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Monthly Archives: September 2023
Waste-derived green ZnO–Fe2O3 photocatalyst for degradation of MB dye pollutant in water
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Terpenoid-based supramolecular materials: fabrications, performances, applications
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Metal organic framework-based photocatalyst-assisted peroxone process for formaldehyde and acetaldehyde removal from waste air stream: intermediates and mineralization
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DOCK 6: Incorporating hierarchical traversal through precomputed ligand conformations to enable large‐scale docking
Molecular docking is a prevalent tool in drug discovery. DOCK 6's extensible design enables implementing and testing new methods in molecular docking. Development in DOCK 3 enabled screening of large databases of billions of small molecules. To allow access to this unprecedented chemical space, we have implemented features from DOCK 3.7 into DOCK 6, including traversal of precomputed ligand conformations stored in a hierarchical database. We test these new features retrospectively.
Abstract
To allow DOCK 6 access to unprecedented chemical space for screening billions of small molecules, we have implemented features from DOCK 3.7 into DOCK 6, including a search routine that traverses precomputed ligand conformations stored in a hierarchical database. We tested them on the DUDE-Z and SB2012 test sets. The hierarchical database search routine is 16 times faster than anchor-and-grow. However, the ability of hierarchical database search to reproduce the experimental pose is 16% worse than that of anchor-and-grow. The enrichment performance is on average similar, but DOCK 3.7 has better enrichment than DOCK 6, and DOCK 6 is on average 1.7 times slower. However, with post-docking torsion minimization, DOCK 6 surpasses DOCK 3.7. A large-scale virtual screen is performed with DOCK 6 on 23 million fragment molecules. We use current features in DOCK 6 to complement hierarchical database calculations, including torsion minimization, which is not available in DOCK 3.7.
The challenge of ab initio calculations of small neon clusters
Weakly bound neon dimer, trimer and tetramers are studied at HF and CCSD(T) levels using Dunning, ANO and SIGMA-s basis sets. Their ground-state binding energies are studied along with some structural properties. SIGMA-s basis sets have been developed explicitly for this issue but in a manner that can be readily applied to other atoms for the study of larger weakly bound systems. The difficulties for attaining accurate results on these systems are assessed by the computation of total, atomization and correlation energies, as well as equilibrium distances, with several basis sets of increasing size, ranging from non-augmented to double-augmented versions. Extrapolations are proposed to predict stabilization energies and the results are compared with previously published data.
Photocatalytic Dehydroformylation of Benzyl Alcohols to Arenes
The combination of photoinduced hydrogen atom transfer (HAT) and cobalt catalysis gives access to a mild dehydroformylation sequence for the defunctionalization of benzyl alcohols to arenes. The transformation proceeds through a stepwise radical pathway, wherein benzylic and acyl radicals are generated as key intermediates. As a result, stable C−C bonds can be cleaved while generating concomitant syngas (CO+H2).
Abstract
In the last decades, many C−C bond-forming reactions have been developed, whereas less attention has been paid to the design of strategies involving C−C bond cleavage. We report a photocatalytic dehydroformylation sequence for the conversion of benzyl alcohols to arenes in a one-pot two-step process. Herein, the initial dehydrogenation of the benzyl alcohols to the corresponding benzaldehydes is combined with an additional decarbonylation step yielding arenes. As a result, a broad range of benzyl alcohols can be easily transformed in short times under mild photocatalytic conditions. The conducted mechanistic studies indicate that our cooperative hydrogen atom transfer (HAT)-cobalt system proceeds through the formation of α-alkoxy- and acyl radicals as key intermediates, involving concomitant syngas (CO+H2) generation.
Vigna unguiculata L. Walp. Leaves as a Source of Phytochemicals of Dietary Interest: Optimization of Ultrasound‐Assisted Extraction and Assessment of Traditional Consumer Habits.
Vigna unguiculata L. Walp. is an African crop spread worldwide mainly for pulses production. Despite being a neglected and under-utilized food, cowpea leaves are a rich source of phytochemicals and micronutrients. The aim of the work is to characterize the phytochemical composition of cowpea leaves by an optimized ultrasound-assisted extraction (USAE) and to compare raw and boiled leaves.A three-level factorial design (Box-Behnken) was employed for the optimization of the USAE considering three different parameters (% ethanol, drug-to-solvent ratio, and number of cycles). The optimized extracts were characterized by LC-MS/MS. Finally, leaves were boiled at 100 °C for 30 min to simulate traditional cooking procedures and compared to raw leaves. The best extraction condition was EtOH/H2O 1:2 v/v, drug to solvent ratio 1:47 w/v, and 3 extraction cycles. The phytochemicals identified mainly belong to the family of phenolic acids, flavonoids, terpenoids, and alkaloids. Boiled leaves revealed a significant loss of most phytochemicals and a net decrease of their antioxidant activity compared to the raw ones. The results highlight the potential nutraceutical value of cowpea leaves whilst the impoverishment triggered by traditional consumer habits pushes the need to evaluate alternative cooking procedures helpful in the maintenance of their phytochemical properties.
Spatial variation in yield, chemical composition, and phytotoxic activity of Cistus ladanifer essential oils.
Cistus ladanifer L. (rockrose) is a widespread shrub species of the Mediterranean region with products highly valued by the perfume and cosmetics industry. In this research, the variability in yield, chemical composition and phytotoxic activity of C. ladanifer essential oils collected from 12 plots belonging to four natural populations and settled on two different types of edaphic substrates were evaluated. The essential oils were analyzed by GC-MS. The essential oil content ranged from 0.19 to 0.42 ml/100 g. The volatile profiles were found to be rich in oxygenated sesquiterpenes and oxygenated monoterpenes. PCA analysis clustered the samples into two groups that were mainly attributed to the type of substrate on which the plants grow. Furthermore, CCA and correlation analysis revealed that soil organic matter was the most effective edaphoclimatic driver accounting for these high levels of variation in essential oil yield and composition. Finally, C. ladanifer essential oils showed strong phytotoxic activity on R. sativus seedlings, indicating its potential use as a natural bio-herbicide in agriculture. The results showed that the effect associated to local edaphoclimatic conditions not only impacted on the quality and quantity of the essential oil, but also on the industrial uses derived from its biological activities.
Asymmetric Synthesis of Pantolactone: Recent Advances
(R)-Pantolactone, an intermediate in the syntheses of Vitamin B5 and coenzyme A, is an important chiral molecule often used as a food additive, chiral auxiliary, and chiral starting material for organic transformations. Enantioenriched pantolactones are predominantly produced by biological fermentation and chemical synthesis approaches. Herein, we present a review of recent developments in the asymmetric synthesis of pantolactone via different methods, and systematically summarize the characteristics and advantageous features of these strategies. Among the strategies discussed herein, the direct asymmetric catalysis of glyoxylate and isobutyraldehyde with small organocatalyst molecules has attracted growing attention owing to its good step-economy, commercially available starting materials, absence of toxic reagents, mild reaction conditions, convenient operation, and low catalyst loading. These characteristics render the direct asymmetric route to pantolactone a particularly attractive procedure. This review provides valuable guidance for the design and synthesis of enantioenriched pantolactone and its analogs.