Self-healing mechanism of metallopolymers investigated by QM/MM simulations and Raman spectroscopy.

Surface Enhanced Raman Scattering of Crystal Violet with Low Concentrations Using Self-Assembled Silver and Gold-Silver Core-Shell Nanoparticles

The active substrates in surface enhanced Raman scattering (SERS) spectroscopy were prepared through self-assembly of nanoparticles on functionalized glasses. Colloidal silver nanoparticles (Ag NPs) were prepared chemically in two different sizes by reduction of AgNO3 using trisodium citrate and sodium borohydride. Gold–silver core–shell nanoparticles were also prepared to compare between the o...

Tracking flavin conformations in protein crystal structures with Raman spectroscopy and QM/MM calculations.

Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation.

A new approach for performing Particle Mesh Ewald in ab initio quantum mechanical/molecular mechanical (QM/MM) simulations with extended atomic orbital basis sets is presented. The new approach, the Ambient-Potential Composite Ewald (CEw) method, does not perform the QM/MM interaction with Mulliken charges nor electrostatically fit charges. Instead the nuclei and electron density interact direc...

Importance of van der Waals Interactions in QM/MM Simulations.

The importance of accurately treating van der Waals interactions between the quantum mechanical (QM) and molecular mechanical (MM) atoms in hybrid QM/MM simulations has been investigated systematically. First, a set of van der Waals (vdW) parameters was optimized for an approximate density functional method, the self-consistent charge-tight binding density functional (SCC-DFTB) approach, based ...

Efficient frequency calculations in QM/MM using the Mobile Block Hessian method

Normal mode analysis (NMA) is a well-known technique which estimates the intrinsic frequencies of chemical systems by assuming a harmonic shape for the potential energy surface. Despite its simplicity, it is still a popular approach to predict vibrational IR and Raman spectra, to identify chemical groups [1], or to study the large motions involved in conformational changes of biomolecules [2]. ...