====== Visualizing molecular structures for analysis of NMR spectra ======
===== Start in ChemDraw =====
NOTE: Chemdraw for ND will ask about URL: https://notredame.signalsresearch2.revvitycloud.com
  - Make a molecule in ChemDraw
  - Select it
  - Copy to clipboard in SMILES format:   ''Edit:Copy As:SMILES''
===== Load a molecule in Avogadro and optimize geometry =====

Avogadro manuals are here: [[https://avogadro.cc/docs/]]

  - Start a new document: ''File:New''
  - ''Build:Insert:SMILES''
  - Paste from clipboard (Cmd-V or Ctrl-V), click OK
  - Set view parameters: ''Display Settings'', check ''Ball and Stick''
  - Right-click to deselect the atoms
  - Optimize molecular geometry by energy minimization: ''Extensions:Optimize Geometry''

Parameters of geometry optimization are set in ''Extensions: Molecular Mechanics: Setup force field''. 
For more details on force fields and optimization see [[https://avogadro.cc/docs/optimizing-geometry/molecular-mechanics/]]


===== Distance measurements in Avogadro =====

  - Rotate the molecule to see both atoms of interest with ''Select Tool'' 
  - Press ''Click to Measure'' button in the toolbar
  - Click first atom, click second atom
  - Read the distance on the bottom of the screen
  - Clicking on the same atom again removes it from the selection