pmmooc

21st century key cases in chemistry: interplay between molecular modeling and experiment

This course aims at complementing the training of students prior to their potential enrollment to the Master in Advanced Catalysis and Molecular Modeling (MACMoM), with the strong intention also to improve its presence in the world wide network.

The course will provide an attractive and solid background in different experimental techniques, synthetic procedures and computer simulation methods, in order to address the issues most innovative modern chemistry problems, from fullerene chemistry to biomimetic catalysts and sustainable processes.

Target public:

It is addressed mainly to BSc students of Chemistry and related areas such as Material Science or Biotechnology, as well as general public with solid background in science.

Structure of the course:

The structure of the course focuses on the study of different real cases in which the interplay between theory and experiment ultimately lead to fruitful results and progress of Science and Chemistry in particular. Namely, we will show how theoretical studies (e.g. reaction mechanisms) pointed towards additional experiments in the lab to verify the predictions, and vice versa, when experimental evidences guided computational simulations and confirmed the theoretical models.

The course will start with three “zero-th order” lessons describing the essential background on quantum chemistry and computational chemistry methods, basic concepts on organometallic chemistry and reaction mechanisms, and chemical reactivity.

0.1) Basic concepts in computational chemistry: what can be modeled and to which accuracy?

We will introduce the essential elements of Quantum Chemistry, from the postulates of Quantum Mechanics and their implication in chemical phenomena, to the practical aspects of electronic structure calculations. Scientific computation: use of computer clusters and supercomputation.

0.2) Basic concepts in catalysis: towards sustainable chemical processes

We will review the basic concepts in organometallic chemistry, the most fundamental organometallic reaction steps and the catalytic cycle (reaction mechanism).

0.3) Basic concepts in chemical reactivity.

We will review key concepts of chemical kinetics and thermodynamics. Kinetic control vs thermodynamic control.

Then, the main body of the course will cover four case studies. The case studies will be based on the following research papers, authored by researchers of the Institut de Química Computacional i Catàlisi

1) M. Swart, A change in oxidation state of iron: scandium is not innocent, Chem. Comm. 2013, 49, 6650-6652

2) O. El Bakouri, D. Cassú, M. Solà, T. Parella, A. Pla-Quintana, A. Roglans. A new mild synthetic route to N-arylated pyridazinones from aryldiazonium salts. Chemical Communications, 2014. DOI: 10.1039/c4cc03190c.

3) M. Parera, A. Dachs, M. Solà, A. Pla-Quintana, A. Roglans. Direct detection of key intermediates in rhodium(I)-catalyzed [2+2+2] cycloadditions of alkynes by ESI-MS, Chemistry, a European Journal, 2012, 18, 13097-13107.

4) Osuna, S.; Rodríguez-Fortea, A.; Poblet, J. M.; Solà, M.; Swart, M. Product Formation in the Prato Reaction on Sc3N@D5h-C80: Preference for [5,6]-bonds, and not Pyracylenic Bonds, Chem. Commun., 2012, 48, 2486-2488.

Along the first-person narration of the multidisciplinary research carried out in each case study, basic concepts of chemistry and physics underlying the experiments and the corresponding computer simulations will be introduced, namely:

A) Methods and techniques for structural and spectroscopic determination

The fundamentals of the techniques listed below will be provided first. Then, practical descriptions of the methods, including actually showing their use and the whole process of data obtaining and processing will be shown in the videos. Finally their relevance in research will be highlighted by pointing out their important role in the case studies.

A.1) Nuclear Magnetic Resonance (NMR)

A.2) Mass Spectrometry (MS)

A.3) X-ray Diffraction (XRD)

A.4) Infrared Spectroscopy (IR)

A.5) UV-VIS Spectroscopy

A.6) Electronic Paramagnetic Resonance (EPR)

A.7) Mössbauer Spectroscopy

A.8) Redox potentials and Pourbaix diagrams

 

B) Methods and techniques for reaction mechanism elucidation

The videos will show the process of getting and interpreting the experimental evidences on mechanistic studies, covering the following aspects:

B.1) Kinetic analysis of reactions

B.2) Isotope analysis: primary and secondary KIE

B.3).Trapping and characterization of reaction intermediates

B.4) Structure-activity analysis

 

These 12fundamental lessons will be embedded into the four different case study modules, delivered as short clips of 4-5 minutes.

A final module will deal with the actual communication of the research undertaken.

3) Classic and 2.0 Scientific Communication

The process of publishing research. Basic issues of writing and organizing scientific papers for publication Use of new technologies in the dissemination of research results: blogs and wikis in education and research.

So, altogether the course will consist of 3 modules that will be developed along eight to ten weeks. A 4-6hrs/week of dedication is expected for the students during the course.

Schedule:

The course will be delivered during in spring of 2015, coinciding with the first pre-registration period to the Master in Advanced Catalysis and Molecular Modeling.

Competences:

Previous knowledge of several aspects is strongly recommended for this course. User-level knowledge of internet resources, Intermediate knowledge of English to understand both the audio and the additional materials online. Obviously, being the target bachelor degree students of chemistry, a previous knowledge of several aspects of chemistry is required.

 The competences/skills the students should acquire, at a very basic level, upon completion of the course are

C.1 To recognize the correlations between the electronic structure of molecular systems with structural features and reactivity. 

C.2 To understand how computational chemistry is integrated with experimental observations, and how one is able to use it as support in solving chemical problems of different nature.

C.3 To distinguish the principles and procedures of spectroscopic and spectrometric analysis for structural elucidation and characterization of chemical compounds.

 

Evaluation:

Each module will be accompanied by supporting documentation, how-to videos and links to related resources available on the internet. The evaluation will consist of a number of multiple choice questions inserted during the fundamental lessons A and B. Also, each module is presented as a real-time story where the experimental and theoretical evidences described in a given clip determine the flow of the story, i.e. the next step in the research process. The student will be repeatedly asked questions like “what would do next?” or “what do you think will be the outcome of the forthcoming experiment?”, which will be unveiled in the next clip, again in a multiple choice fashion.

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