Predicting retrosynthetic pathways using transformer-based models and a hyper-graph exploration strategy

We present an extension of our Molecular Transformer model combined with a hyper-graph exploration strategy for automatic retrosynthesis route planning without human intervention. The single-step retrosynthetic model sets a new state of the art for predicting reactants as well as reagents, solvents and catalysts for each retrosynthetic step. We introduce four metrics (coverage, class diversity, round-trip accuracy and Jensen–Shannon divergence) to evaluate the single-step retrosynthetic models, using the forward prediction and a reaction classification model always based on the transformer architecture. The hypergraph is constructed on the fly, and the nodes are filtered and further expanded based on a Bayesian-like probability. We critically assessed the end-to-end framework with several retrosynthesis examples from literature and academic exams. Overall, the frameworks have an excellent performance with few weaknesses related to the training data. The use of the introduced metrics opens up the possibility to optimize entire retrosynthetic frameworks by focusing on the performance of the single-step model only.

We present an extension of our Molecular Transformer model combined with a hyper-graph exploration strategy for automatic retrosynthesis route planning without human intervention.     

Tridentate Schiff base and 4,4′-bipyridine coordinated di/polynuclear Cu (II) complexes: Synthesis,crystal structure,DNA/protein binding and catecholase activity

4,4′-bipyridine bridged two Cu (II) complexes, [Cu₂L¹₂(4,4′-bipy)(H₂O)₂](ClO₄)₂ ( 1 ) and [Cu₂L²₂(4,4′-bipy)]_n·(2H₂O)_n ( 2 ) (where, HL¹ = 2-[(3-methylamino-propylimino)-methyl]-phenol, H₂L² = 3-[(2-hydroxy-3-methoxy-benzylidene)-amino]-propionic acid, and 4,4′-bipy = 4,4′-bipyridine) have been synthesized and characterized by single crystal structure determination, mass spectrometry, FT-IR, electronic absorption, and emission spectroscopy. Complex 1 is dinuclear cationic compound and counter balanced by perchlorate anion, whereas complex 2 possesses 1D poly-nuclear structure. Both the complexes crystallize in monoclinic system with P2₁/c space group and the copper centers possess square pyramidal geometry. H-bonding, C-H···π, π···π interactions results the formation of two dimentional supramolecular structure for both the complexes. Interactions of complexes with bovine serum albumins (BSA) and human serum albumins (HSA) have been studied by using electronic absorption and emission spectroscopic technique. The calculated values of binding constants (K_b) are (9.22 ± 0.26) × 10⁵ L mol⁻¹ ( 1 -BSA), (7.19 ± 0.16) × 10⁵ L mol⁻¹ ( 1 -HSA), (5.05 ± 0.20) × 10⁵ L mol⁻¹ ( 2 -BSA) and (3.56 ± 0.25) × 10⁵ L mol⁻¹ ( 2 -HSA). The mechanism of serum albumins-complex interactions have been investigated by fluorescence lifetime measurement. Fluorescence spectroscopic studies indicate that both the complexes interact with calf thymas-DNA. Catecholase activity of the complexes has been studied in methanol using 3,5-di-tert-butylcatechol (3,5-DTBC) as substrate and the result show that both the complexes are active for catalytic oxidation of 3,5-DTBC to 3,5-di-tert-butylquinone (3,5-DTBQ) in presence of molecular oxygen. Calculated values of turnover numbers are 71.81 ± 1.04 h⁻¹ and 69.45 ± 0.74 h⁻¹ for 1 and 2 , respectively.     

A Resin‐Linker‐Vector Approach to Radiopharmaceuticals Containing 18F: Application in the Synthesis of O‐(2‐[18F]‐Fluoroethyl)‐L‐tyrosine

A Resin‐linker‐vector (RLV) strategy is described for the radiosynthesis of tracer molecules containing the radionuclide ¹⁸F, which releases the labelled vector into solution upon nucleophilic substitution of a polystyrene‐bound arylsulfonate linker with [¹⁸F]‐fluoride ion. Three model linker‐vector molecules 7 a – c containing different alkyl spacer groups were assembled in solution from (4‐chlorosulfonylphenyl)alkanoate esters, exploiting a lipase‐catalysed chemoselective carboxylic ester hydrolysis in the presence of the sulfonate ester as a key step. The linker‐vector systems were attached to aminomethyl polystyrene resin through amide bond formation to give RLVs 8 a – c with acetate, butyrate and hexanoate spacers, which were characterised by using magic‐angle spinning (MAS) NMR spectroscopy. On fluoridolysis, the RLVs 8 a , b containing the longer spacers were shown to be more effective in the release of the fluorinated model vector (4‐fluorobutyl)phenylcarbamic acid tert‐butyl ester ( 9 ) in NMR kinetic studies and gave superior radiochemical yields (RCY≈60 %) of the ¹⁸F‐labelled vector. The approach was applied to the synthesis of the radiopharmaceutical O‐(2‐[¹⁸F]‐fluoroethyl)‐L ‐tyrosine ([¹⁸F]‐FET), delivering protected [¹⁸F]‐FET in >90 % RCY. Acid deprotection gave [¹⁸F]‐FET in an overall RCY of 41 % from the RLV.     

Antioxidant capacity and antibacterial activity from Annona cherimola phytochemicals by ultrasound-assisted extraction and its comparison to conventional methods

In recent years, the food, pharmacy, and cosmetic industries have focused on the search of natural compounds with antimicrobial and antioxidant properties; commonly, these compounds are obtained from Kingdom plantae. The aim of the present work is comparing antibacterial and antioxidant capacity of Annona cherimola Mill leaves, using different extraction methods. The ultrasound assisted extraction technique (UAE) was compared with conventional techniques: Soxhlet and maceration. Water and ethanol were used as solvents for leaves extractions performed with these three methods. The main acetogenins reported in Annona cherimola Mill and Annona muricata L. species were simulated using the functional hybrid B3LYP and to confirm its presence, analysis of the compound composition was performed using FT-IR, UV–Vis and HPLC. Total phenolics (TP) and flavonoids (TF) were determined by spectroscopy techniques and novel Differential Pulse Voltammetry (DPV) electrochemical technique. Total Antioxidant Capacity (TAC) of the extracts was measured, using the DPPH, FRAP and CUPRAC techniques. The highest antioxidant content was found in the Soxhlet water extracts; even so, the UAE technique presented an attractive alternative due to considerable reduction in extraction time, which was greater than 99%, and possible selectivity in compounds extraction. Finally, antibacterial activity of the extracts was evaluated, obtaining the best results against gram-positive bacteria using UAE water extract. In this way, the UAE technique presents an excellent extraction option due to the considerable reduction in time and energy, as well as the increase in antibacterial activity.     

Zn-Induced Interactions Between SARS-CoV-2 orf7a and BST2/Tetherin

We present in this work a first X-ray Absorption Spectroscopy study of the interactions of Zn with human BST2/tetherin and SARS-CoV-2 orf7a proteins as well as with some of their complexes. The analysis of the XANES region of the measured spectra shows that Zn binds to BST2, as well as to orf7a, thus resulting in the formation of BST2-orf7a complexes. This structural information confirms the the conjecture, recently put forward by some of the present Authors, according to which the accessory orf7a (and possibly also orf8) viral protein are capable of interfering with the BST2 antiviral activity. Our explanation for this behavior is that, when BST2 gets in contact with Zn bound to the orf7a Cys₁₅ ligand, it has the ability of displacing the metal owing to the creation of a new disulfide bridge across the two proteins. The formation of this BST2-orf7a complex destabilizes BST2 dimerization, thus impairing the antiviral activity of the latter.     

Transforming nonlocality into a frequency dependence: a shortcut to spectroscopy

Measurable spectra are often derived from contractions of many-body Green's functions. One calculates hence more information than needed. Here we present and illustrate an in principle exact approach to construct effective potentials and kernels for the direct calculation of electronic spectra. In particular, a dynamical but local and real potential yields the spectral function needed to describe photoemission. We discuss for model solids the frequency dependence of this "photoemission potential" stemming from the nonlocality of the corresponding self-energy.     

Easy Access to Ni3N– and Ni–Carbon Nanocomposite Catalysts

In the search for alternative materials to current expensive catalysts, Ni has been addressed as one of the most promising and, on this trail, its corresponding nitride. However, nickel nitride is a thermally unstable compound, and therefore not easy to prepare especially as nanoparticles. In the present work, a sol–gel‐based process (the urea glass route) is applied to prepare well‐defined and homogeneous Ni₃N and Ni nanoparticles. In both cases, the prepared crystalline nanoparticles (～25 nm) are dispersed in a carbon matrix forming interesting Ni₃N‐ and Ni‐based composites. These nanocomposites were characterised by means of several techniques, such as XRD, HR‐TEM, EELS, and the reaction mechanism was investigated by TGA and IR and herein discussed. The catalytic activity of Ni₃N is investigated for the first time, to the best of our knowledge, for hydrogenation reactions involving H₂, and here compared to the one of Ni. Both materials show good catalytic activities but, interestingly, give a different selectivity between different functional groups (namely, nitro, alkene and nitrile groups).     

Facile Electrochemical Hydrogenation and Chlorination of Glassy Carbon to Produce Highly Reactive and Uniform Surfaces for Stable Anchoring of Thiolated Molecules

Carbon is a highly adaptable family of materials and is one of the most chemically stable materials known, providing a remarkable platform for the development of tunable molecular interfaces. Herein, we report a two‐step process for the electrochemical hydrogenation of glassy carbon followed by either chemical or electrochemical chlorination to provide a highly reactive surface for further functionalization. The carbon surface at each stage of the process is characterized by AFM, SEM, Raman, attenuated total reflectance (ATR) FTIR, X‐ray photoelectron spectroscopy (XPS), and electroanalytical techniques. Electrochemical chlorination of hydrogen‐terminated surfaces is achieved in just 5 min at room temperature with hydrochloric acid, and chemical chlorination is performed with phosphorus pentachloride at 50 °C over a three‐hour period. A more controlled and uniform surface is obtained using the electrochemical approach, as chemical chlorination is observed to damage the glassy carbon surface. A ferrocene‐labeled alkylthiol is used as a model system to demonstrate the genericity and potential application of the highly reactive chlorinated surface formed, and the methodology is optimized. This process is then applied to thiolated DNA, and the functionality of the immobilized DNA probe is demonstrated. XPS reveals the covalent bond formed to be a C?S bond. The thermal stability of the thiolated molecules anchored on the glassy carbon is evaluated, and is found to be far superior to that on gold surfaces. This is the first report on the electrochemical hydrogenation and electrochemical chlorination of a glassy carbon surface, and this facile process can be applied to the highly stable functionalization of carbon surfaces with a plethora of diverse molecules, finding widespread applications.