Finite element approach for the modal analysis of open-boundarywaveguides

A general finite element approach to computing the modes of open-boundary waveguides is presented. This efficient and robust scheme applies equally to situations with real and complex propagation constants. By using a localised boundary impedance condition, the approach preserves the sparsity of the global matrices. A comparison with the well established infinite element technique and the analysis of a 2-D leaky optical structure are given as examples     

Die Komplexe von Dioxocyan (OCN)2 mit TiCl4 und ZrCl4

Complexes of Dioxocyanogen (OCN)₂ with TiCl₄ and ZrCl₄ A solution of (OCN)₂ was obtained by reaction of AgOCN with Br₂ in H₂CCl₂ at ?70°C. From this the complexes TiCl₄(NCO)₂ and ZrCl₄(NCO)₂ were obtained by addition of equimolar amounts of TiCl₄ and ZrCl₄, respectively. According to the i.r. and Raman spectra, the (NCO)₂ ligand is bonded via its N atoms to the metal.     

Forced transverse vibrations of a submerged tensioned string

For a submerged cable, the classical equation of a vibrating string must be modified to account for added mass and damping effects. This can be done with the aid of Morison's formulae. The resulting equation is non-linear. It is solved for the case when one end of the string is forced into sinusoidal transverse motion. The first harmonic approximations for both resonant and non-resonant responses are obtained by the method of matched asymptotic expansions under the assumption that the non-dimensional damping coefficient is small.     

Irradiation of the porphyrin causes unfolding of the protein in the protoporphyrin IX/beta-lactoglobulin noncovalent complex

Porphyrins such as protoporphyrin IX (PPIX) are known to occasionally cause conformational changes in proteins for which they are specific ligands. It has also been established that irradiation of porphyrins noncovalently intercalated between bases or bound to one of the grooves can cause conformational effects on DNA. Conversely, there is no evidence reported in the literature of conformational changes caused by noncovalently bound PPIX to globular proteins for which the porphyrin is not a specific ligand. This study shows that the irradiation of the porphyrin in the PPIX/lactoglobulin noncovalent complex indeed causes a local and limited (approximately 7%) unfolding of the protein near the location of Trp19. This event causes the intrinsic fluorescence spectrum of the protein to shift to the red by 2 nm and the average decay lifetime to lengthen by approximately 0.5 ns. The unfolding of lactoglobulin occurs only at pH >7 because of the increased instability of the protein at alkaline pH. The photoinduced unfolding does not depend on the presence of O2 in solution; therefore, it is not mediated by formation of singlet oxygen and is likely the result of electron transfer between the porphyrin and amino acid residues.     

Organocatalytic conjugate addition of formaldehyde N,N-dialkylhydrazones to beta,gamma-unsaturated alpha-keto esters

(1S,2R)-1-Aminoindan-2-ol-derived thioureas behave as efficient H-bonding organocatalysts for the nucleophilic conjugate addition of formaldehyde hydrazones to beta,gamma-unsaturated alpha-keto esters as enoate surrogates, affording the corresponding adducts in good yields and enantioselectivities.     

Automated discovery of noncovalent inhibitors of SARS-CoV-2 main protease by consensus Deep Docking of 40 billion small molecules

Recent explosive growth of ‘make-on-demand’ chemical libraries brought unprecedented opportunities but also significant challenges to the field of computer-aided drug discovery. To address this expansion of the accessible chemical universe, molecular docking needs to accurately rank billions of chemical structures, calling for the development of automated hit-selecting protocols to minimize human intervention and error. Herein, we report the development of an artificial intelligence-driven virtual screening pipeline that utilizes Deep Docking with Autodock GPU, Glide SP, FRED, ICM and QuickVina2 programs to screen 40 billion molecules against SARS-CoV-2 main protease (Mpro). This campaign returned a significant number of experimentally confirmed inhibitors of Mpro enzyme, and also enabled to benchmark the performance of twenty-eight hit-selecting strategies of various degrees of stringency and automation. These findings provide new starting scaffolds for hit-to-lead optimization campaigns against Mpro and encourage the development of fully automated end-to-end drug discovery protocols integrating machine learning and human expertise.

Deep learning-accelerated docking coupled with computational hit selection strategies enable the identification of inhibitors for the SARS-CoV-2 main protease from a chemical library of 40 billion small molecules.     

Synthesis,Structural Characterization,and In Vitro and In Silico Antifungal Evaluation of Azo-Azomethine Pyrazoles (PhN2(PhOH)CHN(C3N2(CH3)3)PhR,R = H or NO2)

The azo-azomethine imines, R¹-N=N-R²-CH=N-R³, are a class of active pharmacological ligands that have been prominent antifungal, antibacterial, and antitumor agents. In this study, four new azo-azomethines, R¹ = Ph, R² = phenol, and R³ = pyrazol-Ph-R’ (R = H or NO₂), have been synthesized, structurally characterized using X-ray, IR, NMR and UV–Vis techniques, and their antifungal activity evaluated against certified strains of Candida albicans and Cryptococcus neoformans. The antifungal tests revealed a high to moderate inhibitory activity towards both strains, which is regulated as a function of both the presence and the location of the nitro group in the aromatic ring of the series. These biological assays were further complemented with molecular docking studies against three different molecular targets from each fungus strain. Molecular dynamics simulations and binding free energy calculations were performed on the two best molecular docking results for each fungus strain. Better affinity for active sites for nitro compounds at the “meta” and “para” positions was found, making them promising building blocks for the development of new Schiff bases with high antifungal activity.     

A Fluorescent Activatable AND‐Gate Chemokine CCL2 Enables In Vivo Detection of Metastasis‐Associated Macrophages

We report the novel chemical design of fluorescent activatable chemokines as highly specific functional probes for imaging subpopulations of immune cells in live tumours. Activatable chemokines behave as AND‐gates since they emit only after receptor binding and intracellular activation, showing enhanced selectivity over existing agents. We have applied this strategy to produce mCCL2‐MAF as the first probe for in vivo detection of metastasis‐associated macrophages in a preclinical model of lung metastasis. This strategy will accelerate the preparation of new chemokine‐based probes for imaging immune cell function in tumours.     

Mechanism of the base-assisted displacement of chloride by alcohol in sulfinyl derivatives

A computational study with density functional theory (DFT) is carried out on the reaction between methyl sulfinyl chloride (MSC) and methanol in the presence of trimethylamine, a process which is a general model for two different methods used in practice for the obtention of chiral sulfoxides through dynamic kinetic resolution. Two mechanistic options are considered: in one of them, chloride is initially displaced by the base (ion pair mechanism), whereas in the other, chloride stays bound to sulfur until its final displacement by methoxy (neutral mechanism). In both cases, the approach of the alcohol to sulfur is coupled with a hydrogen transfer from methanol to the oxo group of MSC in a single concerted transition state. The presence of a trimethylamine molecule facilitates substantially the reaction by reducing the nucleophilic substitution barrier by more than 10 kcal/mol through the formation of a N-H bond with the hydrogen atom being transferred. The neutral mechanism presents a free energy barrier lower than the ion pair alternative and is thus preferred.