Models in Organic Chemistry: Chair Conformations, Newman Projections

This report provides a comprehensive analysis of the use of models in organic chemistry. It begins with an overview of organic chemistry and then delves into specific models such as chair conformations, Newman projections, and Fischer projections, explaining their uses and relevance. The report also discusses the learning outcomes associated with using these models, particularly for undergraduate students, and highlights the challenges encountered in teaching with them. It references previous research on the impact of models on learning and suggests that model learning is most beneficial for beginners. The report also touches upon the integration of writing skills and models in the curriculum to enhance student performance. The report emphasizes the importance of visual-spatial representations and the benefits of using models in understanding complex chemical structures. The report concludes by discussing the advantages and disadvantages of each model, providing a well-rounded view of their application in organic chemistry education.

UNIVERSITY AFFILIATION
DEPARTMENT OR FACULTY
COURSE ID
COURSE NAME
TITLE:
MODELS IN ORGANIC CHEMISTRY
STUDENT NAME
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DATE OF SUBMISSION
[Year]

EXECUTIVE SUMMARY
This report seeks to do a thorough research on the use of models in organic chemistry. Some of the
models implemented in organic chemistry are chairs conformations, Newman projections, and Fischer
projections. All these modes are well described in the introductory section of the paper. The paper goes further
to discuss the uses of the models, their relevance in organic chemistry, and the drawbacks of using each model.
The report seeks to understand the impact or influence the use of models in scientific units has on the learning
outcomes. Previous researchers have performed case studies that seek to analyze the impact of using the model
for the undergraduate and graduate students. This paper concludes that the model learning is most suitable for
the undergraduate or beginners of the organic chemistry coursework. The beginners need to grasp the concepts
at an early stage of their coursework before they delve into other areas. It goes further to discuss the struggles
associated with teaching using the models and the associated learning outcomes. One key research done in
Turkey shows the impact of integrating writing skills and models in the curriculum to attain the highest
performance from learners.
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TABLE OF CONTENTS
EXECUTIVE SUMMARY.........................................................................................................................1
INTRODUCTION.......................................................................................................................................3
OVERVIEW OF ORGANIC CHEMISTRY...........................................................................................3
MODELS IN ORGANIC CHEMISTRY.....................................................................................................3
CHAIRS CONFORMATIONS...............................................................................................................4
NEWMAN PROJECTIONS....................................................................................................................7
FISCHER PROJECTIONS......................................................................................................................8
SECTION II................................................................................................................................................9
LEARNING OUTCOMES WHILE USING MODELS IN ORGANIC CHEMISTRY..........................9
CHALLENGES ENCOUNTERED IN USE OF MODELS IN ORGANIC CHEMISTRY....................9
APPROACH TAKEN BY TEACHERS TO ADDRESS THE CHALLENGES...................................11
DISCUSSION AND RECOMMENDATIONS.........................................................................................13
LIST OF FIGURES
Figure 1 Illustration of Conformations of the Cyclohexane compound [Source: Dr.Siriwehane, 2008]...............................7
Figure 2 Newman Staggered and Eclipsed conformation [source: Villaen,2010].................................................................9
Figure 3 A sample question from CHM 257 Organic Chemistry Course............................................................................11
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INTRODUCTION
OVERVIEW OF ORGANIC CHEMISTRY
From the industrial age to the technology age, laboratory experiments have been used to collect, test,
analyze and draw conclusions on matter. For chemists and the pharmaceuticals, the studies or experiments are
carried out to determine the connections between molecular structures. There are two main goals in practical
chemistry which are synthesis and analysis. Models tend to provide information that is obtained from molecular
orbital calculations, which include structures, energy, and atomic charges. In organic chemistry, there is a great
focus on the potential energy surfaces as well as the bonding between different atoms especially the carbon and
hydrogen atoms.
The process seeks to connect the reactants to products via a transition state. The models compute the
energy of a given molecular structure. Organic chemistry requires that the learners get a visual-spatial
representation of matter or compounds. These concepts, both visual and spatial, are often offered to students
through the utilization of the technical chemical modeling sets (Bodner & Domin, 2000, p3). The use of a
white-board game with students to practice discerning between cyclohexane substituent directions and
positions, either pointing upward or downward or in an axial or equatorial orientation is a proper way of content
representation using models (Gilbert, 1991, p75). The quick tempo of this activity makes it an engaging method
for students to understand the topic.
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MODELS IN ORGANIC CHEMISTRY
The concept of molecular models in the study of organic chemistry brings out a new perspective on the
analysis of the subject matter. Previously, laboratory experiments formed the basis of study but now the
molecular modelling uses the graphics-intensive computers on a Unix-based platform to run software that
model and modifies the three-dimensional form of the organic matter under study (Al-Balushi & Al-Hajri,
2014, p49). The first pilot project on the use of molecular modelling was carried out during the fall in 1995. It
was run as a three-year project that sought to run the software in undergraduate chemistry related programs to
induct the students as well as test it for future use. One of the most common molecular modelling program to be
implemented was the Spartan that run on Silicon Graphics Indigo series workstations under the Operating
System highlighted above. The system was evaluated over the project period until the system was finally
accepted as a form of practical study on organic chemistry. Models are visual aids or representations that
highlight the main ideas and variables of the system or compound under study.
Models are used to give a perception or direct view of real-world scenarios using the Spartan software or
the ball-to-sticks models. Modelling in organic chemistry requires tools to help in the learning process. Modern
computational methods are seen to provide better theoretical predictions and accuracy while taking
measurements. Many laboratory experiments expose the students to a lot of risk especially if the components
used are hazardous to the skin or respiratory system. Models solve the issue as they are safe, easy to implement,
and very affordable (Dr. Siriwardane, 2008, p12). It is crucial to note that the molecular modelling does not
replace laboratory experiments rather it complements. The molecular modelling process allows a user to define
the problem statement, build models, perform calculations, and later analyze the results. The molecular
modelling approach reduces the material setup process that takes a lot of time in the laboratory experiments and
guarantees very high-quality results with a lot of input from the students performing the experiment.
According to Thompson, there are methodical models that are useful in describing and presenting
findings. The target group for such information is the scientific community as the models develop and make
changes over time. The improvements and updates on the models can be seen over relatively short time spans.
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Oversby (2000, p.227) describes the organic chemistry as a science that needs to use models for study. The unit
is an important facet in science as there are very few of the macroscopic observations which require to be
understood using representations or models. The models in science describe and present the scientific outcomes
which need to be used in the scientific community. According to Gilbert and Justi (2000), the curriculum
developers interpret scientific models and the models are transformed into school science curricula.
CHAIRS CONFORMATIONS
There are atom arrangements in spatial mode that facilitate the rotation of the carbon-carbon single
bonds known as conformations. The different arrangements are the conformers. The conformational isomers are
organic compounds denoted using chemical formulae which indicate the type and number of the atoms in the
molecule. The condensed formula of the organic compound shows the skeletal atoms in a molecule and places
them in a sequential order that indicates bonding. The organic compounds known as isomers are different
compounds that exhibit the same molecular formula with different structural formulas. One of the simplest
conformational structures is reviewed by analyzing the rotation of the two-methyl groups about the C-C bond in
Ethane. The chemical formula for Ethane compound is given as,
Ethane → H3 C−c H3
The structures of conformers tend to differ by the rotation around one or more bonds. One can,
therefore, determine the minima, maxima, and transition states of the structures. For the ethane compound one
can determine the torsion or dihedral angles of the carbon-hydrogen bonds as staggering conformations at
minima. The other position is the maxima where the bonds are referred to as eclipsed conformations. The
eclipsed conformation is as illustrated in the figure below under a 600 rotation where the carbon is directly
aligned with the C-H bonds on the closest carbon. On the other hand, the staggered conformation has one
carbon bisect where the H-C-H bond is on the adjacent carbon.
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It is illustrated as,
± 1800∧± 600−minima
± 1200∧00−maxima
Another common example of conformers is the cyclohexane. Its most stable conformation is the chair
form. The structure of the C-C bonds when observed on an aerial or side view, one can spot the chair form. All
the other bonds between carbon and hydrogen are combined using conformations that are closer to the ethane
staggered conformation structure. The cyclohexane compound is flexible and can take other shapes such as the
boat shape, the twist-boat shape and the half-chair shape. The chair conformation shapes are as illustrated in the
figure below,
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The cyclohexane is a six-membered single bonded carbon ring. The chair conformation appropriately
reflects the angles between the carbos in the ring and the positions of the groups on each carbon in the ring. The
conversion from one chair conformation to another, results in a change of energy in the structure as illustrated
in the figure below,
Figure 1 Illustration of Conformations of the Cyclohexane compound [Source: Dr.Siriwehane, 2008]
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The relationship between the cyclohexane and ethane shows some isomerism besides the chair conformations.
There are diverse connections among the atoms in the skeleton, position, and practical group. These
arrangements have similar connectivity but differ in other attributes such as the conformational geometry and
the spatial orientation. For students in the organic chemistry class, it is difficult to sketch and interpret the chair
conformations of a given compound under analysis (Graulich, 2015, p15). Some of the carbon-hydrogen bonds
are not easy to rotate to form different spatial arrangements. Some of the bonds are so complex to sketch and
the use of the Spartan Software helps in bringing to reality very complex networks and arrangements
demonstrating their orbitals and energy scales.
NEWMAN PROJECTIONS
The constitutional isomers compounds with the same molecular formula but a different connectivity
of their atoms in the skeleton are said to have stereoisomerism. There are two constitutional isomers that have
molecular formula,
C4 H10
These atoms differ in spatial orientation such as geometric, conformational, and optical orientations. The
model is used in the conformational analysis of the alkanes. The Newman projection, as a model used in alkane
stereochemistry, visualizes the confirmation of a chemical bond from the front to the back. The front atom is
represented by a dot and the back carbon as a circle. The front carbon atom is the proximal atom, while the back
atom is the distal. This type of representation clearly illustrates the specific dihedral angle between the proximal
and the distal atoms. The conformation can be illustrated as,
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Figure 2 Newman Staggered and Eclipsed conformation [source: Villaen,2010]
FISCHER PROJECTIONS
The Fischer projections are used to differentiate between the L-and D-molecules. It provides a two-
dimensional representation of three-dimensional molecules and there is little doubt that the ability to construct
and manipulate the 3-dimensional mental images from these drawings is crucial to the organic chemists (Duit &
Glynn, 1996, p174). The question below is a sample question in organic chemistry which can be easily
responded to even without the need for a three-dimensional imaging. This mode allows the penultimate carbon
of D sugars to be depicted with hydrogen on the left and the hydroxyl on the right. L sugars will be shown with
the hydrogen on the right and the hydroxyl on the left. All the horizontal bonds project towards the viewer,
while the vertical bonds project away from the viewer. All the horizontal bonds project towards the viewer
while the vertical bonds project away from the viewer. Unfortunately, the Fischer projection cannot be rotated
by 90 or 270 degrees in the plane of the screen on which it lies. The orientation of bonds relative to one another
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can change and converting a molecule to its enantiomer. On the other hand, the model easily rotates along the
1800 as it doesn’t change the molecule’s representation.
SECTION II
LEARNING OUTCOMES WHILE USING MODELS IN ORGANIC CHEMISTRY
This section seeks to address what is expected that the student will manage to do as a result of using the
models to learn or capture concepts in organic chemistry. The learning outcomes specify what the learner will
know or do as a result of going through the learning activities in their coursework. It is expressed as a skill or
attribute.
(i) To understand the concepts as described in organic chemistry by using the ball-to-stick models or
the Spartan Unix-based computer software to run simulations on the required compounds.
(ii) To come up with personalized designs and answer questions related to organic chemistry as well as
know how to represent the organic compounds in one-dimension, two-dimension and three-
dimension. Some of the processes require that one chooses examination questions wisely.
(iii) To determine the application areas of the organic chemistry especially in the pharmaceutical field.
(iv) To ensure that learners can have a learning module that they can use in the absence of a tutor to do
revision work as well as assignments on. The practical nature of the model learning enables a student
to grasp all the concepts of the content as well as ensuring that the work is well done.
CHALLENGES ENCOUNTERED IN USE OF MODELS IN ORGANIC CHEMISTRY
A study was conducted to determine the ability to use the curved-arrow or electron-pushing formalist as
a vital skill in organic chemist’s repertoire. It allows the chemist to use the technique to visualize the
compounds and thereafter write some mechanisms for the reaction. The participants of the case study were
bright and conscientious, as they had worked hard to master the elements of organic chemistry. A test is
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provided to students in 2-dimensional representation. The questions that have a 3-dimensional feature of a
molecule are solved by manipulating three-dimensional images of the molecules while other questions can
easily be computed by using the 2-dimensional stick structures with which organic molecules are shown.
Figure 3 A sample question from CHM 257 Organic Chemistry Course
Some of the questions require the use of molecules to have the 3-dimensional approach while others use
the 2-dimensional approach (Strickland, Kraft, & Bhattacharyya, 2010, p 297). Another challenge could be
found in the use of structural, molecular, displayed and skeletal formulae. The learning institutions need to
identify the most suitable learning models to ensure that the students grasp the concepts of organic chemistry as
intended.
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