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Compound identification by mass spectrometry needs reference mass spectra. While there are over 102 million compounds in PubChem, less than 300,000 curated electron ionization (EI) mass spectra are available from NIST or MoNA mass spectral databases. Here, we test quantum chemistry methods (QCEIMS) to generate in silico EI mass spectra (MS) by combining molecular dynamics (MD) with statistical methods. To test the accuracy of predictions, in silico mass spectra of 451 small molecules were generated and compared to experimental spectra from the NIST 17 mass spectral library. The compounds covered 43 chemical classes, ranging up to 358 Da. Organic oxygen compounds had a lower matching accuracy, while computation time exponentially increased with molecular size. The parameter space was probed to increase prediction accuracy including initial temperatures, the number of MD trajectories and impact excess energy (IEE). Conformational flexibility was not correlated to the accuracy of predictions. Overall, QCEIMS can predict 70 eV electron ionization spectra of chemicals from first principles. Improved methods to calculate potential energy surfaces (PES) are still needed before QCEIMS mass spectra of novel molecules can be generated at large scale.

Recently, Huang and co‐workers reported a catalytic reaction that utilizes H2 as the sole reductant for a C−C coupling of allyl groups with yields up to 96 %. Here we use computational quantum chemistry to identify several key features of this reaction that provide clarity on how it proceeds. We propose the involvement of a Pd−Pd bound dimer precatalyst, demonstrate the importance of ligand π‐π interactions and counterions, and identify a new, energetically viable, mechanism involving two dimerized, outer‐sphere reductive elimination transition structures that determine both the rate and selectivity. Although we rule out the previously proposed transmetalation step on energetic grounds, we show it to have an unusual aromatic transition structure in which two Pd atoms support rearranging electrons. The prevalence of potential metal‐supported pericyclic reactions in this system suggests that one should consider such processes regularly, but the results of our calculations also indicate that one should do so with caution. [ABSTRACT FROM AUTHOR]

Computational chemistry approaches for studying the formation of terpenes/terpenoids in wines are presented, using five particular terpenes/terpenoids (1,8-cineole, α-ylangene, botrydial, rotundone, and the wine lactone), volatile compounds (or their precursors) found in wine and/or wine grapes, as representative examples. Through these examples, we show how modern computational quantum chemistry can be employed as an effective tool for assessing the validity of proposed mechanisms for terpene/terpenoid formation.

The template‐directed C−H insertion of α,β‐unsaturated esters into quinoline was interrogated by using computational quantum chemistry. An energetically viable mechanism for this complex multistep transformation was elucidated, with attention paid throughout to conformational flexibility and alternative ligand binding modes. The selectivity was found to correlate with distortion from a tetrahedral geometry for the carbon atom involved in C−H insertion, a parameter that can be applied to future template design. [ABSTRACT FROM AUTHOR]

Between 1910 and 1947, Robert Robinson (primarily), among others, published numerous proposed structures for strychnine. Robinson published 17 of his strychnine papers with his doctoral advisor William Henry Perkin, Jr. though all but two appeared after Robinson had taken his first permanent academic position. This Essay analyzes 20 key publications leading up to Robinson's (correct, then incorrect, then correct again though not definitively) proposal and Woodward's assignment of the actual structure of strychnine. We subjected the assignment of the strychnine structure to a modern computational quantum chemistry workflow. By computing, with density functional theory, 1H and 13C NMR chemical shifts for the literature‐proposed strychnine structures, we were able to rule out most incorrect structures. 13C NMR predictions were better at this, but 1H NMR chemical shifts were helpful. A comparison is made between the consequences of publishing erroneous ideas in the first half of the 20th century and doing so in the 21st century. [ABSTRACT FROM AUTHOR]

Quantum chemical methods are useful for probing the energetic viability of chemical mechanisms involved in natural product biosynthesis. Typical computational approaches are described and representative examples of mechanistic studies on radical, pericyclic, and carbocation rearrangement reactions that lead to polycyclic skeletons of complex natural products showcase the utility of such methods in providing understanding and shaping future experimental studies. The importance of inherent substrate reactivity is highlighted and cautions for interpreting computational results are discussed. This article is categorized under:Structure and Mechanism > Reaction Mechanisms and CatalysisTheoretical and Physical Chemistry > Reaction Dynamics and KineticsStructure and Mechanism > Computational Biochemistry and Biophysics [ABSTRACT FROM AUTHOR]

Abstract: Sesterterpenoids are a relatively rare class of plant terpenes. Sesterterpene synthase (STS)‐mediated cyclization of the linear C25 isoprenoid precursor geranylfarnesyl diphosphate (GFPP) defines sesterterpene scaffolds. So far only a very limited number of STSs have been characterized. The discovery of three new plant STSs is reported that produce a suite of sesterterpenes with unprecedented 6/11/5 and 6/6/7/5 fused ring systems when transiently co‐expressed with a GFPP synthase in Nicotiana benthamiana. Structural elucidation, feeding experiments, and quantum chemical calculations suggest that these STSs catalyze an unusual cyclization path involving reprotonation, intramolecular 1,6 proton transfer, and concerted but asynchronous bicyclization events. The cyclization is diverted from those catalyzed by the characterized plant STSs by forming unified 15/5 bicyclic sesterterpene intermediates. Mutagenesis further revealed a conserved amino acid residue implicated in reprotonation. [ABSTRACT FROM AUTHOR]

C-H functionalization, mechanism, Pd catalysts, quantum chemistry, templates Keywords: C-H functionalization; mechanism; Pd catalysts; quantum chemistry; templates EN C-H functionalization mechanism Pd catalysts quantum chemistry templates 1 1 1 05/16/23 20230511 NES 230511 B Like an octopus b trapping its prey with wriggling arms, a palladium catalyst binds its quinoline substrate through multiple conformations en route to selective activation of a particular C-H bond. Cover Feature: Mechanism and Origins of Site-Selectivity of Template-Directed C-H Insertion of Quinolines (Chem. Eur. J. 27/2023). [Extracted from the article]

Substitution of a histidine, comprising part of the catalytic base group in the ent-copalyl diphosphate synthases found in all seed plants for gibberellin phytohormone metabolism, by a larger aromatic residue leads to rearrangements. Through a series of 1,2-hydride and methyl shifts of the initially formed bicycle predominant formation of (-)-kolavenyl diphosphate is observed. Further mutational analysis and quantum chemical calculations provide mechanistic insight into the basis for this profound effect on product outcome. [ABSTRACT FROM AUTHOR]

The results of quantum-chemical calculations aimed at assessing the viability of nonclassical carbocations proposed to be involved in the biosynthesis of atiserne, beyerene, kaurene, and trachylobane diterpenes are presented. While the proposed edge-protonated structure is much lower in energy than the proposed face-protonated structure, neither is predicted to be a viable intermediate energetically. [ABSTRACT FROM AUTHOR]

Biosynthetic production of cyclobutanes leads to many complex natural products. Recently, theoretical work employing quantum chemical calculations has shed light on many of the details of cyclobutane-formation, in particular, for terpene natural products. Specific insights and general principles derived from these theoretical studies are described herein. [ABSTRACT FROM AUTHOR]

This account discusses representative case studies for various applications of quantum chemical calculations in synthetic organic chemistry. These include confirmation of target structures, methodology development, and catalyst design. These examples demonstrate how predictions from quantum chemical calculations can be utilized to streamline synthetic efforts. [ABSTRACT FROM AUTHOR]

Quantum chemical calculations on the transformation of the bisabolyl cation into an array of sesquiterpenes (iso-y-bisabolene, trichodiene, cuprenene, laurene, isochamigrene, chamigrene, chamipinene, sesquithujene, sesquisabinene, micro- biotene, dunniene, cutnacrene, isobazzanene, bazzanene, barbatene, widdradiene, and thujopsene) are described. The bisabolyl cation is the hub of a complicated web of carbocations involved in the construction of diverse and complex molecular architectures present in a large number of Nature's sesquiterpenoids. The results of quantum chemical calculations on the multitude of rearrangements described herein provide reasonable answers to several persistent mechanistic questions in the world of terpene biosynthesis and also provide examples of general reactivity principles for terpene-forming (and other) carbocation rearrangements. [ABSTRACT FROM AUTHOR]

An introduction to the application of quantum chemical dynamics calculations to mechanistic problems in the field of terpene biosynthesis is provided. A bare bones introduction to the fundamentals of chemical dynamics is followed by a brief account of previous applications to terpene-forming carbocation reactions, a discussion of questions in this field that dynamics calculations may help answer, and a description of current problems to which dynamics calculations are being applied. [ABSTRACT FROM AUTHOR]

Covering: up to March, 2013. This article was invited following the 2012 NPR Lectureship presented to Professor Dean Tantillo at the 21st IUPAC International Conference on Physical Organic Chemistry (ICPOC 21) This Highlight describes applications of quantum chemical calculations to problems in natural products chemistry, including the elucidation of natural product structures (distinguishing between constitutional isomers, distinguishing between diastereomers, and assigning absolute configuration) and determination of reasonable mechanisms for their formation. [ABSTRACT FROM AUTHOR]

A complete pathway (structures and energies of intermediates and transition state structures connecting them) from geranylgeranyl diphosphate to taxadiene, obtained using quantum chemical calculations, is described. This pathway is fully consistent with previous labeling experiments, despite differing in several subtle ways (in terms of conformations of certain carbocation intermediates and in the concertedness and synchronicity of certain bond-forming events) from previous mechanistic proposals. Also, on the basis of the theoretical results, it is proposed that the 2-fluoro-geranylgeranyl diphosphate substrate analogue in the recently reported X-ray crystal structure of taxadiene synthase is bound in a nonproductive orientation. [ABSTRACT FROM AUTHOR]

The success of many organocatalysts depends on the proper modulation of electronic properties of amines and their derived enamines and iminium ions. We and others have been fascinated with the differences in reactivity observed for aziridines versus other amines in many reactions. Herein we report a theoretical assessment (using B3LYP/6-31 + G(d,p)) of the π-donating ability of aziridines relative to other amines and discuss the implications for enamine and iminium ion reactivity. Copyright © 2010 John Wiley & Sons, Ltd. Quantum chemical calculations reveal that N-alkenylaziridines are less basic/nucleophilic at their (β)-carbon than are corresponding systems that lack an aziridine ring and their derived iminium ions are more susceptible to attack by nucleophiles. [ABSTRACT FROM AUTHOR]

In this work, covalent hydration energies for a variety of azanaphthalenes and purine analogs have been calculated using a variety of quantum chemical methods. On the basis of these results, we recommend the CPCM(UA0)-B3LYP/6-31+G(d,p) level for rapid prediction of covalent hydration energies. However, we caution the use of this methodology for computing covalent hydration energies for fluorine-containing compounds. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [ABSTRACT FROM AUTHOR]

Quantum chemical calculations on cyclization mechanisms for several sesquiterpene families proposed to be closely related to each other in a biogenic sense (the bisabolene, curcumene, acoradiene, zizaene (zizaene, isozizaene, epi-zizaene, and epi-isozizaene) cedrene (α/β-cedrenes and 7-epi-α/β-cedrenes), duprezianene, and sesquithuriferol families) are described. On the basis of the results of these calculations, we suggest that the conformation of the bisabolyl cation attainable in an enzyme active site is a primary determinant of the structure and relative stereochemistry of the sesquiterpenes formed. We also suggest that substantial conformational changes of initially formed conformers of the bisabolyl cation are necessary in order to form zizaene and epi-cedrene. Given that the productive conformation of the bisabolyl cation does not necessarily reflect the original orientation of farnesyl diphosphate bound in the corresponding enzyme active site, we conclude that folding of farnesyl diphosphate alone does not always dictate the structure and relative stereochemistry of cyclization products. In addition, the potential roles of dynamic matching in determining product distributions and enzyme-promoted formation of secondary carbocations are discussed. [ABSTRACT FROM AUTHOR]

Abstract: Quantum chemical calculations were used to characterize [4,5] sigmatropic shifts in systems containing butadiene and pentadienyl substructures. Cationic, anionic, and radical systems with various tethers connecting these substructures were examined. In many cases, concerted [4,5] sigmatropic shifts with asynchronous bond making and breaking events were observed. The fundamental connections between [4,5] sigmatropic shifts and (5+4) cycloadditions are highlighted. [Copyright &y& Elsevier]

Quantum chemical studies on complexes of the 2-norbornyl cation with ammonia and benzene are described. These calculations demonstrate that the delocalized, bridged, nonclassical geometry that is usually favored for this carbocation can be perturbed significantly toward the normally less favorable classical geometry through appropriately oriented noncovalent interactions. Since such cations have been proposed as intermediates in enzyme and antibody catalyzed reactions, these results have implications for the nature of the cationic species that may be generated in the presence of electron-rich amino acid side chains of the sort that may be present in the active sites of biocatalysts. [ABSTRACT FROM AUTHOR]

In this article, we describe studies, using quantum chemical computations, on possible polycyclization pathways of the farnesyl cation leading to the complex sesquiterpene pentalenene. Two distinct pathways to pentalenene with similar activation barriers are described, each differing from previous mechanistic proposals, and each involving unusual and unexpected intermediates. Direct deprotonation of intermediates on these pathways leads to sesquiterpene byproducts, such as humulene, protoilludene, and asteriscadiene, supporting the notion that a key function of pentalenene synthase, the enzyme that produces pentalenene in Nature, is to regulate the timing and location of proton removal. The implications of the computational results for experimental studies on pentalenene synthase are discussed. [ABSTRACT FROM AUTHOR]

Quantum chemical calculations (B3LYP and Moeller-Plesset second-order perturbation theory) on carbonium ions containing hypercoordinated carbon atoms in distorted square-pyramidal geometries are described. The importance of overall charge (in addition to the delocalization of a certain number of electrons) for the stability of such structures is explored through calculations on isoelectronic systems containing boron atoms. The effects of alkyl substitution as well as variations in the structure of the linker attached to the C5 core substructure are explored systematically for a variety of structures that do not have severe geometric constraints that rigidly enforce unusual geometries. In addition, transition structures for reactions involving the intramolecular attack of tetracoordinate carbons on carbenium ion centers were located; in some cases, such carbenium-to-carbonium rearrangement processes (in which tetracoordinate carbon centers act as nucleophiles) are actually both exothermic and accompanied by low activation barriers. [ABSTRACT FROM AUTHOR]

This paper reports new theoretical evidence that supports previous proposals concerning the similarity between transition structures for electrocyclizations and sigmatropic hydrogen shifts. This evidence was obtained using two recently proposed methodologies, namely the so-called generalized population analysis and the formalism of molecular quantum similarity indices. Analysis of multicenter bond indices shows that the transition structures for cationic [1,n] hydrogen shifts do indeed have three-center indices that are similar to those of other three-center carbocations. In addition, the close resemblance of the electronic structures of electrocyclic and sigmatropic transition structures that differ by only a proton is supported by the values of their quantum molecular similarity indices. [ABSTRACT FROM AUTHOR]

Review: [26 refs. [ABSTRACT FROM AUTHOR]

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The reactivity of macrocyclic bis-enones in Diels--Alder reactions was examined using quantum chemical calculations. Stepwise pathways for these transannular cyclo-addition reactions were shown to predominate. Steric interactions and torsional strain appeared to play a major role in controlling the overall barrier for polycycle formation. [ABSTRACT FROM AUTHOR]

Abstract: The results of quantum chemical calculations on a previously proposed biosynthetic pathway for the formation of calophyline A from rhazimol, which features formally forbidden 4-electron [1,2] and [1,3] sigmatropic shifts, are discussed. The proposed pathway was not found to be energetically viable, despite a surprisingly low predicted barrier for the [1,3] shift, but an alternative route involving a series of tautomerizations and carbonyl addition reactions is shown to be more energetically feasible. [Copyright &y& Elsevier]

Quantum chemical calculations (B3LYP and MP2) are described for the formation and rearrangements of carbocations derived from the biological methylation reaction that produces 24-propyl sterols in pelagophyte algae. Previous mechanistic proposals are discussed in light of the results of these calculations. Of particular note is the prediction of a new triple-shift rearrangement that is inherently preferred for the biosynthetically relevant carbocations. Our calculations also reveal how these reactions may be affected by intermolecular interactions with S-adenosylmethionine. [ABSTRACT FROM AUTHOR]

Abstract: Quantum chemical calculations (B3LYP/6-31G(d)) on carbocation rearrangements that are proposed to occur in the biosynthesis of aspernomine are described. Based on these calculations, a pathway involving a concerted but asynchronous [4+2] cycloaddition that avoids the formation of a secondary carbocation is proposed for small model systems. [Copyright &y& Elsevier]

In this paper, we describe theoretical studies, using gas-phase quantum chemical calculations, on carbocationic rearrangement pathways leading to the sesquiterpenes sativene, cyclosativene, α-ylangene, and β-ylangene. For all four sesquiterpene natural products, viable pathways are presented, and these are compared both to mechanistic proposals found in the literature, and in certain cases to alternative stereochemical and rearrangement possibilities, thus providing a basis for comparison to experimental results. We find that these four sesquiterpenes likely arise from a common bicyclic intermediate and, furthermore, that the computed pathways are mostly in agreement with previous mechanistic proposals, although the few differences that we have uncovered are significant. Additionally, the potential energy profiles of the pathways are found to be very flat, supporting the notion that following the initial ionization of farnesyl diphosphate, minimal enzymatic intervention may be required for the generation of such sesquiterpenes. [ABSTRACT FROM AUTHOR]

Biosynthesis of the complex diterpenoid antibiotic pleuromutilin relies on a bifunctional (di)terpene synthase, and here site-directed mutagenesis was used to knockout either of the two active sites. This enabled characterization of the novel ring contracted intermediate produced by the initiating class II diterpene cyclase active site. Quantum chemical calculations further indicate the importance of reactant configuration for this intriguing ring rearrangement. [ABSTRACT FROM AUTHOR]

Aquatolide has been reisolated from its natural source, and its structure has been revised on the basis of quantum-chemical NMR calculations, extensive experimental NMR analysis, and crystallography. [ABSTRACT FROM AUTHOR]

The article describes an approach that makes applied computational chemistry research accessible to blind and visually impaired (BVI) students. The problems encountered and the solutions adopted are described, along with comments from the blind students involved in the research. The tasks associated with conducting applied computational chemistry research are outlined which include the communication and discussion of the chemical questions to be addressed by using computational methods.

Quantum chemical computations (B3LYP/6-31+G(d,p)) were applied to examine the mechanisms of dyotropic rearrangements of spirolactones in order to assess whether these reactions are concerted. Mechanistic experiments, designed on the basis of the results of these calculations, support the conclusions derived from theory. In particular, Zn(II) salts or Brønsted acids induce stepwise dyotropic processes, whereas dyotropic rearrangements mediated by silyltriflates are concerted processes. Additional products isolated with Zn(II) salts support a stepwise process with a carbocationic intermediate. Furthermore, a facile Grob-type fragmentation emanating from both a tricyclic-β-lactone and a spiro-γ-lactone was identified. [ABSTRACT FROM AUTHOR]

Intramolecular [2 + 2] cycloaddition reactions of allene-ynes offer a quick and efficient route to fused bicyclic ring structures. Insights into the mechanism and regiochemical preferences of this reaction are provided herein on the basis of the results of quantum chemical calculations (B3LYP/6-31 +G(d,p)) and select experiments; both indicate that the reaction likely proceeds through a stepwise diradical pathway where one radical center is stabilized through allylic delocalization. The influences of the length of the tether connecting the alkyne and allene and substituent effects are also discussed. [ABSTRACT FROM AUTHOR]

A combination of physical organic experiments and quantum chemical calculations were used to construct a detailed mechanistic model for the Ni(O)-N-heterocyclic carbene-catalyzed vinylcyclopropane-cyclopentene rearrangement that involves a mutiatep oxidative addition/haptotropic shift/reductive elimination pathway. No evidence for the intermediacy of radicals or zwitterions was found. The roles of substituents on the vinylcyclopropane substrate and variations in the ligands on Ni were evaluated. It is postulated that bulky carbene ligands facilitate formation of the active catalyst species. [ABSTRACT FROM AUTHOR]

Mechanistic proposals for the carbocation cascade reaction leading to the tricycic sesquiterpene pentalenene are assessed in light of the results of isotopically sensitive branching experiments with the H309A mutant of pentalenene synthase. These experimental results support a mechanism for pentalenene formation involving a 7-protoilludyl cation whose intermediacy was first predicted using quantum-chemical calculations. [ABSTRACT FROM AUTHOR]