Structure and stability of the sH binary hydrate cavity and host-guest versus guest-guest interactions therein: A DFT approach.

The intrinsic ability of clathrate hydrates to encage gaseous molecules is explored. Encapsulation ability depends on the cavity size and the type of guest gaseous species in addition to the physical parameters, temperature and pressure. Here we have reported the structure, stability and nature of interaction in dissimilar guest occupied sH hydrate cavity.

Analogue and structure based approaches for modelling HIV-1 integrase inhibitors.

A set of 220 inhibitors belonging to different structure classes and having HIV-1 integrase activity were collected along with their experimental pIC values. Geometries of all the inhibitors were fully optimized using B3LYP/6-31 + G(d) level of theory. These ligands were docked against 4 different HIV-1 integrase receptors (PDB IDs: 4LH5, 5KRS, 3ZSQ and 3ZSV).

Rational design of pincer-nickel complexes for catalytic cyanomethylation of benzaldehyde: A systematic DFT study.

The current study dwells upon the efforts to computationally probe a phosphine-free pincer-nickel complex that would demonstrate an efficiency better than the reported phosphine-based pincer-nickel complex ( POCN )Ni(CH CN) for cyanomethylation reaction. For this purpose, the mechanism of cyanomethylation of benzaldehyde was studied quantum mechanically for a series of 11 pincer-nickel complexes. The energetics of various intermediates and transition states involved in the catalytic cycle for each catalyst was compared with the corresponding energetics of the Miller's catalyst ( POCN )Ni(CH CN) that is reported to accomplish the cyanomethylation at room temperature.

Artificially expanded genetic information systems (AEGISs) as potent inhibitors of the RNA-dependent RNA polymerase of the SARS-CoV-2.

The recent outbreak of the SARS-CoV-2 infection has affected the lives and economy of more than 200 countries. The unavailability of virus-specific drugs has created an opportunity to identify potential therapeutic agents that can control the rapid transmission of this pandemic. Here, the mechanisms of the inhibition of the RNA-dependent RNA polymerase (RdRp), responsible for the replication of the virus in host cells, are examined by different ligands, such as Remdesivir (RDV), Remdesivir monophosphate (RMP), and several artificially expanded genetic information systems (AEGISs) including their different sequences by employing molecular docking, MD simulations, and MM/GBSA techniques.

Selective Catalytic Synthesis of α-Alkylated Ketones and β-Disubstituted Ketones via Acceptorless Dehydrogenative Cross-Coupling of Alcohols.

Herein, a phosphine-free pincer ruthenium(III) catalyzed β-alkylation of secondary alcohols with primary alcohols to α-alkylated ketones and two different secondary alcohols to β-branched ketones are reported. Notably, this transformation is environmentally benign and atom efficient with HO and H gas as the only byproducts. The protocol is extended to gram-scale reaction and for functionalization of complex vitamin E and cholesterol derivatives.

Synthesis of β- and γ-lactam fused dihydropyrazinones from Ugi adducts a sequential ring construction strategy.

A modular approach for the construction of β- and γ-lactam fused dihydropyrazinones from the readily available Ugi adducts has been described. The sequential construction of rings through base-mediated cycloisomerization followed by acid-mediated cyclization yielded β-lactam fused dihydropyrazinones. However, the Ugi-derived dihydropyrazinones afforded γ-lactam fused dihydropyrazinones under base-mediated cycloisomerization.

Parallel Lemniscal and Non-Lemniscal Sources Control Auditory Responses in the Orbitofrontal Cortex (OFC).

The orbitofrontal cortex (OFC) controls flexible behavior through stimulus value updating based on stimulus outcome associations, allowing seamless navigation in dynamic sensory environments with changing contingencies. Sensory cue driven responses, primarily studied through behavior, exist in the OFC. However, OFC neurons' sensory response properties, particularly auditory, are unknown in the mouse, a genetically tractable animal.

Selective and high yield transformation of glycerol to lactic acid using NNN pincer ruthenium catalysts.

The conversion of glycerol selectively to lactic acid has been accomplished in high yields (ca. 90%) by using a NNN pincer-Ru catalyst. DFT explains the role of the Ru-P bond and sterics in favoring the catalysis.

Peptide-like and small-molecule inhibitors against Covid-19.

Coronavirus disease strain (SARS-CoV-2) was discovered in 2019, and it is spreading very fast around the world causing the disease Covid-19. Currently, more than 1.6 million individuals are infected, and several thousand are dead across the globe because of Covid-19.

Modeling antimalarial and antihuman African trypanosomiasis compounds: a ligand- and structure-based approaches.

This study examines the interaction of 137 antimalarial and antihuman African trypanosomiasis compounds [bis(2-aminoimidazolines), bisguanidinediphenyls and polyamines] on three different in vitro assays (Trypanosoma brucei rhodesiense (T.b.r.

Trisulfides over disulfides: highly selective synthetic strategies, anti-proliferative activities and sustained HS release profiles.

Temperature- and solvent-induced selective synthesis of trisulfides and disulfides is demonstrated. A remarkable selectivity was achieved using Na2S as a sulfur-transfer agent under mild, greener, catalyst-free and additive-free conditions. This study reveals trisulfides as a better model than disulfides in general for a sustained release of H2S and potent anti-cancer activities.

Stereospecific Assembly of Fused Imidazolidines via Tandem Ring Opening/Oxidative Amination of Aziridines with Cyclic Secondary Amines Using Photoredox Catalysis.

Sustainable assembly of imidazolidines is accomplished via a sequential stereospecific ring opening and C-H amination using aziridines with secondary cyclic amines under visible light mediated indazoloquinoline photoredox catalysis at ambient conditions. Optically active aziridines are coupled with high enantiomeric purities. The computational studies provide insights on the redox properties of the catalysts as well as a profile of the reaction.

Converting waste Allium sativum peel to nitrogen and sulphur co-doped photoluminescence carbon dots for solar conversion, cell labeling, and photobleaching diligences: A path from discarded waste to value-added products.

Proper waste utilization in order to promote value added product is a promising scientific practice in recent era. Inspiring from the recurring trend, we propose a single step oxidative pyrolysis derived fluorescent carbon dots (C-dots) from Allium sativum peel, which is a natural, nontoxic, and waste raw material. Because of its excellent optical properties, and photostability this C-dots have been used in versatile area of applications.

tert-Butyl Nitrite Mediated Synthesis of 1,2,4-Oxadiazol-5(4 H)-ones from Terminal Aryl Alkenes.

tert-Butyl nitrite (TBN) mediated synthesis of 3-aryl-1,2,4-oxadiazol-5(4 H)-ones has been accomplished using terminal aryl alkenes via a biradical reaction intermediate. Three consecutive sp C-H bond functionalizations of styrenes afforded 3-phenyl-1,2,4-oxadiazol-5(4 H)-ones via the formation of new C═N, C═O, C-O, and two C-N bonds. Both of the N atoms originate from TBN, while the carbonyl oxygen is from the water (moisture) the other oxygen from the N═O part of the TBN.

pH-Regulated anion transport activities of bis(iminourea) derivatives across the cell and vesicle membrane.

Recently, synthetic anion transporters have gained considerable attention because of their ability to disrupt cellular anion homeostasis and promote cell death. Herein, we report the development of bis(iminourea) derivatives as a new class of selective Cl- ion carrier. The bis(iminourea) derivatives were synthesized via a one-pot approach under mild reaction conditions.

Visible-Light-Mediated Ir(III)-Catalyzed Concomitant C3 Oxidation and C2 Amination of Indoles.

A visible-light-mediated concomitant C3 oxidation and C2 amination of indoles has been achieved at room temperature using an Ir (III) photocatalyst. This reaction proceeds without an isatin intermediate via the attack of a singlet oxygen at the C3 position followed by C2 amination leading to difunctionalization of indoles.

Benchmarking of different molecular docking methods for protein-peptide docking.

Background: Molecular docking studies on protein-peptide interactions are a challenging and time-consuming task because peptides are generally more flexible than proteins and tend to adopt numerous conformations. There are several benchmarking studies on protein-protein, protein-ligand and nucleic acid-ligand docking interactions. However, a series of docking methods is not rigorously validated for protein-peptide complexes in the literature.

Geometry-Driven Iminosemiquinone Radical to Cu(II) Electron Transfer and Stabilization of an Elusive Five-Coordinate Cu(I) Complex: Synthesis, Characterization, and Reactivity with KO.

The noninnocent ligand HL contained a bulky phenyl substituent at the ortho position to the aniline moiety. The ligand reacted with 0.5 equiv of CuCl·2HO in the presence of EtN under air and provided the corresponding Cu(II)-bis(imonosemiquinone) complex (1).

Secondary amine salt catalyzed controlled activation of 2-deoxy sugar lactols towards alpha-selective dehydrative glycosylation.

A new organocatalytic glycosylation method exploiting the lactol functionality has been disclosed. The catalytic generation of glycosyl oxacarbenium ions from lactols under forcible conditions via weakly Brønsted-acidic, readily available secondary amine salts affects the diastereoselective glycosylation of 2-deoxypyranoses and furanoses. This operationally simple iminium catalyzed activation of 2-deoxy hemi-acetals is a potential alternative to the existing cumbersome methods that need specialized handling.

One- and Two-Photon Uncaging: Carbazole Fused o-Hydroxycinnamate Platform for Dual Release of Alcohols (Same or Different) with Real-Time Monitoring.

A one- and two-photon activated photoremovable protecting group (PRPG) was designed based on a carbazole fused o-hydroxycinnamate platform for the dual (same or different) release of alcohols. The mechanism for the dual release proceeds through a stepwise pathway and also monitors the first and second photorelease in real time by an increase in fluorescence intensity and color change, respectively. Further, its application in staining live neurons and ex vivo imaging with two-photon excitation is shown.

Metal-Free Sequential C(sp)-H/OH and C(sp)-H Aminations of Nitrosoarenes and N-Heterocycles to Ring-Fused Imidazoles.

Hydrogen bond assisted ortho-selective C(sp)-H amination of nitrosoarenes and subsequent α-C(sp)-H functionalization of aliphatic amines is achieved under metal-free conditions. The annulation of nitrosoarenes and 2-hydroxy-C-nitroso compounds with N-heterocycles provides a facile excess to a wide range of biologically relevant ring-fused benzimidazoles and structurally novel polycyclic imidazoles, respectively. Nucleophilic aromatic hydrogen substitution (SArH) was found to be preferred over classical SAr reaction during the C(sp)-H amination of halogenated nitrosoarenes.

A web server for analysis, comparison and prediction of protein ligand binding sites.

Background: One of the major challenges in the field of system biology is to understand the interaction between a wide range of proteins and ligands. In the past, methods have been developed for predicting binding sites in a protein for a limited number of ligands.

Results: In order to address this problem, we developed a web server named 'LPIcom' to facilitate users in understanding protein-ligand interaction.

Energy decomposition analysis of cation-π, metal ion-lone pair, hydrogen bonded, charge-assisted hydrogen bonded, and π-π interactions.

This study probes the nature of noncovalent interactions, such as cation-π, metal ion-lone pair (M-LP), hydrogen bonding (HB), charge-assisted hydrogen bonding (CAHB), and π-π interactions, using energy decomposition schemes-density functional theory (DFT)-symmetry-adapted perturbation theory and reduced variational space. Among cation-π complexes, the polarization and electrostatic components are the major contributors to the interaction energy (IE) for metal ion-π complexes, while for onium ion-π complexes (NH4+, PH4+, OH3+, and SH3+) the dispersion component is prominent. For M-LP complexes, the electrostatic component contributes more to the IE except the dicationic metal ion complexes with H2 S and PH3 where the polarization component dominates.

Molecular dynamics investigation on a series of HIV protease inhibitors: assessing the performance of MM-PBSA and MM-GBSA approaches.

The binding free energies (ΔG(Bind)) obtained from molecular mechanics with Poisson-Boltzmann surface area (MM-PBSA) or molecular mechanics with Generalized Born surface area (MM-GBSA) calculations using molecular dynamics (MD) trajectories are the most popular procedures to measure the strength of interactions between a ligand and its receptor. Several attempts have been made to correlate the ΔG(Bind) and experimental IC(50) values in order to observe the relationship between binding strength of a ligand (with its receptor) and its inhibitory activity. The duration of MD simulations seems very important for getting acceptable correlation.