Computational Chemistry

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Presentation transcript:

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

First things, first

Thank you!

Valencia 2013. © José R. Valverde

Welcome to the WORLD of TOMORROW

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).

Atoms and Molecules DO NOT EXIST

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.

What we will learn

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

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

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

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

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

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

What you will do

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

Fasten your seat belt

Fasten your seat belt and

Fasten your seat belt and get ready

Fasten your seat belt and get ready for

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

Ready for a quantum leap? Image; © José R. Valverde, 2013. CC-BY.NC-SA

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