Adiabatic Excited-State Molecular Dynamics with an Explicit Solvent: NEXMD-SANDER Implementation.

We present a method to link the Nonadiabatic EXcited-state Molecular Dynamics (NEXMD) package to the SANDER package supplied by AMBERTOOLS to provide excited-state adiabatic quantum mechanics/molecular mechanics (QM/MM) simulations. NEXMD is a computational package particularly developed to perform simulations of the photoexcitation and subsequent nonadiabatic electronic and vibrational energy relaxation in large multichromophoric conjugated molecules involving several coupled electronic excited states. The NEXMD-SANDER exchange has been optimized in order to achieve excited-state adiabatic dynamics simulations of large conjugated materials in a QM/MM environment, such as an explicit solvent. Dynamics of a substituted polyphenylene vinylene oligomer (PPV3-NO2) in vacuum and different explicit solvents has been used as a test case by performing comparative analysis of changes in its optical spectrum, state-dependent conformational changes, and quantum bond orderings. The method has been tested and compared with respect to previous implicit solvent implementations. Also, the impact on the expansion of the QM region by including a variable number of solvent molecules has been analyzed. Altogether, these results encourage future implementations of NEXMD simulations using the same combination of methods.

Electric potential profile of a spherical soft particle with a charged core.

The electrostatic potential profile of a spherical soft particle is derived by solving the Poisson-Boltzmann equations on a spherical system both numerically and analytically. The soft particle is assumed to consist of an ion-permeable charged outer layer and a non-permeable charged core with constant charged density. The contribution of the core to the potential profile is calculated for different charges and dielectric constants. Our results show that the charged core heavily influences the local potential within the soft particle. By contrast, the potential distribution outside the particle in the salt solution is found to be weakly dependent on the core features. These findings are consistent with previous experiments showing the minor impact of the core of the MS2 virus on its overall electrical properties. Our studies also indicate that while a change in temperature from 290 K to 310 K only slightly varies the potential, the ionic strength in the range of 1-600 mM has a significant effect on the potential profile. Our studies would provide good understanding for experimental research in the field of biophysics and nanomedicine.