Molecular-Level Understanding of Surface Roughness Boosting Segregation Behavior at the ZIF-8/Ionic Liquid Interfaces.

Here, we perform a series of classical molecular dynamics simulations for two different [HEMIM][DCA] and [BMIM][BF] ionic liquids (ILs) on the ZIF-8 surface to explore the interfacial properties of metal-organic framework (MOFs)/IL composite materials at the molecular level. Our simulation results reveal that the interfacial structures of anions and cations on the ZIF-8 surface are dominated by the surface roughness due to the steric hindrance, which is extremely different from the driving mechanism based on solid-ion interactions of ILs on flat solid surfaces. At the ZIF-8/IL interfaces, the open sodalite (SOD) cages of the ZIF-8 surface can block most of the large-size cations outside and significantly boost the segregation behavior of anions and cations.

Structures and properties of ionic crystals and condensed phase ionic liquids predicted with the generalized energy-based fragmentation method.

The generalized energy-based fragmentation (GEBF) approach is extended to facilitate ab initio investigations of structures, lattice energies, vibrational spectra and H NMR chemical shifts of ionic crystals and condensed-phase ionic liquids (ILs) with the periodic boundary conditions (PBC). For selected periodic systems, our results demonstrate that the so-called PBC-GEBF approach can provide satisfactory descriptions on ground-state energies, structures, and vibrational spectra of ionic crystals and IL crystals. The PBC-GEBF approach is then applied to three realistic condensed phase systems.

Controlled Fluorescence Enhancement of DNA-Binding Dye Through Chain Length Match between Oligoguanine and TOTO.

Fluorescent DNA-binding dyes are extensively employed as probe and biosensing in biological detection and imaging. Experiments and theoretical calculations of thiazole orange homodimeric (TOTO) dye binding to a single-strand DNA (ssDNA), poly(dG) ( = 2, 4, 6, 8), reveal that the = 6 complex shows about 300-fold stronger fluorescence than = 2, 4 and a slightly stronger one than = 8 complexes, which is benefited from the length match between TOTO and poly(dG). The machine learning, based on molecular dynamics trajectories, indicates that TOTO is featured by the dihedral angle along its backbone and its end-to-end distance, in which the latter one defines the stretch and hairpin structures of TOTO, respectively.

Telomerase and poly(ADP-ribose) polymerase-1 activity sensing based on the high fluorescence selectivity and sensitivity of TOTO-1 towards G bases in single-stranded DNA and poly(ADP-ribose).

Telomerase and poly(ADP-ribose) polymerase-1 (PARP-1) are two potential cancer biomarkers and are closely related to tumor initiation and malignant progression. TOTO-1 is well-known for differentiating ss-DNA from ds-DNA because it is virtually non-fluorescent without DNA and exhibits very low fluorescence with ss-DNA, while it emits strong fluorescence with ds-DNA. In this paper, for the first time, it was found that TOTO-1 has high fluorescence selectivity and sensitivity towards the G bases in single-stranded DNA and poly(ADP-ribose) (PAR).

How intermolecular interactions influence electronic absorption spectra: insights from the molecular packing of uracil in condensed phases.

The photoexcitation mechanism in photochemistry and photophysics is a key to understanding the photostability and photoreaction of nucleobases. Using a combination of the generalized energy-based fragmentation (GEBF) and quantum mechanical and molecular mechanical (GEBF-QM/MM) approach and the QM/MM approach, we have investigated the electronic absorption spectra for the π-π* transition of uracil in aqueous solution, amorphous solid, and crystal. Our results indicate that the intermolecular interactions in terms of molecular packing are crucial for the investigation of the absorption spectra of uracil in different environments.

Unique orientations and rotational dynamics of a 1-butyl-3-methyl-imidazolium hexafluorophosphate ionic liquid at the gas-liquid interface: the effects of the hydrogen bond and hydrophobic interactions.

Here we report a series of molecular dynamics simulations for the orientations and rotational dynamics of the 1-butyl-3-methyl-imidazoliumhexafluorophosphate ([BMIM][PF]) ionic liquid (IL) at the gas-liquid interface. Compared to the bulk phase, the [BMIM] cations at the interface prefer to orientate themselves with their imidazolium rings perpendicular to the gas-IL interface plane and their butyl chains pointing toward the vacuum phase. Such a preferential orientation can be attributed to the combined effect of the hydrophobic interactions and the optimum loss of hydrogen bonds (HBs).