Computational prediction of complex cationic rearrangement outcomes.

Recent years have seen revived interest in computer-assisted organic synthesis1,2. The use of reaction- and neural-network algorithms that can plan multistep synthetic pathways have revolutionized this field1,3-7, including examples leading to advanced natural products6,7. Such methods typically operate on full, literature-derived 'substrate(s)-to-product' reaction rules and cannot be easily extended to the analysis of reaction mechanisms. Here we show that computers equipped with a comprehensive knowledge-base of mechanistic steps augmented by physical-organic chemistry rules, as well as quantum mechanical and kinetic calculations, can use a reaction-network approach to analyse the mechanisms of some of the most complex organic transformations: namely, cationic rearrangements. Such rearrangements are a cornerstone of organic chemistry textbooks and entail notable changes in the molecule's carbon skeleton8-12. The algorithm we describe and deploy at https://HopCat.allchemy.net/ generates, within minutes, networks of possible mechanistic steps, traces plausible step sequences and calculates expected product distributions. We validate this algorithm by three sets of experiments whose analysis would probably prove challenging even to highly trained chemists: (1) predicting the outcomes of tail-to-head terpene (THT) cyclizations in which substantially different outcomes are encoded in modular precursors differing in minute structural details; (2) comparing the outcome of THT cyclizations in solution or in a supramolecular capsule; and (3) analysing complex reaction mixtures. Our results support a vision in which computers no longer just manipulate known reaction types1-7 but will help rationalize and discover new, mechanistically complex transformations.

Computational planning of the synthesis of complex natural products.

Training algorithms to computationally plan multistep organic syntheses has been a challenge for more than 50 years1-7. However, the field has progressed greatly since the development of early programs such as LHASA1,7, for which reaction choices at each step were made by human operators. Multiple software platforms6,8-14 are now capable of completely autonomous planning. But these programs 'think' only one step at a time and have so far been limited to relatively simple targets, the syntheses of which could arguably be designed by human chemists within minutes, without the help of a computer. Furthermore, no algorithm has yet been able to design plausible routes to complex natural products, for which much more far-sighted, multistep planning is necessary15,16 and closely related literature precedents cannot be relied on. Here we demonstrate that such computational synthesis planning is possible, provided that the program's knowledge of organic chemistry and data-based artificial intelligence routines are augmented with causal relationships17,18, allowing it to 'strategize' over multiple synthetic steps. Using a Turing-like test administered to synthesis experts, we show that the routes designed by such a program are largely indistinguishable from those designed by humans. We also successfully validated three computer-designed syntheses of natural products in the laboratory. Taken together, these results indicate that expert-level automated synthetic planning is feasible, pending continued improvements to the reaction knowledge base and further code optimization.

Machine Learning Algorithm Guides Catalyst Choices for Magnesium-Catalyzed Asymmetric Reactions.

Organic-chemical literature encompasses large numbers of catalysts and reactions they can effect. Many of these examples are published merely to document the catalysts' scope but do not necessarily guarantee that a given catalyst is "optimal" - in terms of yield or enantiomeric excess - for a particular reaction. This paper describes a Machine Learning model that aims to improve such catalyst-reaction assignments based on the carefully curated literature data. As we show here for the case of asymmetric magnesium catalysis, this model achieves relatively high accuracy and offers out of-the-box predictions successfully validated by experiment, e.g., in synthetically demanding asymmetric reductions or Michael additions.

Propargylation of CoQ0 through the Redox Chain Reaction.

An efficient catalytic propargylation of CoQ0 is described by employing the cooperative effect of Sc(OTf)3 and Hantzsch ester. It is suggested to work through the redox chain reaction, which involves hydroquinone and dimeric propargylic moiety intermediates. A broad range of propargylic alcohols can be converted into the appropriate derivatives of CoQ0 containing triple bonds in good to excellent yields. The mechanism of the given transformation is also discussed.

Correction to: Comparative Assessment of the New PDE7 Inhibitor - GRMS-55 and Lisofylline in Animal Models of Immune-Related Disorders: A PK/PD Modeling Approach.

There was a mistake in the unit of clearance (Cl) in Table II. In addition, the descriptions of V1(ROL) and V1(GRMS-55) were imprecise and the reference number in the footnote below this table should be (9). The corrected Table appears below.

Comparative Assessment of the New PDE7 Inhibitor - GRMS-55 and Lisofylline in Animal Models of Immune-Related Disorders: A PK/PD Modeling Approach.

PURPOSE: This study aimed to assess the activity of two phosphodiesterase (PDE) inhibitors, namely GRMS-55 and racemic lisofylline ((±)-LSF)) in vitro and in animal models of immune-mediated disorders. METHODS: Inhibition of human recombinant (hr)PDEs and TNF-alpha release from LPS-stimulated whole rat blood by the studied compounds were assessed in vitro. LPS-induced endotoxemia, concanavalin A (ConA)-induced hepatitis, and collagen-induced arthritis (CIA) animal models were used for in vivo evaluation. The potency of the investigated compounds was evaluated using PK/PD and PK/PD/disease progression modeling. RESULTS: GRMS-55 is a potent hrPDE7A and hrPDE1B inhibitor, while (±)-LSF most strongly inhibits hrPDE3A and hrPDE4B. GRMS-55 decreased TNF-alpha levels in vivo and CIA progression with IC50 of 1.06 and 0.26 mg/L, while (±)-LSF with IC50 of 5.80 and 1.06 mg/L, respectively. Moreover, GRMS-55 significantly ameliorated symptoms of ConA-induced hepatitis. CONCLUSIONS: PDE4B but not PDE4D inhibition appears to be mainly engaged in anti-inflammatory activity of the studied compounds. GRMS-55 and (±)-LSF seem to be promising candidates for future studies on the treatment of immune-related diseases. The developed PK/PD models may be used to assess the anti-inflammatory and anti-arthritic potency of new compounds for the treatment of rheumatoid arthritis and other inflammatory disorders.

Asymmetric total synthesis of (+)-asenapine.

Asymmetric total synthesis of (+)-asenapine, an atypical antipsychotic drug, used for treating schizophrenia and acute mania associated with bipolar disorder, is reported. The key steps are the organocatalytic Michael addition of aldehydes to trans-nitroalkenes and subsequent reductive cyclization.

Influence of inflammatory disorders on pharmacokinetics of lisofylline in rats: implications for studies in humans.

1. Despite the number of favourable properties of lisofylline (LSF), clinical trials on this compound have not yielded the expected results yet. 2. The aims of this study were to evaluate the pharmacokinetics of LSF enantiomers in rats following intravenous, oral and subcutaneous administration of (±)-LSF and to assess the influence of experimental inflammatory disorders, such as multiple organ dysfunction syndrome and severe sepsis on LSF pharmacokinetics. 3. In addition, based on the results obtained an attempt was made to elucidate the possible reasons for the failure of LSF therapy in clinical trials carried out in patients with severe inflammatory disorders. 4. A subcutaneous route of (±)-LSF administration to rats is more favourable than an oral one due to a high bioavailability and a fast absorption of both LSF enantiomers. Pharmacokinetics of LSF in rats is significantly influenced by inflammatory diseases. Too low LSF serum levels might have been one of the reasons for clinical trial failures. A long-term i.v. infusion of LSF seems to be more effective compared to short-term multiple infusions that were used in clinical trials, as it may provide concentrations above IC50 for inhibition of both TNF-alpha release and cAMP degradation in serum for a longer period of time.

Chiral Amplification in Nature: Studying Cell-Extracted Chiral Carotenoid Microcrystals via the Resonance Raman Optical Activity of Model Systems.

Carotenoid microcrystals, extracted from cells of carrot roots and consisting of 95 % of achiral ß-carotene, exhibit a very intense chiroptical (ECD and ROA) signal. The preferential chirality of crystalline aggregates that consist mostly of achiral building blocks is a newly observed phenomenon in nature, and may be related to asymmetric information transfer from the chiral seeds (small amount of α-carotene or lutein) present in carrot cells. To confirm this hypothesis, we synthesized several model aggregates from various achiral and chiral carotenoids. Because of the sergeant-and-soldier behavior, a small number of chiral sergeants (α-carotene or astaxanthin) force the achiral soldier molecules (ß- or 11,11'-[D2 ]-ß-carotene) to jointly form supramolecular assemblies of induced chirality. The chiral amplification observed in these model systems confirmed that chiral microcrystals appearing in nature might consist predominantly of achiral building blocks and their supramolecular chirality might result from the co-crystallization of chiral and achiral analogues.

Intramolecular Tandem Seleno-Michael/Aldol Reaction: A Simple Route to Hydroxy Cyclo-1-ene-1-carboxylate Esters.

Intramolecular tandem seleno-Michael/aldol reaction followed by an oxidation-elimination process can be an efficient tool for the construction of hydroxy cyclo-1-ene-1-carboxylate esters from oxo-α,ß-unsaturated esters. Generation of lithium selenolate from elemental selenium and n-BuLi provides a simple and efficient one-pot access to cyclic endo-Morita-Baylis-Hillman adducts.

Total synthesis of pipecolic acid and 1-C-alkyl 1,5-iminopentitol derivatives by way of stereoselective aldol reactions from (S)-isoserinal.

A short synthesis of iminosugars and pipecolic acid derivatives has been realized through aldol addition of a pyruvate, a range of ketones and (S)-isoserinal, followed by catalytic reductive intramolecular amination. The stereoselective aldol reaction was achieved successfully by using tertiary amines or di-zinc aldol catalysts, thus constituting two parallel routes to optically pure products with good yields and high diastereoselectivities. These carbohydrate analogues may be the inhibitors of potent glycosidases and glycosyltransferases.

Iron-Catalyzed Asymmetric Nitro-Mannich Reaction.

The first enantioselective addition of nitroalkanes to imines (nitro-Mannich reaction), mediated by an iron(II) catalyst assembled by a hindered hydroxyethyl-pybox ligand, is described. This valuable carbon-carbon bond-forming reaction proceeds smoothly at room temperature to afford enantioenriched ß-nitro amines in good yields and high enantioselectivity, up to 98% with unprecedentedly low iron catalyst loading (5 mol %).

Application of the EF and GH Fragments to the Synthesis of Idraparinux.

A novel total synthesis of fully protected idraparinux has been achieved. A short and efficient protocol for the synthesis of the EF fragment of idraparinux and its C5'-epi analogue (GH unit) has been developed. The same cellobiose unit was transformed in 14 steps into the fully protected EF and GH disaccharide fragments. The key step of this approach is an epimerization of C5 by an elimination-addition sequence leading to l-ido disaccharide (GH unit) with a total yield of 24% (36% for the EF fragment). 1,6-Anhydro ring opening gave suitable substrates for efficient synthesis of fully protected idraparinux. The fully protected antithrombotic pentasaccharide idraparinux was synthesized in 23 steps for the longest linear route, with a 1.7% overall yield from d-cellobiose and d-glucose.

Self-Enhancement of Rotating Magnetocaloric Effect in Anisotropic Two-Dimensional (2D) Cyanido-Bridged MnII-NbIV Molecular Ferrimagnet.

The rotating magnetocaloric effect (RMCE) is a new issue in the field of magnetic refrigeration. We have explored this subject on the two-dimensional (2D) enantiopure {[MnII(R-mpm)2]2[NbIV(CN)8]}·4H2O (where mpm = α-methyl-2-pyridinemethanol) coordination ferrimagnet. In this study, the magnetic and magnetocaloric properties of single crystals were investigated along the bc//H easy plane and the a*//H hard axis. The observed small easy plane anisotropy is due to the dipole-dipole interactions. For fields higher than 0.5 T, no significant difference in the magnetocaloric effect between both geometries was noticed. The maximal magnetic entropy change for conventional effect was observed at 32 K and the magnetic field change µ0ΔH = 5.0 T attaining the value of ∼5 J mol-1 K-1. The obtained maximal value of -ΔSm is comparable to previously reported results for polycrystalline octacyanidoniobate-based bimetallic coordination polymers. A substantial anisotropy of magnetocaloric effect between the easy plane and hard axis appears in low fields. This includes the presence of inverse magnetocaloric effect only for the a*//H direction. The difference between both geometries was used to study the rotating magnetocaloric effect. We show that the inverse part of magnetocaloric effect can be used to enhance the rotating magnetic entropy change up to 51%. This finding is of key importance for searching efficient materials for RMCE.

Synthesis of 2-Keto-d- and l-gluconic Acid via Stereoselective Direct Aldol Reactions.

Stereoselective direct aldol reaction between optically pure d- or l-glyceraldehyde and hydroxyacetylfuran is demonstrated as an efficient and straightforward methodology for the synthesis of six-carbon atom d- and l-arabino-hex-2-ulosonic acids. syn-Selective aldol reactions realized by using either tertiary amines or a dizinc aldol catalyst constitute two parallel routes to the de novo synthesis of orthogonally protected biologically relevant 2-keto-d- and l-gluconic acids.

Synthesis of l-Pyranosides by Hydroboration of Hex-5-enopyranosides Revisited.

Extensive study of the diastereoselective synthesis of l-pyranosides utilizing hydroboration of substituted exo-glucals (5-enopyranosides) obtained from d-sugars is presented. On the basis of this study we present the empirical rules describing the reaction stereoselectivity and the correlation between the yield of the l-ido product and the size of protecting groups used. Application of these guidelines revealed that the hydroboration of methyl 2,3-O-methyl-6-deoxy-α-d-xylo-hex-5-enopyranoside resulted in exclusive formation of l-ido product with high yield. This method can be successfully applied to the synthesis of l-iduronic acid being an essential component of anticoagulant drugs with diastereoselectivity superior to previously published protocols.

Enantioselective Hydrosilylation of Imines Catalyzed by Chiral Zinc Acetate Complexes.

A series of zinc acetate complexes with optically pure diphenylethanediamine (DPEDA)-derived ligands have been employed as enantioselective catalyst for the hydrosilylation of various imines. High control of stereoselectivity (up to 97% ee) and excellent yields (up to 96%) were gained for a broad range of N-phosphinoylimines by using (R,R)-N,N'-dibenzyl-1,2-diphenylethane-1,2-diamine. This is the first successful application of an air-stable and environmentally friendly chiral Zn(OAc)2 complex instead of the previously used harmful diethylzinc in the asymmetric reduction of the C═N double bond.

Application of 2-substituted benzyl groups in stereoselective glycosylation.

The use of 2-O-(2-nitrobenzyl) and 2-O-(2-cyanobenzyl) groups controls stereoselective formation of 1,2-trans-glycosidic linkages via the arming participation effect. The observed stereoselectivity likely arises from the intramolecular formation of cyclic intermediate between the electron-rich substituent and the donor oxacarbenium ion providing the expected facial selectivity for attack of the glycoside acceptor. The stereodirecting effect of the 2-nitro- and 2-cyanobenzyl groups attached at the remote position (C-3, C-4, and C-6) of the donor molecule have also been investigated. To prove the postulated mechanism based on the participation effect of 2-substituted benzyl groups in the glycosylation stereoselectivity we used DFT theoretical calculation methodology.

Optical Activity and Dehydration-Driven Switching of Magnetic Properties in Enantiopure Cyanido-Bridged Co(II)3W(V)2 Trigonal Bipyramids.

The unique enantiopure {[Λ-Co(II)((R)-mpm)2]3[W(V)(CN)8]2}·9H2O [(R)-1] and {[Δ-Co(II)((S)-mpm)2]3[W(V)(CN)8]2}·9H2O [(S)-1], where mpm = α-methylpyridinemethanol, magnetic spongelike materials, crystallizing in the chiral P21 space group, are constructed of cyanido-bridged {Co3W2} trigonal bipyramids with three cis-[Co(II)(mpm)2(µ-NC)2] moieties in equatorial sites and two [W(V)(CN)8](3-) units in apical positions. The arrangement of {Co3W2} clusters in the crystal lattice is controlled by interactions with crystallization H2O molecules, resulting in two independent hydrogen-bonding systems: the first weaving along open channels in the a direction (weakly bonded H2O) and the second closed in the cages formed by the surrounding [W(CN)8](3-) and mpm fragments (strongly bonded H2O). The strong optical activity of (R)- and (S)-1 together with continuous chirality measure (CCM) analysis confirms the chirality transfer from enantiopure (R)- and (S)-mpm to [Co(mpm)2(µ-NC)2] units, a cyanido-bridged skeleton, and to the whole crystal lattice. Magnetic properties confronted with ab initio calculations prove the ferromagnetic couplings within Co(II)-NC-W(V) linkages inside {Co3W2} molecules, accompanied by weak antiferromagnetic intermolecular interactions. The reversible removal of weakly bonded H2O above 50 °C induces the structural phase transition 1 ⇄ 1deh and strongly affects the magnetic characteristics. The observed changes can be interpreted in terms of the combined effects of the decreasing strength of ferromagnetic Co(II)-W(V) coupling and the increasing role of antiferromagnetic intermolecular correlation, both connected with dehydration-induced structural modifications in the clusters' core and supramolecular network of 1.

Catalytic asymmetric aldol reactions in aqueous media--a 5 year update.

Asymmetric reactions in water and in aqueous solutions have become an area of fast growing interest recently. Although for a long time neglected as a medium for organic reactions, water has attracted attention as the most widely distributed solvent in the world. Indeed, water is the solvent used by nature for biological chemistry including aldol reactions being essential for glycolysis, gluconeogenesis and related processes. Consequently, artificial catalysts designed and used for aldol reactions in water can be promising for the synthesis of enantiopure molecules and are also important for the understanding of complex chemistry of life. This tutorial review summarizes recent developments in the area of aqueous asymmetric aldol reactions highlighting two fundamental directions--development of water compatible chiral Lewis acids and amine-based organocatalysts.