Investigation of hydrogen bonded structure of urea-water mixtures through Infra-red spectroscopy and non-covalent interaction (NCI) theoretical approach

Identification of imidazole-based small molecules to combat cognitive disability caused by Alzheimer's disease: A molecular docking and MD simulations based approach

Alzheimer's disease (AD) is a chronic neurodegenerative disorder that is the primary cause of dementia. It is characterised by the gradual loss of brain cells, which results in memory loss and cognitive dysfunction. One of the hallmarks of AD is an abnormally upregulated glutaminyl-peptide cyclotransferase (QPCT or QC) enzyme. Not only AD, but QC has also been implicated with pathological conditions like Huntington's disease (HD), melanomas, carcinomas, atherosclerosis, and septic arthritis. Therefore, the inhibition of QC emerged as a potential strategy for preventing multiple pathological conditions. Considering this, we screened a library of 153,536 imidazole-based compounds against a doubly mutant (Y115E-Y117E) QC target. Molecular docking based virtual screening and absorption, distribution, metabolism, excretion/toxicity (ADME/T) predictions identified five compounds, namely 118981836, 136459842, 139388116, 139388226, and 139958725. Furthermore, molecular dynamics (MD) simulations of 500 ns were conducted to investigate the behaviour of the identified compounds with the target receptor. The results were compared to the co-ligand by analysing RMSD, RMSF, and SASA parameters. To our knowledge, this is the first computational study that employed a protein with double mutation to identify new imidazole-based QC-inhibitors.

Synthesis, characterization, DFT studies and evaluation of the potential anti-tumour activity of nicotinic hydrazide based Schiff base using in vitro and molecular docking techniques

Breast cancer, one of the most serious issues worldwide, has been raising day by day. It has now become a necessary to develop a suitable drug to combat this terrible illness. Schiff bases are increasingly being used as powerful medications for a number of illnesses. BNH has now synthesized from Benzil and Nicotinic hydrazide and characterized experimentally by FT-IR, UV, 1H NMR,13CNMR and Mass analysis. DFT calculations were done using Gaussian 16 W with B3LYP/6-311 + G (d,p) and geometry of the compound is optimized. Frontier Molecular orbit (FMO), Mullikan atomic charges and Molecular Electrostatic Potential (MEP) were studied. Invitro antimicrobial studies were done using various bacteria and fungi. The synthesized compound is appropriate against bacterial and fungal actions. Invitro study were done using MCF-7 cell lines to analyze the anticancer property of the ligand. The outcome suggests that BNH may be employed in the future as a novel anticancer medication.

Synthesis, solvent role, absorption and emission studies of cytosine derivative

The (E)-4-((4-hydroxy-3-methoxy-5-nitrobenzylidene) amino) pyrimidin-2(1H)-one (C5NV) was synthesized from cytosine and 5-nitrovanilline by simple straightforward condensation reaction. The structural characteristics of the compound was determined and optimized by WB97XD/cc-pVDZ basis set. The vibrational frequencies were computed and subsequently compared to the experimental frequencies. We investiated the electronic properties of the synthesized compound in gas and solvent phases using the time-dependent density functional theory (TD-DFT) approach, and compared them to experimental values. The fluorescence study showed three different wavelengths indicating the nature of the optical material properties. Frontier molecular orbital (FMO) and molecular electrostatic potential (MEP) analyses were conducted for the title compound, and electron localized functions (ELF) and localized orbital locators (LOL) were used to identify the orbital positions of localized and delocalized atoms. Non-covalent interactions (H-bond interactions) were investigated using reduced density gradients (RDGs). The objective of the study was to determine the physical, chemical, and biological properties of the C5NV. The molecular docking study was conducted between C5NV and 2XNF protein, its lowest binding energy score is -7.92 kcal/mol.

Exploration of electronic and vibrational properties of sulfanilic acid through periodic and non-periodic DFT calculations

CONTEXT

The electronic, discrete water solvation, and vibrational properties of zwitterionic sulfanilic acid were thoroughly investigated using periodic and non-periodic DFT approaches. The periodic-DFT results, obtained by employing the PBE-TS functional (Perdew-Burke-Ernzerhof (PBE) functional with the Tkatchenko and Scheffler (TS) dispersion correction) were first presented in order to analyze the band structures of the studied crystal. An attentive reading of the predicted band structures has shown three lowest gap energies calculated at 4.23, 4.24, and 4.29 eV arising from the Γ→Γ, Γ→Z, and Γ→S transitions, respectively. Then, non-periodic calculations were carried out, at the B3LYP-D3 level of theory (B3LYP functional with the D3 Grimme dispersion correction) in order to optimize the sulfanilic acid-(H2O)10 complex. Starting from the optimized structure, non-covalent interaction calculations were performed and the H-bonding, van der Waals, and steric effect interactions were identified. Finally, the PBE-TS calculations were strengthened by conducting anharmonic B3LYP-D3 calculations in order to achieve a complete decryption of the experimental IR spectrum of sulfanilic acid. The spectral analysis is not limited only to the interpretation of both the NH/CH stretching and fingerprint regions but also extended to the 1800-2600 cm-1 region, which is characterized by a strong anharmonic effect. In the latter wavenumber region, the large experimental IR band centered at 1937 cm-1 is reproduced theoretically employing the anharmonic B3LYP-D3 calculations. The similarity of this band with those usually considered as a fingerprint of zwitterionic amino acids is observed, and its origin is elucidated theoretically. In the vibrational spectroscopy field, the calculations presented in this study are probably the most appropriate for achieving vast analysis and accurate assignments of vibrational spectra of hydrogen bonding compounds recorded in the solid state.

METHOD

The periodic and non-periodic calculations were conducted within the Density Functional Theory (DFT) using the Generalized Gradient Approximation (GGA) at the PBE-TS level of theory and B3LYP-D3 functional with the 6-311++G(d,p) basis set, respectively. The PBE-TS and B3LYP-D3/6-311++G(d,p) calculations were performed using the CASTEP and Gaussian 09 programs, respectively. In addition, The non-covalent interactions were calculated by the Multiwfn 3.8 software. The obtained results for different calculations were visualized by employing the visualization tools in Materials Studio, GaussView, VMD, and Gnuplot programs.

Role of Noncovalent Interactions in N,P-Functionalized Luminescent Carbon Dots for Ultrasensitive Detection of Moisture in D2O: Boosting Visible-NIR Light Sensitivity

It is highly desirable to design cost-efficient and eco-friendly fluorometric sensors that can efficiently detect water contamination in D₂O and other expensive organic solvents. Herein, we have synthesized N,P-codoped carbon dots (N,P-CDs) from o-phenylene diamine (o-PDA) and H₃PO₄ through the bottom-up carbonization method. Heteroatom co-doping increases the absorption cross section in the visible-NIR range, followed by the formation of stable emissive states in longer-wavelength regions. We have critically investigated the noncovalent interactions (especially H-bonding interactions) of various surface functional groups with surrounding solvent media through a detailed structure-property correlation. Based on the sensitivity of noncovalent H-bonding interactions to the stability of longer-wavelength emissive domains, we have utilized these N,P-CDs as cost-effective fluorometric sensors of water/moisture contamination in D₂O especially under visible-NIR light; the optical sensitivity reaches up to 0.1 volume (%) level. The detailed sensing mechanism has been further supported by a computational study through a simple visualization approach by mapping and analyzing all possible noncovalent interactions between the CDs and the solvent medium.

Construction of double network hydrogels using agarose and gallic acid with antibacterial and anti-inflammatory properties for wound healing

Gallic acid (GA) has attracted extensive attention due to its excellent health benefits. Our recent work demonstrated that GA could be self-assembled into hydrogels. However, the poor mechanical properties and rapid degradation of GA hydrogels presented challenges for further applications. In this study, agarose (AG), a water-soluble polysaccharide, was used with GA to develop a double network hydrogel (GA-AG). Physical and chemical tests demonstrated that the GA-AG hydrogel at ratio of 4:5 had the highest cross-linked structure, along with excellent porosity, good water retention and a swelling ratio of 9.72 %. In addition, the cross-linked network structure enabled the GA-AG hydrogel to have good mechanical properties and better viscosity than the pure GA hydrogel. The glass transition temperature of the GA-AG hydrogel increased from 59.49 °C to 65.54 °C, while its disintegration rate decreased from 99.07 % to 64.37 % within 48 h. In vitro tests showed that the GA-AG hydrogel had excellent antibacterial activity and biocompatibility. Meanwhile, we demonstrated that this double network hydrogel significantly reduced inflammation and accelerated wound healing in vivo. From the results of our study, we expect that this stable GA-AG double network hydrogel has potential applications in wound healing.

Adsorption properties of metal functionalized fullerene (C59Au, C59Hf, C59Ag, and C59Ir) nanoclusters for application as a biosensor for hydroxyurea (HXU): insight from theoretical computation

This theoretical study was conducted to evaluate the efficiency of fullerene C60 and its metal functionalized nano clusters (C59Au, C59Hf, C59Ag and C59Ir) as a sensor for hydroxyurea (HXU). The various conclusions concerning the adsorption and sensing properties of the studied nano surfaces were achieved using density functional theory (DFT) at the M062X-D3/gen/LanL2DZ/def2svp level of theory. Among the nano clusters studied for this interaction, analysis of the HOMO–LUMO energy differences (E g) showed that HXU@C59Hg (H2) reflects the least energy gap of 3.042 eV, indicating its greater reactivity, sensitivity and conductivity. Also, the adsorption phenomenon in this current study is best described as chemisorptions owing to the negative adsorption enthalpies observed. Thus, the adsorption energy (E Ad) follows an increasing pattern of: HXU@C60 (C1) (−0.218 eV) < HXU@C59Ir (I1) (−1.361 eV) < HXU@C59Au (A1) (−1.986 eV) < HXU@C59Hf (H1) (−2.640 eV) < HXU@C59Hg (H2) (−3.347 eV). Least E g, highest E Ad and non-covalent nature of interaction attributed to C59Hg surface are sufficient to show that, among all studied surfaces, C59Hg surface emerged as the most suitable adsorbent for the adsorption of HXU. Hence, it can be used in modeling future adsorbent material for hydroxyurea.

Synergistic Chaotropic Effect and Cathode Interface Thermal Release Effect Enabling Ultralow Temperature Aqueous Zinc Battery

Although rechargeable zinc-ion batteries are promising candidates for next-generation energy storage devices, their inferior performance at subzero temperatures limits their practical application. Here, a strategy to destroy the H-bond network by adding synergistic chaotropic regents is reported, thus reducing the freezing point of the aqueous electrolyte below -90 °C. Owing to the synergistic chaotropic effect between urea and Zn(ClO₄ )₂ and the thermal release effect on the cathode interface during charging, Zn//VO₂ batteries feature a specific capacity of 111.4 mAh g^-1 and stability after ≈1000 cycles with 81.9% capacity retention at -40 °C. This work demonstrates that the synergistic chaotropic effect and the thermal effect on the interface can effectively widen the operation range of temperature of aqueous electrolytes and maintain fast kinetics, which provides a new design strategy for all-weather aqueous zinc batteries.