Compass: predicting biological activities from molecular surface properties. Performance comparisons on a steroid benchmark.

The analysis of molecular shapes is of major importance in the study of molecular structures and chemical reactivity. Computational analyses of shapes of molecular bodies are usually based on computer graphics techniques and on visual inspection. However, for accurate shape comparisons of a large number of molecules, visual inspection is not the best choice, and fully automatic, non-visual, algorithmic shape analysis by computer is more reliable. The shape group method (SGM) and various shape codes, derived from the 3D topological properties of molecular contour surfaces, provide efficient computational tools for non-visual shape analysis. Molecular shapes are subject to change when electronic excitation or a chemical reaction occurs. Several rules are derived, providing constraints on molecular shape changes in electronic excitations. The shape matrices, defined by the curvature properties of molecular contour surfaces, are applicable for a computer-based, non-visual evaluation of molecular shape and molecular similarity. The invariance domains of shape matrices within the dynamic shape space D suggest a general method for a dynamic description of molecular shapes.

Mixture-based synthetic combinatorial library (MB-SCL) screening is a well-established experimental approach for rapidly retrieving structure-activity relationships (SAR) and identifying hits. Virtual screening is also a powerful approach that is increasingly being used in drug discovery programs and has a growing number of successful applications. However, limited efforts have been made to integrate both techniques. To this end, we combined experimental data from a MB-SCL of bicyclic guanidines screened against the κ-opioid receptor and molecular similarity methods. The activity data and similarity analyses were integrated in a biometric analysis-similarity map. Such a map allows the molecules to be categorized as actives, activity cliffs, low similarity to the reference compounds, or missed hits. A compound with IC(50) = 309 nM was found in the "missed hits" region, showing that active compounds can be retrieved from a MS-SCL via computational approaches. The strategy presented in this work is general and is envisioned as a general-purpose approach that can be applied to other MB-SCLs.

P48 Prediction of intestinal drug absorption from molecular surface properties

Inspired by tetracyclic nitropyrazole-based stable and potential energetic materials, we designed two new C-C and C-N-linked tetrazole-pyrazole-based energetic molecules, with acceptable detonation performance and moderate sensitivity. The heat of formation and performance parameters were analyzed by density functional theory, and the calculations demonstrate that both compounds have a high positive heat of formation (> 930kJ/mol). The designed compounds, A1 (density: 1.79g/cm3, detonation velocity: 7.95km/s, pressure: 25.30 GPa, impact sensitivity: 35J) and A2 (density: 1.87g/cm3, detonation velocity: 8.83km/s, pressure: 33.31 GPa, impact sensitivity: 21J), exhibit moderate to high detonation performance and low sensitivity to impact stimuli. Further, the analysis of bond strength and Mayer bond order of the C-NO2 bond and charge on -NO2 groups suggests the stability of the C-NO2 bond in designed compounds in comparison with reported tetracyclic energetic compounds. These findings demonstrate that the combination of bistetrazole with nitropyrazole and dinitropyrazole rings holds high potential for developing new high-performing and less sensitive energetic materials. The optimization and energy calculations of designed tetracyclic compounds were carried out at the B3LYP/6-311G(d,p) level of theory, utilizing the Gaussian 09 software package. The molecular surface properties were analysed using Multiwfn. The EXPLO5 (V7.01.01) thermochemical code was used to predict the detonation properties.

The earlier, symmetry-independent group theoretical characterization of the shapes of three-dimensional molecular functions, such as electrostatic potentials, electronic charge densities, or molecular orbitals, is extended and compared to a new family of shape descriptors. The incidence graphs and shape graphs, defined by the curvature properties of various molecular contour surfaces, provide an easily visualizable, alternative mathematical technique for a computer-based, non-visual evaluation of molecular shape and molecular similarity. The invariance domains of incidence graphs, shape graphs and shape groups within the dynamic shape spaceD provide the mathematical basis for the development of a general method for a dynamic description of molecular shapes.

In this study, the molecular structure of single crystal containing Schiff bases has been characterized by X-ray diffraction, NMR, IR and UV‒Vis spectral techniques and compared with similar molecules in the literature. For the purpose of supporting X-ray results, geometric parameters and spectroscopic studies of the title compound were theoretically performed by Hartree‒Fock and density functional theory methods. In addition, the title compound’s molecular energies, Mulliken‒ESP‒NPA‒Hirshfeld charges, molecular electrostatic potential surface, Frontier orbitals and thermodynamic properties to elucidate intermolecular interactions were calculated. All the calculations in gas and solid phases were carried out using Gaussian 09 and Quantum Espresso programs. It was found that the studies of X-ray are more compatible with the calculations made in the solid phase.

99/00810 Research on a new type of additive for CWS from low temperature pyrolysis tar

Automotive bezels of polycarbonate (PC) were prepared in this work by varying the amount of recycled polymer in order to estimate an acceptable scrap/virgin ratio that maintains the material properties. Conducted tests allow us to define the limit to don't compromise the performance of recycled pieces. The studied properties were their chemical structure, molecular weight distribution, mechanical and surface properties of the samples. Results showed no change in the chemical structure of PC chains. However, variations in molecular distribution was observed by the addition of recycled material. Last one ascribed to chain scission at the carbonyl group of the PC molecules, and the formation of physical cross-linking as a consequence of degradation due to injection process. Both stiffness and surface properties of the material increased as the percentage of recycled PC rose. Therefore, although the chemical structure of the PC is preserved during the recycling process, fluid and elastic properties are modified limiting their operating conditions and industrial tolerance. Conducted analysis allows to establish that the addition to virgin PC of 20% of recycled material don't affect the physical-chemical properties of pieces, also maintains the quality standars of cosmetics tests.

Mesoporous nanocomposite sensors based on Sn1−xCexO2−δ metastable solid solution with high percentage of Ce3+ valence state for selective detection of H2 and CO

The goal present investigation was to formulate and characterized of biological macromolecules of alginate (ALG) and carboxymethylcellulose sodium (CMC) containing probiotic bacteria of Lactobacillus sporogenes (LS) co-encapsulated with a prebiotics, Bioecolians (α-Gluco-oligosaccharides). The prepared beads were characterized in terms of yield, size, encapsulation efficiency, viabilities in simulated gastric (pH 1.2, 2 hours) and bile (1% w/v, 3 hours) conditions. The beads were also characterized by FTIR, DSC, SEM and XRD to investigate molecular structure, surface properties and morphology of beads. The results showed that spherical beads with size distribution ranging from 1.18 ± 0.11 to 1.45 ± 0.15 mm for ALG and from 1.3 ± 0.12 to 1.5 ± 0.16 mm for ALG-CMC with encapsulation efficiency higher than 90% were achieved. The results indicated that incorporation of carboxymethylcellulose sodium into alginate beads improved viability of the bacteria in simulated gastric conditions as well as bile conditions. According to our in vitro studies, Probiotic beads using combination of ALG-CMC are suitable encapsulating polymer for gastro-intestinal delivery as designed by novel assembly using peristaltic pump for automated production.

In vitro degradation of electrospun poly(l-lactic acid)/segmented poly(ester urethane) blends

Organic corrosion inhibitors have been widely used to prevent and mitigate the damaging effects of corrosion on metal surfaces. However, their underlying mechanisms of action and effectiveness are still not fully understood. In recent years, the use of density functional theory (DFT) has emerged as a powerful tool to investigate the interaction between organic inhibitors and metal surfaces at the molecular level. This review article provides an overview of the principles of DFT, its advantages and limitations, and its application to the study of organic corrosion inhibitors. The factors affecting the performance of organic inhibitors, such as molecular structure, functional groups, and metal surface properties, are discussed in detail. The interaction between organic inhibitors and metal surfaces, including the adsorption and desorption of inhibitors, the role of intermolecular forces, and the effects of pH and temperature, are also explored. Finally, the challenges and future directions in the development of organic inhibitors using DFT are highlighted, including limitations and challenges in using DFT and potential avenues for further research. Overall, this review demonstrates the potential of DFT to provide valuable insights into the mechanism of organic corrosion inhibitors and to guide the development of new and more effective inhibitors for the protection of metal surfaces.

With the rapid advancement of nano-electromechanical systems (NEMS), friction at the nanoscale has become a critical factor influencing the stability, precision, and energy efficiency of moving components. Unlike macroscopic friction, which is primarily governed by mechanical interlocking, nanoscale friction is strongly influenced by molecular interactions and surface properties. Therefore, developing lubricants with low and controllable friction at the nanoscale is of paramount importance for improving the performance and longevity of NEMS devices. Ionic liquids (ILs) have recently garnered significant attention as advanced lubricants due to their unique physicochemical properties, such as negligible vapor pressure, high thermal stability, and excellent lubrication performance. One of the key advantages of ILs is their ability to undergo electrotunable friction, a property arising from the ability of their cations and anions to reorganize in response to applied electric fields. This allows for dynamic control over friction by modulating the adsorption configuration of ions on solid surfaces. While extensive studies have been conducted on the tribological behavior of ILs on atomically smooth surfaces like graphene, their performance on surfaces with nanoscale curvature remains largely unexplored. Understanding this effect is crucial, as real-world applications often involve rough and curved interfaces rather than ideal flat surfaces.The frictional properties of ILs are highly dependent on the location of the slippage plane, where ionic motion occurs. According to the electrical double-layer model, both surface potential and curvature can influence the position of this plane. The surface potential alters electrostatic interactions between the solid substrate and adsorbed ions, while nanoscale curvature introduces steric hindrance effects that impact ion packing density and structural ordering. As curvature increases, the available space for ion adsorption changes, potentially leading to variations in lubrication behavior.To address this knowledge gap, this study investigates the frictional electrotunability of ILs on graphene surfaces with controlled nanoscale curvatures. Single layer graphene will be transferred onto nanoparticles of different diameters (10 nm, 20 nm, and 30 nm) to systematically vary the curvature. The nanofriction tests will be performed using atomic force microscopy (AFM) under single-asperity contact mode, utilizing a sharp tip (radius ~9 nm) to study the friction under varying normal loads. The IL 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([EMIM][TFSI]) will be employed as the lubricant due to its strong π-π interactions with graphene, which significantly influence adsorption behavior and subsequent friction.By applying external electrical potentials to the system, we will evaluate how surface curvature modifies the electrotunable frictional response of the IL. The force-distance curve measurements using AFM will provide insight into the ionic layering and structural organization of ILs on curved graphene surfaces. The correlation between surface curvature, ionic structuring, and electrotunable friction will be analyzed to elucidate the fundamental mechanisms governing this behavior. This work aims to provide a deeper understanding of IL lubrication on non-ideal (curved or rough) surfaces, offering new strategies for designing adaptive nanoscale lubrication systems. The findings will contribute to the development of next-generation lubricants for nanodevices where controlled friction at the nanoscale is crucial.

Naphthenic acid (NA), the predominant organic acid in acidic crude oil, contributes to severe emulsification, complicating the electrostatic demulsification process. To elucidate the mechanism of electro-coalescence in water-in-oil (W/O) emulsions with NA, we employed both molecular dynamics (MD) simulations and experimental methods to examine the dynamic behavior of water droplets when subjected to DC electric fields. The effects of electric field strength (E) and naphthenic acid concentration (cn) on droplet coalescence were explored. Results indicate that the intermolecular interaction between NAs and water droplets diminishes with decreasing solvent accessible surface area (SASA). Graphical interaction analysis shows that NAs adopt a "head-to-head" configuration between droplets, producing a repulsive exchange energy of 26.03 kJ·mol-1 that impedes droplet coalescence. At cn = 0.0441 mol·L-1, both contact and coalescence times were significantly extended. In this scenario, NAs interact in a "head-to-shoulder" configuration, producing a dispersive attraction energy of -11.32 kJ·mol-1, which facilitates droplet coalescence. Furthermore, increasing cn reduces the interfacial tension (IFT) between water and oil. The application of an electric field induces alignment of NA molecules along the field direction, generating steric hindrance that impedes droplet contact. As E increased, the reorientation and alignment of both water molecules and NA intensified, enhancing the formation of H-bonds between the droplets and NAs. This work offers molecular insights into the droplet electro-coalescence mechanisms in acidic W/O emulsions.

Protein-DNA interactions play a crucial role in the translation of genomic information to the biological consequences. Because specific recognition of DNA sequences by proteins is extremely complicated, it is hard to predict how those proteins interact with DNA. Under this circumstance, we carried out the analyses for the interfaces of protein-DNA complexes, using physicochemical properties of protein molecular surfaces, e.g. the electrostatic potentials and the shapes of molecular surface.