INNOCHEM: molecular modelling

Michael Bredol

Fachhochschule M¨unster - University of Applied Sciences Department of Chemical Engineering

9/2015

Bredol (FH) InnoChem FHMS/2015 1/6 History Schrodinger’s¨ heritage

The application of quantum physics to chemistry started back in the 1920s First calculations were posible with paper and pencil only With the advent of electronic computers in the 1950s, first codes for quantum chemistry appeared With the widespread installation of mainframe computers in the 1960s and 1970s, the first useful codes were established Only after the introduction of Personal Computers and graphical interfaces molecular modelling became feasible for the wider scientific community Nowadays, powerful computer clusters have made molecular modelling a routine in many branches

Bredol (FH) InnoChem FHMS/2015 2/6 History Software approaches “Quantum Chemistry” mainly uses two different approaches: ab-initio wave function or electron density functional calculations

Bredol (FH) InnoChem FHMS/2015 3/6 History Software approaches “Quantum Chemistry” mainly uses two different approaches: ab-initio wave function or electron density functional calculations Both approaches today use basis sets based either on Gaussian functions (typical: in molecules) or plane waves (typical: in solids)

Bredol (FH) InnoChem FHMS/2015 3/6 History Software approaches “Quantum Chemistry” mainly uses two different approaches: ab-initio wave function or electron density functional calculations Both approaches today use basis sets based either on Gaussian functions (typical: in molecules) or plane waves (typical: in solids) Meanwhile, a large amount of quantum chemical software packages is available, both in the academic domain (no fees) and on a commercial basis

Bredol (FH) InnoChem FHMS/2015 3/6 History Software approaches “Quantum Chemistry” mainly uses two different approaches: ab-initio wave function or electron density functional calculations Both approaches today use basis sets based either on Gaussian functions (typical: in molecules) or plane waves (typical: in solids) Meanwhile, a large amount of quantum chemical software packages is available, both in the academic domain (no fees) and on a commercial basis Companies like BASF have their own groups of “Computational Chemists”, designing e.g. reaction paths for organic synthesis, mostly in order to weed out unfeasible solutions

Bredol (FH) InnoChem FHMS/2015 3/6 History Software approaches “Quantum Chemistry” mainly uses two different approaches: ab-initio wave function or electron density functional calculations Both approaches today use basis sets based either on Gaussian functions (typical: in molecules) or plane waves (typical: in solids) Meanwhile, a large amount of quantum chemical software packages is available, both in the academic domain (no fees) and on a commercial basis Companies like BASF have their own groups of “Computational Chemists”, designing e.g. reaction paths for organic synthesis, mostly in order to weed out unfeasible solutions Many packages like the well-known “Gaussian” suite have developed over decades and still contain “old” code

Bredol (FH) InnoChem FHMS/2015 3/6 History Software approaches “Quantum Chemistry” mainly uses two different approaches: ab-initio wave function or electron density functional calculations Both approaches today use basis sets based either on Gaussian functions (typical: in molecules) or plane waves (typical: in solids) Meanwhile, a large amount of quantum chemical software packages is available, both in the academic domain (no fees) and on a commercial basis Companies like BASF have their own groups of “Computational Chemists”, designing e.g. reaction paths for organic synthesis, mostly in order to weed out unfeasible solutions Many packages like the well-known “Gaussian” suite have developed over decades and still contain “old” code Due to the nature of the problem, all codes rely on efficient algorithms for large linear algebra systems and compilers generating fast machine code

Bredol (FH) InnoChem FHMS/2015 3/6 History Software organization Graphical capabilities of computers have developed much faster than the basic computational properties: the graphical user interface therefore in most systems is detached from the computational engine doing the quantum chemistry

Bredol (FH) InnoChem FHMS/2015 4/6 History Software organization Graphical capabilities of computers have developed much faster than the basic computational properties: the graphical user interface therefore in most systems is detached from the computational engine doing the quantum chemistry Communication between GUI and computational engine proceeds via text files with commands

Bredol (FH) InnoChem FHMS/2015 4/6 History Software organization Graphical capabilities of computers have developed much faster than the basic computational properties: the graphical user interface therefore in most systems is detached from the computational engine doing the quantum chemistry Communication between GUI and computational engine proceeds via text files with commands Results of calculations are output also in the form of text files

Bredol (FH) InnoChem FHMS/2015 4/6 History Software organization Graphical capabilities of computers have developed much faster than the basic computational properties: the graphical user interface therefore in most systems is detached from the computational engine doing the quantum chemistry Communication between GUI and computational engine proceeds via text files with commands Results of calculations are output also in the form of text files This approach allows for local installation of graphical packages for problem formulation and output analysis, whereas the computation engine can be anywhere on the net

Bredol (FH) InnoChem FHMS/2015 4/6 History Software organization Graphical capabilities of computers have developed much faster than the basic computational properties: the graphical user interface therefore in most systems is detached from the computational engine doing the quantum chemistry Communication between GUI and computational engine proceeds via text files with commands Results of calculations are output also in the form of text files This approach allows for local installation of graphical packages for problem formulation and output analysis, whereas the computation engine can be anywhere on the net Most packages therefore can be compiled on a simple laptop computer as well as on large parallelized computer clusters, without the need to change the user interface

Bredol (FH) InnoChem FHMS/2015 4/6 History Software organization Graphical capabilities of computers have developed much faster than the basic computational properties: the graphical user interface therefore in most systems is detached from the computational engine doing the quantum chemistry Communication between GUI and computational engine proceeds via text files with commands Results of calculations are output also in the form of text files This approach allows for local installation of graphical packages for problem formulation and output analysis, whereas the computation engine can be anywhere on the net Most packages therefore can be compiled on a simple laptop computer as well as on large parallelized computer clusters, without the need to change the user interface Some packages are run and maintained on commercial cloud servers, e.g. https://www.crunchyard.com/, avoiding the need for local installations and maintenance

Bredol (FH) InnoChem FHMS/2015 4/6 History Workshop organization In the workshop, graphical packages are installed locally on individual computers, but the calculations are done externally

Bredol (FH) InnoChem FHMS/2015 5/6 History Workshop organization In the workshop, graphical packages are installed locally on individual computers, but the calculations are done externally MOLDEN is a powerful (compiled) molecular builder, and also allows for visualization of computational results

Bredol (FH) InnoChem FHMS/2015 5/6 History Workshop organization In the workshop, graphical packages are installed locally on individual computers, but the calculations are done externally MOLDEN is a powerful (compiled) molecular builder, and also allows for visualization of computational results JMOL is a Java-based application for the inspection of computational results, just needs (modern) Java environment

Bredol (FH) InnoChem FHMS/2015 5/6 History Workshop organization In the workshop, graphical packages are installed locally on individual computers, but the calculations are done externally MOLDEN is a powerful (compiled) molecular builder, and also allows for visualization of computational results JMOL is a Java-based application for the inspection of computational results, just needs (modern) Java environment Many other solutions are available – the field is under constant development, due to rapid increase in graphical capabilities

Bredol (FH) InnoChem FHMS/2015 5/6 History Workshop organization In the workshop, graphical packages are installed locally on individual computers, but the calculations are done externally MOLDEN is a powerful (compiled) molecular builder, and also allows for visualization of computational results JMOL is a Java-based application for the inspection of computational results, just needs (modern) Java environment Many other solutions are available – the field is under constant development, due to rapid increase in graphical capabilities GAMESS-US is a computational engine with computational methods built-in / most useful for work with molecules

Bredol (FH) InnoChem FHMS/2015 5/6 History Workshop organization In the workshop, graphical packages are installed locally on individual computers, but the calculations are done externally MOLDEN is a powerful (compiled) molecular builder, and also allows for visualization of computational results JMOL is a Java-based application for the inspection of computational results, just needs (modern) Java environment Many other solutions are available – the field is under constant development, due to rapid increase in graphical capabilities GAMESS-US is a computational engine with computational methods built-in / most useful for work with molecules GAMESS-US is free for academic use (maintained at http://www.msg.ameslab.gov/GAMESS/) and under constant development

Bredol (FH) InnoChem FHMS/2015 5/6 History Workshop organization In the workshop, graphical packages are installed locally on individual computers, but the calculations are done externally MOLDEN is a powerful (compiled) molecular builder, and also allows for visualization of computational results JMOL is a Java-based application for the inspection of computational results, just needs (modern) Java environment Many other solutions are available – the field is under constant development, due to rapid increase in graphical capabilities GAMESS-US is a computational engine with computational methods built-in / most useful for work with molecules GAMESS-US is free for academic use (maintained at http://www.msg.ameslab.gov/GAMESS/) and under constant development Definig problems and preparing input files: etherpad!

Bredol (FH) InnoChem FHMS/2015 5/6 History Workshop organization In the workshop, graphical packages are installed locally on individual computers, but the calculations are done externally MOLDEN is a powerful (compiled) molecular builder, and also allows for visualization of computational results JMOL is a Java-based application for the inspection of computational results, just needs (modern) Java environment Many other solutions are available – the field is under constant development, due to rapid increase in graphical capabilities GAMESS-US is a computational engine with computational methods built-in / most useful for work with molecules GAMESS-US is free for academic use (maintained at http://www.msg.ameslab.gov/GAMESS/) and under constant development Definig problems and preparing input files: etherpad! To visualize numerical results, IPython would be a useful resource...

Bredol (FH) InnoChem FHMS/2015 5/6 History Problem

Acetaldehyde, vinyl alcohole and ethyleneoxide are isomers Which one is more stable? Can we draw (perhaps with intermediates) a reaction coordinate? Do solvents change the situation? Can we differentiate by the IR-spectrum? ...

Bredol (FH) InnoChem FHMS/2015 6/6