Halogen vs hydrogen bonding in thiazoline-2-thione stabilization with σ- and π-electron acceptors adducts: theoretical and experimental study

Synthesis and characterization of new 1,3,4-thiadiazole derivatives: study of their antibacterial activity and CT-DNA binding

1,3,4-Thiadiazole molecules (1-4) were synthesized by the reaction of phenylthiosemicarbazide and methoxy cinnamic acid molecules in the presence of phosphorus oxychloride, and characterized with UV, FT-IR, ¹³C-NMR, and ¹H-NMR methods. DFT calculations (b3lyp/6-311++G(d,p)) were performed to investigate the structures' geometry and physiochemical properties. Their antibacterial activity was screened for various bacteria strains such as Enterobacter aerogenes, Escherichia coli ATCC 13048, Salmonella kentucky, Pseudomonas aeruginosa, Klebsiella pneumoniae, Proteus and Gram positive such as Staphylococcus aureus ATCC 25923, Listeria monocytogenes ATCC 7644, Enterococcus faecium, Enterococcus durans, Staphylococcus aureus ATCC, Serratia marcescens, Staphylococcus hominis, Staphylococcus epidermidis, alfa Streptococcus haemolyticus, Enterococcus faecium and found to have an inhibitory effect on Klebsiella pneumoniae and Staphylococcus hominis, while molecules 1, 3 and 4 had an inhibitory effect on Staphylococcus epidermidis and alpha Streptococcus haemolyticus. The experimental results were supported by the docking study using the Kinase ThiM from Klebsiella pneumoniae. All the investigated compounds showed an inhibitory effect for the Staphylococcus epidermidis protein. In addition, the mechanism of the 1-4 molecule interaction with calf thymus-DNA (CT-DNA) was investigated by UV-vis spectroscopic methods.

Spectroscopic study of self-assembly of anti-hepatitis C virus sofosbuvir drug with bio-polymeric nanoparticles for improving the drug release effect

Self-assembly of Sofosbuvir drug (SOF) anti-hepatitis C virus (HCV) with bio-polymeric nanoparticles such as chitosan nanoparticles (Cs NPs) and polyvinyl alcohol nanoparticles (PVA NPs), the novel composites have been characterized successfully by different analysis such as Energy-dispersive X-ray spectroscopy (EDX), Scanning electron microscopy (SEM), UV-Visible spectrophotometer (UV-Vis) and Fourier Transmittance Infrared (FT-IR). The improvement of the Sofosbuvir effect as a result of loading drug on the bio-polymer NPs surface has been detected by the UV-Vis, and fluorescence spectroscopy techniques. The improvement of SOF efficiency was revealed via studying the drug release of SOF from biopolymers NPs surface at pH 7.4, UV-Vis spectra used for the releasing process. The binding constant (K_b) value was reported at 0.000055 and 0.3613 min^-1 for Cs and PVA NPs respectively. Also, the value of K_SV was documented at 0.0014 and 7.16 min^-1 for Cs@SOF and PVA@SOF hybrid nanocomposite. The incorporation rate (k) of SOF on the surface of biopolymer nano molecules was calculated to be 0.00812 and 0.0165 min^-1 for Cs and PVA NPs, respectively. Besides the observed value of (n) was close to the unit 0.74 and 0.86 for Cs and PVA NPs, respectively. The SOF released from Cs NPs surface was documented at 0.09 mg after 24 h, while PVA NPs reported at 0.7 mg at the same time and the release efficiency is 56.5 and 73% for Cs@SOF and PVP@SOF, respectively. From the results, we suggest Cs/SOF and PVA/SOF hybrid nanocomposites have spectroscopic results that make them promising candidate drugs, but need to the clinical trials.

Chloroquine and hydroxychloroquine inhibitors for COVID-19 sialic acid cellular receptor: Structure, hirshfeld atomic charge analysis and solvent effect

COVID-19, the pandemic disease recently discovered in Wuhan (China), severely spread and affected both social and economic activity all over the world. Attempts to find an effective vaccine are challenging, time-consuming though interminable. Hence, re-proposing effective drugs is reliable and effective alternative. Taking into account the genome similarity of COVID-19 with SARS-CoV, drugs with safety profiles could be fast solution. Clinical trials encouraged the use of Chloroquine and Hydroxychloroquine for COVID-19 inhibition. One of the possible inhibition pathways is the competitive binding with the angiotension-converting enzyme-2 (ACE-2), in particular with the cellular Sialic acid (Neu5Ac). Here, we investigate the possible binding mechanism of ClQ and ClQOH with sialic acid both in the gas phase and in water using density functional theory (DFT). We investigated the binding of the neutral, monoprotonated and diprotonated ClQs and ClQOHs to sialic acid to simulate the pH effect on the cellular receptor binding. DFT results reveals that monoprotonated ClQ⁺ and ClQOH⁺, which account for more than 66% in the solution, possess high reactivity and binding towards sialic acid. The Neu5Ac-ClQ and the analogues Neu5Ac-ClQOH adducts were stabilized in water than in the gas phase. The molecular complexes stabilize by strong hydrogen bonding and π - π stacking forces. In addition, proton-transfer in Neu5Ac-ClQOH⁺ provides more stabilizing power and cellular recognition binding forces. These results shed light on possible recognition mechanism and help future breakthroughs for COVID-19 inhibitors.

Noncovalent Bonds, Spectral and Thermal Properties of Substituted Thiazolo[2,3-b][1,3]thiazinium Triiodides

The interrelation between noncovalent bonds and physicochemical properties is in the spotlight due to the practical aspects in the field of crystalline material design. Such study requires a number of similar substances in order to reveal the effect of structural features on observed properties. For this reason, we analyzed a series of three substituted thiazolo[2,3-b][1,3]thiazinium triiodides synthesized by an iodocyclization reaction. They have been characterized with the use of X-ray diffraction, Raman spectroscopy, and thermal analysis. Various types of noncovalent interactions have been considered, and an S…I chalcogen bond type has been confirmed using the electronic criterion based on the calculated electron density and electrostatic potential. The involvement of triiodide anions in the I…I halogen and S…I chalcogen bonding is reflected in the Raman spectroscopic properties of the I–I bonds: identical bond lengths demonstrate different wave numbers of symmetric triiodide vibration and different values of electron density at bond critical points. Chalcogen and halogen bonds formed by the terminal iodine atom of triiodide anion and numerous cation…cation pairwise interactions can serve as one of the reasons for increased thermal stability and retention of iodine in the melt under heating.

Halogen bond triggered aggregation induced emission in an iodinated cyanine dye for ultra sensitive detection of Ag nanoparticles in tap water and agricultural wastewater

Aggregation induced emission (AIE) has emerged as a powerful method for sensing applications. Based on AIE triggered by halogen bond (XB) formation, an ultrasensitive and selective sensor for picomolar detection of Ag nanoparticles (Ag NPs) is reported. The dye (CyI) has an iodine atom in its skeleton which functions as a halogen bond acceptor, and aggregates on the Ag NP plasmonic surfaces as a halogen bond donor or forms halogen bonds with the vacant π orbitals of silver ions (Ag⁺). Formation of XB leads to fluorescence enhancement, which forms the basis of the Ag NPs or Ag⁺ sensor. The sensor response is linearly dependent on the Ag NP concentration over the range 1.0–8.2 pM with an LOD of 6.21 pM (σ = 3), while for Ag⁺ it was linear over the 1.0–10 μM range (LOD = 2.36 μM). The sensor shows a remarkable sensitivity for Ag NPs (pM), compared to that for Ag⁺ (μM). The sensor did not show any interference from different metal ions with 10-fold higher concentrations. This result indicates that the proposed sensor is inexpensive, simple, sensitive, and selective for the detection of Ag NPs in both tap and wastewater samples.

Based on AIE triggered by halogen bond (XB) formation, we established an ultrasensitive and selective sensor for picomolar detection of Ag nanoparticles (Ag NPs).

Phosphorescence of several cocrystals assembled by diiodotetrafluorobenzene and three ring angular diazaphenanthrenes via CI···N halogen bond

X-ray single crystal diffraction reveals that a series of cocrystals are assembled by three ring angular diazaphenanthrenes including 1,7-phenanthroline, 4,7-phenanthroline and 1,10-phenanthroline with 1,4-/1,2-diiodotetrafluorobenzenes via C-I···N halogen bonding (XB) as main driving force. Raman shift of the symmetric CI stretching vibration coupling with ring elongation and lateral ring expansion to a lower frequency by 2 to 7cm^-1 for 1,4-DITFB in cocrystals shows the existence of C-I···N halogen bonding. All cocrystals phosphoresce with a distinct change of colors from yellow, orange, pink to red. Also phosphorescent lifetimes of cocrystals containing 1,4-DITFB are longer than those of others constructed by 1,2-DITFB. These phenanthrolines monomers have almost same phosphorescence wavelength (the max. at 493nm) in β-cyclodextrin solution in the presence of bromocyclohexane as a pure physically heavy atom perturber. The results demonstrate CI···N XB makes heavy atom effect more direct and efficient, and influences significantly the energy level of the lowest lying excited triplet states and the population of electrons to triplet state of the angular diazaphenanthrenes because of greater contribution of lone pair electrons from nitrogen to conjugation systems. Meanwhile, the XB modulates luminescent behaviors due to difference in positions of nitrogen atoms. Good coplanarity, i.e., torsion angles being closer to 0°, in CI···N halogen bonded binary systems also is an important factor affecting the appearance quality of cocrystals.

Orthogonal hydrogen/halogen bonding in 1-(2-methoxyphenyl)-1H-imidazole-2(3H)-thione-I2 adduct: an experimental and theoretical study

The molecular complex between 1-(2-methoxyphenyl)-1H-imidazole-2(3H)-thione (Hmim(OMe)) and iodine (I2) was investigated. Single crystal of [(Hmim(OMe))I2] adduct was grown by slow evaporation technique from chloroform at room temperature. Spectroscopic techniques such as FT-IR and Raman techniques, as well as elemental and thermal analysis were used to characterize the complex. The crystal structure shows that the formed adduct stabilized by two noncovalent interactions, namely, hydrogen bond (HB) and halogen bond (XB). Orthogonal HB/XB associated with iodine atom (I) was observed and fully characterized. The ability of iodine to behave as hydrogen bond acceptor and halogen bond donor was held responsible for the orthogonal HB/XB presence. In addition, the structure of Hmim(OMe)I2 was investigated theoretically using MP2/aug-cc-pVDZ level of theory. Natural bond orbital analysis (NBO) was used to investigate the molecular orbitals interactions and orbitals stabilization energies.