External

OIT (Lund): Organic Chemistry with a Biological Emphasis (Soderberg)

Chemistry

Author: Travis Lund
Publisher: Oregon Institute of Technology
Source: LibreTexts
Language: EN
Category: Basic Sciences

Read online Download PDF (open licence)

Contents· 198 sections

01: Introduction to Organic Structure and Bonding I
1.00: Prelude to Atoms Electron Configurations and Lewis Structures
1.01: Drawing Organic Structures
1.02: Functional groups and organic nomenclature
1.03: Structures of some important biomolecules
1.3.00: Introduction to Amino Acids and Proteins
1.3.01: Introduction to carbohydrate structure
1.3.02: Introduction to Lipid Structure
1.3.03: Introduction to nucleic acid (DNA and RNA) structure
1.04: Solutions to Chapter 1 Exercises
1.E: Problems for Chapter 1
1.00: Solutions to selected Chapter 1 problems
02: Introduction to Organic Structure and Bonding II
2.00: Prelude to Organic Structure and Bonding II
2.01: Valence Bond Theory
2.02: Molecular orbital theory- conjugation and aromaticity
2.03: Resonance
2.04: Non-covalent interactions
2.05: Physical properties of organic compounds
2.06: Solutions to Chapter 2 exercises
2.P: Problems for Chapter 2
1.00: Solutions to selected chapter 2 problems
03: Conformations and Stereochemistry
3.00: Prelude to Conformations and Stereochemistry
3.01: Conformations of open-chain organic molecules
3.02: Conformations of cyclic organic molecules
3.03: Chirality and stereoisomers
3.04: Naming chiral centers- the R and S system
3.05: Optical Activity
3.06: Compounds with multiple chiral centers
3.07: Meso Compounds
3.08: Fischer and Haworth projections
3.09: Stereochemistry of alkenes
3.10: Stereochemistry in biology and medicine
3.11: Prochirality
3.12: Solutions to Chapter 3 exercises
3.P: Problems for Chapter 3
04: Structure Determination I- UV-Vis and Infrared Spectroscopy Mass Spectrometry
4.00: Prelude to Structure Determination I
4.01: Introduction to molecular spectroscopy
4.02: Mass Spectrometry
4.03: Infrared spectroscopy
4.04: Ultraviolet and visible spectroscopy
4.P: Problems for Chapter 4
05: Structure Determination II - Nuclear Magnetic Resonance Spectroscopy
5.00: Prelude to Structure Determination
5.01: The Origin of the NMR Signal
5.02: Chemical Equivalence
5.03: The 1H-NMR experiment
5.04: The Basis for Differences in Chemical Shift
5.05: Spin-Spin Coupling
5.06: 13C-NMR Spectroscopy
5.07: Solving Unknown Structures
5.08: Complex Coupling in Proton Spectra
5.09: Other Applications of NMR
5.E: Structure Determination (Exercises)
5.S: Structure Determination (Summary)
06: Overview of Organic Reactivity
6.00: Prelude to Organic Reactivity
6.01: A First Look at Some Organic Reaction Mechanism
6.02: A Quick Review of Thermodynamics and Kinetics
6.03: Catalysis
6.04: Comparing Biological Reactions to Laboratory Reactions
6.E: Overview of Organic Reactivity (Exercises)
6.S: Overview of Organic Reactivity (Summary)
07: Acid-base Reactions
7.00: Prelude to Acid-base Reactions
7.01: Overview of Acid-Base Reactions
7.02: The Acidity Constant
7.03: Structural Effects on Acidity and Basicity
7.04: Acid-base Properties of Phenols
7.05: Acid-base properties of nitrogen-containing functional groups
7.06: Carbon Acids
7.07: Polyprotic Acids
7.08: Effects of enzyme microenvironment on acidity and basicity
7.E: Acid-base Reactions (Exercises)
7.S: Acid-base Reactions (Summary)
08: Nucleophilic Substitution Reactions
8.00: Prelude to Nucleophilic Substitution Reactions
8.01: Two Mechanistic Models for Nucleophilic Substitution
8.02: Nucleophiles
8.03: Electrophiles
8.04: Leaving Groups
8.05: Regiochemistry of SN1 Reactions with Allylic Electrophiles
8.06: SN1 or SN2 Predicting the Mechanism
8.07: Biological Nucleophilic Substitution Reactions
8.08: Nucleophilic substitution in the Lab
8.E: Nucleophilic Substitution Reactions (Exercises)
8.S: Nucleophilic Substitution Reactions (Summary)
09: Phosphate Transfer Reactions
9.00: Prelude to Phosphate Transfer Reactions
9.01: Overview of Phosphate Groups
9.02: Phosphate Transfer Reactions - An Overview
9.03: ATP The Principal Phosphate Group Donor
9.04: Phosphorylation of Alcohols
9.05: Phosphorylation of Carboxylates
9.06: Hydrolysis of Organic Phosphates
9.07: Phosphate Diesters in DNA and RNA
9.08: The Organic Chemistry of Genetic Engineering
9.09: NMR of phosphorylated compounds
9.E: Phosphate Transfer Reactions (Exercise)
9.S: Phosphate Transfer Reactions (Summary)
10: Nucleophilic Carbonyl Addition Reactions
10.00: Prelude to Nucleophilic Carbonyl Addition Reactions
10.01: Nucleophilic Additions to Aldehydes and Ketones - An Overview
10.02: Hemiacetals Hemiketals and Hydrates
10.03: Acetals and Ketals
10.04: N-glycosidic Bonds
10.05: Imines
10.06: A Look Ahead - Addition of Carbon and Hydride Nucleophiles to Carbonyls
10.E: Nucleophilic Carbonyl Addition Reactions (Exercises)
10.S: Nucleophilic Carbonyl Addition Reactions (Summary)
11: Nucleophilic Acyl Substitution Reactions
11.00: Prelude to Nucleophilic Acyl Substitution Reactions
11.01: Carboxylic Acid Derivatives
11.02: The Nucleophilic Acyl Substitution Mechanism
11.03: Acyl Phosphates
11.04: The Relative Reactivity of Carboxylic Acid Derivatives
11.05: Acyl Phosphates
11.06: Hydrolysis of Thioesters Esters and Amides
11.07: Protein Synthesis on the Ribosome
11.08: Nucleophilic Substitution at Activated Amides and Carbamides
11.09: Nucleophilic Acyl Substitution Reactions in the Laboratory
11.10: A Look Ahead - Acyl Substitution Reactions with a Carbanion or Hydride Ion Nucleophile
11.E: Nucleophilic Acyl Substitution Reactions (Exercises)
11.S: Nucleophilic Acyl Substitution Reactions (Summary)
12: Reactions at the -Carbon Part I
12.00: Prelude to Reactions at the -carbon part I
12.01: Review of Acidity at the -Carbon
12.02: Isomerization at the -Carbon
12.03: Aldol Addition
12.04: -Carbon Reactions in the Synthesis Lab - Kinetic vs. Thermodynamic Alkylation Products
12.05: Nitrosation
12.E: Reactions at the -Carbon Part I (Exercises)
12.S: Reactions at the -Carbon Part I (Summary)
13: Reactions at the -Carbon Part II
13.00: Prelude to Reactions at the -Carbon Part II
13.01: Decarboxylation
13.02: An Overview of Fatty Acid Metabolism
13.03: Claisen Condensation
13.04: Conjugate Addition and Elimination
13.05: Carboxylation
13.E: Reactions at the -Carbon Part II (Exercises)
13.S: Reactions at the -Carbon Part II (Summary)
14: Electrophilic Reactions
14.00: Prelude to Electrophilic Reactions
14.01: Electrophilic Addition to Alkenes
14.02: Elimination by the E1 Mechanism
14.03: Electrophilic Isomerization
14.04: Electrophilic Substitution
14.05: Carbocation Rearrangements
14.6: Cycloaddition reactions
14.E: Electrophilic Reactions (Exercises)
14.S: Electrophilic Reactions (Summary)
15: Oxidation and Reduction Reactions
15.00: Prelude to Oxidation and Reduction Reactions
15.01: Oxidation and Reduction of Organic Compounds - An Overview
15.02: Oxidation and Reduction in the Context of Metabolism
15.03: Hydrogenation of Carbonyl and Imine Groups
15.04: Hydrogenation of alkenes and Dehydrogenation of Alkanes
15.05: Monitoring Hydrogenation and Dehydrogenation Reactions by UV Spectroscopy
15.06: Redox Reactions of Thiols and Disulfides
15.07: Flavin-Dependent Monooxygenase Reactions - Hydroxylation Epoxidation and the Baeyer-Villiger Oxidation
15.08: Hydrogen Peroxide is a Harmful - Reactive Oxygen Species
15.E: Oxidation and Reduction Reactions (Exercises)
15.S: Oxidation and Reduction Reactions (Summary)
16: Radical Reactions
16.00: Prelude to Radical Reactions
16.01: Overview of Single-Electron Reactions and Free Radicals
16.02: Radical Chain Reactions
16.03: Useful Polymers formed by Radical Chain Reactions
16.04: Destruction of the Ozone Layer by a Radical Chain Reaction
16.05: Oxidative Damage to cells Vitamin C and Scurvy
16.06: Flavin as a One-Electron Carrier
16.E: Radical Reactions (Exercises)
17: The Organic Chemistry of Vitamins
17.00: Prelude to the Organic Chemistry of Vitamins
17.01: Pyridoxal Phosphate (Vitamin B6)
17.02: Thiamine Diphosphate (Vitamin B1)
17.03: Thiamine Diphosphate Lipoamide and the Pyruvate Dehydrogenase Reaction
17.04: Folate
17.E: The Oganic Chemistry of Vitamins (Exercises)
17.S: The Oganic Chemistry of Vitamins (Summary)
Appendix I: Index of enzymatic reactions by pathway
Amino acid biosynthesis
Amino acid catabolism
Citric Acid Cycle
Fatty acid metabolism
Glycolysis Gluconeogenesis Fermentation
Isoprenoid biosynthesis
Nucleoside biosynthesis
Nucleotide catabolism
Pentose Phosphate Pathway Calvin Cycle
Appendix: Review of laboratory synthesis reactions
Full Index
Full Table of Contents
Retrosynthetic analysis and metabolic pathway prediction
Pathway prediction practice problems