energy relationships
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Author(s):  
Yipeng Cao ◽  
Rui Yang ◽  
Wei Wang ◽  
Shengpeng Jiang ◽  
Chengwen Yang ◽  
...  

2021 ◽  
Author(s):  
Sanjeev Rachuru ◽  
Jagannadham Vandanapu

Application of Linear Free Energy Relationships (LFER) to pKaH+ data in water at 25o C of deprotonation of protonated fused ring systems like benzimidazolium cations is carried out in the present work. With a good comparison of the sites of substituents with reference to a functional group in benzene ring and the imidazolium ring, an excellent Hammett correlation is observed for the deprotonation of (pKaH+) of protonated fused ring systems like benzimidazolium cations. For the three substituents OH, MeO and Me at position 4 in the benzimidazole satisfy the correlation with I values. A positive Hammet  values of 1.93 indicates that electron withdrawing substituents facilitate the deprotonation. Under the same conditions a Taft * value of 1.11 is obtained for the deprotonation of 2-substituted-benzimidazolium cations. The available pKaH+ data in 5% aq. ethanol at 30o C of 2-methyl benzimidazolium cations and 2-(hydroxyethyl) benzimidazolium cations also followed Hammett correlation. The lower Hammett  value of 0.89 for 2-(hydroxyethyl) benzimidazolium cation series than that of 1.78 of 2-methyl benzimidazolium cation series is explained in terms of strong intramolecular hydrogen bonding in 2-(hydroxyethyl) benzimidazolium cation which resists the easy deprotonation. Deprotonation of 1-substituted-benzimidazolium cations did not follow Hammett relation.


2021 ◽  
Author(s):  
Martin Pfeiffer ◽  
Bernd Nidetzky ◽  
Rory Crean ◽  
Cátia Moreira ◽  
Antonietta Parracino ◽  
...  

Cooperative interplay between the functional devices of a preorganized active site is fundamental to enzyme catalysis. A deepened understanding of this phenomenon is central to elucidating the remarkable efficiency of natural enzymes, and provides an essential benchmark for enzyme design and engineering. Here, we study the functional interconnectedness of the catalytic nucleophile (His18) in an acid phosphatase by analyzing the consequences of its replacement with aspartate. We present crystallographic, biochemical and computational evidence for a conserved mechanistic pathway via a phospho-enzyme intermediate on Asp18. Linear free-energy relationships for phosphoryl transfer from phosphomonoester substrates to His18/Asp18 provide evidence for cooperative interplay between the nucleophilic and general-acid catalytic groups in the wildtype enzyme, and its substantial loss in the H18D variant. As an isolated factor of phosphatase efficiency, the advantage of a histidine compared to an aspartate nucleophile is around 10^4-fold. Cooperativity with the catalytic acid adds ≥10^2-fold to that advantage. Empirical valence bond simulations of phosphoryl transfer from glucose 1-phosphate to His and Asp in the enzyme explain the loss of activity of the Asp18 enzyme through a combination of impaired substrate positioning in the Michaelis complex, as well as a shift from early to late protonation of the leaving group in the H18D variant. The evidence presented furthermore suggests that the cooperative nature of catalysis distinguishes the enzymatic reaction from the corresponding reaction in solution and is enabled by the electrostatic preorganization of the active site. Our results reveal sophisticated discrimination in multifunctional catalysis of a highly proficient phosphatase active site.


2021 ◽  
Author(s):  
Hongbin Wan ◽  
Kristina Spiru ◽  
Sarah Williams ◽  
Robert Alan Pearlstein

We proposed previously that aqueous non-covalent barriers arise from solute-induced perturbation of the H-bond network of solvating water ('the solvation field') relative to bulk solvent, where the association barrier equates to enthalpic losses incurred from incomplete replacement of the H-bonds of expelled H-bond enriched solvation by inter-partner H-bonds, and the dissociation barrier equates to enthalpic + entropic losses incurred during dissociation-induced resolvation of H-bond depleted positions of the free partners (where dynamic occupancy is powered largely by the expulsion of such solvation to bulk solvent during association). We analyzed blockade of the ether-a-go-go-related gene potassium channel (hERG) based on these principles, the results of which suggest that blockers: 1) project a single rod-shaped R-group (denoted as 'BP') into the pore at a rate proportional to the desolvation cost of BP, with the largely solvated remainder (denoted as 'BC') occupying the cytoplasmic 'antechamber' of hERG; and 2) undergo second-order entry to the antechamber, followed by first-order association of BP to the pore. In this work, we used WATMD to qualitatively survey the solvation fields of the pore and a representative set of 16 blockers sampled from the Redfern dataset of marketed drugs spanning a range of pro-arrhythmicity. We show that the highly non-polar pore is solvated principally by H-bond depleted and bulk-like water (incurring zero desolvation cost), whereas blocker BP moieties are solvated by variable combinations of H-bond enriched and depleted water. With a few explainable exceptions, the blocker solvation fields (and implied desolvation/resolvation costs) are qualitatively well-correlated with blocker potency and Redfern safety classification.


2021 ◽  
pp. 2256-2261
Author(s):  
Jose L. Alvarez-Hernandez ◽  
Ji Won Han ◽  
Andrew E. Sopchak ◽  
Yixing Guo ◽  
Kara L. Bren

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