To select a broad concept and be able to synthesize content learning around this concept.
The concept I present for this rubric is the characteristics of carbon bonds. Here I relate the nature of carbon bonding to concepts I learned across the scientific classes from the MCE program.
Characteristics of Carbon Bonds
Carbon is found in a variety of different compounds. It is in the food we eat, clothes we wear, cosmetics we use, and gasoline that fuels our cars.
Carbon is a very special element because it plays a dominant role in chemistry.
The carbon atom
A good way to look at carbon atom is by using energy graph.
Two electrons are found in the 1s orbital close to the nucleus, next two go to the 2s orbital and the remaining ones are in separate 2p orbitals. They are in two separate p orbitals because p orbitals have the same energy and the electrons would rather be in separate orbitals (Hund's rule: orbitals of equal energy are each occupied by one electron before any orbital is occupied by a second electron, and all electrons in singly occupied orbitals must have the same spin state).
The actual location of those electrons cannot really be determined with certainty but the electrons appear to be smeared into orbitals as shown in the figures below.
Since the valence energy shell of carbon can hold eight electrons, each carbon atom can share electrons with up to four different atoms. Carbon can combine with other elements as well as itself. This allows carbon to form many different compounds of varying size and shape.
1. Chem501: Hybridization of carbon molecules
Enduring Understanding: The chemical bond; bonds formed by electron-pair sharing.
Here I reflect about hybridization and how methane has tetrahedral geometry.
Guide line: x number of orbitals = x number of hybrid orbital. Evidence below shows: Hybridization July 6, 2007
#of hybrid orbital = # of sigma bonds + # of lone pairs.
# of hybrid orbital = # of atomic orbitals combined. Lone pair takes up more space than bonding pairs, thus, they compress the bond angle. The box in this evidence below shows 2s+2pz+2py+2px produce 4sp3 hybrid orbital.
Chem. 501. Hybridization
Ground state carbon atom requires ~800kj/mol to form sp3 hybrid orbitals. High energy solution = hybrid orbitals, not the most stable, but high energy solution. We get strong bonds and make the molecule more stable. In the evidence shown below (Hybridization POGIL, July 6, 2007) the formation of 4 CH sigma bonds is an exothermic reaction.
Hybridization POGIL, July 6, 2007
2. Chem503: Polymerization of carbon molecules
Enduring Understanding: Synthetic Organic Polymers permeate every aspect of our material life and are the foundation of our consumer-oriented society.
There are two kinds of synthetic polymers: addition (chain-growth) polymers and condensation polymers.
Chain-growth polymerization of alkenes monomers utilizes free radicals, cationic, anionic initiators, or organ metallic catalysts.
Inquiry question. Cationic polymerization
The evidence on the left (inquiry question-cationic polymerization) is a cationic polymerization of isobutylene. It is not strong enough to serve as a replacement for natural rubber because the cation has no resonance for stabilization. Adding isopropene means adding a double bond and stabilizing the polymer through resonance. Positive sign on 30 carbon exchanges with the double bond for steric reasons and occupies 10 carbon, resulting in a compound with double bond. Next is to Vulcanize; to heat up with sulfur to have a cross-linkage structure that makes it as strong as natural rubber.
Chem. 503. Chain growth
Evidence on the left here (Chem. 503 chain growth) is another kind of synthetic organic polymers: addition polymers. This evidence demonstrates the chain-growth polymerization of alkenes; the monomer utilizes anionic initiators.
3. Chem505: Effect of methane on global warming
Enduring Understanding: atmospheric processes: empirical observations of atmospheric processes in the stratosphere and the troposphere lead to the development of theories about human impacts on the chemistry of the stratospheric ozone depletion, acidic precipitation, urban air pollution, and the green house affect/global warming.
In the troposphere, there are strong interactions between methane and hydroxide which produce ozone. Additionally, in the stratosphere, its reaction with the hydroxide produces water vapor. Both tropospheric ozone and the stratospheric water vapor are green house gases, thereby, bringing additional global warming. In comparison with other greenhouse gases, methane has more atoms. It is the simplest stable hydrocarbon molecule yet its spectroscopy is very complicated. This is mainly due to the high symmetry of the tetrahedral system which leads to the existence of much degeneracy and to its intricate vibration structure; it in fact has four fundamental vibration frequencies. Methane emission has 25 times the impact on temperature than carbon dioxide emission of the same mass over the following 100 years.
Chem. 505. PIM 2
This evidence from Chem. 505 is part of PIM 2 that I created for the environmental chemistry class. The circle graph shows the natural sources of atmospheric methane and the table shows the methane emission inventory by sources.
You will have access to the entire PIM by clicking at the provided link below.
Global warming; the non CO2 story
4. Chem506: Group symmetry and carbon containing molecules
Enduring understanding: attaining the ability to mentally visualize molecules and chemical reactions in 3- dimensions as well as proficient communication of these 3-dimensional concepts using 2- dimensional media is essential to teaching and learning chemistry.
CH4 is an isoelectronic molecule with steric number equals 4: Four identical bonds between carbon and each of the hydrogen atoms, if arranged as far from each other as possible, it will result in tetrahedral shape (angle measures 109.50).
C-H bond has very little polarity but the sum of all bonds is zero because of the symmetry of the molecule.
The example I brought below as evidence (from Chem. 506. Group Symmetry) for learning groups of low and high symmetry is CH4. It has C3, 3C2, S4 6σd and no C4, it is assigned Td group symmetry.
Chem. 506. Group Symmetry.
5. Chem507: The effect of conjugation on alkenes
Enduring Understanding: Atoms obey the laws of quantum mechanics and have energy levels.
- Electronic energy
- Vibration energy
- Rotational energy
- Translational energy
Bathochromic shift results from an increase in the length of a Conjugated system implying that an increase in conjugation decreases the energy required for electron excitation which is explained by using the molecular orbital theory (MO):
For ethene: 2p orbitals Ф1 and ф2 we form two π molecular orbitals Ψ1 and Ψ2* by taking their linear combination.
The bonding orbital Ψ1 results from addition of the wave function of the two p orbitals, and anti bonding, Ψ2 results from the subtraction of these two wave functions. The new bonding orbital (molecular orbital) has energy lower than that of either of the original p orbitals; likewise, the anti bonding orbitals have an elevated energy.
Note: Two atomic orbitals grow two molecular orbitals. There were two electrons, one in each p atomic orbital. As a result of combination, the new π system contains two electrons, and because we fill the lower energy orbitals first, these electrons end up in the Ψ1 bonding orbital.
Electron transition in this system is π à π* transition from Ψ1 à Ψ2*.
1, 3- butadiene, Ψ2 à Ψ3* is a π à π* transition and has a lower energy than the corresponding transition in ethene Ψ1 à Ψ2* because 1, 3 butadiene has four p atomic orbitals that forms the pie system which builds four molecular orbitals. Evidence below Chem. 507. Molecular orbital illustrates the above.
Chem. 507. Molecular Orbitals
As we increase the number of orbitals making up the conjugate system, the transition from highest occupied molecular orbital (HOMO) to the lowest unoccupied molecular orbital (LUMO) has progressively lower energy. The energy gap dividing the bonding and the antibonding orbitals becomes progressively smaller with increasing conjugation.
In application I would like to include the following problem from Chem. 507 Activity 3. Transitional energy.
Chem. 507 Activity 3, Transitional energy.
Assuming pie electrons of 1, 3 butadiene moving along conjugated molecule. I learned to add bond lengths: C = C (135 x 2), one C – C (154) and one half of C – C bond length at the two terminal carbon atoms. Ε1 and Ε2 has four electrons for there are two double bonds and the wave function that describes an electron can hold two electrons with opposite spin in each of the Ε1 or E2. Energy is calculated using an equation described in (c). From the energy value we get to find the wave length to compare it with the experimental value.
6. Chem504/508: Carbon atom in protein
Enduring Understanding: Structures and shapes of biological macromolecules are keys to understanding biological function. Carbon is an essential atom in the molecular basis of life and evolution. Carbon is the major atom in proteins, nucleic acid, and polysaccharides. First evidence in this reflection is from Chem. 508 class. Slides shown below are from the power point I created for my thesis presented this past summer titled; "Molecular Basis of Dark Vision". An amazing carbon macromolecule named 11-cis-retinal is the chromophore portion of Rhodopsin. Rhodopsin: is a member of the seven helix G-protein coupled receptor family (GPCR).
Chromophore is the photopigment of the rods & cones (two types of cells in the retina). Upon absorption of only one photon, 11-cis retinal isomerizes to all-trans. This process called "bleaching", which means Rhodopsin changes to being colorless after being red-purple due to the change of absorption from ~ 498 to below around ~300nm (invisible to our sight). Due to the isomerization of this carbon molecule stimulated by light, activation of transducin (another protein) occurs leading to hyper-polarization/depolarization of the rod cells at night/day.
The COOH terminal is on the intracellular face which corresponds to the cytoplasmic side of the GCPRs backbone emphasizes the fact that the helices are tilted probably to provide flexibility for the conformational changes after photon absorption.
First slide demonstrates the isomerization of 11-cis retinal to all trans and the bleaching due to different absorption. The second slide demonstrates the phototransduction in cone cells.
Rhodopsin Bleaching Phototransduction
The evidences below are from Chem. 504. It demonstrates the clear understanding of the formation of peptide bond and the importance of folding the peptide chain in the formation of the native structure of proteins.
This peptide bond slide shows how the formation of a peptide bond requires a dehydration process as demonstrated in the slide below.
Chem. 504. Peptide bonds
Another evidence from Chem 504 shows the levels of protein structure. In a polypeptide chain or protein, the sequence of the amino acids is called the primary structure. The secondary structure describes how the chain is coiled or otherwise arranged in space.
In a protein, the amino acids side chains may project out in such a way that they often interact with other side chains located at different positions along the protein backbone, such interaction gives the protein its three dimensional shape called tertiary structure.
In some proteins, different polypeptides each of which has its tertiary structure come together to form quaternary structure.
Chem. 504. Protein structure
The evidence below focuses on how the sequence of amino acids dictates the shape and the structure of the protein, which in turn is important to the proteins' biological functions.
The role of the amino acid in protein structure
