The potential thermoelectric material Tl3XSe4 (X = V, Ta, Nb): a first-principles study.

Searching for materials with a high thermoelectric figure of merit (ZT) has always been the goal of scientific researchers in the energy field. Here, we combine first-principles calculations to obtain the thermoelectric characteristics of Tl3XSe4 (X = V, Nb, or Ta). First, we compared the phonon thermal transport characteristics of Tl3XSe4 by solving the Boltzmann transport equation and calculated the thermal conductivity. After that, we obtained the thermoelectric properties of Tl3XSe4 through the relaxation time approximation theory. The results show that Tl3XSe4 has a high Seebeck coefficient, high electrical conductivity, high power factor (PF) and low thermal conductivity contributed by both phonons and electrons. At the same time, the ZT value of Tl3XSe4 shows that it is a potential thermoelectric material with excellent performance. This work demonstrates the thermoelectric transport characteristics of Tl3XSe4 to explore its potential applications in many other fields of thermoelectricity and energy.

Co0.9Co0.1S Nanorods with an Internal Electric Field and Photothermal Effect Synergistically for Boosting Photocatalytic H2 Evolution.

The paper reports a strategy to synthesize Cd0.9Co0.1S nanorods (NRs) via a one-pot solvothermal method. Remarkably, the pencil-shaped Cd0.9Co0.1S NRs with a large aspect ratio and good polycrystalline plane structure significantly shorten the photogenerated carrier transfer path and achieve fast separation. An appropriate amount of Co addition enhances visible light-harvesting and generates a photothermal effect to improve the surface reaction kinetics and increases the charge transfer rate. Moreover, the internal electric field facilitates the separation and transfer of carriers and effectively impedes their recombination. As a result, the optimized Cd0.9Co0.1S NRs yield a remarkable H2 evolution rate of 8.009 mmol·g-1·h-1, which is approximately 7.2 times higher than that of pristine CdS. This work improves the photocatalytic hydrogen production rate by tuning and optimizing electronic structures through element addition and using the photothermal synergistic effect.

Exploring the mechanism of F282L mutation-caused constitutive activity of GPCR by a computational study.

G-protein-coupled receptors (GPCRs) are important drug targets and generally activated by ligands. However, some experiments found that GPCRs also give rise to constitutive activity through some mutations (viz., CAM), which are usually associated with different kinds of diseases. However, the mechanisms of CAMs and their roles in interactions with drug-ligands are unclear in experiments. Herein, we used microsecond molecular dynamics simulations to study the effect of one important F282L mutation on ß2AR in order to address the questions above. With the aid of principle component and correlation analysis, our results revealed that the F282L mutation could increase the instability of the overall structure, increase the dramatic fluctuations of NPxxY and extracellular loops, and decrease restraint of the helices through weakening interhelical H-bonding and correlations between residues, which could partly contribute to the constitutive activity reported by the experiments. The observations from the protein structure network (PSN) analysis indicate that the mutant exhibits less information flow than the wild ß2AR and weakens the role of TM5 and TM6 in the signal transmission, but it enhances the impact of TM3 on the orthosteric pathway and TM4 on the allosteric one. In addition, the results from the virtual screening reveal that the mutant prefers to select agonists rather than antagonists, similar to the active state but opposite of the inactive state, further confirming that the F282L mutation advances the activation of ß2AR. Our observations provide valuable information for understanding the mechanism of the mutation-caused constitutive activity of GPCR and related drug-design.

Understanding the conformation transition in the activation pathway of ß2 adrenergic receptor via a targeted molecular dynamics simulation.

G protein coupled receptors (GPCRs) play a crucial role in regulating signal recognition and transduction through their activation. The conformation transition in the activation pathway is of particular importance for their function. However, it has been poorly elucidated due to experimental difficulties in determining the conformations and the time limitation of conventional molecular dynamics (CMD) simulation. Thus, in this work, we employed a targeted molecular dynamic (TMD) simulation to study the activation process from an inactive structure to a fully active one for ß2 adrenergic receptor (ß2AR). As a reference, 110 ns CMD simulations on wild ß2AR and its D130N mutant were also carried out. TMD results show that there is at least an intermediate conformation cluster in the activation process, evidenced by the principal component analysis and the structural and dynamic differences of some important motifs. It is noteworthy that the activation of the ligand binding site lags the G-protein binding site, displaying uncoupled correlation. Comparisons between the CMD and TMD results show that the D130N mutation significantly speeds up ICL2 and key ionic lock to enter into the intermediate state, which to some extent facilitates the activation involved in the NPxxY, DRY region and the separation between TM3 and TM6. However, the contribution from the D130N mutation to the activation of the ligand binding site could not be observed within the scale of 110 ns time. These observations could provide novel insights into previous studies for better understanding of the activation mechanism for ß2AR.

Synthesis, Crystal Structures and Catalytic Oxidation Property of Two Oxidovanadium(V) Complexes with Schiff bases.

Two new oxidovanadium(V) complexes, [VO2L1] (1) and [V2O2(µ-O)2L2)] (2), where L1 and L2 are the deprotonated form of 5-bromo-2-(((2-(pyrrolidin-1-yl)ethyl)imino)methyl)phenol (HL1) and 5-bromo-2-(((2-((2-hydroxyethyl)amino)ethyl)imino)methyl)phenol (HL2), respectively, have been synthesized and structurally characterized by physico-chemical methods and single crystal X-ray determination. X-ray analysis indicates that the V atom in complex 1 is in square pyramidal coordination, and those in complex 2 are in octahedral coordination. Crystal structures of the complexes are stabilized by hydrogen bonds. The catalytic property for epoxidation of styrene by the complexes was evaluated.

First-Principles Studies on Transition Metal Doped Mo2B2 as Anode Material for Li-Ion Batteries.

New two-dimensional (2D) transition-metal borides have attracted considerable interest in research on electrode materials for Li-ion batteries (LIBs) owing to their promising properties. In this study, 2D molybdenum boride (Mo2 B2 ) with and without transition metal (TM, TM=Mn, Fe, Co, Ni, Ru, and Pt) atom doping was investigated. Our results indicated that all TM-doped Mo2 B2 samples exhibited excellent electronic conductivity, similar to the intrinsic 2D Mo2 B2 metal behavior, which is highly beneficial for application in LIBs. Moreover, we found that the diffusion energy barriers of Li along paths 1 and 2 for all TM-doped Mo2 B2 samples are smaller than 0.30 and 0.24 eV of the pristine Mo2 B2 . In particular, for 2D Co-doped Mo2 B2 , the diffusion energy barriers of Li along paths 1 and 2 are reduced to 0.14 and 0.11 eV, respectively, making them the lowest Li diffusion barriers in both paths 1 and 2. This indicates that TM doping can improve the electrochemical performance of 2D Mo2 B2 and that Co-doped Mo2 B2 is a promising electrode material for LIBs. Our work not only identifies electrode materials with promising electrochemical performance but also provides guidance for the design of high-performance electrode materials for LIBs.

Jasmine waste derived biochar as green sulfate catalysts dominate non-free radical paths efficiently degraded tetracycline.

Because of the potential environmental harm caused by the extensive application of tetracycline (TC), this study used jasmine waste rich in organic matter as a precursor and one-step carbonization into metal-free carbon-based materials to efficiently activate peroxymonosulfate (PMS) toward degrading TC. The jasmine waste biochar (JWB) with a heating rate of 10 °C min-1 and a heating temperature of 700 °C was selected as the most suitable material based on its catalytic performance. The effects of catalyst dose, PMS dose, initial pH value, coexisting inorganic anions and TC concentration on the JWB/PMS/TC system were thoroughly optimized. The results showed that the degradation efficiency of TC by JWB/PMS system was 90%. Meanwhile, the combination of electron paramagnetic resonance, masking experiments and X-ray photoelectron spectrometry confirmed that JWB degraded TC mainly through the non-radical radical pathway of 1O2 oxidation and mediated the electron transfer to PMS. In addition, some degradation products were analyzed by LC-MS and possible degradation pathways of the system were proposed. Therefore, this paper proposes a novel method for recycling jasmine waste and providing a low-cost catalyst for the oxidation treatment of refractory organic matter.

Prediction of Synergistic Drug Combinations for Prostate Cancer by Transcriptomic and Network Characteristics.

Prostate cancer (PRAD) is a major cause of cancer-related deaths. Current monotherapies show limited efficacy due to often rapidly emerging resistance. Combination therapies could provide an alternative solution to address this problem with enhanced therapeutic effect, reduced cytotoxicity, and delayed the appearance of drug resistance. However, it is prohibitively cost and labor-intensive for the experimental approaches to pick out synergistic combinations from the millions of possibilities. Thus, it is highly desired to explore other efficient strategies to assist experimental researches. Inspired by the challenge, we construct the transcriptomics-based and network-based prediction models to quickly screen the potential drug combination for Prostate cancer, and further assess their performance by in vitro assays. The transcriptomics-based method screens nine possible combinations. However, the network-based method gives discrepancies for at least three drug pairs. Further experimental results indicate the dose-dependent effects of the three docetaxel-containing combinations, and confirm the synergistic effects of the other six combinations predicted by the transcriptomics-based model. For the network-based predictions, in vitro tests give opposite results to the two combinations (i.e. mitoxantrone-cyproheptadine and cabazitaxel-cyproheptadine). Namely, the transcriptomics-based method outperforms the network-based one for the specific disease like Prostate cancer, which provide guideline for selection of the computational methods in the drug combination screening. More importantly, six combinations (the three mitoxantrone-containing and the three cabazitaxel-containing combinations) are found to be promising candidates to synergistically conquer Prostate cancer.

Theoretical calculation of a full-dimensional ab initio potential energy surface and prediction of infrared spectra for Xe-CS2.

An effective four-dimensional (4D) ab initio potential energy surface (PES) for Xe-CS2 which explicitly involves the intramolecular Q 1 symmetric stretching and Q 3 antisymmetric stretching vibrational coordinates of CS2 is constructed. The computations are carried out employing single- and double-excitation coupled-cluster theory with a non-iterative perturbation treatment of triple excitations [CCSD(T)] method with a large basis set. Two vibrationally averaged potentials at the ground and ν 1 + ν 3 (ν 1 = 1, ν 3 = 1) excited states are obtained by integrating the 4D potentials over the Q 1 and Q 3 coordinates. The potentials have a T-shaped global minimum and two equivalent linear local minima. The radial discrete variable representation/angular finite basis representation and the Lanczos algorithm are employed to calculate the rovibrational energy levels for Xe-CS2. The infrared band origin shift associated with the fundamental band of CS2 is predicted, which is red-shifted by -1.996 cm-1 in the ν 1 + ν 3 region. In addition, we further predict the spectroscopic parameters for the ground and the ν 1 + ν 3 excited states of Xe-CS2. Compared with the previous Rg-CS2 (Rg = He, Ne, Ar, Kr) complexes, we found that the complexes of the rare gas atoms with CS2 display obvious regularities.

Correction: Theoretical calculation of a full-dimensional ab initio potential energy surface and prediction of infrared spectra for Xe-CS2.

[This corrects the article DOI: 10.1039/C9RA03782A.].

Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model.

Thrombin-binding aptamer (TBA) with the sequence 5'GGTTGGTGTGGTTGG3' could fold into G-quadruplex, which correlates with functionally important genomic regionsis. However, unfolding mechanism involved in the structural stability of G-quadruplex has not been satisfactorily elucidated on experiments so far. Herein, we studied the unfolding pathway of TBA by a combination of molecular dynamics simulation (MD) and Markov State Model (MSM). Our results revealed that the unfolding of TBA is not a simple two-state process but proceeds along multiple pathways with multistate intermediates. One high flux confirms some observations from NMR experiment. Another high flux exhibits a different and simpler unfolding pathway with less intermediates. Two important intermediate states were identified. One is similar to the G-triplex reported in the folding of G-quadruplex, but lack of H-bonding between guanines in the upper plane. More importantly, another intermediate state acting as a connector to link the folding region and the unfolding one, was the first time identified, which exhibits higher population and stability than the G-triplex-like intermediate. These results will provide valuable information for extending our understanding the folding landscape of G-quadruplex formation.

Probing immobilization mechanism of alpha-chymotrypsin onto carbon nanotube in organic media by molecular dynamics simulation.

The enzyme immobilization has been adopted to enhance the activity and stability of enzymes in non-aqueous enzymatic catalysis. However, the activation and stabilization mechanism has been poorly understood on experiments. Thus, we used molecular dynamics simulation to study the adsorption of α-chymotrypsin (α-ChT) on carbon nanotube (CNT) in aqueous solution and heptane media. The results indicate that α-ChT has stronger affinity with CNT in aqueous solution than in heptane media, as confirmed by more adsorption atoms, larger contact area and higher binding free energies. Although the immobilization causes significant structure deviations from the crystal one, no significant changes in secondary structure of the enzyme upon adsorption are observed in the two media. Different from aqueous solution, the stabilization effects on some local regions far from the surface of CNT were observed in heptane media, in particular for S1 pocket, which should contribute to the preservation of specificity reported by experiments. Also, CNT displays to some extent stabilization role in retaining the catalytic H-bond network of the active site in heptane media, which should be associated with the enhanced activity of enzymes. The observations from the work can provide valuable information for improving the catalytic properties of enzymes in non-aqueous media.

Understanding the effects on constitutive activation and drug binding of a D130N mutation in the ß2 adrenergic receptor via molecular dynamics simulation.

G-protein-coupled receptors (GPCRs) are currently one of the largest families of drug targets. The constitutive activation induced by mutation of key GPCR residues is associated closely with various diseases. However, the structural basis underlying such activation and its role in drug binding has remained unclear. Herein, we used all-atom molecular dynamics simulations and free energy calculations to study the effects of a D130N mutation on the structure of ß2 adrenergic receptor (ß2AR) and its binding of the agonist salbutamol. The results indicate that the mutation caused significant changes in some key helices. In particular, the mutation leads to the departure of transmembrane 3 (TM3) from transmembrane 6 (TM6) and marked changes in the NPxxY region as well as the complete disruption of a key ionic lock, all of which contribute to the observed constitutive activation. In addition, the D130N mutation weakens some important H-bonds, leading to structural changes in these regions. Binding free energy calculations indicate that van der Waals and electrostatic interactions are the main driving forces in binding salbutamol; however, binding strength in the mutant ß2AR is significantly enhanced mainly through modifying electrostatic interactions. Further analysis revealed that the increase in binding energy upon mutation stems mainly from the H-bonds formed between the hydroxyl group of salbutamol and the serine residues of TM5. This observation suggests that modifications of the H-bond groups of this drug could significantly influence drug efficacy in the treatment of diseases associated with this mutation.

Effects of the position and manner of hydration on the stability of solvated N-methylacetamides and the strength of binding between N-methylacetamide and water clusters: a computational study.

This work mainly studies the effects of the position (there are two possible hydrated sites) and the manner (i.e., whether water acts as a proton donor or acceptor) of hydration by various numbers of water molecules on the stability of 14 solvated N-methylacetamide structures, NMA-(H(2)O)( n ) (n = 1-3), as well as the binding strength between the NMA and the water cluster, using molecular dynamics (MD) and B3LYP methods. Natural bond orbital (NBO) analysis is used to explore the origin of these effects. Some novel observations are obtained from the work. Our results show that monohydration at the carbonyl site favors stability and binding strength compared to monohydration at the amino site. Similarly, the preferred hydration at the carbonyl site is observed for dihydrated NMAs when the second water is added as a proton donor to the C=O group or the first water is H-bonded to the C=O group. However, unfavorable hydration at the C=O site occurs if the second water acts as a proton acceptor. Trihydration by a ring cluster of three water molecules at either the carbonyl site or the amino one yields relatively stable complexes, but significantly disfavors binding strength. The other trihydrated NMAs show similar behavior to dihydrated NMAs. In addition, our results show that the C=O and N-H frequencies can still be utilized to examine the H-bond effects of the water cluster.

Effects of organic solvent and crystal water on γ-chymotrypsin in acetonitrile media: observations from molecular dynamics simulation and DFT calculation.

The use of enzymes in nonaqueous solvent has been one of the most exciting facets of enzymology in recent times; however, the mechanism of how organic solvent and essential water influence on structure and function of enzyme has been not satisfactorily explained in experiments, which limit its further application. Herein, we used molecular dynamics (MD) simulation to study γ-chymotrypsin in two types of media (viz., acetonitrile media with inclusion of 151 crystal water molecules and aqueous solution). On the basis of the MD result, the truncated active site modes containing two specific solvent molecules are furthered studied at the B3LYP/6-31+G(d,p) level of theory within the framework of PCM model. The results show that the acetontrile solvent gives rise to an extent deviation of enzyme structure from the native one, a drop in the flexibility and the total SASA of enzyme. The QM study further reveals that the structure variation of the active pocket caused by acetonitrile would lead to a weakened strength in the catalytic H-bond network, a drop in the pK(a) value of His57, and an increase in the proton transfer barriers from the Ser195 to the His57 residue, which may contribute to the drop in the enzymatic activity in acetontrile media. In addition, the crystal waters play an importance role in retaining the catalytic H-bond network and weakening the acetonitrile-induced variations above, which may be associated with the fact that the enzyme could retain catalytic activity in microhydration acetonitrile media.