A Reactive Molecular Dynamics Study of Chlorinated Organic Compounds. Part II: A ChemTraYzer Study of Chlorinated Dibenzofuran Formation and Decomposition Processes

In our two-paper series, we first present the development of ReaxFF CHOCl parameters using the recently published ParAMS parametrization tool. In this second part, we update the reactive Molecular Dynamics – Quantum Mechanics coupling scheme ChemTraYzer and combine it with our new ReaxFF parameters from Part I to study formation and decomposition processes of chlorinated dibenzofurans. We introduce a self-learning method for recovering failed transition-state searches that improves the overall ChemTraYzer transition-state search success rate by 10 percentage points to a total of 48 %. With ChemTraYzer, we automatically find and quantify more than 500 reactions using transition state theory and DFT. Among the discovered chlorinated dibenzofuran reactions are numerous reactions that are new to the literature. In three case studies, we discuss the set of reactions that are most relevant to the dibenzofuran literature: (i) bimolecular reactions of the chlorinated-dibenzofuran precursors phenoxy radical and 1,3,5-trichlorobenzene, (ii) dibenzofuran chlorination and pyrolysis, and (iii) oxidation of chlorinated dibenzofurans.     

Asymptotic limit-cycle analysis of oscillating chemical reactions

The asymptotic limit-cycle analysis of mathematical models for oscillating chemical reactions is presented. In this work, after a brief presentation of mathematical preliminaries applied to the biased Van der Pol oscillator, we consider a two-dimensional model of the Chlorine dioxide Iodine Malonic-Acid (CIMA) reactions and the three-dimensional and two-dimensional Oregonator models of the Belousov–Zhabotinsky reactions. Explicit analytical expressions are given for the relaxation-oscillation periods of these chemical reactions that are accurate within 5% of their numerical values. In the two-dimensional CIMA and Oregonator models, we also derive critical parameter values leading to canard explosions and implosions in their associated limit cycles.

     

Synthetic studies on the bryostatins: synthetic routes to analogues containing the tricyclic macrolactone core

[reaction: see text]. Synthesis of the first of a projected series of bryostatin analogues has been accomplished in 26 steps and 2.2% overall yield. In this letter, we detail two approaches to the structural core of these tricyclic macrolactone bryostatin analogues. The key features of the route include BITIP-catalyzed asymmetric allylation reactions and Mukaiyama aldol reactions, a chelation-controlled allylation, pyran annulation reactions, and macrolactonization.     

A versatile catalyst for asymmetric reactions of carbonyl groups working purely by activation through hydrogen bonding: Mukaiyama-aldol, hetero Diels-Alder and Friedel-Crafts reactions

Bis-sulfonamides are demonstrated to be promising candidates for the efficient activation of carbonyl compounds through hydrogen bonding. Exemplified by three carbonyl addition reactions: Mukaiyama-aldol, hetero Diels-Alder and Friedel-Crafts reactions we show that bis-triflamides or bis-nonaflamides of commercially available chiral diamines act as chiral Br?nsted-acid catalysts, leading to the optically active products in moderate to excellent yields and with enantioselectivities up to 73% ee.     

Chemoselective N-Alkylation of Indoles in Aqueous Microdroplets

Many reactions show much faster kinetics in microdroplets than in the bulk phase. Most reported reactions in microdroplets mirror the products found in bulk reactions. However, the unique environment of microdroplets allows different chemistry to occur. In this work, we present the first chemoselective N-alkylation of indoles in aqueous microdroplets via a three-component Mannich-type reaction without using any catalyst. In sharp contrast, bulk reactions using the same reagents with a catalyst yield exclusively C-alkylation products. The N-alkylation yield is moderate in microdroplets, up to 53 %. We extended the scope of the microdroplet reaction and obtained a series of new functionalized indole aminals, which are likely to have biological activities. This work clearly indicates that microdroplet reactions can show reactivity quite different from that of bulk-phase reactions, which holds great potential for developing novel reactivities in microdroplets.     

Chemoselective N‐Alkylation of Indoles in Aqueous Microdroplets

Many reactions show much faster kinetics in microdroplets than in the bulk phase. Most reported reactions in microdroplets mirror the products found in bulk reactions. However, the unique environment of microdroplets allows different chemistry to occur. In this work, we present the first chemoselective N‐alkylation of indoles in aqueous microdroplets via a three‐component Mannich‐type reaction without using any catalyst. In sharp contrast, bulk reactions using the same reagents with a catalyst yield exclusively C‐alkylation products. The N‐alkylation yield is moderate in microdroplets, up to 53 %. We extended the scope of the microdroplet reaction and obtained a series of new functionalized indole aminals, which are likely to have biological activities. This work clearly indicates that microdroplet reactions can show reactivity quite different from that of bulk‐phase reactions, which holds great potential for developing novel reactivities in microdroplets.     

A Liquid-Liquid-Solid System to Manipulate the Cascade Reaction for Highly Selective Electrosynthesis of Aldehyde

Electrocatalytic synthesis of aldehydes from alcohols exhibits unique superiorities as a promising technology, in which cascade reactions are involved. However, the cascade reactions are severely limited by the low selectivity resulting from the peroxidation of aldehydes in a traditional liquid-solid system. Herein, we report a novel liquid-liquid-solid system to regulate the selectivity of benzyl alcohol electrooxidation. The selectivity of benzaldehyde increases 200-fold from 0.4 % to 80.4 % compared with the liquid-solid system at a high current density of 136 mA cm⁻², which is the highest one up to date. In the tri-phase system, the benzaldehyde peroxidation is suppressed efficiently, with the conversion of benzaldehyde being decreased from 87.6 % to 3.8 %. The as-produced benzaldehyde can be in situ extracted to toluene phase and separated from the electrolyte to get purified benzaldehyde. This strategy provides an efficient way to efficiently enhance the selectivity of electrocatalytic cascade reactions.     

Reversible Anionic Redox Activities in Conventional LiNi1/3Co1/3Mn1/3O2 Cathodes

Redox reactions of oxygen have been considered critical in controlling the electrochemical properties of lithium‐excessive layered‐oxide electrodes. However, conventional electrode materials without overlithiation remain the most practical. Typically, cationic redox reactions are believed to dominate the electrochemical processes in conventional electrodes. Herein, we show unambiguous evidence of reversible anionic redox reactions in LiNi_1/3Co_1/3Mn_1/3O₂. The typical involvement of oxygen through hybridization with transition metals is discussed, as well as the intrinsic oxygen redox process at high potentials, which is 75 % reversible during initial cycling and 63 % retained after 10 cycles. Our results clarify the reaction mechanism at high potentials in conventional layered electrodes involving both cationic and anionic reactions and indicate the potential of utilizing reversible oxygen redox reactions in conventional layered oxides for high‐capacity lithium‐ion batteries.     

Progression of Organic Reactions on Resin Supports Monitored by Single Bead FTIR Microspectroscopy

We report the time courses of five solid-phase reactions obtained using single bead FTIR microspectroscopy. This time-resolved information aided in the determination of the required reaction time, the nature of the solid-phase reaction, and resin property, effectively assisting in the initial phase of our combinatorial chemistry efforts. Our results showed that solid-phase organic reactions proceed faster than generally speculated. In addition, we have shown that reactions on the surface and in the interior of the bead occur at the same rate for reactions studied. The reaction on the TentaGel resin was shown to be not faster than reactions on Wang resin, suggesting that the diffusion of the substrate into polystyrene bead copolymerized with 1% divinylbenzene is not rate-limiting. Finally, the capability of obtaining IR spectra from the partial surface of a single bead demonstrated the femtomolar detection limit of single bead FTIR microspectroscopy.     

Bifurcating reactions: distribution of products from energy distribution in a shared reactive mode

Bifurcating reactions yield two different products emerging from one single transition state and are therefore archetypal examples of reactions that cannot be described within the framework of the traditional Eyring''s transition state theory (TST). With the growing number and importance of these reactions in organic and biosynthetic chemistry, there is also an increasing demand for a theoretical tool that would allow for the accurate quantification of reaction outcome at low cost. Here, we introduce such an approach that fulfils these criteria, by evaluating bifurcation selectivity through the energy distribution within the reactive mode of the key transition state. The presented method yields an excellent agreement with experimentally reported product ratios and predicts the correct selectivity for 89% of nearly 50 various cases, covering pericyclic reactions, rearrangements, fragmentations and metal-catalyzed processes as well as a series of trifurcating reactions. With 71% of product ratios determined within the error of less than 20%, we also found that the methodology outperforms three other tested protocols introduced recently in the literature. Given its predictive power, the procedure makes reaction design feasible even in the presence of complex non-TST chemical steps.

Reactive Mode Composition Factor (RMCF) analysis is a powerful tool to forecast the product distribution of bifurcating reactions through analysis of the kinetic energy distribution within the first transition state traversed by the reacting system.     

Michael Addition of Thiols to á,(a)-Unsaturated Carbonyl Compounds Catalyzed by Bifunctional Organocatalysts:Asymmetric Michael Addition and Asymmetric Protonation

Recently the hydrogen-bond activated reactions have attracted much attention.1 Takemoto2 reported a highly enantioselective Michael addition of manolate to nitroolefins catalyzed by a bifunctional organocatalyst with tertiary amine and thiourea moiety. As we known,stereoselective conjugate additions of thiols are interesting due to the standpoint of biological and synthetic importance, however, only very limited good results have been obtained except for the works of Shibasaki3, Kanemasa4 and Deng5 et al.In this letter, we report an efficient catalytic asymmetric Michael reactions of thiols to a,a-unsaturated carbonyl compounds promoted by bifunctional organocatalysts. A series of organocatalysts with chiral amine and thiourea structures were designed and synthesized and have been successfully applied in the conjugated additions of thiols to a,a-unsaturated imides and enones.The reactions got quantitative yields and the ee values were up to 84%. It is noteworthy that the a-asymmetric protonation (up to 43% ee) also could be achieved.The Michael addition between aromatic thiols and a,a-unsaturated carbonyl compounds isdescribed as follows:Works to further increase the enantioselectivity is under investigation in our laboratory.     

Interface Engineering in Two‐Dimensional Heterostructures: Towards an Advanced Catalyst for Ullmann Couplings

The design of advanced catalysts for organic reactions is of profound significance. During such processes, electrophilicity and nucleophilicity play vital roles in the activation of chemical bonds and ultimately speed up organic reactions. Herein, we demonstrate a new way to regulate the electro‐ and nucleophilicity of catalysts for organic transformations. Interface engineering in two‐dimensional heteronanostructures triggered electron transfer across the interface. The catalyst was thus rendered more electropositive, which led to superior performance in Ullmann reactions. In the presence of the engineered 2D Cu₂S/MoS₂ heteronanostructure, the coupling of iodobenzene and para‐chlorophenol gave the desired product in 92 % yield under mild conditions (100 °C). Furthermore, the catalyst exhibited excellent stability as well as high recyclability with a yield of 89 % after five cycles. We propose that interface engineering could be widely employed for the development of new catalysts for organic reactions.     

Microwave-mediated synthesis of a cyclic heptapeptoid through consecutive Ugi reactions

The combination of consecutive Isocyanide-based Multicomponent Reactions (IMCRs) allowed the synthesis of a cyclic heptapeptoid in a reduced number of steps. Herein, we describe this efficient approach using four consecutive Ugi reactions, being three Ugi four-center, four-component reactions, and one Ugi four-center, three-component reaction. Our strategy involved eight steps of which seven in a row were microwave-assisted with reaction times of 3–5?min and yields ranging from 88 to 98%.     

Probing the bioactivity-relevant chemical space of robust reactions and common molecular building blocks

In the search for new bioactive compounds, there is a trend toward increasingly complex compound libraries aiming to target the demanding targets of the future. In contrast, medicinal chemistry and traditional library design rely mainly on a small set of highly established and robust reactions. Here, we probe a set of 58 such reactions for their ability to sample the chemical space of known bioactive molecules, and the potential to create new scaffolds. Combined with ~26,000 common available building blocks, the reactions retrieve around 9% of a scaffold-diverse set of compounds active on human target proteins covering all major pharmaceutical target classes. Almost 80% of generated scaffolds from virtual one-step synthesis products are not present in a large set of known bioactive molecules for human targets, indicating potential for new discoveries. The results suggest that established synthesis resources are well suited to cover the known bioactivity-relevant chemical space and that there are plenty of unexplored regions accessible by these reactions, possibly providing valuable "low-hanging fruit" for hit discovery.     

Efficient Transformation of Polymer Main Chain Catalyzed by Macrocycle Metal Complexes via Pseudorotaxane Intermediate

Post-synthesis modification of polymers streamlines the synthesis of functionalized polymers, but is often incomplete due to the negative polymer effects. Developing efficient polymer reactions in artificial systems thus represents a long-standing objective in the fields of polymer and material science. Here, we show unprecedented macrocycle-metal-complex-catalyzed systems for efficient polymer reaction that result in 100 % transformation of the main chain functional groups presumably via a processive mode reaction. The complete polymer reactions were confirmed in not only intramolecular reaction (hydroamination) but also intermolecular reaction (hydrosilylation) by using Pd- and Pt-macrocycle-catalyzed systems. The most fascinating feature of the both reactions is that higher-molecular-weight polymers reach completion faster. Various studies suggested that the reactions occur in the catalyst cavity via the formation of a supramolecular complex between the macrocycle catalyst and polymer substrate like pseudorotaxane, which should be of characteristic of the efficient polymer reactions progressing in a processive mode.     

Analysis of chemical kinetics at the gas-aqueous interface for submicron aerosols

The effect of kinetics of chemical reactions in the gas-liquid interface between atmospheric gases and reactive solute in dilute aqueous aerosols is analysed in order to see if such processes will affect the overall uptake rate. Accordingly, a parameterization of such heterogeneous reactions was derived, taking into account interfacial reactions. Gibbs surface excess concentration of both reactive compounds and stable compounds leads to higher heterogeneous reaction rates in comparison to aqueous phase bulk reactions. An analytical formulation shows that the surface reactions may be of considerable importance for the uptake process in the case of small liquid aerosols even in the absence of organic film on the surface. In particular, we demonstrate that the uptake rate of atmospheric gas-phase oxidants (such as OH, NO(3) or O(3)) reacting with volatile organic compounds (such as ethanol or methanol) is increased by more than 10% for atmospheric aerosols with diameters lower than 0.1 microm. This effect is in addition intensified in the case of reactions of atmospheric oxidants with liquid aerosols containing organic surfactants, such as semi-volatile organic compounds, i.e., the chemical reactions at the gas-liquid interface may be dominant in the main uptake process for atmospheric submicron aerosols.     

Efficient and rapid synthesis of regioselective functionalized potassium 1,2,3-triazoletrifluoroborates via 1,3-dipolar cycloaddition

In this study, we present a previously unreported method of preparing regiospecific organo-[1,2,3]-triazol-1-aryl-trifluoroborates from haloaryltrifluoroborates via a one-pot 1,3-dipolar cycloaddition reaction. We found that the use of either electron-rich or electron-deficient haloaryltrifluoroborates led to the desired cycloaddition products with good to excellent yields. Furthermore, we successfully carried out the cross-coupling reactions of the obtained triazoles with various aryl halides by means of the Suzuki-Miyaura reaction in the presence of 3 mol % of Pd(PPh₃)₄ catalyst in a 20% aqueous 1,4-dioxane solution at 100 °C; all these reactions yielded complete conversion to the corresponding products. Besides providing a high level of personnel safety, our highly versatile approach allows the preparation of functionalized organotrifluoborates containing 1,2,3-triazoles with retained functionality.     

Extended sugar-assisted glycopeptide ligations: development, scope, and applications

Recently, we reported the development of sugar-assisted ligation (SAL), a novel peptide ligation method for the synthesis of glycopeptides. After screening a large number of glycoprotein sequences in a glycoprotein database, it became evident that a large proportion (approximately 53%) of O-glycosylation sites contain amino acid residues that will not undergo SAL reactions. To overcome these inherent limitations and broaden the scope of the method we report here the development of an extended SAL method. Glycopeptides containing up to six amino acid extensions N-terminal to the glycosylated residue were shown to facilitate ligation reactions with peptide thioesters, and these products were isolated in good yields. Kinetic analysis was used to show that as glycopeptides were extended by further amino acid residues, ligation reactions became slower. This finding was rationalized by molecular dynamics simulations using AMBER9. These studies suggested a general trend whereby the proximal distance between the reactive sites of the thioester intermediate (the N-terminal amine and the carbonyl carbon of the thioester) increased as glycopeptides were extended, thus slowing down the ligation rate. Each of the extended SAL methods showed broad tolerance to a number of different amino acid combinations at the ligation junction. Re-evaluation of the glycoprotein database suggested that 95% of the O-linked glycosylation sites can now be utilized to facilitate SAL or extended SAL reactions. As such, this method represents an extremely valuable tool for the synthesis of naturally occurring glycopeptides and glycoproteins. To demonstrate the applicability of the method, extended SAL was successfully implemented in the synthesis of the starting unit of the cancer-associated MUC1 glycoprotein.     

Microwave-Assisted Solid Phase Organic Synthesis.Application to Indole Library Construction

Microwave-assisted organic synthesis (MAOS) has attained increasing popularity due to recent advancement in the instrumentation of microwave technology. Now, MAOS can be performed under controlled temperature and pressure to yield reproducible results. For combinatorial chemistry,the dramatically increased reaction rate under microwave irradiation at high temperature provides an ideal solution to those sluggish reactions, in particular the combinatorial reactions carried out on solid supports. In this presentation, we describe our results on microwave-assisted solid-phase organic synthesis (MASPOS) applied to the construction of indole libraries such as 5. Compounds 4 were synthesized on the Rink amide resins using IRORI MicroKanTM reactors encoded with a radio-frequency (Rf) tag. The resin-bound terminal alkynes 2, prepared via the amide bond, were cross-coupled with the nitroaryl triflate under the conditions adopted from the solution reactions developed by us1,2. The nitro group of 3 was then reduced and sulfonylated to give 4. Ring closure reactions within 4 with Cu(OAc)2 were examined initially in refluxing DCE for 24 h, but no indole product was detected after cleavage from the resin. Therefore, the same reactions were carried out under microwave irradiation at 200 ℃ for 10 min on a Personal Chemistry Emrys Creator, the desired indoles 5 were obtained in 60-95% overall yields calculated from 1 and in ＞90% purities in most cases3. It is necessary to mention that the IRORI microreactors cannot tolerate the high temperature and the resin-bound 4 must be transferred to the reaction vials for the microwave-assisted ring closure reactions. A traceless synthesis of an indole library via MASPOS will be discussed as well.4