CHEMISTRY 125 

Daily Web Links

Some of these links are external and are freely available through search engines like Google or Bing.

 

Topic Video Web Links
Mass Spectroscopy    Interpreting Mass Spectrum from percent abundancies
Periodic Tables   Periodic Table Live Web
Element Periodic Table

ChemiCool Periodic Table

American Elements

The Pictorial Periodic Table

Chemical Elements - Interactive Periodic Table

Touchspin's Interactive Periodic Table Main Page Touchspin's Interactive Periodic Table

A great Periodic Table (PDF) to print (color) (from http://www.dayah.com/periodic/Other/Periodic%20Table.pdf

Electron Configuration Atoms/Ions Dr J YouTube:  Periods, Rows, Shells, Subshells, and Orbitals

Atomic Orbitals

Better atomic orbitals Jsmol

Electronic Configuration of Ions

Transition Metals:  difference from Main Group Metal

ransition Metals:  difference from Main Group Metal

Transition Metals:  difference from Main Group Meta

 

Periodic Trends Dr J YouTube:   Energy and Forces in Electron Nuclear Attractions

The meaning and measurement of atomic radii

WebElements: Periodicity

 J. Chem Ed: Period Table Live - Charts of Periodic Functions (pick x and y axes variables)

Metals and Unit Cells Adding Atoms to 1 large Face Centered Cubic unit cell
Lattice Structures I with coordination # (YouTube) (8:57) ****
If you have a free hour for extra credit (see syllabus and daily schedule)
Secret of the Viking Sword

Packing and Unit Cells

Bravais lattices: additional unit cells

Great views of Unit Cells - ChemTube3D

Unit Cell Powerpoint (also on Connect)

Face centered cubic = cubic closest packing

Metal Structures

Unit cells of elements

Interactive solid state chemistry: UW Madison

Packing and Holes Lattice Structures 2 - Holes (YouTube)(9:14) **** Unit Cells and Holes show in class
For the 2 links below select buttons to show holes:
Cubic Closest Packing CCP- with Octa/Tetra Holes show in class
Hexagonal CP - with Octa/Teta Holes
another site for holes - for CCP and HCP
Salts and Mineral Structures Fraction of Atoms/Ions in Unit Cell
Dr J YouTube:  number of atoms in hcp unit cell

Solid State - ChemTube3D - Phenomenal site!
Shows Closest Packing (HCP and CCP) salt structures:  Examples of AB, AB2, AB3, A2B, A3B structures with visualization of holes.
Another link for a different view: salts
Crystals at Otterbein: metals and salts

Interactive solid state chemistry: UW Madison

Other sites:

Water  |  Interactive 3 D structures Solid State

Lattice Energy Review YouTube:  unit cells and coordination number
Review Youtube:  holes:
octahedral and tetrahedral holes in Face Centered C;
cubic hole in scp

Lattice Energy Calculator (given in negative number's however)

Changes in Lattices/Unit Cells   Examples of changes in molecules
Deoxy to OxyHemoglobin (with red sphere)
Facilitated Diffusion of Lactose through a membrane
Molecular Shape, Geometry and Perspective Molecular Shape and Perspective (Moodle, passwd required)
Charges and Ions (Moodle passwd required)
Great site on geometry (VSEPR)
Great interactive sites from PHET:
Bond and molecule polarity
Molecular Shapes

IUPAC Nomenclature   Nomenclature
Nomenclature 2
Intro Chirality

Chirality/Enantiomers (1:01)

Stereochemistry - Enantiomers (Jmol)

Chirality: Mirror Planes and Inversion Symmetry

Chirality (7:21)

R and S Isomers

Naming R and S isomers (8:16)

 

R and S (Jmol)
ChemDraw on Network

Priority Rules = and = bonds

Review of stereisomers: more complicated molecules

Stereoisomers, Enantiomers, Diastereomers, Constitutional Isomers and Meso Compounds  view to 11 minute mark (Khan)

Diastereomers (Jmol)
Meso Compounds (Jmol)
Stereochemical Challenge (test yourself) (Jmol)

Meso Compounds

Meso Compounds: (8:51)YouTube
Cis/Trans - E/Z nomenclature (8:31) YouTube

 

9/16 New

Dr J:  Summary isomers

Dr J: Meso or Not

Dr J: Optical Activity


Stereoisomers - A Review
Practice: R/S Determination
R/S Qz with Answers
More than 1 chiral carbon
More than 1 Qz with Answers

For class:
Diastereomers
Meso Compounds
Organic Molecules: search for meso

2,4-dicholorpentane: Stereoch

2-bromo,4-choloropentane: Sterochem

Acylic Conformational Analysis
Cyclic Molecules: Rings and Flips

Ethane Conformation: YouTube
1:04

Conformations Butane: YouTube
13:51

Conformations of Cycloalkanes: YouTube  5:36

Jsmol:  Conformations of Ethane   |   Propane  |    Butane

Alkanes from Chapter 3:  Conformational Analysis of Alkanes and Cycloalkanes by Dr. Ian Hunt, U. Calgary - Follow arrow links at the bottom through cycloalkanes

atom counting and energy

Chair Conformations
Energy Analysis: cyclohexane and substituted cyclohexanes
Diamond Lattice: 6 and 7 atom interactions

Mono and disubstituted cyclohexanes: YouTube (6:41)

9/16 New

Butane in multiple representations:  3D ball/stick, line drawing,

Cyclic Molecules: Angle and Torsional Strain

 Newman projection - Calculating energies. (8:00 min) YouTube - Dr J

Cycloalkanes from Chapter 3:  Conformational Analysis of Alkanes and Cycloalkanes by Dr. Ian Hunt, U. Calgary - Follow arrow links at the bottom

Chair/Boat - Cyclohexane

cycloalkanes other than C6H12

cyclohexane

Steps in drawing chair conformations of cyclohexane (view as slide show!)

Ring Flip with intermediates: Jmol and animation

Newman projection: cyclohexanes

substituted cycloalkanes

polycyclic fused rings

Adding lines ot the diamond lattice and identify 6/7 atom interactions (view as slide show - NEW 10/7)

Diamond Lattice

Diamond Lattice - Oregon State

     
Intermolecular Forces

IMFs: YouTube (5 min)

liquid water and ice  

liquid water and ice with chair

ice and liquid water

dipole- dipole and London Dispersion forces (flash animation)

IMFs

Intermolecular Forces
and properties

Melting Pt Depression and Boiling Point Elevation: YouTube
(mistake at 3:25 - should state lower Melting Pt not Boiling Pt (0-6 minutes)

NaCl dissolving in water (from Iowa State)

Of Mice and Oxygen

Another view

thin layer chromatography

Solutions;
Colligative Properties:
Introduction Vapor Pressure Lowering Boiling Point Elevation Freezing Point Depression

Carbohydrates and Lipids

Carbohydrates 1: Defo and simple examples 
Carbohydrates 2:  Ribose and Glucose - straight and cyclic forms
Carbohydrates 3:  polysaccharides of 1 monossacharides repeats
Carbohydrates 4:  polysaccharides of disaccharide repeats.

Carbohydrates:
Fisher to Ring structure change:  Jmol
Jmol:  Glycogen    Amylose      Amylopectin     cellulose  
  

Lipids Dr J YouTube  -new 10.24.16
Gel to Liquid Crystalline Phase Change in Lipid Bilayers:  Effect of Cholesterol
Lipids:
A micelle
A membrane bilayer

Molecular Dynamics Simulation of a phospholipid with a saturated fatty acids and one with 6 double bonds from Scott Feller, Wabash College (note changes in saturated fatty acid from all trans to some gauche conformations.
Proteins Protein Structure (15:42))

Buried or Not: That is the Question (compare protein structure to micelle)
N-linked Glycoprotein    
How important are links? Influenza  
 Nucleic Acids Nucleic Acid and CHO structures (view web tutorials A and B first)

Questions?
For tutorials by Eric Martz below go to THIS LINK.  Select the Set Preference Link
choice
Then select this icon:
JSmol icon choice

Select tutorial A.  B and D are also good.

Dr Js links:
H bonds and H bonds donors and acceptors in AT and GC base pairs

DNA with major and minor groves AND  H bond donors/acceptors

DNA: protein complex
Molecular Dynamics Simulations - Biomolecules  

Biological Examples 

The movies below are courtesy of the Theoretical and Computational Biophysics Group at the Beckman Institute, University of Illinois, Champaign/Urbana

Go to the following pages and view the following simulations

Channel Proteins

- water channels in membranes:

- Sugar Permeation through LacY

 

- K+ Permeation through Kv1.2 Channel
Protein Folding and Stretching
- Six Microseconds of Protein Folding

Lipoproteins

- Lipoproteins that Circulate in the Blood Collecting Fat

  Covalent Networks, Metallic, and Ionic Crystals: YouTube (9:14)

Network Solids: (3:00)
Zeolites: view 2;00-3:15 and 4:00-5:30 minutes only
liquid water and ice with chair of O atoms in ice   (rotate it to clearly see the chair)
Covalent Network Solids

Build diamond and graphite (notice as you build diamond you are making a diamond lattice) 
Diamond, graphite, graphene, fullerene (follow the links)
Solids: Chem Ed Digital Library: Chose the following from the list of covalent solids:
- Carbon: diamond, graphite, nanotubes, etc

- Silica (SiO2) - turn off polyhedron, turn on thicker bonds Jmol:
- Zeolites

MoS2
   MoS2  

Zeolite Database | Zeolites: Wikipedia Jmol:
"Tetrahedra of Bonding" - metallic, ionic, ,molecular covalent, network covalent
Zeolite: scroll down left hand side to Zeolites
Zeolite Explorer
 
Transtion Metals - Dr J
Tetrahedral vs Square Planar - Dr J


d atomic orbitals Jsmol
great view d orbitals JSmol
overview geometry transition metal complexes: Purdue
Transition Metals from Purdue
TS metal complexes of Cl:  Carleton
 EDTA complex
Cis-platin DNA Interactions
 Square Planar Geometry from Octahedral
Naming TS metal complexes

Calmodulin
Zn2+  Zn finger DNA binding motif
  18 Electron Counting - Dr J
Counting Electrons: A needed review
Questions? (note 1 mistake near end: Pt2+ in cis-platin has 16 electron surrounding it)
18 electron rule with qz (use ionic charged model only; do top right qz example; don't worry about ring ligands

18-Electron rule, and
d electron counting from Wikipedia
  Transition Metal Complexes: YouTube (10:18)
Questions?

Mirror Planes in Octahedral Transition Metal Complexes - Dr J YouTube
 

General Isomerism in TS metal complex

Biomolecules

Octahedral isomers of molecules like Co(en)3,


  Waves and Orbitals - Dr J
0-12:00 min: prop waves and atomic orbitals;
12:00-19:00 min: Intro to molecular orbitals
note: 1 mistake - one mention of  nonbonding orbitals should have been correctly stated as antibonding orbital
Hands Chasing Clouds (prep for Zen Chem MOs)
Questions?
Diffraction – bend around corner
Interference: Constructive and Destructive I
Interference: Constructive and Destructive I
Interference Examples:
Water
Laser
 Electrons 
  Hybrid Orbtials - Dr J (14:00)
Hybrid Orbital Formation - YouTube (1:36)
Questions?
Hybrid Orbitals (Jsmol works)
Great sp2 visualization ethene (Jsmol)
  Resonance and Conjugation Dr J
Note: yellow dots represent atomic nuclei, not nodes; Last slide cursor does not appear.
MOs of Methane - YouTube 4:00
MOs of Ethane - YouTube 5:00
Questions?
conjugation: Jsmol
MOs pi ring systems: not Jsmol
MOs: Linear Combo of atomic orbital: (not Jsmol)
Stefan Immel; Tech. Univ Darmstad
MolCalc**** See and rotate MOs of a variety of molecules.  Select calculate and then observe properties like IR frequencies, MOs, etc. Disregard first set of lowest energy
  Aromaticity Dr J
Questions?
Huckel MOs of Benzene
Interior Angles of a regular  polygon
Aromatic, Antiaromatic, Nonaromatic Rings
Amide Bond:  Resonance, Conjugations, Hybridization, and Huckel MOs
  none Are these the same? - Octahedral complexes
Diamond Lattice
  Lewis Acid/Base reaction mechanism: electron pushing - YouTube Ca2+ calmodulin (calcium modulatory protein) – EF Hand
 Cu1+ copper (I) efflux regulator protein
Fe2+   deoxy and oxy-heme
 K+      valinomycin – a K+ ionophore which transports K+ ions across a membrane Zn2+
  Zn finger DNA binding motif
  Bronsted Acid/Base and pKas - Dr J
Questions?
 
  Bronsted Acid/Base Strength - Dr J (mistake: molecule named as glucose is not glucose, but glucitol)
Questions?
Organic Mechanisms - ChemTube3D
Increased acidity of Hs on C adjacent to a double bond:  resonance, conjugation and MO explanations.
  Acid/Base Rx - Extent, Completion, and Extractions - Dr J (mistake:  in 0.1 M HCl extraction, since HCl is a strong acid, no HCl is present as it is all converted to H3O+ which has a pKa of -1.7.  Rx still goes to completion.)  

The Structure of Atoms

The Periodic Table and Properties of Atoms

A.  Property of Waves

B.  What's wrong with the Rutherford "planetary" model of the atom - 1?

C.  Absorption and Emission (What's wrong with the Rutherford model -2)

D.  Light as particle:  Photoelectric Effect  (What's wrong with our description of light)

E.  Particles as Waves: electron, neutron, and molecule diffraction/interferences (What's wrong with the Rutherford model 3)

F.  Quantum model of the atom:  Bohr Model: 

G.  Quantum model of the atom:  Modern

Misc

 

Covalent Network Solids

October Nobel Prizes

Isomers

 Conformations of Molecules (Jmol)

Intermolecular Forces and the Properties of Substances

 Biological Examples 

The movies below are courtesy of the Theoretical and Computational Biophysics Group at the Beckman Institute, University of Illinois, Champaign/Urbana

Covalent Network Solids

Transition Metals

 

Molecular Orbitals

 

Acids and Bases and other reactions

Biological Examples Lewis Acid/Bases Complex