Nucleophilic Attack by Palladium Species

2005 ◽  
pp. 211-239 ◽  
Author(s):  
Yoshinori Yamamoto ◽  
Itaru Nakamura
Keyword(s):  
Nucleophilic Attack

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

2018 ◽  
Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Rates ◽  
Nucleophilic Attack ◽  
Classical Molecular Dynamics ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

Atom Condensed Fukui Function for Condensed Phases and Biological Systems and Its Application to Enzymatic Fixation of Carbon Dioxide

2019 ◽  
Author(s):  
Javier Oller ◽  
David A. Sáez ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Carbon Dioxide ◽  
Aqueous Solution ◽  
Molecular System ◽  
Chemical Reactivity ◽  
Nucleophilic Attack ◽  
Stable Conformation ◽  
Fukui Functions ◽  
Reactivity Descriptors ◽  
Dynamics Simulations ◽  
Fixation Of Carbon Dioxide

<div><div><div><p>Local reactivity descriptors such as atom condensed Fukui functions are promising computational tools to study chemical reactivity at specific sites within a molecule. Their applications have been mainly focused on isolated molecules in their most stable conformation without considering the effects of the surroundings. Here, we propose to combine QM/MM Born-Oppenheimer molecular dynamics simulations to obtain the microstates (configurations) of a molecular system using different representations of the molecular environment and calculate Boltzmann weighted atom condensed local reac- tivity descriptors based on conceptual DFT. Our approach takes the conformational fluctuations of the molecular system and the polarization of its electron density by the environment into account allowing us to analyze the effect of changes in the molecular environment on reactivity. In this contribution, we apply the method mentioned above to the catalytic fixation of carbon dioxide by crotonyl-CoA carboxylase/reductase and study if the enzyme alters the reactivity of its substrate compared to an aqueous solution. Our main result is that the protein en- vironment activates the substrate by the elimination of solute-solvent hydrogen bonds from aqueous solution in the two elementary steps of the reaction mechanism: the nucleophilic attack of a hydride anion from NADPH on the α, β unsaturated thioester and the electrophilic attack of carbon dioxide on the formed enolate species.</p></div></div></div>

Kinetics of the Imidazolium Ring-Opening of mRNA 5'-cap Analogs in Aqueous Alkali

2006 ◽  
Vol 71 (4) ◽  
pp. 567-578 ◽  
Author(s):  
Alicja Stachelska ◽  
Zbigniew J. Wieczorek ◽  
Janusz Stępiński ◽  
Marzena Jankowska-Anyszka ◽  
Harri Lönnberg ◽  
...  
Keyword(s):  
Electrostatic Interaction ◽  
Ring Opening ◽  
Nucleophilic Attack ◽  
Amino Groups ◽  
Hydroxide Ion ◽  
Methyl Group ◽  
Structural Modifications ◽  
Alkyl Groups ◽  
Imidazolium Ring ◽  
Kinetics Of

Second-order rate constants for the hydroxide-ion-catalyzed imidazolium ring-opening of several mono- and dinucleosidic analogs of mRNA 5'-cap have been determined. Intramolecular stacking of the two nucleobases in the dinucleosidic analogs, m7GpppN (m7G = 7-methylguanosine, N = 5'-linked nucleoside), and electrostatic interaction between the N-alkylated imidazolium ring and phosphate moiety have been shown to shield the m7G moiety against the nucleophilic attack of hydroxide ion. In addition, the effect of methylation of the nucleobase amino groups and replacement of the 7-methyl group with other alkyl groups have been studied. The influence of all the structural modifications studied turned out to be modest, the cleavage rates of the most and least reactive analogs (with the exception of non-phosphorylated nucleosides) differing only by a factor of 5.

scholarly journals Understanding the reaction mechanism of the regioselective piperidinolysis of aryl 1-(2,4-dinitronaphthyl) ethers in DMSO: Kinetic and DFT studies

2021 ◽  
Vol 46 ◽  
pp. 146867832110274
Author(s):  
Yasmen M Moghazy ◽  
Nagwa MM Hamada ◽  
Magda F Fathalla ◽  
Yasser R Elmarassi ◽  
Ezzat A Hamed ◽  
...  
Keyword(s):  
Carbon Atom ◽  
Density Functional ◽  
Function Analysis ◽  
Density Functional Theory Method ◽  
Activation Parameters ◽  
Kinetic Studies ◽  
Nucleophilic Attack ◽  
Common Mechanism ◽  
Slow Step ◽  
Rate Determining Step

Reactions of aryl 1-(2,4-dinitronaphthyl) ethers with piperidine in dimethyl sulfoxide at 25oC resulted in substitution of the aryloxy group at the ipso carbon atom. The reaction was measured spectrophotochemically and the kinetic studies suggested that the titled reaction is accurately third order. The mechanism is began by fast nucleophilic attack of piperidine on C1 to form zwitterion intermediate (I) followed by deprotonation of zwitterion intermediate (I) to the Meisenheimer ion (II) in a slow step, that is, SB catalysis. The regular variation of activation parameters suggested that the reaction proceeded through a common mechanism. The Hammett equation using reaction constant σo values and Brønsted coefficient value showed that the reaction is poorly dependent on aryloxy substituent and the reaction was significantly associative and Meisenheimer intermediate-like. The mechanism of piperidinolysis has been theoretically investigated using density functional theory method using B3LYP/6-311G(d,p) computational level. The combination between experimental and computational studies predicts what mechanism is followed either through uncatalyzed or catalyzed reaction pathways, that is, SB and SB-GA. The global parameters of the reactants, the proposed activated complexes, and the local Fukui function analysis explained that C1 carbon atom is the most electrophilic center of ether. Also, kinetics and theoretical calculation of activation energies indicated that the mechanism of the piperidinolysis passed through a two-step mechanism and the proton transfer process was the rate determining step.

scholarly journals NeissLock provides an inducible protein anhydride for covalent targeting of endogenous proteins

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Arne H. A. Scheu ◽  
Sheryl Y. T. Lim ◽  
Felix J. Metzner ◽  
Shabaz Mohammed ◽  
Mark Howarth
Keyword(s):  
Growth Factor ◽  
Transforming Growth Factor ◽  
Binding Protein ◽  
Growth Factor Receptor ◽  
Molecular Engineering ◽  
Nucleophilic Attack ◽  
High Yield ◽  
Protein Chemistry ◽  
Transforming Growth Factor Α ◽  
Endogenous Proteins

AbstractThe Neisseria meningitidis protein FrpC contains a self-processing module (SPM) undergoing autoproteolysis via an aspartic anhydride. Herein, we establish NeissLock, using a binding protein genetically fused to SPM. Upon calcium triggering of SPM, the anhydride at the C-terminus of the binding protein allows nucleophilic attack by its target protein, ligating the complex. We establish a computational tool to search the Protein Data Bank, assessing proximity of amines to C-termini. We optimize NeissLock using the Ornithine Decarboxylase/Antizyme complex. Various sites on the target (α-amine or ε-amines) react with the anhydride, but reaction is blocked if the partner does not dock. Ligation is efficient at pH 7.0, with half-time less than 2 min. We arm Transforming Growth Factor-α with SPM, enabling specific covalent coupling to Epidermal Growth Factor Receptor at the cell-surface. NeissLock harnesses distinctive protein chemistry for high-yield covalent targeting of endogenous proteins, advancing the possibilities for molecular engineering.

scholarly journals Transition-Metal-Free Boryl Substitution Using Silylboranes and Alkoxy Bases

Synlett ◽  
2017 ◽  
Vol 28 (11) ◽  
pp. 1258-1267 ◽  
Author(s):  
Hajime Ito ◽  
Eiji Yamamoto ◽  
Satoshi Maeda ◽  
Tetsuya Taketsugu
Keyword(s):  
Transition Metal ◽  
Functional Group ◽  
Experimental Studies ◽  
Transition Metal Catalysts ◽  
Alkyl Halides ◽  
Aryl Halides ◽  
Nucleophilic Attack ◽  
Important Class ◽  
Mechanistic Studies ◽  
Induced Reaction

Silylboranes are used as borylation reagents for organohalides in the presence of alkoxy bases without transition-metal catalysts. PhMe2Si–B(pin) reacts with a variety of aryl, alkenyl, and alkyl halides, including sterically hindered examples, to provide the corresponding organoboronates in good yields with high borylation/silylation ratios, showing good functional group compatibility. Halogenophilic attack of a silyl nucleophile on organohalides, and subsequent nucleophilic attack on the boron electrophile are identified to be crucial, based on the results of extensive theoretical and experimental studies. This boryl­ation reaction is further applied to the first direct dimesitylboryl (BMes2) substitution of aryl halides using Ph2MeSi–BMes2 and Na(O-t-Bu), affording aryldimesitylboranes, which are regarded as an important class of compounds for organic materials.1 Introduction2 Boryl Substitution of Organohalides with PhMe2Si–B(pin)/Alkoxy Bases3 Mechanistic Investigations4 DFT Mechanistic Studies Using an Artificial Force Induced Reaction (AFIR) Method5 Dimesitylboryl Substitution of Aryl Halides with Ph2MeSi–BMes2/Na(O-t-Bu)6 Conclusion

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