Comprehensive Theoretical Study of Cp*IrIII-Catalyzed Intermolecular Enantioselective Allylic C-H Amidation: Reaction Mechanism, Electronic Processes, and Regioselectivity.

Density functional theory was used to elucidate the reaction mechanism of Cp*IrIII-catalyzed intermolecular regioselective C(sp3)-H amidation of alkenes with methyl dioxazolones. All substrates, intermediates, and transition states were fully optimized at the ωB97XD/6-31G(d,p) level (LANL2DZ(f) for Ir). The computational results revealed that this amidation occurred through the IrIII/IrV catalytic cycle, involving four important elementary steps: C-H bond activation, oxidative addition of methyl dioxazolone, reductive elimination, and proto-demetalation, and the first was the rate-determining step. The C-H bond activation showed good α- and branch-regioselectivity, decided by the distortion energy of 2-pentene and the interaction energy of the transition state, respectively. The oxidative addition of dioxazolone occurred in one elementary step with CO2 disassociation. The reductive elimination showed good branch-regioselectivity determined by the distorted energy of the allyl group. In the proto-demetalation, hydrogen directly transferred from the oxygen atom to the nitrogen atom. Moreover, to clarify the effect of the substituted groups, selected 12 substrates were also discussed in this text.

Theoretical Study of N-H σ-Bond Activation by Nickel(0) Complex: Reaction Mechanism, Electronic Processes, and Prediction of Better Ligand.

N-H σ-bond activation of alkylamine by Ni(PCy3) was investigated using density functional theory (DFT) calculations. When simple alkylamine NHMe2 is a reactant, both concerted oxidative addition in Ni(PCy3)(NHMe2) and ligand-to-ligand H transfer reaction in Ni(PCy3)(C2H4)(NHMe2) are endergonic and need a high activation energy. When NH(Me)(Bs) (Bs = SO2Ph, a model of tosyl group used in experiments) is a reactant, both reactions are exergonic and occur easily with a much smaller activation energy. The much larger reactivity of NH(Me)(Bs) than that of NHMe2 results from the stronger Ni-N(Me)(Bs) bond than the Ni-NMe2 bond and the presence of the Ni-O bonding interaction between the Bs group and the Ni atom in the product. N-Heterocyclic carbene, 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene (IPr), is computationally predicted to be better than PCy3 because the Ni-NMe2 and Ni-N(Me)(Bs) bonds in the IPr complex are stronger, respectively, than those of the PCy3 complex. The introduction of the electron-withdrawing Bs group to the N atom of amine and the use of IPr as a ligand are recommended for the N-H σ-bond activation. The C-H σ-bond activations of benzene via the oxidative addition and the ligand-to-ligand H transfer reaction were also investigated here for comparison with the N-H σ-bond activation. The differences between the C-H σ-bond activation of benzene and the N-H σ-bond activation of these amines are discussed in terms of the N-H, C-H, Ni-Ph, and Ni-NMe2, and Ni-N(Me)(Bs) bond energies and back-donation to benzene from the Ni atom.

GPress: a framework for querying general feature format (GFF) files and expression files in a compressed form.

MOTIVATION: Sequencing data are often summarized at different annotation levels for further analysis, generally using the general feature format (GFF) or its descendants, gene transfer format (GTF) and GFF3. Existing utilities for accessing these files, like gffutils and gffread, do not focus on reducing the storage space, significantly increasing it in some cases. We propose GPress, a framework for querying GFF files in a compressed form. GPress can also incorporate and compress expression files from both bulk and single-cell RNA-Seq experiments, supporting simultaneous queries on both the GFF and expression files. In brief, GPress applies transformations to the data which are then compressed with the general lossless compressor BSC. To support queries, GPress compresses the data in blocks and creates several index tables for fast retrieval. RESULTS: We tested GPress on several GFF files of different organisms, and showed that it achieves on average a 61% reduction in size with respect to gzip (the current de facto compressor for GFF files) while being able to retrieve all annotations for a given identifier or a range of coordinates in a few seconds (when run in a common laptop). In contrast, gffutils provides faster retrieval but doubles the size of the GFF files. When additionally linking an expression file, we show that GPress can reduce its size by more than 68% when compared to gzip (for both bulk and single-cell RNA-Seq experiments), while still retrieving the information within seconds. Finally, applying BSC to the data streams generated by GPress instead of to the original file shows a size reduction of more than 44% on average. AVAILABILITY AND IMPLEMENTATION: GPress is freely available at https://github.com/qm2/gpress. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Lysine Ethylation by Histone Lysine Methyltransferases.

Biomedicinally important histone lysine methyltransferases (KMTs) catalyze the transfer of a methyl group from S-adenosylmethionine (AdoMet) cosubstrate to lysine residues in histones and other proteins. Herein, experimental and computational investigations on human KMT-catalyzed ethylation of histone peptides by using S-adenosylethionine (AdoEth) and Se-adenosylselenoethionine (AdoSeEth) cosubstrates are reported. MALDI-TOF MS experiments reveal that, unlike monomethyltransferases SETD7 and SETD8, methyltransferases G9a and G9a-like protein (GLP) do have the capacity to ethylate lysine residues in histone peptides, and that cosubstrates follow the efficiency trend AdoMet>AdoSeEth>AdoEth. G9a and GLP can also catalyze AdoSeEth-mediated ethylation of ornithine and produce histone peptides bearing lysine residues with different alkyl groups, such as H3K9meet and H3K9me2et. Molecular dynamics and free energy simulations based on quantum mechanics/molecular mechanics potential supported the experimental findings by providing an insight into the geometry and energetics of the enzymatic methyl/ethyl transfer process.

Theoretical Insight into Ni(0)-Catalyzed Hydroarylation of Alkenes and Arylboronic Acids.

The density functional theory (ωB97XD functional) is employed to clarify nickel(0)/PtBu3-catalyzed hydroarylation of alkenes and arylboronic acids with methanol. The computational results reveal that this reaction goes primarily through the ligand-to-ligand H transfer from the O-H bond to the alkene coordinated with nickel, complexation of arylboronic acid to the nickel-alkyl-methoxyl intermediate, attack of methoxyl on boron, transmetalation, and reductive elimination. The formation of the branched 1,1-diarylalkane, linear 1,1-diarylalkane, and alkene-dimer is also discussed in this work.

Strategy Used to Control the Mechanism of Homogeneous Alkyne/Olefin Hydrogenation: AIMD Simulations and DFT Calculations.

Understanding the mechanism of the catalytic reaction is an effective way to design new high-performance catalysts. The mechanisms of alkyne/olefin hydrogenations catalyzed by a nonclassical Co-N2 catalyst are explored by ab initio molecular dynamics simulations and density functional theory calculations. From the calculated results, the hydrogenation mechanisms, i.e., molecular or atomic mechanisms, can be effectively controlled via employing the different interaction between the catalyst and substrates. The origination of excellent selectivity toward E-olefins for the Co-N2 catalyst is also taken into account with the help of investigating the olefin hydrogenation process. The mechanism indicates that the negligible energy barrier of rotation is the main reason for highly selective semihydrogenation of a Co-N2 catalyst, which leads to the trans-olefin formation. These investigations may provide some useful information and guidelines on the current understanding of the hydrogenation reaction and designing the high-performance catalysts.

Synthesis, characterization and bioactivities of a new covalent copper(II) compound derived from {P2Mo5O23}6- and thiosemicarbazones.

In this article, a new compound H2[{Cu(HL)(H2O)}2(P2Mo5O23)]·5H2O (1) (HL = 2-acetylpyrazine thiosemicarbazone) has been synthesized and structurally characterized by single-crystal X-ray diffraction of and other detection techniques. Interestingly, the structure of 1 is different from many reported copper-based complexes, in which the [P2Mo5O23]6-, two Cu2+ ions and two HL were directly connected by covalent bands. Biological studies demonstrated that 1 indicated moderate antibacterial activity against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus), and a better cytotoxicity against human hepatic cancer line (SMMC-7721) than Mitoxantrone (Mito), the current clinical anticancer drug. Besides, the antibacterial mechanisms of 1 have been studied by the membrane integrity disruption, the destructive reactive oxygen species generation (ROS), the glutathione (GSH) depletion and the depressed enzymatic activity of respiratory chain dehydrogenases (RCD). These results revealed that the combination of HL, Cu2+, [P2Mo5O23]6- shows a higher antibacterial and cytotoxic activity.

Phosphine ligand-coated Cu nanoparticle-catalyzed selective semihydrogenation of alkynes: electronic or hindrance effects of the ligand?

Understanding the mechanism of a catalytic reaction is of fundamental importance not only scientifically but also technologically to the design of high-performance catalysts. In this work, the mechanisms of 1-phenyl-1-propyne and cis-ß-methylstyrene hydrogenations catalyzed by Cu55 and ligand-coated Cu55 are explored in detail by means of density functional theory (DFT). The calculated results indicate that the semihydrogenation selectivity of the catalyst can be effectively controlled by employing a suitable ligand. That is, the PCy3 and PPh3 ligands used to coat Cu55 can largely raise the energy barrier of the rate-determining step for cis-ß-methylstyrene hydrogenation. By the study of energy decomposition analysis (EDA) and charge density difference, it can be found that the deformation energies of the substrate fragments play a crucial role in the energy barriers of the rate-determining steps. The large hindrance effect of the ligands is beneficial for improving the semihydrogenation selectivity of the catalysts. This study provides significant information for future catalyst design and on the physical origin of the phosphine ligand-coated nanoparticle catalysis for semihydrogenation.

Small substituent groups as geometric controllers for tridentate platinum(ii) complexes to effectively suppress non-radiative decay processes.

For phosphorescent emitters, the rigidity of the geometry is a crucial indicator, which can directly determine the non-radiative decay rate. In this article, density functional theory (DFT) calculations were performed to investigate the influence of the small substituent groups on the rigidities of tridentate Pt(ii) complexes in detail. The calculated results indicate that the small substituent groups can serve as geometric controllers to suppress the structural distortion on going from the ground state (S0) to the lowest-lying triplet excited state (T1) (Jahn-Teller distortion). For instance, when electron-donating substituent groups, including -NH2, -N(CH3)2 and -OCH3, were employed, the rigidities of the corresponding Pt(ii) complexes can be effectively enhanced because the highest occupied molecular orbital (HOMO)-HOMO-1 energy gaps could be increased. Different from the electron-donating substituent groups, electron-withdrawing substituent groups, i.e., -NO2 and -COCH3, can cause a negligible change in HOMO and HOMO-1 energies during the S0 → T1 transition process, and therefore, for Pt-NO2 and Pt-COCH3, no Jahn-Teller distortion occurs. According to the calculated results, the rigidities of tridentate Pt(ii) complexes could be raised via tuning the energies of the frontier molecular orbital (FMO) with the help of small substituent groups.

What accounts for the color purity of tetradentate Pt complexes? A computational analysis.

In order to improve the texture of human visual perception and broaden the range of certain optical applications, many phosphorescent complexes exhibiting narrow emission spectra have been prepared through reasonable molecular design. For example, by adding a particular group such as tert-butyl (tbu) to a suitable position of PtON1 and PtON7, the peak width of a relevant vibronic band caused by the specific vibrational normal modes could be dramatically restrained in the emission spectra at room temperature. For the purpose of finding an effective approach to replace the trial-and-error manner, the microscopic mechanism of such high color purity was elucidated by computational investigation. In this study, we aim to identify the reason that causes sharp emission associated with the relevant vibrational normal modes. Here, these modes can be labeled to the emission peak by the vibrationally resolved emission spectra. Based on the displacement vectors of relevant normal modes and the vibrationally resolved spectra, the most possible reason for the higher color purity is that tbu in a specific location can restrain the structural deformation between the first triplet excited state (T1) and the ground state (S0). That is to say, the relevant Huang-Rhys factor (Sk) of specific vibrational modes would be decreased. For these compounds, the total bandwidth and the height of the intermediate and high-frequency regions which are in direct proportion to Sk would be decreased to obtain the higher color purity by tbu in a particular position. What is more, the best position for tbu in order to suppress the structural deformation was also considered. In the meantime, radiative (kr) and nonradiative (knr) decay rates of T1 were investigated to seek the effective phosphorescent complexes.

Effect of needle diameter, type and volume of contrast agent on intervertebral disc degeneration in rats with discography.

PURPOSE: Discography can increase disc degeneration, but the influence of different discography variables on the degeneration of discs has not been reported. The aim of this study was to investigate the effects of discography variables of needle diameter, type of contrast agent and volume of contrast agent on disc degeneration. METHODS: Three separate experiments examined needle diameter, and type and volume of contrast agent. Coccygeal discs (Co7-10) adult male rats were used. X-rays were used to detect the disc height degeneration index at 1, 2 and 4 weeks after the procedure. MRI was used to study the changes in the disc structure and the signal intensity of IVD 2 and 4 weeks after the procedure. Disc water content and histology were measured at 4 weeks after the procedure. RESULTS: A 21-g needle significantly increased disc degeneration when compared with the 30-g needle as detected by X-ray, MRI, disc water content and histology (P < 0.05). Two microlitres of iodine significantly decreased the disc MRI signal and water content at 4 weeks compared with the same volume of normal saline (P < 0.05). Three microlitres of iodine significantly increased disc degeneration when compared with 2 µl iodine, as detected by X-ray, MRI, disc water content and histology at 4 weeks (P < 0.05). CONCLUSION: To reduce disc degeneration after discography, it may be best to choose a smaller needle size, minimize the use of contrast agent and use non-ionic contrast agents with osmotic pressure similar to the intervertebral disc. These slides can be retrieved under Electronic Supplementary Material.

Dyes Adsorption Behavior of Fe3O4 Nanoparticles Functionalized Polyoxometalate Hybrid.

The magnetic adsorbent, Fe3O4@[Ni(HL)2]2H2[P2Mo5O23]·2H2O (Fe3O4@1), is synthesized by employing the nanoparticles Fe3O4 and polyoxometalate hybrid 1. Zero-field-cooled (ZFC) and field-cooled (FC) curves show that the blocking temperature of Fe3O4@1 was at 120 K. Studies of Fe3O4@1 removing cationic and anionic dyes from water have been explored. The characterization of Fe3O4@1, effects of critical factors such as dosage, the concentration of methylene blue (MB), pH, adsorption kinetics, isotherm, the removal selectivity of substrate and the reusability of Fe3O4@1 were assessed. The magnetic adsorbent displayed an outstanding removal activity for the cationic dye at a broad range of pH. The adsorption kinetics and isotherm models revealed that the adsorption process of Fe3O4@1 was mainly governed via chemisorption. The maximum capacity of Fe3O4@1 adsorbing substance was 41.91 mg g-1. Furthermore, Fe3O4@1 showed its high stability by remaining for seven runs of the adsorption-desorption process with an effective MB removal rate, and could also be developed as a valuable adsorbent for dyes elimination from aqueous system.

Novel medical bathing with traditional Chinese herb formula alleviates paraplegia spasticity.

Paraplegia spasm is a kind of chronic disease which lacks effective treatment; the patients have to endure long-term pain, which is a tough problem for nursing practice. Lots of potential candidate medicines are under investigation, and a new Chinese herb formula is introduced in the current study. In the present study, we chose six different well-known Chinese herbs to form a formula, and boiled them into the water with an optimized ratio to make bath water; 80 paraplegic patients received this medicinal bath, and 80 patients received perfume water bath as placebo group. Compared with placebo control patients, the herb-treated patients have significant reduction in paraplegia spasm, visual analogue scale score, clinician global impression and sleep disorder. This novel six-combined formula traditional medicine could be beneficial for alleviating paraplegia spasm, but the underlying action mechanism deserves further study.

Reference-free lossless compression of nanopore sequencing reads using an approximate assembly approach.

The amount of data produced by genome sequencing experiments has been growing rapidly over the past several years, making compression important for efficient storage, transfer and analysis of the data. In recent years, nanopore sequencing technologies have seen increasing adoption since they are portable, real-time and provide long reads. However, there has been limited progress on compression of nanopore sequencing reads obtained in FASTQ files since most existing tools are either general-purpose or specialized for short read data. We present NanoSpring, a reference-free compressor for nanopore sequencing reads, relying on an approximate assembly approach. We evaluate NanoSpring on a variety of datasets including bacterial, metagenomic, plant, animal, and human whole genome data. For recently basecalled high quality nanopore datasets, NanoSpring, which focuses only on the base sequences in the FASTQ file, uses just 0.35-0.65 bits per base which is 3-6[Formula: see text] lower than general purpose compressors like gzip. NanoSpring is competitive in compression ratio and compression resource usage with the state-of-the-art tool CoLoRd while being significantly faster at decompression when using multiple threads (> 4[Formula: see text] faster decompression with 20 threads). NanoSpring is available on GitHub at https://github.com/qm2/NanoSpring .

Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing.

Epigenetic characterization of cell-free DNA (cfDNA) is an emerging approach for detecting and characterizing diseases such as cancer. We developed a strategy using nanopore-based single-molecule sequencing to measure cfDNA methylomes. This approach generated up to 200 million reads for a single cfDNA sample from cancer patients, an order of magnitude improvement over existing nanopore sequencing methods. We developed a single-molecule classifier to determine whether individual reads originated from a tumor or immune cells. Leveraging methylomes of matched tumors and immune cells, we characterized cfDNA methylomes of cancer patients for longitudinal monitoring during treatment.

Resveratrol Suppresses Annulus Fibrosus Cell Apoptosis through Regulating Oxidative Stress Reaction in an Inflammatory Environment.

During disc degeneration, the increase of inflammatory cytokines and decrease of disc cell density are two prominent features. Enhanced inflammatory reaction contributes to disc annulus fibrosus (AF) cell apoptosis. In this study, we investigated whether resveratrol can suppress AF cell apoptosis in an inflammatory environment. Rat disc AF cells were cultured in medium with or without tumor necrosis factor-α (TNF-α). Resveratrol was added along with the culture medium supplemented with TNF-α. Caspase-3 activity, cell apoptosis ratio, expression of apoptosis-associated molecules (Bcl-2, Bax, caspase-3, cleaved PARP, and cleaved caspase-3), reactive oxygen species (ROS) content, and the total superoxide dismutase (SOD) activity were measured. Our results showed that TNF-α significantly increased caspase-3 activity and AF cell apoptosis ratio and upregulated gene/protein expression of Bax, caspase-3, cleaved caspase-3, and cleaved PARP, whereas it downregulated the expression of Bcl-2. Moreover, TNF-α significantly increased ROS content but decreased the total SOD activity. Further analysis demonstrated that resveratrol partly attenuated the effects of TNF-α on AF cell apoptosis-associated parameters, decreased ROS content, and increased the total SOD activity in the AF cells treated with TNF-α. In conclusion, resveratrol attenuates inflammatory cytokine TNF-α-induced AF cell apoptosis through regulating oxidative stress reaction in vitro. This study sheds a new light on the protective role of resveratrol in alleviating disc degeneration.

Osteopontin sequence modified mesoporous calcium silicate scaffolds to promote angiogenesis in bone tissue regeneration.

Sufficient blood supply remains the key issue to be addressed for an optimal performance of implanted bone tissue engineering scaffolds. Host vessel invasion is limited to a depth of only several hundred micrometers from the scaffold/host interface. In this study, an osteopontin sequenced polypeptide SVVYGLR was grafted into/onto mesoporous calcium silicate (MCS) and then 3D-printed into scaffolds. The peptide motifs can be accessed on the scaffold surfaces and released as well. In vitro studies of human umbilical vein endothelial cells (HUVECs) indicated enhanced cell adhesion and vascular-like structure formation on MCS-SVVYGLR scaffolds. At the same time, human bone marrow stromal cells (hBMSCs) showed enhanced osteogenic differentiation capability and higher expression levels of angiogenic genes and proteins as well. The results of in vivo radial defect repair tests of rabbits showed that more tubular vessels formed throughout the whole MCS-SVVYGLR scaffolds, and therefore, a more homogeneous new bone formation pattern was obtained on MCS-SVVYGLR scaffolds instead of a peripheral bone growth pattern on pure MCS scaffolds by Micro-CT and tissue staining techniques over 3 months. Relative gene and protein expressions in PI3K/AKT and ERK1/2 pathways suggested that the SVVYGLR motif on the MCS scaffold surface could initiate the PI3K/AKT signaling pathway and up-regulate ERK1/2 expression, which positively stimulated VEGF expression, to improve angiogenesis.

Mechanisms for nickel(0)/N-heterocyclic carbene-catalyzed intramolecular alkene hydroacylation: insights from a DFT study.

Density functional calculations have been applied to study and elucidate nickel(0)/N-heterocyclic carbene-catalyzed intramolecular alkene hydroacylation. The calculations showed that nickel(0)-catalyzed intramolecular alkene hydroacylation involved four potential reaction channels (I, II, III, and IV), and pathway IV was predicted to be more favorable than the other three. Two pathways, I and II, had three steps (oxidative addition, hydrogen migration, reductive elimination), and the rate-determining step was hydrogen migration. Pathway III proceeded through oxidative cyclization, ß-hydride elimination, and hydrogen migration, and the rate-determining step was ß-hydride elimination. Pathway IV included four steps (oxidative cyclization, dimerization, ß-hydride elimination, hydrogen migration), and the rate-determining step was again ß-hydride elimination. Oxidative cyclization was easy and led to rapid dimerization, greatly reducing the free energy of ß-hydride elimination. The binuclear nickelacycle intermediate was observed in Ogoshi's experiments, and it was identified by nuclear magnetic resonance (NMR). The dominant product was the five-membered benzocyclic ketone p1. All results agreed with Ogoshi's experiments. Graphical Abstract Nickel(0)-catalyzed intramolecular alkene hydroacylation involved four potential reaction channels. The binuclear nickelacycle intermediate was important, and the dimerization greatly reduced the free energy of the ß-hydride elimination.

Mechanisms and reactivity differences for the cobalt-catalyzed enantioselective intramolecular hydroacylation of ketones and alkenes: insights from density functional calculations.

Density functional theory (DFT) was used to study the cobalt(I)-catalyzed enantioselective intramolecular hydroacylation of ketones and alkenes. All intermediates and transition states were fully optimized at the M06/6-31G(d,p) level (LANL2DZ(f) for Co). The results demonstrated that the ketone and alkene present different reactivities in the enantioselective hydroacylation. In ketone hydroacylation catalyzed by the cobalt(I)-(R,R)-Ph-BPE complex, reaction channel "a" to (R)-phthalide was more favorable than channel "b" to (S)-phthalide. Hydrogen migration was both the rate-determining and chirality-limiting step, and this step was endothermic. In alkene hydroacylation catalyzed by the cobalt(I)-(R,R)-BDPP complex, reaction channel "c" leading to the formation of (S)-indanone was the most favorable, both thermodynamically and kinetically. Reductive elimination was the rate-determining step, but the chirality-limiting step was hydrogen migration, which occurred easily. The results also indicated that the alkene hydroacylation leading to (S)-indanone formation was more energetically favorable than the ketone hydroacylation that gave (R)-phthalide, both thermodynamically and kinetically.

Crosstalk between Activated Microglia and Neurons in the Spinal Dorsal Horn Contributes to Stress-induced Hyperalgesia.

Stress has been shown to enhance pain sensitivity resulting in stress-induced hyperalgesia. However, the underlying mechanisms have yet to be elucidated. Using single-prolonged stress combined with Complete Freund's Adjuvant injection model, we explored the reciprocal regulatory relationship between neurons and microglia, which is critical for the maintenance of posttraumatic stress disorder (PTSD)-induced hyperalgesia. In our assay, significant mechanical allodynia was observed. Additionally, activated neurons in spinal dorsal horn were observed by analysis of Fos expression. And, microglia were also significantly activated with the presence of increased Iba-1 expression. Intrathecal administration of c-fos antisense oligodeoxynucleotides (ASO) or minocycline (a specific microglia inhibitor) attenuated mechanical allodynia. Moreover, intrathecal administration of c-fos ASO significantly suppressed the activation of neurons and microglia. Interestingly, inhibition of microglia activation by minocycline significantly suppressed the activation of both neurons and microglia in spinal dorsal horn. P38 inhibitor SB203580 suppressed IL-6 production, and inhibition of IL-6 receptor (IL-6R) activation by tocilizumab suppressed Fos expression. Together, our data suggest that the presence of a "crosstalk" between activated microglia and neurons in the spinal dorsal horn, which might contribute to the stress-induced hyperactivated state, leading to an increased pain sensitivity.