Master of Chem Ed Program Courses – EU’s

Enduring Understandings for ALL MCE Courses:

EU 1: Chemistry is the central science.

EU 2: Chemistry is an experimental science where bridges are built between experimental observations and underlying concepts.

EU 3: Qualitative ideas can be transformed into quantitative expressions.

EU 4: Examples of all levels of chemistry are found in daily life and in modern human developments.

EU 5: The reflective-discussion classroom style exemplified by the PIM is an effective means of teaching and learning chemistry.

EU 6: Teacher-participants become confident life-long learners and reflective practitioners through their MCE coursework and experiences.

CHEM501: General & Organic Chemistry I

Dr. Bryan Roberts

I. Chemistry is the central science.

Chemistry has drawn upon the quantitative insights of physics to create a molecular model of the physical world which has transformed biology and which is the foundation for technological innovations in medicine, engineering, and material science.

II. Chemistry is an experimental science.

Ø Chemists carry out experiments to discover the quantitative relationships on which the underlying concepts for a model of the physical world can be based.

Ø The molecular model is based on experiments which meet statistical standards for reproducibility.

Ø Chemists strive to refine and improve the molecular model through further experimentation.

Ø Chemists use the molecular model to explain how macroscopic observations originate from molecular events.

III. Chemistry is based on nine core ideas.

Core Idea 1: Mole Concept : Matter consists of atoms,

Ø The concept of mole ratio leads to insight into the combining properties of matter.

Core Idea 2: Atomic Structure: Atomic structure accounts for periodicity.

Ø Solution of the Schrödinger leads to atomic wavefunctions.

Ø The shell model of the atom is a useful model for predicting periodic effects.

Ø The Aufbau principle predicts atomic structure.

Ø Coulomb’s law is an important relationship for predicting the energies of electrons in atoms.

Core Idea 3: The Chemical Bond: Bonds form by electron-pair sharing.

Ø Lewis structures describe how atoms are connected in molecules.

Ø Resonance theory is a useful model for describing the distribution of electrons in molecules.

Ø The arrangement of bonds in space can lead to structural isomerism.

Ø The symbolism used in the representation of chemical bonds and molecular structure are important for the rapid transmission of chemical knowledge.

Core Idea 4: Molecular geometry: Shape is especially important

Ø VSEPR predicts shape around an atom.

Ø Conformational analysis predicts molecular shape.

Ø Molecules can exist as stereoisomers.

Core Idea 5: Intermolecular Interactions: There are residual forces between molecules.

Ø Permanent and transient dipole moments lead to attraction between atoms and molecules.

Core Idea 6: Conservation of Energy: Energy is conserved

Ø Quantitative measurement of the interconversion of heat, work, and potential energy leads to insight into the relationship between energy and the structure of matter.

Ø The state functions internal energy and enthalpy are useful concepts for describing how energy is distributed in atoms and molecules.

Core Idea 7: Entropy Concept: Energy and matter tend to disperse.

Ø The entropy concept provides insight into the origins of spontaneous physical and chemical change.

Ø The Gibbs free energy is a fundamentally important concept for measuring the extent of chemical reaction.

Core Idea 8: Chemical Kinetics: There are barriers to reaction.

Ø Experimental study of the rates of chemical reactions leads to a model of how they take place.

Core Idea 9: Reaction Mechanisms: There are only four types of elemental reactions

Ø Single electron transfer

Ø Electron pair donation/acceptance

Ø Electron pairing/unpairing

Ø .Nuclear fission/fusion

CHEM502: Information Technology & Experimental Chemistry

Dr. Bill Dailey

EU & Skills #1: Information technology and computer skills are valuable tools in both the teaching and learning of chemistry.

Content topics & skills:

• creating, maintaining and using (searching, etc.) web pages
• using Excel
• Using PowerPoint
• Using computational chemistry codes
• Using Library and reference resources

EU & skills #2: Chemistry is a laboratory science where bridges are built between experimental observations and underlying concepts.

Content topics & skills:

• Acid/base chemistry
• Intermolecular interactions – solubility, etc
• Separation techniques including distillation and crystallization
• Gas Chromatography
• Bond Energies
• Reactive intermediates and mechanisms

EU & skills #3: Qualitative ideas can be transformed into quantitative expressions.

Content topics & skills:

• Determining the structure and energies of molecules, conformational analysis
• Equilibrium constants and energy
• Calculating and Predicting activation energies

CHEM503: Organic Chemistry II

Dr. Bryan Roberts

Aromatic Compounds

Ø The benzene ring possesses special stability because of cyclic delocalization of p electrons.

Ø Electrophilic aromatic substitution is one of the most important reactions of aromatic compounds because it leads to introduction of substituents on the benzene ring at predictable preferred positions.

Alcohols, Phenols, Ethers, and their Sulfur Analogues

Ø The physical properties of alcohols are dominated by their ability to serve as hydrogen bond donors and acceptors.

Ø Alcohols are important intermediates in organic synthesis and undergo a large number of reactions including dehydration and oxidation.

Ø The larger size of the sulfur atom influences the physical properties and chemistry of thiols, thiophenols, and thioethers.

Aldehydes and Ketones

Ø The polarity of the carbonyl group activates it toward reaction with Lewis acids and Lewis bases.

Ø Chemical tests can be used to distinguish compounds.

Ø Compounds that possess covalent metal-carbon bonds are the most important reagents for creating carbon-carbon bonds.

Enols and Enolates

Ø The reaction of enolates with electrophiles is one of the fundamentally important reactions for forming carbon-carbon bonds.

Ø The aldol condensation is an especially useful reaction for building up more complex carbon skeletons from simpler ones.

Carboxylic Acids and Derivatives

Ø Carboxylic acids and their derivatives are highly versatile organic compounds used widely in synthesis and commerce and participating in many important biochemical processes.

Ø The acidity of carboxylic acids depends upon structure.

Amines

Ø Amines include some of the most physiologically active compounds found in nature or made in the laboratory.

Ø The basicity of amines depends upon structure.

Ø Amines are good nucleophiles and participate in the S_N2 reaction.

Ø Reaction of aniline or related aromatic amines with nitrous acid leads to a diazonium salt which is valuable in synthesis.

Ø The replacement of carbon atoms in aromatic compounds with nitrogen leads to heteroaromatic compounds.

Polymers

Ø Synthetic organic polymers permeate every aspect of our material life and are the foundation of our consumer-oriented society.

Ø There are two kinds of synthetic polymer: addition (chain-growth) polymers and condensation polymers.

Ø Specialized organometallic catalysts may be used to give polymers with regular stereochemistries.

Ø The physical properties of a polymer are a function of polymer structure.

Lipids

Ø Lipids constitute one of the major classes of naturally occurring organic compounds.

Ø Lipids include a diverse array of organic compounds including triglycerides, waxes, fatty acids, phospholipids, glycolipids, steroids, prostaglandins, leukotrienes, and terpenes.

Carbohydrates

Ø Carbohydrates constitute the most abundant class of naturally occurring organic compounds.

Ø In solution, monosaccharides exist as a mixture of the open chain form and cyclic forms.

Ø Monosaccharides combine through acetal linkages to give disaccharides and polysaccharides which perform many specialized functions in the chemistry of life.

Amino Acids, Peptides, and Proteins

Ø a-Amino acids are the building blocks of peptides and proteins.

Ø Peptides and proteins result from the combination of a-amino acids through amide linkages.

Ø Peptides and proteins perform many important functions in the chemistry of life including serving as catalysts, regulatory agents, structural material, and components of the immune system.

Ø A functioning peptide or protein adopts a specific three-dimensional shape which is determined by the geometry of the amide linkages and the interactions of the organic groups attached to the amino acid subunits.

Nucleic Acids

Ø Genetic information is encoded in the sequence of bases in the biopolymer deoxyribonucleic acid (DNA).

Ø DNA exists as a double helix in which complementary base pairs project toward the center of the helix and hydrogen bond with each other.

Ø In cell division, replication of the DNA results from separation of the double helix into template strands and construction of complementary strands on each of these.

Ø The genetic code is a three-letter code in which a sequence of three bases in DNA is transcribed into a sequence of three bases in ribonucleic acid (RNA) that is then translated into an amino acid subunit of a peptide or protein.

Ø A gene is a sequence of DNA which possess start and stop signals and which codes for a specific peptide or protein.

Ø In genetic engineering restriction enzymes are used to cut a gene from the DNA of one organism and to insert it into the DNA of another organism for the purpose of producing the peptide or protein coded for by the gene.

CHEM504: Biochemistry and Molecular Biology

Dr. Stacy Gelhaus

EU #1: Students should understand that the structures and shapes of biological macromolecules are key to understanding biological function.

What is life?
Molecular basis of life & evolution
Three major classes
Proteins
Nucleic acids
Polysaccharides

EU # 2: Students should understand the structure and properties of the peptide bond.

Peptide chemical structure
Conformation
Proteins are chains of amino acids linked by peptide bonds

EU #3 Students should understand how peptide bonds and the amino acid side chains give proteins unique shapes and functions.

Folding
Primary, secondary, & tertiary structure
Noncovalent interactions
Hydrogen bonding
Hydrophobic effect
Solvation
Quaternary structure
Sequence of amino acids determines shape and function
Homology

EU # 4 Students should understand how most biochemical reactions are catalyzed by enzymes.

Enzymes are protein catalysts
Reactivity and selectivity controlled by enzyme shape and functional groups
Binding & specificity
Some amino acid side chains have catalytic properties
Enzyme cofactors

EU # 5 Students should understand how the biological reactions catalyzed by enzymes carry out metabolism.

Anabolism
Catabolism
Biochemical cycles
ATP

EU # 6 Students should understand how nucleic acids are key to genetics.

Double-helix structure of DNA
Replication and cell division
Reverse transcriptases

EU # 7 Students should understand how nucleic acids are key to protein synthesis.

Transcription
Translation
Messenger RNA (mRNA)
Transfer RNA (tRNA)
Ribosome structure & mechanism

EU # 8 Students should understand the molecular basis of cellular signaling processes.

Intracellular signaling
Intercellular signaling
Brain & neurons

CHEM505: Environmental Chemistry

Dr. Mark Hermanson -- February 2005

Course EUs

1. Environmental chemistry is a quantitative science, converting qualitative observations and ideas into quantitative expressions.
2. Environmental chemistry employs statistical analysis to develop quantitative models of complex systems.
3. Environmental chemistry is both empirical and theoretical, making quantitative environmental observations and using processes, mechanisms and theories in chemistry to explain them.
4. Environmental chemistry is a bridge between chemistry and human toxicology.

Unit-level EUs:

1. Statistical analysis of data – most often using the general linear model – is essential for converting qualitative environmental observations into quantitative expressions. The use of statistics does not imply causation, but leads to identifying processes that relate observed variables.
2. Empirical observations of atmospheric processes in the stratosphere and the troposphere lead to development of theories about human impacts on the chemistry of ozone depletion, acid precipitation, urban air pollution (smog, etc.) and the greenhouse effect/global warming.
3. (A) Effective water and wastewater treatment chemistry is vital to human survival, yet is driven mostly by empirical observation because of geographic differences in treatment effectiveness. General chemical principles developed from treatment processes are developed and applied with the understanding that results can be highly variable.

(B) Thermodynamics of natural aqueous systems are largely empirical because of variable water chemistry based on presence or absence of oxygen. General thermodynamic principles regarding the relationship between oxidation/reduction potential (Eh) and pH in natural waters are based on empirical observations, but general chemical principles can be developed using stability field diagrams.

(C) Alkalinity of natural waters is an important regulator of pH, governs the solubility of many metals in water, and is based on presence of carbonates or hydroxides. Alkalinity regulates the effects of acid precipitation. Alkalinity is easily measured in the laboratory, and those observations can be used to make many interpretations about general water quality.

4. Environmental toxins include trace metals and organic compounds. Many of these are subject to global distribution through the atmosphere. The toxicity [usually defined by carcinogenicity] of many organic compounds is related to molecular shape [e.g. planar compounds among organochlorines, potential for epoxidation of PAH]. The observation of hormonal effects of some organic compounds is empirical because molecular shape is not related to endocrine disruption.

CHEM505: Environmental Chemistry

Dr. Mark Hermanson -- February 2008

Course EUs

1. Environmental chemistry involves study of human influences, known as the anthrosphere, on the four physical units of the Earth surface, including the atmosphere, hydrosphere, biosphere and lithosphere.
2. Environmental chemistry is a quantitative science, converting qualitative observations and ideas into quantitative expressions.
3. Environmental chemistry employs statistical analysis to develop quantitative models of complex systems.
4. Environmental chemistry is both empirical and theoretical, making quantitative environmental observations and using processes, mechanisms and theories in chemistry to explain them.
5. Environmental chemistry is a bridge between chemistry and human toxicology.

Unit-level EUs:

1. Statistical analysis of data: The general linear model is most often used for converting qualitative environmental observations into quantitative expressions. The use of statistics does not imply causation, but leads to identifying processes that relate observed variables.
2. Atmospheric processes: Empirical observations of atmospheric processes in the stratosphere and the troposphere lead to development of theories about human (anthrospheric) impacts on the chemistry of stratospheric ozone depletion, acid precipitation, urban air pollution (smog, ground-level ozone) and the greenhouse effect/global warming.
3. Hydrospheric processes:

(A) Water and wastewater treatment chemistry is vital to human well-being, yet is driven mostly by empirical

observation because of geographic and temporal differences in local water chemistry. Chemical principles used in treatment processes are developed and applied with the understanding that results can be variable.

(B) Thermodynamics of natural aqueous systems are largely empirical because of variable water chemistry based on presence or absence of oxygen. General thermodynamic principles regarding the relationship between oxidation/reduction potential (Eh) and pH in natural waters are based on empirical observations, but general principles can be developed using stability field diagrams. Thermodynamics of altered (treated) aqueous systems is also empirical and must be controlled to prevent solubility of toxic metals.

(C) Alkalinity of natural waters is an important regulator of pH and thereby governs the solubility of many metals in water. Alkalinity is the presence of carbonates or, occasionally, hydroxides. Alkalinity regulates the effects of acid precipitation. Alkalinity is easily measured in the laboratory, and those observations can be used to make many interpretations about general water quality.

4. Environmental toxins include organic compounds and trace metals. Many of these are subject to global distribution through the atmosphere. Organic compounds in the gas phase can travel to remote regions where they were never used or produced. This observation can be used to designate the substance as a persistent organic pollutant (POP), subjecting it to international regulation. Other contaminants (organic and inorganic) are associated with particles and can also be transported but likely over shorter distances.
5. Toxic mechanisms.
1. Organic contaminants as carcinogens. The carcinogenicity of many organic compounds is related to molecular shape [e.g. planar compounds or potential for epoxidation].
2. Organic contaminants as endocrine disruptors. The observation of hormonal effects of some organic compounds is empirical because molecular shape is not related to endocrine disruption.
3. Organic contaminants as nerve agents. Organophosphorus compounds, including pesticides and agents of mass destruction, enable excess nerve stimulations by inhibiting the function of acetylcholinestrase.
4. Toxicity of radioactive materials. The most dangerous (carcinogenic) radioactive materials are considered to be those decaying by emission of a particles. These must be ingested and are usually are considered to be carcinogens.
5. Toxicity of trace metals (lead, cadmium, mercury). Trace metals are usually considered to impair nerve function. New research is suggesting a wider toxic role for these metals.

CHEM506: Inorganic Chem

Dr. Don Berry – Spring 2005

Course EU’s:

EU 1: The Periodic Table embodies the trends and properties of all elements and is based on atomic structure and chemical bonding.

EU 2: 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 (paper, chalkboard, etc.) is essential to teaching and learning chemistry at all three levels of representation (macroscopic, microscopic and symbolic).

Topic EU’s:

Atoms and Schrödinger's Equation

• The "particle" and "wave" description of electrons and other subatomic particles are attempts to explain complicated behavior in terms of simplistic models with physical significance to us; neither is "real", nor sufficient and should not be taken literally.
• Solution of Schrödinger's equation (i.e. application of the rules of wave mechanics) for atoms produces two main pieces of information: location in space (shape) and energy

(1) "wave functions" - families of functions describing electron density in different regions of space ("shape"), related by a series of simple numbers ("Quantum numbers" - n,l,ml,ms)

(2) "energy levels" - the energy associated with each wave function, where lower is better ;)

(3) The sign of the wave function in various regions of space does NOT represent charge, but indicates the magnitude of the function. The square of the value of this function at some point (x,y,z) is related to the "probability of finding the electron at that point".

Auf Bau and the Periodic Table

• The periodic table of the elements can be "assembled" by sequentially adding protons and electrons and requiring the latter to occupy the lowest energy configuration of the hydrogenic atomic orbitals constrained by the Pauli Exclusion Principle and Hund's Rule.
• The "Effective Nuclear Charge" (Z_eff) felt by an electron is the result of the nucleus being incompletely screened or shielded by other electron's in an atom due to varying degrees of penetration of different orbitals into the core electrons; the general trend that Z_eff increases going from left to right along a row gives rise to most of the common "periodic" properties of the elements.

Symmetry:

• Three-dimensional objects such as molecules can be systematically analyzed and classified into an unique point group on the basis of symmetry.
• All aspects of molecular symmetry can be defined in terms of five symmetry operations which are performed with respect to symmetry elements.

Transition Metal Coordination Chemistry:

• A "coordination complex" consists of an inner coordination sphere of ligands covalently bonded to a metal in a specific geometry and the outer coordination sphere of counter-ions and solvent molecules loosely held by electrostatic interactions.
• The different energy levels of the partially filled transition metal d-orbitals resulting from the symmetry and strength of the coordinated ligands leads to diverse electronic and magnetic properties.

Molecular Orbitals:

• Molecular Orbitals are wave functions formed from linear combinations of atomic orbitals which can be delocalized over many atoms in a molecule and which can be classified by symmetry (sigma, pi, delta) and the nature of the orbital overlap (bonding or antibonding; constructive or destructive interference).

Orbitals, energy levels, and spectroscopy

• Electronic Spectroscopy is the absorption of energy from light resulting in the excitation of a molecule from the electronic ground state {configuration} to an excited state {configuration}.
• In the presence of an octahedral array of ligands around a transition metal, the five d-orbitals split into two distinct sets - the "2 over 3" pattern - separated by the "Crystal Field Stabilization Energy" or D_oct, whereas a tetrahedral ligand field leads to a "3 over 2" pattern separated by D_tet.
• Different ligands can be arranged into the "Spectrochemical Series", according to the size of the CFSE induced at a metal center; a "strong-field" ligand creates a large CFSE, and can induce a change in spin multiplicity for some electron configurations.

CHEM507: Molecular Spectroscopy

Dr. Susan Philips -- Spring 2004

EU #1: Atoms obey the laws of quantum mechanics and have energy levels.

· Electronic energy

• Vibrational energy
• Rotational energy
• Spin States
• Gaussian/WebMO

EU #2: Understanding light and how light affects matter are paramount to understanding spectroscopy.

· Wave & particle properties of light

· Absorption & emission of light as it relates to energy levels of atoms & molecules

· Lasers

EU #3: All areas of chemistry use spectroscopy.

· This will be tied in throughout the course as we discuss each type of spectroscopy

· The course project will also address this EU.

· The lab exercises also relate to this EU.

EU #1: Atoms obey the laws of quantum mechanics and have energy levels.

Content topics:

· Electronic energy

• Vibrational energy
• Rotational energy

EU #2: Understanding light and how light affects matter are paramount to understanding spectroscopy.

Content topics:

· The electromagnetic spectrum

· Wave & particle properties of light

· Absorption & emission of light as it relates to energy levels of atoms & molecules

o Types of transitions resulting from absorbance of different regions of the electromagnetic spectrum and how this information can be utilized to gain understanding about molecules.

· Boltzmann distribution

· Lasers

EU #3: All areas of chemistry, as well as other fields of science such as biology and astronomy, use spectroscopy.

· This will be tied in throughout the course as we discuss each type of spectroscopy

· The course project will also address this EU.

Labs/PIMS

o “Dissection” of Spec 20; use of Spec-20 to measure absorption spectra (LAB)

§ Components of a spectrometer

§ Relationship between color of light and wavelength

§ Relationship between apparent color of a solution and wavelength(s) of light absorbed

§ Beers’ Law (electronic energy; absorption of light)

o Laser Diffraction (properties of light; lasers) (LAB)

§ Use of light to measure dimensions of small objects

o IR spectroscopy of organic compounds (vibrational energy; absorption of light)

§ Use of IR spectroscopy to identify functional groups in some organic compounds (LAB)

o IR spectroscopy of gases (vibrational energy; rotational energy; absorption of light) (PIM)

§ Greenhouse effect and IR absorption by atmospheric gases

o Laser PIM. Working in small groups, students research types of lasers and create a presentation to be given to the class NMR spectroscopy: mini-lecture and in-class activity on basics of NMR; students identify some compounds from their NMR spectra. (PIM)

o Several activities from Moog “Atoms, Molecules, and Spectroscopy” are utilized

o Raman spectroscopy: mini-lecture, demonstration, and PIM