An efficient and near linear scaling pair natural orbital based local coupled cluster method

CH Bond Activation Mechanism by a High-Valent Dinuclear Copper Complex: Unraveling the Effect of a Base by a Theoretical Study

Recently, an electrochemically monooxidized dinuclear copper(II) complex [Cu2(L)(μ-OH)2]2+ with the dipyridylethane naphthyridine ligand (L) has been shown to activate the recalcitrant aliphatic Csp 3H bond of toluene (bond dissociation free energy, BDFE = 87.0 kcal mol-1) at room temperature. The mechanistic pathway turns from stoichiometric to catalytic upon addition of a base (2,6-lutidine), suggesting a modification of the reactive species. Herein, we report theoretical calculations to characterize the reactive species and obtain a detailed understanding of the reactivity. Since different electronic structures are possible for these high valent systems, we perform DFT calculations coupled to CCSD(T) ones using the DLPNO-CCSD(T) scheme. Our results show that the presence of a base will impact the nature of the reactive species but also the type of mechanism involved in the CH activation.

SpectroIBIS: Automated Data Processing for Multiconformer Quantum Chemical Spectroscopic Calculations

Quantum chemical spectroscopic calculations have grown increasingly popular in natural products research for aiding the elucidation of chemical structures, especially their stereochemical configurations. These calculations have become faster with modern computational speeds, but subsequent data handling, inspection, and presentation remain key bottlenecks for many researchers. In this article, we introduce the SpectroIBIS computer program as a user-friendly tool to automate tedious tasks commonly encountered in this workflow. Through a simple graphical user interface, researchers can drag and drop Gaussian or ORCA output files to produce Boltzmann-averaged ECD, VCD, UV-vis and IR data, optical rotations, and/or 1H and 13C NMR chemical shifts in seconds. Also produced are formatted, publication-quality supplementary data tables containing conformer energies and atomic coordinates, saved to a DOCX file compatible with Microsoft Word and LibreOffice. Importantly, SpectroIBIS can assist researchers in finding common calculation issues by automatically checking for redundant conformers and imaginary frequencies. Additional useful features include recognition of conformer energy recalculations at a higher theory level, and automated generation of input files for quantum chemistry programs with optional exclusion of high-energy conformers. Lastly, we demonstrate the applicability of SpectroIBIS with spectroscopic calculations for five natural products. SpectroIBIS is open-source software available as a free desktop application (https://github.com/bbulcock/SpectroIBIS).

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.

A framework for designing main-group single-molecule magnets

Single-molecule magnets (SMMs) are molecular entities with strongly anisotropic magnetic moment. As a result, SMMs display slow relaxation of magnetization at the macroscopic scale. Up to date all experimentally characterized SMMs are based on either d- or f-block metals with lanthanides proving to be the most successful. In the present work, a framework for constructing SMMs consisting purely of main-group elements will be outlined by computational and theoretical means. The proposed main-group SMMs utilize the strong spin-orbit coupling of a single heavy p-block atom or ion that can lead to strong magnetic anisotropy and pronounced SMM properties. A theoretical crystal-field model is developed to describe the magnetic properties of p-block SMMs with a minimal set of parameters related to the chemical structure of the SMMs. The model is used to establish which p-block elements and oxidation states can lead to SMM behavior. A large number of model structures are studied to establish general features of optimal chemical structures. These include one- and two-coordinate structures involving ligands with different coordination modes and all group 13 to 17 elements in periods 4 to 6. The results show that the most viable structures are based on mono-coordinated complexes of bismuth in oxidation state 0 with σ-donor ligands. Structures with bulkier ligands that sterically protect the bismuth atoms are then proposed as a starting point for the practical realization of main-group SMMs. The calculations show that minimizing the anagostic interactions with the bismuth atom is essential in the ligand design, which along with the low oxidation state of bismuth introduces significant synthetic challenges. The results do, however, show that main-group SMMs are plausible from a practical point of view within a limited set of heavier p-block elements in specific oxidation states. Furthermore, the proposed SMMs display much larger energy barriers for the relaxation of magnetization than even the best lanthanide-based SMMs do. This indicates that it is possible that main-group SMMs can supersede even the best currently known SMMs based on d- or f-block elements.

Direct measurement of fluorocarbon radicals in the thermal destruction of perfluorohexanoic acid using photoionization mass spectrometry

Thermal destruction is a critical cornerstone of addressing the rampant contamination of natural resources with per- and polyfluoroalkyl substances (PFAS). However, grave concerns associated with stack emissions from incineration exist because mechanistic studies have thus far relied on ex situ analyses of end products and theoretical calculations. Here, we used synchrotron-based vacuum ultraviolet photoionization mass spectrometry to study the pyrolysis of a representative PFAS-perfluorohexanoic acid-and provide direct evidence of fluorocarbon radicals and intermediates. A key reaction pathway from perfluorocarboxylic acids to ketenes via acyl fluorides is proposed. We furthermore propose CF2/CF3 radical-centered pyrolysis mechanisms and explain their roles in the formation of other products that may form in full-scale incinerators. These results have not only unveiled the role of radicals and intermediates in thermal PFAS decomposition and recombination mechanisms but also provide unique insight into improving the safety and viability of industrial PFAS incineration.

Overview of Developments in the MRCC Program System

mrcc is a versatile suite of quantum chemistry programs designed for accurate ab initio and density functional theory (DFT) calculations. This contribution outlines the general features and recent developments of the package. The most popular features include the open-ended coupled-cluster (CC) code, state-of-the-art CC singles and doubles with perturbative triples [CCSD(T)], second-order algebraic-diagrammatic construction, and combined wave function theory-DFT approaches. Cost-reduction techniques are implemented, such as natural orbital (NO), local NO (LNO), and natural auxiliary function approximations, which significantly decrease the computational demands of these methods. This paper also details the method developments made over the past five years, including efficient schemes to approach the complete basis set limit for CCSD(T) and the extension of our LNO-CCSD(T) method to open-shell systems. Additionally, we discuss the new approximations introduced to accelerate the self-consistent field procedure and the cost-reduction techniques elaborated for analytic gradient calculations at various levels. Furthermore, embedding techniques and novel range-separated double-hybrid functionals are presented for excited-state calculations, while the extension of the theories established to describe core excitations and ionized states is also discussed. For academic purposes, the program and its source code are available free of charge, and its commercial use is also facilitated.

Determining the Molecular Shape of Progesterone: Insights from Laser Ablation Rotational Spectroscopy

Herein, we present the first experimental observation of isolated progesterone, an endogenous steroid, placed in the gas phase by laser ablation and characterized in a supersonic expansion by Fourier transform microwave techniques. Guided by quantum-chemical calculations, we assigned the rotational spectrum of the most stable structure. The internal rotation of the acetyl methyl group led to the observation of A-E doublets in the spectrum, which were analyzed, resulting in a V3 barrier of 2.4425 ± 0.0025 kJ mol-1. By fitting over 250 transitions, we determined accurate rotational constants that enabled us to compare the gas phase geometrical parameters with those of crystalline forms and complexes with progesterone receptors. Our results indicate that the A ring of progesterone that contains the ketone group is surprisingly flexible, despite its rigid appearance. This finding is particularly significant, since this ring is an active biological site that is involved in strong intermolecular interactions. Notably, progesterone C21H30O2 is the largest molecule investigated using laser ablation rotational spectroscopy.

On the nature of high-spin forms in the S2 state of the oxygen-evolving complex

The Mn4CaO x cluster of the oxygen-evolving complex (OEC) in photosystem II, the site of biological water oxidation, adopts different forms as it progresses through the catalytic cycle of S i states (i = 0-4) and within each S i state itself. This has been amply documented by spectroscopy, but the structural basis of spectroscopic polymorphism remains debated. The S2 state is extensively studied by magnetic resonance spectroscopies. In addition to the common type of g ≈ 2 multiline EPR signal attributed to a low-spin (S = 1/2) form of the manganese cluster, other signals at lower fields (g ≥ 4) associated with the S2 state arise from higher-spin forms. Resolving the structural identity of the high-spin species is paramount for a microscopic understanding of the catalytic mechanism. Hypotheses explored by theoretical studies implicate valence isomerism, proton tautomerism, or coordination change with respect to the low-spin form. Here we analyze structure-property correlations for multiple formulations employing a common high-level protocol based on multiscale models that combine a converged quantum mechanics region embedded within a large protein region treated semiempirically with an extended tight-binding method (DFT/xTB), surpassing conventional quantum mechanics/molecular mechanics (QM/MM) approaches. Our results provide a comprehensive comparison of magnetic topologies, spin states and energetics in relation to experimental observations. Crucial predictions are made about 14N hyperfine coupling constants and X-ray absorption Mn K-pre-edge features as criteria for discriminating between different models. This study updates our view on a persistent mystery of biological water oxidation, while providing a refined and transferable computational platform for future theoretical studies of the OEC.

Another Angle on Benchmarking Noncovalent Interactions

For noncovalent interactions, the CCSD(T)-coupled cluster method is widely regarded as the "gold standard". With localized orbital approximations, benchmarks for ever larger complexes are being published, yet FN-DMC (fixed-node quantum Monte Carlo) intermolecular interaction energies diverge to a progressively larger degree from CCSD(T) as the system size grows, particularly when π-stacking is involved. Unfortunately, post-CCSD(T) methods like CCSDT(Q) are cost-prohibitive, which requires us to consider alternative means of estimating post-CCSD(T) contributions. In this work, we take a step back by considering the evolution of the correlation energy with respect to the number of subunits for such π-stacked sequences as acene dimers and alkadiene dimers. We show it to be almost perfectly linear and propose the slope of the line as a probe for the behavior of a given electron correlation method. By going further into the coupled cluster expansion and comparing with CCSDT(Q) results for benzene and naphthalene dimers, we show that CCSD(T) does slightly overbind but not as strongly as suggested by the FN-DMC results.

Beyond CCSD(T) Accuracy at Lower Scaling with Auxiliary Field Quantum Monte Carlo

We introduce a black-box auxiliary field quantum Monte Carlo (AFQMC) approach to perform highly accurate electronic structure calculations using configuration interaction singles and doubles (CISD) trial states. This method consistently provides more accurate energy estimates than coupled cluster singles and doubles with perturbative triples (CCSD(T)), often regarded as the gold standard in quantum chemistry. This level of precision is achieved at a lower asymptotic computational cost, scaling as O(N6) compared to the O(N7) scaling of CCSD(T). We provide numerical evidence supporting these findings through results for challenging main group and transition metal-containing molecules.

CO2 Reduction at a Borane-Modified Iron Complex: A Secondary Coordination Sphere Strategy

This work addresses fundamental questions that deepen our understanding of secondary coordination sphere effects on carbon dioxide (CO2) reduction using derivatized hydride analogues of the type, [Cp*Fe(diphosphine)H] (Cp* = C5Me5 -) - a well-studied family of organometallic complex - as models. More precisely, we describe the general reactivity of [(Cp*-BR2)Fe(diphosphine)H], which contains an intramolecularly positioned Lewis acid, and its cooperative reactivity with CO2. Control experiments underscore the critical nature of borane incorporation for transforming CO2 to reduced products, a reaction that does not occur for unfunctionalized [Cp*Fe(diphosphine)H]. Additional experiments highlight relevance of borane hybridization and substituent effects. Mechanistic studies performed in the presence and absence of CO2 emphasize the significance of carbonyl substrate to catalyst longevity. Lessons from these reactions were also transferable - with such borane-containing complexes enabling the chemoselective reduction of aldehydes in the presence of alkenes. These findings provide valuable insights into metal-ligand cooperative design strategies for carbonyl reduction and illustrate the versatility of intramolecularly positioned Lewis acids for otherwise challenging chemical transformations.

Linear-Scaling Local Natural Orbital-Based Full Triples Treatment in Coupled-Cluster Theory

We present an efficient, asymptotically linear-scaling implementation of the canonically O ( N 8 ) coupled-cluster method with singles, doubles, and full triples excitations (CCSDT) method. We apply the domain-based local pair natural orbital (DLPNO) approach for computing CCSDT amplitudes. Our method, called DLPNO-CCSDT, uses the converged coupled-cluster amplitudes from a preceding DLPNO-CCSD(T) computation as a starting point for the solution of the CCSDT equations in the local natural orbital basis. To simplify the working equations, we t1-dress our two-electron integrals and Fock matrices, allowing our equations to take on the form of CCDT. With appropriate parameters, our method can recover more than 99.99% of the total canonical CCSDT correlation energy. In addition, we demonstrate that our method consistently yields sub-kJ mol-1 errors in relative energies when compared to canonical CCSDT, and, likewise, when computing the difference between CCSDT and CCSD(T). Finally, to highlight the low scaling of our algorithm, we present timings on linear alkanes (up to 30 carbons and 730 basis functions) and water clusters (up to 131 water molecules and 3144 basis functions).

Intermolecular Forces in Bioactive Resveratrol Complexes with Alcohols: A Study of Stability and Electronic Structure

Noncovalent interactions, particularly hydrogen bonding, play a pivotal role in determining the structural stability and functional properties of molecules, including bioactive compounds like resveratrol. This study focuses on the hydrogen-bonding behavior and other noncovalent interactions in gas-phase resveratrol-ethanol (EtOH) and resveratrol-methanol (MtOH) complexes, referred to as System 1 and System 2, respectively. These systems were optimized using the ωB97XD functional and cc-pVDZ basis set, providing a detailed picture of their stability and intermolecular interactions. By employing advanced methods such as Domain-Based Local Pair Natural Orbital Coupled Cluster (DLPNO-CCSD)(T) for energy decomposition, natural bond orbital (NBO) for charge analysis, atoms in molecule (AIM) for electron density topology, and noncovalent interaction (NCI) techniques, we decompose interaction energies into meaningful components like electrostatic, dispersion, and exchange-repulsion. The findings indicate that, while hydrogen bonding contributes to the stability of these complexes, London dispersion and other attractive interactions are substantial factors as well. The resveratrol-EtOH and resveratrol-MtOH systems demonstrate a robust electronic environment with significant contributions from various intermolecular forces, underscoring the importance of noncovalent interactions in stabilizing bioactive compounds. This study adds to our understanding of molecular interactions in resveratrol complexes, with potential implications for medicinal chemistry and material science, particularly where solvation effects are critical.

Vibrationally Assisted Tunneling through the Bread of a Proton Sandwich─Connections to Dynamic Matching

Proton sandwiches are unusual nonclassical carbocations characterized by a five-center, four-electron bonding array which rapidly isomerize to lower energy isomers with three-center, two-electron bonding arrays via hydrogen migration transition states. These reactions are suspected to involve significant contributions from tunneling, even at relatively high temperatures, where tunneling effects are usually minimal. Machine-learning-accelerated ring-polymer, quasiclassical, and classical ab initio molecular dynamics simulations were used to investigate the effects of a flavor of dynamic matching that involves coupling of vibrational modes of the reactant to the transition structure mode with an imaginary frequency, and how quantum mechanical tunneling affects this coupling. These nonstatistical dynamic effects were quantified by analysis of momentum in the molecular dynamics simulations. We show the importance of momentum for reactivity with and without tunneling, how tunneling amplifies these benefits, and that vibrational modes can be leveraged to generate beneficial momentum.

Metal-Metal Bonding in Tri-Actinide Clusters: A DFT Study of [An3Cl6]z (z=1-6) and [An3Cl6Cp3]z (z=-2-+3; An=Ac, Th, Pa, U, Np, Pu)

The actinide-actinide bonding in tri-actinide clusters [An₃Cl₆]z (An=Ac-Pu, z=1-6) and [An₃Cl₆Cp₃]z (z=-2-+3; Cp=(η5-C5H5)) is studied using density functional theory. We find 3-centre bonding similar to the tri-thorium cluster [{Th(η⁸-C₈H₈)(μ₃-Cl)₂}₃{K(THF)₂}₂]∞, as we previously reported (Nature 2021, 598, 72-75). The population of 3-centre molecular orbitals (3c-MOs) by zero, one or two electrons correlates with shortening of the An-An bond lengths, which also decrease with increasing actinide atomic number, consistent with the contraction of the actinide valence atomic orbitals. Mulliken analyses indicate that these 3c-MOs predominantly involve An 6d and 5 f orbitals. Various methods evidence the presence of An-An bonding in most systems with populated 3c-MOs, including bond orders (Mayer and Wiberg), quantum theory of atoms in molecules metrics (ρ, ∇2ρ, -G/V, H, delocalization indices), electron localization function, and electron density assessments. Additionally, we explore the effect of Cp ligand substitution on uranium complexes, finding that bulkier Cp ligands can induce U-U bond distortions and result in slightly longer U-U bonds. Overall, this study advances our understanding of metal-metal bonding in tri-actinide clusters, highlighting its effects on geometric and electronic structures.

Evaluation of Density-Functional Tight-Binding Methods for Simulation of Protic Molecular Ion Pairs

In this work, we benchmark the accuracy of the density-functional tight-binding (DFTB) method, namely the long-range corrected second-order (LC-DFTB2) and third-order (DFTB3) models, for predicting energetics of imidazolium-based ionic liquid (IL) ion pairs. We compare the DFTB models against popular density functionals such as LC-ωPBE and B3LYP, using ab initio domain-based local pair-natural orbital coupled cluster (DLPNO-CC) energies as reference. Calculations were carried out in the gas phase, as well as in aqueous solution using implicit solvent methods. We find that the LC-DFTB2 model shows excellent performance in the gas phase and agrees well with reference energies in implicit solvent, often outperforming DFTB3 predictions for complexation energetics. Our study identifies a range of opportunities for use of the LC-DFTB method and quantifies its sensitivity to protonation states and the types of chemical interactions between ion pairs.

Synthetically Relevant Post-Transition State Bifurcation Leading to Diradical and Zwitterionic Intermediates: Controlling Nonstatistical Kinetic Selectivity through Solvent Effects

A post-transition state surface intersection (PTSSI) between radical and zwitterionic states that causes a bifurcation in the reaction pathway was discovered through density functional theory calculations on potential energy surfaces and ab initio molecular dynamics simulations of cycloadditions between a bicyclobutane and a triazolinedione (BCB-TAD). It was predicted that changes to the solvent polarity would enable control over the dynamic selectivity in this system; indeed, experimental evidence supported this prediction. This work not only provides new insights into an unusual type of post-transition state bifurcation, but also demonstrates how the nonstatistical dynamic effects that control selectivity for such reactions can be manipulated rationally to increase the yields of synthetically useful reactions.

Phenoxazinone Synthase-Like Catalytic Activity of Bi- and Trinuclear Copper(II) Complexes with 2-Benzylethanolamine: Experimental and Theoretical Investigations

The self-assembly reaction of 2-benzylaminoethanol (Hbae) with CuCl2 or Cu(NO3)2 leads to the formation of binuclear [Cu2(bae)2(Cl)2] (1) and [Cu2(Hbae)2(bae)2](NO3)2 (2) complexes, while the trinuclear [Cu3(Hbae)2(bae)2(dmba)2](NO3)2 (3) compound was obtained using the auxiliar bulky substituted 2,2-dimethylbutyric acid (Hdmba). Crystallographic studies reveal the molecular structures of 1 and 2 based on the similar {Cu2(μ-O)2} core, while the structure of 3 features the {Cu3(μ-O)2} core with consecutive arranement of the metal centres, supported by the additional carboxylate bridges. The strong intermolecular hydrogen bonds join the molecular structures into 1D (for 1 and 3) or 2D (for 2) architectures. All three compounds act as catalysts for the aerobic oxidation of 2-aminophenol to the phenoxazinone chromophore (phenoxazinone synthase-like activity) with the maximum reaction rates up to 2.3×10-8 M s-1. The substrate scope involves methyl-, nitro- and chloro-substituted 2-aminophenols, disclosing the negligible activity of nitro-derivatives, while the 6-amino-m-cresol substrate shows the highest activity with the initial reaction rate of 5.8×10-8 M s-1. The mechanism of the rate-limiting reaction step (copper-catalysed formation of 2-aminophenoxyl radicals) was investigated at the DFT level. The combined DFT and CASSCF studies of the copper superoxo CuII-OO⋅ radical species as possible unconventional reaction intermediates resulted in a rational mechanism of H-atom abstraction, where the activation energies follow the experimental reactivity of substituted 2-aminophenols. The TDDFT and STEOM-DLPNO-CCSD theoretical calculations of the absorption spectra of substrates, phenoxazinone chromophores and putative polynuclear species containing 2-aminophenoxo ligand are reported.

Influence of counterion substitution on the properties of imidazolium-based ionic liquid clusters

Due to their unique physiochemical properties that may be tailored for specific purposes, ionic liquids (ILs) have been investigated for various applications, including chemical separations, catalysis, energy storage, and space propulsion. The different cations and anions comprising ILs may be selected to optimize a range of desired properties, such as thermal stability, ionic conductivity, and volatility, leading to the designation of certain ILs as designer "green" solvents. The effect of counterions on the properties of ILs is of both fundamental scientific interest and technological importance. Herein, we report a systematic experimental and theoretical investigation of the size, charge, stability toward dissociation, and geometric/electronic structure of 1-ethyl-3-methyl imidazolium (EMIM)-based IL clusters containing two different atomic counterions (i.e., bromide [Br-] and iodide [I-]). This work extends our studies of EMIM+ cations with atomic chloride (Cl-) and molecular tetrafluoroborate (BF4-) anions reported previously by Baxter et al. [Chem. Mater. 34, 2612 (2022)] and Zhang et al. [J. Phys. Chem. Lett. 11, 6844 (2020)], respectively. Distributions of anionic IL clusters were generated in the gas phase using electrospray ionization and characterized by high mass resolution mass spectrometry, energy-resolved collision-induced dissociation, and negative ion photoelectron spectroscopy experiments. The experimental results reveal anion-dependent trends in the size distribution, relative abundance, ionic charge state, stability toward dissociation, and electron binding energies of the IL clusters. Complementary global optimization theory provides molecular-level insights into the bonding and electronic structure of a selected subset of clusters, including their low energy structures and electrostatic potential maps, and how these fundamental characteristics are influenced by anion substitution. Collectively, our findings demonstrate how the fundamental properties of ILs, which determine their suitability for many applications, may be tuned by substituting counterions. These observations are critical in the sub-nanometer cluster size regime where phenomena do not scale predictably to the bulk phase, and each atom counts toward determining behavior.

Theoretical Study on the Kinetics of Secondary Oxygen Addition Reactions for N-Butyl Radicals

Chemical kinetics for second oxygen addition reactions (·QOOH + O2) of long-chain alkanes are of great importance in low-temperature combustion technologies. However, kinetic data for key reactions of ·QOOH + O2 systems are often difficult to obtain experimentally and are primarily estimated or calculated by using theoretical methods. In this work, barrier heights (BHs), reaction energies (ΔEs), and relative energies (REs) of stationary points for key reactions of two representative ·QOOH + O2 systems in the low-temperature oxidation of n-butyl as well as pressure-dependent rate constants for the involved reactions are calculated with the high-level quantum chemical method CCSD(T)-F12b/CBS. These results can be employed in the development of low-temperature combustion mechanisms for n-butane and longer straight-chain alkanes. In addition, the performance of some quantum chemistry methods with a lower computational cost on BHs, ΔEs, and REs as well as rate constants is also investigated. Our results indicate that the maximum error on these energies with PNO-LCCSD(T)-F12a is within 1 kcal/mol, and rate constants with this method are in the best agreement with reference values, with a maximum relative error of about half the reference values. Due to its low computational cost and memory requirements, this method is strongly recommended for studying low-temperature combustion reactions involving larger hydrocarbon fuels.

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.

Isolation of a Staudinger-type Intermediate Utilizing a Five-Membered Phosphorus-Centered Biradicaloid

The Staudinger reaction provides chemists with a valuable tool for the reduction of azides, which are notoriously unstable and can decompose explosively. By providing a controlled method for the conversion of azides to amines, the reaction opened up new avenues for the synthesis of various amine-containing compounds that are widely used in natural products, pharmaceuticals and polymers. The Staudinger reaction begins with the nucleophilic attack of a trivalent phosphine (usually triphenylphosphine), leading to the formation of a triazenide intermediate, a highly reactive species. Here we report how a divalent phosphorus-centered biradicaloid reacts with covalent azides and show that it is possible to capture and fully characterize the transient intermediate. The experimental data is supported by quantum chemical calculations of the reaction paths and in terms of thermodynamics and chemical bonding.

Binding Energy Calculations of Anthracene and Rhodamine 6G H-Type Dimers: A Comparative Study of DFT and SMD Methods

With the ever-growing need to study systems of increased size and complexity, modern density functional theory (DFT) methods often encounter problems arising from the growing computational demands. In this work, we have presented a comprehensive DFT validation of the steered molecular dynamics (SMD) approach in estimating the binding energies of aromatic dimers. By performing DFT calculations on optimized and unoptimized anthracene and rhodamine 6G (R6G) dimers using functionals with progressively enhanced exchange-correlation energy description and comparing the obtained results with SMD-predicted values, it was found that SMD predictions are in good agreement with the results obtained from hybrid DFT calculations. The average binding energies for optimized anthracene dimers were found to be 6.46 kcal/mol using DFT at ωB97X-D4/def2-QZVPP and 7.64 ± 1.61 kcal/mol as predicted by the SMD. For the R6G H-type dimer, the binding energies were 17.48 and 19.02 ± 2.22 kcal/mol, respectively. The study also revealed that due to the lack of explicit terms accounting for electron-electron interactions in MD force fields, the proposed method tends to overbind dimers. It is anticipated that the presented method can be applied to more complex dimers, potentially accelerating the calculations of binding energies. Moreover, this study further validates the accuracy of the CHARMM36 FF.

Simulating Ionized States in Realistic Chemical Environments with Algebraic Diagrammatic Construction Theory and Polarizable Embedding

Theoretical simulations of electron detachment processes are vital for understanding chemical redox reactions, semiconductor and electrochemical properties, and high-energy radiation damage. However, accurate calculations of ionized electronic states are very challenging due to their open-shell nature, importance of electron correlation effects, and strong interactions with chemical environment. In this work, we present an efficient approach based on algebraic diagrammatic construction theory with polarizable embedding that allows to accurately simulate ionized electronic states in condensed-phase or biochemical environments (PE-IP-ADC). We showcase the capabilities of PE-IP-ADC by computing the vertical ionization energy (VIE) of thymine molecule solvated in bulk water. Our results show that the second- and third-order PE-IP-ADC methods combined with the basis of set of triple-ζ quality yield a solvent-induced shift in VIE of -0.92 and -0.93 eV, respectively, in an excellent agreement with experimental estimate of -0.9 eV. This work demonstrates the power of PE-IP-ADC approach for simulating charged electronic states in realistic chemical environments and motivates its further development.

Application of modern artificial intelligence techniques in the development of organic molecular force fields

The molecular force field (FF) determines the accuracy of molecular dynamics (MD) and is one of the major bottlenecks that limits the application of MD in molecular design. Recently, artificial intelligence (AI) techniques, such as machine-learning potentials (MLPs), have been rapidly reshaping the landscape of MD. Meanwhile, organic molecular systems feature unique characteristics, and require more careful treatment in both model construction, optimization, and validation. While an accurate and generic organic molecular force field is still missing, significant progress has been made with the facilitation of AI, warranting a promising future. In this review, we provide an overview of the various types of AI techniques used in molecular FF development and discuss both the advantages and weaknesses of these methodologies. We show how AI methods provide unprecedented capabilities in many tasks such as potential fitting, atom typification, and automatic optimization. Meanwhile, it is also worth noting that more efforts are needed to improve the transferability of the model, develop a more comprehensive database, and establish more standardized validation procedures. With these discussions, we hope to inspire more efforts to solve the existing problems, eventually leading to the birth of next-generation generic organic FFs.

An Open-Shell FeIV Nitrido

We report the photogeneration and characterization of an open-shell, terminal iron nitrido (EmL)Fe(N) using a sterically encumbered dipyrrin ligand environment. The Fe-N distance in the solid-state, zero-field 57Fe Mössbauer spectrum, and computational analysis are consistent with a triplet electronic ground state of the iron nitrido. Notably, the attenuation of Fe-N multiple bond character through occupying π*Fe-N enables (i) primary C(sp3)-H amination, (ii) H2 cleavage, (iii) aromatic C-C cleavage, and (iv) photocatalytic N-atom transfer reactivity. These modes of reactivity have not previously been observed in low-spin Fe(N) analogues.

Accurate Enthalpies of Formation for Bioactive Compounds from High-Level Ab Initio Calculations with Detailed Conformational Treatment: A Case of Cannabinoids

Our recently developed approach based on the local coupled-cluster with single, double, and perturbative triple excitation [LCCSD(T)] model gives very efficient means to compute the ideal-gas enthalpies of formation. The expanded uncertainty (95% confidence) of the method is about 3 kJ·mol-1 for medium-sized compounds, comparable to typical experimental measurements. Larger compounds of interest often exhibit many conformations that can significantly differ in intramolecular interactions. Although the present capabilities allow processing even a few hundred distinct conformer structures for a given compound, many systems of interest exhibit numbers well in excess of 1000. In this study, we investigate how to reduce the number of expensive LCCSD(T) calculations for large conformer ensembles while controlling the error of the approximation. The best strategy found was to correct the results of the lower-level, surrogate model (density functional theory, DFT) in a systematic manner. It was also found that the error in the conformational contribution introduced by a surrogate model is mainly driven by a systematic (bias) rather than a random component of the DFT energy deviation from the LCCSD(T) target. This distinction is usually overlooked in DFT benchmarking studies. As a result of this work, the enthalpies of formation for 20 cannabinoid and cannabinoid-related compounds were obtained. Comprehensive uncertainty analysis suggests that the expanded uncertainties of the obtained values are below 4 kJ·mol-1.

Activation and C-C Coupling of Aryl Iodides via Bismuth Photocatalysis

Within the emerging field of bismuth redox catalysis, the catalytic formation of C-C bonds using aryl halides would be highly desirable; yet such a process remains a synthetic challenge. Herein, we present a chemoselective bismuth-photocatalyzed activation and subsequent coupling of (hetero)aryl iodides with pyrrole derivatives to access C(sp2)-C(sp2) linkages through C-H functionalization. This unique reactivity is the result of the bismuth complex featuring two redox state-dependent interactions with light, which 1) activates the Bi(I) complex for oxidative addition via MLCT, and 2) promotes the homolytic cleavage of aryl Bi(III) intermediates through a LLCT process.

Homologation of Alkenyl Carbonyls via a Cyclopropanation/Light-Mediated Selective C-C Cleavage Strategy

We report herein our studies on the direct photoactivation of carbonyl cyclopropanes to give biradical intermediates, leading to selective cleavage of the more substituted carbon-carbon bond. Depending on the substrate structure, extended alkenes were isolated or directly reacted in a photo-Nazarov process to give bicyclic products. Based on these results, a unified reductive ring-opening reaction was developed by using diphenyl disulfide as a hydrogen atom transfer (HAT) reagent. By performing a sequential cyclopropanation/selective ring opening reaction, we achieved a CH2 insertion into the α,β bond of both acyclic and cyclic unsaturated carbonyl compounds. Our protocol provides a further tool for the modification of the carbon framework of organic compounds, complementing the recent progress in "skeletal editing".

Spatial Signatures of Electron Correlation in Least-Squares Tensor Hypercontraction

Least-squares tensor hypercontraction (LS-THC) has received some attention in recent years as an approach to reduce the significant computational costs of wave function-based methods in quantum chemistry. However, previous work has demonstrated that LS-THC factorization performs disproportionately worse in the description of wave function components (e.g., cluster amplitudes T̂2) than Hamiltonian components (e.g., electron repulsion integrals (pq|rs)). This work develops novel theoretical methods to study the source of these errors in the context of the real-space T̂2 kernel, and reports, for the first time, the existence of a "correlation feature" in the errors of the LS-THC representation of the "exchange-like" correlation energy EX and T̂2 that is remarkably consistent across ten molecular species, three correlated wave functions, and four basis sets. This correlation feature portends the existence of a "pair point kernel" missing in the usual LS-THC representation of the wave function, which critically depends upon pairs of grid points situated close to atoms and with interpair distances between one and two Bohr radii. These findings point the way for future LS-THC developments to address these shortcomings.

Mechanism and optimization of ruthenium-catalyzed oxalamide synthesis using DFT

The oxalamide skeleton is a common structural motif in many biologically active molecules. These scaffolds can be synthesized via ruthenium pincer complex-catalyzed acceptorless dehydrogenative coupling of ethylene glycol and amines. In this study, we elucidate the mechanism of this oxalamide synthesis using density functional theory calculations. The rate-determining state is identified as the formation of molecular hydrogen following the oxidation of hydroxyacetamide to oxoacetamide. In predictive catalysis exercises, various modifications to the ruthenium pincer catalyst were investigated to assess their impact on the reactivity.

The divide expand consolidate scheme for unrestricted second order Møller-Plesset perturbation theory ground state energies

The linear scaling divide-expand-consolidate (DEC) framework is expanded to include unrestricted Hartree-Fock references. By partitioning the orbital space and employing local molecular orbitals, the full molecular calculation can be performed as independent calculations on individual fragments, making the method well-suited for massively parallel implementations. This approach also incorporates error control through the fragment optimization threshold (FOT), which maintains precision and consistency throughout the calculations. A benchmark was conducted for correlation energies of open-shell systems and the relative energies of both open- and closed-shell molecules at the MP2 level of theory. The full calculation result is achieved as the FOT approaches zero. For correlation energies, an FOT of 10-3 is sufficient to recover over 98% of the full result in all cases. However, for relative energies and the electronic energy component of oxidation potentials, a tighter FOT of 10-4 is required to keep the DEC error within 10% for both open- and closed-shell molecules. This is likely due to a lack of systematic error cancellation for the molecules with vastly different chemical natures. Therefore, for accurate relative energies, the FOT should be an order of magnitude lower, and additional caution is needed, particularly for large systems. The DEC method extension to unrestricted references maintains favorable features of linear scaling and can be implemented in a massively parallel algorithm to calculate correlation energies for large open-shell systems.

Cluster perturbation theory. XI. Excitation-energy series using a variational excitation-energy function

Traditionally, excitation energies in coupled-cluster (CC) theory have been calculated by solving the CC Jacobian eigenvalue equation. However, based on our recent work [Jørgensen et al., Sci. Adv. 10, eadn3454 (2024)], we propose a reformulation of the calculation of excitation energies where excitation energies are determined as a conventional molecular property. To this end, we introduce an excitation-energy function that depends on the CC Jacobian and the right and left eigenvectors for the Jacobian eigenvalue problem. This excitation-energy function is variational with respect to the right and left eigenvectors but not with respect to the cluster amplitudes. Instead, the cluster amplitudes satisfy the cluster-amplitude equations, and we set up an excitation-energy Lagrangian by adding to the excitation-energy function the cluster-amplitude equations with an undetermined multiplier for each cluster-amplitude constraint. The excitation-energy Lagrangian is variational in all its parameters. Based on the variational property of the Lagrangian, we have determined two quadratically convergent excitation-energy series: the total-order cluster-perturbation (tCP) and variational cluster-perturbation (vCP) excitation-energy series. Calculations of the excitation energies of three small molecules have shown that the vCP series is to be preferred over the tCP series. The test calculations have been carried out for CPS(D) expansions [targeting the CC singles-and-doubles (CCSD) wave function from the CC singles wave function] and the CPSD(T) expansion [targeting the CC singles-doubles-triples (CCSDT) wave function from the CCSD wave function]. For the S(D) and SD(T) orbital excitation space calculations, we obtain in the second vCP iteration excitation energies with a mean deviation from CCSD excitation energies of about 0.04 eV for the S(D) orbital spaces, and for the SD(T) orbital space calculation, we obtain a mean deviation from the CCSDT excitation energies of 0.001 eV.

Modeling Local Aerosol Surface Environments: Clustering of Pyruvic Acid Analogs, Water, and Na+, Cl- Ions

Pyruvic acid is an omnipresent compound in nature and is found both in the gas phase and in the particle phase of the atmosphere as well as in aqueous solution in the hydrosphere. Despite much literature on the photochemical degradation and stability of pyruvic acid in different chemical environments, the study of simultaneous interactions between gas-phase pyruvic acid or similar carboxylic acids with water and ions is not well-understood. Here, we present a study of microhydrated molecular clusters containing pyruvic acid and the structurally analogous carboxylic acids lactic acid, propionic acid, and 2,2-dihydroxypropanoic acid by probing geometries, binding free energies, hydrate distributions, as well as their infrared (IR) absorption spectra. We performed a meticulous configurational sampling protocol for the various hydrated clusters ranging from low level of theory to high level of theory to identify the lowest free energy structure. We find that cluster geometries and especially their water structure are highly sensitive to the presence and character of ions. We show that the hydration of the studied organic acids is thermodynamically unfavorable in the gas phase and ions are necessary for mediating interactions between organic acids and water thus stabilizing the clusters. Finally, we find a clear correlation between decreasing pyruvic acid carboxylic O-H stretching frequencies, increasing intensity when adding more water to the clusters, and a correlation between increasing redshifting of the O-H frequencies upon addition of ions to the clusters. The observations done in this study could pave the way to unravel the mechanisms behind the transitioning of organic acids from the gas phase to the particle phase.

Dyotropic Rearrangement of β-Lactams: Reaction Development, Mechanistic Study, and Application to the Total Syntheses of Tricyclic Marine Alkaloids

An unprecedented dyotropic rearrangement of β-lactams has been developed, which provides an enabling tool for the synthesis of structurally diverse γ-butyrolactams. Unlike the well-established dyotropic rearrangements of β-lactones, the present reaction probably proceeds through a dual-activation mode, and thus displays unusual reactivity and chemoselectivity. The combined computational and experimental results suggest that the dyotropic rearrangement of β-lactams may proceed through different mechanisms depending on the nature of migrating groups (H, alkyl, or aryl). Hinging on a chemoselective H-migration dyotropic rearrangement of β-lactams, we have completed the divergent synthesis of tricyclic marine alkaloids (-)-lepadiformine A, (+)-cylindricine C, and (-)-fasicularin within 11-12 longest linear steps.

Triazolide Complexes of Sodium and Potassium in the Gas Phase

Aromatic organometallic complexes, such as ferrocene and the "inverse sandwich complex" [Na2Cp]+, are stabilized via charge-transfer (C-T) interactions and cation-π interactions (i.e., charge-induced dipole and charge-quadrupole interactions). Much effort has gone into investigating systems that contain organic moieties, such as benzene or cyclopentadienyl ligands, but less attention has been paid to aromatic systems that contain heteroatoms (e.g., N), possibly owing to the complexity arising from a lowering of symmetry and the introduction of electron lone pair density and dipole moments. Here we investigate sodiated and potassiated clusters of 1,2,3-triazolide, [Mx (123T)x-1]+ (x = 3, 4; M = Na, K), and 1,2,4-triazolide, [Mx (124T)x-1]+ (x = 3, 4; M = Na, K), using a combination of infrared ion spectroscopy (IRIS) and DFT calculations. Cluster structures are strongly influenced by charge-dipole interactions and C-T interactions from N lone pairs to the metal cations. IRIS spectra indicated that the geometries of the triazolide moieties are essentially unperturbed by the interaction with the metal ions. Additional spectral features, not predicted by DFT calculations, that are observed in the 1500-1800 cm-1 region seem to be associated with combination bands involving C-H wagging and ring torsion motions.

From boom to bloom: synthesis of diazidodifluoromethane, its stability and applicability in the 'click' reaction

Diazidodifluoromethane was prepared from dibromodifluoromethane, sodium azide and an alkanethiolate initiator. It represents the first example of a diazidomethane that is stable enough to be used in synthesis. The stability of (poly)azidomethanes was explored with ab initio calculations. Copper(I)-catalysed azide-alkyne cycloaddition of the title azide with alkynes afforded difluoromethylene-containing bis(1,2,3-triazoles)amenable to Rh(II)-catalysed transannulation with nitriles to difluoromethylene bis(imidazoles).

Impact of Intracellular Proteins on μ-Opioid Receptor Structure and Ligand Binding

Chronic pain is a prevalent problem affecting approximately one out of every five adults in the U.S. The most effective way to treat chronic pain is with opioids, but they cause dangerous side effects such as tolerance, addiction, and respiratory depression, which makes them quite deadly. Opioids, such as fentanyl, target the μ-opioid receptor (MOR), which can then bind to the intracellular Gi protein or the β-arrestin protein. The Gi pathway is primarily responsible for pain relief and potential side effects, but the β-arrestin pathway is chiefly responsible for the unwanted side effects. Ideally, an effective pain medication without side effects would bind to MOR, which would bias signaling solely through the Gi pathway. We used the Bio3D library to conduct principal component analysis to compare the cryo-electron microscopy MOR structure in complex with the Gi versus an X-ray crystallography MOR structure with a nanobody acting as a Gi mimic. Our results agree with a previous study by Munro, which concluded that nanobody-bound MOR is structurally different than Gi-bound MOR. Furthermore, we investigated the structural diversity of opioids that can bind to MOR. Quantum mechanical calculations show that the low energy solution structures of fentanyl differ from the one bound to MOR in the experimental structure, and pKa calculations reveal that fentanyl is protonated in aqueous solution. Glide docking studies show that higher energy structures of fentanyl in solution form favorable docking complexes with MOR. Our calculations show the relative abundance of each fentanyl conformation in solution as well as the energetic barriers that need to be overcome to bind to MOR. Docking studies confirm that multiple fentanyl conformations can bind to the receptor. Perhaps a variety of conformations of fentanyl can stabilize multiple conformations of the MOR, which can explain why fentanyl can induce different intracellular signaling and multiple physiological effects.

Chemical Bond Overlap Descriptors From Multiconfiguration Wavefunctions

The chemical bond is a fundamental concept in chemistry, and various models and descriptors have evolved since the advent of quantum mechanics. This study extends the overlap density and its topological descriptors (OP/TOP) to multiconfigurational wavefunctions. We discuss a comparative analysis of OP/TOP descriptors using CASSCF and DCD-CAS(2) wavefunctions for a diverse range of molecular systems, including X-O bonds in X-OH (XH, Li, Na, H2B, H3C, H2N, HO, F) and Li-X' (XF, Cl, and Br). Results show that OP/TOP aligns with bonding models like the quantum theory of atoms in molecules (QTAIM) and local vibrational modes theory, revealing insights such as overlap densities shifting towards the more electronegative atom in polar bonds. The Li-F dissociation profile using OP/TOP descriptors demonstrated sensitivity to ionic/neutral inversion during Li-F dissociation, highlighting their potential for elucidating complex bond phenomena and offering new avenues for understanding multiconfigurational chemical bond dynamics.

Improving the Efficiency of Electrostatic Embedding Using the Fast Multipole Method

This paper reports the improvement in the efficiency of embedded-cluster model (ECM) calculations in ORCA thanks to the implementation of the fast multipole method. Our implementation is based on state-of-the-art algorithms and revisits certain aspects, such as efficiently and accurately handling the extent of atomic orbital shell pairs. This enables us to decompose near-field and far-field terms in what we believe is a simple and effective manner. The main result of this work is an acceleration of the evaluation of electrostatic potential integrals by at least one order of magnitude, and up to two orders of magnitude, while maintaining excellent accuracy (always better than the chemical accuracy of 1 kcal/mol). Moreover, the implementation is versatile enough to be used with molecular systems through QM/MM approaches. The code has been fully parallelized and is available in ORCA 6.0.

Key Kinetic Interactions between NOX and Unsaturated Hydrocarbons: H Atom Abstraction from C3-C7 Alkynes, Dienes, and Trienes by NO2

An adequate understanding of the NOx interacting chemistry is a prerequisite for a smoother transition to carbon-lean and carbon-free fuels such as ammonia and hydrogen. In this regard, this study presents a comprehensive study on the H atom abstraction by NO2 from C3 to C7 alkynes, dienes, and trienes forming 3 HNO2 isomers (i.e., TRANS_HONO, HNO2, and CIS_HONO), encompassing 8 hydrocarbons and 24 reactions. Through a combination of high-level quantum chemistry computation, electronic structures, single-point energies, C-H bond dissociation energies, and 1-D hindered rotor potentials of the reactants, transition state (TS), complexes, and products involved in each reaction are determined at DLPNO-CCSD(T)/cc-pVDZ//M06-2X/6-311++g(d,p), from which potential energy surfaces and energy barriers for each reaction are determined. Following this, the rate coefficients for all studied reactions, over a temperature range from 298 to 2000 K, are computed based on TS theory using the Master Equation System Solver program by considering unsymmetric tunneling corrections. Comprehensive analysis of branching ratios elucidates the diversity and similarities between different species, different HNO2 isomers, and different abstraction sites. Incorporating the calculated rate parameters into a recent chemistry model reveals the significant influences of this type of reaction on model performance, where the updated model is consistently more reactive for all the alkynes, dienes, and trienes studied in predicting autoignition characteristics. Sensitivity and flux analyses are further conducted, through which the importance of H atom abstractions by NO2 is highlighted. With the updated rate parameters, the branching ratios in fuel consumption clearly shift toward H atom abstractions by NO2 while away from H atom abstractions by ȮH. The obtained results emphasize the need for adequately representing these kinetics in new alkyne, diene, and triene chemistry models to be developed by using the rate parameters determined in this study, and call for future efforts to experimentally investigate NO2 blending effects on alkynes, dienes, and trienes.

Ligand Many-Body Expansion as a General Approach for Accelerating Transition Metal Complex Discovery

Methods that accelerate the evaluation of molecular properties are essential for chemical discovery. While some degree of ligand additivity has been established for transition metal complexes, it is underutilized in asymmetric complexes, such as the square pyramidal coordination geometries highly relevant to catalysis. To develop predictive methods beyond simple additivity, we apply a many-body expansion to octahedral and square pyramidal complexes and introduce a correction based on adjacent ligands (i.e., the cis interaction model). We first test the cis interaction model on adiabatic spin-splitting energies of octahedral Fe(II) complexes, predicting DFT-calculated values of unseen binary complexes to within an average error of 1.4 kcal/mol. Uncertainty analysis reveals the optimal basis, comprising the homoleptic and mer symmetric complexes. We next show that the cis model (i.e., the cis interaction model solved for the optimal basis) infers both DFT- and CCSD(T)-calculated model catalytic reaction energies to within 1 kcal/mol on average. The cis model predicts low-symmetry complexes with reaction energies outside the range of binary complex reaction energies. We observe that trans interactions are unnecessary for most monodentate systems but can be important for some combinations of ligands, such as complexes containing a mixture of bidentate and monodentate ligands. Finally, we demonstrate that the cis model may be combined with Δ-learning to predict CCSD(T) reaction energies from exhaustively calculated DFT reaction energies and the same fraction of CCSD(T) reaction energies needed for the cis model, achieving around 30% of the error from using the CCSD(T) reaction energies in the cis model alone.

Monomer size effect in inelastic collisional dynamics of non-equilibrium soot nucleation

Molecular dynamics (MD) simulations of the collisional dynamics of the coronene-acepyrene and coronene radical-acepyrene pairs have been carried out to investigate the size effect of monomers of polycyclic aromatic hydrocarbons (PAH) on their non-equilibrium dimerization. The results compared to the previous MD simulations of the smaller pyrene-acepyrene and pyrenyl-acepyrene systems corroborate the non-equilibrium hypothesis of crosslinking PAH dimerization enhanced by physical interaction between the monomers. The phenomenon of inelastic collisional dynamics responsible for non-equilibrium van der Waals dimerization, which fosters a covalent bond formation between the monomers, amplifies with increasing PAH size. The increase in the size of the colliding monomers enhances the non-equilibrium effects as the growing pool of low-frequency modes provides a larger sink for the energy of the colliding PAH monomers. Based on the direct count of the crosslinking reaction events observed in the MD simulations, the forward rate constant for the coronene radical-acepyrene association is estimated at ∼10-11 cm3 molecule-1 s-1, showing a 15-fold increase with respect to the value from the statistical Rice-Ramsperger-Kassel-Marcus calculations. A comparison with the eightfold increase reported previously for the pyrenyl-acepyrene system shows that the statistical (equilibrium-based) calculations increasingly underestimate the reaction rate with the increasing size of the interacting PAHs from pyrene to coronene. The total increase of the MD-assessed rate constant for the coronene radical-acepyrene dimerization reaction as compared to pyrenyl-acepyrene is a factor of 2.4, with the overall collision efficiency to produce dimerized products growing by 30%.

Au-Catalyzed 5C Reaction of Type II Diene-Ynenes toward Dihydrosemibullvalenes: Reaction Development and Mechanistic Study

We report an unexpected gold-catalyzed 5C reaction of type II diene-ynenes to synthesize dihydrosemibullvalenes, which are potential bioisosteres for drug discovery. This 5C reaction occurs through a sequence of elementary reactions of cyclopropanation/Cope rearrangement/carbon shift/cyclopropanation/C-H insertion (shortened here as the 5C reaction), supported by quantum chemistry calculations. Mechanistic studies have also been applied to answer why type-II diene-ynenes cannot access seven-membered carbocycles-embedded bridged molecules under the gold catalysis, finding that the chair-like Cope rearrangement transition state (not the traditional boat-like transition state) is the key to the change of regiochemistry.

Local Wave Function Embedding: Correlation Regions in PNO-LCCSD(T)-F12 Calculations

Many chemical reactions affect only a rather small number of bonds, leaving the largest part of the chemical and geometrical structure of the molecules nearly unchanged. In this work we extended the previously proposed region method [J. Chem. Phys. 128, 144106 (2008)] to PNO-LCCSD(T)-F12. Using this method, we investigate whether accurate reaction energies for larger systems can be obtained by correlating only the electrons in a region of localized molecular orbitals close to the reaction center at high-level (PNO-LCCSD(T)-F12). The remainder is either treated at lower level (PNO-LMP2-F12) or left uncorrelated (Hartree-Fock frozen core). It is demonstrated that indeed the computed reaction energies converge rather quickly with the size of the correlation regions toward the results of the full calculations. Typically, 2-3 bonds from the reacting atoms need to be included to reproduce the results of the full calculations to within ±0.2 kcal/mol. We also computed spin-state energy differences in a large transition metal complex, where a factor of 15 in computation time could be saved, still yielding a result that is within ±0.1 kcal/mol of the one obtained in a full PNO-LCCSD(T)-F12 calculation.

Enantioselective interactions of aminonitrile dimers

Enantioenrichment of amino acids is essential during the early chemical evolution leading to the origin of life. However, the detailed molecular mechanisms remain unsolved. Dimerization of enantiomers is the first molecular process in the nucleation of deposition and crystallization, which are both essential for enantioenrichment. Here, we report the enantioselective interactions of dimers of chiral intermediates, i.e., aminonitriles, in both gas and water environments based on density functional theory (DFT) and more accurate coupled-cluster (CC) calculations. We show that all the aminonitriles stabilize the homochiral dimer preferentially to the heterochiral dimer in the gas phase, while this trend was not observed in water. The energies of the enantioselective interactions in aminonitriles are substantially lower compared to those in amino acids, especially isovaline. These results suggest that prebiotic enhancements of enantiomeric excess are more likely to occur in amino acids than in the aminonitrile intermediates.

Phenyl Radical Activates Molecular Hydrogen Through Protium and Deuterium Tunneling

Activating dihydrogen, H2, is a challenging endeavor typically achieved using transition metal centers. Pure main-group compounds capable of this are rare and have emerged in recent decades. These systems rely on synergistic donor-acceptor interactions with H2's antibonding σ* and bonding σ orbital. An alternative (hydrocarbon) radical-mediated activation is problematic because the H-H bond is stronger (104.2 kcal mol-1) than most C-H bonds. Here, we explore using the phenyl radical to tackle this, forming benzene with a C-H bond energy (112.9 kcal mol-1) that provides a thermodynamic driving force. We mainly observe a benzene-HI complex upon photolysis of iodobenzene in an H2-doped neon matrix at 4.4 K despite a barrier of 7.6 kcal mol-1, while phenyl radical forms in case of the heavier D2 isotopologue. When D2 molecules are allowed to diffuse, mono-deuterated benzene accumulates within hours. Computations using path integral-based instanton theory highlight that primarily the transferred hydrogen atom is moving during the reaction which greatly increases the tunneling probability. In excellent agreement with the experimental results, we predict significant tunneling rate constants for both isotopologues, H2 and D2, featuring a strong kinetic isotope effect of up to four orders of magnitude at the lowest temperatures.

Study of Sterically Crowded Alkanes: Assessment of Non-Empirical Density Functionals Including Double-Hybrid (Cost-Effective) Methods

We theoretically study here the homolytic dissociation reactions of sterically crowded alkanes of increasing size, carrying three different (bulky) substituents such as tert-butyl, adamantyl, and [1.1.1]propellanyl, employing a family of parameter-free functionals ranging from semi-local, to hybrid and double-hybrid models. The study is complemented with the interaction between a pair of HC(CH3)3 molecules at repulsive and attractive regions, as an example of a system composed by a pair of weakly bound sterically crowded alkanes. We also assessed the effect of incorporating reliable dispersion corrections (i. e., D4 or NL) for all the functionals assessed, as well as the use of a tailored basis set (DH-SVPD) for non-covalent interactions, which provides the best trade-off between accuracy and computational cost for a seemingly extended applications to branched or crowded systems. Overall, the PBE-QIDH/DH-SVPD and r2SCAN-QIDH/DH-SVPD methods represent an excellent compromise providing relatively low, and thus very competitive, errors at a fraction of the cost of other quantum-chemical methods in use.

Elementary reactions for glycine production in hot and dense interstellar media from CH 3 COOH , HCOOH, and NH 2 CH

CONTEXT

In this work, we investigate three elementary reactions involved in the production of glycine in the interstellar medium (ISM) employing trustworthy electronic structure and chemical kinetics methodologies. We considered three elementary reactions: HCOOH + NH 2 CH → NH 2 CH 2 COOH (R 1 ),CH 3 COOH + NH → CH 2 COOH + NH 2 (R 2 ) andCH 2 COOH + NH 2 → NH 2 CH 2 COOH ( R 3 ) under conditions consistent with hot molecular cores of massive star-forming regions. Our results indicate that the elementary reactions are feasible in these environments, with reaction barriers of 18.8 ( R 1 ) and 18.4 kcal · mol - 1 ( R 2 ). The rate coefficients for these reactions were calculated to be 1.4 × 10 - 17 and 9.3 × 10 - 16 cm 3 · molecule - 1 · s - 1 at 1000 K. Additionally, if the products of ( R 2 ) couple on a singlet surface, R 3 connects to the ground state of glycine via a barrierless path presenting a rate coefficient equal to 8.7 × 10 - 9 cm 3 · molecule - 1 · s - 1 at 298.15 K. Given that the molecules involved in these reactions have been detected in regions such as Sgr B2, our findings suggest that these elementary reactions should be included in mechanisms to study the production of glycine in such locations.

METHODS

The single-reference electronic structure calculations were carried out with the ORCA 4.1.2 package while the multi-reference calculations were performed with the COLUMBUS 7.0 package. The DFT functionals employed were M06-2X, ω B97X, and ω B97X-D3, with the 6-31+G* and def2-TZVP, and for the wave function-based calculations, the CCSD(T), DLPNO-CCSD(T), MRCI, and CASSF methods were employed using the aug-cc-pVDZ, aug-cc-pVTZ, and aug-cc-pVQZ basis sets. The chemical kinetic calculations for the elementary reactions with well-defined saddle points were performed using the Pilgrim package employing the TST, CVT, and CVT/SCT approaches.

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

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