The classical force field, which is compatible with the Amber force field 99SB, has been obtained for the interaction of Cu(II) with monomer and dimers of amyloid-β peptides using the coordination where Cu(II) is bound to His6, His13 (or His14), and Asp1 with distorted planar geometry. The newly developed force field and molecular dynamics simulation were employed to study the impact of Cu(II) binding on structures and dynamics of Aβ monomer and dimers. It was shown that in the presence of Cu(II) the β content of monomer is reduced substantially compared with the wild-type Aβ suggesting that, in accord with experiments, metal ions facilitate formation of amorphous aggregates rather than amyloid fibrils with cross-β structures. In addition, one possible mechanism for amorphous assembly is that the Asp23-Lys28 salt bridge, which plays a crucial role in β sheet formation, becomes more flexible upon copper ion binding to the Aβ N-terminus. The simulation of dimers was conducted with the Cu(II)/Aβ stoichiometric ratios of 1:1 and 1:2. For the 1:1 ratio Cu(II) delays the Aβ dimerization process as observed in a number of experiments. The mechanism underlying this phenomenon is associated with slow formation of interchain salt bridges in dimer as well as with decreased hydrophobicity of monomer upon Cu-binding.

We present the parametrization and benchmark of long-range corrected second-order density functional tight binding (DFTB), LC-DFTB2, for organic and biological molecules. The LC-DFTB2 model not only improves fundamental orbital energy gaps but also ameliorates the DFT self-interaction error and overpolarization problem, and further improves charge-transfer excited states significantly. Electronic parameters for the construction of the DFTB2 Hamiltonian as well as repulsive potentials were optimized for molecules containing C, H, N, and O chemical elements. We use a semiautomatic parametrization scheme based on a genetic algorithm. With the new parameters, LC-DFTB2 describes geometries and vibrational frequencies of organic molecules similarly well as third-order DFTB3/3OB, the de facto standard parametrization based on a GGA functional. LC-DFTB2 performs well also for atomization and reaction energies, however, slightly less satisfactorily than DFTB3/3OB.

Abstract

Layered titanium carbide (Ti 3 C 2 T x ) MXene is a promising electrode material for use in next-generation electrochemical capacitors. However, the atomic-level information needed to correlate the distribution of intercalated cations with surface redox reactions, has not been investigated in detail. Herein we report on sodium preintercalated MXene with high sodium content (up to 2Na per Ti 3 C 2 T x formula) using a solution of Na-biphenyl radical anion complex (E 0 ≈ −2.6 SHE). Multiple sodiation sites and formation of a twodimensional sodium domain structure at interfaces/surfaces is identified through combined computational simulations with neutron pair distribution function analysis. The induced layer charges and the redox process characterized by the densityfunctional tight-binding method on a local scale are found to greatly depend on the location of sodium ions. Electrochemical testing of the pre-sodiated MXene as an electrode material in a sodium-ion capacitor shows excellent reversibility and promising performance, indicating the feasibility of chemical preintercalation as an approach to prepare MXene electrodes for ion capacitors.