Evaluation of the Performance of the B3LYP, PBE0, and M06 DFT Functionals, and DBLOC-Corrected Versions, in the Calculation of Redox Potentials and Spin Splittings for Transition Metal Containing Systems

Chiroptical Activity Amplification of Chiral Metal Nanoclusters via Surface/Interface Solidification

It remains a grand challenge to amplify the chiroptical activity of chiral metal nanoclusters (NCs) although it is desirable for fundamental research and practical application. Herein, we report a strategy of surface/interface solidification (SIS) for enhancing the chiroptical activity of gold NCs. Structural analysis of [Au19(2R,4R/2S,4S-BDPP)6Cl2]3+ (BDPP is 2,4-bis(diphenylphosphino)pentane) clusters reveals that one of the interfacial gold atoms is flexible between two sites and large space is present on the surface, thus hampering chirality transfer from surface chiral ligands to metal core and leading to low chiroptical activity. Following SIS by filling the flexible sites and replacing chlorides with thiolate ligands affords another pair of [Au20(2R,4R/2S,4S-BDPP)6(4-F-C6H4S)2]4+, which shows a more compact and organized structure and thus an almost 40-fold enhancement of chiroptical activity. This work not only provides an efficient approach for amplifying the chiroptical activity of metal nanoclusters but also highlights the significance of achiral components in shaping chiral nanostructures.

A systematic DFT study of structure and electronic properties of titanium dioxide

DFT functionals are of paramount importance for an accurate electronic and structural description of transition metal systems. In this work, a systematic analysis using some well-known and commonly used DFT functionals is performed. A comparison of the structural and energetic parameters calculated with the available experimental data is made in order to find the adequate functional for an accurate description of the TiO2 bulk and surface of both anatase and rutile structures. In the absence of experimental data on the surface energy, the theoretical predictions obtained using the high-accuracy HSE06 functional were used as a reference to compare against the surface energy values calculated with the other DFT functionals. A clear improvement in the electronic description of both anatase and rutile was observed by introducing the Hubbard U correction term to PBE, PW91, and OptPBE functionals. The OptPBE-U4 functional was found to offer a good compromise between accurately describing the structural and electronic properties of titania.

A Theoretical Benchmark of the Geometric and Optical Properties for 3d Transition Metal Nanoclusters via Density Functional Theory

Understanding structure-property relationships in atomically precise metal nanoclusters is vital in finding selective and tunable catalysts. In this study, density functional theory (DFT) was used to benchmark seven exchange correlation functionals at different basis sets for 17 atomically precise nanoclusters against experimentally determined geometries, band gaps, and optical gaps. The set contains both monometallic and bimetallic clusters that possess at least two types of 3d transition metals (specifically, Cu, Ni, Fe, or Co). The benchmark highlights that PBE0 is a good functional to use regardless of the basis set, and Minnesota functionals do well with respect to specific metals. Further, while long-range corrected functionals overestimate band and optical gaps, they model absorption features better than the other considered functionals. The study additionally looks at the photoinduced hydrogen evolution reaction (HER) and the CO2 reduction mechanism on nanoclusters reported from the literature.

Theoretical Evaluation of Fluorinated Resazurin Derivatives for In Vivo Applications

Primarily owing to the pronounced fluorescence exhibited by its reduced form, resazurin (also known as alamarBlue®) is widely employed as a redox sensor to assess cell viability in in vitrostudies. In an effort to broaden its applicability for in vivo studies, molecular adjustments are necessary to align optical properties with the near-infrared imaging window while preserving redox properties. This study delves into the theoretical characterisation of a set of fluorinated resazurin derivatives proposed by Kachur et al., 2015 examining the influence of fluorination on structural and electrochemical properties. Assuming that the conductor-like polarisable continuum model mimics the solvent effect, the density functional level of theory combining M06-2X/6-311G* was used to calculate the redox potentials. Furthermore, (TD-)DFT calculations were performed with PBE0/def2-TZVP to evaluate nucleophilic characteristics, transition states for fluorination, relative energies, and fluorescence spectra. With the aim of exploring the potential of resazurin fluorinated derivatives as redox sensors tailored for in vivo applications, acid-base properties and partition coefficients were calculated. The theoretical characterisation has demonstrated its potential for designing novel molecules based on fundamental principles.

Magnetic solid phase extraction coupled to HPLC-UV for highly sensitive analysis of mono-hydroxy polycyclic aromatic hydrocarbons in urine

BACKGROUND

As a common pollutant, the carcinogenic properties of polycyclic aromatic hydrocarbons have garnered considerable attention. Trace metabolites of polycyclic aromatic hydrocarbons can be detected in urine as a non-invasively approach to monitor the exposure level. Nonetheless, the urine samples have the disadvantages of being large in volume and containing numerous impurities. Given the growing demand to study metabolites with low abundance and potential biomarkers, there is a pressing need for a preconcentration and high-throughput technique for effectively handling complex liquid samples.

RESULTS

Polystyrene-coated magnetic nanoparticles were used to establish a novel magnetic extraction method for monohydroxy polycyclic aromatic hydrocarbons in urine samples. Polystyrene magnetic nanoparticles are an ideal absorbent for solid-phase extraction. After the material was mixed with the sample and adsorbed the target analyte, the analytes on the material were eluted and quantified using high-performance liquid chromatography. Influencing factors were optimized, and the proposed method achieved desirable sensitivity in analyzing low-abundance metabolites in large volumes of complex urine samples. The recoveries of intra-day and inter-day were 78.0-118.0 % and 81.0 %-115.0 %, respectively. The intra-day and inter-day reproducibility were less than 4.5 % and 8.6 %, respectively. The limits of detection were in the range of 0.009-0.041 ng mL-1, and the limits of quantification were in the range of 0.030-0.135 ng mL-1.

SIGNIFICANCE AND NOVELTY

The application of reusable polystyrene-coated magnetic solid-phase nanoparticles as adsorbents makes the extraction of monohydroxy polycyclic aromatic hydrocarbons from urine samples economical and environmentally benign. The proposed method is simple, sensitive, and efficient compared to existing techniques. The nanoparticles are easy to prepare, showing potential for rapid screening of complex bulk bio-samples in batches with high efficiency and low budget.

Theoretical Insights into the Generation Mechanism of the Tyr122 Radical Catalyzed by Intermediate X in Class Ia Ribonucleotide Reductase

Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides to deoxyribonucleotides in all organisms. There is an ∼35 Å long-range electron-hole transfer pathway during the catalytic process of class Ia RNR, which can be described as Tyr122β ↔ [Trp48β]? ↔ Tyr356β ↔ Tyr731α ↔ Tyr730α ↔ Cys439α. The formation of the Y122• radical initiates this long-range radical transfer process. However, the generation mechanism of Y122• is not yet clear due to confusion over the intermediate X structures. Based on the two reported X structures, we examined the possible mechanisms of Y122• generation by density functional theory (DFT) calculations. Our examinations revealed that the generation of the Y122• radical from the two different core structures of X was via a similar two-step reaction, with the first step of proton transfer for the formation of the proton receptor of Y122 and the second step of a proton-coupled long-range electron transfer reaction with the proton transfer from the Y122 hydroxyl group to the terminal hydroxide ligand of Fe1III and simultaneously electron transfer from the side chain of Y122 to Fe2IV. These findings provide an insight into the formation mechanism of Y122• catalyzed by the double-iron center of the β subunit of class Ia RNR.

One-step preparation of Pt/Ag nanoclusters for CO2 transformation

Structurally precise metal nanoclusters with a facile synthetic process and high catalytic performance have been long pursued. These atomically precise nanocatalysts are regarded as model systems to study structure-performance relationships, surface coordination chemistry, and the reaction mechanism of heterogeneous metal catalysts. Nevertheless, the research on silver-based nanoclusters for driving chemical transformations is sluggish in comparison to gold counterparts. Herein, we report the one-step synthesis of Pt/Ag alloy nanoclusters of [PtAg9(C18H12Br3P)7Cl3](C18H12Br3P), which are highly active in catalysing cycloaddition reactions of CO2 and epoxides. The cluster was obtained in a rather simple way with the reduction of silver and platinum salts in the presence of ligands in one pot. The molecular structure of the titled cluster describes the protection of the Pt-centred Ag9 crown by the shell of phosphine ligands and halides. Its electronic structure, as revealed by density function theoretical calculations, adopts a superatomic geometry with 1S21P6 configuration. Interestingly, the cluster displays high activity in the formation of cyclic carbonates from CO2 under mind conditions.

Toward Benchmark-Quality Ab Initio Predictions for 3d Transition Metal Electrocatalysts: A Comparison of CCSD(T) and ph-AFQMC

Generating accurate ab initio ionization energies for transition metal complexes is an important step toward the accurate computational description of their electrocatalytic reactions. Benchmark-quality data is required for testing existing theoretical methods and developing new ones but is complicated to obtain for many transition metal compounds due to the potential presence of both strong dynamical and static electron correlation. In this regime, it is questionable whether the so-called gold standard, coupled cluster with singles, doubles, and perturbative triples (CCSD(T)), provides the desired level of accuracy─roughly 1-3 kcal/mol. In this work, we compiled a test set of 28 3d metal-containing molecules relevant to homogeneous electrocatalysis (termed 3dTMV) and computed their vertical ionization energies (ionization potentials) with CCSD(T) and phaseless auxiliary-field quantum Monte Carlo (ph-AFQMC) in the def2-SVP basis set. A substantial effort has been made to converge away the phaseless bias in the ph-AFQMC reference values. We assess a wide variety of multireference diagnostics and find that spin-symmetry breaking of the CCSD wave function and the PBE0 density functional correlate well with our analysis of multiconfigurational wave functions. We propose quantitative criteria based on symmetry breaking to delineate correlation regimes inside of which appropriately performed CCSD(T) can produce mean absolute deviations from the ph-AFQMC reference values of roughly 2 kcal/mol or less and outside of which CCSD(T) is expected to fail. We also present a preliminary assessment of density functional theory (DFT) functionals on the 3dTMV set.

Lewis Acids and Electron-Withdrawing Ligands Accelerate CO Coordination to Dinuclear CuI Compounds

A series of dinuclear molecular copper complexes were prepared and used to model the binding and Lewis acid stabilization of CO in heterogeneous copper CO₂ reduction electrocatalysts. Experimental studies (including measurement of rate and equilibrium constants) and electronic structure calculations suggest that the key kinetic barrier for CO binding may be a σ-interaction between Cu^I and the incoming CO ligand. The rate of CO coordination can be increased upon the addition of Lewis acids or electron-withdrawing substituents on the ligand backbone. Conversely, K_eq for CO coordination can be increased by adding electron density to the metal centers of the compound, consistent with stronger π-backbonding. Finally, the electrochemically measured kinetic results were mapped onto an electrochemical zone diagram to illustrate how these system changes enabled access to each zone.

Insights into the deviation from piecewise linearity in transition metal complexes from supervised machine learning models

Virtual high-throughput screening (VHTS) and machine learning (ML) with density functional theory (DFT) suffer from inaccuracies from the underlying density functional approximation (DFA). Many of these inaccuracies can be traced to the lack of derivative discontinuity that leads to a curvature in the energy with electron addition or removal. Over a dataset of nearly one thousand transition metal complexes typical of VHTS applications, we computed and analyzed the average curvature (i.e., deviation from piecewise linearity) for 23 density functional approximations spanning multiple rungs of "Jacob's ladder". While we observe the expected dependence of the curvatures on Hartree-Fock exchange, we note limited correlation of curvature values between different rungs of "Jacob's ladder". We train ML models (i.e., artificial neural networks or ANNs) to predict the curvature and the associated frontier orbital energies for each of these 23 functionals and then interpret differences in curvature among the different DFAs through analysis of the ML models. Notably, we observe spin to play a much more important role in determining the curvature of range-separated and double hybrids in comparison to semi-local functionals, explaining why curvature values are weakly correlated between these and other families of functionals. Over a space of 187.2k hypothetical compounds, we use our ANNs to pinpoint DFAs for which representative transition metal complexes have near-zero curvature with low uncertainty, demonstrating an approach to accelerate screening of complexes with targeted optical gaps.

One-electron self-interaction error and its relationship to geometry and higher orbital occupation

Density Functional Theory (DFT) sees prominent use in computational chemistry and physics; however, problems due to the self-interaction error (SIE) pose additional challenges to obtaining qualitatively correct results. As an unphysical energy an electron exerts on itself, the SIE impacts most practical DFT calculations. We conduct an in-depth analysis of the one-electron SIE in which we replicate delocalization effects for simple geometries. We present a simple visualization of such effects, which may help in future qualitative analysis of the one-electron SIE. By increasing the number of nuclei in a linear arrangement, the SIE increases dramatically. We also show how molecular shape impacts the SIE. Two- and three-dimensional shapes show an even greater SIE stemming mainly from the exchange functional with some error compensation from the one-electron error, which we previously defined [D. R. Lonsdale and L. Goerigk, Phys. Chem. Chem. Phys. 22, 15805 (2020)]. Most tested geometries are affected by the functional error, while some suffer from the density error. For the latter, we establish a potential connection with electrons being unequally delocalized by the DFT methods. We also show how the SIE increases if electrons occupy higher-lying atomic orbitals; seemingly one-electron SIE free methods in a ground are no longer SIE free in excited states, which is an important insight for some popular, non-empirical density functional approximations (DFAs). We conclude that the erratic behavior of the SIE in even the simplest geometries shows that robust DFAs are needed. Our test systems can be used as a future benchmark or contribute toward DFT development.

Performance of Screened-Exchange Functionals for Band Gaps and Lattice Constants of Crystals

Kohn-Sham density functional theory is the most widely used method for electronic structure calculations of solid-state systems. The screened-exchange functionals developed following the influential work of Scuseria and co-workers in 2003-2006 have significantly improved the accuracy of the predictions of solid-state properties. This work assesses six screened-exchange density functionals for the prediction of 60 band gaps (database BG60) and 68 lattice constants (database LC68). The band gaps are calculated with both consistently calculated lattice constants and experimental lattice constants. Results for the nonlocal screened-exchange functionals are compared with those for six widely used or recently developed local functionals. The results show that all the screened-exchange functionals have smaller mean absolute errors (MAEs) than any of the local functionals. All the functionals except HLE17 overestimate (on average) the lattice constants, and M06-SX gives the best performance among the compared functionals, with a MAE of 0.051 Å. All the functionals underestimate (on average) the band gaps, and M06-SX outperforms all other functionals, with a MAE of 0.47 eV. M06-SX also has the lowest root-mean-squared error for both LC68 and BG60. For the subdatabases of BG60, M06-SX shows better performance for ionic crystals and systems with large band gaps, while HSE12s gives better results for semiconductors and systems with small band gaps. Overall, M06-SX shows the best performance for solid-state systems, followed by N12-SX and HSE12s. The best-performing local functionals are M06-L, revM06-L, and HLE17 for band gaps and M06-L and revM06-L for lattice constants. We found that M06-SX, revM06-L, and N12-SX not only are well optimized for a broad array of chemical properties but also have very good performance for the databases in this paper, making them well-suited for applications involving heterogeneous chemistry.

Mechanistic views and computational studies on transition-metal-catalyzed reductive coupling reactions

Transition-metal-catalyzed reductive coupling reactions have been considered as a powerful tool to convert two electrophiles into value-added products. Numerous related reports have shown the fascinating potential. Mechanistic studies, especially theoretical studies, can provide important implications for the design of novel reductive coupling reactions. In this review, we summarize the representative advancements in theoretical studies on transition-metal-catalyzed reductive coupling reactions and systematically elaborate the mechanisms for the key steps of reductive coupling reactions. The activation modes of electrophiles and the deep insights of selectivity generation are mechanistically discussed. In addition, the mechanism of the reduction of high-oxidation-state catalysts and further construction of new chemical bonds are also described in detail.

Bonding and 13 C-NMR properties of coinage metal tris(ethylene) and tris(norbornene) complexes: Evaluation of the role of relativistic effects from DFT calculations

The π-complexes of cationic coinage metal ions (Cu(I), Ag(I), Au(I)) provide useful experimental support for understanding fundamental characteristics of bonding and ¹³ C-NMR patterns of the group 11 triad. Here, we account for the role of relativistic effects on olefin-coinage metal ion interaction for cationic, homoleptic tris-ethylene, and tris-norbornene complexes, [M(η² -C₂ H₄ )₃ ]⁺ and [M(η² -C₇ H₁₀ )₃ ]⁺ (M = Cu, Ag, Au), as representative case of studies. The M-(CC) bond strength in the cationic, tris-ethylene complexes is affected sizably for Au and to a lesser extent for Ag and Cu (48.6%, 16.7%, and 4.3%, respectively), owing to the influence on the different stabilizing terms accounting for the interaction energy in the formation of coinage metal cation-π complexes. The bonding elements provided by olefin → M σ-donation and olefin ← M π-backbonding are consequently affected, leading to a lesser covalent interaction going down in the triad if the relativistic effects are ignored. Analysis of the ¹³ C-NMR tensors provides further understanding of the observed experimental values, where the degree of backbonding charge donation to π₂ *-olefin orbital is the main influence on the observed high-field shifts in comparison to the free olefin. This donation is larger for ethylene complexes and lower for norbornene counterparts. However, the bonding energy in the later complexes is slightly stabilized given by the enhancement in the electrostatic character of the interaction. Thus, the theoretical evaluation of metal-alkene bonds, and other metal-bonding situations, benefits from the incorporation of relativistic effects even in lighter counterparts, which have an increasing role going down in the group.

Calculation of Metallocene Ionization Potentials via Auxiliary Field Quantum Monte Carlo: Toward Benchmark Quantum Chemistry for Transition Metals

The accurate ab initio prediction of ionization energies is essential to understanding the electrochemistry of transition metal complexes in both materials science and biological applications. However, such predictions have been complicated by the scarcity of gas phase experimental data, the relatively large size of the relevant molecules, and the presence of strong electron correlation effects. In this work, we apply all-electron phaseless auxiliary-field quantum Monte Carlo (ph-AFQMC) utilizing multideterminant trial wave functions to six metallocene complexes to compare the computed adiabatic and vertical ionization energies with experimental results. We find that ph-AFQMC yields mean absolute errors (MAEs) of 1.69 ± 1.02 kcal/mol for the adiabatic energies and 2.85 ± 1.13 kcal/mol for the vertical energies. We also carry out density functional theory (DFT) calculations using a variety of functionals, which yields MAEs of 3.62-6.98 kcal/mol and 3.31-9.88 kcal/mol, as well as one variant of localized coupled cluster calculations (DLPNO-CCSD(T₀) with moderate PNO cutoffs), which has MAEs of 4.96 and 6.08 kcal/mol, respectively. We also test the reliability of DLPNO-CCSD(T₀) and DFT on acetylacetonate (acac) complexes for adiabatic energies measured in the same manner experimentally, and we find higher MAEs, ranging from 4.56 to 10.99 kcal/mol (with a different ordering) for DFT and 6.97 kcal/mol for DLPNO-CCSD(T₀). Finally, by utilizing experimental solvation energies, we show that accurate reduction potentials in solution for the metallocene series can be obtained from the AFQMC gas phase results.

The Mechanism of a Retro-Diels-Alder Fragmentation of Luteolin: Theoretical Studies Supported by Electrospray Ionization Tandem Mass Spectrometry Results

The mechanisms of retro-Diels-Alder fragmentation of luteolin are studied theoretically using the Density Functional Theory method (B3LYP hybrid functional) together with the 6-311++G(d,p) basis set and supported by electrospray ionization tandem mass spectrometry (ESI-MS) results. The reaction paths leading to the formation of 1,3A- and 1,3B- fragment ions observed as the main spectral features in the ESI-MS spectrum are described and discussed, including the structures of the transition states and intermediate products. The heights of the activation energy barriers which have to be overcome along the reaction paths corresponding to 1,3-retrocyclization cleavage of the ionized luteolin are predicted to span the 69-94 kcal/mol range (depending on the initial isomeric structure) for the concerted retrocyclization mechanism and the 60-89 kcal/mol (first barrier) and 24-52 kcal/mol (second barrier) barriers for the stepwise mechanism (also depending on the initial isomeric structure). It is also demonstrated that the final fragmentation products (1,3A- and 1,3B-) are in fact represented by various isomeric systems which are not experimentally distinguishable. In addition, the absence of the spectral feature corresponding to the [M-B]- fragment ion formed by the rupture of the C-C bond connecting luteolin's B and C rings (which does not occur during the ESI-MS experiment) is explained by much larger energy barriers predicted for such a process.

Site-Specified Doping of Silver Atoms into Au25 Nanocluster as Directed by Ligand Binding Preference

For the first time site-specific doping of silver into a spherical Au₂₅ nanocluster has been achieved in [Au₁₉Ag₆(MeOPhS)₁₇(PPh₃)₆] (BF₄)₂ (Au₁₉Ag₆) through a dual-ligand coordination strategy. Single crystal X-ray structural analysis shows that the cluster has a distorted centered icosahedral Au@Au₆Ag₆ core of D₃ symmetry, in contrast to the I_h Au@Au₁₂ kernel in the well-known [Au₂₅(SR)₁₈]⁻ (R = CH₂CH₂Ph). An interesting feature is the coexistence of [Au₂(SPhOMe)₃] dimeric staples and [P–Au–SPhOMe] semi-staples in the title cluster, due to the incorporation of PPh₃. The observation of only one double-charged peak in ESI-TOF-MS confirms the ordered doping of silver atoms. Au₁₉Ag₆ is a 6e system showing a distinct absorption spectrum from [Au₂₅(SR)₁₈]⁻, that is, the HOMO–LUMO transition of Au₁₉Ag₆ is optically forbidden due to the P character of the superatomic frontier orbitals.

For the first time site-specific doping of silver into a spherical Au₂₅ nanocluster has been achieved in [Au₁₉Ag₆(MeOPhS)₁₇(PPh₃)₆] (BF₄)₂. It is a 6e system showing quite a different absorption spectrum from [Au₂₅(SR)₁₈]⁻.

Machine learning to tame divergent density functional approximations: a new path to consensus materials design principles

Virtual high-throughput screening (VHTS) with density functional theory (DFT) and machine-learning (ML)-acceleration is essential in rapid materials discovery. By necessity, efficient DFT-based workflows are carried out with a single density functional approximation (DFA). Nevertheless, properties evaluated with different DFAs can be expected to disagree for cases with challenging electronic structure (e.g., open-shell transition-metal complexes, TMCs) for which rapid screening is most needed and accurate benchmarks are often unavailable. To quantify the effect of DFA bias, we introduce an approach to rapidly obtain property predictions from 23 representative DFAs spanning multiple families, “rungs” (e.g., semi-local to double hybrid) and basis sets on over 2000 TMCs. Although computed property values (e.g., spin state splitting and frontier orbital gap) differ by DFA, high linear correlations persist across all DFAs. We train independent ML models for each DFA and observe convergent trends in feature importance, providing DFA-invariant, universal design rules. We devise a strategy to train artificial neural network (ANN) models informed by all 23 DFAs and use them to predict properties (e.g., spin-splitting energy) of over 187k TMCs. By requiring consensus of the ANN-predicted DFA properties, we improve correspondence of computational lead compounds with literature-mined, experimental compounds over the typically employed single-DFA approach.

Machine learning (ML)-based feature analysis reveals universal design rules regardless of density functional choices. Using the consensus among multiple functionals, we identify robust lead complexes in ML-accelerated chemical discovery.

Computational Discovery of Transition-metal Complexes: From High-throughput Screening to Machine Learning

Transition-metal complexes are attractive targets for the design of catalysts and functional materials. The behavior of the metal-organic bond, while very tunable for achieving target properties, is challenging to predict and necessitates searching a wide and complex space to identify needles in haystacks for target applications. This review will focus on the techniques that make high-throughput search of transition-metal chemical space feasible for the discovery of complexes with desirable properties. The review will cover the development, promise, and limitations of "traditional" computational chemistry (i.e., force field, semiempirical, and density functional theory methods) as it pertains to data generation for inorganic molecular discovery. The review will also discuss the opportunities and limitations in leveraging experimental data sources. We will focus on how advances in statistical modeling, artificial intelligence, multiobjective optimization, and automation accelerate discovery of lead compounds and design rules. The overall objective of this review is to showcase how bringing together advances from diverse areas of computational chemistry and computer science have enabled the rapid uncovering of structure-property relationships in transition-metal chemistry. We aim to highlight how unique considerations in motifs of metal-organic bonding (e.g., variable spin and oxidation state, and bonding strength/nature) set them and their discovery apart from more commonly considered organic molecules. We will also highlight how uncertainty and relative data scarcity in transition-metal chemistry motivate specific developments in machine learning representations, model training, and in computational chemistry. Finally, we will conclude with an outlook of areas of opportunity for the accelerated discovery of transition-metal complexes.

Electronic Structure of Molecules, Surfaces, and Molecules on Surfaces with the Local Modified Becke-Johnson Exchange-Correlation Potential

The knowledge of electronic properties of matter is the key to the understanding of its properties and to propose useful applications. To model hybrid organic/inorganic systems with the plane-wave approach, large supercells with many atoms are usually necessary to minimize artificial interactions between periodic images. For such systems, accurate approximations to the exchange-correlation functional of density functional theory, such as hybrid functionals, become computationally expensive, and cheaper approaches need to be considered. Here, we apply the local modified Becke-Johnson exchange-correlation potential to free molecules and surfaces and study its accuracy for calculated ionization potentials. This quantity being important to understand the band alignment of composite heterogeneous systems, we demonstrate the application of the potential to the electronic structure calculation of an exemplary composite semiconductor/molecule system, namely, a F6-TCNNQ molecule adsorbed on a hydrogenated Si(111) surface.

On the mechanism of the formation of alkyl-Ni(I) catalysts

The formation of catalytically active alkyl-Ni(i) complexes by comproportionation of diorgano-Ni(ii) precursors and Ni(0) species proceeds easily through triplet states by alkyl ligand exchange. The process involves inversion of the configuration at the carbon that is transferred.

Understanding of [RuL(ONO)]n+ acting as nitric oxide precursor, a theoretical study of ruthenium complexes of 1,4,8,11-tetraazacyclo- tetradecane having different substituents: How spin multiplicity influences bond angle and bond lengths (Ru-O-NO) in releasing of NO

Generation of nitric oxide has been a great interest in cell biology as it involves a wide range of physiological functions including the blood pressure control; thus the exploitation of ruthenium chemistry has been motivated in biochemical and clinical points of view. Herein, the structural and electronic properties of ruthenium(II) complexes of 1,4,8,11-tetraazacyclotetradecane containing pyridyl, imidazole and benzimidazole (L¹, L², L³) were analyzed theoretically in the context of how spin multiplicity plays a crucial role influencing the NO release from the LRu-ONO moiety. The results show that β-cleavage of nitrito in the complex motivates the release of NO as it depends highly on total spin multiplicity of metal ion altering significantly the geometrical parameters; particularly, a decrease of bond length of Ru-ONO is highly associated with an increase of RuO-NO bond distance that correlates with the decrease of the Ru-O-NO bond angle ultimately leading to the release of NO; apparently, the bending nature of Ru-O-NO defines its release from the complex. This is consistent with orbital energy (d_x²-_y²) where the stabilization of axial Ru-O bond in the complex was observed, and proved by molecular orbital studies. In the excitation of the complex (singlet to triplet or singlet to quintet), the NO release has been facilitated, agreeing with the Gibbs free energy data where a lower energy for NO release was obtained compared to other types of excitations. In the calculated electronic spectra, a visible broad band with relatively high intensity for [RuL¹ONO]⁺ was observed, agreeing approximately with reported experimental results.

Remote Water-Mediated Proton Transfer Triggers Inter-Cu Electron Transfer: Nitrite Reduction Activation in Copper-Containing Nitrite Reductase

The copper-containing nitrite reductase (CuNiR) catalyzes the biological conversion of nitrite to nitric oxide; key long-range electron/proton transfers are involved in the catalysis. However, the details of the electron-/proton-transfer mechanism are still unknown. In particular, the driving force of the electron transfer from the type-1 copper (T1Cu) site to the type-2 copper (T2Cu) site is ambiguous. Here, we explored the two possible proton-transfer channels, the high-pH proton channel and the primary proton channel, by using two-layered ONIOM calculations. Our calculation results reveal that the driving force for electron transfer from T1Cu to T2Cu comes from a remote water-mediated triple-proton-coupled electron-transfer mechanism. In the high-pH proton channel, the water-mediated triple-proton transfer occurs from Glu113 to an intermediate water molecule, whereas in the primary channel, the transfer is from Lys128 to His260. Subsequently, the two channels employ another two or three distinct proton-transfer steps to deliver the proton to the nitrite substrate at the T2Cu site. These findings explain the detailed proton-/electron-transfer mechanisms of copper-containing nitrite reductase and could extend our understanding of the diverse proton-coupled electron-transfer mechanisms in complicated proteins.

Coumarin-Based Dual Chemosensor for Colorimetric and Fluorescent Detection of Cu2+ in Water Media

A novel coumarin derivative (5) was synthesized and used as a colorimetric and fluorescent probe for selective detection of Cu²⁺ ions in the presence of other metal ions, with the detection limits of 5.7 and 4.0 ppb, respectively. Cu²⁺ ion reacts with probe 5 to form a 1:1 stoichiometry complex, resulting in a remarkable redshift of absorption maximum from 460 to 510 nm, as well as almost completely quenching fluorescence intensity of probe 5 at the wavelength of 536 nm. These changes can be distinctly observed by naked eyes. In addition, the working pH range of probe 5 is wide and suitable for physiological conditions, thus probe 5 may be used for detection of Cu²⁺ ions in living cells. The stable structures of probe 5 and its 1:1 complex with Cu²⁺ ion were optimized at the PBE0/6-31+G(d) level of theory. The presence and characteristics of bonds in compounds were studied through atoms in a molecule and natural bond orbital analysis. The formation of the complex led to a strong transfer of electron density from probe 5 as a ligand to Cu²⁺ ion, resulting in breaking the π-electron conjugated system, which is the cause of fluorescence quenching and color change of 5-Cu²⁺ complex.

Accurate Quantum Chemical Calculation of Ionization Potentials: Validation of the DFT-LOC Approach via a Large Data Set Obtained from Experiments and Benchmark Quantum Chemical Calculations

Density functional theory (DFT) is known to often fail when calculating thermodynamic values, such as ionization potentials (IPs), due to nondynamical error (i.e., the self-interaction term). Localized orbital corrections (LOCs), derived from assigning corresponding corrections for the atomic orbitals, bonds, and paired and unpaired electrons, are utilized to correct the IPs calculated from DFT. Some of the assigned parameters, which are physically due to the contraction of and change of the environment around a bond, depend on identifying the location in the molecule from which the electron is removed using differences in the charge density between neutral and oxidized species. In our training set, various small organic and inorganic molecules from the literature with the reported experimental IP were collected using the NIST database. For certain molecules with uncertain or no experimental measurements, we obtain the IP using coupled cluster theory and auxiliary field quantum Monte Carlo. After applying these corrections, as generated by least-squares regression, LOC reduces the mean absolute deviation (MAD) of the training set from 0.143 to 0.046 eV (R² = 0.895), and LOC reduces the MAD of the test set from 0.192 to 0.097 eV (R² = 0.833).

Large-scale comparison of 3d and 4d transition metal complexes illuminates the reduced effect of exchange on second-row spin-state energetics

The origin of distinct 3d vs. 4d transition metal complex sensitivity to exchange is explored over a large data set.

Appraising spin-state energetics in transition metal complexes using double-hybrid models: accountability of SOS0-PBESCAN0-2(a) as a promising paradigm

Through a comprehensive survey, reliable double-hybrid models have been validated and proposed for spin-state energetics in transition metal complexes.

G4 accuracy at DFT cost: unlocking accurate redox potentials for organic molecules using systematic error cancellation

This study presents a cost-effective error cancellation protocol to predict the redox potentials of 46 organic molecules with near-G4 accuracy.

Redox potentials along the redox-active low-barrier H-bonds in electron transfer pathways

Local proton transfer along redox-active low-barrier H-bonds can alter the driving force or electronic coupling for electron transfer, as the redox potential values depend on the H⁺ position in low-barrier H-bonds.

Trans Influence and Substituent Effects on the HOMO-LUMO Energy Gap and Stokes Shift in Ru Mono-Diimine Derivatives

The ground (S0) and excited triplet (T1) electronic states and corresponding optical spectra of a series of cationic complexes [RuH(CO)L(PPh3)2]+ (L=2,2´-bipyridyl) (Rubpy), 4,4´-dicarboxylic-2,2´-bipyridyl (Rudcbpy), bis-4,4'-(N-methylamide)-2,2´-bipyridyl (Rudamidebpy), bis-4,4'-(methyl)-2,2´-bipyridyl (RudMebpy), [Ru(CO)2dcbpy(PPh3)2]2+ (Ru(2CO)dcbpy), and [Ru(H)2dcbpy(PPh3)2] (Ru(2H)dcbpy) have been studied by combined Density Functional/Time-Dependent Density Functional (DFT/TDDFT) techniques using different combinations of DFT exchange-correlation functionals and basis sets. PBE0/LANL2DZ provided more accurate geometries to describe S0 whereas B3LYP/LANL2DZ predicted spectral energies that correlated better with the available experiment data. The Ru (II) complexes with different substituents emit photons ranging from 560-610 nm in the series RudMebpy, Rubpy, Rudamidebpy, Rudcbpy. The calculations predicted a maximum emission at about 540 nm for the complex constructed from two carbonyl π-acceptors ligands trans to the dcbpy, while an emission in the far infrared region is calculated when two H σ-donor ligands trans to the dcbpy. Our calculation results show correlations between HOMO-LUMO energy gap, Stokes shift, and T1 distortion, which reflect the different effects of electron-withdrawing and donating groups. We proposed that these correlations can be used to predict the photophysical properties for new complexes.

Atom-Economical Ni-Catalyzed Diborylative Cyclization of Enynes: Preparation of Unsymmetrical Diboronates

We report a Ni-catalyzed diborylative cyclization of enynes that affords carbo- and heterocycles containing both alkyl- and alkenylboronates. The reaction is fully atom-economical, shows a broad scope, and employs a powerful and inexpensive catalytic Ni-based system. The reaction mechanism seems to involve activation of the enyne by Ni(0) through oxidative cyclometalation of the enyne prior to diboron reagent activation. An unprecedented dinuclear bis(organometallic) Ni(I) intermediate complex was isolated.

Large-Scale Benchmark of Exchange-Correlation Functionals for the Determination of Electronic Band Gaps of Solids

We compile a large data set designed for the efficient benchmarking of exchange–correlation functionals for the calculation of electronic band gaps. The data set comprises information on the experimental structure and band gap of 472 nonmagnetic materials and includes a diverse group of covalent-, ionic-, and van der Waals-bonded solids. We used it to benchmark 12 functionals, ranging from standard local and semilocal functionals, passing through meta-generalized-gradient approximations, and several hybrids. We included both general purpose functionals, like the Perdew–Burke–Ernzerhof approximation, and functionals specifically crafted for the determination of band gaps. The comparison of experimental and theoretical band gaps shows that the modified Becke–Johnson is at the moment the best available density functional, closely followed by the Heyd–Scuseria–Ernzerhof screened hybrid from 2006 and the high-local-exchange generalized-gradient approximation.

A Benchmark of Density Functional Approximations For Thermochemistry and Kinetics of Hydride Reductions of Cyclohexanones

The performance of density functionals and wavefunction methods for describing the thermodynamics and kinetics of hydride reductions of 2-substituted cyclohexanones has been evaluated for the first time. A variety of exchange correlation functionals ranging from generalized gradient approximations to double hybrids have been tested and their performance to describe the facial selectivity of hydride reductions of cyclohexanones has been carefully assessed relative to the CCSD(T) method. Among the tested methods, an approach in which single-point energy calculations using the double hybrid B2PLYP-D3 functional on ωB97X-D optimized geometries provides the most accurate transition state energies for these kinetically-controlled reactions. Moreover, the role of torsional strain, temperature, solvation, noncovalent interactions on the stereoselectivity of these reductions was elucidated. Our results indicate a prominent role of the substituent on the cis/trans ratios driven by the delicate interplay between torsional strain and dispersion interactions.

Iron(II) and Iron(III) Spin Crossover: Toward an Optimal Density Functional

Spin crossover (SCO) plays a major role in biochemistry, catalysis, materials, and emerging technologies such as molecular electronics and sensors, and thus accurate prediction and design of SCO systems is of high priority. However, the main tool for this purpose, density functional theory (DFT), is very sensitive to applied methodology. The most abundant SCO systems are Fe(II) and Fe(III) systems. Even with average good agreement, a functional may be significantly more accurate for Fe(II) or Fe(III) systems, preventing balanced study of SCO candidates of both types. The present work investigates DFT's performance for well-known Fe(II) and Fe(III) SCO complexes, using various design types and customized versions of GGA, hybrid, meta-GGA, meta-hybrid, double-hybrid, and long-range-corrected hybrid functionals. We explore the limits of DFT performance and identify proficient Fe(II)-Fe(III)-balanced functionals. We identify and quantify remarkable differences in the DFT description of Fe(II) and Fe(III) systems. Most functionals become more accurate once Hartree-Fock exchange is adjusted to 10-17%, regardless of the type of functionals involved. However, this typically introduces a clear Fe(II)-Fe(III) bias. The most accurate functionals measured by mean absolute errors <10 kJ/mol are CAMB3LYP-17, B3LYP*, and B97-15 with 15-17% Hartree-Fock exchange, closely followed by CAMB3LYP and CAMB3LYP-15, OPBE, rPBE-10, and B3P86-15. While GGA functionals display a small Fe(II)-Fe(III) bias, they are generally inaccurate, except the O exchange functional. Hybrid functionals (including B2PLYP double hybrids and meta hybrids) tend to favor HS too much in Fe(II) vs Fe(III), which is important in many studies where the oxidation state of iron can vary, e.g. rational SCO design and studies of catalytic processes involving iron. The only functional with a combined bias <5 kJ/mol and a decent MAE (15 kJ/mol) is our customized PBE0-12 functional. Alternatively one has to sacrifice Fe(II)-Fe(III) balance to use the best functionals for each group separately. We also investigated the precision (measured as the standard deviation of errors) and show that the target accuracy for iron SCO is 10 kJ/mol for accuracy and 5 kJ/mol for precision, and DFT is probably not going to break this limit in the near future. Importantly, all four types of functional behavior (accurate/precise, accurate/imprecise, inaccurate/precise, inaccurate/imprecise) are observed. More generally, our work illustrates the importance not only of overall accuracy but also of balanced accuracy for systems likely to occur in context.

Photoelectron spectroscopic and computational studies of [EDTA·M(iii)]− complexes (M = H3, Al, Sc, V–Co)

Photoelectron spectroscopic and computational studies of [EDTA·M(iii)]⁻ complexes reveal their redox chemistry and specific metal bindings.

Computational Spectroscopic Characterization of a Bistable Binuclear Complex [(CO)2(benzoate)FeII/III(terephthalate)CoIII/II(benzoate)(CO)2]+

Electric dipole moments, polarizabilities, and IR, Raman, optical rotatory dispersion, and electronic and vibrational circular dichroism spectra of the four cis–trans isomers of the proposed [(CO)2(benzoate)FeII/III(terephthalate)CoIII/II(benzoate)(CO)2]+ binuclear complex, having bistablity due to intramolecular charge transfer (IMCT), is investigated using the time-dependent density functional theory ((TD)DFT) B3LYP/6–31G(d,p)[LanL2DZ] method. Results show that the two FeII–CoIII and FeIII–CoII IMCT states of this binuclear complex have distinctly different spectroscopic, optical, and electric response properties, and are sensitive to the cis–trans arrangement of the ligands around the two metallic centres. Furthermore, intrinsic reaction coordinates inter-connecting the two IMCT states are identified using the Duschinsky matrix method. Only one or two of the normal coordinates remain almost (above 80 %) intact during the IMCT reaction which denotes global changes in the bonding strengths and potential energy hypersurface of this bistable binuclear complex. Analysis of the calculated spin densities characterizes the IMCT transition state structures of the trans–trans, cis–cis, and trans–cis isomers as early, early, and late transition states, respectively.