Ameloblastoma is a non-cancerous but aggressive oral tumor emerging from odontogenic epithelial tissue involved during odontogenesis. Since there is lack in unravelling the complete molecular pathogenesis of ameloblastoma, chemotherapy is less attempted and a lot of disagreement over the optimal treatment option. Hence, till date, wide surgical resection is considered to be the reliable treatment for ameloblastoma. The Neurotrophin Signaling pathway plays an important role in neuron signaling and it is closely related with the MAPK pathway, which on the other hand regulated cell differentiation, apoptosis, proliferation, plasticity and survival. Protein- Protein Interaction analysis was analysed with STRING tool using WNL value, identified that CTNNB1, HRAS, NGFR, NGFR, and SORT1 having high interacting with BDNF, NT4, p75NTR, NGF, and NT3. The results of ontology analysis revealed that Neurotrophin signaling pathway is associated with Cell surface receptor signaling pathway, regulation of cell differentiation, regulation of development process, EGFR tyrosine kinase inhibitor resistance, MAPK signaling pathway, PI3K-Akt signaling pathway and Ras signaling pathway leading to pathogenesis involving genes. Further, clustering coefficient values of proteins BDNF, NT4, p75NTR, NGF & NT3 were identified as 0.627, 0.708, 0.367, 0.644 & 0.415. The results of molecular docking studies revealed among the selected ligands Methyl-ɣ-oresellinate, N-(4-Hydroxy-phenyl)-2-phenyl-N-phenylacetyl-acetamide, Atranorin and Oresellinate exhibited high binding affinity with selected protein. The key genes involved in Neurotrophin signaling pathway leading to ameloblastoma pathogenesis is revealed, which are closely associated with cell differentiation, cell proliferation, pro-apoptosis, and pro-survival regulations. Further it can be concluded that Neurotrophin signaling pathway could be one of the promising pathway to tailor the targeted drug therapy for Ameloblastoma treatment.
UNASSIGNED: The online version contains supplementary material available at 10.1007/s40203-024-00223-2.

The hydrolysis mechanism of americium was calculated using density functional theory, and the detailed microscopic reaction mechanism was obtained. The results show that americium reacts with water along the octet state to produce oxides and H2, and that this reaction is exothermic. The interaction between Am and O atoms gradually changes from initially electrostatic interaction to covalent interaction, and continues to strengthen. During the reaction process, Am atoms always lose electrons, the 5f orbital is obviously involved, and there is df orbital hybridization. This study provides the necessary theoretical data support for the theoretical and experimental study of the actinide system.

The title SnIV complex, [Sn(C6H5)3Cl(C18H15O4P)], is a formal adduct between triphenyl phosphate (PhO)3P=O and the stannane derivative chlorido-tri-phenyl-tin, SnPh3Cl. The structure refinement reveals that this mol-ecule displays the largest Sn-O bond length for compounds including the X=O→SnPh3Cl fragment (X = P, S, C, or V), 2.6644 (17) Å. However, an AIM topology analysis based on the wavefunction calculated from the refined X-ray structure shows the presence of a bond critical point (3,-1), lying on the inter-basin surface separating the coordinated phosphate O atom and the Sn atom. This study thus shows that an actual polar covalent bond is formed between (PhO)3P=O and SnPh3Cl moieties.

Porous molecular materials are constructed from molecules that assemble in the solid-state such that there are cavities or an interconnected pore network. It is challenging to control the assembly of these systems, as the interactions between the molecules are generally weak, and subtle changes in the molecular structure can lead to vastly different intermolecular interactions and subsequently different crystal packing arrangements. Similarly, the use of different solvents for crystallization, or the introduction of solvent vapour, can result in different polymorphs and pore networks being formed. It is difficult to uniquely describe the pore networks formed, and thus we analyse 1033 crystal structures of porous molecular systems to determine the underlying topology of their void spaces and potential guest diffusion networks. Material-agnostic topology definitions are applied. We use the underlying topological nets to examine whether it is possible to apply isoreticular design principles to porous molecular materials. Overall, our automatic analysis of a large dataset gives a general insight into the relationships between molecular topologies and the topological nets of their pore network. We show that while porous molecular systems tend to pack similarly to non-porous molecules, the topologies of their pore distributions resemble those of more prominent porous materials, such as metal-organic frameworks and covalent organic frameworks.

The emergence and spread of multi-drug resistance among Helicobacter pylori (H. pylori) strain raise more stakes for genetic research for discovering new drugs. The quantity of uncharacterized hypothetical proteins in the genome may provide an opportunity to explore their property and promulgation could act as a platform for designing the drugs, making them an intriguing genetic target. In this context, the present study aims to identify the key hypothetical proteins (HPs) and their biological regulatory processes in H. pylori. This investigation could provide a foundation to establish the molecular connectivity among the pathways using topological analysis of the protein interaction networks (PINs). The giant network derived from the extended network has 374 nodes connected via 925 edges. A total of 43 proteins with high betweenness centrality (BC), 54 proteins with a large degree, and 23 proteins with high BC and large degrees have been identified. HP 1479, HP 0056, HP 1481, HP 1021, HP 0043, HP 1019, gmd, flgA, HP 0472, HP 1486, HP 1478, and HP 1473 are categorized as hub nodes because they have a higher number of direct connections and are potentially more important in understanding HP\'s molecular interactions. The pathway enrichment analysis of the network clusters revealed significant involvement of HPs in pathways such as flagellar assembly, bacterial chemotaxis and lipopolysaccharide biosynthesis. This comprehensive computational study revealed HP\'s functional role and its druggability characteristics, which could be useful in the development of drugs to combat H. pylori infections.

A novel and efficient chemosensor 1 for detecting Cu2+ has recently been developed. However, the photophysical properties of chemosensor 1 and its response mechanism to Cu2+ are still unclear. Herein, the density functional theory and the time-dependent density functional theory approaches are implemented to investigate the excited state behavior of chemosensor 1 and its sensing mechanism for Cu2+ is revealed. Through constructing the potential energy curve with the dihedral angle of hydroxide radical as a variable, the irreversibility of the adjustment of the hydrogen proton direction is determined. This feature provides a favorable geometric configuration condition for the formation of intramolecular hydrogen bond. Moreover, the reduced density gradient analysis and topological analysis are performed to visualize the hydrogen bond strength, it is found that the hydrogen bond is enhanced in first singlet excited state (S1) compared with that in ground state (S0). The chemosensor 1 has only a low potential barrier in the S1 state, indicating that it could undergo an ultra-fast excited state intramolecular proton transfer (ESIPT) process. Furthermore, the reaction sites of chemosensor 1 and Cu2+ is theoretically predicted by the electrostatic potential analysis and the coordination mode of 1 + Cu2+-H+ is confirmed. Thus, we verify that the deprotonation inhibits the ESIPT behavior and leads to fluorescence quenching to achieve the recognition of chemosensor 1 to Cu2+. In addition, the binding energy of Cu2+ with chemosensor 1 is greater than that of Mg2+ and Zn2+, the high selectivity of chemosensor 1 to Cu2+ is illustrated. Our investigation clarifies the sensing mechanism of chemosensor 1 to Cu2+ based on inhibiting ultra-fast ESIPT process, which provides a theoretical basis for the development of new metal ion sensors.

This article uses quantum chemical methods and various wave function analysis methods to firstly analyze the optical absorption spectrum and electron migration mechanism of rhodamine 6G molecular complexes on graphene substrates during electron or hole injection. Secondly, since the light absorption properties are very important during photocatalysis, the intermolecular interaction and electronic structure in both cases were calculated and analyzed. Not only the experimental results of the previous photocatalytic devices were explained, but also the physical mechanism was promoted, and the guiding recommendations for the future catalytic device design.

The present study aimed to investigate the molecular mechanisms underlying glioblastoma multiform (GBM) and its biomarkers. The differentially expressed genes (DEGs) were diagnosed using the limma software package. The ToppGene (ToppFun) was used to perform pathway and Gene Ontology (GO) enrichment analysis of the DEGs. Protein-protein interaction (PPI) networks, extracted modules, miRNA-target genes regulatory network and TF-target genes regulatory network were used to obtain insight into the actions of DEGs. Survival analysis for DEGs was carried out. A total of 590 DEGs, including 243 up regulated and 347 down regulated genes, were diagnosed between scrambled shRNA expression and Lin7A knock down. The up-regulated genes were enriched in ribosome, mitochondrial translation termination, translation, and peptide biosynthetic process. The down-regulated genes were enriched in focal adhesion, VEGFR3 signaling in lymphatic endothelium, extracellular matrix organization, and extracellular matrix. The current study screened the genes in the PPI network, extracted modules, miRNA-target genes regulatory network, and TF-target genes regulatory network with higher degrees as hub genes, which included NPM1, CUL4A, YIPF1, SHC1, AKT1, VLDLR, RPL14, P3H2, DTNA, FAM126B, RPL34, and MYL5. Survival analysis indicated that the high expression of RPL36A and MRPL35 were predicting longer survival of GBM, while high expression of AP1S1 and AKAP12 were predicting shorter survival of GBM. High expression of RPL36A and AP1S1 were associated with pathogenesis of GBM, while low expression of ALPL was associated with pathogenesis of GBM. In conclusion, the current study diagnosed DEGs between scrambled shRNA expression and Lin7A knock down samples, which could improve our understanding of the molecular mechanisms in the progression of GBM, and these crucial as well as new diagnostic markers might be used as therapeutic targets for GBM.

2-(4-(Dimethylamino)phenyl)-3-hydroxy-6,7-dimethoxy-4Hchromen-4-one (HOF) was synthesized in experiment (Wang et al., Sensor. Actuat. B-Chem. 277 (2018) 484), and its photophysical and photochemical properties was reported. However the corresponding full theoretical interpretation of mechanisms is inadequate. In the present research, the intermolecular hydrogen bond structure of HOF-methanol complex (HOF-2M) was found, and mechanism of alcohols monitoring of HOF was deeply studied using the density functional theory (DFT) and time-dependent density functional theory (TDDFT). The enhancing mechanism of the excited state hydrogen bond is verified by analyzing the hydrogen bond parameters, infrared spectra and frontier molecular orbitals. Importantly, the reduced density gradient visual analysis and topological quantificational analysis confirm that the intramolecular hydrogen bond of HOF is broken by strong intermolecular hydrogen bonds of HOF-2M using the Atoms-In-Molecule theory. The obtained absorption and emission spectra are found to agree well with the experimental results and the complete quenched keto-emission in methanol and ethanol solvents provide a suitable sensing mechanism for detecting alcohols. The reaction path of the excited state intramolecular proton transfer for HOF is explained in detail through the constructed potential energy curves.

Isatin oxamohydrazide (L) reacted with the aqueous solution of silver nitrate at room temperature afforded the polymeric silver(I) nitrato complex, [Ag2L\'(NO3)2] n , (1) of the azine ligand (L\'). Similarly, the reaction of L with silver(I) perchlorate gave the [Ag2L\'2(ClO4)2] n , (2) coordination polymer. Careful inspection of the crystals from the nitrato complex preparation showed the presence of another crystalline product which is found to be [Ag(Isatin-3-hydrazone)NO3], (3) suggesting that the reaction between silver(I) nitrate and L proceeds first by the hydrolysis of L to the isatin hydrazone which attacks another molecule of L to afford L\'. Testing metal salts such as Ni2+, Co2+, Mn2+, Cu2+ and Cd2+ did not undergo any reaction with L either under the same reaction conditions or with heating under reflux up to 24 h. Treatment of the warm alcoholic solution of L with few drops of 1 : 1 (v/v) hydrochloric acid gave the free ligand (L\') in good yield. The [Ag2L\'(NO3)2] n complex forms a two-dimensional infinite coordination polymer, while the [Ag2L\'2(ClO4)2] n forms one-dimensional infinite chains with an alternating silver-azine backbone. Quantitative analysis of the intermolecular interactions in their crystals is made using Hirshfeld surface analysis. Density functional theory studies were performed to investigate the coordination bonding in the studied complexes.