reflection 3

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Reflection 3: Synthesis of Scientific Concepts Across Courses

Summary of how the rubric item was addressed in this reflection:

This reflection shows how I have synthesized key ideas across the program content around the idea that:

A SUBSTANCE'S SHAPE IS STRONGLY RELATED TO ITS PROPERTIES AND/ OR ENERGY.

As a participant in the MCE program, I have taken 8 content courses that have reintroduced me to topics in General Chemistry, Organic Chemistry, Spectroscopy, Inorganic Chemistry, Environmental Chemistry, Biochemistry, and Information Technology Associated with Chemistry. I have found that a persistent theme in each course is the importance of molecular shape in influencing chemical behavior.

I present 6 pieces of evidence from various courses that show how I have synthesized various course concepts around this central idea. Shape is important!!!!

COURSE & EVIDENCE

REFLECTION

Chem 501/2:
General Chemistry & Organic Chemistry I
Information & Experimental Chemistry
Dr. Bryan Roberts & Dr. William Dailey
Shape and energy (sterics)

Conformational analysis of butane (Summer 2007):
butane chart

The conformation (shape adopted by rotation around a sigma bond) affects the steric energy of a compound. Conformations that decreases steric repulsions by keeping bulky groups far away from each other have lower energy and are therefore more favored. This concept also applies to the folding of protins. There may be local minima, but the most favored shape has the lowest energy.

Conformational analysis of butane:

The lowest energy, least sterically hindered conformation is the anti- conformation (180 deg). The highest energy, most sterically hindered conformation is the methyl-methyl eclipsed conformation (0 and 360 deg). As butane rotates around its C2-C3 bond, the energy of the molecule changes to reflect the steric hindrance encountered in the particular conformation.

Chem 503:
Organic Chemistry II
Dr. Bryan Roberts
Intermolecular attractions/ polymers (January 2008)

Macrogalleria of polymers web exploration: Polyethylene
(January 2008)

Intermolecular forces/ polymer PIM Question:
(January 2008)
dyneema

Enduring Understanding (January 26, 2008):

V. THE PHYSICAL PROPERTIES OF A POLYMER ARE A FUNCTION OF POLYMER STRUCTURE.
a. Crosslinking increases the rigidity of a polymer.
b. Branching increases the intermolecular contact distances between polymer chains thus decreasing the dipole-dipole and/ or London dispersion attractions and making the polymer more flexible.
c. Polymer chains which interact through dipole-dipole and/ or London dispersion attractions tend to be strong but flexible and suitable for applications like fabrics, ropes, coatings, etc.
d. A highly regular polymer may pack so as to give regions of high crystallinity which make the polymer denser, stronger, and more rigid.

The shape, in particular, the degree of branching, of polethylene affects its physical properties (e.g. strength, rigidity, opacity).

HDPE can be used to make bulletproof vests, while LDPE can be used to make lightweight (relatively flimsy) disposable plastic grocery bags.

HDPE:
Linear polyethylene has a shape conducive to close packing of polyethylene fibers and extensive London dispersion interactions between each strand. This produces a tightly bound, high density product that can be used for applications that require rigidity and strength.

LDPE:
Highly branched polyethylene, however, has a shape that resists close packing, and thus, has low levels of London dispersion forces. This produces a light, low density product that is ideal for applications that do not require strength, but do require flexibility.

Chem 504:
Biochemistry & Molecular Biology
Dr. Stacy Gelhaus
Enzyme substrate specificity/ allosteric inhibition (hemoglobin)

Enzyme/ substrate shape (July 2009 .ppt):

The shape of an enzyme (its active site, in particular) is directly related to the specificity and effectiveness of its function.

Slide 1-3:
The active site of an enzyme is designed to specifically bind to a particular substrate (with a particular shape and polarity) and catalyze a specific reaction by stabilizing the transition state. As mentioned in Slide 2 to the left, "this precision is a result of the intricate three-dimensional structure [i.e. shape and polarity] of the enzyme."

Slide 4:
Because shape plays such an important role in enzyme-substrate interactions, transition state analogs (which are bound by the enzyme, but cannot be acted upon) can effectively inhibit an enzyme.

ALLOSTERIC REGULATION:
A brief discussion of oxyhemoglobin (oxygenated tetramer in blood), deoxyhemoglobin (deoxygenated tetramer in blood), myoglobin (monomer in body tissues), and fetal hemoglobin.

Furthermore, certain enzymes and proteins (such as hemoglobin) can be regulated allosterically--meaning that their function can be altered by a change in shape (i.e. conformation).

When oxygen binds hemoglobin, the protein changes shape, decreasing the size of the "hole" at the center of the protein.
BPG's shape and polarity allow it to bind hemoglobin to stabilize deoxyhemoglobin, so that hemoglobin has a lower affinity for oxygen than myoglobin (this is good--tissue cells can get the oxygen from hemoglobin)
two amino acid in fetal hemoglobin are different (serine for histadine-143 in the beta units), decreasing BPG affinity, this gives fetal hemoglobin a higher affinity for oxygen (this is good--the fetus can get the oxygen from mom's blood)

DENATURING AN ENZYME

Enzymes that lose their shape because of pH changes, heat, or disulfide bond disruption lose their function until they refold into the active conformation.

Chem 505:
Environmental Chemistry
Dr. Mark Hermanson & Leslie Anderson
Shape and biotoxicity

Pesticides: DDT's effectiveness as a pesticide and as a hormone mimic (August 4, 2008 .ppt)

Carcinogenic Toxins: Dioxins, Furans, and planar PCBs (August 11, 2008 .ppt)

The shape of a compound--specifically, how planar it is, impacts its toxicity.

DDT is a nonplanar compound used as a pesticide. Its use is now banned in the US because of its persistence (it is very resistant to oxidative, hydrolytic, or photolytic degradation), its tendency to bioaccumulate (K_ow=100,000), and its interaction with the human estrogen receptor (i.e. action as a hormone mimic). While DDT's ability to bioaccumulate has much to do with its lipophilic phenyl rings,

DDT's nonplanar shape (due to the sp³hybridization of its central carbon) and the steric repulsions of its chlorine substituents are responsible for its potency as an insecticide, and
the shape of its phenyl rings makes it a good mimic for estrogen, which also contains a phenyl ring.

******************************

Other toxins, such as dioxins, furans, and other polyaromatic hydrocarbons can be carcinogenic because of their planar shape. In these compounds, the addition of large halogen substituents can reduce the carcinogenicity of the compounds by forcing the compound (via steric repulsions) into less toxic nonplanar conformations.

Chem 506:
Inorganic Chemistry
Dr. Donald Berry

August 2008 notes and problem set:
Crystal Field Theory & Strong vs. Weak ligands

Activity:
(click on image for larger view)

Problem set:
(click on image for larger view)

Notes:
(click on image for larger view)

The shape of the coordination compound is related to its electron configuration and its crystal field stabilization energy (CFSE)--aka splitting energy (the difference in energy between previously degenerate orbitals).

The magnitude of the CFSE is affected by:

shape of the coordination environment (octahedral, tetrahedral, or square planar (D_4h))
ligand "strength", those ligands with a more intense negative charge will induce greater splitting.
the metal identity (i.e. size, charge, number of electrons)

Greater ligand-d orbital overlap = higher energy

Octahedral coordination environments have a characteristic two over three splitting of d orbitals because the x²-y² and z² orbitals have greater overlap with ligands than the xy, xz, or yz orbitals.

Square Planar coordination environments split further (imagine the effect of removing 2 ligands along the z axis), so that the x²-y² orbital and z² orbital split (in this case x²-y² is the higher energy one) and the three xy, yz, and xz orbitals split (one over two--in this case xy orbital is higher energy than the yz and xz orbitals).

Tetrahedral coordination environments have a characteristic three over two splitting of d orbitals because the xy, xz, or yz orbitals experience greater overlap with ligands than the x²-y² and z² orbitals.

Chem 507:
Molecular Spectroscopy
Dr. Susan Phillips & Dusty Carroll

ChemActivity 21 HW Answers: IR Spectroscopy, Questions #8-10 (January 7, 2009)
(click on image for larger view)

Quiz #6 (March 7, 2009)
(click on image for larger view)

The shape, specifically a molecule's symmetry as it relates to molecular dipole moment, will affect what vibrational modes are detected in IR spectroscopy.

Molecules have various vibrational modes in which their bonds stretch or bend. Any vibrational mode that causes a change in the overall dipole moment of the molecule will absorb IR radiation, and can be detected by IR spectroscopy. Those vibrational modes that do not change the overall dipole moment of the molecule can often be detected by Raman spectroscopy.

CO₂ (symmetric, linear molecule) vs. H₂O (bent molecule) and NH₃ (trigonal pyrimidal)

CO₂ has 4 vibrational modes. Because of the symmetric shape of the molecule, the symmetric stretch is IR inactive because the dipole moment of the molecule does not change. The other 3 modes (2 assymetric bending--in/out of the x-y plane, in/out of the x-z plane; 1 assymetric stretching) are all IR active. (See
http://www.chem.purdue.edu/gchelp/vibs/co2.html, which requires Chime).

In comparison, all the vibrational modes of H₂O and NH3, which are not symmetric, can be detected with IR spectroscopy.

CONCLUSION

In conclusion, through continually having to revisit the connection of shape to various properties throughout the MCE coursework, I have further realized the importance of shape. The natural shape of a molecule is that which confers the most favorable (lowest) energy profile--VSEPR explains how molecules move their bonds and lone pair electrons as far away from each other to minimize e- to e- repulsions. In the case of coordination compounds, the introduction of ligands yields electron configurations that are characteristic to the shape of the coordination environment.

Shape, whether molecular geometry (which is a function of connectivity and atomic composition) or conformation (which is a function of folding or rotation around sigma bonds), directly impacts the energy profile and properties of the substance. Biological interactions, such as those between enzymes and subtrates or between signalling molecules and cell receptors, are often mediated by the "fit" (which is a combination of shape and polar interactions) between two molecules. In polymers and plastics, macroscopic properties are often determined by the intermolecular interactions at the submicroscopic level, which are strongly influenced by molecular shape and how closely molecules can pack. In spectroscopy, the symmetry and/ or shape of a molecule can impact the magnitude (and therefore) type of energy that is absorbed. The symmetry of a compound affects the detection of its vibrational modes in IR spectroscopy (since only vibrational modes that change the molecular dipole moment absorb IR energy). For coordination compounds and complex ions, the shape of the coordination compounds is highly related to the energy levels of the transition metal's d orbital (those with greater overlap with ligands are promoted to higher energies), this affects the absorption of energy and the number of unpaired electrons (whether the complex is dia- or paramagnetic).