Qin Wu

Molecular dynamics (MD) simulations have become increasingly popular in studying the motions and functions of biomolecules. The accuracy of the simulation, however, is highly determined by the molecular mechanics (MM) force field (FF), a set of functions with adjustable parameters to compute the potential energies from atomic positions. However, the overall quality of the FF, such as our previously published ff99SB and ff14SB, can be limited by assumptions that were made years ago. In the updated model presented here (ff19SB), we have significantly improved the backbone profiles for all 20 amino acids. We fit coupled φ/ψ parameters using 2D φ/ψ conformational scans for multiple amino acids, using as reference data the entire 2D quantum mechanics (QM) energy surface. We address the polarization inconsistency during dihedral parameter fitting by using both QM and MM in aqueous solution. Finally, we examine possible dependency of the backbone fitting on side chain rotamer. To extensively validate ff19SB parameters, and to compare to results using other Amber models, we have performed a total of ∼5 ms MD simulations in explicit solvent. Our results show that after amino-acid-specific training against QM data with solvent polarization, ff19SB not only reproduces the differences in amino-acid-specific Protein Data Bank (PDB) Ramachandran maps better but also shows significantly improved capability to differentiate amino-acid-dependent properties such as helical propensities. We also conclude that an inherent underestimation of helicity is present in ff14SB, which is (inexactly) compensated for by an increase in helical content driven by the TIP3P bias toward overly compact structures. In summary, ff19SB, when combined with a more accurate water model such as OPC, should have better predictive power for modeling sequence-specific behavior, protein mutations, and also rational protein design. Of the explicit water models tested here, we recommend use of OPC with ff19SB.

Consider a system with an arbitrary constraint on its electron density (e.g., that there are $N$ charges on a certain group of atoms). We show that in Kohn-Sham density functional theory, the minimum energy state consistent with the constraint is actually a maximum with respect to the constraint potential, and that this solution is unique. This leads us to an efficient algorithm for calculations on constrained systems. Illustrative studies are shown for charge transfer in the zincbacteriochlorin-bacteriochlorin complex, polyene and alkane chains.

Metal−oxos are critical intermediates for the management of oxygen and its activation. The reactivity of the metal−oxo is central to the formation of O−O bonds, which is the essential step for oxygen generation. Two basic strategies for the formation of O−O bonds at metal−oxo active sites are presented. The acid–base (AB) strategy involves the attack of a nucleophilic oxygen species (e.g., hydroxide) on an electrophilic metal−oxo. Here, active-site designs must incorporate the assembly of a hydroxide (or water) proximate to a high-valent metal−oxo of even d electron count. For the radical coupling (RC) strategy, two high-valent metal−oxos of an odd d electron count are needed to drive O−O coupling. This Forum Article focuses on the different electronic structures of terminal metal−oxos that support AB and RC strategies and the design of ligand scaffolds that engender these electronic structures.

The development of highly active and durable catalysts for electrochemical reduction of CO2 (ERC) to CH4 in aqueous media is an efficient and environmentally friendly solution to address global problems in energy and sustainability. In this work, an electrocatalyst consisting of single Zn atoms supported on microporous N-doped carbon was designed to enable multielectron transfer for catalyzing ERC to CH4 in 1 M KHCO3 solution. This catalyst exhibits a high Faradaic efficiency (FE) of 85%, a partial current density of −31.8 mA cm–2 at a potential of −1.8 V versus saturated calomel electrode, and remarkable stability, with neither an obvious current drop nor large FE fluctuation observed during 35 h of ERC, indicating a far superior performance than that of dominant Cu-based catalysts for ERC to CH4. Theoretical calculations reveal that single Zn atoms largely block CO generation and instead facilitate the production of CH4.

Constrained density functional theory (DFT) is a useful tool for studying electron transfer (ET) reactions. It can straightforwardly construct the charge-localized diabatic states and give a direct measure of the inner-sphere reorganization energy. In this work, a method is presented for calculating the electronic coupling matrix element (Hab) based on constrained DFT. This method completely avoids the use of ground-state DFT energies because they are known to irrationally predict fractional electron transfer in many cases. Instead it makes use of the constrained DFT energies and the Kohn-Sham wave functions for the diabatic states in a careful way. Test calculations on the Zn2+ and the benzene-Cl atom systems show that the new prescription yields reasonable agreement with the standard generalized Mulliken-Hush method. We then proceed to produce the diabatic and adiabatic potential energy curves along the reaction pathway for intervalence ET in the tetrathiafulvalene-diquinone (Q-TTF-Q) anion. While the unconstrained DFT curve has no reaction barrier and gives Hab≈17kcal∕mol, which qualitatively disagrees with experimental results, the Hab calculated from constrained DFT is about 3kcal∕mol and the generated ground state has a barrier height of 1.70kcal∕mol, successfully predicting (Q-TTF-Q)− to be a class II mixed-valence compound.

Diabatic states have a long history in chemistry, beginning with early valence bond pictures of molecular bonding and extending through the construction of model potential energy surfaces to the modern proliferation of methods for computing these elusive states. In this review, we summarize the basic principles that define the diabatic basis and demonstrate how they can be applied in the specific context of constrained density functional theory. Using illustrative examples from electron transfer and chemical reactions, we show how the diabatic picture can be used to extract qualitative insight and quantitative predictions about energy landscapes. The review closes with a brief summary of the challenges and prospects for the further application of diabatic states in chemistry.

Dinitrogen conversion to ammonia via electrochemical reduction with over 10% Faradaic efficiency is demonstrated in this work. Co-doped MoS2-x polycrystalline nanosheets with S vacancies as the catalysts are loaded onto carbon cloth by hydrothermal growth from Mo, Co, and S precursors. A sulfur vacancy on the MoS2-x basal plane mimicking the natural Mo-nitrogenase active site is modified by Co doping and exhibits superior dinitrogen-to-ammonia conversion activity. Density-functional simulation reveals that the free energy barrier, which can be compensated by applied overpotential, is reduced from 1.62 to 0.59 eV after Co doping. Meanwhile, dinitrogen tends to be chemically adsorbed to defective MoS2-x, which effectively activates the dinitrogen molecule for the dissociation of the N≡N triple bond. This process is further accelerated by Co doping, resulting from the modulation of Mo–N bonding configuration.

A direct optimization method is developed for the computation of the Kohn–Sham kinetic energy density functional Ts from a given electron density and the exchange–correlation potential vxc if this density is from a ground state. The method is based on the construction of a variational functional of the one-electron potential. This functional is derived from the conventional Levy constrained-search formulation and is shown to be closely related to the Lieb functional construction. The one-electron potential is expanded in terms of some fixed terms plus a linear expansion in a basis set. The determination of the Kohn–Sham kinetic energy for an input density is then turned into the maximization of this functional of potential. The analytic first and second derivatives of the variational functional with respect to the linear basis set expansion coefficients and also the nonlinear parameters in the basis set are derived. This enables very efficient iterative optimization of the potential and hence the calculation of Ts and vxc. The efficiency and accuracy of the method is shown in the numerical implementation for atomic and molecular calculations with Gaussian basis set expansions both for molecular orbitals and for one-electron potentials. Finally, this direct optimization method is extended to general density functionals and the analytic derivatives are also developed for use in optimization methods.

The conventional optimized effective potential method is based on a difficult-to-solve integral equation. In the new method, this potential is constructed as a sum of a fixed potential and a linear combination of basis functions. The energy derivatives with respect to the coefficients of the linear combination are obtained. This enables calculations by optimization methods. Accurate atomic and molecular calculations with Gaussian basis sets are presented for exact exchange functionals. This efficient and accurate method for the optimized effective potential should play an important role in the development and application of density functionals.

Recently, we have proposed an efficient method in the Kohn−Sham density functional theory (DFT) to study systems with a constraint on their density (Phys. Rev. A 2005, 72, 24502). In our approach, the constrained state is calculated directly by running a fast optimization of the constraining potential at each iteration of the usual self-consistent-field procedure. Here, we show that the same constrained DFT approach applies to systems with multiple constraints on the density. To illustrate the utility of this approach, we focus on the study of long-range charge-transfer (CT) states. We show that constrained DFT is size-consistent: one obtains the correct long-range CT energy when the donor−acceptor separation distance goes to infinity. For large finite distances, constrained DFT also correctly describes the 1/R dependence of the CT energy on the donor−acceptor separation. We also study a model donor−(amidinium−carboxylate)−acceptor complex, where experiments suggest a proton-coupled electron-transfer process. Constrained DFT is used to explicitly calculate the potential-energy curves of both the donor state and the acceptor state. With an appropriate model, we obtain qualitative agreement with experiments and estimate the reaction barrier height to be 7 kcal/mol.

It is shown that constrained density functional theory (DFT) can be used to access diabatic potential energy surfaces in the Marcus theory of electron transfer, thus providing a means to directly calculate the driving force and the inner-sphere reorganization energy. We present in this report an analytic expression for the forces in constrained DFT and their implementation in geometry optimization, a prerequisite for the calculation of electron transfer parameters. The method is then applied to study the symmetric mixed-valence complex tetrathiafulvalene-diquinone radical anion, which is observed experimentally to be a Robin-Day class II compound but found by DFT to be in class III. Constrained DFT avoids this pitfall of over-delocalization and provides a way to find the charge-localized structure. In another application, driving forces and inner-sphere reorganization energies are calculated for the charge recombination (CR) reactions in formanilide-anthraquinone (FA-AQ) and ferrocene-formanilide-anthraquinone (Fc-FA-AQ). While the two compounds have similar reorganization energies, the driving force in FA-AQ is 1 eV larger than in Fc-FA-AQ, in agreement with experimental observations and supporting the experimental conclusion that the anomalously long-lived FA-AQ charge-separated state arises because the electron transfer is in the Marcus inverted region.

Existing density functional theory (DFT) methods are typically very effective in capturing dynamic correlation, but run into difficulty treating near-degenerate systems where static correlation becomes important. In this work, we propose a configuration interaction (CI) method that allows one to use a multireference approach to treat static correlation but incorporates DFT's efficacy for the dynamic part as well. The new technique uses localized charge or spin states built by a constrained DFT approach to construct an active space in which the effective Hamiltonian matrix is built. These local configurations have significantly less static correlation compared to their delocalized counterparts and possess an essentially constant amount of self-interaction error. Thus their energies can be reliably calculated by DFT with existing functionals. Using a small number of local configurations as different references in the active space, a simple CI step is then able to recover the static correlation missing from the localized states. Practical issues of choosing configurations and adjusting constraint values are discussed, employing as examples the ground state dissociation curves of H(2) (+), H(2), and LiF. Excellent results are obtained for these curves at all interatomic distances, which is a strong indication that this method can be used to accurately describe bond breaking and forming processes.

We present a detailed theoretical study of the pathway for water oxidation in synthetic ruthenium-based catalysts. As a first step, we consider a recently discovered single center catalyst, where experimental observations suggest a purely single-center mechanism. We find low activation energies (<5 kcal/mol) for each rearrangement in the catalytic cycle. In the crucial step of O-O bond formation, a solvent water acts as a Lewis base and attacks a highly oxidized Ru(V)=O. Armed with the structures and energetics of the single-center catalyst, we proceed to consider a representative Ru-dimer which was designed to form O(2) via coupling between the two centers. We discover a mechanism that proceeds in analogous fashion to the monomer case, with all the most significant steps occurring at a single catalytic center within the dimer. This acid-base mechanism suggests a new set of strategies for the rational design of multicenter catalysts: rather than coordinating the relative orientations of the subunits, one can focus on coordinating solvation-shell water molecules or tuning redox potentials.

The first purely density-based energy decomposition analysis (EDA) for intermolecular binding is developed within the density functional theory. The most important feature of this scheme is to variationally determine the frozen density energy, based on a constrained search formalism and implemented with the Wu-Yang algorithm [Q. Wu and W. Yang, J. Chem. Phys. 118, 2498 (2003)]. This variational process dispenses with the Heitler-London antisymmetrization of wave functions used in most previous methods and calculates the electrostatic and Pauli repulsion energies together without any distortion of the frozen density, an important fact that enables a clean separation of these two terms from the relaxation (i.e., polarization and charge transfer) terms. The new EDA also employs the constrained density functional theory approach [Q. Wu and T. Van Voorhis, Phys. Rev. A 72, 24502 (2005)] to separate out charge transfer effects. Because the charge transfer energy is based on the density flow in real space, it has a small basis set dependence. Applications of this decomposition to hydrogen bonding in the water dimer and the formamide dimer show that the frozen density energy dominates the binding in these systems, consistent with the noncovalent nature of the interactions. A more detailed examination reveals how the interplay of electrostatics and the Pauli repulsion determines the distance and angular dependence of these hydrogen bonds.

Abstract Singlet fission (SF), a multiple exciton generation process that generates two triplet excitons after the absorption of one photon, can potentially enable more efficient solar cell designs by harvesting energy normally lost as heat. While low-bandgap conjugated polymers are highly promising candidates for efficient SF-based solar cells, few polymer materials capable of SF have been reported because the SF process in polymer chains is poorly understood. Using transient spectroscopy, we demonstrate a new, highly efficient (triplet yield of 160–200%) isoindigo-based donor–acceptor polymer and show that the triplet pairs are directly emissive and exhibit a time-dependent energy evolution. Importantly, aggregation in poor solvents and in films significantly lowers the singlet energy, suppressing triplet formation because the energy conservation criterion is no longer met. These results suggest a new design rule for developing intramolecular SF capable low-bandgap conjugated polymers, whereby inter-chain interactions must be carefully engineered.

Single atom catalysts (SACs) have shown high activity and selectivity in a growing number of chemical reactions. Many efforts aimed at unveiling the structure–property relationships underpinning these activities and developing synthesis methods for obtaining SACs with the desired structures are hindered by the paucity of experimental methods capable of probing the attributes of local structure, electronic properties, and interaction with support—features that comprise key descriptors of their activity. In this work, we describe a combination of experimental and theoretical approaches that include photon and electron spectroscopy, scattering, and imaging methods, linked by density functional theory calculations, for providing detailed and comprehensive information on the atomic structure and electronic properties of SACs. This characterization toolbox is demonstrated here using a model single atom Pt/CeO2 catalyst prepared via a sol–gel-based synthesis method. Isolated Pt atoms together with extra oxygen atoms passivate the (100) surface of nanosized ceria. A detailed picture of the local structure of Pt nearest environment emerges from this work involving the bonding of isolated Pt2+ ions at the hollow sites of perturbed (100) surface planes of the CeO2 support, as well as a substantial (and heretofore unrecognized) strain within the CeO2 lattice in the immediate vicinity of the Pt centers. The detailed information on structural attributes provided by our approach is the key for understanding and improving the properties of SACs.

The long-standing problem of the large overestimation of polymer polarizabilities in density-functional theory is reexamined and largely solved using an exact exchange method. We have built an accurate optimized effective potential as the sum of a fixed potential and a linear combination of basis sets based on our direct optimization method. This effective potential properly develops a linear counteracting depolarization field, and it significantly improves recent results from approximate optimized potentials. The controversial case of hydrogen chains is now correctly described and the failure of the local density approach is attributed to the large self-interaction error in systems with a non-integer number of electrons.

We demonstrate an accurate method for extracting Heisenberg exchange-coupling constants (J) from density-functional theory (DFT) calculations. We note that the true uncoupled low-spin state of a given molecule should be identified with the ground state of the system subject to a constraint on the spin density of the atoms. Using an efficient optimization strategy for constrained DFT we obtain these states directly, leading to a simple, physically motivated formula for J. Our method only depends on state energies and their associated electron densities and assigns no unphysical meaning to the Kohn-Sham determinant or individual orbitals. We study several bimetallic transition-metal complexes and find that the constrained DFT approach is competitive with, if not better than, the best broken symmetry DFT results. The success of constrained DFT in these cases appears to result from a balanced elimination of self-interaction error and static correlation from the simulation.

In this work, a constrained density functional theory based configuration interaction approach (CDFT-CI) is applied to calculating transition state energies of chemical reactions that involve bond forming and breaking at the same time. At a given point along the reaction path, the configuration space is spanned by two diabaticlike configurations: reactant and product. Each configuration is constructed self-consistently with spin and charge constraints to maximally retain the identities of the reactants or the products. Finally, the total energy is obtained by diagonalizing an effective Hamiltonian constructed in the basis spanned by these two configurations. By design, this prescription does not affect the energies of the reactant or product species but will affect the energy at intermediate points along the reaction coordinate, most notably by modifying the reaction barrier height. When tested with a large set of reactions that include hydrogen transfer, heavy atom transfer, and nucleophilic substitution, CDFT-CI is found to improve the prediction of barrier heights by a factor of 2-3 for some commonly used local, semilocal, and hybrid functionals. Thus, just as CDFT can be used to cure energy errors in charge localized states, CDFT-CI can recover the correct energy for charge delocalized states by approximating the true wave function as a linear combination of localized configurations (e.g., reactant and product). The well-defined procedure and the promising results of CDFT-CI suggest that it could broaden the applicability of traditional DFT methods for reaction barrier heights.

Abstract We report the synthesis of a tellurophene‐containing low‐bandgap polymer, PDPPTe2T, by microwave‐assisted palladium‐catalyzed ipso ‐arylative polymerization of 2,5‐bis[(α‐hydroxy‐α,α‐diphenyl)methyl]tellurophene with a diketopyrrolopyrrole (DPP) monomer. Compared with the corresponding thiophene analog, PDPPTe2T absorbs light of longer wavelengths and has a smaller bandgap. Bulk heterojunction solar cells prepared from PDPPTe2T and PC 71 BM show PCE values of up to 4.4 %. External quantum efficiency measurements show that PDPPTe2T produces photocurrent at wavelengths up to 1 µm. DFT calculations suggest that the atomic substitution from sulfur to tellurium increases electronic coupling to decrease the length of the carbon–carbon bonds between the tellurophene and thiophene rings, which results in the red‐shift in absorption upon substitution of tellurium for sulfur.

Abstract Weak binding of hydrogen atoms to the 2H‐MoS 2 basal plane renders MoS 2 inert as an electrocatalyst for the hydrogen evolution reaction. Transition‐metal doping can activate neighboring sulfur atoms in the MoS 2 basal plane to bind hydrogen more strongly. Our theoretical studies show strong variation in the degree of activation by dopants across the 3d transition‐metal series. To understand the trends in activation, we propose a model based on the electronic promotion energy required to partially open the full valence shell of a local S atom and therefore enable it to bond with a H atom. In general, the promotion is achieved through an electron transfer from the S to neighboring metal‐atom sites. Furthermore, we demonstrate a specific, electronic‐structure‐based descriptor for the hydrogen‐binding strength: Δ dp , the local interband energy separation between the lowest empty d‐states on the dopant metal atoms and occupied p‐states on S. This model can be used to provide guidelines for chalcogen activation in future catalyst design based on doped transition‐metal dichalcogenides.

We have developed a second-order perturbation theory (PT) energy functional within density-functional theory (DFT). Based on PT with the Kohn-Sham (KS) determinant as a reference, this new ab initio exchange-correlation functional includes an exact exchange (EXX) energy in the first order and a correlation energy including all single and double excitations from the KS reference in the second order. The explicit dependence of the exchange and correlation energy on the KS orbitals in the functional fits well into our direct minimization approach for the optimized effective potential, which is a very efficient method to perform fully self-consistent calculations for any orbital-dependent functionals. To investigate the quality of the correlation functional, we have applied the method to selected atoms and molecules. For two-electron atoms and small molecules described with small basis sets, this new method provides excellent results, improving both second-order Moller-Plesset expression and any conventional DFT results significantly. For larger systems, however, it performs poorly, converging to very low unphysical total energies. The failure of PT based energy functionals is analyzed, and its origin is traced back to near degeneracy problems due to the orbital- and eigenvalue-dependent algebraic structure of the correlation functional. The failure emerges in the self-consistent approach but not in perturbative post-EXX calculations, emphasizing the crucial importance of self-consistency in testing new orbital-dependent energy functionals.

A functional of external potentials and its variational principle for the ground-state energy is constructed. This potential functional formulation is dual to the density functional approach and provides a solution to the $v$-representability problem in the original Hohenberg-Kohn theory. A second potential functional for Kohn-Sham noninteracting systems establishes the foundation for the optimized effective potential approach and results in efficient approaches for ensemble Kohn-Sham calculations.

A variational method for forcing the exchange-correlation potential in density-functional theory (DFT) to have the correct asymptotic decay is developed. The resulting exchange-correlation potentials are much improved while the total energies remain essentially the same, compared with conventional density-functional theory calculations. The highest occupied orbital energies from the asymptotically corrected exchange-correlation potentials are found to provide significantly more accurate approximations to the ionization potential (for a neutral molecule) and the electron affinity (for an anion) than those from conventional calculations, although the results are usually inferior to direct methods by computing energy differences. Extending recent results from exchange-only DFT, we show that exact exchange-correlation potential is nonuniform asymptotically. Correcting the asymptotic decay of approximate exchange-correlation potentials towards the exact functional form binds the highest occupied orbitals for atomic and molecular anions, which supports the use of DFT calculations for negatively charged molecular species. With this technique, even hybrid functionals have local exchange-correlation potentials, effectively removing the largest objection to including these functionals in the panoply of Kohn–Sham DFT methods.

Nearly all common density functional approximations fail to properly describe dispersion interactions responsible for binding in van der Waals complexes. Empirical corrections can fix some of the failures but cannot fully grasp the complex physics and may not be reliable for systems dissimilar to the fitting set. In contrast, the recently proposed nonlocal van der Waals density functional (vdW-DF) was derived from first principles, describes dispersion interactions in a seamless fashion, and yields the correct asymptotics. Implementation of this functional is somewhat cumbersome: Nonlocal dependence on the electron density requires numerical double integration over the space variables and functional derivatives are nontrivial. This paper shows how vdW-DF can be implemented self-consistently with Gaussian basis functions. The gradients of the energy with respect to nuclear displacements have also been derived and coded, enabling efficient geometry optimizations. We test the vdW-DF correlation functional in combination with several exchange approximations. We also study the sensitivity of the method to the basis set size and to the quality of the numerical quadrature grid. For weakly interacting systems, acceptable accuracy in semilocal exchange is achieved only with fine grids, whereas for nonlocal vdW-DF correlation even rather coarse grids are sufficient. The current version of vdW-DF is not well suited for pairing with Hartree–Fock exchange, leading to considerable overbinding.

The nature of charge carriers in conjugated polymers was elucidated through optical spectroscopy following single- and multielectron reduction of 2,7-(9,9-dihexylfluorene) oligomers, F(n), n = 1-10, yielding spectra with the two bands typical of polarons upon single reduction. For short oligomers addition of a second electron gave a single band demonstrating the classic polaron-bipolaron transition. However, for long oligomers double reductions yielded spectra with two bands, better described as two polarons, possibly residing side-by-side in the F(n) chains. The singly reduced anions do not appear to delocalize over the entire length of the longer conjugated systems; instead they are polarons occupying approximately four fluorene repeat units. The polarons of F(3) and F(4) display sharp absorption bands, but for longer oligomers the bands broaden, possibly due to fluctuations of the lengths of these unconfined polarons. DFT calculations with long-range-corrected functionals were fully consistent with the experiments describing polarons in anions, bipolarons in dianions of short oligomers, and side-by-side polarons in dianions of long oligomers, while results from standard functionals were not compatible with the experimental results. The computations found F(10)(2-), for example, to be an open-shell singlet (<S(2)> ≈ 1), with electrons in two side-by-side orbitals, while dianions of shorter oligomers experienced a gradual transition to bipolarons with states of intermediate character at intermediate lengths. The energies and extinction coefficients of each anionic species were measured by ultraviolet-visible-near-infrared absorption spectroscopy with chemical reduction and pulse radiolysis. Reduction potentials determined from equilibria mirrored oxidation potentials reported by Chi and Wegner. Anions of oligomers four or more units in length contained vestigial neutral (VN) absorption bands that arise from neutral parts of the chain. Energies of the VN bands correspond to those of oligomers shorter by four units.

Li–S battery is one of the most promising next-generation rechargeable battery technologies because of its high theoretical energy density and low material cost. However, its success is impeded by the low energy efficiency and fast capacity fade primarily caused by the discharge intermediates, Li-polysulfides (PS), dissolution in the electrolyte. Mitigation of PS dissolution in electrolyte involves the search for a new electrolyte solvent system that exhibits poor solvation to the PS while still having good solvation ability to the electrolyte salt for high ionic conductivity. Applying cosolvents with reduced solvating power but compatible with the state of the art Li–S battery’s ether-based electrolyte is one of the most promising concepts. This route is also advantageous of having a low scale-up cost. With the aid of quantum chemical calculation, we have identified high carbon-to-oxygen (C/O) ratio ethers as cosolvent in the new electrolytes that effectively impede PS dissolution while still maintaining high ionic conductivity. Significantly improved cycle life and cycling Coulombic efficiency are observed for Li–S cells using the new composite electrolytes. Anode analysis with different methods also demonstrate that reducing electrolyte’s PS solubility results in less sulfur total amount on the lithium anode surface and lower ratio of the longer-chain PS, which is probably a sign of suppressed side reactions between the anode and PS in the electrolyte.

We demonstrate layer-dependent electron transfer between core/shell PbS/CdS quantum dots (QDs) and layered MoS2 via energy band gap engineering of both the donor (QDs) and the acceptor (MoS2) components. We do this by (i) changing the size of the QD or (ii) by changing the number of layers of MoS2, and each of these approaches alters the band gap and/or the donor–acceptor separation distance, thus providing a means of tuning the charge-transfer rate. We find the charge-transfer rate to be maximal for QDs of smallest size and for QDs combined with a 5-layer MoS2 or thicker. We model this layer-dependent charge-transfer rate with a theoretical model derived from Marcus theory previously applied to nonadiabatic electron transfer in weakly coupled systems by considering the QD transferring photogenerated electrons to noninteracting monolayers within a few layers of MoS2.

We utilize excited state density functional theory (eDFT) to study Rydberg states in atoms. We show both analytically and numerically that semilocal functionals can give quite reasonable Rydberg energies from eDFT, even in cases where time dependent density functional theory (TDDFT) fails catastrophically. We trace these findings to the fact that in eDFT the Kohn-Sham potential for each state is computed using the appropriate excited state density. Unlike the ground state potential, which typically falls off exponentially, the sequence of excited state potentials has a component that falls off polynomially with distance, leading to a Rydberg-type series. We also address the rigorous basis of eDFT for these systems. Perdew and Levy have shown using the constrained search formalism that every stationary density corresponds, in principle, to an exact stationary state of the full many-body Hamiltonian. In the present context, this means that the excited state DFT solutions are rigorous as long as they deliver the minimum noninteracting kinetic energy for the given density. We use optimized effective potential techniques to show that, in some cases, the eDFT Rydberg solutions appear to deliver the minimum kinetic energy because the associated density is not pure state v-representable. We thus find that eDFT plays a complementary role to constrained DFT: The former works only if the excited state density is not the ground state of some potential while the latter applies only when the density is a ground state density.

Approximate molecular calculations via standard Kohn-Sham Density Functional Theory are exactly reproduced by performing self-consistent calculations on isolated fragments via Partition Density Functional Theory [Phys. Rev. A 82, 024501 (2010)]. We illustrate this with the binding curves of small diatomic molecules. We find that partition energies are in all cases qualitatively similar and numerically close to actual binding energies. We discuss qualitative features of the associated partition potentials.

Intervalence electron transfer reactions were studied computationally by means of density functional theory and constrained density functional theory (CDFT). Two ferrocene moieties, connected via various bridge structures, were used as model mixed-valence compounds in the computational investigation. Features of the frontier orbitals were analyzed to offer a qualitative account of the intervalence characteristics of the model complexes. The effective electronic coupling between the donor and acceptor sites was calculated using the CDFT method, which provided a quantitative measure of the intervalence electronic communication. The relationship between the bridge linkage and the effectiveness of intervalence transfer was discussed on the basis of the theoretical results and compared to experimental data available in the literature.

A common synthetic strategy used to design low-bandgap organic semiconductors employs the use of "push-pull" building blocks, where electron -rich and electron-deficient monomers are alternated along the π-conjugated backbone of a molecule or polymer. Incorporating strong "pull" units with high electron affinity is a means to further decrease the optical gap for infrared optoelectronics or to develop n-type semiconducting materials. Here we show that the use of thiophene-1,1-dioxide as a strong acceptor in "push-pull" oligomers affects the electronic structure and carrier dynamics in unexpected ways. Critically, the overall excited-state lifetime is reduced by several orders of magnitude relative to unoxidized analogs due to the introduction of low-energy optically dark states and low-energy triplet states that allow for fast internal conversion and intramolecular singlet fission. We found that the electronic structure and excited-state lifetime are strongly dependent on the number of sequential thiophene-1,1-dioxide units. These results suggest that both the static and dynamical optical properties are highly tunable via small changes in chemical structure that have drastic effects on the optoelectronic properties, which can impact the types of applications that involve these materials.

We study the Heisenberg exchange couplings in polynuclear transition-metal clusters with strong spin frustration using a variety of theoretical techniques. We present results for a trinuclear Cr(III) molecule, a tetranuclear Fe(III) complex, and an octanuclear Fe(III) molecular magnet. We explore the physics of the exchange couplings in these systems using standard broken-symmetry (BS) techniques and a more recently developed constrained density functional theory (C-DFT) approach. The calculations show that the expected picture of localized spin moments on the metal centers is appropriate, and in each case C-DFT predicts coupling constant values in good agreement with experiment. Furthermore, we demonstrate that all of the C-DFT spin states for a given cluster can be reasonably described by a single Heisenberg Hamiltonian. These findings are significant in part because standard BS calculations are in conflict with the experiments on a number of key points. For example, BS-DFT predicts a doublet (rather than quartet) ground state for the Cr(III) cluster while for the Fe(III) complexes BS-DFT predicts some of the exchange couplings to be ferromagnetic whereas the experimentally derived couplings are all antiferromagnetic. Furthermore, for BS-DFT the best-fit exchange parameters can depend significantly on the set of spin configurations chosen. For example, by choosing configurations with Ms closer to Ms(max) the BS-DFT couplings can typically be made somewhat closer to the C-DFT and experimental results. Thus, in these cases, our results consistently support the experimental findings.

One well-known shortcoming of widely-used biomolecular force fields is the description of the directional dependence of hydrogen bonding (HB). Here we aim to better understand the origin of this difficulty and thus provide some guidance for further force field development. Our theoretical approaches center on a novel density-based energy decomposition analysis (DEDA) method [J. Chem. Phys., 131, 164112 (2009)], in which the frozen density energy is variationally determined through constrained search. This unique and most significant feature of DEDA enables us to find that the frozen density interaction term is the key factor in determining the HB orientation, while the sum of polarization and charge-transfer components shows very little HB directional dependence. This new insight suggests that the difficulty for current non-polarizable force fields to describe the HB directional dependence is not due to the lack of explicit polarization or charge-transfer terms. Using the DEDA results as reference, we further demonstrate that the main failure coming from the atomic point charge model can be overcome largely by introducing extra charge sites or higher order multipole moments. Among all the electrostatic models explored, the smeared charge distributed multipole model (up to quadrupole), which also takes account of charge penetration effects, gives the best agreement with the corresponding DEDA results. Meanwhile, our results indicate that the van der Waals interaction term needs to be further improved to better model directional hydrogen bonding.

Hexaazatriphenylene triimides (HAT) have been shown to be a novel class of disk-shaped π electron acceptors that pair with donors with complementary shape and electron demands, such as triphenylene (TP) derivatives. The donor–acceptor (DA) pair forms a strong charge-transfer complex in CH2Cl2 with an association constant of 2.6 × 104 M−1, which is remarkable for a recognition system that is solely based on electrostatic interactions between two π systems. NMR studies, along with molecular modelling, have revealed a complementary charge distribution and an "eclipsed" conformation in the DA complex. The strong DA interaction results in extended alternating DA stacks in the thin film and mesophases.

By using a chiral cinchona alkaloid-squaramide catalyst, a series of both enantiomers of novel amino-pyrimidine derivatives can be obtained in an enantioselective three-component one-pot Mannich reaction with high yields and excellent enantioselectivities. In addition, these chiral derivatives were found to exhibit higher antiviral activities against tobacco mosaic virus (TMV) in vivo than the commercial agent ningnanmycin. In particular, chiral compounds (R)-4b and (R)-4e showed excellent antiviral activity against TMV at a concentration of 500 μg/mL, with a curative activity of 56.8% and 55.2%, respectively, a protection activity of 69.1% and 67.1%, respectively, and an inactivation activity of 91.5% and 94.3%, respectively. These values are superior to those of the agent ningnanmycin (which has curative, protective, and inactivation activities of 52.9%, 62.8%, and 90.4%, respectively). The antiviral mechanisms and enhanced antiviral activities of these chiral derivatives are interesting subjects for future investigation.

Nanoparticles with a low-Pt content core and a few-layer thick Pt skin are attractive catalysts toward the oxygen reduction reaction (ORR) not only for their low cost, but also because their activity can be enhanced by judiciously choosing the core alloy. Achieving the optimal ORR performance would require fine tuning of the core composition and structure. Previous work studying the enhancement effects has primarily focused on core alloys with a cubic structure, (i.e. disordered alloy or L12 ordered structure) which limits the tuning to composition alone. In this work, using ab initio calculations, we have systemically investigated a new class of Pt0.5M0.5 (M = V, Cr, Fe, Co, Ni and Cu) core alloy that has a face-centered tetragonal L10 intermetallic structure. We have calculated the adsorption energies of O, OH and OOH on various Pt skins and the underlying tetragonally structured alloys, which allows us to not only predict the optimal number of pure Pt skin layers but also tune the activity of the catalysts toward the peak of the ORR volcano plot. More importantly, using adsorption energies on intermediate structures, we are able to decompose the enhancement factor into the ligand, normal and shear strain effects, and reveal the significant contribution of the shear strain that is only possible with a tetragonal core but not a cubic one. Our results point to a new direction in designing tetragonally structured intermetallic core-shell nanoparticles for ORR applications.

The study focused on the structural sensitivity of lignin during the phosphoric acid-acetone pretreatment process and the resulting hydrolysis and phosphorylation reaction mechanisms using density functional theory calculations. The chemical stabilities of the seven most common linkages (β-O-4, β-β, 4-O-5, β-1, 5-5, α-O-4, and β-5) of lignin in H3PO4, CH3COCH3, and H2O solutions were detected, which shows that α-O-4 linkage and β-O-4 linkage tend to break during the phosphoric acid-acetone pretreatment process. Then α-O-4 phosphorylation and β-O-4 phosphorylation follow a two-step reaction mechanism in the acid treatment step, respectively. However, since phosphorylation of α-O-4 is more energetically accessible than phosphorylation of β-O-4 in phosphoric acid, the phosphorylation of α-O-4 could be controllably realized under certain operational conditions, which could tune the electron and hole transfer on the right side of β-O-4 in the H2PO4- functionalized lignin. The results provide a fundamental understanding for process-controlled modification of lignin and the potential novel applications in lignin-based imprinted polymers, sensors, and molecular devices.

The density-based energy decomposition analysis (DEDA) is the first of its kind to calculate the frozen density energy variationally. Defined with the constrained search formulation of density functional theory, the frozen density energy is optimized in practice using the Wu-Yang (WY) method for constrained minimizations. This variational nature of the frozen density energy, a possible reason behind some novel findings of DEDA, will be fully investigated in this work. In particular, we systematically study the dual basis set dependence in WY: the potential basis set used to expand the Lagrangian multiplier function and the regular orbital basis set. We explain how the convergence progresses differently on these basis sets and how an apparent basis-set independence is achieved. We then explore a new development of DEDA in frozen energy calculations of the ethane molecule, focusing on the internal rotation around the carbon-carbon bond and the energy differences between staggered and eclipsed conformations. We argue that the frozen density energy change at fixed bond lengths and bond angles is purely steric effects. Our results show that the frozen density energy profile follows closely that of the total energy when the dihedral angle is the only varying geometry parameter. We can further analyze the contributions from electrostatics and Pauli repulsions. These results lead to a meaningful DEDA of the torsional potential in ethane.

In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.

We report the synthesis, characterization, and detailed comparison of a series of novel Pt-bisacetylide containing conjugated small molecules possessing an unconventional “roller-wheel” shaped structure that is distinctly different from the “dumbbell” designs in traditional Pt-bisacetylide containing conjugated polymers and small molecules. The relationships between the chemical nature and length of the “rollers” and the electronic and physical properties of the materials are carefully studied by steady-state spectroscopy, cyclic voltammetry, differential scanning calorimetry, single-crystal X-ray diffraction, transient absorption spectroscopy, theoretical calculation, and device application. It was revealed that if the roller are long enough, these molecules can “slip-stack” in the solid state, leading to high crystallinity and charge mobility. Organic solar cells were fabricated and showed power conversion efficiencies up to 5.9%, out-performing all existing Pt-containing materials. The device performance was also found to be sensitive to optimization conditions and blend morphologies, which are a result of the intricate interplay among materials crystallinity, phase separation, and the relative positions of the lowest singlet and triplet excited states.

Electrochemical ozone production (EOP), a six-electron water oxidation reaction, offers promising avenues for creating value-added oxidants and disinfectants. However, progress in this field is slowed by a dearth of understanding of fundamental reaction mechanisms. In this work, we combine experimental electrochemistry, spectroscopic detection of reactive oxygen species (ROS), oxygen-anion chemical ionization mass spectrometry, and computational quantum chemistry calculations to determine a plausible reaction mechanism on nickel- and antimony-doped tin oxide (Ni/Sb–SnO2, NATO), one of the most selective EOP catalysts. Antimony doping is shown to increase the conductivity of the catalyst, leading to improved electrochemical performance. Spectroscopic analysis and electrochemical experiments combined with quantum chemistry predictions reveal that hydrogen peroxide (H2O2) is a critical reaction intermediate. We propose that leached Ni4+ cations catalyze hydrogen peroxide into solution phase hydroperoxyl radicals (•OOH); these radicals are subsequently oxidized to ozone. Isotopic product analysis shows that ozone is generated catalytically from water and corrosively from the catalyst oxide lattice without regeneration of lattice oxygens. Further quantum chemistry calculations and thermodynamic analysis suggest that the electrochemical corrosion of tin oxide itself might generate hydrogen peroxide, which is then catalyzed to ozone. The proposed pathways explain both the roles of dopants in NATO and its lack of stability. Our study interrogates the possibility that instability and electrochemical activity are intrinsically linked through the formation of ROS. In doing so, we provide the first mechanism for EOP that is consistent with computational and experimental results and highlight the central challenge of instability as a target for future research efforts.

The resonance Raman spectrum of the simple alkyne bridge in 4,4'-dinitrotolane radical anion shows two distinct bands, providing proof of the solvent-dependent coexistence of charge-localized and -delocalized species. The Raman spectra of normal modes primarily involving the charge-bearing -PhNO(2) units also support the coexistence of two solvent-dependent electronic species. The temperature dependence of the spectra of the bridging unit shows an inverse relationship between the solvent reorganization energy (lambda(s)) and the temperature.

X-ray crystallographic structures are reported for 1(Me)2+(SbCl6−)2·2CH3CN, 2(Et)2+(SbF6−)2·2CH3CN·2CH2Cl2, and 1(iPr)2+(SbF6−)2, which also contained unresolved solvent and is in a completely different conformation than the methyl- and ethyl-substituted compounds. A quite different structure of 1(Me)2+(SbF6−)2 than that previously published was obtained upon crystallizing it from a mixture rich in monocation. It does not contain close intramolecular PD+,PD+ contacts but has close intermolecular ones. Low temperature NMR spectra of 1(Me)2+ and 1(Et)2+ in 2:1 CD3OD/CD3CN showed that both contain three conformations of all-gauche NCCC unit material with close intramolecular PD+,PD+ contacts. In addition to the both PD+ ring syn and anti material that had been seen in the crystal structure of 1(Me)2+(SbF6−)2·2CH3CN published previously, an unsymmetrical conformation having one PD+ ring syn and the other anti (abbreviated uns) was seen, and the relative amounts of these conformations were significantly different for 1(Me)2+ and 1(Et)2+. Calculations that correctly obtain the relative amounts of both the methyl- and ethyl-substituted material as well as changes in the optical spectra between 1(Me)2+ and 1(Et)2+, which contains much less of the uns conformation, are reported.

Stacked against the odds: A bridged mixed-valent compound with direct through-space interactions between the charge-bearing units in its singly charged paramagnetic and its doubly charged diamagnetic forms is isolated and characterized by X-ray crystallography and spectroscopy (see scheme). π-Stacking interactions for the singlet diradical dication were more pronounced than for the doublet monocation, despite the Coulomb repulsion effect in the diradical dication.

We test the feasibility of using nanostructured electrodes in organic bulk heterojunction solar cells to improve their photovoltaic performance by enhancing their charge collection efficiency and thereby increasing the optimal active blend layer thickness. As a model system, small concentrations of single wall carbon nanotubes are added to blends of poly(3-hexylthiophene): [6,6]-phenyl-C61-butyric acid methyl ester in order to create networks of efficient hole conduction pathways in the device active layer without affecting the light absorption. The nanotube addition leads to a 22% increase in the optimal blend layer thickness from 90 nm to 110 nm, enhancing the short circuit current density and photovoltaic device efficiency by as much as ∼10%. The associated incident-photon-to-current conversion efficiency for the given thickness also increases by ∼10% uniformly across the device optical absorption spectrum, corroborating the enhanced charge carrier collection by nanostructured electrodes.

Photoexcitation of conjugated poly-2,7-(9,9-dihexylfluorene) polyfluorenes with naphthylimide (NI) and anthraquinone (AQ) electron-acceptor end traps produces excitons that form charge transfer states at the end traps. Intramolecular singlet exciton transport to end traps was examined by steady state fluorescence for polyfluorenes of 17-127 repeat units in chloroform, dimethylformamide (DMF), tetrahydrofuran (THF), and p-xylene. End traps capture excitons and form charge transfer (CT) states at all polymer lengths and in all solvents. The CT nature of the end-trapped states is confirmed by their fluorescence spectra, solvent and trap group dependence, and DFT descriptions. Quantum yields of CT fluorescence are as large as 46%. This strong CT emission is understood in terms of intensity borrowing. Energies of the CT states from onsets of the fluorescence spectra give the depths of the traps which vary with solvent polarity. For NI end traps, the trap depths are 0.06 (p-xylene), 0.13 (THF), and 0.19 eV (CHCl3). For AQ, CT fluorescence could be observed only in p-xylene where the trap depth is 0.27 eV. Quantum yields, emission energies, charge transfer energies, solvent reorganization, and vibrational energies were calculated. Fluorescence measurements on chains >100 repeat units indicate that end traps capture ∼50% of the excitons, and that the exciton diffusion length is LD = 34 nm, which is much larger than diffusion lengths reported in polymer films or than previously known for diffusion along isolated chains. The efficiency of exciton capture depends on chain length but not on trap depth, solvent polarity, or which trap group is present.

Polymers are desirable optoelectronic materials, stemming from their solution processability, tunable electronic properties, and large absorption coefficients. An exciting development is the recent discovery that singlet fission (SF), the conversion of a singlet exciton to a pair of triplet states, can occur along the backbone of an individual conjugated polymer chain. Compared to other intramolecular SF compounds, the nature of the triplet pair state in SF polymers remains poorly understood, hampering the development of new materials with optimized excited state dynamics. Here, we investigate the effect of solvent polarity on the triplet pair dynamics in the SF polymer polybenzodithiophene-thiophene-1,1-dioxide. We use transient emission measurements to study isolated polymer chains in solution and use the change in the solvent polarity to investigate the role of charge transfer character in both the singlet exciton and the triplet pair multiexciton. We identify both singlet fluorescence and direct triplet pair emission, indicating significant symmetry breaking. Surprisingly, the singlet emission peak is relatively insensitive to solvent polarity despite its nominal “charge-transfer” nature. In contrast, the redshift of the triplet pair energy with increasing solvent polarity indicates significant charge transfer character. While the energy separation between singlet and triplet pair states increases with solvent polarity, the overall SF rate constant depends on both the energetic driving force and additional environmental factors. The triplet pair lifetime is directly determined by the solvent effect on its overall energy. The dominant recombination channel is a concerted, radiationless decay process that scales as predicted by a simple energy gap law.

Inspired by the analysis of Kohn–Sham energy densities by Nakai and coworkers, we extended the energy density analysis to linear-response time-dependent density functional theory (LR-TDDFT) calculations.

Density functional theory (DFT) methods are the working horse in screening new catalytic materials. They are widely used to predict trends in binding energies, which are then used to compare the activity of different materials. The binding strength of CO is an important descriptor to the CO2 reduction catalytic activity of the single transition metal atoms embedded on nitrogen-doped graphene (TM/NG). In this work, however, we show that CO binding strengths in different TM/NG has very different sensitivity to DFT methods. Specifically, Fe/NG CO binding energy changes dramatically with the percentage of exact exchange in the functional; Co/NG does less so, while Ni/NG nearly has no change. Such varying behaviors is a direct result of different local spin configurations, similar to the performance of DFT methods for metal porphyrin complexes. Therefore, caution should be exercised when using DFT binding energies for quantitative predictions in TM/NG single atom catalysis.

We present the calculation of nuclear magnetic resonance shielding constants using a range of different methods. In particular we examine two new methods proposed by Yang and Wu which are based on the Kohn–Sham potential. The first is a method which reproduces an accurate input density (WY) and the second is an implementation of the optimised effective potential method. We find that these methods give results which are very similar to each other and when the methods are applied to a hybrid functional (e.g. B3LYP) we obtain good agreement with experiment.

Abstract We have applied two of our recently developed methods for calculating accurate Kohn–Sham potentials, namely direct optimization of non-interacting kinetic energy of a known electron density and the asymptotic correction of approximate exchange-correlation potentials, to the calculation of excitation energies within time-dependent density functional theory. Our asymptotic correction method is found not to be adequate in improving Rydberg state results, probably because the potential is still affected by the approximate energy functional due to the variational nature of the method. However, Kohn–Sham potentials calculated from coupled cluster singles and doubles densities give excellent results for the He and Be atoms, and consistently much improved results for molecules. Acknowledgement This work has been supported by the National Science Foundation. Notes This paper is dedicated to Professor Nicholas Handy on the occasion of his 63rd birthday. Additional informationNotes on contributorsWeitao Yang * This paper is dedicated to Professor Nicholas Handy on the occasion of his 63rd birthday.

We systematically investigate the capability of hybrid functionals for describing charge self-localization in conjugated polymers, using the critical test that the spatial extension of a localized charge should be polymer length independent. We first compare the new long-range corrected (LRC) hybrids with conventional global hybrids and find that the former has a clear and important advantage over the latter in being significantly less spin contaminated. We then focus on LRC hybrids and investigate in detail the dependence of charge localization on the range parameter. We show that this parameter consistently needs to be about 0.2 bohr−1 or larger to produce self-localized charges across different polymers. We introduce a new measure to determine the charge localization length, and then consider how properties related to localized charges converge with the polymer length and how they depend on the range parameter. These properties include the reorganization energy in the Marcus theory for electron transfer and the lowest excitation energy of a polaron. We discuss parameter tuning to experimental results and also suggest 0.2 bohr−1 without tuning for exploratory studies based on the preference for least spin contaminations.

A series of both enantiomers of chiral β-amino acid ester derivatives containing a 4-(piperidin-1-yl)pyrimidine moiety was prepared in high yield and excellent enantioselectivity excess (up to &gt;99% enantiomeric excess) using a chiral cinchona alkaloid thiourea catalyst under one-pot solvent-free conditions. Antiviral bioassay experimental results showed that some of the chiral products exhibited higher antiviral activities against tobacco mosaic virus (TMV) in vivo than the commercial antiviral agent ningnanmycin.

Abstract A series of novel chiral 5-(substituted aryl)-1,3,4-thiadiazole derivatives was synthesized in an enantioselective three-component Mannich reaction using cinchona alkaloid squaramide catalyst with excellent enantioselectivities (up to &gt;99% enantiomeric excess (ee)). The bioassay results showed that these derivatives possessed good to excellent activities against tobacco mosaic virus (TMV).

In this article, we report a scheme to analyze and visualize the energy density fluctuations during the real-time time-dependent density functional theory (RT-TDDFT) simulations. Using Ag4-N2 complexes as examples, it is shown that the grid-based Kohn-Sham energy density can be computed at each time step using a procedure from Nakai and coworkers. Then the instantaneous energy of each molecular fragment (such as Ag4 and N2) can be obtained by partitioning the Kohn-Sham energy densities using Becke or fragment-based Hirshfeld (FBH) scheme. A strong orientation-dependence is observed for the energy flow between the Ag4 cluster and a nearby N2 molecule in the RT-TDDFT simulations. Future applications of such an energy density analysis in electron dynamics simulations are discussed.

Abstract Weak binding of hydrogen atoms to the 2H‐MoS 2 basal plane renders MoS 2 inert as an electrocatalyst for the hydrogen evolution reaction. Transition‐metal doping can activate neighboring sulfur atoms in the MoS 2 basal plane to bind hydrogen more strongly. Our theoretical studies show strong variation in the degree of activation by dopants across the 3d transition‐metal series. To understand the trends in activation, we propose a model based on the electronic promotion energy required to partially open the full valence shell of a local S atom and therefore enable it to bond with a H atom. In general, the promotion is achieved through an electron transfer from the S to neighboring metal‐atom sites. Furthermore, we demonstrate a specific, electronic‐structure‐based descriptor for the hydrogen‐binding strength: Δ dp , the local interband energy separation between the lowest empty d‐states on the dopant metal atoms and occupied p‐states on S. This model can be used to provide guidelines for chalcogen activation in future catalyst design based on doped transition‐metal dichalcogenides.

Redox flow batteries (RFBs) have emerged as a promising option for large-scale energy storage, owing to their high energy density, low cost, and environmental benefits. However, the identification of organic compounds with high redox activity, aqueous solubility, stability, and fast redox kinetics is a crucial and challenging step in developing an RFB technology. Density functional theory-based computational materials prediction and screening is a time-consuming and computationally expensive technique, yet it has a high success rate. To speed up the discovery of new materials with desired properties, machine-learning-based models can be trained on large data sets. Graph neural networks (GNNs) are particularly well-suited for non-Euclidean data and can model complex relationships, making them ideal for accelerating the discovery of novel materials. In this study, a GNN-based model called MolGAT was developed to predict the redox potential of organic molecules using molecular structures, atomic properties, and bond attributes. The model was trained on a data set of over 15,000 compounds with redox potentials ranging from -4.11 to 2.56. MolGAT outperformed other GNN variants, such as the Graph Attention Network, Graph Convolution Network, and AttentiveFP models. The trained model was used to screen a vast chemical data set comprising 581,014 molecules, namely OMDB, QM9, ZINC, CHEMBL, and DELANEY, and identified 23,467 potential redox-active compounds for use in redox flow batteries. Of those, 20,716 molecules were identified as potential catholytes with predicted redox potentials up to 2.87 V, while 2,751 molecules were deemed potential anolytes with predicted redox potentials as low as -2.88 V. This work demonstrates the capabilities of graph neural networks in condensed matter physics and materials science to screen promising redox-active species for further electronic structure calculations and experimental testing.

Bimolecular equilibria measured the one-electron reduction potentials and triplet free energies (∆G°T) of oligo(9,9-dihexyl)fluorenes and a polymer with lengths of n=1-10 and 57 repeat units.Accurate oneelectron potentials can be measured electrochemically only for the shorter oligomers.Starting at n=1 the free energies change rapidly with increasing length and become constant for lengths longer than the delocalization length.Both the reduction potentials and triplet energies can be understood as the sum of a free energy for a fixed polaron and a positional entropy.The positional entropy increases gradually with length beyond the delocalization length due the possible occupation sites of the charge or the triplet exciton.The results reinforce the view that charges and triplet excitons in conjugated chains exist as polarons and find that positional entropy can replace a popular empirical model of the energetics.

Coexistence of high local charge mobility and an energy gradient can lead to efficient free charge carrier generation from geminate charge transfer states at the donor–acceptor interface in bulk heterojunction organic photovoltaics. It is, however, not clear what polymer microstructures can support such coexistence. Using recent methods from density functional theory, we propose that a stack of similarly curved oligothiophene chains can deliver the requirements for efficient charge separation. Curved stacks are stable because of the polymer’s strong π-stacking ability and because backbone torsions are flexible in neutral chains. However, energy of a charge in a polymer chain has remarkably stronger dependence on torsions. The trend of increasing planarity in curved stacks effectively creates an energy gradient that drives charge in one direction. The curvature of these partially ordered stacks is found to beneficially interact with fullerenes for charge separation. The curved stacks, therefore, are identified as possible building blocks for interfacial structures that lead to efficient free carrier generation in high-performing organic photovoltaic systems.

We examine interatomic interactions for rare gas dimers using the density-based energy decomposition analysis (DEDA) in conjunction with computational results from CCSD(T) at the complete basis set (CBS) limit. The unique DEDA capability of separating frozen density interactions from density relaxation contributions is employed to yield clean interaction components, and the results are found to be consistent with the typical physical picture that density relaxations play a very minimal role in rare gas interactions. Equipped with each interaction component as reference, we develop a new three-term molecular mechanical force field to describe rare gas dimers: a smeared charge multipole model for electrostatics with charge penetration effects, a B3LYP-D3 dispersion term for asymptotically correct long-range attractions that is screened at short-range, and a Born-Mayer exponential function for the repulsion. The resulted force field not only reproduces rare gas interaction energies calculated at the CCSD(T)/CBS level, but also yields each interaction component (electrostatic or van der Waals) which agrees very well with its corresponding reference value.

The analytic energy gradients of the optimized effective potential (OEP) method in density-functional theory are developed. Their implementation in the direct optimization approach of Yang and Wu [Phys. Rev. Lett. 89, 143002 (2002)] and Wu and Yang [J. Theor. Comput. Chem. 2, 627 (2003)] are carried out and the validity is confirmed by comparison with corresponding gradients calculated via numerical finite difference. These gradients are then used to perform geometry optimizations on a test set of molecules. It is found that exchange-only OEP (EXX) molecular geometries are very close to the Hartree-Fock results and that the difference between the B3LYP and OEP-B3LYP results is negligible. When the energy is expressed in terms of a functional of Kohn-Sham orbitals, or in terms of a Kohn-Sham potential, the OEP becomes the only way to perform density-functional calculations and the present development in the OEP method should play an important role in the applications of orbital or potential functionals.

A critical problem in the design of materials for organic photovoltaics is quantifying the driving force needed for efficient charge separation without losses associated with a large overpotential. Here, we directly measured the effect of the molecular driving force on the charge transfer rate in films of low-bandgap push–pull type polymers mixed with a series of fullerene-based molecular acceptors using broadband near-infrared transient absorption spectroscopy. By systematically tuning the absolute energy levels of the donor and acceptor, as well as the relative offset between them, we determine the minimum voltage loss required to achieve a high short circuit current. A molecular donor–acceptor framework provides a quantitative description of the charge transfer rate constants in our system and describes the scaling of the photogenerated current with S1–LUMO energy offset. These results point to potential efficiency gains for high performing polymer devices through recovery of additional voltage without sacrificing current output.

Kinetics of a reaction network that follows mass-action rate laws can be described with a system of ordinary differential equations (ODEs) with polynomial right-hand side. However, it is challenging to derive such kinetic differential equations from transient kinetic data without knowing the reaction network, especially when the data are incomplete due to experimental limitations. We introduce a program, PolyODENet, toward this goal. Based on the machine-learning method Neural ODE, PolyODENet defines a generative model and predicts concentrations at arbitrary time. As such, it is possible to include unmeasurable intermediate species in the kinetic equations. Importantly, we have implemented various measures to apply physical constraints and chemical knowledge in the training to regularize the solution space. Using simple catalytic reaction models, we demonstrate that PolyODENet can predict reaction profiles of unknown species and doing so even reveal hidden parts of reaction mechanisms.

Unsupported FeMo, CoMo and NiMo sulphide hydrodesulphurization (HDS) catalysts have been prepared by one or several different methods: homogeneous sulphide precipitation (HSP), inverse HSP (IHSP), comaceration (CM) and coprecipitation (CP). They have been characterised by (i) differential thermal analysis (DTA) during temperature-programmed reduction/sulphidation (TPR/S) and subsequent air oxidation (TPO), (ii) temperature-programmed sulphur extraction (TPSE), (iii) XPS and (iv) XRD. For catalysts prepared by the HSP, IHSP and CP methods the onset temperature of TPR/S decreases, and the threshold temperature of oxidation, the amount of released H2S in TPSE and the HDS activity all increase in the sequence Mo < FeMo < CoMo < NiMo. XPS reveals a change in the Co 2p3/2 and 2p3/2 binding energies for promoted catalysts with respect to pure Co9S8 and NiS, respectively. The results demonstrate a strong correlation between catalytic activities in HDS of thiophene and hydrogenation of cyclohexene on the one hand, and the reducibility of the catalysts on the other.

ipso-Arylative ring-opening polymerization of 2-bromo-8-aryl-8H-indeno[2,1-b]thiophen-8-ol monomers proceeds to Mn up to 9 kg mol-1 with conversion of the monomer diarylcarbinol groups to pendent conjugated aroylphenyl side chains (2-benzoylphenyl or 2-(4-hexylbenzoyl)phenyl), which influence the optical and electronic properties of the resulting polythiophenes. Poly(3-(2-(4-hexylbenzoyl)phenyl)thiophene) was found to have lower frontier orbital energy levels (HOMO/LUMO=-5.9/-4.0 eV) than poly(3-hexylthiophene) owing to the electron-withdrawing ability of the aryl ketone side chains. The electron mobility (ca. 2×10-3 cm2 V-1 s-1 ) for poly(3-(2-(4-hexylbenzoyl)phenyl)thiophene) was found to be significantly higher than the hole mobility (ca. 8×10-6 cm2 V-1 s-1 ), which suggests such polymers are candidates for n-type organic semiconductors. Density functional theory calculations suggest that backbone distortion resulting from side-chain steric interactions could be a key factor influencing charge mobilities.

Solubility prediction plays a crucial role in energy storage applications, such as redox flow batteries, because it directly affects the efficiency and reliability. Researchers have developed various methods that utilize quantum calculations and descriptors to predict the aqueous solubilities of organic molecules. Notably, machine learning models based on descriptors have shown promise for solubility prediction. As deep learning tools, graph neural networks (GNNs) have emerged to capture complex structure-property relationships for material property prediction. Specifically, MolGAT, a type of GNN model, was designed to incorporate n-dimensional edge attributes, enabling the modeling of intricacies in molecular graphs and enhancing the prediction capabilities. In a previous study, MolGAT successfully screened 23 467 promising redox-active molecules from a database of over 500 000 compounds, based on redox potential predictions. This study focused on applying the MolGAT model to predict the aqueous solubility (log S) of a broad range of organic compounds, including those previously screened for redox activity. The model was trained on a diverse sample of 8494 organic molecules from AqSolDB and benchmarked against literature data, demonstrating superior accuracy compared with other state of the art graph-based and descriptor-based models. Subsequently, the trained MolGAT model was employed to screen redox-active organic compounds identified in the first phase of high-throughput virtual screening, targeting favorable solubility in energy storage applications. The second round of screening, which considered solubility, yielded 12 332 promising redox-active and soluble organic molecules suitable for use in aqueous redox flow batteries. Thus, the two-phase high-throughput virtual screening approach utilizing MolGAT, specifically trained for redox potential and solubility, is an effective strategy for selecting suitable intrinsically soluble redox-active molecules from extensive databases, potentially advancing energy storage through reliable material development. This indicates that the model is reliable for predicting the solubility of various molecules and provides valuable insights for energy storage, pharmaceutical, environmental, and chemical applications.

Electrochemical ozone production (EOP), a six-electron water oxidation, offers potentially sustainable routes for value-added oxidations and disinfectants, but progress in this field is slowed by a dearth in understanding fundamental mechanisms and how to best design improved EOP catalysts. In this work, we combine experimental electrochemistry, spectroscopic detection of reactive oxygen species (ROS), oxygen anion chemical ionization mass spectrometry (CIMS), and computational quantum chemistry calculations to unveil reaction mechanisms and ascertain the key role of corrosion in EOP on nickel and antimony-doped tin oxide (Ni/Sb-SnO2, NATO) electrodes. By comparing experimental potentials with quantum chemistry predictions, hydrogen peroxide is identified as a critical reaction intermediate, and the presence of nickel dopants in NATO catalyzes hydrogen peroxide into solution-phase hydroperoxyl radicals that can be subsequently oxidized into ozone. Isotopic analyses of products show that oxygen atoms in the generated ozone are from both water and the metal oxide lattice. The time evolution of isotopic composition indicates that as NATO catalysts corrode, lattice oxygen is not regenerated. Further analysis suggests that the electrochemical corrosion of tin oxide itself might generate hydrogen peroxide and tin(IV) hydroxide. These implications point to fundamental technological limitations that must be addressed for electrochemical water purification and other future advanced oxidation processes.

Electrochemical ozone production (EOP) is intriguing as a sustainable route for gen- erating powerful chemical oxidants and disinfectants, but atomic scale details of EOP mechanisms on nickel and antimony doped SnO2 (NATO) electrocatalysts have been unclear. We used computational quantum chemistry to evaluate the thermodynamic feasibility of six-electron water oxidation steps based on 1) the adsorbate evolving mech- anism (AEM) and the lattice oxygen mechanism (LOM). This work provides atomic scale insights into the atomic scale nature of tin oxide-based electrocatalysts under highly oxidizing potentials and how and why dopants would influence EOP catalysis on NATO. Importantly, we identify that EOP adsorbates are significantly stabilized by explicit hydrogen bonding networks that arise from H* and OH* intermediates that form from dissociated water molecules, likely over the entire SnO2 surface. The disso- ciated water network is essential to developing computational catalysis model for EOP that is qualitatively consistent with experimental observations.

All the DFT calculations are done with the Vienna Ab Initio Simulation Package (VASP) using the projector augmented wave method. The Bayesian error estimation exchange-correlation functionals (BEEF) with van der Waals interactions are employed. A plane-wave cutoff energy of 400 eV is used together with PAW-PBE potentials where semi core p states are treated as valence. All the calculations allow for spin-polarization. The structures are relaxed until the force is converged to &lt; 0.01 eV/Å. The lattice parameter of MoS2 unit cell, optimized with this functional, is 3.19 Å. A (4×4) supercell is used to model all the transition metal doped MoS2 systems studied here, including those with S vacancies. For calculations in the initial dopant structure exploration, the Brillouin zone is sampled with a 3x3x1 Monkhorst-Pack k-point mesh. A 6×6×1 Monkhorst-Pack k-point mesh is used for the H binding energy and density of states calculations. In all calculations, the vacuum layer is set as 15 Å to eliminate periodic interaction perpendicular to the basal plane.

An efficient asymmetric synthesis of chiral β-amino acid ester derivatives containing a 4-(pyridin-3-yl)pyrimidin-2-yl amine moiety was developed. This catalytic asymmetric Mannich reaction gave target products in high yields (95%) and excellent enantioselectivities (&gt;99% ee) using a cinchona-based squaramide catalyst under solvent-free, one-pot conditions. Antiviral bioassays indicated that some of the chiral products exhibited higher antiviral activities against tobacco mosaic virus than the commercial compound ribavirin.

Abstract ipso ‐Arylative ring‐opening polymerization of 2‐bromo‐8‐aryl‐8 H ‐indeno[2,1‐b]thiophen‐8‐ol monomers proceeds to M n up to 9 kg mol −1 with conversion of the monomer diarylcarbinol groups to pendent conjugated aroylphenyl side chains (2‐benzoylphenyl or 2‐(4‐hexylbenzoyl)phenyl), which influence the optical and electronic properties of the resulting polythiophenes. Poly(3‐(2‐(4‐hexylbenzoyl)phenyl)thiophene) was found to have lower frontier orbital energy levels (HOMO/LUMO=−5.9/−4.0 eV) than poly(3‐hexylthiophene) owing to the electron‐withdrawing ability of the aryl ketone side chains. The electron mobility (ca. 2×10 −3 cm 2 V −1 s −1 ) for poly(3‐(2‐(4‐hexylbenzoyl)phenyl)thiophene) was found to be significantly higher than the hole mobility (ca. 8×10 −6 cm 2 V −1 s −1 ), which suggests such polymers are candidates for n‐type organic semiconductors. Density functional theory calculations suggest that backbone distortion resulting from side‐chain steric interactions could be a key factor influencing charge mobilities.

Room-temperature ionic liquids (RTILs) are one type of electrolytes which have promising applications in batteries, catalysts, supercapacitors, etc. Computational simulations have played an essential role in elucidating many of the RTILs’ properties. Because Coulomb interactions dominate in RTILs, it is important to understand charge fluctuations, i.e., when ions’ charges are significantly less than unity. In this work, we perform calculations from density functional theory methods and the Bader charge analysis to examine ionic charges of 1-ethy-2,3-dimethylimidazolium bis(trifluoromethanesulfonyl)imide ([EMMIM]+[TFSI]−) thin film on the gold (111) surface. For cation and anion of similar sizes, we first identify the most stable ionic arrangement on Au(111) to be a checkerboard pattern. We build the thin film with up to four layers of ions in the most stable configuration and analyze the charge of each ion. In addition to cases of equal numbers of cations and anions, we also study systems where there is one more cation or anion but no net charge. We find that ions mostly maintain a near unity charge. However, when the ion numbers are not equal, and therefore the system is kept neutral by accruing counter charge on the gold, the counter charge is much less than unity, indicating charge reduction in ions. We further find that the charge deviation mostly occurs on the ion in the top layer and the reduction increases with the number of layers. We explain the results through a model of state mixing that includes charge transfer between the gold and ions.

We present a detailed theoretical study of the pathway for water oxidation in synthetic ruthenium-based catalysts. As a first step, we consider a recently discovered single center catalyst, where experimental observations suggest a purely single-center mechanism. We find low activation energies (<5 kcal/mol) for each rearrangement in the catalytic cycle. In the crucial step of O—O bond formation, a solvent water acts as a Lewis base and attacks a highly oxidized RuV−O. Armed with the structures and energetics of the single-center catalyst, we proceed to consider a representative Ru-dimer which was designed to form O2 via coupling between the two centers. We discover a mechanism that proceeds in analogous fashion to the monomer case, with all the most significant steps occurring at a single catalytic center within the dimer. This acid-base mechanism suggests a new set of strategies for the rational design of multicenter catalysts: rather than coordinating the relative orientations of the subunits, one can focus on coordinating solvation-shell water molecules or tuning redox potentials. ∗To whom correspondence should be addressed †Massachusetts Institute of Technology ‡Brookhaven National Laboratory

Abstract The HDS activity of the Co, Ni, or Fe promoted catalysts prepared by homogeneous sulphide precipitation (HSP), inverse HSP, or by coprecipitation, increases in the sequence M0 FeMo CoMo NiMo.