Liquid water is a dynamic polydisperse branched polymer.

We developed the RexPoN force field for water based entirely on quantum mechanics. It predicts the properties of water extremely accurately, with = 273.3 K (273.

Csp-Csp Bond-Forming Reductive Elimination from Well-Defined Copper(III) Complexes.

Carbon-carbon bond-forming reductive elimination from elusive organocopper(III) complexes has been considered the key step in many copper-catalyzed and organocuprate reactions. However, organocopper(III) complexes with well-defined structures that can undergo reductive elimination are extremely rare, especially for the formation of Csp-Csp bonds. We report herein a general method for the synthesis of a series of [alkyl-Cu-(CF)] complexes, the structures of which have been unequivocally characterized by NMR spectroscopy, mass spectrometry, and X-ray crystal diffraction.

The PX Motif of DNA Binds Specifically to Escherichia coli DNA Polymerase I.

The PX motif of DNA is a four-stranded structure in which two parallel juxtaposed double-helical domains are fused by crossovers at every point where the strands approach each other. Consequently, its twist and writhe are approximately half of those of conventional DNA. This property has been shown to relax supercoiled plasmid DNA under circumstances in which head-to-head homology exists within the plasmid; the homology can be either complete homology or every-other-half-turn homology, known as PX homology.

A Highly Active Star Decahedron Cu Nanocatalyst for Hydrocarbon Production at Low Overpotentials.

The electrochemical carbon dioxide reduction reaction (CO RR) presents a viable approach to recycle CO gas into low carbon fuels. Thus, the development of highly active catalysts at low overpotential is desired for this reaction. Herein, a high-yield synthesis of unique star decahedron Cu nanoparticles (SD-Cu NPs) electrocatalysts, displaying twin boundaries (TBs) and multiple stacking faults, which lead to low overpotentials for methane (CH ) and high efficiency for ethylene (C H ) production, is reported.

Discrete Dimers of Redox-Active and Fluorescent Perylene Diimide-Based Rigid Isosceles Triangles in the Solid State.

The development of rigid covalent chiroptical organic materials, with multiple, readily available redox states, which exhibit high photoluminescence, is of particular importance in relation to both organic electronics and photonics. The chemically stable, thermally robust, and redox-active perylene diimide (PDI) fluorophores have received ever-increasing attention owing to their excellent fluorescence quantum yields in solution. Planar PDI derivatives, however, generally suffer from aggregation-caused emission quenching in the solid state.

Molecular Russian dolls.

The host-guest recognition between two macrocycles to form hierarchical non-intertwined ring-in-ring assemblies remains an interesting and challenging target in noncovalent synthesis. Herein, we report the design and characterization of a box-in-box assembly on the basis of host-guest radical-pairing interactions between two rigid diradical dicationic cyclophanes. One striking feature of the box-in-box complex is its ability to host various 1,4-disubstituted benzene derivatives inside as a third component in the cavity of the smaller of the two diradical dicationic cyclophanes to produce hierarchical Russian doll like assemblies.

Catalytic Synthesis of Superlinear Alkenyl Arenes Using a Rh(I) Catalyst Supported by a "Capping Arene" Ligand: Access to Aerobic Catalysis.

Alkyl and alkenyl arenes are used in a wide range of products. However, the synthesis of 1-phenylalkanes or their alkenyl variants from arenes and alkenes is not accessible with current commercial acid-based catalytic processes. Here, it is reported that an air-stable Rh(I) complex, (5-FP)Rh(TFA)(η-CH) (5-FP = 1,2-bis( N-7-azaindolyl)benzene; TFA = trifluoroacetate), serves as a catalyst precursor for the oxidative conversion of arenes and alkenes to alkenyl arenes that are precursors to 1-phenylalkanes upon hydrogenation.

QM-Mechanism-Based Hierarchical High-Throughput in Silico Screening Catalyst Design for Ammonia Synthesis.

We propose and test a hierarchical high-throughput screening (HHTS) approach to catalyst design for complex catalytic reaction systems that is based on quantum mechanics (QM) derived full reaction networks with QM rate constants but simplified to examine only the reaction steps likely to be rate determining. We illustrate this approach by applying it to determine the optimum dopants (our of 35 candidates) to improve the turnover frequency (TOF) for the Fe-based Haber-Bosch ammonia synthesis process. We start from the QM-based free-energy reaction network for this reaction over Fe(111), which contains the 26 most important surface configurations and 17 transition states at operating conditions of temperature and pressure, from which we select the key reaction steps that might become rate determining for the alloy.

Polarizable Charge Equilibration Model for Transition-Metal Elements.

The polarizable charge equilibration (PQEq) method was developed to provide a simple but accurate description of the electrostatic interactions and polarization effects in materials. Previously, we optimized four parameters per element for the main group elements. Here, we extend this optimization to the 24 d-block transition-metal (TM) elements, columns 4-11 of the periodic table including Ti-Cu, Zr-Ag, and Hf-Au.

The quantum mechanics-based polarizable force field for water simulations.

We report here a new force field for water based (QM) calculations with , for all orientations and distances for water dimer plus X3LYP density functional theory (DFT) on 19 larger water clusters. In addition, we included charge and polarization based on the polarizable charge equilibration method and nonbond interactions from DFT-D3 calculations on the H and O crystal. This model, denoted as RexPoN, provides quite excellent agreement with experimental (expr) data for the solid and liquid phase of water: 273.

Reaction Mechanism for the Hydrogen Evolution Reaction on the Basal Plane Sulfur Vacancy Site of MoS Using Grand Canonical Potential Kinetics.

We develop the grand canonical potential kinetics (GCP-K) formulation based on thermodynamics from quantum mechanics calculations to provide a fundamental basis for understanding heterogeneous electrochemical reactions. Our GCP-K formulation arises naturally from minimizing the free energy using a Legendre transform relating the net charge of the system and the applied voltage. Performing this macroscopic transformation explicitly allows us to make the connection of GCP-K to the traditional Butler-Volmer kinetics.

Grain Boundary Sliding and Amorphization are Responsible for the Reverse Hall-Petch Relation in Superhard Nanocrystalline Boron Carbide.

The recent observation of the reverse Hall-Petch relation in nanocrystalline ceramics offers a possible pathway to achieve enhanced ductility for traditional brittle ceramics via the nanosize effect, just as nanocrystalline metals and alloys. However, the underlying deformation mechanisms of nanocrystalline ceramics have not been well established. Here we combine reactive molecular dynamics (RMD) simulations and experimental transmission electron microscopy to determine the atomic level deformation mechanisms of nanocrystalline boron carbide (B_{4}C).

Factors affecting cyclic durability of all-solid-state lithium batteries using poly(ethylene oxide)-based polymer electrolytes and recommendations to achieve improved performance.

A detailed experimental analysis of the factors affecting cyclic durability of all-solid-state lithium batteries using poly(ethylene oxide)-based polymer electrolytes was published in EES by Nakayama et al. We use quantum mechanics to interpret these results, identifying processes involved in the degradation of rechargeable lithium batteries based on polyethylene oxide (PEO) polymer electrolyte with LiTFSI. We consider that ionization of the electrolyte near the cathode at the end of the recharge step is probably responsible for this degradation.

Selective Extraction of C by a Tetragonal Prismatic Porphyrin Cage.

Along with the advent of supramolecular chemistry, research on fullerene receptors based on noncovalent bonding interactions has attracted a lot of attention. Here, we present the design and synthesis of a cationic molecular cage: a cyclophane composed of two tetraphenylporphyrins, bridged face-to-face by four viologen units in a rhomboid prismatic manner. The large cavity inside the cage, as well as the favorable donor-acceptor interactions between the porphyrin panels and the fullerene guests, enables the cage to be an excellent fullerene receptor.

Neighboring Component Effect in a Tri-stable [2]Rotaxane.

The redox properties of cyclobis(paraquat- p-phenylene)cyclophane (CBPQT) render it a uniquely variable source of recognition in the context of mechanically interlocked molecules, through aromatic donor-acceptor interactions in its fully oxidized state (CPBQT) and radical-pairing interactions in its partially reduced state (CBPQT). Although it is expected that the fully reduced neutral state (CBPQT) might behave as a π-donating recognition unit, resulting in a dramatic change in its binding properties when compared with the other two redox states, its role in rotaxanes has not yet been investigated. To address this challenge, we report herein the synthesis of a tri-stable [2]rotaxane in which a CBPQT ring is mechanically interlocked with a dumbbell component containing five recognition sites-(i) a bipyridinium radical cation (BIPY) located centrally along the axis of the dumbbell, straddled by (ii) two tetrafluorophenylene units linked to (iii) two triazole rings.

First-principles-based reaction kinetics from reactive molecular dynamics simulations: Application to hydrogen peroxide decomposition.

This paper presents our vision of how to use in silico approaches to extract the reaction mechanisms and kinetic parameters for complex condensed-phase chemical processes that underlie important technologies ranging from combustion to chemical vapor deposition. The goal is to provide an analytic description of the detailed evolution of a complex chemical system from reactants through various intermediates to products, so that one could optimize the efficiency of the reactive processes to produce the desired products and avoid unwanted side products. We could start with quantum mechanics (QM) to ensure an accurate description; however, to obtain useful kinetics we need to average over ∼10-nm spatial scales for ∼1 ns, which is prohibitively impractical with QM.

Interface dynamics: Mechanisms of stabilization and destabilization and structure of flow fields.

Interfacial mixing and transport are nonequilibrium processes coupling kinetic to macroscopic scales. They occur in fluids, plasmas, and materials over celestial events to atoms. Grasping their fundamentals can advance a broad range of disciplines in science, mathematics, and engineering.

First principles-based multiscale atomistic methods for input into first principles nonequilibrium transport across interfaces.

This issue of PNAS features "nonequilibrium transport and mixing across interfaces," with several papers describing the nonequilibrium coupling of transport at interfaces, including mesoscopic and macroscopic dynamics in fluids, plasma, and other materials over scales from microscale to celestial. Most such descriptions describe the materials in terms of the density and equations of state rather than specific atomic structures and chemical processes. It is at interfacial boundaries where such atomistic information is most relevant.

Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding.

TCR-signaling strength generally correlates with peptide-MHC binding affinity; however, exceptions exist. We find high-affinity, yet non-stimulatory, interactions occur with high frequency in the human T cell repertoire. Here, we studied human TCRs that are refractory to activation by pMHC ligands despite robust binding.

Electrochemical CO Reduction Builds Solvent Water into Oxygenate Products.

Numerous studies have examined the electrochemical reduction of CO (COR) to oxygenates (e.g., ethanol).

High-performance bifunctional porous non-noble metal phosphide catalyst for overall water splitting.

Water electrolysis is an advanced energy conversion technology to produce hydrogen as a clean and sustainable chemical fuel, which potentially stores the abundant but intermittent renewable energy sources scalably. Since the overall water splitting is an uphill reaction in low efficiency, innovative breakthroughs are desirable to greatly improve the efficiency by rationally designing non-precious metal-based robust bifunctional catalysts for promoting both the cathodic hydrogen evolution and anodic oxygen evolution reactions. We report a hybrid catalyst constructed by iron and dinickel phosphides on nickel foams that drives both the hydrogen and oxygen evolution reactions well in base, and thus substantially expedites overall water splitting at 10 mA cm with 1.

Mixed-Valence Superstructure Assembled from a Mixed-Valence Host-Guest Complex.

Herein, we report an unprecedented mixed-valence crystal superstructure that consists of a 2:1 host-guest complex [MV⊂(CBPQT)] [MV = methyl viologen, CBPQT = cyclobis(paraquat- p-phenylene)]. One electron is distributed statistically between three [MV⊂(CBPQT)] composed of a total of 15 viologen units. The mixed-valence state is validated by single-crystal X-ray crystallography, which supports an empirical formula of [MV⊂(CBPQT)]·(PF) for the body-centered cubic superstructure.

Explanation of Dramatic pH-Dependence of Hydrogen Binding on Noble Metal Electrode: Greatly Weakened Water Adsorption at High pH.

Hydrogen oxidation reaction (HOR) and hydrogen evolution reaction (HER) are both 2 orders slower in alkaline electrolyte than in acidic electrolyte, but no explanation has been provided. The first step toward understanding this dramatic pH-dependent HOR/HER performance is to explain the pH-dependent hydrogen binding to the electrode, a perplexing behavior observed experimentally. In this work, we carried out Quantum Mechanics Molecular Dynamics (QMMD) with explicit considerations of solvent and applied voltage ( U) to in situ simulate water/Pt(100) interface in the condition of under-potential adsorption of hydrogen ( H).

Surface Ligand Promotion of Carbon Dioxide Reduction through Stabilizing Chemisorbed Reactive Intermediates.

We have explored functionalizing metal catalysts with surface ligands as an approach to facilitate electrochemical carbon dioxide reduction reaction (CORR). To provide a molecular level understanding of the mechanism by which this enhancement occurs, we combine in situ spectroscopy analysis with an interpretation based on quantum mechanics (QM) calculations. We find that a surface ligand can play a critical role in stabilizing the chemisorbed CO, which facilitates CO activation and leads to a 0.

Synergy between Fe and Ni in the optimal performance of (Ni,Fe)OOH catalysts for the oxygen evolution reaction.

The oxygen evolution reaction (OER) is critical to solar production of fuels, but the reaction mechanism underlying the performance for a best OER catalyst, Fe-doped NiOOH [(Ni,Fe)OOH], remains highly controversial. We used grand canonical quantum mechanics to predict the OER mechanisms including kinetics and thus overpotentials as a function of Fe content in (Ni,Fe)OOH catalysts. We find that density functional theory (DFT) without exact exchange predicts that addition of Fe does not reduce the overpotential much.