Activity 1-Drawing 2D Structures (Step-by-Step).pdf

COLLEGE OF SCIENCE AND MATHEMATICS DEPARTMENT OF CHEMISTRY ACTIVITY NO. 1 Drawing 2D Structures (Step-by-Step) Three Ways to Draw 2D Structures in BIOVIA Draw Sample molecul...

COLLEGE OF SCIENCE AND MATHEMATICS DEPARTMENT OF CHEMISTRY ACTIVITY NO. 1 Drawing 2D Structures (Step-by-Step) Three Ways to Draw 2D Structures in BIOVIA Draw Sample molecule: Aspirin A) Manual Sketching 1) Open BIOVIA Draw. 2) Tip: Start with the carbon skeleton before adding heteroatoms. Click the Single Bond (C-C) button, then the Atom toolbar button below it. Ensure the element C (carbon) is selected. 3) Place 6 carbons on your canvass following a hexagonal shape. 4) Click the Single Bond (C-C) button again. Drag bonds between adjacent carbons to connect them. Continue until you form a cyclohexane ring. 5) To add double bonds, click on any single bond. Ensure there are 3 double bonds in the benzene ring. 6) Select the carbon element again. Place carbon atoms in their correct positions. Repeat this for the oxygen atoms. Don’t worry about hydrogen atoms yet. 7) Click the Single Bond (C-C) button again. Drag bonds between the atoms to connect them. 8) Add the necessary double bonds. C.M. Recto Avenue, Lapasan, Cagayan de Oro City 9000 Philippines Tel Nos. +63 (88) 856 1738; Telefax +63 (88) 856 4696 | http://www.ustp.edu.ph  COLLEGE OF SCIENCE AND MATHEMATICS DEPARTMENT OF CHEMISTRY 9) To display hydrogen atoms, right-click on the oxygen atom with missing hydrogen. Click Hydrogen Display, then Auto. Now, your 2D structure is almost done. 10) Press Ctrl + A. 11) Click the Chemistry tab, then Clean. Now you have a 2D structure of aspirin with standard bond lengths and angles. 12) To save, click File, then Save As. Rename the file as aspirin.mol and save it in your designated folder. 13) Click X to close BIOVIA Draw. Note: Alternatively, you can access predefined templates such as common functional groups, rings, and more complex molecules to prepare your structure. You can find these under the Templates panel. Simply select the desired template and place it on your canvas. B) From IUPAC Name 1) Open BIOVIA Draw again. 2) Click Chemistry, then Generate Structure from Text, and select IUPAC Name. 3) Enter the IUPAC name of aspirin: 2-Acetoxybenzoic acid. Click OK. This will generate a 2D structure of aspirin. Click anywhere on your canvas to place the structure. 4) Ensure polar hydrogens are shown. If not, right-click on the oxygen atom. Click Hydrogen Display, then Auto. 5) To save, click File, then Save As. Rename the file as aspirin2.mol and save it in your designated folder. C) From SMILES String 1) Open BIOVIA Draw again. 2) Click Chemistry, then Generate Structure from Text, and select SMILES String. C.M. Recto Avenue, Lapasan, Cagayan de Oro City 9000 Philippines Tel Nos. +63 (88) 856 1738; Telefax +63 (88) 856 4696 | http://www.ustp.edu.ph  COLLEGE OF SCIENCE AND MATHEMATICS DEPARTMENT OF CHEMISTRY 3) Enter the SMILES string for aspirin: CC(=O)OC1=CC=CC=C1C(=O)O. Click OK. This generates a 2D structure of aspirin. Click anywhere on your canvas to place the structure. 4) Ensure polar hydrogens are shown. If not, right-click on the oxygen atom. Click Hydrogen Display, then Auto. 5) To save, click File, then Save As. Rename the file as aspirin3.mol and save it in your designated folder. C.M. Recto Avenue, Lapasan, Cagayan de Oro City 9000 Philippines Tel Nos. +63 (88) 856 1738; Telefax +63 (88) 856 4696 | http://www.ustp.edu.ph