Ateneo - UPO

The course presents insights and practical applications, through numerical and formal exercises, of the main theoretical and computational modeling techniques in Chemistry. Ab initio calculations will be covered, mainly DFT, post-Hartree Fock and multireference, and classical ones, based on force fields applied to Molecular Dynamics and Monte Carlo simulations.

Christopher J. Cramer, Essentials of Computational Chemistry: Theories and Models, 2nd Edition, John Wiley & Sons, 2004.Foresman, J. B., & Frisch, Æ. (2015). Exploring Chemistry with Electronic Structure Methods (3rd ed.). Gaussian, Inc. Ashcroft, N. W., & Mermin, N. D. (1976). Solid State Physics (1st ed.). Saunders College Publishing.Texts and materials provided by the teacher.

Gain practical and applicative skills in quantum and classical modeling of chemical systems: molecules, solute/solvent systems, porous solids, derivatized surfaces.
Learn the fundamentals of the main simulation and modeling techniques used in theoretical chemistry.

Knowledge of quantum mechanics (at the level provided by the Physical Chemistry courses of the Bachelor's Degree in Chemistry).
The contents of the Theoretical Chemistry course taught in the Master's Degree in Chemical Sciences, even if attended at the same time, are very useful, although not essential.

Frontal lessons in the classroom.
Computer exercises at the Department workstations.

Numerical exercises are carried out on a workstation under in a Unix OS.A practical introduction to Operating System and command shell will be given.

Oral exam.

Fortran Programming for Scientific Computing:

* Introduction to scientific programming and the concept of an algorithm.
* Translation of a scientific problem into input, operations, and output.
* Programming languages and the role of Fortran in scientific computing.
* Installation and use of the GFortran compiler.
* General structure of a Fortran program.
* Declaration of variables and main data types.
* Explicit typing and use of `implicit none`.
* Arithmetic operators, expressions, and type conversions.
* Numerical precision and use of double precision.
* Input and output operations with `read`, `print`, and `write`.
* Formatting of integers, real numbers, strings, and scientific notation.
* Reading from and writing to external files.
* Management of input/output errors using `iostat`.
* Conditional structures `if–then–else`.
* Iterative loops `do` and `do while`.
* One-dimensional and multidimensional arrays.
* Dynamic memory allocation and deallocation.
* Vector operations and intrinsic array functions.
* Implementation of simple physicochemical models.
* Calculation of the average kinetic energy of an ideal gas.
* Modular programming using functions and subroutines.
* Argument passing and `intent` attributes.
* Use of Fortran modules to organize code.
* Quantum-mechanical application to the particle in a box.
* Numerical representation and manipulation of matrices.
* Calculation of eigenvalues and eigenvectors.
* Use of the BLAS and LAPACK numerical libraries.
* Diagonalization of symmetric matrices using `DSYEV`.
* Verification of diagonalization through matrix transformations.
* Jacobi iterative method for diagonalization.
* Numerical integration using the trapezoidal rule.
* String manipulation and substring searching.
* Automatic extraction of data from scientific program output files.
* Extraction of free energies from Gaussian output files.

DFT:

* Geometry optimizations.
* Simulation of vibrational spectra (IR).
* Simulation of UV/Vis spectra using TDDFT.
* Simulation of circular dichroism spectra using TDDFT.
* Simulation of chemical reactions using the IRC approach.
* Calculation of relative energies and Boltzmann populations.
* Introduction to potential energy surfaces.
* Minima, transition states, and saddle points.
* Optimization of transition states with Gaussian.
* TS, QST2, and QST3 methods.
* Analysis of vibrational and imaginary frequencies.
* Qualitative verification of the normal mode associated with the transition state.
* Calculation and interpretation of the Intrinsic Reaction Coordinate.
* Analysis of energy profiles along the reaction path.
* Comparison of different reaction channels and transition states.
* Interpretation of stereochemical selectivity.
* Distinction between kinetic and thermodynamic control.
* Relationship among free energy, equilibrium constant, and rate constant.
* Application of the Eyring equation to the prediction of selectivity.

Post-Hartree–Fock Methods:

* Calculation of multireference electronic structures.
* Simulation of optical spectra using CASSCF.

Classical Methods, Introduction to Solid-State Systems, and Simulations with LCAO and Plane-Wave Codes:

* Molecular dynamics.
* Free-energy calculations using thermodynamic integration.
* Simulation of adsorption processes using Monte Carlo techniques.

Ability to independently design and execute simulations of chemical systems with different theoretical and computational techniques.
Ability to model different chemical problems, and the most appropriate simulation techniques.