Comparison study of exchange-correlation functionals on prediction of ground states and structural properties

Despite significant advances in first-principles calculation methods, there is no single exchange-correlation functional which predicts the ground state of materials without an error yet. We investigated how accurately ground states of binary semiconductors are described using 16 exchange-correlation functionals (with or without van der Waals corrections). LDA, PBEsol, SCAN (with or without rVV10 correction), and PBE with D3 van der Waals correction (zero or Becke-Johnson damping) show good predicting power. The lattice constants of stable phases were slightly better described by SCAN, PBEsol, PBE+D3 (Becke-Johnson damping), and MS2. We also propose a set of functionals to double-check the stability of new materials based on the majority vote.     

Het(aryl)isatin to het(aryl)aminoindoline scaffold hopping: A route to selective inhibitors of matrix metalloproteinases

Matrix metalloproteinases (MMPs) are a large family of zinc-dependent endoproteases known to exert multiple regulatory roles in tumor progression. A variety of chemical classes have been explored for targeting individual MMP isoforms. In the present study, we further developed our isatin based scaffold BB0223107 capable of binding to and inactivating MMP-2 in a zinc-independent manner (Agamennone et al., 2016). Forty four new compounds were synthesized based on the modified BB0223107. All compounds were tested in enzyme inhibition assays against MMP-2, ?8 and ?13. SAR studies demonstrated that 5-het(aryl)-3-aminoindolin-2-ones (37–39) were active toward MMP-2 and MMP-13. The most potent compounds 33 and 37 displayed an IC₅₀ of 3 µM against MMP-13 and showed a negligible activity toward MMP-8; almost all new compounds were inactive toward MMP-8. Replacement of the isatin ring with a biaryl system (compound 33) did not decrease the potency against MMP-13 but reduced the selectivity. Structure-based computational studies were carried out to rationalize the inhibitory activity data. The analysis of binding geometries confirmed that all fragments occupied the S1′ site in the three enzymes while no ligand was able to bind the catalytic zinc ion. To the best of our knowledge, this is the first example of 3-aminoindolin-2-one-based MMP inhibitors that, based on the computer modeling study, do not coordinate the zinc ion. Thus, the het(aryl)-3-aminoindolin-2-one derivatives emerge as a drug-like and promising chemotype that, along with the hetaryl variations, represents an alternative and thrifty tool for chemical space exploration aimed at MMP inhibitor design.     

Well-posedness of two pseudo-parabolic problems for electrical conduction in heterogeneous media

We prove a well-posedness result for two pseudo-parabolic problems, which can be seen as two models for the same electrical conduction phenomenon in heterogeneous media, neglecting the magnetic field. One of the problems is the concentration limit of the other one, when the thickness of the dielectric inclusions goes to zero. The concentrated problem involves a transmission condition through interfaces, which is mediated by a suitable Laplace-Beltrami type equation.     

Bifurcation analysis of visual angle model with anticipated time and stabilizing driving behavior

In the light of the visual angle model (VAM), an improved car-following model considering driver's visual angle, anticipated time and stabilizing driving behavior is proposed so as to investigate how the driver's behavior factors affect the stability of the traffic flow. Based on the model, linear stability analysis is performed together with bifurcation analysis, whose corresponding stability condition is highly fit to the results of the linear analysis. Furthermore, the time-dependent Ginzburg-Landau (TDGL) equation and the modified Korteweg-de Vries (mKdV) equation are derived by nonlinear analysis, and we obtain the relationship of the two equations through the comparison. Finally, parameter calibration and numerical simulation are conducted to verify the validity of the theoretical analysis, whose results are highly consistent with the theoretical analysis.     

Chemical bonding in representative astrophysically relevant neutral,cation, and anion HCnH chains

Most existing studies assign a polyynic and cumulenic character of chemical bonding in carbon-based chains relying on values of the bond lengths. Building on our recent work, in this paper we add further evidence on the limitations of such an analysis and demonstrate the significant insight gained via natural bond analysis. Presently reported results include atomic charges, natural bond order and valence indices obtained from ab initio computations for representative members of the astrophysically relevant neutral and charged HC_2k/2k+1H chain family. They unravel a series of counter-intuitive aspects and/or help naive intuition in properly understanding microscopic processes, e.g., electron removal from or electron attachment to a neutral chain. Demonstrating that the Wiberg indices adequately quantify the chemical bonding structure of the HC_2k/2k+1H chains—while the often heavily advertised Mayer indices do not—represents an important message conveyed by the present study.     

Versatile Near-Infrared Super-Resolution Imaging of Amyloid Fibrils with the Fluorogenic Probe CRANAD-2

CRANAD-2 is a fluorogenic curcumin derivative used for near-infrared detection and imaging in vivo of amyloid aggregates, which are involved in neurodegenerative diseases. We explore the performance of CRANAD-2 in two super-resolution imaging techniques, namely stimulated emission depletion (STED) and single-molecule localization microscopy (SMLM), with markedly different fluorophore requirements. By conveniently adapting the concentration of CRANAD-2, which transiently binds to amyloid fibrils, we show that it performs well in both techniques, achieving a resolution in the range of 45–55 nm. Correlation of SMLM with atomic force microscopy (AFM) validates the resolution of fine features in the reconstructed super-resolved image. The good performance and versatility of CRANAD-2 provides a powerful tool for near-infrared nanoscopic imaging of amyloids in vitro and in vivo.     

Optimization of Transducer Location for Novel Non-Intrusive Methodologies of Diagnosis in Diesel Engines

The health monitoring has been studied to ensure integrity of design of engine structure by detection, quantification, and prediction of damages. Early detection of faults may allow the downtime of maintenance to be rescheduled, thus preventing sudden shutdown of machines. In cylinder pressure developed, vibrations and noise emissions data provide a rich source of information about condition of engines. Monitoring of vibrations and noise emissions are novel non-intrusive methodologies for which positioning of various transducers are important issue. The presented work shows applicability of these diagnosis methodologies adopted in case of diesel engines. The effects of changing various fuel injection parameters was analyzed. Scope of using non-intrusive technique has been analyzed by changing locations of microphone. Novelty of this worklies in exploring signal processing methods for various locations around the engine test set up. Various frequency ranges of contributing noise and vibration sources were identified. Time-Frequency analysis showed the onset of various cyclic. Based on the identification of various frequency bands, it is possible to device suitable filters in order to extract more information.     

Anti-fibrosis attributes: UHPLC-MS/MS-based pharmacokinetics profiling of a novel autotaxin inhibitor with excellent in vivo efficacy in rat

3,4-Difluorobenzyl(1-ethyl-5-(4-((4-hydroxypiperidin-1-yl)-methyl)thiazol-2-yl)-1H-indol-3-yl)carbamate (NAI59), a small molecule with outstanding therapeutic effectiveness to anti-pulmonary fibrosis, was developed as an autotaxin inhibitor candidate compound. To evaluate the pharmacokinetics and plasma protein binding of NAI59, a UPLC–MS/MS method was developed to quantify NAI59 in plasma and phosphate-buffered saline. The calibration curve linearity ranged from 9.95 to 1990.00 ng/mL in plasma. The accuracy was −6.8 to 5.9%, and the intra- and inter-day precision was within 15%. The matrix effect and recovery, as well as dilution integrity, were within the criteria. The chromatographic and mass spectrometric conditions were also feasible to determine phosphate-buffered saline samples, and it has been proved that this method exhibits good precision and accuracy in the range of 9.95–497.50 ng/mL in phosphate-buffered saline. This study is the first to determine the pharmacokinetics, absolute bioavailability, and plasma protein binding of NAI59 in rats using this established method. Therefore, the pharmacokinetic profiles of NAI59 showed a dose-dependent relationship after oral administration, and the absolute bioavailability in rats was 6.3%. In addition, the results of protein binding showed that the combining capacity of NAI59 with plasma protein attained 90% and increased with the increase in drug concentration.     

Influence of acceptor tethering on the performance of nonlinear optical properties for pyrene-based materials with A-π-D-π-D architecture

In this study, we designed a series of pyrene-based donor-π-donor-π-acceptor compounds (HPTC1-HPTC7) by structural tailoring the reference compound (HPTC) using acceptor units. Nonlinear optical (NLO) properties, frontier molecular orbitals (FMOs), natural bonding orbital (NBO), transition density matric (TDM) analysis, and absorption spectra of reference and proposed derivatives were calculated at M06/6-31G(d,p) functional. All the designed compounds have smaller energy bandgaps than the HPTC compound. Moreover, the designed compounds exhibited larger global softness values than the reference. The absorption maxima of HPTC2, HPTC3, and HPTC7 are blue shifted with respect to HPTC. NBO analysis revealed that prolonged hyper conjugative associations and strong interactions between the donor (π) and acceptor (π*) moieties play a crucial part in their stabilization. The FMO and NBO findings supported the NLO responses of entitled compounds, and consequently, the linear and nonlinear properties of designed derivatives elevate compared to the reference molecule. Promisingly, the NLO response for HPTC7 comprises of highest values of <α>, β_total and < γ > as 1.92 × 10^?22 esu, 1.95 × 10^?27 esu, and 4.69 × 10⁷ (a.u). This NLO behavior shows push–pull NLO chromophores for HPTC7 predicting its role in pursuing NLO materials for optoelectronic applications.