This is the wiki for "Chemical Kinetics and Molecular Dynamcis" course, @univgirona BioTech 3r year

Reference textbook:
PW Atkins, "Physical Chemistry"
A textbook to get a more easy introduction:
PW Atkins, "The Elements of Physical Chemistry"

Schedule:

Session 01 20140916

#cqdm1415 Presentation
https://www.dropbox.com/s/qjpwn26eslstnho/cqdm1415.pdf?dl=0

A fun video introducing chemical kinetics
https://www.youtube.com/watch?v=3ow0OJVChSU

Intro to kinetics, by the Khan Academy
https://www.youtube.com/watch?v=__zy-oOLPug

Videos from Coursera MOOC Univ Kentucky course
search youtube for "respect chemistry chemical kinetics"
https://www.youtube.com/results?search_query=respect+chemistry+chemical+kinetics

“Chemical Kinetics and Catalysis” is available at
http://pediapress.com/books/show/chemical-kinetics-and-catalysis-a-wiki-ov/

Session 02 20140917

ChemWiki UCDavis
http://chemwiki.ucdavis.edu/Physical_Chemistry/Kinetics

Interesting webpages and references:

Application of graph theory to chemical kinetics: Part 1. Kinetics of complex reactions

The major trends in applying graph theory to chemical kinetics and the mechanistic theory of complex reactions.

J. Chem. Educ., 1992, 69 (7), p 544 http://pubs.acs.org/doi/pdf/10.1021/ed069p544


Simulation of First-Order Chemical Kinetics Using Cellular Automata

http://pubs.acs.org/doi/abs/10.1021/ci960103u?journalCode=jcics1
J. Chem. Inf. Comput. Sci., 1997, 37 (2), pp 386–391,


Cellular automata are dynamical systems composed of arrays of cells that change their states in a discrete manner following local, but globally applied, rules. It is shown that a two-dimensional asynchronous cellular automaton simulates both the deterministic and the stochastic features of first-order chemical kinetic processes in an especially simple manner, avoiding the chore of solving either the deterministic coupled differential rate equations or the stochastic master equation. Processes illustrated include first-order decay, opposing first-order reactions, consecutive reactions, the steady-state approximation, a rate-limiting step, pre-equilibrium, and parallel competing reactions. The deterministic solutions are seen to emerge as statistical averages in the limit of large cell numbers. Some additional stochastic and statistical features of the solutions are examined.

ARRHENIUS Temperature Dependence of Reaction Rates

At Chemwiki: http://chemwiki.ucdavis.edu/Physical_Chemistry/Kinetics/Modeling_Reaction_Kinetics/Temperature_Dependence_of_Reaction_Rates/The_Arrhenius_Law/Arrhenius_Equation

An interesting paper in J. Chem. Educ. on the "exponential behavior" http://pubs.acs.org/doi/pdf/10.1021/ed075p1186

Nice,simple interpretation at
http://www.chem1.com/acad/webtext/dynamics/dynamics-3.html with a beautiful concept map for reaction mechanisms: dynmap4.jpg
A couple of videos are found at http://ch302.cm.utexas.edu/kinetics/temp-depend/selector.php?name=arrhenius-law

On Chain reactions:
UCDavis ChemWiki:
[lecture] http://chemwiki.ucdavis.edu/Organic_Chemistry/Organic_Chemistry_With_a_Biological_Emphasis/Chapter_17%3A_Radical_reactions/Section_17.2%3A_Radical_chain_reactions
Lecture 18 - Chain reactions (presented actually)
[lecture] http://www.dstuns.iitm.ac.in/teaching-and-presentations/teaching/undergraduate%20courses/cy102-equilibrium-and-dynamics-of-chemical-systems/lectures-2004/L18.pdf

Chain-growth polymerization
Wikipedia:
https://en.wikipedia.org/wiki/Chain-growth_polymerization
Kinetic of Condensation (Step-Growth) Polymerization
http://infochem.hanyang.ac.kr/courses/polylec/11.%20Kinetic%20of%20Condensation%20(Step-Growth)%20Polymerization.pdf
Video:
https://www.youtube.com/watch?v=Els5JNYfHQE

Video on step-growth polymerization:
https://www.youtube.com/watch?v=0r2F70_kmUA

Well covered in Wikipedia: Polymerization
[lecture]https://en.wikipedia.org/wiki/Polymerization

Explosions
[lecture] http://soliton.ae.gatech.edu/people/jseitzma/classes/ae6766/kineticsChainH2.pdf

Numerical solutions:
http://chemistry.illinoisstate.edu/standard/che38056/lecture_notes/380.56chapter12-S06.pdf

[lecture] Tenua simulator
Tenua-the kinetics simulator for Java
Tenua allows you to write out chemical reactions and calculate the concentrations of all the species over time. It can also compare the simulation to real data and automatically calculate the correct rate constants and other parameters to fit the data.
http://bililite.com/tenua/
See example in http://www.chm.davidson.edu/vce/kinetics/IntegratedRateLaws.html

CLASSICAL COLLISION THEORY, POTENTIAL ENERGY SURFACES AND TRANSITION STATE THEORY


OVERVIEW
http://www.fysik.su.se/~rdt/Molecular%20Physics/FK7012-Lecture_16.pdf

Scholarpedia:
http://www.scholarpedia.org/article/Chemical_reaction_kinetics

CLASSICAL COLLISION THEORY
https://en.wikipedia.org/wiki/Collision_theory

Intro video worth viewving:
https://www.youtube.com/watch?v=NO413LiI6QA

Useful:
https://www.youtube.com/watch?v=BBU6LP5ByTo&list=PLNo63t_rsUnKOVDYSHSeLxe7FBE6u-aQM

Fun video:
https://www.youtube.com/watch?v=WeBE-_LRb2s

Good info:
http://www.umich.edu/~elements/03chap/html/collision/
Microscopic theory:
[lecture] https://chemistry.tcd.ie/assets/pdf/sf-chemistry/megl/SF%20Chemical%20Kinetics%20Michaelmas%202011%20L5.pdf

MOLECULAR REACTION DYNAMICS
http://vallance.chem.ox.ac.uk/pdfs/ReactionDynamicsLectureNotes2012.pdf

TrANSITION STATE THEORY
Good:
http://www.umich.edu/~elements/03chap/html/transition/index.htm