Statistics of layered zigzags: a two-dimensional generalization of TASEP

A novel discrete growth model in 2+1 dimensions is presented in three equivalent formulations: i) directed motion of zigzags on a cylinder, ii) interacting interlaced TASEP layers, and iii) growing heap over 2D substrate with a restricted minimal local height gradient. We demonstrate that the coarse-grained behavior of this model is described by the two-dimensional Kardar-Parisi-Zhang equation. The coefficients of different terms in this hydrodynamic equation can be derived from the steady state flow-density curve, the so called `fundamental' diagram. A conjecture concerning the analytical form of this flow-density curve is presented and is verified numerically.Comment: 5 pages, 4 figure

Daytime ozone loss term in the mesopause region

For the retrieval of atomic oxygen via ozone observations in the extended mesopause region under sunlight conditions, two assumptions are used: first, the photochemical equilibrium of ozone and, second, that the ozone losses are dominated by ozone's dissociation from solar UV radiation, silently ignoring the O3 destruction by atomic hydrogen. We verify both by 3-D modeling. We found that ozone approaches photochemical equilibrium at 75–100 km for daytime conditions. Hence, the first assumption is valid. However, the reaction of ozone with atomic hydrogen was found to be an important loss process and should not be omitted in retrieving atomic oxygen

DFT study of dihydrogen addition to molybdenum π-heteroaromatic complexes: a prerequisite step for the catalytic hydrodenitrogenation process

International audienceThe range of molybdenum hydride complexes that are sought to participate in the important catalytic hydrodenitrogenation process (HDN) of nitrogen containing polycyclic aromatic hydrocarbons were evaluated by DFT studies. The previously synthesized stable (η6-quinoline)Mo(PMe3)3 complex 1N, in which molybdenum is bonded to the heterocyclic ring, was chosen as a model. The hydrogenation of the quinone heterocycle, which was postulated as the initial step in the overall HDN reaction, is found to occur via three consecutive steps of the oxidative addition of dihydrogen to Mo in 1N. Successive transfer of hydrogen atoms from the metal to the heterocycle leads to the ultimate formation of the tetrahydrido molybdenum intermediate Mo(PMe3)4H413 and 2,2,3,3-tetrahydroquinoline C9H11N 14. All the involved intermediates and transition states have been fully characterized by DFT. This computational modeling of the hydrogenation of quinoline, as a part of extended HDN catalytic processes, provides a fundamental understanding of such mechanism

The Mechanism of Release of P-TEFb and HEXIM1 from the 7SK snRNP by Viral and Cellular Activators Includes a Conformational Change in 7SK

The positive transcription elongation factor, P-TEFb, is required for the production of mRNAs, however the majority of the factor is present in the 7SK snRNP where it is inactivated by HEXIM1. Expression of HIV-1 Tat leads to release of P-TEFb and HEXIM1 from the 7SK snRNP in vivo, but the release mechanisms are unclear.We developed an in vitro P-TEFb release assay in which the 7SK snRNP immunoprecipitated from HeLa cell lysates using antibodies to LARP7 was incubated with potential release factors. We found that P-TEFb was directly released from the 7SK snRNP by HIV-1 Tat or the P-TEFb binding region of the cellular activator Brd4. Glycerol gradient sedimentation analysis was used to demonstrate that the same Brd4 protein transfected into HeLa cells caused the release of P-TEFb and HEXIM1 from the 7SK snRNP in vivo. Although HEXIM1 binds tightly to 7SK RNA in vitro, release of P-TEFb from the 7SK snRNP is accompanied by the loss of HEXIM1. Using a chemical modification method, we determined that concomitant with the release of HEXIM1, 7SK underwent a major conformational change that blocks re-association of HEXIM1.Given that promoter proximally paused polymerases are present on most human genes, understanding how activators recruit P-TEFb to those genes is critical. Our findings reveal that the two tested activators can extract P-TEFb from the 7SK snRNP. Importantly, we found that after P-TEFb is extracted a dramatic conformational change occurred in 7SK concomitant with the ejection of HEXIM1. Based on our findings, we hypothesize that reincorporation of HEXIM1 into the 7SK snRNP is likely the regulated step of reassembly of the 7SK snRNP containing P-TEFb

Pyridine-, Pyridazine‑, Pyrimidine‑, and Pyrazine-Derived Carbenes as Ligands for Transition-Metal Complexes: Perspectives from DFT Calculations

A comprehensive theoretical analysis of the electronic structure, reactivity, and ligand properties of various types of carbenes derived from pyridine and diazines (pyridazine, pyrimidine, and pyrazine) was performed. These carbenes are divided into three classes: “normal” N-heterocyclic carbenes (NHCs) bearing one nitrogen atom at the ylidene carbon (1N-NHC), mesoionic carbenes (MIC), and remote-NHCs (r-NHC). These species have a singlet ground state. Carbenes under study bear high-lying lone electron pairs localized on the ylidene carbon atoms making them bases 2–18 pKaH units stronger than the reference imidazol-2-ylidenes. However, such carbenes are thermodynamically and kinetically less stable than conventional imidazol-2-ylidenes. Pyridinium and diazinium carbenes have exceptional ligand properties evaluated using a model (NHC)Rh(CO)2Cl complex: high metal–ligand binding energies and significantly higher electron donation and steric stabilization than those provided by its five-membered ring counterparts. Diazinium carbenes can act as ditopic ligands that bind Lewis acids to both ylidene carbon and nitrogen atoms. Protonation of diazinium carbenes transforms them from strong donors into strong π-acceptors comparable to phosphites. Theoretical calculations have shown that diazinium carbenes are promising ligands for the construction of complexes photoactive in the NIR region. A new type of chiral ligand C-PyBOX has been developed, promising for use in transition-metal-mediated enantioselective catalytic transformations

Pyridine-, Pyridazine‑, Pyrimidine‑, and Pyrazine-Derived Carbenes as Ligands for Transition-Metal Complexes: Perspectives from DFT Calculations

A comprehensive theoretical analysis of the electronic structure, reactivity, and ligand properties of various types of carbenes derived from pyridine and diazines (pyridazine, pyrimidine, and pyrazine) was performed. These carbenes are divided into three classes: “normal” N-heterocyclic carbenes (NHCs) bearing one nitrogen atom at the ylidene carbon (1N-NHC), mesoionic carbenes (MIC), and remote-NHCs (r-NHC). These species have a singlet ground state. Carbenes under study bear high-lying lone electron pairs localized on the ylidene carbon atoms making them bases 2–18 pKaH units stronger than the reference imidazol-2-ylidenes. However, such carbenes are thermodynamically and kinetically less stable than conventional imidazol-2-ylidenes. Pyridinium and diazinium carbenes have exceptional ligand properties evaluated using a model (NHC)Rh(CO)2Cl complex: high metal–ligand binding energies and significantly higher electron donation and steric stabilization than those provided by its five-membered ring counterparts. Diazinium carbenes can act as ditopic ligands that bind Lewis acids to both ylidene carbon and nitrogen atoms. Protonation of diazinium carbenes transforms them from strong donors into strong π-acceptors comparable to phosphites. Theoretical calculations have shown that diazinium carbenes are promising ligands for the construction of complexes photoactive in the NIR region. A new type of chiral ligand C-PyBOX has been developed, promising for use in transition-metal-mediated enantioselective catalytic transformations

Mechanisms in the reaction of palladium(II)–π-allyl complexes with aryl halides: evidence for NHC exchange between two palladium complexes

A detailed experimental and DFT study (PBE level) of the reaction of [Pd(η3-C3H5)(tmiy)(PR3)]BF4 (tmiy=tetramethylimidazolin-2-ylidene, PR3=phosphane), precursors to monoligated Pd0 species, with aryl electrophiles yielding 2-arylimidazolium salt is reported. Experiments establish that an autocatalytic ligand transfer mechanism is preferred over PdIV and σ-bond metathesis pathways, and that transmetalation is the rate-determining step. Calculations indicate that the key step involves the concerted exchange of NHC and iodo ligands between two different PdII complexes. This is corroborated by experimental results showing the slower reaction of complexes containing the bulkier dipdmiy (dipdmiy = diisopropyldimethylimidazolin-2-ylidene)

ADAPTATION OF SOFTWARE SYSTEMS TO USER TASKS BASED ON THE METHOD OF CONFIGURATION MODELING

In this paper, we discuss task of adaptation of software systems (PCs) and complexes (PCs) on the basis of the configuration modeling (MCM) method is considered. The article describes designated purpose of MCM in the field of SSs development, describes background and justification for the development of adap- tive SSs, and many of the advantages of creating configurable SSs. The main attention is paid to the analysis and research of the software engineering and implementation of adaptive SSs using the configuration mechanism as a mean of adapting SSs to the problem of interest. The potential for using configuration modeling in this area is determined. The meaning of the concepts «configurator», «configuration» and «reconfiguration» in the context of the description of MCM implementation of adaptive SSs creation is considered. The article gives a real example of an adaptive SS describing MCMs application in the process of software engineering. A conceptual model of such a SS is described, and its interpretation is implement- ed in the form of a modular complex data processing system (CDPS). The example of the CDPS shows the structural scheme of the conceptual model of the data handling process, decomposes the CDPS into the basic modules, including the built-in configuration module. Special attention to a detailed description of the problem of interest and the functionality of each module is paid, as well as to the description of the relationships between them. On the basis of the CDPS, the solution of the problem of adapting PSs with the elements of dynamic configuration based on the input data is realized. The example of the CDPS describes user-accessible operating modes of the SS corresponding to various system configurations determined according to the tasks to be solved. The article makes it possible to obtain an abstract presentation on the methods and principles for the creation of adaptive SS. Moreover, a concrete understanding of the imple- mentation of adaptation by using the configuration management mechanism is covered. Additionally, the article highlights direct benefits and potential profit from using of configurator in software engineering

Acid-Switchable Synthesis of Trifluoromethylated Triazoles and Isoxazoles via Reaction of CF3-Ynones with NaN3: DFT Study of the Reaction Mechanism

A detailed study of the reaction of CF3-ynones with NaN3 was performed. It was found that the reaction permits the selective synthesis of either 4-trifluoroacetyltriazoles or 5-CF3-isoxazoles. The chemoselectivity of the reaction was switchable via acid catalysis. The reaction of CF3-ynones with NaN3 in EtOH produced high yields of 4-trifluoroacetyltriazoles. In contrast, the formation of 5-CF3-isoxazoles was observed under catalysis by acids. This acid-switchable procedure can be performed at sub-gram scale. The possible reaction mechanism was supported by DFT calculations. The synthetic utility of the prepared 4-trifluoroacetyltriazoles was demonstrated