Thiolase: A Versatile Biocatalyst Employing Coenzyme A-Thioester Chemistry for Making and Breaking C-C Bonds.

Thiolases are CoA-dependent enzymes that catalyze the thiolytic cleavage of 3-ketoacyl-CoA, as well as its reverse reaction, which is the thioester-dependent Claisen condensation reaction. Thiolases are dimers or tetramers (dimers of dimers). All thiolases have two reactive cysteines: (a) a nucleophilic cysteine, which forms a covalent intermediate, and (b) an acid/base cysteine. The best characterized thiolase is the Zoogloea ramigera thiolase, which is a bacterial biosynthetic thiolase belonging to the CT-thiolase subfamily. The thiolase active site is also characterized by two oxyanion holes, two active site waters, and four catalytic loops with characteristic amino acid sequence fingerprints. Three thiolase subfamilies can be identified, each characterized by a unique sequence fingerprint for one of their catalytic loops, which causes unique active site properties. Recent insights concerning the thiolase reaction mechanism, as obtained from recent structural studies, as well as from classical and recent enzymological studies, are addressed, and open questions are discussed.

Salinity-mediated water self-purification via bond network distorting of H2O molecules on DRC-surface.

High salinity has plagued wastewater treatment for a long time by hindering pollutant removal, thereby becoming a global challenge for water pollution control that is difficult to overcome even with massive energy consumption. Herein, we propose a novel process for rapid salinity-mediated water self-purification in a dual-reaction-centers (DRC) system with cation-π structures. In this process, local hydrogen bond networks of H2O molecules can be distorted through the mediation of salinity, thereby opening the channels for the preferential contact of pollutants on the DRC interface. As the result, the elimination rate of pollutants increased approximately 32-fold at high salinity (100 mM) without any external energy consumption. Our findings provide a novel technology for high-efficiency and low-consumption water self-purification, which is of great significance in environmental remediation and even fine chemical industry.

Mutation-induced shift of the photosystem II active site reveals insight into conserved water channels.

Photosystem II (PSII) is the water-plastoquinone photo-oxidoreductase central to oxygenic photosynthesis. PSII has been extensively studied for its ability to catalyze light-driven water oxidation at a Mn4CaO5 cluster called the oxygen-evolving complex (OEC). Despite these efforts, the complete reaction mechanism for water oxidation by PSII is still heavily debated. Previous mutagenesis studies have investigated the roles of conserved amino acids, but these studies have lacked a direct structural basis that would allow for a more meaningful interpretation. Here, we report a 2.14-Å resolution cryo-EM structure of a PSII complex containing the substitution Asp170Glu on the D1 subunit. This mutation directly perturbs a bridging carboxylate ligand of the OEC, which alters the spectroscopic properties of the OEC without fully abolishing water oxidation. The structure reveals that the mutation shifts the position of the OEC within the active site without markedly distorting the Mn4CaO5 cluster metal-metal geometry, instead shifting the OEC as a rigid body. This shift disturbs the hydrogen-bonding network of structured waters near the OEC, causing disorder in the conserved water channels. This mutation-induced disorder appears consistent with previous FTIR spectroscopic data. We further show using quantum mechanics/molecular mechanics methods that the mutation-induced structural changes can affect the magnetic properties of the OEC by altering the axes of the Jahn-Teller distortion of the Mn(III) ion coordinated to D1-170. These results offer new perspectives on the conserved water channels, the rigid body property of the OEC, and the role of D1-Asp170 in the enzymatic water oxidation mechanism.

Anomalous water transport in narrow-diameter carbon nanotubes.

Carbon nanotubes (CNTs) mimicking the structure of aquaporins support fast water transport, making them strong candidates for building next-generation high-performance membranes for water treatment. The diffusion and transport behavior of water through CNTs or nanoporous graphene can be fundamentally different from those of bulk water through a macroscopic tube. To date, the nanotube-length-dependent physical transport behavior of water is still largely unexplored. Herein, on the basis of molecular dynamics simulations, we show that the flow rate of water through 0.83-nm-diameter (6,6) and 0.96-nm-diameter (7,7) CNTs exhibits anomalous transport behavior, whereby the flow rate increases markedly first and then either slowly decreases or changes slightly as the CNT length l increases. The critical range of l for the flow-rate transition is 0.37 to 0.5 nm. This anomalous water transport behavior is attributed to the l-dependent mechanical stability of the transient hydrogen-bonding chain that connects water molecules inside and outside the CNTs and bypasses the CNT orifice. The results unveil a microscopic mechanism governing water transport through subnanometer tubes, which has important implications for nanofluidic manipulation.

Viscoelastic Response in Hydrous Polymers: The Role of Hydrogen Bonds and Microstructure.

Water responsive polymers represent a remarkable group of soft materials, acting as a laboratory for diverse water responsive physical phenomena and cutting-edge biology-electronics interfaces. We report on peculiarly distinctive viscoelastic behaviors of the biobased water responsive polymer cellulose 10-undecenoyl ester, while biobased regenerated cellulose displays stronger hydroplastic behaviors. We discovered a novel hydrous deformation mechanism involving the stretching of hydrogen bonds mediated by hydroxyl groups and water molecules, serving as a crucial factor in accommodating deformations. In parallel, the microstructure of cellulose 10-undecenoyl ester with unique coexisting nanoparticles and a continuous phase of entangled chains is mechanically resilient in the anhydrous state but enhances structural stiffness in the hydrous state. This variation arises from a different hydration level within the hydrous microstructure. Such a fundamental discovery offers valuable insights into the connection between the microscopic physical properties that can be influenced by water and the corresponding viscoelastic responses, extending its applicability to a wide range of hygroscopic materials.

Reorientation of Hydrogen Bonds Renders Unusual Enhancement in Thermal Transport of Water in Nanoconfined Environments.

Liquid confined in a nanochannel or nanotube has exhibited a superfast transport phenomenon, providing an ideal heat and mass transfer platform to meet the increasingly stringent challenge of thermal management in developing high-power-density nanoelectronics and nanochips. However, understanding the thermal transport of confined liquid is currently lacking and is speculated to be fundamentally different from that of bulk counterparts due to the unprecedented thermodynamics of liquid in nanoconfined environments. Here, we report that the thermal conductivity of water confined in a silica nanotube is nearly 2-fold as that of bulk status. Further molecular dynamics simulations reveal that this unusual enhancement originates from the densification and reorientation of local hydrogen bonds close to the nanotubes. Thermal-confinement scaling law is established and quantitatively supported by comprehensive simulations with remarkable agreement. Our findings lay a theoretical foundation for designing nanofluidics-enabled cooling strategies and devices.

Neutron crystallography and quantum chemical analysis of bilin reductase PcyA mutants reveal substrate and catalytic residue protonation states.

PcyA, a ferredoxin-dependent bilin pigment reductase, catalyzes the site-specific reduction of the two vinyl groups of biliverdin (BV), producing phycocyanobilin. Previous neutron crystallography detected both the neutral BV and its protonated form (BVH+) in the wildtype (WT) PcyA-BV complex, and a nearby catalytic residue Asp105 was found to have two conformations (protonated and deprotonated). Semiempirical calculations have suggested that the protonation states of BV are reflected in the absorption spectrum of the WT PcyA-BV complex. In the previously determined absorption spectra of the PcyA D105N and I86D mutants, complexed with BV, a peak at 730 nm, observed in the WT, disappeared and increased, respectively. Here, we performed neutron crystallography and quantum chemical analysis of the D105N-BV and I86D-BV complexes to determine the protonation states of BV and the surrounding residues and study the correlation between the absorption spectra and protonation states around BV. Neutron structures elucidated that BV in the D105N mutant is in a neutral state, whereas that in the I86D mutant is dominantly in a protonated state. Glu76 and His88 showed different hydrogen bonding with surrounding residues compared with WT PcyA, further explaining why D105N and I86D have much lower activities for phycocyanobilin synthesis than the WT PcyA. Our quantum mechanics/molecular mechanics calculations of the absorption spectra showed that the spectral change in D105N arises from Glu76 deprotonation, consistent with the neutron structure. Collectively, our findings reveal more mechanistic details of bilin pigment biosynthesis.

Noncovalent interactions that tune the reactivities of the flavins in bifurcating electron transferring flavoprotein.

Bifurcating electron transferring flavoproteins (Bf-ETFs) tune chemically identical flavins to two contrasting roles. To understand how, we used hybrid quantum mechanical molecular mechanical calculations to characterize noncovalent interactions applied to each flavin by the protein. Our computations replicated the differences between the reactivities of the flavins: the electron transferring flavin (ETflavin) was calculated to stabilize anionic semiquinone (ASQ) as needed to execute its single-electron transfers, whereas the Bf flavin (Bfflavin) was found to disfavor the ASQ state more than does free flavin and to be less susceptible to reduction. The stability of ETflavin ASQ was attributed in part to H-bond donation to the flavin O2 from a nearby His side chain, via comparison of models employing different tautomers of His. This H-bond between O2 and the ET site was uniquely strong in the ASQ state, whereas reduction of ETflavin to the anionic hydroquinone (AHQ) was associated with side chain reorientation, backbone displacement, and reorganization of its H-bond network including a Tyr from the other domain and subunit of the ETF. The Bf site was less responsive overall, but formation of the Bfflavin AHQ allowed a nearby Arg side chain to adopt an alternative rotamer that can H-bond to the Bfflavin O4. This would stabilize the anionic Bfflavin and rationalize effects of mutation at this position. Thus, our computations provide insights on states and conformations that have not been possible to characterize experimentally, offering explanations for observed residue conservation and raising possibilities that can now be tested.

Allosteric modulation of fluorescence revealed by hydrogen bond dynamics in a genetically encoded maltose biosensor.

Genetically encoded fluorescent biosensors (GEFBs) proved to be reliable tracers for many metabolites and cellular processes. In the simplest case, a fluorescent protein (FP) is genetically fused to a sensing protein which undergoes a conformational change upon ligand binding. This drives a rearrangement in the chromophore environment and changes the spectral properties of the FP. Structural determinants of successful biosensors are revealed only in hindsight when the crystal structures of both ligand-bound and ligand-free forms are available. This makes the development of new biosensors for desired analytes a long trial-and-error process. In the current study, we conducted µs-long all atom molecular dynamics (MD) simulations of a maltose biosensor in both the apo (dark) and holo (bright) forms. We performed detailed hydrogen bond occupancy analyses to shed light on the mechanism of ligand induced conformational change in the sensor protein and its allosteric effect on the chromophore environment. We find that two strong indicators for distinguishing bright and dark states of biosensors are due to substantial changes in hydrogen bond dynamics in the system and solvent accessibility of the chromophore.

Location of S-nitrosylated cysteines in protein three-dimensional structures.

Although S-nitrosylation of cysteines is a common protein posttranslational modification, little is known about its three-dimensional structural features. This paper describes a systematic survey of the data available in the Protein Data Bank. Several interesting observations could be made. (1) As a result of radiation damage, S-nitrosylated cysteines (Snc) are frequently reduced, at least partially. (2) S-nitrosylation may be a protection against irreversible thiol oxidation; because the NO group of Snc is relatively accessible to the solvent, it may act as a cork to protect the sulfur atoms of cysteines from oxidation by molecular oxygen to sulfenic, sulfinic, and sulfonic acid; moreover, Snc are frequently found at the start or end of helices and strands and this might shield secondary structural elements from unfolding.

C and G are frequently mutated into T and A in coding regions of human genes.

Nucleotide mutations in human genes have long been a hot subject for study because some of them may lead to severe human diseases. Understanding the general mutational process and evolutionary trend of human genes could help answer such questions as why certain diseases occur and what challenges we face in protecting human health. In this study, we conducted statistics on 89,895 single-nucleotide variations identified in coding regions of 18,339 human genes. The results show that C and G are frequently mutated into T and A in human genes. C/G (C or G)-to-T/A mutations lead to reduction of hydrogen bonds in double-stranded DNA because C-G and T-A base pairs are maintained by three and two hydrogen bonds respectively. C-to-T and G-to-A mutations occur predominantly in human genes because they not only reduce hydrogen bonds but also belong to transition mutation. Reduction of hydrogen bonds could reduce energy consumption not only in separating double strands of mutated DNA for transcription and replication but also in disrupting stem-loop structure of mutated mRNA for translation. It is thus considered that to reduce hydrogen bonds (and thus to reduce energy consumption in gene expression) is one of the driving forces for nucleotide mutation. Moreover, codon mutation is positively correlated to its content, suggesting that most mutations are not targeted on changing any specific codons (amino acids) but are merely for reducing hydrogen bonds. Our study provides an example of utilizing single-nucleotide variation data to infer evolutionary trend of human genes, which can be referenced to conduct similar studies in other organisms.

Exploring the influence of metal cations on individual hydrogen bonds in Watson-Crick guanine-cytosine DNA base pair: An interacting quantum atoms analysis.

This study delves into the nature of individual hydrogen bonds and the relationship between metal cations and hydrogen bonding in the Watson-Crick guanine-cytosine (GC) base pair and its alkali and alkaline earth cation-containing complexes (Mn+-GC). The findings reveal how metal cations affect the nature and strength of individual hydrogen bonds. The study employs interacting quantum atoms (IQA) analysis to comprehensively understand three individual hydrogen bonds within the GC base pair and its cationic derivatives. These analyses unveil the nature and strength of hydrogen bonds and serve as a valuable reference for exploring the impact of cations (and other factors) on each hydrogen bond. All the H ⋯ $$ \cdots $$ D interactions (H is hydrogen and D is oxygen or nitrogen) in the GC base pair are primarily electrostatic in nature, with the charge transfer component playing a substantial role. Introducing a metal cation perturbs all H ⋯ $$ \cdots $$ D interatomic interactions in the system, weakening the nearest hydrogen bond to the cation (indicated by a) and reinforcing the other (b and c) interactions. Notably, the interaction a, the strongest H ⋯ $$ \cdots $$ D interaction in the GC base pair, becomes the weakest in the Mn+-GC complexes. A broader perspective on the stability of GC and Mn+-GC complexes is provided through interacting quantum fragments (IQF) analysis. This approach considers all pairwise interactions between fragments and intra-fragment components, offering a complete view of the factors that stabilize and destabilize GC and Mn+-GC complexes. The IQF analysis underscores the importance of electron sharing, with the dominant contribution arising from the inter-fragment exchange-correlation term, in shaping and sustaining GC and Mn+-GC complexes. From this point of view, alkaline and alkaline earth cations have distinct effects, with alkaline cations generally weakening inter-fragment interactions and alkaline earth cations strengthening them. In addition, IQA and IQF calculations demonstrate that the hydration of cations led to small changes in the hydrogen bonding network. Finally, the IQA interatomic energies associated with the hydrogen bonds and also inter-fragment interaction energies provide robust indicators for characterizing hydrogen bonds and complex stability, showing a strong correlation with total interaction energies.

Hydrogen bond energy estimation (H-BEE) in large molecular clusters: A Python program for quantum chemical investigations.

A procedure, derived from the fragmentation-based molecular tailoring approach (MTA), has been proposed and extensively applied by Deshmukh and Gadre for directly estimating the individual hydrogen bond (HB) energies and cooperativity contributions in molecular clusters. However, the manual fragmentation and high computational cost of correlated quantum chemical methods make the application of this method to large molecular clusters quite formidable. In this article, we report an in-house developed software for automated hydrogen bond energy estimation (H-BEE) in large molecular clusters. This user-friendly software is essentially written in Python and executed on a Linux platform with the Gaussian package at the backend. Two approximations to the MTA-based procedure, viz. the first spherical shell (SS1) and the Fragments-in-Fragments (Frags-in-Frags), enabling cost-effective, automated evaluation of HB energies and cooperativity contributions, are also implemented in this software. The software has been extensively tested on a variety of molecular clusters and is expected to be of immense use, especially in conjunction with correlated methods such as MP2, CCSD(T), and so forth.

Hydrogen Bonding Competition Mediated Phase Separation with Abnormal Moisture-Induced Stiffness Boosting.

Moisture usually deteriorates polymers' mechanical performance owing to its plasticizing effect, causing side effects in their practical load-bearing applications. Herein, a simple binary ionogel consisting of an amphiphilic polymer network and a hydrophobic ionic liquid (IL) is developed with remarkable stiffening effect after moisture absorption, demonstrating a complete contrast to water-induced softening effect of most polymer materials. Such a moisture-induced stiffening behavior is induced by phase separation after hydration of this binary ionogel. Specifically, it is revealed that hydrogen (H)-bonding structures play a dominant role in the humidity-responsive behavior of the ionogel, where water will preferentially interact with polymer chains through H-bonding and break the polymer-IL H-bonds, thus leading to phase separation structures with modulus boosting. This work may provide a facile and effective molecular engineering route to construct mechanically adaptive polymers with water-induced dramatic stiffening for diverse applications.

A Universal Additive Design Strategy to Modulate Solvation Structure and Hydrogen Bond Network toward Highly Reversible Fe Anode for Low-Temperature All-Iron Flow Batteries.

Aqueous all-iron redox flow batteries (RFBs) are promising competitors for next-generation grid-scale energy storage applications. However, the high-performance operation of all-iron RFBs in a wider temperature range is greatly hindered by inferior iron plating/stripping reaction and low solid-liquid transition temperature at Fe anode. Herein, a universal electrolyte additive design strategy for all-iron RFBs is reported, which realizes a highly reversible and dendrite-free Fe anode at low temperatures. Quantum chemistry calculations first screen several organic molecules with oxygen-containing functional groups and identify N,N-Dimethylacetmide (DMAc) as a potential candidate with low cost, high solubility, and strong interactions with Fe2+ and H2 O. Combined experimental characterizations and theoretical calculations subsequently demonstrate that adding DMAc into the FeCl2 solution effectively reshapes the primary solvation shell of Fe2+ via the Fe2+ -O (DMAc) bond and breaks hydrogen-bonding network of water through intensified H-bond interaction between DMAc and H2 O, thereby affording the Fe anode with enhanced Fe/Fe2+ reversibility and lower freezing point. Consequently, the assembled all-iron RFB achieves an excellent combination of high power density (25 mW cm-2 ), long charge-discharge cycling stability (95.59% capacity retention in 103 h), and preeminent battery efficiency at -20 °C (95% coulombic efficiency), which promise a future for wider temperature range operation of all-iron RFBs.

Hydrogen Bond Boosted Ferroelectric Polarization Enables High Rate Capability Lithium Metal Batteries.

Lithium metal is considered as a promising anode material for next generation lithium-based batteries due to its highest specific capacity and lowest reduction potential. However, irreversible lithium stripping/depositing gives rise to severe dendritic growth and countless dead lithium, which lead to rapid electrochemical performance degradation and increased safety hazards, and thus limit its large-scale application. Herein, this work demonstrates a universal hydrogen-bond-induced strategy to in situ form a highly polarized ferroelectric polyvinylidene fluoride (PVDF) coating on the anode current collector. The localized electric field induced by the polarized ferroelectric PVDF can accelerate the migration of lithium ions and alleviate the shortage of lithium ions and uneven ion/electron distribution and transfer at the anode/electrolyte interface, thus promoting uniform deposition and stripping of Li+ at high-rate situations. As a result, the symmetrical Li || Li batteries with polarized PVDF coating exhibit a long cycling lifespan over 900 h under 2 mA cm-2 with marginal voltage polarization, and an ultra-high-rate performance up to 8.85 mA cm-2 . The full cells using LiFePO4 cathode also display enhanced electrochemical performance. The innovative strategy of ferroelectric polarization sheds light on interface engineering to circumvent Li dendrite growth in lithium metal batteries (LMBs).

Interfacial Hydrogen-Bond Interactions Driven Assembly toward Polychromatic Copper Nanoclusters.

Constructing versatile metal nanoclusters (NCs) assemblies through noncovalent weak interactions between inter-ligands is a long-standing challenge in interfacial chemistry, while compelling interfacial hydrogen-bond-driven metal NCs assemblies remain unexplored so far. Here, the study reports an amination-ligand o-phenylenediamine-coordinated copper NCs (CuNCs), demonstrating the impact of interfacial hydrogen-bonds (IHBs) motifs on the luminescent behaviors of metal NCs as the alteration of protic solvent. Experimental results supported by theoretical calculation unveil that the flexibility of interfacial ligand and the distance of cuprophilic CuI···CuI interaction between intra-/inter-NCs can be tailored by manipulating the cooperation between the diverse IHBs motifs reconstruction, therewith the IHBs-modulated fundamental structure-property relationships are established. Importantly, by utilizing the IHBs-mediated optical polychromatism of aminated CuNCs, portable visualization of humidity sensing test-strips with fast response is successfully manufactured. This work not only provides further insights into exploring the interfacial chemistry of NCs based on inter-ligands hydrogen-bond interactions, but also offers a new opportunity to expand the practical application for optical sensing of metal NCs.

A Short-Range Ordered α-MoO3 with Modulated Interlayer Structure via Hydrogen Bond Chemistry for NH4 + Storage.

The layered orthorhombic molybdenum trioxide (α-MoO3) is a promising host material for NH4 + storage. But its electrochemical performances are still unsatisfactory due to the absence of fundamental understanding on the relationship between structure and property. Herein, NH4 + storage properties of α-MoO3 are elaborately studied. Electrochemistry together with ex situ physical characterizations uncover that irreversible H+/NH4 + co-intercalation in the initial cycle confines the electrochemically reactive domain to the near surface of α-MoO3 thus resulting in a low reversible NH4 + storage capacity. This issue can be resolved by decreasing ion diffusion pathway to construct short-range ordered α-MoO3 (SMO), which improves the specific capacity to 185 mAh g-1. SMO suffers from dissolution issue. In view of this the interlayer structure of SMO is reconstructed via hydrogen bond chemistry to reinforce the structural stability and it is discovered that the hydrogen bond network only with moderate intensity endows SMO with both high capacity and ability against dissolution. This work presents a new avenue to improve the NH4 + storage properties of α-MoO3 and highlights the important role of hydrogen bond intensity in optimizing electrochemical properties.

Mitigating Surface Defects in Tin-Based Perovskite Films with α-Tocopherol for Enhanced Photovoltaic Performance.

Surface defects in tin-based perovskite films disrupt the periodic arrangement of atoms in crystals, making surface atoms more susceptible to interactions with water and oxygen molecules in the surrounding environment. The diffusion of oxygen ions into the perovskite interior leads to the formation of severe bulk defects, which compromises the performance of tin-based perovskite solar cells (PSCs). As a result, surface defects are recognized as the primary source of degradation and require special attention. In this study, α-Tocopherol (also known as vitamin E) into tin-based perovskite films is introduced. Experimental results show that because of its larger volume, α-Tocopherol does not enter the perovskite lattice. Instead, it forms van der Waals and hydrogen bond interactions with the formamidine ion (FA+) and the [SnI6]4- octahedron at the perovskite terminals. Through α-Tocopherol passivation, both surface and interior oxidation of the perovskite are significantly suppressed as α-Tocopherol firmly embeds itself on the perovskite surface. Density functional theory analysis confirms the inhibition of I─Sn antisite defects (ISn) and Sn interstitial defects (Sni), which possess deep trap states within the bandgap. Ultimately, it is demonstrated that α-Tocopherol enhances the power conversion efficiency (PCE) from 9.19% to 13.14% and prolongs the lifetime of tin-based PSCs to over 50 days.

Electron Reservoir Effect of Adjacent Fe Nanoclusters Boosts Atomic Fe Active Sites on Porous Carbon for the Both Electrocatalytic Oxygen Reduction and CO2 Reduction Reaction.

Electrochemical oxygen reduction reaction (ORR) and carbon dioxide reduction reaction (CO2RR) are greatly significant in renewable energy-related devices and carbon-neutral closed cycle, while the development of robust and highly efficient electrocatalysts has remained challenges. Herein, a hybrid electrocatalyst, featuring axial N-coordinated Fe single atom sites on hierarchically N, P-codoped porous carbon support and Fe nanoclusters as electron reservoir (FeNCs/FeSAs-NPC), is fabricated via in situ thermal transformation of the precursor of a supramolecular polymer initiated by intermolecular hydrogen bonds co-assembly. The FeNCs/FeSAs-NPC catalyst manifests superior oxygen reduction activity with a half-wave potential of 0.91 V in alkaline solution, as well as high CO2 to CO Faraday efficiency (FE) of surpassing 90% in a wide potential window from -0.40 to -0.85 V, along with excellent electrochemical durability. Theoretical calculations indicate that the electron reservoir effect of Fe nanoclusters can trigger the electron redistribution of the atomic Fe moieties, facilitating the activation of O2 and CO2 molecules, lowering the energy barriers for rate-determining step, and thus contributing to the accelerated ORR and CO2RR kinetics. This work offers an effective design of electron coupling catalysts that have advanced single atoms coexisting with nanoclusters for efficient ORR and CO2RR.