Subject | Description |
---|---|
Advanced Organic Chemistry | bonding, organic reactions, reactivity |
Computational Chemistry | tutorials on how to use Gaussian |
NMR Spectroscopy | 1D and 2D methods, coupling constants, stereochemistry, pulse sequences |
Experimental Organic Chemistry | lab procedures for advanced undergraduates |
These course notes are a reinterpretation of the Chem 206 course notes created by Professor David A. Evans. If you would like to use them, please contact me. I can provide the corresponding ChemDraw files on request.
Energy and Reactivity
free energy surface, Hammond postulate, Curtin–Hammett principle, Mayr scales, reactivity-selectivity
Bonding
multielectron atoms, LCAO method, natural bond orbitals, resonance, anomeric effect, Bent’s rule
Pericyclic Reactions
π-bonding, aromaticity, Dewar–Zimmerman, electrocyclizations, cycloadditions, sigmatropic shifts
Acyclic Conformational Analysis
gauche and syn-pentane interactions, olefins, allylic strain, Thorpe–Ingold
Acyclic Stereocontrol
hydroboration, directed reactions, epoxidation, Burgi–Dunitz, Cram chelate, Felkin–Anh–Eisenstein
Aldol Reaction
Zimmerman–Traxler, enolate and aldehyde facial selectivity, double stereodifferentiating reactions
Aldol Reactions Cheat Sheet
the key diastereoselective reactions and their transition structures
Small Ring Conformational Analysis
types of strain, A values, Furst-Plattner, fused systems, oxocarbenium ions
Conformational Analysis of Macrocycles
medium and large rings, peripheral attack, transannular reactions; courtesy of Dr. Joe Wzorek
Computational Chemistry I
potential energy surface, optimization, basis sets, single point energies, accuracy
Computational Chemistry II
computed KIEs, Singleton method, distinguishing between mechanisms, solvation
Nucleophilic Substitution
endocyclic restriction, Baldwin’s rules, ion pairing, S_{N}1 vs S_{N}2
Acidity
measurement, gas vs. solution phase, hybridization, induction vs. resonance, solvation effects
Organolithium Aggregates
aggregates, enthalpy vs. entropy, HMPA and TMEDA, continuous variation, kinetics, optimizing reactions
Tetrahedral Intermediates
ester and acetal hydrolysis, linear free energy, direct observation, Weinreb amides
Hydrogen Bonding
donor-acceptor vs. electrostatic views, optimal geometry, charge and resonance asssistance, cooperativity
π-π Stacking and Cation-π Interactions
optimal geometries, electrostatics and dispersion, Hunter–Sanders/Houk–Wheeler models, catalysis
N-Heterocyclic Carbenes
bonding, Wanzlick equilibrium, benzoin reaction, Stetter reaction, asymmetric catalysis
First-Order Kinetics
rate laws, approach to equilibrium, two-step system, Michaelis–Menten system, “1+rate” laws
Applications of Kinetics
Halpern–Landis hydrogenation, reaction progress kinetic analysis, same vs. different excess
Rate Laws
elementary reactions, differential vs. integral methods, two-step system, catalytic rate laws
Linear Free Energy Relationships
Hammett equation, curvature, alternative references, Taft/Charton/Sterimol parameters, 2D LFERs
Kinetic Isotope Effects
zero-point energy, hybridization, geometry, Hammond postulate, tunnelling, heavy atom effects
Competitive KIEs
absolute rates vs. competition, inter- vs. intramolecular KIEs, competition equations
Rates and Temperature
Arrehnius vs. Eyring, data analysis, interpretation of enthalpy and entropy
This is a series of tutorials designed to cover the basics of performing routine calculations in Gaussian. The instructions are tailored for the Odyssey Cluster at Harvard University, but will mostly work for Gaussian in general.
Exercise 0: Odyssey Setup
accessing Odyssey, basic shell commands, transfering files, GaussView, vim
Exercise 1: Conformers of Pentane
drawing structures, running Gaussian jobs, extracting energies, thermochemistry
Exercise 2: Transition State for an SN2 Reaction
scanning bond lengths, minimum energy path, calculating barriers, solvation
Exercise 3: Choosing the Right Method: Benzene Dimer
single point energies, introduction to scripting, dispersion, counterpoise corrections
Exercise 4: Selectivity in a Diels-Alder Reaction
finding diastereomeric transition states, composite level single points, selectivity
Exercise 5: Conformational Analysis of Thiourea Catalysts
rapid optimization, conformational analysis with dispersion
Exercise 6: Water Dimer: Complete Basis Set Extrapolation
complete basis set extrapolation, additivity of energy corrections
Exercise 7: Molecular Properties
making pictures with CYLview, molecular orbitals, electrostatic potentials, point charges
These course notes were previously used to teach Chem 117 at Harvard University.
Introduction to NMR
1D spectra, chemical shift, integration, coupling, magnetic and chemical equivalence
The Chemical Shift
diamagnetic effects, carbon chemical shifts, spin-orbit coupling, hydrogen bonding
The Coupling Constant
energy diagrams, size of couplings, positive vs. negative values, second-order effects
1D NMR Techniques
heteronuclear NMR, isotope effects, NOE, vector model, relaxation, inversion recovery, CPMG
Data Acquisition and Processing
sample preparation, pulse-acquire, Ernst angle, quadrature, ADC and dynamic range, Nyquist theorem
Polarization Transfer
quantitative integration, selective population transfer, INEPT/DEPT, spectral editing/APT
Computational Methods
the PES, conformational searching, molecular mechanics, DFT methods, optimization
Chemical Exchange
exchange regimes, selective inversion, saturation transfer, spin-locking, Bloch equations
The Nuclear Overhauser Effect
transverse vs. longitudinal relaxation, mechanisms for relaxation, transient vs. steady state, NOE vs ROE
Experimental Methods
kinetics, no-D NMR, titration, composite and adibatic pulses, composite pulse decoupling
NMR: Relative and Configuration
acetonides, NOE/ROE, homonuclear decoupling, J-based methods, Mosher-type analysis, DFT strategies
Coupling Constant Practice
second-order coupling patterns (courtesy Dr. Andy Phillips), Hoye’s method practice
Fluorine Couplings in Carbon-13 Spectra
size of couplings, practice problems
2D NMR Methods
COSY/TOCSY, HSQC vs. HMQC, HMBC, phase-cycling vs. gradients, linear prediction
2D NMR Problem Solving
structural elucidation strategies, tabulating data, sample problems
NMR Practice: 2D Problems
1D and 2D spectra
NMR Practice: Naringenin
1D and 2D spectra
2D NMR Solutions
detailed solutions to 2D NMR problems
Caveman Guide to NMR Experiments
for Varian/Agilent systems; courtesy of Dr. Brian Sparling
Spectral Reference Guide
frequently used spectral reference tables; courtesy of Dr. Brian Sparling
These lab experiments have been used in the past for Chem 135 at Harvard University. If you would like to use them, please contact me. I thank Dr. Andreas Roetheli for helping me to develop these laboratory procedures.
Spectroscopy Primer
introduction to UV-vis, IR, NMR, and mass spectrometry
Experiment 1: 9-BBN
synthesis of 9-BBN and hydroboration of 1-decene
Experiment 2: Cross-Coupling
preparation of Buchwald pre-catalyst and Suzuki cross-coupling
Experiment 3: Auxiliary Alkylation
Myers pseudoephenamine alkylation and cleavage
Experiment 4: Dess–Martin Periodinane
preparation of DMP and Horner–Wadsworth–Emmons olefination