Large-scale snake genome analyses provide insights into vertebrate development.

Snakes are a remarkable squamate lineage with unique morphological adaptations, especially those related to the evolution of vertebrate skeletons, organs, and sensory systems. To clarify the genetic underpinnings of snake phenotypes, we assembled and analyzed 14 de novo genomes from 12 snake families. We also investigated the genetic basis of the morphological characteristics of snakes using functional experiments. We identified genes, regulatory elements, and structural variations that have potentially contributed to the evolution of limb loss, an elongated body plan, asymmetrical lungs, sensory systems, and digestive adaptations in snakes. We identified some of the genes and regulatory elements that might have shaped the evolution of vision, the skeletal system and diet in blind snakes, and thermoreception in infrared-sensitive snakes. Our study provides insights into the evolution and development of snakes and vertebrates.

Ionic liquids intercalation in titanium carbide MXenes: A first-principles investigation.

Herein, we present a density functional theory with dispersion correction (DFT-D) calculations that focus on the intercalation of ionic liquids (ILs) electrolytes into the two-dimensional (2D) Ti3C2Tx MXenes. These ILs include the cation 1-ethyl-3-methylimidazolium (Emim+), accompanied by three distinct anions: bis(trifluoromethylsulfonyl)imide (TFSA-), (fluorosulfonyl)imide (FSA-) and fluorosulfonyl(trifluoromethanesulfonyl)imide (FTFSA-). By altering the surface termination elements, we explore the intricate geometries of IL intercalation in neutral, negative, and positive pore systems. Accurate estimation of charge transfer is achieved through five population analysis models, such as Hirshfeld, Hirshfeld-I, DDEC6 (density derived electrostatic and chemical), Bader, and VDD (voronoi deformation density) charges. In this work, we recommend the DDEC6 and Hirshfeld-I charge models, as they offer moderate values and exhibit reasonable trends. The investigation, aimed at visualizing non-covalent interactions, elucidates the role of cation-MXene and anion-MXene interactions in governing the intercalation phenomenon of ionic liquids within MXenes. The magnitude of this role depends on two factors: the specific arrangement of the cation, and the nature of the anionic species involved in the process.

Multifunctional Deep Eutectic Solvent-Based Microemulsion for Transdermal Delivery of Artemisinin.

As a serious public health issue, malaria threatens the health of millions of people. Artemisinin, a gift from traditional Chinese medicine, has been used in the treatment of malaria and has shown good therapeutic efficiency. However, due to its low solubility, poor bioavailability, and short half-life time, some smart delivery strategies are still required. Herein, a multifunctional DES prepared from ibuprofen and menthol was prepared. This DES was shown to efficiently promote the solubility of artemisinin up to 400-fold. Then, it was further applied as the oil phase to construct an O/W microemulsion with the help of Tween-80 + Span-20 mixed surfactants. The prepared microemulsion displayed high efficiency in improving the permeability of artemisinin, which can be ascribed to the presence of the permeation enhancer menthol in DES and the microstructure of the O/W microemulsion. Moreover, the simultaneous permeation of artemisinin and ibuprofen further indicated the potential benefits of the presented formulation in the treatment of malaria. To sum up, the microemulsion based on multifunctional DES presented herein provided an effective method for transdermal delivery of artemisinin.

One-Dimensional Covalent Organic Frameworks for the 2e- Oxygen Reduction Reaction.

Two-dimensional covalent organic frameworks (2D COFs) are often employed for electrocatalytic systems because of their structural diversity. However, the efficiency of atom utilization is still in need of improvement, because the catalytic centers are located in the basal layers and it is difficult for the electrolytes to access them. Herein, we demonstrate the use of 1D COFs for the 2e- oxygen reduction reaction (ORR). The use of different four-connectivity blocks resulted in the prepared 1D COFs displaying good crystallinity, high surface areas, and excellent chemical stability. The more exposed catalytic sites resulted in the 1D COFs showing large electrochemically active surface areas, 4.8-fold of that of a control 2D COF, and thus enabled catalysis of the ORR with a higher H2 O2 selectivity of 85.8 % and activity, with a TOF value of 0.051 s-1 at 0.2 V, than a 2D COF (72.9 % and 0.032 s-1 ). This work paves the way for the development of COFs with low dimensions for electrocatalysis.

The Genome of Shaw's Sea Snake (Hydrophis curtus) Reveals Secondary Adaptation to Its Marine Environment.

The transition of terrestrial snakes to marine life ∼10 Ma is ideal for exploring adaptive evolution. Sea snakes possess phenotype specializations including laterally compressed bodies, paddle-shaped tails, valvular nostrils, cutaneous respiration, elongated lungs, and salt glands, yet, knowledge on the genetic underpinnings of the transition remains limited. Herein, we report the first genome of Shaw's sea snake (Hydrophis curtus) and use it to investigate sea snake secondary marine adaptation. A hybrid assembly strategy obtains a high-quality genome. Gene family analyses date a pulsed coding-gene expansion to ∼20 Ma, and these genes associate strongly with adaptations to marine environments. Analyses of selection pressure and convergent evolution discover the rapid evolution of protein-coding genes, and some convergent features. Additionally, 108 conserved noncoding elements appear to have evolved quickly, and these may underpin the phenotypic changes. Transposon elements may contribute to adaptive specializations by inserting into genomic regions around functionally related coding genes. The integration of genomic and transcriptomic analyses indicates independent origins and different components in sea snake and terrestrial snake venom; the venom gland of the sea snake harbors the highest PLA2 (17.23%) expression in selected elapids and these genes may organize tandemly in the genome. These analyses provide insights into the genetic mechanisms that underlay the secondary adaptation to marine and venom production of this sea snake.

Investigations of CO2 Capture from Gas Mixtures Using Porous Liquids.

Porous liquids, a new porous material with fluidity, can be applied in numerous fields, such as gas storage and/or separation. In this work, the separation of binary gas mixtures CO2/N2 and CO2/CH4 with porous liquids was examined by molecular dynamics (MD) simulations. The pure gas adsorption capacity was analyzed with different concentrations of porous liquids. The dependence of the separation effect of a gas mixture on the total pressure and temperature was investigated. Meanwhile, for both CO2/N2 and CO2/CH4 systems, the adsorption and separation effects of porous liquids with a cage:solvent ratio of 1:12 are better than those of 1:91 and 1:170. The results of the spatial distribution function and/or trajectories indicated that porous liquids prefer CO2, leading to the location of CO2 in the channels formed in porous liquids. However, N2 and CH4 are hardly adsorbed into the bulk. The diffusion of gas molecules follows the order of CO2 > N2 (for CO2/N2) and CH4 > CO2 (for CO2/CH4) in the bulk and N2 > CO2 (for CO2/N2) and CH4 > CO2 (for CO2/CH4) at the interface of porous liquids. Upon increasing the concentrations of porous liquids, the working capacities of CO2 show small decreases in CO2/N2 and CO2/CH4 systems, but the sorbent selection parameters are higher in pressure- and temperature-swing adsorption processes. The porous liquid with a cage:solvent ratio of 1:12 is more suitable for the separation of CO2/N2 and CO2/CH4 systems than ratios of 1:91 and 1:170.

Construction of Covalent Organic Frameworks with Crown Ether Struts.

Crown ethers are a class of macrocyclic molecules with unique flexible structures but they are rarely integrated in covalent organic frameworks (COFs). To date, employing flexible organic units such as crown ethers to construct COFs with high crystallinity and surface area are still a challenge. In this work, two new COFs with different flexible crown ethers as backbone rather than side chains are synthesized and further employed for alkali metal ions separation. Both of COFs possess high surface areas, good crystallinity, and excellent chemical stability. Interestingly, these two new COFs with 18-crown-6 or 24-crown-8 units showed remarkable binding ability of K+ or Cs+ owing to the size-fit effect. This work demonstrated that the unique structural features of crown ethers will lead to increase interest in fabricating COFs with crown ethers.

The first draft genome of Lophophorus: A step forward for Phasianidae genomic diversity and conservation.

The monal genus (Lophophorus) is a branch of Phasianidae and its species inhabit the high-altitude mountains of the Qinghai-Tibet Plateau. The Chinese monal, L. lhuysii, is a threatened endemic bird of China that possesses high-altitude adaptability, diversity of plumage color and potentially low reproductive life history. This is the first study to describe the monal genome using next generation sequencing technology. The Chinese monal genome size is 1.01 Gb, with 16,940 protein-coding genes. Gene annotation yielded 100.93 Mb (9.97%) repeat elements, 785 ncRNA, 5,465,549 bp (0.54%) SSR and 15,550 (92%) genes in public databases. Compared to other birds and mammals, the genome evolution analysis showed numerous expanded gene families and positive selected genes involved in high-altitude adaptation, especially related to the adaptation of low temperature and hypoxia. Consequently, this gene data can be used to investigate the molecular evolution of high-altitude adaptation in future bird research. Our first published genome of the genus Lophophorus will be integral for the study of monal population genetic diversity and conservation, genomic evolution and Galliformes species differentiation in the Qinghai-Tibetan Plateau.

pH Responsiveness of Hexosomes and Cubosomes for Combined Delivery of Brucea javanica Oil and Doxorubicin.

We report pH-responsive liquid crystalline lipid nanoparticles, which are dual-loaded by Brucea javanica oil (BJO) and doxorubicin hydrochloride (DOX) and display a pH-induced inverted hexagonal (pH = 7.4) to cubic (pH = 6.8) to emulsified microemulsion (pH = 5.3) phase transition with a therapeutic application in cancer inhibition. BJO is a traditional herbal medicine that strongly inhibits the proliferation and metastasis of various cancers. Doxorubicin is an antitumor drug, which prevents DNA replication and hampers protein synthesis through intercalation between the base pairs of the DNA helices. Its dose-dependent cardiotoxicity imposes the need for safe delivery carriers. Here, pH-induced changes in the structural and interfacial properties of designed multicomponent drug delivery (monoolein-oleic acid-BJO-DOX) systems are determined by synchrotron small-angle X-ray scattering and the Langmuir film balance technique. The nanocarrier assemblies display good physical stability in the studied pH range and adequate particle sizes and ζ-potentials. Their interaction with model lipid membrane interfaces is enhanced under acidic pH conditions, which mimic the microenvironment around tumor cells. In vitro cytotoxicity and apoptosis studies with BJO-DOX dual-loaded pH-switchable liquid crystalline nanoparticles are performed on the human breast cancer Michigan Cancer Foundation-7 (MCF-7) cell line and MCF-7 cells with doxorubicin resistance (MCF-7/DOX), respectively. The obtained pH-sensitive nanomedicines exhibit enhanced antitumor efficacy. The performed preliminary studies suggest a potential reversal of the resistance of the MCF-7/DOX cells to DOX. These results highlight the necessity for further understanding the link between the established pH-dependent drug release profiles of the nanocarriers and the role of their pH-switchable inverted hexagonal, bicontinuous cubic, and emulsified microemulsion inner organizations for therapeutic outcomes.

Theoretical and experimental investigations of BiOCl for electrochemical adsorption of cesium ions.

BiOCl was found to have excellent electrochemical adsorption properties for cesium ions (Cs+) in electrochemically switched ion exchange (ESIX). In this work, BiOCl nanosheets were synthesized by a hydrothermal method and used for electrochemical adsorption of Cs+. The experimental results showed that BiOCl exhibited higher electrochemical adsorption selectivity for Cs+ than Li+ and Na+. Quantum chemical calculations based on density functional theory (DFT) were first performed to compare the adsorption and migration mechanisms of three ions Li+, Na+, and Cs+ in BiOCl crystals. The calculation results revealed that the excellent electrochemical adsorption performance of BiOCl for Cs+ is due to the interaction of embedded Cs with Cl and Bi in BiOCl crystals. This makes it have a higher adsorption energy and a lower ion migration energy barrier due to the balance of interaction forces. In this work experimental and theoretical calculations were used to systematically analyze the adsorption and migration of three ions in BiOCl, which has important guiding significance for the design of highly-efficient electroactive materials for electrochemical adsorption of Cs+.

Theoretical and experimental investigations of the electronic/ionic conductivity and deprotonation of Ni3-xCoxAl-LDHs in an electrochemical energy storage system.

The remarkable effect of divalent transition metal ions on the electrochemical performance of transition metal-based layered double hydroxides (LDHs) was systematically investigated via computational and experimental approaches. Ni3-xCoxAl-LDHs (x = 0, 1, 2, and 3) were synthesized on carbon paper by a unipolar pulse electrodeposition (UPED) method and used as electrodes in energy storage systems. The structures were characterized by X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS). Their electrochemical performance was evaluated by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The mechanism of different electrochemical performances with various divalent transition metal ions was investigated by the density functional theory (DFT) plus U method and molecular dynamics (MD) simulations. The computational and experimental data demonstrated that the electronic and ionic conductivity and deprotonation of NiAl-LDHs were improved by doping Co species, and the incorporation of Co and Ni cations enabled LDHs to exhibit a larger interlayer spacing which can facilitate the diffusion of OH- ions, indicating that NiCo2Al-LDHs had the highest specific capacitance.

Comparative genome-wide survey of single nucleotide variation uncovers the genetic diversity and potential biomedical applications among six Macaca species.

Macaca is of great importance in evolutionary and biomedical research. Aiming at elucidating genetic diversity patterns and potential biomedical applications of macaques, we characterized single nucleotide variations (SNVs) of six Macaca species based on the reference genome of Macaca mulatta. Using eight whole-genome sequences, representing the most comprehensive genomic SNV study in Macaca to date, we focused on discovery and comparison of nonsynonymous SNVs (nsSNVs) with bioinformatic tools. We observed that SNV distribution patterns were generally congruent among the eight individuals. Outlier tests of nsSNV distribution patterns detected 319 bins with significantly distinct genetic divergence among macaques, including differences in genes associated with taste transduction, homologous recombination, and fat and protein digestion. Genes with specific nsSNVs in various macaques were differentially enriched for metabolism pathways, such as glycolysis, protein digestion and absorption. On average, 24.95% and 11.67% specific nsSNVs were putatively deleterious according to PolyPhen2 and SIFT4G, respectively, among which the shared deleterious SNVs were located in 564⁻1981 genes. These genes displayed enrichment signals in the 'obesity-related traits' disease category for all surveyed macaques, confirming that they were suitable models for obesity related studies. Additional enriched disease categories were observed in some macaques, exhibiting promising potential for biomedical application. Positively selected genes identified by PAML in most tested Macaca species played roles in immune and nervous system, growth and development, and fat metabolism. We propose that metabolism and body size play important roles in the evolutionary adaptation of macaques.

An absorption mechanism and polarity-induced viscosity model for CO2 capture using hydroxypyridine-based ionic liquids.

A series of new hydroxypyridine-based ionic liquids (ILs) are synthesized and applied in CO2 capture through chemical absorption, in which one IL, i.e., tetrabutylphosphonium 2-hydroxypyridine ([P4444][2-Op]), shows a viscosity as low as 193 cP with an absorption capacity as high as 1.20 mol CO2 per mol IL. Because the traditional anion-CO2 absorption mechanism cannot provide an explanation for the influences of cations and temperature on CO2 absorption capacity, herein, a novel cation-participating absorption mechanism based on the proton transfer is proposed to explain the high absorption capacity and the existence of a turning point of absorption capacity with the increase of temperature for the capture of CO2 using [P4444][n-Op] (n = 2, 3, 4) ILs. Also, the relationship between the viscosity of ILs and the linear interaction energy is proposed for the first time, which can guide how to design and synthesize ILs with low viscosity. Quantum chemistry calculations, which are based on the comprehensive analysis of dipole moment, cation-anion interaction energy and surface electrostatic potential, indicate that the different viscosities of hydroxypyridine-based ILs and the changes after CO2 absorption mainly resulted from the different distribution of negative charges in the anion.

The Interactions between Imidazolium-Based Ionic Liquids and Stable Nitroxide Radical Species: A Theoretical Study.

In this work, the interactions between imidazolium-based ionic liquids and some stable radicals based on 2,2,6,6-tetramethylpiperidine-1-yloxyl (TEMPO) have been systematically investigated using density functional theory calculations at the level of M06-2x. Several different substitutions, such as hydrogen bonding formation substituent (OH) and ionic substituents (N(CH3)3(+) and OSO3(-)), are presented at the 4-position of the spin probe, which leads to additional hydrogen bonds or ionic interactions between these substitutions and ionic liquids. The interactions in the systems of the radicals containing ionic substitutions with ionic liquids are predicted much stronger than those in the systems of neutral radicals, resulting in a significant reduction of the mobility of ionic radicals in ionic liquids. To further understand the nature of these interactions, the natural bond order, atoms in molecules, noncovalent interaction index, electron density difference, energy decomposition analysis, and charge decomposition analysis schemes were employed. The additional ionic interactions between ionic radicals and counterions in ionic liquids are dominantly contributed from the electrostatic term, while the orbital interaction plays a major role in other interactions. The results reported herein are important to understand radical processes in ionic liquids and will be very useful in the design of task-specific ionic liquids to make the processes more efficient.

The acidity/basicity of metal-containing ionic liquids: insights from surface analysis and the Fukui function.

Metal-containing ionic liquids (ILs) have been recognized as potential solvents, catalysts, catalyst precursors and reagents for many organic processes. In this work, several quantum-chemical parameters, including the surface electrostatic potential (Vs,max and Vs,min), the lowest surface average local ionization energy (I̅s,min), and the electrostatic potential at the position of an atom (EPnuc), were adopted to understand the acidity/basicity of metal-containing ILs. Chlorometallate-based ILs show stronger acidity than conventional ILs, because of the increased electron-deficiency of the imidazole ring upon the incorporation of metal chloride. For the ILs with the Ag-coordinated cations, the acidity tends to attenuate while the basicity becomes stronger, as compared to traditional ILs. In addition, the regional Fukui function was also used to assess the molecular distribution of the Lewis acidity/basicity of the ILs under study. Overall, the introduction of metals into either the cations or the anions influences the acidity/basicity of ILs to a large degree, which would be beneficial for their certain applications, such as catalysis and extraction. We hope that the results presented here will assist in the development of novel metal-containing ILs with desirable properties.

Structures and electronic properties of transition metal-containing ionic liquids: insights from ion pairs.

Transition metal-containing ionic liquids (TM-ILs) have attracted a great deal of attention in recent years, due to their unique physical and chemical properties. In this work, several representative TM-ILs, such as the cations consisting of silver(I) center coordinated by two n-alkylimidazole ligands ([(C(n)(im))Ag(mim)](+)) and the anions involving mercury(II) (HgCl3(-)), zinc(II) (ZnCl3(-)), and rhenium(VII) (ReO4(-)), were investigated using density functional theory calculations. First, the structural and energetic properties of the ion pairs for these TM-ILs have been examined in detail and compared with properties for conventional ILs. It was found that the interactions between the cations and anions, including hydrogen bonds and electrostatic interactions, in TM-ILs become weaker in strength than those in traditional ILs. In particular, the calculated geometric and energetic features compare fairly well with the experimental results, such as melting points and X-ray crystal structures of these TM-ILs. Then, the structures and energetics of ion-pair dimers for three ILs containing HgCl3(-), ZnCl3(-), and ReO4(-) were also explored, to gain a deeper understanding of the properties of TM-ILs. Finally, a survey of the Cambridge Structural Database (CSD) was undertaken to provide some crystallographic implications of TM-ILs.

Dipole moment regulation for enhancing internal electric field in covalent organic frameworks photocatalysts.

Covalent organic frameworks (COFs) have recently emerged as a kind of promising photocatalytic platform in addressing the growing threat of trace pollutants in aquatic environments. Along this, we propose a strategy of constructing internal electric field (IEF) in COFs through the dipole moment regulation, which intrinsically facilitates the separation and transfer of photogenerated excitons. Two COFs of BTT-TZ-COF and BTT-TB-COF are developed by linking the electron-donor of benzotrithiophene (BTT) block and the electron-acceptor of triazine (TZ) or tribenzene (TB) block, respectively. DFT calculations demonstrate TZ block with larger dipole moment can achieve more efficient IEF due to the stronger electron-attractive force and hence narrower bandgap. Moreover, featuring the highly-order crystalline structure for accelerating photo-excitons transfer and rich porosity for facilitating the adsorption, BTT-TZ-COF exhibited an excellent universal performance of photocatalytic degradations of various dyes. Specifically, a superior photodegradation efficiency of 99% Rhodamine B (RhB) is achieved within 20 min under the simulated sunlight. Therefore, this convenient construction approach of enhanced IEF in COFs through rational regulation of the dipole moment can be a promising way to realize high photocatalytic activity.

The Interactions between Ionic Liquids and Lithium Polysulfides in Lithium-Sulfur Batteries: A Systematic Density Functional Theory Study.

Ionic liquids (ILs) based on hybrid anions have recently garnered attention as beguiling alternative electrolytes for energy storage devices. This attention stems from the potential of these asymmetric anions to reduce the melting point of ILs and impede the crystallization of ILs. Furthermore, they uphold the advantages associated with their more conventional symmetric counterparts. In this study, we employed dispersion-corrected density functional theory (DFT-D) calculations to scrutinize the interplay between two hybrid anions found in ionic liquids [FTFSA]- and [MCTFSA]- and the [C4mpyr]+ cation, as well as in lithium polysulfides in lithium-sulfur batteries. For comparison, we also examined the corresponding ILs containing symmetric anions, [TFSA]- and [FSA]-. We found that the hybrid anion [MCTFSA]- and its ionic liquid exhibited exceptional stability and interaction strength. Additionally, our investigation unveiled a remarkably consistent interaction between ionic liquids (ILs) and anions with lithium polysulfides (and S8) during the transition from octathiocane (S8) to the liquid long-chain Li2Sn (4 ≤ n ≤ 8). This contrasts with the gradual alignment observed between cations and lithium polysulfides during the intermediate state from Li2S4 to the solid short-chain Li2S2 and Li2S1. We thoroughly analyzed the interaction mechanism of ionic liquids composed of different symmetry anions and their interactions with lithium polysulfides.

Noncovalent interactions in halogenated ionic liquids: theoretical study and crystallographic implications.

In recent years, several specific imidazolium-based ionic liquids with halogen substituents on the imidazole ring as well as on the alkyl chains have been reported. In this work, noncovalent interactions in four halogenated ionic liquids, i.e. 2-bromo-/iodo- and 4,5-dibromo-/diiodo-1,3-dimethylimidazolium trifluoromethanesulfonates, were systematically investigated using density functional theory calculations. The structural and energetic properties of the ion pairs for such ionic liquids have been fully examined and compared with the non-halogenated ones. It was found that C-X···O halogen bonds, C-H···O hydrogen bonds, and electrostatic interactions with the anion located over the imidazole ring in the ion pairs. In addition, the structures and energetics of two ion pairs for such ionic liquids were also explored to reproduce experimental observations. The halogen-bonded ring structures and the conformers with the concurrent C-H···O and C-X···O contacts were predicted, consistent with the X-ray crystal structures of corresponding organic salts. Finally, the implications of the observed structural and energetic features of ion pairs on the design of halogen-bonding ionic liquids were discussed. The results presented herein should provide useful information in the development of novel halogenated ionic liquids used for specific tasks ranging from organic synthesis to gas absorption.