Synthesis, characterization, molecular modeling, binding energies of β-cyclodextrin-inclusion complexes of quercetin: Modification of photo physical behavior upon β-CD complexation

We prepared a naturally occurring flavanoid namely quercetin from tea leaves and analyzed by Absorption, Emission, FT-IR, 1H, 13C nmr spectra and ESI-MS analysis. The inclusion behavior of quercetin in cyclodextrins like α-, β-, γ-, per-6-ABCD and mono-6-ABCD cavities were supported such as UV-vis., Emission, FT-IR and ICD spectra and energy minimization studies. From the absorption and emission results, the type of complexes formed were found to depend on stoichiometry of Host:Guest. FT-IR data of CD complexes of quercetin supported inclusion complex formation of the substrate with α-, β- and γ-CDs. The inclusion of host-guest complexation of quercetin with α-, β-, γ-CDs, per-6-ABCD and mono-6-ABCDs provides very valuable information about the CD:quercetin complexes, the study also shows that β-CD complexation improves water solubility, chemical stability and bioavailability of quercetin. Besides, phase solubility studies also supported the formation of 1:1 drug-CD soluble complexes. All these spectral results provide insight into the binding behavior of substrate into CD cavity in the order per-6-ABCD > Mono-6-ABCD > γ-CD > β-CD > α-CD. The proposed model also finds strong support from the fact with excess CD this exciton coupling disappears indicates the formation of only 1:1 complex.

Aging effects of titanium dioxide on Cu toxicity to Daphnia magna: Exploring molecular docking and significance of surface properties

Cosmetics and personal care products containing titanium dioxide nanoparticles (TiO2 NPs) may enter aquatic environments, where the surface coatings of TiO2 NPs may change with aging due to environmental factors such as light, and potentially affect their bioaccumulation and toxicity. This study examined how aging impacted the physicochemical properties of three commercially available TiO2 NPs and subsequent influence on the bioaccumulation and toxicity of copper (Cu) in Daphnia magna (D. magna). We demonstrated that aging significantly affected the hydrophobicity of TiO2 NPs, which affected their binding to water molecules and adsorption of Cu. Changes of bioaccumulation of TiO2 NPs and Cu in D. magna ultimately affected the activities of intracellular antioxidant enzymes such as SOD, CAT, GSH-Px, and the transmembrane protein Na+/K+-ATPase. Molecular docking calculations demonstrated that changes of activities of these biological enzymes were due to the interaction between TiO2 NPs, Cu, and amino acid residues near the sites with the lowest binding energy and active center of the enzyme. Such effect was closely related to the hydrophobicity of TiO2 NPs. Our study demonstrated the close relationship between surface properties of TiO2 NPs and their biological effects, providing important evidence for understanding the behavior of nanomaterials in aquatic environments.

Hydrophobic substrate binding pocket remodeling of echinocandin B deacylase based on multi-dimensional rational design

Actinoplanes utahensis deacylase (AAC)-catalyzed deacylation of echinocandin B (ECB) is a promising method for the synthesis of anidulafungin, the newest of the echinocandin antifungal agents. However, the low activity of AAC significantly limits its practical application. In this work, we have devised a multi-dimensional rational design strategy for AAC, conducting separate analyses on the substrate-binding pocket's volume, curvature, and length. Furthermore, we quantitatively analyzed substrate properties, particularly on hydrophilic and hydrophobic. Accordingly, we tailored the linoleic acid-binding pocket of AAC to accommodate the extended long lipid chain of ECB. By fine-tuning the key residues, the resulting AAC mutants can accommodate the ECB lipid chain with a lower curvature binding pocket. The D53A/I55F/G57M/F154L/Q661L mutant (MT) displayed 331 % higher catalytic efficiency than the wild-type (WT) enzyme. The MT product conversion was 94.6 %, reaching the highest reported level. Utilizing a multi-dimensional rational design for a customized mutation strategy of the substrate-binding pocket is an effective approach to enhance the catalytic efficiency of enzymes in handling complicated substrates.

Unsupervised machine learning reveals eigen reactivity of metal surfaces

The reactivity of metal surfaces is a cornerstone concept in chemistry, as metals have long been used as catalysts to accelerate chemical reactions. Although fundamentally important, the reactivity of metal surfaces has hitherto not been explicitly defined. For example, in order to compare the activity of two metal surfaces, a particular probe adsorbate, such as O, H, or CO, has to be specified, as comparisons may vary from probe to probe. Here we report that the metal surfaces actually have their own intrinsic/eigen reactivity, independent of any probe adsorbate. By employing unsupervised machine learning algorithms, specifically, principal component analysis (PCA), two dominant eigenvectors emerged from the binding strength dataset formed by 10 commonly used probes on 48 typical metal surfaces. According to their chemical characteristics revealed by vector decomposition, these two eigenvectors can be defined as the covalent reactivity and the ionic reactivity, respectively. Whereas the ionic reactivity turns out to be related to the work function of the metal surface, the covalent reactivity cannot be indexed by simple physical properties, but appears to be roughly connected with the valence-electron number normalized density of states at the Fermi level. Our findings expose that the metal surface reactivity is essentially a two-dimensional vector rather than a scalar, opening new horizons for understanding interactions at the metal surface.

A computational study to determine the role of σ-hole in Br/OH substituted nido-carborane and its binding capabilities

A detailed investigation of the σ-hole on the halogen atom present in the nido-heteroboranes is made by employing quantum mechanical methods. The bromide and the hydroxyl groups are incorporated in the exo-substituents of the nido-boranes. The potential of the bromide σ-hole was compared to that of electrostatic potential of hydroxyl group counterpart. The presence of a carbon atom vertex, in a different position of a system, influences the σ-hole and hence its binding abilities. Bromide substituted nido-carboranes have less potential and hence weaker binding ability compared to their closo-counterparts. Binding affinity with aliphatic is found to be more compared to that of aromatic system. The presence of solvent dampened the electrostatic interactions. Apart from the neutral system, the binding capabilities of charged nido-heteroboranes were also studied. The results of this study will be further useful for several applications viz., crystal engineering, drug designing (Pharmaceuticals), medicine, material science, energy storage devices, etc.

Synergistic effect of hydrophilic polyglycerol fatty acid esters and protein on the stability of interfacial membrane in low-fat aerated emulsions with different homogenization conditions

This study investigates the impact of various chain lengths of hydrophilic polyglycerol fatty acid esters (HPGEs), namely SWA-10D, M-7D and M-10D on protein interactions and their influence on the surface morphology and interfacial properties of low-fat aerated emulsions under different pressures conditions. M-7D and M-10D samples exhibited larger particle sizes, higher ζ-potential and rougher surface compared to SWA-10D sample at 1 % concentration of HPGEs. Consequently, M-7D and M-10D samples demonstrated lower values of G', G'', and higher values tan δ at the oil-water interface as pressure increased, thereby promoting the formation of less viscoelastic structures. M-7D sample, characterized by lower content of α-helix structures, resulted in an observable redshift in the NH and CO groups of the protein. Molecular docking analysis affirmed that M-7D sample exhibited a lower absolute binding energy value, indicating stronger interaction with the protein compared to other samples, ultimately contributing to the unstable interfacial membrane formed.

Neurotoxicant effects of bisphenol A, nonylphenol, and tert‑butyl phenol in the Nile tilapia (Oreochromis niloticus)

Worldwide production of alkyl phenols and ethoxylated alkyl phenols is high due to their broad industrial uses. It has been widely documented that they are endocrine disruptors, and it has been suggested that they could exert neurotoxic effects. However, a lack of information about the neurotoxic effects of APs and APEs prevails. In this study, the bisphenol A (BPA), 4-nonylphenol (NP), and 3‑tert-butylphenol (tertBP) effects on brain and spinal cord of Nile tilapia exposed to environmental concentrations were evaluated by assessing acetylcholinesterase (AChE), butyrylcholinesterase (BuChE), and carboxylesterases (CES) activities, and γ-aminobutyric acid (GABA) levels and their effects were evaluated by molecular docking. BPA and NP, tertBP behave as agonists and antagonists of AChE, BuChE, CES, and GABA, with notable differences among organs. However, none of these compounds or their metabolites interact with the enzymes' catalytic triad, suggesting an indirect alteration of enzymatic activities. While inhibiting these enzymes stand out hydrophobic interactions with the peripheral anion site, contacts with the inner face of the active site and blocking the mouth of the gorge of the active site, and steric hindrance in the enzyme pocket of glutamate decarboxylase (GAD). In contrast, inductions probably are by homotropic pseudo-cooperative phenomenon, where APEs behave as anchors favoring the active site to remain open and interactions that confer a conservative stabilization of the regulatory domain. Although the results of this study are complex, with notable differences between organs and toxicants, they are some of the first evidence of the neurotoxicity of alkylphenols and their ethoxylated derivatives.

Theoretical investigation of electronic, energetic, and mechanical properties of polyvinyl alcohol/cellulose composite hydrogel electrolyte

Hydrogels are a new class of electrolytic materials employed in zinc-air batteries due to their significant on the battery's performance. However, the effectiveness of electrolytic hydrogel is affected by factors such as water content, temperature, additives, etc. Using DMol3 and molecular dynamics modeling techniques, this research aimed at investigating the electronic properties, effect of water content, and temperature on the binding energy, cohesive energy, and the mechanical properties of polyvinyl alcohol/cellulose-based composite hydrogel at the molecular level. The electronic optimized structures of the polymeric materials and parameters such as frontier molecular orbitals, band gap and electron density were analyzed. The results revealed that the binding energies of hydrogel polymer composite increased as the number of water molecules in the composite increased up to 60 % after which the binding energy decreased. In addition, the temperature increase led to a decrease in the binding energy of the composite. The cohesive energy density of the composite was highest at 40 % water content while higher temperatures decreased the cohesive energy density of the hydrogel. As the number of water molecules increased from 29 to 256, the tensile modulus increased from 0.707 × 10-3 to 2.821 × 10-3 Gpa; while the bulk modulus (K) increased in the order of K 40 > 50 > 30 > 20 > 10 respectively. These results serve as a theoretical enlightenment and a guide for experimental works in the field of energy conversion and storage devices.

Molecular dynamics simulation and performance analysis of polyimide/aramid blends

CONTEXT

Polyimide (PI) and aramid, as functional polymer materials, have significant application prospects in special fields such as fire prevention and arc resistance. Blends of materials can not only improve the physical and chemical properties of a single material, but also save costs, so in order to improve the performance of polyimide, it is of great practical importance to study the properties of PI and aramid blends. Molecular dynamics simulation results showed that the two materials are compatible. The solubility parameters of PI tend to stabilize when the polymerization degree exceeded 10; aramid-1313 and aramid-1414 tend to stabilize at polymerization degrees of 10 and 15 or more, respectively. On this basis, the binding energy, diffusion coefficient, and mechanical properties of PI/aramid-1313 and PI/aramid-1414 blends with different mass ratios were analyzed. It was found that with the continuous increase of aramid content, the binding energy of the blends continue to improve, limiting the gas molecules diffusion ability. The mechanical properties of the materials also continue to improve. The simulation results provided in this paper can provide theoretical guidance for experiments on PI blends and shorten the research time and cost.

METHODS

To investigate the properties of PI and aramid blends, the PI/aramid composite system models were constructed using the Amorphous Cell module in Materials Studio software. Subsequently, molecular dynamics simulations of the PI/aramid composite system were performed using the Forcite module, while the interactions between atoms and molecules were described using the COMPASS II force field.

In silico evaluation of some commercially available terpenoids as spike glycoprotein of SARS-CoV-2 - inhibitors using molecular dynamic approach

Coronavirus, an extremely contagious infections disease had a harmful effect on the world's population. It is a family of enveloped, single-stranded, positive-strand RNA viruses of Nidovirales order belongs to coroviridae family. At present, worldwide several lakhs of deaths and several billions of infections have been reported. Hence, the focus of the present study was to assess the SARS-CoV-2 enzyme inhibitory potential of certain commercially available terpenoids using Lamarckian genetic algorithm as a working principle and molecular dynamic studies was also performed. AutoDock 4.2 software was used to perform the computational docking calculations of terpenoids against SARS-CoV-2 enzyme. The terpenoids such as, Andrographolide, Betulonic acid, Erythrodiol, Friedelin, Mimuscopic acid, Moronic acid, and Retinol were selected based on the drug likeness properties. Remdesivir a well-known anti-viral drug was selected as the standard drug. Molecular dynamic simulation studies were carried using Desmond module of Schrodinger Suite. In the current study we observed that, Friedelin was exhibited excellent SARS-CoV-2 enzyme inhibitory potential than the standard drug and other selected terpenoids. Friedelin and the standard Remdesivir was undergone the molecular dynamic studies and Friedelin showed a good number of hydrogen bonds over the simulation time of 100 ns. Based on the in silico computational evaluation, it can be concluded that Friedelin could be worthwhile terpenoid against SARS-CoV-2 spike protein. A further study on Friedelin is required to develop a potential chemical entity against the management of COVID disease.Communicated by Ramaswamy H. Sarma.

Chemical characterization of the crude extract of Sauromatum venosum (voodoo lily) and docking study with 12-O-acetylingol 8-tiglate for cytotoxicity testing in SaOS2 (osteoblastic osteosarcoma cells)

The current study was carried out to investigate the anticancer potential of Sauromatum venosum (SV) tuber by gas chromatography with high-resolution mass spectrometry (GC-HRMS) analysis of ethanolic (eSV), hydroalcoholic (hSV), and aqueous extracts (wSV), and in silico study were performed to investigate the main targets of 12-O-acetylingol 8-tiglate by computational docking. The GC-HRMS analysis of three plant samples was carried out on a system equipped with a high-resolution mass spectrometer. The major compounds were identified in all crude extracts. Computation docking analysis was performed for the prediction of the main target of the cancer proliferation of active compound of the Sauromatum venosum tuber extract in cancer therapy. A total of 45 phytocompounds were detected including diterpenoids, esters of fatty acid, hydrocarbons, and alkanes in the tuber of SV. Among all the crude samples tested, eSV showed the lowest IC50 value treated with SaOS2 cells. 12-O-acetylingol 8-tiglate is one of the phytocompounds identified in eSV extract and has been found to exhibit cytotoxic effects against various cancer cells, as reported in the research. It shows the optimum binding affinity with - 8.59 kcal/mol binding energy with a molecular target protein TNF-α (PDB ID: 7PKA). The observed interactions strongly support the anticancer activity of 12-O-acetylingol 8-tiglate and its role in the medicinal efficacy of the plant. These findings highlight the potential of the compound as a valuable source for the development of a therapeutic agent aimed at combating cancer. However, it is important to note that additional in vitro and in vivo studies are required to validate these findings and establish the therapeutic potential.

An efficient end-capped engineering of pyrrole-based acceptor molecules for high-performance organic solar cells

CONTEXT

Various innovative molecules have been designed and explored for use in organic photovoltaics. In this study, we devised novel molecules (KZ1-KZ7) specifically for organic solar cells (OSCs). The newly formulated acceptor compounds possess a lower bandgap (Eg = 1.85-2.02), along with bathochromic shift (λmax = 713-788 nm) compared to the reference (Eg = 2.04 eV and λmax = 774 nm). Moreover, the FMO results identified the distinct charge transfer from HOMO to LUMO, which was strongly corroborated by the TDM maps. Similarly, the new designed molecules show less excitation energy (Ex = 1.31-1.54(gas)) than reference (Ex = 1.72). Likewise, all designed molecules (KZ1-KZ7) have demonstrated an analogous open circuit voltage (Voc) with the donor polymer PTB7-Th. All seven designed molecules (KZ1-KZ7) exhibited more fill factor ranging from 97.08 to 97.29 than reference 95.25 and PCE of between 8 and 20% at short circuit current densities of 9, 12, and 15 mA cm-2. Overall, the findings support that designed molecules can be potential molecules for future practical applications.

METHODS

Geometric calculations were conducted with Gaussian 09W software, and the findings were visualized using Gauss View software. DFT and TD-DFT were employed to evaluate various parameters for R and designed molecules (KZ1-KZ7). Firstly, four functionals including B3LYP, CAM-B3LYP, MPW1PW91, and ωB97XD with 6-31G(d,p) DFT level were applied to R to decide the best level for results. After appropriate analysis, the MPW1PW91/6-31G(d,p) was selected for further examination by comparing the experimental and DFT-based absorption graphs of R. External and internal reorganization energy are the two main factors contributing to reorganization energy. External energy refers to changes in external environment, while internal energy deals with information related to internal geometrical symmetry or the internal environment. The effect of outside factors or external reorganizational energy is omitted because it creates too little change.

Toward a mechanistic understanding of Rhenium(VII) adsorption behavior onto aminated polymeric adsorbents: Batch experiments, spectroscopic analyses, and theoretical computations

Rhenium, a rare and critical metal, existing in the industrial wastewater has been aroused extensive interests recently, due to its environmental and resource issues. Chitosan, an easily available, low-cost and eco-friendly biopolymer, was prepared and modified by grafting primary, secondary, tertiary and quaternary amino groups, respectively. Adsorption behaviors and interactions between ReO4- and these four types of aminated adsorbents were investigated through batch experiments, spectroscopic analysis, and theoretical computations. Chitosan modified with secondary amines showed an extremely high uptake of ReO4- with 742.0 mg g-1, which was higher than any reported adsorbents so far. Furthermore, a relatively high adsorption selectivity for Re(VII), as well as the stable and facile regeneration of these aminated adsorbents revealed a promising approach for Re(VII) recovery in full-scale applications. The electrostatic attraction was illustrated to be the main adsorption mechanism by Fourier Transform Infrared Spectroscopy and X-ray Photoelectron Spectroscopy analyses. Significantly, the sub-steps of the adsorption process, encompassing the transformation of binding sites and the subsequent binding between these sites and the adsorbate, have been thoroughly investigated through the density functional theory (DFT) calculation method. This approach was firstly proposed to clearly demonstrate the differences in Re(VII) adsorption behavior onto four types of aminated adsorbents, resulting the importance of not only strong binding energy but also an appropriate binding spatial environmental for effective Re(VII) adsorption.

Computer-aided Affinity Enhancement of a Cross-reactive Antibody against Dengue Virus Envelope Domain III

The dengue virus (DENV), composed of four distinct but serologically related Flaviviruses, causes the most important emerging viral disease, with nearly 400 million infections yearly. Currently, there are no approved therapies. Although DENV infection induces lifelong immunity against the same serotype, the antibodies raised contribute to severe disease in heterotypic infections. Therefore, understanding the mechanism of DENV neutralization by antibodies is crucial in the design of vaccines against all serotypes. This study reports a comparative structural and energetic analysis of the monoclonal antibody (mAb) 4E11 in complex with its target domain III of the envelope protein for all four DENV serotypes. We use extensive replica molecular dynamics simulations in conjunction with the binding free energy calculations. Further single point and double mutations were designed through computational site-directed mutagenesis and observed that the re-engineered antibody exhibits high affinity to binding and broadly neutralizing activity against serotypes. Our results showed improved binding affinity by the gain of enthalpy, which could be attributed to the stabilization of salt-bridge and hydrogen bond interactions at the antigen-antibody interface. The findings provide valuable results in understanding the structural dynamics and energetic contributions that will be helpful to the design of high-affinity antibodies against dengue infections.

Improving the accuracy of the FMO binding affinity prediction of ligand-receptor complexes containing metals

Polarization and charge transfer strongly characterize the ligand-receptor interaction when metal atoms are present, as for the Au(I)-biscarbene/DNA G-quadruplex complexes. In a previous work (J Comput Aided Mol Des2022, 36, 851-866) we used the ab initio FMO2 method at the RI-MP2/6-31G* level of theory with the PCM [1] solvation approach to calculate the binding energy (ΔEFMO) of two Au(I)-biscarbene derivatives, [Au(9-methylcaffein-8-ylidene)2]+ and [Au(1,3-dimethylbenzimidazole-2-ylidene)2]+, able to interact with DNA G-quadruplex motif. We found that ΔEFMO and ligand-receptor pair interaction energies (EINT) show very large negative values making the direct comparison with experimental data difficult and related this issue to the overestimation of the embedded charge transfer energy between fragments containing metal atoms. In this work, to improve the accuracy of the FMO method for predicting the binding affinity of metal-based ligands interacting with DNA G-quadruplex (Gq), we assess the effect of the following computational features: (i) the electron correlation, considering the Hartree-Fock (HF) and a post-HF method, namely RI-MP2; (ii) the two (FMO2) and three-body (FMO3) approaches; (iii) the basis set size (polarization functions and double-ζ vs. triple-ζ) and (iv) the embedding electrostatic potential (ESP). Moreover, the partial screening method was systematically adopted to simulate the solvent screening effect for each calculation. We found that the use of the ESP computed using the screened point charges for all atoms (ESP-SPTC) has a critical impact on the accuracy of both ΔEFMO and EINT, eliminating the overestimation of charge transfer energy and leading to energy values with magnitude comparable with typical experimental binding energies. With this computational approach, EINT values describe the binding efficiency of metal-based binders to DNA Gq more accurately than ΔEFMO. Therefore, to study the binding process of metal containing systems with the FMO method, the adoption of partial screening solvent method combined with ESP-SPCT should be considered. This computational protocol is suggested for FMO calculations on biological systems containing metals, especially when the adoption of the default ESP treatment leads to questionable results.

Analyzing the potential of selected plant extracts and their structurally diverse secondary metabolites for α-glucosidase inhibitory activity: in vitro and in silico approach

Inhibiting α-glucosidase activity is a therapeutic method to regulate post-prandial hyperglycemia in humans. Here, in-vitro and in-silico studies were used to find α-glucosidase inhibitory plant secondary metabolites (PSM). Among 408 solvent extracts from 70 plants tested for α-glucosidase inhibition, 174 had IC50 ≤ 3 mg/ml. α-glucosidase inhibitory PSM is found in several plant species and solvent extracts, indicating their diversity. Further, ensemble molecular docking and structural activity relationship analysis supported this hypothesis where the top 100 PSM with the least binding energy (BE) among the 539 PSM belonged to sesquiterpenoids (34%), catechols (11%), flavonoids (9%) and steroidal lactones (8%). Shortlisted 11 PSM were subjected to molecular dynamic simulation. Withanolide J recorded the least BE of -66.424 ± 22.333 kJ/mol, followed by Withacoagulin I (-64.665 ± 24.030 kJ/mol). When different simulation frames were analyzed, PSM of withanolide groups was stabilized in the narrow entrance of the active pocket forming H-bond with LYS156, TYR158, PHE159, PHE303 PRO312, LEU313, ARG315 and PHE134. Similarly, Hydroxytuberosone and 1, 8-Dihydroxy-3-carboxy-9, 10-anthraquinone (DHCA) formed H-bond with ASP307 located on the loop at the entrance of the active pocket. In the case of Neoliquiritin and Kaempferol-3-o-alpha-L-rhamnoside (KALR), glucose moiety interacted with the GLU277 and ASP215 (catalytic amino acid residues) through H-bonds. In addition, these 11 PSM were found to fulfil the criteria of drug-likeness as per Lipinski's rule of five and pharmacokinetic profile. The present study strengthens the library of α-glucosidase inhibitory plants and PSM, providing valuable information for Type-II Diabetes mellitus management.Communicated by Ramaswamy H. Sarma.

In silico guided screening of active components of C. lanceolata as 3-chymotrypsin-like protease inhibitors of novel coronavirus

Despite the intense worldwide efforts towards the identification of potential anti-CoV therapeutics, no antiviral drugs have yet been discovered. Numerous vaccines are now approved for use, but they all serve as preventative measures. To effectively treat viral infections, it is crucial to find new antiviral drugs that are derived from natural sources. Various compounds with potential activity against 3 chymotrypsin-like protease (3CLpro) were reported and some are validated by bioassay studies. Therefore, we performed the computational screening of phytoconstituents of Codonopsis lanceolata to search for potential antiviral hit candidates. The curated compounds of the plant C. lanceolata were collected and downloaded from the literature. The binding affinity of the curated datasets was predicted for the target 3CLpro. Stigmasterol exhibits the highest docking score for the 3CLpro target. In addition, molecular dynamics (MD) simulations were conducted for the validation of docking results using root mean square deviation and root mean square fluctuation plots. The MD results indicated that the docked complex was stable and retained hydrogen bonding and non-bonding interactions. Furthermore, the calculation of pharmacokinetic parameters and Lipinski's rule of five suggest that C. lanceolata has the potential for drug-likeness. In order to develop new medicines for this debilitating disease, we will focus on the primary virus-based and host-based targets that can direct medicinal chemists to identify novel treatments to produce new drugs for it.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03745-2.

Two Biexciton Types Coexisting in Coupled Quantum Dot Molecules

Coupled colloidal quantum dot molecules (CQDMs) are an emerging class of nanomaterials, manifesting two coupled emission centers and thus introducing additional degrees of freedom for designing quantum-dot-based technologies. The properties of multiply excited states in these CQDMs are crucial to their performance as quantum light emitters, but they cannot be fully resolved by existing spectroscopic techniques. Here we study the characteristics of biexcitonic species, which represent a rich landscape of different configurations essentially categorized as either segregated or localized biexciton states. To this end, we introduce an extension of Heralded Spectroscopy to resolve the different biexciton species in the prototypical CdSe/CdS CQDM system. By comparing CQDMs with single quantum dots and with nonfused quantum dot pairs, we uncover the coexistence and interplay of two distinct biexciton species: A fast-decaying, strongly interacting biexciton species, analogous to biexcitons in single quantum dots, and a long-lived, weakly interacting species corresponding to two nearly independent excitons. The two biexciton types are consistent with numerical simulations, assigning the strongly interacting species to two excitons localized at one side of the quantum dot molecule and the weakly interacting species to excitons segregated to the two quantum dot molecule sides. This deeper understanding of multiply excited states in coupled quantum dot molecules can support the rational design of tunable single- or multiple-photon quantum emitters.

Evidences of noncovalent interactions between indole and dichloromethane under different solvent conditions

CONTEXT

Theoretical investigation of indole (IND) and its binary combination with dichloromethane (DC) in various solvents were computed to track the impact of molecular interactions on spectral characteristics. When transitioning from plain drug to complexes, different modes of IND display a substantial shift in peak location. The 3561.26 cm^-1 band shows (~15.58 cm^-1) red shift upon dilution. The geometry in various solvents was calculated using quantum chemical calculation utilizing density functional theory (DFT). The highest ALIE values are located at the indole skeleton and on complexation with DC, and the ring atoms become more electron rich. The atom-centered density matrix propagation (ADMP) molecular dynamic (MD) calculation shows that the geometries optimized through the DFT calculation match the global minima effectively. MD simulations indicate that indole is more stable in water and methanol.

METHODS

DFT studies have been employed to study the interaction between indole and dichloromethane. CAM-B3LYP/6-311++G(d)(6D,7F) level of theory was employed using Gaussian 16 W suite. Quantum topological descriptors were discussed using quantum theory of atoms in molecules (QTAIM) with the help of Multiwfn software. Reduced density gradient (RDG) plot describes the nature of the interaction, while average local ionization energy (ALIE) explained the variation in local ionization energy of the molecular surface before and after complexation.

Synergistic effect of lecithin and alginate, CMC, or PVP in stabilizing curcumin and its potential mechanism

This work aims to advance the understanding of the synergistic mechanism of lecithin and polymers (alginate, CMC, and PVP) in stabilizing curcumin, with a major focus on understanding the nanocomplex formation process and the main binding energy between molecules. It is demonstrated that lecithin and polymers have a synergistic effect in increasing the thermal acid, light, and digestion stability of curcumin. The potential mechanism is that the hydrophobic parts of curcumin molecules are first anchored at the region of the hydrophobic cavity of lecithin by van der Waals, while the hydrophilic parts are outward and are further encapsulated by hydrophilic polymers by van der Waals and electrostatic interaction to form a protective shell. This study contributes to our understanding of the synergistic mechanism of lecithin, polymers, and hydrophobic compounds, which can promote the synergistic use of lecithin and polymers to prepare nanocomplexes as an important tool for delivering bioactive compounds.

Computational analysis of the phytocompounds of Mimusops elengi against spike protein of SARS CoV2 - An Insilico model

The COVID-19 pandemic has been a global health crisis for over three years now, with the virus causing widespread illness and death. The urgent need for safe and effective therapeutic drugs has prompted the exploration of alternative medicine systems such as Ayurveda and Siddha. This study focuses on the potential therapeutic properties of the Ayurvedic plant, Mimusops elengi. In silico techniques were employed to analyze the bioactivity of the plant, including target prediction, gene ontology analysis, OMIM analysis, and molecular docking analysis. The results revealed 36 phytocompounds that interacted with 1431 receptors in the human body, and two compounds - hederagenin and quercetin - showed exceptionally high binding affinities toward their corresponding receptors, IL6 and MMP9. These results provide important insight into the potential therapeutic activity of M. elengi and its compounds in combating COVID-19. However, further research and clinical trials are necessary to validate these findings and develop safe and effective drugs. The study highlights the importance of combining traditional medicine with modern scientific methods to find effective treatments for global health challenges.

Molecular dynamics simulation of CL20/DNDAP cocrystal-based PBXs

CONTEXT

CL-20/DNDAP cocrystal is a promising new type of explosive with exceptional energy density and detonation parameters. However, compared to TATB, FOX-7 and other insensitive explosives, it still has higher sensitivity. In order to decrease the sensitivity of CL20/DNDAP cocrystal explosive, in this article, a CL20/DNDAP cocrystal model was established, and six different types of polymers, including butadiene rubber (BR), ethylene-vinyl acetate copolymer (EVA), polyethylene glycol (PEG), hydroxyl-terminated polybutadiene (HTPB), fluoropolymer (F₂₆₀₃), and polyvinylidene difluoride (PVDF), were added to the three cleaved surfaces of (1 0 0), (0 1 0) and (0 0 1) to obtain polymer-bonded explosives (PBXs). Predict the effects of different polymers on the stability, trigger bond length, mechanical properties, and detonation performance of PBXs. Among the six PBX models, CL-20/DNDAP/PEG model exhibited the highest binding energy and the lowest trigger bond length, indicating that CL-20/DNDAP/PEG model had the best stability, compatibility, and the least sensitivity. Furthermore, although the CL-20/DNDAP/F₂₆₀₃ model demonstrated superior detonation capabilities, it should be noted that this model displayed low levels of compatibility. Overall, CL-20/DNDAP/PEG model exhibited the superior comprehensive properties, thereby demonstrating that PEG is a more suitable binder option for PBXs based on the CL20/DNDAP cocrystal.

METHODS

The properties of CL-20/DNDAP cocrystal-based PBXs were predicted by molecular dynamics (MD) method under Materials Studio software. The MD simulation time step was set at 1fs and the total MD simulation time was 2ns. The Isothermal-isobaric (NPT) ensemble was used for the 2ns of MD simulation. The COMPASS force field was used, and the temperature was set at 295K.

Molecular Docking and Molecular Dynamics Simulation of New Potential JAK3 Inhibitors

INTRODUCTION

JAK3 kinase inhibitor has become an effective means to treat tumors and autoimmune diseases.

METHOD

In this study, molecular docking and molecular dynamics simulation were used to study the theoretical interaction mechanism between 1-phenylimidazolidine-2-one molecules and JAK3 protein.

RESULT

The results of molecular docking showed that the six 1-phenylimidazolidine-2-one derivatives obtained by virtual screening were bound to the ATP pocket of JAK3 kinase, which were competitive inhibitors of ATP, and were mainly bound to the pocket through hydrogen bonding and hydrophobic interaction. Further, MM/GBSA based on molecular dynamics simulation sampling was used to calculate the binding energy between six molecules and the JAK3 kinase protein. Subsequently, the binding energy was decomposed into the contribution of each amino acid residue, of which Leu905, Lys855, Asp967, Leu956, Tyr904, and Val836 were the main energy-contributing residues. Among them, the molecule numbered LCM01415405 can interact with the specific amino acid Arg911 of JAK3 kinase, suggesting that the molecule may be a selective JAK3 kinase inhibitor. The root-mean-square fluctuation (RMSF) of JAK3 kinase pocket residues during molecular dynamics simulation showed that the combination of six new potential small molecule inhibitors with JAK3 kinase could reduce the flexibility of JAK3 kinase pocket residues.

CONCLUSION

These findings reveal the mechanism of 1-phenylimidazolidine-2-one derivatives on JAK3 protein and provide a relatively solid theoretical basis for the development and structural optimization of JAK3 protein inhibitors.

Docking, Synthesis, and In vitro Anti-depressant Activity of Certain Isatin Derivatives

BACKGROUND

In vitro, the molecular docking method has been suggested for estimating the biological affinity of the pharmacophores with physiologically active compounds. It is the latter stage in molecular docking, and the docking scores are examined using the AutoDock 4.2 tool program. The chosen compounds can be evaluated for in vitro activity based on the binding scores, and the IC50 values can be computed.

OBJECTIVE

The purpose of this work was to create methyl isatin compounds as potential antidepressants, compute physicochemical characteristics, and carry out docking analysis.

METHODS

The protein data bank of the RCSB (Research Collaboratory for Structural Bioinformatics) was used to download the PDB structures of monoamine oxidase (PDB ID: 2BXR) and indoleamine 2,3-dioxygenase (PDB ID: 6E35). Based on the literature, methyl isatin derivatives were chosen as the lead chemicals. By determining their IC50 values, the chosen compounds were tested for in vitro anti-depressant activity.

RESULTS

The binding scores for the interactions of SDI 1 and SD 2 with indoleamine 2,3 dioxygenase were found to be -10.55 kcal/mol and -11.08 kcal/mol, respectively, while the scores for their interactions with monoamine oxidase were found to be -8.76 kcal/mol and -9.28 kcal/mol, respectively, using AutoDock 4.2. The relationship between biological affinity and pharmacophore electrical structure was examined using the docking technique. The chosen compounds were tested for their ability to inhibit MAO, and the IC50 values for each were found to be 51.20 and 56, respectively.

CONCLUSION

This investigation has identified many novel and effective MAO-A inhibitors from the family of chemicals known as methyl isatin derivatives. Lead optimization was applied to the SDI 1 and SDI 2 derivatives. The superior bioactivity, pharmacokinetic profile, BBB penetration, pre-ADMET profiles, such as HIA (human intestinal absorption) and MDCK (Madin-Darby canine kidney), plasma protein binding, toxicity assessment, and docking outcomes, have been obtained. According to the study, synthesised isatin 1 and SDI 2 derivatives exhibited a stronger MAO inhibitory activity and effective binding energy, which may help prevent stress-induced depression and other neurodegenerative disorders caused by a monoamine imbalance.

Theoretical Prediction on Properties of 3,4-Bisnitrofurazanfuroxan (DNTF) Crystal and its Polymer Bonded Explosives (PBXs) Through Molecular Dynamics (MD) Simulation

CONTEXT

3,4-Bisnitrofurazanfuroxan (DNTF) is a typical high energy density compound (HEDC), it has high crystal density and detonation parameters, but also high mechanical sensitivity. To decrease its mechanical sensitivity, the DNTF based polymer bonded explosives (PBXs) was designed. The pure DNTF crystal and PBXs models were established. The stability, sensitivity, detonation performance and mechanical properties of DNTF crystal and PBXs models were predicted. Results show that PBXs models containing fluorine rubber (F₂₃₁₁) and fluorine resin (F₂₃₁₄) have higher binding energy, meaning that DNTF/F₂₃₁₁ and DNTF/F₂₃₁₄ is relatively more stable. PBXs models have higher value of cohesive energy density (CED) than pure DNTF crystal, DNTF/F₂₃₁₁ and DNTF/F₂₃₁₄ have the highest value of CED, implying that the sensitivity of PBXs is effectively decreased, DNTF/F₂₃₁₁ and DNTF/F₂₃₁₄ is more insensitive. PBXs have lower crystal density and detonation parameters than DNTF, the energy density is declined, DNTF/F₂₃₁₄ has higher energetic performance than other PBXs. Compared with pure DNTF crystal, engineering moduli (tensile modulus, shear modulus, bulk modulus) of PBXs models are obviously decreased, but Cauchy pressure is increased, implying that the mechanical properties of PBXs is superior to pure DNTF component, the PBXs containing F₂₃₁₁ or F₂₃₁₄ have more preferable mechanical properties. Consequently, DNTF/F₂₃₁₁ and DNTF/F₂₃₁₄ have the best comprehensive properties and is more attractive among the designed PBXs, indicating that F₂₃₁₁ and F₂₃₁₄ are more advantageous and promising in ameliorating properties of DNTF.

METHODS

The properties of DNTF crystal and PBXs models were predicted through molecular dynamics (MD) method under Materials Studio 7.0 package. The MD simulation was performed with isothermal-constant volume (NVT) ensemble, and the force field was chosen as COMPASS force field. The temperature was set as 295 K, the time step was 1 fs and the total MD simulation time was 2 ns.

The deconstruction and recombination of endogenous active units of carbon@chitosan@montmorillonite nanosheet microsphere adsorbent caused by cadmium and copper cations benefit for high adsorption performance

The highly efficient removal of heavy metals is one of the important factors to evaluate adsorbents. In our study, carbon@chitosan@montmorillonite nanosheet (C@CS@MTN) was successfully prepared via layer-by-layer assembly for the removal of Cu2+ and Cd2+ from solution. High-intensity ultrasound peeling technology was used to release Si-O tetrahedron and Al-O octahedron from montmorillonite in order to exert their optimal adsorption potential. Fourier transform infrared spectroscopy, an X-ray diffractometer, BET surface area measurement, and the inductively coupled plasma emission spectrometry were adopted to investigate the morphology, functional groups, and adsorption capacity of C@CS@MTN. Batch experiment results indicated that both Cu2+ and Cd2+ were effectively removed from solution with the range of pH from 2 to 6. The removal ratio of Cu2+ and Cd2+ onto C@CS@MTN increased with the rise of reaction temperature and their maximum adsorption capacities reached 1108.8 mg·g-1 and 237.4 mg·g-1, respectively, under the condition of the reaction temperature 40 °C, the reaction time 4 h, and the pH = 6. The molecular simulation calculation indicated that there was an obvious electron transfer between Si-O tetrahedron and metal cations, but not for Al-O octahedron. In comparison to Al-O octahedron, the bonding of Cu-O and Cd-O caused the Si-O bond to be broken, resulting in the deconstruction of Si-O tetrahedron and their recombination via the junction of O atoms. It was exactly the deconstruction and recombination of endogenous active units that provide more sites for metal ion adsorption.

Designing and property prediction of a novel three-component CL-20/HMX/TNAD energetic cocrystal explosive by MD method

CONTEXT

Cocrystallization technology can effectively regulate crystal structure, alter packing mode, and improve physicochemical performances of energetic materials at molecule level. CL-20/HMX cocrystal explosive has high energy density than HMX, but it also exhibits high mechanical sensitivity. To decrease the sensitivity and improve the properties of CL-20/HMX energetic cocrystal, the three-component energetic cocrystal CL-20/HMX/TNAD was designed. The properties of CL-20, CL-20/HMX, and CL-20/HMX/TNAD cocrystal models were predicted. The results show that CL-20/HMX/TNAD cocrystal models have better mechanical properties than CL-20/HMX cocrystal model, implying that the mechanical properties can be effectively improved. The binding energy of CL-20/HMX/TNAD cocrystal models is higher than CL-20/HMX cocrystal model, indicating that the three-component energetic cocrystal is more stable, and the cocrystal model with the ratio 3:4:1 is predicted to be the most stable phase. CL-20/HMX/TNAD cocrystal models have higher value of trigger bond energy than pure CL-20 and CL-20/HMX cocrystal models, meaning that the three-component energetic cocrystal is more insensitive. The crystal density and detonation parameters of CL-20/HMX and CL-20/HMX/TNAD cocrystal models are lower than CL-20, illustrating that the energy density is declined. The CL-20/HMX/TNAD cocrystal has higher energy density than RDX and can be regarded as a potential high energy explosive.

METHODS

This paper was performed with molecular dynamics (MD) method with the software of Materials Studio 7.0 under COMPASS force field. The MD simulation was performed under isothermal-isobaric (NPT) ensemble, the temperature and pressure was 295 K and 0.0001 GPa, respectively.

Atomistic insights into migration mechanism of graphene-based membranes on soil mineral phases

Graphene-based membranes (GBM) will migrate in the soil and enter the groundwater system or plant roots, which will eventually pose potential risks to human beings. The migration mechanism of GBM depends on the interface behavior of complex soil components. Herein, we use molecular dynamics (MD) simulations to probe the interface behavior between GBM and three type minerals (quartz, calcite and kaolinite). Based on the investigation of binding energy, maximum pulling force and barrier energy, the order of the difficulty of GBM adsorption and desorption on the three minerals from small to large is roughly: quartz, calcite and kaolinite respectively. The graphene-oxide (GO), improves the binding energy and energy barrier, making GBM difficult to migrate in soil. Remarkably, a larger GBM sheet and high velocity external load improve GBM migration in soil to a certain extent. These investigations give the dynamic information on the GBM/mineral interaction and provide nanoscale insights into the migration mechanisms of GBM in soil.

In silico analysis decodes transthyretin (TTR) binding and thyroid disrupting effects of per- and polyfluoroalkyl substances (PFAS)

Transthyretin (TTR) is a homo-tetramer protein involved in the transport of thyroid hormone (thyroxine; T4) in the plasma and cerebrospinal fluid. Many pollutants have been shown to bind to TTR, which could be alarming as disruption in the thyroid hormone system can lead to several physiological problems. It is also indicated that the monomerization of tetramer and destabilization of monomer can lead to amyloidogenesis. Many compounds are identified that can bind to tetramer and stabilize the tetramer leading to the inhibition of amyloid fibril formation. Other compounds are known to bind tetramer and induce amyloid fibril formation. Among the pollutants, per- and polyfluoroalkyl substances (PFAS) are known to disrupt the thyroid hormone system. The molecular mechanisms of thyroid hormone disruption could be diverse, as some are known to bind with thyroid hormone receptors, and others can bind to membrane transporters. Binding to TTR could also be one of the important pathways to alter thyroid signaling. However, the molecular interactions that drive thyroid-disrupting effects of long-chain and short-chain PFASs are not comprehensively understood at the molecular level. In this study, using a computational approach, we show that carbon chain length and functional group in PFASs are structural determinants, in which longer carbon chains of PFASs and sulfur-containing PFASs favor stronger interactions with TTR than their shorter-chained counterparts. Interestingly, short-chain PFAS also showed strong binding capacity, and the interaction energy for some was as close to the longer-chain PFAS. This suggests that short-chain PFASs are not completely safe, and their use and build-up in the environment should be carefully regulated. Of note, TTR homologs analysis suggests that thyroid-disrupting effects of PFASs could be most likely translated to TTR-like proteins and other species.

Discovery of allosteric SHP2 inhibitors through ensemble-based consensus molecular docking, endpoint and absolute binding free energy calculations

SHP2 (Src homology-2 domain-containing protein tyrosine phosphatase-2) is a cytoplasmic protein -tyrosine phosphatase encoded by the gene PTPN11. It plays a crucial role in regulating cell growth and differentiation. Specifically, SHP2 is an oncoprotein associated with developmental pathologies and several different cancer types, including gastric, leukemia and breast cancer and is of great therapeutic interest. Given these roles, current research efforts have focused on developing SHP2 inhibitors. Allosteric SHP2 inhibitors have been shown to be more selective and pharmacologically appealing compared to competitive catalytic inhibitors targeting SHP2. Nevertheless, there remains a need for novel allosteric inhibitor scaffolds targeting SHP2 to develop compounds with improved selectivity, cell permeability, and bioavailability. Towards this goal, this study applied various computational tools to screen over 6 million compounds against the allosteric site within SHP2. The top-ranked hits from our in-silico screening were validated using protein thermal shift and biolayer interferometry assays, revealing three potent compounds. Kinetic binding assays were employed to measure the binding affinities of the top-ranked compounds and demonstrated that they all bind to SHP2 with a nanomolar affinity. Hence the compounds and the computational workflow described herein provide an effective approach for identifying and designing a generation of improved allosteric inhibitors of SHP2.

Potential inhibitory properties of structurally modified quercetin/isohamnetin glucosides against SARS-CoV-2 Mpro; molecular docking and dynamics simulation strategies

Concerned organizations and individuals are fully engaged in seeking appropriate measures towards managing Severe Acute Respiratory Syndrome Coronavirus 2 (SAR-CoV-2) infection because of the unprecedented economic and health impact. SAR-CoV-2 Main protease (SARS-CoV-2 Mpro) is unique to the survival and viability of the virus. Therefore, inhibition of Mpro can block the viral propagation. Thirty (30) derivatives were built by changing the glucosides in the Meta and para position of quercetin and isohamnetin. Molecular docking analysis was used for the screening of the compounds. Dynamics simulation was performed to assess the stability of the best pose docked complex. Molecular mechanics binding free energy calculation was done by Molecular Mechanics/Poisson-Boltzmann Surface Area (MMPBSA). Overall analysis showed that the compounds are allosteric inhibitors of SARS-CoV-2 Mpro. Dynamic simulation analysis established the stability of Mpro-ISM-1, Mpro-ISD-3, Mpro-IST-2, Mpro-QM-2, and Mpro-QD-6 complexes with a maximum of 7 hydrogen bonds involved in their interaction. The MMPBSA binding free energies for ISM-1, ISD-3, IST-2, QM-2, and QD-6 were -92.47 ± 9.06, -222.27 ± 32.5, 180.72 ± 47.92, 156.46 ± 49.88 and -93.52 ± 48.75 kcal/mol respectively. All the compounds showed good pharmacokinetic properties, while only ISM-1 inhibits hERG and might be cardio-toxic. Observations in this study established that the glucoside position indeed influenced the affinity for SARS-CoV-2 Mpro. The study also suggested the potentials of ISD-3, QM-2 and QD-6 as potent inhibitors of the main protease, further experimental and clinical studies are however necessary to validate and establish the need for further drug development processes. Therefore, future studies will be on the chemical synthesis of the compounds and investigation of the in-vitro inhibition of SARS-CoV-2.

Site specific interactions of amino acids with (ZnO)12 cluster: Density functional approach

The Stability and electronic properties of bio-hybrid molecules are investigated in the framework of the first-principles density functional theory. The site-specific interactions between (ZnO)₁₂ nano-cluster and arginine/aspartic acid are investigated. There are partially ionic and covalent bonds between the interacting atoms, higher binding energy 8.86 eV is observed at -COOH site of arginine, and 7.60 eV at -CN site of aspartic acid during the interaction with a nano-cluster. Higher HOMO-LUMO gap 4.3 eV is found in arginine, and smaller 2.6 eV in a cluster, it becomes zero with -COOH site of arginine, and 0.8 eV at -CN site of aspartic acid during the formation of bio-hybrids, i.e. highly stable amino acids arg/asp-nano-cluster (ZnO)₁₂ bio-hybrids are formed with small forbidden energy-gap. This study will support in the formation of drugs which will improve the response in wound healing, immune functioning in burn injuries, and in the treatment of bone dysfunction.HighlightsThe binding energy is higher in a bio-hybrid at -COOH site of Arg, and -CN site of Asp.HOMO-LUMO gap is higher in a pristine Arg (4.3 eV), smaller in a cluster (2.6 eV), zero gap in a bio-hybrid with -COOH site of Arg, smaller 0.8 eV at -CN site of Asp.Higher binding energy is found with the small forbidden energy-gap of bio-hybrid molecules.This study will support in the formation of drugs which will improve the response in wound healing, immune functioning in burn injuries, and in the treatment of bone dysfunction.Communicated by Ramaswamy H. Sarma.

Computational and data mining studies to understand the distribution and dynamics of Temoneria (TEM) β-lactamase and their interaction with β-lactam and β-lactamase inhibitors

β-lactams are large group of antibiotics widely used to suppress the bacterial growth by inhibiting cell wall synthesis. Bacterial resistance against β-lactam antibiotics is primarily mediated through the production of Temoneria (TEM) β-lactamase (BLs), with almost 474 variants identified in Lactamase Engineering Database (LacED). The present study aims to develop a model to track the evolution of TEM BLs and their interactions with β-lactam and BLs inhibitors through data mining and computational approaches. Further, the model will be used to predict the effective combinations of β-lactam and BLs inhibitors to treat the bacterial infection harbouring emerging variants of β-lactamase. The molecular docking study results demonstrated that most TEM mutants recorded the least binding energy to penicillin and cephalosporin (I/II/III/IV/V generations) class of antibiotics. On the contrary, the same mutants recorded higher binding energy to carbapenem and Monobactam class of antibiotics. Among the BLs inhibitors, tazobactam recorded the least binding energy against most of the TEM mutants, indicating that it can lower the catalytic activity of TEM BLs, thereby potentiating antibiotic action. Similarly, data mining work has assisted us in creating a database of TEM mutants that has comprehensive data on mutations, bacterial diversity, Km, MIC, and IRT types. It has been noted that earlier released antibiotics like amoxicillin and ampicillin had lower Km and higher MIC values, which indicates the prevalence of bacterial resistance. By analysing the differential binding energy (ΔBE) of the selected TEM mutants against β-lactam and BLs inhibitors, the most effective combination of β-lactam (carbapenem and monobactam class of antibiotics) and BLs inhibitors (tazobactam) was identified, to cure bacterial diseases/infections and to prevent similar antibiotic resistance outbreaks. Therefore, our study opens a new avenue in developing strategies to manage antibiotic resistance in bacteria.

The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study

In this work, the ab initio fragment molecular orbital (FMO) method was applied to calculate and analyze the binding energy of two biscarbene-Au(I) derivatives, [Au(9-methylcaffein-8-ylidene)₂]⁺ and [Au(1,3-dimethylbenzimidazol-2-ylidene)₂]⁺, to the DNA G-Quadruplex structure. The FMO2 binding energy considers the ligand-receptor complex as well as the isolated forms of energy-minimum state of ligand and receptor, providing a better description of ligand-receptor affinity compared with simple pair interaction energies (PIE). Our results highlight important features of the binding process of biscarbene-Au(I) derivatives to DNA G-Quadruplex, indicating that the total deformation-polarization energy and desolvation penalty of the ligands are the main terms destabilizing the binding. The pair interaction energy decomposition analysis (PIEDA) between ligand and nucleobases suggest that the main interaction terms are electrostatic and charge-transfer energies supporting the hypothesis that Au(I) ion can be involved in π-cation interactions further stabilizing the ligand-receptor complex. Moreover, the presence of polar groups on the carbene ring, as C = O, can improve the charge-transfer interaction with K⁺ ion. These findings can be employed to design new powerful biscarbene-Au(I) DNA-G quadruplex binders as promising anticancer drugs. The procedure described in this work can be applied to investigate any ligand-receptor system and is particularly useful when the binding process is strongly characterized by polarization, charge-transfer and dispersion interactions, properly evaluated by ab initio methods.

Silver cluster interactions with Pterin: Complex structure, binding energies and spectroscopy

Metal nanoclusters (NCs) are widely present today in biosensing, bioimaging, and diagnostics due to their small size, great biocompatibility, and sensitivity to the biomolecular environment. Silver (Ag) NCs often possess intense fluorescence, photostability, and low photobleaching, which is in high demand during the detection of organic molecules. Pterins are small compounds, which are used in medicine as biomarkers of oxidative stress, cardiovascular diseases, neurotransmitter synthesis, inflammation and immune system activation. It is experimentally possible to detect pterin (Ptr) through the adsorption on Ag colloid. We optimized geometries and evaluated the binding energy in Ptr-Ag_n^q complexes (n = 1-6; q = 0, +1, +2) using quantum chemistry methods. Different Ptr atoms were preferential for silver attachment depending on NC charge and size. The highest E_b was obtained for the complexes between the Ptr⁰ and Ag₃²⁺ (-50.8 kcal mol^-1), between Ptr^-1 and Ag₃²⁺ (-64.8 kcal mol^-1), which means that these complexes should be formed preferably in aqueous solutions in acidic and alkaline media, respectively. The colorimetric detection of pterin with silver clusters does not seem to be promising. However, intense S_0→S₁ transitions of Ag₅⁺ complexes look promising for luminescent Ptr detection. SERS detection of pterin is better to be done at pH > 8 since deprotonated pterin Raman undergo more dramatic changes upon addition of Ag than the neutral pterin. The characteristics of absorption and vibrational spectra of silver-pterin should be exploited during biosensor development.

Bivalent binding mode of an amino-pyrazole inhibitor indicates the potentials for CK2α1-selective inhibitors

Casein kinase 2 (CK2) is a vital protein kinase that consists of two catalytic subunits (CK2α1 and/or CK2α2) and two regulatory subunits (CK2β). CK2α1 is a drug target for nephritis and cancers, while CK2α2 is a serious off-target because its inhibition causes testicular toxicity. High similarity between the isozymes CK2α1 and CK2α2 make it difficult to design CK2α1-specific inhibitors. Herein, the crystal structures of CK2α1 and CK2α2 complexed with a 3-amino-pyrazole inhibitor revealed the remarkable differences in the protein-inhibitor interaction modes. This inhibitor bound to the ATP binding sites of both isozymes in apparently distinct orientations. In addition, another molecule of this inhibitor bound to CK2α1, but not to CK2α2, at the CK2β protein-protein interface. Binding energy calculations and biochemical experiments suggested that this inhibitor possesses the conventional ATP-competitive characteristics with moderate allosteric function in a molecular glue mechanism. These results will assist the potential design of potent and selective CK2α1 inhibitors.

In silico design of novel quinazoline-based compounds as potential Mycobacterium tuberculosis PknB inhibitors through 2D and 3D-QSAR, molecular dynamics simulations combined with pharmacokinetic predictions

Serine/threonine protein kinase B (PknB) is essential to Mycobacterium tuberculosis (M. tuberculosis) cell division and metabolism and a potential anti-tuberculosis drug target. Here we apply Hologram Quantitative Structure Activity Relationship (HQSAR) and three-dimensional QSAR (Comparative Molecular Similarity Indices Analysis (CoMSIA)) methods to investigate structural requirements for PknB inhibition by a series of previously described quinazoline derivatives. PknB binding of quinazolines was evaluated by molecular dynamics (MD) simulations of the catalytic domain and binding energies calculated by Molecular Mechanics/Poisson Boltzmann Surface Area (MM-PBSA) and Molecular Mechanics/Generalized Born Surface Area (MM-GBSA) methods. Evaluation of a training set against experimental data showed both HQSAR and CoMSIA models to reliably predict quinazoline binding to PknB, and identified the quinazoline core and overall hydrophobicity as the major contributors to affinity. Calculated binding energies also agreed with experiment, and MD simulations identified hydrogen bonds to Glu93 and Val95, and hydrophobic interactions with Gly18, Phe19, Gly20, Val25, Thr99 and Met155, as crucial to PknB binding. Based on these results, additional quinazolines were designed and evaluated in silico, with HQSAR and CoMSIA models identifying sixteen compounds, with predicted PknB binding superior to the template, whose activity spectra and physicochemical, pharmacokinetic, and anti-M. tuberculosis properties were assessed. Compound, D060, bearing additional ortho- and meta-methyl groups on its R₂ substituent, was superior to template regarding PknB inhibition and % caseum fraction unbound, and equivalent in other aspects, although predictions identified hepatotoxicity as a likely issue with the quinazoline series. These data provide a structural basis for rational design of quinazoline derivatives with more potent PknB inhibitory activity as candidate anti-tuberculosis agents.

Synthesis and greener pastures biological study of bis-thiadiazoles as potential Covid-19 drug candidates

A novel series of bis- (Abdelhamid et al., 2017, Banerjee et al., 2018, Bharanidharan et al., 2022)thiadiazoles was synthesized from the reaction of precursor dimethyl 2,2'-(1,2-diphenylethane-1,2-diylidene)-bis(hydrazine-1-carbodithioate) and hydrazonyl chlorides in ethanol under ultrasonic irradiation. Spectral tools (IR. NMR, MS, elemental analyses, molecular dynamic simulation, DFT and LUMO and HOMO) were used to elucidate the structure of the isolated products. Molecular docking for the precursor, 3 and ligands 6a-i to two COVID-19 important proteins M^pro and RdRp was compared with two approved drugs, Remdesivir and Ivermectin. The binding affinity varied between the ligands and the drugs. The highest recorded binding affinity of 6c with M^pro was (-9.2 kcal/mol), followed by 6b and 6a, (-8.9 and -8.5 kcal/mol), respectively. The lowest recorded binding affinity was (-7.0 kcal/mol) for 6 g. In comparison, the approved drugs showed binding affinity (-7.4 and -7.7 kcal/mol), for Remdesivir and Ivermectin, respectively, which are within the range of the binding affinity of our ligands. The binding affinity of the approved drug Ivermectin against RdRp recoded the highest (-8.6 kcal/mol), followed by 6a, 6 h, and 6i are the same have (-8.2 kcal/mol). The lowest reading was found for compound 3 ligand (-6.3 kcal/mol). On the other side, the amino acids also differed between the compounds studied in this project for both the viral proteins. The ligand 6a forms three H-bonds with Thr 319(A), Sr 255(A) and Arg 457(A), whereas Ivermectin forms three H-bonds with His 41(A), Gly143(A) and Gln 18(A) for viral M^pro. The RdRp amino acids residues could be divided into four groups based on the amino acids that interact with hydrogen or hydrophobic interactions. The first group contained 6d, 6b, 6 g, and Remdesivir with 1-4 hydrogen bonds and hydrophobic interactions 1 to 10. Group 2 is 6a and 6f exhibited 1 and 3 hydrogen bonds and 15 and 14 hydrophobic interactions. Group 3 has 6e and Ivermectin shows 4 and 3 hydrogen bonds, respectively and 11 hydrophobic interactions for both compounds. The last group contains ligands 3, 6c, 6 h, and 6i gave 1-3 hydrogen bonds and 6c and 3 recorded the highest number of hydrophobic interactions, 14 for both 6c and 6 h. Pro Tox-II estimated compounds' activities as Hepatoxic, Carcinogenic and Mutagenic, revealing that 6f-h were inactive in all five similar to that found with Remdesivir and Ivermectin. The drug-likeness prediction was carried out by studying physicochemical properties, lipophilicity, size, polarity, insolubility, unsaturation, and flexibility. Generally, some properties of the ligands were comparable to that of the standards used in this study, Remdesivir and Ivermectin.

A novel cocrystal of metformin hydrochloride with citric acid: Systematic synthesis and computational simulation

Pharmaceutical cocrystals have matured into an effective technique for tuning the physicochemical and mechanical properties of drugs in solid form simultaneously. Herein, in order to provide a novel cocrystal form of oral medicine metformin hydrochloride (MH), citric acid (CA) was selected as an efficient ligand after screening a variety of inorganic and organic acids. Thus, based on the principle of crystal engineering, we report a novel cocrystal: metformin hydrochloride - citric acid (MHCA) after the systematic screening, which was experimentally proved to be constituted with 1:1 stoichiometry. Compared with pure MH, MHCA has been proved higher solubility in water, methanol, and ethanol from 283.15 to 313.15 K. Through single-crystal X-ray diffraction (SC-XRD), the particular molecular structure of MHCA has been determined as the orthorhombic system and Pbca space group. Besides, the binding model of MH-CA was built for investigating the binding energy and stability between two components at 278, 298, and 318 K, which were found to be essential for the prediction and analysis of cocrystals. The contribution of different intermolecular interactions and the strength of molecular packing in the cocrystal also have been investigated by Hirshfeld surface analysis. It was found that the cocrystal structure was mainly stabilized by intermolecular hydrogen bonds existing as N-H···O between components, which indicated that the diffusion-combination trend of molecules enhanced the regular array of cocrystal. The results revealed that the molecules of MH and CA formed supramolecular cocrystals mainly induced by hydrogen bonds after passive contacts, such as co-crystallization or grind.

MurC ligase of multi-drug resistant Salmonella Typhi can be inhibited by novel Curcumin derivative: Evidence from molecular docking and dynamics simulations

Emerging multi-drug resistance in recent Salmonella Typhi isolates, causative agent of enteric Typhoid fever, compelled us to investigate alternative therapeutic strategies. The present study encompassed virtual screening, ADMET screening as well as antibacterial activity prediction to shortlist potent lead molecules whose binding affinities (BAs) were checked against major druggable S. Typhi targets. BA profile revealed a deoxy-tetradeutero- curcumin derivative to be novel bioactive compound having high BA towards UDP-N-acetylmuramate-L-alanine ligase (MurC) protein involved in peptidoglycan synthesis. Molecular docking indicated that our lead {Binding energy (BE)= -8.00 ± 0.02 kcal/mol}could competitively bind to MurC with respect to its natural ligand ATP (BE= -7.65 ± 0.19 kcal/mol). The lead also possessed superior binding and inhibition profile against MurC than other commercial antibiotics. This BE was contributed by Hydrogen (H-) bonds and numerous non-canonical interactions with the evolutionary conserved active-site residues. From molecular docking and coarse-grained dynamics simulations, it was inferred that the novel curcumin derivative was predicted to be potential competitive inhibitor of ATP for MurC-catalytic domain having low relative RMSF (0.59 Å) to inhibit MurC-induced peptidoglycan biosynthesis. The inferences drawn from the study can open new portals for designing efficient therapeutic strategies against S. Typhi.

In-silico modelling studies of 5-benzyl-4-thiazolinone derivatives as influenza neuraminidase inhibitors via 2D-QSAR, 3D-QSAR, molecular docking, and ADMET predictions

Influenza virus disease is one of the most infectious diseases responsible for many human deaths, and the high mutability of the virus causes drug resistance effects in recent times. As such, it became necessary to explore more inhibitors that could avert future influenza pandemics. The present research utilized some in-silico modelling concepts such as 2D-QSAR, 3D-QSAR, molecular docking simulation, and ADMET predictions on some 5-benzyl-4-thiazolinone derivatives as influenza neuraminidase (NA) inhibitors. The 2D-QSAR modelling results revealed GFA-MLR (R train 2 =0.8414, Q2 = 0.7680) and GFA-ANN (R train ​ 2 =0.8754, Q2 = 0.8753) models with the most relevant descriptors (MATS3i, SpMax5_Bhe, minsOH and VE3_D) for predicting the inhibitory activities of the molecules which has passed the global criteria of accepting QSAR models. The results of the 3D-QSAR modelling results showed that CoMFA_ES (R train ​ 2 =0.9030, Q2 = 0.5390) and CoMSIA_EA (R train 2 =0.880, Q2 = 0.547) models are having good predicting ability among other developed models. The molecules were virtually screened via molecular docking simulation with the active site of NA protein receptor (pH1N1) which confirms their resilient potency when compared with zanamivir standard drug. Molecule 11 as the most potent molecule formed more H-bond interactions with the key residues such as TRP178, ARG152, ARG292, ARG371, and TYR406 that triggered the catalytic reactions for NA inhibition. Furthermore, six (6) molecules (9, 10, 11, 17, 22, and 31) with relatively high inhibitory activities and docking scores were identified as the possible leads for in-silico exploration of novel NA inhibitors. The drug-likeness and ADMET predictions of the lead molecules revealed non-violation of Lipinski's rule and good pharmacokinetic profiles respectively, which are important guidelines for rational drug design. Hence, the outcome of this study overlaid a solid foundation for the in-silico design and exploration of novel NA inhibitors with improved potency.

Computational drug design of novel COVID-19 inhibitor

BACKGROUND

In 2003, the first case of severe acute respiratory syndrome coronavirus (SARS-CoV) was recorded. Coronaviruses (CoVs) have caused a major outbreak of human fatal pneumonia. Currently, there is no specific drug or treatment for diseases caused by SARS CoV 2. Computational approach that adopts dynamic models is widely accepted as indispensable tool in drug design but yet to be exploited in covid-19 in Zaria, Nigeria. In this study, steps were taken to advance on the successful achievements in the field of covid-19 drug, with the aid of in silico drug design technique, to create novel inhibitor drug candidates with better activity. In this study, one thousand human immunodeficiency virus (HIV1) antiviral chemical compounds from www.bindingBD.org were docked on the SARS CoV 2 main protease protein data bank identification number 6XBH (PDB ID: 6XBH) and the molecular docking score were ranked in order to identify the compounds with the highest inhibitory effects, and easy selection for future studies.

RESULTS

The docking studies showed some interesting results. Inhibitors with Index numbers 331, 741, and 819 had the highest binding affinity. Similarly, inhibitors with Index number 441, 847, and 46 had the lowest hydrogen bond energy. Inhibitor with index number 331 was reported with the lowest value (- 48.38kCal/mol). Five new compounds were designed from the selected six (6) compounds with the best binding score giving a total of thirty (30) novel compounds. The low binding energy of inhibitor with index no. 847b is unique, as most of the interaction energies are of H-bond type with amino acids (Thr26, Gly143, Ser144, Cys145, Glu166, Gln189, Hie164, Met49, Thr26, Thr25, Thr190, Asn142, Met165) resulting in an overall negative value (-16.31 kCal/mol) making it the best of all the newly designed inhibitors.

CONCLUSIONS

The novel inhibitor is 2-(2-(5-amino-2-((((3-aminobenzyl)oxy)carbonyl)amino)-5-oxopentanamido)-4-(2-(tert-butyl)-4-oxo-4-(pentan-3-ylamino) butanamido)-3-hydroxybutyl) benzoic acid. The improvement it has over the parent inhibitor is from the primary amine group attached to meta position of first benzene ring and the carboxyl group attached to the ortho position of the second benzene ring. The molecular dynamics studies also show that the novel inhibitor remains stable after the study. This result makes it a better drug candidate against SARS CoV 2 main protease when compared with the co-crystallized inhibitor or any of the 1000 docked inhibitors.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s42269-022-00892-z.

Computational studies evidenced the potential of steroidal lactone to disrupt surface interaction of SARS-CoV-2 spike protein and hACE2

The critical event in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogenesis is recognition of host cells by the virus, which is facilitated by protein-protein interaction (PPI) of viral Spike-Receptor Binding Domain (S-RBD) and Human Angiotensin Converting Enzyme 2-Receptor (hACE2-R). Thus, disrupting the interaction between S-RBD and hACE2-R is widely accepted as a primary strategy for managing COVID-19. The purpose of this study is to assess the ability of three steroidal lactones (SL) (4-Dehydrowithaferin A, Withaferin A, and Withalongolide A) derived from plants to disrupt the PPI of S-RBD and hACE2-R under two conditions (CON-I and CON-II) using in-silico methods. Under CON-I, 4-Dehydrowithaferin A destabilizing the interactions between S-RBD and hACE2-R, as indicated by an increase in binding energy (BE) from -1028.5 kJ/mol (control) to -896.12 kJ/mol 4-Dehydrowithaferin A exhibited a strong interaction with S-RBD GLY496 with a hydrogen bond occupancy (HBO) of 37.33%. Under CON-II, Withalongolide A was capable of disrupting all types of PPI, as evidenced by an increased BE from -913 kJ/mol (control) to -133.69 kJ/mol and an increased distance (>3.55 nm) between selected AAR combinations of S-RBD and hACE2-R. Withalongolide A formed a hydrogen bond with TYR453 (97%, HBO) of S-RBD, which is required for interaction with hACE2-R's HIS34. Our studies demonstrated that SL molecules have the potential to disrupt the S-RBD and hACE2-R interaction, thereby preventing SARS-CoV-2 from recognizing host cells. The SL molecules can be considered for additional in-vitro and in-vivo studies with this research evidence.

Protein-protein interaction of RdRp with its co-factor NSP8 and NSP7 to decipher the interface hotspot residues for drug targeting: A comparison between SARS-CoV-2 and SARS-CoV

In this study we explored the molecular mechanism of RdRp (Non-Structural Protein, NSP12) interaction with its co-factors NSP7 and NSP8 which is the main toolbox for RNA replication and transcription of SARS-CoV-2 and SARS-CoV. The replication complex is a heterotetramer consists of one NSP12, one NSP7 and two NSP8. Extensive molecular dynamics (MD) simulations were applied on both the heterotetramer complexes to generate the conformations and were used to estimate the MMPBSA binding free energy (BFE) and per-residue energy decomposition of NSP12-NSP8 and NSP12-NSP7 and NSP7-NSP8 complexes. The BFE of SARS-CoV-2 heterotetramer complex with its corresponding partner protein was significantly higher as compared to SARS-CoV. Interface hotspot residues were predicted using different methods implemented in KFC (Knowledge-based FADA and Contracts), HotRegion and Robetta web servers. Per-residue energy decomposition analysis showed that the predicted interface hotspot residues contribute more energy towards the formation of complexes and most of the predicted hotspot residues are clustered together. However, there is a slight difference in the residue-wise energy contribution in the interface NSPs on heterotetramer viral replication complex of both coronaviruses. While the overall replication complex of SARS-CoV-2 was found to be slightly flexible as compared to SARS-CoV. This difference in terms of structural flexibility/stability and energetic characteristics of interface residues including hotspots at PPI interface in the viral replication complexes may be the reason of higher rate of RNA replication of SARS-CoV-2 as compared to SARS-CoV. Overall, the interaction profile at PPI interface such as, interface area, hotspot residues, nature of bonds and energies between NSPs, may provide valuable insights in designing of small molecules or peptide/peptidomimetic ligands which can fit into the PPI interface to disrupt the interaction.

Talazoparib Dual-targeting on Poly (ADP-ribose) Polymerase-1 and -16 Enzymes Offers a Promising Therapeutic Strategy in Small Cell Lung Cancer Therapy: Insight from Biophysical Computations

In recent times, inhibition of poly (ADP-ribose) polymerase (PARP) enzymes by pharmacological drugs has attracted much attention as an anticancer therapy. As reported, PARP-16 has been discovered as a novel anticancer target for small cell lung cancer, and that the inhibition of both PARP-16 and PARP-1 by talazoparib can increase the overall effectiveness of talazoparib in the SCLC treatment. In this study, we employed computational approaches to investigate the differential inhibitory potency of Talazoparib on PARP-1 and PARP-16. Talazoparib has excellent PARP-1 and PARP-16 binding activities, as revealed by the ΔG_bind (total binding energy). Pp16-tpb had binding energy of -34.85 kcal/mol, while pp1-tpb had a binding energy of -26.36 kcal/mol. The binding activity of Talazoparib on both PARP-1 and PARP-16 was significantly influenced by van der Waal and electrostatic interactions. Correspondingly, according to the findings of this study, binding residues with total binding energy greater than 1.00 kcal/mol contributed considerably to the Talazoparib's binding activities on PARP-1 and PARP-16. We believe the findings of this study will pave the way for developing dual targeting of PARP enzymes as a strategy for small-cell lung cancer treatment.

A descriptor for the structural stability of organic-inorganic hybrid perovskites based on binding mechanism in electronic structure

The poor stability of organic-inorganic hybrid perovskites hinders its commercial application, which motivates a need for greater theoretical insight into its binding mechanism. To date, the binding mode of organic cation and anion inside organic-inorganic hybrid perovskites is still unclear and even contradictory. Therefore, in this work based on density functional theory (DFT), the binding mechanism between organic cation and anion was systematically investigated through electronic structure analysis including an examination of the electronic localization function (ELF), electron density difference (EDD), reduced density gradient (RDG), and energy decomposition analysis (EDA). The binding strength is mainly determined by Coulomb effect and orbital polarization. Based on the above analysis, a novel 2D linear regression descriptor that E_b =  - 9.75Q²/R₀ + 0.00053 V∙E_HL - 6.11 with coefficient of determination R² = 0.88 was proposed to evaluate the binding strength (the units for Q, R₀, V, and E_HL are |e|, Å, bohr³, and eV, respectively), revealing that larger Coulomb effect (Q²/R₀), smaller volume of perovskite (V), and narrower energy difference (E_HL) between the lowest unoccupied molecular orbital (LUMO) of organic cation and the highest occupied molecular orbital (HOMO) of anion correspond to the stronger binding strength, which guides the design of highly stable organic-inorganic hybrid perovskites.

Binding sites of miRNA on the overexpressed genes of oral cancer using 7mer-seed match

The microRNAs having a length of ~ 19-22 nucleotides are the small, non-coding RNAs. The evolution of microRNAs in many disorders may hold the key to tackle complex challenges. Oral cancer belongs to the group of head and neck cancer. It occurs in the mouth region that appears as an ulcer. In this study, we collected information on the overexpressed genes of oral cancer. The coding sequences of the genes were derived from NCBI and the entire set of human microRNAs present in miRBASE 21 was retrieved. The human microRNAs that can target the overexpressed genes of oral cancer were determined with the aid of our in-house software. The interaction between microRNAs and the overexpressed genes was evaluated with 7mer-m8 model of microRNA targeting. The genes DKK1 and APLN paired with only one miRNA i.e., miR-447 and miR-6087, respectively. But the genes INHBA and MMP1 were found to be targeted by 2 miRNAs, while the genes FN1, FAP, TGFPI, COL4A1, COL4A2, and LOXL2 were found to be targeted by 16, 5, 9, 18, 29, and 11 miRNAs. Subsequently, several measures such as free energy, translation efficiency, and cosine similarity metric were used to estimate the binding process. It was found that the target region's stability was higher than the upstream and downstream zones. The overexpressed genes' GC contents were calculated, revealing that the codons in target miRNA region were overall GC rich as well as GC3 rich. Lastly, gene ontology was performed to better understand each gene's involvement in biological processes, molecular function, and cellular component. Our study showed the role of microRNAs in gene repression, which could possibly aid in the prognosis and diagnosis of oral cancer.

Density functional theory studies on C20 with substitutional TinNn impurities

In this paper, we have performed systematic theoretical surveys of C₂₀ and its C_20-2nTi_nN_n nanocages with n = 1-8 at DFT. Full optimization indicates none of the structures collapse to open deformed as segregated heterofullerene. Also, in order to avoid the resulted strain of fused five-pentagon configuration, some of them deform their cage at the Ti-N bonds and appear cubic-like. Binding energy (E_b) increases, and the absolute heat of atomization │ΔH_at│ of the designed C_20-2nTi_nN_n structures decreases, respectively, as the number of substituting Ti-N units increases. The calculated E_b of 57.05 eV/atom and │ΔH_at│ of 2437.40 kcal/mol display C₄Ti₈N₈ as the most thermodynamic stable heterofullerene where including eight separated Ti-N units through two double C═C bonds. In contrast, the calculated band gap of 2.06 eV shows C₁₈Ti₁N₁ as the best-insulated heterofullerene. Here isolable or extractable open-shell C₁₈Ti₁N₁ heterofullerene must be kinetic stable species, and closed-shell C₄Ti₈N₈ should be thermodynamic stable species. Compared to the suggested Ti-decorated B₃₈ fullerene as a high capacity hydrogen storage material with large E_b (5.67 eV/atom), our studied C_20-2nTi_nN_n heterofullerenes show the higher E_b with a range of 13.78 to 57.05 eV/atom, the higher stability, and the higher capacity hydrogen storage. Each Ti-N unit can bind up to two hydrogen molecules with an average adsorption energy of 0.073 eV/H₂. While the C₄Ti₈N₈ fullerene substituted with 8 Ti-N units can store 16 H₂ molecules, the hydrogen gravimetric density (the hydrogen storage capacity) reaches up to 5.61 wt% with an average adsorption energy of 0.587 eV/H₂. Based on these results, we infer that C₄Ti₈N₈ fullerene is a potential material for hydrogen storage with high capacity and might motivate active experimental efforts in designing hydrogen storage media.

Photophysics of nanographenes: from polycyclic aromatic hydrocarbons to graphene nanoribbons

Graphene quantum dots (GQDs) and nanoribbons (GNRs) are classes of nanographene molecules that exhibit highly tunable photophysical properties. There have been great strides in recent years to advance our understanding of nanographene photophysics and develop their use in light-harvesting systems, such as artificial photosynthesis. Here, we review the latest studies of GQDs and GNRs which have shed new light onto their photophysical underpinnings through computational and advanced spectroscopic techniques. We discuss how the size, symmetry, and shape of nanographenes influence their molecular orbital structures and, consequentially, their spectroscopic signatures. The scope of this review is to comprehensively lay out the general photophysics of nanographenes starting with benzene and building up to larger polycyclic aromatic hydrocarbons, GQDs, and GNRs. We also explore a collection of publications from recent years that build upon the current understanding of nanographene photophysics and their potential application in light-driven processes from display, lasing, and sensing technology to photocatalytic water splitting.

Simultaneous enantioseparation and simulation studies of atenolol, metoprolol and propranolol on Chiralpak® IG column using supercritical fluid chromatography

Enantioseparation of three β-blockers, i.e., atenolol, metoprolol and propranolol, was studied on amylose tris(3-chloro-5-methylphenylcarbamate) immobilized chiral stationary phase using supercritical fluid chromatography (SFC). The effect of organic modifiers (methanol, isopropanol and their mixture), column temperature and back pressure on chiral separation of β-blockers was evaluated. Optimum chromatographic separation with respect to resolution, retention, and analysis time was achieved using a mixture of CO₂ and 0.1% isopropyl amine in isopropanol: methanol (50:50, V/V), in 75:25 (V/V) ratio. Under the optimized conditions, the resolution factors (R_s) and separation factors (α) were greater than 3.0 and 1.5, respectively. Further, with increase in temperature (25–45 °C) and pressure (100–150 bars) there was corresponding decrease in retention factors (k), α and R_s. However, a reverse trend (α and R_s) was observed for atenolol with increase in temperature. The thermodynamic data from van't Hoff plots revealed that the enantioseparation was enthalpy driven for metoprolol and propranolol while entropy driven for atenolol. To understand the mechanism of chiral recognition and the elution behavior of the enantiomers, molecular docking studies were performed. The binding energies obtained from simulation studies were in good agreement with the elution order found experimentally and also with the free energy values. The method was validated in the concentration range of 0.5–10 μg/mL for all the enantiomers. The limit of detection and limit of quantitation ranged from 0.126 to 0.137 μg/mL and 0.376–0.414 μg/mL, respectively. The method was used successfully to analyze these drugs in pharmaceutical preparations.

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Simultaneous enantioseparation of three β-blockers in a single analysis using chiral SFC

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Separation efficiency was mainly dependent on the nature and composition of mobile phase

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van't Hoff plots revealed enthalpy driven process for metoprolol and propranolol and entropy driven for atenolol

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Binding energies from molecular docking study were in good agreement with the elution order

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The results suggested hydrogen bonding and hydrophobic interactions, as the dominant interaction modes.