1. Computational Chemistry
A teaser introduction
José R. Valverde
CNB/CSIC
Welcome to a quick introduction to Computational Chemistry.
© José R. Valverde, 2014
CC-BY-NC-SA

2. First things, first

3. Thank you!

4. Valencia 2013. © José R. Valverde

5. Welcome to
the
WORLD of
TOMORROW

6. Introduction
Computational chemistry is a branch of chemistry that uses principles of computer science to assist in solving chemical problems.
Taken from Wikipedia (don't forget your contribution).

7. Atoms and Molecules DO NOT EXIST

8. What we believe that might possibly exist:
Space/Time distortions (energy) that concentrate on deep wells (particles) that are more or less likely (wave function) to be found somewhere (orbitals) in Space/Time.

9. What we will learn

10. Cheminformatics Information management in relation to Chemistry
Closely related to Bioinformatics
Closely related to Immunoinformatics
Closely related to Medinformatics
Collect, manage and access data in databases
Work with “textual” (1D) information (sequences, knowledge, etc...)
Analyze “textual” data (comparisons, motifs, NN, HMM, relationships, tc...)
Data mining

11. Computational Chemistry
Carry on calculations using multidimensional molecular data
Closely related to Computational Biology
Work with structural descriptions of molecules
Ab initio
Simplified
Shared properties and abstractions
Strongly dependent on mathematical calculations

12. Molecular structures Analysis of macromolecular structures
Visualization
Exploration
Prediction of macromolecular structures
Homology modeling
Threading
Ab initio modeling

13. Molecular Mechanics Compute properties from 3D molecular description
Atoms are considered as charged “soft balls”
Bonds are considered as “springs”
Typical calculations
Structure optimization
Molecular Dynamics
Average ensemble properties

14. Molecular interactions
Mainly receptor-ligand interactions, where
Receptor is a biological macromolecule
Ligand is a small compound (or another macromolecule)
Typical analyses
Protein-Protein interactions
Protein-Drug interactions
Drug screening

15. Quantum Mechanics Compute properties from 3D molecular description
Atoms do NOT exist
Molecules are a cloud of electrons moving around nuclei
Requires solution of Schroedinger wavefunction or Kohn-Sham electronic density
Typical calculations
Structural refinement
Quantum Dynamics
Reaction dynamics

16. What you will do

17. Practical sessions Protein function prediction
Visualization of macromolecules
Modelling protein structures from sequence
Molecular Dynamics
Molecular interactions (docking)
Quantum Mechanics
Quantum Dynamics
Modelling reactions

18. Fasten your seat belt

19. Fasten your seat belt and

20. Fasten your seat belt and get ready

21. Fasten your seat belt and get ready for

22. Fasten your seat belt and get ready for the Magical Mistery Tour

23. Ready for a quantum leap?
Image; © José R. Valverde, CC-BY.NC-SA