Non-covalent interactions between epinephrine and nitroaromatic compounds: A DFT study

A detailed TD-DFT and intermolecular interaction study of vitamin K in soluble, poorly soluble and insoluble solvents, as well as an ADME and molecular docking study

Vitamin K is one of the most important fat-soluble vitamins and while there are two main types of vitamin K in nature, known as K1 (phylloquinone) and K2 (menaquinones), there is also a synthetic type of vitamin K known as K3 (menadione). Recent studies have shown that it is crucial to know the non-covalent interactions, ADME and molecular docking of molecules in different solvent media. Therefore, we have performed some quantum chemical calculations, ADME and intra-and intermolecular interaction calculations of a number of K1, K2 and K3 such as K1-water (K1 + W), K1-methanol (K1 + M), K1-triacetin (K1 + T), K2-water (K2 + W), K2-methanol (K2 + M), K2-triacetin (K2 + T), K3-water (K3 + W), K3-methanol (K3 + M), K3-triacetin (K3 + T) performed by Density Functional Theory (DFT) and Multiwfn: A multifunctional wavefunction analyzer. Molecular structures, HOMO-LUMO energies, MEP and electronic properties have been calculated and described using DFT at the level of B3LYP/6-311G (d,p) level. The nature of the molecular interactions between vitamin K and solvents such as water, methanol and triacetin were also investigated using topological analyses such as atoms in molecule (AIM), non-covalent interaction index (NCI), reduced density gradient (RDG), Localized orbital locator (LOL) and electron localization function (ELF). In addition, FMO for electronic transitions, MEP for electrophilic and nucleophilic attack, ADME to investigate how a chemical is processed by a living organism, and Fukui functions to determine electron density are explained. Finally, molecular docking was used to determine the biological activity of the vitamin K.

Activatable NIR Fluorescence Probe for Epinephrine Detection and Bioimaging Based on Anionic Heptamethine Cyanine

Epinephrine (EP) is an essential catecholamine in the human body. Currently, most EP detection methods are not suitable for in vivo detection due to material limitations. An organic small molecule fluorescent probe based on a chemical cascade reaction for the detection of EP was designed. Anionic heptamethine cyanine dye was selected as a fluorescent dye because of its NIR fluorescence emission with excellent biocompatibility. The secondary amine of EP nucleophilically attacks the carbonate of the probe with its stronger nucleophilicity and further undergoes intramolecular nucleophilic cyclization to release the fluorophore. Other substances containing only primary amines or no β-OH lack reaction competitiveness due to their weaker nucleophilicity or inability to undergo further cyclization. The fluorescence recovery of the probe was linearly related to the EP concentration of 2-75 μmol/L. The detection limit was 0.4 μmol/L. The recovery rate was 94.78-111.32%. Finally, we successfully achieved bioimaging of EP in living cells and EP analogue in nematodes.

Evolution from basic to advanced structure of fulvic acid and humic acid prepared by food waste

Fulvic acid (FA) and humic acid (HA) are common polyacids in nature. However, the evolutionary process of their basic and advanced structures is still unclear. FA and HA were separated into five molecular weight components to investigate the process of evolution from small to large molecules. The primary structure analysis showed that FA were rich in CN, COOH and OH content, while HA were rich in (CH2)n, NH2 and CC. Moreover, with the molecular weight increasing, the structures could complement each other to maintain the hydrophilic or hydrophobic balance. The 2D-COS spectroscopy demonstrated that during the growth of FA, COOH, NH2 and OH firstly respond. On the other hand, during the growth of HA, NH2 and (CH2)n firstly respond. In addition, advanced structure of FA was affected by intramolecular hydrogen bonds and π - π interaction. HA was affected by hydrophobic interactions due to the abundance of hydrophobic groups, primarily (CH2)n and benzene rings. 3D conformational fitting and particle size characterization confirmed that the interaction forces determine that FA and HA become tightly and loosely molecules respectively. This study is to further explore the geochemical formation and evolution process of FA and HA molecules.

Unveiling the Potential of B3O3 Nanoflake as Effective Transporter for the Antiviral Drug Favipiravir: Density Functional Theory Analysis

In this study, for the first time, boron oxide nanoflake is analyzed as drug carrier for favipiravir using computational studies. The thermodynamic stability of the boron oxide and favipiravir justifies the strong interaction between both species. Four orientations are investigated for the interaction between the favipiravir and the B3O3 nanoflake. The Eint of the most stable orientation is -26.98 kcal/mol, whereas the counterpoise-corrected energy is -22.59 kcal/mol. Noncovalent interaction index (NCI) and quantum theory of atoms in molecules (QTAIM) analyses are performed to obtain insights about the behavior and the types of interactions that occur between B3O3 nanoflake and favipiravir. The results indicate the presence of hydrogen bonding between the hydrogen in the favipiravir and the oxygen in the B3O3 nanoflake in the most stable complex (FAV@B3O3-C1). The electronic properties are investigated through frontier molecular orbital analysis, dipole moments and chemical reactivity descriptors. These parameters showed the significant activity of B3O3 for favipiravir. NBO charge analysis transfer illustrated the charge transfer between the two species, and UV-VIS analysis confirmed the electronic excitation. Our work suggested a suitable drug carrier system for the antiviral drug favipiravir, which can be considered by the experimentalist for better drug delivery systems.

Fluorescence Quenching and the Chamber of Nitroaromatics: A Dinaphthoylated Oxacalix[4]arene's (DNOC) Adventure Captured through Computational and Experimental Study

This research presents the application of Dinaphthoylated Oxacalix[4]arene (DNOC) as a novel fluorescent receptor for the purpose of selectively detecting nitroaromatic compounds (NACs). The characterization of DNOC was conducted through the utilization of spectroscopic methods, including 1H-NMR, 13C-NMR, and ESI-MS. The receptor demonstrated significant selectivity in acetonitrile towards several nitroaromatic analytes, such as MNA, 2,4-DNT, 2,3-DNT, 1,3-DNB, 2,6-DNT, and 4-NT. This selectivity was validated by the measurement of emission spectra. The present study focuses on the examination of binding constants, employing Stern-Volmer analysis, as well as the determination of the lowest detection limit (3σ/Slope) and fluorescence quenching. These investigations aim to provide insights into the inclusion behavior of DNOC with each of the six analytes under fluorescence spectra investigation. Furthermore, the selectivity trend of the ligand DNOC for NAC detection is elucidated using Density Functional Theory (DFT) calculations conducted using the Gaussian 09 software. The examination of energy gaps existing between molecular orbitals, namely the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), provides a valuable understanding of electron-transfer processes and electronic interactions. Smaller energy gaps are indicative of heightened selectivity resulting from favorable electron-transfer processes, whereas bigger gaps suggest less selectivity attributable to weaker electronic contacts. This work integrates experimental and computational methodologies to provide a full understanding of the selective binding behavior of DNOC. As a result, DNOC emerges as a viable chemical sensor for detecting nitroaromatic explosives.

Intramolecular Hydrogen Bonding Effect on the Electron-Transfer Thermodynamics of a Series of o-Nitrobenzyl Alcohol Derivatives

From thermoelectrochemical experiments and electronic structure calculations of a series of nitrobenzyl alcohol derivatives, the effect of intramolecular hydrogen bonding (IHB) on the electron transfer thermodynamics is discussed on a molecular basis. A linear correlation between formal reduction potential (E1/2) values and temperature was obtained for the temperature range from 300 to 350 K. Estimated electron transfer entropy values (ΔS)─determined from this dependence─and the enthalpy (ΔΔH) changes relative to o-nitrobenzyl alcohol confirmed that the effect of the formation of IHB proved to be decisive in the charge-transfer thermodynamics. The possibility of intermolecular hydrogen bonding is further discussed upon comparing thermodynamic data among three different solvents.

Effects of Site-Directed Mutagenesis of Cysteine on the Structure of Sip Proteins

Bacillus thuringiensis, a gram-positive bacteria, has three insecticidal proteins: Vip (vegetative insecticidal protein), Cry (crystal), and Sip (secreted insecticidal protein). Of the three, Sip proteins have insecticidal activity against larvae of Coleoptera. However, the Sip1Aa protein has little solubility in the supernatant because of inclusion bodies. This makes it more difficult to study, and thus research on Sip proteins is limited, which hinders the study of their mechanistic functions and insecticidal mechanisms. This highlights the importance of further investigation of the Sip1Aa protein. Disulfide bonds play an important role in the stability and function of proteins. Here, we successfully constructed mutant proteins with high insecticidal activity. The tertiary structure of the Sip1Aa protein was analyzed with homologous modeling and bioinformatics to predict the conserved domain of the protein. Cysteine was used to replace amino acids via site-directed mutagenesis. We successfully constructed Sip149-251, Sip153-248, Sip158-243, and Sip178-314 mutant proteins with higher solubility than Sip1Aa. Sip153-248 and Sip158-243 were the most stable compared to Sip1Aa, followed by Sip149-251 and Sip178-314. The insecticidal activity of Sip153-248 (Sip158-243) was 2.76 (2.26) times higher than that of Sip1Aa. The insecticidal activity of Sip149-251 and Sip178-314 did not differ significantly from that of Sip1Aa. Basic structural properties, physicochemical properties, and the spatial structure of the mutation site of Sip1Aa and the mutant proteins were analyzed. These results provide a molecular basis for using Sip1Aa to control Coleopteran insects and contribute to the study of the Sip1Aa insecticidal mechanism.

Investigation of optical properties for N- and F-doped triangular shaped carbon molecules

Optical properties of N- and F-doping triangular-shaped carbon molecules have been investigated in theory and experiment. The theoretical results showed that carbon molecules with impurity F and Cl have the same characters with pure carbon. Doping N into pure carbon molecule would change the optical rotation at 589 nm. For doping N replacing hydrogen atom structures (N-doping 1 and N-doping 2 molecules), the absorption spectra of them are similar to pure carbon molecule. However, for molecules with impurity N atom in benzene ring (N-doping 3 and N-doping 4 molecules), the peaks of wavelength of absorption spectra shift to long wavelength compared to that of pure carbon molecule. Moreover, the delocalization of molecular orbital (MO) is different from pure carbon molecule, which is caused by the impurity N changing the electrons distribution of benzene ring. We have calculated 3 without H and 4 without H molecules which are removing hydrogen atom in nitrogen atom from N-doping 3 and 4. 3 without H and 4 without H molecules have similar optical properties with pure carbon molecule. The results testified that the impurity N and F would not change the optical properties of carbon molecule if impurity did not change the delocalization of all benzene rings. Optical properties of nitrogen- and fluorine-doping carbon molecules investigating in theory and experiment.

Chitosan and chitosan/PEG nanoparticles loaded with indole-3-carbinol: Characterization, computational study and potential effect on human bladder cancer cells

Indole-3-carbinol (I3C) is a plant molecule known to be active against several types of cancer, but some chemical characteristics limit its clinical applications. In order to overcome these limitations, polymeric nanoparticles can be used as carrier systems for targeted delivery of I3C. In this study, chitosan and chitosan/polyethylene glycol nanoparticles (CS NP and CS/PEG NP, respectively) were prepared to encapsulate I3C by ionic gelation method. The polymeric nanoparticles were characterized by Dynamic Scattering Light (DLS), Zeta Potential (ZP), Fourier Transform Infrared (FTIR) spetroscopy, X-Ray Diffraction (XRD), Thermogravimetric Analysis (TGA), Differential Scanning Calorimetry (DSC), and Field Emission Gun Scanning Electron Microscopy (FEG-SEM). I3C release testing was performed at an acidic media and the interactions between I3C and chitosan or PEG were evaluated by Density Functional Theory (DFT). Cytotoxicity of nanoparticles in bladder cancer T24 cell line was evaluated by the Methyl-thiazolyl-tetrazolium (MTT) colorimetric assay. The average size of the nanoparticles was observed to be in the range from 133.3 ± 3.7 nm to 180.4 ± 2.7 nm with a relatively homogeneous distribution. Samples had relatively high positive zeta potential values (between +20.3 ± 0.5 mV and + 24.3 ± 0.5 mV). Similar encapsulation efficiencies (about 80%) for both nanoparticles were obtained. Physicochemical and thermal characterizations pointed to the encapsulation of I3c. electron microscopy showed spherical particles with smooth or ragged surface characteristics, depending on the presence of PEG. The mathematical fitting of the release profile demonstrated that I3C-CS NP followed the Higuchi model whereas I3C-CS/PEG NP the Korsmeyer-Peppas model. Chemical differences between the nanoparticles as based on the I3C/CS or I3C/PEG interactions were demonstrate by computational characterization. The assessment of cell viability by the MTT test showed that the presence of both free I3C and I3C-loaded nanoparticles lead to statistically significant reduction in T24 cells viability in the concentrations from 500 to 2000 μM, when comparison to the control group after 24 h of exposure. Thus, CS and CS/PEG nanoparticles present as feasible I3C carrier systems for cancer therapy.