DFT studies of the degradation mechanism of methyl mercury activated by a sulfur-rich ligand

Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3′3′-cyclic GMP–AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5′-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5′-pGpG-Ca2+ structure, β5–α5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5′-pGpG-Ca2+ structure quite different from other 5′-pGpG bound structures reported earlier.

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Stereodivergent Alkyne Hydrofluorination Using a Simple Practical Reagent

10.26434/chemrxiv.11962629.v3 ◽

2020 ◽

Author(s):

Rui Guo ◽

Xiaotian Qi ◽

Hengye Xiang ◽

Paul Geaneoates ◽

Ruihan Wang ◽

...

Keyword(s):

Bond Formation ◽

Biologically Active ◽

Dft Studies ◽

Thermodynamic Control ◽

Important Goal ◽

Peptide Bonds ◽

Metal Free ◽

Vinyl Cation ◽

E And Z Isomers ◽

Vinyl Fluorides

Vinyl fluorides play an important role in drug development as they serve as bioisosteres for peptide bonds and are found in a range of biologically active molecules. The discovery of safe, general and practical procedures to prepare vinyl fluorides remains an important goal and challenge for synthetic chemistry. Here we introduce an inexpensive and easily-handled reagent and report simple, scalable, and metal-free protocols for the regioselective and stereodivergent hydrofluorination of alkynes to access both the E and Z isomers of vinyl fluorides. These conditions were suitable for a diverse collection of alkynes, including several highly-functionalized pharmaceutical derivatives. Mechanistic and DFT studies support C–F bond formation through a vinyl cation intermediate, with the (E)- and (Z)-hydrofluorination products forming under kinetic and thermodynamic control, respectively.

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Copper Catalyzed sp3 C-H α-Acetylation

10.26434/chemrxiv.11407116.v1 ◽

2019 ◽

Author(s):

Otome Okoromoba ◽

Eun Sil Jang ◽

Claire McMullin ◽

Thomas Cundari ◽

Timothy H. Warren

Keyword(s):

Natural Products ◽

Dft Studies ◽

Alkyl Radicals ◽

Important Chemical ◽

Alkyl Electrophiles ◽

Synthetic Intermediates ◽

Alkylation Reactions

α-substituted ketones are important chemical targets as synthetic intermediates as well as functionalities in in natural products and pharmaceuticals. We report the sp3 C-H α-acetylation of sp3 C-H substrates R-H with arylmethyl ketones ArC(O)Me to provide α-alkylated ketones ArC(O)CH2R at RT with tBuOOtBu as oxidant via copper(I) β-diketiminato catalysts. Proceeding via alkyl radicals R•, this method enables α-substitution with bulky substituents without competing elimination that occurs in more traditional alkylation reactions between enolates and alkyl electrophiles. DFT studies suggest the intermediacy of copper(II) enolates [CuII](CH2C(O)Ar) that capture alkyl radicals R• to give R-CH2C(O)Ar under competing dimerization of the copper(II) enolate to give the 1,4-diketone ArC(O)CH2CH2C(O)Ar.

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Copper Catalyzed sp3 C-H α-Acetylation

10.26434/chemrxiv.11407116 ◽

2019 ◽

Author(s):

Otome Okoromoba ◽

Eun Sil Jang ◽

Claire McMullin ◽

Thomas Cundari ◽

Timothy H. Warren

Keyword(s):

Natural Products ◽

Dft Studies ◽

Alkyl Radicals ◽

Important Chemical ◽

Alkyl Electrophiles ◽

Synthetic Intermediates ◽

Alkylation Reactions

α-substituted ketones are important chemical targets as synthetic intermediates as well as functionalities in in natural products and pharmaceuticals. We report the sp3 C-H α-acetylation of sp3 C-H substrates R-H with arylmethyl ketones ArC(O)Me to provide α-alkylated ketones ArC(O)CH2R at RT with tBuOOtBu as oxidant via copper(I) β-diketiminato catalysts. Proceeding via alkyl radicals R•, this method enables α-substitution with bulky substituents without competing elimination that occurs in more traditional alkylation reactions between enolates and alkyl electrophiles. DFT studies suggest the intermediacy of copper(II) enolates [CuII](CH2C(O)Ar) that capture alkyl radicals R• to give R-CH2C(O)Ar under competing dimerization of the copper(II) enolate to give the 1,4-diketone ArC(O)CH2CH2C(O)Ar.

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Radical Capture at Ni(II) Complexes: C-C, C-N, and C-O Bond Formation

10.26434/chemrxiv.8115860.v1 ◽

2019 ◽

Author(s):

Abolghasem (Gus) Bakhoda ◽

Stefan Wiese ◽

Christine Greene ◽

Bryan C. Figula ◽

Jeffery A. Bertke ◽

...

Keyword(s):

Functional Groups ◽

Bond Formation ◽

Dft Studies ◽

Bond Forming ◽

Aryl Amines ◽

Shed Light ◽

Competing Pathways

The dinuclear b-diketiminato NiIItert-butoxide {[Me3NN]Ni}2(μ-OtBu)2 (2), synthesized from [Me3NN]Ni(2,4-lutidine) (1) and di-tert-butylperoxide, is a versatile precursor for the synthesis of a series of NiIIcomplexes [Me3NN]Ni-FG to illustrate C-C, C-N, and C-O bond formation at NiII via radicals. {[Me3NN]Ni}2(μ-OtBu)2 reacts with nitromethane, alkyl and aryl amines, acetophenone, benzamide, ammonia and phenols to deliver corresponding mono- or dinuclear [Me3NN]Ni-FG species (FG = O2NCH2, R-NH, ArNH, PhC(O)NH, PhC(O)CH2, NH2and OAr). Many of these NiII complexes are capable of capturing the benzylic radical PhCH(•)CH3 to deliver corresponding PhCH(FG)CH3 products featuring C-C, C-N or C-O bonds. DFT studies shed light on the mechanism of these transformations and suggest two competing pathways that depend on the nature of the functional groups. These radical capture reactions at [NiII]-FG complexes outline key C-C, C-N, and C-O bond forming steps and suggest new families of nickel radical relay catalysts.

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Spectroscopic (FT-IR, NMR, UV-Vis, fluorescence) and DFT studies (molecular structure, IR and NMR spectral assignments, NBO and Fukui function) of Schiff bases derived from 2-chloro-3-quinolinecarboxaldehyde

Журнал структурной химии ◽

10.26902/jsc20180613 ◽

2018 ◽

Vol 59 (6) ◽

Keyword(s):

Molecular Structure ◽

Schiff Bases ◽

Fukui Function ◽

Dft Studies ◽

Ft Ir

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Stochastic Models of Particle Trajectories in Turbulent Atmosphere Flows by Using the LANGEVIN Equations

Proceedings ◽

10.3390/proceedings2020063032 ◽

2020 ◽

Vol 1 (1) ◽

Author(s):

Youssra El Qasemy ◽

Abdelfatah Achahbar ◽

Abdellatif Khamlichi

Keyword(s):

Wind Speed ◽

Wind Turbine ◽

Classical Method ◽

Degradation Mechanism ◽

Transformation Process ◽

Langevin Equations ◽

Turbulence Data ◽

Power Curves ◽

And Diffusion ◽

Fluctuating Wind

The stochastic behavior of wind speed is a particular characteristic of wind energy production, which affects the degradation mechanism of the turbine, resulting in stochastic charging on the wind turbine. A model stochastic is used in this study to evaluate the efficiency of wind turbine power of whatever degree given fluctuating wind turbulence data. This model is based on the Langevin equations, which characterize, by two coefficients, drift and diffusion functions. These coefficients describe the behavior of the transformation process from the input wind speed to the output data that need to be determined. For this present work, the computation of drift and diffusion functions has been carried out by using the stochastic model to assess the output variables in terms of the torque and power curves as a function of time, and it is compared by the classical method. The results show that the model stochastic can define the efficiency of wind turbine generation more precisely.

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Synthesis, Characterization and Thermal Degradation of Some New 3,5-dimethyl Pyrazole Derivatives

Revista de Chimie ◽

10.37358/rc.17.2.5444 ◽

2017 ◽

Vol 68 (2) ◽

pp. 317-322

Author(s):

Anca Mihaela Mocanu ◽

Constantin Luca ◽

Alina Costina Luca

Keyword(s):

Thermal Degradation ◽

Degradation Mechanism ◽

New Products ◽

Analysis Data ◽

Biological Properties ◽

Elemental Analysis Data ◽

Ftir Analysis ◽

Spectral Measurements ◽

Chemical Structures ◽

And Storage

The purpose of this research is to synthetize, characterize and thermal degradation of new heterolytic derivates with potential biological properties. The derivates synthesis was done by obtaining new molecules with pyralozone structure which combine two pharmacophore entities: the amidosulfonyl-R1,R2 phenoxyacetil with the 3,5-dimethyl pyrazole which can have potential biological properties. The synthesis stages of the new products are presented as well as the elemental analysis data and IR, 1H-NMR spectral measurements made for elucidating the chemical structures and thermostability study which makes evident the temperature range proper for their use and storage. The obtained results were indicative of a good correlation of the structure with the thermal stability as estimated by means of the initial degradation temperatures as well as with the degradation mechanism by means of the TG-FTIR analysis.

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Methyl mercury in the dutch rhine delta

Water Science & Technology ◽

10.2166/wst.1994.0530 ◽

1994 ◽

Vol 30 (10) ◽

pp. 213-219 ◽

Cited By ~ 2

Author(s):

Hendrik Pieters ◽

Victor Geuke

Keyword(s):

Suspended Matter ◽

Methyl Mercury ◽

Mercury Contamination ◽

Benthic Organisms ◽

Considerable Decrease ◽

Continuous Sedimentation ◽

Highly Correlated ◽

High Level ◽

Almost All

Samples of yellow eel from various locations in the Dutch Rhine area have been analyzed for trend monitoring of mercury since 1977. In the western Rhine delta mercury levels in eels have hardly changed since the seventies, whereas in the eastern part of the Dutch Rhine area a considerable decrease of mercury concentrations in eel has occurred. Because of continuous sedimentation of contaminated suspended matter transported from upstream regions, accumulation rates and concentrations of mercury in eel in the western Rhine delta remained at a relatively high level. Analyses of methyl mercury in biota have been performed to elucidate the role of methyl mercury in the mercury contamination of the Dutch Rhine ecosystem. Low percentages of methyl mercury were observed in zooplankton (3 to 35%). In benthic organisms (mussels) percentages of methyl mercury ranged from 30 to 57%, while in fish species and liver of aquatic top predator birds almost all the mercury was present in the form of methyl mercury (> 80%). During the period 1970-1990 mercury concentrations of suspended matter in the eastern Rhine delta have drastically decreased. These concentrations seemed to be highly correlated with mercury concentrations of eel (R = 0.84). The consequences of this relation are discussed.

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