Templated DNA Ag Nanocluster Computational Data and Analysis

The following files were used for ab-initio DFT calculations and subsequent data analysis for the "Topology-Enforced Synthesis of Atomically-Precise Silver Nanoclusters in 3D DNA Lattices" publication (preprint)Directory StructureRoot DirectoryAgCluster UV-vis.xlsx - All collected UV-Vis spectrum in one workbook. The sheets Ag4Q2, Ag4Q3, and Ag4Q2Benchmarking were used for figure S20, while the sheet DNAAg4Q2Q3Comparison was used for Figure 4 in the main text.DNANanoclusterStudies/Contains Gaussian input (.gjf) and output (.log) files for single cluster DNA-nanocluster studies. The format of these files is:SingleCAgNCQXMY_[desc].[gjf/log]which refers to the three basepair structure coordinating the AgN nanocluster with charge X and spin multiplicity Y. For the sake of clarity, higher spin states not used in the final figures were not uploaded but can be re-generated by modifying the spin multiplicity (Y) in the corresponding input file and comparing the final DFT energies and optimized geomtries. For each case, there are three types of files used for processing:SingleCAgNCQXMY_opt - Input and output files for the initial B3LYP optimizations, used for initial structure screening (Figure S19) and spin state comparison, as well as input geometries for the second optimization step.SingleCAgNCQXMY_opt_CAMB3LYP - Input and output files for the second CAM-B3LYP optimizations, used to generate structures for TD-DFT calculations.SingleCAgNCQXMY_td - Input and output files for the CAM-B3LYP TD-DFT calculations: used to generate Figure 4, Figure 5b and Figure S20aExcitedStateOptimization/Input and output files for the TDDFT modeling of vibronic reorganization in the first excited state. The second excited state can be generated by updating the Gaussian route line to td=(root=2). Each file has the format:AgNQXS1.[gjf/log]which refers to the AgN nanocluster with charge X.ThreeNanoclusterStudies/Contains Gaussian output files and analysis scripts for three-nanocluster studies (Figure 5c, Figure S20b/c):Ag4Q[2/3].log - Isolated cluster TDDFT output fileAg4Q[2/3]_2nm_rot.log - Two cluster TDDFT output fileAg4Q[2/3]_2nm_2nm_rot.log - Three cluster TDDFT output fileAg4Q3_2nm_2nm_rot_a[1-3].cub - Gaussian cube files for the three singly occupied orbitals (α-HOMO to α-HOMO-2) for the three-cluster Q=+3 statethreeDNAAg4Q3.log - Three DNA-coordinated Q=+3 cluster orbital generation log filethreeDNAAg4Q3_a[1-3].cub - Gaussian cube files for the three singly occupied orbitals (α-HOMO to α-HOMO-2) states of the three DNA-coordinated Q=+3 cluster systemcubeparser.py - Python script for parsing and visualizing cube filesRotateCluster.py - Python script for generating C3 symmetric cluster arrangementsFile Formats.gjf - Gaussian input files (text format).log - Gaussian output files (text format).cub - Gaussian cube files (volumetric data format).xlsx - Excel spreadsheet.py - Python scripts (Python 3)