RESUMO
A recently proposed extended Hamiltonian approach to switching interaction potentials is generalized to enable adaptive partitioning molecular dynamics simulations. Switching is performed along a fictitious classical degree of freedom whose value determines the mixing ratio of the two potentials on a time scale determined by its associated mass. We propose to choose this associated fictitious mass adaptively so as to ensure a constant time scale for all switching processes. For different model systems, including a harmonic oscillator and a Lennard-Jones fluid, we investigate the window of switching time scales that guarantees the conservation of the extended Hamiltonian for a large number of switching events. The methodology is first applied in the microcanonical ensemble and then generalized to the canonical ensemble using a Nosé-Hoover chain thermostat. It is shown that the method is stable for thousands of consecutive switching events during a single simulation, with constant temperature and a conserved extended Hamiltonian. A slight modification of the original Hamiltonian is introduced to avoid accumulation of small numerical errors incurred after each switching process.
RESUMO
Charge transport properties of a P3HT:DIPBI bulk heterojunction solar cell are modelled by kinetic Monte Carlo simulations based on a morphology obtained from coarse-grained molecular dynamics. Different methods for calculating the hopping integrals entering the charge transfer rates are compared and calibrated for hole transport in amorphous P3HT. The influence of intermolecular and intramolecular charge transfer on the total charge carrier mobility and hence the power conversion efficiency is investigated in detail. An analysis of the most probable pathways with low resistance for hole transport is performed, establishing a connection between charge mobility and morphology.
RESUMO
Quantum mechanical (QM) and hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations of a recently reported dinuclear mercury(II)-mediated base pair were performed aiming to analyse its intramolecular bonding pattern, its stability, and to obtain clues on the mechanism of the incorporation of mercury(II) into the DNA. The dynamic distance constraint was employed to find initial structures, control the dissociation process in an unbiased fashion and to determine the free energy required. A strong influence of the exocyclic carbonyl or amino groups of neighbouring base pairs on both the bonding pattern and the mechanism of incorporation was observed. During the dissociation simulation, an amino group of an adenine moiety of the adjacent base pair acts as a turnstile to rotate the mercury(II) ion out of the DNA core region. The calculations provide an important insight into the mechanism of formation of this dinuclear metal-mediated base pair and indicate that the exact location of a transition metal ion in a metal-mediated base pair may be more ambiguous than derived from simple model building.
Assuntos
Pareamento de Bases , DNA/química , Mercúrio/química , DNA/metabolismo , Simulação de Dinâmica Molecular , TermodinâmicaRESUMO
Different N3-substituted derivatives of the new ligand 3H-imidazo[4,5-f]quinolin-5-ol were synthesized. The three pKa values of its nucleoside derivative 1 were determined as 2.72 ± 0.09, 5.2 ± 0.2 and 9.7 ± 0.2. Sophisticated computational methods were used to explain these experimental acidity constants. The artificial nucleoside analogue 1 containing the new ligand was introduced into various DNA duplexes. Upon the addition of Cu(ii) ions to the DNA, highly stabilizing 1-Cu(ii)-1 base pairs were formed, with an increase in the DNA melting temperature upon Cu(ii) insertion of up to 38 °C. The ligand represents the largest artificial nucleobase used for Cu(ii)-mediated base pairing. It was also applied in Cu(ii)-mediated base pairing with the smallest Cu(ii)-binding nucleoside 2, involving the ligand 4-carboxyimidazole. The thermal duplex stabilization upon 2-Cu(ii)-1 base pair formation is smaller than that of 1-Cu(ii)-1 and comes close to that of the previously reported 2-Cu(ii)-2. Important design principles for Cu(ii)-mediated base pairs can be derived by comparing the homoleptic complexes of the largest and the smallest Cu(ii)-binding nucleosides with the heteroleptic complexes comprising both nucleosides.
