TIGER

Other Resources: 60 results
JavaScript Programs To Calculate Thermodynamic Properties Using Cubic Equations of State  Patrick J. Barrie
Cubic equations of state are widely used by chemists and chemical engineers to predict the thermodynamic properties of both pure substances and mixtures. In particular, these equations enable predictions concerning the temperature and pressure at which vapor liquid equilibrium occurs. These two educational JavaScript programs perform calculations using cubic equations of state and, equally importantly, explain how the calculations are performed.
Mathematics / Symbolic Mathematics |
Chemometrics |
Thermodynamics |
Equilibrium |
Enrichment / Review Materials
Physical Properties  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Crystals / Crystallography |
Physical Properties
Chemical Properties  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Ionic Bonding
Properties of Alkanes  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Chirality / Optical Activity
Properties of Gases  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Gases
Colligative Properties of Solutions  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Solutions / Solvents |
Physical Properties
Bubbles-Solids, Liquids & Gases  
ACS Science for Kids activities explore the properties of gases and how these properties explain the formation of bubbles.
Water / Water Chemistry |
Lipids |
Gases
Binary Ionic Compounds and Their Properties  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Ionic Bonding
Lewis Diagrams and Biological and Chemical Properties  Ed Vitz
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Lewis Structures |
Bioinorganic Chemistry
Physical Properties Lecture Demonstrations  Ed Vitz
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Physical Properties
Macroscopic Properties and Microscopic Models  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Molecular Properties / Structure
Slime and Goo  American Chemical Society
ACS Science for Kids activities exploring the properties of polymers.
Polymerization
Crystals  American Chemical Society
ACS Science for Kids activities explore crystals and their properties.
Crystals / Crystallography
Food  American Chemical Society
ACS Science for Kids activities that explore the chemical properties of foods.
Plant Chemistry |
Dyes / Pigments |
Lipids |
Proteins / Peptides |
Carbohydrates |
Molecular Properties / Structure |
Applications of Chemistry |
Nutrition |
Acids / Bases |
Chromatography
Polymers-Characteristics of Materials  American Chemical Society
ACS Science for Kids explores the properties of polymers.
Polymerization
Air-Solids, Liquids & Gases  American Chemical Society
ACS Science for Kids activities explore the properties of gases.
Atmospheric Chemistry |
Acids / Bases |
Reactions |
Applications of Chemistry |
Water / Water Chemistry |
Gases
Water-Solids, Liquids & Gases  American Chemical Society
ACS Science for Kids activities explore the properties of water.
Water / Water Chemistry
Electricity  American Chemical Society
ACS Science for Kids activities that explore the properties of electricity.a
Electrochemistry |
Magnetic Properties |
Metals |
Applications of Chemistry
Sound and Light  American Chemical Society
ACS Science for Kids activities explore the properties of sound and light.
Applications of Chemistry
Plants-ACS Science for Kids  American Chemical Society
ACS Science for Kids activities exploring the properties and chemistry of plants.
Plant Chemistry |
Natural Products |
Photosynthesis |
Transport Properties
Magnets and Metals  American Chemical Society
ACS Science for Kids activities explore the properties of magnets, metals, and electricity.
Magnetic Properties |
Metals
Soap and Detergent  American Chemical Society
ACS Science for Kids activities explore the properties of soap in aqueous solutions.
Lipids |
Polymerization |
Water / Water Chemistry |
Solutions / Solvents
Gases-Solids, Liquids & Gases  American Chemical Society
ACS Science for Kids activities explore the chemical and physical properties of gases.
Gases
States of Matter  American Chemical Society
ACS Science for Kids activities explore phase changes of matter and their properties.
Gases |
Physical Properties |
Phases / Phase Transitions / Diagrams
Motion-Science for Kids  American Chemical Society
ACS Science for Kids activities explore the properties of objects in motion and the effects of friction.
Physical Properties |
Applications of Chemistry
Nutrition  American Chemical Society
ACS Science for Kids activities that explore the chemical properties of food and nutrition.
Lipids |
Physical Properties |
Proteins / Peptides |
Nutrition |
Carbohydrates
Chemical and Biological Properties of Some Groups of Elements  Ed Vitz
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Descriptive Chemistry
Fundamental Properties of Electrons-Frogs Legs to Electron Transport  Ed Vitz
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Atomic Properties / Structure |
Atomic Properties / Structure
The Hydrophobic Effect and Properties of Small Polyatomic Molecules  Ed Vitz
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Noncovalent Interactions
Properties of Organic Compounds and Other Covalent Substances in Astronomy  Robert Hetue
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Bioorganic Chemistry |
Astrochemistry
Solids, Liquids & Gases  American Chemical Society
ACS Science for Kids resources explore the chemical and physical properties of solids, liquids, and gases.
Applications of Chemistry |
Gases |
Solids |
Liquids
Land-Science for Kids  American Chemical Society
ACS Science for Kids activities explore the geological process that occur on earth in relation to chemical properties.
Water / Water Chemistry |
Geochemistry
The Chemical Name Game  Robert M. Hanson
Provides practice in learning about names and properties of chemical species. You can play this game by yourself or as a group with a moderator to work the mouse and check answers.
Nomenclature / Units / Symbols
Luminescent Molecular Thermometers  William F. Coleman
The Featured Molecules this month come from the paper "Luminescent Molecular Thermometers" by Uchiyama, Prasanna de Silva, and Iwai exploring the many ways that photophysical properties can be used as temperature probes. They introduce a variety of molecule types, many of them now in our molecule collection. Excited states play a central role in this paper and it provides an opportunity to introduce students to some excited state properties.
Molecular Modeling |
Molecular Properties / Structure |
Photochemistry
Acids and Bases (Netorials)  Rachel Bain, Mithra Biekmohamadi, Liana Lamont, Mike Miller, Rebecca Ottosen, John Todd, and David Shaw
Acids and Bases: this is a resource in the collection "Netorials". In this module there is an introduction to the chemical properties of acids and bases. Afterwards, the sections include topics such as Molecular Structures of Acids and Bases, Ionization constants, properties of salts, buffers and Lewis theory of Acids and Bases. The Netorials cover selected topics in first-year chemistry including: Chemical Reactions, Stoichiometry, Thermodynamics, Intermolecular Forces, Acids & Bases, Biomolecules, and Electrochemistry.
Acids / Bases
The Relation of Temperature to Energy Spreadsheet  Christopher King
The relation between temperature, energy, and the properties of a material is well developed. While this relation is not clearly elaborated in most physical chemistry textbooks, these relationships can easily be included in the early part of a physical chemistry course on thermodynamics, and this interactive Excel spreadsheet can help.
Theoretical Chemistry |
Thermodynamics
Characteristics of Materials  American Chemical Society
What makes diapers absorbent? Is peanut butter stickier than syrup or jelly? Strong, stretchy, sticky, or sweet—everything around us has special properties which make them unique. See if you can identify and compare the characteristics of materials.
Industrial Chemistry |
Physical Properties |
Reactions |
Consumer Chemistry |
Gases |
Carbohydrates |
Proteins / Peptides |
Crystals / Crystallography |
Water / Water Chemistry |
Plant Chemistry |
Dyes / Pigments |
Lipids |
Molecular Properties / Structure |
Applications of Chemistry |
Nutrition |
Acids / Bases |
Chromatography |
Magnetic Properties |
Metals |
Polymerization |
Solutions / Solvents |
Descriptive Chemistry |
Food Science
Quantum States of Atoms and Molecules  Theresa Julia Zielinski, Erica Harvey, Robert Sweeney, David M. Hanson
Quantum States of Atoms and Molecules is an introduction to quantum mechanics as it relates to spectroscopy, the electronic structure of atoms and molecules, and molecular properties. A digital, living textbook, it provides opportunities not found in conventional textbooks opportunities that allow students to develop skills in information processing, critical thinking or analytical reasoning, and problem solving that are so important for success.
Quantum Chemistry
Strong Acids (GCMP)  David M. Whisnant
Strong Acids: this is a resource in the collection "General Chemistry Multimedia Problems". This problem will explore the properties of common strong acids. General Chemistry Multimedia Problems ask students questions about experiments they see presented using videos and images. The questions asked apply concepts from different parts of an introductory course, encouraging students to decompartmentalize the material.
Acids / Bases
Interactive Molecular Orbital Diagrams  William F. Coleman
Here is an application for constructing the molecular orbital electron configurations of heteronuclear diatomic molecules. Energy level diagrams are given for the two different cases encountered in heteronuclear diatomics of the first short period (Li2 - Ne2). This is a useful tool for having students explore questions of bond order, magnetic properties and numbers of unpaired electrons.
Covalent Bonding |
MO Theory |
Enrichment / Review Materials
Inorganic Molecules; A Visual Database  Charles E. Ophardt, Evan M. Davis, Dustin Underwood
Inorganic Molecules: A Visual Data Base contains text and graphics describing 66 molecules and ions commonly used as examples in general chemistry courses. For each molecule, fifteen molecular properties are presented visually by eight or nine different molecular models created by the CAChe Scientific Molecular Modeling program.
Atomic Properties / Structure |
MO Theory |
Molecular Properties / Structure
Acids and Salts (GCMP)  David M. Whisnant
Acids and Salts: this is a resource in the collection "General Chemistry Multimedia Problems". This problem will explore a few properties of common acids and their salts. General Chemistry Multimedia Problems ask students questions about experiments they see presented using videos and images. The questions asked apply concepts from different parts of an introductory course, encouraging students to decompartmentalize the material.
Acids / Bases
Oxides (GCMP)  David M. Whisnant
Oxides: this is a resource in the collection "General Chemistry Multimedia Problems". In this problem we will explore the properties of the oxides of a few elements. We will add samples of the oxides to universal indicator solution and learn about the acid-base character of the oxides. General Chemistry Multimedia Problems ask students questions about experiments they see presented using videos and images. The questions asked apply concepts from different parts of an introductory course, encouraging students to decompartmentalize the material.
Acids / Bases
Water #1 (GCMP)  David M. Whisnant
Water #1: this is a resource in the collection "General Chemistry Multimedia Problems". Isotopes are forms of the same element composed of atoms that have different numbers of neutrons. In this problem we will begin by observing the properties of water containing two isotopes of hydrogen. General Chemistry Multimedia Problems ask students questions about experiments they see presented using videos and images. The questions asked apply concepts from different parts of an introductory course, encouraging students to decompartmentalize the material.
Water / Water Chemistry
Water #2 (GCMP)  David M. Whisnant
Water #2: this is a resource in the collection "General Chemistry Multimedia Problems". Isotopes are forms of the same element composed of atoms that have different numbers of neutrons. In this problem we will begin by observing the properties of water containing two isotopes of hydrogen. General Chemistry Multimedia Problems ask students questions about experiments they see presented using videos and images. The questions asked apply concepts from different parts of an introductory course, encouraging students to decompartmentalize the material.
Water / Water Chemistry
Radius Ratio  William F. Coleman
This is a set of animations that demonstrates properties of the spherical holes formed when uniform spheres are packed. Cubic, octahedral and tetrahedral packing arrangements may be examined without anything in the holes,and with the repective holes filled. The sizes of the various holes relative to the spheres being packed are shown, which can lead students into an exploration of the radius ratio concept. An example is given of computing the relative size of an octahedral hole.
Crystals / Crystallography |
Ionic Bonding |
Solids |
Enrichment / Review Materials
JCE Cheminfo; Organic  Collection Curator; Hans J. Reich
JCE ChemInfo: Organic is a collection of Web pages containing information useful to teachers, researchers, and students in organic chemistry, biochemistry, and medicinal chemistry. The pages have been selected for ease of use, broad applicability, and quality of coverage. Topics will include structural information, organic reactions, nomenclature, physical properties, and spectroscopic data. These Web pages will be updated when possible and additional Web pages will be added as they become available.
Quartz and Cholesterol  William F. Coleman, Randall J. Wildman
The WebWare molecules of the month for June are from two articles in this issue. The article, "Cement: Its Chemistry and Properties", featured on the cover, dicusses the constituents of cement. Silica is one of the main components of cement, and the most common form of pure silica (SO2) is α-quartz. In "Bromination and Debromination of Cholesterol: An Inquiry-Based Lab Involving Structure Elucidation, Reaction Mechanism, and 1H NMR", Grant and Latimer describe an experiment suitable for upper-level organic chemistry students.
Menthol Steioisomers  William F. Coleman
The JCE Featured Molecules for July come from the paper An Engaging Illustration of the Physical Differences among Menthol Stereoisomers by Edward M. Treadwell and T. Howard Black on the use of commercially available stereoisomers of menthol to illustrate properties of enantiomers and diastereomers. The paper describes the use of four of the eight possible stereoisomers. Structures of all eight stereoisomers are included in this month's molecule collection, labeled by the chirality of the three chiral atoms. In addition to the exercises described in the paper, students can be asked to match the appropriate structures to those shown in the paper, or to generate structures for the isomers that are not discussed.
Molecular Modeling |
Molecular Properties / Structure
Universal Algorithm for Acid-Base Equilibrium Calculations  Pavol Tarapèík
These Microsoft Excel workbooks facilitate the calculation of the equilibrium composition of simple to complex acid-base systems. Three workbooks are available: 1. pH-mix calculates the equilibrium composition for any mixture of protolytes. 2. pH-titr calculates and presents titration curves. 3. pH-titrd calculates and presents titration curves with derivative curves included. The workbooks require only basic knowledge about Excel and almost no calculation abilities. However, they do require a description of chemical properties of the system components. Thus they allow students to concentrate on chemistry skills rather than laborious algebra and arithmetic.
Acids / Bases
Copoly; A Tool for Understanding Copolymerization and Monomer Sequence Distribution of Copolymers  Massoud Miri, Juan A. Morales-Tirado
The study of the composition and monomer sequence distribution of binary copolymers is often complicated because of the many definitions of representative properties for the sequence distribution, the numerous calculations required, and occasionally the abstract treatment of the statistical processes describing the copolymer formation. Copoly resolves these issues with a user-friendly, highly visual interface to perform all calculations. Using Microsoft Excel and Word, Copoly is compatible with Windows and Mac OS. In Copoly the students enter up to five independent data parameters using the Data Input Window, and immediately see the results. To obtain diagrams for a copolymerization obeying a second-order Markovian process, the fraction of one monomer, A, and the reactivity ratios, rA, rB, rA´ and rB´ need to be entered; for a first-order Markovian process only the first three of these are required. For a Bernoullian- or zeroth-order Markovian process only A and rA are required. The results are displayed on separate sheets labeled: 1. Copolymerization Diagrams, 2. Dyads and Triads, 3. Sequence Length Distribution, 4. Simulated Copolymer Design, and 5. Summary.
Polymerization
Molecular Models of Dyes  William F. Coleman
The paper on the synthesis of several dyes by James V. McCullagh and Kelly A. Daggett (1) provides us with the JCE Featured Molecules for this month. The authors mention various applications of these dyes, ranging from commercial dyeing to techniques for determining the course of complex biochemical processes. One of the reaction products, rhodamine B, is a member of a family of molecules that are widely used as tunable laser dyes. In this application, the rhodamines are most commonly encountered in a cationic form, rather than in the neutral form shown in the paper. In the cations, the carboxyl group is no longer part of a ring system. Several different members of the rhodamine family are included in the molecule collection because substituents have a marked effect on the effective lasing range of a given dye. Additionally, the solvent and the excitation source also influence the lasing range (2). Students can learn more about the relationship between structure, absorption and emission properties, and lasing ranges of various dyes by consulting ref 2 and from PhotochemCAD, Jonathan Lindsey's free application (3).
Dyes / Pigments
Molecular Models of Leaf Extracts  William F. Coleman
Our Featured Molecules this month come from the paper by Pelter et. al. on the analysis of leaf extracts by thin-layer chromatography (1). As the authors discuss, their experiment may be used in courses at various levels of the curriculum. The molecules discussed in the paper are also of wide interest both for their structural properties and their wide-ranging appearance in both natural and synthetic substances. Included in the molecule collection are all of the isomers for the molecules pictured in the text with the exception of menthyl acetate, for which only one structure is given (see below). All of these molecules have been optimized at the HF/631-G(d) level. The menthol family enantiomeric pairs of menthol, isomenthol, neomenthol and neoisomenthol provide a rich yet coherent group of molecules on which to base discussion of chirality, enantiomers and diastereomers. Treadwell and Black have described some of the differences in physical properties of four members of this family, and several other experiments using one or more menthols have been published in this Journal (2, 3). I have created a Web page in which the eight molecules are embedded in no particular order, and with no rational file names. This is being used in at least one of our organic sections to give students experience at identifying enantiomers, and diastereomers, and in applying R/S notation (4). As access to computational software becomes more common, and as efforts are being made to incorporate more relevant modeling experiments into all levels of the curriculum, the menthols again present some interesting possibilities. While students at the organic level know about enantiomers differing in their optical rotation, and about chiral molecules interacting with chiral and achiral environments, it is instructive for them to think of other ways in which enantiomers and diastereomers are the same or different. Three useful ways of checking to see whether two structures are truly enantiomers is to compute their total energies, vibrational spectra, and dipole moments. These calculations are available in most common computational packages. Figure 1 shows the results of energy calculations on optimized structures of the eight isomers. The enantiomeric pairs have, as expected, exactly the same total energy, while the various diastereomers differ in energy. The computation of the vibrational spectra is a very sensitive probe to determine whether two structures are optimized and enantiomeric or not. Structures that are almost enantiomeric, but not quite optimized, may exhibit similar energies, but the low frequency vibrations will be sensitive to any deviation from optimization. If two supposedly enantiomeric structures do not have the same computed vibrations, or if either shows a negative frequency, the structures need to be optimized more carefully. As with the vibrational frequencies, enantiomers should show identical dipole moments. Only one structure of the eight isomers in the menthyl acetate family is included in the collection, giving students the chance to build the other seven and verify their computed properties. Because of the central role that chirality plays in chemistry, and particularly in biochemistry, it seems appropriate to introduce some of these visualization and modeling exercises early in the curriculum, and in courses designed for students majoring in other areas. Students in various courses could pursue other aspects of these same molecules including odor and cooling properties, and green chemistry approaches to synthesizing menthols.
Plant Chemistry
Molecular Models of Rosmarinic Acid and DPPH  William F. Coleman
The paper by Canelas and da Costa (1) introduces students to the antioxidant rosmarinic acid, and its interaction with the free radical DPPH. Those two molecules are the featured species this month. The original paper shows the 2-dimensional structure of the cis isomer of rosmarinic acid, although the trans isomer exhibits very similar antioxidant properties. Calculations at the DFT/B3LYP 631-G(d) level show that the trans isomer is more stable than the cis isomer in the gas phase, a situation that is expected to carry over into solution. Many antioxidants are phenols, and rosmarinic acid has four such groups available for radical formation. A DFT study by Cao et al. (2) examines the relative stabilities of the radicals formed from loss of each of the phenolic hydrogens. That paper focuses on the trans isomer, and a useful student project would be to repeat the calculations with the cis isomer. An HPLC separation of the isomers of rosmarinic acid has been published (3), and might well lead to an extension of the experiment described in ref 1 in which relative antioxidant efficiencies of the two isomers could be evaluated. DPPH has been used extensively as a standard for determining antioxidant activity. An examination of the molecular orbital occupied by the lone electron shows significant delocalization, providing a partial explanation for the stability of the neutral radical. Our gas phase structure for DPPH, also at the DFT/B3LYP 631-G(d) level, is quite consistent with several crystal structures on DPPH and DPPH in the presence of another species (4).
Natural Products
Molecular Models of Reactants and Products from an Asymmetric Synthesis of a Chiral Carboxylic Acid  William F. Coleman
Our JCE Featured Molecules for this month come from the paper by Thomas E. Smith, David P. Richardson, George A. Truran, Katherine Belecki, and Megumi Onishi (1). The authors describe the use of a chiral auxiliary, 4-benzyl-2-oxazolidinone, in the synthesis of a chiral carboxylic acid. The majority of the molecules used in the experiment, together with several of the pharmaceuticals mentioned in the paper, have been added to our molecule collection. In many instances multiple enantiomeric and diastereomeric forms of the molecules have been included. This experiment could easily be extended to incorporate various aspects of computation for use in an advanced organic or integrated laboratory. Here are some possible exercises using the R and S forms of the 4-benzyl-2-oxazolidinone as the authors point out that both forms are available commercially. Calculation of the optimized structures and energies of the enantiomers at the HF/631-G(d) level using Gaussian03 (2) produces the results shown in Table 1. Evaluation of the vibrational frequencies results in no imaginary frequencies and the 66 real frequencies are identical for the two forms. Examination of the computed IR spectra also shows them to be identical. Additionally, the Raman and NMR spectra can be calculated for the enantiomers and compared to experimental values and spectral patterns. A tool that is becoming increasingly important for assigning absolute configuration is vibrational circular dichroism (VCD). Although the vibrational spectra of an enantiomeric pair are identical, the VCD spectra show opposite signs, as shown in Figure 1. One can imagine a synthesis, using an unknown enantiomer of the chiral auxiliary, followed by calculations of the electronic and vibrational properties of all of the intermediates and the product, and determination of absolute configuration of reactants and products by comparison of experimental and computed VCD spectra. Using a viewer capable of displaying two molecules that can be moved independently, students could more easily visualize the origin of the enantiomeric preference in the reaction between the chelated enolate and allyl iodide.
Green Chemistry
Molecular Models of Polymers Used in Sports Equipment  William F. Coleman
In keeping with the 2008 National Chemistry Week theme of Having a Ball with Chemistry, the Featured Molecules this month are a number of monomers and their associated polymers taken from a paper by Sandy Van Natta and John P. Williams on polymers used in making equipment for a variety of high-impact sports (1). The molecules provide students with an introduction to an important area of applied chemistry and also enable them to examine complex structures using the models they have seen applied to small molecules.It is certainly instructive for students to build small polymer fragments using molecular model kits. Holding a model of n-decane, for example, and twisting it in various ways, provides real insight into the multiplicity of conformations available to supermolecules of polyethylene. Computer-based 3-dimensional structure drawing and visualization programs make it possible to construct large oligomers of known polymers and to begin to explore structural properties of new systems. Two such programs, free for academic use, are DSVisualizer and ArgusLab (2). DSVisualizer includes a useful set of tools for building and viewing structures and a clean geometry option that applies a Dreiding-like force field. ArgusLab adds the ability to perform both molecular mechanics and semi-empirical geometry optimization and to display various molecular surfaces. Using ArgusLab, or a similar program, students can explore the relative energies of various conformations of the substances they have built electronically. Students who are being introduced to molecular modeling and the use of more sophisticated software can easily explore the effects of the modeling and convergence parameters on the stable structures that are found, and can begin to explore the difference between global and local minima on a molecular potential energy surface. Using the conformational search program in HyperChem 7.5 on a tetramer of vinyl chloride (terminated with H; of SRRS stereochemistry; only CCCC torsions varied), approximately half of the 500 structures examined fell within 6 kcal/mol of the lowest energy structure (3). This number would increase significantly if other torsion angles were included.The use of computational software allows us to introduce students in introductory chemistry to the idea of multiple conformations, which is so important in biochemistry and much of organic chemistry. In teaching ideas behind conformational stability care should be taken when attributing conformational stability solely to non-bonded repulsions between peripheral atoms on adjacent carbon atoms. Weinhold and co-workers have recently presented strong evidence that the stability of the staggered conformer of ethane relative to the eclipsed form arises from more favorable interactions of C-H sigma bonding orbitals on adjacent carbons (4). The multiplicity of such interactions could well be responsible for conformational stability in more complex systems. Any discussion of conformational stability should also introduce students to the ultimate conformational problem, the folding of proteins and to the Folding@home project (5).
Polymerization |
Applications of Chemistry
Molecular Models of Products and Reactants from Suzuki and Heck Syntheses  William F. Coleman
Our Featured Molecules this month come from the paper by Evangelos Aktoudianakis, Elton Chan, Amanda R. Edward, Isabel Jarosz, Vicki Lee, Leo Mui, Sonya S. Thatipamala, and Andrew P. Dicks (1), in which they describe the synthesis of 4-phenylphenol using an aqueous-based Suzuki reaction. The authors describe the various ways in which this reaction addresses concerns of green chemistry, and point out that their product bears structural similarity to two non-steroidal anti-inflammatory drugs (NSAIDs), felbinac and diflunisal. A number of molecules from this paper and its online supplemental material have been added to the Featured Molecules collection. Students will first notice that the aromatic rings in the molecules based on a biphenyl backbone are non-planar, as is the case in biphenyl. If they look carefully at diflunisal, they will notice that the carbon atoms are in a different chemical environment. One way in which to see the effect of these differing environments is to examine the effect of atom charge on the energies of the carbon 1s orbitals. Figure 1 shows this effect using charges and energies from an HF/631-G(d) calculation. A reasonable question to ask students would be to assign each of the data points to the appropriate carbon atom. As an extension of this exercise students could produce similar plots using different computational schemes. Are the results the same; are they parallel. This would be a useful problem when dealing with the tricky question of exactly what is meant by atom charge in electronic structure calculations. Students with more expertise in organic chemistry could explore extending the synthesis of 4-phenylphenol to produce more complex bi- and polyphenyl-based drugs. This may well be the first time that they have seen coupling reactions such as the Suzuki and Heck reactions. Students in introductory and non-science-major courses might well find the NSAIDs to be an interesting group of molecules, and could be asked to find information on the variety of molecules that display the anti-inflammatory properties associated with NSAIDs. Do they find structural similarities? Are there various classes of NSAIDs? Are they familiar with any of these molecules? Have they taken any NSAIDs? If so, for what reason? Is there any controversy about any of the NSAIDs? As with all of the molecules in the Featured Molecules collections, those added this month provide us with a number of ways of showing students the practical relevance of what they sometime see only as lines on a page. Molecules do matter.
Synthesis
Molecular Models of Antioxidants and Radicals  William F. Coleman
This month's featured molecules come from the paper by John M. Berger, Roshniben J. Rana, Hira Javeed, Iqra Javeed, and Sandi L. Schulien (1) describing the use of DPPH to measure antioxidant activity. DPPH was one of the featured molecules in September 2007 (2) and the basics of antioxidant activity were introduced in last month's column (3). In addition, some of the other molecules in the paper are already in the featured molecules collection (4). The remaining structures in the Figure 1 and Table 1 of the paper have been added to the collection. All structures have been optimized at the 6-311G(D,P) level. These molecules suggest a number of possible student activities, some reminiscent of previous columns and some new. (R,R,R)-α-tocopherol is one of the molecules in the mixture that goes by the name vitamin E. These molecules differ in the substituents on the benzene ring and on whether or not there are alternating double bonds in the phytyl tail. In (R,R,R)-α-tocopherol the R's refer to the three chiral carbon atoms in tail while α refers to the substituents on the ring. (R,R,R)-α-Tocopherol is the form found in nature. An interesting literature problem would be to have students learn more about the vitamin E mixture and the differing antioxidant activity of the various constituents. Additionally they could be asked to explore the difference between the word natural as used by a chemist, and "natural" as used on vitamin E supplements. Can students find regulations governing the use of the term "natural"? Can they suggest alternative legislation, and defend their ideas? If students read about vitamin C they will discover that only L-ascorbic acid is useful in the body. It would be interesting to extend the experiment described in the Berger et al. paper (1) to include D-ascorbic acid. How do the antioxidant abilities of the enantiomers, as determined by reaction with DPPH compare? Is this consistent with the behavior in the body? Why or why not? Berger et al. mention two other stable neutral radicals, TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl) and Fremy's salt. In a reversal from the use of stable radicals to measure antioxidant properties, these two molecules have proven to be very versatile oxidation catalysts in organic synthesis, and would make a rich source of research papers for students in undergraduate organic courses.
Free Radicals |
Natural Products
Molecular Models of Annatto Seed Components  William F. Coleman
In January 2008 the focus of this column was on the plant pigments lycopene and beta-carotene (1). Our attention this month returns to two papers discussing the pigments in annatto seeds (Figure 1), including direct precursors to lycopene. The paper by Teixeira, Dur�n, and Guterres describes the extraction and encapsulation of annatto seed components (2). The McCullagh and Ramos paper describes the separation of the pigment bixin from these seeds by TLC and column chromatography (3). These molecules could form the basis of interesting exercises across the chemistry curriculum. In courses designed for non-majors, students could choose a molecule from the table and search the literature for both scientific and non-scientific sources. Are the claims made in the latter sources regarding the health benefits of these molecules consistent with the scientific data? That discussion could be expanded to the more general question of how one tests the validity of statements made in what are essentially advertisements. Are any of these precursor molecules to lycopene considered to have anticancer properties (4)? In introductory or general chemistry courses, students could explore the various bond lengths and bond angles in the molecules to see whether they are consistent with their expectations based on simple bonding models. In introductory, organic, or biochemistry classes, the thermodynamics of hydrogenation and dehydrogenation could be examined. This might make an interesting alternative to the oft-discussed Haber Process. What conditions would one propose for a dehydrogenation process? Why are dehydrogenation reactions important? What enzymes catalyze the various dehydrogenation steps from phytoene to lycopene? These molecules could also be used in a variety of computational exercises in introductory and physical chemistry courses. Hartree�Fock calculations on a molecule such as phytoene may prove time-consuming depending on the nature of the computing system available. A good place to begin would be to perform semi-empirical calculations on the various molecules. Do the optimized structures match experimental results or the results of larger calculations? Does the HOMO�LUMO gap correlate with the observed electronic absorption spectra? Which is more important in determining the difference in absorption between phytoene and phytofluene, the total number of double bonds or the number of bonds in the region of conjugation? Of course the aspect of these molecules that is most likely to capture student attention is their color, and they provide nice examples of the origin of color, the relationship between color observed and color absorbed, and, in upper level courses, the more detailed relationships of the energies of the ground and excited states.
Plant Chemistry |
Natural Products
Molecular Models of Peroxides and Albendazoles  William F. Coleman
This month our featured molecules come from two sources, the paper by Marina Canepa Kittredge, Kevin W. Kittredge, Melissa S. Sokol, Arlyne M. Sarquis, and Laura M. Sennet on the stability of benzoyl peroxide (1) and the paper by Graciela Mahler, Danilo Davyt, Sandra Gordon, Marcelo Incerti, Ivana Núñez, Horacio Pezaroglo, Laura Scarone, Gloria Serra, Mauricio Silvera, and Eduardo Manta on the synthesis of an albendazole metabolite (2).The benzoyl peroxide paper is targeted at non-majors courses, but the molecule and related peroxides contain a number of interesting structural features that could be explored in traditional introductory and in upper-level courses. The first feature is the OO bond itself. In the three examples included in the collection the bond length computed at the B3LYP/6-311++G(d,p) level ranges from 133.8 pm for dimethyl peroxide to 144.9 pm for hydrogen peroxide. The experimental value for the latter is 147.5 pm and the Computational Chemistry Comparison and Benchmark DataBase (CCCBD) gives a wide range of computed OO bond lengths in H2O2 for more than 20 model chemistries (3).The XOOXʹ dihedral angle in these peroxides also shows interesting properties that have been difficult to reproduce theoretically. In hydrogen peroxide the experimental value is 119.8°, while our calculation gives 121.5°. Again the CCCBD reports a wide variation in this angle, including methods that produce a value of 180°. On the other hand, our model of benzoyl peroxide has a dihedral angle of 86.6°, and dimethyl peroxide shows a dihedral angle of 180°. Weinhold and Landis discuss the angle in hydrogen peroxide in terms of a stabilization of the gauche form through an nσ* interaction between oxygen lone pairs and empty CO σ* orbitals (4). Many levels of theory produce 180° dihedral angles for dimethyl peroxide and, as Tonmunphean, Parasuk, and Karpfen have pointed out, minima in the 120° range are not observed until coupled-cluster models are applied (5). The accepted experimental structure with a 119 ± 10° dihedral angle comes from an electron diffraction study (6). These experimental and high-level theoretical calculations lead us to conclude that the model proposed by Weinhold and Landis applies to more complex peroxides as well as to H2O2.In the case of albendazole and the oxygenated albendazoles, it is interesting to monitor the computed charges on the sulfur atoms with oxygenation. The charges on the sulfur atoms, computed at the B3LYP/6-311++G(d,p) level, are 0.066, 0.768 and 1.123 for 0, 1 and 2 oxygens on the sulfur atom respectively. Students could be asked to predict and explain the order of the charges, and to comment on how the charges inform the description of bonding about the sulfur atom. To what extent is the hypervalent species ionic? Does this influence how we should think of d-orbital participation in such molecules?
Molecular Modeling