Chem 222 Prep and Review-archived
الخطوط العريضة للقسم
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A fundamental understanding of chemical structure and bonding is required to understand organic biological chemistry. As such, CHEM 111 is a prerequisite for CHEM 222. We have created this Moodle page as a resource for those of you who have taken General Chemistry elsewhere or simply wish to review material from CHEM 111 that is most relevant to CHEM 222.
You are expected to have seen the material from Soderberg Chapter 1-5 prior to enrolling in CHEM 222. Below we have broken these down into 13 topics and provided vdeo and pencast resources (from CHEM 111) to help guide you through each concept. We will review this material at the beginning of the semester, but we plan to move quickly!
A note on pencasts: Pencasts are interactive documents that allow you to hear the lecturer's talk while also seeing the lecturer's notes just as they were written. To watch these digital lectures, please download the pencast file, open it in a pdf reader such as Adobe Acrobate Pro, and press play!
Want to test your knowledge? We will be posting practice questions on this Moodle site later in the summer! -
Learning Goals: Differentiate between VB and MO approaches to describing bonding in molecules and know the relative strengths of each. Know how to apply VB theory and VSEPR to describe common motifs in organic molecules involving H, C, N, O, S and halogen atoms. Know that double and triple bonds in organic molecules involve one sigma and one or two pi bonds, and the effect that pi bonds have on restricting rotation around bonds.
Readings: Soderberg, sections on molecular orbital theory, and valence bond theory.
Notes: The four pdf files below have notes that describe VBT, MO and the most important features of organic bonding and how to draw line structures, as also described in Soderberg chapter 1. They were originally created as Pencasts using the Livescribe Echo pen, and because of this you may see an annotation saying that you need to use the latest version of Adobe Reader in order to hear the audio portion of the pencast. You should ignore this message, because Adobe has discontinued support for Pencasts in its most recent versions, and so, unless you have a computer not updated since 2017, you will not be able to hear the audio portion. However, the notes are likely still to be helpful supplements to the reading, even without the audio.
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Learning Goals: Apply MO theory and Lewis theory to molecules with adjacent single and double bonds, and use this to understand the concepts of "conjugation" and "aromaticity".
Readings: Soderberg, section on resonance.
Pencasts: Watch the video lecture by Emeritus Prof. Claude Wintner (he was doing blended learning before it was cool).
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Learning Goals: To know the bonding patterns that correspond to the most common functional groups in organic compounds. To understand systematic names of organic compounds and go from a name to a line structure and chemical formula. To know which functional groups are associated with acidic and basic properties.
Readings: Soderberg, sections on organic structure and nomenclature. This reading describes the various functional groups I'd like you to know about, but treats nomenclature rather briefly. If you want a more thorough discussion of nomenclature (than given in the Pencasts), you could look at other Organic Chemistry textbooks on reserve in the Science Library, or you could look at the section from Reusch's Virtual Textbook of Organic Chemistry on Nomenclature.
Notes (old Pencasts): (pencast audio is not accessible - see comment from first topic above). There are two multipage pencasts - one on Alkanes and their nomenclature, and the other on common functional groups and the nomenclature of organic compounds containing these groups. Since it's hard to draw chemical structures on pencasts, the second "3A" pencast has structures redrawn for clarity.
Software resource: The link below allows you to download ChemBioDraw software (Haverford has a site license). This software allows you to draw line structures of organic molecules, and contains commands to convert names to structures or structures to names. This is useful for learning nomenclature and checking what you have learned.
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Learning Goals: Introduce forms of non-covalent molecular interactions: ion-ion, ion-dipole, van der Waals (dispersion), & hydrogen bonding. Be able to rank these in terms of strength. Apply these to understand the physical properties of molecules, specifically solubility, melting point and boiling point trends.
Readings: Soderberg, section on non-covalent interactions.
Notes (old pencasts)/Videos: Watch the two video lectures on intermolecular interactions, and two old pencasts (audio unavailable - see comment in the top section) on the effects of intermolecular interactions on solubility and boiling point/melting point.
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Learning Goals: Learn how relatively free rotation around single bonds in linear and branched alkanes (and other organic compounds) generates many conformations. Understand the meaning of dihedral angle and how it is measured, and the reasons why energy changes with dihedral angles around single (and double) bonds. Know that rotational barriers less than 10 kcal/mol (single, triple bonds) result in a range of conformations, while rotational barriers greater than 30 kcal/mol (double bonds) result in geometric isomerism (cis/trans).
Reading: Soderberg section on open-chain organic molecules.
Notes: A two-page old pencast* describes conformations in alkanes, including definitions of dihedral angles. A single page pencast* compares the energy effects of rotation about single, double and triple bonds and describes why only double bonds result in geometric isomerism. The end of this pencast* describe the C-N bonds in amides, which behave as if they have partial double bond character. Finally, there is a brief pencast* on alkene nomenclature. (*-Audio from old pencasts does not work. Ignore the warning about needing to update to latest Adobe Reader - see note in first topic).
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Learning Goals: Know what is meant by "strain energy" of cycloalkanes and be able to explain why it is largest for ring sizes of 3 and 4, but also why it is small but non-zero for cyclopentane. Know what is meant by chair and boat forms of cyclohexane, and which is more stable. Also know the difference between axial and equatorial positions in cyclohexane and which one of these is energetically preferred by substituents, and why. Be able to explain this using guache and anti conformational analysis.
Reading: Soderberg section on cyclic compounds.
Video lectures: There are no pencasts for this topic, but please use the link below (and follow the instructions below the link) to view about 45 minutes of Claude Wintner's video lecture. (The sections 5.03, 5.04 and 5.06 that I have you skip over won't make sense until we talk more about stereoisomerism next week).
You-tube video: Shows a molecular dynamics simulation of a molecule interconverting between chair, twist boat and boat forms. The twist boat form is twisted just slightly from the pure boat form, and is slightly more stable because it minimizes the steric clash between H atoms on the "bow" and "stern" found in pure boat form.
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Learning Goals:
Molecular Models: It is very important that you get out your molecular models and make 3-D models of, for instance, the simple R & S enantiomeric pairs described in the readings, pencasts and video lectures, so that you can convince yourself that they are not "conformable", and become comfortable with the 3-dimensionality expressed by wedge structures and by Fischer structures.
Reading: Soderberg sections on chirality, labeling chiral centers, optical rotations, molecules with multiple chiral centers, and meso compounds.
Notes: Review the pencasts* below. (*-Audio from old pencasts does not work. Ignore the warning about needing to update to latest Adobe Reader - see note in first topic).
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Learning Goals: Learn when it is and isn't appropriate to use cis,trans to label alkenes, and how to use the E,Z designations of the CIP system. Learn what is meant by prochirality (pro-R and pro-S H atoms or methyl groups), and why it might be important for biological reactivity. Also be able to use the terms enantiotopic, diastereotopic, and homotopic to describe pairs of hydrogen atoms on the same carbon.
Reading: Soderberg sections on alkenes and pro-chirality.
Notes: A pencast* describes E,Z Stereoisomers, and another one describes prochirality. (*-Audio from old pencasts does not work. Ignore the warning about needing to update to latest Adobe Reader - see note in first topic).
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Learning Goals: Understand basic theories of mass spectrometry, ultraviolet/visible (UV/vis) spectroscopy, and infrared spectroscopy. Learn how to interpret data to facilitate molecular structure identification.
Readings: Soderberg Sections on mass spectrometry, molecular spectroscopy, infrared spectroscopy, and UV/vis.
Pencasts/Videos: Review videos below!
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Learning Goals: Understand the fundamentals of Nuclear Magnetic Resonance and which common nuclei are NMR active. NMR frequency depends to large extent on which nucleus is being observed and to a small extent on the chemical environment of the nucleus. Number of signals in 1H NMR = distinct H environments in the molecule structure. Areas of signals (integrations) proportional to numbers of H in a particular (homotopic or enantiotopic) environment.
Reading: Soderberg sections on NMR, chemical inequivalence, NMR experiments, and chemical shift. If you want another perspective on NMR, you could try the NMR chapter of Reusch's online organic chemistry text.
Notes: Review the two pencasts* below. (*-Audio from old pencasts does not work. Ignore the warning about needing to update to latest Adobe Reader - see note in first topic).
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Learning Goals: Understand why different protons in a molecule have different chemical shifts, including the role of shielding by electrons, deshielding caused by nearby electronegative elements, and the role of ring currents for protons bound to carbons that are part of pi bonding systems. Understand what leads to NMR Splitting. Know that "J" represents the splitting between peaks and is measured in Hz (not ppm). Know intensity patterns for equal J splitting by 2, 3, 4, 5, or 6 nuclei. Also be able to use chemical shift charts and tables of functional group effects upon chemical shifts to predict chemical shifts for a given structure.
Reading: Soderberg sections on coupling.
Resource: The two-page document "NMR Chemical Shift Prediction for Chem 111" is a resource you should print out. You will need it to understand pencast 11B.
Notes: Review the pencasts* below. (*-Audio from old pencasts does not work. Ignore the warning about needing to update to latest Adobe Reader - see note in first topic).
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Learning Goals: Understand that 13C spectra don't show C-C coupling because of the low natural abundance of C, and are collected using "proton decoupling" so that they don't show C-H coupling either. Integrations are untrustworthy, but quaternary carbons show up at about 1/4 the size of carbons with H attached. Various DEPT experiments can distinguish primary, secondary and tertiary carbons (know what these are). Know what kinds of peaks occur in 0-100 ppm range, in 100-165 ppm range, and 165-230 ppm range (you can look these up on the chart on p. 2 of the chemical shift prediction handout)
Reading: Soderberg section on carbon NMR.
Notes: The first page of the pencast is "6 things to know about 13C NMR" and the second page shows a sketch of the 13C NMR (regular, + DEPT 90 + DEPT 135) for ethylbenzoate and shows how the spectrum can be analyzed for consistency with the structure of the molecule. (*-Audio from old pencasts does not work. Ignore the warning about needing to update to latest Adobe Reader - see note in first topic).
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Learning Goals: Understand what leads to NMR Splitting. Know that "J" represents the splitting between peaks and is measured in Hz (not ppm). Know intensity patterns for equal J splitting by 2, 3, 4, 5, or 6 nuclei.
Reading: Soderberg section on coupling (again).
Notes: See below. (*-Audio from old pencasts does not work. Ignore the warning about needing to update to latest Adobe Reader - see note in first topic).
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Learning Goals: Understand the Index of Hydrogen Deficiency (IHD, also called "degree of unsaturation" or "unsaturation #") and how it gives clues as to the organic structure. Recognize common patterns (shifts/splittings/integrations) in NMR spectra. Know how to integrate data from MS, IR and NMR to determine molecular structure, and be able to explain your structure assignments based on the spectral data.
Reading: Soderberg section on determining unknown structures.
Resources: Review the resources below and practice, practice, practice!