Molecular modeling teaching

The aim of the series is to present the latest fundamental material for research chemists, lecturers and students across the breadth of the subject, reaching into the various applications of theoretical techniques and modelling. The series concentrates on teaching the fundamentals of chemical structure, symmetry, bonding, reactivity, reaction mechanism, solid-state chemistry and applications in molecular modelling. It will emphasize the transfer of theoretical ideas and results to practical situations so as to demonstrate the role of theory in the solution of chemical problems in the laboratory and in industry. 

Over the span of two decades, molecular modeling has emerged as a viable and powerful approach to chemistry. Molecular mechanics calculations coupled with computer graphics are now widely used in lieu of tactile models to visualize molecular shape and quantify steric demands. Quantum chemical calculations, once a mere novelty, continue to play an ever increasing role in chemical research and teaching. They offer the real promise of being able to complement experiment as a means to uncover and explore new chemistry. 

In his constant search for better methods of teaching he made a 60-minute color-sound movie Techniques of Organic Chemistry, and developed a set of precise plastic molecular models, which are larger than, but have the same relative dimensions as, Dreiding models. Unlike the latter, however, the Fieser models have been so inexpensive to manufacture that even undergraduate students have been able to afford a set. 

The increasing use of computational chemistry in teaching and research has created a burgeoning market for software. Today the potential user or purchaser of molecular modeling software is faced with a bewildering array of products. 

A discussion of the properties of various molecular models and what they teach us about the connections between intermolecular forces and phase diagrams ... 

Hardwicke, A. J. (1995). Using molecular models to teach chemistry Part 1 modelling molecules. School Science Review, 77(278), 59-64. 

The facile conversion of sequences into 3D structures that can be displayed and manipulated on the computer screen (molecular graphics) has greatly improved molecular modeling as an essential tool in biochemical research and teaching. The ID sequences can be converted into 2D structural representations by the use of ISIS Draw, which can be down-... 

The chapter is outlined as follows. First we present some curriculum issues related to molecular modeling and to quantum chemistry. Then we give a brief introduction to the fields of quantum chemistry, molecular mechanics, and molecular dynamics. Following this, we survey the use of molecular mechanics in the curriculum, particularly as it relates to articles that have appeared in the Journal of Chemical Education. Finally, we each present material that outlines our use of computers in the curriculum. This approach allows us to review the literature in each of the areas we cover. We each teach in an undergraduate institution, but many of the topics we discuss also can be included in a graduate course, albeit at a greater depth than at the undergraduate level. 

In 1968 Bartell published an article on the use of molecular models in the curriculum. In this paper the qualitative valence shell electron pair repulsion (VSEPR) model and the relative role of bonded and nonbonded interaaion in directed valence is discussed. The author correctly predicted the increasing importance of model force fields for geometry prediction. An early discussion of the use of molecular mechanics in teaching can be found in a paper by Cox. 07 A cursory description of the methodology of force field calculations is presented, along with computational results on the relative energy of the rotamers of butane and the conformers of cyclohexane. 

Thus, although the model pair potential might not be realistic, it can still be useful in application to complex systems. Sometimes, the water-like particles are non-realistic from the outset (such as 1-D or 2-D models see Secs. 2.4 and 2.5). Nevertheless, the study of such systems can teach us what features of the molecular model are essential for the manifestation of some macroscopic properties of the system. From such studies, one can draw similar conclusions about the features of the models in 3-D that account for the specific and outstanding macroscopic properties of real liquid water. 

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