Electric field gradient (EFG) fluctuations for the monoatomic ions (7)Li(+), (23)Na(+), (35)Cl(-), (81)Br(-), and (127)I(-) in aqueous solution are studied using Car-Parrinello ab initio molecular dynamics (aiMD) simulations based on density functional theory. EFG calculations are typically performed with 1024 ion-solvent configurations from the aiMD simulation, using the Zeroth Order Regular Approximation (ZORA) relativistic Hamiltonian. Autocorrelation functions for the spherical EFG tensor elements are computed, transformed into the corresponding spectral densities (under the extreme narrowing condition), and subsequently converted into NMR quadrupolar relaxation rates for the ions. The relaxation rates are compared with experimental data. The order of magnitude is correctly predicted by the simulations. The computational protocol is tested in detail for (81)Br(-).

Three-dimensional (3D) structural models of the Green River kerogen based on the two-dimensional (2D) structure proposed by Siskin were generated using a combination of ab initio and molecular mechanics calculations. Several initial monomer conformations were generated using the simulated annealing procedure, followed by minimization via quantum mechanical calculations. 13 C solid state nuclear magnetic resonance (SSNMR) spectra and atomic pair distribution functions (PDFs) were calculated based on these 3D models and compared to experimental results obtained on a Green River kerogen sample. The results show reasonably good agreement between calculated and experimental results, showing that this type of 3D modeling can be of value in the evaluation of 2D models. Moreover, this paper establishes a general methodology to develop 3D models for any existing or future 2D model of kerogens.

In this study, we construct novel RNA nanoclusters, RNA nanotubes made of several nanorings up to the size of 20 nm, utilizing the molecular dynamics simulation, and study their structural properties [i.e., the root mean square deviation, the radius of gyration and the radial distribution function (RDF)] in physiological solutions that can be used for drug delivery into the human body. The patterns of energy and temperature variations of the systems are also discussed. Furthermore, we study the concentration of ions around the tube as a function of time at a particular temperature. We have found that when the temperature increases, the number of ions increases within a certain distance of the tube. We report that the number of ions within this distance around the tubes decreases in quenched runs. This indicates that some ions evaporate with decrease in temperature, as has been observed in the case of the nanoring. RDF plots also demonstrate a similar trend with temperature, as was found in the case of RNA nanorings.

This paper presents calculations of 13 C solid state NMR (SSNMR) spectra of model asphaltenes. The overall goal of this work is to assess how valuable 13 C SSNMR studies of asphaltenes can be in guiding the development of representative 3D (three-dimensional) models of asphaltenes. The calculations were done using 3D models based on previously published 2D (two-dimensional) models. The calculated spectra show overall agreement with the existing data, and the results show that the 13 C SSNMR spectra of model asphaltenes are quite sensitive to both the 2D and the 3D structures, indicating that this property can be used to guide further model development.

We investigate the in-plane oscillations of the relaxed shape graphene due to externally applied tensile edge stress along both the armchair and zigzag directions. We show that the total elastic energy density is enhanced with temperature for the case of applied tensile edge stress along the zigzag direction. Thermo-electromechanical effects are treated via pseudomorphic vector potentials to analyze the influence of these coupled effects on the bandstructures of bilayer graphene quantum dots (QDs). We report that the level crossing between ground and first excited states in the localized edge states can be achieved with the accessible values of temperature. In particular, the level crossing point extends to higher temperatures with decreasing values of externally applied tensile edge stress along the armchair direction. This kind of level crossings is absent in the states formed at the center of the graphene sheet due to the presence of three fold symmetry.