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 a...Read More

UNIVERSITY AFFILIATION
DEPARTMENT OR FACULTY
COURSE ID
COURSE NAME
TITLE:
MODELS IN ORGANIC CHEMISTRY
STUDENT NAME
STUDENT REGISTRATION ID
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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The institutions have embraced computational modeling packages which are useful for studying but still
have some difficulties involved in the use of the software. The software packages are yet to supersede the
traditional methods of teaching organic chemistry as the molecular modeling kits are still used in the laboratory
environment for testing; that is, the ball-and-stick kits. The test kits used in analysis are mainly tailor made for
educational purposes to enlighten the students on various concepts of the organic chemistry units. The
molecular modeling tools are used on a 2-dimensional and 3-dimensional scale to bring out the spatial
arrangements. Unfortunately, the modeling techniques may not be used outside the confines of education such
as projects, examinations, and assignments.
The study of organic chemistry in graduate school or college can be difficult for students. The spatial
understanding required for success in organic chemistry is not readily accessible via old textbook and lecture
delivery methods. A study was carried out correlating the spatial ability with the tests performance in organic
chemistry. The study found out that the students with better ability to manipulate the three-dimensional images
as two-dimensional pictures had a higher probability of success on the exam questions (Bhattacharyya &
Bodner, 2005). This applied to questions that required that kind of mental interpretation and manipulation. The
question becomes how to help students make sense of the spatial reasoning of organic chemistry to attain
success in the class.
APPROACH TAKEN BY TEACHERS TO ADDRESS THE CHALLENGES.
Employing a model for representing the structures of molecules as well as their properties is a common
practice, which educators and other scientists use to comprehend the complex behavior of these molecules in a
more tangible manner. An abundant number of papers in the educational literature describe innovative models,
visualization materials or activities for this matter. The model systems will provide a similar representation and
can roughly convey the same information compared to the actual systems with much less effort. The method re-
emphasizes the reason behind the use of models which enables the learners to observe at the macroscopic scale
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what the systems are which is crucial for understanding of chemical concepts (Barnea, 2000 p312). The
beginner students can adopt to the models form of learning as the models have become a popular tool for
teaching and learning main concepts of organic chemistry. The common methods of learning involve written
material such as books, journals, laboratory experiment manuals, and peer-reviewed reports. The images in
these materials can only be in one-dimension or two-dimension. When the learning system introduces the three-
dimensional molecular models for learning, it grasps the student’s attention and makes learning and
understanding of organic chemistry concepts much easier.
Some of the beginner units in undergraduate organic chemistry studies are stereochemistry and
conformational studies of molecules (Boutler, 2000 p301). When the model learning is introduced to students at
this stage, it makes the learning process very easy and adaptable. The students can, thereafter, explain concepts
from a clearer vision unlike when subjected to other written learning materials. Some students tend to have
difficulties with the imagination and simulation of molecules or other relative shapes in the 3D environment.
Teaching these subjects can be tedious over the years as it is repetitive year after year; the model learning,
however, gives the teaching experience a new perspective (Coll & Treagust, 2001 p379). A number of pilot
tests were done on the model teaching in organic chemistry and a number of computational modelling packages
have been introduced in the curriculums to improve learning and practical works.
Some of the steps taken by teachers to make the model learning very effective are such that the teacher
needs to recognize the basic roles of representations such as complementary, enticing and captivating
interpretation of concepts using models and the construction of deeper understanding. These steps enable the
teacher to gain awareness on the issues and the construction of an improved learning environment. The study of
model learning in Turkey discusses that the student’s ability to acquire knowledge employing the scientific
approach while engaging in conceptual learning requires the identification and implementation of the models in
the education or learning process (Gilbert, K 1998 p89).
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Learning should be structured based on learner's prior knowledge. Starting with known and ending up to
unknown gives learners the necessary jumpstart in their thinking, giving their minds time to restructure what
they know and what they ought to have covered and relating it to the current situation. This gives the instructor
a less time in pumping ideas required to have been learned at an early stage by learners. For example, in
learning conformational analysis of alkanes, it is believed that learners know what are alkanes in organic
chemistry (Gilbert & Boulter, 1998 p59).
In teaching, it is important to put into consideration that learners have individual differences and that the
ability differs across a group of students. So as to say, different methods of instruction should be put into
practice. This ensures that for different learners, content absorption varies depending on how it is delivered. The
learners will have a varied means of choosing which learning method matches their abilities and select also
based on their comfort. There are multiple ways in which chemistry phenomena can be represented. The
meaning and definition of terms in organic chemistry needs to be well expounded as it provides learners with a
very wide scope of information. More materials can be provided to the students to supplement the model
learning approach that only give the students the ability to perceive compounds in a 2-D or 3-D manner (Gunel
& Yesildag-Hasancebi, 2016, p112). Providing them with organic chemistry articles pamphlets journals will
assist them in broadening their minds and cater for voluminous organic chemistry words. It is important to have
the students fully engaged in the learning process for them to gain comprehension on various concepts. Such
participatory actions make the learning environment pleasant for both the teachers and the learners.
There are a number of resources available to help the learners improve and understand various concepts
which may be available from different sources. When learning it is important to use the pre-existing materials in
written form as well as the modelling tools to learn. It also builds confidence that the particular material or
model will deliver the content in the discussion. If learners do not have the basic organic chemistry knowledge
it will be hard for them to grasp content based on models used in the representation of organic compounds
(Gergen, 1995 p28). The use of models should be emphasized in all levels of organic chemistry. Learners tend
to grasp content delivered with the help of hands-on activities better than the one presented in a mere lecture
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method. Inorganic models, students will make it easy to convert the 3-D object seen and touched to a 2-D image
and that is what we call a learning experience. The learning experience takes different forms such that the user
thinks or does the practical work in 3-dimensional concrete model and then simplifies the design to 2-
dimensional spatial arrangement. The 2-dimensional arrangement is used in the compound analysis as well as in
the suggested pedagogical sequence. (Gabel & Sherwood, 1980, p79).
DISCUSSION AND RECOMMENDATIONS
Writing is a common practice in the learning process. It has been embraced globally as a key method of
teaching and learning. It is defined as an integral part of generating complementary ideas, gaining
understanding, and reporting on investigations made. A case study of Turkey shows that the curriculum
designers have not yet embraced the modal representation as part of their curriculum. There are strategies in
place to introduce the model learning so as to improve teaching and learners’ performance in the science units.
The use of model learning would require that the ministry of education performs a number of changes in the
education system at Turkey. Unfortunately, in some nations the education system is influenced by very many
external factors such as political changes, policy changes, modern practices, and social changes. Instructors
should give learners not only the skeleton part but also the meat in understanding organic chemistry models.
Learners need to be guided and the teacher should act as a facilitator of learning so as to make learners able to
discover on their own and among peers (H.M, 1999, p38).
Curriculum developers insist on discussing the different types of diagrams during the teaching of
organic chemistry and they suggest that the students ought to draw and describe the two-dimensional diagrams
with reference to the ball and stick models (Tang & Moje,2010 p83). Finally, the art of using models to deliver
feedback to students in a way that allows them to confront illusions of understanding or over-confidence in
performance, providing an opportunity to develop rich internal models that can be applied to the manipulation
of representations in the future (Treagust & Mamiala, 2004, p18). It is also important, as highlighted earlier in
the introduction, for the models to be introduced at both the onset of secondary and tertiary levels. There are so
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many drawings that represent compounds in science materials which may range from the simple Lewis
structures that show the atom connectivity through line-bonds. In the common setup in laboratories the carbon
to hydrogen bonds are demonstrated using the ball and stick structures as shown in the figures above. This
represents the 3-dimensional design of compounds or molecules but the images are simplified to 2-dimensional
molecules for analysis and for written form (Sevian, Szteinberg, Auguste, & Perez, 2015, p440).
There are different representations performed for different forms of matter or situations. Each
representation has a number of merits and demerits associated with it and the explanation of the models used
needs to be clear, concise, and in line with the previously done work which could be in written form. Some of
the attributes that a student should possess to enhance learning are active participation, reflective sessions after
classes, and the zeal to perform research after the classes or learning sessions are over. The students need to
have an overview of the coursework before they proceed with it so that they can acquire the knowledge of any
concepts introduced in the course of learning. The teaching models adopted influence the learning abilities of a
student (Duit & Treagust, 1998). The instructor behavior is a crucial determinant in the establishment of a safe
or comfortable learning behavior. The learners need to be aware of the fact that the comments that are not fully
explained invoked stereotypes and promote incorrect summaries. The quick acceptance of responses from the
learner on the correct answers to questions asked in a classroom or practical laboratory session may only seek to
favour the fast thinkers.
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