

#### Treatment of Silylene–Phosphinidene with Chalcogens Resulted Exclusively in the Formation of Silicon‐Bonded Chalcogens ﻿

Chemistry – A European Journal 2019; 25(49) p.11422-11426
Chalcogen-bonded silicon phosphinidenes LSi(E)-P-Me cAAC (E=S (1); Se (2); Te (3); L=PhC(NtBu)2 ; Me cAAC=C(CH2 )(CMe2 )2 N-2,6-iPr2 C6 H3 )) were synthesized from the reactions of silylene-phosphinidene LSi-P-Me cAAC (A) with elemental chalcogens. All the compounds reported herein have been characterized by multinuclear NMR, elemental analyses, LIFDI-MS, and single-crystal X-ray diffraction techniques. Furthermore, the regeneration of silylene-phosphinidene (A) was achieved from the reactions of 2-3 with L'Al (L'=HC{(CMe)(2,6-iPr2 C6 H3 N)}2 ). Theoretical studies on chalcogen-bonded silicon phosphinidenes indicate that the Si-E (E=S, Se, Te) bond can be best represented as charge-separated electron-sharing σ-bonding interaction between [LSi-P-Me cAAC]+ and E- . The partial double-bond character of Si-E is attributed to significant hyperconjugative donation from the lone pair on E- to the Si-N and Si-P σ*-molecular orbitals.
• Journal Article

#### A Neutral “Aluminocene” Sandwich Complex: η1 - versus η5-Coordination Modes of a Pentaarylborole with ECp* (E=Al, Ga; Cp*=C5 Me5) ﻿

Angewandte Chemie International Edition 2019; 58(42) p.15051-15056
The pentaaryl borole (Ph*C)4 BXylF [Ph*=3,5-tBu2 (C6 H3 ); XylF =3,5-(CF3 )2 (C6 H3 )] reacts with low-valent Group 13 precursors AlCp* and GaCp* by two divergent routes. In the case of [AlCp*]4 , the borole reacts as an oxidising agent and accepts two electrons. Structural, spectroscopic, and computational analysis of the resulting unprecedented neutral η5 -Cp*,η5 -[(Ph*C)4 BXylF ] complex of AlIII revealed a strong, ionic bonding interaction. The formation of the heteroleptic borole-cyclopentadienyl "aluminocene" leads to significant changes in the 13 C NMR chemical shifts within the borole unit. In the case of the less-reductive GaCp*, borole (Ph*C)4 BXylF reacts as a Lewis acid to form a dynamic adduct with a dative 2-center-2-electron Ga-B bond. The Lewis adduct was also studied structurally, spectroscopically, and computationally.
• Journal Article

#### A μ-Phosphido Diiron Dumbbell in Multiple Oxidation States ﻿

Angewandte Chemie International Edition 2019; 58(40) p.14349-14356
The reaction of the ferrous complex [LFe(NCMe)2 ](OTf)2 (1), which contains a macrocyclic tetracarbene as ligand (L), with Na(OCP) generates the OCP- -ligated complex [LFe(PCO)(CO)]OTf (2) together with the dinuclear μ-phosphido complex [(LFe)2 P](OTf)3 (3), which features an unprecedented linear Fe-(μ-P)-Fe motif and a "naked" P-atom bridge that appears at δ=+1480 ppm in the 31 P NMR spectrum. 3 exhibits rich redox chemistry, and both the singly and doubly oxidized species 4 and 5 could be isolated and fully characterized. X-ray crystallography, spectroscopic studies, in combination with DFT computations provide a comprehensive electronic structure description and show that the Fe-(μ-P)-Fe core is highly covalent and structurally invariant over the series of oxidation states that are formally described as ranging from FeIII FeIII to FeIV FeIV . 3-5 now add a higher homologue set of complexes to the many systems with Fe-(μ-O)-Fe and Fe-(μ-N)-Fe core structures that are prominent in bioinorganic chemistry and catalysis.
• Journal Article

#### Functional Mononitrosyl Diiron(II) Complex Mediates the Reduction of NO to N2O with Relevance for Flavodiiron NO Reductases ﻿

Journal of the American Chemical Society 2017; 139(41) p.14380-14383
Reaction of [Fe2(N-Et-HPTB)(CH3COS)](BF4)2 (1) with (NO)(BF4) produces a nonheme mononitrosyl diiron(II) complex, [Fe2(N-Et-HPTB)(NO)(DMF)3](BF4)3 (2). Complex 2 is the first example of a [FeII{Fe(NO)}7] species and is also the first example of a mononitrosyl diiron(II) complex that mediates the reduction of NO to N2O. This work describes the selective synthesis, detailed characterization and NO reduction activity of 2 and thus provides new insights regarding the mechanism of flavodiiron nitric oxide reductases.
• Journal Article

#### Synthesis of Gb3 Glycosphingolipids with Labeled Head Groups: Distribution in Phase-Separated Giant Unilamellar Vesicles ﻿

Angewandte Chemie International Edition
The receptor lipid Gb3 is responsible for the specific internalization of Shiga toxin (STx) into cells. The head group of Gb3 defines the specificity of STx binding, and the backbone with different fatty acids is expected to influence its localization within membranes impacting membrane organization and protein internalization. To investigate this influence, a set of Gb3 glycosphingolipids labeled with a BODIPY fluorophore attached to the head group was synthesized. C24 fatty acids, saturated, unsaturated, α-hydroxylated derivatives, and a combination thereof, were attached to the sphingosine backbone. The synthetic Gb3 glycosphingolipids were reconstituted into coexisting liquid-ordered (lo )/liquid-disordered (ld ) giant unilamellar vesicles (GUVs), and STx binding was verified by fluorescence microscopy. Gb3 with the C24:0 fatty acid partitioned mostly in the lo phase, while the unsaturated C24:1 fatty acid distributes more into the ld phase. The α-hydroxylation does not influence its partitioning.
• Journal Article

#### Organoaluminum Compounds as Catalysts for Monohydroboration of Carbodiimides ﻿

Chemistry – A European Journal 2019; 25(51) p.11918-11923
he effectivecatalytic activity of organoaluminumcompoundsfor the monohydroboration of carbodiimideshas beendemonstrated. Twoaluminumcomplexes,2and3,weresynthesizedandcharacterized.Theefficientcatalyticperformances of fouraluminum hydridecomplexes L1AlH2(L1=HC(CMeNAr)2,Ar=2,6-Et2C6H3;1), L2AlH2(NMe3)(L2=o-C6H4F(CH=N-Ar),Ar=2,6-Et2C6H3;2), L3AlH(L3=2,6-bis(1-methylethyl)-N-(2-pyridinylmethylene)phenylamine;3), andL4AlH(NMe3)(L4=o-C6H4(N-Dipp)(CH=N-Dipp),Dipp=2,6-iPr2C6H3;4), andan aluminum alkylcomplex L1AlMe2(5)wereusedfor the monohydroboration of carbodiimidesin-vestigatedundersolvent-free andmildconditions. Com-pounds1–3and5can produce monohydroboratedN-boryl-formamidine, whereas4can affordtheC-borylformamidineproduct. Asuggested mechanismof this reactionwas ex-plored, andthe aluminumformamidinate compound6wascharacterized by single-crystal X-ray,also astoichiometricre-actionwas investigated.
• Journal Article

#### Quantitation of eumelanin and pheomelanin markers in diverse biological samples by HPLC-UV-MS following solid-phase extraction ﻿

PLOS ONE 2019; 14(10): Art. e0223552
Eumelanin and pheomelanin are well known and common pigments found in nature. However, their complex polymer structure and high thermostability complicate their direct chemical identification. A widely used analytical method is indirect determination using HPLC with UV detection of both types of melanin by their most abundant oxidation products: pyrrole-2,3-dicarboxylic acid (PDCA), pyrrole-2,3,5-tricarboxylic acid (PTCA), thiazole-4,5-dicarboxylic acid (TDCA), and thiazole-2,4,5-tricarboxylic acid (TTCA). An increasing interest in pigmentation in biological research led us to develop a highly sensitive and selective method to identify and quantify these melanin markers in diverse biological samples with complex matrices. By introducing solid-phase extraction (SPE, reversed-phase) following alkaline oxidation we could significantly decrease background signals while maintaining recoveries greater than 70%. Our HPLC-UV-MS method allows for confident peak identification via exact mass information in corresponding UV signals used for quantitation. In addition to synthetic melanin and Sepia officinalis ink as reference compounds eumelanin markers were detected in brown human hair and a brown bivalve shell (Mytilus edulis). Brown feathers from the common chicken (Gallus g. domesticus) yielded all four eumelanin and pheomelanin markers. The present method can be easily adapted for a wide range of future studies on biological samples with unknown melanin content.