SIMULATION OF MOLECULAR AND PERIODIC SYSTEMS

The course falls within the compulsive training activities characterizing the Master Study Programme in Science and Technology of Bio and Nano Materials, The aim of the programme is to train graduates with a solid multidisciplinary preparation in chemistry, physics and biology and with the ability to manage complex processes such as design, synthesis and characterization of materials, including biological ones. The training course includes both theoretical and laboratory lessons concerning the preparation and characterization of nano and biomaterials. In particular, the properties, the chemical-physical characteristics and the methods of preparation of nanostructured materials and their applications are studied in depth. The specific objective of Simulation of Molecular and Periodic Systems is to give competences concerning the use of molecular mechanics and quantum mechanics methods to obtain information about biological molecules and polymers, organic and inorganic materials, nanoscale compounds. The target of the course is the knowledge of advantages and limits of each method, in order to be able to select the most supportive computational approach for the system to be studied.

1. Knowledge and understanding.
I) Knowing the theoretical bases of molecular mechanics – based methods and understanding the fields of application and the limits.
II) Knowing the theoretical bases of Hartree-Fock and the role of basis sets. Basis knowledge about post-Hartree-Fock methods and semi-empirical methods. Knowledge about the theoretical bases of density functional theory (DFT) – based methods. Understanding the fields of application and the limits. Knowledge about the use of quantum mechanical methods for non-periodic and periodic systems, also in the presence of solvent.
III) Understanding the properties that can be predicted from computational simulation of non-periodic and periodic systems.
IV) Understanding advantages and limits of combining molecular mechanics and quantum mechanics methods in hybrid calculations.
2. Ability to apply knowledge and understanding.
I) Being able to apply computational methods for the correct modelling of bio- and nanomaterials.
II) Being able to use computational approaches for the prediction of properties of bio- and nanomaterials.
3. Ability to judge
I) Being able to evaluate the limits of a computational methods depending upon the system to be studied.
II) Being able to balance computational effort and quality of a simulation.
4. Communication skills
I) Being able to use the right terminology and symbols to discuss the subjects of the course.
II) Being able to constructive interact with the teacher and the other students.
5. Learning skills
I) Being able to correctly summarize and connect the most important arguments described during the lessons.
II) Being able to competently carry out a computer simulation on the basis of the theoretical arguments described during the lessons.

Basic mathematic knowledge is required. The usual mathematic courses in scientific Bachelor study programmes are sufficient. Basic chemistry knowledge is required. In particular, the student should be aware about the electronic structure of the elements and about chemical bonds in organic and inorganic compounds. Preliminary information concerning spectroscopy (UV-VIS and IR) and thermodynamics is also required.

In relation to the training objectives and expected learning outcomes, shown in the relevant sections, the contents of the course can be divided as follows:
I) Potential energy surfaces and geometry optimization. Monte-Carlo method. Basic aspects of molecular dynamics.
II) Hartree-Fock method. LCAO approach, basis sets, pseudopotentials. Application of the Hartree-Fock method to periodic systems.
III) Overview of multiconfigurational methods. UV-VIS simulation based on configuration interaction (CIS).
IV) Semiempirical methods. NDO and NDDO approximations to interelectronic repulsion. Related methods and fields of application.
V) DFT theory. Approximations to exchange-correlation energy and related methods. Application to periodic and non-periodic systems.
VI) Molecular and periodic properties. Population analyses, role of frontier orbitals, prediction of reactivity.
VII) IR simulation (harmonic approximation) and estimation of thermodynamic quantities.
VIII) Implicit solvation models (Generalized Born, Onsager, PCM, COSMO). Approximations and limits.
IX) Hybrid molecular mechanics / quantum mechanics methods. General equations, approximations and limits.

For the study and the deepening of the theory:
I) C. J. Cramer, Essentials of Computational Chemistry, 2rd edition, Wiley, 204.
II) F. Jensen, Introduction to Computational Chemistry, 3rd edition, Wiley, 2017.
III) W. J. Hehre, A Guide to Molecular Mechanics and Quantum Chemical Calculations, Wavefunction Inc., 2003.
IV) R. Dronskowski, Computational Chemistry of Solid State Materials, Wiley, 2005.
Possible alternative in Italian:
M. Bortoluzzi, Approccio qualitativo alla chimica computazionale, Aracne editrice, 2009, with supporting information available at https://drive.google.com/drive/folders/0B6EkDs_UUlhBbjVNNkI5MVNqYkE?usp=sharing .

The assessment of learning takes place through an oral test, which consists of a series of questions to which the student must respond by demonstrating to know and be able to expose the topics of the entire program (see the content section) with properties of language. The oral exam lasts from 25 minutes to 35 minutes depending upon the clarity and consistency of the answers to the questions asked. There are at least three questions, the first on a chosen topic. A question must concern examples of application of simulation methods to biological or nano-structured materials.

Teaching is organized in lectures including examples and computer exercises. At the end of each theoretical subject relevant exercises are carried out in the classroom with proper computational software. About the 25% of the course is devoted to computer exercises.

English

Accessibility, Disability and Inclusion
Accommodation and support services for students with disabilities and students with specific learning impairments: Ca’ Foscari abides by Italian Law (Law 17/1999; Law 170/2010) regarding support services and accommodation available to students with disabilities. This includes students with mobility, visual, hearing and other disabilities (Law 17/1999), and specific learning impairments (Law 170/2010). In the case of disability or impairment that requires accommodations (i.e., alternate testing, readers, note takers or interpreters) please contact the Disability and Accessibility Offices in Student Services: disabilita@unive.it.

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