Molecular Design
Faculteit  Science and Engineering 
Jaar  2017/18 
Vakcode  CHMD11 
Vaknaam  Molecular Design 
Niveau(s)  bachelor 
Voertaal  Engels 
Periode  semester II b 
ECTS  5 
Rooster  rooster.rug.nl 
Uitgebreide vaknaam  Molecular Design  
Leerdoelen  At the end of the course, the student is able to: 1. reproduce a number of concepts and quantification related to rational molecular design: (free) energy landscapes, intermolecular interactions, StructureProperty relationships; 2. explain the origin of intermolecular interactions and calculate Boltzmann and orientationally averaged interaction energies between molecules represented by charge distributions as a function of distance; 3. explain the molecular driving forces energy and entropy and their implications for molecular assembly and shape (folding); 4. reproduce a number of molecular descriptors used in Quantitative StructureProperty Relationships and be able to perform regression analysis leading to such relationships; 5. reproduce the general ideas behind molecular modeling techniques and be able to generate and analyze data using modeling software; 6. collect primary scientific literature pertaining to the selfassembly or folding behavior of a class of molecules and summarize this material in an essay written in English; 7. point out the assumptions made in the derivations of the equations and their limitations in relation to the techniques used in rational molecular design and chemical reality. 

Omschrijving  Molecular Design is any activity with the aim to predict what the properties of (a collection of) molecules are other than through trial and error. As such, a 5 ECTS course on Molecular Design can only discuss backgrounds and principles and provide some practical experience. Indeed, this course is very much handson. The students are supposed to apply the concepts in practice using literature retrieval software, Mathematica and modeling software  there is no separation between lectures, tutorials, and practicals. Here, we choose to focus on developing an understanding intermolecular interactions, ultimately deriving from the interactions between the charged building blocks of molecules: nuclei and electrons. Their collective interactions can be represented in a simplified manner through the multipole expansion, leading to a hierarchy of interactions between ions, dipoles, quadrupoles, etc. from which a qualitative prediction of much of the intra and intermolecular organization is possible, in combination with the application of statistical thermodynamical techniques (Boltzmannweighted averaging over possible conformations). More detailed molecular models can nowadays be simulated in the computer and an introduction to Molecular Dynamics simulations will be given, including handson experience. Literature survey of a particular class of molecules will illustrate how these interactions lead to macroscopic properties, e.g. selfassembled structures or molecular switches in folding. Detailed molecular modeling is often too expensive and molecular design often relies on statistical correlations between structure and properties; in particular drug design uses these. An introduction to molecular descriptors and their use in statistical correlations is part of the course. Mathematica is used to quantitatively correlate the boiling point of organic compounds to various molecular descriptors. The theoretical material is described in Ch. 16 of Atkins' and De Paula's Physical Chemistry and in a Reader. Additional material will be made available via the NESTOR website. Essays written by the students are part of the material for the written exam. 

Uren per week  
Onderwijsvorm 
Hoorcollege (LC), Practisch werk (PRC), Werkcollege (T)
(Total hours of lectures/tutorials: 40 hours, computer practicals: 12 hours, library instruction and literature search: 8 hours, feedback: 4 hours, self study: 76 hours.) 

Toetsvorm 
Opdracht (AST), Practisch werk (PR), Schriftelijk tentamen (WE)
(Computer practical exam, assignment with report) 

Vaksoort  bachelor  
Coördinator  dr. A.H. de Vries  
Docent(en)  dr. A.H. de Vries ,prof. dr. S.J. Marrink  
Verplichte literatuur 


Entreevoorwaarden  The course unit assumes prior knowledge acquired from Calculus, Molecules: Structure, Reactivity and Function, and Physical Chemistry I, bachelor programme Chemistry and Chemical Technology (year 1) and Quantum Chemistry and Physical Chemistry II, bachelor programme Chemistry (year 2).  
Opmerkingen  Assessment criteria: The written tests assess the ability of the students to explain and apply the concepts of intermolecular interactions and molecular driving forces to theoretical problems and practical examples taken from the literature. Assessments of these skills reward correct use of standard formulae and equations, clear presentation of derivations of formulae, correct numerical calculations, and correct use of units. As far as explaining concepts, assumptions, and limitations are concerned, correct statements and sound reasoning are rewarded. A template for answers including a points scheme is provided for each test, and I refer to those documents for details. The computer practical test is assessed on correctness of the implementation, readability of the implementation, structure of the report, style of presentation of the results, and comments on the results. There is no strict adherence to a template required. The essay is assessed on the structure and clarity of the material, appropriateness to the subject, depth of the discussion, correct use and representation of literature citations. There is no strict adherence to a template required, but the essay must be compatible with a scientific journal style. A number of more specific questions is provided as a guideline to what type of material to include in the essay. The final mark for the course unit is determined as a weighted average over the theoretical (1 part), computer practical (1 part), and essay (1 part) test marks. The theoretical test mark is calculated as the number of points (maximum 100) scored on the final written exam divided by 10, with a maximum of 10. There is a requirement that the number of points on the final written exam is at least 45. 

Opgenomen in 
