Engineering the interfacial orientation of MoS2/Co9S8 bidirectional catalysts with highly exposed active sites for reversible Li-CO2 batteries.

Sluggish CO2 reduction reaction (CO2RR) and evolution reaction (CO2ER) kinetics at cathodes seriously hamper the applications of Li-CO2 batteries, which have attracted vast attention as one kind of promising carbon-neutral technology. Two-dimensional transition metal dichalcogenides (TMDs) have shown great potential as the bidirectional catalysts for CO2 redox, but how to achieve a high exposure of dual active sites of TMDs with CO2RR/CO2ER activities remains a challenge. Herein, a bidirectional catalyst that vertically growing MoS2 on Co9S8 supported by carbon paper (V-MoS2/Co9S8@CP) has been designed with abundant edge as active sites for both CO2RR and CO2ER, improves the interfacial conductivity, and modulates the electron transportation pathway along the basal planes. As evidenced by the outstanding energy efficiency of 81.2% and ultra-small voltage gap of 0.68 V at 20 µA cm-2, Li-CO2 batteries with V-MoS2/Co9S8@CP show superior performance compared with horizontally growing MoS2 on Co9S8 (H-MoS2/Co9S8@CP), MoS2@CP, and Co9S8@CP. Density functional theory calculations help reveal the relationship between performance and structure and demonstrate the synergistic effect between MoS2 edge sites and Co9S8. This work provides an avenue to understand and realize rationally designed electronic contact of TMDs with specified crystal facets, but more importantly, provides a feasible guide for the design of high-performance cathodic catalyst materials in Li-CO2 batteries.

From Criegee to Breslow: How π-Donors Steer the Route of Olefin Ozonolysis.

While π-bonds typically undergo cycloaddition with ozone, resulting in the release of much-noticed carbonyl O-oxide Criegee intermediates, lone-pairs of electrons tend to selectively accept a single oxygen atom from O3, producing singlet dioxygen. We questioned whether the introduction of potent electron-donating groups, akin to N-heterocyclic olefins, could influence the reactivity of double bonds - shifting from cycloaddition to oxygen atom transfer or generating lesser-known, yet stabilized, donor-substituted Criegee intermediates. Consequently, we conducted a comparative computational study using density functional theory on a series of model olefins with increasing polarity due to (asymmetric) π-donor substitution. Reaction path computations indicate that highly polarized double bonds, instead of forming primary ozonides in their reaction with O3, exhibit a preference for accepting a single oxygen atom, resulting in a zwitterionic species formally identified as a carbene-carbonyl adduct. This previously unexplored reactivity potentially introduces aldehyde umpolung chemistry (Breslow intermediate) through olefin ozonolysis. Considering solvent effects implicitly reveals that increased solvent polarity further directs the trajectories toward a single oxygen atom transfer reactivity by stabilizing the zwitterionic character of the transition state. The competing modes of chemical reactivity can be explained by a bifurcation of the reaction valley in the post-transition state region.

Toward Ab Initio Reaction Discovery Using the Artificial Force Induced Reaction Method.

Predicting the whole process of a chemical reaction while solving kinetic equations presents an opportunity to realize an on-the-fly kinetic simulation that directly discovers chemical reactions with their product yields. Such a simulation avoids the combinatorial explosion of reaction patterns to be examined by narrowing the search space based on the kinetic analysis of the reaction path network, and would open a new paradigm beyond the conventional two-step approach, which requires a reaction path network prior to performing a kinetic simulation. The authors addressed this issue and developed a practical method by combining the artificial force induced reaction method with the rate constant matrix contraction method. Two algorithms are available for this purpose: a forward mode with reactants as the input and a backward mode with products as the input. This article first numerically verifies these modes for known reactions and then demonstrates their application to the actual reaction discovery. Finally, the challenges of this method and the prospects for ab initio reaction discovery are discussed.

Molecularly Tunable Heterostructured Co-Polymers Containing Electron-Deficient and -Rich Moieties for Visible-Light and Sacrificial-Agent-Free H2O2 Photosynthesis.

As an alternative to hydrogen peroxide (H2O2) production by complex anthraquinone oxidation process, photosynthesis of H2O2 from water and oxygen without sacrificial agents is highly demanded. Herein, a covalently connected molecular heterostructure is synthesized via sequential C-H arylation and Knoevenagel polymerization reactions for visible-light and sacrificial-agent-free H2O2 synthesis. The subsequent copolymerization of the electron-deficient benzodithiophene-4,8-dione (BTD) and the electron-rich biphenyl (B) and p-phenylenediacetonitrile (CN) not only expands the π-conjugated domain but also increases the molecular dipole moment, which largely promotes the separation and transfer of the photoinduced charge carriers. The optimal heterostructured BTDB-CN0.2 manifested an impressive photocatalytic H2O2 production rate of 1920 µmol g-1 h-1, which is 2.2 and 11.6 times that of BTDB and BTDCN. As revealed by the femtosecond transient absorption (fs-TA) and theoretical calculations, the linkage serves as a channel for the rapid transfer of photogenerated charge carriers, enhancing the photocatalytic efficiency. Further, in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) uncovers that the oxygen reduction reaction occurs through the step one-electron pathway and the mutual conversion between C=O and C-OH with the anchoring of H+ during the catalysis favored the formation of H2O2. This work provides a novel perspective for the design of efficient organic photocatalysts.

Curvature-weighted nudged elastic band method using the Riemann curvature.

The nudged elastic band (NEB) method is utilized to find reaction paths (RPs) using discretized intermediate structures called "images" between a reactant and a product. In fact, NEB calculations do not always converge because of the bent of RPs. Mathematically, more images are needed for complex curves, and here, we focused on the curvature. In this study, we propose a new method for calculating the curvature of the RPs as well as a method for weighting the spring constant of the NEB with the curvature, which we named the curvature weighted NEB (CW-NEB) method. In addition, we will propose the CW-NEB method with the climbing image (CI) method (CW-CI-NEB). To show the efficiency of our method, calculations for the ene-reaction of the CW-CI-NEB method were performed and compared with those of the CI-NEB methods. The CW-CI-NEB methods converged in shorter iteration times than the CI-NEB calculation, which was found by gathering the bent of RPs.

Solvent and Substituent Size Influence on the Cyclochiral Rigidity of Aminomethylene Derivatives of Resorcin[4]arene.

Resorcin[4]arenes (R[4]A) are a group of macrocyclic compounds whose peculiar feature is the presence of eight hydroxyl groups in their structure. The directional formation of intramolecular hydrogen bonds with their participation leads to the formation of a cyclochiral racemic mixture of these compounds. Their stability strongly depends on the substituent and especially the environment in which they are located. The paper discusses the cyclochiral nature of aminomethylene derivatives of R[4]A (AMD-R[4]A). Their cyclochiral rigidity in non-polar solvents has been shown. The influence of the size of the alkyl groups in the amino substituents of AMD-R[4]A on their cyclochiral nature was noted. To calculate the reaction paths for their racemization, the nudged elastic band (NEB) method was employed using the semi-empirical DFT (GFN1-xTB) approach. The calculated activation barrier energies for their racemization in chloroform, obtained through various semi-empirical quantum chemical methods (SE), Hartree-Fock (HF), and density functionals theory (DFT), show good correlation with experimental observations. Among the tested methods, the B38LYP-D4 method is highly recommended due to its fast computational speed and accuracy, which is comparable to the time-consuming double-hybrid DH-revDSD-PBEP86 approach.

Understanding the Synthesis Kinetics of Single-Crystal Co-Free Ni-Rich Cathodes.

Non-equilibrium kinetic intermediates are usually preferentially generated instead of thermodynamic stable phases in the solid-state synthesis of layered oxides. Understanding the inherent complexity between thermodynamics and kinetics is important for designing high cationic ordering cathodes. Single-crystal strategy is an effective way to solve the intrinsic chemo-mechanical problems of Ni-rich cathodes. However, the synthesis of high-performance single-crystal is very challenging. Herein, the kinetic reaction path and the formation mechanism of non-equilibrium intermediates in the synthesis of single-crystal Co-free Ni-rich were explored. We demonstrate that the formation of non-equilibrium intermediate and the electrochemical-thermo-mechanical failure can be effectively inhibited by driving low-temperature topotactic lithiation. This work provides a basis for designing high-performance single-crystal Ni-rich layered oxides by regulating the defective structures.

Promoting Solar-driven Hydrogen Peroxide Production over Thiazole-based Conjugated Polymers via Generating and Converting Singlet Oxygen.

Solar-driven synthesis of hydrogen peroxide (H2 O2 ) from water and air provides a low-cost and eco-friendly alternative route to the traditional anthraquinone method. Herein, four thiazole-based conjugated polymers (Tz-CPs: TTz, BTz, TBTz and BBTz) are synthesized via aldimine condensation. BBTz exhibits the highest H2 O2 production rate of 7274 µmol g-1 h-1 in pure water. Further, the reaction path is analyzed by electron paramagnetic resonance (EPR), in situ diffuse reflectance infrared Fourier transform (DRIFT) and theoretical calculation, highlighting the prominent role of singlet oxygen (1 O2 ). The generation of 1 O2 occurs through the oxidation of superoxide radical (⋅O2 - ) and subsequent conversion into endoperoxides via [4+2] cycloaddition over BBTz, which promotes charge separation and reduces the barrier for H2 O2 production. This work provides new insight into the mechanism of photocatalytic O2 reduction and the molecular design of superior single-polymer photocatalysts.

Automated input structure generation for single-ended reaction path optimizations.

The exploration of a reaction network requires highly automated workflows to avoid error-prone and time-consuming manual steps. In this respect, a major bottleneck is the search for transition-state (TS) structures, which frequently fails and, therefore, makes (manual) revision necessary. In this work, we present a technique for obtaining suitable input structures for automated TS searches based on single-ended reaction path optimization algorithms, which makes subsequent TS searches via this method significantly more robust. First, possible input structures are generated based on the spatial alignment of the reactants. The appropriate orientation of reacting groups is achieved via stepwise rotations along selected torsional degrees of freedom. Second, a ranking of the obtained structures is performed according to selected geometric criteria. The main goals are to properly align the reactive atoms, to avoid hindrance within the reaction channel and to resolve steric clashes between the reactants. The developed procedure has been carefully tested on a variety of examples and provides suitable input structures for TS searches within seconds. The method is in daily use in an industrial setting.

Arsenic polluted waters: Application of geochemical modelling as a tool to understand the release and fate of the pollutant in crystalline aquifers.

Arsenic (As) is one of the most investigated elements worldwide due to its negative impact on the natural system. Its geochemical behavior depends on several geogenic processes, which can cause hazardous enrichment into natural waters, even in remote areas, far from anthropogenic sources. In this work the arsenic pollution issue has been addressed by studying water-rock interaction processes and applying reaction path modelling as a tool to understand the rock-to-water release of As and the fate of this natural pollutant in crystalline aquifers. In-depth geochemical characterization of several water samples discharging from crystalline aquifers was performed. The obtained data were used to fix the boundary conditions and validate the modelling outcomes. The performed modelling allowed to reconstruct the water-rock interaction processes which occur (i) in shallow and relatively shallow crystalline aquifers in which no As anomalies were observed and (ii) in As-rich areas, coupling reaction path modelling of granite dissolution with adsorption of dissolved As onto precipitating crystalline and amorphous Fe(III)-oxyhydroxides given the widespread presence of these phases in the studied environment. The results of the geochemical modelling are in agreement with the analytical data and reproduce them satisfactorily. The performed geochemical modelling is of high environmental significance because it is a flexible and powerful tool that correctly defines the water-rock interaction processes occurring in crystalline aquifers, providing valuable data to improve the knowledge on As behavior, not only in the study area, but also in similar geological settings worldwide. Therefore, the present research has broad future perspectives in the environmental field.

Reaction Mechanism for the Removal of NOx by Wet Scrubbing Using Urea Solution: Determination of Main and Side Reaction Paths.

Secondary problems, such as the occurrence of side reactions and the accumulation of by-products, are a major challenge in the application of wet denitrification technology through urea solution. We revealed the formation mechanism of urea nitrate and clarified the main and side reaction paths and key intermediates of denitrification. Urea nitrate would be separated from urea absorption solution only when the concentration product of [urea], [H+] and [NO3-] was greater than 0.87~1.22 mol3/L3. The effects of the urea concentration (5-20%) and reaction temperature (30-70 °C) on the denitrification efficiency could be ignored. Improving the oxidation degree of the flue gas promoted the removal of nitrogen oxides. The alkaline condition was beneficial to the dissolution process, while the acidic condition was beneficial to the reaction process. As a whole, the alkaline condition was the preferred process parameter. The research results could guide the optimization of process conditions in theory, improve the operation efficiency of the denitrification reactor and avoid the occurrence of side reactions.

Geometric analysis of anharmonic downward distortion following paths.

A mathematical aspect of the anharmonic downward distortion following (ADDF) path is discussed. The ADDF method is utilized as an automated reaction path search method, which can explore transition state geometries on a potential energy surface from a potential minimum. We show that the maximum number of the ADD stationary paths intersecting the potential minimum is 2f + 1 - 2, where f denotes the degree of freedom of the system. We also show that the bifurcation of the ADD stationary path is essential to detect all the transition states connected from a given minimum. The ADDF computation is demonstrated for a H2 O molecule in which pitchfork bifurcation is observed.

Catalytic Descriptors to Investigate Catalytic Power in the Reaction of Haloalkane Dehalogenase Enzyme with 1,2-Dichloroethane.

Enzymes play a fundamental role in many biological processes. We present a theoretical approach to investigate the catalytic power of the haloalkane dehalogenase reaction with 1,2-dichloroethane. By removing the three main active-site residues one by one from haloalkane dehalogenase, we found two reactive descriptors: one descriptor is the distance difference between the breaking bond and the forming bond, and the other is the charge difference between the transition state and the reactant complex. Both descriptors scale linearly with the reactive barriers, with the three-residue case having the smallest barrier and the zero-residue case having the largest. The results demonstrate that, as the number of residues increases, the catalytic power increases. The predicted free energy barriers using the two descriptors of this reaction in water are 23.1 and 24.2 kcal/mol, both larger than the ones with any residues, indicating that the water solvent hinders the reactivity. Both predicted barrier heights agree well with the calculated one at 25.2 kcal/mol using a quantum mechanics and molecular dynamics approach, and also agree well with the experimental result at 26.0 kcal/mol. This study shows that reactive descriptors can also be used to describe and predict the catalytic performance for enzyme catalysis.

Multistructural microiteration technique for geometry optimization and reaction path calculation in large systems.

We propose a multistructural microiteration (MSM) method for geometry optimization and reaction path calculation in large systems. MSM is a simple extension of the geometrical microiteration technique. In conventional microiteration, the structure of the non-reaction-center (surrounding) part is optimized by fixing atoms in the reaction-center part before displacements of the reaction-center atoms. In this method, the surrounding part is described as the weighted sum of multiple surrounding structures that are independently optimized. Then, geometric displacements of the reaction-center atoms are performed in the mean field generated by the weighted sum of the surrounding parts. MSM was combined with the QM/MM-ONIOM method and applied to chemical reactions in aqueous solution or enzyme. In all three cases, MSM gave lower reaction energy profiles than the QM/MM-ONIOM-microiteration method over the entire reaction paths with comparable computational costs. © 2017 Wiley Periodicals, Inc.

A minimization principle for transition paths of maximum flux for collective variables.

Considered is the construction of transition paths of conformational changes for proteins and other macromolecules, using methods that do not require the generation of dynamics trajectories. Special attention is given to the use of a reduced set of collective variables for describing such paths. A favored way to define transition paths is to seek channels through the transition state having cross sections with a high reactive flux (density of last hitting points of reactive trajectories). Given here is a formula for reactive flux that is independent of the parameterization of "collective variable space." This formula is needed for the principal curve of the reactive flux (as in the revised finite temperature string method) and for the maximum flux transition (MaxFlux) path. Additionally, a resistance functional is derived for narrow tubes, which when minimized yields a MaxFlux path. A strategy for minimization is outlined in the spirit of the string method. Finally, alternative approaches based on determining trajectories of high probability are considered, and it is observed that they yield paths that depend on the parameterization of collective variable space, except in the case of zero temperature, where such a path coincides with a MaxFlux path.

Efficiently computing pathway free energies: New approaches based on chain-of-replica and Non-Boltzmann Bennett reweighting schemes.

BACKGROUND: Accurately modeling condensed phase processes is one of computation's most difficult challenges. Include the possibility that conformational dynamics may be coupled to chemical reactions, where multiscale (i.e., QM/MM) methods are needed, and this task becomes even more daunting. METHODS: Free energy simulations (i.e., molecular dynamics), multiscale modeling, and reweighting schemes. RESULTS: Herein, we present two new approaches for mitigating the aforementioned challenges. The first is a new chain-of-replica method (off-path simulations, OPS) for computing potentials of mean force (PMFs) along an easily defined reaction coordinate. This development is coupled with a new distributed, highly-parallel replica framework (REPDstr) within the CHARMM package. Validation of these new schemes is carried out on two processes that undergo conformational changes. First is the simple torsional rotation of butane, while a much more challenging glycosidic rotation (in vacuo and solvated) is the second. Additionally, a new approach that greatly improves (i.e., possibly an order of magnitude) the efficiency of computing QM/MM PMFs is introduced and compared to standard schemes. Our efforts are grounded in the recently developed method for efficiently computing QM-based free energies (i.e., QM-Non-Boltzmann Bennett, QM-NBB). Again, we validate this new technique by computing the QM/MM PMF of butane's torsional rotation. CONCLUSIONS: The OPS-REPDstr method is a promising new approach that overcomes many limitations of standard pathway simulations in CHARMM. The combination of QM-NBB with pathway techniques is very promising as it offers significant advantages over current procedures. GENERAL SIGNIFICANCE: Efficiently computing potentials of mean force is a major, unresolved, area of interest. This article is part of a Special Issue entitled Recent developments of molecular dynamics.

Symmetry calculation for molecules and transition states.

The symmetry of molecules and transition states of elementary reactions is an essential property with important implications for computational chemistry. The automated identification of symmetry by computers is a very useful tool for many applications, but often relies on the availability of three-dimensional coordinates of the atoms in the molecule and hence becomes less useful when these coordinates are a priori unavailable. This article presents a new algorithm that identifies symmetry of molecules and transition states based on an augmented graph representation of the corresponding structures, in which both topology and the presence of stereocenters are accounted for. The automorphism group order of the graph associated with the molecule or transition state is used as a starting point. A novel concept of label-stereoisomers, that is, stereoisomers that arise after labeling homomorph substituents in the original molecule so that they become distinguishable, is introduced and used to obtain the symmetry number. The algorithm is characterized by its generic nature and avoids the use of heuristic rules that would limit the applicability. The calculated symmetry numbers are in agreement with expected values for a large and diverse set of structures, ranging from asymmetric, small molecules such as fluorochlorobromomethane to highly symmetric structures found in drug discovery assays. The new algorithm opens up new possibilities for the fast screening of the degree of symmetry of large sets of molecules.

Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions.

Hybrid quantum mechanics and molecular mechanics (QM/MM) computer simulations have become an indispensable tool for studying chemical and biological phenomena for systems too large to treat with QM alone. For several decades, semiempirical QM methods have been used in QM/MM simulations. However, with increased computational resources, the introduction of ab initio and density function methods into on-the-fly QM/MM simulations is being increasingly preferred. This adaptation can be accomplished with a program interface that tethers independent QM and MM software packages. This report introduces such an interface for the BOSS and Gaussian programs, featuring modification of BOSS to request QM energies and partial atomic charges from Gaussian. A customizable C-shell linker script facilitates the interprogram communication. The BOSS-Gaussian interface also provides convenient access to Charge Model 5 (CM5) partial atomic charges for multiple purposes including QM/MM studies of reactions. In this report, the BOSS-Gaussian interface is applied to a nitroaldol (Henry) reaction and two methyl transfer reactions in aqueous solution. Improved agreement with experiment is found by determining free-energy surfaces with MP2/CM5 QM/MM simulations than previously reported investigations using semiempirical methods.

Exploring transition state structures for intramolecular pathways by the artificial force induced reaction method.

Finding all required transition state (TS) structures is an important but hard task in theoretical study of complex reaction mechanisms. In the present article, an efficient automated TS search method, artificial force induced reaction (AFIR), was extended to intramolecular reactions. The AFIR method has been developed for intermolecular associative pathways between two or more reactants. Although it has also been applied to intramolecular reactions by dividing molecules manually into fragments, the fragmentation scheme was not automated. In this work, we propose an automated fragmentation scheme. Using this fragmentation scheme and the AFIR method, a fully automated search algorithm for intramolecular pathways is introduced. This version for intramolecular reactions is called single-component AFIR (SC-AFIR), to distinguish it from multicomponent AFIR for intermolecular reactions. SC-AFIR was tested with two reactions, the Claisen rearrangement and the first step of cobalt-catalyzed hydroformylation, and successfully located all important pathways reported in the literature.

Exploring the formation pathway and antioxidant properties of the sugar-smoking pigment 5-GGMF.

The present study aimed to elucidate the pathway of pigment formation and identify the source of antioxidant activity during sugar smoking. Building upon previous research, this investigation replicated the sucrose cleavage process involved in sugar-smoking through model reactions to obtain distinct model reaction products. The products were analyzed using various techniques such as ultraviolet-visible spectrometry, Fourier-transform infrared spectroscopy, high-performance liquid chromatography, and high-performance liquid chromatography-tandem mass spectrometry. The findings revealed that the pyrolysis of sucrose at 330 °C yielded glucose and fructose, with fructose pyrolysis producing significantly more 5-HMF than glucose. Moreover, the antioxidant capacity of 5-HMF was found to make a substantial contribution. The primary source of 5-HMF was identified as fructose resulting from the cleavage of sucrose at 330 °C, while the primary pathway for the formation of the sugar-smoking pigment 5-GGMF was attributed to the intermolecular dehydration of 5-HMF and glucose at 150 °C.