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Register a new userSelf-Assembly of Diamondoid Molecules and Derivatives (MD Simulations and DFT Calculations)
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We report self-assembly and phase transition behavior of lower diamondoid molecules and their primary derivatives using molecular dynamic (MD) simulation and density functional theory (DFT) calculations. Two lower diamondoids (adamantane and diamantane), three adamantane derivatives (amantadine, memantine and rimantadine) and two artificial molecules (Adamantane+Na and Diamantane+Na) are studied separately in 125-molecule simulation systems. We performed DFT calculations to optimize their molecular geometries and obtain atomic electronic charges for the corresponding MD simulation, by which we obtained self-assembly structures and simulation trajectories for the seven molecules. Radial distribution functions and structure factors studies showed clear phase transitions for the seven molecules.
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Although common in nature, the self-assembly of small molecules at sold-liquid interfaces is difficult to control in artificial systems. The high mobility of dissolved small molecules limits their residence at the interface, typically restricting the self-assembly to systems under confinement or with mobile tethers between the molecules and the surface. Small hydrogen-bonding molecules can overcome these issues by exploiting group-effect stabilization to achieve non-tethered self-assembly at hydrophobic interfaces. Significantly, the weak molecular interactions with the solid makes it possible to influence the interfacial hydrogen bond network, potentially creating a wide variety of supramolecular structures. Here we investigate the nanoscale details of water and alcohols mixtures self-assembling at the interface with graphite through group effect. We explore the interplay between inter-molecular and surface interactions by adding small amounts of foreign molecules able to interfere with the hydrogen bond network and systematically varying the length of the alcohol hydrocarbon chain. The resulting supramolecular structures forming at room temperature are then examined using atomic force microscopy with insights from computer simulations. We show that the group-based self-assembly approach investigated here is general and can be reproduced on other substrates such as molybdenum disulphide and graphene oxide, potentially making it relevant for a wide variety of systems.
Applying ab initio calculation and molecular dynamics simulation methods, we have been calculating and predicting the essential self-assemblies and phase transitions of two lower diamondoids (adamantane and diamantane), three of their important derivatives (amantadine, memantine and rimantadine), and two organometallic molecules that are built by substituting one hydrogen ion with one sodium ion in both adamantane and diamantine molecules (ADM-Na and Optimized DIM-Na). To study their self-assembly and phase transition behaviors, we built seven different MD simulation systems, and each system consisting of 125 molecules. We obtained self-assembly structures and simulation trajectories for the seven molecules. Radial distribution function studies showed clear phase transitions for the seven molecules. Higher aggregation temperatures were observed for diamondoid derivatives. We also studied the density dependence of the phase transition which demonstrates that the higher the density - the higher the phase transition points.
Accurate description of the excess charge in water cluster anions is challenging for standard semi-local and (global) hybrid density functional approximations (DFAs). Using the recent unitary invariant implementation of the Perdew-Zunger self-interaction correction (SIC) method using Fermi-Lowdin orbitals, we assess the effect of self-interaction error on the vertical detachment energies of water clusters anions with the local spin density approximation (LSDA), Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation, and the strongly constrained and appropriately normed (SCAN) meta-GGA functionals. Our results show that for the relative energies of isomers with respect to reference CCSD(T) values, the uncorrected SCAN functional has the smallest deviation of 21 meV, better than that for the MP2 method. The performance of SIC-SCAN is comparable to that of MP2 and is better than SIC-LSDA and SIC-PBE, but it reverses the ordering of the two lowest isomers for water hexamer anions. Removing self interaction error (SIE) corrects the tendency of LSDA, PBE, and SCAN to over-bind the extra electron. The vertical detachment energies (VDEs) of water cluster anions, obtained from the total energy differences of corresponding anion and neutral clusters, are significantly improved by removing self-interaction and are better than the hybrid B3LYP functional, but fall short of MP2 accuracy. Removing SIE results in substantial improvement in the position of the eigenvalue of the extra electron. The negative of the highest occupied eigenvalue after SIC provides an excellent approximation to the VDE, especially for SIC-PBE where the mean absolute error with respect to CCSD(T) is only 17 meV, the best among all approximations compared in this work.
We describe extensions to the siesta density functional theory (dft) code [30], for the simulation of isolated molecules and their absorption spectra. The extensions allow for: - Use of a multi-grid solver for the Poisson equation on a finite dft mesh. Non-periodic, Dirichlet boundary conditions are computed by expansion of the electric multipoles over spherical harmonics. - Truncation of a molecular system by the method of design atom pseudo- potentials of Xiao and Zhang[32]. - Electrostatic potential fitting to determine effective atomic charges. - Derivation of electronic absorption transition energies and oscillator stren- gths from the raw spectra produced by a recently described, order O(N3), time-dependent dft code[21]. The code is furthermore integrated within siesta as a post-processing option.
Ionic liquids (IL) are promising electrolytes for electrochemical applications due to their remarkable stability and high charge density. Molecular dynamics simulations are essential for better understanding the complex phenomena occurring at the electrode-IL interface. In this work, we have studied the interface between graphene and 1-ethyl-3-methyl-imidazolium tetrafluoroborate IL, using density functional theory-based molecular dynamics simulations at variable surface charge densities. We have disassembled the electrical double layer potential drop into two main components: one involving atomic charges and the other - dipoles. The latter component arises due to the electronic polarisation of the surface and is related to concepts hotly debated in the literature, such as the Thomas-Fermi screening length, effective surface charge plane, and quantum capacitance.
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