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 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_N 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_N 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>

本数据集为预印本论文《3D DNA晶格中拓扑调控合成原子级精确银纳米团簇》（Topology-Enforced Synthesis of Atomically-Precise Silver Nanoclusters in 3D DNA Lattices）的从头算密度泛函理论（Density Functional Theory, DFT）计算及后续数据分析所用文件。

目录结构
根目录下的<code>AgCluster UV-vis.xlsx</code>：收录所有采集的紫外-可见吸收光谱（Ultraviolet-visible spectroscopy, UV-Vis）数据的Excel工作簿。其中工作表<i>Ag4Q2</i>、<i>Ag4Q3</i>与<i>Ag4Q2Benchmarking</i>用于补充图S20，工作表<i>DNAAg4Q2Q3Comparison</i>用于正文章节图4。

<code>DNANanoclusterStudies/</code>目录：包含单团簇DNA-纳米团簇研究的高斯（Gaussian）输入（.gjf）与输出（.log）文件。文件命名格式为：
<pre>SingleCAgNCQXMY_[desc].[gjf/log]</pre>
该命名对应配位于三碱基对结构、带电荷<code>X</code>且自旋多重度为<code>Y</code>的Ag_N纳米团簇。需说明的是，最终插图未采用的高自旋态文件未上传，但可通过修改对应输入文件中的自旋多重度（<code>Y</code>）重新生成，并对比最终DFT能量与优化后的几何结构。
该目录下每类研究包含三类处理用文件：
1. <code>SingleCAgNCQXMY_opt</code>：初始B3LYP泛函优化的输入与输出文件，用于初始结构筛选（补充图S19）与自旋态对比，同时作为第二步优化的初始几何结构。
2. <code>SingleCAgNCQXMY_opt_CAMB3LYP</code>：第二步CAM-B3LYP泛函优化的输入与输出文件，用于生成含时密度泛函理论（Time-Dependent Density Functional Theory, TD-DFT）计算所需的结构。
3. <code>SingleCAgNCQXMY_td</code>：CAM-B3LYP水平下TD-DFT计算的输入与输出文件，用于生成正文章节图4、图5b及补充图S20a。

<code>ExcitedStateOptimization/</code>目录：包含第一激发态振动-电子重构的TDDFT建模输入与输出文件。第二激发态的建模可通过将Gaussian的路由行修改为<code>td=(root=2)</code>来生成。所有文件命名格式为：
<pre>AgNQXS1.[gjf/log]</pre>
对应带电荷<code>X</code>的Ag_N纳米团簇。

<code>ThreeNanoclusterStudies/</code>目录：包含三团簇研究（对应正文章节图5c、补充图S20b/c）所用的高斯输出文件与分析脚本：
- <code>Ag4Q[2/3].log</code>：孤立团簇的TDDFT输出文件
- <code>Ag4Q[2/3]_2nm_rot.log</code>：双团簇的TDDFT输出文件
- <code>Ag4Q[2/3]_2nm_2nm_rot.log</code>：三团簇的TDDFT输出文件
- <code>Ag4Q3_2nm_2nm_rot_a[1-3].cub</code>：三团簇Q=+3态的三个单占据轨道（α-最高占据分子轨道（Highest Occupied Molecular Orbital, HOMO）至α-HOMO-2）的高斯立方体（Gaussian cube）文件
- <code>threeDNAAg4Q3.log</code>：三个DNA配位的Q=+3团簇的轨道生成日志文件
- <code>threeDNAAg4Q3_a[1-3].cub</code>：三个DNA配位的Q=+3团簇体系的三个单占据轨道（α-HOMO至α-HOMO-2）的高斯立方体文件
- <code>cubeparser.py</code>：用于解析与可视化立方体文件的Python 3脚本
- <code>RotateCluster.py</code>：用于生成C3对称团簇排布的Python 3脚本

文件格式说明
- <b>.gjf</b>：高斯输入文件（纯文本格式）
- <b>.log</b>：高斯输出文件（纯文本格式）
- <b>.cub</b>：高斯立方体文件（体数据格式）
- <b>.xlsx</b>：Excel电子表格
- <b>.py</b>：Python 3脚本