Comprehensive Topological Analysis Research Articles

Solvation and its influence on the electronic structure and pharmacological activity of 2-fluoro-6-trifluromethyl acetophenone

The molecular framework and vibrational spectra of 2′-Fluoro-6′-Trifluoromethyl Acetophenone (MA3) in diverse solvent environments are being studied using quantum chemistry methods like DFT. The structure was successfully optimized using gas phase and solvent phases such as ethanol, diethyl sulfoxide, chloroform, and diethyl ether. Using FT-Raman and FT-IR techniques, both theoretical and experimental scenarios were examined. The IEFPCM model was used to explore the electronic properties, including HOMO-LUMO gaps, UV–Vis spectra, NBO, Mulliken analysis, and MEP, in various solvents. The TD-DFT approach and IEFPCM model were utilized to replicate the UV spectra. The Fukui function helped locate reactive sites and understand chemical interactions. Comprehensive topological analysis using Multiwfn – 3.8 suite integrated RDG, ALIE, ELF, and LOL to identify key binding sites and weak interactions. The molecular docking studies highlighted the compound’s binding affinities with target proteins, showcasing its potential pharmacological applications. This research underscores the critical role of solvation in determining the electronic and structural properties of MA3, paving the way for its application in drug development and other fields.

Exploring kinematic stability of vortex structures: A topological approach to fluid flow around staggered square cylinders

In this study, a detailed fluid dynamics analysis is conducted around two identical square cylinders in a staggered configuration at a Reynolds number (Re) of 40, using a stabilized finite-element method to investigate the kinematic stability of vortex structures. By varying the horizontal spacing (S/D) between 2 and 30 and examining transverse gaps (T/D) of 0.25, 0.8, and 1.25, the research uncovers significant flow behavior variations from the tandem configuration, highlighting complex fluid-structure interactions. The presence of “separation bubbles” at lower S/D values across all T/D ratios indicates the dynamic impact of the upstream cylinder's proximity on the flow field, particularly on the stagnation points of the downstream cylinder. Through a comprehensive topological analysis, the study identifies various flow regimes and topological bifurcations, revealing transitions between stable states that maintain the number of critical points constant, and the kinematic stability of these vortical structures is established by the critical point theory. The effect of cylinder configurations and diverse flow structures on fluid loading is also analyzed by examining surface pressure coefficients. The asymmetry present in the cylinder configuration is manifested through the asymmetric values of lift coefficients.

3D scanning technique for morphological analysis of behind armour blunt trauma

In this paper, a 3D scanning method was used to measure behind armour blunt trauma (BABT). Ballistic tests were performed using two different bimetallic projectiles against armour panels consisting of 36 plies of DYNEEMA® SB21, mounted on blocks of red Weible® plastilina. The deformed surfaces of the witness material were meticulously scanned to isolate the imprinted indentations, allowing a comprehensive topological analysis to estimate various BABT quantifiers. In addition, detailed examinations of the deformed projectiles and damaged armour panels were carried out, including counting of the number of perforated plies. The added value of using 3D scanning techniques to more precisely assess the performance of armour panels in mitigating BABT was demonstrated. This approach facilitates more accurate measurements compared to conventional methods. It provides not only the depth of the imprinted cavities, but also the access to a more complete set of topological information to potentially further the understanding of ballistic trauma mechanics. In addition, these records allow the information contained in the imprints to be preserved for possible additional analysis.

Conservation of knotted and slipknotted topology in transmembrane transporters

The existence of nontrivial topology is well accepted in globular proteins but not in membrane proteins. Our comprehensive topological analysis of the Protein Data Bank structures reveals 18 families of transmembrane proteins with nontrivial topology, showing that they constitute a significant number of membrane proteins. Moreover, we found that they comprise one of the largest groups of secondary active transporters. We classified them based on their knotted fingerprint into four groups: three slipknotted and one knotted. Unexpectedly, we found that the same protein can possess two distinct slipknot motifs that correspond to its outward- and inward-open conformational state. Based on the analysis of structures and knotted fingerprints, we show that slipknot topology is directly involved in the conformational transition and substrate transfer. Therefore, entanglement can be used to classify proteins and to find their structure-function relationship. Furthermore, based on the topological analysis of the transmembrane protein structures predicted by AlphaFold, we identified new potentially slipknotted protein families.

A Comprehensive Topological Analysis of a Novel Flavonoid Extracted from Brazilian Cerrado Plants

AbstractEpicatechin is a bioactive compound that has several biological functions, and can be found in a number of Brazilian Cerrado plants. The compound (2R,3R)‐2‐(3,4‐dihydroxyphenyl)‐3,4‐dihydro‐2H‐1‐benzopyran‐3,5,7‐triol (EPC) was extracted from Salacia crassifolia and its molecular architecture and supramolecular arrangement were characterized by X‐ray diffraction and Hirshfeld Surface. Theoretical calculations such as QTAIM, frontier molecular orbital, MEP and infrared spectra assignments were calculated at M06‐2X/6‐311++G(d,p) basis set. MEP revealed most positive region around hydrogen atoms of the hydroxyl group. X‐ray diffraction and QTAIM results showed that EPC forms a tetramer linked by classical hydrogen bonds O–H…O due to the number of hydroxyl groups available. The crystalline packing and supramolecular arrangement are stabilized by non‐classical hydrogen C–H…O and C–H…π interactions.

A Comprehensive Topological Analysis on a New Bromine-Chalcone with Potential Nonlinear Optical Properties.

The application of organic crystals on nonlinear optical (NLO) materials has been increasing in recent years, and compounds like chalcones are interesting due to their significant third-order nonlinear properties. Hereof, we describe the synthesis, molecular structure, supramolecular arrangement, and theoretical calculations for a bromine-chalcone 3-(4-bromophenyl)-1-[3-(2-oxo-2-phenylethoxy)phenyl]-propenone (BC), which crystallized into noncentrosymmetric space group Pc. Also, a comprehensive topological analysis performed by QTAIM highlights the observed halogen bonds on solid state. In addition, the thermal stability was studied in temperatures smaller than 800 °C showing BC crystal as potential optical devices at temperatures up to 250 °C. Finally, the NLO properties indicate a photonic application based on strong third-order nonlinear response.

An integrative approach using systems biology, mutational analysis with molecular dynamics simulation to challenge the functionality of a target protein.

Visceral leishmaniasis affects millions of people worldwide in areas where Leishmania donovani is endemic. The protozoan species serves a greater threat as it has gradually evolved drug resistance whereby requiring newer approaches to treat the infection. State-of-art techniques are mostly directed toward finding better targets extracted from the available proteome data. In light of recent computational advancements, we ascertain and validate one such target, adenylosuccinate lyase (ADSL) by implementation of in-silico methods which led to the identification of critical amino acid residues that affects its functional attributes. Our target selection was based on comprehensive topological analysis of a knowledge-based protein-protein interaction network. Subsequently, mutations were incorporated and the dynamic behavior of mutated and native proteins was traced using MD simulations for a total time span of 600ns. Comparative analysis of the native and mutated structures exhibited perceptible changes in the ligand-bound catalytic region with respect to time. The unfavorable changes in the orientations of specific catalytic residues, His118 and His196, induced by generated mutations reduce the enzyme specificity. In summary, this integrative approach is able to select a target against pathogen, identify crucial residues, and challenge its functionality through the selected mutations.

PyLink: a PyMOL plugin to identify links.

Links are generalization of knots, that consist of several components. They appear in proteins, peptides and other biopolymers with disulfide bonds or ions interactions giving rise to the exceptional stability. Moreover because of this stability such biopolymers are the target of commercial and medical use (including anti-bacterial and insecticidal activity). Therefore, topological characterization of such biopolymers, not only provides explanation of their thermodynamical or mechanical properties, but paves the way to design templates in pharmaceutical applications. However, distinction between links and trivial topology is not an easy task. Here, we present PyLink-a PyMOL plugin suited to identify three types of links and perform comprehensive topological analysis of proteins rich in disulfide or ion bonds. PyLink can scan for the links automatically, or the user may specify their own components, including closed loops with several bridges and ion interactions. This creates the possibility of designing new biopolymers with desired properties. The PyLink plugin, manual and tutorial videos are available at http://pylink.cent.uw.edu.pl.

Proteins' Knotty Problems

Knots in proteins are increasingly being recognized as an important structural concept, and the folding of these peculiar structures still poses considerable challenges. From a functional point of view, most protein knots discovered so far are either enzymes or DNA-binding proteins. Our comprehensive topological analysis of the Protein Data Bank reveals several novel structures including knotted mitochondrial proteins and the most deeply embedded protein knot discovered so far. For the latter, we propose a novel folding pathway based on the idea that a loose knot forms at a terminus and slides to its native position. For the mitochondrial proteins, we discuss the folding problem from the perspective of transport and suggest that they fold inside the mitochondria. We also discuss the evolutionary origin of a novel class of knotted membrane proteins and argue that a novel knotted DNA-binding protein constitutes a new fold. Finally, we have also discovered a knot in an artificially designed protein structure.

Four New Families of Polynuclear Zn-Ln Coordination Clusters. Synthetic, Topological, Magnetic, and Luminescent Aspects

The employment of three structurally related Schiff bases H2L1, H2L2, and H3L3 with zinc and lanthanide salts under various reaction conditions, gave four families of compounds formulated as [ZnII2LnIII2(L1)4(EtOH)6][ClO4]2 (1–3), [ZnII5Ln(OH)(L1)6(H2O)] (4–6), [ZnII4LnIII2(OH)2(L2)4 (OAc)2(NO3)2(DMF)3]·DMF (7–9), and [ZnII2LnIII2(L3)2(NO3)2(CO3)2(CH3OH)2] (10–12) with robust and novel topologies. Synthetic aspects are discussed. A comprehensive topological analysis of all reported ZnII/LnIII CCs with a core nuclearity of four and above is presented and identifies that families (4–6) and (7–9) are the first examples of the 2,3,4M6–1 motif in ZnII/LnIII chemistry. Magnetic studies are presented for the DyIII analogues (1, 7, and 10) are presented, 7 demonstrates field-induced slow relaxation of the magnetization. Fluorescence studies are also discussed.

Topology of 2-Periodic Coordination Networks: Toward Expert Systems in Crystal Design

We have performed comprehensive topological analysis of 2-periodic coordination networks in 10 371 metal–organic compounds. Both local and overall topologies of complex groups were determined, classified, and stored in the electronic databases. Two plane nets, square lattice (sql) and honeycomb (hcb), were found to compose two-thirds of all the coordination networks. Strong correlations were found between local topological characteristics (coordination numbers of atoms or complex groups, coordination figures, formalized coordination modes of ligands and coordination formula) and the overall topology that in many cases allowed us to predict possible topological motifs from the data on chemical composition with high probability. The possibility to develop an expert system that could envisage local and overall topology of periodic coordination networks is discussed, and an example is given of how such a system can work.

Comprehensive Topological Analysis of Conductive and Inductive Charging Solutions for Plug-In Electric Vehicles

The impending global energy crisis has opened up new opportunities for the automotive industry to meet the ever-increasing demand for cleaner and fuel-efficient vehicles. This has necessitated the development of drivetrains that are either fully or partially electrified in the form of electric and plug-in hybrid electric vehicles (EVs and HEVs), respectively, which are collectively addressed as plug-in EVs (PEVs). PEVs in general are equipped with larger on-board storage and power electronics for charging or discharging the battery, in comparison with HEVs. The extent to which PEVs are adopted significantly depends on the nature of the charging solution utilized. In this paper, a comprehensive topological survey of the currently available PEV charging solutions is presented. PEV chargers based on the nature of charging (conductive or inductive), stages of conversion (integrated single stage or two stages), power level (level 1, 2, or 3), and type of semiconductor devices utilized (silicon, silicon carbide, or gallium nitride) are thoroughly reviewed in this paper.