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][BF4] 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. In comparison with the [BMIM][BF4] IL, the [HEMIM][DCA] IL has much more anions entering into the open SOD cages owing to the combination of stronger ZIF-8-[DCA]- interactions and more ordered arrangement of [DCA]- anions on the ZIF-8 surface. Furthermore, more and stronger ZIF-8-[BF4]- hydrogen bonds (HBs) are found to exist on the cage edges than the ZIF-8-[DCA]- HBs, further preventing [BF4]- anions from entering into SOD cages. By more detailed analyses, we find that the hydrophobic interaction has an important influence on the interfacial structures of the side chains of [HEMIM]+ and [BMIM]+ cations, while the π-π stacking interaction plays a key role in determining the interfacial structures of the imidazolium rings of both cations. Our simulation results in this work provide a molecular-level understanding of the underlying driving mechanism on segregation behavior at the ZIF-8/IL interfaces.

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 1 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. For three ionic crystals (LiCl, NaCl, and KCl), we apply the PBC-GEBF approach with MP2 theory as well as some popular DFT methods to investigate their crystal structures and lattice energies. Our calculations indicate that the crystal structures obtained with PBC-GEBF-MP2/6-311 + G** are very close to the corresponding X-ray structures, while PBC-GEBF-ωB97X-D/6-311 + G** provides satisfactory prediction for crystal structures and lattice energies. For two polymorphs of [n-C4 mim][Cl] crystals, we find that the PBC-GEBF approach at the M06-2X/6-311 + G** level can give a satisfactory descriptions on structures and Raman spectra of these two crystals. Furthermore, for [C2 mim][BF4 ] ILs, we demonstrate that their 1 H NMR chemical shifts can be estimated from averaging over 5 typical snapshots (extracted from MD simulations) with the PBC-GEBF approach at the B97-2/pcSseg-2 level. The calculated results account for the observed experimental data quite well. Therefore, we expect that the PBC-GEBF approach, combined with various quantum chemistry methods, will become an effective tool in predicting structures and properties of ionic crystals and condensed-phase ILs.

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)n (n = 2, 4, 6, 8), reveal that the n = 6 complex shows about 300-fold stronger fluorescence than n = 2, 4 and a slightly stronger one than n = 8 complexes, which is benefited from the length match between TOTO and poly(dG)6. 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. The time-dependent density functional theory calculations on the low-lying excited states show that the stretched TOTO with π-π end-stacking binding mode can bring about strong fluorescence with localized π-π* transitions. For the n = 2, 4, and 8 complexes, the linear scaling quantum mechanics calculations indicate that the dominant hairpin TOTO with intercalative binding modes have relatively larger binding energies, leading to fluorescence quenching by intramolecular charge transfer. Our results may provide an insight for modulating the DNA-dye binding modes to tune the degree of charge transfer and designing fluorescent probes for the recognition of specific DNA sequences.

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). Poly(dG) was used as the model target to explore its possible mechanism. Molecular dynamics (MD) simulation proved that intramolecular π-π stacking existed in TOTO-1 (in an aqueous solution), while intermolecular π-π stacking formed between TOTO-1 and poly(dG) in a similar way as that observed for dsDNA. Interestingly, telomerase and PARP-1 catalyzed the formation of G-rich DNA and PAR in vivo, respectively. Therefore, TOTO-1 was explored in detecting both of them, obtaining satisfactory results. To the best of our knowledge, no probe has been reported to recognize PAR. It is also the first time where telomerase is detected based on the specific recognition of G bases. Importantly, integrating multiple functions into one probe that can detect not only telomerase but also PARP-1 will significantly raise the specificity of screening cancer and decrease false positive proportion, which make TOTO-1 a promising candidate probe for clinical diagnosis and pharmaceutical screening.

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. There is a large red-shift (relative to uracil in the gas-phase) for uracil in the amorphous phase, which arises from hydrogen-bonding (HB) and close π-π stacking interactions. In contrast, the relatively smaller red-shift of uracil in aqueous solution can be attributed to the cooperative HB and long-range electrostatic and polarization interactions. Due to the HB and weak π-π interactions, the red-shift of the crystal is smaller than that of amorphous uracil. Furthermore, the results suggest that a large system is required to obtain the accurate absorption spectra of solutions, whereas small electrostatically embedded cluster models could be used to obtain the corresponding results for amorphous solids and molecular crystals.

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][PF6]) 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). More interestingly, our simulation results demonstrate that the butyl chains of cations exhibit a two-stage rotational behavior at the interface, where the butyl chains are always in the vacuum phase at the first stage and the second stage corresponds to the butyl chains migrating from the vacuum phase into the liquid phase. A further detailed analysis reveals that their rotational motions at the first stage are mainly determined by the weakened HB strength at the interface while those at the second stage are dominated by their hydrophobic interactions. Such a unique rotational behavior of the butyl chains is significantly different from those of the anions and the imidazolium rings of cations at the interface due to the lack of existence of hydrophobic interaction in the cases of the latter two. In addition, a new and simple time correlation function (TCF) was constructed here for the first time to quantitatively identify the relevant hydrophobic interaction of alkyl chains. Therefore, our simulation results provide a molecular-level understanding of the effects of HB and hydrophobic interactions on the unique properties of imidazolium-based ILs at the gas-liquid interface.