Experimental and computational modeling of the biological activity of benzaldehyde sulphur trioxide as a potential drug for the treatment of Alzheimer disease

Impact of Polythiophene ((C4H4S)n; n = 3, 5, 7, 9) Units on the Adsorption, Reactivity, and Photodegradation Mechanism of Tetracycline by Ti-Doped Graphene/Boron Nitride (Ti@GP_BN) Nanocomposite Materials: Insights from Computational Study

This study addresses the formidable persistence of tetracycline (TC) in the environment and its adverse impact on soil, water, and microbial ecosystems. To combat this issue, an innovative approach by varying polythiophene ((C4H4S)n; n = 3, 5, 7, 9) units and the subsequent interaction with Ti-doped graphene/boron nitride (Ti@GP_BN) nanocomposites was applied as catalysts for investigating the molecular structure, adsorption, excitation analysis, and photodegradation mechanism of tetracycline within the framework of density functional theory (DFT) at the B3LYP-gd3bj/def2svp method. This study reveals a compelling correlation between the adsorption potential of the nanocomposites and their corresponding excitation behaviors, particularly notable in the fifth and seventh units of the polythiophene configuration. These units exhibit distinct excitation patterns, characterized by energy levels of 1.3406 and 924.81 nm wavelengths for the fifth unit and 1.3391 and 925.88 nm wavelengths for the seventh unit. Through exploring deeper, the examination of the exciton binding energy emerges as a pivotal factor, bolstering the outcomes derived from both UV-vis transition analysis and adsorption exploration. Notably, the calculated exciton binding energies of 0.120 and 0.103 eV for polythiophene units containing 5 and 7 segments, respectively, provide compelling confirmation of our findings. This convergence of data reinforces the integrity of our earlier analyses, enhancing our understanding of the intricate electronic and energetic interplay within these intricate systems. This study sheds light on the promising potential of the polythiophene/Ti-doped graphene/boron nitride nanocomposite as an efficient candidate for TC photodegradation, contributing to the advancement of sustainable environmental remediation strategies. This study was conducted theoretically; hence, experimental studies are needed to authenticate the use of the studied nanocomposites for degrading TC.

Anti-inflammatory biomolecular activity of chlorinated-phenyldiazenyl-naphthalene-2-sulfonic acid derivatives: perception from DFT, molecular docking, and molecular dynamic simulation

In this study, two novel derivatives of naphthalene-2-sulfonic acid: 6-(((1S,5R)-3,5-dichloro-2,4,6-triazabicyclo [z3.1.0]hex-3-en-1-yl)amino)-5-((E)-phenyldiazenyl)naphthalene-2-sulfonic acid (DTPS1) and (E)-6-((4,6-dichloro-1,3,5-triazine2-yl)amino)-4-hydroxy-3-(phenyldiazenyl)naphthalene-2-sulfonic acid (DTPS2) have been synthesized and characterized using FT-IR, UV-vis, and NMR spectroscopic techniques. Applying density functional theory (DFT) at the B3LYP, APFD, PBEPBE, HCTH, TPSSTPSS, and ωB97XD/aug-cc-pVDZ level of theories for the electronic structural properties. In-vitro analysis, molecular docking, molecular dynamic (MD) simulation of the compounds was conducted to investigate the anti-inflammatory potential using COXs enzymes. Docking indicates binding affinity of -9.57, -9.60, -6.77 and -7.37 kcal/mol for DTPS1, DTPS2, Ibuprofen and Diclofenac which agrees with in-vitro assay. Results of MD simulation, indicates sulphonic group in DTPS1 has > 30% interaction with the hydroxyl and oxygen atoms in amino acid residues, but > 35% interaction with the DTPS2. It can be said that the DTPS1 and DTPS2 can induce inhibitory effect on COXs to halt biosynthesis of prostaglandins (PGs), a chief mediator of inflammation and pain in mammals.Communicated by Ramaswamy H. Sarma.

Synthesis, characterization, and molecular modeling of phenylenediamine-phenylhydrazine-formaldehyde terpolymer (PPHF) as potent anti-inflammatory agent

Inflammation, a characteristic physiological response to infections and tissue damage, commences with processes involving tissue repair and pathogen elimination, contributing to the restoration of homeostasis at affected sites. Hence, this study presents a comprehensive analysis addressing diverse aspects associated with this phenomenon. The investigation encompasses the synthesis, spectral characterizations (FT-IR, ¹H NMR, and ¹³C NMR), and molecular modeling of p-phenylenediamine-phenylhydrazine-formaldehyde terpolymer (PPHF), a potent agent in promoting inflammation. To explore the reactivity, bonding nature, and spectroscopy, as well as perform molecular docking for in-silico biological evaluation, density functional theory (DFT) utilizing the def2svp/B3LYP-D3BJ method was employed. The results reveal significant biological activity of the tested compound in relation to anti-inflammatory proteins, specifically 6JD8, 5TKB, and 4CYF. Notably, upon interaction between PPHF and 6JD8, a binding affinity of -4.5 kcal/mol was observed. Likewise, the interaction with 5TKB demonstrated an affinity of -7.8 kcal/mol. Furthermore, a bonding affinity of -8.1 kcal/mol was observed for the interaction with 4CYF. Importantly, these values closely correspond to those obtained from the interaction between the proteins and the standard drug ibuprofen (IBF), which exhibited binding affinities of -5.9 kcal/mol, -7.0 kcal/mol, and -6.1 kcal/mol, respectively. Thus, these results provide compelling evidence affirming the tremendous potential of p-phenylenediamine-phenylhydrazine-formaldehyde (PPHF) as a highly promising anti-inflammatory agent, owing to the presence of nitrogen-a heteroatom within the compound.

Metals (Ga, In) decorated fullerenes as nanosensors for the adsorption of 2,2-dichlorovinyldimethylphosphate agrochemical based pollutant

Owing to the fact that the use of 2,2-dichlorovinyldimethylphosphate (DDVP) as an agrochemical has become a matter of concern due to its persistence and potential harm to the environment and human health. Detecting and addressing DDVP contamination is crucial to protect human health and mitigate ecological impacts. Hence, this study focuses on harnessing the properties of fullerene (C60) carbon materials, known for their biological activities and high importance, to develop an efficient sensor for DDVP. Additionally, the sensor's performance is enhanced by doping it with gallium (Ga) and indium (In) metals to investigate the sensing and trapping capabilities of DDVP molecules. The detection of DDVP is carefully examined using first-principles density functional theory (DFT) at the Def2svp/B3LYP-GD3(BJ) level of theory, specifically analyzing the adsorption of DDVP at the chlorine (Cl) and oxygen (O) sites. The adsorption energies at the Cl site were determined as - 57.894 kJ/mol, - 78.107 kJ/mol, and - 99.901 kJ/mol for Cl_DDVP@C60, Cl_DDVP@Ga@C60, and Cl_DDVP@In@C60 interactions, respectively. At the O site, the adsorption energies were found to be - 54.400 kJ/mol, - 114.060 kJ/mol, and - 114.056 kJ/mol for O_DDVP@C60, O_DDVP@Ga@C60, and O_DDVP@In@C60, respectively. The adsorption energy analysis highlights the chemisorption strength between the surfaces and the DDVP molecule at the Cl and O sites of adsorption, indicating that the O adsorption site exhibits higher adsorption energy, which is more favorable according to the thermodynamics analysis. Thermodynamic parameters (∆H and ∆G) obtained from this adsorption site suggest considerable stability and indicate a spontaneous reaction in the order O_DDVP@Ga@C60 > O_DDVP@In@C60 > O_DDVP@C60. These findings demonstrate that the metal-decorated surfaces adsorbed on the oxygen (O) site of the biomolecule offer high sensitivity for detecting the organophosphate molecule DDVP.

Structure-based drug design, molecular dynamics simulation, ADMET, and quantum chemical studies of some thiazolinones targeting influenza neuraminidase

The genetic mutability of the influenza virus leads to the existence of drug-resistant strains which is dangerous, particularly with the lingering coronavirus disease (COVID-19). This necessitated the need for the search and discovery of more potential anti-influenza agents to avert future outbreaks. In furtherance of our previous in-silico studies on 5-benzyl-4-thiazolinones as anti-influenza neuraminidase (NA) inhibitors, molecule 11 was selected as the template scaffold for the structure-based drug design due to its good binding, pharmacokinetic profiling, and better NA inhibitory activity. As such, eighteen (18) new molecules (11a-r) were designed with better MolDock scores as compared with the template scaffold and the zanamivir reference drug. However, the dynamic stability of molecule 11a in the binding cavity of the NA target (3TI5) showed water-mediated hydrogen and hydrophobic bondings with the active residues such as Arg118, Ile149, Arg152, Ile222, Trp403, and Ile427 after the MD simulation for 100 ns. The drug-likeness and ADMET assessment of all designed molecules predicted non-violation of the stipulated thresholds of Lipinski's rule and good pharmacokinetic properties respectively. In addition, the quantum chemical calculations also suggested the significant chemical reactivity of molecules with their smaller band energy gap, high electrophilicity, high softness, and low hardness. The results obtained in this study proposed a reliable in-silico viewpoint for anti-influenza drug discovery and development.Communicated by Ramaswamy H. Sarma.

Anticancer Activities of Re(I) Tricarbonyl and Its Imidazole-Based Ligands: Insight from a Theoretical Approach

Rhenium complexes have been observed experimentally to exhibit good inhibitory activity against malignant cells. Hence, our motivation is to explore this activity from a theoretical perspective. In the present study, density functional theory (DFT) and in silico molecular docking approaches were utilized to unravel the unique properties of metal-based rhenium tricarbonyl complexes as effective anticancer drugs. All DFT calculations and geometric optimizations were conducted using the well-established hybrid functional B3LYP-GD(BJ)/Gen/6-311++G(d,p)/LanL2DZ computational method. The FT-IR spectroscopic characterization of the complexes: fac-[Re(Pico)(CO)₃(Pz)] (R1), fac-[Re(Pico)(CO)₃(Py)] (R2), fac-[Re(Dfpc)(CO)₃(H₂O)] (R3), fac-[Re(Dfpc)(CO)₃(Pz)] (R4), fac-[Re(Dfpc)(CO)₃(Py)] (R5), fac-[Re(Tfpc)(CO)₃(H₂O)] (R6), fac-[Re(Tfpc)(CO)₃(Py)] (R7), and fac-[Re(Tfpc)(CO)₃(Im)] (R8) was explored. To gain insights into the electronic structural properties, bioactivity, and stability of these complexes, the highest occupied molecular orbital-lowest unoccupied molecular orbital analysis, binding energy, and topological analysis based on quantum theory of atoms-in-molecules were considered. The anticancer activities of the complexes were measured via in silico molecular docking against human BCL-2 protein (IG5M) and proapoptotic (agonist) BAX 1 protein (450O). The results showed that the studied complexes exhibited good binding affinity (-3.25 to -10.16 kcal/mol) and could cause significant disruption of the normal physiological functions of the studied proteins. The results of DFT calculations also showed that the studied complexes exhibited good stability and are suitable candidates for the development of anticancer agents.

High-performance non-fullerene acceptor-analogues designed from dithienothiophen [3,2-b]-pyrrolobenzothiadiazole (TPBT) donor materials

CONTEXT

Density functional theory (DFT) method was employed to investigate the electronic structure properties, excited state dynamics, charge transfer, and photovoltaic potential of benzo [1,2,5] thiadiazole fused to 3,7-dimethyl-3a,6,7,7b-tetrahydro-5H-thieno[2',3':4,5]thieno[3,2-b]pyrrole to form 3,9,12,13-tetramethyl-12,13-dihydro-[1,2,5]thiadiazolo[3,4-e]thieno[2″,3″:4,5]pyrrolo[3.2-g]thieno[2',3':4,5]thieno[3,2-b]indole as the acceptor (A), bridge with thiophene as π-spacer to the donor moieties (D) which are 2,3-dihydrobenzo [b]thiophene-6-carboxylic acid (M4) and functionalized R, M1, M2, M3, and M5 to give a D-π-A-π-D. Here is the reverse combination for our molecules: the A-π-D-π-A type of chromophore configuration. It is also observed that tuning the dono-bridge configuration significantly increases the ease of charge transfer as the energy gap decreases in the order of 1.29 eV in M4 < 1.59 eV in M3 < 1.67 eV < 1.99 in M2 and 2.06 eV. The reorganization energy (RE) of M3 (0.0031) and M5 (0.0031) indicates an increase in the order of M3 > M5 > R > M2 > M4 > M1. The HOMO-LUMO indicates that the reactivity decreased, while the stability increased for the reference R at 0.990 eV, compared to the designed molecules M1-M5, with M1 being the least stable at 0.970 eV, while M4 exhibited the highest stability at 1.550 eV. The stability of the designed molecule decreased in the order of M4:1.550 > M3:1.257 > M5:1.197 > M2:1.010 > M1:0.970. Therefore, all results point to the electron-deficient core as an effective end-capped electron acceptor in M1-M5 compounds. As the ideal pair for successfully optimizing optoelectronic properties by reducing the HOMO-LUMO energy levels, reorganization energy, and binding energy and enhancing the absorption maximum and open-circuit voltage values in these designed molecules.

METHODS

DFT and TDDFT calculations were performed with Gaussian 16 program. The modelled compounds were optimized fully using the CAM-B3LYP, WB97XD, B3LYP, and MPW1PW91 functionals with the 6-31 G (d,p) basis set. The graphs for the density of states were plotted using the PyMOlyze software. Other molecular properties like the transition density matrix (TDM) and electron density difference maps (EDD) were rendered via the Multiwfn software.

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.

Detection of Carbon, Sulfur, and Nitrogen Dioxide Pollutants with a 2D Ca12O12 Nanostructured Material

In recent times, nanomaterials have been applied for the detection and sensing of toxic gases in the environment owing to their large surface-to-volume ratio and efficiency. CO₂ is a toxic gas that is associated with causing global warming, while SO₂ and NO₂ are also characterized as nonbenign gases in the sense that when inhaled, they increase the rate of respiratory infections. Therefore, there is an explicit reason to develop efficient nanosensors for monitoring and sensing of these gases in the environment. Herein, we performed quantum chemical simulation on a Ca₁₂O₁₂ nanocage as an efficient nanosensor for sensing and monitoring of these gases (CO₂, SO₂, NO₂) by employing high-level density functional theory modeling at the B3LYP-GD3(BJ)/6-311+G(d,p) level of theory. The results obtained from our studies revealed that the adsorption of CO₂ and SO₂ on the Ca₁₂O₁₂ nanocage with adsorption energies of -2.01 and -5.85 eV, respectively, is chemisorption in nature, while that of NO₂ possessing an adsorption energy of -0.69 eV is related to physisorption. Moreover, frontier molecular orbital (FMO), global reactivity descriptors, and noncovalent interaction (NCI) analysis revealed that the adsorption of CO₂ and SO₂ on the Ca₁₂O₁₂ nanocage is stable adsorption, while that of NO₂ is unstable adsorption. Thus, we can infer that the Ca₁₂O₁₂ nanocage is more efficient as a nanosensor in sensing CO₂ and SO₂ gases than in sensing NO₂ gas.