Bond user manual Guide de l'utilisateur

ChemBioDraw 13.0 User Guide

IntroductionDesigned for scientists, students, and scientific authors, ChemBioDraw 13.0 is a powerful yet easy-to use tool for pro-ducing biological a

5. Point to the atom shown below and click twice to create two bonds.6. Pointing to the bond shown below, right-click, and select Double>Plain from

3. With the Text tool selected, click the atom shown below, and then type 'OH' in the text box that appears.Displaying stereochemical marker

The Wedged bond becomes hashed and the (R) stereochemistry is preserved.Tutorial 7: TemplatesChemBioDraw 13.0 comes with an extensive template library

2. Click the bottom bond in the center ring.3. Click the double bond at the top of the ring. It is now a single bond.4. In the Main toolbar, select th

Advanced drawing techniquesThe advanced features help you save time or let you perform functions that simply can’t be accomplished using thebasic tool

Figure 7.1: A) The mitochondrion structure in its default color; B) The structure colored blue as a group; C) The struc-ture colored blue as an integr

Note: If the area of the structure you contract contains errors, an error dialog box appears. Click Ignore to viewother errors. Click Ignore All to ig

Expanded:Adding a label of multiple atoms1. Using the text tool, click an atom in the structure where you need to place the label.2. Type the formula

Adding from the start of an atom label creates bonds that try to attain the chain angle setting in the Drawing Set-tings dialog box. If that angle can

For example, you can explicitly draw the three isomers of dibromobenzene as shown below. Alternately, you canexpress all three isomers as a single par

Figure 1.1: A)Status bar displaying information about solid bond.Serial number and technical supportFor more information on obtaining serial numbers a

Note: After you draw a bond from an attachment point, the asterisk disappears. To view an attachment point, posi-tion the cursor over it with either a

Note: When you type a new indicator, the counter resets to the new style and you can continue numbering in thatstyle with the standard means. For exam

1. Select the structure with either a selection tool or the Structure Perspective tool.2. With the Structure Perspective tool, click-drag the selected

You can reposition the formula and mass displays or delete them.Synthesis and retrosynthesisChemBioDraw 13.0 includes two tools to help you draw synth

Drawing an arrowStarting with 2-propanone (see "Tutorial 1: Drawing a structure" on page 77), draw the reaction arrow:1. On the Arrows toolb

Copy the structure:1. Select the 2-propanone structure and its caption.2. Press and hold the CTRL key.The hand pointer with a plus sign indicates that

Replace the product caption:1. Select the caption with the Text tool and type 4-hydroxy-4-methyl-2-pentanone, press the ENTER and type 1mole.2. Using

Figure 7.8: The reaction after applying the Clean Up Reaction commandNote: The Clean Up Reaction is available only for single-step reactions.Note: The

1. Go to View>Show Reaction Interpretation.2. Hover your cursor over the reaction arrow.For a reaction to be interpreted:Each reactant and product

2. Click+drag the mouse from the source object to the target object and release the mouse. A half-head arrow sig-nifying only one electron transfer ap

Install more physical RAM. The more you have, the less ChemBioOffice Desktop Applications will have to accessyour hard disk to use Virtual Memory.Incr

Note: If a catalyst or condition label is above the reaction arrow, right+click the label and deselect Interpret Chem-ically in the context menu befor

Value CommentsMolarity Default units: MDensity Default units: g/mlAfter you enter the minimum amount of information the values are calculated.The valu

To hide a column, right -click the column and select Hide Column from the context menu.To display hidden rows or columns, select Show All from the con

Customizing templatesYou can modify template palette and create your own palette. When you create a palette, a set of empty templatepanes appear above

3. Specify a new name for the template in the Content text box.4. Click OK.5. Click Save. The annotation appears as a tooltip, when you point to the a

if you expand the structure H-Leu-OH, the hydrogen is bonded to the first attachment point in leucine and the hydroxylgroup to the second.For more inf

As in ChemBioDraw 12.0, Nicknames can also be defined by carving a substructure out of a structure.Nicknames and atom labelsIf you use a nickname that

Incorrect CorrectabChemScriptChemScript is the cheminformatics Software Development Kit (SDK). It contains the programming algorithms thatare common t

Launch external applications from ChemBioDraw.Automate workflow from ChemBioDraw.The input data for the script consists of CDXML data from the current

Struct=NameChemBioDraw 13.0 incudes two features for generating structures and chemical names—Name>Struct andStruct>Name. Collectively, these fe

Getting startedThis section will help you become familiar with the user interface.ChemBioDraw user interfaceBy default, the user interface displays co

Non-ringed structuresIsolating and naming the functional groupsIdentifying the base chain of the moleculeIdentifying and building substituentsNomencla

Figure 8.1: An example of a ring assembly structure: 1,1':2',1''-terphenyl.Fused ring systemsStruct>Name supports fused ring sy

PolymersPolymer structures cannot be expressed by SMILES. However, Struct>Name supports many homopolymers, copol-ymers and alternating polymers. Fo

Sulfones and chalcogen analogsIsotopically modified compoundsRadicals, ions, and radical ionsAuto updateYou can include chemical properties, including

Converting clipboard namesTo paste a name on the clipboard as a structure:1. Click in the document window.2. Go to Edit>Paste Special>Name as St

Some stereochemistry designators: +, -, +/-, +-, D, l, dl, endo, exo, syn, anti, r, t, cChemBioDraw 13.0Chapter 8: Struct=Name 126 of 401

Chemistry featuresStructure analysisYou can display the chemical formula, exact mass, molecular weight, m/z, and elemental analysis for the entire doc

2. Go to View>Show Analysis Window. The analysis windows displays values for the parts of the drawing youselect or the entire drawing if nothing is

StereochemistryChemBioDraw 13.0 calculates the absolute stereochemistry according to the Cahn-Ingold-Prelog (CIP) priority rules.For more information,

ChemBioDraw updates the stereochemistry indicators as you change the drawing.Hiding indicators1. Select the indicator to hide.2. Right-click and selec

ToolbarsIn ChemBioDraw 13.0, several new toolbars have been introduced, such as Structure, Curves, Windows, and Bio-polymer toolbars. To display or hi

To indicate an exact location:1. Select the indicator.2. Right-click and choose Position. The Position Indicator dialog box appears.3. Click the appro

Figure 9.2: beta-CypermethrinTwo stereo-centers have the &1 designation because of their fixed relative configuration: when one is (R) the othermu

Display the Info window to view the orbital’s length and angle relative to the X-axis while you draw it. To constrain thelength and angle of an orbita

d-orbitalsThe d-orbital is shown below:To draw a d orbital(‘dxy’):1. Hold down the mouse button over the Orbital tool and drag to select the d-orbital

RadicalUse the radical symbol to indicate a single non-bonded electron.1. Hold down the mouse button over the Chemical Symbols tool and drag to select

Rotating a symbolYou can rotate the radical anion, cation, and lone pair symbols around the same end from which they were originallydrawn. For example

CLogP/CMRMGMelting pointGibbs free energy MRAbout Molecular Networks*MOSES.pKa, MOSES.logS and MOSES.logP for predicting acid dissociation constants,

Critical pressureReported in bars, this is the least applied pressure required at the critical temperature to liquefy a gas.Critical temperatureReport

Heat of formationReported in KJ/mole, the heat of formation is the increase in enthalpy resulting from the formation of one mole of a sub-stance from

Where ‘T’ is the temperature at the melting point, ‘DS’ is the change in entropy of melting, and ‘DH’ is the change inenthalpy of melting.MRThe Molar

BioDraw toolbarThe BioDraw toolbar contains drawing tools for adding biological and biochemical elements to your drawings. See"BioDraw" on p

Connolly Solvent Accessible SurfaceAreaL Polar surface area Vapor pressureConnolly Solvent-Excluded Volume LogP R WE M Radius Water solubilityExact Ma

Exact Mass Mass RMS ForceF Melting Point SFormal Charge Mol Formula SCF EnergyFrequencies Mol Formula HTML Shape AttributeMol Refractivity Shape Coeff

3D viewingAs you create your drawing, you may be curious to see it in three-dimensions. There are two features in Chem-BioDraw that lets you do just t

With the preview window open, you can change the structure’s appearance, in either the document window or the pre-view window.In the document windowWi

Launch Chem 3D. The structure will appear in ChemBio3D as a model that you can edit.Display Mode. Choose display options for the model: wire frame, st

If you want to... then...2. Right-click in the plate.3. Select the appropriate action.4. (Optional) To delete a lane, click it with the Erasertool.Mov

If you change the Rfthe spot will move to the new position indicated.If you edit the Rfto have different precision, that precision will be preserved.R

Option ActionSet Range...A dialog box prompting for the new range appears. The expectedvalues entered in this dialog are always “kDa”. The default val

Option ActionShow size. The current value of the band appears above it. The value isalways shown on top of the band, and is always bound to it.If you

ChemNMRUsing ChemNMR, you can estimate and display proton and Carbon-13 chemical shifts for a selected molecule.As with ChemBioDraw, you can also use

b. Enter a keyword in the New Keyword text box.c. In the New Content text box, enter the notes to apply to the document and click Add.3. Click OK.Dele

"NMR references" on page 156 (source citations)NMR shiftsChemNMR estimates chemical shifts for all hydrogen or carbon atoms for which additi

The change in the frequency is not indicated in the output NMR spectra, and the modified frequency value remains seteven after you exit ChemDraw. Henc

> <SHIFT1>2,9.61,0.0> <SHIFT2>3,8.92,0.0The correction data for each molecule must appear after the molecule’s structural data. For

4.6062 -1.3275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 04.6062 -3.9825 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 03.4547 -1.9992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 03.4547 -3

M ZZC 10 7M ZZC 11 8M ZZC 12 11M ZZC 13 12M END> <ID>1> <solvent>d6-DMSO> <SHIFT1>2,9.61,0.0> <SHIFT2>3,8.92,0.0&g

In case of13C NMR, it estimates over 95% of the shifts with a mean deviation of -0.29 ppm and standard deviation of2.8 ppm.NMR referencesSources for C

ChemDraw/ExcelChemDraw/Excel is an add-in for MicrosoftExcel for Windows. You can add chemical structures and other data fromChemBioDraw 13.0 or a Che

Note: To import CFW files into Excel, save them with the “allow CAL/OLE Automation access” security settingchecked. See “Setting Security Options” in

2. Go to ChemOffice13>Import/Export>Export Table.3. In the Save Table To dialog box, type the file name and click Save. The status bar displays

Adding structuresYou can add chemical structures to a worksheet from any file format that ChemBioDraw 13.0 supports.ChemDraw/Excel assigns the chemica

2. Enter the description and click OK.AutosaveYou can configure ChemBioDraw 13.0 to periodically save an open document.1. Go to File>Preferences. T

3. Go to ChemOffice13>Convert>Inchi to Molecule. If the cell does not contain a valid Inchi string, an error mes-sage appears.Adding structures

R-Group analysisOpening a databaseBefore searching, you must open a structure database.1. In Excel, go to ChemOffice13>New ChemOffice Worksheet.2.

R-Group analysisAn R-group analysis returns all molecules in the query database that include a template structure that you provide. Forexample, assume

Note: You can remove a structure name by clicking Clear. If you select Use Default , the name of the structure will bereplaced by the default name i.e

Displaying structuresYou can display or hide structures in you spreadsheet. You can also adjust the size of cells to display their entire con-tents.To

Each property is calculated using the “best available” method. If the cell reference argument does not point to a validstructure cell, #N/A appears in

Molecular weightDisplays the average molecular mass of the structure, where atomic masses are based on the weighted average of allisotope masses for t

ExamplesIn cell: =CHEM_NUM_ATOMS(A2)Result: 27In cell: =CHEM_NUM_ATOMS(A2, "C")Result: 12Number of hydrogen-bond acceptorsDisplays the numbe

Does cell have a structure drawing?Returns TRUE if the cell has a ChemOffice/Excel structure drawing or reaction drawings, returns FALSE otherwise.Fun

Vapor pressureThe vapor pressure for the structure at 25° C.UnitsPaFunctionCHEMPROPPRO_VAPOR_PRESSURE(cell ref)ExampleIn cell: =CHEMPROPPRO_VAPOR_PRES

2. Enter your Dropbox username and then click OK. The Authorization Confirmation dialog box appears.3. Click OK. The Cloud Linking Confirmation window

ExampleIn cell: =CHEMPROPPRO_CRITICAL_VOLUME(A2)Result: 562.5Gibbs free energyThe Gibbs free energy for the structure at 298.15 K and 1 atm.UnitskJ/mo

FunctionsCHEMPROPPRO_LOGP(cell ref)CLOGP_DRIVER_PARTITION_COEFFICIENT(cell ref)ExamplesIn cell: =CHEMPROPPRO_LOGP(A2)Result: 2.233In cell: =CLOGP_DRIV

FunctionCHEMPROPSTD_CONNOLLY_ACCESSIBLE_AREA(cell ref)ExampleIn cell: =CHEMPROPSTD_CONNOLLY_ACCESSIBLE_AREA(A2)Result: 428.557Note: The default probe

FunctionCHEMPROPSTD_OVALITY(cell ref)ExampleIn cell: =CHEMPROPSTD_OVALITY(A2)Result: 1.428947Principal moments of Inertia (X, Y, Z)The moments of iner

Number of rotatable bondsFunctionMOLECULAR_TOPOLOGY_NUM_ROTATABLE_BONDS(cell ref)ExampleIn cell: =MOLECULAR_TOPOLOGY_NUM_ROTATABLE_BONDS(A2)Result: 2P

Sum of degreesFunctionMOLECULAR_TOPOLOGY_SUM_OF_DEGREES(cell ref)ExampleIn cell: =MOLECULAR_TOPOLOGY_SUM_OF_DEGREES(A2)Result: 28Sum of valence degree

Wiener indexFunctionMOLECULAR_TOPOLOGY_WIENER_INDEX(cell ref)ExampleIn cell: =MOLECULAR_TOPOLOGY_WIENER_INDEX(A2)Result: 249MOLECULAR_NETWORKS_LOGPThe

1. TheLipinski rule of five.2. The Ghose modifications3. The Congreve Rule-of-Three.Lipinski rule of fiveThe Lipinski rule uses five criteria to deter

2. Verify that the value returned by the functions meets the Ghose modification criteria. For example, if the valuereturned by the function CHEMPROPPR

Property predictions in ChemDraw/ExcelChemDraw/Excel includes a variety of functions for reporting properties for a given structure. Each property is

5. Select a folder location to save the file. You can create a new folder by either double-clicking within the folder listcolumn, or double-clicking t

Where:q is the number of edges in the molecular graph.m= (q-n+1) is the cyclomatic number of molecular graph.n is the number of atoms in the molecular

Critical temperatureReported in Kelvin, this is the temperature above which a gas cannot be liquefied, regardless of the pressure applied.Critical vol

V is volume (SI unit: m3)T is the temperature (SI unit: Kelvin)S is the entropy (SI unit: joule per Kelvin)H is the enthalpy (SI unit: Joule)Note: H a

Where ‘H’ is the enthalpy of the gas, calculated as: H = U + pV.MOLECULAR_NETWORKS_LOGPThe partition coefficient is a ratio of concentrations of un-io

Where ‘NA’ is the Avogadro constant and a is the mean polarizability.Molecular formulaThis is the molecular formula of the compound.Molecular weightTh

Distances are established along each line proportional to the reciprocal of the square root of I on either side of thecenter of mass. The locus of the

Total connectivityIs the connectivity considered over all the heteroatoms.Total Valence ConnectivityIs the valence connectivity considered over all th

Search Results- by default the search result appears in the same worksheet on which the search is performed.The "Display in a new worksheet"

You use the generic reaction to search your chemical database for compounds that match the reactant query struc-tures. Once all the matching compounds

3. In ChemBioDraw, draw the generic reaction.4. In ChemBioDraw, go to File>Exit. You will be returned to Excel and the reaction will appear in the

Table of ContentsWhat’s new viChapter 1: Introduction 1About this manual 1Chapter 2: Getting started 4ChemBioDraw user interface 4Toolbars 5Documents

Note: You can specify a time limit for the download process to complete, by specifying a value in ‘seconds’ in theTime out limit textbox. You can spec

After launching, ChemBioFinder uses the form you entered to search its corresponding database for records thatmatch the generic reactant. You can brow

For example, you can take all the reactants you imported and enumerate an experiment containing all possible com-binations of reactants. After calcula

Note: Whenever you create a new experiment, existing experiment worksheets are retained. If you want to deletethem, right-click each experiment tab an

Three columns are added to the reactant or product worksheet: Well Plate, Well Row, and Well Column.To change specific plate assignments, edit the val

2. Go to ChemOffice13>CombiChem>Highlight Related Records.The related records on the Experiment Reactant and Experiment Product sheet are displa

3. Click the Analysis tab. An analysis of the reaction steps appears below the reaction display and a new tab isadded for each generic reactant in the

Query structuresA query is simply a search for information that is stored in a database. If you have ever searched the Internet using aWeb browser, th

You can use other generic labels to indicate other types of query criteria. The generic labels that Chem & Bio Office13.0 supports are listed belo

Note: For the Windows version, you need both the Reaxys Structure Editor plug-in and either the ChemDraw v11or v12 plugin installed on your system.In

Labels MeaningCYC CyclicCYH Cyclic or HCBC CarbocyclicCBH Carbocyclic or HARY ArylARH Aryl or HCAL CycloalkylCAH Cycloalkyl or HCEL CycloalkenylCEH Cy

Basic drawingsChemBioDraw 13.0 provides a variety of tools for drawing everything from simple chemical structures to complexreactions. In this section

Query indicatorsQuery indicators display the atom properties that you assign to a structure, as shown below. If more than one propertyis assigned, an

1. Select the structure.2. Right-click and go to Atom> or Bond>Show Query Indicator on the context menu.Positioning query indicatorsYou can posi

For example, in the figure below, the carbonyl carbon (B) has a substituents count of two, the alpha carbon (A) and thealdehyde oxygen. (hydrogen atom

Query Finds Does not findUptoExactImplicit hydrogensAn implicit hydrogen is a hydrogen atom in which it or its bond is implied but is not visible. An

Any. Default. Finds compounds in which the selected atoms can be a member of any type of ring, or a member of noring at all.No ring bonds. Finds compo

Figure 11.4: The reaction stereo indicator (circled).Any. Default. Finds all compounds regardless of the stereochemistry at the selected atoms.Inversi

Figure 11.2: 4-(cyclohexylidenemethyl)anilineFigure 11.3: (E)-3-(4-aminophenyl)-2-phenylacrylic acidTo increase the number of free sites:1. To display

Narrow. Translates query superatoms to corresponding specific atoms or groups in the database.Any. Translates generic or specific terms to any term.Fo

Go to Structure>Bond Properties. On the Bond Properties tab, select the desired properties from the drop-down lists and click OK.Point to bond and

1. Select the bonds.2. Go to Structure>Bond Properties.3. Click Use Defaults.To remove specific bond properties:1. Select the bond.2. Do one of the

Quadruple bondsThere are three ways to draw a quadruple bond:Draw a bond using the Quadruple Bond tool.Using the Solid, Dashed, or Bold Bond tool, dra

Reaction centerThe Reaction Center property specifies how the selected bonds are affected in a reaction. This property is meaningfulonly when searchin

(A) indicates that the atom must match any atom except hydrogen. The indicator (B) near the bond indicates that thebond must be single or double, S/D.

To enclose structures with brackets:1. To display the Bracket toolbar, go to View>Other Toolbars>Bracket.2. On the Bracket toolbar, select one o

You can also use the bracket usage types “Crosslink(xl)”, “Graft (grf)”, and “Modification (mod)” to represent types ofrepeating units in a structure

Figure 11.6: Brackets used to indicate mixturesBracket type “Mixture, ordered (f)” is primarily used to describe manufacturing processes, where compon

Repeat patternFor simple linear polymers, the repeating units may connect head-to-tail or head-to-head (or their repeat pattern mightbe a mixture or u

1. Open an atom label text box.2. Type the link node in this format:[CH2]3-7Flip typeFor ladder polymers (polymers with two connecting bonds on each s

Defining alternative groupsYou can create alternative group definitions (R, G, etc.) that represent a set of substituents, each of which is used inthe

Figure 11.9: Defining an alternative groupSpecify where the fragments should bond to the parent structure on the alternative group label by defining a

Multiple attachment pointsYou can use R-groups that contain more than one attachment point, such as:For this type of R-group, you must indicate in you

Moving AtomsLayering bondsChanging bond typesChange a single bond from one type to another by doing either of the following:Select a bond tool and cli

3. Draw the structure fragments and label them with attachment points.When the alternative group definition is complete, the attachment point symbols

The figure below shows an alternative group definition and a parent structure with the attachment rank indicators hid-den.Figure 11.14: Hidden attachm

Figure 11.15: Sample r-group reactant queryA likely hit for the above query is shown below:Searching for productsIf you know the desired end product b

2. Type an open bracket “[”followed by a list of elements, fragments, nicknames, or generic nicknames separated bycommas, followed by a close bracket

definition exampleDefinitions are expanded into multiple complete molecules. If more than one site is present in the selection, the expan-sion include

This structure indicates that both R1sites must consist of either a fluorine or chlorine atom and that the R2site mustbe either a bromine or iodine at

When a reaction map is established, you can point to an atom in one structure with the Reaction Atom-Atom Map toolto highlight the mapped atom in the

you can manually readjust the reaction mapping.The figure below shows the initial mapping being amended by using the Reaction Atom-Atom Map tool.Figur

Figure 11.20: Finalized mappingYou can set or change the mapping for other atoms in the reaction.Clearing reaction mappingTo clear reaction mapping:1.

1. To display the Query tools, go to View>Other Toolbars>Query Tools or click the Query Tools icon on the MainTool palette.2. On the Query tools

Reducing ring sizeYou can reduce the number of atoms in a ring. For example, you can convert cyclohexane to cyclopentane. To reducethe ring size, do o

Geometry and constraint objects update when you change the structure; they cannot be moved independently. Theymay be used with CDX, MOL, SKC, and TGF

Exported Query Properties ISIS™ Mol RxnUnspecifiedX X XMust be absentMust be presentX X XReaction ChangeMay be anythingX XMust be as specifiedX XReact

Exported Query Properties ISIS™ Mol RxnWedgedX X XWavyX X XHollow Wedgede e eDativef f fDoubleXgX XDouble EitherX X XDouble Boldh h hAromaticX X XTaut

Exported Query Properties ISIS™ Mol RxnNot CenterX XOther Query AttributesGeneric NicknamesXjXjXjElement ListsXkoXkoXkoElement Not ListsXkXkXkAlternat

Sharing informationMany of the system commands you commonly use to transfer content from one place to another can also be used inChemBioDraw:copy/past

SMILES supports an alternate notation for aromatic structures using lowercase letters. ChemBioDraw 13.0 generatesthis type of SMILES string for any st

standard makes InChIKey strings useful for Web searching and database indexing.To copy a structure as an InChIKey string to other documents:1. Select

Except for the foreground and background color, the colors present in the selection to be pasted are added to the des-tination document’s Color palett

b. Select a file format.c. Click OK.Some file formats do not support atom labels that contain nicknames or structural fragments. When you save in thes

2. In the Insert Object dialog box, click Create from File.3. Browse to the object file and click OK.Note: If you choose a file type that ChemBioDraw

The bonds in the new structure appear at standard 120° angles.Changing fixed valuesBy default, bond lengths are .4176 inches and bond angles in a chai

Graphics export border preferenceYou can specify the border size when exporting pictures. This preference affects the output of all graphical formats,

Format WindowsEnhancedMetafile (EMF) YESChemDraw Templates CTP) YESChemDraw Templates Style sheets (CTS) YESPDF NOMDL Molfile V3000 YESReaction Molfil

Format Import ExportGraphic Image Format (GIF) YES YESISIS (SKC, TGF, RXN) YES YESJCAMP (JDX, DX) YES NOJPEG (JPG, JPEG) YES YESMDL MolFile (MOL) YES

Preferences and settingsYou can customize ChemBioDraw 13.0 by configuring Preferences and Document Settings for the way you work.Preferences allow you

To activate the I/Draw mode, go to File>Preferences and click I/Draw Mode.Default document locationYou can set the default file directory for each

The ChemDraw items folderThe folder contains the preferences, hotkeys, nicknames, and isotopes files; scripts, and the generic nicknames file.It also

To save a document’s setting as a style sheet:1. Go to File>Save As. The Save As dialog box appears.2. Name the file and change the type (in OS X:

Default document locationYou can set the default file directory for each time you open a file.1. Go to File>Preferences. The Preferences dialog box

The ChemDraw items folderThe folder contains the preferences, hotkeys, nicknames, and isotopes files; scripts, and the generic nicknames file.It also

To save a document’s setting as a style sheet:1. Go to File>Save As. The Save As dialog box appears.2. Name the file and change the type (in OS X:

Click a symbol to highlight the atom and activate the Text tool. Move the mouse across the table to highlight eachatom.To add an atom. Select the desi

Default document locationYou can set the default file directory for each time you open a file.1. Go to File>Preferences. The Preferences dialog box

The ChemDraw items folderThe folder contains the preferences, hotkeys, nicknames, and isotopes files; scripts, and the generic nicknames file.It also

To save a document’s setting as a style sheet:1. Go to File>Save As. The Save As dialog box appears.2. Name the file and change the type (in OS X:

Default document locationYou can set the default file directory for each time you open a file.1. Go to File>Preferences. The Preferences dialog box

The ChemDraw items folderThe folder contains the preferences, hotkeys, nicknames, and isotopes files; scripts, and the generic nicknames file.It also

To save a document’s setting as a style sheet:1. Go to File>Save As. The Save As dialog box appears.2. Name the file and change the type (in OS X:

Default document locationYou can set the default file directory for each time you open a file.1. Go to File>Preferences. The Preferences dialog box

The ChemDraw items folderThe folder contains the preferences, hotkeys, nicknames, and isotopes files; scripts, and the generic nicknames file.It also

To save a document’s setting as a style sheet:1. Go to File>Save As. The Save As dialog box appears.2. Name the file and change the type (in OS X:

Apply settings to the entire current document from an existing document.Apply settings to selected objects in the current document from an existing do

1. Draw the phenol structure.2. Using the Text tool, click below the drawing and type “Phenol” in the text box.3. Click outside the text box.To edit t

An absolute value you choose in the units specified for your document.Bold Width. Set the width of the line used when bold and wedge bonds are drawn.

Configuring objectsTo configure the drawing settings for a selected object:1. Select the object.2. Go to Object>Object Settings.3. Configure the se

6. Repeat step 4 for other properties, as desired.7. Click OK.Formatting captionsText settings affect how captions and atom labels for the current doc

Style indicatorsSelect any text in the document window and go to Text>Style to view the styles that have been applied. A check indi-cates the style

Figure 13.1: Atom label justification. A) stacked above; B) centered; C) flush left; D) flush right.Automatic alignmentWhen you justify atom labels au

If you label C1, the second and third tokens are placed above the first token since there are bonds below the atom.If you label C4, the second and thi

The format is applied to the typed text. Subsequent text you type uses the default document settings.Changing text spacingYou can change the text sett

1. Go to File>Document Settings. The Document Settings dialog box appears.2. Click the Drawing tab.3. Type a new Margin Width value.4. Click OK.The

"DNA": Hotkeys that sets the label for the DNA sequence."RNA": Hotkeys that sets the label for the RNA sequence.“Generic”: Hotkeys

PEN CYCLOBUTANEHASHEDBOND CYCLOPROPANEARROW TEMPLATEHASHEDWEDGEDBOND SNAKINGCHAINORBITAL ACYCLICCHAINBOLDBOND QUERYDRAWINGELEMENTS TABLEWEDGEDBOND ARC

To specify a font, style, and size for selected text, do one of the following:Choose the font and size from the Text menu.Right-click and choose the f

1. Go to File>Document Settings and select the Colors tab.2. Select the background and foreground colors.3. Click OK.Color by elementYou can now co

The color paletteUse the color palette to specify the color of objects and text in the document in the active window. A palette is storedin every docu

9. Click Add to Custom Colors.10.Click OK.Templates and colorThe background and foreground colors in a template from the template pop-up palette are n

Line Width: 0.6 ptMargin Width: 1.6 ptHash Spacing: 2.5 ptChain Angle (degrees): 120Bond Spacing (% of length): 18Atom Label Font :Atom Label Size: 10

Caption Font :Caption Size: 12 ptDrawing Area (Width x Height): 693 pt x 918 ptPage Size: US LetterReduction (%): 80J. Mol. Mod. (1 column)Fixed Lengt

Bold Width: 4 ptLine Width: 1.6 ptMargin Width: 2 ptHash Spacing: 2.7 ptChain Angle (degrees): 120Bond Spacing (% of length): 15Atom Label Font :Atom

Atom Label Size: 9 ptCaption Font :Caption Size: 9 ptDrawing Area (Width x Height): 8.9 cm x 25.4 cm (1 col-umn); 19 cm x 27.7 cmPage Size: US LetterR

Verlag Helvetica Chimica ActaFixed Length: 17 ptBold Width: 2.9 ptLine Width: 0.54 ptMargin Width: 2 ptHash Spacing: 2 ptChain Angle (degrees): 120Bon

Page layoutObject alignment, page size, orientation, and other factors affect the presentation quality of your document.The drawing areaThe document w

4. Select whether to Print Registration Marks.5. Create Headers and Footers.6. Click OK.Headers and footersFor posters, only one header and footer app

2. Choose a color from the Color menu.Caption widthTo edit the width of a caption:1. Select the caption using the Text tool. A resize handle appears o

Figure 14.2: A) The filename is displayed center aligned in the header; B)The page number is displayed aligned right inthe footer.Page setupTo setup t

1. Select the document to print.2. Go to File>Print. ChemBioDraw 13.0 opens and the Print dialog box appears.3. Make your selections in the Print d

Two 35mm Slide Boundary Guides appear in the orientation chosen in the Page Setup dialog box. These guidesappear in every document.Viewing drawingsMag

Figure 14.1: How rulers indicate position. A) The cursor; B) Ruler guides indicating vertical and horizontal location ofthe cursor.When you select an

Click and drag in the document window to create the table. The table has two rows and two columns.Click in the document window. Type the numbers of ro

To add or delete rows or columns in the table:1. Point to the top or left border where you want to add or delete the row or column. A border appears a

1. Select the caption.2. Move the caption with the arrow keys.For more information on moving objects,see "Moving objects" on page 42.3. To c

Chemical interpretationChemBioDraw 13.0 converts lines, characters, and other symbols into chemically meaningful figures as you work.This occurs in th

A successful search in one database might not produce results in another. When in doubt, consult the documentationfor the conventions your database us

A single bond near a closed circle is recognized as aromatic:Atom labelsA simple atom label may contain any of the following:A single element.An eleme

Merging sidechains with residue 66Hybrid biopolymers 69IUPAC codes 70Disulfide bridges 74Lactam bridges 75Chapter 6: Tutorials 77Tutorial 1: Drawing a

HotkeysHotKeys are keys on your keyboard that are linked to specific atom labels. Use ChemBioDraw hotKeys to quicklylabel atoms and apply atom propert

atom label. Multi-attached atom labels are always parsed from beginning to end, but the beginning might be on theright if the atom label was in Automa

Chemically significant textOften, it is simpler to write a chemical formula like MeOH or H2O than to draw an atoms-and-bonds structure. Chem-BioDraw 1

Charges that follow other repeating units are distributed among thoseunits.Charges may be superscripted.Multiple charges are recognized appropriately.

Isotopes can be included anywhere that regular elements can.Deuterium and Tritium appear as one-letter symbols.RadicalsRadicals are indicated with the

Multi-center attachmentsMulti-center attachments are meaningful only when created using Structure>Add Multi-Center Attachment. Multi-center attachm

Cahn-Ingold-PrelogAbsolute stereochemistry is calculated for tetrahedral atoms and double bonds according to the Cahn-Ingold-Prelog(CIP) priority rule

Figure 15.2: The Absolute flag indicates the exact stereoisomer as drawn.Figure 15.3: The relative flag indicates the exact stereoisomer as drawn, or

Figure 15.4: The racemic flag indicates a mixture of the exact stereoisomer as drawn and its enantiomer.Polymer representationsPolymers are represente

Message DescriptionFilled valences include sum of bond orders, charge, radicals, and free sites.Aromatic bonds count 1.5 each, rounded down unless it

Message DescriptionPart of a molecule is outside of thealternative group definition.Displayed for any Alternative Group Box whose border crosses part

NicknamesThe simplest way to add an atomic symbol to a structure is to type the symbol into a text box. However, you are notlimited to entering atoms

Property calculationsYou can calculate predicted values of selected physical and thermodynamic properties for structures of up to 200heavy atoms. This

pKa, CLogP, and CMRSpecific algorithms for calculating LogP and molar refractivity from fragment-based methods developed by the Medic-inal Chemistry P

CLogP (CLogP driver Partition Coefficient)MR (ChemPropPro Mol Refractivity)CMR (CLogP driver Mol Refractivity).The ChemBio3D MOPAC interfaceCalculates

Shortcuts and hotkeysHotkeys are organized into atom labels, bond types, and functions (such as adding a charge or displaying a bond.Shortcuts are org

Atom Label KeyC cNa NX xCl C or lO oCOOCH3 ED dOTs TCH2OH 6Et eP pB BBond hotkeysTo modify a bond, place your mouse over the bond and select a key lis

Function KeyPosition a double bond to the right rChange to wedged bond wBring bond to front fChange to hashed bond HOpen a bond properties text box /

Function KeyOpen an atom label text box. <Enter>Remove an atom label. <Backspace>, <Delete> or<space>ShortcutsBelow is a list

Command Key CombinationClear DeleteViewCommand Key CombinationActual size F5Reduce F8Magnify F7Fit to window F6Toggle ruler F11Toggle crosshair CTRL+H

Command Key CombinationRotate... (opens Rotate Objectsdialog box)CTRL+RScale...(opens Scale Objectsdialog box)CTRL+KStructureCommand Key CombinationCl

DrawingCommand Key CombinationCopy a selected object CTRL+dragCopy a selected object(constrained to X and Yaxes)SHIFT+CTRL+dragDistort (limit resize t

To select a nickname to apply to an atom using a hotkey:1. Point to an atom.2. Press the hotkey “=” (equal sign). The nickname list appears.3. Select

Ac-MeAsp BzOM Cy DMTr Gly m-PhenyleneBenzoyl c-C3H5 cyclobutyl DNP His m-TolylBenzyl c-C4H7 cycloheptyl Dnp i-Am MDIPSBn c-C5H9 cyclooctyl Dns i-Bu MD

The PerkinElmer Informatics web siteThe PerkinElmer Informatics Web site is a valuable source of helpful information. There you can:Register your soft

1. In ChemBioDraw 13.0, select a structure you have drawn.2. Go to Online>Find Suppliers on ChemACX.com.The ChemACX.Com page opens with information

PerkinElmer InformaticsTo open the PerkinEmer Informatics Home Page, go to Online>Browse CambridgeSoft.com. Check the Per-kinElmer Informatics Web

Index113C, 1H shifts, estimating 151335 mm slide boundary lines 2823D query properties 230Aabnormal valence 208absolute flag, drawing 229ACX informati

attachment point symbol 219attachment rank indicators 219defining 218description 217multiple attachment points 220amino acidsbeta amino acids 61D-amin

atomnumbers 101query properties 200atom-to-atom mapping 226atom label text boxes, closing 245, 248, 251, 254, 257atom labelsautomatic justification 26

atom, to add an 17atomsmoving 14attached data 240attachment pointdefining 218numbering 221symbol 219tool 135, 218attachment points 135attachment point

bio instruments template 53BioDraw 6drawing a helix protein 55drawing a membrane arc 55drawing a membrane line 55drawing DNA 56templates 113BioDraw ob

types 210bond properties, assigningbondsproperties, assigning 208properties, assigningassigingbond properties 208bond spacing, description 260bonding

To select the amino acid, double-click the nickname as shown:To expand atom nicknames,1. Select the selection tool.2. Select the label to expand or do

single 36tool 35usage 213branched peptides 73branching peptides 72branching, calculating 186bridgesdisulfide 74lactam 75CCahn-Ingold-Prelog 296calcula

Table column spacing 287carbon-13 shifts, see 13C, 1H shifts, estimating 151cation, drawing 135CDX see file formats 7chain angle, description 261chain

ChemDraw items folderisotope table 208scripts 268templates 113ChemDraw Items folderdescription 246, 249, 252, 255, 258ChemDraw laser prep 273ChemDraw/

freezing point 303Gibbs free energy 303heat of formation 303Henry’s Law 301ideal gas thermal capacity 303LogP 301molar refractivity 301thermal capacit

ChemNMR directory 153ChemOffice SDK, accessing 314ChemPropcritical pressure 303ChemScript 118ChemSpider database 128chirality, see stereochemistry, fl

Combi experimentscreating 191commandsnew 6open 6save 7Congreve Rule-of-Three 179Connolly accessible area 181Connolly molecular surface area 173, 181Co

critical pressure 138, 170, 181calculation 303critical temperature 138, 170, 182calculation 303critical volume 138, 170, 182critical volume, calculati

database conventions, in structure drawings 288dative bonds, drawing 13defaultatom properties, resetting 202bond properties, resetting 209document loc

document settingsAdv. Synth.Catal. 274J. Mol. Mod. 275new document 275new slide 275overview 259phytomedicine 276RSC document 276Science of Synthesis 2

orientation 14double either bonds, drawing 12drawingacyclic chains 29arcs 35benzene and cyclopentadiene rings 28charge symbols 135curves 36d-orbitals

Deleting a keywordWhen you delete a keyword, all the notes for that keyword are also deleted.1. In the Annotate dialog box, select the keyword from th

triple bonds 12drawing a structure tutorial 77drawing area 279drawing elementsautoscaling 237color 34fill patterns 34drawing settingsmargin width, eff

enlargedocument window 279page size 282error checking 48error messages 298exact mass 167, 182definition 127exportingcompatibility 231mapping 229query

flush right justification 264fontnew captions 266footers, creating 280formal charge 168, 182formatatom labels 264text 263formula commanddescription 12

Gibbs free energy 138, 171, 182grouping objects 44groupsintegral 45HH-Dot and H-Dashspecification 294H–dash 134H–dot 134half-head arrow 110Hapticity 9

hotkeys .xml file 270how to use this guide 1hybrid orbitals, drawing 133hydrogens, implicit 204hyphens, font submenu 263Iideal gas thermal capacity 17

integral groups, creating 45internet, CambridgeSoft web site 314ISISV3000 support 240isotopesspecifications 293isotopes table file 208isotopes text fi

contracting 96lactam bridges 75Lasso toolselecting objects 38launch Chem & Bio 3D 145layeringatom labels 267Lewis dot symbol, see lone pair symbol

mappingatom 226clearing 229exporting 229manual 227reaction 226margin widthadjusting 261description 261effect on bond crossings 261setting 267specifyin

minus (symbol) 134mirror images, creating 43mol formula 185mol refractivity 184mol weight 185molar refractivity 172, 301molecular mass, definition 127

new document 275new slide 275Newman projections tutorial 87nicknames 22, 304defining 115deleting 117NMR datarestoring default 153NMR, see ChemNMR, spe

To add or remove a terminal carbon label, right-click the atom and select or deselect Show Terminal CarbonLabels.Chemical significanceBy default, capt

joining 44moving 42selecting 38ungrouping 45using crosshair with 284using rulers with 283objects ungrouping 45objects, coloring 95OLE 238Online menubr

Pp-orbitals, drawing 133pageborder 279overlap 279page setupsaving settings 282paged documents 279paired brackets 36palettearcs 35brackets 36color 272s

plasmid map 57-58adding markers to 58resizing regions 58Plasmid map, customizing 54plate assignmentsremoving 194to change 194plus (symbol) 134polar su

principal moment 185principal moments of inertia (X, Y, Z) 174printingbackground color 273ChemDraw laser prep 273drawing elements fill 34overview 281P

Qquadruple bonds 13queriesmultiple rings 216query indicatorsbond 201editing 201query properties3D 230exported 231query structuresexporting 231Query St

reactant worksheets 190recreating 191reaction atom-to-atom mapping 226reaction center 211reaction interpreter 108reaction mappingclearing 229exporting

repositioningstereochemistry indicators 130reset defaultsatom properties 202bond properties 209residuesadding 68numbering 69removing 67replacing 68res

ringsdrawing with fixed length 27rings tutorial 78rotatable bonds 185rotatechemical symbols 136command 41dialog box 41objects 41rotating objects 41RS,

objects 45when transferring information 237scaling objects 45Science of Synthesis 277SciStore.com 313scrap files 237scripts 118SDK Online, accessing 3

pasting as text strings 63-64settingpreferences 244, 247, 250, 253, 256setting preferences 25settingsdocument 259shape attribute 175, 186shape coeffic

Figure 3.1: a)cyclopropane; b)cyclopentane; c)cycloheptane; d)cyclo hexane chair(1); e)cyclopentadiene; f)c-yclobutane; g)cyclohexane; h)cyclooctane;

creating 235SMIRKS, overview 235spectraremoving assignments 152spectrum-structure assignmentsremoving 152viewing 152spiro and sprout rings 27squiggly

Struct=Name 120, 124Struct=Name, structure types supported 125structurechecking 48chemical warning 48converting to name 120selecting 39shortcut keys 3

synthesis 104Synthesis/Synlett document 277TTableadjusting rows and columns 285adjusting the whole table 285alignment 285clearing cells 285column spac

text conventions 1text line notation 235text settingscaptions, font, size, and style 266TLC 145TLC spotscrescent 146custom, about 147custom, adding 14

bond 12bracket 35cyclohexane chair 26cyclohexane ring 78, 84cyclooctane ring 26cyclopentadiene ring 26cyclopropane ring 26dashed bond 12dative bond 12

transferring informationacross platforms 243keeping in scale 237transferring objects 237translation (query property) 207triple bonds, drawing 12tRNA 5

use defaultsatom properties 202bond properties 209bracket properties 213user guide, online 312using nicknames 22VV3000, support for 240vapor pressure

work area 4113C, 1H shifts, estimating 151335 mm slide boundary lines 2823D query properties 230Aabnormal valence 208absolute flag, drawing 229ACX inf

alternative groupsattachment point numbering 221attachment point symbol 219attachment rank indicators 219defining 218description 217multiple attachmen

assigningatom mapping 226asymmetry, see stereochemistry indicators 296atomnumbers 101query properties 200atom-to-atom mapping 226atom label text boxes

1. Click one of the Cyclohexane Chair Ring tools.2. Click+drag in the structure to the orientation you want.Figure 3.2: a)Horizontal orientation; b)Ve

substituents 202unsaturation 205atom, changing to a different 17atom, to add an 17atomsmoving 14attached data 240attachment pointdefining 218numbering

benzene ringchanging orientation 28drawing 28beta amino acids 61bio instruments template 53BioDraw 6drawing a helix protein 55drawing a membrane arc 5

query indicators 209reaction center 211removing 209topology 210types 210bond properties, assigningbondsproperties, assigning 208properties, assigninga

braces 35bracketsdrawing 36paired 36single 36tool 35usage 213branched peptides 73branching peptides 72branching, calculating 186bridgesdisulfide 74lac

justification 264setting font, size and styles 266subscript 263superscript 263Table column spacing 287carbon-13 shifts, see 13C, 1H shifts, estimating

ChemClub.com 312ChemDrawHotkeys file 268ChemDraw for Excel 196ChemDraw items folderisotope table 208scripts 268templates 113ChemDraw Items folderdescr

CLogP 302CMR 302critical temperature 303critical volume 303freezing point 303Gibbs free energy 303heat of formation 303Henry’s Law 301ideal gas therma

ChemNMRexample supplementary data 151, 153NMR shifts 151using 151ChemNMR database 153ChemNMR directory 153ChemOffice SDK, accessing 314ChemPropcritica

color palette 272Coloring groups 95colors, maximum number of 237, 270, 272Column spacing 287Combi experimentscreating 191commandsnew 6open 6save 7Cong

creatingHotkeys 268SLN strings 236tables 286critical pressure 138, 170, 181calculation 303critical temperature 138, 170, 182calculation 303critical vo

To draw, click in the document window with either the cyclopentadiene or benzene drawing tool.To shift the orientation so the first bond drawn is a si

DD-amino acids vi, 60-61d-orbitals, drawing 134daggers 36data Sgroup, support for 240database conventions, in structure drawings 288dative bonds, draw

disulfide bridges 74DNA tool, customizing 54documentlocation, default 245, 248, 251, 254, 257posters 279setting up multi-paged 279document settingsAdv

Does cell have a reaction drawing? 169Does cell have a structure drawing? 169DOS prompt 153double bondchanging type 14drawing 12orientation 14double e

s-orbitals 133sigma orbitals 133single bonds 12single lobe orbitals 133stereochemical symbols 229structure automatically from name 124triple bonds 12d

element lists 211elemental analysisdescription 127embedding objects 238empirical formulas 292enantiomers, describing 131enlargedocument window 279page

fixed angle bonds 15fixed lengthsdescription 260scaling 45flip type 217flush left justification 264flush right justification 264fontnew captions 266fo

gamma subunit, customizing 54generic groups 217generic nicknames 198generic structures, expanding 224, 265, 301-302get ChemDraw/Excel list 158Ghose 17

highlight boxselecting 39home page, CambridgeSoft 314hot-linked properties 124Hotkeys 246, 249, 252, 255, 258creating 268hotkeys.xml file 268hotkeys .

Info window 43displaying fixed angles 15insert name as structure 124insertingname as structure 124Insertingrows in tables 287integral groups, creating

LL-amino acids viL amino-acids 60lab supplies, purchasing online 313label, to edit a 17labels 17, 115auto-update 124automatic terminal carbons 261cont

1. Select the Acyclic Chain tool.2. Click an existing atom or an empty area in a document window. The Add Chain dialog box appears.3. Type the number

Mm/z, displaying 127magnification control 279magnifyingwith View menu 283Main toolbar 5, 12, 27MakeChemNMRUserDB.exe 153manual mappingclearing 229over

melting point 139melting/freezing point 169membrane (arc), customizing 54membrane (ellipse), customizing 54membrane (line), customizing 54merging side

Nnameinserting as structure 124of structure, inserting 120name to structure see Name=Struct 124name, automatic structure from 124Name=Struct 124conver

Oobjects3D rotation 34aligning 284bioDraw, customizing 54copying 42deleting 44distributing 46framing 36grouping 44joining 44moving 42selecting 38ungro

openingChemDraw/Excel 157organelles template 53orientationbenzene ring tool 28cyclopentadiene ring tool 28double bonds 14ovality 173, 185overlap, mult

pen tools 36peptidesbranched 72crosslinked 72cyclic 72periodic table 16perspective drawings tutorial 83phytomedicine 276picture layersatom labels 267p

rulers 283stereochemistry indicators 130posters, setup 279PostScriptprinting 268preferences 195overview 244, 247, 250, 253, 256print 273require CTRL+E

atom, substituents 202atom, unsaturation 205bond 208bond query indicators 209bond types 210bond, reaction center 211bond, removing 209bond, topology 2

R groups 217racemic flag, drawing 229Radical 135Radical Anion 135Radical Cation 135radicalsdrawing 135specification 294radius 175, 186reactant lists 1

registration marks 279registration, online 312relative flag, drawing 229relative stereochemistry 131removing residues 67repeat command, rotations 41re

Structure analysis 127ChemBioFinder hotlink 128Stereochemistry 129Chemical annotations 132Chemical properties 1363D viewing 143TLC 145ChemNMR 150Chapt

Figure 3.3: A) Arc adjustment handleSelect an arc arrow from the Arrows palette.You can customize arc arrows as easily as straight arrows. Here are so

retrosynthesis tool 104reversing actions 7Rf display 146ribosome 57ribosomes A and B 57Ribosomes, customizing 54ring assemblies 121ring bond count 204

save commanddefault file format 8savingstructures in ChemDraw/Excel 161saving changes automatically 8saving documents 7saving page setup settings 282s

selection tooldeleting 44deselecting objects 39highlight box 39joining 44Sequence 267sequencesnonlinear 69pasting 63pasting as text strings 63-64setti

similarity searches in ChemDraw/Excel 162single bonds, drawing 12single brackets 36single lobe orbitals, drawing 133SLN strings 236copy as 235SMILES s

indicators, repositioning 130relative 131removing markers 130see also indicators 296showing 129terms supported 129stereochemistry tutorial 90stoichiom

supplier, finding online 312supported structures 120, 125symbols, chemicalcircle minus 134circle plus 134minus (symbol) 134plus (symbol) 134Synchroniz

textatom label format 264atom labels, automatic justification 265caption, creating tables 286formatting 263shortcut keys 309text boxclosing 245, 248,

toolbarstearing off 5toolsacyclic chain 29alternative group 218arc 35attachment point 218BioDraw 6bold bond 12bold wedge bond 12bond 12bracket 35cyclo

wavy bond 12topological diameter 176, 186topological index 174topological polar surface area 303topology 210total connectivity 176, 187total valence c

Uundo, redo, and repeat 7ungroup command 45ungrouping objects 45unsaturation 205unspecified atom properties, in queries 203unsupported structures 123u

Connecting arrowsYou can connect a new arrow to an existing arrow at either end or at the midpoint.Note: The terms “left” and “right” in the context m

water solubility 172, 187Web site, CambridgeSoft, accessing 314wedged bonds, drawing 13Weiner index 187What’s New viwhite space, adjusting in atom lab

Finally, arrows can be rotated with the Structure Perspective tool as well as the Lasso or Marquee. For more infor-mation on Structure Perspective too

3. On the context menu, choose either Filled, Faded, or Shaded.Drawing elementsDrawing elements are simple shapes such as circles and rectangles.To gr

ArcsYou can draw solid or dashed arcs of different angles: 90°, 120°, 180°, and 270°.To draw an arc:1. Do one of the following:In ChemDraw Standard, p

Single bracketsYou can draw a single bracket in any orientation. Select a single bracket tool from the Brackets palette.1. Point where you want the br

The cursor appears as a hand with a “+” sign inside . However, when the cursor is positioned exactly over thepoints on the curve, the '+' sy

arbitrarily shaped arrows to be created. To add color, select a color in the Color menu.Figure 3.5: A freehand curve with different properties; A) A s

To set one selection tool to behave like the other, click either one of the tools while pressing ALT .To toggle a selection tool and the last drawing

Resizing objectsYou can resize objects by dragging the resize handle of a selected object or by scaling.To resize a selected object proportionately:1.

Polymers 212Link nodes 216Alternative groups 217Anonymous alternative groups 223Expand generic structures 224Atom-to-Atom mapping 226Stereochemical sy

Shift+drag the Resize handle in the desired direction. Shift modifies the resize operation so that you can distortobjects along the X-axis or Y-axis.R

To move the center of rotation:1. Select the object. A center of rotation indicator (‘+’) appears in the center of the object, as shown in the figure:

To constrain the copy to move only vertically or horizontally while positioning it, hold down the SHIFT+CTRL keys.The info windowThis window shows the

Deleting objectsTo delete selected objects, do one of the following:Press the DELETE key.Go to Edit>Clear.Use the Eraser tool.Joining structuresTo

To select grouped objects, move the selection tool over an object in the group until it is highlighted and double-click it.Ungrouping objectsTo ungrou

.To scale the bonds to a new fixed length that you specify, select Scale selected objects so that medianbond is option, and type the new median bond l

Clean Up StructureThe Clean Up Structure command is used to neaten the appearance of molecules by regularizing bond lengths andangles. Graphic objects

You can also clean up a reaction or a biopolymer. For more information, see "Clean Up Reaction" on page 107 and"Clean Up Biopolymer&quo

When Display Warnings is disabled for an object:A red box does not appear around the object.Problems are reported by the Check Structure command (Go t

Warning DescriptionLinear AtomAn unlabeled atom is attached to exactly two identical bonds that create a 180 degreeangle.ChemBioDraw 13.0Chapter 3: Ba

Viewing drawings 283Tables 284Chapter 15: Chemical interpretation 288Database conventions 288Chapter 16: Property calculations 301Chapter 17: Shortcut

BioDrawChemBioDraw 13.0 includes a variety of tools for drawing metabolic pathways, such as enzymes and receptors. Todisplay the BioDraw toolbars, go

Advanced BioDrawAnatomy templatesChemBioDraw 13.0Chapter 4: BioDraw 52 of 401

AnimalsBio InstrumentsMicroorganismsOrganellesChemBioDraw 13.0Chapter 4: BioDraw 53 of 401

For more information, see "Templates" on page 113.Customizable objectsThe table below describes the BioDraw objects in the BioDraw toolbar w

Membrane line1. Select the membrane line tool from the BioDraw toolbar.2. Click and drag to draw a membrane line of the size you want or click for the

The helix protein has four adjustment handles: height, width of the strands, width of the cylinders, and spacing.Figure 4.1: Adjustment handles on a h

RibosomesTo draw a Ribosome:1. On either the Ribosome or BioDraw toolbar, select a Ribosome tool.2. Click and drag in the workspace until the Ribosome

Adding regionsRegions represent the fragments in the plasmid. You can add as many regions to you map as you want or none.To add regions:1. Right-click

To extend an arrow, click and drag its center handle as indicated by the cursor ( ) in the figure above.Enhancing the drawingA plasmid map is like any

Drawing biopolymersBiopolymers are complex molecular assemblies that adopt precise and defined shapes and structures. Their definedshape and structure

What’s newChemBioDraw has long been the preferred tool for illustrating chemical and biological concepts. ChemBioDraw 13.0introduces a variety of impr

Note: The SHIFT key acts as a toggle. Hence, to enter D-amino acids, press SHIFT while entering a single-lettersequence while in L mode. Alternatively

You can also overwrite and replace the sequence atoms using the residue replacement button in the biopolymereditor. For more information, see "Re

If no leaving group is found, after you enter ’)’, a dialog box will prompt you to specify the attachment point.You can expand and contract protected

Select one of these options:Paste FASTA PeptidePaste FASTA RNAPaste FASTA DNAWhen you hover your mouse over the residue, a description of the residue

Note: The labels in the text string must correspond to explicit nicknames.Expanding sequencesAfter creating a sequence, you can expand the whole seque

Figure 5.1: Two expanded serine residues. The residue on the left has been modified to create homoserine.To contract a label:1. Using a selection tool

The residue is selected and you can edit the residue label.Removing residuesWhen you remove a residue, the bonds are automatically re-created between

Replacing residuesThe Biopolymer toolbar has two distinct modes of data entry- Insertion mode and Replacement mode. Insertion modeis the default mode.

2. Click a label you want the new label to be adjacent to. An orange chevron indicates the insertion point.3. Type the new label. The new label is add

Branched biopolymersResidue labels typically have two attachment points. However, you can add attachment points so that the sequencebranches. For exam

Lactam bridges -You can form lactam bridges between residues with available amino and carboxylic acid leavinggroups, such as Lys-Asp and Lys-Glu. For

C Cytosine C Cys CysteineG Guanine D Asp Aspartic AcidT (or U) Thymine (or Uracil) E Glu Glutamic AcidR A or G [EitherpuRine]F Phe PhenylalanineY C or

V Val ValineW Trp TryptophanY Tyr TyrosineThe tables below list the three letter codes for non-specific and non-proteinogenic amino acids.IUPAC aminoa

You can create a crosslinked peptide such as insulin, using the biopolymer tool and bond tool.Branched peptidesA branched peptide is formed where a re

2. Using the solid-bond tool, drag from the lower chain's Gly-3 to the upper chain's Arg-3. The terminal hydrogen onthe lower chain is remov

Insulin consists of two chains, an A chain and a B chain, connected by disulfide bridges.A chainGIVEQCCTSICSLYQLENYCNB chainFVNQHLCGSHLVEALYLVCGERGFFY

ChemBioDraw 13.0Chapter 5: Drawing biopolymers 76 of 401

TutorialsThe tutorials illustrate fundamental drawing techniques. Each tutorial introduces new techniques, or variations of tech-niques from previous

Adding atom labels1. Using the Text tool, click the end of the double-bond shown below. A text box appears at the end of the bond.2. Type an uppercase

Figure 6.1: To change the bond order, type ‘1’.5. To create the double bond in the second ring, either hover the mouse over the bond and type ‘2’ or c

8. Hover the mouse over the right-most terminal carbon and type the letter ‘o’ to create the ketone functional group.9. To connect the left terminal c

Polymer Bead Enhancements. You can resize polymer beads. For more information on polymer beads and otherattachment points, see "Attachment points

Figure 6.2: Fischer projectionsTo draw the first bond:1. Click the Solid Bond tool.2. Point in the document window. Drag downward to draw the first bo

Note: When you drag the pointer along the length of the bonds, the pointer alternates between an arrow and across. The arrow indicates you are pointin

Figure 6.6: Adding repeating atom labelsTip: Double click an atom with the text tool to repeat the last label.3. Click one of the remaining atoms and

Note: If you are following the tutorials in order, ChemBioDraw 13.0 will remember your last drawing used the ACSstyle sheet and open it as the default

Enlarge the ring:1. Go to Edit>Select All (or type CTRL+A).2. Click-drag the ring a corner adjustment handle increase the size of the ring to 150%.

Figure 6.8: Adding the OH labels3. Move the pointer to the other atoms as shown, and triple-click to repeat the atom label.Tip: If the drawing is too

2. Click the bond shown in the figure.3. The cursor changes to a bold arrow as you point to the bond.4. Click the Wedge bond tool.5. Click each ring b

Draw ethane:1. Click the Solid Bond tool.2. In the document window, click-drag downward to create the first bond.3. Click the atom at the bottom of th

Drawing the Newman projectionIn this step, you draw the hollow circle that is particular to Newman projections.1. Click the Orbital tool, and select t

Note: If chemical warnings are turned on, a red warning box appears when you overlay the structure, because thecarbon atoms overlay the C-C bond. To t