How reliable are DFT transition structures? Comparison of GGA, hybrid-meta-GGA and meta-GGA functionals

Transferable Machine Learning Interatomic Potential for Bond Dissociation Energy Prediction of Drug-like Molecules

We present a transferable MACE interatomic potential that is applicable to open- and closed-shell drug-like molecules containing hydrogen, carbon, and oxygen atoms. Including an accurate description of radical species extends the scope of possible applications to bond dissociation energy (BDE) prediction, for example, in the context of cytochrome P450 (CYP) metabolism. The transferability of the MACE potential was validated on the COMP6 data set, containing only closed-shell molecules, where it reaches better accuracy than the readily available general ANI-2x potential. MACE achieves similar accuracy on two CYP metabolism-specific data sets, which include open- and closed-shell structures. This model enables us to calculate the aliphatic C-H BDE, which allows us to compare reaction energies of hydrogen abstraction, which is the rate-limiting step of the aliphatic hydroxylation reaction catalyzed by CYPs. On the "CYP 3A4" data set, MACE achieves a BDE RMSE of 1.37 kcal/mol and better prediction of BDE ranks than alternatives: the semiempirical AM1 and GFN2-xTB methods and the ALFABET model that directly predicts bond dissociation enthalpies. Finally, we highlight the smoothness of the MACE potential over paths of sp3C-H bond elongation and show that a minimal extension is enough for the MACE model to start finding reasonable minimum energy paths of methoxy radical-mediated hydrogen abstraction. Altogether, this work lays the ground for further extensions of scope in terms of chemical elements, (CYP-mediated) reaction classes and modeling the full reaction paths, not only BDEs.

Mechanistic studies of HF/BF3-catalyzed anthracene polymerization to prepare mesophase pitch

CONTEXT

The mesophase pitch prepared by acid catalytic method typically had the advantages of low softening point and high solubility. To fully understand the mechanism of acid-catalyzed reactions and gain a deeper understanding of the microstructure of mesophase pitch, this article studied the mechanism of hydrofluoride/boron trifluoride (HF/BF3)-catalyzed anthracene using molecular simulation methods. The results showed that there might be two types of carbocations present in the system: classical and non-classical carbocations, and five reactions might occur, protonation reaction, chain elongation reaction, intramolecular cyclization reaction, deprotonation reaction, and dehydrogenation reaction. Classical carbocations acted as reactive intermediates in the chain elongation reaction and intramolecular cyclization reaction. When anthracene occurred chain elongation reactions with carbocations to form polymers, the generation of the tetramer required lager energy barriers than that of the dimer and trimer. The stiffness and flatness of molecules could be increased via intramolecular cyclization reactions. The polymers of anthracene might also occurred dehydrogenation reactions when the non-classical carbocations played the role of reactive intermediates. The dehydrogenation reactions required large energy barriers, which might be the reason for the product having a high aliphatic hydrogen content.

METHOD

The Materials Studio (MS) 2020 software was used to complete the simulation. The atomic charge distribution calculation and the structure optimization of molecules were carried out using the B3LYP functional and DNP basis. The DFT-D (TS) dispersion corrections were added to calculate the dispersion interaction between aromatic molecules. The complete LST/QST method was used to search the transition states and calculate the reaction energy barrier.

Chemical Mechanism of Fireworm Bioluminescence - A Theoretical Proposition

Odontosyllis undecimdonta is a marine worm, commonly known as a fireworm, that exhibits bluish-green bioluminescence (BL). The luciferin (L) and oxyluciferin (OL) during fireworm BL have been experimentally identified in vitro. The L and OL are the respective starting point and ending point of a series of complicated chemical reactions in the BL. However, the chemical mechanism of the fireworm BL remains largely unknown. Before the experiments provided strong evidence for the mechanism, based on our previously successful studies on several bioluminescent systems, we theoretically proposed the chemical mechanism of the fireworm BL in this article. By means of the spin-flip and time-dependent density functional calculations, we clearly described the complete process from L to OL: under the catalysis of luciferase, L undergoes deprotonation and reacts with 3O2 to form a dioxetanone anion via the single-electron transfer mechanism; the dioxetanone anion decomposes into the OL at the first singlet excited state (S1) by the gradually reversible charge-transfer-induced luminescence mechanism; and the S1-OL emits light and deexcites to OL in the ground state.

Recent Advancements in Mechanistic Studies of Palladium- and Nickel-Catalyzed Ethylene Copolymerization with Polar Monomers

The introduction of polar functional groups into polyolefin chain structures creates opportunities to enhance specific properties, such as adhesion, dyeability, printability, compatibility, thermal stability, and electrical conductivity, which widen the range of potential applications for these modified materials. Transition metal catalysts, especially late transition metals, have proven to be highly effective in copolymerization processes due to their reduced Lewis acidity and electrophilicity. However, when compared to the significant progress and summary of synthetic methods, there is a distinct lack of a comprehensive summary of mechanistic studies pertaining to the catalytic systems involved in ethylene copolymerization catalyzed by palladium and nickel catalysts. In this review, we have provided a comprehensive summary of the latest developments in mechanistic studies of ethylene copolymerization with polar monomers catalyzed by late-transition-metal complexes. Experimental and computational methods were employed to conduct a detailed investigation of these organic and organometallic systems. It is mainly focused on ligand substitution, changes in binding modes, ethylene/polar monomer insertion, chelate opening, and β-H elimination. Factors that control the catalytic activity, molecular weight, comonomer incorporation ratios, and branch content are analyzed, these include steric repulsions between ligands and monomers, electronic effects arising from both ligands and monomers, and so on.

First-Principles Calculations to Investigate the Stability and Thermodynamic Properties of a Newly Exposed Lithium-Gallium-Iridium-Based Full-Heusler Compound

The structural, optical, electrical, thermodynamic, superconducting, and mechanical characteristics of LiGa₂Ir full-Heusler alloys with the MnCu₂Al configuration were comprehensively examined in this work using the first-principles computation approach premised upon density functional analysis. This theoretical approach is the first to investigate the influence of pressure on the mechanical and optical characteristics of LiGa₂Ir. The structural and chemical bonding analysis shows that hydrostatic pressure caused a decrease in the lattice constant, volume, and bond length of each cell. According to the mechanical property calculations, the LiGa₂Ir cubic Heusler alloy exhibits mechanical stability. It also has ductility and anisotropic behavior. This metallic substance shows no band gap throughout the applied pressure range. The physical characteristics of the LiGa₂Ir full-Heusler alloy are analyzed in the operating pressure range of 0-10 GPa. The quasi-harmonic Debye model is employed to analyze thermodynamic properties. The Debye temperature (291.31 K at 0 Pa) increases with hydrostatic pressure. A newly invented structure attracted a lot of attention around the globe for its superior superconductivity (T_c ∼ 2.95 K). Optical functions have also been improved after applying stress to utilize it in optoelectronic/nanoelectric devices. The optical function analysis is supported strongly by the electronic properties. Due to these reasons, LiGa₂Ir imposed an essential guiding principle for relevant future research and could be a credible candidate substance for industrial settings.

Predicting Regioselectivity of Cytosolic Sulfotransferase Metabolism for Drugs

Cytosolic sulfotransferases (SULTs) are a family of enzymes responsible for the sulfation of small endogenous and exogenous compounds. SULTs contribute to the conjugation phase of metabolism and share substrates with the uridine 5'-diphospho-glucuronosyltransferase (UGT) family of enzymes. UGTs are considered to be the most important enzymes in the conjugation phase, and SULTs are an auxiliary enzyme system to them. Understanding how the regioselectivity of SULTs differs from that of UGTs is essential from the perspective of developing novel drug candidates. We present a general ligand-based SULT model trained and tested using high-quality experimental regioselectivity data. The current study suggests that, unlike other metabolic enzymes in the modification and conjugation phases, the SULT regioselectivity is not strongly influenced by the activation energy of the rate-limiting step of the catalysis. Instead, the prominent role is played by the substrate binding site of SULT. Thus, the model is trained only on steric and orientation descriptors, which mimic the binding pocket of SULT. The resulting classification model, which predicts whether a site is metabolized, achieved a Cohen's kappa of 0.71.

Investigating the Association Reactions of HOCH2CO and HOCHCHO with O2: A Quantum Computational and Master Equation Study

Glycolaldehyde, HOCH₂CHO, is an important multifunctional atmospheric trace gas formed in the oxidation of ethylene and isoprene and emitted directly from burning biomass. The initial step in the atmospheric photooxidation of HOCH₂CHO yields HOCH₂CO and HOCHCHO radicals; both of these radicals react rapidly with O₂ in the troposphere. This study presents a comprehensive theoretical investigation of the HOCH₂CO + O₂ and HOCHCHO + O₂ reactions using high-level quantum chemical calculations and energy-grained master equation simulations. The HOCH₂CO + O₂ reaction results in the formation of a HOCH₂C(O)O₂ radical, while the HOCHCHO + O₂ reaction yields (HCO)₂ + HO₂. Density functional theory calculations have identified two open unimolecular pathways associated with the HOCH₂C(O)O₂ radical that yield HCOCOOH + OH or HCHO + CO₂ + OH products; the former novel bimolecular product pathway has not been previously reported in the literature. Master equation simulations based on the potential energy surface calculated here for the HOCH₂CO + O₂ recombination reaction support experimental product yield data from the literature and indicate that, even at total pressures of 1 atm, the HOCH₂CO + O₂ reaction yields ∼11% OH at 298 K.

Formation of Larger Molecular Weight Disinfection Byproducts from Acetaminophen in Chlorine Disinfection

Acetaminophen is widely used to treat mild to moderate pain and to reduce fever. Under the worldwide COVID-19 pandemic, this over-the-counter pain reliever and fever reducer has been drastically consumed, which makes it even more abundant than ever in municipal wastewater and drinking water sources. Chlorine is the most widely used oxidant in drinking water disinfection, and chlorination generally causes the degradation of organic compounds, including acetaminophen. In this study, a new reaction pathway in the chlorination of acetaminophen, i.e., oxidative coupling reactions via acetaminophen radicals, was investigated both experimentally and computationally. Using an ultraperformance liquid chromatograph coupled to an electrospray ionization-triple quadrupole mass spectrometer, we detected over 20 polymeric products in chlorinated acetaminophen samples, some of which have structures similar to the legacy pollutants "polychlorinated biphenyls". Both C-C and C-O bonding products were found, and the corresponding bonding processes and kinetics were revealed by quantum chemical calculations. Based on the product confirmation and intrinsic reaction coordinate computations, a pathway for the formation of the polymeric products in the chlorination of acetaminophen was proposed. This study suggests that chlorination may cause not only degradation but also upgradation of a phenolic compound or contaminant.

Predicting Regioselectivity of AO, CYP, FMO, and UGT Metabolism Using Quantum Mechanical Simulations and Machine Learning

Unexpected metabolism in modification and conjugation phases can lead to the failure of many late-stage drug candidates or even withdrawal of approved drugs. Thus, it is critical to predict the sites of metabolism (SoM) for enzymes, which interact with drug-like molecules, in the early stages of the research. This study presents methods for predicting the isoform-specific metabolism for human AOs, FMOs, and UGTs and general CYP metabolism for preclinical species. The models use semi-empirical quantum mechanical simulations, validated using experimentally obtained data and DFT calculations, to estimate the reactivity of each SoM in the context of the whole molecule. Ligand-based models, trained and tested using high-quality regioselectivity data, combine the reactivity of the potential SoM with the orientation and steric effects of the binding pockets of the different enzyme isoforms. The resulting models achieve κ values of up to 0.94 and AUC of up to 0.92.

The performance of exchange-correlation functionals in describing electron density parameters of saddle point structures along chemical reactions

This work is focused on evaluating the performance of exchange-correlation functionals from density functional theory in providing descriptor values derived from the electron density of saddle point structures (transition states) in chemical reactions. The properties investigated were obtained from the quantum theory of atoms in molecules, including atomic charges and electron density topological data at the bond critical points. In addition, parameters from the Interacting quantum atom energy partition were used as well in this comparative study. The reference values are attained in coupled cluster calculations with iterative single and double excitations (CCSD). Six elementary reactions are considered here: CO + H₂  ↔ H₂ CO, CO + H₂ O ↔ HCOOH, HCN ↔ HNC, H + F₂  ↔ HF + F, H + N₂  ↔ HN₂ , and H + CO ↔ HCO. In general, the BB1K functional (hybrid-meta-generalized gradient approximation) provides the best description of these properties. Our study indicates that an intermediate percentage of nonlocal exact exchange, around 40%-55% (perhaps even larger), is probably required for attaining more accurate values with actual functionals, although this condition is not able of explaining all the trends observed.

Remarkably enhanced dynamic oxygen migration on graphene oxide supported by copper substrate

The dynamic covalent properties of graphene oxide (GO) are of fundamental interest to a broad range of scientific areas and technological applications. It remains a challenge to access feasible dynamic reactions for reversibly breaking/reforming the covalent bonds of oxygen functional groups on GO, although these reactions can be induced by photonic or mechanical routes, or mediated by adsorbed water. Here, using density functional theory calculations, we demonstrate the remarkably enhanced dynamic oxygen migration along the basal plane of GO supported by copper substrate (GO@copper), with C-O bond breaking reactions and proton transfer between neighboring epoxy and hydroxyl groups. Compared to reactions on GO, the energy barriers of oxygen migrations on GO@copper are sharply reduced to be less than or comparable to thermal fluctuations, and meanwhile the crystallographic match between GO and copper substrate induces new oxygen migration paths on GO@copper. This work sheds light on understanding of the metal substrate-enhanced dynamic properties of GO, and evidences the strategy to tune the activity of two-dimensional-interfacial oxygen groups for various potential applications.

Mechanisms, Challenges, and Opportunities of Dual Ni/Photoredox-Catalyzed C(sp2)-C(sp3) Cross-Couplings

The merging of photoredox and nickel catalysis has revolutionized the field of C-C cross-coupling. However, in comparison to the development of synthetic methods, detailed mechanistic investigations of these catalytic systems are lagging. To improve the mechanistic understanding, computational tools have emerged as powerful tools to elucidate the factors controlling reactivity and selectivity in these complex catalytic transformations. Based on the reported computational studies, it appears that the mechanistic picture of catalytic systems is not generally applicable, but is rather dependent on the specific choice of substrate, ligands, photocatalysts, etc. Given the complexity of these systems, the need for more accurate computational methods, readily available and user-friendly dynamics simulation tools, and data-driven approaches is clear in order to understand at the molecular level the mechanisms of these transformations. In particular, we anticipate that such improvement of theoretical methods will become crucial to advance the understanding of excited-state properties and dynamics of key species, as well as to enable faster and unbiased exploration of reaction pathways. Further, with greater collaboration between computational, experimental, and spectroscopic communities, the mechanistic investigation of photoredox/Ni dual-catalytic reactions is expected to thrive quickly, facilitating the design of novel catalytic systems and promoting our understanding of the reaction selectivity.

Graphene-induced planarization of cyclooctatetraene derivatives

Stable equilibrium compounds containing a planar antiaromatic cyclooctatetraene (COT) ring are promising candidates for organic electronic devices such as organic semiconductor transistors. The planarization of COT by incorporation into rigid planar π-systems, as well as by oxidation or reduction has attracted considerable attention in recent years. Using dispersion-corrected density functional theory calculations, we explore an alternative approach of planarizing COT derivatives by adsorption onto graphene. We show that strong π-π stacking interactions between graphene and COT derivatives induce a planar structure with an antiaromatic central COT ring. In addition to being reversible, this strategy provides a novel approach for planarizing COT without the need for incorporation into a rigid structure, atomic substitution, oxidation, or reduction.

Exploring the evolution patterns of melem from thermal synthesis of melamine to graphitic carbon nitride

In the exploration of synthesizing graphitic carbon nitride (g-C₃N₄), the existence of secondary anime bridging units shows the incompleteness of related theories. Thus, taking the thermal synthesis of melamine as an example, this work finds a possible reaction path with Density Functional Theory (DFT) for forming melem during the thermal synthesis of g-C₃N₄. Combined with transition state theory (TST), it indicates that the formation of melem results from the condensation of melamine and isomerization of melam. Meanwhile, the weak signal near 2135 cm⁻¹ in the Fourier Transform Infrared Spectra (FTIR) corresponds to the vibration of carbodi-imines (–N Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> CN–), which further proves the proposed reaction path. Thus, this work can explain the formation of g-C₃N₄ and its monomer, which may contribute to the successful formation of ideal g-C₃N₄ in the future.

In the exploration of synthesizing graphitic carbon nitride (g-C₃N₄), the existence of secondary anime bridging units shows the incompleteness of related theories.

Identifying the true origins of selectivity in chiral phosphoric acid catalyzed N-acyl-azetidine desymmetrizations

The first catalytic intermolecular desymmetrization of azetidines was reported by Sun and coworkers in 2015 using a BINOL-derived phosphoric acid catalyst (J. Am. Chem. Soc. 2015, 137, 5895-5898). To uncover the mechanism of the reaction and the origins of the high enantioselectivity, Density Functional Theory (DFT) calculations were performed at the B97D3/6-311+G(2d,2p)/SMD(toluene)//B97D3/6-31G(d,p)/CPCM(toluene) level of theory. Comparison of four possible activation modes confirms that this reaction proceeds through the bifunctional activation of the azetidine nitrogen and the thione tautomer of the 2-mercaptobenzothiazole nucleophile. Upon thorough conformational sampling of the enantiodetermining transition structures (TSs), a free energy difference of 2.0 kcal mol-1 is obtained, accurately reproducing the experimentally measured 88% e.e. at 80 °C. This energy difference is due to both decreased distortion and increased non-covalent interactions in the pro-(S) TS. To uncover the true origins of selectivity, the TSs optimized with the full catalyst were compared to those optimized with a model catalyst through steric maps. It is found that the arrangements displayed by the substrates are controlled by strict primary orbital interaction requirements at the transition complex, and their ability to fit into the catalyst pocket drives the selectivity. A general model of selectivity for phosphoric acid-catalyzed azetidine desymmetrizations is proposed, which is based on the preference of the nucleophile and benzoyl group to occupy empty quadrants of the chiral catalyst pocket.

Nazarov Cyclizations Catalyzed by BINOL Phosphoric Acid Derivatives: Quantum Chemistry Struggles To Predict the Enantioselectivity

Quantum chemical calculations have successfully predicted the stereoselectivities of many BINOL phosphoric acid catalyzed reactions over the past 10-15 years. Herein we report a contrasting example: a reaction for which standard quantum chemistry techniques have proven unexpectedly ineffective at explaining the stereoselectivity. The Nazarov cyclizations of a divinyl ketone catalyzed by a BINOL phosphoric acid or H₈-BINOL dithiophosphoric acid were studied with a conventional contemporary quantum chemical approach, consisting of transition state optimizations with B3LYP-D3(BJ) and single-point calculations with several functionals in implicit solvent. Unexpectedly, different functionals gave widely different predictions of the level of enantioselectivity and were unable even to agree on which enantiomer of the product would predominate. Molecular dynamics simulations with the OPLS-AA force field provided evidence that the transition state geometries optimized with DFT in the gas phase or in implicit solvent are not good representations of the true transition states of these reactions in solution. One possible reason for this, which may also explain the failure of quantum chemical techniques to reliably predict the enantioselectivity, is the fact that the transition states contain ion pairs which are not highly organized and do not contain any strongly directional noncovalent interactions between the substrate and the catalyst.

Chiral Phosphoric Acid Catalysis: The Terada Model Revisited

Since Akiyama and Terada independently reported the introduction of chiral phosphoric acids (CPAs) as effective catalysts for Mannich-type reactions in 2004, the field of CPA catalysis has grown immensely. Terada reported in 2008 the first example of the activation of aldehydes by a CPA. Based on density functional theory (DFT) calculations, Terada proposed a dual activation mode for this enantioselective aza-ene-type reaction between an aldehyde and an enecarbamate. In this model, hydrogen bonds between the catalyst's hydroxyl group and the carbonyl oxygen and the catalyst's P═O and the formyl proton were observed; the nucleophile then attacks without coordination to the catalyst. This reaction model provided the mechanistic basis for understanding Terada's reaction and many other asymmetric transformations. In the present study, DFT calculations are reported that identify a lower-energy mechanism for this landmark reaction. In this new model, hydrogen bonds between the catalyst's hydroxyl group and the aldehyde oxygen and the catalyst's P═O and the NH group of the enecarbamate are seen. The new model rationalizes the stereoselective outcome of Terada's reaction and offers insight into why a more sterically demanding catalyst gives lower levels of enantioselectivity.

Tetrahedral Pt10- Cluster with Unique Beta Aromaticity and Superatomic Feature in Mimicking Methane

Utilizing a customized metal cluster source in tandem with a flow tube reactor and a reflectron time-of-flight mass spectrometer, we have obtained well-resolved pure metal clusters Pt_n^- and observed their gas-phase reactions with a few small gas molecules. Interestingly, the remarkable inertness of Pt₁₀^- was repeatedly observed in different reactions. Meanwhile, we have determined the structure of Pt₁₀^- within a regular tetrahedron. Considering that Pt possesses 5d⁹6s¹ electron configuration, the tetrahedral Pt₁₀^- exhibits unexpected stability at neither a magic number of valence electrons nor a shell closure of geometric structure. Comprehensive theoretical calculations unveil the stability of Pt₁₀^- is significantly associated with the all-metal aromaticity. In addition to the classical total aromaticity, which is mainly due to 6s electrons, there is unique beta-aromaticity ascribed to spin-polarized beta 5d electrons pertaining to singly occupied multicenter bonds. Further, we demonstrate the superatomic feature of such a transition metal cluster Pt₁₀^-, as Pt₆@Pt₄^-, in mimicking methane.

Understanding the mechanism of the chiral phosphoric acid-catalyzed aza-Cope rearrangement

The first catalytic enantioselective aza-Cope rearrangement was reported in 2008 by Rueping et al. The reaction is catalyzed by a 1,1'-bi-2-naphthol-derived (BINOL-derived) phosphoric acid and achieved high yields and enantioselectivities (up to 97 : 3 er with 75% yield). This work utilizes Density Functional Theory to understand the mechanism of the reaction and explain the origins of the enantioselectivity. An extensive conformational search was carried out to explore the different activation modes by the catalyst and, the Transition State (TS) leading to the major product was found to be 1.3 kcal mol-1 lower in energy than the TS leading to the minor product. The origin of this stabilization was rationalized with NBO and NCI analysis: it was found that the major TS has a greater number of non-bonding interactions between the substrate and the catalyst, and shows stronger H-bond interactions between H atoms in the substrate and the O atoms in the phosphate group of the catalyst.

Topography of the free energy landscape of Claisen-Schmidt condensation: solvent and temperature effects on the rate-controlling step

Recent studies have found that hydroxide elimination and the C[double bond, length as m-dash]C bond formation step in base-promoted aldol condensation have a strong influence on the overall rate of the reaction, in contrast to the well-accepted first enolization or C-C bond formation step. Here, applying theoretical models to the prototypical reaction of chalcone formation, the complete free energy profile of Claisen-Schmidt condensation is assessed, revealing how a protic solvent and a slight increase in temperature can induce the second enolization as the rate-controlling step (RCS). It is also observed: i) the nonexistence of a step with a much higher energetic barrier than the others, making the concept of RCS debatable; and ii) that the overall inverse kinetic isotopic effect does not exclude second enolization as a RCS in protic continuum medium. We expect that these results can expand the understanding of the decisive role of physicochemical factors on the choose of the RCS in the aldol condensation.

How Lewis Acids Catalyze Ring-Openings of Cyclohexene Oxide

We have quantum chemically studied the Lewis acid-catalyzed epoxide ring-opening reaction of cyclohexene epoxide by MeZH (Z = O, S, and NH) using relativistic dispersion-corrected density functional theory. We found that the reaction barrier of the Lewis acid-catalyzed epoxide ring-opening reactions decreases upon ascending in group 1 along the series Cs+ > Rb+ > K+ > Na+ > Li+ > H+. Our activation strain and Kohn-Sham molecular orbital analyses reveal that the enhanced reactivity of the Lewis acid-catalyzed ring-opening reaction is caused by the reduced steric (Pauli) repulsion between the filled orbitals of the epoxide and the nucleophile, as the Lewis acid polarizes the filled orbitals of the epoxide more efficiently away from the incoming nucleophile. Furthermore, we established that the regioselectivity of these ring-opening reactions is, aside from the "classical" strain control, also dictated by a hitherto unknown mechanism, namely, the steric (Pauli) repulsion between the nucleophile and the substrate, which could be traced back to the asymmetric orbital density on the epoxide. In all, this work again demonstrates that the concept of Pauli-lowering catalysis is a general phenomenon.

Quantum chemical study of gas-phase reactions of isoprene with OH radicals producing highly oxidised second-generation products

The formation of secondary organic aerosols caused by atmospheric oxidation of isoprene is harmful to human health and the climate; thus, isoprene oxidation is further mandatory to obtain less harmful or harmless highly oxidised products. In this numerical investigation, 2-hydroperoxy-2-methylbut-3-en-1-ol (ISOPOOH) was considered the model compound to investigate the formation of three RO₂ radicals (C₅H₁₁O₄, C₅H₁₁O₆ and C₅H₁₁O₅) and two saturated highly oxidised products (C₅H₁₂O₆ and C₅H₁₀O₆). The complete reaction network and its thermodynamics and kinetics were analysed to obtain the most probable and feasible reaction pathways. Four different levels of theories (HF, B3LYP, M06-2X and ωB97XD with basis set of 6-31+g(d,p)) were employed to explore a global minimum of ISOPOOH. All theories provided approximately close energetics; however, because of the novelty of the functional and parameterisation of the basis set, the ωB97XD functional was selected to examine the reaction mechanism. C₅H₁₂O₆ was formed as the second-generation highly oxidised product during ISOPOOH oxidation.

Direct Observation of Structural Heterogeneity and Tautomerization of Single Hypericin Molecules

Tautomerization is a fundamental chemical reaction which involves the relocation of a proton in the reactants. Studying the optical properties of tautomeric species is challenging because of ensemble averaging. Many molecules, such as porphines, porphycenes, or phenanthroperylene quinones, exhibit a reorientation of the transition dipole moment (TDM) during tautomerization, which can be directly observed in single-molecule experiments. Here, we study single hypericin molecules, which is a prominent phenanthroperylene quinone showing antiviral, antidepressive, and photodynamical properties. Observing abrupt flipping of the image pattern combined with time-dependent density functional theory calculations allows drawing conclusions about the coexistence of four tautomers and their conversion path. This approach allows the unambiguous assignment of a TDM orientation to a specific tautomer and enables the determination of the chemical structure in situ. Our approach can be applied to other molecules showing TDM reorientation during tautomerization, helping to gain a deeper understanding of this important process.

Mechanistic insights on CO2 utilization using sustainable catalysis

Caffeinium halides were used to catalyse the cycloaddition of CO2 to form cyclic carbonates. The reaction intermediates were isolated and characterized experimentally. The reaction mechanism has been confirmed by DFT calculations.

Flow synthesis kinetics for lomustine, an anti-cancer active pharmaceutical ingredient

An original reaction mechanism and kinetic parameter estimation has been achieved for lomustine, an anti-cancer active pharmaceutical ingredient (API).

The origin of the regiospecificity of acrolein dimerization

The NCI at the transition state are the key factor controlling the regiospecificity in the acrolein dimerization.

Reactivity prediction in aza-Michael additions without transition state calculations: the Ames test for mutagenicity

Animal testing remains a contentious ethical issue in predictive toxicology. Thus, a fast, versatile, low-cost quantum chemical model is presented for predicting the risk of Ames mutagenicity in a series of 1,4 Michael acceptor type compounds. This framework eliminates the need for transition state calculations, and uses an intermediate structure to probe the reactivity of aza-Michael acceptors. This model can be used in a variety of settings e.g., the design of targeted covalent inhibitors and polyketide biosyntheses.

Density Functional Theory in the Prediction of Mutagenicity: A Perspective

As a field, computational toxicology is concerned with using in silico models to predict and understand the origins of toxicity. It is fast, relatively inexpensive, and avoids the ethical conundrum of using animals in scientific experimentation. In this perspective, we discuss the importance of computational models in toxicology, with a specific focus on the different model types that can be used in predictive toxicological approaches toward mutagenicity (SARs and QSARs). We then focus on how quantum chemical methods, such as density functional theory (DFT), have previously been used in the prediction of mutagenicity. It is then discussed how DFT allows for the development of new chemical descriptors that focus on capturing the steric and energetic effects that influence toxicological reactions. We hope to demonstrate the role that DFT plays in understanding the fundamental, intrinsic chemistry of toxicological reactions in predictive toxicology.

Predicting reactivity to drug metabolism: beyond P450s-modelling FMOs and UGTs

We present a study based on density functional theory calculations to explore the rate limiting steps of product formation for oxidation by Flavin-containing Monooxygenase (FMO) and glucuronidation by the UDP-glucuronosyltransferase (UGT) family of enzymes. FMOs are responsible for the modification phase of metabolism of a wide diversity of drugs, working in conjunction with Cytochrome P450 (CYP) family of enzymes, and UGTs are the most important class of drug conjugation enzymes. Reactivity calculations are important for prediction of metabolism by CYPs and reactivity alone explains around 70-85% of the experimentally observed sites of metabolism within CYP substrates. In the current work we extend this approach to propose model systems which can be used to calculate the activation energies, i.e. reactivity, for the rate-limiting steps for both FMO oxidation and glucuronidation of potential sites of metabolism. These results are validated by comparison with the experimentally observed reaction rates and sites of metabolism, indicating that the presented models are suitable to provide the basis of a reactivity component within generalizable models to predict either FMO or UGT metabolism.

DFT study on dibenzofuran conversion to cyclohexane and benzene in gas, water and methanol solvents

Hydrodeoxygenation (HDO) of dibenzofuran is studied using density functional theory (DFT) with SMD implicit solvation model to give products like benzene and cyclohexane. Water and methanol are used as solvents, and gas-phase calculations are also performed for comparison. HDO is proposed via two major route- 1) saturation of phenyl rings followed by deoxygenation, 2) cleavage of C-O bond for oxy -removal followed by ring saturation. First, thermochemical parameters like Gibbs free energy change and enthalpy change are calculated at varying temperature in gas, water and methanol. Then, the solvation free energy is calculated for methanol and water to determine the ease of separation of products from the solvents. Finally, a Single Point Energy calculation is performed in the gas phase. It is found that water is the best solvent among three mediums and offers a significant advantage in some reactions such as the conversion of dibenzofuran to 1,2,3,4,4a,9b-hexahydrodibenzo[b,d]furan, 2-cyclohexyl phenol to bicyclo-hexan-2-ol and biphenyl to cyclohexyl benzene. Water is also found to be a better medium for separation of all the intermediates and products from the solvent over methanol. The effect of temperature was also studied, and it was found that the increase in temperature is unfavourable in all mediums for almost all reactions.

Functionalized Double Strain-Promoted Stapled Peptides for Inhibiting the p53-MDM2 Interaction

The Sondheimer dialkyne reagent has previously been employed in strain-promoted double-click cycloadditions with bis-azide peptides to generate stapled peptide inhibitors of protein-protein interactions. The substituted variants of the Sondheimer dialkyne can be used to generate functionalized stapled peptide inhibitors with improved biological properties; however, this remains a relatively underdeveloped field. Herein, we report the synthesis of new substituted variants of Sondheimer dialkyne and their application in the stapling of p53-based diazido peptides to generate potent stapled peptide-based inhibitors of the oncogenic p53-MDM2 interaction. The functionalized stapled peptide formed from a meta-fluoro-substituted Sondheimer dialkyne was found to be the most potent inhibitor. Furthermore, through experimental studies and density functional theory calculations, we investigated the impact of the substituent on the strain-promoted double-click reactivity of Sondheimer dialkyne.

Vinylidene Homologation of Boronic Esters and its Application to the Synthesis of the Proposed Structure of Machillene

Alkenyl boronic esters are important reagents in organic synthesis. Herein, we report that these valuable products can be accessed by the homologation of boronic esters with lithiated epoxysilanes. Aliphatic and electron-rich aromatic boronic esters provided vinylidene boronic esters in moderate to high yields, while electron-deficient aromatic and vinyl boronic esters were found to give the corresponding vinyl silane products. Through DFT calculations, this divergence in mechanistic pathway has been rationalized by considering the stabilization of negative charge in the C-Si and C-B bond breaking transition states. This vinylidene homologation was used in a short six-step stereoselective synthesis of the proposed structure of machillene, however, synthetic and reported data were found to be inconsistent.

Theoretical study of the 1,3-DC reaction between fluorinated alkynes and azides: Reactivity indices, transition structures, IGM and ELF analysis

DFT/B3LYP/6-31 + g(d,p) calculations were performed and reactivity indices, transition structures theory were applied to elucidate the molecular mechanism of the reaction between fluorinated alkynes and different azides. The process of cycloaddition operates through a one-step mechanism and an asynchronous transition states. Examination of the energy profile in the gas phase show two possible 1,4 and 1,5 addition channels for amid, the former is preferred. Furthermore, the Parr functions have used to elucidate the reaction's regioselectivity. It was noted that the addition of solvent (DMSO) does not affect the regioselectivity of the reactions. Analysis of charge transfer in the transition structures shows a moderate polar character for the majority of the studied reactions. Moreover, the independent gradient model based on promolecular density (IGM) has been used to evaluate the asynchronicity of the formation of the two new sigma bonds. Finally, the ELF calculation has been performed to clearly describe the formation of the previous bonds along the IRC path.

Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols

Targeted covalent inhibitor drugs require computational methods that go beyond simple molecular-mechanical force fields in order to model the chemical reactions that occur when they bind to their targets. Here, several semiempirical and density-functional theory (DFT) methods are assessed for their ability to describe the potential energy surface and reaction energies of the covalent modification of a thiol by an electrophile. Functionals such as PBE and B3LYP fail to predict a stable enolate intermediate. This is largely due to delocalization error, which spuriously stabilizes the prereaction complex, in which excess electron density is transferred from the thiolate to the electrophile. Functionals with a high-exact exchange component, range-separated DFT functionals, and variationally optimized exact exchange (i.e., the LC-B05minV functional) correct this issue to various degrees. The large gradient behavior of the exchange enhancement factor is also found to significantly affect the results, leading to the improved performance of PBE0. While ωB97X-D and M06-2X were reasonably accurate, no method provided quantitative accuracy for all three electrophiles, making this a very strenuous test of functional performance. Additionally, one drawback of M06-2X was that molecular dynamics (MD) simulations using this functional were only stable if a fine integration grid was used. The low-cost semiempirical methods, PM3, AM1, and PM7, provide a qualitatively correct description of the reaction mechanism, although the energetics is not quantitatively reliable. As a proof of concept, the potential of mean force for the addition of methylthiolate to methylvinyl ketone was calculated using quantum mechanical/molecular mechanical MD in an explicit polarizable aqueous solvent. © 2019 Wiley Periodicals, Inc.

Reassessment of the Mechanisms of Thermal C-H Bond Activation of Methane by Cationic Magnesium Oxides: A Critical Evaluation of the Suitability of Different Density Functionals

The mechanisms of the thermal reactions of the two iconic magnesium oxide cations MgO^.+ and Mg₂ O₂ ^.+ with methane have been re-evaluated at the CCSD(T)/CBS//CCSD/def2-TZVP level of theory. For the reaction of MgO^.+ with CH₄ , only the classical hydrogen-atom transfer (HAT) was found; in contrast, for the Mg₂ O₂ ^.+ /CH₄ couple, both HAT and proton-coupled electron-transfer (PCET) exist as mechanistic variants. In order to evaluate the suitability of density functional theory (DFT) methods, the reactions were computed by using 27 density functionals. The results obtained demonstrate that the various DFT methods often deliver rather different results for both geometric and energetic features. As to the prediction of the apparent barriers, pure functionals give the largest mean absolute errors. BMK, ωB97XD, and the double-hybrid functional mPW2PLYP were confirmed to come closest to the results provided by CCSD(T)/CBS. Thus, mechanistic conclusions based on a single DFT method should be viewed with great caution. In summary, this study may assist in the selection of a suitable quantum chemical method to unravel the mechanistic details of C-H bond activation by charged metal oxides.

DFT investigation on thermochemical analyses of conversion of xylose to linear alkanes in aqueous phase

Xylose is an integral part of hemicellulose fraction of lignocellulosic biomass. Its abundance in the lignocellulose makes it a desirable component for converting into various value-added compounds. In this study, conversion of xylose to four linear alkanes has been discussed by five different schemes including their thermochemistry under the framework of density functional theory. Main products are butane, pentane, octane and tridecane whereas the intermediate products include furfural, tetrahydrofuran, pentane-1,5-diol, etc. The simulations have been performed at B3LYP/6-31 + g(d,p) and M06-2X/6-31 + g(d,p) level of theories in aqueous phase using SMD solvation model. Thermochemical parameters (ΔG, ΔH and K_eq) are obtained at a wide range of temperature, i.e. 298-698 K. Single point energy change (ΔE) of all the conversion steps has also been calculated at M05-2X/6-311++g(3df,2p) level of theory in the aqueous phase. It is observed that temperature plays a vital role in the formation of products. At high temperature, only scheme RS 1 (i.e. xylose to butane) can proceed to produce butane. The absolute difference between two functionals, B3LYP and M06-2X, was found to be small (<2 kcal/mol) for ring opening reactions making both the functionals suitable for a qualitative study. For saturation of cyclic compounds, a large difference (>10 kcal/mol) was observed between the two functionals making higher accuracy method more suitable for them. For all other reactions, use of M06-2X can be preferred.