Modelling non-equilibrium self-assembly from dissipation

Non-equilibrium self-assembly is ubiquitous in physico-chemical and biological systems, and manifests itself at different scales, ranging from the molecular to the cosmological. The formation of microtubules, gels, cells and living beings among many others takes place through self-assembly under nonequilibrium conditions. We propose a general thermodynamic non-equilibrium model to understand the formation of assembled structures such as gels and Liesegang patterns and at the same time able to describe the kinetics and the energetics of the structure formation process. The model is supported for a global mechanism to obtain self-assembled structures from building blocks via activation, deactivation, assembly, and disassembly processes. It is proposed that the resulting structures can be characterised by a structural parameter. Our model may contribute to a better understanding of non-equilibrium self-assembly processes and give deeper insight as to how to obtain a specific structural architecture to materials, such as hydrogels which are of great importance in the design of advanced devices and novel materials.     

Unraveling the mechanism of catalytic reactions through combined kinetic and thermodynamic analyses: Application to the condensation of ethanol

The combination of kinetic and thermodynamic analyses can provide an in-depth knowledge of the crucial steps of catalyzed reactions. Earlier examples are recalled to stress how a reaction mechanism can be supported or rejected based on trivial reactant and product concentration analyses. The method is then applied to the important reaction of alcohol condensation, the so-called Guerbet reaction, which enables converting ethanol, a renewable feedstock, into higher alcohols. Important conclusions regarding the design of ethanol condensation processes can be drawn, as the main reaction mechanism occurring at high temperatures (ca. 350–420 °C) appears to be different from that proposed at low temperatures (< 250 °C). In the former case, the pathway involving acetaldehyde is negligible, and therefore a multi-step process based on ethanol dehydrogenation followed by acetaldehyde self-aldolization would be irrelevant.     

An asymmetric N-rim partially substituted calix[4]pyrrole: Its affinity for Ag(I) and its destruction by Hg(II)

A new partially substituted calix[4] pyrrole derivative obtained by the introduction of three thioamide functionalities in the N-rim has been synthesised and fully characterised by ¹H, ¹³C, HSQC, ROESY NMR and mass spectroscopy. Computer modelling suggested an alternate conformation which was confirmed through ROESY ¹H NMR. The receptor interacts only with the silver cation as shown by ¹H NMR. The strength of interaction is quantitatively assessed by titration calorimetry. N-rim modification eliminates the possibility of interaction with anions. Unlike calix[4] pyrrole derivatives obtained by the introduction of functionalities through the meso-position, addition of Hg(NO₃)₂ leads to the degeneration of the receptor as demonstrated by ¹H NMR, FTIR and XPS analyses. This is for the first time reported. Molecular simulation studies show significant strain in the mercury bound ligand in bonds, angles, torsions leading to the destruction of the receptor. Given the negative environmental impact produced by the availability of silver ions in aquatic organisms, the fundamental studies indicate that this receptor offers potential applications for monitoring silver (ion selective electrode) or indeed as a decontaminating material for removing silver ions from water.     

Computer-aided design of formulated products

Formulated products represent a particular class of complex chemical products, and their design is typically based on experience and extensive experimentation. Although still at an early stage, and despite that their potential is not fully accessed and not fully used by the industry, computer-aided design (CAD) methods and tools offer many possibilities in the design of formulated products. The CAD methodology based on computerized models enables the formulation chemists to speed up the design process, without completely replacing experiments.In this work, we summarize previous studies in the field and present important elements of the CAD framework, emphasizing estimation methods for key target properties, link to specifications, and finally, some case studies will illustrate how the CAD framework can be used in practice for formulated products.     

Synthesis of a Porous [14]Annulene Graphene Nanoribbon and a Porous [30]Annulene Graphene Nanosheet on Metal Surfaces

The electrical and mechanical properties of graphene-based materials can be tuned by the introduction of nanopores, which are sensitively related to the size, morphology, density, and location of nanopores. The synthesis of low-dimensional graphene nanostructures containing well-defined nonplanar nanopores has been challenging due to the intrinsic steric hindrance. Herein, we report the selective synthesis of one-dimensional (1D) graphene nanoribbons (GNRs) containing periodic nonplanar [14]annulene pores on Ag(111) and two-dimensional (2D) porous graphene nanosheet containing periodic nonplanar [30]annulene pores on Au(111), starting from a same precursor. The formation of distinct products on the two substrates originates from the different thermodynamics and kinetics of coupling reactions. The reaction mechanisms were confirmed by a series of control experiments, and the appropriate thermodynamic and kinetic parameters for optimizing the reaction pathways were proposed. In addition, the combined scanning tunneling spectroscopy (STS) and density functional theory (DFT) calculations revealed the electronic structures of porous graphene structures, demonstrating the impact of nonplanar pores on the π-conjugation of molecules.     

Thermodynamic characterization of proflavine–DNA binding through microcalorimetric studies

The interaction of an important acridine dye, proflavine hydrochloride, with double stranded DNA was investigated using isothermal titration calorimetry and differential scanning calorimetry. The equilibrium constant for the binding reaction was calculated to be (1.60 ± 0.04) · 10⁵ · M⁻¹ at T = 298.15 K. The binding of proflavine hydrochloride to DNA was favored by both negative enthalpy and positive entropy contributions to the Gibbs energy. The equilibrium constant for the binding reaction decreased with increasing temperature. The standard molar enthalpy change became increasingly negative while the standard molar entropy change became less positive with rise in temperature. However, the standard molar Gibbs free energy change varied marginally suggesting the occurrence of enthalpy–entropy compensation phenomenon. The binding reaction was dominated by non-polyelectrolytic forces which remained virtually unchanged at all the salt concentrations studied. The binding also significantly increased the thermal stability of DNA against thermal denaturation.     

Thermodynamic properties,detonation characterisation and free radical of N-acetyl-3,3-dinitroazetidine

N-acetyl-3,3-dinitroazetidine (ADNAZ) is an important precursor for synthesizing new multinitroazetidine energetic compounds. Its thermal behaviour was studied under a non-isothermal condition by DSC and TG/DTG methods, the results show that there are one melting process and one endothermic decomposition process. The specific molar heat capacity (C_p,m) of ADNAZ was determined by a continuous C_p mode of micro-calorimeter and theoretical calculation, and the C_p,m of ADNAZ was 240.37 J · K⁻¹ · mol⁻¹ at T = 298.15 K. The detonation velocity (D) and detonation pressure (P) of ADNAZ were estimated using the nitrogen equivalent equation according to the experimental density, the value of D and P are (6685.83 ± 3.12) m · s⁻¹ and (18.36 ± 0.02) GPa, respectively. The free radical signals of ADNAZ were detected by electron spin resonance (ESR) technique, which is used to estimate its sensitivity.     

Aqueous solutions of ionic liquids. Description of osmotic coefficients within the Binding Mean Spherical Approximation

The Binding Mean Spherical Approximation (BiMSA) is used to describe osmotic coefficients of aqueous solutions of salts containing imidazolium cations and bulky anions over the whole concentration range at temperature in the range (25 to 60) °C. A total of 13 salts have been considered altogether. The ion diameters, the permittivity of solution and the association constant were taken as adjustable parameters. Ionic liquids are described as being weakly associated in water, and association constants values obtained within the BiMSA model are in good agreement with those from the literature. Diameter values were assigned to 1-alkyl-3-methylimidazolium cations. The adjusted values obtained for the cation diameters increased with the number of carbons on the alkyl chain. For all systems studied, average relative deviations were found to be satisfactory.     

A model for the deformations and thermodynamics of liquids involving a dislocation kinetics

A model for the deformation and thermodynamics of liquids is developed that depends on dislocation kinetics. The approach uses concepts from statistical mechanics to model a stochastic evolution equation for a scalar dislocation density function. The dislocation density is used in an idealized model for the discrete discontinuous deformation due to dislocation motion and dislocation creation kinetics. The total deformation functional for a liquid is modelled as a continuum deformation of an idealized lattice structure plus the discontinuous deformation due to dislocation kinetics. This results in a thermodynamic model that has an elastic response from the continuum lattice structure and a fluid response from the dislocation kinetics.In the thermodynamics, a generalized internal energy functional is assumed to exist and to have a dependence on the functions of entropy, continuum lattice strain, scalar dislocation density, velocity, and mass density. The continuum lattice strain is termed the recoverable strain and its conjugate variable is the thermodynamic stress. The conjugate variable to the scalar dislocation density is the thermodynamic chemical potential for a dislocation configuration, somewhat analogous to Gibbs' treatment of chemical potential for various mass species.This model implies that a liquid and a crystalline solid have analogous deformation and thermodynamic responses. Their differences appear in the dislocation densities and in the dislocation chemical potentials. To illustrate the deformation response analogy, some solutions are developed for simple laminar shear flows. Also, using some concepts primarily from Kuhlmann-Wilsdorf's melting model, a definition for a specific dislocation creation heat equivalent is given. This thermodynamic formalism suggests that the melting process can be modelled as the consequence of a continuous change in the dislocation density function.Work performed under the auspices of the U.S. Department of Energy by the Lawrence Livermore National Laboratory under contract No. W-7405-ENG-48.     

Representation invariant Geometrothermodynamics: Applications to ordinary thermodynamic systems

In this work we employ a recently devised metric within the Geometrothermodynamics program to study ordinary thermodynamic systems. The new feature of this metric is that, in addition to Legendre symmetry, it exhibits invariance under a change of representation. This metric was derived in a previous work by the authors while addressing the problem of the conformal structure of the thermodynamic metrics for different representations. Here, we present a thorough analysis for the ideal gas, the van der Waals fluid, the one dimensional Ising model and some other systems of cosmological interest.