Branched isomeric 1,2,3-triazolium-based ionic liquids: new insight into structure-property relationships.

A series of four isomeric 1,2,3-triazolium-based ionic liquids (ILs) with vary degree of branching were synthesized and characterized to investigate the effect of ion branching on thermal and physical properties of the resulting IL. It was found that increased branching led to a higher ionicity and higher viscosity. The thermal properties were also altered significantly and spectral changes in the near edge X-ray absorption fine structure (NEXAFS) spectra show that branching affects intermolecular interaction. While the ionicity and viscosity varying linearly with branching, the MDSC and NEXAFS measurements show that the cation shape has a stronger influence on the melting temperature and absorptive properties than the number of branched alkyl substituents.

Zeolite screening for the separation of gas mixtures containing SO2, CO2 and CO.

We used a combination of experiments and molecular simulations to investigate at the molecular level the effects of zeolite structure on the adsorption and diffusion of sulfur dioxide, carbon dioxide and carbon monoxide as well as separation processes of their mixtures. Our study involved different zeolite topologies and revealed numerous structure-property trends depending on the temperature and pressure conditions. Sulfur dioxide, which has the strongest interactions with zeolites due to its size and polarity, showed the largest adsorption across investigated temperatures and pressures. Our results indicate that structures with channel-type pore topology and low pore volume are the most promising for selective adsorption of sulfur dioxide over carbon dioxide and carbon monoxide under room conditions, while structures with higher pore volume exhibit better storage capacity at higher pressure. Our results emphasize the need for considering both adsorption and diffusion processes in the selection of the optimal structure for a given separation process. Our findings help to identify the best materials for effective separation processes under realistic operating conditions.

Navigating molecular worms inside chemical labyrinths.

Predicting whether a molecule can traverse chemical labyrinths of channels, tunnels, and buried cavities usually requires performing computationally intensive molecular dynamics simulations. Often one wants to screen molecules to identify ones that can pass through a given chemical labyrinth or screen chemical labyrinths to identify those that allow a given molecule to pass. Because it is impractical to test each molecule/labyrinth pair using computationally expensive methods, faster, approximate methods are used to prune possibilities, "triaging" the ability of a proposed molecule to pass through the given chemical labyrinth. Most pruning methods estimate chemical accessibility solely on geometry, treating atoms or groups of atoms as hard spheres with appropriate radii. Here, we explore geometric configurations for a moving "molecular worm," which replaces spherical probes and is assembled from solid blocks connected by flexible links. The key is to extend the fast marching method, which is an ordered upwind one-pass Dijkstra-like method to compute optimal paths by efficiently solving an associated Eikonal equation for the cost function. First, we build a suitable cost function associated with each possible configuration, and second, we construct an algorithm that works in ensuing high-dimensional configuration space: at least seven dimensions are required to account for translational, rotational, and internal degrees of freedom. We demonstrate the algorithm to study shortest paths, compute accessible volume, and derive information on topology of the accessible part of a chemical labyrinth. As a model example, we consider an alkane molecule in a porous material, which is relevant to designing catalysts for oil processing.

Estimating persistence of brominated and chlorinated organic pollutants in air, water, soil, and sediments with the QSPR-based classification scheme.

We have estimated degradation half-lives of both brominated and chlorinated dibenzo-p-dioxins (PBDDs and PCDDs), furans (PBDFs and PCDFs), biphenyls (PBBs and PCBs), naphthalenes (PBNs and PCNs), diphenyl ethers (PBDEs and PCDEs) as well as selected unsubstituted polycyclic aromatic hydrocarbons (PAHs) in air, surface water, surface soil, and sediments (in total of 1,431 compounds in four compartments). Next, we compared the persistence between chloro- (relatively well-studied) and bromo- (less studied) analogs. The predictions have been performed based on the quantitative structure-property relationship (QSPR) scheme with use of k-nearest neighbors (kNN) classifier and the semi-quantitative system of persistence classes. The classification models utilized principal components derived from the principal component analysis of a set of 24 constitutional and quantum mechanical descriptors as input variables. Accuracies of classification (based on an external validation) were 86, 85, 87, and 75% for air, surface water, surface soil, and sediments, respectively. The persistence of all chlorinated species increased with increasing halogenation degree. In the case of brominated organic pollutants (Br-OPs), the trend was the same for air and sediments. However, we noticed that the opposite trend for persistence in surface water and soil. The results suggest that, due to high photoreactivity of C-Br chemical bonds, photolytic processes occurring in surface water and soil are able to play significant role in transforming and removing Br-OPs from these compartments. This contribution is the first attempt of classifying together Br-OPs and Cl-OPs according to their persistence, in particular, environmental compartments.

Structure and energetics of clustered damage sites.

Quantum calculations on duplex DNA trimers were used to model the changes in structure, hydrogen bonding, stacking properties, and electrostatic potential induced by oxidized purine bases and abasic (AP) sites. Results for oxidized purine bases were consistent with experimental data that show small structural and energetic perturbations induced by isolated 8-oxoguanine (8oG). Watson-Crick base pairing was preserved, and no major distortions of the backbone were induced. The thermal destabilization of DNA induced by 8oG was comparable to the energy of a single hydrogen bond. In contrast, AP sites caused substantial distortions of the DNA backbone that were accompanied by relocation of counterions. The loss of Watson-Crick hydrogen bonds in AP sites had the potential to destabilize DNA by 10-20 kcal/mol (0.4-0.8 eV); however, new inter- and intrastrand hydrogen bonds formed after removal of a nucleic acid base that significantly affected the energy of AP sites and introduced a strong dependence on sequence context. Quantum calculations on small DNA fragments provided starting conformations and force-field parameters for classical molecular dynamics simulations of radiation-induced single-strand breaks that most often combine hydrolysis of a phosphate-oxygen (P-O) bond with an AP site and fully or partially degraded sugar ring. P-O bond hydrolysis increased the freedom in backbone torsion angles, which allowed the broken strand to compress and partially fill the hole in the DNA created by the AP site. Results for strand breaks with a 3'phosphoglycolate were similar to those with phosphate end groups.