Path-integral molecular dynamics simulations of glycine·(H2O)n (n=1–7) clusters on semi-empirical PM6 potential energy surfaces

Unveiling Zwitterionization of Glycine in the Microhydration Limit

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.

Formation of free radicals by direct photolysis of halogenated phenols (HPs) and effects of DOM: A case study on monobromophenols

The free radicals play an important role to understand direct/indirect transformation mechanisms of organic pollutants. However, very few efforts have been made to elucidate the radicals produced by direct photolysis. In this study, the short-lived radicals generated under simulated sunlight irradiation from representative halogenated phenols (HPs), monobromophenols, were investigated by electron paramagnetic resonance (EPR). The results showed that three radicals, carbon-centered radical (C), hydrogen radical (H) and hydroxyl radical (OH), were generated from the direct irradiation of HPs. Compared to other substitutions, halogenated atom at para-position led to the highest production of these radicals which is in accordance with the energies calculated by density functional theory. Based on the analyses of the reactive species and corresponding intermediate adducts, the possible reaction pathways for these radicals were tentatively proposed. Dissolved organic matters (DOM) could enhance the photodegradation of HPs by directly affecting the radicals' formation, mainly due to generation of excited triplet DOM (³DOM*). A positive correlation was found between the concentrations of hydrated electron and the steady state ³DOM* from different DOM. Our findings provided insights into environmental photochemical fate of HPs through their direct photolysis and will help more accurately understand their phototransformation mechanisms in the environment.

Efficient Computational Research Protocol to Survey Free Energy Surface for Solution Chemical Reaction in the QM/MM Framework: The FEG-ER Methodology and Its Application to Isomerization Reaction of Glycine in Aqueous Solution

In solution chemical reaction, we often need to consider a multidimensional free energy (FE) surface (FES) which is analogous to a Born-Oppenheimer potential energy surface. To survey the FES, an efficient computational research protocol is proposed within the QM/MM framework; (i) we first obtain some stable states (or transition states) involved by optimizing their structures on the FES, in a stepwise fashion, finally using the free energy gradient (FEG) method, and then (ii) we directly obtain the FE differences among any arbitrary states on the FES, efficiently by employing the QM/MM method with energy representation (ER), i.e., the QM/MM-ER method. To validate the calculation accuracy and efficiency, we applied the above FEG-ER methodology to a typical isomerization reaction of glycine in aqueous solution, and reproduced quite satisfactorily the experimental value of the reaction FE. Further, it was found that the structural relaxation of the solute in the QM/MM force field is not negligible to estimate correctly the FES. We believe that the present research protocol should become prevailing as one computational strategy and will play promising and important roles in solution chemistry toward solution reaction ergodography.

Direct photolysis of MeO-PBDEs in water and methanol: focusing on cyclization product MeO-PBDFs

Polybrominated diphenyl ethers (PBDEs) and hydroxylated PBDEs can transform into polybrominated dibenzofurans (PBDFs) via photocyclization. However, it is unclear whether methoxylated PBDEs (MeO-PBDEs) can photocyclize to form MeO-PBDFs. In this study, 5-MeO-BDE-47, 5'-MeO-BDE-99 and 6-MeO-BDE-85 were selected as models to investigate their direct photolysis, especially photocyclization in two solvent environments (water and methanol) using simulated photochemical experiments and density functional theory (DFT) calculations. The experimental results showed that MeO-PBDEs had faster direct photolysis reactions and higher quantum yields in methanol, and MeO-PBDFs could only be formed in a methanol solution of 5-MeO-BDE-47. The DFT results indicated that the lowest excited triplet state MeO-PBDEs can form dibenzofurans via direct cyclization pathways. Intra-annular H-elimination was found to be the rate-determining step for most cyclization pathways with high reaction barriers (⩾19.7kcal/mol), while 5-MeO-BDE-47 was found to have a distinct pathway for which the rate-determining step is ring closure with a low barrier (13.8kcal/mol) in a methanol environment. For this pathway, H-elimination assisted by Br cleaved from an ortho-C-Br bond was observed with a 2.0kcal/mol barrier. Thus, the DFT results reasonably explained the experimental findings, and the photocyclization of MeO-PBDEs depended on the specific Br-substitution patterns and specific effects of the environmental media.

Theoretical strategy to build structural models of microhydrated inorganic systems for the knowledge of their vibrational properties: the case of the hydrated nitrate aerosols

This study provides theoretical anharmonic calculations for microhydrated NaNO3-labeled (NaNO3, nH2O)x with a water-to-solute ratio (n) ranging from 1 to 3. A representative geometrical model of these forms was first investigated by simulating the molecular clusters as (NaNO3,1H2O)x with x = 1 to 4. The comparison between the calculated time independent anharmonic frequencies using the B3LYP-D/6-311+G(d,p) method and their experimental counterparts led to the choice of a supercluster model. The most probable structures of (NaNO3,nH2O)3 molecular system were investigated by using our global search algorithm we developed recently (GSAM code) both at the B3LYP/6-311+G(d,p) and the B3LYP-D/6-311+G(d,p) levels of theory. The quality of the structural model is illustrated by comparing the B3LYP/6-311+G(d,p) and B3LYP-D/6-311+G(d,p) anharmonic vibrational signatures with those obtained from IR experiments. While an average deviation of 16 cm(-1) is observed in the case of the B3LYP computations, the deviation is reduced to 7 cm(-1) for the B3LYP-D computations.

Quantum proton transfer in hydrated sulfuric acid clusters: a perspective from semiempirical path integral simulations

We have carried out path-integral molecular dynamics simulations for hydrated sulfuric acid clusters to understand acid-dissociation and hydrogen-bonded structural rearrangement processes in these clusters from a quantum mechanical viewpoint. The simulations were performed using the PM6 semiempirical electronic structure level whose parameters were modified on the basis of the specific reaction parameters strategy so that relative energies of optimized structures, as well as water binding energies reproduce ab initio and density-functional theory calculations. We have found that the acid dissociation processes, first and second deprotonation, effectively occur in a hydrated cluster with a specific cluster size. The mechanisms of the proton-transfer processes were analyzed in detail and it was found that the distance between O in sulfuric acid and O in the proton-accepting water is playing an important role. We also found that the water coordination number of the poton-accepting water is important in the proton-transfer processes.