Fully Automatized Optimization of Ring-Opening Reactions in Lactone Derivatives via Two-Step Machine Learning.

Cyclization and cycloreversion of organic compounds are fundamental kinetic processes in the design of functional molecules, molecular machines, nanoscale sensors, and switches in the field of molecular and nanoelectronics. We present a fully automatic computational platform for the design of a class of five- and six-membered ring lactones by optimizing the ring-opening reaction rate. Starting from a minimal initial parent set, our algorithm generates iteratively cascades of pools of candidate lactone derivatives where optimization and down-selection are performed without human supervision. We employ the density functional theory combined with the transition state theory to elucidate the exact mechanism leading to the lactone ring-opening reaction. On the basis of the analysis of the reaction pathway and the frontier molecular orbitals, we identify a simple descriptor that can easily correlate with the reaction rate. Consequently, we can omit computationally expensive transition state calculations and deduce the reaction rate from simple ground-state and ionic calculations. To accelerate the platform, we use a data set of the order of 800 molecules to train machine learning models for the prediction of targeted chemical properties, reducing the computational time by a 90% factor. We developed an evolutionary algorithm capable of generating data sets 3 orders of magnitude larger than the initial parent set. Thus, we can explore a large domain of chemical space using minimal computational effort. Our entire platform is modular, and our current implementation for lactone can be further generalized to more complex systems via substitution of the quantum chemical and fingerprinting modules.

Tailoring the work function of graphene via defects, nitrogen-doping and hydrogenation: A first principles study.

The effect of defects, nitrogen doping, and hydrogen saturation on the work function of graphene is investigated via first principle calculations. Whilst Stone-Wales defects have little effect, single and double vacancy defects increase the work function by decreasing charge density in theπ-electron system. Substitutional nitrogen doping in defect-free graphene significantly decreases the work function, because the nitrogen atoms donate electrons to theπ-electron system. In the presence of defects, these competing effects mean that higher nitrogen content is required to achieve similar reduction in work function as for crystalline graphene. Doping with pyridinic nitrogen atoms at vacancies slightly increases the work function, since pyridinic nitrogen does not contribute electrons to theπ-electron system. Meanwhile, hydrogen saturation of the pyridinic nitrogen atoms significantly reduces the work function, due to a shift from pyridinic to graphitic-type behavior. These findings clearly explain some of the experimental work functions obtained for carbon and nitrogen-doped carbon materials in the literature, and has implications in applications such as photocatalysis, photovoltaics, electrochemistry, and electron field emission.

Curvature Effect in Polydimethylsiloxane Interaction with CO2. Insights from Theory.

In this study we employ density functional theory to investigate the binding interaction between polydimethylsiloxane and CO2 for application in gas separation membranes. The binding strength has been studied systematically as a function of the monomer conformational rotations in the polymer chain. Our work identified major differences between the CO2 interaction with the helical conformation and the linear conformation of polydimethylsiloxane polymer chains. We have further estimated dependence between the CO2 binding strength and the polydimethylsiloxane polymer chain curvature by systematically evaluating the CO2 binding to cyclic polydimethylsiloxane oligomers. The enhanced CO2 interaction with helical chains and cyclic oligomers was attributed to cooperative, confinement effects, and local electron density distribution at the Si-O-Si fragments. The binding modes were identified using vibration frequency analysis.

Density functional theory analysis for H2S adsorption on pyridinic N- and oxidized N-doped graphenes.

Biomass discharged from primary industries can be converted into methane by fermentation. This methane is used for generating electricity with solid oxide fuel cells (SOFCs). This methane fermentation provides H2S, which reduces the efficiency of SOFCs even at a level as low as a few parts per million. It has been experimentally reported that a nitrogen (N)-doped graphene-based material known as pyridinic N removes H2S via an oxidation reaction compared with another graphene-based material known as oxidized N. To understand this experimental result, we investigated H2S adsorption on pyridinic N and oxidized N by a density functional theory analysis and further examined the activation barrier of dissociation reactions. We found that the adsorption of H2S on pyridinic N is more stable than that on oxidized N. In addition, the H2S dissociation reaction occurs only on pyridinic N.

Heterointerface Created on Au-Cluster-Loaded Unilamellar Hydroxide Electrocatalysts as a Highly Active Site for the Oxygen Evolution Reaction.

The oxygen evolution reaction (OER) is a critical element for all sorts of reactions that use water as a hydrogen source, such as hydrogen evolution and electrochemical CO2 reduction, and novel design principles that provide highly active sites on OER electrocatalysts push the limits of their practical applications. Herein, Au-cluster loading on unilamellar exfoliated layered double hydroxide (ULDH) electrocatalysts for the OER is demonstrated to fabricate a heterointerface between Au clusters and ULDHs as an active site, which is accompanied by the oxidation state modulation of the active site and interfacial direct OO coupling ("interfacial DOOC"). The Au-cluster-loaded ULDHs exhibit excellent activities for the OER with an overpotential of 189 mV at 10 mA cm-2 . X-ray absorption fine structure measurements reveal that charge transfer from the Au clusters to ULDHs modifies the oxidation states of trivalent metal ions, which can be active sites on the ULDHs. The present study, supported by highly sensitive spectroscopy combining reflection absorption infrared spectroscopy and modulation-excitation spectroscopy and density functional theory calculations, indicates that active sites at the interface between the Au clusters and ULDHs promote a novel OER mechanism through interfacial DOOC, thereby achieving outstanding catalytic performance.

A flavin-Cu2+ supramolecular complex for highly selective sorting of semiconducting single-walled carbon nanotubes with specific chiralities.

We introduce thio-substituents at the 7- and 8-positions of a flavin analogue, which allows for the coordination of metal ions, and demonstrate, based on both experimental and theoretical methods, that the formed Cu2+-based supramolecular assembled complex shows very high selective sorting of semiconducting single-walled carbon nanotubes with (8,6)- and (9,4)-chiralities.

Supramolecular Chemistry-Based One-Pot High-Efficiency Separation of Solubilizer-Free Pure Semiconducting Single-Walled Carbon Nanotubes: Molecular Strategy and Mechanism.

Single-walled carbon nanotubes (SWCNTs) have the potential to revolutionize nanoscale electronics and power sources; however, their low purity and high separation cost limit their use in practical applications. Here we present a supramolecular chemistry-based one-pot, less expensive, scalable, and highly efficient separation of a solubilizer/adsorbent-free pure semiconducting SWCNT (sc-SWCNT) using flavin/isoalloxazine analogues with different substituents. On the basis of both experimental and computational simulations (DFT study), we have revealed the molecular requirements of the solubilizers as well as provided a possible mechanism for such a highly efficient selective sc-SWCNT separation. The present sorting method is very simple (one-pot) and gives a promising sc-SWCNT separation methodology. Thus, the study provides insight for the molecular design of an sc-SWCNT solubilizer with a high (n,m)-chiral selectivity, which benefits many areas including semiconducting nanoelectronics, thermoelectric, bio and energy materials, and devices using solubilizer-free very pure sc-SWCNTs.

Computational Study on the Light-Induced Oxidation of Iridium-Aqua Complex to Iridium-Oxo Complex over WO3(001) Surface.

An iridium aqua complex [IrIII(η5-C5Me5){bpy(COOH)2}(H2O)]2+ under visible light irradiation has been experimentally reported to form an iridium-oxo (Ir-oxo) complex [IrV(η5-C5Me5){bpy(COOH)2}(O)]2+, which oxidizes H2O to O2. However, the mechanism for the formation of this Ir-oxo complex remains unclear, due to the difficulties in observing the unstable Ir-oxo complex and computing light-induced systems having different numbers of electrons. In this study, we perform density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations to investigate more in detail our previously proposed deprotonation and light-induced oxidation reactions composing the formation of the Ir-oxo complex. In particular, we discuss effects of light irradiation and WO3 support on the formation of the Ir-oxo complex. We suggest two distinct mechanisms, that is, direct and indirect for the light-induced oxidation. In the direct mechanism electrons are directly transferred from the occupied π* orbitals of IrIII-OH or IrIV=O• to the conduction band of the WO3 surface, whereas in the indirect mechanism electrons are first excited from the valence band to the conduction band of the WO3 surface due to the UV light, and then the resultant electron hole oxidizes the Ir complex. In the direct mechanism, in particular, we found that the lowest energy of the anode's conduction band determines the adsorption wavelength of the light irradiation, enabling us to predict alternative semiconductor anodes for more efficient formation of the Ir-oxo complex.

Dual Catalytic Cycle of H2 and H2O Oxidations by a Half-Sandwich Iridium Complex: A Theoretical Study.

While hydrogenase and photosystem II enzymes are known to oxidize H2 and H2O, respectively, a recently reported iridium aqua complex [IrIII(η5-C5Me5){bpy(COOH)2}(H2O)]2+ is able to oxidize both of the molecules and generate energies as in the fuel and solar cells ( Ogo ChemCatChem 2017 , 9 , 4024 - 4028 ). To understand the mechanism behind such an interesting bifunctional catalyst, in the present study, we perform density functional theory (DFT) calculations on the dual catalytic cycle of H2 and H2O oxidations by the iridium aqua complex. In the H2 oxidation, we found that the H-H bond is easily cleaved in a heterolytic fashion, and the resultant iridium hydride complex is significantly stabilized by the presence of H2O molecules, due to dihydrogen bond. The rate-determining step of this reaction is found to be the H2O → H2 ligand substitution with an activation energy of 10.7 kcal/mol. In the H2O oxidation, an iridium oxo complex originating from an oxidation of the iridium aqua complex forms a hydroperoxide complex, where an O-O bond is formed with an activation energy of 21.0 kcal/mol. Such a relatively low activation barrier is possible only when at least two H2O molecules are present in the reaction, allowing the water nucleophilic attack (WNA) mechanism to take place. The present study suggests and discusses in detail six reaction steps required for the dual catalytic cycle to complete.

Theoretical Overview of Methane Hydroxylation by Copper-Oxygen Species in Enzymatic and Zeolitic Catalysts.

As fossil-based energy sources become more depleted and with renewable-energy technologies still in a very early stage of development, the utilization of highly abundant methane as a transitional solution for current energy demands is highly important despite difficulties in transport and storage. Technologies enabling the conversion of methane to liquid/condensable energy carriers that can be easily transported and integrated into the existing chemical infrastructures are therefore essential. Although there commercially exists a two-step gas-to-liquid process involving syngas production, a novel route of methane conversion that can circumvent the high-cost production of syngas should be developed. Among all of the conceptually possible methods for converting methane to methanol, methane hydroxylation (CH4 + 1/2O2 → CH3OH) at low temperature seems to be the most viable since it provides a direct route of conversion and allows a much lower operational cost. However, it is hampered by the fact that the complete oxidation to CO2 is thermodynamically more favored. To overcome this, an effective catalyst that is able to "mildly" oxidize methane and stabilize the resultant methyl radical toward methanol formation is required. Particulate methane monooxygenase (pMMO) and copper-exchanged zeolites are two catalysts known to hydroxylate methane into methanol at low temperature with high selectivity. Having been studied for more than 30 years, these copper-cored catalysts are still relevant topics of discussion since the actual structure of the active sites has not been agreed upon, and thus, the reaction mechanism and factors influencing their reactivity and productivity are yet to be understood. Density functional theory (DFT) has provided us with a powerful computational tool for accomplishing these tasks. This Account presents an overview of the recent progress in the computational elucidation of the catalytic mechanism of methane hydroxylation by mono-, di-, and trinuclear copper sites in pMMO and Cu-exchanged zeolites as well as its correlations to the influencing factors that must be controlled to achieve higher reactivity. First, we briefly introduce the catalytic mechanism of a bare CuO+ cation as the simplest copper-oxo system in methane hydroxylation. The system is then extended to the copper-oxo species in pMMO and zeolites, and the radical and nonradical mechanisms are examined. Investigations of the reactivities of mononuclear and dinuclear copper-oxo species in the pMMO active site suggest that the bis(µ-oxo)CuIICuIII, (µ-oxo)(µ-hydroxo)CuIICuIII, and CuIIIO species are important for the catalytic activity of pMMO. In the case of Cu-exchanged zeolites, as the mono(µ-oxo)CuIICuII and tris(µ-oxo)CuIICuIIICuIII active sites have been fully characterized in experiments, here we discuss the effects of zeolite structures on the geometry and reactivity of the active sites.

Dioxygen Activation on Cu-MOR Zeolite: Theoretical Insights into the Formation of Cu2O and Cu3O3 Active Species.

The utilization of low-cost and abundant oxygen (O2) as an oxidant in the activation of copper-exchanged zeolites is highly important for the direct, selective oxidation of methane to methanol at low temperatures. While two motifs of active sites, i.e., the [Cu2(µ-O)]2+ and [Cu3(µ-O)3]2+, have been experimentally observed in mordenite (MOR) zeolite, the mechanisms of their formation from the reaction of Cu-MOR with O2 are still unclear. In this study, we performed density functional theory (DFT) calculations for O2 activation over 2[Cu2]2+-MOR and [Cu3O]2+-MOR zeolites. For the reaction on the dicopper species, we found two possible reaction routes: O-O bond cleavage leading to (1) formation of a [Cu2(µ-O)]2+ active species and a trans-µ-1,2-peroxo-Si2 species and (2) simultaneous formation of two [Cu2(µ-O)]2+ active species neighboring to each other. These routes are both exothermic but require completely different O-O bond activation energies. For the reaction on the tricopper species, we suggest a peroxo-Cu3O species as the intermediate structure with two transition states (TSs) involved in the reaction. The first TS where a significant rearrangement of the tricopper site occurs is found to be rate-determining, while the second TS where the peroxo bond is cleaved results in a smaller activation barrier. This reaction, in contrast to the dicopper case, is slightly endothermic. The present study provides theoretical insights that may help design of better Cu-exchanged zeolite catalysts for methane hydroxylation to methanol.

Electronic properties and surface reactivity of SrO-terminated SrTiO3 and SrO-terminated iron-doped SrTiO3.

Surface reactivity and near-surface electronic properties of SrO-terminated SrTiO3 and iron doped SrTiO3 were studied with first principle methods. We have investigated the density of states (DOS) of bulk SrTiO3 and compared it to DOS of iron-doped SrTiO3 with different oxidation states of iron corresponding to varying oxygen vacancy content within the bulk material. The obtained bulk DOS was compared to near-surface DOS, i.e. surface states, for both SrO-terminated surface of SrTiO3 and iron-doped SrTiO3. Electron density plots and electron density distribution through the entire slab models were investigated in order to understand the origin of surface electrons that can participate in oxygen reduction reaction. Furthermore, we have compared oxygen reduction reactions at elevated temperatures for SrO surfaces with and without oxygen vacancies. Our calculations demonstrate that the conduction band, which is formed mainly by the d-states of Ti, and Fe-induced states within the band gap of SrTiO3, are accessible only on TiO2 terminated SrTiO3 surface while the SrO-terminated surface introduces a tunneling barrier for the electrons populating the conductance band. First principle molecular dynamics demonstrated that at elevated temperatures the surface oxygen vacancies are essential for the oxygen reduction reaction.

Multiscale Computational Design of Functionalized Photocathodes for H2 Generation.

We present an integrated computational approach combining first-principles density functional theory (DFT) calculations with wxAMPS, a solid-state drift/diffusion device modeling software, to design functionalized photocathodes for high-efficiency H2 generation. As a case study, we have analyzed the performance of p-type Si(111) photocathodes functionalized with a set of 20 mixed aryl/methyl monolayers, which have a known synthetic route for attachment to Si(111). DFT is used to screen for high-performing monolayers by calculating the surface dipole induced by the functionalization. The trend in the calculated surface dipoles was validated using previously published experimental measurements. We find that the molecular dipole moment is a descriptor of the surface dipole. wxAMPS is used to predict the open-circuit voltage (efficiency) of the photocathode by calculating the photocurrent versus voltage behavior using the DFT surface dipole calculations as inputs to the simulation. We find that Voc saturates beyond a surface dipole of ∼0.3 eV, suggesting an upper limit for achievable device performance. This computational approach provides a possibility for the rational design of functionalized photocathodes for enhanced H2 generation by combining the angstrom-scale results obtained using DFT with the micron-to-nanometer scale capabilities of wxAMPS.

Theoretical Investigation of Methane Hydroxylation over Isoelectronic [FeO]2+- and [MnO]+-Exchanged Zeolites Activated by N2O.

While the most likely structure of the active site in iron-containing zeolites has been recently identified as [FeO]2+ (Snyder et al. Nature 2016, 536, 317-321), the mechanism for the direct conversion of methane to methanol over this active species is still debatable between the direct-radical-rebound or nonradical (concerted) mechanism. Using density functional theory on periodic systems, we calculated the two reaction mechanisms over two d4 isoelectronic systems, [FeO]2+ and [MnO]+ zeolites. We found that [FeO]2+ zeolites favor the direct-radical-rebound mechanism with low CH4 activation energies, while [MnO]+ zeolites prefer the nonradical mechanism with higher CH4 activation energies. These contrasts, despite their isoelectronic structures, are mainly due to the differences in the metal coordination number and Oα (oxo) spin density. Moreover, molecular orbital analyses suggest that the zeolite steric hindrance further degrades the reactivity of [MnO]+ zeolites toward methane. Two types of zeolite frameworks, i.e., medium-pore ZSM-5 (MFI framework) and small-pore SSZ-39 (AEI framework) zeolites, were evaluated, but no significant differences in the reactivity were found. The rate-determining reaction step is found to be methanol desorption instead of methane activation. Careful examination of the most stable sites hosting the active species and calculation for N2O decomposition over [Fe]2+-MFI and -AEI zeolites were also performed.

Modulation of the catalytic activity of Pt nanoparticles through charge-transfer interactions with metal-organic frameworks.

We employed metal-organic framework (MOF) supports to modulate the electronic states of loaded Pt nanoparticles (NPs) in their composite catalysts (Pt/MOFs). Pt NPs were homogenously deposited on four MOFs characterized with different electronic states (Zn-MOF-74, Mg-MOF-74, HKUST-1, and UiO-66-NH2). Theoretical and experimental studies demonstrated that a charge-transfer interaction between Pt NPs and MOFs is a critical factor for controlling the catalytic activity of Pt NPs supported on MOFs.

Ni-Fe Nitride Nanoplates on Nitrogen-Doped Graphene as a Synergistic Catalyst for Reversible Oxygen Evolution Reaction and Rechargeable Zn-Air Battery.

Obtaining bifunctional electrocatalysts with high activity for the oxygen evolution reaction (OER) and oxygen reduction reaction (ORR) is a main hurdle in the application of rechargeable metal-air batteries. Earth-abundant 3d transition metal-based catalysts have been developed for the OER and ORR; however, most of these are based on oxides, whose insulating nature strongly restricts their catalytic performance. This study describes a metallic Ni-Fe nitride/nitrogen-doped graphene hybrid in which 2D Ni-Fe nitride nanoplates are strongly coupled with the graphene support. Electronic structure of the Ni-Fe nitride is changed by hybridizing with the nitrogen-doped graphene. The unique heterostructure of this hybrid catalyst results in very high OER activity with the lowest onset overpotential (150 mV) reported, and good ORR activity comparable to that for commercial Pt/C. The high activity and durability of this bifunctional catalyst are also confirmed in rechargeable zinc-air batteries that are stable for 180 cycles with an overall overpotential of only 0.77 V at 10 mA-2 .

Macroscale Superlubricity of Multilayer Polyethylenimine/Graphene Oxide Coatings in Different Gas Environments.

Friction and wear decrease the efficiency and lifetimes of mechanical devices. Solving this problem will potentially lead to a significant reduction in global energy consumption. We show that multilayer polyethylenimine/graphene oxide thin films, prepared via a highly scalable layer-by-layer (LbL) deposition technique, can be used as solid lubricants. The tribological properties are investigated in air, under vacuum, in hydrogen, and in nitrogen gas environments. In all cases the coefficient of friction (COF) significantly decreased after application of the coating, and the wear life was enhanced by increasing the film thickness. The COF was lower in dry environments than in more humid environments, in contrast to traditional graphite and diamond-like carbon films. Superlubricity (COF < 0.01) was achieved for the thickest films in dry N2. Microstructural analysis of the wear debris revealed that carbon nanoparticles were formed exclusively in dry conditions (i.e., N2, vacuum), and it is postulated that these act as rolling asperities, decreasing the contact area and the COF. Density functional theory (DFT) simulations were performed on graphene oxide sheets under pressure, showing that strong hydrogen bonding occurs in the presence of intercalated water molecules compared with weak repulsion in the absence of water. It is suggested that this mechanism prevents the separation graphene oxide layers and subsequent formation of nanostructures in humid conditions.

Lattice Strain Mapping of Platinum Nanoparticles on Carbon and SnO2 Supports.

It is extremely important to understand the properties of supported metal nanoparticles at the atomic scale. In particular, visualizing the interaction between nanoparticle and support, as well as the strain distribution within the particle is highly desirable. Lattice strain can affect catalytic activity, and therefore strain engineering via e.g. synthesis of core-shell nanoparticles or compositional segregation has been intensively studied. However, substrate-induced lattice strain has yet to be visualized directly. In this study, platinum nanoparticles decorated on graphitized carbon or tin oxide supports are investigated using spherical aberration-corrected scanning transmission electron microscopy (Cs-corrected STEM) coupled with geometric phase analysis (GPA). Local changes in lattice parameter are observed within the Pt nanoparticles and the strain distribution is mapped. This reveals that Pt nanoparticles on SnO2 are more highly strained than on carbon, especially in the region of atomic steps in the SnO2 lattice. These substrate-induced strain effects are also reproduced in density functional theory simulations, and related to catalytic oxygen reduction reaction activity. This study suggests that tailoring the catalytic activity of electrocatalyst nanoparticles via the strong metal-support interaction (SMSI) is possible. This technique also provides an experimental platform for improving our understanding of nanoparticles at the atomic scale.

Synthesis and Investigation of the Effect of Substitution on the Structure, Physical Properties, and Electrochemical Properties of Anthracenodifuran Derivatives.

A series of syn/anti mixtures of anthradifuran (ADF) and substituent compounds were systematically synthesized, and the effect of substitution at the 5,11-positions on the neutral and radical states of ADF was investigated. All compounds were measured and analyzed by absorption and fluorescence spectroscopy, cyclic voltammetry, electrochemical absorption spectroscopy, and DFT calculations. The absorption spectra of 5,11-substituent compounds in their neutral state were red-shifted. In addition, the substituted compounds exhibited increased thermal stability with respect to the parent 1a because of elongation of the π-conjugation and an increased steric hindrance effect due to the bulky ethynyl substituent groups. The cyclic voltammograms of all of the compounds exhibited irreversible reduction potentials and irreversible oxidation potentials, except in the case of (trimethylsilyl)silylethynyl-substituted ADF. When the materials were subjected to oxidation/reduction potentials, the radical cation and anion species were generated. The absorption spectra of the radical-cation species of the compounds exhibited similar characteristics and similar absorption ranges (550-1400 nm), whereas the spectra of the radical anion species were blue-shifted (550-850 nm) compared than that of the parent 1a(•-) (550-1100 nm). The DFT computation results suggested that the radical states of lowest energy transitions occurred primarily from π to π(SOMO) or from π(SOMO) to π*.

Orbital views of molecular conductance perturbed by anchor units.

Site-specific electron transport phenomena through benzene and benzenedithiol derivatives are discussed on the basis of a qualitative Hückel molecular orbital analysis for better understanding of the effect of anchoring sulfur atoms. A recent work for the orbital control of electron transport through aromatic hydrocarbons provided an important concept for the design of high-conductance connections of a molecule with anchoring atoms. In this work the origin of the frontier orbitals of benzenedithiol derivatives, the effect of the sulfur atoms on the orbitals and on the electron transport properties, and the applicability of the theoretical concept on aromatic hydrocarbons with the anchoring units are studied. The results demonstrate that the orbital view predictions are applicable to molecules perturbed by the anchoring units. The electron transport properties of benzene are found to be qualitatively consistent with those of benzenedithiol with respect to the site dependence. To verify the result of the Hückel molecular orbital calculations, fragment molecular orbital analyses with the extended Hückel molecular orbital theory and electron transport calculations with density functional theory are performed. Calculated results are in good agreement with the orbital interaction analysis. The phase, amplitude, and spatial distribution of the frontier orbitals play an essential role in the design of the electron transport properties through aromatic hydrocarbons.