Transcriptional Hubs Within Cliques in Ensemble Hi-C Chromatin Interaction Networks

Chromatin conformation capture technologies permit the study of chromatin spatial organization on a genome-wide scale at a variety of resolutions. Despite the increasing precision and resolution of high-throughput chromatin conformation capture (Hi-C) methods, it remains challenging to conclusively link transcriptional activity to spatial organizational phenomena. We have developed a clique-based approach for analyzing Hi-C data that helps identify chromosomal hotspots that feature considerable enrichment of chromatin annotations for transcriptional start sites and, building on previously published work, show that these chromosomal hotspots are not only significantly enriched in RNA polymerase II binding sites as identified by the ENCODE project, but also identify a noticeable increase in FANTOM5 and GTEx transcription within our identified cliques across a variety of tissue types. From the obtained data, we surmise that our cliques are a suitable method for identifying transcription factories in Hi-C data, and outline further extensions to the method that may make it useful for locating regions of increased transcriptional activity in datasets where in-depth expression or polymerase data may not be available.

Topological Analysis and Structural Determination of 3D Covalent Organic Frameworks

3D covalent organic frameworks (3D COFs) constitute a new type of crystalline materials that consist of a range of porous structures with numerous applications in the fields of adsorption, separation, and catalysis. However, because of the complexity of the three-periodic net structure, it is desirable to develop a thorough structural comprehension, along with a means to precisely determine the actual structure. Indeed, such advancements would considerably contribute to the rational design and application of 3D COFs. In this review, the reported topologies of 3D COFs are introduced and categorized according to the configurations of their building blocks, and a comprehensive overview of diffraction-based structural determination methods is provided. The current challenges and future prospects for these materials will also be discussed.

A Tiny Viral Protein, SARS-CoV-2-ORF7b: Functional Molecular Mechanisms

This study presents the interaction with the human host metabolism of SARS-CoV-2 ORF7b protein (43 aa), using a protein-protein interaction network analysis. After pruning, we selected from BioGRID the 51 most significant proteins among 2753 proven interactions and 1708 interactors specific to ORF7b. We used these proteins as functional seeds, and we obtained a significant network of 551 nodes via STRING. We performed topological analysis and calculated topological distributions by Cytoscape. By following a hub-and-spoke network architectural model, we were able to identify seven proteins that ranked high as hubs and an additional seven as bottlenecks. Through this interaction model, we identified significant GO-processes (5057 terms in 15 categories) induced in human metabolism by ORF7b. We discovered high statistical significance processes of dysregulated molecular cell mechanisms caused by acting ORF7b. We detected disease-related human proteins and their involvement in metabolic roles, how they relate in a distorted way to signaling and/or functional systems, in particular intra- and inter-cellular signaling systems, and the molecular mechanisms that supervise programmed cell death, with mechanisms similar to that of cancer metastasis diffusion. A cluster analysis showed 10 compact and significant functional clusters, where two of them overlap in a Giant Connected Component core of 206 total nodes. These two clusters contain most of the high-rank nodes. ORF7b acts through these two clusters, inducing most of the metabolic dysregulation. We conducted a co-regulation and transcriptional analysis by hub and bottleneck proteins. This analysis allowed us to define the transcription factors and miRNAs that control the high-ranking proteins and the dysregulated processes within the limits of the poor knowledge that these sectors still impose.

Investigating the X-aminopyridine (X = 2 and 3) molecules sensing by Al12N12 and B12N12 fullerene-like nanocages: DFT, QTAIM, RDG and TD-DFT insights

DeThe adsorption of 2-aminopyridine (2-AP) and 3-aminopyridine (3-AP) on the external surface of B12N12 and Al12N12 fullerene-like nanocages (FLNs) is probed herein via DFT/M06-2X/6-311G(d,p) level of theory. It came out from the study that all FLN@X-AP states investigated are spontaneously formed. Moreover, topological analysis demonstrated that the boron nitride FLN can strongly adsorbed the APs through B-N covalent interactions. A significant change in the HOMO-LUMO band gap of B12N12, with values of 22.01 and 32.71% have been obtained following the adsorption of 2-AP and 3-AP respectively. Accordingly, the conductivity of B12N12 is greatly enhanced by the adsorption of the APs. The above mentioned observations, combined with those found from the analysis of dipole moments and molecular electrostatic potential maps predict B12N12 to be more sensitive to the aminopyridines investigated than the Al12N12 FLN from the theoretical point of view.Communicated by Ramaswamy H. Sarma.

Artificial Intelligence as a Decision-Making Tool in Forensic Dentistry: A Pilot Study with I3M

Expert determination of the third molar maturity index (I3M) constitutes one of the most common approaches for dental age estimation. This work aimed to investigate the technical feasibility of creating a decision-making tool based on I3M to support expert decision-making. Methods: The dataset consisted of 456 images from France and Uganda. Two deep learning approaches (Mask R-CNN, U-Net) were compared on mandibular radiographs, leading to a two-part instance segmentation (apical and coronal). Then, two topological data analysis approaches were compared on the inferred mask: one with a deep learning component (TDA-DL), one without (TDA). Regarding mask inference, U-Net had a better accuracy (mean intersection over union metric (mIoU)), 91.2% compared to 83.8% for Mask R-CNN. The combination of U-Net with TDA or TDA-DL to compute the I3M score revealed satisfying results in comparison with a dental forensic expert. The mean ± SD absolute error was 0.04 ± 0.03 for TDA, and 0.06 ± 0.04 for TDA-DL. The Pearson correlation coefficient of the I3M scores between the expert and a U-Net model was 0.93 when combined with TDA and 0.89 with TDA-DL. This pilot study illustrates the potential feasibility to automate an I3M solution combining a deep learning and a topological approach, with 95% accuracy in comparison with an expert.

Age-Related Differences of Cortical Topology Across the Adult Lifespan: Evidence From a Multisite MRI Study With 1427 Individuals

BACKGROUND

Healthy aging is usually accompanied by alterations in brain network architecture, influencing information processing and cognitive performance. However, age-associated coordination patterns of morphological networks and cognitive variation are not well understood.

PURPOSE

To investigate the age-related differences of cortical topology in morphological brain networks from multiple perspectives.

STUDY TYPE

Prospective, observational multisite study.

POPULATION

A total of 1427 healthy participants (59.1% female, 51.75 ± 19.82 years old) from public datasets.

FIELD STRENGTH/SEQUENCE

1.5 T/3 T, T1-weighted magnetization prepared rapid gradient echo (MP-RAGE) sequence.

ASSESSMENT

The multimodal parcellation atlas was used to define regions of interest (ROIs). The Jensen-Shannon divergence-based individual morphological networks were constructed by estimating the interregional similarity of cortical thickness distribution. Graph-theory based global network properties were then calculated, followed by ROI analysis (including global/nodal topological analysis and hub analysis) with statistical tests.

STATISTICAL TESTS

Chi-square test, Jensen-Shannon divergence-based similarity measurement, general linear model with false discovery rate correction. Significance was set at P < 0.05.

RESULTS

The clustering coefficient (q = 0.016), global efficiency (q = 0.007), and small-worldness (q = 0.006) were significantly negatively quadratic correlated with age. The group-level hubs of seven age groups were found mainly distributed in default mode network, visual network, salient network, and somatosensory motor network (the sum of these hubs' distribution in each group exceeds 55%). Further ROI-wise analysis showed significant nodal trajectories of intramodular connectivities.

DATA CONCLUSION

These results demonstrated the age-associated reconfiguration of morphological networks. Specifically, network segregation/integration had an inverted U-shaped relationship with age, which indicated age-related differences in transmission efficiency.

EVIDENCE LEVEL

2 TECHNICAL EFFICACY: Stage 1.

Computational Simulations of Fabrication of Aluminum-Based Josephson Junctions: Topological Aspects of the Barrier Structure

Although the performance of qubits has been improved in recent years, the differences in the microscopic atomic structure of the Josephson junctions, the core devices prepared under different preparation conditions, are still underexplored. In this paper, the effects of the oxygen temperature and upper aluminum deposition rate on the topology of the barrier layer in the aluminum-based Josephson junctions have been presented by classical molecular dynamics simulations. We apply a Voronoi tessellation method to characterize the topology of the interface and central regions of the barrier layers. We find that when the oxygen temperature is 573 K and the upper aluminum deposition rate is 4 Å/ps, the barrier has the fewest atomic voids and the most closely arranged atoms. However, if only the atomic arrangement of the central region is considered, the optimal rate of the aluminum deposition is 8 Å/ps. This work provides microscopic guidance for the experimental preparation of Josephson junctions, which helps to improve the performance of qubits and accelerate the practical application of quantum computers.

Anti-Symmetric Electromagnetic Interactions' Response in Electron Circular Dichroism and Chiral Origin of Periodic, Complementary Twisted Angle in Twisted Bilayer Graphene

Many novel physical properties of twisted bilayer graphene have been discovered and studied successively, but the physical mechanism of the chiral modulation of BLG by a twisted angle lacks theoretical research. In this work, the density functional theory, the wavefunction analysis of the excited state, and the quantum theory of atoms in molecules are used to calculate and analyze the anti-symmetric chiral characteristics of zigzag-edge twisted bilayer graphene quantum dots based on periodic complementary twisted angles. The analysis of the partial density of states shows that Moiré superlattices can effectively adjust the contribution of the atomic basis function of the fragment to the transition dipole moment. The topological analysis of electron density indicates that the Moiré superlattices structure can enhance the localization of the system, increasing the electron density of the Moiré central ring, reducing the electron surge capacity in general and inducing the reversed helical properties of the top and underlying graphene, which can be used as the origin of the chiral discrimination; it also reveals the mole in the superlattice chiral physical mechanism. On this basis, we will also study the nonlinear optical properties of twisted bilayer graphene based on a twisted angle.

Distinct brain structural-functional network topological coupling explains different outcomes in tinnitus patients treated with sound therapy

Topological properties, which serve as the core of the neural network, and their couplings can reflect different therapeutic effects in tinnitus patients. We hypothesized that tinnitus patients with different outcomes after sound therapy (narrowband noise) would have distinct brain network topological alterations. Diffusion tensor imaging and resting‐state functional magnetic resonance imaging (fMRI) were prospectively performed in 60 patients with idiopathic tinnitus and 57 healthy controls (HCs). Graph‐theoretical network analyses of structural connectivity (SC), functional connectivity (FC), and SC and FC coupling were performed. Associations between clinical performance and graph‐theoretical features were also analyzed. Treatment was effective (effective group; EG) in 28 patients and ineffective (ineffective group; IG) in 32 patients. For FC, the patients in the EG showed higher local efficiency than patients in the IG. For SC, patients in both the EG and IG displayed lower normalized characteristic path length, characteristic path length, and global efficiency than the HCs. More importantly, patients in the IG had higher coupling than the HCs, whereas there was no difference in coupling between patients in the EG and HCs. Additionally, there were significant associations between the SC features and clinical performance in patients in the EG. Our findings demonstrate that tinnitus patients exhibited significant brain network topological alterations, especially in the structural brain network. More importantly, patients who demonstrated different curative effects showed distinct SC‐FC topological coupling properties. SC‐FC coupling could be an indicator that could be used to predict prognoses in patients with idiopathic tinnitus before sound therapy.

Two Tautomers of Thiobarbituric Acid in One Crystal: The Experimental Charge Density Perspective

High-quality crystals of a certain polymorphic form of thiobarbituric acid containing both keto and enol tautomers in the asymmetric unit were obtained. High-resolution X-ray diffraction data up to sinθ/λ = 1.0 Å^-1 were collected and subsequently successfully used for the refining of the multipolar model of electron density distribution. The use of a crystal containing both ketone and enol forms allowed a direct comparison of the topological analysis results and a closer look at the differences between these two forms. The similarities and differences between the deformation densities, electrostatic potentials, Laplacian maps and bond characteristics of the tautomers were analysed. Additionally, the spectrum of the intermolecular interactions was identified and studied from classical, relatively strong N-H···O and O-H···O hydrogen bonds through weaker N-H···S hydrogen bonds to weak interactions (for instance, C-H···O, C-H···S and N···O). The results of these studies point toward the importance of including both the geometrical features and the details of the electron density distribution in the analysis of such weak interactions.

A Network Pharmacology Study on the Molecular Mechanism of Protocatechualdehyde in the Treatment of Diabetic Cataract

Purpose

Protocatechualdehyde (PCA) is a phenolic compound found in the roots of Salvia miltiorrhiza with anti-proliferative and antioxidant activities. At present, there are few studies on protocatechualdehyde against diabetic cataract (DC), and there is also lack of systematic research on the mechanism of protocatechualdehyde. Therefore, this study tried to comprehensively clarify the targets and complex mechanisms of PCA against DC from the perspective of network pharmacology.

Materials and Methods

Through collecting relevant targets from the databases, GO and KEGG enrichment analysis were performed on the potential targets. Moreover, core genes were identified by topological analysis of protein-protein interaction (PPI) network and gene-phenotype correlation analysis.

Results

The results indicated that protocatechualdehyde may be closely related to targets such as AKT1, MAPK3 and HDAC3, as well as signal pathways such as MAPK signaling pathway, PI3K-Akt signaling pathway and AGE-RAGE signaling pathway in diabetic complications.

Conclusion

Together, the present study systematically clarified the possible mechanisms of protocatechualdehyde in the treatment of diabetic cataract and provided new ideas for the drug research of this disease.

Network Pharmacology-Based Analysis on the Potential Biological Mechanisms of Sinisan Against Non-Alcoholic Fatty Liver Disease

Non-alcoholic fatty liver disease (NAFLD) has become the most prevalent liver disease in China. Sinisan (SNS) is a traditional Chinese medicine formula that has been widely used in treating chronic liver diseases, including NAFLD. However, its underlying biological mechanisms are still unclear. In this study, we employed a network pharmacology approach consisting of overlapped terms- (genes or pathway terms-) based analysis, protein-protein interaction (PPI) network-based analysis, and PPI clusters identification. Unlike the previous network pharmacology study, we used the shortest path length-based network proximity algorithm to evaluate the efficacy of SNS against NAFLD. And we also used random walk with restart (RWR) algorithm and Community Cluster (Glay) algorithm to identify important targets and clusters. The screening results showed that the mean shortest path length between genes of SNS and NAFLD was significantly smaller than degree-matched random ones. Six PPI clusters were identified and ten hub targets were obtained, including STAT3, CTNNB1, MAPK1, MAPK3, AGT, NQO1, TOP2A, FDFT1, ALDH4A1, and KCNH2. The experimental study indicated that SNS reduced hyperlipidemia, liver steatosis, and inflammation. Most importantly, JAK2/STAT3 signal was inhibited by SNS treatment and was recognized as the most important signal considering the network pharmacology part. This study provides a systems perspective to study the relationship between Chinese medicines and diseases and helps to discover potential mechanisms by which SNS ameliorates NAFLD.

Scaling Up DNA Origami Lattice Assembly

The surface-assisted hierarchical assembly of DNA origami nanostructures is a promising route to fabricate regular nanoscale lattices. In this work, the scalability of this approach is explored and the formation of a homogeneous polycrystalline DNA origami lattice at the mica-electrolyte interface over a total surface area of 18.75 cm2 is demonstrated. The topological analysis of more than 50 individual AFM images recorded at random locations over the sample surface showed only minuscule and random variations in the quality and order of the assembled lattice. The analysis of more than 450 fluorescence microscopy images of a quantum dot-decorated DNA origami lattice further revealed a very homogeneous surface coverage over cm2 areas with only minor boundary effects at the substrate edges. At total DNA costs of € 0.12 per cm2 , this large-scale nanopatterning technique holds great promise for the fabrication of functional surfaces.

Novel Ba2+ and Pb2+ metal-organic frameworks based on a semi-rigid tetracarboxylic acid: syntheses, structures, topologies and luminescence properties

Multidentate carboxylate ligands have been widely used in the construction of metal-organic frameworks (MOFs) owing to the rich variety of their coordination modes, which can lead to crystalline products with interesting structures and properties. Two new main-group MOFs, namely, poly[[di-μ-aqua-diaqua(dimethylformamide)[μ₇-5,5'-methylenebis(2,4,6-trimethylbenzene-1,3-dicarboxylato)]dibarium(II)] trihydrate], {[Ba₂(C₂₃H₂₀O₈)(C₃H₇NO)(H₂O)₄]·3H₂O}_n or {[Ba₂(BTMIPA)(DMF)(H₂O)₄]·3H₂O}_n (1), and poly[[diaqua[μ₆-5,5'-methylenebis(2,4,6-trimethylbenzene-1,3-dicarboxylato)]dilead(II)] 2.5-hydrate], {[Pb₂(C₂₃H₂₀O₈)(H₂O)₂]·2.5H₂O}_n or {[Pb₂(BTMIPA)(H₂O)₂]·2.5H₂O}_n (2), were prepared by the self-assembly of metal salts with the semi-rigid tetracarboxylic acid ligand 5,5'-methylenebis(2,4,6-trimethylisophthalic acid) (H₄BTMIPA). Both structures were characterized by elemental analysis (EA), single-crystal X-ray diffraction, powder X-ray diffraction (PXRD), IR spectroscopy and thermogravimetric analysis (TGA). Complex 1 reveals a three-dimensional (3D) flu network formed via bridging tetranuclear secondary building units (SBUs) and complex 2 displays a 3D framework with an sqp topology based on one-dimensional metal chains. The BTMIPA^4- ligands adopt a rare coordination mode in 2, although the ligands in both 1 and 2 are X-shaped. The luminescence properties of both complexes were investigated in the solid state.

Weak Intermolecular Interactions in a Series of Bioactive Oxazoles

The intermolecular interactions in a series of nine similar 4,5-phenyl-oxazoles were studied on the basis of crystal structures determined by X-ray diffraction. The crystal architectures were analyzed for the importance and hierarchies of different, weak intermolecular interactions using three approaches: the geometrical characteristics, topological analysis (for the model based on the transfer of multipolar parameters), and energetics of the molecule–molecule interactions. The geometries of the molecules were quite similar and close to the typical values. The results of the analysis of the interactions suggest that the number of nonspecific interactions is more important than the apparent strength of the specific interactions. The interactions involving covalently bound bromine and divalent sulfur atoms were classified as secondary, they certainly did not define the crystal packing, and they played a minor role in the overall crystal cohesion energies. Incidentally, another method for confirming the degree of isostructurality, according to the topologies of the interactions, is described.

Construction and topological analysis of an endometriosis-related exosomal circRNA-miRNA-mRNA regulatory network

Novel biomarkers are needed to accelerate the diagnosis and treatment of endometriosis. We performed RNA sequencing to explore the expression profiles of exosomal circular RNAs (circRNAs), microRNAs (miRNAs) and mRNAs in patients with ovarian endometriomas, eutopic endometria and normal endometria. Differentially expressed genes between the different pairs of groups were analyzed and functionally annotated. Then, miRNA-target RNA pairs were identified, competing endogenous RNA (ceRNA) scores were calculated, gene expression characteristics were determined, and these parameters were used to construct an exosomal ceRNA network. We identified 36 candidate hub genes with high degrees of gene connectivity. We also topologically analyzed the ceRNA network to obtain a hub ceRNA network of circRNAs with the highest closeness and ceRNA efficiency. Twelve genes overlapped between the 36 candidate hub genes and the genes in the hub ceRNA network. These 12 genes were considered to be exosomal RNA-based biomarkers, and circ_0026129/miRNA-15a-5p/ATPase H+ transporting V1 subunit A (ATP6V1A) were at the center of the ceRNA network. By determining the exosomal RNA expression profiles of endometriosis patients and constructing a circRNA-associated ceRNA network, these findings provide insight into the molecular pathways of endometriosis and new resources for its diagnosis and treatment.

Identification of the Key Regulators of Spina Bifida Through Graph-Theoretical Approach

Spina Bifida (SB) is a congenital spinal cord malformation. Efforts to discern the key regulators (KRs) of the SB protein-protein interaction (PPI) network are requisite for developing its successful interventions. The architecture of the SB network, constructed from 117 manually curated genes was found to self-organize into a scale-free fractal state having a weak hierarchical organization. We identified three modules/motifs consisting of ten KRs, namely, TNIP1, TNF, TRAF1, TNRC6B, KMT2C, KMT2D, NCOA3, TRDMT1, DICER1, and HDAC1. These KRs serve as the backbone of the network, they propagate signals through the different hierarchical levels of the network to conserve the network’s stability while maintaining low popularity in the network. We also observed that the SB network exhibits a rich-club organization, the formation of which is attributed to our key regulators also except for TNIP1 and TRDMT1. The KRs that were found to ally with each other and emerge in the same motif, open up a new dimension of research of studying these KRs together. Owing to the multiple etiology and mechanisms of SB, a combination of several biomarkers is expected to have higher diagnostic accuracy for SB as compared to using a single biomarker. So, if all the KRs present in a single module/motif are targetted together, they can serve as biomarkers for the diagnosis of SB. Our study puts forward some novel SB-related genes that need further experimental validation to be considered as reliable future biomarkers and therapeutic targets.

Plant multiscale networks: charting plant connectivity by multi-level analysis and imaging techniques

In multicellular and even single-celled organisms, individual components are interconnected at multiscale levels to produce enormously complex biological networks that help these systems maintain homeostasis for development and environmental adaptation. Systems biology studies initially adopted network analysis to explore how relationships between individual components give rise to complex biological processes. Network analysis has been applied to dissect the complex connectivity of mammalian brains across different scales in time and space in The Human Brain Project. In plant science, network analysis has similarly been applied to study the connectivity of plant components at the molecular, subcellular, cellular, organic, and organism levels. Analysis of these multiscale networks contributes to our understanding of how genotype determines phenotype. In this review, we summarized the theoretical framework of plant multiscale networks and introduced studies investigating plant networks by various experimental and computational modalities. We next discussed the currently available analytic methodologies and multi-level imaging techniques used to map multiscale networks in plants. Finally, we highlighted some of the technical challenges and key questions remaining to be addressed in this emerging field.

Gene Set Enrichment Analysis of Interaction Networks Weighted by Node Centrality

Gene set enrichment analysis (GSEA) is a powerful tool to associate a disease phenotype to a group of genes/proteins. GSEA attributes a specific weight to each gene/protein in the input list that depends on a metric of choice, which is usually represented by quantitative expression data. However, expression data are not always available. Here, GSEA based on betweenness centrality of a protein–protein interaction (PPI) network is described and applied to two cases, where an expression metric is missing. First, personalized PPI networks were generated from genes displaying alterations (assessed by array comparative genomic hybridization and whole exome sequencing) in four probands bearing a 16p13.11 microdeletion in common and several other point variants. Patients showed disease phenotypes linked to neurodevelopment. All networks were assembled around a cluster of first interactors of altered genes with high betweenness centrality. All four clusters included genes known to be involved in neurodevelopmental disorders with different centrality. Moreover, the GSEA results pointed out to the evidence of “cell cycle” among enriched pathways. Second, a large interaction network obtained by merging proteomics studies on three neurodegenerative disorders was analyzed from the topological point of view. We observed that most central proteins are often linked to Parkinson’s disease. The selection of these proteins improved the specificity of GSEA, with “Metabolism of amino acids and derivatives” and “Cellular response to stress or external stimuli” as top-ranked enriched pathways. In conclusion, betweenness centrality revealed to be a suitable metric for GSEA. Thus, centrality-based GSEA represents an opportunity for precision medicine and network medicine.

Identification of Functional lncRNAs Associated With Ovarian Endometriosis Based on a ceRNA Network

Background

Endometriosis is a common gynecological disease affecting women of reproductive age; however, the mechanisms underlying this condition are not fully clear. The aim of this study was to identify functional long non-coding RNAs (lncRNAs) associated with ovarian endometriosis for potential use as biomarkers and therapeutic targets.

Methods

RNA-seq profiles of paired ectopic (EC) and eutopic (EU) endometrial samples from patients with ovarian endometriosis were downloaded from the publicly available Gene Expression Omnibus (GEO) database. Bioinformatics algorithms were used to construct a network of ovarian endometriosis-related competing endogenous RNAs (ceRNAs) and to detect functional lncRNAs.

Results

A total of 4,213 mRNAs, 1,474 lncRNAs, and 221 miRNAs were identified as being differentially expressed between EC and EU samples, and an ovarian endometriosis-related ceRNA network was constructed through analysis of these differentially expressed RNAs. H19 and GS1-358P8.4 were identified as key ovarian endometriosis-related lncRNAs through topological feature analysis, and RP11-96D1.10 was identified using a random walk with restart algorithm.

Conclusion

Based on bioinformatics analysis of a ceRNA network, we identified the lncRNAs H19, GS1-358P8.4, and RP11-96D1.10 as being strongly associated with ovarian endometriosis. These three lncRNAs hold potential as targets for medical therapy and as diagnostic biomarkers. Further studies are needed to elucidate the detailed biological function of these lncRNAs in the pathogenesis of endometriosis.

Topological analysis of chemical bonding in the layered FePSe3 upon pressure-induced phase transitions

Two pressure-induced phase transitions have been theoretically studied in the layered iron phosphorus triselenide (FePSe₃ ). Topological analysis of chemical bonding in FePSe₃ has been performed based on the results of first-principles calculations within the periodic linear combination of atomic orbitals (LCAO) method with hybrid Hartree-Fock-DFT B3LYP functional. The first transition at about 6 GPa is accompanied by the symmetry change from R 3 ¯ to C2/m, whereas the semiconductor-to-metal transition (SMT) occurs at about 13 GPa leading to the symmetry change from C2/m to P 3 ¯ 1 m . We found that the collapse of the band gap at about 13 GPa occurs due to changes in the electronic structure of FePSe₃ induced by relative displacements of phosphorus or selenium atoms along the c-axis direction under pressure. The results of the topological analysis of the electron density and its Laplacian demonstrate that the pressure changes not only the interatomic distances but also the bond nature between the intralayer and interlayer phosphorus atoms. The interlayer P-P interactions are absent in two non-metallic FePSe₃ phases while after SMT the intralayer P-P interactions weaken and the interlayer P-P interactions appear.

Seven new metal-organic frameworks assembled from semi-rigid polycarboxylate and auxiliary N-donor ligands: syntheses, structures and properties

Seven new metal-organic frameworks (MOFs), namely, [Zn₂(L¹)(H₂O)₃]_n (1), [Zn₂(L¹)(dib)(H₂O)₂]_n (2), {[Zn₂(L¹)(4,4'-bipy)(H₂O)₂]·H₂O}_n (3), [Cd₂(L¹)(1,10-phen)]_n (4), [Ni₂(HL¹)(4,4'-bipy)(μ₃-OH)(μ₂-H₂O)]_n (5), {[Co₄(L¹)(4,4'-bibp)₃]·(4,4'-bibp)₃}_n (6), and [Co₂(L²)(4,4'-bibp)₂(H₂O)]_n (7), where H₄L¹ and H₄L² are semi-rigid 3-(3,5-dicarboxylphenoxy)phthalic acid and 4-(3,5-dicarboxylphenoxy)phthalic acid, respectively, and 4,4'-bipy is 4,4'-bipyridine, dib is 1,4-bis(1H-imidazol-1-yl)benzene, 1,10-phen is 1,10-phenanthroline and 4,4'-bipb is 1,4-bis(pyridin-4-yl)benzene, have been prepared under solvothermal conditions with Zn^II, Cd^II, Co^II and Ni^II ions in the presence of auxiliary N-donor ligands. The crystal structures and photoluminescence and magnetic properties of these compounds have been investigated. Compound 1 displays a 3,4,6-connected two-dimensional (2D) topology with a Schläfli symbol of (4².5)₂(4³.5².7)(4⁵.5⁶.6³)₂, and the 2D structure was further assembled to form a three-dimensional (3D) framework by intermolecular O-H...O hydrogen bonds. Compound 2 features a novel 3,3,4-connected structure and the point symbol is (4.10²)(4.6.8⁴)(6².8). Compound 3 exhibits a 3,4,6-connected 3-nodal net having a 3,4,6 T53 type topology, with the point symbol (4.6²)₂(4².6⁴)₂(4².6⁸.8².10³). Compound 4 shows a 2D→3D supramolecular structure formed by π-π stacking interactions. Compound 5 possesses a 3D framework with a tfz-d net topology. Compounds 6 and 7 are constructed from the same auxiliary ligand and metal salt at the same temperature, but with different main ligands and exhibiting different topologies. Compound 6 presents a 3D 4,6-connected topological network with a Schläfli symbol of (3.4⁴.6)(3².4⁴.5⁶.6³), while compound 7 has a 3D topological network with a Schläfli symbol of (4¹².6¹⁶). Magnetic analyses indicate that compounds 5 and 7 show weak antiferromagnetic interactions.

Biosensing Cytokine IL-6: A Comparative Analysis of Natural and Synthetic Receptors

Cytokines are a family of proteins which play a major role in the regulation of the immune system and the development of several diseases, from rheumatoid arthritis to cancer and, more recently, COVID-19. Therefore, many efforts are currently being developed to improve therapy and diagnosis, as well as to produce inhibitory drugs and biosensors for a rapid, minimally invasive, and effective detection. In this regard, even more efficient cytokine receptors are under investigation. In this paper we analyze a set of IL-6 cytokine receptors, investigating their topological features by means of a theoretical approach. Our results suggest a topological indicator that may help in the identification of those receptors having the highest complementarity with the protein, a feature expected to ensure a stable binding. Furthermore, we propose and discuss the use of these receptors in an idealized experimental setup.

Bringing a New Flexible Mercaptoacetic Acid Linker to the Design of Coordination Polymers

Two new 3D coordination polymers (CPs), formulated as [Zn(p-XBT)]_n (1H) and [Cd(p-XBT)]_n (2H), were assembled from a virtually unexplored p-xylylene-bis(2-mercaptoacetic) acid linker (p-XBTA) and characterized by infrared spectroscopy (FTIR), powder X-ray diffraction (PXRD), thermal analysis methods (TG-DSC, TG-FTIR), single-crystal X-ray diffraction, and topological analysis. Two different synthetic strategies were explored, namely the precipitation (P) and hydrothermal (H) methods, resulting in a Zn(II) derivative [Zn(p-XBT)·H₂O]_n (1P) and its dehydrated analogue [Zn(p-XBT)]_n (1H), respectively. In the Cd(II)-containing system, the same [Cd(p-XBT)]_n (2P = 2H) products were generated by both synthetic methods. Upon dehydration, 1P undergoes a “crystal-to-crystal” phase transition in the 170−185 °C temperature range, producing an anhydrous polycrystalline sample (1H). Both CPs 1H and 2H are isostructural and feature polymeric 3D metal-organic nets of the cds topological type, which are driven by the 4-linked metal and p-XBT²⁻ nodes. These compounds represent unique examples of coordination polymers derived from p-xylylene-bis(2-mercaptoacetic) acid, thus opening up the use of this flexible S,O-heterodonor building block in the design of polymeric metal-organic architectures.

Two ZnII-based MOFs constructed with biphenyl-2,2',5,5'-tetracarboxylic acid and flexible N-donor ligands: syntheses, structures and properties

Two new Zn²⁺-based metal-organic frameworks (MOFs) based on biphenyl-2,2',5,5'-tetracarboxylic acid, i.e. H₄(o,m-bpta), and N-donor ligands, namely, poly[[(μ₄-biphenyl-2,2',5,5'-tetracarboxylato)bis{[1,3-phenylenebis(methylene)]bis(1H-imidazole)}dizinc(II)] dimethylformamide monosolvate dihydrate], {[Zn₂(C₁₆H₆O₈)(C₁₄H₁₄N₄)₂]·C₃H₇NO·2H₂O}_n or {[Zn₂(o,m-bpta)(1,3-bimb)₂]·C₃H₇NO·2H₂O}_n (1) {1,3-bimb = [1,3-phenylenebis(methylene)]bis(1H-imidazole)}, and poly[[(μ₄-biphenyl-2,2',5,5'-tetracarboxylato)bis{[1,4-phenylenebis(methylene)]bis(1H-imidazole)}dizinc(II)] monohydrate], {[Zn₂(C₁₆H₆O₈)(C₁₄H₁₄N₄)₂]·H₂O}_n or {[Zn₂(o,m-bpta)(1,4-bimb)₂]·H₂O}_n (2) {1,4-bimb = [1,4-phenylenebis(methylene)]bis(1H-imidazole)}, have been synthesized under solvothermal conditions. The complexes were characterized by IR spectroscopy, elemental analysis, single-crystal X-ray diffraction and powder X-ray diffraction analysis. Structurally, the (o,m-bpta)^4- ligands are fully deprotonated and combine with Zn²⁺ ions in μ₄-coordination modes. Complex 1 is a (3,4)-connected porous network with honeycomb-like [Zn₂(o,m-bpta)]_n sheets formed by 4-connected (o,m-bpta)^4- ligands. Complex 2 exhibits a (2,4)-connected network formed by 4-connected (o,m-bpta)^4- ligands linking Zn²⁺ ions in left-handed helical chains. The cis-configured 1,3-bimb and 1,4-bimb ligands bridge Zn²⁺ ions to form multi-membered [Zn₂(bimb)₂] loops. Optically, the complexes show strong fluorescence and display larger red shifts compared to free H₄(o,m-bpta). Complex 2 shows ferroelectric properties due to crystallizing in the C_2v polar point group.

An Integrative Pharmacology-Based Analysis of Refined Qingkailing Injection Against Cerebral Ischemic Stroke: A Novel Combination of Baicalin, Geniposide, Cholic Acid, and Hyodeoxycholic Acid

Stroke is the second leading cause of death after heart disease globally and cerebral ischemic stroke accounts for approximately 70% of all incident stroke cases. We selected four main compounds from a patent Chinese medicine, Qingkailing (QKL) injection, including baicalin from Scutellaria baicalensis Georgi (Huang Qin), geniposide from Gardenia jasminoides J. Ellis (Zhizi), and cholic acid and hyodeoxycholic acid from Bovis Calculus (Niuhuang) with a ratio of 4.4:0.4:3:2.6 m/m, to develop a more efficacious and safer modern Chinese medicine injection against ischemic stroke, refined QKL (RQKL). In this study, we investigated multiple targets, levels, and pathways of RQKL by using an integrative pharm\acology combining experimental validation approach. In silica study showed that RQKL may regulate PI3K-Akt, estrogen, neurotrophin, HIF-1, MAPK, Hippo, FoxO, TGF-beta, NOD-like receptor, apoptosis, NF-kappa B, Wnt, chemokine, TNF, Toll-like receptor signaling pathways against ischemic stroke. The experimental results showed that RQKL improved neurological function and prevented infract volume and blood-brain-barrier damage. RQKL inhibited microgliosis and astrogliosis, and protected neurons from ischemic/reperfusion injury. RQKL also inhibited cell apoptosis and affecting the ratio of the anti-apoptosis protein B-cell lymphoma-2 (Bcl2) and pro-apoptosis protein Bcl2-associated X protein (Bax). Western blot analysis showed that RQKL activated AKT/PI3K signaling pathway and antibody array showed RQKL inhibited inflammatory response and decreased proinflammatory factor Tnf, Il6, and Il1b, and chemokines Ccl2, Cxcl2, and Cxcl3, and increased anti-inflammatory cytokine Il10. In conclusion, RQKL protected tissue against ischemic stroke through multiple-target, multiple signals, and modulating multiple cell-types in brain. This study not only promoted our understanding of the role of RQKL against ischemic stroke, but also provided a pattern for the study of Chinese medicine combining pharmaceutical Informatics and system biology methods.

Metal-directed supramolecular architectures based on the bifunctional ligand 2,5-bis(1H-1,2,4-triazol-1-yl)terephthalic acid

By the solvothermal reactions of 2,5-bis(1H-1,2,4-triazol-1-yl)terephthalic acid (H₂L) with transition-metal ions, two novel polymeric complexes, namely, poly[diaqua[μ₄-2,5-bis(1H-1,2,4-triazol-1-yl)terephthalato]cobalt(II)], [Co(C₁₂H₆N₆O₄)(H₂O)₂]_n, (1), and poly[[diaqua[μ₄-2,5-bis(1H-1,2,4-triazol-1-yl)terephthalato]nickel(II)] dihydrate], {[Ni(C₁₂H₆N₆O₄)(H₂O)₂]·2H₂O}_n, (2), were isolated. Both polymers have been characterized by FT-IR spectroscopy, elemental analysis and single-crystal X-ray diffraction analysis. The complexes have similar two-dimensional layered structures and coordination modes. Furthermore, the two-dimensional layered structures bear distinct intermolecular hydrogen-bonding interactions and π-π stacking interactions to form two different three-dimensional supramolecular networks based on 4⁴-subnets. The structural variation depends on the nature of the metal cations. The results of variable-temperature magnetization measurements (χ_MT-T and χ_M^-1-T) show that complexes (1) and (2) display antiferromagnetic behaviour.

One-pot concomitant preparation of two copper(II) coordination polymers with different configurations of bridging bithiophene ligands

By employing the conjugated bithiophene ligand 5,5'-bis(1H-imidazol-1-yl)-2,2'-bithiophene (bibp), which can exhibit trans and cis conformations, two different Cu^II coordination polymers, namely, poly[[μ-5,5'-bis(1H-imidazol-1-yl)-2,2'-bithiophene-κ²N:N'](μ₂-4,4'-oxydibenzoato-κ²O:O')copper(II)], [Cu(C₁₄H₈O₅)(C₁₄H₁₀N₄S₂)]_n or [Cu(bibp)(oba)]_n, (I), and catena-poly[μ-aqua-bis[μ-5,5'-bis(1H-imidazol-1-yl)-2,2'-bithiophene-κ²N:N']bis(μ₃-4,4'-oxydibenzoato)-κ³O:O':O'';κ⁴O:O',O'':O'-dicopper(II)], [Cu₂(C₁₄H₈O₅)₂(C₁₄H₁₀N₄S₂)(H₂O)]_n or [Cu₂(bibp)(oba)₂(H₂O)]_n, (II), have been prepared through one-pot concomitant crystallization and characterized by single-crystal X-ray diffraction, IR spectroscopy, elemental analysis, powder X-ray diffraction (PXRD) and thermogravimetric (TG) analysis. Single-crystal X-ray diffraction indicates that the most interesting aspect of the structure is the existence of sole trans and cis conformations of the bibp ligand in a single net of (I) and (II), respectively. Compound (I) displays a threefold interpenetrating three-dimensional framework with a 4-connected {6⁵.8} cds topology, whereas (II) features a one-dimensional chain structure. In the crystal of (II), the polymeric chains are further extended through C-H...O hydrogen bonds and C-H...π interactions into a three-dimensional supramolecular architecture. In addition, strong intramolecular O-H...O hydrogen bonds formed between the bridging water molecules and the carboxylate O atoms improve the stability of the framework of (II). Furthermore, solid-state UV-Vis spectroscopy experiments show that compounds (I) and (II) exhibit optical band gaps which are characteristic for optical semiconductors, with values of 2.70 and 2.26 eV, respectively.

Europium-Functionalized Flexible Luminescent Zeolite-like Supramolecular Assembly for Ratiometric Anthrax Biomarker Determination

Anthrax spores have been a determining risk to human beings and animals across the world. As such, the qualitative monitoring toward dipicolinic acid (DPA), the unique biomarker of bacillus anthracis, is highly desired and being moved forward in health management. Herein, a breathing zeolite-like supramolecular assembly (ZSA), with the sra topology and 1D hexagon channel, is designed by controlling the bridging angle of the ditopic ligand after systematic analysis in topology. The solvent-dependent dynamic behavior is illustrated by powder X-ray diffraction and reflected in tunable luminescent emission based on solvent polarity parameters. According to the structural result and theoretical analysis, Eu³⁺ is anchored within the framework to form a ratiometric luminescent sensor successfully because of the abundant potential active site. After DPA addition, the resulting composite shows a sensitive and selective response in the linear range of 0-7.0 μM stemmed from absorbance energy-transfer emission and preferential coordination. The work we presented here may enrich the sensing platforms containing lanthanides and expand the potential application of ZSAs in clinical analysis.

Identification of cancer/testis antigen 2 gene as a potential hepatocellular carcinoma therapeutic target by hub gene screening with topological analysis

The 5-year survival rate of hepatocellular carcinoma (HCC) is <20%; thus, identifying new potential therapeutic targets or novel biomarkers for prognosis prediction is crucial. The present study aimed to screen hub genes by constructing protein-protein interaction (PPI) subnetworks using topological analysis methods, as well as reveal their clinical significance through big data analytics and their association with the clinicopathological features. Firstly, the PPI subnetworks were constructed using four topological analysis methods, including the MCC, DMNC, MNC and degree methods, to obtain 6 hub genes. Subsequently, the hub gene cancer/testis antigen 2 (CTAG2), which affects the prognosis of HCC (overall survival, P=0.035), was acquired by analysing clinical data in The Cancer Genome Atlas database. Meanwhile, CTAG2 expression was significantly associated with the age at diagnosis (P=0.003), T stage (P=0.028), TNM stage (P=0.028) and α-fetoprotein (AFP) expression (P=0.045). Further immunohistochemical analysis of samples collected in our hospital revealed that the expression level of CTAG2 in 46 HCC tissues was significantly higher in comparison with that in paired adjacent tissues. The clinical data indicated that the expression of CTAG2 was significantly correlated with the hepatitis B virus status (P=0.010) and AFP expression (P=0.004). These results were then found to be consistent with the results of big data analytics. Furthermore, Gene Set Enrichment Analysis demonstrated that the function of CTAG2 in HCC may be associated with the cell cycle. Taken together, these findings suggest that CTAG2 may serve as a new potential therapeutic target for HCC patients.

Synthesis, structure and photocatalytic degradation of organic dyes of a copper(II) metal-organic framework (Cu-MOF) with a 4-coordinated three-dimensional CdSO4 topology

Metal-organic frameworks (MOFs) have attracted much interest in the fields of gas separation and storage, catalysis synthesis, nonlinear optics, sensors, luminescence, magnetism, photocatalysis gradation and crystal engineering because of their diverse properties and intriguing topologies. A Cu-MOF, namely poly[[(μ₂-succinato-κ²O:O'){μ₂-tris[4-(1,2,4-triazol-1-yl)phenyl]amine-κ²N:N'}copper(II)] dihydrate], {[Cu(C₄H₄O₄)(C₂₄H₁₈N₁₀)]·2H₂O}_n or {[Cu(suc)(ttpa)]·2H₂O}_n, (I), was synthesized by the hydrothermal method using tris[4-(1,2,4-triazol-1-yl)phenyl]amine (ttpa) and succinate (suc^2-), and characterized by IR, powder X-ray diffraction (PXRD), luminescence, optical band gap and valence band X-ray photoelectron spectroscopy (VB XPS). Cu-MOF (I) shows a twofold interpenetrating 4-coordinated three-dimensional CdSO₄ topology with point symbol {6⁵·8}. It presents good photocatalytic degradation of methylene blue (MB) and rhodamine B (RhB) under visible-light irradiation. A photocatalytic mechanism was proposed and confirmed.

Two CoII coordination polymers of biphenyl-2,2',5,5'-tetracarboxylic acid with flexible N-donor ligands: syntheses, structures and magnetic properties

Two Co^II-based coordination polymers, namely poly[(μ₄-biphenyl-2,2',5,5'-tetracarboxylato){μ₂-1,3-bis[(1H-imidazol-1-yl)methyl]benzene}dicobalt(II)], [Co₂(C₁₆H₆O₈)(C₁₄H₁₄N₄)₂]_n or [Co₂(o,m-bpta)(1,3-bimb)₂]_n (I), and poly[[aqua(μ₄-biphenyl-2,2',5,5'-tetracarboxylato){1,4-bis[(1H-imidazol-1-yl)methyl]benzene}dicobalt(II)] dihydrate], {[Co₂(C₁₆H₆O₈)(C₁₄H₁₄N₄)₂(H₂O)₂]·4H₂O}_n or {[Co₂(o,m-bpta)(1,4-bimb)₂(H₂O)₂]·4H₂O}_n (II), were synthesized from a mixture of biphenyl-2,2',5,5'-tetracarboxylic acid, i.e. [H₄(o,m-bpta)], CoCl₂·6H₂O and N-donor ligands under solvothermal conditions. The complexes were characterized by IR spectroscopy, elemental analysis, single-crystal X-ray diffraction and powder X-ray diffraction analysis. The bridging (o,m-bpta)^4- ligands combine with Co^II ions in different μ₄-coordination modes, leading to the formation of one-dimensional chains. The central Co^II atoms display tetrahedral [CoN₂O₂] and octahedral [CoN₂O₄] geometries in I and II, respectively. The bis[(1H-imidazol-1-yl)methyl]benzene (bimb) ligands adopt trans or cis conformations to connect Co^II ions, thus forming two three-dimensional (3D) networks. Complex I shows a (2,4)-connected 3D network with left- and right-handed helical chains constructed by (o,m-bpta)^4- ligands. Complex II is a (4,4)-connected 3D novel network with ribbon-like chains formed by (o,m-bpta)^4- linkers. Magnetic studies indicate an orbital contribution to the magnetic moment of I and II due to the longer Co...Co distances. An attempt has been made to fit the χ_MT results to the magnetic formulae for mononuclear Co^II complexes, the fitting indicating the presence of weak antiferromagnetic interactions between the Co^II ions.

Investigation of Precise Molecular Mechanistic Action of Tobacco-Associated Carcinogen `NNK´ Induced Carcinogenesis: A System Biology Approach

Cancer is the second deadliest disease listed by the WHO. One of the major causes of cancer disease is tobacco and consumption possibly due to its main component, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). A plethora of studies have been conducted in the past aiming to decipher the association of NNK with other diseases. However, it is strongly linked with cancer development. Despite these studies, a clear molecular mechanism and the impact of NNK on various system-level networks is not known. In the present study, system biology tools were employed to understand the key regulatory mechanisms and the perturbations that will happen in the cellular processes due to NNK. To investigate the system level influence of the carcinogen, NNK rewired protein–protein interaction network (PPIN) was generated from 544 reported proteins drawn out from 1317 articles retrieved from PubMed. The noise was removed from PPIN by the method of modulation. Gene ontology (GO) enrichment was performed on the seed proteins extracted from various modules to find the most affected pathways by the genes/proteins. For the modulation, Molecular COmplex DEtection (MCODE) was used to generate 19 modules containing 115 seed proteins. Further, scrutiny of the targeted biomolecules was done by the graph theory and molecular docking. GO enrichment analysis revealed that mostly cell cycle regulatory proteins were affected by NNK.

A fourfold interpenetrating diamond-like three-dimensional zinc(II) coordination polymer: synthesis, crystal structure and physical properties

Excellent fluorescence properties are exhibited by d¹⁰ metal compounds. The novel three-dimensional Zn^II coordination framework, poly[[{μ₂-bis[4-(2-methyl-1H-imidazol-1-yl)phenyl] ether-κ²N³:N^3'}(μ₂-furan-2,5-dicarboxylato-κ²O²:O⁵)zinc(II)] 1.76-hydrate], {[Zn(C₆H₂O₅)(C₂₀H₁₈N₄O)]·1.76H₂O}_n, has been prepared and characterized using IR spectroscopy, elemental analysis and single-crystal X-ray diffraction. The crystal structure analysis revealed that the compound exhibits a novel fourfold interpenetrating diamond-like network. This polymer also displays a strong fluorescence emission in the solid state at room temperature.

On the Nature of the Positronic Bond

Recently it has been proposed that the positron, the anti-particle analog of the electron, is capable of forming an anti-matter bond in a composite system consists of two hydride anions and a positron [Angew. Chem. Int. Ed. 57, 8859-8864 (2018)]. In order to dig into the nature of this novel bond the newly developed multi-component quantum theory of atoms in molecules (MC-QTAIM) is applied to this positronic system. The topological analysis reveals that this species is composed of two atoms in molecules, each containing a proton and half of the electronic and the positronic populations. Further analysis elucidates that the electron exchange phenomenon is virtually non-existent between the two atoms and no electronic covalent bond is conceivable in between. On the other hand, it is demonstrated that the positron density enclosed in each atom is capable of stabilizing interactions with the electron density of the neighboring atom. This electrostatic interaction suffices to make the whole system bonded against all dissociation channels. Thus, the positron indeed acts like an anti-matter glue between the two atoms.

Interpreting Aromaticity and Antiaromaticity through Bifurcation Analysis of the Induced Magnetic Field

In all molecules, a current density is induced when the molecule is subjected to an external magnetic field. In turn, this current density creates a particular magnetic field. In this work, the bifurcation value of the induced magnetic field is analyzed in a representative set of aromatic, non-aromatic and antiaromatic monocycles, as well as a set of polycyclic hydrocarbons. The results show that the bifurcation value of the ring-shaped domain adequately classifies the studied molecules according to their aromatic character. For aromatic and nonaromatic molecules, it is possible to analyze two ring-shaped domains, one diatropic (inside the molecular ring) and one paratropic (outside the molecular ring). Meanwhile, for antiaromatic rings, only a diatropic ring-shaped domain (outside the molecular ring) is possible to analyze, since the paratropic domain (inside the molecular ring) is irreducible with the maximum value (attractor) at the center of the molecular ring. In some of the studied cases, i. e., in heteroatomic species, bifurcation values do not follow aromaticity trends and present some inconsistencies in comparison to ring currents strengths, showing that this approximation provides only a qualitative estimation about (anti)aromaticity.

Synthesis, structure and selective luminescence sensing for iron(III) ions of a three-dimensional zinc(II) (4,6)-connected coordination network

Coordination polymers constructed from conjugated organic ligands and metal ions with a d¹⁰ electronic configuration exhibit intriguing properties for chemical sensing and photochemistry. A Zn^II-based coordination polymer, namely poly[aqua(μ₆-biphenyl-3,3',5,5'-tetracarboxylato)(μ₂-4,4'-bipyridine)dizinc(II)], [Zn₂(C₁₆H₆O₈)(C₁₀H₈N₂)(H₂O)₂]_n or [Zn₂(m,m-bpta)(4,4'-bipy)(H₂O)₂]_n, was synthesized from a mixture of biphenyl-3,3',5,5'-tetracarboxylic acid [H₄(m,m-bpta)], 4,4'-bipyridine (4,4'-bipy) and Zn(NO₃)₂·6H₂O under solvothermal conditions. The title complex has been structurally characterized by IR spectroscopy, elemental analysis, single-crystal X-ray diffraction and powder X-ray diffraction analysis, and features a μ₆-coordination mode. The Zn^II ions adopt square-pyramidal geometries and are bridged by two syn-syn carboxylate groups to form [Zn₂(COO)₂] secondary buildding units (SBUs). The SBUs are crosslinked by (m,m-bpta)^4- ligands to produce a two-dimensional grid-like layer that exhibits a stair-like structure along the a axis. Adjacent layers are linked by 4,4'-bipy ligands to form a three-dimensional network with a {4⁴.6¹⁰.8}{4⁴.6²} topology. In the solid state, the complex displays a strong photoluminescence and an excellent solvent stability. In addition, the luminescence sensing results indicate a highly selective and sensitive sensing for Fe³⁺ ions.

Syntheses, supramolecular networks and Hirshfeld surface and thermal analyses of two new cadmium chloride coordination polymers with an N,O-chelating ligand

Two new coordination polymers, namely poly[[(3-aminopyrazin-4-ium-2-carboxylate-κ²N¹,O)di-μ-chlorido-cadmium(II)] monohydrate], {[CdCl₂(C₅H₅N₃O₂)]·H₂O}_n, (1), and poly[2-amino-3-carboxypyrazin-1-ium [(3-aminopyrazine-2-carboxylato-κ²N¹,O)di-μ-chlorido-cadmium(II)] monohydrate], {(C₅H₆N₃O₂)[Cd(C₅H₄N₃O₂)Cl₂]·H₂O}_n, (2), have been synthesized from the reaction of cadmium(II) chloride and 3-aminopyrazine-2-carboxylic acid (Hapca) under mild conditions in acidic media. The two coordination polymers have been characterized by single-crystal X-ray diffraction and show chloride-bridged zigzag chains with octahedrally coordinated metal ions, where Hapca acts as a bidentate ligand via the π-conjugated N atom and a carboxylate O atom. The chains are further interconnected via noncovalent interactions into three-dimensional supramolecular networks. The dominant H...O and H...Cl interactions for both compounds were quantified using Hirshfeld surface analysis. The thermal stability and topological analysis of the two-dimensional networks of (1) and (2) are also discussed.

Direct air capture of CO-2 - topological analysis of the experimental electron density (QTAIM) of the highly insoluble carbonate salt of a 2,6-pyridine-bis(iminoguanidine), (PyBIGH2)(CO3)(H2O)4

Chemical bonding and all intermolecular interactions in the highly insoluble carbonate salt of a 2,6-pyridine-bis(iminoguanidine), (PyBIGH2)(CO3)(H2O)4, recently employed in the direct air capture of CO2 via crystallization, have been analyzed within the framework of the quantum theory of atoms in molecules (QTAIM) based on the experimental electron density derived from X-ray diffraction data obtained at 20 K. Accurate hydrogen positions were included based on an analogous neutron diffraction study at 100 K. Topological features of the covalent bonds demonstrate the presence of multiple bonds of various orders within the PyBIGH2 2+ cation. Strong hydrogen bonds define ribbons comprising carbonate anions and water molecules. These ribbons are linked to stacks of essentially planar dications via hydrogen bonds from the guanidinium moieties and an additional one to the pyridine nitro-gen. The linking hydrogen bonds are approximately perpendicular to the anion-water ribbons. The observation of these putative interactions provided motivation to characterize them by topological analysis of the total electron density. Thus, all hydrogen bonds have been characterized by the properties of their (3,-1) bond critical points. Weaker interactions between the PyBIGH2 2+ cations have similarly been characterized. Integrated atomic charges are also reported. A small amount of cocrystallized hydroxide ion (∼2%) was also detected in both the X-ray and neutron data, and included in the multipole model for the electron-density refinement. The small amount of additional H+ required for charge balance was not detected in either the X-ray or the neutron data. The results are discussed in the context of the unusually low aqueous solubility of (PyBIGH2)(CO3)(H2O)4 and its ability to sequester atmospheric CO2.

Polarizable ab initio QM/MM Study of the Reaction Mechanism of N-tert-Butyloxycarbonylation of Aniline in [EMIm][BF₄]

N-t e r t-butoxycarbonylation of amines in solution (water, organic solvents, or ionic liquids) is a common reaction for the preparation of drug molecules. To understand the reaction mechanism and the role of the solvent, quantum mechanical/molecular mechanical simulations using a polarizable multipolar force field with long⁻range electrostatic corrections were used to optimize the minimum energy paths (MEPs) associated with various possible reaction mechanisms employing the nudged elastic band (NEB) and the quadratic string method (QSM). The calculated reaction energies and energy barriers were compared with the corresponding gas-phase and dichloromethane results. Complementary Electron Localization Function (ELF)/NCI analyses provide insights on the critical structures along the MEP. The calculated results suggest the most likely path involves a sequential mechanism with the rate⁻limiting step corresponding to the nucleophilic attack of the aniline, followed by proton transfer and the release of CO 2 without the direct involvement of imidazolium cations as catalysts.

Synthesis, crystal structure and topological analysis of a three-dimensional polymeric network based on zinc(II), potassium and 5-sulfobenzene-1,3-dicarboxylate (SIP)

Aromatic polycarboxylate linkers provide structural rigidity and strong interactions among the metal centre and the carboxylate O atoms. A new three-dimensional coordination polymer namely, catena-poly[potassium [tetraaqua(μ-5-sulfobenzene-1,3-dicarboxylato)zinc(II)]], {K[Zn(C₈H₃O₇S)(H₂O)₄]}_n or {K[Zn(SIP)(H₂O)₄]}_n, where SIP is 5-sulfobenzene-1,3-dicarboxylate or 5-sulfoisophthalate, was obtained and characterized by elemental analysis and IR vibrational spectroscopy, and the single-crystal structure was determined by X-ray diffraction analysis. The compound crystallizes in the monoclinic space group P2₁/n with Z = 4. Topological analysis revealed that K-O interactions form a two-dimensional network, which is uninodal 4-connected and can be described with a point symbol (4⁴.6²), and this plane network is classified as sql/Shubnikov. The layers are connected by Zn²⁺ ions coordinated to the SIP linker, forming a three-dimensional network. This net is a trinodal (3,5,6)-connected system with point symbol (3.4⁴.5².6².7³.8³).(3.4⁴.5².6².7).(3.7²).

TopoMS: Comprehensive topological exploration for molecular and condensed-matter systems

We introduce TopoMS, a computational tool enabling detailed topological analysis of molecular and condensed-matter systems, including the computation of atomic volumes and charges through the quantum theory of atoms in molecules, as well as the complete molecular graph. With roots in techniques from computational topology, and using a shared-memory parallel approach, TopoMS provides scalable, numerically robust, and topologically consistent analysis. TopoMS can be used as a command-line tool or with a GUI (graphical user interface), where the latter also enables an interactive exploration of the molecular graph. This paper presents algorithmic details of TopoMS and compares it with state-of-the-art tools: Bader charge analysis v1.0 (Arnaldsson et al., 01/11/17) and molecular graph extraction using Critic2 (Otero-de-la-Roza et al., Comput. Phys. Commun. 2014, 185, 1007). TopoMS not only combines the functionality of these individual codes but also demonstrates up to 4× performance gain on a standard laptop, faster convergence to fine-grid solution, robustness against lattice bias, and topological consistency. TopoMS is released publicly under BSD License. © 2018 Wiley Periodicals, Inc.

Nasopharyngeal Carcinoma Protein Interaction Mapping Analysis via Proteomic Approaches

Nasopharyngeal carcinoma (NPC), although not very common in many parts of the world, is a major concern in some countries, including Iran. Molecular studies are very helpful to provide essential information regarding underlying carcinogenetic mechanisms. Here, considering NPC proteomic approaches, established biomarkers were designated for protein-protein interaction network construction and analysis with corresponding plug-ins. A network of reported protein markers was constructed and topological and biological process features were investigated. Centrality analysis showed that JUN, CALM1, HSB1, and SOD1 are more important than other differentially expressed proteins in an interacting pattern. What is more, by extending the network, Tp53, PRDM10, AKT1, ALB, HSP90AA1, and EGFR achieved the highest values for NPC network strength. It can be concluded that these proteins as well as their contributing processes, particularly in a second network, may be important for NPC onset and development. Targeting these candidate proteins may allow novel treatment approaches following appropriate validation.

Topological study of diverse hydrogen-bonded patterns found in a system of a nickel(II) complex and the sulfate anion

A nickel(II) coordination complex, bis[2,6-bis(1H-benzimidazol-2-yl-κN³)pyridine-κN]nickel(II) sulfate, [Ni(C₁₉H₁₃N₅)₂]SO₄ or [Ni(H₂L)₂]SO₄, having four peripheral tetrahedrally oriented N-H donor units, combines with sulfate bridges to create hydrogen-bonded structures of varied dimensionality. The three crystal structures reported herein in the space groups P2₁2₁2₁, I-4 and Pccn are defined solely by strong charge-assisted N-H...O hydrogen bonds and contain disordered guests (water and dimethylformamide) that vary in size, shape and degree of hydrophilicity. Two of the compounds are channelled solids with three-dimensional structures, while the third is one-dimensional in nature. In spite of their differences, all three present a striking resemblance to the previously reported anhydrous relative [Guo et al. (2011). Chin. J. Inorg. Chem. 27, 1517-1520], which is considered as the reference framework from which all three title compounds are derived. The hydrogen-bonded frameworks are described and compared using crystallographic and topological approaches.

Informatics and machine learning to define the phenotype

INTRODUCTION

For the past decade, the focus of complex disease research has been the genotype. From technological advancements to the development of analysis methods, great progress has been made. However, advances in our definition of the phenotype have remained stagnant. Phenotype characterization has recently emerged as an exciting area of informatics and machine learning. The copious amounts of diverse biomedical data that have been collected may be leveraged with data-driven approaches to elucidate trait-related features and patterns. Areas covered: In this review, the authors discuss the phenotype in traditional genetic associations and the challenges this has imposed.Approaches for phenotype refinement that can aid in more accurate characterization of traits are also discussed. Further, the authors highlight promising machine learning approaches for establishing a phenotype and the challenges of electronic health record (EHR)-derived data. Expert commentary: The authors hypothesize that through unsupervised machine learning, data-driven approaches can be used to define phenotypes rather than relying on expert clinician knowledge. Through the use of machine learning and an unbiased set of features extracted from clinical repositories, researchers will have the potential to further understand complex traits and identify patient subgroups. This knowledge may lead to more preventative and precise clinical care.

Why Bond Critical Points Are Not "Bond" Critical Points

Equating (3,-1) critical points (CPs), derived from the topological analysis of the electron densities, to chemical bonds has triggered a lot of confusion in recent years. Part of this confusion stems from calling these CPs "bond" CPs (BCPs). While the origin of this terminology is traceable to the late seventies and beginning of eighties, when it sounded reasonable, new computational studies conducted on molecular electron densities cast serious doubt on the supposed universal equivalence between the chemical bonds and (3,-1) CPs. Herein, recent computational studies are briefly reviewed to demonstrate why (3,-1) CPs are not indicators of chemical bonds. It is discussed why this confusing terminology needs to be changed and reemphasized that (3,-1) CPs should be called "line" critical points (LCPs). The proposed terminology detaches the topological properties of molecular electron densities from any a priori chemical interpretation. Such detachment, if adopted by other authors, will hopefully prevent further misinterpretation of the data emerging from the quantum theory of atoms in molecules (QTAIM).

A new CdII coordination polymer with a self-penetrating architecture induced by the molecular conformation of a rigid bithiophene ligand

The design and synthesis of coordination polymers with a self-penetrating architecture has attracted much interest not only due to their interesting structures but also due to their potential applications. 5,5'-Bis(pyridin-4-yl)-2,2'-bithiophene (bpbp), as a conjugated bithiophene ligand, can exhibit trans and cis conformations and this can lead to the construction of a self-penetrating architecture. In addition, the semi-rigid ancillary ligand 4,4'-oxybis(benzoic acid) (H₂oba) can adopt different coordination modes, resulting in coordination polymers with high-dimensional skeletons. A new Cd^II coordination polymer based on mixed ligands, namely poly[diaquapentakis[μ-5,5'-bis(pyridin-4-yl)-2,2'-bithiophene-κ²N:N']bis(nitrato-κ²O,O')tetrakis(μ₃-4,4'-oxydibenzoato)-κ¹⁰O:O,O':O'',O''';κ⁶O:O':O''-pentacadmium(II)], [Cd₅(C₁₄H₁₄O₅)₄(NO₃)₂(C₁₈H₁₂N₂S₂)₅(H₂O)₂]_n, (I), has been synthesized under solvothermal conditions and characterized by single-crystal X-ray diffraction, IR spectroscopy and elemental analysis. Single-crystal X-ray diffraction indicates that there are three crystallographically independent Cd^II cations, three bpbp ligands, two deprotonated oba^2- ligands, one nitrate ligand and one coordinated water molecule in the asymmetric unit. One Cd^II centre is seven-coordinated, exhibiting a distorted {CdN₂O₅} pentagonal bipyramidal geometry, while the other two Cd centres are both six-coordinated, showing slightly distorted {CdN₂O₄} octahedral geometries. The most interesting feature is the co-existence of trans and cis conformations in a single net, allowing structural interpenetration via self-threading and yet the expected self-penetrating structure was obtained. Topological analysis shows that the whole three-dimensional framework can be classified as a 3-nodal (4,6,6)-c net with Schläfli symbol {6¹³.8²}₂{6⁶}, which is a new topology. Furthermore, the luminescence properties of (I) were examined in the solid state at room temperature.

Synthesis and crystal structure of a new polymorph of potassium europium(III) bis(sulfate) mono-hydrate, KEu(SO4)2·H2O

In comparison with the known polymorph of KEu(SO₄)₂·H₂O (monoclinic, P2₁/c), the new polymorph crystallizes in the trigonal crystal system (space group P3₁21).

The mixed-metal sulfate, KEu(SO₄)₂·H₂O, has been obtained as a new polymorph using hydro­thermal conditions. The crystal structure is isotypic with NaCe(SO₄)₂·H₂O and shows a three-dimensional connectivity of the tetra­hedral sulfate units with Eu^III and K^I ions. Tricapped trigonal–prismatic EuO₉ units and square-anti­prismatic KO₈ units link the SO₄ tetra­hedra, building the three-dimensional structure. Topological analysis reveals the existence of two nodes with 6- and 10-connected nets. The compound was previously reported [Kazmierczak & Höppe (2010 ▸). J. Solid State Chem.183, 2087–2094] in the monoclinic space group P2₁/c with a similar structural connectivity and coordination environments to the present compound.

A three-dimensional ZnII coordination polymer constructed from 1,1'-biphenyl-2,2',4,4'-tetracarboxylate and 1,4-bis(1H-imidazol-1-yl)benzene ligands exhibiting photoluminescence

Ligands based on polycarboxylic acids are excellent building blocks for the construction of coordination polymers; they may bind to a variety of metal ions and form clusters, as well as extended chain or network structures. Among these building blocks, biphenyltetracarboxylic acids (H₄bpta) with C₂ symmetry have recently attracted attention because of their variable bridging and multidentate chelating modes. The new luminescent three-dimensional coordination polymer poly[(μ₅-1,1'-biphenyl-2,2',4,4'-tetracarboxylato)bis[μ₂-1,4-bis(1H-imidazol-1-yl)benzene]dizinc(II)], [Zn₂(C₁₆H₆O₈)(C₁₂H₁₀N₄)]_n, was synthesized solvothermally and characterized by single-crystal X-ray diffraction, elemental analysis and IR spectroscopy. The crystal structure contains two crystallographically independent Zn^II cations. Both metal cations are located on twofold axes and display distorted tetrahedral coordination geometries. Neighbouring Zn^II centres are bridged by carboxylate groups in the syn-anti mode to form one-dimensional chains. Adjacent chains are linked through 1,1'-biphenyl-2,2',4,4'-tetracarboxylate and 1,4-bis(1H-imidazol-1-yl)benzene ligands to form a three-dimensional network. In the solid state, the compound exhibits blue photoluminescence and represents a promising candidate for a thermally stable and solvent-resistant blue fluorescent material.

Interactive cooperation and hierarchical operation of microRNA and transcription factor crosstalk in human transcriptional regulatory network

Transcriptional regulation of gene expression is an essential cellular process that is arranged by transcription factors (TFs), microRNAs (miRNA) and their target genes through a variety of mechanisms. Here, we set out to reconstruct a comprehensive transcriptional regulatory network of Homo sapiens consisting of experimentally verified regulatory information on miRNAs, TFs and their target genes. We have performed topological analyses to elucidate the transcriptional regulatory roles of miRNAs and TFs. When we thoroughly investigated the network motifs, different gene regulatory scenarios were observed; whereas, mutual TF-miRNA regulation (interactive cooperation) and hierarchical operation where miRNAs were the upstream regulators of TFs came into prominence. Otherwise, biological process specific subnetworks were also constructed and integration of gene and miRNA expression data on ovarian cancer was achieved as a case study to observe dynamic patterns of the gene expression. Meanwhile, both co-operation and hierarchical operation types were determined in active ovarian cancer and process-specific subnetworks. In addition, the analysis showed that multiple signals from miRNAs were integrated by TFs. Our results demonstrate new insights on the architecture of the human transcriptional regulatory network, and here we present some lessons we gained from deciphering the reciprocal interplay between miRNAs, TFs and their target genes.