DOI: 10.6084/m9.figshare.30837419.v1
title: Templated DNA Ag Nanocluster Computational Data and Analysis

description: 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 Directory<code>AgCluster UV-vis.xlsx</code> - All collected UV-Vis spectrum in one workbook. The sheets <i>Ag4Q2</i>, <i>Ag4Q3</i>, and <i>Ag4Q2Benchmarking</i> were used for figure S20, while the sheet <i>DNAAg4Q2Q3Comparison</i> 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:<pre><pre>SingleCAgNCQXMY_[desc].[gjf/log]<br></pre></pre>which refers to the three basepair structure coordinating the Ag<sub>N</sub> nanocluster with charge <code>X</code> and spin multiplicity <code>Y</code>. 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 (<code>Y</code>) 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:<code>SingleCAgNCQXMY_opt</code> - 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.<code>SingleCAgNCQXMY_opt_CAMB3LYP</code> - Input and output files for the second CAM-B3LYP optimizations, used to generate structures for TD-DFT calculations.<code>SingleCAgNCQXMY_td</code> - 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 <code>td=(root=2)</code>. Each file has the format:<pre><pre>AgNQXS1.[gjf/log]<br></pre></pre>which refers to the Ag<sub>N</sub> nanocluster with charge <code>X</code>.ThreeNanoclusterStudies/Contains Gaussian output files and analysis scripts for three-nanocluster studies (Figure 5c, Figure S20b/c):<code>Ag4Q[2/3].log</code> - Isolated cluster TDDFT output file<code>Ag4Q[2/3]_2nm_rot.log</code> - Two cluster TDDFT output file<code>Ag4Q[2/3]_2nm_2nm_rot.log</code> - Three cluster TDDFT output file<code>Ag4Q3_2nm_2nm_rot_a[1-3].cub</code> - Gaussian cube files for the three singly occupied orbitals (α-HOMO to α-HOMO-2) for the three-cluster Q=+3 state<code>threeDNAAg4Q3.log</code> - Three DNA-coordinated Q=+3 cluster orbital generation log file<code>threeDNAAg4Q3_a[1-3].cub</code> - Gaussian cube files for the three singly occupied orbitals (α-HOMO to α-HOMO-2) states of the three DNA-coordinated Q=+3 cluster system<code>cubeparser.py</code> - Python script for parsing and visualizing cube files<code>RotateCluster.py</code> - Python script for generating C3 symmetric cluster arrangementsFile Formats<b>.gjf</b> - Gaussian input files (text format)<b>.log</b> - Gaussian output files (text format)<b>.cub</b> - Gaussian cube files (volumetric data format)<b>.xlsx</b> - Excel spreadsheet<b>.py</b> - Python scripts (Python 3)<br>