Reaction of 3‐Hydroxyquinoline‐2,4‐diones with Inorganic Thiocyanates in the Presence of Ammonium or Alkylammonium Ions: the Unexpected Replacement of a Hydroxy Group by an Amino Group

3‐Hydroxyquinoline‐2,4‐diones react with KSCN in the presence of the NH$\rm{{_{4}^{+}}}$ ions to generate 2,3‐dihydro‐3‐thioxoimidazo[1,5‐c]quinazolin‐5(6H)‐ones, 2,3‐dihydro‐2‐thioxo‐1H‐imidazo[4,5‐c]quinolin‐4(5H)‐ones, and products of molecular rearrangement of the 3‐aminoquinolinedione intermediates. Starting compounds with a benzyl (Bn) group at C(3) afford 3‐aminoquinolinediones, even when only AcONH₄ is used. The results of the reaction between 3‐hydroxyquinoline‐2,4‐diones and KSCN in the presence of BuNH₂ show that replacing a OH group with a secondary NH₂ group is also possible.     

Tuning of the Temperature Window for Unit‐Cell and Pore‐Size Enlargement in Face‐Centered‐Cubic Large‐Mesopore Silicas Templated by Swollen Block Copolymer Micelles

The unit‐cell size and pore diameter as functions of temperature are investigated in the syntheses of FDU‐12 silicas with face‐centered cubic structure templated by Pluronic (PEO‐PPO‐PEO) block copolymer micelles swollen by toluene. The temperature range in which the unit‐cell size and pore size strongly increase as temperature decreases is correlated with the critical micelle temperature (CMT) of the surfactant. While Pluronic F127 affords a wide range of unit‐cell parameters (28–51 nm) and pore diameters (16–32 nm), it renders moderately enlarged pore sizes at 25 °C. The use of Pluronic F108 with higher CMT affords FDU‐12 with very large unit‐cell size (～49 nm) and large pore diameter (27 nm) at 23 °C. Large unit‐cell size (40–41 nm) and pore size (22 nm) were obtained even at 25 °C. The application of Pluronics F87 and F88 with much smaller molecular weights and higher CMTs also allows one to synthesize FDU‐12 with quite large unit‐cell parameters and pore sizes at room temperature. The present work demonstrates that one can judiciously select Pluronic surfactants with appropriate CMT to shift the temperature range in which the pore diameter is readily tunable.     

Determination of volatile and non-volatile products of milk fermentation processes using capillary zone electrophoresis and solid phase microextraction coupled to gas chromatography

The aim of the investigations was to develop analytical methods for the determination of selected volatile and non-volatile organic compounds numbering among the final products of milk fermentation. The analyzed compounds were as follows: biacetyl and carboxylic acids (formic, acetic, citric, and lactic). The model yogurt was prepared under controlled conditions in our laboratory by addition of the selected bacteria (Lactobacillus bulgaricus and Streptococcus thermophilus) to the milk sample. The temperature, time, and stirring were controlled during the fermentation process. Factors considered in SPMPE-GC-FID method development included fiber exposure time, salt addition, temperature of extraction, and temperature of desorption. Various SPME fibers, for example with PDMS, CAR/PDMS, PA, and PDMS/DVB coatings, were tested to obtain the highest recovery of the investigated compounds extracted from yogurt samples. Based on these preliminary experiments, qualitative and quantitative analyses for the determination of biacetyl were performed by SPME-GC-FID. Moreover, a capillary zone electrophoresis method was developed for the determination of carboxylic acids in the yogurt samples. The buffer composition as well as deproteinization by acetonitrile were found to have a crucial effect on the analysis.     

Emergence of charge-transfer-to-solvent band in the absorption spectra of hydrogen halides on ice nanoparticles: spectroscopic evidence for acidic dissociation

Extensive ab initio calculations complemented by a photodissociation experiment at 193 nm elucidate the nature of hydrogen halide molecules bound on free ice nanoparticles. Electronic absorption spectra of small water clusters (up to 5 water molecules) and water clusters doped with hydrogen fluoride, hydrogen chloride and hydrogen bromide were calculated. The spectra were modeled at the time-dependent density functional (TDDFT) level of theory with the BHandHLYP functional using the reflection principle. We observe the emergence of a charge-transfer-to-solvent (CTTS) band in the absorption spectra upon the acidic dissociation of the hydrogen halides. The CTTS band provides a spectroscopically observable feature for the acidic dissociation. The calculated spectra were compared with our new experimental photodissociation data for larger water clusters doped with HCl and HBr. We conclude that HCl and HBr dissociate to a large extent on the surface of ice nanoparticles at temperatures near 120 K and photoactive products are formed. The acidic dissociation of HX leads to an enhancement by about 4 orders of magnitude of the HCl photolysis rate in the 200-300 nm region, which is potentially relevant for the halogen budget in the atmosphere.     

Influence of the solvent description on the predicted mechanism of SN2 reactions

The influence of the implicit solvent model on transition state structures of two S N2 reactions of biochemical importance is presented. In the considered methyl transfer reaction, we show experimentally that the rate constant in blood serum is about 60% slower than in the aqueous solution and that the implicit solvent model with slightly modified parameters for water captures correctly the energetics of this reaction. With the example of the reaction between 4-methyl-1,2,4-triazol-3-thione and ethyl bromoacetate, we show that relative stabilities of the conformationally different transition states depend upon the solvent inclusion strategy.     

Polymer Lamellae as Reaction Intermediates in the Formation of Copper Nanospheres as Evidenced by In Situ X‐ray Studies

The classical nucleation theory (CNT) is the most common theoretical framework used to explain particle formation. However, nucleation is a complex process with reaction pathways which are often not covered by the CNT. Herein, we study the formation mechanism of copper nanospheres using in situ X‐ray absorption and scattering measurements. We reveal that their nucleation involves coordination polymer lamellae as pre‐nucleation structures occupying a local minimum in the reaction energy landscape. Having learned this, we achieved a superior monodispersity for Cu nanospheres of different sizes. This report exemplifies the importance of developing a more realistic picture of the mechanism involved in the formation of inorganic nanoparticles to develop a rational approach to their synthesis.     

Bifunctional Nanoscale Assemblies: Multistate Electrochromics Coupled with Charge Trapping and Release

We demonstrate controlled charge trapping and release, accompanied by multiple color changes in a metallo‐organic bilayer. The dual functionality of the metallo‐organic materials provides fundamental insight into the metal‐mediated electron transport pathways. The electrochemical processes are visualized by distinct, four color‐to‐color transitions: red, transparent, orange, and brown. The bilayer is composed of two elements: 1) a nanoscale gate consisting of a layer of well‐defined polypyridyl ruthenium complexes bound to a flexible transparent electrode, and 2) a charge storage layer consisting of isostructural iron complexes attached to the surface of the gate. This gate mediates or blocks electron transport in response to an applied voltage. The charge storage and release depend on the oxidation state of the layer of ruthenium complexes (=gate). Combining electrochemistry with optical data revealed mechanistic information: the brown coloration of the bilayer directly relates to the formation of intermediate ruthenium species, providing evidence for catalytic positive charge release mediated through the gate.     

Toward calculations of the 129Xe chemical shift in Xe@C60 at experimental conditions: relativity, correlation, and dynamics

We calculate the 129Xe chemical shift in endohedral Xe@C60 with systematic inclusion of the contributing physical effects to model the real experimental conditions. These are relativistic effects, electron correlation, the temperature-dependent dynamics, and solvent effects. The ultimate task is to obtain the right result for the right reason and to develop a physically justified methodological model for calculations and simulations of endohedral Xe fullerenes and other confined Xe systems. We use the smaller Xe...C6H6 model to calibrate density functional theory approaches against accurate correlated wave function methods. Relativistic effects as well as the coupling of relativity and electron correlation are evaluated using the leading-order Breit-Pauli perturbation theory. The dynamic effects are treated in two ways. In the first approximation, quantum dynamics of the Xe atom in a rigid cage takes advantage of the centrosymmetric potential for Xe within the thermally accessible distance range from the center of the cage. This reduces the problem of obtaining the solution of a diatomic rovibrational problem. In the second approach, first-principles classical molecular dynamics on the density functional potential energy hypersurface is used to produce the dynamical trajectory for the whole system, including the dynamic cage. Snapshots from the trajectory are used for calculations of the dynamic contribution to the absorption 129Xe chemical shift. The calculated nonrelativistic Xe shift is found to be highly sensitive to the optimized molecular structure and to the choice of the exchange-correlation functional. Relativistic and dynamic effects are significant and represent each about 10% of the nonrelativistic static shift at the minimum structure. While the role of the Xe dynamics inside of the rigid cage is negligible, the cage dynamics turns out to be responsible for most of the dynamical correction to the 129Xe shift. Solvent effects evaluated with a polarized continuum model are found to be very small.     

Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints

The rapidly growing number of theoretically predicted protein structures requires robust methods that can utilize low-quality receptor structures as targets for ligand docking. Typically, docking accuracy falls off dramatically when apo or modeled receptors are used in docking experiments. Low-resolution ligand docking techniques have been developed to deal with structural inaccuracies in predicted receptor models. In this spirit, we describe the development and optimization of a knowledge-based potential implemented in Q-Dock, a low-resolution flexible ligand docking approach. Self-docking experiments using crystal structures reveals satisfactory accuracy, comparable with all-atom docking. All-atom models reconstructed from Q-Dock's low-resolution models can be further refined by even a simple all-atom energy minimization. In decoy-docking against distorted receptor models with a root-mean-square deviation, RMSD, from native of approximately 3 A, Q-Dock recovers on average 15-20% more specific contacts and 25-35% more binding residues than all-atom methods. To further improve docking accuracy against low-quality protein models, we propose a pocket-specific protein-ligand interaction potential derived from weakly homologous threading holo-templates. The success rate of Q-Dock employing a pocket-specific potential is 6.3 times higher than that previously reported for the Dolores method, another low-resolution docking approach.