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© 2020 National Academy of Sciences. All rights reserved. Escalating global water scarcity necessitates high-performance desalination membranes, for which fundamental understanding of structure–property–performance relationships is required. In this study, we comprehensively assess the ionization behavior of nanoporous polyamide selective layers in state-of-the-art nanofiltration (NF) membranes. In these films, residual carboxylic acids and amines influence permeability and selectivity by imparting hydrophilicity and ionizable moieties that can exclude coions. We utilize layered interfacial polymerization to prepare physically and chemically similar selective layers of controlled thickness. We then demonstrate location-dependent ionization of carboxyl groups in NF polyamide films. Specifically, only surface carboxyl groups ionize under neutral pH, whereas interior carboxyl ionization requires pH >9. Conversely, amine ionization behaves invariably across the film. First-principles simulations reveal that the low permittivity of nanoconfined water drives the anomalous carboxyl ionization behavior. Furthermore, we report that interior carboxyl ionization could improve the water–salt permselectivity of NF membranes over fourfold, suggesting that interior charge density could be an important tool to enhance the selectivity of polyamide membranes. Our findings highlight the influence of nanoconfinement on membrane transport properties and provide enhanced fundamental understanding of ionization that could enable novel membrane design.

© 2019 American Chemical Society. Methyl transferases (MTases) are a well-studied class of enzymes for which competing enzymatic enhancement mechanisms have been suggested, ranging from structural methyl group CH···X hydrogen bonds (HBs) to electrostatic- and charge-transfer-driven stabilization of the transition state (TS). We identified all Class I MTases for which reasonable resolution (<2.0 Å) crystal structures could be used to form catalytically competent ternary complexes for multiscale (i.e., quantum-mechanical/molecular-mechanical or QM/MM) simulation of the SN2 methyl transfer reaction coordinate. The four Class I MTases studied have both distinct functions (e.g., protein repair or biosynthesis) and substrate nucleophiles (i.e., C, N, or O). While CH···X HBs stabilize all reactant complexes, no universal TS stabilization role is found for these interactions in MTases. A consistent picture is instead obtained through analysis of charge transfer and electrostatics, wherein much of cofactor-substrate charge separation is maintained in the TS region, and electrostatic potential is correlated with substrate nucleophilicity (i.e., intrinsic reactivity).

© 2020 National Academy of Sciences. All rights reserved. Escalating global water scarcity necessitates high-performance desalination membranes, for which fundamental understanding of structure–property–performance relationships is required. In this study, we comprehensively assess the ionization behavior of nanoporous polyamide selective layers in state-of-the-art nanofiltration (NF) membranes. In these films, residual carboxylic acids and amines influence permeability and selectivity by imparting hydrophilicity and ionizable moieties that can exclude coions. We utilize layered interfacial polymerization to prepare physically and chemically similar selective layers of controlled thickness. We then demonstrate location-dependent ionization of carboxyl groups in NF polyamide films. Specifically, only surface carboxyl groups ionize under neutral pH, whereas interior carboxyl ionization requires pH >9. Conversely, amine ionization behaves invariably across the film. First-principles simulations reveal that the low permittivity of nanoconfined water drives the anomalous carboxyl ionization behavior. Furthermore, we report that interior carboxyl ionization could improve the water–salt permselectivity of NF membranes over fourfold, suggesting that interior charge density could be an important tool to enhance the selectivity of polyamide membranes. Our findings highlight the influence of nanoconfinement on membrane transport properties and provide enhanced fundamental understanding of ionization that could enable novel membrane design.

SpnF is the first monofunctional Diels-Alder/[6+4]-ase that catalyzes a reaction leading to both Diels-Alder and [6+4] adducts through a single transition state. The environment-perturbed transition-state sampling method has been developed to calculate free energies, kinetic isotope effects, and quasi-classical reaction trajectories of enzyme-catalyzed reactions and the uncatalyzed reaction in water. Energetics calculated in this way reproduce the experiment and show that the normal Diels-Alder transition state is stabilized by H bonds with water molecules, while the ambimodal transition state is favored in the enzyme SpnF by both intramolecular hydrogen bonding and hydrophobic binding. Molecular dynamics simulations show that trajectories passing through the ambimodal transition state bifurcate to the [6+4] adduct and the Diels-Alder adduct with a ratio of 1:1 in the gas phase, 1:1.6 in water, and 1:11 in the enzyme. This example shows how an enzyme acts on a vibrational time scale to steer post-transition state trajectories toward the Diels-Alder adduct.

This thesis focuses on the study of time-resolved mechanism of organic reactions with molecular reaction dynamics simulations. Gas-phase trajectory simulations were performed on (1) dimethyldioxirane C-H oxidation, which show how polar acetone solvation favors diradical recombination, leading to the retention of stereospecificity; (2) dehydro-Diels-Alder reactions, which reveal intrinsic dynamic features for concerted and stepwise pathways, where concerted pathway involves a vibrational excitation, while stepwise pathway involves a rotational excitation; (3) cyclopentadiene dimerization, in which two-stage pathway, as originally proposed by Woodward and Katz, is involved in 13% of the reactive trajectories, presenting a typical “dynamically stepwise” feature with time gap between formation of two bonds longer than 60 fs; and (4) sixteen reactions with potential energy surface bifurcation, where a linear correlation was found between TS bond lengths and the product ratio, serving as an empirical model to assist the discovery of new bifurcating reactions, and estimate product ratio without the expense of MD simulations. The thesis reports the development of a new computational method, environment-perturbed transition state sampling, (EPTSS) to enable the study of reaction dynamics in solvent and in enzyme. EPTSS integrates the conformational sampling of solvent/enzyme and quasi-classical sampling of reacting molecules, which was inspired by Truhlar and Gao’s ensemble-average variational transition state theory. The method has been applied to (1) water-accelerated Diels-Alder reaction, which shows how water molecules dynamically participate the reaction and forms enhanced hydrogen bonds; (2) phosphoric acid-catalyzed allylboration reactions, in which an intrinsic synergy of enhancement between the CH���O and OH���O hydrogen bonds were observed, and the enhancement is diminished in toluene solvent; and (3) SpnF-catalyzed Diels-Alder reaction, which first dem

This thesis focuses on the study of time-resolved mechanism of organic reactions with molecular reaction dynamics simulations. Gas-phase trajectory simulations were performed on (1) dimethyldioxirane C-H oxidation, which show how polar acetone solvation favors diradical recombination, leading to the retention of stereospecificity; (2) dehydro-Diels-Alder reactions, which reveal intrinsic dynamic features for concerted and stepwise pathways, where concerted pathway involves a vibrational excitation, while stepwise pathway involves a rotational excitation; (3) cyclopentadiene dimerization, in which two-stage pathway, as originally proposed by Woodward and Katz, is involved in 13% of the reactive trajectories, presenting a typical “dynamically stepwise” feature with time gap between formation of two bonds longer than 60 fs; and (4) sixteen reactions with potential energy surface bifurcation, where a linear correlation was found between TS bond lengths and the product ratio, serving as an empirical model to assist the discovery of new bifurcating reactions, and estimate product ratio without the expense of MD simulations. The thesis reports the development of a new computational method, environment-perturbed transition state sampling, (EPTSS) to enable the study of reaction dynamics in solvent and in enzyme. EPTSS integrates the conformational sampling of solvent/enzyme and quasi-classical sampling of reacting molecules, which was inspired by Truhlar and Gao’s ensemble-average variational transition state theory. The method has been applied to (1) water-accelerated Diels-Alder reaction, which shows how water molecules dynamically participate the reaction and forms enhanced hydrogen bonds; (2) phosphoric acid-catalyzed allylboration reactions, in which an intrinsic synergy of enhancement between the CH���O and OH���O hydrogen bonds were observed, and the enhancement is diminished in toluene solvent; and (3) SpnF-catalyzed Diels-Alder reaction, which first dem

Enzymes have evolved to facilitate challenging reactions at ambient conditions with specificity seldom matched by other catalysts. Computational modeling provides valuable insight into catalytic mechanism, and the large size of enzymes mandates multi-scale, quantum mechanical-molecular mechanical (QM/MM) simulations. Although QM/MM plays an essential role in balancing simulation cost to enable sampling with the full QM treatment needed to understand electronic structure in enzyme active sites, the relative importance of these two strategies for understanding enzyme mechanism is not well known. We explore challenges in QM/MM for studying the reactivity and stability of three diverse enzymes: i) Mg[supercript 2+]-dependent catechol O-methyltransferase (COMT), ii) radical enzyme choline trimethylamine lyase (CutC), and iii) DNA methyltransferase (DNMT1), which has structural Zn[superscript 2+] binding sites. In COMT, strong non-covalent interactions lead to long range coupling of electronic structure properties across the active site, but the more isolated nature of the metallocofactor in DNMT1 leads to faster convergence of some properties. We quantify these effects in COMT by computing covariance matrices of by-residue electronic structure properties during dynamics and along the reaction coordinate. In CutC, we observe spontaneous bond cleavage following initiation events, highlighting the importance of sampling and dynamics. We use electronic structure analysis to quantify the relative importance of CHO and OHO non-covalent interactions in imparting reactivity. These three diverse cases enable us to provide some general recommendations regarding QM/MM simulation of enzymes., NEC Corporation, National Institute of Environmental Health Sciences (Grant P30-ES002109), Burroughs Wellcome Fund (Career Award at the Scientific Interface), United States. Department of Energy (Computational Science Graduate Fellowship)

Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry.

Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry.

Vinyl carbocations have been the subject of extensive experimental and theoretical studies over the past five decades. Despite this long history in chemistry, the utility of vinyl cations in chemical synthesis has been limited, with most reactivity studies focusing on solvolysis reactions or intramolecular processes. Here we report synthetic and mechanistic studies of vinyl cations generated through silylium-weakly coordinating anion catalysis. We find that these reactive intermediates undergo mild intermolecular carbon-carbon bond-forming reactions, including carbon-hydrogen (C-H) insertion into unactivated sp3 C-H bonds and reductive Friedel-Crafts reactions with arenes. Moreover, we conducted computational studies of these alkane C-H functionalization reactions and discovered that they proceed through nonclassical, ambimodal transition structures. This reaction manifold provides a framework for the catalytic functionalization of hydrocarbons using simple ketone derivatives.

Pericyclic reactions-which proceed in a concerted fashion through a cyclic transition state-are among the most powerful synthetic transformations used to make multiple regioselective and stereoselective carbon-carbon bonds. They have been widely applied to the synthesis of biologically active complex natural products containing contiguous stereogenic carbon centres. Despite the prominence of pericyclic reactions in total synthesis, only three naturally existing enzymatic examples (the intramolecular Diels-Alder reaction, and the Cope and the Claisen rearrangements) have been characterized. Here we report a versatile S-adenosyl-l-methionine (SAM)-dependent enzyme, LepI, that can catalyse stereoselective dehydration followed by three pericyclic transformations: intramolecular Diels-Alder and hetero-Diels-Alder reactions via a single ambimodal transition state, and a retro-Claisen rearrangement. Together, these transformations lead to the formation of the dihydropyran core of the fungal natural product, leporin. Combined in vitro enzymatic characterization and computational studies provide insight into how LepI regulates these bifurcating biosynthetic reaction pathways by using SAM as the cofactor. These pathways converge to the desired biosynthetic end product via the (SAM-dependent) retro-Claisen rearrangement catalysed by LepI. We expect that more pericyclic biosynthetic enzymatic transformations remain to be discovered in naturally occurring enzyme 'toolboxes'. The new role of the versatile cofactor SAM is likely to be found in other examples of enzyme catalysis.

Pericyclic reactions-which proceed in a concerted fashion through a cyclic transition state-are among the most powerful synthetic transformations used to make multiple regioselective and stereoselective carbon-carbon bonds. They have been widely applied to the synthesis of biologically active complex natural products containing contiguous stereogenic carbon centres. Despite the prominence of pericyclic reactions in total synthesis, only three naturally existing enzymatic examples (the intramolecular Diels-Alder reaction, and the Cope and the Claisen rearrangements) have been characterized. Here we report a versatile S-adenosyl-l-methionine (SAM)-dependent enzyme, LepI, that can catalyse stereoselective dehydration followed by three pericyclic transformations: intramolecular Diels-Alder and hetero-Diels-Alder reactions via a single ambimodal transition state, and a retro-Claisen rearrangement. Together, these transformations lead to the formation of the dihydropyran core of the fungal natural product, leporin. Combined in vitro enzymatic characterization and computational studies provide insight into how LepI regulates these bifurcating biosynthetic reaction pathways by using SAM as the cofactor. These pathways converge to the desired biosynthetic end product via the (SAM-dependent) retro-Claisen rearrangement catalysed by LepI. We expect that more pericyclic biosynthetic enzymatic transformations remain to be discovered in naturally occurring enzyme 'toolboxes'. The new role of the versatile cofactor SAM is likely to be found in other examples of enzyme catalysis.

SpnF, an enzyme involved in the biosynthesis of spinosyn A, catalyzes a transannular Diels-Alder reaction. Quantum mechanical computations and dynamic simulations now show that this cycloaddition is not well described as either a concerted or stepwise process, and dynamical effects influence the identity and timing of bond formation. The transition state for the reaction is ambimodal and leads directly to both the observed Diels-Alder and an unobserved [6+4] cycloadduct. The potential energy surface bifurcates and the cycloadditions occur by dynamically stepwise modes featuring an "entropic intermediate". A rapid Cope rearrangement converts the [6+4] adduct into the observed [4+2] adduct. Control of nonstatistical dynamical effects may serve as another way by which enzymes control reactions.