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     

Morphological studies of blends of conjugated polymers and acceptor molecules using langevin dynamics simulations

We use coarse‐grained Langevin dynamics simulations of blends of generic conjugated polymers and acceptor molecules to show how architecture (e.g., side chains, backbone flexibility of oligomers) and the pair‐wise interactions between the constituents of the blend affect morphology and phase transition. Alkyl side chains on the conjugated oligomer backbones shift the liquid crystal (LC) transition temperature from that of bare conjugated backbones and the direction of the shift depends on backbone–backbone interactions. Rigid backbones and constrained side chains cause a layer‐by‐layer morphology of conjugated polymers and amorphous acceptors, whereas flexible backbones and unconstrained side chains facilitate highly ordered acceptor arrangement. Strong backbone–backbone attraction shifts LC transition to higher temperatures than weak backbone–backbone attraction, and strong acceptor–acceptor attraction increases acceptor aggregation. Pure macro‐phase separated domains form when all pair‐wise interactions in the blend are strongly attractive, whereas interconnected domains form at intermediate acceptor–acceptor attraction and strong polymer–polymer attractions. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2013     

Effect of homopolymer matrix on diblock copolymer grafted nanoparticle conformation and potential of mean force: A molecular simulation study

We study the effect of homopolymer A or B matrix on the conformations and effective interactions of AB diblock copolymer grafted particles using coarse‐grained molecular dynamics simulations. In an A homopolymer matrix we observe patchy conformations within the AB diblock copolymer grafted layer, where the number of B patches is controlled by the A‐A attractive interaction strength. In a B homopolymer matrix the grafted particle takes on a core‐corona conformation, where the inner A block aggregates near the particle surface and the outer B block forms a corona that interacts with the B matrix. The potential of mean force (PMF) between two particles in an A homopolymer matrix has a long‐ranged attractive well with a minima at intermediate distances corresponding to the location of the outer B block patches. The PMF between two particles in a B homopolymer matrix has an attractive well at short interparticle distances corresponding to the size of the inner A block. We isolate the contribution of the homopolymer matrix on the PMF between the two diblock copolymer grafted particles, by deducting the PMF in the absence of a matrix, assuming the contributions of the grafted particle and matrix to the PMF to be additive. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 76–88     

A fluorescent di-zinc(II) complex of bis-calix[4]arene conjugate as chemosensing-ensemble for the selective recognition of ATP

A triethylene glycol di-imine locked triazole linked bis-calix[4]arene conjugate L has been synthesised and characterised. Conjugate L exhibits high fluorescence enhancement towards Zn²⁺ among the 13 metal ions studied down to a lower detection limit of ～12 ppb. The absorption and visual colour change experiments differentiated the Zn²⁺ from the other metal ions studied. The isolated zinc complex, [Zn₂L] has been used as a chemo-sensing ensemble for the recognition of anions based on their binding affinities towards Zn²⁺. [Zn₂L] was found to be sensitive and selective towards phosphate-bearing species and in particular to adenosine triphosphate (ATP^2 ? ) among the other 20 anions studied as observed based on the changes occurred in the fluorescence intensity. The selectivity of the ATP^2 ?  has been shown on the basis of the changes observed in the emission and absorption spectral studies. The lowest detectable concentration for ATP^2 ?  with the chemo-sensing ensemble [Zn₂L] is 348 ppb in methanol. The fluorescence quenching by the phosphate-based anions has been modelled by molecular mechanics studies and found that the anions possessing two or more phosphate moieties can only bridge between the two zinc centres, and hence those possessing only one phosphate moiety (H₂PO₄^?  and AMP^2 ? ) are ineffective.     

Monte carlo simulations of polydisperse polymers grafted on spherical surfaces

This article presents effects of polydispersity in polymers grafted on spherical surfaces on grafted polymer chain conformations, grafted layer thickness, and free‐end monomer distribution within the grafted layer. At brush‐like grafting densities, as polydispersity index (PDI) increases, the scaling exponent of radius of gyration of grafted chains approaches that of a single chain grafted on the same nanoparticle, because polydispersity alleviates monomer crowding within the brush. At high PDI, the chains shorter than the number average chain length, N_n, have more compressed conformations, and the chains longer than N_n overall stretch less than in the monodisperse case. As seen in polydisperse flat brushes at high grafting densities, the grafted layer thickness on spherical nanoparticle increases with PDI. Polydispersity eliminates the region near the surface devoid of free‐end monomers seen in monodisperse cases, and it reduces the width of free‐end monomer distribution and shifts the free‐end monomer distribution close to the surface. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2012     

Effect of additive length and chemistry on the morphology of blends of conjugated thiophenes and fullerene derivative acceptor molecules

Small molecule additives have been shown to increase the device efficiency of conjugated polymer (donor) and fullerene derivative (acceptor) based organic solar cells by modifying the morphology of the device active layer. In this paper we conduct a systematic study of how additives affect the donor‐acceptor morphology using molecular dynamics simulations of blends of thiophene‐based oligomers, mimicking poly(3‐dodecylthiophene) (P3DDT) or poly(2,2′:5′,2”‐3,3”‐didocyl‐terthiophene) (PTTT), and fullerene derivatives with additives of varying length and chemical functionalization, mimicking experimentally used additives like methyl ester additives, diiodooctane, and alkanedithiols. We find that functionalization of additives with end groups that are attracted to acceptor molecules are necessary to induce increased donor‐acceptor macrophase separation. In blends where acceptors intercalate between oligomer alkyl side chains, functionalized additives decrease acceptor intercalation. Functionalized additives with shorter alkyl segments increase acceptor macrophase separation more than additives with same chemical functionalization but longer alkyl segments. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 1046–1057     

Sample Treatment Approaches for Trace Level Determination of Cesium in Hepatitis B Vaccine by Suppressed Ion Chromatography

The hepatitis B surface antigen manufactured by recombinant DNA technology is extracted from the culture media by density gradient centrifugation using cesium salts. Cesium is considered to be toxic, because it affects active ion transport by blocking potassium channels. The residual trace levels of cesium in hepatitis B vaccine samples are determined by suppressed ion chromatography. Hepatitis B vaccines contain various buffer salts, aluminum-containing adjuvants, proteins and traces of iron. The polyvalent cations (Al³⁺, Fe³⁺) and proteins degrade the chromatographic performance in terms of decreased retention time and poor reproducibility. Different sample preparation approaches were evaluated with the aim of eliminating these foulants: (1) filtration, (2) digestion and (3) digestion-protein precipitation. Quantitative elimination of these foulants was achieved in the digestion-protein precipitation sample clean-up approach. Cesium was separated on the IonPac CS17 column with suppressed conductivity detection. The results of the ion chromatography (IC) method were compared with ICP-MS analysis. The precision of determination was better than 6.5% (relative standard deviation) with a method detection limit of 45 ng mL⁻¹. The expanded uncertainty in the measurement at 95% confidence level (coverage factor 2) is better than 16.3%.

     

Nondoped blue fluorescent OLED based on cyanophenanthrimidazole‐styryl‐triphenylamine/carbazole materials

New 2‐(4′‐9H‐carbazole‐9‐yl)‐styryl‐1H‐phenathro[9,10‐d]imidazole‐1‐yl)benzonitrile (SPICN‐Cz) and 4‐(2‐(4‐(diphenylamino)phenyl‐styryl‐1H‐phenathro[9,10‐d]imidazole‐1‐yl)benzonitrile (SPICN‐TPA) have been synthesised, and their photophysical, electrochemical, and electroluminescent properties were analysed in comparison with their cyano‐free parent compounds, SPI‐Cz, and SPI‐TPA. Solvatochromic effects show the transformation of an excited state character from locally excited (LE) state to charge transfer (CT) state. Using time‐dependent density functional theory calculation, the excited state properties of these donor‐acceptor blue emissive materials have been analysed. Their excited state properties have been tuned by replacing the strong donor triphenylamine to weak donor carbazole to achieve the combination of high photoluminance efficiency locally excited (LE) component and high exciton‐utilizing CT component in one excited state. Hybridization processes between LE and CT components of SPICN‐Cz and SPICN‐TPA in the emissive state have been discussed. The nondoped organic light emitting diode device based on SPICN‐Cz exhibit better electroluminescent performances than those of SPICN‐TPA–based device: high external quantum efficiency of 2.58 %, current efficiency of 2.90 cd A^‐1, and power efficiency of 2.26 lm W^‐1 with Commission Internationale de l'Éclairage (CIE) coordinates of (0.15, 0.12). The excited state modulation and the composition of LE and CT states in the donor‐acceptor system could be useful to design low‐cost, high‐efficiency fluorescent organic light emitting diode materials.