Reactivity for the Diels–Alder Reaction of Cumulenes: A Distortion-Interaction Analysis along the Reaction Pathway

Theoretical investigations of 2-vinylpyridine stereoselective polymerization catalyzed by cationic yttrium complexes with different ancillary ligands

The polymerization mechanism of 2-vinylpyridine catalyzed by cationic yttrium complexes with diverse ancillary ligands, specifically [L1Y(CH2SiMe3)(THF)]+ [L1 = (2,6-Et2C6H3)NC(Me)CHC(Me)N(2,6-Et2C6H3)] (Y-1), [L2Y(CH2SiMe3)(THF)]+ [L2 = (2,6-Cl2C6H3)NC(Me)CHC(Me)N(2,6-Cl2C6H3)] (Y-2), and [L3Y(CH2SiMe3)(THF)]+ [L3 = (2,6-C6H5)NC(Me)CHC(Me)N(2,6-iPr2C6H3)] (Y-3), was studied using density functional theory (DFT) calculations. Having achieved an agreement between theory and experiment, it is found that isotactic selectivity induced by Y-1 or Y-2 results from a combination of smaller deformation of the catalyst and stronger electronic effects. Conversely, the Y-3 complex exhibits comparable energy barriers for proceeding via either isotactic or syndiotactic pathways, aligning with the production of atactic polymers as seen experimentally. To examine the steric effects on the kinetic and thermodynamic properties, a computational model of an analogue complex [L4Y(CH2SiMe3)(THF)]+ [L4 = (2,6-Cl2C6H3)NC(Me)CHC(Me)N(iPr2C6H3)] (Y-4), featuring increased steric hindrance, was analyzed. Distortion-interaction and topographic steric map analyses further affirmed that steric hindrance significantly influences stereoselectivity. A direct relationship was identified between the energy barriers of isotactic insertion transition states and the bulkiness of ancillary ligands; greater distortion energy of the catalyst correlates with higher barriers for isotactic polymerization. These findings enhance the mechanistic comprehension of 2-vinylpyridine polymerization and are expected to contribute valuable insights for the improvement of catalytic polymerization systems of 2-vinylpyridine.

DFT Insight into a Strain-Release Mechanism in Bicyclo[1.1.0]butanes via Concerted Activation of Central and Lateral C-C Bonds with Rh(III) Catalysis

Transition-metal-catalyzed, strain-release-driven transformations of "spring-loaded" bicyclo[1.1.0]butanes (BCBs) are considered potent tools in synthetic organic chemistry. Previously proposed strain-release mechanisms involve either the insertion of the central C-C bond of BCBs into a metal-carbon bond, followed by β-C elimination, or the oxidative addition of the central or lateral C-C bond on the transition metal center, followed by reductive elimination. This study, employing DFT calculations on a Rh(III)-catalyzed model system in a three-component protocol involving oxime ether, BCB ester, and ethyl glyoxylate for constructing diastereoselective quaternary carbon centers, introduces an unusual strain-release mechanism for BCBs. In this mechanism, the catalytic reaction is initiated by the simultaneous cleavage of two C-C bonds (the central and lateral C-C bonds), resulting in the formation of a Rh-carbene intermediate. The new mechanism exhibits a barrier of 21.0 kcal/mol, making it energetically more favorable by 11.1 kcal/mol compared to the previously suggested most favorable pathway. This unusual reaction mode rationalizes experimental observation of the construction of quaternary carbon centers, including the excellent E-selectivity and diastereoselectivity. The newly proposed strain-release mechanism holds promise in advancing our understanding of transition-metal-catalyzed C-C bond activation mechanisms and facilitating the synthesis of transition metal carbene complexes.

How Strain-Release Determines Chemoselectivity: A Mechanistic Study of Rhodium-Catalyzed Bicyclo[1.1.0]butane Activation

Bicyclo[1.1.0]butane (BCB) derivatives are versatile coupling partners, and various reaction modes for their activation and transformation have been proposed. In this work, three BCB-activation modes in Rh-catalyzed BCB transformations that construct diastereoselective α-quaternary β-lactones were investigated by density functional theory calculations. Our results show that, compared with C1-C3 insertion and C-C3 oxidative addition, C2-C3 oxidative addition is more favorable. The whole catalytic cycle involves five main steps: C-H activation, oxidative addition, β-C elimination/reductive elimination, Rh walking, and aldehyde insertion/protonation. Independent gradient model, intrinsic reaction coordinate, distortion-interaction energy, and Laplacian electron-density analyses were carried out to investigate the mode of BCB activation. Our calculation also showed that aldehyde-insertion is the diastereoselectivity determining step, which is controlled by the steric effect between the ligand, methyl group, and aldehyde.

Computational biotransformation of polyethylene terephthalate by depolymerase: A QM/MM approach

Despite increasing environmental concerns on ever-lasting Polyethylene Terephthalate (PET), its global production is continuously growing. Effective strategies that can completely remove PET from environment are urgently desired. Here biotransformation processes of PET by one of the most effective enzymes, leaf-branch compost cutinase (LCC), were systematically explored with Molecular Dynamics and Quantum Mechanics/Molecular Mechanics approaches. We found that four concerted steps are required to complete the whole catalytic cycle. The last concerted step, deacylation, was determined as the rate-determining step with Boltzmann-weighted average barrier of 13.6 kcal/mol and arithmetic average of 16.1 ± 2.9 kcal/mol. Interestingly, unprecedented fluctuations of hydrogen bond length during LCC catalyzed transformation process toward PET were found. This fluctuation was also observed in enzyme IsPETase, indicating that it may widely exist in other catalytic triad (Ser-His-Asp) containing enzymes as well. In addition, possible features (bond, angle, dihedral angle and charge) that influence the catalytic reaction were identified and correlations between activation energies and key features were established. Our results present new insights into catalytic mechanism of hydrolases and shed light on the efficient recycling of the ever-lasting PET.

Palladium-Catalyzed Regio- and Chemoselective Double-Alkoxycarbonylation of 1,3-Diynes: A Computational Study

The palladium-catalyzed double-alkoxycarbonylation of 1,3-diynes provides an efficient approach for the selective synthesis of 1,2,3,4-tetrasubstituted conjugated dienes. In this report, density functional theory calculations have been performed to elucidate the...

BH9, a New Comprehensive Benchmark Data Set for Barrier Heights and Reaction Energies: Assessment of Density Functional Approximations and Basis Set Incompleteness Potentials

The calculation of accurate reaction energies and barrier heights is essential in computational studies of reaction mechanisms and thermochemistry. To assess methods regarding their ability to predict these two properties, high-quality benchmark sets are required that comprise a reasonably large and diverse set of organic reactions. Due to the time-consuming nature of both locating transition states and computing accurate reference energies for reactions involving large molecules, previous benchmark sets have been limited in scope, the number of reactions considered, and the size of the reactant and product molecules. Recent advances in coupled-cluster theory, in particular local correlation methods like DLPNO-CCSD(T), now allow the calculation of reaction energies and barrier heights for relatively large systems. In this work, we present a comprehensive and diverse benchmark set of barrier heights and reaction energies based on DLPNO-CCSD(T)/CBS called BH9. BH9 comprises 449 chemical reactions belonging to nine types common in organic chemistry and biochemistry. We examine the accuracy of DLPNO-CCSD(T) vis-a-vis canonical CCSD(T) for a subset of BH9 and conclude that, although there is a penalty in using the DLPNO approximation, the reference data are accurate enough to serve as a benchmark for density functional theory (DFT) methods. We then present two applications of the BH9 set. First, we examine the performance of several density functional approximations commonly used in thermochemical and mechanistic studies. Second, we assess our basis set incompleteness potentials regarding their ability to mitigate basis set incompleteness errors. The number of data points, the diversity of the reactions considered, and the relatively large size of the reactant molecules make BH9 the most comprehensive thermochemical benchmark set to date and a useful tool for the development and assessment of computational methods.

Chiral Phosphoric Acid Catalyzed Conversion of Epoxides into Thiiranes: Mechanism, Stereochemical Model, and New Catalyst Design

Computations and experiments leading to new chiral phosphoric acids (CPAs) for epoxide thionations are reported. Density functional theory calculations reveal the mechanism and origin of the enantioselectivity of such CPA‐catalyzed epoxide thionations. The calculated mechanistic information was used to design new efficient CPAs that were tested experimentally and found to be highly effective. Bulky ortho‐substituents on the 3,3′‐aryl groups of the CPA are important to restrict the position of the epoxide in the key transition states for the enantioselectivity‐determining step. Larger para‐substituents significantly improve the enantioselectivity of the reaction.

π-Facial Stereoselectivity in Acyl Nitroso Cycloadditions to 5,5-Unsymmetrically Substituted Cyclopentadienes: Computational Exploration of Origins of Selectivity and the Role of Substituent Conformations on Selectivity

The π-facial selectivity of Diels-Alder cycloadditions of 5-monosubstituted cyclopentadienes is known experimentally and has been extensively studied computationally. Previous studies on 5-monosubstituted cyclopentadienes by the Burnell and Houk groups showed that facial selectivity arises principally from hyperconjugative aromaticity or antiaromaticity of polar groups that cause distortion of the cyclopentadiene; steric effects of nonpolar groups can also be important. We have now explored the stereoselective cycloaddition of 5,5-unsymmetrically substituted cyclopentadienes to an acyl nitroso dienophile reported by Kan and co-workers. Computational studies with M06-2X/6-311+G(d,p) indicate that the stereoselectivity in the cycloadditions of 5,5-unsymmetrically substituted cyclopentadienes is not just a simple combination of effects found for monosubstituted counterparts. Substituent conformations and diene-dienophile steric and electronic interaction effects all influence stereoselectivity. Predictions are made about several as-yet-unstudied cyclopentadiene cycloadditions.

Understanding the intermolecular Diels-Alder cycloaddition promotion: Activation strain model/energy decomposition analysis model and conceptual density functional theory viewpoints

The present work reports the computational study of the major Diels-Alder reaction between 2-bromocycloalkenone and a variety of mono- and di-substituted dienes. Through density functional theory (DFT) calculations and subsequent activation strain model/energy decomposition analysis/conceptual DFT (C-DFT) analyses, the key factors governing the activation barriers heights, and thus reactivity, are characterized. In contrast with a previous study, steric effects do not appear to control reactivity. Conversely, in all presented cases, a subtle interplay between deformation and interaction energies is evidenced at transition states. In the end, neither term alone is enough to explain or predict reactivity. Yet a simple C-DFT descriptor allows to predict with a reasonable efficiency the activation barriers: the excitation energy needed to observe a charge transfer from the diene to the dienophile. Theoretical elements are provided to support the use of this descriptor.

Quantifying Frustrations for Molecular Complexes with Noncovalent Interactions

Molecular systems bound together through noncovalent interactions are involved in a lot of life-essential processes such as molecular recognition, signal transduction, and allosteric regulation. While cooperation as an important effect discovered in these systems focuses on the behavior of system's entirety, we need also examine the behavior of individual parts. In this work, using the distortion energy as the descriptor, we quantify frustration as the energetic loss of individual parts due to the formation of nonadditive molecular complexes. The applicability of our approach has been illustrated by a few simple clusters. Our results show that the frustration effect is smaller than the cooperation effect, but same as cooperativity, it can be both positive and negative. The ultimate benefit of a system made of multiple parts is dictated by the balance between the cooperative behavior among parts and the sacrifice from its individuals. This conflicting yet complementary conceptual pair of cooperation and frustration provides us with a different perspective from the systems' viewpoint for molecular complexes. This new angle of appreciating molecular complexes can be applied in conformational changes, enzymatic catalysis, and many more.

A computational investigation of the selectivity and mechanism of the Lewis acid catalyzed oxa-Diels-Alder cycloaddition of substituted diene with benzaldehyde

The selectivity and the mechanism of the uncatalyzed and AlCl₃ catalyzed hetero-Diels-Alder reaction (HDR) between ([E]-4-methylpenta-2,4-dienyloxy)(tert-butyl)dimethylsilane 1 and benzaldehyde 2 have been studied using density functional theory at the MPWB1K/6-31G(d) level of theory. The uncatalyzed HDR between diene 1 and alkene 2 is characterized by a polar character and proceeds via an asynchronous one-step mechanism for the meta paths and synchronous for the ortho ones. In the presence of AlCl₃ catalyst, the mechanism changes to be stepwise, while the first step is the rate-determining step. The activation energies widely decrease, and the polar character increases dramatically. A large analysis of the mechanism is performed using the activation strain model/energy decomposition analysis (ASM/EDA) model, the natural bond orbital (NBO) and state specific dual descriptors (SSDDs). The obtained results indicate that the combined interaction energy associated with the distortion of the reactants in these HDR are at the origin of the observed kinetics. NBO analyses were applied to estimate the Lewis-acid catalyst donor-acceptor interaction with the molecular system. The SSDD analysis shed light into the orientation effects on the reaction kinetics by providing important information about charge transfer interactions during the chemical reaction. It indicates that the more favorable HDR pathway have the lowest excitation energies, facilitating the interaction between diene 1 and benzaldehyde 2 moieties. Non-covalent interaction (NCI) and QTAIM analyses of the meta-endo structure indicate that the presence of several weak NCIs formed at this approach is at the origin of the meta-endo selectivity.

Soft Materials by Design: Unconventional Polymer Networks Give Extreme Properties

Hydrogels are polymer networks infiltrated with water. Many biological hydrogels in animal bodies such as muscles, heart valves, cartilages, and tendons possess extreme mechanical properties including being extremely tough, strong, resilient, adhesive, and fatigue-resistant. These mechanical properties are also critical for hydrogels' diverse applications ranging from drug delivery, tissue engineering, medical implants, wound dressings, and contact lenses to sensors, actuators, electronic devices, optical devices, batteries, water harvesters, and soft robots. Whereas numerous hydrogels have been developed over the last few decades, a set of general principles that can rationally guide the design of hydrogels using different materials and fabrication methods for various applications remain a central need in the field of soft materials. This review is aimed at synergistically reporting: (i) general design principles for hydrogels to achieve extreme mechanical and physical properties, (ii) implementation strategies for the design principles using unconventional polymer networks, and (iii) future directions for the orthogonal design of hydrogels to achieve multiple combined mechanical, physical, chemical, and biological properties. Because these design principles and implementation strategies are based on generic polymer networks, they are also applicable to other soft materials including elastomers and organogels. Overall, the review will not only provide comprehensive and systematic guidelines on the rational design of soft materials, but also provoke interdisciplinary discussions on a fundamental question: why does nature select soft materials with unconventional polymer networks to constitute the major parts of animal bodies?

Rhodium(i)/bisoxazolinephosphine-catalyzed regio- and enantioselective amination of allylic carbonates: a computational study

DFT calculations were performed to investigate the rhodium(i)/bisoxazolinephosphine-catalyzed regio- and enantioselective amination of allylic carbonates.

Understanding chemical reactivity using the activation strain model

Understanding chemical reactivity through the use of state-of-the-art computational techniques enables chemists to both predict reactivity and rationally design novel reactions. This protocol aims to provide chemists with the tools to implement a powerful and robust method for analyzing and understanding any chemical reaction using PyFrag 2019. The approach is based on the so-called activation strain model (ASM) of reactivity, which relates the relative energy of a molecular system to the sum of the energies required to distort the reactants into the geometries required to react plus the strength of their mutual interactions. Other available methods analyze only a stationary point on the potential energy surface, but our methodology analyzes the change in energy along a reaction coordinate. The use of this methodology has been proven to be critical to the understanding of reactions, spanning the realms of the inorganic and organic, as well as the supramolecular and biochemical, fields. This protocol provides step-by-step instructions-starting from the optimization of the stationary points and extending through calculation of the potential energy surface and analysis of the trend-decisive energy terms-that can serve as a guide for carrying out the analysis of any given reaction of interest within hours to days, depending on the size of the molecular system.

PyFrag 2019-Automating the exploration and analysis of reaction mechanisms

We present a substantial update to the PyFrag 2008 program, which was originally designed to perform a fragment-based activation strain analysis along a provided potential energy surface. The original PyFrag 2008 workflow facilitated the characterization of reaction mechanisms in terms of the intrinsic properties, such as strain and interaction, of the reactants. The new PyFrag 2019 program has automated and reduced the time-consuming and laborious task of setting up, running, analyzing, and visualizing computational data from reaction mechanism studies to a single job. PyFrag 2019 resolves three main challenges associated with the automated computational exploration of reaction mechanisms: it (1) computes the reaction path by carrying out multiple parallel calculations using initial coordinates provided by the user; (2) monitors the entire workflow process; and (3) tabulates and visualizes the final data in a clear way. The activation strain and canonical energy decomposition results that are generated relate the characteristics of the reaction profile in terms of intrinsic properties (strain, interaction, orbital overlaps, orbital energies, populations) of the reactant species. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.

Energy Decomposition Analyses Reveal the Origins of Catalyst and Nucleophile Effects on Regioselectivity in Nucleopalladation of Alkenes

Nucleopalladation is one of the most common mechanisms for Pd-catalyzed hydro- and oxidative functionalization of alkenes. Due to the electronic bias of the π-alkene-palladium complexes, nucleopalladations with terminal aliphatic alkenes typically deliver the nucleophile to the more substituted sp² carbon to form the Markovnikov-selective products. The selective formation of the anti-Markovnikov nucleopalladation products requires the inherent electronic effects to be overridden, which is still a significant challenge for reactions with simple aliphatic alkenes. Because the interactions between the nucleophile and the alkene substrate are influenced by a complex combination of multiple types of steric and electronic effects, a thorough understanding of the interplay of these underlying interactions is needed to rationalize and predict the regioselectivity. Here, we employ an energy decomposition approach to quantitatively separate the different types of nucleophile-substrate interactions, including steric, electrostatic, orbital interactions, and dispersion effects, and to predict the impacts of each factor on regioselectivity. We demonstrate the use of this approach on the origins of catalyst-controlled anti-Markovnikov-selectivity in Hull's Pd-catalyzed oxidative amination reactions. In addition, we evaluated the regioselectivity in a series of nucleopalladation reactions with different neutral and anionic Pd catalysts and N- and O-nucleophiles with different steric and electronic properties. On the basis of these computational analyses, a generalized scheme is established to identify the dominant nucleophile-substrate interaction affecting the regioselectivity of nucleopalladations with different Pd catalysts and nucleophiles.

Theoretical study of the ligand effect on NHC–cobalt-catalyzed hydrogenation of ketones

Theoretical study of ketone hydrogenation revealed that the catalyst regeneration step is more sensitive to the ligand effect.

Factors Controlling the Diels-Alder Reactivity of Hetero-1,3-Butadienes

We have quantum chemically explored the Diels-Alder reactivities of a systematic series of hetero-1,3-butadienes with ethylene by using density functional theory at the BP86/TZ2P level. Activation strain analyses provided physical insight into the factors controlling the relative cycloaddition reactivity of aza- and oxa-1,3-butadienes. We find that dienes with a terminal heteroatom, such as 2-propen-1-imine (NCCC) or acrolein (OCCC), are less reactive than the archetypal 1,3-butadiene (CCCC), primarily owing to weaker orbital interactions between the more electronegative heteroatoms with ethylene. Thus, the addition of a second heteroatom at the other terminal position (NCCN and OCCO) further reduces the reactivity. However, the introduction of a nitrogen atom in the backbone (CNCC) leads to enhanced reactivity, owing to less Pauli repulsion resulting from polarization of the diene HOMO in CNCC towards the nitrogen atom and away from the terminal carbon atom. The Diels-Alder reactions of ethenyl-diazene (NNCC) and 1,3-diaza-butadiene (NCNC), which contain heteroatoms at both the terminal and backbone positions, are much more reactive due to less activation strain compared to CCCC.

Ruthenium(II)-Catalyzed C-H Difluoromethylation of Ketoximes: Tuning the Regioselectivity from the meta to the para Position

A highly para-selective C_Ar -H difluoromethylation of ketoxime ethers under ruthenium catalysis has been developed. A wide variety of ketoxime ethers are compatible with the reaction, which leads to the corresponding para-difluoromethylated products in moderate to good yield. A mechanistic study clearly showed that chelation-assisted cycloruthenation is the key factor in the para selectivity of the difluoromethylation of ketoxime ethers. Density functional theory was used to gain a theoretical understanding of the para selectivity.

C–H bond cleavage occurring on a Rh(v) intermediate: a theoretical study of Rh-catalyzed arene azidation

Our theoretical calculations indicated that the oxidation of Rh(iii) to Rh(v) by PhI(OAc)OTs is a facile process. Subsequent electrophilic deprotonation was shown to occur from a Rh(v) intermediate rather than a Rh(iii) intermediate.

Fluorine substituent effect on the stereochemistry of catalyzed and non-catalyzed Diels–Alder reactions. The case of R-butenone with cyclopentadiene: a computational assessment of the mechanism

A semiquantitative prediction of stereoselectivity due to substitutions of dienophile is obtained.

Bioinspired Total Synthesis of Homodimericin A

Homodimericin A is a remarkable fungal metabolite. This highly oxygenated racemic unsaturated polyketide poses a significant synthetic challenge owing to its sterically demanding central cagelike core containing eight contiguous stereogenic centers (including three quaternary stereocenters) and several carbonyl functionalities. On the basis of its proposed biogenetic synthesis, we designed a total synthesis of homodimericin A that proceeds in seven steps and features a double Michael reaction, an intramolecular Diels-Alder reaction, and an ene reaction.