ID:
511802
Duration (hours):
48
CFU:
6
SSD:
CHIMICA ORGANICA
Year:
2025
Overview
Date/time interval
Secondo Semestre (02/03/2026 - 12/06/2026)
Syllabus
Course Objectives
By the end of the course, students should be able to:
* Have a general idea of what computational chemistry is and how it could integrate and guide experimental chemistry, starting from organic chemistry
* Learn the computational chemist’s mindset and “take it into the lab”, for example:
** Through a better understanding of and ability to speculate on reaction mechanisms
** By proposing reasonable modifications in the laboratory whenever a particular compound does not exhibit a set of desired properties
** By practising how to explain unexpected results in a specific experiment.
* Have a general idea of the theoretical aspects that are behind the main types of chemical calculations, and of the required software packages.
* Be able to consider potential career options inside and outside of academia.
* Have a general idea of what computational chemistry is and how it could integrate and guide experimental chemistry, starting from organic chemistry
* Learn the computational chemist’s mindset and “take it into the lab”, for example:
** Through a better understanding of and ability to speculate on reaction mechanisms
** By proposing reasonable modifications in the laboratory whenever a particular compound does not exhibit a set of desired properties
** By practising how to explain unexpected results in a specific experiment.
* Have a general idea of the theoretical aspects that are behind the main types of chemical calculations, and of the required software packages.
* Be able to consider potential career options inside and outside of academia.
Course Prerequisites
None.
However, students are recommended to familiarise with Linux commands and a programming language such as Python.
However, students are recommended to familiarise with Linux commands and a programming language such as Python.
Teaching Methods
Frontal lecturing and hands-on sessions (theory, software characteristics, etc.)
Detailed protocols on how to carry out each session
Assistance in carrying out the hands-on sessions, projecting some examples if necessary.
Hands-on sessions will be interactive: each session will pose simple problems to solve, and questions aiming to verify how much students have understood calculations and how able they are to interpret their results.
Detailed protocols on how to carry out each session
Assistance in carrying out the hands-on sessions, projecting some examples if necessary.
Hands-on sessions will be interactive: each session will pose simple problems to solve, and questions aiming to verify how much students have understood calculations and how able they are to interpret their results.
Assessment Methods
A written report on one practical session chosen out of the last three will count towards one third of the final grade. (Maximum ten marks for this part). Reports will have to be submitted two weeks before the exam session one wishes to partake in.
Evaluated aspects will include:
1) Form (2 marks)
2) Theoretical accuracy (4 marks)
3) Proposals for future work (4 marks)
The remaining two thirds of the final grade will be awarded through an oral examination, with five random questions, each about theoretical aspects, concepts encountered during the hands-on sessions, and the submitted report. Maximum of four marks per question (maximum 20 marks for this part).
Evaluated aspects will include:
1) Form (2 marks)
2) Theoretical accuracy (4 marks)
3) Proposals for future work (4 marks)
The remaining two thirds of the final grade will be awarded through an oral examination, with five random questions, each about theoretical aspects, concepts encountered during the hands-on sessions, and the submitted report. Maximum of four marks per question (maximum 20 marks for this part).
Texts
Lecture notes, materials and handouts provided by the lecturer (including for hands-on sessions).
“Understanding Molecular Simulation”, D. Frenkel, B. Smit
“Computer Simulation of Liquids”, M. P. Allen, D. J. Tildesley
“Molecular Modelling - Principles and Applications”, A. R. Leach
“Introduction to Computational Chemistry”, F. Jensen
“Oxford Chemistry Primers — Computational Chemistry”, J. Harvey
“Introduzione alla Chimica Organica Computazionale”, A. Bottoni – IN ITALIAN
“Understanding Molecular Simulation”, D. Frenkel, B. Smit
“Computer Simulation of Liquids”, M. P. Allen, D. J. Tildesley
“Molecular Modelling - Principles and Applications”, A. R. Leach
“Introduction to Computational Chemistry”, F. Jensen
“Oxford Chemistry Primers — Computational Chemistry”, J. Harvey
“Introduzione alla Chimica Organica Computazionale”, A. Bottoni – IN ITALIAN
Contents
The 48 hours will comprise at least 4 practical sessions, intercalated with theory. Each lecture will last 3 hours.
Practical Sessions:
Molecular Formats, Molecular Modelling, Molecular Visualisation
Molecular Dynamics Simulations of a Small Protein
QM Calculations to Study Simple Organic Molecules
Virtual Screening of Drug Libraries through Molecular Docking
Examples of Software packages employed include: Gaussian, Amber, VMD, PyMOL, AutodockVINA
Theoretical Aspects, intercalated with case studies where possible:
Theory and principles behind molecular dynamics (MD) simulations, with elements of statistical thermodynamics
How to read MD simulation results: elements of geometry, RMSD, density profiles, radial distribution functions, principal component analysis
Clustering
Enhanced sampling methods for the simulation of rare events
Introduction to Monte Carlo methods
QM methods: basis sets, pseudopotentials, Hartree-Fock method, DFT method, post-SCF methods (multideterminantal and perturbative), semiempirical methods.
Hybrid (QM/MM) methods
Free energy simulations
Molecular simulations in the pharmaceutical and agrochemical industry: structure- and ligand-based drug design techniques, pharmacophores, molecular docking, cheminformatics and bioinformatics, folding prediction and homology modelling
Molecular simulations in materials industry
Introduction to Artificial Intelligence
Practical Sessions:
Molecular Formats, Molecular Modelling, Molecular Visualisation
Molecular Dynamics Simulations of a Small Protein
QM Calculations to Study Simple Organic Molecules
Virtual Screening of Drug Libraries through Molecular Docking
Examples of Software packages employed include: Gaussian, Amber, VMD, PyMOL, AutodockVINA
Theoretical Aspects, intercalated with case studies where possible:
Theory and principles behind molecular dynamics (MD) simulations, with elements of statistical thermodynamics
How to read MD simulation results: elements of geometry, RMSD, density profiles, radial distribution functions, principal component analysis
Clustering
Enhanced sampling methods for the simulation of rare events
Introduction to Monte Carlo methods
QM methods: basis sets, pseudopotentials, Hartree-Fock method, DFT method, post-SCF methods (multideterminantal and perturbative), semiempirical methods.
Hybrid (QM/MM) methods
Free energy simulations
Molecular simulations in the pharmaceutical and agrochemical industry: structure- and ligand-based drug design techniques, pharmacophores, molecular docking, cheminformatics and bioinformatics, folding prediction and homology modelling
Molecular simulations in materials industry
Introduction to Artificial Intelligence
Course Language
English
More information
This 2025-26 academic year is the first one in which this course is offered.
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CHEMISTRY
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