scholarly journals Proton transfers in the Strecker reaction revealed by DFT calculations

2014 ◽  
Vol 10 ◽  
pp. 1765-1774 ◽  
Author(s):  
Shinichi Yamabe ◽  
Guixiang Zeng ◽  
Wei Guan ◽  
Shigeyoshi Sakaki

The Strecker reaction of acetaldehyde, NH3, and HCN to afford alanine was studied by DFT calculations for the first time, which involves two reaction stages. In the first reaction stage, the aminonitrile was formed. The rate-determining step is the deprotonation of the NH3 + group in MeCH(OH)-NH3 + to form 1-aminoethanol, which occurs with an activation energy barrier (ΔE ≠) of 9.6 kcal/mol. The stereochemistry (R or S) of the aminonitrile product is determined at the NH3 addition step to the carbonyl carbon of the aldehyde. While the addition of CN− to the carbon atom of the protonated imine 7 appears to scramble the stereochemistry, the water cluster above the imine plane reinforces the CN− to attack the imine group below the plane. The enforcement hinders the scrambling. In the second stage, the aminonitrile transforms to alanine, where an amide Me-CH(NH2)-C(=O)-NH2 is the key intermediate. The rate-determining step is the hydrolysis of the cyano group of N(amino)-protonated aminonitrile which occurs with an ΔE ≠ value of 34.7 kcal/mol. In the Strecker reaction, the proton transfer along the hydrogen bonds plays a crucial role.

2013 ◽  
Vol 9 ◽  
pp. 1073-1082 ◽  
Author(s):  
Shinichi Yamabe ◽  
Guixiang Zeng ◽  
Wei Guan ◽  
Shigeyoshi Sakaki

A Bamberger rearrangement of N-phenylhydroxylamine, Ph–N(OH)H, to p-aminophenol was investigated by DFT calculations for the first time. The nitrenium ion, C6H5–NH+, suggested and seemingly established as an intermediate was calculated to be absent owing to the high nucleophilicity of the water cluster around it. First, a reaction of the monoprotonated system, Ph–N(OH)H + H3O+(H2O) n (n = 4 and 14) was examined. However, the rate-determining transition states involving proton transfers were calculated to have much larger activation energies than the experimental one. Second, a reaction of the diprotonated system, Ph–N(OH)H + (H3O+)2(H2O)13, was traced. An activation energy similar to the experimental one was obtained. A new mechanism of the rearrangement including the aniline dication-like transition state was proposed.


2013 ◽  
Vol 9 ◽  
pp. 185-196 ◽  
Author(s):  
Shinichi Yamabe ◽  
Wei Guan ◽  
Shigeyoshi Sakaki

Reaction paths of base-catalyzed hydrolyses of isoelectronic substrates, Ph–C(=O)–X–Et [X = O (ethyl benzoate) and X = NH (N-ethylbenzamide)], were traced by DFT calculations. To simulate bond interchanges accompanied by proton transfers, a cluster model of Ph–C(=O)–X–Et + OH−(H2O)16 was employed. For X = O, three elementary processes and for X = NH four ones were obtained. The rate-determining step of X = O is the first TS (TS1, the OH− addition step), while that of X = NH is TS2. TS2 of X = NH leads to a novel Mulliken charge-transfer complex, Ph–(OH)(O=)C∙∙∙N(H2)–Et. The superiority or inferiority between the direct nucleophilic process or the general base-catalyzed process for TS1 was examined with the model Ph–C(=O)–X–Et + OH−(H2O) n , n = 3, 5, 8, 12, 16, 24 and 32. The latter process was calculated to be more favorable regardless of the number (n, except n = 3) of water molecules. The counter ion Na+ works unfavorably on the ester hydrolysis, particularly on TS1. A minimal model of TS1 was proposed and was found to be insensitive to n.


2019 ◽  
Author(s):  
Raghu Nath Dhital ◽  
keigo nomura ◽  
Yoshinori Sato ◽  
Setsiri Haesuwannakij ◽  
Masahiro Ehara ◽  
...  

Carbon-Fluorine (C-F) bonds are considered the most inert organic functionality and their selective transformation under mild conditions remains challenging. Herein, we report a highly active Pt-Pd nanoalloy as a robust catalyst for the transformation of C-F bonds into C-H bonds at low temperature, a reaction that often required harsh conditions. The alloying of Pt with Pd is crucial to activate C-F bond. The reaction profile kinetics revealed that the major source of hydrogen in the defluorinated product is the alcoholic proton of 2-propanol, and the rate-determining step is the reduction of the metal upon transfer of the <i>beta</i>-H from 2-propanol. DFT calculations elucidated that the key step is the selective oxidative addition of the O-H bond of 2-propanol to a Pd center prior to C-F bond activation at a Pt site, which crucially reduces the activation energy of the C-F bond. Therefore, both Pt and Pd work independently but synergistically to promote the overall reaction


Chemistry ◽  
2021 ◽  
Vol 3 (1) ◽  
pp. 116-125
Author(s):  
Yi-Fan Li ◽  
Amit Ghosh ◽  
Pronay Kumar Biswas ◽  
Suchismita Saha ◽  
Michael Schmittel

Three distinct four-component supramolecular nanorotors were prepared, using, for the first time, bipyridine instead of phenanthroline stations in the stator. Following our established self-sorting protocol to multicomponent nanodevices, the nanorotors were self-assembled by mixing the stator, rotators with various pyridine head groups, copper(I) ions and 1,4-diazabicyclo[2.2.2]octane (DABCO). Whereas the exchange of a phenanthroline vs. a bipyridine station did not entail significant changes in the rotational exchange frequency, the para-substituents at the pyridine head group of the rotator had drastic consequences on the speed: 4-OMe (k298 = 35 kHz), 4-H (k298 = 77 kHz) and 4-NO2 (k298 = 843 kHz). The exchange frequency (log k) showed an excellent linear correlation with both the Hammett substituent constants and log K of the copper(I)–ligand interaction, proving that rotator–copper(I) bond cleavage is the key determining factor in the rate-determining step.


2021 ◽  
Vol 22 (7) ◽  
pp. 3677
Author(s):  
Zuzana Rosenbergová ◽  
Kristína Kántorová ◽  
Martin Šimkovič ◽  
Albert Breier ◽  
Martin Rebroš

Myrosinase is a plant defence enzyme catalysing the hydrolysis of glucosinolates, a group of plant secondary metabolites, to a range of volatile compounds. One of the products, isothiocyanates, proved to have neuroprotective and chemo-preventive properties, making myrosinase a pharmaceutically interesting enzyme. In this work, extracellular expression of TGG1 myrosinase from Arabidopsis thaliana in the Pichia pastoris KM71H (MutS) strain was upscaled to a 3 L laboratory fermenter for the first time. Fermentation conditions (temperature and pH) were optimised, which resulted in a threefold increase in myrosinase productivity compared to unoptimised fermentation conditions. Dry cell weight increased 1.5-fold, reaching 100.5 g/L without additional glycerol feeding. Overall, a specific productivity of 4.1 U/Lmedium/h was achieved, which was 102.5-fold higher compared to flask cultivations.


2004 ◽  
Vol 380 (3) ◽  
pp. 749-756 ◽  
Author(s):  
Yong-Xin SUN ◽  
Kazuhito TSUBOI ◽  
Yasuo OKAMOTO ◽  
Takeharu TONAI ◽  
Makoto MURAKAMI ◽  
...  

Anandamide (an endocannabinoid) and other bioactive long-chain NAEs (N-acylethanolamines) are formed by direct release from N-acyl-PE (N-acyl-phosphatidylethanolamine) by a PLD (phospholipase D). However, the possible presence of a two-step pathway from N-acyl-PE has also been suggested previously, which comprises (1) the hydrolysis of N-acyl-PE to N-acyl-lysoPE by PLA1/PLA2 enzyme(s) and (2) the release of NAEs from N-acyllysoPE by lysoPLD (lysophospholipase D) enzyme(s). In the present study we report for the first time the characterization of enzymes responsible for this pathway. The PLA1/PLA2 activity for N-palmitoyl-PE was found in various rat tissues, with the highest activity in the stomach. This stomach enzyme was identified as group IB sPLA2 (secretory PLA2), and its product was determined as N-acyl-1-acyl-lysoPE. Recombinant group IB, IIA and V of sPLA2s were also active with N-palmitoyl-PE, whereas group X sPLA2 and cytosolic PLA2α were inactive. In addition, we found wide distribution of lysoPLD activity generating N-palmitoylethanolamine from N-palmitoyl-lysoPE in rat tissues, with higher activities in the brain and testis. Based on several lines of enzymological evidence, the lysoPLD enzyme could be distinct from the known N-acyl-PE-hydrolysing PLD. sPLA2-IB dose dependently enhanced the production of N-palmitoylethanolamine from N-palmitoyl-PE in the brain homogenate showing the lysoPLD activity. N-Arachidonoyl-PE and N-arachidonoyl-lysoPE as anandamide precursors were also good substrates of sPLA2-IB and the lysoPLD respectively. These results suggest that the sequential actions of PLA2 and lysoPLD may constitute another biosynthetic pathway for NAEs, including anandamide.


Microbiology ◽  
2004 ◽  
Vol 150 (7) ◽  
pp. 2257-2266 ◽  
Author(s):  
Helmuth Adelsberger ◽  
Christian Hertel ◽  
Erich Glawischnig ◽  
Vladimir V. Zverlov ◽  
Wolfgang H. Schwarz

Four extracellular enzymes of the thermophilic bacterium Clostridium stercorarium are involved in the depolymerization of de-esterified arabinoxylan: Xyn11A, Xyn10C, Bxl3B, and Arf51B. They were identified in a collection of eight clones producing enzymes hydrolysing xylan (xynA, xynB, xynC), β-xyloside (bxlA, bxlB, bglZ) and α-arabinofuranoside (arfA, arfB). The modular enzymes Xyn11A and Xyn10C represent the major xylanases in the culture supernatant of C. stercorarium. Both hydrolyse arabinoxylan in an endo-type mode, but differ in the pattern of the oligosaccharides produced. Of the glycosidases, Bxl3B degrades xylobiose and xylooligosaccharides to xylose, and Arf51B is able to release arabinose residues from de-esterified arabinoxylan and from the oligosaccharides generated. The other glycosidases either did not attack or only marginally attacked these oligosaccharides. Significantly more xylanase and xylosidase activity was produced during growth on xylose and xylan. This is believed to be the first time that, in a single thermophilic micro-organism, the complete set of enzymes (as well as the respective genes) to completely hydrolyse de-esterified arabinoxylan to its monomeric sugar constituents, xylose and arabinose, has been identified and the enzymes produced in vivo. The active enzyme system was reconstituted in vitro from recombinant enzymes.


Author(s):  
Т.А. Богумил

В статье предлагается концепция жизни и творческого роста В.М. Шукшина сквозь призму тезаурусного и кластерного подходов. Объяснительными «персональными моделями» для интерпретации биографического текста писателя являются кластеры Мартина Идена, Гамлета и Степана Разина. Ранее биографы и литературоведы указывали на важность этих персон для Шукшина, но разрозненно. Впервые предпринята попытка свести указанные персональные модели воедино, в целостный сюжет становления писателя в пространстве культуры. На разных этапах эволюции автора доминирует одна из указанных моделей, последовательно сменяя друг друга, но не вытесняя, а «внахлест». Ранний этап творчества, ориентированный на стратегию Мартина Идена, является попыткой «вписаться» в наличный культурный мейнстрим. Выражено это в следовании поэтике соцреализма. Второй этап подспудно начинается с реабилитации отца Шукшина в 1956 года, когда актуализируется «гамлетовский комплекс», проявляющийся в чувстве вины перед отцом, через стратегию утаивания подлинного «я», мотивы чудаковатости. Третий этап связан с личностью реального исторического лица, Степана Разина, и выражается в открытом протесте против власти. Все важные для В.М. Шукшина поведенческие модели объединены мотивом одинокого противостояния враждебному социуму и имеют трагический финал, что обусловило ранний уход писателя и порождение мифов о насильственном характере его смерти. В.М. Шукшин одновременно был фигурой неординарной и типичной, что позволило его биографии стать «персональной моделью» для последующих авторов, выходцев из сельской глубинки. The article proposes the concept of life and creative growth of V.M. Shukshin through the prism of the thesaurus and cluster approach. The explanatory "personal models" for interpreting the biographical text of the writer are clusters of Martin Eden, Hamlet and Stepan Razin. Earlier, biographers and literary critics pointed out the importance of these people for Shukshin, but it was scattered. For the first time, an attempt was made to bring these personal models together into an integral plot of the formation of the writer in the space of culture. At different stages of the writer’s evolution, one of these models dominates, successively replacing each other, but not crowding out, but “overlapping”. The early stage of creativity, focused on Martin Eden’s strategy, is an attempt to “fit in” the current cultural mainstream. This is expressed in following the poetics of socialist realism. The second stage implicitly begins with the rehabilitation of Shukshin’s father in 1956, when the “Hamletian complex” is actualized. It is manifested in a sense of guilt towards his father, the strategy of concealing the true “I”, eccentricities. The third stage is connected with the personality of a real historical person, Stepan Razin, and is expressed in an open protest against the authorities. All important for V.M. Shukshin's behavioral models are united by the motive of a lonely confrontation with a hostile society and have a tragic ending, which led to the early departure of the writer and the generation of myths about the violent nature of his death. V.M. Shukshin was an extraordinary and typical figure at the same time. That allowed his biography to become a “personal model” for subsequent authors who came from the rural outback.


Author(s):  
Ik-Hwan Um ◽  
Seungjae Kim

Second-order rate constants (kN) for reactions of p-nitrophenyl acetate (1) and S-p-nitrophenyl thioacetate (2) with OH‒ have been measured spectrophotometrically in DMSO-H2O mixtures of varying compositions at 25.0 ± 0.1 oC. The kN value increases from 11.6 to 32,800 M‒1s‒1 for the reactions of 1 and from 5.90 to 190,000 M‒1s‒1 for those of 2 as the reaction medium changes from H2O to 80 mol % DMSO, indicating that the effect of medium on reactivity is more remarkable for the reactions of 2 than for those of 1. Although 2 possesses a better leaving group than 1, the former is less reactive than the latter by a factor of 2 in H2O. This implies that expulsion of the leaving group is not advanced in the rate-determining transition state (TS), i.e., the reactions of 1 and 2 with OH‒ proceed through a stepwise mechanism, in which expulsion of the leaving group from the addition intermediate occurs after the rate-determining step (RDS). Addition of DMSO to H2O would destabilize OH‒ through electronic repulsion between the anion and the negative-dipole end in DMSO. However, destabilization of OH‒ in the ground state (GS) is not solely responsible for the remarkably enhanced reactivity upon addition of DMSO to the medium. The effect of medium on reactivity has been dissected into the GS and TS contributions through combination of the kinetic data with the transfer enthalpies (ΔΔHtr) from H2O to DMSO-H2O mixtures for OH‒ ion.


Author(s):  
Wei Liu ◽  
Yunbo Yuan ◽  
Tao He ◽  
Donghua Wang

Considering the effect of teeth surface sliding friction, free vibration of two-stage planetary gears (TPG) is studied theoretically for the first time. The lateral-torsional coupling dynamic model and equation are established with three degrees of freedom: two translations and one rotation. The change rule of natural frequency is discussed with the case of first stage planetary gear’s number 4 and second stage planetary gear’s number 3, 4 and 5. Afterwards three vibration modes are summarized by calculating the free vibration. In order to understand the behavior of friction, the effect of friction on natural frequencies is analyzed for the case of considering friction and not considering friction. Furthermore, the ‘self-coupling’ phenomenon is obtained from the vibration of center component of TPG Meanwhile, the ‘mutual coupling’ is obtained between the first-stage planetary gear (FPG) and the second-stage planetary gear (SPG).


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