Hollow bonds are equal to more common up stereo bonds

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Unformatted text preview: ACD/ChemSketch Tutorial 32 Drawing More Complex Structures • Quadruple bonds are used to describe the structure of some organometallic complexes. Ph N Ph Ph N N N Cr N Ph 2+ Ph N Cr N Ph 2+ N N N Ph N Ph N - 7. On the General toolbar, click Save File , then click New Page . 3.13 Changing Atom Properties If you want to display the valency or the isotopic mass of an atom of a structure drawn in ACD/ChemSketch—or even change the typeface or the size of the atom identification—you should use the Properties panel. You can use the structure drawn in Section 3.11. We are going to change the size of the plus sign and make the visible atom symbols bold: Br H3C + H CH3 CH3 1. On the Structure toolbar, click Select/Move . 2. Point to the plus sign and double-click. This will make the Properties panel appear. Switch to the Atom tab: ACD/ChemSketch Tutorial 33 Drawing More Complex Structures 3. As you can see, the buttons below the preview area allow you to change the atom symbol and . For font sizes, select 14. charge 4. Click Apply to view the result on the selected element: 5. By selecting other structure parts or the whole structure and double-clicking the selection, try modifying various attributes in the Properties panel. 6. On the General toolbar, click Save File , then click New Page . ACD/ChemSketch Tutorial 34 4. Advanced Structures, SMILES and InChI Notations, Reaction Schemes 4.1 Objectives This chapter is the next step to drawing even more sophisticated structures. Two kinds of optimization are covered: optimizing for display purposes (2D) and optimizing according to a simple force-field model (3D). If you are using ACD/ChemSketch for the first time, it is recommended that you do the exercises described here only after completing the previous chapters. In this chapter, you will learn how to: • Draw structures of cyclic Alkanes and Peptides using the 2D optimization (Clean Structure) tool; • Convert structures to SMILES format and vice versa; • Convert structures to InChI string and vice versa • Use the 3D Optimization tool for drawing “spectacular” 3D structures of Bicyclo[2.2.2]octane, triptycene, cubane, and dodecahedrane; • Draw reaction schemes and reflect the reaction conditions on it; • Map reactions; and • Use the Reaction Calculator—Commercial version only! 4.2 2D-Optimization The Clean Structure tool can be considered to be a 2D-optimization of the drawn structure, i.e. redrawing and resizing it to standardize all the bond lengths and angles. Using this tool you can easily draw a perfect structure. Some examples are put below: 4.2.1 Creating the Structure of Cyclic Alkanes This section is based on the movie cycloalk.exe which can be downloaded from our Web site or found in the \\MOVIES folder. Using the following technique you can quickly draw cyclic alkanes perfectly. Here's how to draw a cyclononane: ACD/ChemSketch Tutorial 35 Advanced Structures, SMILES and InChI Notations, Reaction Schemes 1. On the Atoms toolbar (Structure mode), click Carbon . and drag in the workspace to draw a 92. On the Structure toolbar, click Draw Chains member chain. Note that the informative cursor shows the number of atoms in the chain if the Informative Cirsor check box is selected in the Preferences dialog box (General tab). H3C CH3 3. On the Structure toolbar, click Flip Top to Bottom the structure is turned upside down: H3C 4. Right-click to quickly switch to the Draw Normal another in order to connect them with a bond. CH3 tool and drag from one end atom to 5. Click Clean Structure to obtain the following structure: Try to draw C10- and C8-rings using the above technique. 6. On the General toolbar, click Save File , then click New Page . 4.2.2 Creating the Structure of a Cyclic Peptide This section is based on the movie pept.exe which can be downloaded from our Web site or found in the \\MOVIES folder. Let’s draw the cyclic Tyr-Ala-Trp. Again we will find Clean Structure useful. 1. Make sure you are in the Structure mode. 2. In the Template Window that can be displayed with the Open Template Window button, switch to the Amino Acids tab. 3. From the set of amino acids, click Tyrosine and click in the workspace to copy the structure. ACD/ChemSketch Tutorial 36 Advanced Structures, SMILES and InChI Notations, Reaction Schemes 4. From the Table of Radicals , choose sequentially Alanine and then Tryptophan and attach the corresponding radicals as indicated: Tip You can flip the template shadow before placing it in the workspace by pressing TAB. 5. Right-click to quickly switch to the Select/Move group as shown: tool and drag the NH2 group to the OH 6. Click Clean Structure to obtain the following structure: Try to draw any other cyclic peptide, for instance Gramicidine S: ACD/ChemSketch Tutorial 37 Advanced Structures, SMILES and InChI Notations, Reaction Schemes 4.3 SMILES Notations ACD/ChemSketch can convert SMILES (Simplified Molecular Input Line Entry Specification) strings to structures, and convert structures to SMILES 4.3.1 Generating SMILES Notations Now we will try to create a SMILES string for the cyclic...
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