Computational Organic Chemistry: The Frontier for Understanding and Designing Bioorthogonal Cycloadditions.

Computational organic chemistry has become a valuable tool in the field of bioorthogonal chemistry, offering insights and aiding in the progression of this branch of chemistry. In this review, I present an overview of computational work in this field, including an exploration of both the primary computational analysis methods used and their application in the main areas of bioorthogonal chemistry: (3 + 2) and [4 + 2] cycloadditions. In the context of (3 + 2) cycloadditions, detailed studies of electronic effects have informed the evolution of cycloalkyne/1,3-dipole cycloadditions. Through computational techniques, researchers have found ways to adjust the electronic structure via hyperconjugation to enhance reactions without compromising stability. For [4 + 2] cycloadditions, methods such as distortion/interaction analysis and energy decomposition analysis have been beneficial, leading to the development of bioorthogonal reactants with improved reactivity and the creation of orthogonal reaction pairs. To conclude, I touch upon the emerging fields of cheminformatics and machine learning, which promise to play a role in future reaction discovery and optimization.

Is Mn(I) More Promising Than Fe(II)-A Comparison of Mn vs Fe Complexes for Olefin Metathesis.

Olefin metathesis is one of the most significant transformations in organic chemistry and is an excellent example for efficient homogeneous catalysis. Although most currently used catalysts are primarily based on 4d and 5d metals, cycloaddition and cycloreversion reactions can also be attributed to first-row transition metals, such as Fe. Surprisingly, the potential of Mn(I)-based catalysts for olefin metathesis has been unexplored despite their prominence in homogeneous catalysis and their diagonal relationship to Ru(II). In the present study, we have investigated the prospective capabilities of Mn complexes for cycloaddition and reversion reactions using density functional theory. Therefore, we have initially compared the literature known iron model systems and their isoelectronic Mn counterparts regarding their reactivity and electronic structure. Next, we constructed potential Mn complexes derived from synthetically accessible species, including carbonyl ligands and obeying octahedral geometry. Based on thermodynamic parameters and the calculation of electronic descriptors, we were able to validate the isodiagonal relationship. Our study serves as guidance for the experimental chemist.

Directionality of Halogen-Bonds: Insights from 2D Energy Decomposition Analysis.

Halogen bonds are typically observed to have a linear arrangement with a 180° angle between the nucleophile and the halogen bond acceptor X-R. This linearity is commonly explained using the σ-hole model, although there have been alternative explanations involving exchange repulsion forces. We employ two-dimensional Distortion/Interaction and Energy Decomposition Analysis to examine the archetypal H3 N⋯X2 halogen bond systems. Our results indicate that although halogen bonds are predominantly electrostatic, their directionality is largely due to decreased Pauli repulsion in linear configurations as opposed to angled ones in the I2 and Br2 systems. As we move to the smaller halogens, Cl2 and F2 , the influence of Pauli repulsion diminishes, and the energy surface is shaped by orbital interactions and electrostatic forces. These results support the role of exchange repulsion forces in influencing the directionality of strong halogen bonds. Additionally, we demonstrate that the 2D Energy Decomposition Analysis is a useful tool for enhancing our understanding of the nature of potential energy surfaces in noncovalent interactions.

How cycloalkane fusion enhances the cycloaddition reactivity of dibenzocyclooctynes.

Dibenzoannulated cyclooctynes have emerged as valuable compounds for bioorthogonal reactions. They are commonly used in combination with azides in strain-promoted 1,3-dipolar cycloadditions. They are typically, however, unreactive towards 3,6-disubstituted tetrazines in inverse electron-demand Diels-Alder cycloadditions. Recently a dibenzoannulated bicyclo[6.1.0]nonyne derivative (DMBO) with a cyclopropane fused to the cyclooctyne core was described, which showed surprising reactivity towards tetrazines. To elucidate the unusual reactivity of DMBO, we performed density functional theory calculations and revealed that a tub-like structure in the transition state results in a much lower activation barrier than in the absence of cyclopropane fusion. The same transition state geometry is found for different cycloalkanes fused to the cyclooctyne core albeit higher activation barriers are observed for increased ring sizes. This conformation is energetically unfavored for previously known dibenzoannulated cyclooctynes and allows tetrazines and azides to approach DMBO from the face rather than the edge, a trajectory that was hitherto not observed for this class of activated dieno- and dipolarophiles.

To Bond or Not to Bond: Metal-Metal Interaction in Heterobimetallic Rare-Earth Metal-Silver Complexes.

The reaction of 2,4-tBu2-6-(PPh2)PhOH (HOArP) with silver(I) triflate in a 3:1 molar ratio gave the mononuclear coinage metal complex (HOArP-κP)3AgIOTf (1). Treatment of HOArP with LnIII[N(SiMe3)2]3 (Ln = La, Sm, Y, Yb) in a 3:1 molar ratio yielded the mononuclear rare-earth metal complexes LnIII(OArP-κ2O,P)3 (2-Ln). The heterobimetallic rare-earth metal-silver complexes LnIII(OTf)(µ-OArP-1κ1O,2κ1P)3AgI (3-Ln) were prepared from monometallic precursors by reactions of equimolar amounts of 1 with LnIII[N(SiMe3)2]3 or 2-Ln with silver(I) triflate, respectively. The compounds were characterized by NMR, ultraviolet-visible (UV-vis), and infrared (IR) spectroscopy, single-crystal X-ray diffraction, elemental analysis, and the effective magnetic moments of the paramagnetic complexes were determined via the Evans NMR method. Computational studies were conducted on 3-La and 3-Y.

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.

"Holographic" Autostereoscopic Displays: A Perspective on Their Technology and Potential Impact in Chemistry.

The three-dimensional arrangement of atoms in molecules is essential for understanding their properties and behavior. Traditional 2D representations and digital 3D models presented on 2D media often fall short in conveying the complexity of molecular structures. Autostereoscopic displays, often marketed as "holographic" displays, pose a potential solution to this challenge. These displays, with their multi-view and single-view configurations, promise to advance chemistry education and research by offering accurate 3D representations with depth and parallax. In this perspective, I delve into the possibilities and limitations of autostereoscopic displays in chemistry, discussing the underlying technology and potential applications, from research to teaching and science communication. Multi-view autostereoscopic displays excel in facilitating collaborative work by enabling multiple viewers to simultaneously perceive the same 3D structure from different angles. However, they currently suffer from low resolution and high cost, which could limit their immediate widespread adoption. Conversely, single-view autostereoscopic displays with eye-tracking, while limited to one viewer at a time, provide higher resolution at a lower cost, thus suggesting that they might become the technology of the future given the balance of price to performance. Despite current limitations, autostereoscopic displays possess undeniable potential for shaping the future of chemistry education and research.

Orthogonal Inverse-Electron-Demand Cycloaddition Reactions Controlled by Frontier Molecular Orbital Interactions.

Chemoselective pairs of bioorthogonal reactants enable the simultaneous labeling of several biomolecules. Here, we access orthogonal click reactions by exploiting differences in frontier molecular orbital interaction energies in transition states. We establish that five-membered cyclic dienes are inert to isonitriles but readily react with strained alkynes, while tetrazines with bulky substituents readily react with isonitriles. Strained alkynes show an opposite reactivity pattern. The approach was demonstrated by orthogonally labeling two proteins with different fluorophores.

Substituent Effects in Bioorthogonal Diels-Alder Reactions of 1,2,4,5-Tetrazines.

1,2,4,5-Tetrazines are increasingly used as reactants in bioorthogonal chemistry due to their high reactivity in Diels-Alder reactions with various dienophiles. Substituents in the 3- and 6-positions of the tetrazine scaffold are known to have a significant impact on the rate of cycloadditions; this is commonly explained on the basis of frontier molecular orbital theory. In contrast, we show that reactivity differences between commonly used classes of tetrazines are not controlled by frontier molecular orbital interactions. In particular, we demonstrate that mono-substituted tetrazines show high reactivity due to decreased Pauli repulsion, which leads to a more asynchronous approach associated with reduced distortion energy. This follows the recent Vermeeren-Hamlin-Bickelhaupt model of reactivity increase in asymmetric Diels-Alder reactions. In addition, we reveal that ethylene is not a good model compound for other alkenes in Diels-Alder reactions.

Oxidative Desymmetrization Enables the Concise Synthesis of a trans-Cyclooctene Linker for Bioorthogonal Bond Cleavage.

Modified trans-cyclooctenes (TCO) are capable of highly efficient molecular manipulations in biological environments, driven by the bioorthogonal reaction with tetrazines (Tz). The development of click-cleavable TCO has fueled the field of in vivo chemistry and enabled the design of therapeutic strategies that have already started to enter the clinic. A key element for most of these approaches is the implementation of a cleavable TCO linker. So far, only one member of this class has been developed, a compound that requires a high synthetic effort, mainly to fulfill the multilayered demands on its chemical structure. To tackle this limitation, we developed a dioxolane-fused cleavable TCO linker (dcTCO) that can be prepared in only five steps by applying an oxidative desymmetrization to achieve diastereoselective introduction of the required functionalities. Based on investigation of the structure, reaction kinetics, stability, and hydrophilicity of dcTCO, we demonstrate its bioorthogonal application in the design of a caged prodrug that can be activated by in-situ Tz-triggered cleavage to achieve a remarkable >1000-fold increase in cytotoxicity.

Cycloaddition Reactivities Analyzed by Energy Decomposition Analyses and the Frontier Molecular Orbital Model.

This Account describes our quest to understand and predict organic reactivity, a principal goal of physical and theoretical organic chemistry. The focus is on the development and testing of models for the prediction of cycloaddition reactivities and selectivities. We describe the involvement of the Houk group, and other groups, in the evolution of theoretical models that can achieve ever greater accuracy as well as provide practical heuristic models for understanding and prediction.Is the venerable frontier molecular orbital (FMO) model, the basis of Kenichi Fukui's 1981 Nobel Prize, still useful, or must it be replaced with more advanced models? In particular, models such as Conceptual Density Functional, the Pauli Exclusion Model, and the recent popularity of Electrostatic Potential Plots and Dispersion Energies have not only added to our understanding, but they have also created uncertainty about whether the simple FMO heuristic model has a place in 21st century discussions. This Account addresses this issue and asserts the value of the FMO model.Beginning with brief descriptions of selected models for cycloaddition reactivity starting with early donor-acceptor (nucleophile-electrophile) charge-transfer concepts, this Account reviews Fukui's frontier molecular orbital model, Salem and Klopman's orbital, electrostatic and Pauli repulsion model, the conceptual DFT model by Parr and later by Domingo and others, the recent Houk and Bickelhaupt Distortion/Interaction Activation Strain model, and the Bickelhaupt-Hamlin's Pauli-repulsion lowering model.Computations and analyses of four well-studied Diels-Alder cycloadditions, both normal and inverse electron-demand types, are presented. Most were studied earlier in our published work but are presented here with new insights from calculations with modern methods. Depending on the types of substrates (cycloaddends), the dominant factors controlling reactivity can be orbital interactions, electrostatics and polarization, or Pauli repulsion and dispersion effects, or a combination of all of these.By comparing orbital interactions, especially the frontier molecular orbital interactions, with the other factors that influence reactivity, we show why the FMO model is such a powerful─and theoretically meaningful─heuristic for understanding and predicting reactivity. We also present a method to understand Pauli repulsion effects on activation barriers, ρ(1.1). The use of a new reaction coordinate, the extent of Pauli repulsion along the reaction path, is advocated to emphasize the role of repulsive occupied orbital interactions on reactivity.Fukui's frontier molecular orbital model is effective because FMO interactions parallel all the quantities that influence reactivity. The FMO model continues to provide a practical model to understand and guide experiments.

Mechanistic Insights into the Reaction of Amidines with 1,2,3-Triazines and 1,2,3,5-Tetrazines.

1,2,3-Triazines and 1,2,3,5-tetrazines react rapidly, efficiently, and selectively with amidines to form pyrimidines/1,3,5-triazines, exhibiting an orthogonal reactivity with 1,2,4,5-tetrazine-based conjugation chemistry. Whereas the mechanism of the reaction of the isomeric 1,2,4-triazines and 1,2,4,5-tetrazines with alkenes is well understood, the mechanism of the 1,2,3-triazine/1,2,3,5-tetrazine-amidine reaction as well as its intrinsic reactivity remains underexplored. By using 15N-labeling, kinetic investigations, and kinetic isotope effect studies, complemented by extensive computational investigations, we show that this reaction proceeds through an addition/N2 elimination/cyclization pathway, rather than the generally expected concerted or stepwise Diels-Alder/retro Diels-Alder sequence. The rate-limiting step in this transformation is the initial nucleophilic attack of an amidine on azine C4, with a subsequent energetically favored N2 elimination step compared with a disfavored stepwise formation of a Diels-Alder cycloadduct. The proposed reaction mechanism is in agreement with experimental and computational results, which explains the observed reactivity of 1,2,3-triazines and 1,2,3,5-tetrazines with amidines.

Uncovering the Key Role of Distortion in Bioorthogonal Tetrazine Tools That Defy the Reactivity/Stability Trade-Off.

The tetrazine/trans-cyclooctene ligation stands out from the bioorthogonal toolbox due to its exceptional reaction kinetics, enabling multiple molecular technologies in vitro and in living systems. Highly reactive 2-pyridyl-substituted tetrazines have become state of the art for time-critical processes and selective reactions at very low concentrations. It is widely accepted that the enhanced reactivity of these chemical tools is attributed to the electron-withdrawing effect of the heteroaryl substituent. In contrast, we show that the observed reaction rates are way too high to be explained on this basis. Computational investigation of this phenomenon revealed that distortion of the tetrazine caused by intramolecular repulsive N-N interaction plays a key role in accelerating the cycloaddition step. We show that the limited stability of tetrazines in biological media strongly correlates with the electron-withdrawing effect of the substituent, while intramolecular repulsion increases the reactivity without reducing the stability. These fundamental insights reveal thus far overlooked mechanistic aspects that govern the reactivity/stability trade-off for tetrazines in physiologically relevant environments, thereby providing a new strategy that may facilitate the rational design of these bioorthogonal tools.

Synergistic Experimental and Computational Investigation of the Bioorthogonal Reactivity of Substituted Aryltetrazines.

Tetrazines (Tz) have been applied as bioorthogonal agents for various biomedical applications, including pretargeted imaging approaches. In radioimmunoimaging, pretargeting increases the target-to-background ratio while simultaneously reducing the radiation burden. We have recently reported a strategy to directly 18F-label highly reactive tetrazines based on a 3-(3-fluorophenyl)-Tz core structure. Herein, we report a kinetic study on this versatile scaffold. A library of 40 different tetrazines was prepared, fully characterized, and investigated with an emphasis on second-order rate constants for the reaction with trans-cyclooctene (TCO). Our results reveal the effects of various substitution patterns and moreover demonstrate the importance of measuring reactivities in the solvent of interest, as click rates in different solvents do not necessarily correlate well. In particular, we report that tetrazines modified in the 2-position of the phenyl substituent show high intrinsic reactivity toward TCO, which is diminished in aqueous systems by unfavorable solvent effects. The obtained results enable the prediction of the bioorthogonal reactivity and thereby facilitate the development of the next generation of substituted aryltetrazines for in vivo applications.

Direct Cu-mediated aromatic 18F-labeling of highly reactive tetrazines for pretargeted bioorthogonal PET imaging.

Pretargeted imaging can be used to visualize and quantify slow-accumulating targeting vectors with short-lived radionuclides such as fluorine-18 - the most popular clinically applied Positron Emission Tomography (PET) radionuclide. Pretargeting results in higher target-to-background ratios compared to conventional imaging approaches using long-lived radionuclides. Currently, the tetrazine ligation is the most popular bioorthogonal reaction for pretargeted imaging, but a direct 18F-labeling strategy for highly reactive tetrazines, which would be highly beneficial if not essential for clinical translation, has thus far not been reported. In this work, a simple, scalable and reliable direct 18F-labeling procedure has been developed. We initially studied the applicability of different leaving groups and labeling methods to develop this procedure. The copper-mediated 18F-labeling exploiting stannane precursors showed the most promising results. This approach was then successfully applied to a set of tetrazines, including highly reactive H-tetrazines, suitable for pretargeted PET imaging. The labeling succeeded in radiochemical yields (RCYs) of up to approx. 25%. The new procedure was then applied to develop a pretargeting tetrazine-based imaging agent. The tracer was synthesized in a satisfactory RCY of ca. 10%, with a molar activity of 134 ± 22 GBq µmol-1 and a radiochemical purity of >99%. Further evaluation showed that the tracer displayed favorable characteristics (target-to-background ratios and clearance) that may qualify it for future clinical translation.

Origin of Increased Reactivity in Rhenium-Mediated Cycloadditions of Tetrazines.

Pyridyl tetrazines coordinated to metals like rhenium have been shown to be more reactive in [4 + 2] cycloadditions than their uncomplexed counterparts. Using density functional theory calculations, we found a more favorable interaction energy caused by stronger orbital interactions as the origin of this increased reactivity. Additionally, the high regioselectivity is due to a greater degree of charge stabilization in the transition state, leading to the major product.

Lipophilicity and Click Reactivity Determine the Performance of Bioorthogonal Tetrazine Tools in Pretargeted In Vivo Chemistry.

The development of highly selective and fast biocompatible reactions for ligation and cleavage has paved the way for new diagnostic and therapeutic applications of pretargeted in vivo chemistry. The concept of bioorthogonal pretargeting has attracted considerable interest, in particular for the targeted delivery of radionuclides and drugs. In nuclear medicine, pretargeting can provide increased target-to-background ratios at early time-points compared to traditional approaches. This reduces the radiation burden to healthy tissue and, depending on the selected radionuclide, enables better imaging contrast or higher therapeutic efficiency. Moreover, bioorthogonally triggered cleavage of pretargeted antibody-drug conjugates represents an emerging strategy to achieve controlled release and locally increased drug concentrations. The toolbox of bioorthogonal reactions has significantly expanded in the past decade, with the tetrazine ligation being the fastest and one of the most versatile in vivo chemistries. Progress in the field, however, relies heavily on the development and evaluation of (radio)labeled compounds, preventing the use of compound libraries for systematic studies. The rational design of tetrazine probes and triggers has thus been impeded by the limited understanding of the impact of structural parameters on the in vivo ligation performance. In this work, we describe the development of a pretargeted blocking assay that allows for the investigation of the in vivo fate of a structurally diverse library of 45 unlabeled tetrazines and their capability to reach and react with pretargeted trans-cyclooctene (TCO)-modified antibodies in tumor-bearing mice. This study enabled us to assess the correlation of click reactivity and lipophilicity of tetrazines with their in vivo performance. In particular, high rate constants (>50 000 M-1 s-1) for the reaction with TCO and low calculated logD 7.4 values (below -3) of the tetrazine were identified as strong indicators for successful pretargeting. Radiolabeling gave access to a set of selected 18F-labeled tetrazines, including highly reactive scaffolds, which were used in pretargeted PET imaging studies to confirm the results from the blocking study. These insights thus enable the rational design of tetrazine probes for in vivo application and will thereby assist the clinical translation of bioorthogonal pretargeting.

Origins of Endo Selectivity in Diels-Alder Reactions of Cyclic Allene Dienophiles.

Strained cyclic allenes, first discovered in 1966 by Wittig and co-workers, have recently emerged as valuable synthetic building blocks. Previous experimental investigations, and computations reported here, demonstrate that the Diels-Alder reactions of furans and pyrroles with 1,2-cyclohexadiene and oxa- and azaheterocyclic analogs proceed with endo selectivity. This endo selectivity gives the adduct with the allylic saturated carbon of the cyclic allene endo to the diene carbons. The selectivity is very general and useful in synthetic applications. Our computational study establishes the origins of this endo selectivity. We analyze the helical frontier molecular orbitals of strained cyclic allenes and show how secondary orbital and electrostatic effects influence stereoselectivity. The LUMO of carbon-3 of the allene (C-3 is not involved in primary orbital interactions) interacts in a stabilizing fashion with the HOMO of the diene in such a way that the carbon of the cyclic allene attached to C-1 favors the endo position in the transition state. The furan LUMO, allene HOMO interaction reinforces this preference. These mechanistic studies are expected to prompt the further use of long-avoided strained cyclic allenes in chemical synthesis.

The Influence of Substitution on Thiol-Induced Oxanorbornadiene Fragmentation.

Oxanorbornadienes (ONDs) undergo facile Michael addition with thiols and then fragment by a retro-Diels-Alder (rDA) reaction, a unique two-step sequence among electrophilic cleavable linkages. The rDA reaction rate was explored as a function of the furan structure, with substituents at the 2- and 5-positions found to be the most influential and the fragmentation rate to be inversely correlated with electron-withdrawing ability. Density functional theory calculations provided an excellent correlation with the experimentally measured OND rDA rates.