A QM/MM approach for the study of monolayer-protected gold clusters

Abstract

We report the development and implementation of hybrid methods that combine Quantum Mechanics (QM) with Molecular Mechanics (MM) to theoretically characterize thiolated gold clusters. We use, as training systems, structures such as Au 25 (SCH 2 -R) 18 and Au 38 (SCH 2 -R) 24 , which can be readily compared with recent crystallographic data. We envision that such an approach will lead to an accurate description of key structural and electronic signatures at a fraction of the cost of a full quantum chemical treatment. As an example, we demonstrate that calculations of the 1 H and 13 C NMR shielding constants with our proposed QM/MM model maintain the qualitative features of a full DFT calculation, with an order-of-magnitude increase in computational efficiency.

Understanding and Designing the Gold–Bio Interface: Insights from Simulations

“…This issue has been a strong motivator behind the also popular GolP family of FFs. [82b,83b,84b,121,141]…”

“…Within this small size regime, capturing the quantum chemical nature (no longer bulk metal band structuring) and vastly different morphology of AuNCs presents a significant FF design challenge for classical all‐atom molecular simulation. This is primarily due to limited availability of experimental data and how recently they have been chemically characterized, which is reflected by the fact that only very few all‐atom (staple motif containing) thiolate‐AuNC FFs have appeared, namely for Au 25 (SR) 18 , Au 38 (SR) 24 [84a,152] and Au 144 (SR) 60. Within these FFs, gold can be designated different atom types depending on the coordination to metallic and/or ligand atoms (i.e., Au–Au–Au, Au–Au–S or S–Au–S) .…”

“…This is primarily due to limited availability of experimental data and how recently they have been chemically characterized, which is reflected by the fact that only very few all‐atom (staple motif containing) thiolate‐AuNC FFs have appeared, namely for Au 25 (SR) 18 , Au 38 (SR) 24 [84a,152] and Au 144 (SR) 60. Within these FFs, gold can be designated different atom types depending on the coordination to metallic and/or ligand atoms (i.e., Au–Au–Au, Au–Au–S or S–Au–S) . This allows for interaction parameters to be optimized for each gold type much like different atom types are treated in biological FFs.…”

“…Many biomolecule adsorption studies are used to parameterize FFs for the MM treatment of nano–bio systems where water is modeled explicitly (discussed in detail in Section ) . Analogous studies have been done to derive gold biomolecular parameters for smaller nanoclusters . In the development of the GolP‐CHARMM FF, Wright et al utilized Plane Wave DFT (with the vdW‐DF to treat dispersion and revPBE functionals) to examine the binding of small molecules representing the functional groups found in amino acids to the Au(111) and Au(100) surfaces.…”

Recent advances in first principles computations in materials research

“…The last three articles provide examples of such strategies. Banerjee et al [35] present a hybrid quantum mechanics/molecular mechanics approach aimed at a study of gold clusters protected by surfactants, Chernatynskiy et al [36] provide a critical assessment of various flavors of inter-atomic potentials used in studies of UO 2 fuels aimed at thermal conductivity calculations, and Sukumar et al [37] provide insights into how cheminformatics strategies such as quantitative structure property relationships may be used to extract knowledge from first principles (or other) data. These methods are synergistic to first principles methods and are seen to be essential to bridge the (inevitable) gaps between situations realistically accessible by means of purely first principles methods and complex real-life situations.…”