Light-Fueled Transformations of a Dynamic Cage-Based Molecular System

In a chemical equilibrium, the formation of high-energy species—in a closed system—is inefficient due to microscopic reversibility. Here, we demonstrate how this restriction can be circumvented by coupling a dynamic equilibrium to a light-induced E/Z isomerization of an azobenzene imine cage. The stable E-cage resists intermolecular imine exchange reactions that would “open” it. Upon switching, the strained Z-cage isomers undergo imine exchange spontaneously, thus opening the cage. Subsequent isomerization of the Z-open compounds yields a high-energy, kinetically trapped E-open species, which cannot be efficiently obtained from the initial E-cage, thus shifting an imine equilibrium energetically uphill in a closed system. Upon heating, the nucleophile is displaced back into solution and an opening/closing cycle is completed by regenerating the stable all-E-cage. Using this principle, a light-induced cage-to-cage transformation is performed by the addition of a ditopic aldehyde.     

Steric Effects on Reaction Rates. Part IX. Force-Field Parameters for Bridgehead and Rigid Tertiary Carbenium Ions

Molecular-mechanics calculations for strain of carbenium ions are tested using Bentley's unified reactivity scale for bridgehead solvolysis as reference. Excellent correlations are obtained for solvolytic bridgehead reactivity with the calculated steric-energy difference (ΔE_st) between substrate (R? H or R? OH) and cation (R⁺). After adjustment of appropriate force-field parameters, the approach is successfully extended to the rigid, but planar cations derived from structures 15 – 20 ; however, the general set of parameters cannot be applied to highly strained systems such as the cation formed from 17 . With all of the 18 sets of parameters tested, the 2-endo-norbornyl derivative 16 , is adequately correlated, while the exo isomer 15 exhibits enhanced reactivity by a factor of ca. 10² to 10³.     

A Metabolic-Tag-Based Method for Assessing the Permeation of Small Molecules Across the Mycomembrane in Live Mycobacteria**

The general lack of permeability of small molecules observed for Mycobacterium tuberculosis (Mtb) is most ascribed to its unique cell envelope. More specifically, the outer mycomembrane is hypothesized to be the principal determinant for access of antibiotics to their molecular targets. We describe a novel assay that combines metabolic tagging of the peptidoglycan, which sits directly beneath the mycomembrane, click chemistry of test molecules, and a fluorescent labeling chase step, to measure the permeation of small molecules. We showed that the assay workflow was robust and compatible with high-throughput analysis in mycobacteria by testing a small panel of azide-tagged molecules. The general trend is similar across the two types of mycobacteria with some notable exceptions. We anticipate that this assay platform will lay the foundation for medicinal chemistry efforts to understand and improve uptake of both existing drugs and newly-discovered compounds into mycobacteria.     

Inside Cover: Structural and Mechanistic Studies on Substrate and Stereoselectivity of the Indole Monooxygenase VpIndA1: New Avenues for Biocatalytic Epoxidations and Sulfoxidations (Angew. Chem. Int. Ed. 17/2023)

Flavoprotein monooxygenases are a versatile group of enzymes for biocatalytic transformations. Among these, group E monooxygenases (GEMs) catalyze enantioselective epoxidation and sulfoxidation reactions. Here, we describe the crystal structure of an indole monooxygenase from the bacterium Variovorax paradoxus EPS, a GEM designated as VpIndA1. Complex structures with substrates reveal productive binding modes that, in conjunction with force-field calculations and rapid mixing kinetics, reveal the structural basis of substrate and stereoselectivity. Structure-based redesign of the substrate cavity yielded variants with new substrate selectivity (for sulfoxidation of benzyl phenyl sulfide) or with greatly enhanced stereoselectivity (from 35.1 % to 99.8 % ee for production of (1S,2R)-indene oxide). This first determination of the substrate binding mode of GEMs combined with structure-function relationships opens the door for structure-based design of these powerful biocatalysts.     

Steric Effects on Reaction Rates. VI. Application of a New MM2 Force-Field for Carbenium Ions to Solvolysis Rates of Secondary p-Toluenesulfonates

An empirical force-field for carbenium ions has been incorporated in Allinger's MM2 programme. Structural parameters of secondary carbenium ions calculated by this method are compared with those obtained with Schleyer's BIGSTRN calculations. The strain changes occurring upon solvolysis of secondary p-toluenesulfonates are evaluated by means of this force-field and correlated with the rate constants for solvolysis. The equation for correlation of acetolysis, relative to cyclohexyl p-toluenesulfonate, of 28 k_c substrates is ΔG = 0.67 ΔE_st - 0.20 (r = 0.958).     

A Versatile Strategy for Screening Custom-Designed Warhead-Armed Cyclic Peptide Inhibitors

Demand for peptide-based pharmaceuticals has been steadily increasing, but only limited success has been achieved to date. To expedite peptide-based drug discovery, we developed a general scheme for cell-based screening of cyclic peptide inhibitors armed with a user-designed warhead. We combined unnatural amino acid incorporation and split intein-mediated peptide cyclization techniques and integrated a yeast-based colorimetric screening assay to generate a new scheme that we call the custom-designed warhead-armed cyclic peptide screening platform (CWCPS). This strategy successfully discovered a potent inhibitor, CY5-6Q, that targets human histone deacetylase 8 (HDAC8) with a K_D value of 15 nM. This approach can be a versatile and general platform for discovering cyclic peptide inhibitors.     

Prediction of viscosities and COSMO-RS analyses in binary mixtures of N,N-dimethylformamide with acetone

Experimental viscosities, η, for pure N,N-dimethylformamide (DMF) and acetone (ACT) and their binary mixtures are measured over the whole composition range as a function of temperature between 298.15 and 313.15 K. The deviations in viscosity, ?η, Gibbs free energy of activation ?G, entropies ?S*, enthalpies ?H of activation of viscous flow have been calculated. The determination of excess molar volumes, Vη^E, was calculated from the experimental viscosities for the binary mixtures. The conductor-like screening model is applied to interpret the intermolecular forces. The σ-profile is computed for the N,N-DMF and ACT with conductor-like screening model for real solvents. The experimental results were found to be in good agreement with the theoretical predictions. Moreover, viscosity data were calculated from the theoretical equations of Grunberg and Nissan, Hind et al. and Wilke for the entire systems. All results obtained were averaged experimentally and theoretically in terms of average deviations.     

Modified MM2 scheme for computation of O?C?N-containing systems

A modification of Allinger's MM2 force field for the anomeric effect in O? C? N systems is presented. For optimal consistency, it was parameterized by alternate use of ab initio (3-21G level) and X-ray results to account for the energetic and structural manifestations of the effect in the gas or condensed phase, respectively. The results obtained with the modified force field are in good agreement with those from both theoretical and experimental methods. The parameterization scheme explicitly treats all structural parameters of the C? O? C? N? C moiety as well as C? N bond lengths in tertiary amines contained within an anomeric unit. In addition, it includes directional H-bond type interactions. A limited number of parameters is put forward, in accord with the general MM2 force-field approach. © 1993 John Wiley & Sons, Inc.     

A surface site interaction point methodology for macromolecules and huge molecular databases

Determining the position and magnitude of Surface Site Interaction Points (SSIP) is a useful technique for understanding intermolecular interactions. SSIPs have been used for the prediction of solvation properties and for virtual co‐crystal screening. To determine the SSIPs for a molecule, the Molecular Electrostatic Potential Surface (MEPS) is first calculated using ab initio methods such as Density Functional Theory. This leads to a high cost in terms of computation time and is not compatible with the analysis of huge molecular databases. Herein, we present a method for the fast estimation of SSIPs, which is based on the MEPS calculated from MMFF94 atomic partial charges. The results show that this method can be used to calculate SSIPs for large molecular databases with a much higher speed than the original ab initio methodology. © 2017 Wiley Periodicals, Inc.     

Empirical force field and ab initio calculations on allyl cations

Allyl cation geometries optimized using an extended version of MMP2, newly parameterized for localized and delocalized classical cations, compare favorably with those obtained at the MP2(full) /6–31G^* level. Hence, the force field should provide good starting structures for ab initio calculations. The π-electron densities obtained by these two very different methods are quite similar. The relative energies of various isomers at MP4/6–31G^*//MP2(full)/6–31G^* are reproduced well by the force-field calculations. The heats of formation calculated by MMP2, as well as those predicted from the ab initio data, agree with experimentally determined values. The force-field method provides interpretive capabilities. Energy differences between isomers can be separated into electronic and steric contributions, reasonable estimates of resonance energies are given, and nonbonded resonance energies in delocalized cations can be evaluated. The stabilizing 1–3 π-interactions in allyl cations are quite significant, but are reduced by alkyl groups hyperconjugatively and sterically. © 1997 by John Wiley & Sons, Inc.     

Steric Effects in the Reduction of Ketones with Sodium Borohydride

The rates for the reduction of ketones with sodium borohydride are interpreted in terms of two parameters, both derived from force-field calculations; i.e. the strain difference between alcohol and ketone (Δ strain) and the steric hindrance towards approach of the hydride R. Models for the evaluation of R are discussed. With this approach reduction rates over a range of 10⁸ can be rationalized within a factor of 6–10.     

New Prediction Model of Surface and Interfacial Energies Based on COSMO-UCE**

The nature and strength of intermolecular and surface forces are the key factors that influence the solvation, adhesion and wetting phenomena. The universal cohesive energy prediction equation based on conductor-like screening model (COSMO-UCE) was extended from like molecules (pure liquids) to unlike molecules (dissimilar liquids). A new molecular-thermodynamic model of interfacial tension (IFT) for liquid-liquid and solid-liquid systems was developed in this work, which can predict the surface free energy of solid materials and interfacial energy directly through cohesive energy calculations based on COSMO-UCE. The applications of this model in prediction of IFT for water-organic, solid (n-hexatriacontane, polytetrafluoroethylene (PTFE) and octadecyl-amine monolayer)-liquid systems have been verified extensively with successful results; which indicates that this is a straightforward and reliable model of surface and interfacial energies through predicting intermolecular interactions based on merely molecular structure (profiles of surface segment charge density), the dimensionless wetting coefficient R_A/C can characterize the wetting behavior (poor adhesive (non-wetting), wetting, spreading) of liquids on the surface of solid materials very well.     

Catalytic Asymmetric 1,6‐Conjugate Addition of para‐Quinone Methides: Formation of All‐Carbon Quaternary Stereocenters

Described herein is a general and mild catalytic asymmetric 1,6‐conjugate addition of para‐quinone methides (p‐QMs), a class of challenging reactions with previous limited success. Benefiting from chiral Brønsted acid catalysis, which allows in situ formation of p‐QMs, our reaction expands the scope to general p‐QMs with various substitution patterns. It also enables efficient intermolecular formation of all‐carbon quaternary stereocenters with high enantioselectivity.     

Synthesis of 1‐Aryl‐1H‐indazoles via a Ligand‐Free Copper‐ Catalyzed Intramolecular Amination Reaction

A general synthesis of 1‐aryl‐1‐H‐indazoles from o‐halogenated aryl aldehydes or ketones and aryl hydrazines was described. This protocol included an intermolecular condensation and a ligand‐free copper‐catalyzed intramolecular Ullmann‐type coupling reaction. This method was applied to a wide range of substrates to produce the indazole products in good yields.     

Trivalent‐Intermediate Valent Cerium Ordering in CeRuSn – A Static Intermediate Valent Cerium Compound with a Superstructure of the CeCoAl Type

New equiatomic stannide CeRuSn was synthesized from the elements by arc‐melting. CeRuSn was investigated by X‐ray powder and single crystal diffraction: C2/m, a = 1156.1(4), b = 475.9(2) and c = 1023.3(4) pm, β = 102.89(3)°, wR2 = 0.0466, 1229 F² values and 38 variables. CeRuSn adopts a superstructure of the monoclinic CeCoAl type through a doubling of the subcell c axis. In the superstructure two crystallographically independent cerium sites occur. Based on the interatomic distances the two sites can be assigned to trivalent Ce2 and intermediate valent Ce1. This trivalent‐intermediate valent cerium ordering is underlined by magnetic susceptibility measurements χ_m(T): below 150 K χ_m, measured with decreasing temperature, follows a Curie‐Weiss law χ_m = C_m/(T–θ_p) giving C_m = 0.38 emuK/mol as Curie constant per CeRuSn mol; a value showing that only half of the cerium atoms are trivalent in CeRuSn (C_m = 0.807 emuK/mol for one free Ce³⁺ ion). A remarkable feature of the CeRuSn structure are the short Ce1–Ru1 (233 pm) and Ce1–Ru2 (246 pm) distances. The crystal chemistry of CeRuSn is discussed on the basis of a group‐subgroup scheme.     

Endocyclische SN-Reaktionen am gesättigten Kohlenstoff? Vorläufige Mitteilung

Fig. 1 illustrates a definition of the terms endocyclic and exocyclic SN-reactions, referring to intramolecular nucleophilic substitution processes that occur by an SN₂-analogous mechanism. Crossing experiments show that the methyl transfer I → II (see scheme 1) does not follow the formally appealing mechanism of the endocyclic SN-process III; the reaction proceeds intermolecularly under all conditions investigated. Kinetic measurements indicate that the methyl transfer XI → XII (see scheme 3) occurs in a similar fashion. This behaviour is believed to follow from the preference of tetrahedral carbon for backside attack by the nucleophile in SN₂-reactions. The general experience, according to which intramolecular reaction paths over cyclic transition states with ring sizes of 5 or 6 are preferred to their intermolecular counterparts, is not to be extrapolated to SN₂-reactions at tetrahedral carbon.     

Solubilization of organics I: 1H NMR chemical shift perturbations,diffusometry, and NOESY indicate biphenyls internalize in micelles formed by cetyltrimethylammonium bromide

Polychlorinated biphenyls are a class of persistent environmental contaminants, and micellar solubilization can be applied to remediate them. The intermolecular aggregates of biphenyl (BP) analogs and cetyltrimethyl ammonium bromide (CTAB) were studied by chemical shift perturbation, nuclear magnetic resonance (NMR) diffusometry, quantitative proton NMR, and nuclear Overhauser effect (NOE) spectroscopy to understand the structural determinants of their solubilization. The micelles of CTAB solubilized BPs readily, but its capacity depended strongly on the nature of the functional group (BPCH₂OH > > BPCHO > BPCOOH ≈ BPCl ≈ BP). Upon internalization, the BPs diffused much slower, introduced significant low-frequency ¹H chemical shift changes for CTAB, and displayed strong intermolecular NOEs. The semiquantitative analysis of NOEs revealed further that the BPs are located in the palisade layer closer to the N⁺(CH₃)₃ head group, away from the hydrophobic core. ¹H NMR offers a simple high-throughput screening assay for evaluating and quantitating the solubilization of organics in micelles. The intermolecular NOEs and site-specific perturbation of chemical shifts add further insights on the location of solubilizates in micelles, which may be important for designing surfactants specific for environmental pollutants.     

C64 Nanographene Tetraimide—A Receptor for Phthalocyanines with Subnanomolar Affinity

Phthalocyanines are extensively used by the dye and pigment industry and in photovoltaic and photodynamic therapy research due to their intense absorption of visible light, outstanding stability, and versatility. As pigments, the unsubstituted phthalocyanines are insoluble owing to strong intermolecular π-π-stacking interactions, which causes limitations for the solution chemistry for both free base and metalated phthalocyanines. Here we show a supramolecular host–guest strategy to dissolve phthalocyanines into solution. C₆₄ nanographene tetraimide ( 1 ) binds two free base/zinc/copper phthalocyanines in a 1 : 2 stoichiometry to solubilize phthalocyanines as evidenced by ¹H NMR spectroscopy, UV/Vis absorption and single-crystal X-ray analysis. Binding studies using a tetra-tert-butyl-substituted soluble phthalocyanine revealed binding affinities of up to 10⁹ M⁻¹ in tetrachloromethane, relating to a Gibbs free energy of −52 kJ mol⁻¹. Energy decomposition analysis revealed that complexes between 1 and phthalocyanines are stabilized by dispersion interactions followed by electrostatics as well as significant charge-transfer interactions.     

Structural Aspects of the O-glycosylation Linkage in Glycopeptides via MD Simulations and Comparison with NMR Experiments

A powerful conformational searching and enhanced sampling simulation method, and unbiased molecular dynamics simulations have been used along with NMR spectroscopic observables to provide a detailed structural view of O-glycosylation. For four model systems, the force-field parameters can accurately predict experimental NMR observables (J couplings and NOE's). This enables us to derive conclusions based on the generated ensembles, in which O-glycosylation affects the peptide backbone conformation by forcing it towards to an extended conformation. An exception is described for β-GalNAc-Thr where the α content is increased and stabilized via hydrogen bonding between the sugar and the peptide backbone, which was not observed in the rest of the studied systems. These observations might offer an explanation for the evolutionary preference of α-linked GalNAc glycosylation instead of a β link.