A thorough benchmark of density functional methods for general main group thermochemistry, kinetics, and noncovalent interactions

Design and structure of overlapping regions in PCA via deep learning

Polymerase cycling assembly (PCA) stands out as the predominant method in the synthesis of kilobase-length DNA fragments. The design of overlapping regions is the core factor affecting the success rate of synthesis. However, there still exists DNA sequences that are challenging to design and construct in the genome synthesis. Here we proposed a deep learning model based on extensive synthesis data to discern latent sequence representations in overlapping regions with an AUPR of 0.805. Utilizing the model, we developed the SmartCut algorithm aimed at designing oligonucleotides and enhancing the success rate of PCA experiments. This algorithm was successfully applied to sequences with diverse synthesis constraints, 80.4 % of which were synthesized in a single round. We further discovered structure differences represented by major groove width, stagger, slide, and centroid distance between overlapping and non-overlapping regions, which elucidated the model's reasonableness through the lens of physical chemistry. This comprehensive approach facilitates streamlined and efficient investigations into the genome synthesis.

Mechanisms of C(sp3)-H Functionalization of Acetonitrile or Acetone with Alkynes: A DFT Investigation

The mechanisms for the C(sp3)-H activation and addition reactions between acetonitrile (or acetone) and alkynes have been investigated with the M06-2X-D3/ma-def2-TZVP method and basis set. The SMD (solvation model based on solute electron density) model was applied to simulate the solvent effect. In the first and second reactions, 2-phenylbut-3-yn-2-ol reacted with acetonitrile and acetone, respectively. First, the C(sp3)-H activations of acetonitrile and acetone could be achieved by PhCOO• and t-BuO• radicals. Then, addition reactions converted 2-phenylbut-3-yn-2-ol into final products P1 and P2. Gibbs free energy surfaces of these two reactions suggest that blue lines would be the favorable paths with lower Gibbs energy barriers, and the terminal C atom of the C≡C bond is the best reactive site. Moreover, the analysis of the IRI (Interaction Region Indicator) reveals the Z- and E-configuration transformations. While in the third and fourth reactions, methyl(2-(phenylethynyl)phenyl)sulfane has interactions with acetonitrile and acetone via some paths, respectively. Gibbs free energy profiles show that the C10 atom, rather than the C11 atom, has priority, and the blue lines are favorable. Furthermore, the action mode of Na2HPO4 could reduce the energy barrier and benefit the reaction. vdW (van der Waals) interactions play an important role in the choice for the reactive site. In the fifth (or sixth) reaction, it happened between 1-(2-(methylthio)phenyl)-3-phenylprop-2-yn-1-one and acetontrile (or acetone) to yield the final product P5 (or P6). The computational results uncovered the blue line is the best path, and the choice for the reactive site depends on the vdW interactions, which reveals the origin of selectivity. In addition, the investigation for the byproducts have been carried out, and these can explain the reason that only the main product is produced. Both of those can agree with the experimental results. The localized orbital locator (LOL) isosurfaces, Laplacian bond order (LBO), electron density of the bond critical point (ρBCP), electron spin density isosurface graphs, and IRI graphs can be used to analyze the structure and reveal the reaction substances.

A Cross-Linked Polymer Coating Strategy to Enhance the Performance of NaNi0.33Fe0.33Mn0.33O2 Cathode for Sodium-Ion Batteries

O3-type layered oxide materials are regarded as optimal cathode candidates for sodium-ion batteries (SIBs) on account of their exceptional energy density. Nevertheless, the rapid decline in capacity resulting from the instability of the interface structure represents a significant challenge to the practical implementation of these materials. In this study, we propose an innovative method to modify the O3-type NaNi0.33Fe0.33Mn0.33O2 (NFM) cathode material by applying a cross-linked polymer (CLP) coating. X-ray photoelectron spectroscopy (XPS) analysis demonstrates that the CLP coating effectively inhibits the decomposition of the cathode electrolyte interface (CEI) membrane in the course of cycling, leading to a substantial improvement in the stability of the electrode material's interface. Moreover, the oxygen-containing groups within the coating can compete with propylene carbonate (PC) solvent molecules in the electrolyte for Na+ coordination, reducing the coordination between Na+ and PC molecules. This process facilitates more efficient diffusion of Na+, thereby enhancing the rate performance. Consequently, CLP-coated NFM (NFM@CLP) materials exhibit enhanced electrochemical performance. After 300 cycles at 25 °C, NFM@CLP retains 72.36% of its capacity, compared to 62.59% for pristine NFM. Even at elevated temperatures (65 °C), the capacity retention of NFM@CLP remains high at 63.84% after 200 cycles, whereas pristine NFM drops to 3.65%. In full-cell tests (vs hard carbon), the NFM@CLP also exhibits better capacity retention (85.07% after 150 cycles). This study offers an effective and simple approach to enhancing the capacity retention and rate performance of O3-type layered materials in SIBs, providing unique insights into advanced energy storage materials.

Improving the Reliability of, and Confidence in, DFT Functional Benchmarking through Active Learning

Validating the performance of exchange-correlation functionals is vital to ensure the reliability of density functional theory (DFT) calculations. Typically, these validations involve benchmarking data sets. Currently, such data sets are usually assembled in an unprincipled manner, suffering from uncontrolled chemical bias, and limiting the transferability of benchmarking results to a broader chemical space. In this work, a data-efficient solution based on active learning is explored to address this issue. Focusing─as a proof of principle─on pericyclic reactions, we start from the BH9 benchmarking data set and design a chemical reaction space around this initial data set by combinatorially combining reaction templates and substituents. Next, a surrogate model is trained to predict the standard deviation of the activation energies computed across a selection of 20 distinct DFT functionals. With this model, the designed chemical reaction space is explored, enabling the identification of challenging regions, i.e., regions with large DFT functional divergence, for which representative reactions are subsequently acquired as additional training points. Remarkably, it turns out that the function mapping the molecular structure to functional divergence is readily learnable; convergence is reached upon the acquisition of fewer than 100 reactions. With our final updated model, a more challenging─and arguably more representative─pericyclic benchmarking data set is curated, and we demonstrate that the functional performance has changed significantly compared to the original BH9 subset.

Efficient Sampling for Machine Learning Electron Density and Its Response in Real Space

Electron density is a fundamental quantity that can in principle determine all ground state electronic properties of a given system. Although machine learning (ML) models for electron density based on either an atom-centered basis or a real-space grid have been proposed, the demand for a number of high-order basis functions or grid points is enormous. In this work, we propose an efficient grid-point sampling strategy that combines targeted sampling favoring a large density and a screening of grid points associated with linearly independent atomic features. This new sampling strategy is integrated with a field-induced recursively embedded atom neural network model to develop a real-space grid-based ML model for the electron density and its response to an electric field. This approach is applied to a QM9 molecular data set, a H2O/Pt(111) interfacial system, an Au(100) electrode, and an Au nanoparticle under an electric field. The number of training points is found to be much smaller than previous models, while yielding comparably accurate predictions for the electron density of the entire grid. The resultant machine-learned electron density model enables us to properly partition partial charge onto each atom and analyze the charge variation upon proton transfer in the H2O/Pt(111) system. The machine-learning electronic response model allows us to predict charge transfer and the electrostatic potential change induced by an electric field applied to an Au(100) electrode or an Au nanoparticle.

Data-Driven Improvement of Local Hybrid Functionals: Neural-Network-Based Local Mixing Functions and Power-Series Correlation Functionals

Local hybrid functionals (LHs) use a real-space position-dependent admixture of exact exchange (EXX), governed by a local mixing function (LMF). The systematic construction of LMFs has been hampered over the years by a lack of exact physical constraints on their valence behavior. Here, we exploit a data-driven approach and train a new type of "n-LMF" as a relatively shallow neural network. The input features are of meta-GGA character, while the W4-17 atomization-energy and BH76 reaction-barrier test sets have been used for training. Simply replacing the widely used "t-LMF" of the LH20t functional by the n-LMF provides the LH24n-B95 functional. Augmented by DFT-D4 dispersion corrections, LH24n-B95-D4 remarkably improves the WTMAD-2 value for the large GMTKN55 test suite of general main-group thermochemistry, kinetics, and noncovalent interactions (NCIs) from 4.55 to 3.49 kcal/mol. As we found the limited flexibility of the B95c correlation functional to disfavor much further improvement on NCIs, we proceeded to replace it by an optimized B97c-type power-series expansion. This gives the LH24n functional. LH24n-D4 gives a WTMAD-2 value of 3.10 kcal/mol, the so far lowest value of a rung 4 functional in self-consistent calculations. The new functionals perform moderately well for organometallic transition-metal energetics while leaving room for further data-driven improvements in that area. Compared to complete neural-network functionals like DM21, the present more tailored approach to train just the LMF in a flexible but well-defined human-designed LH functional retains the possibility of graphical LMF analyses to gain deeper understanding. We find that both the present n-LMF and the recent x-LMF suppress the so-called gauge problem of local hybrids without adding a calibration function as required for other LMFs. LMF plots show that this can be traced back to large LMF values in the small-density region between the interacting atoms in NCIs for n- and x-LMFs and low values for the t-LMF. We also find that the trained n-LMF has relatively large values in covalent bonds without deteriorating binding energies. The current approach enables fast and efficient routine self-consistent calculations using n-LMFs in Turbomole.

Approaching coupled-cluster accuracy for molecular electronic structures with multi-task learning

Machine learning plays an important role in quantum chemistry, providing fast-to-evaluate predictive models for various properties of molecules; however, most existing machine learning models for molecular electronic properties use density functional theory (DFT) databases as ground truth in training, and their prediction accuracy cannot surpass that of DFT. In this work we developed a unified machine learning method for electronic structures of organic molecules using the gold-standard CCSD(T) calculations as training data. Tested on hydrocarbon molecules, our model outperforms DFT with several widely used hybrid and double-hybrid functionals in terms of both computational cost and prediction accuracy of various quantum chemical properties. We apply the model to aromatic compounds and semiconducting polymers, evaluating both ground- and excited-state properties. The results demonstrate the model's accuracy and generalization capability to complex systems that cannot be calculated using CCSD(T)-level methods due to scaling.

Theoretical and Electrochemical Evaluation of Cannabis Sativa L. Extracts as Corrosion Inhibitors for Mild Steel in Acidic Medium

The corrosion of metals in acidic environments remains a significant challenge, driving the search for sustainable and eco-friendly inhibitors derived from natural sources. This study evaluates the corrosion inhibition potential of three extracts from Cannabis sativa L., namely ethanol extract (EET), hexane extract (EHX), and dichloromethane extract (EDM), for mild steel in a 1 M HCl acidic medium. The investigation employed weight loss (WL) measurements, electrochemical impedance spectroscopy (EIS), and potentiodynamic polarization (PDP) techniques. To understand their inhibitive performance, density functional theory (DFT) was used. For a more comprehensive theoretical analysis, Monte Carlo (MC) and molecular dynamics (MD) simulations were used. The corrosion inhibition efficiency increased with the increase of EET, EHX, and EDM concentrations up to 91 %, 89 %, and 83 %, respectively, obtained at 308 K for a 0.8 g/L concentration. Polarization studies classify EET, EHX, and EDM as mixed-type inhibitors with a predominantly anodic effect, functioning through adsorption on the metal surface. The adsorption of these extracts on mild steel conforms to the Langmuir isotherm model, with adsorption equilibrium constants (Kads) of 3.0143 M, 5.1245 M, and 2.2009 M for EET, EHX, and EDM, respectively, highlighting their potential as effective corrosion inhibitors. The EET extract exhibits a high activation energy (Ea) of 101.70 kJ/mol, while the EHX and EDM extracts show Ea values of 79.05 kJ/mol and 82.93 kJ/mol, respectively, all significantly higher than the Ea of blank, which is 30.23 kJ/mol, indicating that the extracts effectively inhibit corrosion by increasing the activation energy, with EET being the most potent inhibitor. Theoretical approaches based on DFT, MC, and MD simulations clearly explain the mode of adsorption of the majority of molecules on the metal surface. The inhibition process may result from a synergistic intermolecular effect of the major compounds in the extract, which interact at various active adsorption sites on the metal surface. Simulations indicate that catechin dihydrate in EET (52.42 %), linoleic acid in EHX (42.92 %), and naringenin in EDM (41.92 %) are close to the metal surface, suggesting strong interactions with the material. The results obtained from experimental measurements and theoretical calculations agree, highlighting the potential for developing more sustainable corrosion inhibitors based on plant-derived compounds.

A Benchmark Study of DFT-Computed p-Block Element Lewis Pair Formation Enthalpies Against Experimental Calorimetric Data

The quantification of Lewis acidity is of fundamental and applied importance in chemistry. While the computed fluoride ion affinity (FIA) is the most widely accepted thermodynamic metric, only sparse experimental values exist. Accordingly, a benchmark of methods for computing Lewis pair formation enthalpies, also with a broader set of Lewis bases against experimental data, is missing. Herein, we evaluate different density functionals against a set of 112 experimentally determined Lewis acid/base binding enthalpies and gauge influences such as solvation correction in structure optimization. From that, we can recommend r2SCAN-3c for robust quantification of this omnipresent interaction.

Assessment of the applicability of DFT methods to [Cp*Rh]-catalyzed hydrogen evolution processes

The present computational study provides a benchmark of density functional theory (DFT) methods in describing hydrogen evolution processes catalyzed by [Cp*Rh]-containing organometallic complexes. A test set was composed of 26 elementary reactions featuring chemical transformations and bonding situations essential for the field, including the emerging concept of non-innocent Cp* behavior. Reference values were obtained from a highly accurate 3/4 complete basis set and 6/7 complete PNO space extrapolated DLPNO-CCSD(T) energies. The performance of lower-level extrapolation procedures was also assessed. We considered 84 density functionals (DF) (including 13 generalized gradient approximations (GGA), nine meta-GGAs, 33 hybrids, and 29 double-hybrids) and three composite methods (HF-3c, PBEh-3c, and r2SCAN-3c), combined with different types of dispersion corrections (D3(0), D3BJ, D4, and VV10). The most accurate approach is the PBE0-DH-D3BJ (MAD of 1.36 kcal mol-1) followed by TPSS0-D3BJ (MAD of 1.60 kcal mol-1). Low-cost r2SCAN-3c composite provides a less accurate but much faster alternative (MAD of 2.39 kcal mol-1). The widely used Minnesota-family M06-L, M06, and M06-2X DFs should be avoided (MADs of 3.70, 3.94, and 4.01 kcal mol-1, respectively).

Construction of S-scheme heterojunction via coating ZIF-8-derived Zn0.7Cd0.3S on Ni2P hydrangea for efficient photocatalytic hydrogen evolution coupled with benzyl alcohol oxidation

Coupling light-driven hydrogen (H2) evolution with benzyl alcohol (BA) oxidation is regard as a prospective strategy for obtaining value-added fuels as well as chemicals to deal with energy and environment crisis. In this contribution, a series of dual-functional noble metal-free S-scheme heterojunctions (Zn1-xCdxS@yNi2P) with spatially separated and precise redox sites were constructed by synthesizing Zn1-xCdxS with regular morphology uniformly coated on Ni2P nanosheets via the template method for coupling H2 evolution with BA oxidation. The optimized Zn0.7Cd0.3S@15 %Ni2P photocatalytic produced H2 (40.33 mmol g-1 h-1) and benzaldehyde (BAD) (43.38 mmol g-1 h-1), remarkably exceeding pure Ni2P and Zn0.7Cd0.3S. Notably, the Zn0.7Cd0.3S@15 %Ni2P gave a significant advantage in coupling H2 evolution and BA oxidation performance than the catalysts reported previously. The S-scheme heterojunction constructed between Zn0.7Cd0.3S and Ni2P was demonstrated by Density functional theory (DFT) calculations, in-situ radiation X-ray photoelectron spectroscopy (XPS), Kelvin probe force microscope (KPFM) and electron paramagnetic resonance (EPR). The effect of S-scheme heterointerfaces and internal electric field promoted photo-induced charge separation and transfer efficiency, greatly enhancing the photocatalysis performance. This work emphasizes the significance of rational engineering of heterojunctions, providing an enlightening guidance on synthesis of dual-functional photo-redox catalysts to improve economical solar fuel exploitation and production of value-added chemicals.

Synthesis of the Bulky Phosphanide [P(SiiPr3)2]- and Its Stabilization of Low-Coordinate Group 12 Complexes

Here, we report an improved synthesis of the bulky phosphanide anion [P(SiiPr3)2]- in synthetically useful yields and its complexation to group 12 metals. The ligand is obtained as the sodium salt NaP(SiiPr3)2 1 in a 42% isolated yield and a single step from red phosphorus and sodium. This is a significantly higher-yielding and safer preparation compared to the previously reported synthesis of this ligand, and we have thus applied 1 to the synthesis of the two-coordinate complexes M[P(SiiPr3)2]2 (M = Zn, Cd, Hg). These group 12 complexes are all monomeric and with nonlinear P-M-P angles in the solid state, with DFT calculations suggesting that this bending is due to the steric demands of the ligand. Multinuclear NMR spectroscopy revealed complex second-order splitting patterns due to strong PP' coupling. This work demonstrates that the synthesis of 1 is viable and provides a springboard for the synthesis of low-coordinate complexes featuring this unusual bulky ligand.

Toward High-Performance Electrochemical Ammonia Synthesis by Circumventing the Surface H-Mediated N2 Reduction

The rapid performance decay with potentials is a significant obstacle to achieving an efficient electrocatalytic N2 reduction reaction (eNRR), which is typically attributed to competition from hydrogen evolution. However, the potential-dependent competitive behavior and reaction mechanism are still under debate. Herein, we theoretically defined N2 adsorption, H mediation, and H2 evolution as three crucial regions along the potentials by revisiting the potential-dependent competitive adsorption between N2 and H on FeN4 and RuN4 catalysts. We revealed that the surface H-mediated mechanism makes eNRR feasible at low potentials but introduces sluggish reaction kinetics, showing a double-edged sword nature. In view of this, we proposed a new possibility to achieve high-performance NH3 synthesis by circumventing the H-mediated mechanism, where the ideal catalyst should have a wide potential interval with N2-dominated adsorption to trigger direct eNRR. Using this mechanistic insight as a new criterion, we proposed a theoretical protocol for eNRR catalyst screening, but almost none of the theoretically reported electrocatalysts passed the assessment. This work not only illustrates the intrinsic mechanism behind the low-performance dilemma of eNRR but also points out a possible direction toward designing promising catalysts with high selectivity and high current density.

Structural and energetic properties of cluster models of anatase-supported single late transition metal atoms: a density functional theory benchmark study

CONTEXT

Single-atom catalytic systems constitute an intriguing research topic due to their inherently different chemical behavior as compared to classic heterogeneous catalysts. In this study, cluster systems representing single late transition metal atoms adsorbed on anatase were constructed starting from previously generated periodic models and subjected to a density functional theory (DFT) benchmark study. The ability of different density functional approximations representing all rungs of the Jacob's Ladder classification to accurately describe bond lengths and adsorption energies was assessed for these clusters with the aim of revealing the functional that allows to retain the structural characteristics of the initial periodic system, while also delivering reliable energetics. In this regard, our results indicate that optimisation of the clusters with the meta-GGA functionals TPSS or RevTPSS provides the lowest mean unsigned error and root-mean-square deviations with respect to the periodic models. Moreover, these functionals and, to a slightly lesser degree, PW91 were also found to provide adsorption energies that are statistically the least deviating from the CCSD(T) reference data. More complex hybrid functionals appear to be performing less well.

METHODS

Cluster geometries were determined at the Kohn-Sham DFT level using the LANL2DZ basis set for the transition metals and the Pople 6-31G(d) basis set for O and H. The density functional approximations considered were SVWN, PBE, BP86, BLYP, PW91, TPSS, RevTPSS, M06L, M11L, B3LYP, PBE0, M06, M06-2X, MN15, ωB97X-D, CAM-B3LYP, M11, and MN12-SX. Reference adsorption energies of the metals on the support cluster were obtained at the CCSD(T)/LANL2TZ (transition metals)/6-311 +  + G(d,p)//RevTPSS/LANLD2DZ (transition metals)/6-31G*. Besides the above-mentioned functionals, energy calculations using the double-hybrid functionals, DSDPBEP86, PBE0-DH, and B2PLYP, were also performed. All adsorption energy calculations were carried out on the RevTPSS geometries.

From unbound to bound states: Ab initio molecular dynamics of ammonia clusters with an excess electron

Ab initio molecular dynamics simulations of negatively charged clusters of 2-48 ammonia molecules were performed to elucidate the electronic stability of the excess electron as a function of cluster size. We show that while the electronic stability of finite temperature clusters increases with cluster size, as few as 5-7 ammonia molecules can bind an excess electron, reaching a vertical binding energy slightly less than half of the bulk value for the largest system studied. These results, which are in agreement with previous studies wherever available, allowed us to analyze the excess electron binding patterns in terms of its radius of gyration and shape anisotropy and provide a qualitative interpretation based on a particle-in-a-spherical-well model.

Density isobar of water and melting temperature of ice: Assessing common density functionals

We investigate the density isobar of water and the melting temperature of ice using six different density functionals. Machine-learning potentials are employed to ensure computational affordability. Our findings reveal significant discrepancies between various base functionals. Notably, even the choice of damping can result in substantial differences. Overall, the outcomes obtained through density functional theory are not entirely satisfactory across most utilized functionals. All functionals exhibit significant deviations either in the melting temperature or equilibrium volume, with most of them even predicting an incorrect volume difference between ice and water. Our heuristic analysis indicates that a hybrid functional with 25% exact exchange and van der Waals damping averaged between zero and Becke-Johnson dampings yields the closest agreement with experimental data. This study underscores the necessity for further enhancements in the treatment of van der Waals interactions and, more broadly, density functional theory to enable accurate quantitative predictions for molecular liquids.

Exploring non-covalent interactions in excited states: beyond aromatic excimer models

Time-dependent density functional theory (TD-DFT) offers a relatively accurate and inexpensive approach for excited state calculations. However, conventional TD-DFT may suffer from the same poor description of non-covalent interactions (NCIs) which is known from ground-state DFT. In this work we present a comprehensive benchmark study of TD-DFT for excited-state NCIs. This is achieved by calculating dissociation curves for excited complexes ('exciplexes'), whose binding strength depends on excited-state NCIs including electrostatics, Pauli repulsion, charge-transfer, and London dispersion. Reference dissociation curves are calculated with the reasonably accurate wave function method SCS-CC2/CBS(3,4) which is used to benchmark a range of TD-DFT methods. Additionally, we test the effect of ground-state dispersion corrections, DFT-D3(BJ) and VV10, for exciplex binding. Overall, we find that TD-DFT methods generally under-bind exciplexes which can be explained by the missing dispersion forces. Underbinding errors reduce going up the rungs of Jacob's ladder. Further, the D3(BJ) dispersion correction is essential for good accuracy in most cases. Likewise, the VV10-type non-local kernel yields relatively low errors and has comparable performance in either its fully self-consistent implementation or as a post-SCF additive correction, but its impact is solely on ground-state energies and not on excitation energies. From our analysis, the most robust TD-DFT methods for exciplexes with localised excitations in their equilibrium and non-equilibrium geometries are the double hybrids B2GP-PLYP-D3(BJ) and B2PLYP-D3(BJ). Their range-separated versions ωB2(GP-)PLYP-D3(BJ) or the spin-opposite scaled, range-separated double hybrid SOS-ωB88PP86 can be recommended when charge transfer plays a role in the excitations. We also identify the need for a state-specific dispersion correction as the next step for improved TD-DFT performance.

Supramolecular architecture of theophylline polymorphs, monohydrate and co-crystals with iodine: study from the energetic viewpoint

The regularities of crystal structure organization were thoroughly studied in all to date known polymorphic modifications of theophylline (THP) using an energetic approach. The monohydrate and a co-crystal of theophylline with one half equivalent of an iodine molecule were similarly investigated. The calculations of pairwise interaction energies have showed that the crystals studied can be divided into two groups according to their basic structural motifs: columnar-layered or columnar. The energetic approach also allows the role of different interactions in the crystal structure formation to be estimated. It was found that strong N-H⋯N, N-H⋯O hydrogen bonds and stacking interactions play the most important roles in polymorphic modifications of THP and the THP monohydrate. In the case of the co-crystal with iodine, N-H⋯O hydrogen bond participates in the dimeric building unit formation. However, instead of a stacking interaction the π⋯π interaction between carbonyl groups of neighboring molecules plays the highest role in the supramolecular architecture of this crystal. The lattice energies calculations in periodic conditions for polymorphic structures have shown that polymorph with the most anisotropic energetic structure may be considered as stable and all others forms metastable. In the polymorphic modification 1 of THP a zwitter-ionic resonance form is predominant, which affects significantly the solubility and the intermolecular interactions of this modification.

Implementing reactivity in molecular dynamics simulations with harmonic force fields

The simulation of chemical reactions and mechanical properties including failure from atoms to the micrometer scale remains a longstanding challenge in chemistry and materials science. Bottlenecks include computational feasibility, reliability, and cost. We introduce a method for reactive molecular dynamics simulations using a clean replacement of non-reactive classical harmonic bond potentials with reactive, energy-conserving Morse potentials, called the Reactive INTERFACE Force Field (IFF-R). IFF-R is compatible with force fields for organic and inorganic compounds such as IFF, CHARMM, PCFF, OPLS-AA, and AMBER. Bond dissociation is enabled by three interpretable Morse parameters per bond type and zero energy upon disconnect. Use cases for bond breaking in molecules, failure of polymers, carbon nanostructures, proteins, composite materials, and metals are shown. The simulation of bond forming reactions is included via template-based methods. IFF-R maintains the accuracy of the corresponding non-reactive force fields and is about 30 times faster than prior reactive simulation methods.

Computational Design of Ligands for the Ir-Catalyzed C5-Borylation of Indoles through Tuning Dispersion Interactions

The indole moiety is ubiquitous in natural products and pharmaceuticals. C-H borylation of the benzenoid moiety of indoles is a challenging task, especially at the C5 position. We have combined computational and experimental studies to introduce multiple noncovalent interactions, especially dispersion, between the substrate and catalytic ligand to realize C5-borylation of indoles with high reactivity and selectivity. The successful computational predictions of new ligands should be suitable for ligand design in other transition-metal catalyzed reactions.

Tuning the Properties of Hydrazone/Isosorbide-Based Switchable Chiral Dopants

The long-range supramolecular interactions in liquid crystals (LCs) can be used to amplify and subsequently propagate microscopic structural changes into macroscopic events. Here, we report on a systematic structure-property analysis using 16 chiral photoswitchable dopants composed of bistable hydrazones and chiral isosorbide moieties. Our findings showcase the relationship between the dopant's structure and its helical twisting power (β), and hence, the photophysical properties of the host LC. We show that an increase in the hydrazone CNNH dihedral angle results in an increase in the β value, while alkoxy chains do not lead to such an increase. These results contradict established rules of thumb, stating that structural rigidity and long alky chains are needed for high β values. We also found that the position of the substitution, whether at the 2' or 5' positions of the isosorbide unit, or the attachment of the chiral unit to the rotor or stator phenyl units can have negative or positive additive effects that can either increase or decrease the β values. These results made us hypothesize that unsymmetrically functionalized dopants should result in large Δβ values, which we corroborated experimentally. Moreover, a fluorine-functionalized dopant resulted in higher overall β values, most likely because of π-π interactions. Finally, the dopants were used in modulating and locking in the reflective properties of LC films, yielding multicolor LC canvases that can reflect light from the ultraviolet to the infrared range (i.e., a manipulation of up to ca. 1500 nm of reflected light).

Unraveling the Roles of Ionic Size and Hydrogen Bonding in Electric Field-Driven Ion Emission from Hydroxylamine Nitrate-Based Ionic Liquids

Ionic size and hydrogen bonding (HB) may play significant roles in controlling ion emission from HAN (hydroxylamine nitrate)-based ionic liquids (ILs) but have received little attention. In this paper, the ion emission behavior and mechanism in an external electric field are meticulously investigated using the molecular dynamics (MD) method and density functional theory. We find that the higher the proportion of ionic HAN in the blend of ILs, the longer the delay time of the ion start-up emission. In the positive mode, cations can evaporate directly from the surface of the studied ILs and manifest exclusively as the [EMIM]+ monomers within the simulation time scale, whereas in the negative mode, a variety of complicated anion clusters are emitted. As a result, the average charge-to-mass ratio of the positively charged species remarkably exceeds that of the negatively charged species. This large difference is attributed to the relatively larger size of the [EMIM]+ ion and the absence of substantial HB interactions between the [EMIM]+ ion and any other monomer, leading to diminished binding energies. Conversely, the strong HB interactions, primarily constituted by N-H--O and O-H--O hydrogen bonds, are clearly found in the [EtSO4]--based and HAN-based clusters. In addition, the [NO3]- and [EtSO4]- ions tend to combine with the small-sized [HA]+ ions to form large anion clusters rather than with the [EMIM]+ ions. The energy decomposition results further elucidate that the orbital interaction plays a pivotal role in the [NO3]- and [EtSO4]--based clusters. The findings clearly elucidate the experimental phenomena observed in previous studies and have implications for the formulation of multimode IL propellants.

Quasi-one-dimensional hydrogen bonding in nanoconfined ice

The Bernal-Fowler ice rules stipulate that each water molecule in an ice crystal should form four hydrogen bonds. However, in extreme or constrained conditions, the arrangement of water molecules deviates from conventional ice rules, resulting in properties significantly different from bulk water. In this study, we employ machine learning-driven first-principles simulations to identify a new stabilization mechanism in nanoconfined ice phases. Instead of forming four hydrogen bonds, nanoconfined crystalline ice can form a quasi-one-dimensional hydrogen-bonded structure that exhibits only two hydrogen bonds per water molecule. These structures consist of strongly hydrogen-bonded linear chains of water molecules that zig-zag along one dimension, stabilized by van der Waals interactions that stack these chains along the other dimension. The unusual interplay of hydrogen bonding and van der Waals interactions in nanoconfined ice results in atypical proton behavior such as potential ferroelectric behavior, low dielectric response, and long-range proton dynamics.

Benchmarking Charge-Transfer Excited States in TADF Emitters: ΔDFT Outperforms TD-DFT for Emission Energies

Charge-transfer (CT) excited states are crucial to organic light-emitting diodes (OLEDs), particularly to those based on thermally activated delayed fluorescence (TADF). However, accurately modeling CT states remains challenging, even with modern implementations of (time-dependent) density functional theory [(TD-)DFT], especially in a dielectric environment. To identify shortcomings and improve the methodology, we previously established the STGABS27 benchmark set with highly accurate experimental references for the adiabatic energy gap between the lowest singlet and triplet excited states (ΔEST). Here, we diversify this set to the STGABS27-EMS benchmark by including experimental emission energies (Eem) and use this new set to (re)-evaluate various DFT-based approaches. Surprisingly, these tests demonstrate that a state-specific (un)restricted open-shell Kohn-Sham (U/ROKS) DFT coupled with a polarizable continuum model for perturbative state-specific nonequilibrium solvation (ptSS-PCM) provides exceptional accuracy for predicting Eem over a wide range of density functionals. In contrast, the main workhorse of the field, Tamm-Dancoff-approximated TD-DFT (TDA-DFT) paired with the same ptSS-PCM, is distinctly less accurate and strongly functional-dependent. More importantly, while TDA-DFT requires the choice of two very different density functionals for good performance on either ΔEST or Eem, the time-independent U/ROKS/PCM approaches deliver excellent accuracy for both quantities with a wide variety of functionals.

The effect of tethered bi-naphthyls on visible-light promoted alkene-alkene [2 + 2] cycloadditions

Dispersion interactions are ubiquitous weak interactions that can play a role in many chemical events. Tailor-made catalysts and additives can lead to more selective reactions by properly exploiting dispersion interactions. Although radical-π dispersion interactions are known to have an important stabilizing role, this concept has been so far overlooked in synthetic photochemistry. We recently proved that similar dispersion interactions can play a profound impact on several reactions involving an energy transfer step. We present herein a study on the co-catalytic effect of tethered bi-naphthyl derivatives on the visible-light-promoted alkene-alkene [2 + 2] cycloaddition. A library of tethered bi-naphthyl derivatives was prepared in order to evaluate the impact of the tether on the efficiency of the prototypical [2 + 2] cycloaddition. The best performing additives showed a dramatic effect on the efficiency of the cyclization, and a rationalization of their relative efficiency was carried out through DFT modeling. The best co-catalyst allowed one to isolate desired products in good to excellent yields even employing several challenging substrates. These results offer new tools to devise optimized [2 + 2] photocycloaddition methods and provide valuable information for the design of organic co-catalyst that can boost photochemical reactions by exploiting dispersion interactions.

Introducing a new correlation functional in density functional theory

The correlation functional holds significance in density functional theory as it addresses electron-electron interactions beyond the mean-field approximation, enhancing the accuracy of total energy calculations, electronic excitations, and the prediction of materials properties. There are several expressions to describe this energy, and each of them has a unique set of errors in calculating particular properties of materials. This work offers a new correlation functional by employing the density's dependence on ionization energy. We theoretically derived this functional and combined it with the previously reported ionization energy dependent exchange functional to investigate its effect on the total energy, bond energy, dipole moment, and zero-point energy of 62 molecules. The comparison of this new functional in respect to existing widely used correlation models including QMC, PBE, B3LYP and Chachiyo models shows how well it works in producing accurate results with minimal mean absolute error.

Position of substituents directs the electron transfer properties of entatic state complexes: new insights from guanidine-quinoline copper complexes

In a previous study, we showed that the properties and the ability as an entatic state model of copper guanidine quinoline complexes are significantly influenced by a methyl or methyl ester substituent in the 2-position. To prove the importance of the 2-position of the substituent, two novel guanidine quinoline ligands with a methyl or methyl ester substituent in the 4-position and the corresponding copper complexes were synthesized and characterized in this study. The influence of the substituent position on the copper complexes was investigated with various experimental and theoretical methods. The molecular structures of the copper complexes were examined in the solid state by single-crystal X-ray diffraction (SCXRD) and by density functional theory (DFT) calculations indicating a strong dependency on the substituent position compared to the systems substituted in the 2-position from the previous study. Further, the significantly different influence on the donor properties in dependency on the substituent position was analyzed with natural bond orbital (NBO) calculations. By the determination of the redox potentials, the impact on the electrochemical stabilization was examined. With regard to further previously analyzed guanidine quinoline copper complexes, the electrochemical stabilization was correlated with the charge-transfer energies calculated by NBO analysis and ground state energies, revealing the substituent influence and enabling a comparatively easy and accurate possibility for the theoretical calculation of the relative redox potential. Finally, the electron transfer properties were quantified by determining the electron self-exchange rates via the Marcus theory and by theoretical calculation of the reorganization energies via Nelsen's four-point method. The results gave important insights into the dependency between the ability of the copper complexes as entatic state model and the type and position of the substituent.

One- and Two-Photon Photophysical Properties, Ultrafast Dynamics, and DFT Study of Three Modified Zinc Phthalocyanines

As two-photon absorption (TPA) materials, phthalocyanine molecules have promising application prospects due to their large TPA absorption cross-section, high third-order nonlinear optical susceptibility, and ultrafast response characteristics. In this work, optical properties and the ultrafast response of three modified zinc phthalocyanine molecules (P-HPcZn, Pc-P-Pc, and (DR1)4PcZn) were analyzed. No obvious side-shoulder absorption peaks in the Q-band can be observed from the steady-state absorption spectra of the three molecules, confirming the lack of aggregation products in the solutions of our measurement. Open-aperture Z-scan results show relatively large TPA cross-section values of 136.4 and 55.3 GM for Pc-P-Pc and (DR1)4PcZn, respectively. The nonlinear optical results show that the absorption process observed under the excitation of femtosecond pulses is a reverse saturable absorption (RSA) mechanism. Up-conversion fluorescence spectra of (DR1)4PcZn in THF solution indicate that the fluorescence emission mechanism is TPA. In the study of ultrafast dynamics, the transient absorption spectra were investigated and the decay lifetime of the dynamic traces corresponding to some representative probe wavelengths was obtained through data fitting with a multi-exponential function. Finally, the charge transfer and excited state properties of the modified zinc phthalocyanine molecules were discussed in depth by the DFT method. The energy gaps of P-HPcZn, Pc-P-Pc, and (DR1)4PcZn are 2.16, 1.39, and 2.13 eV, respectively. The results indicate that the Pc-P-Pc of donor-acceptor-donor (D-A-D) structure has the smallest energy gap as well as the best charge transfer properties.

Ultrafast Knock-Off Li+ Diffusion and Subtle Structural Evolution of Li5V3O8 Anode in Lithium-Ion Batteries

Li5V3O8, a lithiation product derived from the LiV3O8 cathode, has emerged as a promising intercalation-type anode material, boasting a theoretical capacity of 256 mA h g-1. Through a comprehensive combination of experimental and theoretical approaches, we demonstrate its capability to intercalate a substantial amount of Li+ at extremely high rates. Experimental findings reveal that Li5V3O8 exhibits outstanding high-rate capability (with a specific capacity of 152 mA h g-1, 60% of the theoretical capacity at 40 C) and exceptional cyclability (with a capacity retention of 80% after 11,000 cycles at 20 C). The structural changes in Li5V3O8 during the lithiation/delithiation cycles are subtle and reversible. First-principles calculations highlight a knock-off mechanism in Li+ diffusion within Li5V3O8, with an estimated energy barrier ranging from 0.16 to 0.38 eV, considerably lower than that of a direct hopping mechanism (0.62-1.44 eV). These ultrafast ion diffusion properties are attributed to interlock interactions among interstitial tetrahedral Li+ and neighboring octahedral lattice Li+, facilitating long-distance and chain-like Li+ diffusion. This study not only introduces an influential vanadium-based anode material with practical implications for fast-charging lithium-ion batteries but also provides fundamental insights into solid state Li+ diffusion kinetics.

Mutual synergistic regulation of chloride anion and cesium cation binding using a new designed macrocyclic multi-functional sites receptor: A case of DFT computational prediction

The mutual synergistic regulation of the multi-functional sites on a single receptor molecule for ion-binding/recognition is vital for the new receptor design and needs to be well explored from experiment and theory. In this work, a new macrocyclic ion receptor (BEBUR) with three functional zones, including two ether holes and one biurea groups, is designed expecting to mutually enhance the ion-binding performance. The binding behaviors of BEBUR mainly for Cl- and Cs+ are deeply investigated by using density functional theoretical calculations. It is found that Cl-/Cs+ binding can be mutually enhanced and synergistically regulated via corresponding conformational changes of the receptor, well reflecting an electrical complementary matching and mutual reinforcement effect. Moreover, solvent effect calculations indicate that BEBUR may be an excellent candidate structure for Cl--binding with the enhancement of counter ion (Cs+) in water and toluene. In addition, visualization of intermolecular noncovalent interaction is used for analysis on the nature of the binding interactions between receptor and ions.

Quantum chemical calculations of nitrosamine activation and deactivation pathways for carcinogenicity risk assessment

N-nitrosamines and nitrosamine drug substance related impurities (NDSRIs) became a critical topic for the development and safety of small molecule medicines following the withdrawal of various pharmaceutical products from the market. To assess the mutagenic and carcinogenic potential of different N-nitrosamines lacking robust carcinogenicity data, several approaches are in use including the published carcinogenic potency categorization approach (CPCA), the Enhanced Ames Test (EAT), in vivo mutagenicity studies as well as read-across to analogue molecules with robust carcinogenicity data. We employ quantum chemical calculations as a pivotal tool providing insights into the likelihood of reactive ion formation and subsequent DNA alkylation for a selection of molecules including e.g., carcinogenic N-nitrosopiperazine (NPZ), N-nitrosopiperidine (NPIP), together with N-nitrosodimethylamine (NDMA) as well as non-carcinogenic N-nitrosomethyl-tert-butylamine (NTBA) and bis (butan-2-yl) (nitros)amine (BBNA). In addition, a series of nitroso-methylaminopyridines is compared side-by-side. We draw comparisons between calculated reaction profiles for structures representing motifs common to NDSRIs and those of confirmed carcinogenic and non-carcinogenic molecules with in vivo data from cancer bioassays. Furthermore, our approach enables insights into reactivity and relative stability of intermediate species that can be formed upon activation of several nitrosamines. Most notably, we reveal consistent differences between the free energy profiles of carcinogenic and non-carcinogenic molecules. For the former, the intermediate diazonium ions mostly react, kinetically controlled, to the more stable DNA adducts and less to the water adducts via transition-states of similar heights. Non-carcinogenic molecules yield stable carbocations as intermediates that, thermodynamically controlled, more likely form the statistically preferred water adducts. In conclusion, our data confirm that quantum chemical calculations can contribute to a weight of evidence approach for the risk assessment of nitrosamines.

Computational methods for investigating organic radical species

Computational analysis of organic radical species presents significant challenges. This study compares the efficacy of various DFT and wavefunction methods in predicting radical stabilisation energies, bond dissociation energies, and redox potentials for organic radicals. The hybrid meta-GGA M062X-D3(0), and the range-separated hybrids ωB97M-V and ωB97M-D3(BJ) emerged as the most reliable functionals, consistently providing accurate predictions across different basis sets including 6-311G**, cc-pVTZ, and def2-TZVP.

Synergistic regulation of chloride anion recognition using a triple-functional sites receptor with two different cationic effectors

The synergistic regulation of the multi-functional sites on one receptor molecule with different cationic effectors for anion recognition is scarce to be well understood from the experiment and theory. In this work, a new anion receptor with three functional zones including ether hole, biurea and double bipyridine groups (EUPR) is designed expecting to enhance the chloride anion recognition together with a rational synthesis path being proposed based on four simple and mature organic reaction steps. The conformational structures of the designed receptor EUPR and the binding behaviors for three kinds of ions (Cl-, Na+, and Ag+) are deeply investigated by using density functional theoretical calculations. It is found that Cl- binding via the hydrogen bond interaction can be significantly enhanced and synergistically regulated by the two kinds of cations and the corresponding conformational changes of receptor EUPR. Especially, the conformational pre-organization of receptor caused by the encapsulation of sodium ion into ether hole is benefit to the binding for Cl- in both thermodynamics and kinetics. Na+ binding, in turn, can ever be enhanced by chloride anion, whereas it seems that Ag+ binding cannot always be enhanced by chloride anion, reflecting an electrical complementary matching and mutual enhancement effect for different counter ions. Moreover, solvent effect calculations indicate that EUPR may be an ideal candidate structure for Cl- recognition by strategy of counter ion enhancement in water. Additionally, a visual study of intermolecular noncovalent interaction (NCI) and molecular electrostatic potential (ESP) are used for the analysis on the nature of interactions between receptor and bound ions.

How do spin-scaled double hybrids designed for excitation energies perform for noncovalent excited-state interactions? An investigation on aromatic excimer models

Time-dependent double hybrids with spin-component or spin-opposite scaling to their second-order perturbative correlation correction have demonstrated competitive robustness in the computation of electronic excitation energies. Some of the most robust are those recently published by our group (M. Casanova-Páez, L. Goerigk, J. Chem. Theory Comput. 2021, 20, 5165). So far, the implementation of these functionals has not allowed correctly calculating their ground-state total energies. Herein, we define their correct spin-scaled ground-state energy expressions which enables us to test our methods on the noncovalent excited-state interaction energies of four aromatic excimers. A range of 22 double hybrids with and without spin scaling are compared to the reasonably accurate wavefunction reference from our previous work (A. C. Hancock, L. Goerigk, RSC Adv. 2023, 13, 35964). The impact of spin scaling is highly dependent on the underlying functional expression, however, the smallest overall errors belong to spin-scaled functionals with range separation: SCS- and SOS- ω PBEPP86, and SCS-RSX-QIDH. We additionally determine parameters for DFT-D3(BJ)/D4 ground-state dispersion corrections of these functionals, which reduce errors in most cases. We highlight the necessity of dispersion corrections for even the most robust TD-DFT methods but also point out that ground-state based corrections are insufficient to completely capture dispersion effects for excited-state interaction energies.

Multitask methods for predicting molecular properties from heterogeneous data

Data generation remains a bottleneck in training surrogate models to predict molecular properties. We demonstrate that multitask Gaussian process regression overcomes this limitation by leveraging both expensive and cheap data sources. In particular, we consider training sets constructed from coupled-cluster (CC) and density functional theory (DFT) data. We report that multitask surrogates can predict at CC-level accuracy with a reduction in data generation cost by over an order of magnitude. Of note, our approach allows the training set to include DFT data generated by a heterogeneous mix of exchange-correlation functionals without imposing any artificial hierarchy on functional accuracy. More generally, the multitask framework can accommodate a wider range of training set structures-including the full disparity between the different levels of fidelity-than existing kernel approaches based on Δ-learning although we show that the accuracy of the two approaches can be similar. Consequently, multitask regression can be a tool for reducing data generation costs even further by opportunistically exploiting existing data sources.

Next-generation of BBQ analogues that selectively target breast cancer

We previously reported on the interaction of 10-chloro-7H-benzo[de]benzo[4,5]imidazo[2,1-a]isoquinolin-7-one (10-Cl-BBQ) with the Aryl hydrocarbon Receptor (AhR) and selective growth inhibition in breast cancer cell lines. We now report on a library of BBQ analogues with substituents on the phenyl and naphthyl rings for biological screening. Herein, we show that absence of the phenyl Cl of 10-Cl-BBQ to produce the simple BBQ molecule substantially enhanced the growth inhibitory effect with GI50 values of 0.001-2.1 μM in select breast cancer cell lines MCF-7, T47D, ZR-75-1, SKBR3, MDA-MB-468, BT20, BT474 cells, while having modest effects of 2.1-7 μM in other cell lines including HT29, U87, SJ-G2, A2780, DU145, BE2-C, MIA, MDA-MB-231 or normal breast cells, MCF10A (3.2 μM). The most potent growth inhibitory effect of BBQ was observed in the triple negative cell line, MDA-MB-468 with a GI50 value of 0.001 μM, presenting a 3,200-fold greater response than in the normal MCF10A breast cells. Additions of Cl, CH3, CN to the phenyl ring and ring expansion from benzoimidazole to dihydroquinazoline hindered the growth inhibitory potency of the BBQ analogues by blocking potential sites of CYP1 oxidative metabolism, while addition of Cl or NO2 to the naphthyl rings restored potency. In a cell-based reporter assay all analogues induced 1.2 to 10-fold AhR transcription activation. Gene expression analysis confirmed the induction of CYP1 oxygenases by BBQ. The CYP1 inhibitor α-naphthoflavone, and the SULT1A1 inhibitor quercetin significantly reduced the growth inhibitory effect of BBQ, confirming the importance of both phase I and II metabolic activation for growth inhibition. Conventional molecular modelling/docking revealed no significant differences between the binding poses of the most and least active analogues. More detailed DFT analysis at the DSD-PBEP86/Def-TZVPP level of theory could not identify significant geometric or electronic changes which would account for this varied AhR activation. Generation of Fukui functions at the same level of theory showed that CYP1 metabolism will primarily occur at the phenyl head group of the analogues, and substituents within this ring lead to lower cytotoxicity.

Intramolecularly O,N,O-Coordinated Tin(II) Salts: Syntheses, Structures, Cyclization, and Transition Metal Complexation

We report the syntheses of tin(II) salts of the types [L1SnX]SnX3 [L1=2,6-{(i-PrO)2(O)P}2C5H3N: 1, X=Cl; 2, X=Br], [L2SnCl]SnCl3 [L2=2-{(i-PrO)Ph(O)P}-6-{(i-PrO)2(O)P}C5H3N: 3], [L3SnX]SnX3 [L3=2,6-{MeO(O)C}2C5H3N: 4, X=Cl; 5, X=Br], [L4SnX]SnX3 [L4=2,6-{Et2N(O)C}2C5H3N: 6, X=Cl; 7, X=Br]. These compounds were obtained by addition of SnX2 to the corresponding ligand inducing autoionization of the respective tin(II) halide. The thermal stability of 1, 3, and 4 was elucidated, giving, under ester cleavage and cyclisation, the tin(II) derivatives 8-12. The reaction of [L1SnCl]SnCl3 (1) with W(CO)4(thf)2 afforded the tungsten tetracarbonyl complex [{L1SnCl}{SnCl3}W(CO)4] (13), representing the first example in which a tin(II) stannate anion and a tin(II) stannylium cation simultaneously coordinate to a transition metal centre. The compounds were characterized by single crystal X-ray diffraction analyses and in part by elemental analyses, IR and NMR spectroscopy, electrospray ionization mass spectrometry. DFT calculations accompany the experimental work.

DszA Catalyzes C-S Bond Cleavage through N5-Hydroperoxyl Formation

Due to its detrimental impact on human health and the environment, regulations demand ultralow sulfur levels on fossil fuels, in particular in diesel. However, current desulfurization techniques are expensive and cannot efficiently remove heteroaromatic sulfur compounds, which are abundant in crude oil and concentrate in the diesel fraction after distillation. Biodesulfurization via the four enzymes of the metabolic 4S pathway of the bacterium Rhodococcus erythropolis (DszA-D) is a possible solution. However, the 4S pathway needs to operate at least 500 times faster for industrial applicability, a goal currently pursued through enzyme engineering. In this work, we unveil the catalytic mechanism of the flavin monooxygenase DszA. Surprisingly, we found that this enzyme follows a recently proposed atypical mechanism that passes through the formation of an N5OOH intermediate at the re side of the cofactor, aided by a well-defined, predominantly hydrophobic O2 pocket. Besides clarifying the unusual chemical mechanism of the complex DszA enzyme, with obvious implications for understanding the puzzling chemistry of flavin-mediated catalysis, the result is crucial for the rational engineering of DszA, contributing to making biodesulfurization attractive for the oil refining industry.

Accurate Enthalpies of Formation for PFAS from First-Principles: Combining Different Levels of Theory in a Generalized Thermochemical Hierarchy

The enthalpies of formation are computed for a large number of per- and poly fluoroalkyl substances (PFAS) using a connectivity-based hierarchy (CBH) approach. A combination of different electronic structure methods are used to provide the reference data in a hierarchical manner. The ANL0 method, in conjunction with the active thermochemical tables, provides enthalpies of formation for smaller species with subchemical accuracy. Coupled-cluster theory with explicit correlations are used to compute enthalpies of formation for intermediate species, based upon the ANL0 results. For the largest PFAS, including perfluorooctanoic acid (PFOA) and heptafluoropropylene oxide dimer acid (GenX), coupled-cluster theory with local correlations is used. The sequence of homodesmotic reactions proposed by the CBH are determined automatically by a new open-source code, AutoCBH. The results are the first reported enthalpies of formation for the majority of the species. A convergence analysis and global uncertainty quantification confirm that the enthalpies of formation at 0 K should be accurate to within ±5 kJ/mol. This new approach is not limited to PFAS, but can be applied to many chemical systems.

Big data benchmarking: how do DFT methods across the rungs of Jacob's ladder perform for a dataset of 122k CCSD(T) total atomization energies?

Total atomization energies (TAEs) are a central quantity in density functional theory (DFT) benchmark studies. However, so far TAE databases obtained from experiment or high-level ab initio wavefunction theory included up to hundreds of TAEs. Here, we use the GDB-9 database of 133k CCSD(T) TAEs generated by Curtiss and co-workers [B. Narayanan, P. C. Redfern, R. S. Assary and L. A. Curtiss, Chem. Sci., 2019, 10, 7449] to evaluate the performance of 14 representative DFT methods across the rungs of Jacob's ladder (namely, PBE, BLYP, B97-D, M06-L, τ-HCTH, PBE0, B3LYP, B3PW91, ωB97X-D, τ-HCTHh, PW6B95, M06, M06-2X, and MN15). We first use the A25[PBE] diagnostic for nondynamical correlation to eliminate systems that potentially include significant multireference effects, for which the CCSD(T) TAEs might not be sufficiently reliable. The resulting database (denoted by GDB9-nonMR) includes 122k species. Of the considered functionals, B3LYP attains the best performance relative to the G4(MP2) reference TAEs, with a mean absolute deviation (MAD) of 4.09 kcal mol-1. This first-generation hybrid functional, in which the three mixing coefficients were fitted against a small set of TAEs, is one of the few functionals that are not systematically biased towards overestimating the G4(MP2) TAEs, as demonstrated by a mean-signed deviation (MSD) of 0.45 kcal mol-1. The relatively good performance of B3LYP is followed by the heavily parameterized M06-L meta-GGA functional, which attains a MAD of 6.24 kcal mol-1. The PW6B95, M06, M06-2X, and MN15 functionals tend to systematically overestimate the G4(MP2) TAEs and attain MADs ranging between 18.69 (M06) and 28.54 (MN15) kcal mol-1. However, PW6B95 and M06-2X exhibit particularly narrow error distributions. Thus, scaling their TAEs by an empirical scaling factor reduces their MADs to merely 3.38 (PW6B95) and 2.85 (M06-2X) kcal mol-1. Empirical dispersion corrections (e.g., D3 and D4) are attractive, and therefore, their inclusion worsens the performance of methods that systematically overestimate the TAEs.

Incorporation of Carboxylate Pendant Arms into 18-Membered Macrocycles: Effects on [nat/203Pb]Pb(II) Complexation

We present a detailed investigation on the coordination chemistry of [nat/203Pb]Pb(II) with chelators H4PYTA and H4CHX-PYTA. These chelators belong to the family of ligands derived from the 18-membered macrocyclic backbone PYAN and present varying degrees of rigidity due to the presence of either ethyl or cyclohexyl spacers. A complete study of the stable Pb(II) complexes is carried out via NMR, X-Ray crystallography, stability constant determination and computational studies. While these studies indicated that Pb(II) complexation is achieved, and the thermodynamic stability of the resulting complexes is very high, a certain degree of fluxionality does exist in both cases. Nevertheless, radiolabeling studies were carried out using SPECT (single photon emission computed tomography) compatible isotope lead-203 (203Pb, t1/2=51.9 h), and while both chelators complex the radioisotope, the incorporation of carboxylate pendant arms appears to be detrimental towards the stability of the complexes when compared to the previously described amide analogues. Additionally, incorporation of a cyclohexyl spacer does not improve the kinetic inertness of the system.

Experimental detection of the diamino-pentazolium cation and theoretical exploration of derived high energy materials

In this work, we realized the detection of diamino-pentazolium cation (DAPZ+) in the reaction solution experimentally and proved it to be meta-diamino-pentazole based on the transition state theory. Quantum chemical methods were used to predict its spectral properties, charge distribution, stability and aromaticity. Considering that DAPZ+ has excellent detonation properties, it was further explored by assembling it with N5-, N3- and C(NO2)3- anions, respectively. The results show a strong interaction between DAPZ+ and the three anions, which will have a positive effect on its stability. Thanks to the high enthalpy of formation and density, the calculated detonation properties of the three systems are exciting, especially [DAPZ+][N5-] (D: 10,016 m·s-1; P: 37.94 GPa), whose actual detonation velocity may very likely exceed CL-20 (D: 9773 m·s-1). There is no doubt that this work will become the precursor for the theoretical exploration of new polynitrogen ionic compounds.

Ground and excited state charge transfer at aqueous nanodiamonds

Nanodiamonds (NDs) are unique carbonaceous materials with exceptionally high stability, hardness, and notable electronic properties. Their applications in photocatalysis, biomedicine, and energy materials are usually carried out in aqueous environments, where they interact with aqueous adsorbates. Especially, electron density may rearrange from the diamond material toward oxidative adsorbates such as oxygen, which is known as charge transfer doping. In this article, we quantify the charge transfer doping for NDs with inhomogeneous surface coverings (hydroxyl, fluorine, and amorphous carbon), as well as NDs doped with heteroatoms (B, Si, N) using hybrid density functional theory (DFT) calculations. The transfer doping magnitude is largely determined by the NDs' highest occupied molecular orbital energies, which can in turn be modified by the surface covering and doping. However, local modifications of the ND structures do not have any local effects on the magnitude of the charge transfer. We furthermore analyze the impact of aqueous adsorbates on the excited states of an aqueous ND in the context of photocatalysis via time-dependent DFT. Here, we find that the excited electrons are biased to move in the direction of the respective oxidative adsorbate. Surprisingly, we find that also unreactive species such as nitrous oxide may attract the excited electrons, which is probably due to the positive partial charge that is induced by the local N2 O solvation geometry.

The influence of model building schemes and molecular dynamics sampling on QM-cluster models: the chorismate mutase case study

Most QM-cluster models of enzymes are constructed based on X-ray crystal structures, which limits comparison to in vivo structure and mechanism. The active site of chorismate mutase from Bacillus subtilis and the enzymatic transformation of chorismate to prephenate is used as a case study to guide construction of QM-cluster models built first from the X-ray crystal structure, then from molecular dynamics (MD) simulation snapshots. The Residue Interaction Network ResidUe Selector (RINRUS) software toolkit, developed by our group to simplify and automate the construction of QM-cluster models, is expanded to handle MD to QM-cluster model workflows. Several options, some employing novel topological clustering from residue interaction network (RIN) information, are evaluated for generating conformational clustering from MD simulation. RINRUS then generates a statistical thermodynamic framework for QM-cluster modeling of the chorismate mutase mechanism via refining 250 MD frames with density functional theory (DFT). The 250 QM-cluster models sampled provide a mean ΔG‡ of 10.3 ± 2.6 kcal mol-1 compared to the experimental value of 15.4 kcal mol-1 at 25 °C. While the difference between theory and experiment is consequential, the level of theory used is modest and therefore "chemical" accuracy is unexpected. More important are the comparisons made between QM-cluster models designed from the X-ray crystal structure versus those from MD frames. The large variations in kinetic and thermodynamic properties arise from geometric changes in the ensemble of QM-cluster models, rather from the composition of the QM-cluster models or from the active site-solvent interface. The findings open the way for further quantitative and reproducible calibration in the field of computational enzymology using the model construction framework afforded with the RINRUS software toolkit.

Augmentation of NIR Circularly Polarized Luminescence Activity in Shibasaki-Type Lanthanide Complexes Supported by the Spirane Sphenol

We report two new circularly polarized luminescence (CPL)-active lanthanide complexes emissive in the near-infrared (NIR) region; using sphenol as a supporting ligand, we provide the first reported example of an NIR-emissive lanthanide complex supported by a chiral spirane. Inclusion of a quaternary carbon to impart axial chirality results in dramatic augmentation of the CPL strength of the resultant sphenolate complexes (glum ≤ 0.77 for [(sphenol)3ErNa3(thf)6]) compared to that of their contemporary biaryl-based axially chiral analogues (glum ≤ 0.47 for [(binol)3ErNa3(thf)6]). Despite similar structural parameters, the rigid spiro carbon of sphenol enables the strongest dissymmetry factors observed to date from Shibasaki-type complexes for both Yb and Er. We also demonstrate the sensitivity of the reported chiroptical measurements to small variations in instrumental parameters, such as bandpass, and suggest a standardized method or at least that additional detail should be included in future reports to allow for direct comparisons between newly published CPL emitters.

Synthesis and Structural Studies of peri-Substituted Acenaphthenes with Tertiary Phosphine and Stibine Groups

Two mixed peri-substituted phosphine-chlorostibines, Acenap(PiPr2)(SbPhCl) and Acenap(PiPr2)(SbCl2) (Acenap = acenaphthene-5,6-diyl) reacted cleanly with Grignard reagents or nBuLi to give the corresponding tertiary phosphine-stibines Acenap(PiPr2)(SbRR') (R, R' = Me, iPr, nBu, Ph). In addition, the Pt(II) complex of the tertiary phosphine-stibine Acenap(PiPr2)(SbPh2) as well as the Mo(0) complex of Acenap(PiPr2)(SbMePh) were synthesised and characterised. Two of the phosphine-stibines and the two metal complexes were characterised by single-crystal X-ray diffraction. The peri-substituted species act as bidentate ligands through both P and Sb atoms, forming rather short Sb-metal bonds. The tertiary phosphine-stibines display through-space J(CP) couplings between the phosphorus atom and carbon atoms bonded directly to the Sb atom of up to 40 Hz. The sequestration of the P and Sb lone pairs results in much smaller corresponding J(CP) being observed in the metal complexes. QTAIM (Quantum Theory of Atoms in Molecules) and EDA-NOCV (Energy Decomposition Analysis employing Naturalised Orbitals for Chemical Valence) computational techniques were used to provide additional insight into a weak n(P)→σ*(Sb-C) intramolecular bonding interaction (pnictogen bond) in the phosphine-stibines.

Predicting valence tautomerism in diverse cobalt-dioxolene complexes: elucidation of the role of ligands and solvent

The ability of molecular switches to reversibly interconvert between different forms promises potential applications at the scale of single molecules up to bulk materials. One type of molecular switch comprises cobalt-dioxolene compounds that exhibit thermally-induced valence tautomerism (VT) interconversions between low spin Co(iii)-catecholate (LS-CoIII-cat) and high spin Co(ii)-semiquinonate (HS-CoII-sq) forms. Two families of these compounds have been investigated for decades but have generally been considered separately: neutral [Co(diox)(sq)(N2L)] and cationic [Co(diox)(N4L)]+ complexes (diox = generic dioxolene, N2L/N4L = bidentate/tetradentate N-donor ancillary ligand). Computational identification of promising new candidate compounds prior to experimental exploration is beneficial for environmental and cost considerations but requires a thorough understanding of the underlying thermochemical parameters that influence the switching. Herein, we report a robust approach for the analysis of both cobalt-dioxolene families, which involved a quantitative density functional theory-based study benchmarked with reliable quasi-experimental references. The best-performing M06L-D4/def2-TZVPP level of theory has subsequently been verified by the synthesis and experimental investigation of three new complexes, two of which exhibit thermally-induced VT, while the third remains in the LS-CoIII-cat form across all temperatures, in agreement with prediction. Valence tautomerism in solution is markedly solvent-dependent, but the origin of this has not been definitively established. We have extended our computational approach to elucidate the correlation of VT transition temperature with solvent stabilisation energy and change in dipole moment. This new understanding may inform the development of VT compounds for applications in soft materials including films, gels, and polymers.

A Synergistic Bimetallic Ti/Co-Catalyzed Isomerization of Epoxides to Allylic Alcohols Enabled by Two-State Reactivity

Isomerization of epoxides into versatile allylic alcohols is an atom-economical synthetic method to afford vicinal bifunctional groups. Comprehensive density functional theory (DFT) calculations were carried out to elucidate the complex mechanism of a bimetallic Ti/Co-catalyzed selective isomerization of epoxides to allyl alcohols by examining several possible pathways. Our results suggest a possible mechanism involving (1) radical-type epoxide ring opening catalyzed by Cp2Ti(III)Cl leading to a Ti(IV)-bound β-alkyl radical, (2) hydrogen-atom transfer (HAT) catalyzed by the Co(II) catalyst to form the Ti(IV)-enolate and Co(III)-H intermediate, (3) protonation to give the alcohols, and (4) proton abstraction to form the Co(I) species followed by electron transfer to regenerate the active Co(II) and Ti(III) species. Moreover, bimetallic catalysis and two-state reactivity enable the key rate-determining HAT step. Furthermore, a subtle balance between dispersion-driven bimetallic processes and entropy-driven monometallic processes determines the most favorable pathway, among which the monometallic process is energetically more favorable in all steps except the vital hydrogen-atom transfer step. Our study should provide an in-depth mechanistic understanding of bimetallic catalysis.

Puzzling Structure of the Key Intermediates in Gold(I)-catalyzed Cyclization Reactions of Enynes and Allenenes

We identify the dominant structures of the intermediates of gold(I)-catalyzed cyclizations of 1,5-enynes and 1,5-allenenes through computational analysis as gold(I) cyclopropylcarbenes, endocyclic vinylgold complexes and previously unreported non-classical carbocationic minima. In contrast to 1,6-enynes, the exocyclic carbocations are found to be less stable. Cyclopropylcarbene structures are consistently favoured as the most stable intermediates for all studied substitution patterns. We validate the computational methods used by using DLPNO-CCSD(T) energies as a benchmark, indicating that the B3LYP-D3 and M06-D3 functionals are most accurate for energy determination, while NPA charges are mostly insensitive to functional. The evolution of a 1,6-enyne in a single-cleavage or double-cleavage rearrangement is attributed to the barrierless evolution of a common cyclopropyl-gold(I) carbocation non-stationary geometry. Our findings provide insights into reaction pathways and substrate dependence of the cycloisomerization processes.

Effects of Several Auxiliary Acceptors and Anchoring Groups on Charge Transfer and Photophysical Properties of D-A-π-A Type DSSCs: A DFT Study

In this paper, we performed theoretical studies on the twelve D-A-π-A type organic dyes (G-1 ~ G-3, M-1 ~ M-3, J-1 ~ J-3, and S-1 ~ S-3) with 9-phenylcarbazole as the electron donor in anticipation of the application of these dyes in dye-sensitized solar cells (DSSCs). DFT and TD-DFT methods are applied to investigate in detail the molecular geometries, frontier molecular orbitals (FMOs), absorption spectra, charge density difference (CDD), and transition density matrix (TDM) of several dyes. The results show that the M-series (M-1 ~ M-3) dyes have the largest dihedral angles between the electron donor and the auxiliary acceptor and also has the largest energy gaps in HOMO-LUMO orbitals, which greatly reduces the charge transfer efficiency. Finally, the UV-Vis absorption spectra inferred that the anchoring groups modified with o-nitrobenzoic acid (G-3, M-3, J-3, S-3) can red-shift the absorption peaks of the dyes, which results in higher light-harvesting efficiency and improves the power conversion efficiency of DSSCs. Overall, all of these dyes contribute to the improvement of photovoltaic power conversion efficiency and have potential for application in DSSCs devices.