DOI: 10.5061/dryad.cfxpnvxbk
title: Coordinates of the low-lying energy Agn isomers and the Agn-Tyr complexes

description: Noble metal clusters with a size around the Fermi wavelength of electrons
 display quantum confinement effects and properties such as
 photoluminescence, two-photon absorption, and second and third-harmonic
 generation. As a result of these unique features, noble metal clusters are
 increasingly gaining popularity in optics and catalysis. Being highly
 reactive, it is standard practice to use capping agents to stabilize them.
 This dataset contains the structural parameters for the low-lying energy
 Agn isomers and the Agn-Tyr complexes from n = 3–12, all fully optimized
 at the B3PW91 functional combined with the def2-TZVP basis set. The
 structural parameters were obtained using a global search strategy
 combined with DFT calculations to explore the potential energy surface of
 clusters of atoms and molecules.
description: We determine the putative global minima for the bare
 Ag<sub>n</sub> (n = 3–12) clusters and the corresponding
 Ag<sub>n</sub>-Tyr complexes via the GLobal Optimization of
 MOlecular Systems (GLOMOS). GLOMOS is a code written in Python that,
 through different strategies, can explore the potential energy surface of
 atomic and molecular clusters by evaluating the energy through electronic
 structure codes. The global optimization strategy choice was a stochastic
 approach. GLOMOS generates trial structures with random atomic
 coordinates, ensuring all the atoms meet a proximity criterion and form a
 bonded assembly. To minimize the possibility of collapse into a funnel
 associated with a dominant morphology, GLOMOS generates trial structures
 with different morphological patterns. GLOMOS identifies and discriminates
 the equivalent configurations via the Ultrafast Shape-Recognition
 Algorithm with Mass Ponderation (USRAMP). The local
 optimization of the test structures Ag<sub>n</sub> was done in
 two steps. All trial structures were fully optimized without symmetry
 constraints in the first stage using the B3PW91 hybrid functional with the
 LanL2DZ basis set. This functional-basis combination has delivered
 structural and electronic results in good agreement with the experimental
 data for small Ag naked clusters. In the second stage, after the
 similarity discrimination process, the final structures were again fully
 optimized at the B3PW91 functional with the def2-TZVP basis set. The
 highest multiplicities were not explored because the lowest spin state in
 small silver clusters is the ground state. A harmonic frequency analysis
 was also performed to verify a stationary local minimum for all the
 optimized structures. The punctual group for each cluster was determined
 using the SYVA program and the symmetry analyzer module included in the
 Python Materials Genomics library. On the other hand,
 the strategy to find the most energetically favorable
 Ag<sub>n</sub>-Tyr (n = 3–12) complexes consists of fixing the
 putative global minimum (GM) of each Ag<sub>n</sub> cluster at
 the center of a coordinate system and trying different binding sites for
 tyrosine. For each silver cluster, 30n possibilities were estimated by
 randomly changing the binding site and the spatial orientation of the
 molecule in its Euler angles. All the candidate
 Ag<sub>n</sub>-Tyr complexes thus built were fully optimized
 at the B3PW91/def2-TZVP level, including the Grimme D3 dispersion
 scheme.
description: Use Molden, VESTA (Visualization for Electronic and STructural
 Analysis), Avogadro, or any molecular visualization program.