The Organic Chem Lab Survival Manual

Chapter 1 Safety First, Last, and Always 1 Accidents Will Not Happen 5 Disposing of Waste 5 Mixed Waste 7 Material Safety Data Sheet (Msds) 8 Green Chemistry and Planning an Organic Synthesis 8 An iBag for Your iThing 10 Exercises 10 Chapter 2 Keeping a Notebook 11 A Technique Experiment 12 Notebook Notes 12 A Synthesis Experiment 16 Notebook Notes 17 The Six Maybe Seven Elements in Your Experimental Write-Up 20 The Acid Test 21 Notebook Mortal Sin 21 Calculation of Percent Yield (Not Yeild!) 22 Estimation Is Your Friend 24 Exercises 24 Chapter 3 Mining Your Own Data 25 Google and the Wiki 26 The Terphenyl Anomaly 29 Exercises 29 Chapter 4 Jointware 30 Stoppers With Only One Number 31 Another Episode of Love of Laboratory 33 Hall of Blunders and Things Not Quite Right 34 Round-Bottom Flasks 34 Columns and Condensers 34 The Adapter with Lots of Names 35 Forgetting the Glass 36 Inserting Adapter Upside Down 36 Inserting Adapter Upside Down sans Glass 37 The O-Ring and Cap Branch Out 38 Greasing the Joints 38 To Grease or Not to Grease 38 Preparation of the Joints 39 Into the Grease Pit 39 Storing Stuff and Sticking Stoppers 40 Corking a Vessel 40 Chapter 5 Microscale Jointware 41 Microscale: A Few Words 41 Uh-Oh Rings 42 The O-Ring Cap Seal 42 Skinny Apparatus 42 Not-So-Skinny Apparatus 43 Sizing Up the Situation 43 Why I Don’t Really Know How Vacuum-Tight These Seals Are 44 The Comical Vial (That’s Conical!) 45 The Conical Vial as Vial 45 Packaging Oops 46 Tare to the Analytical Balance 46 The Electronic Analytical Balance 46 Heating These Vials 47 The Microscale Drying Tube 48 Gas Collection Apparatus 48 Generating the Gas 49 Isolating the Product 51 Chapter 6 Other Interesting Equipment 52 Funnels, and Beakers, and Flasks—Oh My! 53 The Flexible Double-Ended Stainless Steel Spatula 54 Transferring a Powdered Solid with the Spatula 55 Chapter 7 Pipet Tips 56 Pre-Preparing Pasteur Pipets 56 Calibration 56 Operation 57 Amelioration 58 Pipet Cutting 58 Pipet Filtering—Liquids 60 Pipet Filtering—Solids 61 Chapter 8 Syringes, Needles, and Septa 63 The Rubber Septum 65 Chapter 9 Clean and Dry 66 Drying Your Glassware When You Don’t Need To 67 Drying Your Glassware When You Do Need To 67 Chapter 10 Drying Agents 68 Typical Drying Agents 68 Using a Drying Agent 69 Following Directions and Losing Product Anyway 70 Drying Agents: Microscale 70 Drying in Stages: The Capacity and Efficiency of Drying Agents 70 Exercises 71 Chapter 11 On Products 72 Solid Product Problems 72 Liquid Product Problems 72 The Sample Vial 73 Hold It! Don’t Touch That Vial 73 Chapter 12 The Melting-Point Experiment 74 Sample Preparation 75 Loading the Melting-Point Tube 75 Closing Off Melting-Point Tubes 76 Melting-Point Hints 77 The Mel-Temp Apparatus 77 Operation of the Mel-Temp Apparatus 79 The SRS DigiMelt 80 The Fisher-Johns Apparatus 82 Operation of the Fisher-Johns Apparatus 83 The Thomas-Hoover Apparatus 84 Operation of the Thomas-Hoover Apparatus 85 Using the Thiele Tube 88 Cleaning the Tube 89 Getting the Sample Ready 89 Dunking the Melting-Point Tube 90 Heating the Sample 91 Exercises 91 Chapter 13 Recrystallization 92 Finding a Good Solvent 93 General Guidelines for a Recrystallization 94 My Product Disappeared 95 Gravity Filtration 95 The Buchner Funnel and Filter Flask 97 Just a Note 100 The Hirsch Funnel and Friends 101 Activated Charcoal 101 The Water Aspirator: A Vacuum Source 102 The Water Trap 102 Working with a Mixed-Solvent System—The Good Part 103 The Ethanol—Water System 103 A Mixed-Solvent System—The Bad Part 104 Salting Out 105 World-Famous Fan-Folded Fluted Paper 105 Exercises 107 Chapter 14 Recrystallization: Microscale 108 Isolating the Crystals 109 Craig Tube Filtration 109 Centrifuging the Craig Tube 113 Getting the Crystals Out 113 Chapter 15 Extraction and Washing 114 Never-Ever Land 115 Starting an Extraction 115 Dutch Uncle Advice 116 The Separatory Funnel 117 The Stopper 117 The Teflon Stopcock 118 How to Extract and Wash What 119 The Road to Recovery—Back-Extraction 120 A Sample Extraction 121 Performing an Extraction or Washing 123 Extraction Hints 124 Theory of Extraction 125 Exercises 127 Chapter 16 Extraction and Washing: Microscale 128 Mixing 128 Separation: Removing the Bottom Layer 128 Separation: Removing the Top Layer 129 Separation: Removing Both Layers 130 Chapter 17 Sources of Heat 131 Boiling Stones 131 The Steam Bath 132 The Bunsen Burner 133 Burner Hints 134 The Heating Mantle 135 Proportional Heaters and Stepless Controllers 137 Exercise 139 Chapter 18 Clamps and Clamping 140 Clamping a Distillation Setup 142 Clipping a Distillation Setup 147 CHAPTER 19 Distillation 150 Distillation Notes 151 Class 1: Simple Distillation 151 Sources of Heat 151 The Three-Way Adapter 152 The Distilling Flask 152 The Thermometer Adapter 153 The Ubiquitous Clamp 153 The Thermometer 154 The Condenser 154 The Vacuum Adapter 154 The Receiving Flask 154 The Ice Bath 154 The Distillation Example 155 The Distillation Mistake 155 Class 2: Vacuum Distillation 156 Pressure Measurement 157 Manometer Hints 158 Leaks 158 Pressure and Temperature Corrections 159 Vacuum Distillation Notes 162 Class 3: Fractional Distillation 164 How This Works 164 Fractional Distillation Notes 167 Azeotropes 168 Class 4: Steam Distillation 168 External Steam Distillation 168 Internal Steam Distillation 170 Steam Distillation Notes 171 Simulated Bulb-to-Bulb Distillation: Fakelrohr 172 Exercises 173 Chapter 20 Microscale Distillation 175 Like the Big Guy 175 Class 1: Simple Distillation 175 Class 2: Vacuum Distillation 175 Class 3: Fractional Distillation 176 Class 4: Steam Distillation 176 Microscale Distillation II: The Hickman Still 176 The Hickman Still Setup 176 Hickman Still Heating 177 Recovering Your Product 178 A Port in a Storm 178 Chapter 21 The Rotary Evaporator 179 Exercises 182 Chapter 22 Reflux and Addition 183 Standard Reflux 183 A Dry Reflux 185 Addition and Reflux 186 Funnel Fun 186 How to Set Up 188 Exercise 189 Chapter 23 Reflux: Microscale 190 Addition and Reflux: Microscale 190 Chapter 24 Sublimation 192 Chapter 25 Microscale Boiling Point 195 Microscale Boiling Point 195 Ultramicroscale Boiling Point 197 Chapter 26 Chromatography: Some Generalities 199 Adsorbents 199 Separation or Development 200 The Eluatropic Series 200 Chapter 27 Thin-Layer Chromatography: TLC 202 We Don’t Make Our Own TLC Plates Any More, But… 202 Pre-prepared TLC Plates 203 The Plate Spotter 203 Spotting the Plates 204 Developing a Plate 205 Visualization 206 Interpretation 207 Multiple Spotting 209 Cospotting 210 Other TLC Problems 210 Preparative TLC 212 Exercises 212 Chapter 28 Wet-Column Chromatography 214 Preparing the Column 214 Compounds on the Column 216 Visualization and Collection 217 Wet-Column Chromatography: Microscale 218 Flash Chromatography 219 Microscale Flash Chromatography 220 Exercises 221 Chapter 29 Refractometry 222 The Abbé Refractometer 223 Before Using the Abbé Refractometer: A Little Practice 224 Using the Abbé Refractometer 225 Refractometry Hints 226 Chapter 30 Gas Chromatography 227 The Mobile Phase: Gas 227 GC Sample Preparation 228 GC Sample Introduction 228 Sample in the Column 230 Sample at the Detector 231 Electronic Interlude 232 Sample on the Computer 233 Parameters, Parameters 234 Gas Flow Rate 234 Temperature 234 Exercises 235 Chapter 31 HP Liquid Chromatography 236 The Mobile Phase: Liquid 237 A Bubble Trap 238 The Pump and Pulse Dampener Module 239 HPLC Sample Preparation 239 HPLC Sample Introduction 241 Sample in the Column 242 Sample at the Detector 242 Sample on the Computer 243 Parameters, Parameters 243 Eluent Flow Rate 244 Temperature 244 Eluent Composition 244 Exercises 244 Chapter 32 Infrared Spectroscopy (and a bit of uv-vis, too ) 245 Molecules As Balls On Springs 245 Ah, Quantum Mechanics 247 The Dissonant Oscillator 247 But Wait! There’s More 248 More Complicated Molecules 248 Correlation Tables to the Rescue 250 Troughs and Reciprocal Centimeters 254 Some Functional Group Analysis 254 A Systematic Interpretation 256 Infrared Sample Preparation 258 Liquid Samples 258 Solid Samples 259 Running the Spectrum 262 Interpreting IR Spectra—Finishing Touches 263 The Fourier Transform Infrared (FTIR) 264 The Optical System 264 A Reflectance Attachment: Something to Think About 268 And UV-VIS Too! 268 Electrons Get to Jump 268 Instrument Configuration 269 Source 270 Sample (and Reference) Cells 270 Solvents 270 Exercises 271 Chapter 32 On The Dual -Beam Infra-Red Instrument (ONLINE)1 The Perkin-Elmer 710B IR 2 Using the Perkin-Elmer 710B 4 The 100% Control: An Important Aside 5 Calibration of the Spectrum 6 IR Spectra: The Finishing Touches 7 Chapter 33 Nuclear Magnetic Resonance 272 Nuclei Have Spin, Too 272 The Magnetic Catch 273 Everybody Line Up, Flip, and Relax 273 A More Sensitive Census 274 The Chemical Shift 274 T For One and Two 275 Be It Better Resolved... 275 Incredibly Basic Ft-Nmr 276 Nmr Sample Preparation 276 Some Nmr Terms and Interpretations 280 The Chemical Shift and Tms Zero 280 Integration and Labeling 282 Threaded Interpretations: Spectrum #1 (t-butyl alcohol) 283 Threaded Interpretations: Spectrum #2 (Toluene) and Spectrum #3 (p-Dichlorobenzene) 283 Threaded Interpretations: Spectrum #4 (Ethylbenzene) and Spectrum #5 (A Double Resonance Experiment) 285 Use a Correlation Chart 288 Exercises 290 Chapter 34 Theory of Distillation (Online) 1 Class 1: Simple Distillation 1 Clausius and Clapeyron 3 Class 3: Fractional Distillation 5 A Hint from Dalton 5 Dalton and Raoult 5 A Little Algebra 6 Clausius and Clapeyron Meet Dalton and Raoult 7 Dalton Again 8 What Does It All Mean? 10 Reality Intrudes I: Changing Composition 12 Reality Intrudes II: Nonequilibrium Conditions 12 Reality Intrudes III: Azeotropes 13 Other Deviations 16 Class 4: Steam Distillation 16 Index 291