Understanding the reactivity of polycyclic aromatic hydrocarbons and related compounds

Buckybowl Molecular Tweezers for Recognition of Fullerenes

Buckybowl tweezers are a relatively young research area closely associated with the development of non-planar polycyclic aromatic systems and supramolecular chemistry. Since the appearance of the first prototypes in the early 2000s, the tweezers have undergone evolutionary changes. Nowadays they are able to effectively interact with fullerenes and the results opened up prospects for development in the field of sensing, nonlinear optics, and molecular switchers. In the present study, examples of corannulene-based and other buckybowl tweezers for the recognition of C60 and C70 fullerenes were summarized and analyzed. The main structural components of the tweezers were also reviewed in detail and their role in the formation of complexes with fullerenes was evaluated. The revealed structural patterns should trigger the development of novel recognition systems and materials with a wide range of applications.

Carbene-Decorated Geometrically Constrained Borylenes for Bond Activations

While metal-ligand cooperativity is well-known, studies on element-ligand cooperativity involving main group species are comparatively much less explored. In this study, we computationally designed a few geometrically constrained borylenes supported by different carbenes. Our density functional theory studies indicate that they possess enhanced nucleophilicity as well as electrophilicity, thus rendering them promising candidates for exhibiting borylene-ligand cooperativity. The cooperation between the boron and adjacent carbene centers facilitates different bond activation processes, including the cycloaddition of acetylene across the boron-carbene bond as well as B-H/Si-H bond activation reactions, which have been analyzed in detail. To the best of our knowledge, the borylenes proposed in this study represent the first examples of theoretically proposed geometrically constrained bis(carbene)-stabilized borylenes capable of cooperative activation of enthalpically strong bonds.

COMPAS-3: a dataset of peri-condensed polybenzenoid hydrocarbons

We introduce the third installment of the COMPAS Project - a COMputational database of Polycyclic Aromatic Systems, focused on peri-condensed polybenzenoid hydrocarbons. In this installment, we develop two datasets containing the optimized ground-state structures and a selection of molecular properties of ∼39k and ∼9k peri-condensed polybenzenoid hydrocarbons (at the GFN2-xTB and CAM-B3LYP-D3BJ/cc-pvdz//CAM-B3LYP-D3BJ/def2-SVP levels, respectively). The manuscript details the enumeration and data generation processes and describes the information available within the datasets. An in-depth comparison between the two types of computation is performed, and it is found that the geometrical disagreement is maximal for slightly-distorted molecules. In addition, a data-driven analysis of the structure-property trends of peri-condensed PBHs is performed, highlighting the effect of the size of peri-condensed islands and linearly annulated rings on the HOMO-LUMO gap. The insights described herein are important for rational design of novel functional aromatic molecules for use in, e.g., organic electronics. The generated datasets provide a basis for additional data-driven machine- and deep-learning studies in chemistry.

A Deeper Insight into the Supramolecular Activation of Oxidative Addition Reactions Involving Pincer-Rhodium(I) Complexes

The factors governing the acceleration of the oxidative addition of methyl iodide to pincer rhodium(I)-complexes induced by coronene have been computationally explored in detail using quantum chemical methods. Both the parent reaction and the coronene-mediated process proceed via a stepwise SN2-type mechanism. It is found that the acceleration of the process derives from the formation of an initial supramolecular complex, mainly stabilized by electrostatic and π-π interactions, which significantly increases the electron richness of the complex. The impact of this effect on the reaction barrier has been quantitatively analyzed by applying the activation strain model in combination with the energy decomposition analysis method. In addition, the influence of other polycyclic aromatic hydrocarbons on the oxidative reaction has been also considered.

Design and Advanced Manufacturing of NU-1000 Metal-Organic Frameworks with Future Perspectives for Environmental and Renewable Energy Applications

Metal-organic frameworks (MOFs) represent a relatively new family of materials that attract lots of attention thanks to their unique features such as hierarchical porosity, active metal centers, versatility of linkers/metal nodes, and large surface area. Among the extended list of MOFs, Zr-based-MOFs demonstrate comparably superior chemical and thermal stabilities, making them ideal candidates for energy and environmental applications. As a Zr-MOF, NU-1000 is first synthesized at Northwestern University. A comprehensive review of various approaches to the synthesis of NU-1000 MOFs for obtaining unique surface properties (e.g., diverse surface morphologies, large surface area, and particular pore size distribution) and their applications in the catalysis (electro-, and photo-catalysis), CO2 reduction, batteries, hydrogen storage, gas storage/separation, and other environmental fields are presented. The review further outlines the current challenges in the development of NU-1000 MOFs and their derivatives in practical applications, revealing areas for future investigation.

Cyanocyclopentadiene-Annulated Polycyclic Aromatic Radical Anions: Predicted Negative Ion Photoelectron Spectra and Singlet-Triplet Energies of Cyanoindene and Cyanofluorene Radical Anions

Isomer-specific negative ion photoelectron spectra (NIPES) of cyanoindene (C9H7CN) and cyanofluorene (C14H9N), acquired through the computation of Franck-Condon (FC) factors that utilize harmonic vibrational frequencies and normal mode vectors derived from density functional theory (DFT) at the B3LYP/aug-cc-pVQZ and 6-311++G(2d,2p) basis sets, are reported. The adiabatic electron affinity (EA) values of the ground singlet (S0) and the lowest lying triplet (T1) states are used to predict site-specific S0-T1 energies (ΔEST). The vibrational spectra of the S0 and T1 states are typified by ring distortion and ring C-C stretching vibrational progressions. Among all the S0 isomers in C9H7CN, the 2-cyanoindene (2-C9H7CN) is found to be the most stable at an EA of 0.716 eV, with the least stable isomer being the 1-C9H7CN at an EA of 0.208 eV. In C14H9N, the most stable S0 isomer, 2-cyanofluorene (2-C14H9N), has an EA of 0.781 eV. The least stable S0 isomer in C14H9N is the 9-C14H9N, with an EA of 0.364 eV. The FC calculations are designed to mimic simulations that would be performed to aid in the analysis of experimental spectra obtained in NIPE spectroscopic techniques. The vibrational spectra, adiabatic EAs, and ΔEST values reported in this study are intended to act as a guide for future gas-phase ion spectroscopic experiments and astronomical searches, especially with regard to the hitherto largely unexplored C14H9N isomers.

Beyond Planar Structure: Curved π-Conjugated Molecules for High-Performing and Stable Perovskite Solar Cells

Perovskite solar cell (PSC) shows a great potential to become the next-generation photovoltaic technology, which has stimulated researchers to engineer materials and to innovate device architectures for promoting device performance and stability. As the power conversion efficiency (PCE) keeps advancing, the importance of exploring multifunctional materials for the PSCs has been increasingly recognized. Considerable attention has been directed to the design and synthesis of novel organic π-conjugated molecules, particularly the emerging curved ones, which can perform various unmatched functions for PSCs. In this review, the characteristics of three representative such curved π-conjugated molecules (fullerene, corannulene and helicene) and the recent progress concerning the application of these molecules in state-of-the-art PSCs are summarized and discussed holistically. With this discussion, we hope to provide a fresh perspective on the structure-property relation of these unique materials toward high-performance and high-stability PSCs.

Metal Influence on Cyaphide-Azide 1,3-Dipolar Cycloaddition Reactions: Aromaticity and Activation Strain

The factors governing 1,3-dipolar cycloaddition reactions involving C≡P-containing compounds are computationally explored in detail using quantum chemical tools. To this end, the parent process involving tBuN3 and tBuCP is analyzed and compared to the analogous reaction involving organometallic cyaphide complexes (metal=Au, Pt, Ge, Mg), in order to understand the role of the metal fragment in such transformations. It is found that while the metal fragment does not significantly influence the aromaticity of the corresponding concerted transition states or the regioselectivity of the transformation, it may modify the reactivity of the cyaphide complexes (i. e. Ge and Mg cyaphide complexes are comparatively more reactive). The computed reactivity trends and the factors behind the regioselectivity of the cycloaddition reaction are quantitatively analyzed with the help of the activation strain model in combination with the energy decomposition analysis method.

Mono(Lewis Base)-Stabilized Gallium Iodide: An Unexplored Class of Promising Ligands

Quantum-chemical (DFT) calculations on hitherto unknown base(carbene)-stabilized gallium monoiodides (LB→GaI) suggest that these systems feature one lone pair of electrons and a formally vacant p-orbital - both centered at the central gallium atom - and exhibit metallomimetic behavior. The calculated reaction free energies as well as bond dissociation energies suggest that these LB→GaI systems are capable of forming stable donor-acceptor complexes with group 13 trichlorides. Examination of the ligand exchange reactions with iron and nickel complexes indicates their potential use as ligands in transition metal chemistry. In addition, it is found that the title compounds are also able to activate various enthalpically robust bonds. Further, a detailed mechanistic investigation of these small molecule activation processes reveals the non-innocent behavior of the carbene (base) moiety attached to the GaI fragment, thereby indicating the cooperative nature of these bond activation processes. The energy decomposition analysis (EDA) and activation strain model (ASM) of reactivity were also employed to quantitatively understand and rationalize the different activation processes.

Mechanistic Insights into the DABCO-Catalyzed Cloke-Wilson Rearrangement: A DFT Perspective

The mechanism and selectivity patterns of the DABCO-catalyzed Cloke-Wilson rearrangement were computationally studied in detail using density functional theory calculations. Our computations suggest that the process occurs stepwise involving the initial ring opening of the cyclopropane promoted by a DABCO molecule followed by a ring-closure reaction of the readily formed zwitterionic intermediate. The regioselectivity of the initial nucleophilic ring-opening step strongly depends on the nature of the substituent attached to the cyclopropane moiety. The physical factors governing the preference for the more sterically hindered C2 (tertiary) position have been quantitatively analyzed by applying the combined activation strain model-energy decomposition analysis method. In addition, our calculations revealed a new mechanism for the analogous transformation involving vinylcyclopropanes consisting of an initial SN2' ring-opening process followed by a 5-exo-trig cyclization step, which proceeds without facial selectivity.

Unraveling the Bürgi-Dunitz Angle with Precision: The Power of a Two-Dimensional Energy Decomposition Analysis

Understanding the geometrical preferences in chemical reactions is crucial for advancing the field of organic chemistry and improving synthetic strategies. One such preference, the Bürgi-Dunitz angle, is central to nucleophilic addition reactions involving carbonyl groups. This study successfully employs a novel two-dimensional Distortion-Interaction/Activation-Strain Model in combination with a two-dimensional Energy Decomposition Analysis to investigate the origins of the Bürgi-Dunitz angle in the addition reaction of CN- to (CH3)2C═O. We constructed a 2D potential energy surface defined by the distance between the nucleophile and carbonylic carbon atom and by the attack angle, followed by an in-depth exploration of energy components, including strain and interaction energy. Our analysis reveals that the Bürgi-Dunitz angle emerges from a delicate balance between two key factors: strain energy and interaction energy. High strain energy, as a result of the carbonyl compound distorting to avoid Pauli repulsion, is encountered at high angles, thus setting the upper bound. On the other hand, interaction energy is shaped by a dominant Pauli repulsion when the angles are lower. This work emphasizes the value of the 2D Energy Decomposition Analysis as a refined tool, offering both quantitative and qualitative insights into chemical reactivity and selectivity.

Understanding the reactivity and selectivity of Diels-Alder reactions involving furans

The reactivity and endo/exo selectivity of the Diels-Alder cycloaddition reactions involving furan and substituted furans as dienes have been computationally explored. In comparison to cyclopentadiene, it is found that furan is comparatively less reactive and also less endo-selective in the reaction with maleic anhydride as the dienophile. Despite that, both the reactivity and the selectivity can be successfully modified by the presence of substituents at either 2- or 3-positions of the heterocycle. In this sense, it is found that the presence of strong electron-donor groups significantly increases the reactivity of the system while the opposite is found in the presence of electron-withdrawing groups. The observed trends in both the reactivity and selectivity are analyzed quantitatively in detail by means of the activation strain model of reactivity in combination with the energy decomposition analysis methods.

A two-step access to fused-/spiro-polycyclic frameworks via double Heck cascade and acid-driven processes

This report illustrates the rapid construction of two divergent classes of polycyclic frameworks, benzo[a]fluorenones and spiro-chromenone indenes, via a double Heck cascade and an acid-driven cyclization from easily accessible precursors, alkyl 2-bromocinnamate esters and diphenylacetylenes. The present strategy has surveyed a broad substrate scope and delivered an array of products with interesting structural features. Besides, fluorescence studies were performed for the synthesized benzo[a]fluorenones.

Lewis Acid-Catalyzed Carbonyl-Ene Reaction: Interplay between Aromaticity, Synchronicity, and Pauli Repulsion

The physical factors governing the catalysis in Lewis acid-promoted carbonyl-ene reactions have been explored in detail quantum chemically. It is found that the binding of a Lewis acid to the carbonyl group directly involved in the transformation greatly accelerates the reaction by decreasing the corresponding activation barrier up to 25 kcal/mol. The Lewis acid makes the process much more asynchronous and the corresponding transition state less in-plane aromatic. The remarkable acceleration induced by the catalyst is ascribed, by means of the activation strain model and the energy decomposition analysis methods, mainly to a significant reduction of the Pauli repulsion between the key occupied π-molecular orbitals of the reactants and not to the widely accepted stabilization of the LUMO of the enophile.

Interpretable Deep-Learning Unveils Structure-Property Relationships in Polybenzenoid Hydrocarbons

In this work, interpretable deep learning was used to identify structure-property relationships governing the HOMO-LUMO gap and the relative stability of polybenzenoid hydrocarbons (PBHs) using a ring-based graph representation. This representation was combined with a subunit-based perception of PBHs, allowing chemical insights to be presented in terms of intuitive and simple structural motifs. The resulting insights agree with conventional organic chemistry knowledge and electronic structure-based analyses and also reveal new behaviors and identify influential structural motifs. In particular, we evaluated and compared the effects of linear, angular, and branching motifs on these two molecular properties and explored the role of dispersion in mitigating the torsional strain inherent in nonplanar PBHs. Hence, the observed regularities and the proposed analysis contribute to a deeper understanding of the behavior of PBHs and form the foundation for design strategies for new functional PBHs.

Evaluation of the cancer risk from PAHs by inhalation: Are current methods fit for purpose?

There is ample evidence from occupational studies that exposure to a mixture of Polycyclic Aromatic Hydrocarbons (PAHs) is causally associated with an increased incidence of lung cancers. In both occupational atmospheres and ambient air, PAHs are present as a mixture of many compounds, but the composition of the mixture in ambient air differs from that in the occupational atmosphere, and varies in time and space in ambient air. Estimates of cancer risk for PAH mixtures are based upon unit risks which derive from extrapolation of occupational exposure data or animal model data, and in the case of the WHO use one compound, benzo[a]pyrene as a marker for the entire mixture, irrespective of composition. The U.S. EPA has used an animal exposure study to derive a unit risk for inhalation exposure to benzo[a]pyrene alone, and there have been a number of rankings of relative carcinogenic potency for other PAHs which many studies have used to calculate a cancer risk from the PAHs mixture, frequently incorrectly by adding the estimated relative risks of individual compounds, and applying the total "B[a]P equivalent" to the WHO unit risk, which already applies to the entire mixture. Such studies are often based upon data solely for the historic US EPA group of 16 compounds which do not include many of the apparently more potent carcinogens. There are no data for human cancer risk of individual PAHs, and conflicting evidence of additivity of PAH carcinogenicity in mixtures. This paper finds large divergences between risk estimates deriving from the WHO and U.S. EPA methods, as well as considerable sensitivity to the mixture composition, and assumed PAH relative potencies. Of the two methods, the WHO approach appears more likely to provide reliable risk estimates, but recently proposed mixture-based approaches using in vitro toxicity data may offer some advantages.

η6 -Metalated Aryl Iodides in Diels-Alder Cycloaddition Reactions: Mode of Activation and Catalysis

The potential application of η⁶ -metalated aryl iodides as organocatalyst has been explored by means of computational methods. It is found that the enhanced halogen bonding donor ability of these species, in comparison with their demetalated counterparts, translates into a significant acceleration of the Diels-Alder cycloaddition reaction involving cyclohexadiene and methyl vinyl ketone. The factors behind this acceleration, the endo-exo selectivity of the process and the influence of the nature of the transition metal fragment in the activity of these species are quantitatively explored in detail by means of the combination of the Activation Strain Model of reaction and the Energy Decomposition Analysis methods.

Dinaphthooxepine Bisimide Undergoes Oxygen Extrusion Reaction upon Electron Injection at Room Temperature

We report the synthesis and properties of a dinaphthooxepine bisimide (DNOBI), a nonplanar perylene bisimide (PBI) analogue with an inserted oxygen atom. A DNOBI underwent an oxygen-extrusion reaction smoothly upon electron injection at room temperature, affording PBI in good yield. Studies on the reaction mechanism suggest that the injection of two electrons triggers the isomerization of DNOBI to dinaphthooxanorcaradiene bisimide, which is a key step in inducing the oxygen-extrusion reaction.

Automotive Diesel Fuel Internal Stability Testing with the Use of UV and Temperature as Degradation Factors

Diesel fuel stability can be considered from many points of view, of which the two considered most important are stability in contact with the environment and internal stability. Fuel stability in touch with the environment is often defined as oxidation stability, of which measurement procedures are well developed. The presented paper shows that fuel's internal stability can also be important. The internal stability of diesel fuel with the local use of thermal and ultraviolet radiation (UV) as degradation factors and fluorescence signals as a probe is presented in this paper. We show that the internal degradation of fuel with temperature use differs from that with UV and simultaneous both factors use. Our study shows that using temperature as a degradation factor introduces significant fluorescence fading. Moreover, the fluorescence signal restores significantly later than the sample stabilizes at room temperature. The novelty proposed based on examination is hybrid degradation and an examination cycle that enables the simultaneous use of degradation factors and fluorescence reading. For this purpose, a dedicated measurement setup of signal control and processing was constructed and programmed. The measurement procedure of the data series for specific wavelength enables calculation of signal shifts that allow the internal stability classification of diesel fuel samples in less than 30 min with the cost of a single disposable capillary probe and one polymer plug. Premium and regular fuel examination results show that internal fuel stability can be related to polycyclic aromatic hydrocarbons (PAH) concentrations and can be modified with dedicated additives.

An advanced bath model to simulate association followed by ensuing dissociation dynamics of benzene + benzene system: a comparative study of gas and condensed phase results

The role of the environment (N₂ molecules) on the association followed by the ensuing dissociation reaction of benzene + benzene system is studied here with the help of a new code setup. Chemical dynamics simulations are performed to investigate this reaction in vacuum as well as in a bath of 1000 N₂ molecules, equilibrated at 300 K. Bath densities of 20 and 324 kg m^-3 are considered with a few results from the latter density. The simulations are performed at three different excitation temperatures of benzene, namely, 1000, 1500, and 2000 K, with an impact parameter range of 0-12 Å for both vacuum and bath models. Higher association probabilities and hence, higher temperature dependent association rate constants are obtained in the condensed phase. In the condensed phase, when a trajectory takes a longer time for the monomers to associate, the associated complex is formed with a longer lifetime and provides a lower rate of ensuing dissociation. Higher association rate and lower dissociation rate in condensed phase dynamics are due to the energy transfer process. Hence, the energy transfer phenomenon plays a decisive role in the association/dissociation dynamics, which is completely ignored in the same reaction when studied in vacuum.

Designing drugs when there is low data availability: one-shot learning and other approaches to face the issues of a long-term concern

INTRODUCTION

Modern drug discovery generally is accessed by useful information from previous large databases or uncovering novel data. The lack of biological and/or chemical data tends to slow the development of scientific research and innovation. Here, approaches that may help provide solutions to generate or obtain enough relevant data or improve/accelerate existing methods within the last five years were reviewed.

AREAS COVERED

One-shot learning (OSL) approaches, structural modeling, molecular docking, scoring function space (SFS), molecular dynamics (MD), and quantum mechanics (QM) may be used to amplify the amount of available data to drug design and discovery campaigns, presenting methods, their perspectives, and discussions to be employed in the near future.

EXPERT OPINION

Recent works have successfully used these techniques to solve a range of issues in the face of data scarcity, including complex problems such as the challenging scenario of drug design aimed at intrinsically disordered proteins and the evaluation of potential adverse effects in a clinical scenario. These examples show that it is possible to improve and kickstart research from scarce available data to design and discover new potential drugs.

Influence of chemical structure of organic micropollutants on the degradability with ozonation

The increasing environmental problems due to various organic micropollutants in water cause the search of suitable additional water treatment methods. Gaining experimental data for the large amount and variety of pollutants would consume a lot of time as well as economic and ecologic resources. An alternative approach is predictive quantitative structure-property relationship (QSPR) modeling, which establishes a correlation between the structural properties of a molecules with a biological, physical, or chemical property. Therefore, in this study, QSPR modeling has been conducted using extensive validation techniques and statistical test to investigate the structural influence on the degradability of organic micropollutants with ozonation. In contrast to most of the other studies, the underlying dataset - rate constants for 92 organic molecules - were obtained under standardized conditions with defined experimental parameters. QSPR modeling was executed using a combination of the software PaDEL for descriptor calculation and QSARINS for the modeling process respecting all five OECD-requirements for applicable QSAR/QSPR-models. The final model was selected using a multi-criteria decision-making tool to evaluate the model quality based on all calculated statistical quality parameters. The model included 10 selected descriptors and fingerprints and showed good regression abilities, predictive power, and stability (R² = 0.8221, CCC_tr = 0.9024, Q²_loo = 0.7436, R²_ext = 0.8420, Q²_F1 = 0.8104). The applicability domain of the QSPR model was defined and an interpretation of selected model descriptors has been connected to previous experimental studies. A significant influence of the interpretable descriptors was put into experimental context and compared with previous studies and models. For example, the molar refractivity as a measure of size and polarizability of a molecule and the occurrence of important substructures such as a formamide group seem to decrease the removal rate constant. The contribution of lone electrons entering into resonance as well as the occurrence of fused rings were identified as influences for the increase of the degradability of micropollutants by ozonation.

Origin of Catalysis and Selectivity in Lewis Acid-Promoted Diels-Alder Reactions Involving Vinylazaarenes as Dienophiles

The poorly understood factors controlling the catalysis and selectivity in Lewis acid-promoted Diels-Alder cycloaddition reactions involving vinylazaarenes as dienophiles have been quantitatively explored in detail by means of computational methods. With the help of the activation strain model and the energy decomposition analysis methods, it is found that the remarkable acceleration induced by the catalysis is mainly due to a significant reduction of the Pauli repulsion between the key occupied π-molecular orbitals of the reactants and not due to the proposed stabilization of the lowest unoccupied molecular orbital (LUMO) of the dienophile. This computational approach has also been helpful to understand the reasons behind the extraordinary regio- and diastereoselectivity observed experimentally. The insight gained in this work allows us to predict even more reactive vinylazaarene dienophiles, which may be useful in organic synthesis.

Stepwise reduction of a corannulene-based helical molecular nanographene with Na metal

The chemical reduction of a corannulene-based molecular nanographene, C₇₆H₆₄ (1), with Na metal in the presence of 18-crown-6 afforded the doubly-reduced state of 1. This reduction provokes a distortion of the helicene core and has a significant impact on the aromaticity of the system.

Understanding the reactivity of frustrated Lewis pairs with the help of the activation strain model-energy decomposition analysis method

This Feature article presents recent representative applications of the combination of the Activation Strain Model of reactivity and the Energy Decomposition Analysis methods to understand the reactivity of Frustrated Lewis Pairs (FLPs). This approach has been helpful to not only gain a deeper quantitative insight into the factors controlling the cooperative action between the Lewis acid/base partners but also to rationally design highly active systems for different bond activation reactions. Issues such as the influence of the nature of the FLP antagonists or the substituents directly attached to them on the reactivity are covered herein, which are crucial for the future development of this fascinating family of compounds.

An Access to Benzo[a]fluorenes, Benzo[b]fluorenes, and Indenes Triggered by Simple Lewis Acid

This report illustrates BF₃·OEt₂ promoted intramolecular cascade cycloaromatization of 1,7-ynones toward synthesizing structurally diverse benzofluorene scaffolds. Remarkably, the present protocol promotes the formation of two consecutive C-C bonds intramolecularly and undergoes aromatization under mild reaction conditions to afford the tetracyclic benzo[a]fluorene frameworks. Besides, the formation of indenes was observed when 1-bromo-2-iodoarenes are relatively more electron-rich when compared with the one originating from the terminal arylacetylenes, under controlled conditions, wherein triple bond polarity has been just reversed due to the change of electronic effects exerted by the strong +M group of 1-bromo-2-iodoarenes, which is in conjugation to the connected triple bond. The same concept to generate indenes has also been extended by using aliphatic alkyne tethered ynones. Further, it was noticed that 1,7-ynones bearing the more electron-rich 1-bromo-2-iodoarenes than the arene ring arriving from the terminal arylacetylenes lead to benzo[b]fluorenes, under thermodynamic conditions, instead of delivering the benzo[a]fluorenes. In addition, this method features metal-free conditions, easily accessible starting materials, operational simplicity, gram-scale synthesis, and a wide range of substrate scopes.

B-DNA Structure and Stability: The Role of Nucleotide Composition and Order

We have quantum chemically analyzed the influence of nucleotide composition and sequence (that is, order) on the stability of double-stranded B-DNA triplets in aqueous solution. To this end, we have investigated the structure and bonding of all 32 possible DNA duplexes with Watson-Crick base pairing, using dispersion-corrected DFT at the BLYP-D3(BJ)/TZ2P level and COSMO for simulating aqueous solvation. We find enhanced stabilities for duplexes possessing a higher GC base pair content. Our activation strain analyses unexpectedly identify the loss of stacking interactions within individual strands as a destabilizing factor in the duplex formation, in addition to the better-known effects of partial desolvation. Furthermore, we show that the sequence-dependent differences in the interaction energy for duplexes of the same overall base pair composition result from the so-called "diagonal interactions" or "cross terms". Whether cross terms are stabilizing or destabilizing depends on the nature of the electrostatic interaction between polar functional groups in the pertinent nucleobases.

Stable N-heterocyclic borylenes with promising ligand properties: a contribution from theory

DFT calculations reveal the power of ylides in stabilizing neutral singlet cyclic borylenes that are found to be capable of activating a variety of small molecules having enthalpically strong bonds.

Rationalizing the influence of α-cationic phospholes on π-catalysis

The physical factors behind the experimentally observed high activity of gold(I)-catalysts having an α-cationic phosphole as a ligand have been computationally explored. To this end, the gold(I)-catalysed hydroarylation reactions of phenylacetylene and mesitylene involving both neutral and cationic phosphole as well as phosphine ligands have been quantitatively analyzed in detail with the help of the activation strain model of reactivity in combination with the energy decomposition analysis method. It is found that the cationic phosphole ligands induce a dramatic change in both the geometry and the electronic structure of the initially formed π-complex which significantly enhances its electrophilicity. This results in an enhancement of the key π(mesitylene) → π*(LAu-acetylene complex) molecular orbital interaction which is the main factor responsible for the activating effect of these cationic ligands.

Influence of the CH/B replacement on the Reactivity of Boranthrene and Related Compounds

The influence of the replacement of CH groups by boron atoms on the reactivity of planar polycyclic aromatic hydrocarbons has been explored by means of computational tools. To this end, [4 + 2]-cycloaddition reactions involving anthracene and neutral boranthrene with different dienophiles such as ethylene, acetylene, and CO₂ have been compared. In addition, the influence of additional fused aromatic rings (pentacene or borapentacene) on the reactivity of these species has been also explored. It was found that the B-doped systems are systematically much more reactive than their all-carbon counterparts from both kinetic and thermodynamic points of view. The observed trends in reactivity are quantitatively analyzed in detail using state-of-the-art methods, namely, the activation strain model of reactivity and the energy decomposition analysis method. Our calculations reveal the importance of molecular orbital interactions as the key factor responsible for the enhanced reactivity of the B-doped systems.

Origin of asynchronicity in Diels-Alder reactions

Asynchronicity in Diels-Alder reactions plays a crucial role in determining the height of the reaction barrier. Currently, the origin of asynchronicity is ascribed to the stronger orbital interaction between the diene and the terminal carbon of an asymmetric dienophile, which shortens the corresponding newly formed C-C bond and hence induces asynchronicity in the reaction. Here, we show, using the activation strain model and Kohn-Sham molecular orbital theory at ZORA-BP86/TZ2P, that this rationale behind asynchronicity is incorrect. We, in fact, found that following a more asynchronous reaction mode costs favorable HOMO-LUMO orbital overlap and, therefore, weakens (not strengthens) these orbital interactions. Instead, it is the Pauli repulsion that induces asynchronicity in Diels-Alder reactions. An asynchronous reaction pathway also lowers repulsive occupied-occupied orbital overlap which, therefore, reduces the unfavorable Pauli repulsion. As soon as this mechanism of reducing Pauli repulsion dominates, the reaction begins to deviate from synchronicity and adopts an asynchronous mode. The eventual degree of asynchronicity, as observed in the transition state of a Diels-Alder reaction, is ultimately achieved when the gain in stability, as a response to the reduced Pauli repulsion, balances with the loss of favorable orbital interactions.

Factors Controlling the Aluminum(I)-meta-Selective C-H Activation in Arenes

The so far poorly understood factors controlling the complete meta-selectivity observed in the C-H activation reactions of alkylarenes promoted by aluminyl anions have been explored in detail by means of Density Functional Theory calculations. To this end, a combination of state-of-the-art computational methods, namely the activation strain model of reactivity and energy decomposition analysis, has been applied to quantitatively unveil the origin of the selectivity of the transformation as well as the influence of the associated potassium cation. It is found that the selectivity takes place during the initial nucleophilic addition step where the key LP(Al)→π*(C=C) molecular orbital interaction is more stabilizing for the meta-pathway, which results in a stronger interaction between the reactants along the entire transformation.

Extension and Quantification of the Fries Rule and Its Connection to Aromaticity: Large-Scale Validation by Wave-Function-Based Resonance Analysis

The Fries rule is a simple, intuitive tool to predict the most dominant Kekulé structures of polycyclic aromatic hydrocarbons (PAHs), which is valuable for understanding the structure, stability, reactivity, and aromaticity of these conjugated compounds. However, it still remains an empirical hypothesis, with limited qualitative applications. Herein, we verify, generalize, and quantify the Fries rule based on the recently developed resonance analysis of the DFT wave functions of over 1500 PAH and fullerene molecules with over a billion Kekulé structures. The extended rules, counting the numbers of electrons within all rings (not just sextets), are able to rank the relative importance of all Kekulé structures for all considered systems. The statistically meaningful quantification also opens a way to evaluate ring aromaticity based on the resonance theory, which generally agrees well with conventional aromaticity descriptors. Furthermore, we propose a purely graph-based aromaticity indicator nicely applicable to PAHs and fullerenes, with no need of any quantum chemistry calculations, so that it can make valuable predictions for molecular properties that are related to local aromaticity.

Lewis Acid-Catalyzed Diels-Alder Reactions: Reactivity Trends across the Periodic Table

The catalytic effect of various weakly interacting Lewis acids (LAs) across the periodic table, based on hydrogen (Group 1), pnictogen (Group 15), chalcogen (Group 16), and halogen (Group 17) bonds, on the Diels-Alder cycloaddition reaction between 1,3-butadiene and methyl acrylate was studied quantum chemically by using relativistic density functional theory. Weakly interacting LAs accelerate the Diels-Alder reaction by lowering the reaction barrier up to 3 kcal mol-1 compared to the uncatalyzed reaction. The reaction barriers systematically increase from halogen Collapse

Key Words

• Diels-Alder reaction
• Lewis acids
• activation strain model
• density functional calculations
• reactivity

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MESH Headings Collapse

Grants

• Netherlands Organization for Scientific Research (NWO)
• Dutch Astrochemistry Network (DAN)
• PID2019-106184GB-I00 Spanish MICIIN
• RED2018-102387-T Spanish MICIIN
• Nederlandse Organisatie voor Wetenschappelijk Onderzoek
• Dutch Astrochemistry Network
• Nederlandse Organisatie voor Wetenschappelijk Onderzoek

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Affiliation(s)

Pascal Vermeeren Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands
Marco Dalla Tiezza Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands
Michelle van Dongen Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands
Israel Fernández Departamento de Química Orgánica I and Centro de Innovación en Química Avanzada (ORFEO-CINQA)Facultad de Ciencias QuímicasUniversidad Complutense de Madrid28040MadridSpain
F. Matthias Bickelhaupt Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands Institute for Molecules and MaterialsRadboud UniversityHeyendaalseweg 1356525 AJNijmegen (TheNetherlands
Trevor A. Hamlin Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdam (TheNetherlands

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Non-Planar Perylene Bisimide Analogues with Inserted Carbonyl and Methylene Subunits

The synthesis and properties of dinaphthotropone bisimide (DNTrBI) and dinaphthocycloheptatriene bisimide (DNCHepBI) are described. Their molecular design is conceptually based on the insertion of a carbon atom into a perylene bisimide (PBI) core. These molecules adopt non-planar structures due to the presence of a seven-membered ring. The PBI derivative into which a carbonyl group was inserted (DNTrBI) immediately underwent nonradiative decay and/or intersystem crossing in its excited state. The PBI derivative into which a methylene group was inserted (DNCHepBI) was susceptible to deprotonation on account of the two electron-withdrawing naphthalene monoimide units. Subsequent aerobic oxidation resulted in the formation of a C-C bond at the central methylene unit, thus affording a σ-dimer. The formation of this C-C bond is dynamically redox-active, i.e., electron injection into the σ-dimer almost quantitatively regenerated the deprotonated DNCHepBI.

Transformation from triple helicene to double helicene embedding adjacent stereogenic carbon atoms and axial stereogenicity

Transformation of triple helicene (TH) to double helicene (DH) with adjacent stereogenic carbon atoms and axial stereogenicity was achieved by the unexpected conjugate addition to the central aromatic ring of TH-1. We also studied the boundary at which different reactivities to addition reactions occur in some helicenes with different π-extension.

Gas-phase synthesis of benzene via the propargyl radical self-reaction

Polycyclic aromatic hydrocarbons (PAHs) have been invoked in fundamental molecular mass growth processes in our galaxy. We provide compelling evidence of the formation of the very first ringed aromatic and building block of PAHs-benzene-via the self-recombination of two resonantly stabilized propargyl (C₃H₃) radicals in dilute environments using isomer-selective synchrotron-based mass spectrometry coupled to theoretical calculations. Along with benzene, three other structural isomers (1,5-hexadiyne, fulvene, and 2-ethynyl-1,3-butadiene) and o-benzyne are detected, and their branching ratios are quantified experimentally and verified with the aid of computational fluid dynamics and kinetic simulations. These results uncover molecular growth pathways not only in interstellar, circumstellar, and solar systems environments but also in combustion systems, which help us gain a better understanding of the hydrocarbon chemistry of our universe.

The Pauli Repulsion-Lowering Concept in Catalysis

Organic chemistry has undoubtedly had a profound impact on humanity. Day in and day out, we find ourselves constantly surrounded by organic compounds. Pharmaceuticals, plastics, fuels, cosmetics, detergents, and agrochemicals, to name a few, are all synthesized by organic reactions. Very often, these reactions require a catalyst in order to proceed in a timely and selective manner. Lewis acids and organocatalysts are commonly employed to catalyze organic reactions and are considered to enhance the frontier molecular orbital (FMO) interactions. A vast number of textbooks and primary literature sources suggest that the binding of a Lewis acid or an iminium catalyst to a reactant (R1) stabilizes its LUMO and leads to a smaller HOMO(R2)-LUMO(R1) energy gap with the other reactant (R2), thus resulting in a faster reaction. This forms the basis for the so-called LUMO-lowering catalysis concept. Despite the simplicity and popularity of FMO theory, a number of deficiencies have emerged over the years, as a consequence of these FMOs not being the operative factor in the catalysis. LUMO-lowering catalysis is ultimately incomplete and is not always operative in catalyzed organic reactions. Our groups have recently undertaken a concerted effort to generate a unified framework to rationalize and predict chemical reactivity using a causal model that is rooted in quantum mechanics. In this Account, we propose the concept of Pauli repulsion-lowering catalysis to understand the catalysis in fundamental processes in organic chemistry. Our findings emerge from state-of-the-art computational methods, namely, the activation strain model (ASM) of reactivity in conjunction with quantitative Kohn-Sham molecular orbital theory (KS-MO) and a matching energy decomposition analysis (EDA). The binding of the catalyst to the substrate not only leads to a stabilization of its LUMO but also induces a significant reduction of the two-orbital, four-electron Pauli repulsion involving the key molecular orbitals of both reactants. This repulsion-lowering originates, for the textbook Lewis acid-catalyzed Diels-Alder reaction, from the catalyst polarizing the occupied π orbital of the dienophile away from the carbon atoms that form new bonds with the diene. This polarization of the occupied dienophile π orbital reduces the occupied orbital overlap with the diene and constitutes the ultimate physical factor responsible for the acceleration of the catalyzed process as compared to the analogous uncatalyzed reaction. We show that this physical mechanism is generally applicable regardless of the type of reaction (Diels-Alder and Michael addition reactions) and the way the catalyst is bonded to the reactants (i.e., from pure covalent or dative bonds to weaker hydrogen or halogen bonds). We envisage that the insights emerging from our analysis will guide future experimental developments toward the design of more efficient catalytic transformations.

An Aromatic Universe-A Physical Chemistry Perspective

This Perspective presents recent advances in our knowledge of the fundamental elementary mechanisms involved in the low- and high-temperature molecular mass growth processes to polycyclic aromatic hydrocarbons in combustion systems and in extraterrestrial environments (hydrocarbon-rich atmospheres of planets and their moons, cold molecular clouds, circumstellar envelopes). Molecular beam studies combined with electronic structure calculations extracted five key elementary mechanisms: Hydrogen Abstraction-Acetylene Addition, Hydrogen Abstraction-Vinylacetylene Addition, Phenyl Addition-DehydroCyclization, Radical-Radical Reactions, and Methylidyne Addition-Cyclization-Aromatization. These studies, summarized here, provide compelling evidence that key classes of aromatic molecules can be synthesized in extreme environments covering low temperatures in molecular clouds (10 K) and hydrocarbon-rich atmospheres of planets and their moons (35-150 K) to high-temperature environments like circumstellar envelopes of carbon-rich Asymptotic Giant Branch Stars stars and combustion systems at temperatures above 1400 K thus shedding light on the aromatic universe we live in.

Catalysis by Bidentate Iodine(III)-Based Halogen Donors: Surpassing the Activity of Strong Lewis Acids

The poorly understood mode of activation and catalysis of bidentate iodine(III)-based halogen donors have been quantitatively explored in detail by means of state-of-the-art computational methods. To this end, the uncatalyzed Diels–Alder cycloaddition reaction between cyclohexadiene and methyl vinyl ketone is compared to the analogous process mediated by a bidentate iodine(III)-organocatalyst and by related, highly active iodine(I) species. It is found that the bidentate iodine(III)-catalyst accelerates the cycloaddition by lowering the reaction barrier up to 10 kcal mol^–1 compared to the parent uncatalyzed reaction. Our quantitative analyses reveal that the origin of the catalysis is found in a significant reduction of the steric (Pauli) repulsion between the diene and dienophile, which originates from both a more asynchronous reaction mode and a significant polarization of the π-system of the dienophile away from the incoming diene. Notably, the activity of the iodine(III)-catalyst can be further enhanced by increasing the electrophilic nature of the system. Thus, novel systems are designed whose activity actually surpasses that of strong Lewis acids such as BF₃.

Bifunctional Hydrogen Bond Donor-Catalyzed Diels-Alder Reactions: Origin of Stereoselectivity and Rate Enhancement

The selectivity and rate enhancement of bifunctional hydrogen bond donor-catalyzed Diels-Alder reactions between cyclopentadiene and acrolein were quantum chemically studied using density functional theory in combination with coupled-cluster theory. (Thio)ureas render the studied Diels-Alder cycloaddition reactions exo selective and induce a significant acceleration of this process by lowering the reaction barrier by up to 7 kcal mol-1 . Our activation strain and Kohn-Sham molecular orbital analyses uncover that these organocatalysts enhance the Diels-Alder reactivity by reducing the Pauli repulsion between the closed-shell filled π-orbitals of the diene and dienophile, by polarizing the π-orbitals away from the reactive center and not by making the orbital interactions between the reactants stronger. In addition, we establish that the unprecedented exo selectivity of the hydrogen bond donor-catalyzed Diels-Alder reactions is directly related to the larger degree of asynchronicity along this reaction pathway, which is manifested in a relief of destabilizing activation strain and Pauli repulsion.

Synthesis of azahelicenes through Mallory reaction of imine precursors: corannulene substrates provide an exception to the rule in oxidative photocyclizations of diarylethenes

Typically, the synthesis of phenanthrene-based polycyclic aromatic hydrocarbons relies on the Mallory reaction. In this approach, stilbene (PhCH[double bond, length as m-dash]CHPh)-based precursors undergo an oxidative photocyclization reaction to join the two adjacent aromatic rings into an extended aromatic structure. However, if one C[double bond, length as m-dash]C carbon atom is replaced by a nitrogen atom (C[double bond, length as m-dash]N), the synthesis becomes practically infeasible. Here, we show the very first examples of a successful Mallory reaction on stilbene-like imine precursors involving the molecularly curved corannulene nucleus. The isolated yields exceed 90% and the resulting single and double aza[4]helicenes exhibit adjustable high affinity for electrons.

Unusual reversibility in molecular break-up of PAHs: the case of pentacene dehydrogenation on Ir(111)

In this work, we characterise the adsorption of pentacene molecules on Ir(111) and their dissociation behaviour as a function of temperature.

Rationalizing the AlI -Promoted Oxidative Addition of C-C Versus C-H Bonds in Arenes

The factors controlling the oxidative addition of C-C and C-H bonds in arenes mediated by Al^I have been computationally explored by means of Density Functional Theory calculations. To this end, we compared the processes involving benzene, naphthalene and anthracene which are promoted by a recently prepared anionic Al^I -carbenoid. It is found that this species exhibits a strong tendency to oxidatively activate C-H bonds over C-C bonds, with the notable exception of benzene, where the C-C bond activation is feasible but only under kinetic control reaction conditions. State-of-the-art computational methods based on the combination of the Activation Strain Model of reactivity and the Energy Decomposition Analysis have been used to rationalize the competition between both bond activation reactions as well as to quantitatively analyze in detail the ultimate factors controlling these transformations.

Origin of rate enhancement and asynchronicity in iminium catalyzed Diels-Alder reactions

The Diels-Alder reactions between cyclopentadiene and various α,β-unsaturated aldehyde, imine, and iminium dienophiles were quantum chemically studied using a combined density functional theory and coupled-cluster theory approach. Simple iminium catalysts accelerate the Diels-Alder reactions by lowering the reaction barrier up to 20 kcal mol-1 compared to the parent aldehyde and imine reactions. Our detailed activation strain and Kohn-Sham molecular orbital analyses reveal that the iminium catalysts enhance the reactivity by reducing the steric (Pauli) repulsion between the diene and dienophile, which originates from both a more asynchronous reaction mode and a more significant polarization of the π-system away from the incoming diene compared to aldehyde and imine analogs. Notably, we establish that the driving force behind the asynchronicity of the herein studied Diels-Alder reactions is the relief of destabilizing steric (Pauli) repulsion and not the orbital interaction between the terminal carbon of the dienophile and the diene, which is the widely accepted rationale.