Adrea's Academic Notebook and Journal
Module 13
Initializing search
Notebook and Journal
Coding Stats
Cheat Sheets and Play
Honours
Honours Thesis
PhD
Undergrad
Adrea's Academic Notebook and Journal
Notebook and Journal
Coding Stats
Cheat Sheets and Play
Cheat Sheets and Play
Cheat Sheets
Cheat Sheets
Basis Sets
GAMESS
LaTeX in Sublime Text (LaTeXTools) setup guide
MultiWFN
ORCA
Psi4
Pymol
Homeless Equations
Homeless Equations
Computational Thermo Equations
Other Homeless Equations
Statistics
Jupyter Notebooks
Jupyter Notebooks
Jupyter Notebooks
MD Play
MD Play
Gromacs Single Molecule Sovation (CGenFF)
LAMMPS/LigParGen/fftool
NAMD QM/MM (CGenFF)
Parameterising TiO2 From MP2 (function fitting in python)
SDL
SDL
SDL Guide
MCSCF Methods
Neil Dickson
Chris Cramer
Chris Cramer
Computational Chemistry
Computational Chemistry
2. The PES
2. The PES
Preamble: Part 1
Preamble: Part 2
Basic Force Field: Part 1
Basic Force Field: Part 2
Basic Force Field: Part 3
MM Force Fields: Part 1
MM Force Fields: Part 2
MM Force Fields: Part 3
The Takeaway
3. MO Theory
3. MO Theory
LCAO Wave Functions
Effective Hamiltonians
Semiempirical Methods
4. Ab Iniio
4. Ab Iniio
Electron Correlation and CI
Molecular Properties
6. Solvation
6. Solvation
Chemical Phenomena
Explicit Solvation
Free Energy Perturbation
Continuum Solvent Electrostatics
Continuum Solvent Non-Electrostatics
Phase-Phase Partitioning
Hybrid Models
7. Excited States
7. Excited States
Configuration Interaction (CI)
Perturbation and Time-Dependent DFT
Conical Intersections
Solvatochromism
Statistical Molecular Thermodynamics
Statistical Molecular Thermodynamics
Energy Levels
Gases
Atomic Partition Functions
Molecular Partition Functions
Internal Energy and Enthalpy
CHE10002 - Enthalpy
CHE10002 - Entropy/Gibbs Free Energy
Free Energy
Module 11
Module 12
Module 13
Katya Pas
Katya Pas
Principles of Quantum Chemistry
PES and BO Approximation
Solutions of Schrödinger’s Equation
Electron Correlation
Density functional Theory
Kinetics
Kinetics
Equations
Chemical Kinetics
The Rate Law
The Relationship Between Reactant Concentration and Time
Honours
Honours
Thesis Defence Prep
Diary
Diary
Week 0 - Intro
Week 1
Week 3
Week 4
Week n
Week n+1
Week n+2
Week n+3
Week n+4
Week n+5
Week n+6
Week n+7
Week n+8
Week n+9
Week n+10
Week n+11
Week n+12
Week n+13
Week n+14
Week n+15
Week n+16
Week n+17
Week n+18
Week n+19/20
Final Week
Notes
Notes
Main Group Chemistry
Main Group Chemistry
Inert Pair Effect
Group 13
Group 14
Metallosupramolecular Chemistry
Metallosupramolecular Chemistry
Crystal Engineering Grammar
Crystal Engineering Design
Crystal Engineering Applications
Supramolecular Chemistry
Host-guest Systems
Honours Thesis
Honours Thesis
1. Introduction
2. Computational Details
3. Results and Discussion
4. Conclusion and Future Research
Acknowledgements
Appendices
PhD
PhD
Misc. Notes
Misc. Notes
PCM
Gas-Phase Fluorophore Dataset Notes
Solvated Fluorophore Dataset Notes
Dataset Procurement Protocol
Experimental Notes
Excited States in Solution
Notebook
Notebook
Pre-PhD Playground
PhD Prep
PhD Begin
May 2022
June 2022
July 2022
August 2022
September 2022
October 2022
November 2022
December 2022
January 2023
February 2023
March 2023
April 2023
May 2023
June 2023
July 2023
August 2023
Undergrad
Undergrad
Notes
Notes
Sem 2. Chemistry 2
Sem 2. Chemistry 2
Solubility Equilibria
pH of Weak Acids
Common Ion Effect
Redox Reactions
Complex Ions
Galvanic Cells - Standard Conditions
Galvanic Cells - Non Standard Conditions
Thermochemistry
Thermochemistry
Calorimetry
Enthalpy
Entropy and Gibbs Free Energy
Sem 3. Organic
Sem 3. Organic
Organic Synthesis Reaction Types
Organic Synthesis
Functional Groups of Interest
Curved Arrow
Electrophiles
Nucleophiles
Acids and Bases
SN1 and SN2 Reactions
β-Elimination
Aromatic Compounds
Carbonyl Chemistry
Stereochemistry Representations
Stereoisomers
Cis-Trans Isomerism
Optical Rotation
(R)/(S) Designation (Absolute Stereochemistry)
Sem 4. Spectroscopy
Sem 4. Spectroscopy
Introduction to Spectroscopy
Interaction of Light with Matter
Colour
Absorption and emission
Molecular Spectra
The Analytical Process
Signals
Components of a Spectrophotometer
Flame Spectroscopy AA-AES
IR Spectroscopy
Reading FTIR
Proton NMR Spectroscopy
MO Diagrams
UV-Vis Spectrophotometers
UV-Vis Spectra
Sem 5. Comp Chemistry
Sem 5. Comp Chemistry
How to plan your calculations
Why we need to optimise
Basics of Quantum Chemistry
Basis Sets
Ab Initio
Density Functional Theory
Model Chemistry
Energy Calculations
Energy Calculations
Vibrational Spectra
UV-Vis Spectra
NMR Spectra
Sem 5. Inorganic Chemistry
Sem 5. Inorganic Chemistry
Applications and Techniques
Applications and Techniques
Coordination
Ligand/Crystal Field Theory
XRD
Bioinorganic Chemistry
Medical Imaging
Environmental Chemistry
Energy Materials
Photovoltaics
Batteries
Physical Thoery
Physical Thoery
Quantum Numbers - Revised
Periodic Trends
Atomic Structure and Spectra
Ionic Bonding
Lattice Energy
Covalent Bonding
MO Theory
Solid Metals
Transition Metals and Complexes
Sem 6. Advanced Analytical
Sem 6. Advanced Analytical
Electrochemistry
Electrochemistry
Electrochemistry
Electrochemical Cells
Electrode Processes
Electrochemical Methods
Electrical Storage
NMR and MS
NMR and MS
NMR Recap
CNMR vs HNMR and Intramolecular H-Bonding
NMR - Aromatics, Timescales, Coupling and Deuteration
2D NMR
MS Recap
MS Fragmentation and Molecular Formula
Checklists
Sample Prep and Chromatography
Sample Prep and Chromatography
Sample Preparation Techniques
Advanced Chromatographic Techniques
Further Chromatographic Developments
Surface Analytical Tech
Surface Analytical Tech
Surface Analytical Techniques
X-ray Photoelectron Spectroscopy (XPS)
XPS Continued
XPS Damage and Scanning
Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS)
Sem 6. Food Science
Sem 6. Food Science
Food Composition Analysis
Proteins and Enzymes
Protein Determination Methods
Carbohydrates
Lipids
Lipid Extraction and Analysis
Water Content and Drying
Micronutrients and Calories
Chemical Additives in Food
More Chemical Additives in Food
Heavy Metals in Foods
Foods Toxins
Sem 6. Research Skills
Sem 6. Research Skills
Research Overview
Types of Research Deign
Sampling Methods
Measurement in Research
Data Collection (Social)
Writing For Research: Part 1
Writing For Research: Part 2
Research Metrics
Sem 6. Surface and Colloids
Sem 6. Surface and Colloids
Colloids
Colloids
Introduction to Colloids
Forces Acting on Colloids
Attractive Forces Between Colloids
Surface Charge (\(\sigma_o\))
Charge & Potential at the Interface
Repulsion Between Colloids
DLVO Theory
Zeta Potential (\(\zeta\))
Emulsions
Emulsions
Emulsions 1
Emulsions 2
Emulsions 3
Polymers and Proteins
Polymers and Proteins
Proteins and Polymers at the Surface
Quantifying Protein Adsorption - 1
Quantifying Protein Adsorption - 2
Matrix Assisted Laser Desorption/Ionisation - Time of Flight Mass Spectrometry (MALDI-TOF)
Surfaces That Prevent Adsorption
Surface Chemistry
Surface Chemistry
Introduction and Surface Tension
Vapour Pressure
Orientation and Spreading at Interfaces
Adsorption at Interfaces
X Contact Angle
Detergency
Sem 7. Advanced Organic Chemistry
Sem 7. Advanced Organic Chemistry
David Lupton
David Lupton
Introduction to Catalysis
Biocatalysis
Organocatalysis
Transition Metal Catalysis 1
Transition Metal Catalysis 2
Kellie tuck
Kellie tuck
Chemoselectivity - Reduction
Retrosynthesis
Chemoselectivity - Oxidation
Chemoselectivity - Hydrogenation
Thermodynamic Control and Conformational Analysis of Linear/Cyclic Alkanes
Protecting Groups
Conformational Analysis
Pericyclic Reactions
Pericyclic Reactions
Types of Reactions, Diels-Alder and FMO diagrams
Cycloadditions
Woodward-Hoffman Description
Sigmatropic Rearrangements
Electrocyclic Reactions
Philip Chan
Philip Chan
Aromatic NMR
NMR Coupling
Aromaticity
Aromatic EAS Directing Groups
Aromatic NAS
Aromatic - Pyridine
Pyrrole
Furan and Thiophene
Heterocycle Retrosynthesis
Sem 7. Consumer Chemistry
Sem 7. Consumer Chemistry
Surfactants as Detergents
Surfactants as Emulsifiers
Lab - Conductimetry and Gravimetry
Agrochemicals - Fertilisers
Agrochemicals - Herbicides, Soil Chem and Pesticides
Carbohydrates
Fats and Oils
Food Additives
Vitamins
Research
Research
2018 Summer
2018 Summer
Pre Semester
Pre Semester
Friday 4/1/2018
Week 1
Week 1
Monday 7/1/2018
Wednesday 9/1/2018
Thursday 10/1/2018
Friday 11/1/2018
Week 2
Week 2
Monday 14/1/2018
Tuesday 15/1/2018
Wednesday 16/1/2018
Thursday 17/1/2018
Friday 18/1/2018
Week 3
Week 3
Monday 21/1/2018
Tuesday 22/1/2018
Wednesday 23/1/2018
Thursday 24/1/2018
Friday 25/1/2018
Week 4
Week 4
Tuesday 29/1/2018
Wednesday 30/1/2018
Thursday 31/1/2018
Friday ½/2018
Week 5
Week 5
Monday 4/2/2018
Wednesday 6/2/2018
Thursday 7/2/2018
Friday 8/2/2018
Week 6
Week 6
Tuesday 12/2/2018
2020 Grand Challenges
2020 Grand Challenges
Week 1
Week 2
Week 4
Week 5
Week 6
Mid Sem Break
Week 7
Week 8
Week 9
Week 10
Week 11
2020 Summer
2020 Summer
Monday, 6. January 2020
Tuesday, 7. January 2020
Wednesday, 8. January 2020
Thursday, 9. January 202
Friday, 10. January 2020
Saturday, 11. January 2020
Monday, 13. January 2020
Tuesday, 14. January 2020
Wednesday, 15. January 2020
Thursday, 16. January 2020
Friday, 17. January 2020
Monday, 20. January 2020
Tuesday, 21. January 2020
Wednesday, 22. January 2020
Thursday , 23. January 2020
Friday , 24. January 2020
Aus Day Long Weekend , 25/26/27. January 2020
Tuesday, 28. January 2020
Wednesday, 29. January 2020
Thursday, 30. January 2020
Friday, 31. January 2020
Monday, 3. February 2020
Tuesday, 4. February 2020
Wednesday, 5. February 2020
Thursday, 6. February 2020
Friday, 7. February 2020
Monday, 10. February 2020
Tuesday, 11. February 2020
Wednesday, 12. February 2020
Thursday, 13. February 2020
Friday, 14. February 2020
Monday, 17. February 2020
Tuesday, 18. February 2020
Wednesday, 19. February 2020
Thursday, 20. February 2020
Thursday, 20. February 2020
Saturday, 22. February 2020
Module 13
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