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Bond user manual User's Guide (108 pages)


Brand: Bond | Category: Barbecues & grills | Size: 3.42 MB |

 

Table of contents

User’s Guide

1

Table of Contents

5

1. WebMO Introduction

9

C. Quickstart Tutorial

10

Job Manager

11

Build Molecule

11

Choose Computational Engine

13

Configure Job Options

14

View Job

16

D. WebMO Pro

18

2. Building Molecules

19

B. WebMO Editor

21

C. Build Tool

24

D. View Tool

25

E. Adjust Tool

26

F. Cleaning-Up Structures

28

H. Working With Selections

30

I. Z-Matrix Editor (Pro)

31

J. Preferences

33

K. Help

33

3. Running Jobs

34

B. Calculation Types

35

Geometry Optimization

36

UV-Vis Spectrum

36

Coordinate Scan (Pro)

37

IRC Calculation

37

Saddle Calculation

37

Molecular Orbitals (Pro)

37

C. Gamess

38

D. Gaussian

40

E. Mopac

42

F. Failed Calculations

44

4. Visualizing Results

46

B. Calculated Quantities

47

D. Normal Modes

49

F. Coordinate Scans (Pro)

52

G. MOViewer (Pro)

54

H. Export Molecule

58

J. Output Files (Pro)

60

A. Job Manager

61

B. Folders (Pro)

62

C. Download

64

D. Import

64

E. Rename

65

F. Delete

65

G. Edit Profile

66

6. WebMO Administration

67

B. User Manager

68

C. Job Manager

69

D. System Manager

70

E. Version Manager

71

F. Fragment Manager

72

H. Interface Manager

74

J. Customization

76

Calculation Templates

77

Basis Set Choices

77

B. Input and Output Files

79

C. Molecular Properties

79

D. Geometry Optimizations

81

E. Frequency Calculations

84

18. Thermochemistry of CH

86

CHO → CO + CH

86

in the gas phase

86

F. Model Chemistry

87

G. Partial Charge

88

Substitution Reactions

90

O Inversion (Pro)

91

Formaldehyde

96

Spreadsheet button to

98

7. Exercises

101

8. Appendices

102

$ cd WebMO.install

104

$ perl upgrade.pl

104

Bond user manual User's Guide (410 pages)


Brand: Bond | Category: Barbecues & grills | Size: 5.66 MB |

 

Table of contents

ChemBioDraw 13.0 User Guide

1

Table of Contents

2

Table of Contents ii

3

Table of Contents iii

4

Table of Contents iv

5

Table of Contents v

6

What’s new

7

What’s new vii

8

What’s new viii

9

Introduction

10

Troubleshooting

11

Performance

11

Applications and drivers

12

Getting started

13

Toolbars

14

Documents

15

Deleting a keyword

16

Discarding changes

16

Undo, redo, and repeat

16

Saving documents

16

Autosave

17

Default file format

17

Dropbox interface

17

Signing into Dropbox

17

Upload files

18

Download files

19

Basic drawings

21

Quadruple bonds

22

Dative bonds

22

Wedged bonds

22

Changing bonds

22

Changing bond types

23

Changing double bonds

23

Aligning double bonds

23

Moving atoms

23

Reducing ring size

24

Bond crossing

24

Fixed bonds

24

Drawing fixed length bond

24

Drawing fixed angle bonds

24

Changing fixed values

25

Periodic table

25

Captions

26

Formatting

27

Coloring text

28

Caption width

29

About fonts

29

Character map

29

Using hotkeys

30

Nicknames

31

Using nicknames

31

Applying nicknames

31

Expanding nicknames

32

Annotations

33

Drawing rings

35

Spiro and sprout rings

36

Cyclohexane chair rings

36

Aromatic structures

37

Delocalized rings

37

Resonance structures

37

Changing chain direction

38

Fixed length

38

Fixed angle

38

Adding chains to structures

38

Specifying chain length

38

Arrow heads

39

Arrow types

39

Hollow arrows

40

Connecting arrows

41

Curved arrows

42

Colored arrows

42

Coloring block arrows

42

Drawing elements

43

Circles and ovals

43

Brackets

44

Freehand shapes

46

Selecting objects

47

The lasso tool

47

The marquee tool

47

Selecting entire structures

48

Selecting objects by clicking

48

Selecting multiple objects

48

Deselecting all objects

48

Deselecting one object

48

Resizing objects

49

Rotating objects

50

Moving the center of rotation

50

Moving objects

51

Copying objects

51

The info window

52

Mirror images

52

Deleting objects

53

Joining structures

53

Grouping objects

53

Ungrouping objects

54

Scaling objects

54

Centering objects

55

Aligning objects

55

Distributing objects

55

Clean Up Structure

56

Check structure

57

Chemical warnings

57

Warning preferences

58

Warning Description

59

Linear Atom

59

BioDraw templates

60

Advanced BioDraw

61

Anatomy templates

61

Bio Instruments

62

Microorganisms

62

Organelles

62

Customizable objects

63

Membrane line

64

Membrane arc

64

Helix proteins

64

DNA molecules

65

Coloring residues

65

Ribosomes

66

Plasmid maps

66

Creating a plasmid map

66

Adding regions

67

Adding markers

67

Moving markers

67

Resizing regions

67

Enhancing the drawing

68

Drawing biopolymers

69

Biopolymer editor

70

Protecting groups

71

Pasting sequences

72

Paste text strings

73

Expanding sequences

74

Contracting labels

74

Modifying sequence residues

74

Removing residues

76

Replacing residues

77

Adding residues

77

Hybrid biopolymers

78

IUPAC codes

79

Branched peptides

82

Disulfide bridges

83

Lactam bridges

84

Tutorials

86

Tutorial 2: Drawing rings

87

The structure is complete

89

Drawing the Newman projection

98

Tutorial 6: Stereochemistry

99

Adding atom labels

100

Tutorial 7: Templates

102

Advanced drawing techniques

104

Creating labels

105

Expanding labels

106

Multiple atoms

106

Attachment points

108

Atom numbering

110

Structure perspective

111

Mass fragmentation

112

Drawing reactions

113

Drawing an arrow

114

Drawing the product

114

Clean Up Reaction

116

The reaction interpreter

117

Electron and radical pushing

118

Stoichiometry grid

119

Templates

122

Adding a template

123

Annotating a template

123

Customizing templates

123

Modifying a template

123

Defining nicknames

124

Nicknames and atom labels

126

Deleting nicknames

126

Troubleshooting nicknames

126

ChemScript

127

Struct=Name

129

Non-ringed structures

130

Ringed structures

130

Fused ring systems

131

Bridged fused ring systems

131

Polymers

132

Other compounds

132

Unsupported structures

132

Name>Struct

133

Converting clipboard names

134

Converting captions

134

Supported structures

134

ChemBioDraw 13.0

135

Chemistry features

136

ChemBioFinder hotlink

137

Stereochemistry

138

Hiding indicators

139

Formatting indicators

139

Removing indicators

139

Positioning indicators

139

Relative stereochemistry

140

Chemical annotations

141

S-orbitals

142

Sigma orbitals

142

Single lobe orbitals

142

Hybrid orbitals

142

Chemical symbols

143

H–dot and H–dash

143

Lone pair/diradical

143

Charge symbols

144

Chemical properties

145

Boiling point

146

Critical pressure

147

Critical temperature

147

Critical volume

147

CLogP/CMR

147

Gibbs free energy

147

Heat of formation

148

Henry’s law constant

148

Melting point

148

ChemBioFinder properties

151

Viewing chemical properties

151

3D viewing

152

In the document window

153

In ChemBio3D preview

153

Resizing spots

156

Custom spots

156

Gel electrophoresis tool

156

Parameters in ChemNMR

159

Spectrometer frequency

159

NMR shifts

160

Modifying NMR frequency

160

Viewing spectral assignments

161

Removing spectral assignments

161

Custom shift correction data

161

NMR data format

161

Updating the ChemNMR database

162

Restoring default NMR data

162

Example supplementary data

162

ChemNMR limitations

164

NMR references

165

ChemDraw/Excel

166

Importing hit lists

167

Exporting tables

167

Synchronizing tables

168

Adding structures

169

Searching

170

Opening a database

171

Normal searches

171

Similarity searches

171

R-Group analysis

172

Working with structures

172

Using the clipboard

173

ChemDraw/Excel functions

174

Chemical name

175

Chemical composition

175

Chemical formula

175

Molecular weight

176

Exact mass

176

Number of atoms

176

SMILES string

177

Formal charge

177

Melting/freezing point

178

Vapor pressure

179

Ideal gas thermal capacity

180

Molar refractivity

181

Water solubility

181

Balaban index

183

Cluster count

183

Topological index

183

Number of rotatable bonds

184

Polar surface area

184

Shape attribute

184

Shape coefficient

184

Sum of degrees

185

Sum of valence degrees

185

Topological diameter

185

Total connectivity

185

Total valence connectivity

185

Wiener index

186

Lipinski rule of five

187

Ghose modifications

187

Henry’s Law constant

192

Total Valence Connectivity

196

CombiChem

197

Entering a generic reaction

198

Creating reactant worksheets

199

Searching for reactants

199

Creating an experiment

200

Experiment worksheets

201

Configuring plates

202

Assigning plates

202

Browsing plates

203

Viewing related structures

203

ChemBioFinder/Office

204

Editing the hitlist

205

ChemDraw for Excel

205

Query structures

206

Generic nickname hotkeys

207

Defining generic nicknames

207

Atom properties

209

Query indicators

210

Positioning query indicators

211

Hiding a query indicators

211

Removing atom properties

211

Atom property options

211

Substituents

211

Implicit hydrogens

213

Ring bond count

213

Unsaturation

214

Reaction change

214

Reaction stereo

214

Free sites

215

Translation

216

Bond properties

217

Viewing bond properties

218

Removing bond properties

218

Bond property options

219

Bond types

219

Topology

219

Element lists

220

Setting bracket properties

222

Bracket usage

222

Structure-based polymers

222

Source-based polymers

223

Multiple groups

224

Link nodes

225

Alternative groups

226

Defining alternative groups

227

Multiple attachment points

229

Attachment point numbering

230

Hiding rank indicators

230

R-group reaction queries

231

Anonymous alternative groups

232

Expand generic structures

233

R-Logic queries

234

Atom-to-Atom mapping

235

Displaying and printing

236

Automatic mapping

236

Manual mapping

236

Stereochemical symbols

238

3D properties

239

Export compatibility

240

Sharing information

244

Pasting SMILES

245

Creating SLN strings

245

Creating InChI™ strings

245

Creating InChIKey strings

245

Transferring objects

246

Embedding objects

247

Exporting

247

Importing

248

ISIS™ compatibility

249

Attached data

249

Modifying attached data

249

File formats

250

Transferring across platforms

252

Preferences and settings

253

Default document location

254

Default open file format

254

Setting the default tool

254

Highlight box tolerance

254

The ChemDraw items folder

255

Default styles

255

Saving customized styles

255

Setting preferences

256

Windows XP

258

Windows Vista

258

Customizing toolbars

268

Document and object settings

268

Drawing settings

269

Configuring documents

270

Configuring objects

271

Analysis and properties

271

Formatting captions

272

Style indicators

273

Specifying line spacing

273

Aligning text

273

Automatic alignment

274

Changing the default format

275

Biopolymer settings

276

Customizing hotkeys

277

{description}”/>

278

Working with color

279

Color by element

280

The color palette

281

Customizing colors

281

Document settings

282

Adv. Synth Catal

283

J.Chin. Chem. Soc

283

J. Mol. Mod. (1 column)

284

New Document

284

New Slide

284

Phytomedicine

285

Science of Synthesis

286

Synthesis, Synlett

286

Verlag Helvetica Chimica Acta

287

Wiley Document

287

Page layout

288

Headers and footers

289

Printing

290

Saving page setup settings

291

35mm slide boundary guides

291

Viewing drawings

292

The crosshairs

293

Moving the crosshair

293

Positioning objects

293

Creating a table

293

Resizing tables

294

Customizing borders

294

Using the text tool

295

Creating a new row

296

Inserting a new row

296

Chemical interpretation

297

Bond conventions

298

Atom labels

299

Chemically significant text

301

Isotopes and elements

302

Radicals

303

H-Dot/H-Dash

303

Complexes

303

Multi-center attachments

304

Cahn-Ingold-Prelog

305

Stereochemical indicators

305

Stereochemical flags

305

Polymer representations

307

References

307

Analysis messages

307

Property calculations

310

The ChemBio3D MOPAC interface

312

Other properties

312

Miscellaneous properties

312

Shortcuts and hotkeys

313

Bond hotkeys

314

Function hotkeys

315

Shortcuts

316

Structure

318

Registering online

321

User’s guide

321

Technical support

321

ACX structures and numbers

322

ACX structures

322

ACX numbers

322

ChemBio3D ActiveX Control

322

SciStore.com

322

PerkinElmer Informatics

323

Using the ChemOffice SDK

323

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Bond user manual User's Guide (77 pages)


Brand: Bond | Category: Barbecues & grills | Size: 0.55 MB |

 

Table of contents

ACD/ChemSketch

1

Table of Contents

3

1. Introduction

6

1.3 What’s New in 4.5

7

1.4 About this Guide

8

1.5 Useful Definitions

8

1.6 Demo Versions

9

1.7 Freeware Version

9

1.8 For More Information…

9

1.8.1 How to Get Hold of Us

10

2. Basics of ACD/ChemSketch

11

2.3 Structure and Draw Mode

12

2.3.2 Draw Mode Screen

13

3. Drawing Simple Structures

15

3.2.3 Using Mouse Drag

17

3.2.6 Editing Atom Labels

18

3.3 Flipping Structures

20

3.5 Clearing the Screen

21

4.1 Objectives

22

4.3 Using Ring Structures

23

4.5 Replacing Atoms

24

4.8 Changing Atom Properties

28

5.1 Objectives

29

5.2 2D Optimization

29

5.3 3D Optimization

31

6.1 Objectives

39

6.2 Overview

39

6.3 Instant Template Tool

40

Click + Shift

44

6.5.1.2 Adding the bases

45

6.7 Defining a User Template

47

6.7.1 The Template.cfg File

48

6.7.2 Available Templates

48

7.1 Objectives

49

7.6.1 Drawing the lipid

60

7.7 Creating a Poster

62

11. Attach the pages

63

8.1 Overview

64

8.3.1 Molar Volume, MV

66

8.3.7 Dielectric Constant

68

(Permittivity)

68

8.3.8 Polarizability

68

9. Special Function Keys

72

9.2 Dictionary

73

10. Goodies

74

Button Function How to use

75

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