Portable Models for Entropy Effects on Kinetic Selectivity

Woodward and Hoffmann. Hoffmann and Woodward. A Close Collaboration Had Yet to Begin

In 1965, R. B. Woodward and Roald Hoffmann published five communications in the Journal of the American Chemical Society in which they outlined the mechanisms of electrocyclizations, cycloadditions, and sigmatropic reactions - today known as the Woodward-Hoffmann rules. Over the next several years, the organic chemistry community rushed to test the validity of the W-H rules and expand the range of reactions covered by them. Meanwhile, Woodward and Hoffmann were besieged with invitations to lecture and write expositions on these concepts. In this publication, I present an analysis of Woodward and Hoffmann's next publications in 1966 and 1967 on the W-H rules. Two of these publications were based on lectures Woodward or Hoffmann presented in late 1965 and 1966. I also discuss their own continuing research on the topic in this time period (all by Hoffmann; none by Woodward). I conclude that the assumed intimate collaboration of Woodward and Hoffmann had actually not yet begun.

N-Oxide Insertion into LDA Dimeric Aggregates for Azomethine Ylide Formation: Explicit Solvation in Quantum Mechanical Treatment of Polarized Intermediates

The physical model used to compute natural phenomena is crucial for accurate structural and mechanism elucidation. Specifically, we examine the mechanistic consequences of an explicit LDA dimer, THF, and N-oxide aggregate formation at the rate-limiting step for two competing reaction pathways involving nitrogen-oxygen dissociation and alpha-hydrogen deprotonation for azomethine ylide formation. We compute the free energies of activation using the M06-2x, B3LYP, and HCTH407 functionals and second-order Møller-Plesset perturbation theory with Dunning's correlation consistent basis sets cc-pV[D,T]Z, and corrected entropy by using Whitesides' free volume theory. Our discrete-continuum approach uses Tomasi's polarizable continuum model to complement the quantum system by incorporating bulk solvent effects. Building off the LDA aggregation work developed by Collum and coworkers, we demonstrate that the explicit inclusion of solvent can have a profound impact on the predicted free energy barriers and alignment with experimental product distributions. In the polarized N-oxide system, the use of a more sophisticated and balanced model of the reaction mechanism underscores the importance of explicit solvent and the correct pattern of aggregation. Our results identify a unique aggregate that incorporates the N-oxide, THF, and LDA for azomethine ylide formation, which suggests a third dimension to the John Pople diagram to enhance the accuracy through model sophistication.

Interplay between Energy and Entropy Mediates Ambimodal Selectivity of Cycloadditions

One ambimodal transition state can lead to the formation of multiple products. However, it remains fundamentally unknown how the energy and entropy along the post-TS pathways mediate ambimodal selectivity. Here, we investigated the energy and entropy profiles along the post-TS pathways in four [4 + 2]/[6 + 4] cycloadditions. We observe that the pathway leading to the minor product involves a more pronounced entropic trap. These entropic traps, resulting from the conformational change in the dynamic course of ring closure, act as a reservoir of longer-lived dynamic intermediates that roam on the potential energy surface and have a higher likelihood of redistributing to form the other product. The SpnF-catalyzed Diels-Alder reaction produces [4 + 2] and [6 + 4] adducts with nearly equal product distribution and relatively flat energy profiles, in contrast to other cycloadditions. Unexpectedly, the entropy profiles for these two adducts are distinctly different. The formation of the [6 + 4] adduct encounters an entropic barrier acting as a dynamical bottleneck, while the [4 + 2] adduct involves a substantial entropic trap to maintain long-lived intermediates. These opposing effects hinder both product formations and likely cancel each other out so that an equal product distribution is observed.

On the prediction by density functional theory of entropies in solution within implicit solvation models

CONTEXT

Entropies are fundamental contributions to Gibbs energies that carry important chemical information, in particular when investigating reaction mechanisms. However, evaluating them in solution is far from being straightforward. In this paper, we focus on its evaluation within the framework of implicit solvation models. To this aim, successive corrections (with increased complexity) involving only contributions available from any standard quantum chemistry code and macroscopic solvent properties are built and assessed by comparison to more than one hundred experimental entropy values measured in a liquid phase. It turns out that significant improvement with respect to the standard ideal gas approximation can be achieved at an almost negligible computational cost, affording a robust and transferable predictive model.

METHODS

DFT calculations with the ADF software at the PBE or PBE0/TZ2P level of theory with COSMO solvent model. Python scripts for regressions.

Going Beyond Woodward and Hoffmann's Electrocyclizations and Cycloadditions: Sigmatropic Rearrangements

On June 1, 1965, R. B. Woodward and Roald Hoffmann published their third communication in the Journal of the American Chemical Society in which they applied orbital symmetry control to explain the mechanism of a wide variety of valence isomerizations that they termed "sigmatropic reactions." This publication reveals the research trajectory taken by Hoffmann from which this portion of the no-mechanism problem was solved. Hoffmann used five different quantum chemical tools, all based on either extended Hückel theoretical calculations or frontier molecular orbital theory, in his research. Hoffmann's laboratory notebooks and his three draft manuscripts along with Woodward's four subsequent drafts have survived the past 59 years and provide an excellent window into the thinking and manuscript-writing processes used by these Nobel laureates in February-April 1965.

Eureka Moments Shared by Chemists. Hints at Enhancing One's Own Creativity (and Even One's Joy)

Eureka moments can occur during all steps of discovery. Eighteen chemists and molecular scientists described their Eureka moments herein. Hints at fostering one's own Eureka moments are provided.

Exceptions, Paradoxes, and Their Resolutions in Chemical Reactivity

Progress in chemistry has primarily been framed through inductive processes, leading to the frequent emergence of exceptions and unexpected reactivities. These anomalies─ranging from surprising reactivity trends and paradoxical understandings to unanticipated parameter influences and unexpected successes or failures in synthetic methods─offer valuable insights that can drive scientific discovery. While it is commonly accepted that such exceptions can drive progress, many have been passively accepted without being explored for opportunities. Although numerous chemists have addressed exceptions and refined chemical models and theories, employing a systematic framework for actively exploring and understanding the underlying causes of exceptions could resolve paradoxes in broader contexts and create a greater impact than treating anomalies as isolated occurrences. This perspective demonstrates a proactive epistemic approach to uncovering the opportunities presented by exceptions and promotes deliberate, thoughtful engagement with paradoxes and anomalies. While the examples primarily focus on physical organic chemistry, the concepts are broadly applicable across various fields in chemical science. The thinking framework presented here is neither exhaustive nor prescriptive, but it outlines one of many potentially possible ways to inspire further development in how these anomalies could be harnessed for advancement.

Counterintuitive Isomerization of TFSI- and TFSI--Cation Correlated Isomerization: Insights into the Low Melting Points of TFSI--Based Ionic Liquids

Ionic liquids (ILs), particularly bis(trifluoromethane)sulfonamide (TFSI-)-based ILs, have attracted substantial attention in electrochemical energy storage, ionic gating for superconductivity, and iontronic sensing. However, underestimating TFSI- isomerization and overlooking TFSI--cation correlation make the origin of their most characteristic property, low melting points (Tm), ambiguous. Traditional static electronic structure calculations assume that C2-symmetric trans enantiomers of TFSI- easily isomerize into cis enantiomers through four symmetrically equivalent pathways over a barrier of 7.1 kJ mol-1. Herein, ab initio molecular dynamics (AIMD) simulations combined with metadynamics reveal that the unusual oscillation of the central nitrogen atom promotes TFSI- to undergo complex isomerization. Specifically, asymmetric trans-to-cis diastereomers of TFSI- experience restricted interconversion (20-52 kJ mol-1) through four distinct asymmetric pathways. The adaptive oscillation and hybridization of chiral nitrogen boost nN → σ*S-C negative hyperconjugation for stabilizing conformational structures and enlarging energy barriers. The orientational distortion of oxygen atoms' lone pairs enhances conjugation but breaks the C2-symmetry. The coexistence of both helicity and chiral nitrogen breaks the enantiomeric relationship. Furthermore, Raman characterization and AIMD simulations confirm the positive correlation between the relative stability of cis-TFSI- and its countercation's polarity. TFSI- and countercations make a mutual conformational selection instead of free isomerization. Surprisingly, Tm increases with the cation-dependent conformational rigidity of TFSI-, offering new fundamental insights into the low Tm of ILs. This descriptor encoding the dependence of thermal property on cation-anion correlated isomerization provides material design guidelines and property prediction capability.

Revisiting a classic carbocation - DFT, coupled-cluster, and ab initio molecular dynamics computations on barbaralyl cation formation and rearrangements

Density functional theory computations were used to model the formation and rearrangement of the barbaralyl cation (C9H+ 9). Two highly delocalized minima were located for C9H+ 9, one of C s symmetry and the other of D 3h symmetry, with the former having lower energy. Quantum chemistry-based NMR predictions affirm that the lower energy structure is the best match with experimental spectra. Partial scrambling was found to proceed through a C 2 symmetric transition structure associated with a barrier of only 2.3 kcal mol-1. The full scrambling was found to involve a C 2v symmetric transition structure associated with a 5.0 kcal mol-1 barrier. Ab initio molecular dynamics simulations initiated from the D 3h C9H+ 9 structure revealed its connection to six minima, due to the six-fold symmetry of the potential energy surface. The effects of tunneling and boron substitution on this complex reaction network were also examined.

Mechanism of Methyl Transfer Reaction between CH3Co(dmgBF2)2py and PPh3Ni(Triphos)

DFT calculations were performed for the methyl group transfer reaction between CH3Co (dmgBF2)py and PPh3Ni(Triphos). The reaction mechanism and its energetics were investigated. This reaction is relevant to the catalytic mechanism of the enzyme acetyl coenzyme A synthase. BP86 and PBE functionals and dispersion corrections were used. It was found that intermolecular interactions are very important for this reaction. The influence of the solvent on the reaction was studied.

Combined Computational and Experimental Study Reveals Complex Mechanistic Landscape of Brønsted Acid-Catalyzed Silane-Dependent P═O Reduction

The reaction mechanism of Brønsted acid-catalyzed silane-dependent P═O reduction has been elucidated through combined computational and experimental methods. Due to its remarkable chemo- and stereoselective nature, the Brønsted acid/silane reduction system has been widely employed in organophosphine-catalyzed transformations involving P(V)/P(III) redox cycle. However, the full mechanistic profile of this type of P═O reduction has yet to be clearly established to date. Supported by both DFT and experimental studies, our research reveals that the reaction likely proceeds through mechanisms other than the widely accepted "dual activation mode by silyl ester" or "acid-mediated direct P═O activation" mechanism. We propose that although the reduction mechanisms may vary with the substitution patterns of silane species, Brønsted acid generally activates the silane rather than the P═O group in transition structures. The proposed activation mode differs significantly from that associated with traditional Brønsted acid-catalyzed C═O reduction. The uniqueness of P═O reduction originates from the dominant Si/O═P orbital interactions in transition structures rather than the P/H-Si interactions. The comprehensive mechanistic landscape provided by us will serve as a guidance for the rational design and development of more efficient P═O reduction systems as well as novel organophosphine-catalyzed reactions involving P(V)/P(III) redox cycle.

Metal-Free Activation of Molecular Oxygen by Quaternary Ammonium-Based Ionic Liquid: A Detail Mechanistic Study

Most oxidation processes in common organic synthesis and chemical biology require transition metal catalysts or metalloenzymes. Herein, we report a detailed mechanistic study of a metal-free oxygen (O2) activation protocol on benzylamine/alcohols using simple quaternary alkylammonium-based ionic liquids to produce products such as amide, aldehyde, imine, and in some cases, even aromatized products. NMR and various control experiments established the product formation and reaction mechanism, which involved the conversion of molecular oxygen into a hydroperoxyl radical via a proton-coupled electron transfer process. Detection of hydrogen peroxide in the reaction medium using colorimetric analysis supported the proposed mechanism of oxygen activation. Furthermore, first-principles calculations using density functional theory (DFT) revealed that reaction coordinates and transition state spin densities have a unique spin conversion of triplet oxygen leading to formation of singlet products via a minimum energy crossing point. In addition to DFT, domain-based local pair natural orbital coupled cluster, (DLPNO-CCSD(T)), and complete active space self-consistent field, CASSCF(20,14) methods complemented the above findings. Partial density of states analysis showed stabilization of π* orbital of oxygen in the presence of ionic liquid, making it susceptible to hydrogen abstraction in a mild, metal-free condition. Inductively coupled plasma atomic emission spectroscopic (ICP-AES) analysis of reactant and ionic liquids clearly showed the absence of any significant transition metal contamination. The current results described the origin of O2 activation within the context of molecular orbital (MO) theory and opened up a new avenue for the use of ionic liquids as inexpensive, multifunctional and high-performance alternative to metal-based catalysts for O2 activation.

Monitoring the Evolution of Relative Product Populations at Early Times during a Photochemical Reaction

Identifying multiple rival reaction products and transient species formed during ultrafast photochemical reactions and determining their time-evolving relative populations are key steps toward understanding and predicting photochemical outcomes. Yet, most contemporary ultrafast studies struggle with clearly identifying and quantifying competing molecular structures/species among the emerging reaction products. Here, we show that mega-electronvolt ultrafast electron diffraction in combination with ab initio molecular dynamics calculations offer a powerful route to determining time-resolved populations of the various isomeric products formed after UV (266 nm) excitation of the five-membered heterocyclic molecule 2(5H)-thiophenone. This strategy provides experimental validation of the predicted high (∼50%) yield of an episulfide isomer containing a strained three-membered ring within ∼1 ps of photoexcitation and highlights the rapidity of interconversion between the rival highly vibrationally excited photoproducts in their ground electronic state.

The Intrinsic Barrier Width and Its Role in Chemical Reactivity

Chemical reactions are in virtually all cases understood and explained on the basis of depicting the molecular potential energy landscape, i.e., the change in atomic positions vs the free-energy change. With such landscapes, the features of the reaction barriers solely determine chemical reactivities. The Marcus dissection of the barrier height (activation energy) on such a potential into the thermodynamically independent (intrinsic) and the thermodynamically dependent (Bell-Evans-Polanyi) contributions successfully models the interplay of reaction rate and driving force. This has led to the well-known and ubiquitously used reactivity paradigm of "kinetic versus thermodynamic control". However, an analogous dissection concept regarding the barrier width is absent. Here we define and outline the concept of intrinsic barrier width and the driving force effect on the barrier width and report experimental as well as theoretical studies to demonstrate their distinct roles. We present the idea of changing the barrier widths of conformational isomerizations of some simple aromatic carboxylic acids as models and use quantum mechanical tunneling (QMT) half-lives as a read-out for these changes because QMT is particularly sensitive to barrier widths. We demonstrate the distinct roles of the intrinsic and the thermodynamic contributions of the barrier width on QMT half-lives. This sheds light on resolving conflicting trends in chemical reactivities where barrier widths are relevant and allows us to draw some important conclusions about the general relevance of barrier widths, their qualitative definition, and the consequences for more complete descriptions of chemical reactions.

Revolutions in Chemistry: Assessment of Six 20th Century Candidates (The Instrumental Revolution; Hückel Molecular Orbital Theory; Hückel's 4n + 2 Rule; the Woodward-Hoffmann Rules; Quantum Chemistry; and Retrosynthetic Analysis)

Six 20th century candidates for revolutions in chemistry are examined, using a definitional scheme published recently by the author. Six groupings of 13 characteristics of revolutions in science are considered: causes and birthings of revolutions, relationships between the old and the new, conceptual qualities of the candidate revolutions, instrumental and methodological functions, social construction of knowledge and practical considerations, and testimonials. The Instrumental Revolution was judged to be a revolution in chemistry because of the enormous increase in community-wide knowledge provided by the new instruments and the intentionality in the identification of specific target instruments, in the mindfulness in their design, manufacture, testing, use, and ultimately commercialization. The Woodward-Hoffmann rules were judged to precipitate the Quantum Chemistry Revolution because of theoretical, practical, and social construction of knowledge characteristics. Neither Hückel molecular orbital theory nor Hückel's 4n + 2 rule was considered an initiator of a revolution in chemistry but rather participants in the Quantum Chemistry Revolution. Retrosynthetic analysis was not judged to initiate a revolution in chemistry.

The entropic penalty for associative reactions and their physical treatment during routine computations

A systematic study of the entropic penalty for associative reactions is presented. It is shown that computed solution-phase Gibbs free energies typically overestimate entropic contributions. This entropic penalty for associative reactions in solution, i.e., if the number of particles decreases along the reaction coordinate (sum of stoichiometric numbers ), originates from the insufficient treatment of entropic effects by implicit solvent models. We propose an additive correction scheme to Gibbs free energies that is suitable for routine applications by non-expert users. This correction is based on Garza's formalism for the solution-phase entropy [A. J. Garza, J. Chem. Theory Comput., 2019, 15, 3204.] that is physically sound and embedded into an efficient black-box type algorithm. To critically evaluate the entropic penalty and its proposed treatment, we compiled an experimental benchmark set of 31 Δ_rG and 22 in 15 different solvents. Using a representative best-practice computational protocol (at wave function theory (WFT) based DLPNO-CCSD(T) and density functional theory (DFT) based revDSD-PBEP86-D4 level with an implicit solvent model), we determined a sizeable entropic penalty ranging from 2-11 kcal mol^-1. Using the correction scheme presented herein, the entropic penalty is corrected to the chemical accuracy of ≤1 kcal mol^-1 (WFT and DFT). The same applies to at the WFT level. Barriers at the DFT level are overestimated by 2 kcal mol^-1 (classic) and underestimated by 2 kcal mol^-1 (corrected). This effect is attributed to the finding that barriers computed at the DFT level are systematically 2-3 kcal mol^-1 lower than barriers obtained with WFT.

Computational Strategies for Entropy Modeling in Chemical Processes

Computational simulations of entropy are important in understanding the thermodynamic forces that drive chemical reactions on a molecular scale. In recent years, various algorithms have been developed and applied in conjunction with molecular modeling techniques to evaluate the change of entropy in solvation, hydrophobic interactions, and chemical reactions. The aim of this review is to highlight four specific computational entropy calculation methods: normal mode analysis, free volume theory, two-phase thermodynamics, and configurational entropy modeling. The technical aspects, applications, and limitations of each method will be discussed in detail.

Why Woodward and Hoffmann? And Why 1965?

Previous publications in this series on the history of the development of the Woodward-Hoffmann rules revealed why Woodward and Hoffmann were prime candidates to solve the pericyclic no-mechanism problem. This publication explains why it was the collaborative team of R. B. Woodward and Roald Hoffmann who did solve this mechanistic problem in a series of five communications in the Journal of the American Chemical Society in 1965. That is, the reasons why Woodward and Hoffmann were the perfect team, and why their individual capabilities, experiences, and qualities provided the perfect synergy are described. In part, this was the right time and the right place for them both, but the synergies were fundamental, intrinsic and idiosyncratic as a collaborative pair. Their orbital symmetry rules provided the mechanism of all concerted pericyclic reactions including electrocyclizations, cycloadditions, and sigmatropic rearrangements. Why it was 1965 and not earlier is also discussed.