A Benchmark Study of Quantum Mechanics and Quantum Mechanics-Molecular Mechanics Methods for Carbocation Chemistry

DFT Study on Retigerane-Type Sesterterpenoid Biosynthesis: Initial Conformation of GFPP Regulates Biosynthetic Pathway, Ring-Construction Order and Stereochemistry

Retigerane-type sesterterpenoids, which feature a unique 5/6/5/5/5 fused pentacyclic structure with an angular-type triquinane moiety, are biosynthesized via successive carbocation-mediated reactions triggered by terpene cyclases. However, the precise biosynthetic pathways/mechanisms, wherein steric inversion of the carbon skeleton occurs at least once, remain elusive. Two plausible reaction pathways have been proposed, which differ in the order of ring cyclization: A → B/C → D/E-ring(s) (Route 1) and A → E → B → C/D-ring(s) (Route 2). Since the reaction intermediates of these complicated domino-type reaction sequences are experimentally inaccessible, we employed comprehensive density functional theory (DFT) calculations to evaluate these routes. The results indicate that retigeranin biosynthesis proceeds via Route 2 involving a multistep carbocation cascade, in which the order of ring cyclization (A → E → B → C/D) is the key to constructing the angular 5/5/5 triquinane structure with the correct stereochemistry at C3. The result also suggests that slight differences in the initial conformation have a significant effect on the order of cyclization and steric inversion. The computed pathway/mechanism also provides a rational basis for the formation of various related terpenes/terpenoids.

Asymmetric Synthesis and Biological Evaluation of Platensilin, Platensimycin, Platencin, and Their Analogs via a Bioinspired Skeletal Reconstruction Approach

Platensilin, platensimycin, and platencin are potent inhibitors of β-ketoacyl-acyl carrier protein synthase (FabF) in the bacterial and mammalian fatty acid synthesis system, presenting promising drug leads for both antibacterial and antidiabetic therapies. Herein, a bioinspired skeleton reconstruction approach is reported, which enables the unified synthesis of these three natural FabF inhibitors and their skeletally diverse analogs, all stemming from a common ent-pimarane core. The synthesis features a diastereoselective biocatalytic reduction and an intermolecular Diels-Alder reaction to prepare the common ent-pimarane core. From this intermediate, stereoselective Mn-catalyzed hydrogen atom-transfer hydrogenation and subsequent Cu-catalyzed carbenoid C-H insertion afford platensilin. Furthermore, the intramolecular Diels-Alder reaction succeeded by regioselective ring opening of the newly formed cyclopropane enables the construction of the bicyclo[3.2.1]-octane and bicyclo[2.2.2]-octane ring systems of platensimycin and platencin, respectively. This skeletal reconstruction approach of the ent-pimarane core facilitates the preparation of analogs bearing different polycyclic scaffolds. Among these analogs, the previously unexplored cyclopropyl analog 47 exhibits improved antibacterial activity (MIC80 = 0.0625 μg/mL) against S. aureus compared to platensimycin.

Stability trends in carbocation intermediates stemming from germacrene A and hedycaryol

In the current work, we analyzed the origin of difference in stabilities among the germacrene A and hedycaryol-derived carbocations. This study focused on twelve hydrocarbons derived from germacrene A and twelve from hedycaryol, which can be divided into three groups: four molecules containing 6-6 bicyclic rings, four 5-7 bicyclic compounds with the carbocation being on the seven-membered ring and the remaining four 5-7 bicyclic compounds with the carbocation on the five-membered ring. The variations in energy within the groups of carbocations (i.e., 6-6 and two kinds of 5-7 bicyclic carbocations) can be ascribed to intramolecular repulsion interactions, as seen from non-covalent interactions plots. Despite the structural similarities between germacrene A and hedycaryol cations, they possess a somewhat different stability trend. These differences are attributed to C+···OH intramolecular interactions present in some hedycaryol cations, which are absent in the carbocations derived from germecrene A.

Docking carbocations into terpene synthase active sites using chemically meaningful constraints-The TerDockin approach

Terpenes are a diverse class of natural products which have long been sought after for their chemical properties as medicine, perfumes, and for food flavoring. Computational docking studies of terpene mechanisms have been a challenge due to the lack of strong directing groups which many docking programs rely on. In this chapter, we dive into our computational method Terdockin (Terpene-Docking) as a successful methodology in modeling terpene synthase mechanisms. This method could also be used as inspiration for any multi-ligand docking project.

Homogeneous and heterogeneous atmospheric ozonolysis of chlorobenzene:Mechanism, kinetics and ecotoxicity assessment

The reactions between chlorobenzene(CB) and ozone have been studied comprehensively in this paper. Chlorobenzene is a commonly found chlorinated aromatic volatile organic compound(VOC), and its emission into the atmosphere can cause harm to the ecosystem and human health. The frequent occurrence of mineral particles from sandstorms exerts a significant influence on the atmospheric chemistry of the troposphere. Mineral particles are abundant in SiO2 and Al2O3 content. Therefore, we investigated the homogeneous and heterogeneous reaction processes of CB and ozone in the atmosphere by using density functional theory (DFT) method at the M06-2X/6-311++g(3df,2p)//M06-2X/6-31+g(d,p) level. The atmospheric fate, reaction rate and toxicity evaluation of CB ozonation were studied in the gas-phase section. Toxicity evaluation results showed that ozonation of CB could effectively reduce its toxicity. For the heterogeneous process, we simulated three types of SiO2 clusters and nine types of (Al2O3)n clusters, and studied the configurations of CB adsorbed on the cluster surfaces. We found that adsorption of CB on the SiO2 clusters was achieved through hydrogen bonding, while adsorption of CB on the Al2O3 clusters was achieved through both hydrogen bonding and metal bonding. The energy for CB adsorption on the (Al2O3)n cluster surface was higher than that for the SixOy(OH)z cluster surface, and both types of clusters exhibited efficient adsorption of CB. As the SixOy(OH)z clusters grew larger, the rates for the reactions between O3 and CB increased. CB travelled long distances along the Al2O3 clusters, leading to an extended influence range.

Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set

We present a new benchmark set of metalloenzyme model reaction energies and barrier heights that we call MME55. The set contains 10 different enzymes, representing eight transition metals, both open and closed shell systems, and system sizes of up to 116 atoms. We use four DLPNO-CCSD(T)-based approaches to calculate reference values against which we then benchmark the performance of a range of density functional approximations with and without dispersion corrections. Dispersion corrections improve the results across the board, and triple-ζ basis sets provide the best balance of efficiency and accuracy. Jacob's ladder is reproduced for the whole set based on averaged mean absolute (percent) deviations, with the double hybrids SOS0-PBE0-2-D3(BJ) and revDOD-PBEP86-D4 standing out as the most accurate methods for the MME55 set. The range-separated hybrids ωB97M-V and ωB97X-V also perform well here and can be recommended as a reliable compromise between accuracy and efficiency; they have already been shown to be robust across many other types of chemical problems, as well. Despite the popularity of B3LYP in computational enzymology, it is not a strong performer on our benchmark set, and we discourage its use for enzyme energetics.

Easy and accurate computation of energy barriers for carbocation solvation: an expeditious tool to face carbocation chemistry

An expeditious procedure for the challenging computation of the free energy barriers (ΔG≠) for the solvation of carbocations is presented. This procedure is based on Marcus Theory (MT) and the popular B3LYP/6-31G(d)//PCM method, and it allows the easy, accurate and inexpensive prediction of these barriers for carbocations of very different stability. This method was validated by the fair mean absolute error (ca. 1.5 kcal mol-1) achieved in the prediction of 19 known experimental barriers covering a range of ca. 50 kcal mol-1. Interestingly, the new procedure also uses an original method for the calculation of the required inner reorganization energy (Λi) and free energy of reaction (ΔG). This procedure should pave the way to face computationally the pivotal issue of carbocation chemistry and could be easily extended to any bimolecular organic reaction.

Unraveling the role of prenyl side-chain interactions in stabilizing the secondary carbocation in the biosynthesis of variexenol B

Terpene cyclization reactions involve a number of carbocation intermediates. In some cases, these carbocations are stabilized by through-space interactions with π orbitals. Several terpene/terpenoids, such as sativene, santalene, bergamotene, ophiobolin and mangicol, possess prenyl side chains that do not participate in the cyclization reaction. The role of these prenyl side chains has been partially investigated, but remains elusive in the cyclization cascade. In this study, we focus on variexenol B that is synthesized from iso-GGPP, as recently reported by Dickschat and co-workers, and investigate the possibility of through-space interactions with prenyl side chains using DFT calculations. Our calculations show that (i) the unstable secondary carbocation is stabilized by the cation-π interaction from prenyl side chains, thereby lowering the activation energy, (ii) the four-membered ring formation is completed through bridging from the exomethylene group, and (iii) the annulation from the exomethylene group proceeds in a barrier-free manner.

QM/MM Modeling Aided Enzyme Engineering in Natural Products Biosynthesis

Natural products and their derivatives are widely used across various industries, particularly pharmaceuticals. Modern engineered biosynthesis provides an alternative way of producing and meeting the growing need for diverse natural products. Natural enzymes, on the other hand, often exhibit unsatisfactory catalytic characteristics and necessitate further enzyme engineering modifications. QM/MM, as a powerful and extensively used computational tool in the field of enzyme catalysis, has been increasingly applied in rational enzyme engineering over the past decade. In this review, we summarize recent advances in QM/MM computational investigation on enzyme catalysis and enzyme engineering for natural product biosynthesis. The challenges and perspectives for future QM/MM applications aided enzyme engineering in natural product biosynthesis will also be discussed.

Tryptophan Stabilization of a Biochemical Carbocation Evaluated by Analysis of π Complexes of 3-Ethylindole with the t-Butyl Cation

Understanding how the highly unstable carbocation intermediates in terpenoid biosynthesis are stabilized and protected during their transient existence in enzyme active sites is an intriguing challenge which has to be addressed computationally. Our efforts have focused on evaluating the stabilization afforded via carbocation-π complexation between a biochemical carbocation and an aromatic amino acid residue. This has involved making measurements on an X-ray structure of an enzyme active site that shows a π donor proximate to a putative carbocation site and using these to build models which are analyzed computationally to provide an estimated stabilization energy (SE). Previously, we reported estimated SEs for several such carbocation-π complexes involving phenylalanine. Herein, we report the first such estimate involving tryptophan as the π donor. Because there was almost no published information about indole as a π-complexation donor, we first located computationally equilibrium π and σ complexes of 3-ethylindole with the t-butyl cation as relevant background information. Then, measurements on the X-ray structure of the enzyme CotB2 complexed with geranylgeranyl thiodiphosphate (GGSPP), specifically on the geometric relationship of the putative carbocation at C15 of GGSPP to W186, were used to build a model that afforded a computed SE of -15.3 kcal/mol.

Role of Noncovalent Interactions in Inducing High Enantioselectivity in an Alcohol Reductive Deoxygenation Reaction Involving a Planar Carbocationic Intermediate

The involvement of planar carbocation intermediates is generally considered undesirable in asymmetric catalysis due to the difficulty in gaining facial control and their intrinsic stability issues. Recently, suitably designed chiral catalyst(s) have enabled a guided approach of nucleophiles to one of the prochiral faces of carbocations affording high enantiocontrol. Herein, we present the vital mechanistic insights from our comprehensive density functional theory (B3LYP-D3) study on a chiral Ir-phosphoramidite-catalyzed asymmetric reductive deoxygenation of racemic tertiary α-substituted allenylic alcohols. The catalytic transformation relies on the synergistic action of a phosphoramidite-modified Ir catalyst and Bi(OTf)₃, first leading to the formation of an Ir-π-allenyl carbocation intermediate through a turn-over-determining S_N1 ionization, followed by a face-selective hydride transfer from a Hantzsch ester analogue to yield an enantioenriched product. Bi(OTf)₃ was found to promote a significant number of ionic interactions as well as noncovalent interactions (NCIs) with the catalyst and the substrates (allenylic alcohol and Hantzsch ester), thus providing access to a lower energy route as compared to the pathways devoid of Bi(OTf)₃. In the nucleophilic addition, the chiral induction was found to depend on the number and efficacy of such key NCIs. The curious case of reversal of enantioselectivity, when the α-substituent of the allenyl alcohol is changed from methyl to cyclopropyl, was identified to originate from a change in mechanism from an enantioconvergent pathway (α-methyl) to a dynamic kinetic asymmetric transformation (α-cyclopropyl). These molecular insights could lead to newer strategies to tame tertiary carbocations in enantioselective reactions using suitable combinations of catalysts and additives.

A comprehensive benchmark investigation of quantum chemical methods for carbocations

The application of various density functional approximations (DFAs) and an emphasis on popular methods without any consensus have prevailed in computational studies dedicated to carbocations. More importantly, an extensive and rigorous benchmark investigation on density functionals for the class is still lacking. To close this gap, we present a comprehensive benchmark study of quantum chemical methods on a series of classical and nonclassical carbocations, the CARBO33 dataset. We evaluate a total of 107 DFT methods from all rungs giving particular attention to double hybrid density functionals as the potential of the class has been largely undermined in the context of carbocations. To support our findings, DLPNO-CCSD(T) at the complete basis set (CBS) limit and W1-F12 are used as reference methods. Our results indicate that the composite CBS-QB3 method performs poorly and should not be adopted for target energies. Oftentimes, the tested DFAs of a lower rung perform better than several DFAs in a higher rung of Perdew's "Jacob's ladder". Nonetheless, double hybrids DSD-PBEP86-NL and ωB97X-2-D3(BJ) stand out by showing the overall best performance. Among the hybrids evaluated, about half of them show mean absolute deviation (MAD) below 1.1 kcal mol^-1, including the popular hybrids M06-2X and mPW1PW91. In this family, MN15-D3(BJ) performs particularly well (MAD = 0.77 kcal mol^-1) displaying reliable results across various tests. Highly popular B3LYP exhibited one of the worst performances (MAD = 4.74 kcal mol^-1), and we do not recommend its application to carbocations. We also assess the 24 general-purpose basis sets of single- up to quadruple-ζ quality. The best compromise between accuracy and computational cost is achieved with cc-pVTZ followed by def2-TZVP. Computations on larger structures of general interest, including terpene carbocations, are also presented for selected DFT methods confirming general trends in the results.

Understanding the competing pathways leading to hydropyrene and isoelisabethatriene

Terpene synthases are responsible for the biosynthesis of terpenes, the largest family of natural products. Hydropyrene synthase generates hydropyrene and hydropyrenol as its main products along with two byproducts, isoelisabethatrienes A and B. Fascinatingly, a single active site mutation (M75L) diverts the product distribution towards isoelisabethatrienes A and B. In the current work, we study the competing pathways leading to these products using quantum chemical calculations in the gas phase. We show that there is a great thermodynamic preference for hydropyrene and hydropyrenol formation, and hence most likely in the synthesis of the isoelisabethatriene products kinetic control is at play.