An example of a stepwise mechanism for the catalyst-free 1,3-dipolar cycloaddition between a nitrile oxide and an electron rich alkene

The Puzzle of the Regioselectivity and Molecular Mechanism of the (3+2) Cycloaddition Reaction Between E-2-(Trimethylsilyl)-1-Nitroethene and Arylonitrile N-Oxides: Molecular Electron Density Theory (MEDT) Quantumchemical Study

The regioselectivity and molecular mechanism of the (3+2) cycloaddition reaction between E-2-(trimethylsilyl)-1-nitroethene and arylonitrile N-oxides were explored on the basis of the ωB97XD/6-311+G(d) (PCM) quantumchemical calculations. It was found that the earlier postulate regarding the regioselectivity of the cycloaddition stage should be undermined. Within our research, several aspects of the title reaction were also examined: interactions between reagents, electronic structures of alkenes and nitrile oxides, the nature of transition states, the influence of the polarity solvent on the reaction selectivity and mechanism, substituent effects, etc. The obtained results offer a general conclusion for all of the important aspects of some groups of cycloaddition processes.

Carbon fixation of CO2 via cyclic reactions with borane in gaseous atmosphere leading to formic acid (and metaboric acid); A potential energy surface (PES) study

Carbon dioxide (CO₂), a stable gaseous species, occupies the troposphere layer of the atmosphere. Following it, the environment gets warmer, and the ecosystem changes as a consequence of disrupting the natural order of our life. Due to this, in the present reasearch, the possibility of carbon fixation of CO₂ by using borane was investigated. To conduct this, each of the probable reaction channels between borane and CO₂ was investigated to find the fate of this species. The results indicate that among all the channels, the least energetic path for the reaction is reactant complex (RC) to TS (A-1) to Int (A-1) to TS (A-D) to formic acid (and further meta boric acid production from the transformation of boric acid). It shows that use of gaseous borane might lead to controlling these dangerous greenhouse gases which are threatening the present form of life on Earth, our beautiful, fragile home.

On the Question of Zwitterionic Intermediates in the [3 + 2] Cycloaddition Reactions between C-arylnitrones and Perfluoro 2-Methylpent-2-ene

The molecular mechanism of the [3 + 2] cycloaddition reaction between C-arylnitrones and perfluoro 2-methylpent-2-ene was explored on the basis of DFT calculations. It was found that despite the polar nature of the intermolecular interactions, as well as the presence of fluorine atoms near the reaction centers, all reactions considered cycloaddition proceed via a one-step mechanism. All attempts for the localization of zwitterionic intermediates on the reaction paths were not successful. Similar results were obtained regardless of the level of theory applied.

Understanding the molecular mechanism of γ-elimination of nitrous acid in the framework of the molecular electron density theory

The reactions of γ-dehydronitration of furaxanenitrolic acids have been studied within the density functional theory using molecular electron density theory scheme at the MPWB1K(PCM)/6-311G(d,p) level of theory. The alteration of bonding along the course of the reaction is studied in the topology of the electron density functional within the bonding evolution theory perspective. The characteristics of electron density changes indicate that we can distinguish six different phases in the nitrous acid extrusion from furaxanenitrolic acid 1a. These different phases related to the intrinsic reaction coordinate path of the analyzed reaction denote the non-concerted nature of the molecular mechanism.

An Urgent Industrial Scheme both for Total Synthesis, and for Pharmaceutical Analytical Analysis of Umifenovir as an Anti-Viral API for Treatment of COVID-19

BACKGROUND

This paper is prepared to reveal about an urgent industrial scheme for a fast and facile total synthesis of umifenovir (arbidol) (by one-pot stages) as an antiviral agent for treating 2019-nCoV virus via inhibiting its viral replication in the human cells. As COVID-19, takes thousands of lives all around the world, it seems that the medicinal resources would not be enough to supply billions of peoples, currently living on the planet earth. Thus, this pandemic and its subsequent impacts on the natural order of our life, would be one of the most important threats against the entire human race. Aims & Objective: Due to this, in this project, we have made attempts to find an operative approach for synthesizing this compound as an active pharmaceutical ingredient (API), which showed it could be effective in inhibiting the newly emerged coronavirus.

RESULTS

The designed scheme uses relatively cheap precursors, and contains one pot stages, instead of seven time consuming, and more costly, linear steps. Also, it is tried to use safe and cheap solvents like water, and ethanol, instead of toxic ones like methanol, and pyridine which could cause rejection of the API in the organic volatile impurities (OVI) test of pharmacopeia analysis, as well as increasing the concern of inflammability, explosive, and carcinogenic properties of those common solvents.

CONCLUSION

The most important pharmaceutical analytical methods containing OVI test (mainly ethanol (about 171 ppm) much lower than the limits, by gas chromatography-Flame Ionization Detector (GC-FID) instrument), Assay content (about 99.6% by potentiometric titration), and related purity analysis (by High performance liquid chromatography-Ultraviolet Detector (HPLC-UV)) (about 99.8%) were performed and described to give a more clear industrial scheme.

On the Question of Zwitterionic Intermediates in the [3+2] Cycloaddition Reactions: A Critical Review

New discoveries require a fundamental revision of the view on the mechanism of the 32CAreaction (according to the older nomenclature defined as 1,3-dipolar cycloaddition reactions). The view of the one-step, “concerted” mechanism of such processes developed in the 20-century is very popular today, both in academic literature and among organic chemists who do not specialize in such transformations. Meanwhile, more and more reports bring examples of reactions that clearly cannot be treated as processes without intermediates. However, these examples are documented very differently. In addition to comprehensive studies using many complementary research techniques, there are also reports in which the presence of intermediates in the cycloaddition environment is postulated on the basis of very unreliable premises. This review is an attempt at a critical analysis and systematization of data in the presented area.

Molecular mechanism of Hetero Diels-Alder reactions between (E)-1,1,1-trifluoro-3-nitrobut-2-enes and enamine systems in the light of Molecular Electron Density Theory

The molecular mechanism of the reaction of (E)-1,1,1-trifluoro-3-nitrobut-2-ene 1 with 3,3-dimethyl-2-morpholinobutene 2 has been studied within the Molecular Electron Density Theory (MEDT). This theoretical study confirm the possibility of the formation of zwitterionic structures in the first reaction stage. Interestingly, that localized zwitterions are however not common intermediates for identified in the postreaction mixture products. The further Bonding Evolution Theory (BET) study show, that the key, HDA reaction takes place in one-step but in a non-concerted manner since three stages are clearly identified. First the C5-C6 double bond breaks, then the C1-C2 bond breaks, and in the last phase we observed the formation of the C1-C6 single bond and V(C2) and V' (C2) pseudoradical centers in Z1 molecule. In turn, the molecular mechanism of the conversion of zwitterion Z1 to product 3 can be divided also in three groups in which we observed the disappearance of the two pseudoradical centers and formation O4-C5 single and C3-N3 double bonds, respectively.

A [1 + 2] cycloaddition instead of usual [2 + 3] cycloaddition between the B12N12 cluster and methyl azide: Potential energy surface calculations and Born–Oppenheimer molecular dynamics simulations

We have examined here the possibility of functionalization of the B12N12 cluster by methyl azide by means of a [2 + 3] cycloaddition reaction in analogy with the spontaneous functionalization of C20 fullerene using the same reaction. To achieve more reliable data, all possible interactions at different positions and orientations were considered by reaction channel study and potential energy surface calculations. Also, Born–Oppenheimer molecular dynamics simulations were used to find probable species which could emerge during the reactions.

Understanding the mechanism of the 1,3-dipolar cycloaddition reaction between a thioformaldehyde S-oxide and cyclobutadiene: Competition between the stepwise and concerted routes

Changing the mechanism of the widely used 1,3-dipolar cycloaddition reaction from its usual asynchronous one-step pattern to the rarely observed stepwise form leads to the emergence of intermediates, side products, and other impurities. Thus, it is crucial to determine the nature of the mechanism of the 1,3-dipolar cycloaddition reaction between a special 1,3-dipole and a specified dipolarophile (by theoretical methods) before using them for synthesizing a desired product. In this study, therefore, we have investigated the possibility of some probable intermediates emergence in the 1,3-dipolar cycloaddition reaction between cyclobutadiene and thioformaldehyde S-oxide. The results showed that emergence of Int (B) (−52.1 kcal mol−1) via transition state (B-1) is favorable both thermodynamically and kinetically (in comparison with all other stepwise routes). That is, developing probable impurities should not be neglected at least in the cases of the reactions between some thioformaldehyde S-oxide and some dipolarophiles.

On Searching for a Stepwise Channel for the Mechanism of a 1,3-Dipolar Cycloaddition between a Thiocarbonyl S-Oxide and C20 Fullerene using Born–Oppenheimer ab Initio QM/MM Molecular Dynamics

The probability of existence of a stepwise route which is in parallel with the well-known concerted pathway for the mechanism of 1,3-dipolar cycloaddition is debated by many researchers. As the route is stepwise, it would lead to emergence of at least a metastable intermediate which would produce some stereoisomers such as enantiomers and diastereomers. In 1986 the first clear stepwise example for a 1,3-dipolar cycloaddition was reported by Huisgen where an electron-poor alkene was reacted with a thiocarbonyl ylide. Since then, researchers have focused on the thiocarbonyl ylide 1,3-dipolar group in finding more stepwise examples. It was found that some reactions of a thiocarbonyl ylide with some dipolarophiles proceeded by a stepwise route, while others did not.

This situation led us to investigate the probability of existence a stepwise route in parallel with the concerted path for the reaction of methyl thiocarbonyl S-oxide and C20 fullerene as a chemically active and nano-dimension electronegative alkene. To give more reliable data, Born–Oppenheimer ab initio QM/MM molecular dynamics was used.

A DFT computational study of the molecular mechanism of [3 + 2] cycloaddition reactions between nitroethene and benzonitrile N-oxides

DFT calculations were performed to shed light on the molecular mechanism of [3 + 2] cycloadditions of simple conjugated nitroalkenes to benzonitrile N-oxides. In particular, it was found that these processes proceed by a one-step mechanism through asynchronous transition states. According to the latest terminology, they should be considered polar but not stepwise processes.

Beyond the Alternatives that Switch the Mechanism of the 1,3-Dipolar CyCloadditions from Concerted to Stepwise or Vice Versa: A Literature Review

For several decades, the concerted or stepwise character of the mechanism of the 1,3-dipolar cycloaddition reaction has been one of the most debated issues in the field of organic chemistry. The significance of this problem is due to the fact that in a catalyst-free 1,3-dipolar cycloaddition, when the mechanism switches from concerted to stepwise, the stereospecificity is lost and thus unwanted stereoisomers may emerge. The first proposals about the mechanism of the 1,3-dipolar reaction were due to Huisgen (concerted model) and subsequently by Firestone (two-step diradical channel) in the 1960s. After a decade of debate, most researchers accepted the concerted model for the reaction, but during these years, researchers reported some examples of the stepwise mechanism for catalyst-free 1,3-dipolar cycloadditions. This review attempts to find a number of factors that could influence the reaction channels and switch the mechanism from concerted to stepwise, or vice versa.

Selective sensing of ozone and the chemically active gaseous species of the troposphere by using the C20 fullerene and graphene segment

OZONE is a key species in forming a layer in the atmosphere of earth that brings vita for our planet and supports the complex life. This three-atom molecule in the ozone-layer, is healing the earth's ecosystem by protecting it from dangerous rays of the sun. Until this molecule is in the stratosphere, it would support the natural order of the life; but, when it appears in our environment, damages will begin against us. In this project, we have tried to find a new way for beaconing ozone species in our environment via physical adsorption by the C₂₀ fullerene and graphene segment as a sensor. To find the selectivity of this nano-sized segment in sensing ozone (O₃), compared to the usual chemically active gasses of the troposphere like O₂, N₂, CO₂, H₂O, CH₄, H₂, and CO, the density of state (DOS) plots were analyzed, for each interacting species. The results showed that ozone could significantly change the electrical conductivity of C₂₀ fullerene, for each adsorption step. Thus, this fullerene could clearly sense ozone in different adsorption steps; while, the graphene segment could do this only at the second step adsorption (/ΔE_g-B/=0.016eV) (at the first adsorption step the /ΔE_g-A/ is 0.00eV).

Diradical reaction mechanisms in [3 + 2]-cycloadditions of hetaryl thioketones with alkyl- or trimethylsilyl-substituted diazomethanes

Reactions of dihetaryl and aryl/hetaryl thioketones with 2-diazopropane, diazoethane, and (trimethylsilyl)diazomethane were studied at variable temperature. The experiments showed that reactions with 2-diazopropane carried out at -75 °C occur mainly via the initially formed, relatively stable 1,3,4-thiadiazolines as products of the [3 + 2]-cycloaddition of the diazo dipole onto the C=S bond. The latter decompose only at higher temperature (ca. -40 °C) to generate thiocarbonyl S-isopropanide. In the absence of the starting thioketone, the corresponding thiiranes and/or ethene derivatives, formed from them via spontaneous desulfurization, are the main products. In contrast, reactions with diazoethane occurred predominantly via initially formed diradicals, which in cascade processes gave sterically crowded 4,4,5,5-tetrahetaryl-1,3-dithiolanes as major products. Finally, the reaction of dihetaryl thioketones with (trimethylsilyl)diazomethane occur smoothly at -75 °C leading to the corresponding 4,4,5,5-tetrahetaryl-1,3-dithiolanes as the exclusive [3 + 2]-cycloadducts formed via a cascade of postulated diradicals. The presence of S or Se atoms in the hetaryl rings is of importance for stabilizing diradical intermediates. Remarkably, in no single case, the 'head-to-head dimerization' of aryl/hetaryl and dihetaryl substituted thiocarbonyl ylides was observed.