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Charge separation under solvation stress conditions is a fundamental process that comes in many forms in doped water clusters. Yet, the mechanism of intramolecular charge separation, where constraints due to the molecular structure might be intricately tied to restricted solvation structures, remains largely unexplored. Microhydrated amino acids are such paradigmatic molecules. Ab initio simulations are carried out at 300 K in the frameworks of metadynamics sampling and thermodynamic integration to map the thermal mechanisms of zwitterionization using Gly(H2O) n with n = 4 and 10. In both cases, a similar water-mediated proton transfer chain mechanism is observed; yet, detailed analyses of thermodynamics and kinetics demonstrate that the charge-separated zwitterion is the preferred species only for n = 10 mainly due to kinetic stabilization. Structural analyses disclose that bifurcated H-bonded water bridges, connecting the cationic and anionic sites in the fluctuating microhydration network at room temperature, are enhanced in the transition-state ensemble exclusively for n = 10 and become overwhelmingly abundant in the stable zwitterion. The findings offer potential insights into charge separation under solvation stress conditions beyond the present example.

Ruthenium-based CO releasing molecules (CO-RMs), CORM-2 and CORM-3, have been widely used as surrogates of CO for studying its biological effects in vitro and in vivo with much success. However, several previous solution-phase and in-vitro studies have revealed the ability for such CO-RMs to chemically modify proteins and reduce aromatic nitro groups due to their intrinsic chemical reactivity under certain conditions. In our own work of studying the cytoprotective effects of CO donors, we were in need of assessing chemical factors that could impact the interpretation of results from CO donors including CORM-2,3 in various in-vitro assays. For this, we examined the effects of CORM-2,3 toward representative reagents commonly used in various bioassays including resazurin, tetrazolium salts, nitrites and azide-based H(2)S probes. We have also examined the effect of CORM-2,3 on glutathione disulfide (GSSG), which is a very important redox regulator. Our studies show the ability for these CO-RMs to induce a number of chemical and/or spectroscopic changes for several commonly used biological reagents under near physiological conditions. These reactions/spectroscopic changes cannot be duplicated with CO-deleted CO-RMs (iCORMs), which are often used as negative controls. Further, both CORM-2 and -3 are capable of consuming and reducing GSSG in solution. We hope the results described will help future design of control experiments in using Ru-based CO-RMs in similar experiments.

We previously reported a series of p53-elevating anthraquinone compounds with considerable cytotoxicity for acute lymphatic leukemia (ALL) cells. To further develop this class of compounds, we examined the effect of a few key structural features on the anticancer structure-activity relationship in ALL cells. The active analogs showed comparable cytotoxicity and upregulation of p53 but did not induce significant downregulation of MDM2 as seen with the lead compound AQ-101, indicating the importance of the anthraquinone core scaffold for MDM2 regulation. The result from the current study not only contributes to the SAR framework of these anthraquinone derivatives but also opens up new chemical space for further optimization work.

Understanding the molecular details of antibiotic resistance by the bacterial enzymes β-lactamases is vital for the development of novel antibiotics and inhibitors. In this spirit, the detailed mechanism of deacylation of the acyl-enzyme complex formed by cephalothin and class C β-lactamase is investigated here using hybrid quantum-mechanical/molecular-mechanical molecular dynamics methods. The roles of various active-site residues and substrate in the deacylation reaction are elucidated. We identify the base that activates the hydrolyzing water molecule and the residue that protonates the catalytic serine (Ser64). Conformational changes in the active sites and proton transfers that potentiate the efficiency of the deacylation reaction are presented. We have also characterized the oxyanion holes and other H-bonding interactions that stabilize the reaction intermediates. Together with the kinetic and mechanistic details of the acylation reaction, we analyze the complete mechanism and the overall kinetics of the drug hydrolysis. Finally, the apparent rate-determining step in the drug hydrolysis is scrutinized.

Enhanced sampling of large number of collective variables (CVs) is inevitable in molecular dynamics (MD) simulations of complex chemical processes such as enzymatic reactions. Because of the computational overhead of hybrid quantum mechanical/molecular mechanical (QM/MM)-based MD simulations, especially together with density functional theory, predictions of reaction mechanism, and estimation of free-energy barriers have to be carried out within few tens of picoseconds. We show here that the recently developed temperature-accelerated sliced sampling method allows one to sample large number of CVs, thereby enabling us to obtain rapid convergence in free-energy estimates in QM/MM MD simulation of enzymatic reactions. Moreover, the method is shown to be efficient in exploring flat and broad free-energy basins that commonly occur in enzymatic reactions. We demonstrate this by studying deacylation and reverse acylation reactions of aztreonam drug catalyzed by a class-C β lactamase (CBL) bacterial enzyme. Mechanistic details and nature of kinetics of aztreonam hydrolysis by CBL are elaborated here. The results of this study point to characteristics of the aztreonam drug that are responsible for its slow hydrolysis.\ud \ud

Summary The nucleotidyl transfer reaction, catalyzed by sugar nucleotidyltransferases (SNTs), is assisted by two active site Mg 2+ ions. While studying this reaction using X-ray crystallography, we captured snapshots of the pyrophosphate (product) as it exits along a pocket. Surprisingly, one of the active site Mg 2+ ions remains coordinated to the exiting pyrophosphate. This hints at the participation of Mg 2+ in the process of product release, besides its role in catalyzing nucleotidyl transfer. These observations are further supported by enhanced sampling molecular dynamics simulations. Free energy computations suggest that the product release is likely to be rate limiting in SNTs, and the origin of the high free energy barrier for product release could be traced back to the "slow" conformational change of an Arg residue at the exit end of the pocket. These results establish a dual role for Mg 2+ , and propose a general mechanism of product release during the nucleotidyl transfer by SNTs.

HCN is clearly associated with the prebiotic chemical evolution of life. It has been known for decades that the radiolysis of HCN solutions produces sugars, amino acids and nucleobases. Remarkably, recent experimental studies have shown that the photolytic reduction of aqueous HCN by a photoredox reagent [Cu(CN)3](2-) specifically yields sugars, which are the essential building blocks of RNA. Although a mechanistic understanding of such reductions with solvated electrons is poor, the general consensus is that they involve neutral free radicals. We show herein through the use of electronic structure studies and molecular simulations that the reduction of the nitrile bond of HCN is initiated through the formation of a molecular dipole-bound anion from the photoredox reagent. Our theoretical studies show how HCN binds to the photoexcited reagent and then extracts an electron from the reagent and is ultimately detached as a dipole-bound anion. The dipole-bound anionic form of [HCN](-) can easily convert into a solvated valence-bound form of [HCN](-). After the formation of solvated [HCN](-), an extraordinary chemical event ensues through a counter-intuitive coupling of two valence-bound anions to form a solvated molecular dianionic intermediate, [HCN]2(2-). Finally, a proton-coupled electron transfer occurs within the dianionic entity to complete the reduction. This mechanistic scenario is applicable to the reduction of other prebiotic nitrile species and avoids neutral radical-based pathways, thereby preventing the proliferation of reactive species and preserving chemical selectivity. Furthermore, we show how such similar nitrile reduction pathways operate to yield the sugar precursors.