Tutorial 1 - Orbitals and Vibrational Frequencies in Lactic Acid
1.1 Building the Lactic Acid molecule
1.2 Creating a PQS input file
1.3 Submitting the PQS job
1.4 Visualizing the PQS job output
Tutorial 2 - VCD spectrum of CHFClBr
2.1 Building CHFClBr
2.2 Creating a PQS input file
2.3 Submitting a PQS job
2.4 Visualizing the PQS job output
Tutorial 3 - Methoxy Substitution in Perfluoroanthracene
3.1 Building Perfluoroanthracene
3.2 Creating a PQS input file
3.3 Submitting a PQS job
3.4 Visualizing the PQS job output
3.5 Building 1-Methoxy-Perfluoroanthracene
3.6 Visualizing the PQS job output
3.7 Building 2- and 9-Methoxy-Perfluoroanthracene and Visualizing the PQS job outputs
3.8 Comparing the NMR Spectra of perfluoroanthracene, 1-, 2-, and 9-methoxy- perfluoroanthracene
Tutorial 1 - Lactic Acid
Tutorial 1 - Lactic Acid
To get you started using PQSMOL and PQS , we will begin the tutorials with a simple example molecule - Lactic Acid.
Lactic acid, also known as milk acid or 2-hydroxypropanoic acid, is used in several biochemical processes in the human body. Its chemical formula is C3H6O3. It is schematically shown in Figures and .
Lactic acid structure diagram
Lactic acid structure
In this example we will:
build the molecule
perform an initial optimization, using the Sybyl5.2 force field
create a PQS input file
run a PQS calculation
examine the molecular orbitals and display the vibrational frequencies