Study-unit Code
In all curricula
Gabriele Cruciani
  • Gabriele Cruciani
  • Jenny Desantis (Codocenza)
  • 35 ore - Gabriele Cruciani
  • 7 ore (Codocenza) - Jenny Desantis
Course Regulation
Coorte 2021
Learning activities
Attività formative affini o integrative
Academic discipline
Type of study-unit
Opzionale (Optional)
Type of learning activities
Attività formativa monodisciplinare
Language of instruction
Most common molecular modeling methods for the building and representation of organic molecules aimed at the design of chemical compounds with optimal properties
Reference texts
Material provided by teacher
Educational objectives
The main knowledge gained will be:
- Basic elements of molecular design
- Knowledge of the most popular molecular modeling methods
- Construction and representation of organic molecules aimed at the design of chemical compounds
- Calculation of molecular properties and complex systems
- Properties optimization
- Relationships between molecular structure and biological and pharmaceutical chemical properties.

The main skills are:
- Ability to build and represent molecules and complex systems by computer
- Ability to use the most commonly used force fields in molecular modeling
- Ability to calculate molecular and biological properties
- Ability to propose the use of semi-empirical models for structure-property relationships.
It is useful to have basic organic chemistry notions
Teaching methods
The course is organized as follows:
- Lectures on all topics of the course
- Classroom computer exercises
Other information
Gabriele Cruciani: gabriele.cruciani@unipg.it
Learning verification modality
The exam includes a final oral examination. The test consists of an interview on the main issues addressed in the course and in the solution proposed by the student to a complex problem. The problem to be solved consists of a practical application of the concepts of molecular design in the field of industrial, pharmaceutical, synthetic and environmental chemistry. The lecturer will assess the degree of understanding of the concepts, the deepening of the study, the appropriateness of the scientific language of exposure, the validity of the proposed solutions.
The exam evaluation will take into account the following aspects: correctness and adequacy of responses, processing skills and conceptual connection, mastery and language skills, according to the following percentages: 60%, 30%, 10%.
Extended program
In silico representation of molecular structures. Molecular models. Molecular mechanics. Force fields. Energetic minimization. GRID force field for organic molecules. Proteins and crystallography. GRID and macromolecular structures. Molecular descriptors. VolSurf for QSAR and ADME. The pharmacophoric concept. The FLAP method for small molecules and macromolecules. Practical exercitations on:
Use of force fields to model (macro)molecules
Molecular building
Conformational analysis
Multivariate statistics on molecular descriptors
pKa computation
LogP computation
Virtual screening template
Introduction to Proteolysis Targeted Chimeras (PROTACs): design prociples, PK properties and applications.
Obiettivi Agenda 2030 per lo sviluppo sostenibile
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