Unraveling Hydrogen Adsorption on Transition Metal-Doped [Mo3S13]2- Clusters: Insights from Density Functional Theory Calculations.

Molecular and dissociative hydrogen adsorption of transition metal (TM)-doped [Mo3S13]2- atomic clusters were investigated using density functional theory calculations. The introduced TM dopants form stable bonds with S atoms, preserving the geometric structure. The S-TM-S bridging bond emerges as the most stable configuration. The preferred adsorption sites were found to be influenced by various factors, such as the relative electronegativity, coordination number, and charge of the TM atom. Notably, the presence of these TM atoms remarkably improved the hydrogen adsorption activity. The dissociation of a single hydrogen molecule on TM[Mo3S13]2- clusters (TM = Sc, Cr, Mn, Fe, Co, and Ni) is thermodynamically and kinetically favorable compared to their bare counterparts. The extent of favorability monotonically depends on the TM impurity, with a maximum activation barrier energy ranging from 0.62 to 1.58 eV, lower than that of the bare cluster (1.69 eV). Findings provide insights for experimental research on hydrogen adsorption using TM-doped molybdenum sulfide nanoclusters, with potential applications in the field of hydrogen energy.

Density Functional Study of Size-Dependent Hydrogen Adsorption on Ag n Cr (n = 1-12) Clusters.

Increasing interest has been paid for hydrogen adsorption on atomically controlled nanoalloys due to their potential applications in catalytic processes and energy storage. In this work, we investigate the interaction of H2 with small-sized Ag n Cr (n = 1-12) using density functional theory calculations. It is found that the cluster structures are preserved during the adsorption of H2 either molecularly or dissociatively. Ag3Cr-H2, Ag6Cr-H2, and Ag9Cr-H2 clusters are identified to be relatively more stable from computed binding energies and second-order energy difference. The dissociation of adsorbed H2 on Ag2Cr, Ag3Cr, Ag6Cr, and Ag7Cr clusters is favored both thermodynamically and kinetically. The dissociative adsorption is unlikely to occur because of a considerable energy barrier before reaching the final state for Ag4Cr or due to energetic preferences for n = 1, 5, and 8-12 species. Comprehensive analysis shows that the geometric structure of clusters, the relative electronegativity, and the coordination number of the Cr impurity play a decisive role in determining the preferred adsorption configuration.

A computationally affordable approach for accurate prediction of the binding affinity of JAK2 inhibitors.

Janus kinase 2 (JAK2) inhibitors are potential anticancer drugs in the treatment of lymphoma, leukemia, thrombocytosis and particularly myeloproliferative diseases. However, the resemblance among JAK family members has challenged the identification of highly selective inhibitors for JAK2 to reduce undesired side effects. As a result, a robust search for promising JAK2 inhibitors using a computational approach that can effectively nominate new potential candidates to be further analyzed through laborious experimental operations has become necessary. In this study, the binding affinities of JAK2 inhibitors were rapidly and precisely estimated using the fast pulling of ligand (FPL) simulations combined with a modified linear interaction energy (LIE) method. The approach correlates with the experimental binding affinities of JAK2 inhibitors with a correlation coefficient of R = 0.82 and a root-mean-square error of 0.67 kcal•mol-1. The data reveal that the FPL/LIE method is highly approximate in anticipating the relative binding free energies of known JAK2 inhibitors with an affordable consumption of computational resources, and thus, it is very promising to be applied in in silico screening for new potential JAK2 inhibitors from a large number of molecules available.

First-row transition metal doped germanium clusters Ge16M: some remarkable superhalogens.

A theoretical study of geometric and electronic structures, stability and magnetic properties of both neutral and anionic Ge16M0/- clusters with M being a first-row 3d transition metal atom, is performed using quantum chemical approaches. Both the isoelectronic Ge16Sc- anion and neutral Ge16Ti that have a perfect Frank-Kasper tetrahedral T d shape and an electron shell filled with 68 valence electrons, emerge as magic clusters with an enhanced thermodynamic stability. The latter can be rationalized by the simple Jellium model. Geometric distortions from the Frank-Kasper tetrahedron of Ge16M having more or less than 68 valence electrons can be understood by a Jahn-Teller effect. Remarkably, DFT calculations reveal that both neutral Ge16Sc and Ge16Cu can be considered as superhalogens as their electron affinities (≥3.6 eV) exceed the value of the halogen atoms and even that of icosahedral Al13. A detailed view of the magnetic behavior of Ge16M0/- clusters shows that the magnetic moments of the atomic metals remain large even when they are quenched upon doping. When M goes from Sc to Zn, the total spin magnetic moment of Ge16M0/- increases steadily and reaches the maximum value of 3 µ B with M = Mn before decreasing towards the end of the first-row 3d block metals. Furthermore, the IR spectra of some tetrahedral Ge16M are also predicted.

Systematic Investigation of the Structure, Stability, and Spin Magnetic Moment of CrM n Clusters (M = Cu, Ag, Au, and n = 2-20) by DFT Calculations.

Binary clusters of transition-metal and noble-metal elements have been gathering momentum for not only advanced fundamental understanding but also potential as elementary blocks of novel nanostructured materials. In this regard, the geometries, electronic structures, stability, and magnetic properties of Cr-doped Cu n , Ag n , and Au n clusters (n = 2-20) have been systematically studied by means of density functional theory calculations. It is found that the structural evolutions of CrCu n and CrAg n clusters are identical. The icosahedral CrCu12 and CrAg12 are crucial sizes for doped copper and silver species. Small CrAu n clusters prefer the planar geometries, while the larger ones appear as on the way to establish the tetrahedral CrAu19. Our results show that while each noble atom contributes one s valence electron to the cluster shell, the number of chromium delocalized electrons is strongly size-dependent. The localization and delocalization behavior of 3d orbitals of the chromium decide how they participate in metallic bonding, stabilize the cluster, and give rise to and eventually quench the spin magnetic moment. Moreover, molecular orbital analysis in combination with a qualitative interpretation using the phenomenological shell model is applied to reveal the complex interplay between geometric structure, electronic structure, and magnetic moment of clusters. The finding results are expected to provide greater insight into how a host material electronic structure influences the geometry, stability, and formation of spin magnetic moments in doped systems.

The binary aluminum scandium clusters Al x Sc y with x + y = 13: when is the icosahedron retained?

Geometrical and electronic structures of the 13-atom clusters Al x Sc y with x + y = 13, as well as their thermodynamic stabilities were investigated using DFT calculations. Both anionic and neutral isomers of Al x Sc y were found to retain an icosahedral shape of both Al13 and Sc13 systems in which an Al atom occupies the endohedral central position of the icosahedral cage, irrespective of the number of Al atoms present. Such a phenomenon occurs to maximize the number of stronger Al-Al and Sc-Al bonds instead of the weaker Sc-Sc bonds. NBO analyses were applied to examine their electron configurations and rationalize the large number of open shells and thereby high multiplicities of the mixed clusters having more than three Sc atoms. The SOMOs are the molecular orbitals belonged to the irreducible representations of the symmetry point group of the clusters studied, rather than to the cluster electron shells. Evaluation of the average binding energies showed that the thermodynamic stability of Al x Sc y clusters is insignificantly altered as the number y goes from 0 to 7 and then steadily decreases when y attains the 7-13 range. Increase of the Sc atom number also reduces the electron affinities of the binary Al x Sc y clusters, and thus they gradually lose the superhalogen characteristics with respect to the pure Al13.

Correction: The binary aluminum scandium clusters Al x Sc y with x + y = 13: when is the icosahedron retained?

[This corrects the article DOI: 10.1039/D1RA06994B.].

Design, synthesis, structure, in vitro cytotoxic activity evaluation and docking studies on target enzyme GSK-3ß of new indirubin-3'-oxime derivatives.

The addition of chalcone and amine components into indirubin-3'-oxime resulted in 15 new derivatives with high yields. Structures of new derivatives were also elucidated through 1D, 2D-NMR and HR-MS(ESI) spectra and X-ray crystallography. All designed compounds were screened for cytotoxic activity against four human cancer cell lines (HepG2, LU-1, SW480 and HL-60) and one human normal kidney cell line (HEK-293). Compound 6f exhibited the most marked cytotoxicity meanwhile cytotoxicity of compounds 6e, 6h and 6l was more profound toward cancer cell lines than toward normal cell. These new derivatives were further analyzed via molecular docking studies on GSK-3ß enzyme. Docking analysis shows that most of the derivatives exhibited potential inhibition activity against GSK-3ß with characteristic interacting residues in the binding site. The fast pulling of ligand scheme was then employed to refine the binding affinity and mechanism between ligands and GSK-3ß enzyme. The computational results are expected to contribute to predicting enzyme target of the trial inhibitors and their possible interaction, from which the design of new cytotoxic agents could be created in the future.

Estimation of the ligand-binding free energy of checkpoint kinase 1 via non-equilibrium MD simulations.

Checkpoint kinase 1 (CHK1) is a serine/threonine-protein kinase that is involved in cell cycle regulation in eukaryotes. Inhibition of CHK1 is thus considered as a promising approach in cancer therapy. In this study, the fast pulling of ligand (FPL) process was applied to predict the relative binding affinities of CHK1 inhibitors using non-equilibrium molecular dynamics (MD) simulations. The work of external harmonic forces to pull the ligand out of the binding cavity strongly correlated with the experimental binding affinity of CHK1 inhibitors with the correlation coefficient of R = -0.88 and an overall root mean square error (RMSE) of 0.99 kcal/mol. The data indicate that the FPL method is highly accurate in predicting the relative binding free energies of CHK1 inhibitors with an affordable CPU time. A new set of molecules were designed based on the molecular modeling of interactions between the known inhibitor and CHK1 as inhibitory candidates. Molecular docking and FPL results exhibited that the binding affinities of developed ligands were similar to the known inhibitor in interaction with the catalytic site of CHK1, producing very potential CHK1 inhibitors of that the inhibitory activities should be further evaluated in vitro.

Prediction of AChE-ligand affinity using the umbrella sampling simulation.

Acetylcholinesterase (AChE) is characterized as a key target for designing inhibitors to prevent Alzheimer's disease (AD). The binding free energy of a ligand to the AChE enzyme is a critical factor to screen the potential inhibitor in addition to pharmacokinetics and pharmacology estimation. The biased sampling or umbrella sampling (US) method emerges as a reliable technique to estimate the AChE-inhibitor affinity. The affinity is computed as the difference between the largest and smallest values of the free energy change, obtained by using a potential of mean force (PMF) analysis. The obtained affinities overestimate the experimental ones with a value of ∼4.10 kcal/mol. However, a very good correlation coefficient (R=0.94) between the computational and experimental values is observed. Consequently, the obtained precision is high since the mean error of the free energy value is of δ=1.17 kcal/mol. The binding affinity of a new ligand can be consistently appraised via the US technique. Therefore, the absolute binding free energy of a ligand to the AChE protein can be obtained via the linear regression with the root-mean-square errors (RMSE) of 0.98 kcal/mol. The small value of RMSE implies that ligands revealing the similar binding affinities are able to be discriminated through the US simulations. In addition, the derivatives of Cordyceps were recently reported that they are able to inhibit the AChE enzyme, resulting in an improvement in learning and cognitive ability for curing AD. The active metabolites of Cordyceps were thus evaluated as the potential inhibitors for the AChE enzyme, and the 5-Carboxy-2'-deoxyuridine compound can inhibit the activity of the AChE enzyme. These compounds are also passed the testing of Lipinski's rule of five, toxicity, crossing blood-brain barrier (BBB) ability, and human intestinal absorption.

Social and ecological challenges of market-oriented shrimp farming in Vietnam.

Vietnam is one of the largest shrimp exporters in the world. Since 2010, Vietnam has earned about two billion dollars annually through shrimp exports. As a fertile area of greatest potential for agricultural production in Vietnam, the Mekong Delta has been a major contributor to the country's achievements, especially in the agricultural sector. During recent decades, trade liberation along with various policies in support of aquaculture has accelerated the development of shrimp production in the Delta. Based on an ethnographic study of shrimp farming in the Mekong Delta of Vietnam, I assert that along with great rewards arising from the expansion of shrimp farming areas, productivity, and export value, the shrimp industry has brought various environmental, economic and social challenges. Consequently, shrimp farming is a risky business and local inhabitants have relied on various strategies to cope with these challenges. Risk mitigation in shrimp production and labor migration are the two important strategies of local inhabitants for securing their livelihoods. Water pollution and poor quality post-larvae shrimp are direct consequences of market-oriented production.