Stereoselective Construction of ß-, γ-, and δ-Lactam Rings via Enzymatic C-H Amidation.

Lactam rings are found in many biologically active natural products and pharmaceuticals, including important classes of antibiotics. Methods for the asymmetric synthesis of these molecules are therefore highly desirable, particularly through the selective functionalization of unreactive aliphatic C-H bonds. Here we show the development of a strategy for the asymmetric synthesis of ß-, γ-, and δ-lactams via hemoprotein-catalysed intramolecular C-H amidation reaction with readily available dioxazolone reagents. Engineered myoglobin variants serve as excellent biocatalysts for this transformation yielding the desired lactam products in high yields, high enantioselectivity, and on preparative scale. Mechanistic and computational studies elucidate the nature of the C-H amination and enantiodetermining steps and provide insights into protein-mediated control of regioselectivity and stereoselectivity. Additionally, an alkaloid natural product and a drug molecule were synthesized chemoenzymatically in much fewer steps (7-8 vs. 11-12) than previously reported, further demonstrating the power of biosynthetic strategy for the preparation of complex bioactive molecules.

Biocatalytic strategy for the construction of sp3-rich polycyclic compounds from directed evolution and computational modelling.

Catalysis with engineered enzymes has provided more efficient routes for the production of active pharmaceutical agents. However, the potential of biocatalysis to assist in early-stage drug discovery campaigns remains largely untapped. In this study, we have developed a biocatalytic strategy for the construction of sp3-rich polycyclic compounds via the intramolecular cyclopropanation of benzothiophenes and related heterocycles. Two carbene transferases with complementary regioisomer selectivity were evolved to catalyse the stereoselective cyclization of benzothiophene substrates bearing diazo ester groups at the C2 or C3 position of the heterocycle. The detailed mechanisms of these reactions were elucidated by a combination of crystallographic and computational analyses. Leveraging these insights, the substrate scope of one of the biocatalysts could be expanded to include previously unreactive substrates, highlighting the value of integrating evolutionary and rational strategies to develop enzymes for new-to-nature transformations. The molecular scaffolds accessed here feature a combination of three-dimensional and stereochemical complexity with 'rule-of-three' properties, which should make them highly valuable for fragment-based drug discovery campaigns.

Molecular Dynamics of the Norbornyl Cation in Solution and Its Generation in Winstein-Trifan Solvolysis: The Timing of Sigma Bridging.

Molecular dynamics simulations were performed on the solvolyses of exo- and endo-norbornyl brosylate and for the "nonclassical" σ-bridged norbornyl cation in an acetic acid solution. This computational modeling of the original Winstein-Trifan experiment confirms that exo-solvolysis is accompanied by σ-bridging in the transition state, while endo-solvolysis is not; σ-bridging eventually occurs in a dynamically stepwise fashion. Simulations of the norbornyl cation in solution show typical vibrations due to zero-point and thermal vibrations but no tendency to sample localized "classical cation" geometries.

Origins of Periselectivity and Regioselectivity in Ambimodal Tripericyclic [8+6]/[6+4]/[4+2] Intramolecular Cycloadditions of a Heptafulvenyl-Fulvene.

Quantum mechanical calculations and molecular dynamics simulations have elucidated the reaction mechanism for intramolecular cycloadditions of a heptafulvenyl-fulvene tethered by a trimethylene chain. Prior experiments by Liu and Houk reported the formation of only an endo-[8+6] cycloadduct at 185 °C. Liu et al. later reported an exo-[4+2] Diels-Alder cycloadduct as the major product at 140 °C (Tetrahedron, 1999, 55, 9171). Cycloadditions involve Diels-Alder and an ambimodal intramolecular tripericyclic [8+6]/[6+4]/[4+2] cycloaddition. The mechanistic details explain the experimental reports of temperature dependence on the periselectivity of intramolecular cycloadditions. Additional calculations with multireference-based methods CASSCF and NEVPT2 highlight the artifacts of DFT methods and single-reference wavefunction-based CCSD(T) in the description of complete potential energy surface involving various cycloadditions of the heptafulvenyl-fulvene.

Approaching Coupled Cluster Accuracy with Density Functional Theory Using the Generalized Connectivity-Based Hierarchy.

This Perspective reviews connectivity-based hierarchy (CBH), a systematic hierarchy of error-cancellation schemes developed in our group with the goal of achieving chemical accuracy using inexpensive computational techniques ("coupled cluster accuracy with DFT"). The hierarchy is a generalization of Pople's isodesmic bond separation scheme that is based only on the structure and connectivity and is applicable to any organic and biomolecule consisting of covalent bonds. It is formulated as a series of rungs involving increasing levels of error cancellation on progressively larger fragments of the parent molecule. The method and our implementation are discussed briefly. Examples are given for the applications of CBH involving (1) energies of complex organic rearrangement reactions, (2) bond energies of biofuel molecules, (3) redox potentials in solution, (4) pKa predictions in the aqueous medium, and (5) theoretical thermochemistry combining CBH with machine learning. They clearly show that near-chemical accuracy (1-2 kcal/mol) is achieved for a variety of applications with DFT methods irrespective of the underlying density functional used. They demonstrate conclusively that seemingly disparate results, often seen with different density functionals in many chemical applications, are due to an accumulation of systematic errors in the smaller local molecular fragments that can be easily corrected with higher-level calculations on those small units. This enables the method to achieve the accuracy of the high level of theory (e.g., coupled cluster) while the cost remains that of DFT. The advantages and limitations of the method are discussed along with areas of ongoing developments.

Stereoselective Construction of ß-, γ-, and δ-Lactam Rings via Enzymatic C-H Amidation.

Lactam rings are found in many biologically active natural products and pharmaceuticals, including important classes of antibiotics. Given their widespread presence in bioactive molecules, methods for the asymmetric synthesis of these molecules, in particular through the selective functionalization of ubiquitous yet unreactive aliphatic C-H bonds, are highly desirable. In this study, we report the development of a novel strategy for the asymmetric synthesis of 4-, 5-, and 6-membered lactams via an unprecedented hemoprotein-catalyzed intramolecular C-H amidation reaction with readily available dioxazolone reagents. Engineered myoglobin variants serve as excellent biocatalysts for this transformation producing an array of ß-, γ-, and δ-lactam molecules in high yields, with high enantioselectivity, and on preparative scale. Mechanistic and computational studies elucidate the nature of the C-H amination and enantiodetermining steps in these reactions and provide insights into protein-mediated control of regioselectivity and stereoselectivity. Using this system, it was possible to accomplish the chemoenzymatic total synthesis of an alkaloid natural product and a drug molecule in much fewer steps (7-8 vs. 11-12) than previously possible, which showcases the power of this biosynthetic strategy toward enabling the preparation of complex bioactive molecules.

Probative Evidence and Quantitative Energetics for the Unimolecular Mechanism of the 1,5-Sigmatropic Hydrogen Shift of Cyclopentadiene.

While the 1,5-sigmatropic hydrogen shift in cyclopentadiene is generally thought to be a unimolecular pericyclic reaction, Yamabe proposed a more complex bimolecular mechanism proceeding through the exo dimer of cyclopentadiene. DFT computations by Yamabe were claimed to show that the bimolecular mechanism was kinetically more favorable than the unimolecular mechanism. Reinvestigation of the unimolecular concerted mechanism and Yamabe's bimolecular mechanism with ωB97X-D and DLPNO-CCSD(T) calculations demonstrates a 25 kcal/mol preference for the unimolecular mechanism relative to the bimolecular mechanism. While Yamabe's calculations were performed with the less accurate B3LYP functional, the incorrect conclusion was the result of a different error discovered here. We have also computed corrections for tunneling that result in computed activation barriers within 1.5 kcal/mol of the experimental values.

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.

An Enzymatic Platform for Primary Amination of 1-Aryl-2-alkyl Alkynes.

Propargyl amines are versatile synthetic intermediates with numerous applications in the pharmaceutical industry. An attractive strategy for efficient preparation of these compounds is nitrene propargylic C(sp3)-H insertion. However, achieving this reaction with good chemo-, regio-, and enantioselective control has proven to be challenging. Here, we report an enzymatic platform for the enantioselective propargylic amination of alkynes using a hydroxylamine derivative as the nitrene precursor. Cytochrome P450 variant PA-G8 catalyzing this transformation was identified after eight rounds of directed evolution. A variety of 1-aryl-2-alkyl alkynes are accepted by PA-G8, including those bearing heteroaromatic rings. This biocatalytic process is efficient and selective (up to 2610 total turnover number (TTN) and 96% ee) and can be performed on preparative scale.

Cycloadditions of Cyclopentadiene and Cycloheptatriene with Tropones: All Endo-[6+4] Cycloadditions Are Ambimodal.

The cycloadditions of cyclopentadiene and cycloheptatriene with tropone are some of the earliest published examples of [6+4] cycloaddition reactions. We report quantum mechanical studies (ωB97X-D and DLPNO-CCSD(T)) of transition structures and products of these reactions, as well as quasi-classical molecular dynamics simulations of reaction trajectories. The study reveals that these cycloadditions involve ambimodal transition states resulting in a web of products by pericyclic interconversion pathways. Combined with these studies, calculations of simple parent systems and a thorough meta-analysis of literature examples reveal the general concept that all endo-[6+4] cycloadditions are ambimodal.

Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models.

Monovalent ions play significant roles in various biological and material systems. Recently, four new water models (OPC3, OPC, TIP3P-FB, and TIP4P-FB), with significantly improved descriptions of condensed phase water, have been developed. The pairwise interaction between the metal ion and water necessitates the development of ion parameters specifically for these water models. Herein, we parameterized the 12-6 and the 12-6-4 nonbonded models for 12 monovalent ions with the respective four new water models. These monovalent ions contain eight cations including alkali metal ions (Li+, Na+, K+, Rb+, Cs+), transition-metal ions (Cu+ and Ag+), and Tl+ from the boron family, along with four halide anions (F-, Cl-, Br-, I-). Our parameters were designed to reproduce the target hydration free energies (the 12-6 hydration free energy (HFE) set), the ion-oxygen distances (the 12-6 ion-oxygen distance (IOD) set), or both of them (the 12-6-4 set). The 12-6-4 parameter set provides highly accurate structural features overcoming the limitations of the routinely used 12-6 nonbonded model for ions. Specifically, we note that the 12-6-4 parameter set is able to reproduce experimental hydration free energies within 1 kcal/mol and experimental ion-oxygen distances within 0.01 Å simultaneously. We further reproduced the experimentally determined activity derivatives for salt solutions, validating the ion parameters for simulations of ion pairs. The improved performance of the present water models over our previous parameter sets for the TIP3P, TIP4P, and SPC/E water models (Li, P. et al J. Chem. Theory Comput. 2015 11 1645 1657) highlights the importance of the choice of water model in conjunction with the metal ion parameter set.

Thermodynamics of Transition Metal Ion Binding to Proteins.

Modeling the thermodynamics of a transition metal (TM) ion assembly be it in proteins or in coordination complexes affords us a better understanding of the assembly and function of metalloclusters in diverse application areas including metal organic framework design, TM-based catalyst design, the trafficking of TM ions in biological systems, and drug design in metalloprotein platforms. While the structural details of TM ions bound to metalloproteins are generally well understood via experimental and computational approaches, accurate studies describing the thermodynamics of TM ion binding are rare. Herein, we demonstrate that we can obtain accurate structural and absolute binding free energies of Co2+ and Ni2+ to the enzyme glyoxalase I using an optimized 12-6-4 (m12-6-4) potential. Critically, this model simultaneously reproduces the solvation free energy of the individual TM ions and reproduces the thermodynamics of TM ion-ligand coordination as well as the thermodynamics of TM ion binding to a protein active site unlike extant models. We find the incorporation of the thermodynamics associated with protonation state changes for the TM ion (un)binding to be crucial. The high accuracy of m12-6-4 potential in this study presents an accurate route to explore more complicated processes associated with TM cluster assembly and TM ion transport.

Eliminating Systematic Errors in DFT via Connectivity-Based Hierarchy: Accurate Bond Dissociation Energies of Biodiesel Methyl Esters.

We present a computational study focusing on the determination of accurate bond dissociation energies (BDEs) involved in the combustion of biodiesel methyl esters. We have adapted our previously developed efficient error-cancellation protocols, based on the systematic "connectivity-based hierarchy" (CBH), to derive accurate BDEs of biodiesel molecules at a modest computational cost. Using DFT energies on the full biodiesel molecule in conjunction with accurate G4 energies on the small fragments involved in the CBH reaction schemes, systematic errors in the DFT methods can be cancelled efficiently. Herein, we apply our G4-corrected ΔCBH-2 and ΔCBH-3 schemes in conjunction with several popular DFT methods to determine accurate bond dissociation energies of different C-C, C-H, and C-O bonds in biodiesel surrogate molecules. We first evaluate the performance of different DFT methods using a test set of 21 reactions involving various bond dissociations in small to medium biodiesel surrogates (up to methyl decanoate, a C10-methyl ester) by calibration against accurate values calculated with multireference methods (MRACPF2), reported by Carter and co-workers. The CBH-2 corrections for all tested dispersion-corrected functionals yield mean absolute deviations (MADs) in a narrow range of 1.3-1.5 kcal/mol, the best performance being obtained for B97-D3 and ωB97X-D functionals (MAD = 1.3 kcal/mol). Further, significant improvement yielding a MAD of only 0.9 kcal/mol is obtained using the G4-corrected CBH-3 scheme. Finally, the protocol has been applied to derive accurate BDEs of eight different bonds in the larger biodiesel molecule, methyl linolenate, yielding a MAD of only 1.13 kcal/mol using the ΔCBH-3 error correction scheme. The results suggest that our protocol in conjunction with different DFT methods should be broadly applicable to yield accurate BDEs for a variety of large biodiesel molecules.

Fragment-Based Approaches for Supramolecular Interaction Energies: Applications to Foldamers and Their Complexes with Anions.

We explore the application of our multilayer Molecules-in-Molecules (MIM) fragment-based method for the study of the energies in supramolecular systems, viz. foldamers and their anion bound complexes. The performance of five different density functional theory (DFT) methods in conjunction with the fragmentation-based method is evaluated against the unfragmented energies for a test set of 5 foldamers (82 to 170 atoms). A systematic protocol has been developed to account for the π···π interactions in such systems in addition to the traditional fragmentation of the system along the backbone comprised of covalently bonded dimer (or trimer) units. We find a significant improvement in the performance of the method on going from a one-layer MIM1 model (errors >10 kcal/mol) to a two-layer MIM2 model (errors 0-2 kcal/mol), due to the incorporation of long-range interactions in the latter approach. Furthermore, we extend the applicability of MIM2 models to determine accurate binding energies of macromolecular receptor-anion complexes. For three different anion bound macrocycles, our MIM2 protocol provides total energies within 1.5 kcal/mol of the unfragmented energies for most of the DFT methods. The corresponding anion binding energies are calculated within 0.5 kcal/mol of the unfragmented binding energies due to systematic error cancellation between the macrocycle and the macrocycle-anion complex. Finally, we have calibrated the absolute accuracy in the calculated binding energies by comparison with unfragmented DLPNO-CCSD(T) calculations on three macromolecule-chloride anion complexes. The most accurate results are obtained using a MIM2 model using DLPNO-CCSD(T) calculations on trimer units as the high level and DFT-D3 (e.g., M06-2X-D3) as the low level of theory, yielding sub kcal/mol errors in the anion binding energies. Our protocol can be an accurate method to calculate anion binding energies for very large supramolecular systems.

Simulating the Chelate Effect.

Despite the rich history of experimental studies focusing on the thermochemistry and kinetics associated with the chelate effect, molecular-level computational studies on the chelate ring opening/ring closure are scarce. The challenge lies in an accurate description of both the metal ion and its aqueous environment. Herein, we demonstrate that an optimized 12-6-4 Lennard-Jones (LJ) model can capture the thermodynamics and provide detailed structural and mechanistic insights into the formation of ethylenediamine (en) complexes with metal ions. The water molecules in the first solvation shell of the metal ion are found to facilitate the chelate ring formation. The optimized parameters further simulate the formation of bis and tris(en) complexes representing the wide applicability of the model to simulate coordination chemistry and self-assembly processes.

Anion-Binding Macrocycles Operate Beyond the Electrostatic Regime: Interaction Distances Matter.

Anion recognition impacts many areas of chemistry and often relies on receptors with multiple hydrogen-bond donors. Previous studies of these donors in small molecules have long promoted the idea that electrostatic interactions alone correlate with association strength, yet this correlation has not been critically evaluated in the framework of larger, macrocyclic receptors. Here, we provide that assessment by evaluating how much electrostatics contributes to the gas-phase binding energy of macrocyclic receptors with various anions. Whereas small-molecule complexes behave as expected, we find that electrostatic interactions fail to accurately describe total binding energies of many common macrocyclic receptors: calix[4]pyrroles, dipyrrolyldiketones, indolocarbazoles, amido-pyrroles, triazolophanes, and cyanostars. This deviation arises from the fact that most macrocycles have multiple points of contact with the anion. Whereas the hydrogen-bond donors collectively stabilize the anion, the interaction distances are typically larger than equilibrium values seen with small molecules. This leads to increases in the relative contributions of the attractive components such as induction (e.g., induced dipoles) and dispersion, which are found to be as high as 32 % for CH-donor based tricarbazole triazolophane complex with large polarizable ClO4- . This study augments previous observations of the importance of dispersion and induction towards anion binding of macrocyclic receptors in solution.

Accurate Thermochemistry for Organic Cations via Error Cancellation using Connectivity-Based Hierarchy.

Connectivity-Based Hierarchy (CBH) is an effective error-cancellation scheme for the determination of chemically accurate thermochemical properties of a variety of organic and biomolecules. Neutral molecules and open-shell radicals have already been treated successfully by this approach utilizing inexpensive computational methods such as density functional theory. Herein, we present an extension of the method to a new class of molecules, specifically, organic cations. Because of the presence of structural rearrangements involving hydrogen migrations as well as unusual structures such as bridged cations, the application of the standard CBH protocol to a test set of 25 cations leads to significant errors due to ineffective bond-type matching. We propose an adjusted protocol to overcome such limitations to achieve highly effective error cancellation. The modified CBH methods, in conjunction with a wide range of density functionals, reproduce G4 energies for the test set of organic cations accurately within 1-2 kcal/mol at a reduced computational cost.

Solving the Density Functional Conundrum: Elimination of Systematic Errors To Derive Accurate Reaction Enthalpies of Complex Organic Reactions.

The failure of available density functional methods to compute accurate reaction enthalpies of common organic reactions is well documented. Herein, we demonstrate that the disparate results from different functionals stem from the systematic errors in the underlying elementary reactions that represent the changes in the bonding environment between reactants and products. We develop a rigorous protocol to correct for these systematic errors and obtain dramatically improved results with deviations of only 1-2 kcal/mol for most functionals.