Self-interaction corrected SCAN functional for molecules and solids in the numeric atom-center orbital framework.

Semilocal density-functional approximations (DFAs), including the state-of-the-art SCAN functional, are plagued by the self-interaction error (SIE). While this error is explicitly defined only for one-electron systems, it has inspired the self-interaction correction method proposed by Perdew and Zunger (PZ-SIC), which has shown promise in mitigating the many-electron SIE. However, the PZ-SIC method is known for its significant numerical instability. In this study, we introduce a novel constraint that facilitates self-consistent localization of the SIC orbitals in the spirit of Edmiston-Ruedenberg orbitals [Rev. Mod. Phys. 35, 457 (1963)]. Our practical implementation within the all-electron numeric atom-centered orbitals code FHI-aims guarantees efficient and stable convergence of the self-consistent PZ-SIC equations for both molecules and solids. We further demonstrate that our PZ-SIC approach effectively mitigates the SIE in the meta-generalized gradient approximation SCAN functional, significantly improving the accuracy for ionization potentials, charge-transfer energies, and bandgaps for a diverse selection of molecules and solids. However, our PZ-SIC method does have its limitations. It cannot improve the already accurate SCAN results for properties such as cohesive energies, lattice constants, and bulk modulus in our test sets. This highlights the need for new-generation DFAs with more comprehensive applicability.

Developing correlation-consistent numeric atom-centered orbital basis sets for krypton: Applications in RPA-based correlated calculations.

Localized atomic orbitals are the preferred basis set choice for large-scale explicit correlated calculations, and high-quality hierarchical correlation-consistent basis sets are a prerequisite for correlated methods to deliver numerically reliable results. At present, numeric atom-centered orbital (NAO) basis sets with valence correlation consistency (VCC), designated as NAO-VCC-nZ, are only available for light elements from hydrogen (H) to argon (Ar) [Zhang et al., New J. Phys. 15, 123033 (2013)]. In this work, we extend this series by developing NAO-VCC-nZ basis sets for krypton (Kr), a prototypical element in the fourth row of the periodic table. We demonstrate that NAO-VCC-nZ basis sets facilitate the convergence of electronic total-energy calculations using the Random Phase Approximation (RPA), which can be used together with a two-point extrapolation scheme to approach the complete basis set limit. Notably, the Basis Set Superposition Error (BSSE) associated with the newly generated NAO basis sets is minimal, making them suitable for applications where BSSE correction is either cumbersome or impractical to do. After confirming the reliability of NAO basis sets for Kr, we proceed to calculate the Helmholtz free energy for Kr crystal at the theoretical level of RPA plus renormalized single excitation correction. From this, we derive the pressure-volume (P-V) diagram, which shows excellent agreement with the latest experimental data. Our work demonstrates the capability of correlation-consistent NAO basis sets for heavy elements, paving the way toward numerically reliable correlated calculations for bulk materials.

Improving XYG3-type doubly hybrid approximation using self-interaction corrected SCAN density and orbitals via the PZ-SIC framework: The xDH@SCAN(SIC) approach.

XYG3-type doubly hybrid (xDH) approximations have gained widespread recognition for their accuracy in describing a diverse range of chemical and physical interactions. However, a recent study [Song et al., J. Phys. Chem. Lett. 12, 800-807 (2021)] has highlighted the limitation of xDH methods in calculating the dissociation of NaCl molecules. This issue has been related to the density and orbitals used for evaluating the energy in xDH methods, which are obtained from lower-rung hybrid density functional approximations (DFAs) and display substantial density errors in the dissociation limit. In this work, we systematically investigate the influence of density on several challenging datasets and find that xDH methods are less sensitive to density errors compared to semi-local and hybrid DFAs. Furthermore, we demonstrate that the self-interaction corrected SCAN density approach offers superior accuracy compared to the self-consistent SCAN density and Hartree-Fock density approaches, as evidenced by performing charge analysis on the dissociation of heterodimers, such as NaCl and LiF. Building on these insights, we propose a five-parameter xDH method using the SCAN density and orbitals corrected by the PZ-SIC scheme. This new xDH@SCAN(SIC) method provides a balanced and accurate description across a wide range of challenging systems.

Utilization of Fe-Ethylenediamine-N,N'-Disuccinic Acid Complex for Electrochemical Co-Catalytic Activation of Peroxymonosulfate under Neutral Initial pH Conditions.

The ethylenediamine-N,N'-disuccinic acid (EDDS) was utilized to form Fe-EDDS complex to activate peroxymonosulfate (PMS) in the electrochemical (EC) co-catalytic system for effective oxidation of naphthenic acids (NAs) under neutral pH conditions. 1-adamantanecarboxylic acid (ACA) was used as a model compound to represent NAs, which are persistent pollutants that are abundantly present in oil and gas field wastewater. The ACA degradation rate was significantly enhanced in the EC/PMS/Fe(III)-EDDS system (96.6%) compared to that of the EC/PMS/Fe(III) system (65.4%). The addition of EDDS led to the formation of a stable complex of Fe-EDDS under neutral pH conditions, which effectively promoted the redox cycle of Fe(III)-EDDS/Fe(II)-EDDS to activate PMS to generate oxidative species for ACA degradation. The results of quenching and chemical probe experiments, as well as electron paramagnetic resonance (EPR) analysis, identified significant contributions of •OH, 1O2, and SO4•- in the removal of ACA. The ACA degradation pathways were revealed based on the results of high resolution mass spectrometry analysis and calculation of the Fukui index. The presence of anions, such as NO3-, Cl-, and HCO3-, as well as humic acids, induced nonsignificant influence on the ACA degradation, indicating the robustness of the current system for applications in authentic scenarios. Overall results indicated the EC/PMS/Fe(III)-EDDS system is a promising strategy for the practical treatment of NAs in oil and gas field wastewater.

Identification of Water Hexamer on Cu(111) Surfaces.

While being considered as the building block of ice on a hydrophobic metal surface, the global minimum of the water hexamer is still elusive, which has impeded our understanding of water/metal interfaces. Herein, we comprehensively investigate water hexamer on Cu(111) theoretically and propose the boat configuration as the new in situ adsorption configuration from the scanning tunneling microscope experiments. All existing experimental measurements can therefore be well reproduced. Calculations in high-level theories reveal that the boat configuration is indeed the global minimum under experimental conditions, solving a long-standing discrepancy.

Understanding band gaps of solids in generalized Kohn-Sham theory.

The fundamental energy gap of a periodic solid distinguishes insulators from metals and characterizes low-energy single-electron excitations. However, the gap in the band structure of the exact multiplicative Kohn-Sham (KS) potential substantially underestimates the fundamental gap, a major limitation of KS density-functional theory. Here, we give a simple proof of a theorem: In generalized KS theory (GKS), the band gap of an extended system equals the fundamental gap for the approximate functional if the GKS potential operator is continuous and the density change is delocalized when an electron or hole is added. Our theorem explains how GKS band gaps from metageneralized gradient approximations (meta-GGAs) and hybrid functionals can be more realistic than those from GGAs or even from the exact KS potential. The theorem also follows from earlier work. The band edges in the GKS one-electron spectrum are also related to measurable energies. A linear chain of hydrogen molecules, solid aluminum arsenide, and solid argon provide numerical illustrations.

Polyvinylpyrrolidone-Coordinated Single-Site Platinum Catalyst Exhibits High Activity for Hydrogen Evolution Reaction.

The essence of developing a Pt-based single-atom catalyst (SAC) for hydrogen evolution reaction (HER) is the preparation of well-defined and stable single Pt sites with desired electrocatalytic efficacy. Herein, we report a facile approach to generate uniformly dispersed Pt sites with outstanding HER performance via a photochemical reduction method using polyvinylpyrrolidone (PVP) molecules as the key additive to significantly simplify the synthesis and enhance the catalytic performance. The as-prepared catalyst displays remarkable kinetic activities (20 times higher current density than the commercially available Pt/C) with excellent stability (76.3 % of its initial activity after 5000 cycles) for HER. EXAFS measurements and DFT calculations demonstrate a synergetic effect, where the PVP ligands and the support together modulate the electronic structure of the Pt atoms, which optimize the hydrogen adsorption energy, resulting in a considerably improved HER activity.

Accurate heats of formation of polycyclic saturated hydrocarbons predicted by using the XYG3 type of doubly hybrid functionals.

Polycyclic saturated hydrocarbons (PSHs) are attractive candidates as hydrocarbon propellants. To assess their potential values, one of the key factors is to determine their energy contents, such as to calculate their heats of formation (HOF). In this work, we have calculated HOFs for a set of 36 PSHs including exo-Tricyclo[5.2.1.0(2,6) ] decane, the principal component of the high-energy density hydrocarbon fuel commonly identified as JP-10. The results from B3LYP, B3LYP-D3BJ, M06-2X, B2PLYP, B2PLYP-D3BJ, and the XYG3 type of doubly hybrid (xDH) functionals are presented. It is demonstrated here that the xDH functionals yield accurate HOFs in good agreement with those from experiments or the G4 theory. In particular, XYGJ-OS, a low scaling xDH functional, is shown to hold the promise for accurate prediction of HOFs for PSHs of larger sizes. © 2018 Wiley Periodicals, Inc.

Resolving the chemical identity of H2SO4 derived anions on Pt(111) electrodes: they're sulfate.

Understanding how electrolyte composition controls electrocatalytic reactions requires molecular-level insight into electrode/electrolyte interaction. Perhaps the most basic aspect of this interaction, the speciation of the interfacial ion, is often controversial for even relatively simple systems. For example, for Pt(111) in 0.5 M H2SO4 it has long been debated whether the adsorbed anion is SO42-, HSO4- or an H3O+SO42- ion pair. Here we apply interface-specific vibrational sum frequency (VSF) spectroscopy and theory to this problem and perform an isotope exchange study: we collect VSF spectra of Pt(111) in H2SO4(H2O) and D2SO4(D2O) as a function of bias and show that at all potentials they are identical. This is the most direct spectroscopic evidence to date that SO42- is the dominant adsorbate, despite the fact that at 0.5 M H2SO4 bulk solution is dominated by HSO4-. This approach is based on the unique selection rule of the VSF spectroscopy and thus offers a new way of accessing general electrode/electrolyte interaction in electrocatalysis.

Understanding the Nonplanarity in Aromatic Metallabenzenes: A σ-Control Mechanism.

Metallabenzenes, the organometallic counterparts of benzene with one of the C atoms being replaced by a metal atom, expand the family of aromatics and further create prospective candidates for novel applications as functional materials. One intriguing feature of these complexes is that their MC5 rings do not always constrict into a planar configuration as in the C6 ring of benzene. Such a deviation has often been attributed to the unfavorable antibonding interactions between an occupied metal d orbital and the π orbitals of the C5 moiety. We herein scrutinize the frontier orbital interactions in both σ and π spaces in a plethora of metallabenzene complexes using extensive density functional theory calculations. Unexpectedly, the nonplanarity in metallabenzenes is found to be hardly related to the π orbitals. It is the antibonding interaction between an occupied metal d orbital and the σ orbitals of the C5 moiety that dominates the observed distortion. Such a σ-control mechanism not only provides an explanation for the commonly observed nonplanarity in metallabenzenes but also points out a novel direction toward the rational design of functional materials with enhanced metalla-aromaticity.

Towards Efficient Orbital-Dependent Density Functionals for Weak and Strong Correlation.

We present a new paradigm for the design of exchange-correlation functionals in density-functional theory. Electron pairs are correlated explicitly by means of the recently developed second order Bethe-Goldstone equation (BGE2) approach. Here we propose a screened BGE2 (sBGE2) variant that efficiently regulates the coupling of a given electron pair. sBGE2 correctly dissociates H_{2} and H_{2}^{+}, a problem that has been regarded as a great challenge in density-functional theory for a long time. The sBGE2 functional is then taken as a building block for an orbital-dependent functional, termed ZRPS, which is a natural extension of the PBE0 hybrid functional. While worsening the good performance of sBGE2 in H_{2} and H_{2}^{+}, ZRPS yields a remarkable and consistent improvement over other density functionals across various chemical environments from weak to strong correlation.

Insight into organic reactions from the direct random phase approximation and its corrections.

The performance of the random phase approximation (RPA) and beyond-RPA approximations for the treatment of electron correlation is benchmarked on three different molecular test sets. The test sets are chosen to represent three typical sources of error which can contribute to the failure of most density functional approximations in chemical reactions. The first test set (atomization and n-homodesmotic reactions) offers a gradually increasing balance of error from the chemical environment. The second test set (Diels-Alder reaction cycloaddition = DARC) reflects more the effect of weak dispersion interactions in chemical reactions. Finally, the third test set (self-interaction error 11 = SIE11) represents reactions which are exposed to noticeable self-interaction errors. This work seeks to answer whether any one of the many-body approximations considered here successfully addresses all these challenges.

A fast doubly hybrid density functional method close to chemical accuracy using a local opposite spin ansatz.

We develop and validate the XYGJ-OS functional, based on the adiabatic connection formalism and Görling-Levy perturbation theory to second order and using the opposite-spin (OS) ansatz combined with locality of electron correlation. XYGJ-OS with local implementation scales as N(3) with an overall accuracy of 1.28 kcal/mol for thermochemistry, bond dissociation energies, reaction barrier heights, and nonbonded interactions, comparable to that of 1.06 kcal/mol for the accurate coupled-cluster based G3 method (scales as N(7)) and much better than many popular density functional theory methods: B3LYP (4.98), PBE0 (4.36), and PBE (12.10).

Analytic derivatives for the XYG3 type of doubly hybrid density functionals: Theory, implementation, and assessment.

We present a theoretical development of the equations required to perform an analytic geometry optimization of a molecular system using the XYG3 type of doubly hybrid (xDH) functionals. In contrast to the well-established B2PLYP type of DH functionals, the energy expressions in the xDH functionals are constructed by using density and orbital information from another standard Kohn-Sham (KS) functional (e.g., B3LYP) for doing the self-consistent field calculations. Thus, the xDH functionals are nonvariational in both the hybrid density functional part and the second-order perturbation part, each of which requires formally to solve a coupled-perturbed KS equation. An implementation is reported here which combines the two parts by defining a total Lagrangian such that only a single set of the Z-vector equations need to be solved. The computational cost with our implementation is of the same order as those for the conventional Møller-Plesset theory to the second order (MP2) and B2PLYP. Systematic test calculations are provided for covalently bonded molecules as well as compounds involving the intramolecular nonbonded interactions for the main group elements. Satisfactory performance of the xDH functionals demonstrates that the extra computer time on top of the conventional KS procedure is well-invested, in particular, when the standard KS functionals and MP2 as well, are problematic.

Nonfitting protein-ligand interaction scoring function based on first-principles theoretical chemistry methods: development and application on kinase inhibitors.

Targeted therapy is currently a hot topic in the fields of cancer research and drug design. An important requirement for this approach is the development of potent and selective inhibitors for the identified target protein. However, current ways to estimate inhibitor efficacy rely on empirical protein-ligand interaction scoring functions which, suffering from their heavy parameterizations, often lead to a low accuracy. In this work, we develop a nonfitting scoring function, which consists of three terms: (1) gas-phase protein-ligand binding enthalpy obtained by the eXtended ONIOM hybrid method based on an integration of density functional theory (DFT) methods (XYG3 and ωB97X-D) and the semiempirical PM6 method, (2) solvation free energy based on DFT-SMD solvation model, and (3) entropy effect estimated by using DFT frequency analysis. The new scoring function is tested on a cyclin-dependent kinase 2 (CDK2) inhibitor database including 76 CDK2 protein inhibitors and a p21-activated kinase 1 (PAK1) inhibitor database including 20 organometallic PAK1 protein inhibitors. From the results, good correlations are found between the calculated scores and the experimental inhibitor efficacies with the square of correlation coefficient R(2) of 0.76-0.88. This suggests a good predictive power of this scoring function. To the best of our knowledge, this is the first high level theory-based nonfitting scoring function with such a good level of performance. This scoring function is recommended to be used in the final screening of lead structure derivatives.

Accurate prediction of nuclear magnetic resonance shielding constants: towards the accuracy of CCSD(T) complete basis set limit.

In this work, we have calculated the nuclear magnetic resonance (NMR) shielding constants for 42 molecules at the levels of second order Mo̸ller-Plesset perturbation (MP2) and coupled-cluster singles and doubles model augmented by perturbative corrections for triple excitations CCSD(T). Basis set extrapolations to the complete basis set (CBS) limit have been performed. A focal-point analysis method for magnetic parameters was proposed here, which adds the [σ(e)(CCSD(T)) - σ(e)(MP2)] difference to the MP2∕CBS number to approximate the corresponding CCSD(T)∕CBS value. Systematical comparison has demonstrated the usefulness of this FPA-M∕CBS scheme.

Pulsed versus direct current electrochemical co-catalytic peroxymonosulfate-based system: Elevated degradation and energy efficiency with enhanced oxidation mechanisms.

In this work, the pulsed electrochemical (PE) system was investigated to activate peroxymonosulfate (PMS) with the addition of Fe(III) to achieve efficient degradation of sulfamethoxazole (SMX) with reduced energy consumption, in comparison with the direct current (DC) electrochemical system. The operational conditions of PE/PMS/Fe(III) system were optimized as 4 kHz pulse frequency, 50% duty cycle, and pH 3, at which 67.6% reduction of energy consumption and enhanced degradation performance were achieved compared to the DC/PMS/Fe(III) system. Results of electron paramagnetic resonance spectroscopy analysis and quenching and chemical probe experiment revealed the presence of •OH, SO4•-, and 1O2 in the system, with •OH being the dominant role. The concentrations of these active species were averagely 15 ± 1% higher in the PE/PMS/Fe(III) system than those of the DC/PMS/Fe(III) system. Identification of SMX byproducts was achieved based on high resolution mass spectrometry analysis to predict the degradation pathways. The SMX byproducts could eventually be eliminated by the PE/PMS/Fe(III) system with extended treatment time. Overall, the PE/PMS/Fe(III) system was demonstrated with high energy and degradation performance, and is appear to be an robust strategy for practical treatment of wastewater.

Efficient removal of recalcitrant naphthenic acids with electro-cocatalytic activation of peroxymonosulfate by Fe(III)-nitrilotriacetic acid complex under neutral initial pH condition.

This work investigated the activation of peroxymonosulfate by electrochemical (EC) system assisted with Fe(III)-nitrilotriacetic acid (NTA) complex for degradation of persistent naphthenic acids (NAs) under neutral initial pH conditions. As NAs are a complicated mixture, 1-adamantanecarboxylic acid (ACA) was selected as the model NA compound for degradation experiment. The addition of NTA is to chelate with Fe(III), gaining stability under neutral pH condition to facilitate the circulation of Fe(II)/Fe(III) by the electrochemical process to activate PMS. The EC/Fe(III)-NTA/PMS system was explored with applicable pH range of 3-9 and an optimized molar ratio 1: 2 for Fe: NTA. Results of quenching and chemical probe experiment together with results of electron paramagnetic resonance (EPR) analysis revealed the main reactive species of the system, including •OH, SO4•-, 1O2 and possibly Fe(IV). With the addition of NTA, the yields of •OH, SO4•-, 1O2 were enhanced. Results of mass spectrometry analysis and DFT calculations indicated the formation of 9 degradation byproducts of ACA via three primary degradation pathways such as hydroxyl substitution, carbonyl substitution, and decarboxylation. Furthermore, the EC/Fe(III)-NTA/PMS system could achieve excellent removal efficiency of ACA with different anions such as Cl-, HCO3-, NO3- and H2PO4- in the background. The practical applicability of the system was also verified with the high removal of commercial NAs mixture standard. Overall results have indicated the EC/Fe(III)-NTA/PMS system could be utilized for efficient reclamation of authentic oil and gas industrial wastewater under natural pH conditions.

Hydrogen sulfide functions as a micro-modulator bound at the copper active site of Cu/Zn-SOD to regulate the catalytic activity of the enzyme.

The present study examines whether there is a mechanism beyond the current concept of post-translational modifications to regulate the function of a protein. A small gas molecule, hydrogen sulfide (H2S), was found to bind at active-site copper of Cu/Zn-SOD using a series of methods including radiolabeled binding assay, X-ray absorption near-edge structure (XANES), and crystallography. Such an H2S binding enhanced the electrostatic forces to guide the negatively charged substrate superoxide radicals to the catalytic copper ion, changed the geometry and energy of the frontier molecular orbitals of the active site, and subsequently facilitated the transfer of an electron from the superoxide radical to the catalytic copper ion and the breakage of the copper-His61 bridge. The physiological relevance of such an H2S effect was also examined in both in vitro and in vivo models where the cardioprotective effects of H2S were dependent on Cu/Zn-SOD.

XO: an extended ONIOM method for accurate and efficient modeling of large systems.

Calculation of large complex systems remains to be a great challenge, where there is always a trade-off between accuracy and efficiency. Recently, we proposed the extended our own n-layered integrated molecular orbital (ONIOM) method (XO) (Guo, Wu, Xu, Chem. Phys. Lett. 2010, 498, 203) which surmounts some inherited limitations of the popular ONIOM method by introducing the inclusion-exclusion principle used in the fragmentation methods. The present work sets up general guidelines for the construction of a good XO scheme. In particular, force-error test is proposed to quantitatively validate the usefulness of an XO scheme, taking accuracy, efficiency and scalability all into account. Representative studies on zeolites, polypeptides and cyclodextrins have been carried out to demonstrate how to strive for high accuracy without sacrificing efficiency. As a natural extension, XO is applied to calculate the total energy, fully optimized geometry and vibrational spectra of the whole system, where ONIOM becomes inapplicable.