Reformulation of the D3(Becke–Johnson) Dispersion Correction without Resorting to Higher than C6 Dispersion Coefficients

One-pot complexation of phytic acid and polyethyleneimine on cellulosic microfibers towards insulative and flame-resistant foam

Flame resistance is required for the deployment of bio-based materials, especially those forming cellular structures that endow thermal insulation. This study proposes a one-pot strategy to prepare cellular lignocellulosic composites with excellent flame resistance. Lignocellulosic microfibers were used as the substrate onto which a flame-retardant complex consisting of P-containing phytic acid (PA) and N-containing polyethyleneimine (PEI) was formed. Following the prediction of ab initio molecular dynamics simulation, PA and PEI are integrated onto MF-CTMP following a single-step complexation assembly triggered by pH effects. The PA-PEI modified MF-CTMP can be readily transformed into a composite solid foam by dewatering a wet foam followed by oven drying. At the expense of a slightly reduced thermal insulation (thermal conductivity increase from 33.6 ± 0.6 to 40.0 ± 0.6 mW/(m·K)) the presence of PA-PEI complexes significantly improved the mechanical performance of the foam and uniquely endows it with flame resistance. Compared to unmodified MF-CTMP foams, the composite foams showed significant improvement in the Young's, specific compression, and flexural moduli (increased by 13.5, 5.5, and 7.3 folds, respectively), a high oxygen index (up to 40.8 %) and self-extinguishing effects. The results suggest the suitability of the introduced lignocellulosic foam as an alternative to traditional synthetic polymer-based counterparts as well as inorganic matter for insulation, particularly relevant to the building sector.

A novel nanoparticle fluorescent probe based on a water-soluble conjugated polymer for real-time monitoring of ATP fluctuation and configuration of the Golgi apparatus during the inhibition of glycolysis

BACKGROUND

Adenosine 5'-triphosphate (ATP) plays an important role in cell metabolism and has been regarded as an indicator of cell survival and damage. Golgi apparatus participates in the signal transduction processes of substance transport, ion homeostasis and stress when extracellular substances enter cells. Till now, there is no fluorescent probe for monitoring Golgi ATP level fluctuation and visualizing the configuration change of the Golgi apparatus during the inhibition of glycolysis.

RESULTS

Herein, we report the synthesis of a novel water-soluble cationic polythiophene derivative (PEMTEA) that can be employed as a fluorescent sensor for measuring ATP in the Golgi apparatus. PEMTEA self-assembles into PT-NP nanoparticles in aqueous solution with a diameter of approximately 2 nm. PT-NP displays high sensitivity and superb selectivity towards ATP with a detection limit of 90 nM and a linear detection range from 0 to 3.0 μM. The nanoparticles show low toxicity to HepG2 cells and good photostability in the Golgi apparatus. With the stimulation of Ca2+, PT-NP was practically applied to real-time monitor of endogenous ATP levels in the Golgi apparatus through fluorescence microscopy. Finally, we studied the relationship between the concentration of ATP and configuration of the Golgi apparatus during the inhibition of glycolysis using PT-NP.

SIGNIFICANCE

We have demonstrated that PT-NP can not only indicate the fluctuation and distribution of ATP in the Golgi apparatus, but also give the information of the configuration change of the Golgi apparatus at the single-cell level during the inhibition of glycolysis.

Exploring Raloxifene-Based Metallodrugs: A Versatile Vector Combined with Platinum(II), Palladium(II) and Nickel(II) Dichlorides and Carborates against Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) poses challenges in therapy due to the absence of target expression such as estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). Frequently, the treatment of TNBC involves the combination of several therapeutics. However, an enhanced therapeutic effect can be also achieved within a single molecule. The efficacy of raloxifene can be improved by designing a raloxifene-based hybrid drug bearing a 2,2'-bipyridine moiety (2). Integration of platinum(II), palladium(II), and nickel(II) complexes into this structure dramatically changed the cytotoxicity. The platinum(II) dichloride complex 3 did not demonstrate any activity, while palladium(II) and nickel(II) dichloride complexes 4 and 5 exhibited various cytotoxic behavior towards different types of hormone-receptor positive (HR+) cancer and TNBC cell lines. The replacement of the two chlorido ligands in 3-5 with a dicarbollide (carborate) ion [C2B9H11]2- resulted in reduced activity of compounds 6, 7, and 8. However, the palladacarborane complex 7 demonstrated higher selectivity towards TNBC. Furthermore, the mechanism of action was shifted from cytotoxic to explicitly cytostatic with detectable proliferation arrest and accelerated aging, characterized by senescence-associated phenotype of TNBC cells. This study provides valuable insights into the development of hybrid therapeutics against TNBC.

Integrating density functional theory and chemical ionization mass spectrometry techniques to assess benzophenone derivatives in food packaging: implications for enhancing food quality and safety

Benzophenone and related derivatives are widely used as photoinitiators for food packaging to cure inks or lacquers with ultraviolet (UV) light on cardboard and paper. However, there are concerns about the potential health risks of their migration into food. Knowing the physical and chemical properties of benzophenone and its derivatives could play a significant role in their quantification and analysis using chemical ionization mass spectrometry (CI-MS) methods. These parameters are evaluated using B3LYP/6-311++** density functional theory (DFT) implemented on Gaussian code. Ion-molecule chemistry through the selection of reagent ions, reaction energetics and kinetics, thermodynamic stability, and reactivity of molecules deemed to foster VOC identification and quantification via CI-MS techniques. The VOCs under study are expected to undergo exothermic reactions from H3 O+ , NH4 + , NO+ , and O2 + ions, except endothermic proton transfer from NH4 + to 2-hydroxy-4-methoxybenzophenone and 2,3,4-trihydroxy benzophenone. These compounds possess less proton affinities than NH3 and are least stable in their protonated forms. The DFT computed properties provide the basis for developing reliable and accurate methods to detect and measure the presence of benzophenone and its derivatives in packaging materials and food products.

Exploring the potential of tamoxifen-based copper(ii) dichloride in breast cancer therapy

For decades, tamoxifen-based hormone therapy has effectively addressed oestrogen receptor positive (ER+) luminal A breast cancer. Nonetheless, the emergence of tamoxifen resistance required innovative approaches, leading to hybrid metallodrugs with several therapeutic effects besides the inhibition of oestrogen receptor α (ERα). Drawing inspiration from tamoxifen metabolite structures (4-hydroxytamoxifen and 4,4'-dihyroxytamoxifen), a phenyl ring was replaced by a bidentate 2,2'-bipyridine donor moiety to give 4-[1,1-bis(4-methoxyphenyl)but-1-en-2-yl]-2,2'-bipyridine (L), enabling coordination of bioactive transition metal compounds such as copper(ii) dichloride, yielding [CuCl(μ-Cl)(L-κ2N,N')]2 (1). Notably, copper(ii) complex 1 exhibited remarkable activity within the low micromolar concentration range against ER+ human glioblastoma U251, as well as breast carcinomas MDA-MB-361 and MCF-7, surpassing the efficacy of previously reported palladium(ii) and platinum(ii) dichloride analogs against these cell lines. The pronounced efficacy of complex 1 against triple-negative MDA-MB-231 cells highlights its potential multitherapeutic approach, evident through induction of apoptosis and antioxidant activity. This study evaluates the potential of copper-tamoxifen hybrid complex 1 as a potent therapeutic candidate, highlighting its diverse mechanism of action against challenging breast cancer subtypes.

Bipyridil-based chelators for Gd(III) complexation: kinetic, structural and relaxation properties

In the last 20 years, research in the field of MRI (magnetic resonance imaging) contrast agents (CAs) has been intensified due to the emergence of a disease called nephrogenic systemic fibrosis (NSF). NSF has been linked to the in vivo dissociation of certain Gd(III)-based compounds applied in MRI as CAs. To prevent the dechelation of the probes after intravenous injection, the improvement of their in vivo stability is highly desired. The inertness of the Gd(III) chelates can be increased through the rigidification of the ligand structure. One of the potential ligands is (2,2',2'',2'''-(([2,2'-bipyridine]-6,6'-diylbis(methylene))bis(azanetriyl))tetraacetic acid) (H4DIPTA), which has been successfully used as a fluorescent probe for lanthanides; however, it has never been considered as a potential chelator for Gd(III) ions. In this paper, we report the thermodynamic, kinetic and structural features of the complex formed between Gd(III) and DIPTA. Since the solubility of the [Gd(DIPTA)]- chelate is very low under acidic conditions, hampering its thermodynamic characterization, we can only assume that its stability is close to that determined for the structural analogue [Gd(FENTA)]- (H4FENTA: (1,10-phenanthroline-2,9-diyl)bis(methyliminodiacetic acid)), which is similar to that determined for the agent [Gd(DTPA)]2- routinely used in clinical practice. Unfortunately, the inertness of [Gd(DIPTA)]- is significantly lower (t1/2 = 1.34 h) than that observed for [Gd(EGTA)]- and [Gd(DTPA)]2- as a result of its spontaneous dissociation pathway during dechelation. The relaxivity values of [Gd(DIPTA)]- are comparable with those of [Gd(FENTA)]- and somewhat higher than the values characterizing [Gd(DTPA)]2-. Luminescence lifetime measurements indicate the presence of one water molecule (q = 1) in the inner sphere of the complex with a relatively high water exchange rate (k298ex = 43(5) × 106 s-1). DFT calculations suggest a rigid distorted tricapped trigonal prismatic polyhedron for the Gd(III) complex. On the basis of these results, we can conclude that the bipyridine backbone is not favourable with respect to the inertness of the chelate.

Modulation of Delayed Fluorescence Guided by Conformational Effect-Mediated Thermally Enhanced Phosphorescence in Phenothiazines-Quinoline-Cl Conjugates

Triplet energy harvesting via thermally activated delayed fluorescence (TADF) from pure organic systems has attracted great attention in organic light-emitting diodes, sensing, and photocatalysis. However, the realization of thermally enhanced phosphorescence (TEP)-guided efficient TADF with a high rate of reverse intersystem crossing (kRISC) still needs to be discovered. Herein, we report two phenothiazine-quinoline conjugates (P2QC, P2QMC) comprising two phenothiazine donors covalently attached to the chlorine-substituted quinolinyl acceptor. Spectroscopic analysis in conjunction with quantum chemistry calculations reveals that TEP in P2QC originated due to slow internal conversion from higher-lying triplet to lowest triplet (T2' → T1') of the quasi-axial (QA) conformer and TADF (kRISC = 1.44 × 108 s-1) originated from the quasi-equatorial (QE) conformer caused by a low singlet-triplet gap (ΔES1-T1 = 0.11 eV) and triplet energy transfer from QA to QE owing to the degenerate ground state of the conformers. In contrast, TADF (kRISC = 0.74 × 108 s-1) and dual phosphorescence under ambient conditions are observed in P2QMC. This study provides a sustainable guideline for developing efficient TADF emitters via conformation effects and energy transfer mechanisms.

Molecular simulation of Cu, Ag, and Au-decorated Si-doped graphene quantum dots (Si@QD) nanostructured as sensors for SO2 trapping

In view of the numerous environmental hazards and health challenges linked to sulfur (iv) oxide (SO2), an indirect greenhouse gas, and the resultant need to develop efficient gas nanosensor devices, this research had as its principal focus on the theoretical evaluation of the gas sensing potential of metals: Ag, Au and Cu functionalized silicon-doped quantum dots (Si@QD) for the detection and adsorption of SO2 gas investigated using the first-principles density functional theory (DFT) computation at the B3LYP-D3(BJ)/def2-SVP level of theory. Eight (8) possible adsorption modes: SO2_O_Si@QD, SO2_O_Ag_Si@QD, SO2_O_Au_Si@QD, SO2_O_Cu_Si@QD, SO2_S_Si@QD, SO2_S_Ag_Si@QD, SO2_S_Au_Si@QD, and SO2_S_Cu_Si@QD were considered based on SO2 interactions with the studied materials at the -S and -O sites of the SO2 molecule. The counterpoise correction (BSSE) showed that five of the eight interactions had favorable Ead + BSSE values ranging from -0.31 to -1.98 eV. All the eight interactions were observed to be thermodynamically favorable with ΔG and ΔH ranging from -129.01 to -200.24 kcal/mol and -158.26 to -229.73 kcal/mol respectively. Results from the topology analysis reveal that van der Waals forces occurred the greatest at the gas-sensor interphase while SO2_S_ Cu_Si@QD is predicted to have the highest sensing potency based on the conductivity and recovery time estimations. These results confirm the potential efficient feasibility of real-world device application of the metals (Ag, Au, Cu) functionalized Si-doped QDs.

N-Sulfonyl-1,2,3,4-tetrahydroisoquinoline Derivatives: Synthesis, Antimicrobial Evaluations, and Theoretical Insights

Microbial contamination remains a significant economic challenge in the food industry, emphasizing the need for innovative antimicrobial solutions. In this study, we synthesized N-sulfonyl-1,2,3,4-tetrahydroisoquinolines (NSTHIQ) derivatives using an environmentally friendly Preyssler heteropolyacid catalyst, obtaining moderate to high yields (35-91 %) under mild conditions. Two derivatives (5 and 6) exhibited significant antifungal properties against various fungal species, including Aspergillus spp, Penicillium spp, and Botrytis cinerea. ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) analysis revealed the absence of hepatic toxicity in all compounds, making derivatives 2, 3, 4, and 5 potential candidates for further development. However, derivatives 6 and 7 exhibited immunotoxicity. In support of our experimental findings, reactivity indices were computed using Density Functional Theory principles, deriving valuable insights into the chemical properties of these derivatives. This study underscores the potential of NSTHIQ compounds as potent antifungal agents, coupled with the importance of employing environmentally friendly catalysts in drug discovery.

Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering

CRISPR-Cas9 tools have transformed genetic manipulation capabilities in the laboratory. Empirical rules-of-thumb have been developed for only a narrow range of model organisms, and mechanistic underpinnings for sgRNA efficiency remain poorly understood. This work establishes a novel feature set and new public resource, produced with quantum chemical tensors, for interpreting and predicting sgRNA efficiency. Feature engineering for sgRNA efficiency is performed using an explainable-artificial intelligence model: iterative Random Forest (iRF). By encoding quantitative attributes of position-specific sequences for Escherichia coli sgRNAs, we identify important traits for sgRNA design in bacterial species. Additionally, we show that expanding positional encoding to quantum descriptors of base-pair, dimer, trimer, and tetramer sequences captures intricate interactions in local and neighboring nucleotides of the target DNA. These features highlight variation in CRISPR-Cas9 sgRNA dynamics between E. coli and H. sapiens genomes. These novel encodings of sgRNAs enhance our understanding of the elaborate quantum biological processes involved in CRISPR-Cas9 machinery.

The Role of Water in the Adsorption of Nitro-Organic Pollutants on Activated Carbon

The density functional theory (DFT) is applied to theoretically study the capture and storage of three different nitro polycyclic aromatic hydrocarbons, 4-nitrophenol, 2-nitrophenol, and 9-nitroanthracene by activated carbon, with and without the presence of water. These species are pollutants derived from vehicle and industry emissions. The modeling of adsorption is carried out at the molecular level using a high-level density functional theory with the B3LYP-GD(BJ)/6-31+G(d,p) level of theory. The adsorption energies of polluting gases considered isolated and in a humid environment are compared to better understand the role of water. The calculations reveal different possible pathways involving the formation of chemical bonds between adsorbent and adsorbate on the formation of intermolecular van der Waals interactions. The negative adsorption energy on AC for the three species is obtained when they are treated individually and in mixture with H2O. The basis-set superposition error, estimated using the counterpoise correction, varies the adsorption energies by 2-13%. Dispersion effects were also taken into account. The adsorption energy ranges from -10 to -414 kJ/mol suggesting a diversity of pathways. The resulting analysis suggests three preferred pathways for capture. The main pathway is physical interaction due to π-π stacking. Other means are capture due to the formation of hydrogen bonds resulting from water adsorbed on the surface and the simultaneous adsorption of pollutant and water where water can act as a link that promotes adsorption. The thermodynamic properties give a clue to the most eco-friendly approaches for molecular adsorption.

Modular Synthesis of Phosphino Hydrazones and Their Use as Ligands in a Palladium-Catalysed Cu-Free Sonogashira Cross-Coupling Reaction

Phosphino hydrazones represent a versatile class of nitrogen-containing phosphine ligands. Herein, we report a modular synthesis of phosphino hydrazone ligands by hydrazone condensation reaction of three different aryl hydrazines with 3-(diphenylphosphino)propanal (PCHO). Complexation reactions of these phosphino hydrazone ligands with palladium(II) and platinum(II) were investigated and the catalytic activity of the palladium(II) complexes was explored in a Cu-free Sonogashira cross-coupling reaction achieving yields up to 96 %. Additionally it was shown that the catalytically active species is homogeneous.

Comparison of the Performance of Density Functional Methods for the Description of Spin States and Binding Energies of Porphyrins

This work analyzes the performance of 250 electronic structure theory methods (including 240 density functional approximations) for the description of spin states and the binding properties of iron, manganese, and cobalt porphyrins. The assessment employs the Por21 database of high-level computational data (CASPT2 reference energies taken from the literature). Results show that current approximations fail to achieve the "chemical accuracy" target of 1.0 kcal/mol by a long margin. The best-performing methods achieve a mean unsigned error (MUE) <15.0 kcal/mol, but the errors are at least twice as large for most methods. Semilocal functionals and global hybrid functionals with a low percentage of exact exchange are found to be the least problematic for spin states and binding energies, in agreement with the general knowledge in transition metal computational chemistry. Approximations with high percentages of exact exchange (including range-separated and double-hybrid functionals) can lead to catastrophic failures. More modern approximations usually perform better than older functionals. An accurate statistical analysis of the results also casts doubts on some of the reference energies calculated using multireference methods. Suggestions and general guidelines for users are provided in the conclusions. These results hopefully stimulate advances for both the wave function and the density functional side of electronic structure calculations.

Rupturing aromaticity by periphery overcrowding

The balance between strain relief and aromatic stabilization dictates the form and function of non-planar π-aromatics. Overcrowded systems are known to undergo geometric deformations, but the energetically favourable π-electron delocalization of their aromatic ring(s) is typically preserved. In this study we incremented the strain energy of an aromatic system beyond its aromatic stabilization energy, causing it to rearrange and its aromaticity to be ruptured. We noted that increasing the steric bulk around the periphery of π-extended tropylium rings leads them to deviate from planarity to form contorted conformations in which aromatic stabilization and strain are close in energy. Under increasing strain, the aromatic π-electron delocalization of the system is broken, leading to the formation of a non-aromatic, bicyclic analogue referred to as 'Dewar tropylium'. The aromatic and non-aromatic isomers have been found to exist in rapid equilibrium with one another. This investigation demarcates the extent of steric deformation tolerated by an aromatic carbocycle and thus provides direct experimental insights into the fundamental nature of aromaticity.

Metallodrugs against Breast Cancer: Combining the Tamoxifen Vector with Platinum(II) and Palladium(II) Complexes

The luminal A-subtype of breast cancer, where the oestrogen receptor α (ERα) is overexpressed, is the most frequent one. The prodrug tamoxifen (1) is the clinically used agent, inhibiting the ERα activity via the formation of several active metabolites, such as 4-hydroxytamoxifen (2) or 4,4'-dihydroxytamoxifen (3). In this study, we present the tamoxifen derivative 4-[1,1-bis(4-methoxyphenyl)but-1-en-2-yl]-2,2'-bipyridine (4), which was combined with platinum or palladium dichloride, the former a well-known scaffold in anticancer treatment, to give [PtCl₂(4-κ²N,N')] (5) or [PdCl₂(4-κ²N,N'] (6). To prevent fast exchange of weakly coordinating chlorido ligands in aqueous solution, a bulky, highly stable and hydrophobic nido-carborate(-2) ([C₂B₉H₁₁]^2-) was incorporated. The resulting complexes [3-(4-κ²N,N')-3,1,2-PtC₂B₉H₁₁] (7) and [3-(4-κ²N,N')-3,1,2-PdC₂B₉H₁₁] (8) exhibit a dramatic change in electronic and biological properties compared to 5 and 6. Thus, 8 is highly selective for triple-negative MDA-MB-231 cells (IC₅₀ = 3.7 μM, MTT test), while 7 is completely inactive against this cell line. The observed cytotoxicity of compounds 4-6 and 8 against this triple-negative cell line suggests off-target mechanisms rather than only ERα inhibition, for which these compounds were originally designed. Spectroscopic properties and electronic structures of the metal complexes were investigated for possible explanations of the biological activities.

Unveiling the structural features that regulate carbapenem deacylation in KPC-2 through QM/MM and interpretable machine learning

Resistance to carbapenem β-lactams presents major clinical and economical challenges for the treatment of pathogen infections. The fast hydrolysis of carbapenems by carbapenemase-producing bacterial strains enables the effective deactivation of carbapenem antibiotics. In this study, we aim to unravel the structural features that distinguish the notable deacylation activity of carbapenemases. The deacylation reactions between imipenem (IPM) and the KPC-2 class A serine-based β-lactamases (ASβLs) are modeled with combined quantum mechanical/molecular mechanical (QM/MM) minimum energy pathway (MEP) calculations and interpretable machine-learning (ML) methods. We first applied a dual-level computational protocol to achieve fast sampling of QM/MM MEPs. A tree-based ensemble ML model was employed to learn the MEP activation barriers from the conformational features of the KPC-2/IPM active site. The barrier-predicting model was then unboxed using the Shapley additive explanation (SHAP) importance attribution methods to derive mechanistic insights, which were also verified by additional QM/MM wavefunction analysis. Essentially, we show that potential hydrogen bonding interactions of the general base and the tautomerization states of the carbapenem pyrroline ring could concertedly regulate the activation barrier of KPC-2/IPM deacylation. Nonetheless, we demonstrate the efficacy of interpretable ML to assist the analysis of QM/MM simulation data for robust extraction of human-interpretable mechanistic insights.

Range-dependence of two-body intermolecular interactions and their energy components in molecular crystals

Routinely assessing the stability of molecular crystals with high accuracy remains an open challenge in the computational sciences. The many-body expansion decomposes computation of the crystal lattice energy into an embarrassingly parallel collection of computations over molecular dimers, trimers, and so forth, making quantum chemistry techniques tractable for many crystals of small organic molecules. By examining the range-dependence of different types of energetic contributions to the crystal lattice energy, we can glean qualitative understanding of solid-state intermolecular interactions as well as practical, exploitable reductions in the number of computations required for accurate energies. Here, we assess the range-dependent character of two-body interactions of 24 small organic molecular crystals using the physically interpretable components from symmetry-adapted perturbation theory (electrostatics, exchange repulsion, induction/polarization, and London dispersion). We also examine correlations between the convergence rates of electrostatics and London dispersion terms with molecular dipole moments and polarizabilities, to provide guidance for estimating convergence rates in other molecular crystals.

Chirality-Puckering correlation and intermolecular interactions in Sphingosines: Rotational spectroscopy of jaspine B3 and its monohydrate

Chirality is determinant for sphingosine biofunctions and pharmacological activity, yet the reasons for the biological chiral selection are not well understood. Here, we characterized the intra- and intermolecular interactions at the headgroup of the cytotoxic anhydrophytosphingosine jaspine B, revealing chirality-dependent correlations between the puckering of the ring core and the formation of amino-alcohol hydrogen bond networks, both in the monomer and the monohydrate. Following the specific synthesis of a shortened 3-carbon side-chain molecule, denoted jaspine B3, six different isomers were observed in a jet expansion using broadband (chirped-pulsed) rotational spectroscopy. Additionally, a single isomer of the jaspine B3 monohydrate was observed, revealing the insertion of water in between the hydroxy and amino groups and the formation of a network of O-H···N-H···O_ring hydrogen bonds. The specific jaspine B3 stereochemistry thus creates a double-faced molecule where the exposed lone-pair electrons may easily catalyze the formation of intermolecular aggregates and determine the sphingosine biological properties.

Engineering the geometric and electronic structure of Ru via Ru–TiO2 interaction for enhanced selective hydrogenation

Ru/TiO2-Vo-250H with the structure of TiO2-Vo-partially encapsulated Ru nanoparticles, balances the active sites for H2 dissociation and the adsorption sites for 6-chloroquinoline, achieving the selective hydrogenation even at room temperature.

Oxidative addition, reduction and reductive coupling: the versatile reactivity of subvalent gallium cations

Inspired by the successful oxidative addition of a P-H bond to univalent Ga[Al(OR^F)₄] that gives the unprecedented dicationic gallium hydride complex [H-Ga(PPh₃)₃][Al(OR^F)₄]₂ (OR^F = OC(CF₃)₃), the oxidative addition of E-Cl containing substrates was investigated. The reductive coupling of three PPh₂Cl to the catenated phosphorus cation [P₃Ph₆]⁺ hinted towards a formal two-electron-three-halide reduction (2e^--3X^- reduction). Similarly, from SbCl₃, a cationic formal Sb^I compound and from RhCl₃, [Rh^I(HMB)(COD)]⁺ and [Rh^I(COD)₂]⁺ (HMB = C₆Me₆, COD = 1,5-cyclooctadiene) are formed as [Al(OR^F)₄]^- salts when reacted with Ga⁺. Thus, Ga[Al(OR^F)₄] allows for a one-pot 2e^--3X^- reduction with the concomitant introduction of a weakly coordinating anion (WCA).

A Metallic Ion-Induced Self-Assembly Enabling Nanowire-Based Aerogels

The controlled assembly of nanowires is one of the key challenges in the development of a range of functional 3D aerogels with unique physicochemical properties for practical applications. However, the deep understanding of the dynamic assemble process for fabricating nanowire aerogels remains elusive. Herein, a facile strategy is presented for the metallic ion-induced assembly of nanowires into macroscopic aerogels via a solution-based process. This method enables the interconnecting between polymer-decorated nanowires via metallic coordination, resulting in plenty of nanowire bundles with the same orientation. Besides, the coordinated binding strength of nanowires with different metallic ions is also discussed. The assembly mechanism that the metallic ions induced dynamic behavior of nanowires is revealed via molecular dynamics theoretical evaluation. These findings benefit for constructing nanowire-based aerogels with unique structural features and multi-function, which pave new opportunities for other material systems.

Benchmark test of a dispersion corrected revised Tao-Mo semilocal functional for thermochemistry, kinetics, and noncovalent interactions of molecules and solids

In the density functional theory, dispersion corrected semilocal approximations are often used to benchmark weekly interacting finite and extended systems. Here, the focus is on providing a broad overview of the performance of D3 dispersion corrected revised Tao-Mo (revTM) semilocal functionals [A. Patra et al., J. Chem. Phys. 153, 084 117 (2020)] for thermochemistry and kinetics of molecules, molecular crystals, ice polymorphs, metal-organic systems, atom/molecular adsorption on solids, water interacting with nano-materials, binding energies of layered materials, and properties of weekly and strongly bonded solids. We show that the most suitable "optimized power" function for the revTM functional needs a modification to make it suitable for properties related to the diverse nature of finite and extended systems. The present work is an extension of the previously proposed revTM+D3 method with the motivation to design and benchmark the dispersion corrected cost-effective method based on this semilocal approximation. We show that the revised revTM+D3 functional provides various general purpose molecular and solid properties with the closest to experimental findings than its predecessor. The present assessment and benchmarking can be practically useful for performing cost-effective method based simulations of various molecular and solid-state properties.

Palladium Goes First: A Neutral Asymmetric Heteroditopic N,P Ligand Forming Pd-3d Heterobimetallic Complexes

A facile two-step synthesis of bis(1-methylhydrazinyl)pyrimidine from pyridine-2-carbaldehyde and 2-diphenylphosphanylbenzaldehyde gave access to the new asymmetric ligand 1. The phosphane selectively guides Pd^II into the softer tridentate N,N,P pocket, yielding monometallic complex 2. A second reaction with a 3d transition metal complex precursor (groups 7 to 12) fills the vacant N,N,N pocket and thus provides a variety of heterobimetallic complexes of the type Pd^II/M^II (M = Mn (3), Fe (4), Co (5), Ni (6), Cu (7), Zn (8)). Single-crystal X-ray diffraction studies were performed for all complexes. The assembly of μ₂-chlorido-bridged dimers was observed for complexes 5-7 in the solid state, while DOSY NMR experiments have shown that 5-7 are unbridged monomers in solution. As an exception, Fe^II prefers to form the homoleptic meridional complex [Fe{PdCl(1)}₂](OTf)₄ (4). The electrochemical behavior and the effective magnetic moment in solution were investigated for all complexes by cyclic voltammetry and Evans method, respectively. Experimental UV/vis results were interpreted by performing TD-DFT calculations on 1, 2, and 3.

Identifying the key steps determining the selectivity of toluene methylation with methanol over HZSM-5

Methylation of toluene with methanol to produce p-xylene has been investigated for decades, but the origin of selectivity is still under debate. Here we report computational studies based on ab initio molecular dynamics simulations and free energy sampling methods to identify the key steps determining the selectivity. The steps of toluene methylation to protonated-xylene, deprotonation of protonated-xylenes, and diffusion of xylene in HZSM-5 channels are compared. We find the pathways of formation for protonated p-/m-xylenes have similar free energy barriers. Meanwhile, the methylation is found rate-determining, thus the probability to generate p-/m-xylenes at the active site are similar. We then find that the diffusion for m-xylene along the zigzag channel is more difficult than its isomerization to p-xylene, which in turn further promotes the selectivity of p-xylene formation. These insights obtained at the molecular level are crucial for further development of high-performance zeolite catalysts for toluene methylation.

The selectivity of zeolite catalyzed toluene methylation is still under debate. Here the authors report a comprehensive theoretical investigation based on ab-initio molecular dynamics to identify the key-steps of methylation of toluene with methanol over a zeolite to produce p-xylene.

A theoretical study of supramolecular aggregation of polydopamine tetramer subunits in aqueous solution

Conformational search for the most stable geometry connection of 16 sets of polydopamine (PDA) tetramer subunits has been systematically investigated using density functional theory (DFT) calculations. Our results indicated that the more planar subunits are, the more stable they are. This finding is in good agreement with recent experimental observations, which have suggested that PDA are composed of the nearly planar subunits that appear to be stacked together via the π-π interactions to form graphite-like layered aggregates associated with the balance of the intramolecular hydrogen bonds and steric effects from the indole and catechol moieties. Molecular dynamics (MD) simulations of 16 spherical clusters of the tetramer subunits of PDA in the gas and aqueous phase were performed at 298 K and confirmed the stability of supramolecular tetramer aggregates. The complex formation and binding energy of all 16 clusters are very strong although the shapes of the clusters in aqueous solution are not spherical and are very much different from those in the gas phase. The aggregations of all 16 clusters in aqueous solution were also confirmed from the profiles of the Kratky plot and the radius of gyration of all clusters. Our MD results in both gas phase and aqueous solution pointed out that there are high possibilities of aggregations of the 16 kinds of tetramer subunits although the conformations of each tetramer subunit are not flat. In summary, this work brings an insight into the controversial structure of PDA tetramer units and explains some of the important structural features found in the aqueous phase in comparison to the gas phase.

Interaction of Aromatic Molecules with Forsterite: Accuracy of the Periodic DFT-D4 Method

Density functional theory (DFT) has provided deep atomic-level insights into the adsorption behavior of aromatic molecules on solid surfaces. However, modeling the surface phenomena of large molecules on mineral surfaces with accurate plane wave methods (PW) can be orders of magnitude more computationally expensive than localized atomic orbitals (LCAO) methods. In the present work, we propose a less costly approach based on the DFT-D4 method (PBE-D4), using LCAO, to study the interactions of aromatic molecules with the {010} forsterite (Mg2SiO4) surface for their relevance in astrochemistry. We studied the interaction of benzene with the pristine {010} forsterite surface and with transition-metal cations (Fe2+ and Ni2+) using PBE-D4 and a vdW-inclusive density functional (Dion, Rydberg, Schröder, Langreth, and Lundqvist (DRSLL)) with LCAO methods. PBE-D4 shows good agreement with coupled-cluster methods (CCSD(T)) for the binding energy trend of cation complexes and with PW methods for the binding energy of benzene on the forsterite surface with a difference of about 0.03 eV. The basis set superposition error (BSSE) correction is shown to be essential to ensure a correct estimation of the binding energies even when large basis sets are employed for single-point calculations of the optimized structures with smaller basis sets. We also studied the interaction of naphthalene and benzocoronene on pristine and transition-metal-doped {010} forsterite surfaces as a test case for PBE-D4. Yielding results that are in good agreement with the plane wave methods with a difference of about 0.02-0.17 eV, the PBE-D4 method is demonstrated to be effective in unraveling the binding structures and the energetic trends of aromatic molecules on pristine and transition-metal-doped forsterite mineral surfaces. Furthermore, PBE-D4 results are in good agreement with its predecessor PBE-D3(BJM) and with the vdW-inclusive density functionals, as long as transition metals are not involved. Hence, PBE-D4/CP-DZP has been proven to be a robust theory level to study the interaction of aromatic molecules on mineral surfaces.

Electronic Structure Modeling of Metal-Organic Frameworks

Owing to their molecular building blocks, yet highly crystalline nature, metal-organic frameworks (MOFs) sit at the interface between molecule and material. Their diverse structures and compositions enable them to be useful materials as catalysts in heterogeneous reactions, electrical conductors in energy storage and transfer applications, chromophores in photoenabled chemical transformations, and beyond. In all cases, density functional theory (DFT) and higher-level methods for electronic structure determination provide valuable quantitative information about the electronic properties that underpin the functions of these frameworks. However, there are only two general modeling approaches in conventional electronic structure software packages: those that treat materials as extended, periodic solids, and those that treat materials as discrete molecules. Each approach has features and benefits; both have been widely employed to understand the emergent chemistry that arises from the formation of the metal-organic interface. This Review canvases these approaches to date, with emphasis placed on the application of electronic structure theory to explore reactivity and electron transfer using periodic, molecular, and embedded models. This includes (i) computational chemistry considerations such as how functional, k-grid, and other model variables are selected to enable insights into MOF properties, (ii) extended solid models that treat MOFs as materials rather than molecules, (iii) the mechanics of cluster extraction and subsequent chemistry enabled by these molecular models, (iv) catalytic studies using both solids and clusters thereof, and (v) embedded, mixed-method approaches, which simulate a fraction of the material using one level of theory and the remainder of the material using another dissimilar theoretical implementation.

A proton transfer mechanism along the PO4 anion chain in the [Zn(HPO4)(H2PO4)]2- coordination polymer

In this study, we revisit the proton transfer mechanism in [Zn(HPO4)(H2PO4)]2-, a coordination polymer possessing high proton conductivity. In a previous report [N. Phattharasupakun, J. Wutthiprom, S. Kaenket, Th. Maihom, J. Limtrakul, M. Probst, S. S. Nagarkar, S. Horike and M. Sawangphruk, Chem. Commun., 2017, 53, 11786-11789], it was hypothesized that protons could move along the ImH+ chain involving phosphate anions within the polymer structure, with energy barriers >1.3 eV. Adopting M06-2X calculations to examine the reaction pathway, we observe that it is much more favorable for H+ to move along a one-dimensional channel formed by HPO42- and H2PO4- anions. Within a unit cell, the proton hopping process can be divided into three elementary steps. For the forward proton transfer direction, the maximum energy barrier is only 0.04 eV, while that of the backward direction is 0.27 eV. Even though the barriers of the backward direction seem to outreach the barriers of the forward direction, both are still low in comparison with those reported in the literature. Moreover, we also point out the involvement of PO4 rotation during the proton transfer process. Activation energies of 0.37 eV and 0.15 eV are required for single steps of rotation of the phosphate anion. Both H+ translation (hopping) and rotation steps of PO4 anions simultaneously participate in the course of proton transfer in the coordination polymer.

A generally applicable atomic-charge dependent London dispersion correction

The so-called D4 model is presented for the accurate computation of London dispersion interactions in density functional theory approximations (DFT-D4) and generally for atomistic modeling methods. In this successor to the DFT-D3 model, the atomic coordination-dependent dipole polarizabilities are scaled based on atomic partial charges which can be taken from various sources. For this purpose, a new charge-dependent parameter-economic scaling function is designed. Classical charges are obtained from an atomic electronegativity equilibration procedure for which efficient analytical derivatives with respect to nuclear positions are developed. A numerical Casimir-Polder integration of the atom-in-molecule dynamic polarizabilities then yields charge- and geometry-dependent dipole-dipole dispersion coefficients. Similar to the D3 model, the dynamic polarizabilities are precomputed by time-dependent DFT and all elements up to radon (Z = 86) are covered. The two-body dispersion energy expression has the usual sum-over-atom-pairs form and includes dipole-dipole as well as dipole-quadrupole interactions. For a benchmark set of 1225 molecular dipole-dipole dispersion coefficients, the D4 model achieves an unprecedented accuracy with a mean relative deviation of 3.8% compared to 4.7% for D3. In addition to the two-body part, three-body effects are described by an Axilrod-Teller-Muto term. A common many-body dispersion expansion was extensively tested, and an energy correction based on D4 polarizabilities is found to be advantageous for larger systems. Becke-Johnson-type damping parameters for DFT-D4 are determined for more than 60 common density functionals. For various standard energy benchmark sets, DFT-D4 slightly but consistently outperforms DFT-D3. Especially for metal containing systems, the introduced charge dependence of the dispersion coefficients improves thermochemical properties. We suggest (DFT-)D4 as a physically improved and more sophisticated dispersion model in place of DFT-D3 for DFT calculations as well as other low-cost approaches like semi-empirical models.

Statistically representative databases for density functional theory via data science

Cluster analysis applied to quantum chemistry: a new broad database of chemical properties with a reasonable computational cost.

A Trip to the Density Functional Theory Zoo: Warnings and Recommendations for the User

This account is written for general users of density functional theory (DFT) methods as well as experimental researchers who are new to the field and would like to conduct such calculations. Its main emphasis lies on how to find a way through the confusing ‘zoo’ of DFT by addressing common misconceptions and highlighting those modern methods that should ideally be used in calculations of energetic properties and geometries. A particular focus is on highly popular methods and the important fact that popularity does not imply accuracy. In this context, we present a new analysis of the openly available data published in Swart and co-workers’ famous annual ‘DFT poll’ (http://www.marcelswart.eu/dft-poll/) to demonstrate the existing communication gap between the DFT user and developer communities. We show that despite considerable methodological advances in the field, the perception of some parts of the user community regarding their favourite approaches has changed little. It is hoped that this account makes a contribution towards changing this status and that users are inspired to adjust their current computational protocols to accommodate strategies that are based on proven robustness, accuracy, and efficiency rather than popularity.

Semi-empirical or non-empirical double-hybrid density functionals: which are more robust?

The development of non-empirical double-hybrid density functionals (DHDFs) is a very active research area with the number of approaches in this field having increased rapidly. At the same time, there is a lack of published work that provides a fair assessment and comparison between non-empirical and semi-empirical DHDFs on an equal footing. Herein, we close this gap and present a thorough analysis of both classes of DHDFs on the large GMTKN55 benchmark database for general main-group thermochemistry, kinetics, and noncovalent interactions [Goerigk et al., Phys. Chem. Chem. Phys., 2017, 19, 32184-32215]. In total, 115 variations of dispersion-corrected and -uncorrected DHDFs are tested, which will be condensed to an in-depth assessment of 31 methods: 19 non-empirical and 12 semi-empirical DHDFs. As such, our study represents the largest DHDF study ever conducted and can serve as an important benchmark informing method developers and users alike. Our results show that semi-empirical DHDFs are the most robust density functional approximations and more reliable and accurate than non-empirical ones. In fact, some non-empirical approaches are even outperformed by hybrid approaches or even dispersion-corrected and -uncorrected MP2 and SCS-MP2. SOS0-PBE0-2-D3(BJ) is the only exception and the only non-empirical DHDF that we can safely recommend for general applicability. However, it is still outperformed by six semi-empirical DHDFs, of which we would like to particularly recommend the following five: ωB97X-2-D3(BJ), DSD-BLYP-D3(BJ), DSD-PBEP86-D3(BJ), B2NC-PLYP-D3(BJ), and B2GPPLYP-D3(BJ). Our findings seriously question current trends in the field and they highlight that novel strategies have to be found in order to outperform the currently best density functional theory methods on the market. We hope that our study can function as an important cornerstone inspiring such a change of direction in the field.

Understanding titanium-catalysed radical-radical reactions: a DFT study unravels the complex kinetics of ketone-nitrile couplings

The computational investigation of a titanium-catalysed reductive radical-radical coupling is reported. The results match the conclusions from an earlier experimental study and enable a further interpretation of the previously observed complex reaction kinetics. Furthermore, the interplay between neutral and cationic reaction pathways in titanium(iii)-catalysed reactions is investigated for the first time. The results show that hydrochloride additives and reaction byproducts play an important role in the respective equilibria. A full reaction profile is assembled and the computed activation barrier is found to be in reasonable agreement with the experiment. The conclusions are of fundamental importance to the field of low-valent titanium catalysis and the understanding of related catalytic radical-radical coupling reactions.