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     

Improved semiempirical heats of formation through the use of bond and group equivalents

Deficiencies in energetics obtained using the common semiempirical methods, AM1, PM3, and MNDO, may partly be traced to the use of pseudoatomic equivalents for conversion of molecular energies to heats of formation at 298 K. We present an alternative scheme based on the use of bond and group equivalents. Values for the 61 bond and group equivalents necessary for treatment of molecules containing the common organic elements, hydrogen, carbon, nitrogen, and oxygen have been derived. For a set of 583 neutral, closed-shell molecules mean absolute errors in AM1, PM3, and MNDO heats of formation are reduced from 6.6, 4.2, and 8.2 kcal/mol to 2.3, 2.2, and 3.0 kcal/mol, respectively. Several systematic problems are overcome in the present scheme including relative stabilities of branched hydrocarbons, energetics of conjugated systems, heats of formation of long chain hydrocarbons, and enthalpies of molecules containing multiple heteroatoms. Although the approach is restricted to molecules with well-defined functional groups, the equivalents are easy to incorporate and are chemically relevant. This revised procedure allows semiempirical methods to be used for far more reliable evaluations of heats of reactions. Estimates are made of the errors inherent in these semiempirical formalisms, arising from integral approximations and the neglect of explicit treatment of electron correlation effects, while excluding those from inadequate parameterization.     

D-branes on Calabi–Yau Manifolds and Superpotentials

We show how to compute terms in an expansion of the world-volume superpotential for fairly general D-branes on the quintic Calabi-Yau using linear sigma model techniques, and show in examples that this superpotential captures the geometry and obstruction theory of bundles and sheaves on this Calabi-Yau.Louis Michel Professor     

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     

Validity of the equivalent-photon approximation for the production of massive spin-1 particles

We point out that the equivalent-photon approximation (EPA) for processes with massive spin-1 particles in the final state would have validity in a more restricted kinematic domain than for processes where it is commonly applied, viz., those with spin-1/2 or spin-0 particles in the final state. We obtain the criterion for the validity ofEPA for the two-photon production of a pair of charged, massive, point-like spin-1 particlesV ^±, each of massM and with a standard magnetic moment (κ=1). In a process in which one of the photons is real and the other virtual with four-momentumq, the condition for the validity ofEPA is |q ²|≪M ², in addition to the usual condition |q ²|≪W ²,W being theV ⁺ V ⁻ invariant mass. In a process in which both photons are virtual (with four-momentaq andq′), our condition is |q ²||q′²|W ⁴ ≪ 16M ⁸, in addition to |q ²| ≪M ², |q′²| ≪M ² and |q ²| ≪W ², |q′²| ≪W ². Even when these extra conditions permitting the use ofEPA are not fulfilled, convenient approximate expressions may still be obtained assuming merely |q ²| ≪W ² and |q′²| ≪W ². We also discuss how the extra conditions are altered when the vector bosons are incorporated in a spontaneously broken gauge theory. Examples ofW boson production in Weinberg-Salam model are considered for which the condition |q ²||q′²|W ⁴ ≪ 16M ⁸ is shown to be removed.     

A method for computing the solubility limit of solids: application to sodium chloride in water and alcohols

We present an adaptable method to compute the solubility limit of solids by molecular simulation, which avoids the difficulty of reference state calculations. In this way, the method is highly adaptable to molecules of complex topology. Results are shown for solubility calculations of sodium chloride in water and light alcohols at atmospheric conditions. The pseudosupercritical path integration method is used to calculate the free energy of the solid and gives results that are in good agreement with previous studies that reference the Einstein crystal. For the solution phase calculations, the self-adaptive Wang-Landau transition-matrix Monte Carlo method is used within the context of an expanded isothermal-isobaric ensemble. The method shows rapid convergence properties and the uncertainty in the calculated chemical potential was 1% or less for all cases. The present study underpredicts the solubility limit of sodium chloride in water, suggesting a shortcoming of the molecular models. Importantly, the proper trend for the chemical potential in various solvents was captured, suggesting that relative solubilities can be computed by the method.     

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%.

     

Light-induced enantiospecific 4π ring closure of axially chiral 2-pyridones: enthalpic and entropic effects promoted by H-bonding

Nonbiaryl axially chiral 2-pyridones were synthesized and employed for light-induced electrocyclic 4π ring closure leading to bicyclo-β-lactam photoproducts in solution. The enantioselectivity in the photoproducts varied from 22 to 95% depending on the reaction temperature and the ability of the axially chiral chromophore to form intramolecular and/or intermolecular H-bonds with the solvent. On the basis of the differential activation parameters, entropic control of the enantiospecificity was observed for 2-pyridones lacking the ability to form H-bonds. Conversely, enthalpy played a significant role for 2-pyridones having the ability to form H-bonds.