Sumanene and its adsorption properties towards CO, CO2 and NH3 molecules

Supramolecular Chemistry of Sumanene

Sumanene is a buckybowl molecule that is continuously attracting the attention of the scientific community because of its unique geometrical and physicochemical properties. This Minireview systematically summarizes advances and considerations regarding the applied supramolecular chemistry of sumanene. This work highlights the major fields in which potential or real applications of sumanene molecule have been reported to date, such as the design of sumanene-containing functional supramolecular materials and architectures, sumanene-based drug-delivery systems, or sumanene-tethered ion-selective molecular receptors. An assessment of the current status in the applied supramolecular chemistry of sumanene is provided, together with an emphasis on the key advances being made. Discussion on those milestones that are still to be achieved within this emerging field is also provided.

Design, Molecular Modeling, MD Simulations, Essential Dynamics, ADMET, DFT, Synthesis, Anti-proliferative, and Apoptotic Evaluations of a New Anti-VEGFR-2 Nicotinamide Analogue

OBJECTIVES

This study aims to design and evaluate (in silico and in vitro) a new nicotinamide derivative as an inhibitor of VEGFR-2, a major mediator of angiogenesis Methods: The following in silico studies were performed; DFT calculations, molecular modelling, MD simulations, MM-GBSA, PLIP, and PCAT studies. The compound's in silico (ADMET) analysis was also conducted. Subsequently, the compound ((E)-N-(4-(1-(2-(4-(4-Chlorobenzamido)benzoyl)hydrazono)ethyl) phenyl)nicotinamide) was successfully synthesized and designated as compound X. In vitro, VEGFR-2 inhibition and cytotoxicity of compound X against HCT-116 and A549 cancer cell lines and normal Vero cell lines were conducted. Apoptosis induction and migration assay of HCT-116 cell lines after treatment with compound X were also evaluated.

RESULTS

DFT calculations assigned stability and reactivity of compound X. Molecular docking and MD simulations indicated its excellent binding against VEGFR-2. Furthermore, MM-GBSA analysis, PLIP experiments, and PCAT studies confirmed compound X's correct binding with optimal dynamics and energy. ADMET analysis expressed its general likeness and safety. The in vitro assays demonstrated that compound X effectively inhibited VEGFR-2, with an IC50 value of 0.319 ± 0.013 μM and displayed cytotoxicity against HCT-116 and A549 cancer cell lines, with IC50 values of 57.93 and 78.82 μM, respectively. Importantly, compound X exhibited minimal toxicity towards the non-cancerous Vero cell lines, (IC50 = 164.12 μM). Additionally, compound X significantly induced apoptosis of HCT-116 cell lines and inhibited their potential to migrate and heal.

CONCLUSION

In summary, the presented study has identified compound X as a promising candidate for the development of a novel apoptotic lead anticancer drug.

Trimetallic clusters in the sumanene bowl for dinitrogen activation

It is of great importance to find catalysts for the nitrogen reduction reaction (NRR) with high stability and reactivity. A series of M₃ clusters (M = Ti, Zr, V, and Nb) supported on sumanene (C₂₁H₁₂) were designed as potential catalysts for the NRR by taking advantage of the high reactivity of trimetallic clusters and the unique geometric and electronic properties of sumanene, a bowl-like organic molecule. Detailed mechanisms of NN bond cleavage on C₂₁H₁₂-M₃ were investigated by DFT calculations and compared with those on bare M₃ clusters. M₃ in the sumanene bowl is very stable with large binding energies, which prohibits the cohesion of M₃ into M₆. In the bowl, M₃ has a (quasi-) equilateral triangle structure with lengthened M-M bonds, which is particularly beneficial to the N₂ transfer process on Ti₃ and V₃ clusters. The N-N bond can be dissociated by both M₃ and C₂₁H₁₂-M₃ clusters without the overall energy barriers. A blurring effect is found in which some geometric and electronic properties of different metal types become similar when M₃ is supported on the substrate. Our work demonstrates that sumanene is a suitable substrate to support M₃ in the activation of N₂ with enhanced stability and maintained a high level of reactivity compared to bare M₃.

Exploration of phosphorene as doxorubicin nanocarrier: An atomistic view from DFT calculations and MD simulations

Potential capability of phosphorene nanosheet (PNS) as doxorubicin (DOX) nanocarrier was investigated using density functional theory (DFT) method and molecular dynamics (MD) simulations. Both DFT calculations and MD simulations revealed that the DOX molecule is adsorbed horizontally onto the PNS surface with the nearest interaction distance of 2.5 Å. The binding energy of DOX is predicted to be about - 49.5 kcal.mol^-1, based on the DFT calculations. After DOX adsorption, the E_g value of PNS remains almost constant in both gas and solvent phases. The dynamical behavior of PNS-DOX was studied at T = 298, 310, and 326 K that reminiscent of room temperature, body temperature, and temperature of tumor after exposure to 808 nm laser radiation, respectively. The diffusion coefficient values of DOX molecule are proportional to temperature. We found that PNS can hold a high amount of DOX on both sides of its surface (66% in weight). MD simulations showed that the dynamical behavior of simulated systems are not affected by pH variances.

Buckybowls as gas adsorbents: binding of gaseous pollutants and their electric-field induced release

The adsorption of nitric oxide and nitrogen dioxide (NOx) to the Buckybowls sumanene and corannulene was investigated. Binding energies were up to 1.8× larger than for coronene as the planar analogue, demonstrating the advantages of Buckybowls for gas adsorption. In agreement with previous reports on carbon dioxide and methane adsorption, the favorable binding energies for NOx were shown to be associated with the curvature of the Buckybowls. It is shown that applying an electric field along the bowl symmetry axis modifies the bowl curvatures and impacts adsorbate binding energies, including the potential to desorb adsorbates. As a proof of concept, it is shown that applying electric fields of different strengths and orientations selectively controls sumanene's preference to bind nitric oxide, nitrogen dioxide, and carbon dioxide, suggesting potential applications for dynamically tunable gas adsorption. Moreover, it is demonstrated that adsorbates can be desorbed by applying suitable electric field strengths, allowing cleaning of the Buckybowls for renewed usage.

Synthetic approaches to bowl-shaped π-conjugated sumanene and its congeners

Since the first synthetic report in 2003 by Sakurai et al., sumanene (derived from the Indian 'Hindi as well as Sanskrit word' "Suman", which means "Sunflower"), a beautifully simple yet much effective bowl-shaped C 3-symmetric polycyclic aromatic hydrocarbon having three benzylic positions clipped between three phenyl rings in the triphenylene framework has attracted a tremendous attention of researchers worldwide. Therefore, since its first successful synthesis, a variety of functionalized sumanenes as well as heterosumanenes have been developed because of their unique physiochemical properties. For example, bowl-to-bowl inversion, bowl depth, facial selectivity, crystal packing, metal complexes, intermolecular charge transfer systems, cation-π complexation, electron conductivity, optical properties and so on. Keeping the importance of this beautiful scaffold in mind, we compiled all the synthetic routes available for the construction of sumanene and its heteroatom derivatives including Mehta's first unsuccessful effort up to the latest achievements. Our major goal to write this review article was to provide a quick summary of where the field has been, where it stands at present, and where it might be going in near future. Although several reviews have been published on sumanene chemistry dealing with different aspects but this is the first report that comprehensively describes the 'all-in-one' chemistry of the sumanene architecture since its invention to till date. We feel that this attractive review article will definitely help the scientific community working not only in the area of organic synthesis but also in materials science and technology.

Modelling the adsorption of natural organic matter on Ag (111) surface: Insights from dispersion corrected density functional theory calculations

Understanding the nature of the interactions between natural organic matter (NOM) and engineered nanoparticles (ENPs) is of crucial importance in understanding the fate and behaviour of engineered nanoparticles in the environment. In the present study, dispersion-corrected density functional theory (DFT-D) has been used to elucidate the molecule-surface interactions of higher molecular weight (HMW) NOM ambiguously present in the aquatic systems, namely: humic acid (HA), fulvic acid (FA) and protein Cryptochrome (Cry) on Ag (111) surface. Investigations were done in the gas phase and to mimic real biological environment, water has been used as a solvent within the conductor-like screening model (COSMO) framework. The calculated adsorption energies for HA, FA and Cry on Ag (111) surface were -27.90 (-18.45) kcal/mol, -38.28 (-18.68) kcal/mol and -143.89 (-150.82) kcal/mol respectively in the gas (solvent) phase and the equilibrium distances between the surface and HA, FA and Cry molecules were 1.87 (2.18) Å, 2.31(2.31) Å and 1.91 (1.70) Å respectively in the gas (solvent) phase. In both gas and water phase Cry showed stronger adsorption which means it has a stronger interaction with Ag (111) surface compared to HA and FA. The results for adsorption energy, solvation energy, isosurface of charge deformation difference, total density of state and partial density of states indicated that indeed these chosen adsorbates do interact with the surface and are favourable on Ag (111) surface. In terms of charge transfer, one of many calculated descriptors in this study, electrophilicity (ω) concur that charge transfer will take place from the adsorbates to Ag (111) surface.

Influence of nitrogen doping in sumanene framework toward hydrogen storage: A computational study

Two conditions are important to obtain appropriate substances for hydrogen storage; high surface area and fitting binding energy (BE). Doping is a key strategy that improves BE. We investigated hydrogen adsorption onto twenty six nitrogen disubstituted isomers of sumanene (C₁₉N₂H₁₂) by MP2/6-311++G(d,p)//B3LYP/6-31+G(d) and M06-2X/6-31+G(d) levels of theory. Effect of nitrogen doping in different positions of sumanene was checked. To obtain better BE, basis set superposition error (BSSE) and zero point energy (ZPE) corrections were used. Anticipating of adsorption sites and extra details about adsorption process was done by molecular electrostatic potential (MEP) surfaces. Various types of density of state (DOS) diagrams such as total DOS (TDOS), projected DOS (PDOS) and overlap population DOS (OPDOS) and natural bond orbital (NBO) analysis were used to find better insight on the adsorption properties. In addition of temperature depending of the BE, HOMO-LUMO gap (HLG), dipole moment, reactivity and stability, bowl depth and natural population analysis (NPA) of the isomers were studied. A physisorption mechanism for adsorption was proposed and a trivial change was seen. Place of nitrogen atoms in sumanene frame causes to binding energy increases or decreases compared with pristine sumanene. The best and the worst isomers and category of isomers were suggested.

Influence of sumanene modifications with boron and nitrogen atoms to its hydrogen adsorption properties

We investigate the influence of sumanene modifications on its adsorption properties towards the hydrogen molecule.

Carbon monoxide interactions with pure and doped B11XN12 (X = Mg, Ge, Ga) nano-clusters: a theoretical study

The influence of CO adsorption on the electronic and optical properties of the B₁₁XN₁₂ nano-cluster has been studied by DFT calculations.