Enzyme Catalysis “Reilluminated”

In a new light : The NADPH:protochlorophyllide (Pchlide) oxidoreductase (POR; see structure, green Pchlide, yellow NADPH) is a good model to investigate catalytical processes in enzymes, as its light activation allows an immediate start of the catalyzed reaction. By irradiation with weak, short laser pulses it is possible to detect conformation changes during the reaction and thus to uncover the elementary steps of the catalytic process.

     

A novel “green” synthesis of starch-capped CdSe nanostructures

This paper reports a “green” facile, room temperature, one-pot synthesis of starch-capped CdSe nanostructures with an obvious quantum confinement effect via a novel non-organometallic method. It is found that by simply tuning the Cd:Se molar ratio, dots and elongated particles of high aspect ratio could be prepared selectively in the presence of the same ligand concentration without any post-treatment. Spherical particles were produced at 1:1 ratio, while elongated particles were produced at 0.5:1 Cd:Se ratio. The X-ray diffraction (XRD) analysis showed that the particles were predominantly of wurtzite structure, with sharp diffraction patterns regardless of their size and shapes. We inferred that the elongated particles are formed by self-reorganisation occurring via adhesion between the spherical nanoparticles as a result of dipole–dipole interactions.     

DNA Responds to Ionizing Radiation as an Insulator,Not as a “Molecular Wire”

The yields of radicals trapped on DNA, measured by EPR spectroscopy of oligodeoxyribonucleotide crystals (the EPR spectrum of a single crystal of d(CCCTAGGG) is shown), are found to be very high (0.7 μmol J⁻¹) and insensitive to long-range (>10⁶ base pairs) versus short-range stacking (8 base pairs) of the bases. These observations are evidence that DNA at 4 K has the properties of an insulator and argue against DNA acting as a “molecular wire”.     

Cyclic Voltammetry—“Electrochemical Spectroscopy”. New Analytical Methods (25)

Polarography is still the best known classical measuring method in electroanalytical chemistry. However, in recent years its position has been challenged by cyclic voltammetry (CV). Simple diagnostic criteria and relatively easily acquired measuring techniques have hastened this development. Cyclic voltammetry has the further attraction of providing information not only on the thermodynamics of redox processes but also on the kinetics of heterogeneous electron-transfer reactions and coupled chemical reactions. The characteristic shapes of the voltammetric waves and their unequivocal position on the potential scale virtually fingerprint the individual electrochemical properties of redox systems. For this reason the method has been labeled “electrochemical spectroscopy”.     

The “Speedy” Synthesis of Atom‐Specific 15N Imino/Amido‐Labeled RNA

Although numerous reports on the synthesis of atom‐specific ¹⁵N‐labeled nucleosides exist, fast and facile access to the corresponding phosphoramidites for RNA solid‐phase synthesis is still lacking. This situation represents a severe bottleneck for NMR spectroscopic investigations on functional RNAs. Here, we present optimized procedures to speed up the synthesis of ¹⁵N(1) adenosine and ¹⁵N(1) guanosine amidites, which are the much needed counterparts of the more straightforward‐to‐achieve ¹⁵N(3) uridine and ¹⁵N(3) cytidine amidites in order to tap full potential of ¹H/¹⁵N/¹⁵N‐COSY experiments for directly monitoring individual Watson–Crick base pairs in RNA. Demonstrated for two preQ₁ riboswitch systems, we exemplify a versatile concept for individual base‐pair labeling in the analysis of conformationally flexible RNAs when competing structures and conformational dynamics are encountered.     

Pentagermapyramidane: Crystallizing the “Transition‐State” Structure

The first example of the homonuclear pyramidanes, pentagermapyramidane, was synthesized, fully characterized, and computationally studied to reveal its peculiar structural features and the nature of its apex‐to‐base bonding interactions. Both solid‐state and solution structures of pentagermapyramidane are discussed based on the computed stabilities of its square‐pyramidal and distorted forms.     

Thiol–Ene “Click” Reaction Triggered by Neutral Ionic Liquid: The “Ambiphilic” Character of [hmim]Br in the Regioselective Nucleophilic Hydrothiolation

Thiol–ene “click” chemistry has emerged as a powerful strategy to construct carbon–heteroatom (C? S) bonds, which generally results in the formation of two regioisomers. To this end, the neutral ionic liquid [hmim]Br has been explored as a solvent cum catalyst for the synthesis of linear thioethers from activated and inactivated styrene derivatives or secondary benzyl alcohols and thiols without the requirement of using a metal complex, base, or free radical initiator. Furthermore, detailed mechanistic investigations using ¹H NMR spectroscopy and quadrupole time‐of‐flight electrospray ionization mass spectrometry (Q‐TOF ESI‐MS) revealed that the “ambiphilic” character of the ionic liquid promotes the nucleophilic addition of thiol to styrene through an anti‐Markovnikov pathway. The catalyst recyclability and the extension of the methodology for thiol–yne click chemistry are additional benefits. A competitive study among thiophenol, styrene, and phenyl acetylene revealed that the rate of reaction is in the order of thiol–yne>thiol–ene>dimerization of thiol in [hmim]Br.     

Tunable Keplerate Type‐Cluster “Mo132” Cavity with Dicarboxylate Anions

The internal functionalization of the Keplerate‐type capsule Mo₁₃₂ has been carried out by ligand exchange leading to the formation of glutarate and succinate containing species isolated as ammonium or dimethylammonium salts. Solution NMR analysis is consistent with asymmetric inner dicarboxylate ions containing one carboxylato group grafted onto the inner side of the spheroidal inorganic shell while the second hangs toward the center of the cavity. Such a disposition has been confirmed by the single‐crystal X‐ray diffraction analysis of the glutarate containing {Mo₁₃₂} species. A detailed NMR solution study of the ligand‐exchange process allowed determining the binding constant K_L of acetate (AcO^?), succinate (HSucc^?) or glutarate (HGlu^?) ligands at the 30 inner coordinating sites, which vary such as K<K<K‐supported by the associated thermodynamic parameters Δ_rS* and Δ_rH*. Such a variation is mainly explained by a positive entropic gain attenuated by unfavorable steric effect. Furthermore, these results are completed by ¹H DOSY and ¹H EXSY NMR experiments which are in agreement with bulky guests firmly trapped within the cavity. At last, variable temperature ¹H NMR study below 290 K revealed a striking line broadening occurring abruptly within a 5 K range. Such an effect appears closely related to the presence of the ammonium cations suspected to be present within the cavity and then has been interpreted as an inner‐phase transition leading to a frozen state.     

“Push‐pull” supramolecular chromophores supported on cyclopolymers

Well‐defined macromolecules have been obtained through free‐radical cyclopolymerization and cyclocopolymerization of difunctional and acrylic‐like monomers, which contained “push‐pull” supramolecular chromophores, able to form 1:1 complexes with Eu³⁺ ions in solution. The monomeric molecular modules are built around bismalonate crown ethers in a convergent fashion, in which one of the malonate moiety is derivatized as the ylidene malonate push‐pull fragment, and the other malonate moiety is elaborated to introduce two polymerizable and acrylic‐like substituents. The free‐radical induced cyclopolymerization of these monomers, or their cyclocopolymerization with UV/Vis “silent” but structurally related monomers, afforded macromolecular architectures characterized by GPC, NMR and DSC techniques. UV/Vis titration studies, performed with Eu(OTf)₃ as the supramolecular probe, revealed how adjacent chromophores within the polymeric backbone are virtually independent from each other, and how the binding ability towards the probe of these multivalent, highly packed cyclopolymeric architectures, although reduced, is still clearly detectable. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 5202–5213, 2008     

Comment on “CCSD study of anharmonic Raman cross sections of fundamental,overtone, and combination transitions”

Equations (36) and (37) in L. N. Vidal, P. A. M. Vazquez, Int. J. Quantum Chem. 2012, 112, 3205 are wrong. The agreement between theoretical and experimental Raman cross sections is greatly improved with use of the corrected expressions. © 2013 Wiley Periodicals, Inc.     

“Batch” Kinetics in Flow: Online IR Analysis and Continuous Control

Currently, kinetic data is either collected under steady‐state conditions in flow or by generating time‐series data in batch. Batch experiments are generally considered to be more suitable for the generation of kinetic data because of the ability to collect data from many time points in a single experiment. Now, a method that rapidly generates time‐series reaction data from flow reactors by continuously manipulating the flow rate and reaction temperature has been developed. This approach makes use of inline IR analysis and an automated microreactor system, which allowed for rapid and tight control of the operating conditions. The conversion/residence time profiles at several temperatures were used to fit parameters to a kinetic model. This method requires significantly less time and a smaller amount of starting material compared to one‐at‐a‐time flow experiments, and thus allows for the rapid generation of kinetic data.     

“Inverted” Solvent Effect on Charge Transfer in the Excited State

Faster in cyclohexane than in acetonitrile is the fluorescence quenching of the azoalkane 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) by amines and sulfides. Although this photoreaction is induced by charge transfer (CT; see picture) and exciplexes are formed, the increase in the dipole moment of the exciplex is not large enough to offset the solvent stabilization of the excited reactants, and an “inverted” solvent effect results.     

“Invisible” Conformers of an Antifungal Disulfide Protein Revealed by Constrained Cold and Heat Unfolding,CEST‐NMR Experiments,and Molecular Dynamics Calculations

Transition between conformational states in proteins is being recognized as a possible key factor of function. In support of this, hidden dynamic NMR structures were detected in several cases up to populations of a few percent. Here, we show by two‐ and three‐state analysis of thermal unfolding, that the population of hidden states may weight 20–40 % at 298 K in a disulfide‐rich protein. In addition, sensitive ¹⁵N‐CEST NMR experiments identified a low populated (0.15 %) state that was in slow exchange with the folded PAF protein. Remarkably, other techniques failed to identify the rest of the NMR “dark matter”. Comparison of the temperature dependence of chemical shifts from experiments and molecular dynamics calculations suggests that hidden conformers of PAF differ in the loop and terminal regions and are most similar in the evolutionary conserved core. Our observations point to the existence of a complex conformational landscape with multiple conformational states in dynamic equilibrium, with diverse exchange rates presumably responsible for the completely hidden nature of a considerable fraction.     

“Inverted” Deep Eutectic Solvents Based on Host‐Guest Interactions

Herein, the concept of “inverted” (the mode “molecules mainly interact with cations”) deep eutectic solvents (DESs) is proposed. A strategy to form inverted DESs by host‐guest interactions was developed, and thus numerous DESs could be designed and formed by a combination of host and guest molecules. These liquids are expected to be used as nonaqueous electrolytes in potassium‐ion batteries or other fields for further exploration.     

NMR Spectroscopic Structural Determination of Organozinc Reagents: Evidence for “Highly Coordinated” Zincates

The structures of ¹³ C-labeled methylzinc reagents have been studied by NMR spectroscopy. Analysis of the spectra gives information on the number of chemically equivalent methyl groups that are attached to the metal centers. Shown is the structure of trimethylzincate with the spin couplings that form the basis of the spin system used in the calculation.     

Efficient “On‐the‐Fly” calculation of Raman Spectra from Ab‐Initio molecular dynamics: Application to hydrophobic/hydrophilic solutes in bulk water

We present a novel computational method to accurately calculate Raman spectra from first principles. Together with an extension of the second‐generation Car‐Parrinello method of Kühne et al. (Phys. Rev. Lett. 2007, 98, 066401) to propagate maximally localized Wannier functions together with the nuclei, a speed‐up of one order of magnitude can be observed. This scheme thus allows to routinely calculate finite‐temperature Raman spectra “on‐the‐fly” by means of ab‐initio molecular dynamics simulations. To demonstrate the predictive power of this approach we investigate the effect of hydrophobic and hydrophilic solutes in water solution on the infrared and Raman spectra. © 2015 Wiley Periodicals, Inc.