Exploration of Chemical Compound, Conformer, and Reaction Space with Meta-Dynamics Simulations Based on Tight-Binding Quantum Chemical Calculations

Hypertums A-J, bioactive polycyclic polyprenylated acylphloroglucinols with diverse skeletons from Hypericum perforatum L. (St. John's wort)

Ten previously undescribed polycyclic polyprenylated acylphloroglucinols (PPAPs), hypertums A-J (1-10), together with eighteen known analogues (11-28), belonging to five subclasses of PPAPs, were isolated from the aerial parts of Hypericum perforatum L. (St. John's wort). The chemical structures and the absolute configurations of these compounds were elucidated by comprehensive analysis of NMR spectra, HR-ESI-MS data, quantum chemical calculations, chemical transformation, and X-ray crystallography. The carbon skeletons of compounds 1-5 were first characterized from H. perforatum. Compounds 6 and 7 were rare congeners assembled with two different polyprenylated acylphloroglucinol moieties through an ester bond. The plausible biosynthetic pathways for 1-10 were postulated. Compound 3, yezo'otogirin A (27) and yezo'otogirin B (28) exhibited weak acetylcholinesterase inhibitory activities at 50 μM. The isolated PPAPs were also evaluated for their anti-neuroinflammatory activity. Compound 3 inhibited nitric oxide (NO) production in LPS-stimulated BV-2 microglial cells with IC50 value of 34.34 μM and also suppressed the expressions of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2). Moreover, anti-neuroinflammatory effect of 3 was also supported in zebrafish model.

Automating the Analysis of Substrate Reactivity through Environment Interaction Mapping

Exploring the interaction configurations between substrates and atomic or molecular systems is crucial for various scientific and technological applications, such as characterizing catalytic reactions, solvation structures, and molecular interactions. Traditional approaches for generating substrate-reactant configurations often rely on chemical intuition, symmetry operations, or random initial states, which can be inefficient and challenging for systems with low symmetry or unknown interaction mechanisms. This work introduces a systematic and automated methodology to explore the configuration space between substrates and adsorbates using symmetry-invariant features that characterize the local atomistic topology of the substrate. The approach involves three key components: (1) defining and discretizing a contact space surrounding the substrate, (2) utilizing symmetry-invariant descriptors to capture local atomic environments, and (3) employing unsupervised machine-learning techniques for clustering and hierarchical analysis of interaction sites. The method ensures comprehensive yet nonredundant sampling of the configuration space, independent of the substrate dimensionality. Applications to simple ideal substrates show that symmetry intuition and high-symmetry sites are correctly recovered. Moreover, the method is shown to translate seamlessly to less symmetric substrates.

Enantioselective Photochemical Generation of a Short-Lived, Twisted Cycloheptenone Isomer: Catalytic Formation, Detection, and Consecutive Chemistry

Cyclohept-2-enone-3-carboxylic acid undergoes a photochemical isomerization from its cis- to its trans-form either upon direct irradiation (λ = 366 nm) or in the presence of a triplet sensitizer (λ = 459 nm). The intermediate chiral trans-isomer was detected by step-scan FTIR, displaying a lifetime of 130 µs (r.t., CH2Cl2). Ensuing Diels-Alder reactions of the trans-isomer occurred smoothly and produced chiral trans-fused cycloaddition products (14 examples, 24%-98% yield). Benzylation led to esters, which were separated by chiral HPLC and which were employed to evaluate a possible enantioselective reaction course. It was discovered that a chiral phosphoric acid with a pendant sensitizing group induces a notable enantioselectivity in the photoisomerization step. The planar chirality of the trans-cycloheptene translates into point chirality in the Diels-Alder reaction (seven examples, up to 38% ee). Computational studies suggest that the chiral conformation of the cis-isomer adopted within the assembly to the chiral phosphoric acid induces the enantioselectivity in a one-bond flip (OBF) toward the trans-isomer. Trajectory surface hopping (TSH) simulations showed exemplarily how a chiral trans-cyclohept-2-enone is formed from a chiral cis-conformer. For the Diels-Alder reaction, a weak ground state selectivity was found to attenuate the enantioselectivity achieved in the photochemical step.

Organodichalcogenide Structure and Stability: Hierarchical Ab Initio Benchmark and DFT Performance Study

We conducted a double-hierarchical ab initio benchmark and DFT performance study of the organodichalcogenide bonding motif CH3Ch1Ch2(O)nCH3 with Ch1, Ch2 = S, Se and n = 0, 1, 2. The organodichalcogenide model systems were optimized at ZORA-CCSD(T)/ma-ZORA-def2-TZVPP. Our ab initio benchmark involved a hierarchical series of all-electron relativistically contracted variants of the Karlsruhe basis sets (ZORA-def2-SVP, ZORA-def2-TZVPP, ZORA-def2-QZVPP), both with and without diffuse functions (ma-basis set), in conjunction with a hierarchical series of ZORA-relativistic quantum chemical methods [HF, MP2, CCSD, and CCSD(T)]. Counterpoise correction was applied to account for the basis set superposition error (BSSE). We assessed the performance of 33 ZORA-relativistic DFT functionals (ZORA-[XC functional]/TZ2P//ZORA-[XC functional]/TZ2P) against our benchmark energies and found that M06 and MN15 furnish accurate geometries and bond energies within a mean absolute error of 1.2 kcal mol-1 relative to our best ab initio reference data.

Predicting the Brain-To-Plasma Unbound Partition Coefficient of Compounds via Formula-Guided Network

Blood-brain barrier (BBB) permeability plays a crucial role in determining drug efficacy in the brain, with the brain-to-plasma unbound partition coefficient (Kp,uu) recognized as a key parameter of BBB permeability in drug development. However, Kp,uu data are scarce and mostly in-house. In predicting Kp,uu the generality and applicability of existing empirical scoring models remain underexplored. To address this, we established a public rat Kp,uu data set through data mining and developed a formula-guided deep learning model, CMD-FGKpuu, which performed well on multiple benchmark tests, marking good demonstration of the potential of deep learning for Kp,uu prediction. Additionally, the model can be fine-tuning with project-specific experimental data, thus improving its practical utility. The findings offer an effective tool for predicting BBB permeability in drug development and introduce a new perspective for applying few-shot learning in the pharmaceutical field.

Deciphering the Underlying Mechanism of Anion Binding by Asymmetrical Squaramide-Based Dipeptides

Anions are involved in many important processes, which has led to growing interest in designing new molecules to bind them effectively. Squaramides have gained considerable attention as effective anion receptors due to their dual hydrogen bond donor capability. Combining squaramide with biomolecules is a promising approach for designing and developing biomimetic receptors for anions with enhanced H-bonding abilities, particularly due to their functional versatility. The present study explores the mechanism of interaction of H2PO4- and HSO4- anions with three asymmetrical squaramide-based dipeptide receptors, emphasizing the role of noncovalent interactions. The conformational states of the receptors and the amino acids of the dipeptide with varying side chain lengths are the two major factors that influence these interactions. The conformational analysis of the receptors and their anion complexes performed using conformer-rotamer ensemble sampling tool (CREST) and molecular dynamics (MD) simulations, shows that the anti/anti conformations are the most abundant. Following the MD simulations, density functional theory (DFT) was used to perform electronic structure calculations on the 1:1 receptor-anion complexes. Our findings indicate that the N-H···O and O-H···O═C interactions primarily drive the formation of the receptor-anion complexes. Energy decomposition analysis based on absolutely localized molecular orbitals (ALMO-EDA) highlighted the role of the electrostatic energy (ΔEelst) in stabilizing the receptor-anion complexes. Further confirmation of the intermolecular N-H···O and O-H···O═C interactions in the complexes was attained through several analytic tools. This outcome lays a foundation for designing and developing more efficient and selective dipeptide-based anion receptors.

Quantum Tunneling Fingerprints of Chirality-Induced Symmetry Preferences in Methyl Lactate Dimer

Methyl lactate, a chiral molecule with multiple functional groups, has played a pivotal role in advancing experimental and theoretical chiroptical methods. Leveraging conformer-specific jet-cooled rotational spectroscopy in tandem with extensive conformational searches and quantum chemical calculations, we investigated chirality self-recognition in the methyl lactate dimer. The experimental fingerprint-like spectral patterns, including methyl rotor tunneling splittings, allowed the definite identification of one heterochiral and two homochiral binary conformers from a large number of low-energy candidates. Nuclear spin statistics analyses and methyl internal rotor parameters reveal different nuclear tunneling dynamics in the homochiral versus heterochiral environments and highlight the associated chirality-driven symmetry preference in the observed conformers. The results provide comprehensive experimental data for benchmarking quantum chemical calculations of chiral properties and pave the way for the exploration of this prototypical dimer across different frequency ranges using other spectroscopic tools.

Heterophyllin B: Combining Isotropic and Anisotropic NMR for the Conformational Analysis of a Natural Occurring Cyclic Peptide

Heterophyllin B is a natural occurring cyclic peptide with diverse attributed bioactivities. NMR-based conformational analysis of cyclic peptides often poses a challenge due to limited isotropic solution-state NMR data. In this study, we combined isotropic and anisotropic NMR observables including J-coupling, NOEs, amide proton temperature coefficients, and residual dipolar couplings (RDCs), which enabled the determination of a minimal conformational ensemble of heterophyllin B in methanol at density functional theory (DFT) accuracy. For conformational sampling of a cyclic peptide with a high degree of conformational freedom, we proposed a computational strategy that combines the Conformer-Rotamer Ensemble Sampling Tool (CREST) with the Commandline Energetic SOrting (CENSO). This combined computational and NMR-based approach offers a robust framework for the conformational analysis of cyclic peptides.

Analytical First Derivatives of the SCF Energy for the Conductor-Like Polarizable Continuum Model With Non-Static Radii

Within this work, we present the derivation and implementation of analytical gradients for the Gaussian-switching (SwiG) Conductor-like Polarizable Continuum Model (CPCM) with general nuclear coordinate-dependent non-static radii used for the creation of van der Waals-type cavities. This is done using the recently presented dynamic radii adjustment for continuum solvation (Draco) scheme. This allows for efficient geometry optimization and reasonable numerical Hessian calculations. The derived gradient is implemented in ORCA, and therefore is easily applicable. The derivation and implementation is validated by comparing analytical and numerical gradients and testing geometry optimizations on a diverse test set, including small organic compounds, metal-organic complexes, and highly charged species. We additionally test the continuity of the potential energy surface using an example where very strong changes in the radii occur. The computational efficiency of the derived gradient is investigated.

2-(2-Phenylethyl)chromone-Sesquiterpene Hybrids from Agarwood of Aquilaria sinensis: Characterization and Biological Activity Evaluation

Aquisinenins G-I (1-3), three new 2-(2-phenylethyl)chromone-sesquiterpene hybrids, were isolated from the ethanol extract of Hainan agarwood derived from Aquilaria sinensis. Spectroscopic techniques, such as 1D and 2D NMR and HRESIMS, were used to determine their structures. Experimental and computed ECD data were compared to confirm their absolute configurations. Compounds 1-3 are uncommon dimeric derivatives of 2-(2-phenylethyl)chromone-sesquiterpene, characterized by the fusion of 5,6,7,8-tetrahydro-2-(2-phenylethyl)chromone with agarofuran or agarospirane-type sesquiterpene units by an ester linkage. Compound 1 inhibited nitric oxide production in lipopolysaccharide-stimulated RAW264.7 cells, showing an IC50 value of 22.31 ± 0.42 μM. The neuroprotective effects of compounds 1 and 3 against H2O2-induced apoptosis were assessed in human neuroblastoma SH-SY5Y cells. Compound 1 demonstrated cytotoxicity with IC50 values of 72.37 ± 0.20 μM against K562 and 61.47 ± 0.22 μM against BEL-7402, while compounds 2 and 3 showed cytotoxicity across all five tested human cancer cell lines.

The Amsterdam Modeling Suite

In this paper, we present the Amsterdam Modeling Suite (AMS), a comprehensive software platform designed to support advanced molecular and materials simulations across a wide range of chemical and physical systems. AMS integrates cutting-edge quantum chemical methods, including Density Functional Theory (DFT) and time-dependent DFT, with molecular mechanics, fluid thermodynamics, machine learning techniques, and more, to enable multi-scale modeling of complex chemical systems. Its design philosophy allows for seamless coupling between components, facilitating simulations that range from small molecules to complex biomolecular and solid-state systems, making it a versatile tool for tackling interdisciplinary challenges, both in industry and in academia. The suite also emphasizes user accessibility, with an intuitive graphical interface, extensive scripting capabilities, and compatibility with high-performance computing environments.

GOAT: A Global Optimization Algorithm for Molecules and Atomic Clusters

In this work, we propose a new Global Optimization Algorithm (GOAT) for molecules and clusters of atoms and show how it can find the global energy minima for both systems without resorting to molecular dynamics (MD). This avoids the potential millions of time-consuming gradient calculations required by a long MD run. Because of that, it can be used with any regular quantum chemical method, even with the costlier hybrid DFT. We showcase its accuracy by running it on various systems, from organic molecules to water clusters, metal complexes, and metal nanoparticles, comparing it with state-of-the-art methods such as the Conformer-Rotamer Ensemble Sampling Tool (CREST). We also discuss its underlying theory and mechanisms for succeeding in challenging cases. GOAT is, in general, more efficient and accurate than previous algorithms in finding global minima and succeeds in cases where others cannot due to the free choice for the Potential Energy Surface (PES).

Conclusive Insight into the Coordination Complexes of a Flexible Bis(β-diketonato) Ligand and Their Phase-Dependent Structure: A Multi-Technique Approach

Multichelating ligands with nuclear spin-free donor atoms are of particular interest for creating stable electronic spin qubits based on paramagnetic transition metal ions. We recently focused on the coordinating ability of the bis(β-diketonato) ligand bdhb2-, featuring two "acac" moieties connected through a 1,3-phenylene bridge (H2bdhb = 1,3-bis(3,5-dioxo-1-hexyl)benzene). The two crystalline complexes of bdhb2- so far isolated and structurally characterized, namely [(VO)2(bdhb)2] (1) and [Co2(bdhb)2(py)4] (2), are dimeric and contain bridging bdhb2- ligands; however, they become mononuclear and quasi-macrocyclic in organic solution. To investigate this unique structural isomerism by high-resolution 1H NMR spectroscopy, we have now synthesized a diamagnetic Zn2+ analogue of 1 and 2, namely [Zn2(bdhb)2(py)2] (3). Although both 2 and 3 are dimeric and contain the same ligands, 3 features only one pyridine molecule per metal ion, whose coordination geometry is square pyramidal rather than tetragonally elongated octahedral. The ESI-MS spectra of 3 in THF and CH2Cl2 contain peaks from both monomeric and dimeric species. However, molecular weight determinations by DOSY and conformational studies based on J-coupling analysis and DFT calculations conclusively prove the rearrangement of 3 into quasi-macrocyclic monomers in THF-d8 and CD2Cl2 solution at room temperature.

Analytical SA-HCISCF Nuclear Gradients from Spin-Adapted Heat-Bath Configuration Interaction

This work reports an implementation of the analytical nuclear gradients and nonadiabatic couplings with state-averaged SCF wave functions from a spin-pure selected configuration interaction (SCI) method. At the core of the implementation lies the evaluation of the Lagrange multipliers required for the variational calculation of the nuclear gradient. Using the same code infrastructure, we developed a fully CI-coupled second-order orbital optimization method. Both the calculation of the nuclear gradient and the second-order orbital optimization make use of density fitting in order to accelerate the calculation of the two-electron integrals. We demonstrate the use of analytical nuclear gradients in excited-state geometry optimizations for conjugated molecules. In addition, the first triplet excited-state geometry of a transition-metal catalyst, Fe(PDI), was optimized with up to 30 orbitals in the active space. Our results outline the capabilities of the implemented methods as well as directions for future work.

Wiggle150: Benchmarking Density Functionals and Neural Network Potentials on Highly Strained Conformers

Accurate benchmarks are key to assessing the accuracy and robustness of computational methods, yet most available benchmark sets focus on equilibrium geometries, limiting their utility for applications involving nonequilibrium structures such as ab initio molecular dynamics and automated reaction-path exploration. To address this gap, we introduce Wiggle150, a benchmark comprising 150 highly strained conformations of adenosine, benzylpenicillin, and efavirenz. These geometries─generated via metadynamics and scored using DLPNO-CCSD(T)/CBS reference energies─exhibit substantially larger deviations in bond lengths, angles, dihedrals, and relative energies than other conformer benchmarks. We evaluate a diverse array of computational methods, including density-functional theory, composite quantum chemical methods, semiempirical models, neural network potentials, and force fields, on predicting relative energies for this challenging benchmark set. The results highlight multiple methods along the speed-accuracy Pareto frontier and identify AIMNet2 as particularly robust among the NNPs surveyed. We anticipate that Wiggle150 will be used to validate computational protocols involving nonequilibrium systems and guide the development of new density functionals and neural network potentials.

Tunable G-Quadruplex Ligands: Azobenzene Derivatives for Light-Controlled DNA Modulation

During transcription, replication, and DNA repair, DNA unwinds to reveal guanine-rich sequences that form stable G-quadruplexes. In cancer cells, increased transcription and replication promote G4 formation, making them attractive therapeutic targets. G4 s block DNA and RNA polymerases, inducing replication stress and causing toxic single- and double-strand breaks. Small-molecule ligands can stabilize G4 structures, prolonging their effects and exacerbating replication stress. However, most G4 ligands operate through a one-way mechanism that remains permanent over time. A more versatile approach involves systems that can switch between active and inactive states on demand using external stimuli, such as light. This study aims to deepen knowledge of the current state of the design of photoactive G4-ligand through the synthesis of azobenzene-based compounds that vary in substitution patterns, size of the substituent, electronic effects, and molecular structure. Using orthogonal biophysical methods and quantum-chemical calculations, we evaluate how these factors affect the compounds' ability to bind and stabilize G4 structures. Importantly, our results demonstrate that the interaction mode of the trans isomer with G4 influences its ability to modulate G4 properties bidirectionally. These findings provide insights for designing photoactive G4 ligands with tunable on-off functionality, paving the way for precise control of G4 structures in biological systems.

An enzymatic dual-oxa Diels-Alder reaction constructs the oxygen-bridged tricyclic acetal unit of (-)-anthrabenzoxocinone

The hetero-Diels-Alder (HDA) reaction is a key method for synthesizing six-membered heterocyclic rings in natural products and bioactive compounds. Despite its importance in synthetic chemistry, naturally occurring enzymatic HDA reactions are rare and limited to a single heteroatom. Here we report Abx(-)F, a bifunctional vicinal oxygen chelate (VOC)-like protein that catalyses dehydration and dual-oxa Diels-Alder reactions to stereoselectively form the oxygen-bridged tricyclic acetal of (-)-anthrabenzoxocinone ((-)-ABX). Isotope assays and density functional theory calculations reveal a dehydration-coordinated, concerted HDA mechanism. The crystal structure of Abx(-)F and NMR complex structures of Abx(-)F with its substrate analogue and (-)-ABX define the reaction's structural basis. Mutational analysis identifies Asp17 as a general base that mediates dehydration, forming an o-quinone methide intermediate for stereoselective dual-oxa HDA. This work establishes the molecular and structural basis of a polyheteroatomic Diels-Alderase, paving the way for designing polyheteroatomic DA enzymatic tools.

Toward Symmetric Organic Aqueous Flow Batteries: Triarylamine-Based Bipolar Molecules and Their Characterization via an Extended Koutecký-Levich Analysis

Symmetric organic flow batteries (SOFBs) can potentially address membrane crossover problems by employing bipolar redox-active organic molecules (BROMs). Herein, a triarylamine (TAA) skeleton was chosen as a posolyte moiety for a new class of bipolar molecules for pH-neutral aqueous flow batteries (FBs). Pyridinium and viologen derivatives were tethered to the posolyte moiety, and the new compounds were characterized. Cyclic voltammetry revealed that only viologen with a highly hydrophilic substituent, connected to the TAA moiety via a Zincke reaction, could be reversibly reduced. Varying the supporting electrolyte concentration on the selected derivative revealed water solubility as a challenge for further development. The selected derivative, MeO-TPA-Vi-DMAE, was subjected to hydrodynamic voltammetry, and a modified Koutecký-Levich analysis was developed to investigate the observed potential-dependent currents at the hydrodynamically dominated region, which are often seen with redox-active organic molecules. This model discarded a purely Ohmic effect, showing a useful Levich slope at a certain overpotential before the onset of a secondary reaction. TAA-based BROMs hold promise for pH-neutral aqueous SOFBs, and the results will guide the design of new derivatives. The three-term Koutecký-Levich relation here introduced will be useful not only to develop BROM-based FBs but will most likely appeal to a much broader audience.

Response of a Tethered Zn-Bis-Terpyridine Complex to an External Mechanical Force: A Computational Study of the Roles of the Tether and Solvent

Polymeric materials containing weak sacrificial bonds can be designed to engineer self-healing and higher toughness, improve melt-processing, or facilitate recycling. However, they usually exhibit a lower mechanical strength and are subject to creep and fatigue. For improving their design, it is of interest to investigate their mechanical response on the molecular scale. We report on a computational study of the response to a mechanical external force of a Zinc(II) bis-methyl phenyl-terpyridine ([Zn-bis-Terpy]2+) complex included in a cyclic poly(ethylene glycol) (PEG) tether designed to maintain the two partners of the metal-ligand bonds in close proximity after the rupture of the complex. The mechanical response is studied as a function of the pulling distortion by using the CoGEF isometric protocol, including interactions with a polar solvent (DMSO). We show that tethering favors recombination but destabilizes the complex before bond rupture because of the interactions of the PEG units with Terpy ligands. Similar effects occur between the DMSO molecules and the complex. Our results on the molecular scale are relevant for single-molecule force spectroscopy experiments. Interactions of the complex with solvent molecules and/or with the tether lead to a dispersion of the rupture force values, which could obscure the interpretation of the results.

Evaluation of Semiempirical Quantum Mechanical Methods for Zr-Based Metal-Organic Framework Catalysts

Zr-based metal-organic frameworks (MOFs) are typically employed in heterogeneous catalysis due to their porosity, chemical and thermal stability, and well-defined active sites. Density functional theory (DFT) is the workhorse to compute their electronic structure; however, it becomes very costly when dealing with reaction mechanisms involving large unit cells and vast configurational spaces. Semiempirical quantum mechanical (SQM) methods appear as an alternative approach to simulate such chemical systems at low computational cost, but their feasibility to model catalysis with MOFs is still unexplored. Thus, here we present a benchmark study on UiO-66 to evaluate the performance of SQM methods (PM6, PM7, GFN1-xTB, GFN2-xTB) against hybrid DFT (M06). We evaluate defective nodes, ligand exchange reactions, barrier heights, and host-guest interactions with metal nanoclusters. Despite some caveats, GFN1-xTB on properly constrained models is the best SQM method across all studied properties. Under proper supervision, this protocol holds promise for application in exploratory high-throughput screenings of Zr-based MOF catalysts, subject to further refinement with more accurate methods.

Rotational and vibrational spectroscopy of a weakly bound hexafluoroisopropanol⋯dinitrogen complex: 14N hyperfine splittings, molecular geometry, and experimental benchmarks

The rotational spectrum of a weakly bound binary complex of hexafluoroisopropanol (HFIP) with molecular nitrogen was measured using chirped-pulse and cavity-based Fourier transform microwave spectrometers. In addition, its infrared spectrum was measured in the OH stretching region. An extensive conformational search identified multiple binding sites on HFIP, with the global minimum structure featuring a trans-HFIP conformation and nitrogen weakly bound at the acidic proton (HtNH). Good agreement between the experimentally determined rotational constants and the relative intensity patterns of a-, b-, and c-type transitions with theoretical predictions conclusively identified the HtNH conformer. This assignment is further corroborated by an analysis of the 14N nuclear quadrupole hyperfine structure. The non-equivalence of the two 14N nuclei in HtNH is confirmed through a detailed molecular symmetry group analysis, as well as the 14N nuclear quadrupole hyperfine analysis. Examination of the experimental nuclear quadrupole coupling constants offers additional insights into the orientation and large-amplitude vibrational motions of the N2 subunit. Furthermore, the experimentally derived rotational constants and the OH stretching band position of the complex, compared with previously known values for the isolated monomer, serve as complementary benchmarks for evaluating the systematic quality of predictions from electronic structure calculations across several levels of theory. This combined examination of vibrational energy levels and structural parameters aids in distinguishing fortuitously accurate predictions of individual properties.

Uncertainty quantification with graph neural networks for efficient molecular design

Optimizing molecular design across expansive chemical spaces presents unique challenges, especially in maintaining predictive accuracy under domain shifts. This study integrates uncertainty quantification (UQ), directed message passing neural networks (D-MPNNs), and genetic algorithms (GAs) to address these challenges. We systematically evaluate whether UQ-enhanced D-MPNNs can effectively optimize broad, open-ended chemical spaces and identify the most effective implementation strategies. Using benchmarks from the Tartarus and GuacaMol platforms, our results show that UQ integration via probabilistic improvement optimization (PIO) enhances optimization success in most cases, supporting more reliable exploration of chemically diverse regions. In multi-objective tasks, PIO proves especially advantageous, balancing competing objectives and outperforming uncertainty-agnostic approaches. This work provides practical guidelines for integrating UQ in computational-aided molecular design (CAMD).

Predicting pK a of flexible polybasic tetra-aza macrocycles

We present physics-based pK a predictions for a library of tetra-aza macrocycles. These flexible, polybasic molecules exhibit highly charged states and substantial prototropic tautomerism, presenting a challenge for pK a prediction. Our computational protocol combines CREST/xTB conformational sampling, density functional theory (DFT) refinement in continuum solvent, and a linear empirical correction (LEC). This approach predicts known tetra-aza macrocycle pK a to within a root-mean-square deviation 1.2 log units. This approach also provides reasonable predictions for the most stable protomers at different pH. We use this protocol to predict pK a values for four novel, synthetically achievable, previously un-synthesized tetra-aza macrocycles, providing new leads for future experiments.

Proline-based tripodal cages with guest-adaptive features for capturing hydrophilic and amphiphilic fluoride substances

Proteins exhibit remarkable molecular recognition by dynamically adjusting their conformations to selectively interact with ligands at specialized binding sites. To bind hydrated ligands, proteins leverage amino acid residues with similar water affinities as the substrate, minimizing the energy required to strip water molecules from the hydrophilic substrates. In synthetic receptor design, replicating this sophisticated adaptability remains a challenge, as most artificial receptors are optimized to bind desolvated substances. Here, we show that proline-based synthetic receptors can mimic the conformational dynamics of proteins to achieve selective binding of hydrophilic and amphiphilic fluoride substances in aqueous environments. This finding highlights the critical role of receptor flexibility and strategic hydrophilicity in enhancing ligand recognition and affinity in water. Moreover, it establishes a new framework for designing versatile synthetic receptors with tunable hydrophobicity and hydrophilicity profiles.

Kapok fibers modified with cationic surfactants: Structural insights and efficient removal of Cr(VI) and bisphenol A

In this study, kapok fiber (KF) a hollow and hydrophobic fiber, was modified with cetyltrimethylammonium bromide (CTAB) or cetylpyridinium chloride (CPC), rendering adsorbed amount of ∼0.75 × 10-3 mol/g. Small-angle X-ray scattering (SAXS) measurements of dry KF/CTAB and KF/CPC evidenced a periodic distance of ∼2.6 nm and 2.8 nm, respectively, suggesting the presence of hemimicelles on the surface. KF/CTAB and KF/CPC were used as adsorbents in batch and column adsorption experiments to remove Cr(VI) ions, Bisphenol A (BPA), and their binary mixtures from synthetic solution and fresh water. The adsorbed amounts of Cr(VI) ions on KF/CTAB and KF/CPC, as determined from batch experiments, were 48.62 mg/g and 34.17 mg/g, respectively. X-ray photoelectron spectroscopy (XPS) analysis showed that Cr(VI) adsorption on KF/CTAB involved bromide displacement, while chloride remained on KF/CPC. Moreover, Cr(VI) ions were reduced to Cr(III) ions due to a possible oxidation of γ-sitosterol, one component of the KF wax. Density Functional Theory (DFT) calculations indicated that the interaction energy of CTAB- Cr(VI) pair (-167.8 kcal/mol) is more favorable than that of the CPC-Cr(VI) pair (-147.8 kcal/mol). The adsorbed amounts of BPA on KF/CTAB and KF/CPC were 41.66 mg/g and 22.62 mg/g, respectively. XPS analysis indicated the appearance of an OH peak at 533 eV after the adsorption of BPA, aligning with DFT calculations that predicted interactions between the counter-ions (Br or Cl) and BPA hydroxy groups. In column adsorption experiments, Cr(VI) ions were more effectively adsorbed onto KF/CTAB in the presence of BPA, demonstrating the potential of KF/CTAB for the simultaneous remediation of mixed contaminants in water treatment.

Computational Insights into the Mechanism of Lewis Acid-Catalyzed Alkene-Aldehyde Coupling

The Lewis acid-catalyzed coupling of alkenes and aldehydes presents a modern, versatile synthetic alternative to classical carbonyl addition chemistry, offering exceptional regio- and stereoselectivity. In this work, we present a comprehensive computational investigation into the reaction mechanism of this transformation. Our findings confirm the occurrence of an enantioselective transannular [1,5]-hydride shift step and demonstrate that the enantioselectivity of the reaction arises predominantly from steric clashes between functional groups in the cyclization step. Combining computational and experimental results, we establish that the Lewis acid catalyst facilitates the initial C-O coupling step between the alkene and the activated aldehyde. Investigations into systems with longer alkyl chains reveal that while they follow a similar mechanistic pathway, cyclization becomes kinetically hindered, preventing the reaction from proceeding. These insights illuminate the factors governing reaction outcomes and limitations, paving the way for future developments in this area.

Overview on Building Blocks and Applications of Efficient and Robust Extended Tight Binding

The extended tight binding (xTB) family of methods opened many new possibilities in the field of computational chemistry. Within just 5 years, the GFN2-xTB parametrization for all elements up to Z = 86 enabled more than a thousand applications, which were previously not feasible with other electronic structure methods. The xTB methods provide a robust and efficient way to apply quantum mechanics-based approaches for obtaining molecular geometries, computing free energy corrections or describing noncovalent interactions and found applicability for many more targets. A crucial contribution to the success of the xTB methods is the availability within many simulation packages and frameworks, supported by the open source development of its program library and packages. We present a comprehensive summary of the applications and capabilities of xTB methods in different fields of chemistry. Moreover, we consider the main software packages for xTB calculations, covering their current ecosystem, novel features, and usage by the scientific community.

Facilitating Transition State Search with Minimal Conformational Sampling Using Reaction Graph

Elucidating transition states (TSs) is crucial for understanding chemical reactions. The reliability of traditional TS search approaches depends on input conformations that require significant effort to prepare. Previous automated methods for generating input reaction conformations typically involve extensive exploration of a large conformational space. Such exhaustive search can be complicated by the rapid growth of the conformational space, especially for reactions involving many rotatable bonds, multiple reacting molecules, and numerous bond formations and dissociations. To address this problem, we propose a new approach that generates reaction conformations for TS searches with minimal reliance on sampling. This method constructs a pseudo-TS structure based on a reaction graph containing bond formation and dissociation information and modifies it to produce reactant and product conformations. Tested on three different benchmarks, our method consistently generated suitable conformations without necessitating extensive sampling, demonstrating its potential to significantly improve the applicability of automated TS searches. This approach offers a valuable tool for a broad range of applications such as reaction mechanism analysis and network exploration.

Cambered Bipyridyl Ligand with Extended Aryl System Enables Electrochemical Reduction of Carbon Dioxide and Bicarbonate by Mn(bpy)(CO)3Br-type Catalyst Immobilized on Carbon Nanotubes

Heterogeneous materials containing molecular catalytic sites show promise for electrocatalytic reduction of CO2 to energy-enriched carbon products. Interactions between the catalyst and the heterogeneous support increasingly are recognized as important in governing product selectivity and rate. Recent work on Mn(R-bpy)(CO)3Br type catalysts immobilized on multiwalled carbon nanotubes (MWCNT) demonstrated control of electrocatalytic behavior with steric modification of the molecular catalyst. Phenyl groups installed in the 4,4' positions of the bipyridine ligand (ph-bpy) maximized performance through π-π interactions with the MWCNT support. Herein we report the outcome of extending the ligand π system with Mn(nap-bpy)(CO)3Br (nap-bpy = 4,4'-di(naphthalen-1-yl)-2,2'-bipyridine) and Mn(pyr-bpy)(CO)3Br (pyr-bpy = 4,4'-di(pyren-1-yl)-2,2'-bipyridine) immobilized on MWCNT. We demonstrate exceptional electrocatalysis with Mn(nap-bpy)(CO)3Br/MWCNT (FECO > 92%; JCO = 16.5 mA/cm2) and find that this catalyst electrochemically reduces bicarbonate in the absence of deliberately added CO2 at a remarkable overall selectivity of >80% for carbon products (FEHCOO- = 52% and FECO = 29%). We show diminishing returns to simply adding aromatic character to the bipyridyl ligand with Mn(pyr-bpy)(CO)3Br/MWCNT and observe a unique cambering of the Mn(nap-bpy)(CO)3Br bipyridyl ligand that we believe enables selective catalysis. Mechanistic studies were carried out on Mn(nap-bpy)(CO)3Br/MWCNT using a novel thin-film infrared spectroelectrochemical (IR-SEC) technique. These experiments observe the immobilized Mn(nap-bpy)(CO)3Br undergo single electron reduction to a Mn-centered radical that binds CO2 in a reduction-coupled process.

Cytochalasins and orsellinic acid derivatives with cytotoxicity from the soil-derived fungus Trichocladium asperum

Four undescribed cytochalasins (1-4), three undescribed orsellinic acid derivatives (5-7) and two known metabolites including methyl lecanorate (8) and methyl orsellinate (9) were isolated from the solid-state cultivation of a soil-derived fungus Trichocladium asperum SQ2-3 collected in Qinghai-Tibet Plateau. Their structures were elucidated by analysis of NMR (1D and 2D) and mass spectrometry data. The absolute configurations of 1-7 were assigned by a combination of the modified Mosher's method, microscale derivatization and Mo2(OAc)4-induced circular dichroism experiment. Compounds 1, 2, 3 and 6 showed significant cytotoxicity against HL-60, A3494, SMMC-7721, MDA-MB-231 and SW480 cell lines with IC50 values ranging from 4.74 to 15.84 μM, respectively. Meanwhile, compound 1 could obviously damage mitochondrial membrane potential and induce G2/M cell cycle arrest in A549 cells.

Computational Study of Hypervalent Chalcogen Bond Catalysis on the Hydroarylation of Styrene with Phenol: O-Activation vs π-Activation

Chalcogen bond catalysis is gaining recognition in organocatalysis due to its environmental benignity and relatively low cost. The hypervalent selenium salts can drive the hydroarylation of styrene and phenol, and hypervalent chalcogen···π catalysis has been proposed [Zhang, Q. Angew. Chem., Int. Ed. 2022, 61, e202208009]. In this work, the hydroarylation of styrene and phenol catalyzed by cyclic hypervalent selenium-based catalysts is investigated by density functional theory (DFT) calculations, and two activation modes are observed: one is on the styrene (π-activation mode), and the other is on the phenol (O-activation mode). The energy barriers via the O-activation mode are lower than those of the π-activation mode, and our proposed O-activation mode in this work may be more favorable. For the O-activation mode, energy barriers for the ortho-hydroarylation are lower than those for the para-hydroarylation, which is consistent with the experimental observation that the ortho-hydroarylation product is the major product and supports our proposed O-activation mode. Further investigation revealed that the stronger electrostatic interaction is the main factor leading to the ortho-hydroarylation in the O-activation mode compared to the para-hydroarylation. Moreover, the substituent effect of cyclic hypervalent selenium-based catalysts on the reactivity was investigated. This work would provide a valuable perspective on expanding applications for chalcogen bond catalysis.

Impact of nitrogen configuration on the electronic properties of tailored triphenylamine derivatives as hole transport materials for perovskite solar cells: a computational chemistry study

Physical properties associated with charge transfer processes of tailored triphenylamine derivative molecules, generated from six nitrogen-containing heterocyclic aromatic cores (nTPAM), were theoretically studied. The conformer-rotamer ensemble sampling tool (CREST) was employed to study the geometric arrangements of n-TPAM monomers and dimers. Essential chemical parameters, such as reorganisation energies, spin densities, and chemical reactivity, were computed utilising the M06 and ωB97X-3c DFT functionals. The ω parameter of the ωB97X-3c functional was optimised through a non-empirical tuning method. Time-dependent DFT computations yielded insights into the maximum absorption wavelength and transition density matrix of n-TPAM monomers. The electronic coupling between dimers was assessed using M06 and ωB97X-3c. The HOMO energy levels of the n-TPAM derivatives correspond with the perovskite conduction band, situated between YZ22 and spiro-OMeTAD hole transport materials (HTMs). n-TPAM molecules demonstrated enhanced electronic coupling for hole transfer, except for C-TPAM (Jeff(h) = 52.0 meV), in contrast to YZ22 (Jeff(h) = 79.7 meV). Nonetheless, n-TPAM exhibited elevated reorganisation energies, varying from 268.76 to 346.31 meV, compared to YZ22 (149.78 meV). Among the analysed derivatives, A-TPAM exhibited the highest chemical hardness and was the only molecule with absorption extending beyond the visible spectrum. Although A-TPAM exhibited superior electronic properties, its high reorganisation energy may limit its performance as an HTM compared to YZ22. Our analysis revealed that the electronic properties relevant to the hole extraction process can be tuned by modifying the nitrogen core configuration. Additionally, the degree of charge delocalisation in cationic compounds significantly influences charge transfer rates; therefore, an optimised DFT functional that effectively represents charge delocalisation is crucial for anticipating accurate trends in physical characteristics.

A Unique Intramolecular Redox Reaction by Unidirectional Migration of Three Hydrogen Atoms: Theoretical Elucidation of the 3H-Transfer Sequence

The intramolecular migration of three hydrogen atoms from one moiety of a gaseous radical cation to the other prior to fragmentation is an extremely rare type of redox reaction. Within the scope of this investigation, this scenario requires an ionized but electron-rich arene acceptor bearing a para-(3-hydroxyalkyl) residue. The precise mechanism of such unidirectional 3H transfer processes, including the order of the individual H transfer steps, has remained unclear in spite of previous isotope labelling and recent infrared ion spectroscopy (IRIS) studies. Herein, the details of this peculiar process have been investigated for ionized 4-(N,N-dimethylaminophenyl)-2-butanol, 2, by state-of-the-art density functional theory (DFT) calculations. The energetically most favorable pathway consists of a sequence of successive 1,4-, 1,6- and 1,5-H steps. During these steps the secondary alcohol functionality is oxidized to a carbonyl group and the radical-cationic aniline ring is reduced to an ionized 2,3-dihydroaniline unit. Several alternative sequences, such as three successive 1,5-H shifts, could be excluded. A concomitant unidirectional 2H migration reaction of ion 2 was also investigated and the intermediacy of ion-neutral complexes (INCs) enabling sequential hydride and proton transfer was confirmed by the calculations.

Absolute Saturation Vapor Pressures of Three Fatty Acid Methyl Esters around Room Temperature

We report measurements of absolute saturation vapor pressures around room temperature for three fatty acid methyl esters (methyl octanoate, methyl decanoate, and methyl dodecanoate) using a recently developed experimental method in which the saturation vapor pressures are determined from the vaporization dynamics of a cooled sample during thermalization to a higher chamber temperature.

Glucose-derived receptors for photo-controlled binding of amino acid esters in water

Selective receptors of amino acids in aqueous media are highly sought after as they may enable the creation of novel diagnostic and sensing tools. Photoswitchable receptors are particularly attractive for such purposes as their response and selectivity towards bioanalytes can be modulated using light. Herein we report glucose-based photoswitchable receptors of amino-acid methyl esters and biogenic amines in water. The tetra-ortho-fluoroazobenzene unit in the receptors structure allows to control the distance between their binding sites using light. The Z-isomers of both receptors, having these sites in closer proximity, bind lysine, ornithine and arginine esters significantly stronger compared to E-isomers, where the binding sites are further apart.

Critical Evaluation of Childs Method for the NMR Spectroscopic Scaling of Effective Lewis Acidity: Limitations and Resolution of Earlier Discrepancies

Quantifying Lewis acidity is essential for understanding and optimizing the performance of Lewis acids in diverse applications. Next to the widely accepted Gutmann-Beckett (GB) method, using triethyl phosphine oxide (TEPO) as a probe, the Childs method-employing trans-crotonaldehyde (TCA)-gained attention as an NMR-based technique for measuring effective Lewis acidity (eLA). Despite its steady use, the robustness of Childs method and its correlation with other measures remain underexplored. Previous comparisons between the GB and Childs scales revealed significant discrepancies, suggesting that hard and soft acid/base (HSAB) characteristics may be operative. In this study, we compare thermodynamic data for TCA binding to 117 Lewis acids (representing global Lewis acidity, gLA) with their corresponding NMR-induced chemical shifts in TCA. Our findings showcase notable deviations that reinforce key distinctions between eLA and gLA perspectives. Moreover, we identify significant limitations in the Childs method. First, the weak donor strength of TCA limits its applicability to only the strongest Lewis acids. Second, the exposed protons of TCA are prone to secondary interactions, obscuring the measurement of true Lewis acidity. Finally, our analysis reconciles discrepancies, refuting earlier assumptions that these arise from HSAB effects.

OH-Detected Aromatic Microsolvation of an Organic NO Radical: Halogenation Controls the Solvation Side

The persistent organic radical 2,2,6,6-tetramethylpiperidinyloxyl (TEMPO) protects its NO radical center by four methyl groups. Two of them are arranged tightly (t) on one side of the six-membered puckered heterocycle, and the other two more openly (o) on the other side. It is shown by OH stretching infrared spectroscopy in heated supersonic jet expansions that the hydrogen bond and aromatic ring of a first solvating benzyl alcohol have almost no preference for either side. An increased preference for the t side develops in para-halogenated benzyl alcohols, and it is inverted for ortho-halogenated benzyl alcohols. The experimental dependence on the actual halogen (Cl, Br, and I) is weak, whereas different quantum chemical approaches predict more or less pronounced trends along the halogen series. Some of the benzyl alcohol in the pre-expansion reservoir reduces the TEMPO radical to the closed-shell heterocyclic hydroxylamine TEMPO-H (1-hydroxy-2,2,6,6-tetramethylpiperidine), to the extent that the TEMPO-H···TEMPO complex is observed as an impurity.

Tensor Train Optimization for Conformational Sampling of Organic Molecules

Exploring the conformational space of molecules remains a challenge of fundamental importance to quantum chemistry: identification of relevant conformers at ambient conditions enables predictive simulations of almost arbitrary properties. Here, we propose a novel approach, called TTConf, to enable conformational sampling of large organic molecules where the combinatorial explosion of possible conformers prevents the use of a brute-force systematic conformer search. We employ tensor trains as a highly efficient dimensionality reduction algorithm, effectively reducing the scaling from exponential to polynomial. In our approach, the conformational search is expressed as global energy minimization task in a high-dimensional grid of dihedral angles. Dimensionality reduction is achieved through a tensor train representation of the high-dimensional torsion space. The performance of the approach is assessed on a variety of drug-like molecules in direct comparison to the state-of-the-art metadynamics based conformer search as implemented in CREST. The comparison shows significant acceleration of up to an order of magnitude, while maintaining comparable accuracy. More importantly, the presented approach allows treatment of larger molecules than typically accessible with metadynamics.

Chiroptical Spectroscopy, Theoretical Calculations, and Symmetry of a Chiral Transition Metal Complex with Low-Lying Electronic States

Vibrational circular dichroism (VCD) enhancement by low-lying electronic states (LLESs) is a fascinating phenomenon, but accounting for it theoretically remains a challenge despite significant research efforts over the past 20 years. In this article, we synthesized two transition metal complexes using the tetradentate Schiff base ligands (R,R)- and (S,S)-N,N'-Bis(3,5-di-tert-butylsalicylidene)-1,2-cyclohexanediamine with Co(II) and Mn(III), referred to as Co(II)-salen-chxn and Mn(III)-Cl-salen-chxn, respectively. Their stereochemical properties were explored through a combined experimental chiroptical spectroscopic and theoretical approach, with a focus on Co(II)-salen-chxn. Extensive conformational searches in CDCl3 for both high- and low-spin states were carried out and the associated infrared (IR), VCD, ultraviolet-visible (UV-Vis) absorption, and electronic circular dichroism (ECD) spectra were simulated. A good agreement between experimental and simulated data was achieved for IR, VCD, UV-Vis, and ECD, except in the case of VCD of Co(II)-salen-chxn which exhibits significant intensity enhancement and monosignate VCD bands, attributed to the LLESs. Interestingly, detailed comparisons with Mn(III)-Cl-salen-chxn and previously reported Ni(II)-salen-chxn and Cu(II)-salen-chxn complexes suggest that the enhancement factor is predicted by the current density functional theory simulations. However, the monosignate signatures observed in the experimental Co(II) VCD spectrum were not captured theoretically. Based on the experiment and theoretical VCD and ECD comparison, it is tentatively suggested that Co(II)-salen-chxn exists in both low- and high-spin states, with the former being dominant, while Mn(III)-Cl-salen-chxn in the high-spin state. The study indicates that VCD enhancement by LLESs is at least partially captured by the existing theoretical simulation, while the symmetry consideration in vibronic coupling provides further insight into the mechanisms behind the VCD sign-flip.

Automated search of minimum-energy conical intersections with projected metadynamics

We present a new method for the automated search of minimum-energy conical intersections (MECIs) based on metadynamics. In this method, two independent forces are constructed and projected into the minimization subspace and the constraint subspace, respectively. One force is directed toward the minimum-energy point, while the other is directed toward the conical intersection seam. The root-mean-square deviation based bias potential is added to the potential energy surface to force the structure escape from the already explored regions. The additional constraint function is used to enable the structure reach different intersection seams. This method can be used for systematically and automatically searching MECIs or exploring conical intersection seams. Compared to the penalty function-based metadynamics method, this new method is more effective and stable in searching MECIs. Furthermore, this method can be combined with any kind of constraint, whether geometric or non-geometric, making it a generalized tool for the automated search of constrained minimum.

Predicting Carbonic Anhydrase Binding Affinity: Insights from QM Cluster Models

A systematic series of QM cluster models has been developed to predict the trend in the carbonic anhydrase binding affinity of a structurally diverse dataset of ligands. Reference DLPNO-CCSD(T)/CBS binding energies were generated for a cluster model and used to evaluate the performance of contemporary density functional theory methods, including Grimme's "3c" DFT composite methods (r2SCAN-3c and ωB97X-3c). It is demonstrated that when validated QM methods are used, the predictive power of the cluster models improves systematically with the size of the cluster models. This provided valuable insights into the key interactions that need to be modeled quantum mechanically and could inform how the QM region should be defined in hybrid quantum mechanics/molecular mechanics (QM/MM) models. The use of r2SCAN-3c on the largest cluster model composed of 16 residues appears to be an economical approach to predicting binding trends compared with using more robust DFT methods such as ωB97M-V and provides a significant improvement compared with docking.

Structurally diverse chromane meroterpenoids from Rhododendron capitatum with multifunctional neuroprotective effects

Eleven new chromane meroterpenoids (1-11), along with 24 known ones (12-35) were isolated from Rhododendron capitatum, a Tibetan medicine. Their structures were determined via extensive spectroscopic methods. The absolute configurations of 1 and 2 were determined by comparison of the experimental and theoretically calculated ECD data. For compounds 3-9, the absolute configurations at the C-2 were assigned according to the empirical chromane helicity rule. The stereochemistry of the chiral alcohols at C-13 in 3 and C-15 in 4 were determined using the Rh2(OCOCF3)4-induced ECD spectra based on the bulkiness rule. Additionally, the absolute configurations of secondary alcohols at C-13 in 8 and 9 were unambiguously established by Mosher's method. Neuroprotection evaluations in vitro and in vivo revealed that compounds 1, 18, and 21 can significantly inhibit the inducible nitric oxide synthase (iNOS) and cyclooxygenase 2 (COX-2) protein expressions. Compound 21 also down-regulated MAPK signal pathway in BV-2 cells. The PC-12 cell damage induced by H2O2 and 6-hydroxydopamine (6-OHDA) was attenuated by compounds 1, 21, and 22, especially for 22. Moreover, compounds 3, 6, 22, 23, and 28 significantly enhanced NGF-induced neurite growth in PC-12 cells. Notably, compound 6 demonstrated the most potent neurite growth promotion with a rate of 22.93 ± 2.24 % at 10 μM, which was approximately 3-fold higher than that induced by nerve growth factor (NGF). In AD Caenorhabditis elegans CL4176 model, compounds 1 and 21 delayed Aβ-induced paralysis and reduced ROS expression levels. These studies provide new potential neuroprotective agents for the prevention and treatment of neurodegenerative diseases.

Understanding and quantifying the impact of solute-solvent van der Waals interactions on the selectivity of asymmetric catalytic transformations

The majority of enantioselective organocatalytic reactions occur in apolar or weakly polar organic solvents. Nevertheless, the influence of solute-solvent van der Waals forces on the relative kinetics of competitive pathways remains poorly understood. In this study, we provide a first insight into the nature and strength of these interactions at the transition state level using advanced computational tools, shedding light into their influence on the selectivity. In addition, we introduce a series of computational tools tailored for detailed exploration of the role of the organic solvent across diverse research disciplines. As a case study, we selected a highly relevant asymmetric organocatalytic transformation catalyzed by a chiral Brønsted acid. Our analysis reveals that strong dispersion interactions exist between the transition state and the solvent, predominantly involving specific groups of the catalyst rather than being uniformly distributed around the solute. Short-range repulsion between the transition state and the solvent often counteracts the effect of these dispersion forces on the transition state energy, resulting in a minimal overall influence of solute-solvent van der Waals forces on enantioselectivity. However, for certain geometric configurations of the transition states, the effect these interactions remains significant, favoring specific reaction channels. These results suggest that integrating solvent structural and electronic information into catalyst design strategies could offer new avenues for tuning selectivity of organocatalytic processes.

Probing London Dispersion in Proton-Bound Onium Ions: Are Alkyl-Alkyl Steric Interactions Reliably Modeled?

We report spectroscopic and spectrometric experiments that probe the London dispersion interaction between tert-butyl substituents in three series of covalently linked, protonated bis-pyridines in the gas phase. Molecular ions in the three test series, along with several reference molecules for control, were electrosprayed from solution into the gas phase and then probed by infrared multiphoton dissociation spectroscopy and trapped ion mobility spectrometry. The observed N-H stretching frequencies provided an experimental readout diagnostic of the ground-state geometry of each ion, which could be furthermore compared to a second, independent structural readout via the collision cross section. In each of the three series, the strength of a London dispersion interaction could be modulated systematically by a progressive increase in the size of substituents from H to Me to tert-Bu. Parallel to the experimental study, extensive dispersion-corrected density functional theory (DFT-D3BJ) calculations were performed with a range of exchange correlation functionals. A full analysis of the conformational space for the flexible members of the series, and an analysis of the vibrational spectra in the context of a general double-well potential, finds that DFT-D3BJ appears to significantly overbind alkyl-alkyl interactions, specifically interactions between tert-Bu groups, even failing to predict the minimum energy structures reliably in the case of molecules in which London dispersion competes with other noncovalent interactions such as hydrogen bonding.

Exploring the constitutive activation mechanism of the class A orphan GPR20

GPR20, an orphan G protein-coupled receptor (GPCR), shows significant expression in intestinal tissue and represents a potential therapeutic target to treat gastrointestinal stromal tumors. GPR20 performs high constitutive activity when coupling with Gi. Despite the pharmacological importance of GPCR constitutive activation, determining the mechanism has long remained unclear. In this study, we explored the constitutive activation mechanism of GPR20 through large-scale unbiased molecular dynamics simulations. Our results unveil the allosteric nature of constitutively activated GPCR signal transduction involving extracellular and intracellular domains. Moreover, the constitutively active state of the GPR20 requires both the N-terminal cap and Gi protein. The N-terminal cap of GPR20 functions like an agonist and mediates long-range activated conformational shift. Together with the previous study, this study enhances our knowledge of the self-activation mechanism of the orphan receptor, facilitates the drug discovery efforts that target GPR20.

The Best of Both Worlds: ΔDFT Describes Multiresonance TADF Emitters with Wave-Function Accuracy at Density-Functional Cost

With their narrow-band emission, high quantum yield, and good chemical stability, multiresonance thermally activated delayed fluorescence (MR-TADF) emitters are promising materials for OLED technology. However, accurately modeling key properties, such as the singlet-triplet (ST) energy gap and fluorescence energy, remains challenging. While time-dependent density functional theory (TD-DFT), the workhorse of computational materials science, suffers from fundamental issues, wave function-based coupled-cluster (CC) approaches, like approximate CC of second-order (CC2), are accurate but suffer from high computational cost and unfavorable scaling with system size. This work demonstrates that a state-specific ΔDFT approach based on unrestricted Kohn-Sham (ΔUKS) combines the best of both worlds: on a diverse benchmark set of 35 MR-TADF emitters, ΔUKS performs as good as or better than CC2, recovering experimental ST gaps with a mean absolute deviation (MAD) of 0.03 eV at a small fraction of the computational cost of CC2. When combined with a tuned range-separated LC-ωPBE functional, the excellent performance extends to fluorescence energies and ST gaps of MR- and donor-acceptor TADF emitters and even molecules with an inverted ST gap (INVEST), rendering this approach a jack of all trades for organic electronics.

Ultrafast Dissociation Dynamics of the Sensitive Explosive Ethylene Glycol Dinitrate

Ethylene glycol dinitrate (EGDN) is a nitrate ester explosive widely used in military ordnance and missile systems. This study investigates the decomposition dynamics of the EGDN cation using a comprehensive approach that combines femtosecond time-resolved mass spectrometry (FTRMS) experiments with ab initio electronic structure and molecular dynamics computations. We identify three distinct dissociation time scales for the metastable EGDN cation of approximately 40-60 fs, 340-450 fs, and >2 ps. The observed dissociation time scales are rationalized by electronic and geometric relaxation of multiple EGDN conformers. These insights are crucial for advancing knowledge of the initial molecular decomposition processes that are central to the detonation physics of nitrate esters, which can lead to improving safety protocols and optimizing the performance of nitrate ester explosives in various applications.

The Elusive Ternary Intermediates of Chiral Phosphoric Acids in Ion Pair Catalysis─Structures, Conformations, and Aggregation

In ion-pair catalysis, the last intermediate structures prior to the stereoselective transition states are of special importance for predictive models due to the high isomerization barrier between E- and Z-substrate double bonds connecting ground and transition state energies. However, in prior experimental investigations of chiral phosphoric acids (CPA) solely the early intermediates could be investigated while the key intermediate remained elusive. In this study, the first experimental structural and conformational insights into ternary complexes with CPAs are presented using a special combination of low temperature and relaxation optimized 15N HSQC-NOESY NMR spectroscopy to enhance sensitivity. Combined NMR investigations and theoretical calculations revealed three conformers of the ternary complex, of which one also closely resembles the previously calculated transition states. In addition, a 2:1:1 ternary complex as well as an unprecedent [3:3] dimeric species consisting of two ternary complexes was revealed. Given the importance of the ground state energies for the transition state interpretation in ion pair catalysis we believe that the presented experimental insight into the structural and conformational variety of the ternary complexes is a key to the future development of predictive models in ion pair catalysis.

Increasing the Donor Strength of Alkenylphosphines by Twisting the C=C Double Bond

Electron-rich phosphines play a crucial role in transition metal-based homogeneous catalysis. While alkyl groups have traditionally been employed to increase the phosphine donor strength, recent studies have shown that zwitterionic functional groups such as phosphorus ylides can result in a further enhancement. Herein we report the concept of twisting a C=C double bond to introduce a zwitterionic substituent by the synthesis and application of N-heterocyclic olefin phosphines with a sulfonyl substituent (sNHOP). This sulfonyl group enables the twisting of the olefin moiety due to steric and electronic stabilization of the carbanionic center. The resulting zwitterionic structure leads to a significant increase of the donor strength of the sNHOP ligands compared to conventional NHOP systems with a planar N-heterocyclic olefin moiety. The potential of this new ligand platform for catalysis is demonstrated by its application in the gold-catalyzed hydroamination and cyclo-isomerization of alkynes. Here, the ligands outperform the original NHOP ligands suggesting favorable properties for future catalysis applications.

Absorption Spectrum of Hydroperoxymethyl Thioformate: A Computational Chemistry Study

Hydroperoxymethyl thioformate (or HPMTF) is a compound relevant to the chemistry of sulfur in the marine atmosphere. The chemical cycling of this molecule in the atmosphere is still uncertain due in part to the lack of accurate knowledge of its photolytic behavior. Only approximations based on the properties of its chromophores are used in previous studies. In this work, we calculated the absorption spectra of the molecule in gas and aqueous phases using the Nuclear Ensemble Approach (NEA) and the CASPT2 method. Furthermore, we used such information to obtain relative photolysis rates. We found that the chromophore approximation overestimates the photolysis rates in the gas phase by twice the value obtained with the NEA-CASPT2 protocol. Furthermore, for the aqueous phase, we predict a lower role of photolysis as compared to the gas phase.