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     

Van't Hoff analysis in chiral chromatography

The present review discusses the theory and application of van't Hoff analysis in chiral chromatography, with main focus on liquid chromatography. The topics considered include the physical meaning of van't Hoff equation's parameters, interpretation of thermodynamic data in terms of retention and enantioseparation mechanisms, abnormal behavior of van't Hoff plots, and best practices to avoid biased results.     

1,2‐Dimethoxyethane Degradation Thermodynamics in Li−O2 Redox Environments

The reaction thermodynamics of the 1,2‐dimethoxyethane (DME), a model solvent molecule commonly used in electrolytes for Li?O₂ rechargeable batteries, has been studied by first‐principles methods to predict its degradation processes in highly oxidizing environments. In particular, the reactivity of DME towards the superoxide anion O₂^? in oxygen‐poor or oxygen‐rich environments is studied by density functional calculations. Solvation effects are considered by employing a self‐consistent reaction field in a continuum solvation model. The degradation of DME occurs through competitive thermodynamically driven reaction paths that end with the formation of partially oxidized final products such as formaldehyde and methoxyethene in oxygen‐poor environments and methyl oxalate, methyl formate, 1‐formate methyl acetate, methoxy ethanoic methanoic anhydride, and ethylene glycol diformate in oxygen‐rich environments. This chemical reactivity indirectly behaves as an electroactive parasitic process and therefore wastes part of the charge exchanged in Li?O₂ cells upon discharge. This study is the first complete rationale to be reported about the degradation chemistry of DME due to direct interaction with O₂^?/O₂ molecules. These findings pave the way for a rational development of new solvent molecules for Li?O₂ electrolytes.     

Sublimation Properties of α,ω-Diamines Revisited from First-Principles Calculations

Sublimation enthalpies of alkane-α,ω-diamines exhibit an odd-even pattern within their homologous series. First-principles calculations coupled with the quasi-harmonic approximation for crystals and with the conformation mixing model for the ideal gas are used to explain this phenomenon from the theoretical point of view. Crystals of the odd and even alkane-α,ω-diamines distinctly differ in their packing motifs. However, first-principles calculations indicate that it is a delicate interplay of the cohesive forces, phonons, molecular vibrations and conformational equilibrium which governs the odd-even pattern of the sublimation enthalpies within the homologous series. High molecular flexibility of the alkane-α,ω-diamines predetermines higher sensitivity of the computational model to the quality of the optimized geometries and relative conformational energies. Performance of high-throughput computational methods, such as the density functional tight binding (DFTB, GFN2-xTB) and the explicitly correlated dispersion-corrected Møller - Plesset perturbative method (MP2C-F12), are benchmarked against the consistent state-of-the-art calculations of conformational energies and interaction energies, respectively.     

Energy conditions of the f(T,B) gravity dark energy model with the validity of thermodynamics

In this article, the analysis of Tsallis holographic dark energy(which turns into holographic dark energy for a particular choice of positive non-additivity parameter δ) in modified f(T, B) gravity with the validity of thermodynamics and energy conditions for a homogeneous and isotropic FLRW Universe has been studied. The enlightenment of the field equation towards f(T,B)=αT~m+βB~n, made possible by the fact that the model is purely accelerating,corresponds to q=-0.54(Mamon and Das 2017 Eur. Phys.J.C 77 49). The generalized second law of thermodynamics is valid not only for the same temperature inside the horizon, but also for the apparent horizon for a change in temperature. The essential inspiration driving this article is to exhibit the applicability that the holographic dark energy achieved from standard Tsallis holographic dark energy and the components acquired from f(T, B) gravity are identical for the specific bounty of constants. The analysis of energy conditions confirms that the weak energy condition and the null energy condition are fulfilled throughout the expansion, while violation of the strong energy condition validates the accelerated expansion of the Universe.With the expansion, the model becomes a quintessence dominated model. The dominant energy condition is not observed initially when the model is filled with genuine baryonic matter,whereas it appears when the model is in the quintessence dominated era.     

Structural and Thermodynamic Peculiarities of Core-Shell Particles at Fluid Interfaces from Triangular Lattice Models

A triangular lattice model for pattern formation by core-shell particles at fluid interfaces is introduced and studied for the particle to core diameter ratio equal to 3. Repulsion for overlapping shells and attraction at larger distances due to capillary forces are assumed. Ground states and thermodynamic properties are determined analytically and by Monte Carlo simulations for soft outer- and stiffer inner shells, with different decay rates of the interparticle repulsion. We find that thermodynamic properties are qualitatively the same for slow and for fast decay of the repulsive potential, but the ordered phases are stable for temperature ranges, depending strongly on the shape of the repulsive potential. More importantly, there are two types of patterns formed for fixed chemical potential—one for a slow and another one for a fast decay of the repulsion at small distances. In the first case, two different patterns—for example clusters or stripes—occur with the same probability for some range of the chemical potential. For a fixed concentration, an interface is formed between two ordered phases with the closest concentration, and the surface tension takes the same value for all stable interfaces. In the case of degeneracy, a stable interface cannot be formed for one out of four combinations of the coexisting phases, because of a larger surface tension. Our results show that by tuning the architecture of a thick polymeric shell, many different patterns can be obtained for a sufficiently low temperature.     

The Fundamental Equations of Change in Statistical Ensembles and Biological Populations

A recent article in Nature Physics unified key results from thermodynamics, statistics, and information theory. The unification arose from a general equation for the rate of change in the information content of a system. The general equation describes the change in the moments of an observable quantity over a probability distribution. One term in the equation describes the change in the probability distribution. The other term describes the change in the observable values for a given state. We show the equivalence of this general equation for moment dynamics with the widely known Price equation from evolutionary theory, named after George Price. We introduce the Price equation from its biological roots, review a mathematically abstract form of the equation, and discuss the potential for this equation to unify diverse mathematical theories from different disciplines. The new work in Nature Physics and many applications in biology show that this equation also provides the basis for deriving many novel theoretical results within each discipline.