Melting thermodynamics of oligonucleic acids conjugated with relatively solvophobic linear polymers: A coarse‐grained molecular simulation study

Oligonucleic acids (ONAs), such as DNA and RNA, are used in various biotechnology and nanotechnology applications due to their ability to form a double helix that is stable at low temperature and melts at high temperatures. The melting temperature (T_m) of ONA duplexes can be tuned by the ONA composition, sequence, length and concentration, solvent quality, and salt concentration and by conjugation to other macromolecules. In this article, we use coarse‐grained (CG) molecular simulations to study ONAs conjugated with linear homopolymers that are relatively more solvophobic than the ONA. We study charged and stiff 8‐mer ONAs (e.g., DNA) and neutral and flexible 8‐mer ONAs (e.g., peptide nucleic acids or PNA), and vary the composition (or G‐C content) and sequence of ONA, conjugated homopolymer lengths and solvent quality for the polymer. For neutral and flexible ONAs, as the solvent quality worsens for the polymer, the ONA melting temperature increases from that of unconjugated ONA. The melting curves broaden with polymer length and worsening solvent quality, especially for ONAs with higher G‐C content. For charged and stiff ONAs, as the solvent quality worsens, the ONA melting temperature decreases compared to unconjugated ONA while the width of the melting curve remains the same. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 1196–1208     

Solvent‐free ring‐opening polymerization of lactones with hydrogen‐bonding bisurea catalyst

Development of effective organocatalysts for the living ring‐opening polymerization (ROP) of lactones is highly desired for the preparation of biocompatible and biodegradable polyesters with controlled microstructures and physical properties. Herein, a new class of hydrogen‐bond donating bisurea catalysts is reported for the ROP of lactones under solvent‐free conditions. ROP of lactones mediated by the bisurea/7‐methyl‐1,5,7‐triazabicyclo[4.4.0]dec‐5‐ene (MTBD) catalyst exhibits a living/controlled manner, affording the polymers and copolymers with the well‐defined structure, predictable molecular weight, narrow molecular weight distribution, and high selectivity for monomer at low catalyst loadings at ambient temperature. The possible mechanism of bisurea/MTBD‐catalyzed ROP of lactones is proposed, in which the bisurea activates the carbonyl group of lactones while MTBD facilitates the nucleophilic attack of the initiating/propagating alcohol by hydrogen bonding. Moreover, the poly(ε‐caprolactone‐co‐δ‐valerolactone) [P(CL‐co‐VL)] random copolymers with various compositions were synthesized using the bisurea/MTBD catalyst. The measurements of thermal properties and crystalline structure demonstrate that the CL and VL units are cocrystallized in the crystalline phase of P(CL‐co‐VL) copolymers. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019 , 57, 90–100     

The Special “Morse Code” between Solvent Polarity and Morphology Flexibility in a POSS–Dendrimer Supramolecular System

An amazing phenomenon of the relative magnitude of modulus of two liquid-crystal (LC) gels is found inverted under/above their phase transition temperature T_LC-iso, which is further proved to be caused by their diverse morphology flexibility. By testing the polarity of two LCs, gelator POSS-G1-Boc (POSS=polyhedral oligomeric silsesquioxane) was discovered to self-assemble into more flexible structures in a relatively low polar LC, whereas more rigid ones are formed in higher polar LC. Hence, a fitting function to connect morphology flexibility with solvent polarity was established, which can even be generalized to a number of common solvents. Experimental observations and coarse-grained molecular dynamics simulations revealed that solvent polarity mirrors a “Morse code”, with each “code” corresponding to a specific morphology flexibility.     

Excited-State Dynamics of Thienoguanosine,an Isomorphic Highly Fluorescent Analogue of Guanosine

Thienoguanosine (^thG) is an isomorphic analogue of guanosine with promising potentialities as fluorescent DNA label. As a free probe in protic solvents, ^thG exists in two tautomeric forms, identified as the H1, being the only one observed in nonprotic solvents, and H3 keto–amino tautomers. We herein investigate the photophysics of ^thG in solvents of different polarity, from water to dioxane, by combining time-resolved fluorescence with PCM/TD-DFT and CASSCF calculations. Fluorescence lifetimes of 14.5–20.5 and 7–13 ns were observed for the H1 and H3 tautomers, respectively, in the tested solvents. In methanol and ethanol, an additional fluorescent decay lifetime (≈3 ns) at the blue emission side (λ≈430 nm) as well as a 0.5 ns component with negative amplitude at the red edge of the spectrum, typical of an excited-state reaction, were observed. Our computational analysis explains the solvent effects observed on the tautomeric equilibrium. The main radiative and nonradiative deactivation routes have been mapped by PCM/TD-DFT calculations in solution and CASSCF in the gas phase. The most easily accessible conical intersection, involving an out-of plane motion of the sulfur atom in the five-membered ring of ^thG, is separated by a sizeable energy barrier (≥0.4 eV) from the minimum of the spectroscopic state, which explains the large experimental fluorescence quantum yield.     

Nano-liquid chromatography combined with a sustainable microextraction based on natural deep eutectic solvents for analysis of phthalate esters

The separation of 11 phthalic acid ester (PAEs) was carried out by nano-liquid chromatography coupled to ultraviolet and MS detection. Preliminary experiments were achieved in order to select suitable stationary phases and chromatographic conditions. The baseline separation was obtained, for all compounds, with an XBridge^TM C₁₈ column in less than 15 min, working in step gradient mode. The sensitivity of the method was improved by on-column focusing. PAEs were extracted from alcoholic and nonalcoholic beverages using vortex-assisted emulsification dispersive liquid–liquid microextration and natural deep eutectic solvents. The whole method was validated in terms of linearity, sensitivity, precision, recovery, and repeatability. Combination of both off-line sample preparation preconcentration and large injection volume led to obtain LOQs in the range 5–47 ng/mL. The developed nano-LC-UV method was extended to MS detection to confirm the presence of PAEs in some beverages commercialized in different types of packaging.     

How Does Solvation Affect the Binding of Hydrophilic Amino Saccharides to Cucurbit[7]uril with Exceptional Anomeric Selectivity?

Cucurbit[7]uril (CB[7]) is known to bind strongly to hydrophilic amino saccharide guests with exceptional α‐anomer selectivities under aqueous conditions. Single‐crystal X‐ray crystallography and computational methods were used to elucidate the reason behind this interesting phenomenon. The crystal structures of protonated galactosamine (GalN) and glucosamine (GluN) complexes confirm the inclusion of α anomers inside CB[7] and disclose the details of the host–guest binding. Whereas computed gas‐phase structures agree with these crystal structures, gas‐phase binding free energies show preferences for the β‐anomer complexes over their α counterparts, in striking contrast to the experimental results under aqueous conditions. However, when the solvation effect is considered, the binding structures drastically change and the preference for the α anomers is recovered. The α anomers also tend to bind more tightly and leave less space in the CB[7] cavity toward inclusion of only one water molecule, whereas loosely bound β anomers leave more space toward accommodating two water molecules, with markedly different hydrogen‐bonding natures. Surprisingly, entropy seems to contribute significantly to both anomeric discrimination and binding. This suggests that of all the driving factors for the strong complexation of the hydrophilic amino saccharide guests, water mediation plays a crucial role in the anomer discrimination.     

Solvent‐free Liquid Crystals and Liquids from DNA

As DNA exhibits persistent structures with dimensions that exceed the range of their intermolecular forces, solid‐state DNA undergoes thermal degradation at elevated temperatures. Therefore, the realization of solvent‐free DNA fluids, including liquid crystals and liquids, still remains a significant challenge. To address this intriguing issue, we demonstrate that combining DNA with suitable cationic surfactants, followed by dehydration, can be a simple generic scheme for producing these solvent‐free DNA fluid systems. In the anhydrous smectic liquid crystalline phase, DNA sublayers are intercalated between aliphatic hydrocarbon sublayers. The lengths of the DNA and surfactant are found to be extremely important in tuning the physical properties of the fluids. Stable liquid‐crystalline and liquid phases are obtained in the ?20 °C to 200 °C temperature range without thermal degradation of the DNA. Thus, a new type of DNA‐based soft biomaterial has been achieved, which will promote the study and application of DNA in a much broader context.     

Normal halogen dependence of 13C NMR chemical shifts of halogenomethanes revisited at the four‐component relativistic level

The ‘Normal Halogen Dependence’ of ¹³C NMR chemical shifts in the series of halogenomethanes is revisited at the four‐component relativistic level. Calculations of ¹³C NMR chemical shifts of 70 halogenomethanes have been carried out at the density functional theory (DFT) and MP2 levels with taking into account relativistic effects using the four‐component relativistic theory of Dirac‐Coulomb within the different computational methods (4RPA, 4OPW91) and hybrid computational schemes (MP2 + 4RPA, MP2 + 4OPW91). The most efficient computational protocols are derived for practical purposes. Relativistic shielding effect reaches as much as several hundreds of ppm for heavy halogenomethanes, and to account for this effect in comparison with experiment at the qualitative level, relativistic Dyall's basis sets of triple‐zeta quality or higher are to be used within the framework of the four‐component relativistic theory taking into account solvent effects. Relativistic geometrical optimization (as compared with the non‐relativistic level) is essential for the molecules containing at least two iodines at one carbon atom. Copyright © 2016 John Wiley & Sons, Ltd.     

Charge transport properties of MDMO PPV thin films cast in different solvents

Charge transport properties in thin films of Poly(2‐methoxy‐5‐(3′,7′‐dimethyloctyloxy)‐1,4‐phenylenevinylene) (MDMO PPV) cast using either chloroform (CF), toluene (TOL), or chlorobenzene (CB) as solvent were investigated. Hole mobility (μ) in these thin films measured using time‐of‐flight transient photoconductivity showed an increasing trend with respect to the solvent used in the same order, that is, μ_CF (2.4 × 10^?7 cm²/Vs) < μ_TOL (6.9 × 10^?7 cm²/Vs) < μ_CB (2.3 × 10^?6 cm²/Vs). Observed variations in mobilities were attributed to different morphologies of MDMO PPV chains in thin films cast using the aforesaid solvents. Nature of the interchain interactions and aggregate formation were obtained using photoluminescence (PL), Raman spectroscopy, and AFM studies. Ratio of PL peak intensities of 0–0 and 0–1 transitions, which is a direct measure of interchain interaction, was the highest in CB and lowest in CF. Variation in the relative intensities of out‐of‐plane wagging of vinylene group (～963 cm^?1 mode) in Raman spectra suggested different extent of coiling of polymer chains in these thin films. From these observations, it was elicited that aggregate size and interchain interactions are highest in CB and least in CF. AFM‐based topographic images of thin films further supported these variations in the size of aggregates. Variation in the aggregate sizes and interchain interactions explained the corresponding variation in the mobility. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 1431–1439