TIGER

Other Resources: 32 results
The Free Energy  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Thermodynamics
Gibbs Free Energy in Biology  John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Thermodynamics |
Metabolism |
Bioenergetics
Galvanic Cells and Free Energy  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Electrolytic / Galvanic Cells / Potentials
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
ChemPaths 104 W Mar 30  John W. Moore
Today in Chem 104: * Lecture: Gibbs Free Energy * Reading: Kotz: Ch. 19, Sec. 5-7 Moore: Ch. 18, Sec. 5-8 * Homework #8 due by 11:55 PM F Apr 1 * Quiz in second discussion section this week. * Lab this week is #11, Electrochemical Cells
Thermodynamics
Quinine and Urea  William F. Coleman
The WebWare molecules of the month are discussed in two laboratory articles in this issue. Quinine is studied in the article "A Fluorimetric Approach to Studying the Effects of Ionic Strength on Reaction Rates: An Undergraduate Steady-State Fluorescence Laboratory Experiment" by Stephen W. Bigger, Peter J. Watkins, and Bruce Verity. Urea, a typical protein denaturant, is used as a cosolvent in the article "Transfer Free Energy and the Hydrophobic Effect" by Joseph M. Serafin.
Molecular Modeling |
Molecular Properties / Structure
The Effect of Temperature  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Reactions |
Kinetic-Molecular Theory
The Thermodynamics of Pizza  Ed Vitz
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Thermodynamics
Critical Temperature and Pressure  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Phases / Phase Transitions / Diagrams |
Physical Properties
The Effect of a Change in Temperature  Ed Vitz, John W. Moore
A section of ChemPrime, the Chemical Educations Digital Library's free General Chemistry textbook.
Thermodynamics
A Pedagogical Simulation of Maxwell's Demon Paradox  D. López, C. Criado
Maxwell's demon was conceived by James Clerk Maxwell in 1871 to illustrate the statistical basis of thermodynamics (1), and the concept has since formed an arena for investigation and clarification of many concepts in thermodynamics (2). Chemistry students often have difficulty developing an intuitive knowledge of some concepts in thermodynamics. A Pedagogical Simulation of Maxwell's Demon aims to help make these concepts more understandable for students. Teaching thermodynamics from the microscopic point of view can help students develop an intuitive understanding of its concepts. This program simulates, at the microscopic level, two gas chambers with an opening between them. The program allows students or their instructors to set up simulations that illustrate the thermodynamics and statistical behavior of the system. The user determines the basis for whether the demon permits or denies passage of particles through the opening using information from the microscopic level, such as specific particle velocity. Students can track and analyze how this affects particle distribution, thermal equilibrium, relaxation time, diffusion, and distribution of particle velocities.
Thermodynamics
Chemical Reactions (Netorials)  Rachel Bain, Mithra Biekmohamadi, Liana Lamont, Mike Miller, Rebecca Ottosen, John Todd, and David Shaw
Chemical Reactions: this is a resource in the collection "Netorials". The Netorials cover selected topics in first-year chemistry including: Chemical Reactions, Stoichiometry, Thermodynamics, Intermolecular Forces, Acids & Bases, Biomolecules, and Electrochemistry.
Reactions
Biomolecules (Netorials)  Rachel Bain, Mithra Biekmohamadi, Liana Lamont, Mike Miller, Rebecca Ottosen, John Todd, and David Shaw
Biomolecules: this is a resource in the collection "Netorials". This set of modules will provide you with a descriptive overview of the four major classes of biomolecules found in all living organisms: carbohydrates, lipids, proteins, and nucleic acids. The Netorials cover selected topics in first-year chemistry including: Chemical Reactions, Stoichiometry, Thermodynamics, Intermolecular Forces, Acids & Bases, Biomolecules, and Electrochemistry.
Bioorganic Chemistry |
Carbohydrates |
Nucleic Acids / DNA / RNA |
Lipids |
Proteins / Peptides
Electrochemistry (Netorials)  Rachel Bain, Mithra Biekmohamadi, Liana Lamont, Mike Miller, Rebecca Ottosen, John Todd, and David Shaw
Electrochemistry: this is a resource in the collection "Netorials". This modules about electrochemistry includes topics such as oxidation-reduction and half reactions, voltaic and electrolytic cells, standard cell potentials and batteries. The Netorials cover selected topics in first-year chemistry including: Chemical Reactions, Stoichiometry, Thermodynamics, Intermolecular Forces, Acids & Bases, Biomolecules, and Electrochemistry.
Electrochemistry
ChemPaths 104 M Apr 4  John W. Moore
Today in Chem 104: * Lecture: Acids and Bases * Reading: Kotz: Ch. 17, Sec. 1-2 Moore: Ch. 16, Sec. 1-2 * Homework #9 due by 11:55 PM F Apr 8 * Quiz in second discussion section this week * Lab this week is #10, Chemical Equilibrium and Thermodynamics
Acids / Bases
ChemPaths 104 W Apr 6  John W. Moore
Today in Chem 104: * Lecture: Bronsted Acids and Bases * Reading: Kotz: Ch. 17, Sec. 3-5 Moore: Ch. 16, Sec. 3-5 * Homework #9 due by 11:55 PM F Apr 8 * Quiz in second discussion section this week * Lab this week is #10, Chemical Equilibrium and Thermodynamics
Brønsted-Lowry Acids / Bases
Thermometer (ChemPages Lab)  John W. Moore, Jerrold J. Jacobsen, Joe L. March
Thermometer: this is a resource in the collection "ChemPages Laboratory Resources". A thermometer is used to measure the temperature of solids, liquids, or gases. A thermometer contains a liquid (usually mercury or an alcohol solution) in a reservoir whose volume is linearly dependent on the temperature (as the temperature increases, the volume increases). The ChemPages Laboratory Resources are a set of web pages that include text, images, video, and self check questions. The topics included are those that are commonly encountered in the first-year chemistry laboratory. They have been put together for use as both a pre-laboratory preparation tool and an in-laboratory reference source.
Laboratory Equipment / Apparatus
Two Solids (GCMP)  David M. Whisnant
Two Solids: this is a resource in the collection "General Chemistry Multimedia Problems". When two solids barium hydroxide octahydrate, Ba(OH)2. 8H2O and ammonium thiocyanate, NH4SCN are mixed, they react. We will explore the thermodynamics of the reaction. 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.
Thermodynamics
Stoichiometry (Netorials)  Rachel Bain, Mithra Biekmohamadi, Liana Lamont, Mike Miller, Rebecca Ottosen, John Todd, and David Shaw
Stoichiometry: this is a resource in the collection "Netorials". Stoichiometry shows how to balance chemical equations, deal with limiting reactants, computing yelds, working with molarity and different concentrations as well as the use of stoichiometry principles in the chemical analysis of a mixture. The Netorials cover selected topics in first-year chemistry including: Chemical Reactions, Stoichiometry, Thermodynamics, Intermolecular Forces, Acids & Bases, Biomolecules, and Electrochemistry.
Stoichiometry
Intermolecular Forces (Netorials)  Rachel Bain, Mithra Biekmohamadi, Liana Lamont, Mike Miller, Rebecca Ottosen, John Todd, and David Shaw
Intermolecular Forces: this is a resource in the collection "Netorials". In this resource there is a review of Lewis structures, molecular geometry, electronegativity, or molecular polarity. After that, you can learn about the forces of attraction that exist between molecules. This module explores London forces and dipole-dipole forces (including hydrogen bonds). The Netorials cover selected topics in first-year chemistry including: Chemical Reactions, Stoichiometry, Thermodynamics, Intermolecular Forces, Acids & Bases, Biomolecules, and Electrochemistry.
Noncovalent Interactions
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
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
Nitrogen Oxides (GCMP)  David M. Whisnant
Nitrogen Oxides: this is a resource in the collection "General Chemistry Multimedia Problems". Two of the most important nitrogen oxides, N2O4 and NO2, are in equilibrium with each other. We are interested in how this equilibrium shifts with temperature. 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.
Equilibrium
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
Calorimeter, Coffee Cup (ChemPages Lab)  John W. Moore, Jerrold J. Jacobsen, Joe L. March
Calorimeter, Coffee Cup: this is a resource in the collection "ChemPages Laboratory Resources". A coffee cup calorimeter is a useful, simple device that can be used to measure the temperature change that accompanies a reaction. A Styrofoam cup is used because it is a good insulator. The cup will absorb (or supply) negligible amounts of heat during most General Chemistry experiments. Thus, any change in temperature is assumed to be due only to the reaction, and the heat transferred in the reaction may be calculated. The ChemPages Laboratory Resources are a set of web pages that include text, images, video, and self check questions. The topics included are those that are commonly encountered in the first-year chemistry laboratory. They have been put together for use as both a pre-laboratory preparation tool and an in-laboratory reference source.
Laboratory Equipment / Apparatus |
Calorimetry / Thermochemistry
Melting Points (ChemPages Lab)  John W. Moore, Jerrold J. Jacobsen, Joe L. March
Melting Points: this is a resource in the collection "ChemPages Laboratory Resources". The melting point is a characteristic property of a substance. It can be used for sample identification and purity determination. The melting point is observed by slowly heating a sample and observing the temperature when the sample has changed from a solid to a liquid. The ChemPages Laboratory Resources are a set of web pages that include text, images, video, and self check questions. The topics included are those that are commonly encountered in the first-year chemistry laboratory. They have been put together for use as both a pre-laboratory preparation tool and an in-laboratory reference source.
Laboratory Equipment / Apparatus
Contrail. A Module from the Physical Chemistry On-Line Project  Franklin M. C. Chen
The condensation trail, or contrail, that trails behind a jet plane is an everyday observable phenomenon. These manmade cirrus clouds can persist for hours, or even days and can spread over thousands of square kilometers. This is a concern because clouds are major variables that control Earth's atmospheric temperature and climate. Understanding the impact of contrails on Earth's climate is an active area of research. Further, contrail formation can be examined in terms of the operative thermodynamic phenomena. The process of contrail formation involves combustion, cooling, and ice formation, all common topics in the undergraduate physical chemistry curriculum. The project when it is subdivided into separate manageable subjects is a good, comprehensive exercise for physical chemistry students.
Thermodynamics |
Equilibrium
Molecular Models of Ruthenium(II) Organometallic Complexes  William F. Coleman
The featured molecules for this month come from the paper "Experiments in Thermodynamics and Kinetics of Phosphine Substitution in (p-Cymene)RuCl2(PR3)" by Ozerov, Moura, and Hoffman in which they study the reactions of a number of "piano stool" complexes of ruthenium(II). The synthesis of compound 2a offers students an alternative to the preparation of ferrocene if they are only preparing one metal-arene complex, and the use of the (p-cymene)RuCl2 dimer as a starting material introduces them to a compound that has become important for the synthesis of a number of ruthenium catalysts. Two structures are found for the dimer in the gas phase, one with the chlorides cis to one another and a more stable form with the chlorides trans. DFT calculations using the LanL2MB basis set and the B3LYP functional in Gaussian 03 (1) show the trans form to be about 90 kJ/mol more stable than the cis form. The structures of the trans form of the dimer and of compound 2a are presented in 2 formats with bonds from the ruthenium ion to all of the carbons in the aryl ring and with a single line to a ghost atom in the center of the ring. These are the two common ways of representing such structures but students should be made aware that the overall coordination about the ruthenium in both the dimer and in compound 2a is octahedral, and should look at the structures to convince themselves of that fact. It is also instructive to look at compound 2a, and the other piano stool complexes that are made in the paper, to see how deceptive representation of the triphenylphosphine moiety as PR3 is in terms of the stereochemical bulk of that group.
Organometallics
Molecular Models of EDTA and Other Chelating Agents  William F. Coleman
Deirdre Bell-Oudry presents a variation on an old theme in her paper on using an indirect EDTA titration for sulfate analysis (1). EDTA and (often loosely) related species are this month's Featured Molecules.EDTA is a hexaprotic acid (H6Y2+) having the pKa values given in the featured paper (1). Figure 1 shows a distribution diagram for the EDTA system (2). At the pH of normal waters, the predominant species have one or both of the nitrogen atoms protonated.Complexation, however, requires that both nitrogens be deprotonated and it is generally assumed that the form that complexes with metal ions is Y4−. Structures of several forms of EDTA are included in the molecule collection (Figure 2). These structures are quite flexible having many conformations that are readily accessible at room temperature.An introduction to EDTA chemistry leads to broader questions of metal ion chelation or sequestration. Related chelating agents included in the molecule collection are EGTA, DCTA, NTA, BAPTA, and DTPA. Molecular dynamics and Hartree-Fock calculations on BAPTA (Figure 2) confirm that many conformations, ranging from those with the phenyl rings parallel to one another, to more elongated forms, are essentially isoenergetic in room temperature aqueous solution (3).Also included in the molecule collection are several crown ethers, an isophore (nonactin), and a cryptand. These not only provide students with a glimpse of the types of molecules being employed for metal ion sequestration but open a wide range of topics of current research in a variety of areas of inorganic, industrial, environmental, and biological chemistry.
Aqueous Solution Chemistry
Chromatography, Gas (ChemPages Lab)  John W. Moore, Jerrold J. Jacobsen, Joe L. March
Chromatography, Gas: this is a resource in the collection "ChemPages Laboratory Resources". Gas chromatography is a method for separating the components of a solution and measuring their relative quantities. It is a useful technique for chemicals that do not decompose at high temperatures and when a very small quantity of sample (micrograms) is available. The use of gas chromatography is limited by the decomposition temperature of the components of the mixture and the composition of the column. Most columns cannot withstand temperatures greater than 250-350 °C. The ChemPages Laboratory Resources are a set of web pages that include text, images, video, and self check questions. The topics included are those that are commonly encountered in the first-year chemistry laboratory. They have been put together for use as both a pre-laboratory preparation tool and an in-laboratory reference source.
Laboratory Equipment / Apparatus
Molecular Models of Resveratrol  William F. Coleman
The featured molecules this month are from the paper "Resveratrol Photoisomerization: An Integrative Guided-Inquiry Experiment" by Bernard, Gernigon, and Britz-McKibbin exploring trans to cis photoisomerization in resveratrol. Examination of Figure 1 in that paper, where the hydrogen atoms have been omitted, might lead one to conclude that the structures are relatively straightforward. These isomers provide students an excellent opportunity to test their ability to take a two-dimensional representation and envision the three-dimensional structure of the molecule and to consider the competing factors that might lead to the three-dimensional structures being non-planar. The two-dimensional models focus attention on the possibility of extended pi-electron delocalization. Addition of the hydrogen atoms clearly suggests that delocalization will compete with non-bonded H-H repulsions in the cis isomer. Further examination of the trans isomer shows that such non-bonded interactions are, in what one might call a first-order approximation, like those in biphenyl interactions that lead biphenyl to be non-planar in both the gas phase and in a variety of solvents. The backbone of the trans isomer of resveratrol, trans-stilbene, has been the subject of a number of theoretical and experimental investigations (1, 2). In general, Hartree-Fock calculations predict a non-planar geometry for this molecule while Density Functional Calculations, using the same basis sets, predict an essentially planar structure. Spectroscopic evidence supports a temperature-dependent structure for trans-stilbene with the molecule being planar at low temperature and non-planar at high temperatures. Our calculations on trans-resveratrol produce similar results. Hartree-Fock calculations using the 6-31G** (6- 31G(d,p)) basis set predict a dihedral angle of approximately 24 degrees between each ring and the central carbon-carbon double bond. This result is consistent with the reported value of 23 degrees using the 6-31G* basis set. We also find that DFT calculations using the B3LYP functional and the 6- 31G** basis set, lead to a planar configuration. We include several versions of trans-stilbene and trans-resveratrol in the molecule collection so that students can explore these structural questions in more detail. For each molecule, structures obtained from PM3, HF(6-31G**), and DFT(B3LYP/6-31G**) calculations are included, as well as planar and non-planar structures of biphenyl. Measurement of the various bond and torsion angles using Jmol will help students develop a sense of the distance dependence of the non-bonded interactions and their importance in determining the actual structure. They might also wish to consider what additional degree(s) of freedom resveratrol and stilbene have that biphenyl does not, allowing the trans-form of the former molecules to remain planar under certain conditions, while minimizing the effect of the non-bonded repulsions.
Plant Chemistry |
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