Molecular dynamics simulation study on the binding mechanism between carbon nanotubes and RNA-dependent RNA polymerase.

Carbon nanotubes (CNTs) have potential prospects in disease treatment, so it is of great significance to study CNTs as the possible inhibitors of RNA-dependent RNA polymerase (RdRp). Through the way of using the RdRp of SARS-COV-2 as a model, five armchair single-walled carbon nanotubes (SWCNTs) (namely Dn, which stands for CNTs (n, m = n), n = 3-7) and RdRp have been selected to study the interactions by means of molecular docking and molecular dynamics simulation. After five SWCNT-RdRp complex systems have been subjected to the molecular dynamics simulations of 100 ns, and Molecular Mechanics Poisson - Boltzmann Surface Area (MMPBSA) has been used to calculate the binding free energy, it is found that the binding free energy of the D6 system (-189.541 kJ/mol) is significantly higher than that of the other four systems, and most of the amino acids with strong positive effects on binding are usually basic amino acids. What's more, in the further investigation of the specific interaction mechanism between CNT (6,6) and RdRp, it is revealed that the three amino acid residues LYS545, ARG553 and ARG555 located in the nucleoside triphosphate (NTP) entry channel all have strong effects. In addition, it is also observed that when ARG555 has been inserted into SWCNT, a stable structure will be formed, which will break the original NTP entry channel structure and inhibit virus replication. Therefore, it can be concluded that certain specific types of SWCNT, such as CNT (6,6), could be potential small molecule inhibitors in the treatment of coronavirus.Communicated by Ramaswamy H. Sarma.

Dynamical properties of a room temperature ionic liquid: Using molecular dynamics simulations to implement a dynamic ion cage model.

The transport behavior of ionic liquids (ILs) is pivotal for a variety of applications, especially when ILs are used as electrolytes. Many aspects of the transport dynamics of ILs remain to be understood. Here, a common ionic liquid, 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (BmimNTf2), was studied with molecular dynamics simulations. The results show that BmimNTf2 displays typical structural relaxation, subdiffusive behavior, and a breakdown of the Stokes-Einstein diffusion relation as in glass-forming liquids. In addition, the simulations show that the translational dynamics, reorientation dynamics, and structural relaxation dynamics are well described by the Vogel-Fulcher-Tammann equation like fragile glass forming liquids. Building on previous work that employed ion cage models, it was found that the diffusion dynamics of the cations and anions were well described by a hopping process random walk where the step time is the ion cage lifetime obtained from the cage correlation function. Detailed analysis of the ion cage structures indicated that the electrostatic potential energy of the ion cage dominates the diffusion dynamics of the caged ion. The ion orientational relaxation dynamics showed that ion reorientation is a necessary step for ion cage restructuring. The dynamic ion cage model description of ion diffusion presented here may have implications for designing ILs to control their transport behavior.

Effect of silkworm peptide on inducting M1 type polarization and Th1 activation via TLR2-induced MyD88-dependent pathway.

The aim of this study was to explore immune activity and molecular mechanism of silkworm peptide. The cell subsets induced by silkworm peptides were detected by flow cytometry. The IFN-γ and IL-4 levels in CD4+ cells were measured by ELISA. TLR2 mRNA expression in mouse CD4+ T cells was detected by qRT-PCR. Western blot was used to detect the protein expression levels of MyD88 and p-IκB. The growth rate of Lewis lung cancer xenografts in mice of the medium-dose group was significantly reduced, and the tumor volume was significantly smaller than that of the control group on the 14th day. The relative vitality values of spleen lymphocytes in the medium-dose and high-dose groups were higher than the control group. The IFN-γ levels in the medium-dose and high-dose groups were significantly higher than the control group. The levels of IL-4 were no significant change among different groups. Compared with the control group, different doses of silkworm peptide groups could increase the levels of NO, IL-6, IL-12, and IL-1ß. Compared with the control group, the protein expression levels of MyD88 and p-IκB in 10 µg/ml group and 20 µg/ml groups were significantly increased compared with the control group. Silkworm peptide could induce Th1 activation and M1 type polarization, which was dose-dependent and was relative to the effect of silkworm peptide on inhibiting tumor growth. Silkworm peptide could directly induce M1 type polarization and Th1 activation via TLR2-induced MyD88-dependent pathway in vitro.

Origin of heterogeneous dynamics in local molecular structures of ionic liquids.

Room-temperature ionic liquids (ILs) are generally considered as structurally heterogeneous with inherent polar/apolar phase separation. However, even after a decade of research, local dynamics in the heterogeneous structures of ILs remain neglected. Such local dynamics may influence the ion transport of electrolytes, as well as the reaction rate of solvents. In this study, we performed molecular dynamics simulation to analyze the local dynamics for the structural heterogeneity of ILs. Calculations of the diffusion, reorientation, and association dynamics showed a distinct heterogeneous dynamics between the polar and apolar regions of ILs. Further studies demonstrated that such local dynamic differences originate from local structural heterogeneity. Different energy barriers determine a predominant fast reorientation dynamics in apolar regions and a locally vibrating behavior in polar regions. Additionally, we suggested a new jumping mechanism to clarify the dynamic heterogeneity of ions in the polar regions. The results will help determine the origin of the heterogeneous dynamics in IL local structures and provide a theoretical basis for tuning the dynamic properties of ILs used as electrolytes or reaction solvents.

Dilute or Concentrated Electrolyte Solutions? Insight from Ionic Liquid/Water Electrolytes.

When room-temperature ionic liquids (IL) are used as an electrolyte, their transport behaviors are still under heavy debate due to their complicated ion-associations. In this article, we conducted molecular dynamics simulations to study the molecular scale ion associations from the very dilute 1-butyl-3-methylimidazolium iodide/water solution to the pure IL. It revealed that ions are localized in a multicoordinated ion cage structure with nanoseconds in concentrated IL solutions. Dynamics analyses indicate that the transport of this solution can be depicted by the Debye-Hückel model only in dilute IL/water electrolyte. The velocity and rotational correlation functions showed that the lifetime of translational and rotational motions are at the level of picoseconds and nanoseconds, respectively, because of the ion cage effect. The lifetime of ion association demonstrated that the recombination of association ions was prevalent in IL solutions. It means that the dipolar or stable contact ion-pairs model may not be suitable for depicting the IL transport.

Photoinduced electron transfer between 2-methylanthraquinone and triethylamine in an ionic liquid: time-resolved EPR and transient absorption spectroscopy study.

Photoinduced electron transfer between 2-methylanthraquinone (MeAQ) and triethylamine (TEA) in a room-temperature ionic liquid, 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]), was investigated by comparing the time-resolved electron paramagnetic resonance (TR-EPR) spectroscopy and the transient absorption spectroscopy. The results of TR-EPR spectroscopy, in which MeAQ was 8 mmol L(-1) and TEA was 150 mmol L(-1), indicated that the transient radical would exist longer time in [bmim][PF6] than in acetonitrile. At the delay time of 8 µs after laser excitation, the TR-EPR signal transformed from an emissive peak into an absorptive peak when the experiment was performed in [bmim][PF6]. The results of the transient absorption spectroscopy, in which MeAQ was 0.1 mmol L(-1) and TEA was 2.2 mmol L(-1), showed that the efficiency and the rate of the photoinduced electron transfer reaction in [bmim][PF6] were obviously lower than that in acetonitrile. It was concluded that various factors, such as concentration, viscosity and local structural transformation of the solution, have an influence on the process of photoinduced electron transfer in [bmim][PF6].

Molecular insights into the electric double layers of ionic liquids on Au(100) electrodes.

The electric double layer structure and differential capacitance of single crystalline Au(100) electrodes in the ionic liquid 1-butyl-3-methyl-imidazolium hexafluorophosphate are investigated using molecular dynamics simulations. Results show strong adsorption on the electrode surface. The potential of zero charge (pzc) and maxima of differential capacitance are strongly dependent on the adsorption layer structure. At potentials near the pzc, cations and anions adjacent to the electrode surface are coadsorbed on the same screening layer. This strong adsorption layer results in overscreening effects on the compact layer and induces both a bell-shaped differential capacitance curve and a positive pzc. Moreover, the potential required for transition from overscreening to overcrowding is about 4.0 V. This transition potential may be attributed to the higher interaction energy between the Au(100) electrode and ions compared with the binding energy in our cation-anion system.

A comparative study on the ionic liquid [bmim][BF4] and its solution with transient absorption spectroscopy.

A detailed study was explored to compare the transient absorption spectra of the neat 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF(4)]) with its solution in water or acetonitrile. It was concluded that the excited triplet state (3)[bmim](+*) was produced after 266 nm laser irradiation, and then the neutral radical [bmim] and the cation radical [bmim] (2+) were formed through two possible paths. The transient absorption spectra of the neat [bmim][BF(4)] and its solution were similar but the reaction kinetics were different due to their different local structures such as dimeric or cluster. The energy transfer between excited [bmim][BF(4)] and ß-carotene further affirmed the existence of (3)[bmim](+*). And the reaction that the hydrated electron captured by [bmim](+) to produce [bmim] in solution was observed.

Etiology and pathology of epidermal papillomas in allogynogenetic crucian carp Carassius auratus gibelio (female) x Cyprinus carpio var. singuonensis (male).

Allogynogenetic crucian carp Carassius auratus gibelio (female) x Cyprinus carpio var. singuonensis (male) is one of the main freshwater aquaculture species in China. In recent years, epidermal papillomas have been observed on the scales, fins and opercula of adult fish in many fish farms in the Chongming county of Shanghai, China. The disease appears in the late autumn of the first year and becomes more severe in winter. It gradually regresses in the late spring or summer of the second year, as water temperature increases. Our study revealed that the disease pathogen was likely to be a herpes-like virus, as indicated by enveloped viral particles in the cytoplasm, empty capsids in the nucleus and a virus-like morphology of the pathogen. The size of the enveloped herpes-like virus was 118.18 +/- 10.53 (SD) nm (n = 22) and its nucleocapsid was 78.64 +/- 7.74 nm (n = 22) in diameter. Histopathological examination of tumours revealed that both epithelial and stromal cells proliferated to form papillomas. The nuclei of epithelial tumour cells were irregular in shape and in size. Most of the mucous cells were located in clusters near the middle of each papilloma. Cytoplasmic organelles were sparse in tumour cells. Numerous granulocytes and lymphocytes infiltrated into the tumour tissue. There were no inclusion bodies in the cytoplasm and nuclei of tumour cells. The lesions only occurred in adult allogynogenetic crucian carp, even though they were cultured together with other fish species. There was marked variation in incidence: in some ponds, only a few fish were affected, while the incidence was up to 90% in other ponds.

Effects of ionic liquid [bmim][PF6] on absorption spectra and reaction kinetics of the duroquinone triplet state in acetonitrile.

The transient absorption spectra and photoinduced electron-transfer process of duroquinone (DQ) in mixed binary solutions of ionic liquid (IL) [bmim][PF6] and acetonitrile (MeCN) have been investigated by laser photolysis at an excitation wavelength of 355 nm. A spectral blue shift of 3DQ* was observed in the IL/MeCN mixtures compared to MeCN. At lower VIL(volume fraction of IL), the interaction between DQ and the solvent is dominant, and the decay rate constant (kobs) of 3DQ* increases steadily with the increasing of VIL; to the contrary, at higher VIL, the network structures due to the hydrogen bond and viscosity are dominant, and the decay rate constant decreases obviously with increasing VIL. A critical point (turnover) was observed at VIL = approximately 0.30. The dependence of the observed growth rate (kgr) of the photoinduced electron-transfer (PET) products on VIL is complex and shows a special change; kgr first decreases with increasing VIL, then increases, and finally decreases slowly with further increasing of VIL. It is speculated that the PET process in the mixture can be affected by factors including the local structure and the reorganization energy of the solvent and salt and cage effects. The change of local structure of [bmim][PF6]/MeCN is supported by following the steady-state fluorescence behavior of the mixture, in combination with the molecular dynamics simulation of the thermodynamic property. The results revealed that the degree of self-aggregation of monomeric cations (bmim+) to associated forms increases with increasing VIL. This is in good agreement with the laser photolysis results for the same solutions.

Noncovalently modified carbon nanotubes with carboxymethylated chitosan: a controllable donor-acceptor nanohybrid.

We report here the modification of multiwalled carbon nanotubes (MWNTs) with a kind of polysaccharide, carboxymethylated chitosan (cmCs), and their potential usage as donor-acceptor nanohybrids. The modified composites (cmCs/MWNTs) were characterized by high-resolution TEM, FT-IR, TGA and time-resolved spectroscopy. The time-resolved spectroscopic experiments revealed that interfacial electron transfer readily takes place between MWNTs and surface immobilized cmCs chains. The forward electron transfer is fast (< 20 ns) while the backward recombination is slow. The recombination process strongly depends on the chain length of carboxylmethylated chitosan, i.e. a shorter recombination lifetime (~1.1 micros) for the shorter-chain cmCs coated MWNTs against that of the longer-chain cmCs coated MWNTs (~3.5 micros). The results demonstrated that the cmCs/MWNTs composite may be applied as a controllable donor-acceptor nanohybrid.