# online Gaussian Workshop + troubleshooting

Gaussian 16 is a modern computational chemistry package used by scientists and researchers in chemistry, biochemistry, physics, and materials science. It offers a comprehensive set of quantum chemical and molecular mechanics methods for performing a wide range of molecular modelling and analyses, including molecular structure optimizations, vibrational spectroscopy, thermochemistry calculations, reaction mechanism studies, and more. The Gaussian software is a popular package because of its accuracy, flexibility, and user-friendly interface. Thanks to its powerful algorithms and advanced features, Gaussian 16 is a powerful tool for scientists looking to enhance their knowledge of molecular systems and chemical reactions.

## How we conduct this online Gaussian workshop

Computational chemistry is a complicated art that needs training and practice, as well as a solid theoretical foundation. Also, you may encounter many problems in practice. We know these as a fact. Thus, the Insilicosci online Gaussian workshop is **more than just an online course**.

Our Gaussian workshop has two major components: **online content** and **troubleshooting meetings**. The online content includes video tutorials and some assignments. In each session, first we explain the theory behind the computational methods, then we use those methods in practice. At the end, there are a few exercises to solidify your understanding. You can expect an average of 1.5 hours of video in each session on average. In addition, each session includes a 1-hour troubleshooting meeting during which you can discuss any problems that may have occurred during that session.

## Syllabus

### Session One: Theoretical Fundamentals and Getting Started with Gaussian 16

Introduction To Computational Methods

Explaining The Concept of Basis-Sets

Open-Shell and Closed-Shell Calculations

How To Choose A Suitable Computational Level

Installing and Running Gaussian 16 and GaussView on a Windows Machine

Batching Gaussian 16 Calculations on Windows

Installing and Running Gaussian 16 and GaussView on a Linux Machine

Batching Gaussian Calculations on Linux

### Session Two: Gaussian 16 Input and Output Files

- The Anatomy of Gaussian Input and Output Files
- Creating Gaussian 16 Input Files
- Making Multi-Step Gaussian Input Files
- Restarting Gaussian 16 Calculations
- Introduction to the GaussView Software
- Explaining Internal Molecular Coordinates
- Drawing Molecular Structures using GaussView
- Hands-On Practice: Writing Various Gaussian Input Files
- Hands-On Practice: Drawing Various Organic and Organometallic Molecules

### Session Three: Geometry Optimisation

- Introduction to the Self-Consistent Field Method
- Geometry Optimisation Calculation
- HOMO-LUMO Energy Calculation
- Visualising HOMO-LUMO Orbitals
- Visualising Electron-Density Surfaces
- Conformational Analysis using Gaussian 16
- Calculating the Interaction Energy of Two Molecules
- Introduction to Basis-Set Superposition Error (BSSE)
- BSSE Calculation with Gaussian 16
- Hands-On Practice: Optimising the Molecular Structure of the Dopamine Molecule
- Hands-On Practice: Visualising the Frontier Orbitals and Electron Density Surface of Dopamine
- Hands-On Practice: Calculating Cytosine-Guanine Interaction Energy and Its BSSE

### Session Four: Spectroscopy and Thermochemistry

- Calculating NMR Spectra using Gaussian 16
- Calculating IR and Raman Spectra using Gaussian 16
- Calculating Free Energy and Enthalpy of Chemical Reactions
- Ionisation Energy Calculation
- Accurate Thermo-Chemistry Calculations with Complete Basis Set Methods
- Hands-On Practice: Calculating the IR and NMR Spectra of the Dopamine Molecule
- Hands-On Practice: Calculating the Free Energy and Enthalpy of Methane Combustion

### Session Five: Examining the Mechanics of Chemical Reactions

Explaining Potential Energy Surface (PES)

Introduction to Redundant Internal Coordinates

How to Freeze and Scan Potential Energy Surface

Finding Transition Structures with QST2 And QST3 Methods

Intrinsic Reaction Coordinate (IRC) Calculation

Investigating Chemical Reaction Mechanisms with Gaussian 16

Hands-On Practice: Studying the Mechanism of the Alkyl Nitrate Hydrolysis

### Session Six: Solution Modelling and Excited States

- Introduction to Continuum Solvation Models
- Setting Up Solvation Calculations
- Calculating the Free Energy of Solvation
- Overview of Excited State Modelling
- Semi-Empirical Excited State Methods
- Time-Dependent Excited State Methods
- High-Accuracy Excited State Modelling with Coupled Cluster Methods
- UV/Visible Spectrum Prediction with Gaussian 16
- Hands-On Practice: Calculating the Free Energy of Solvation of the Dopamine Molecule
- Hands-On Practice: Calculating the UV/Vis Spectrum of Dopamine in An Aqueous Solution

### Session Seven: Wave-Function Analysis

- Introduction to Natural Bond Orbital (NBO) Theory
- NBO Analysis with Gaussian 16
- Interpretation of the NBO Analysis
- Introduction to Atoms in Molecules (AIM) Theory
- Creating Wave-Function Files using Gaussian 16
- AIM Analysis with the AIMAll Software
- Drawing Electron Density Counter Maps with the AIMAll Software
- Hands-On Practice with Performing NBO Analysis on the Malondialdehyde Molecule

### Session Eight: A Hybrid QM/MM Method for Large Molecules

Introduction to the ONIOM Method

Preparing ONIOM Input for Biomolecules

Understanding the PDB File Format

Preparing and Trimming PDB Structures for Gaussian 16

Completing the Missing Force-Field Parameters

Calculating Molecular Mechanics Charges for Ligands

Combining Protein and Ligand Structures

Defining ONIOM Layers

Setting Up ONIOM Calculations in Gaussian 16

Hands-On Practice: Studying the Effect of Metal Exchange in the Azurin Protein

## Certification

After finishing the Gaussian workshop, you can apply for certification. The certification does not include a grade and only confirms that you participated in the Gaussian workshop. The certification requirement is that you complete all the sessions and submit at least 80 percent of the assignments correctly.