Search Results (8)

A simplified molecular-dynamics-based electronic circular dichroism (ECD) approach was tested on three condensed derivatives with limited conformational flexibility and an isochroman-2H-chromene hybrid, the ECD spectra of which could not be precisely reproduced by the conventional ECD calculation protocol. Application of explicit solvent molecules at the molecular mechanics (MD) level in the dynamics simulations and subsequent TDDFT-ECD calculation for the unoptimized MD structures was able to improve the agreements between experimental and computed spectra. Since enhancements were achieved even for molecules with limited conformational flexibility, deformations caused by the solvent molecules and multitudes of conformers produced with unoptimized geometries seem to be key factors for better agreement. The MD approach could confirm that aggregation of the phenanthrene natural product luzulin A had a significant contribution to a specific wavelength range of the experimental ECD. The MD approach has proved that dimer formation occurred in solution and this was responsible for the anomalous ECD spectrum. The scope and limitations of the method have also been discussed. Full article

The electronic circular dichroism (ECD) spectra of aqueous d-glucose and d-galactose were modeled using a theoretical–computational approach combining molecular dynamics (MD) simulations and perturbed matrix method (PMM) calculations, hereafter termed MD-PMM. The experimental spectra were reproduced with a satisfactory accuracy, confirming the good performances of MD-PMM in modeling different spectral features in complex atomic–molecular systems, as already reported in previous studies. The underlying strategy of the method was to perform a preliminary long timescale MD simulation of the chromophore followed by the extraction of the relevant conformations through essential dynamics analysis. On this (limited) number of relevant conformations, the ECD spectrum was calculated via the PMM approach. This study showed that MD-PMM was able to reproduce the essential features of the ECD spectrum (i.e., the position, the intensity, and the shape of the bands) of d-glucose and d-galactose while avoiding the rather computationally expensive aspects, which were demonstrated to be important for the final outcome, such as (i) the use of a large number of chromophore conformations; (ii) the inclusion of quantum vibronic coupling; and (iii) the inclusion of explicit solvent molecules interacting with the chromophore atoms within the chromophore itself (e.g., via hydrogen bonds). Full article

To improve the performance of electrochemical deburring for microhole drilling (MD-ECD), the distribution and dynamic change of the current density in the machining area during the electrolysis process were analyzed, and the synchronous change relationship between the current density and the burr profile was studied. The effects of process parameters, such as machining voltage U, initial machining gap d, electrolyte concentration C, and electrode radius r₁ on the deburring process, were studied. The results show that the magnitude of the current density value in the burr area reflects the MD-ECD’s deburring performance. The current density near the burr tip is high, and the material is preferentially removed. The non-processed area has a low current density and slow material removal. As the machining progresses, the burr tip becomes blunt and the current in the burr area gradually transfers to the non-machining area, resulting in the transfer of the material removal area from the burr area to the adjacent non-machining area. Then, a chamfer is formed at the orifice; the chamfer width is larger than the chamfer height. When U = 4 V, d = 0.35 mm, C = 12%, and r₁ = 0.4 mm, the burr removal efficiency and accuracy can be guaranteed. The chamfer width and chamfer height obtained from the test are 29 μm and 17 μm, and the burr removal effect is good. Full article

Interleukin-1 receptor type 1 (IL-1R1) is a key player in inflammation and immune responses. This receptor regulates IL-1 activity in two forms: as a membrane-bound form and as a soluble ectodomain. The details and differences between the conformational dynamics of the membrane-bound and the soluble IL-1R1 ectodomains (ECDs) remain largely elusive. Here, we study and compare the structural dynamics of the soluble and membrane-bound IL-1R1-ECDs using molecular dynamics (MD) simulations, focusing on the flexible interdomain linker of the ECD, as well as the spatial rearrangements between the Ig-like domains of the ECD. To explore the membrane-bound conformations, a full-length IL-1R1 structural model was developed and subjected to classical equilibrium MD. Comparative analysis of multiple MD trajectories of the soluble and the membrane-bound IL-1R1-ECDs reveals that (i) as somewhat expected, the extent of the visited “open-to-closed” transitional states differs significantly between the soluble and membrane-bound forms; (ii) the soluble form presents open-closed transitions, sampling a wider rotational motion between the Ig-like domains of the ECD, visiting closed and “twisted” conformations in higher extent, whereas the membrane-bound form is characterized by more conformationally restricted states; (iii) interestingly, the backbone dihedral angles of residues Glu202, Glu203 and Asn204, located in the flexible linker, display the highest variations during the transition between discrete conformational states detected in IL-1R1, thus appearing to work as the “central wheel of a clock’s movement”. The simulations and analyses presented in this contribution offer a deeper insight into the structure and dynamics of IL-1R1, which may be explored in a drug discovery setting. Full article

Inhibition of cancer cell adhesion is an effective approach to killing adherent cancer cells. B49 and its analog B49Mod1 peptides, derived from the extracellular domain (ECD) of bone marrow stromal antigen 2 (BST-2), display anti-adhesion activity on breast cancer cells. However, the minimal sequence required for this anti-adhesion activity is unknown. Here, we further characterized the anti-adhesion activity of B49Mod1. We show that the anti-adhesion activity of B49Mod1 may require cysteine-linked disulfide bond and that the peptide is susceptible to proteolytic deactivation. Using structure-activity relationship studies, we identified an 18-Mer sequence (B18) as the minimal peptide sequence mediating the anti-adhesion activity of B49Mod1. Atomistic molecular dynamic (MD) simulations reveal that B18 forms a stable complex with the ECD of BST-2 in aqueous solution. MD simulations further reveal that B18 may cause membrane defects that facilitates peptide translocation across the bilayer. Placement of four B18 chains as a transmembrane bundle results in water channel formation, indicating that B18 may impair membrane integrity and form pores. We hereby identify B18 as the minimal peptide sequence required for the anti-adhesion activity of B49Mod1 and provide atomistic insight into the interaction of B18 with BST-2 and the cell membrane. Full article

Change detection (CD) of natural land cover is important for environmental protection and to maintain an ecological balance. The Landsat series of satellites provide continuous observation of the Earth’s surface and is sensitive to reflection of water, soil and vegetation. It offers fine spatial resolutions (15–80 m) and short revisit times (16–18 days). Therefore, Landsat imagery is suitable for monitoring natural land cover changes. Clustering-based CD methods using evolutionary algorithms (EAs) can be applied to Landsat images to obtain optimal changed and unchanged clustering centers (clusters) with minimum clustering index. However, they directly analyze difference image (DI), which finds itself subject to interference by Gaussian noise and local brightness distortion in Landsat data, resulting in false alarms in detection results. In order to reduce image interferences and improve CD accuracy, we proposed an unsupervised CD method based on multi-feature clustering using the differential evolution algorithm (M-DECD) for Landsat Imagery. First, according to characteristics of Landsat data, a multi-feature space is constructed with three elements: Wiener de-noising, detail enhancement, and structural similarity. Then, a CD method based on differential evolution (DE) algorithm and fuzzy clustering is proposed to obtain global optimal clusters in the multi-feature space, and generate a binary change map (CM). In addition, the control parameters of the DE algorithm are adjusted to improve the robustness of M-DECD. The experimental results obtained with four Landsat datasets confirm the effectiveness of M-DECD. Compared with the results of conventional methods and the current state-of-the-art methods based on evolutionary clustering, the detection accuracies of the M-DECD on the Mexico dataset and the Sardinia dataset are very close to the best results. The accuracies of the M-DECD in the Alaska dataset and the large Canada dataset increased by about 3.3% and 11.9%, respectively. This indicates that multiple features are suitable for Landsat images and the DE algorithm is effective in searching for an optimal CD result. Full article

This communication presents the performance evaluation and comparative study between two different techniques: a membrane-based dehumidification system (MDS) and evaporative cooling dehumidification (ECD) for a typical climate of South Korea. Although there are different ways to dehumidify the air in living and work spaces, the membrane-based dehumidification system (MDS) is the most effective way as it neither causes a change in the temperature nor harms the environment. Moreover, it consumes significantly less energy when compared to other methods. There are also limitations concerning products that are sensitive to temperature such as food and pharmaceutical products; the method of evaporative cooling dehumidification is not suitable for such applications. The present work demonstrated the excellent energy-saving performance of the membrane-based dehumidification system against evaporative cooling dehumidification by comparing the performance of these two systems during the rainy season using a transient system simulation. The results showed that the MDS helped to reduce the dehumidification load by more than 47.6% when compared to the ECD system, which is a significant achievement in this regard. Full article

Twenty-nine new limonoids—named xylomolins A₁–A₇, B₁–B₂, C₁–C₂, D–F, G₁–G₅, H–I, J₁–J₂, K₁–K₂, L₁–L₂, and M–N, were isolated from the seeds of the mangrove plant, Xylocarpus moluccensis. Compounds 1–13 are mexicanolides with one double bond or two conjugated double bonds, while 14 belongs to a small group of mexicanolides with an oxygen bridge between C1 and C8. Compounds 15–19 are khayanolides containing a Δ^8,14 double bond, whereas 20 and 21 are rare khayanolides containing a Δ^14,15 double bond and Δ^8,9, Δ^14,15 conjugated double bonds, respectively. Compounds 22 and 23 are unusual limonoids possessing a (Z)-bicyclo[5.2.1]dec-3-en-8-one motif, while 24 and 25 are 30-ketophragmalins with Δ^8,9, Δ^14,15 conjugated double bonds. Compounds 26 and 27 are phragmalin 8,9,30-ortho esters, whereas 28 and 29 are azadirone and andirobin derivatives, respectively. The structures of these compounds, including absolute configurations of 15–19, 21–23, and 26, were established by HRESIMS, extensive 1D and 2D NMR investigations, and the comparison of experimental electronic circular dichroism (ECD) spectra. The absolute configuration of 1 was unequivocally established by single-crystal X-ray diffraction analysis, obtained with Cu Kα radiation. The diverse cyclization patterns of 1–29 reveal the strong flexibility of skeletal plasticity in the limonoid biosynthesis of X. moluccensis. Compound 23 exhibited weak antitumor activity against human triple-negative breast MD-MBA-231 cancer cells with an IC₅₀ value of 37.7 μM. Anti-HIV activities of 1, 3, 8, 10, 11, 14, 20, 23–25, and 27 were tested in vitro. However, no compounds showed potent inhibitory activity. Full article