Undergraduate Physical Chemistry Course Research Articles

A Computer Laboratory for the Calculation of the Heat Capacity of a Peptide Unfolding Transition

ABSTRACT We present the implementation of a computer simulation laboratory for the calculation of the heat capacity of the folding-unfolding pseudo phase transition of a polyalanine Ala30α-helix, using molecular dynamics simulations. Unlike conventional calorimetry experiments, which provide a macroscopic interpretation of the heat capacity, the computer laboratory additionally offers a molecular perspective of the energy exchange processes that lead to the peak of the heat capacity at the phase transition, as well as the statistical mechanical interpretation of the phase transition. The exercise is targeted toward 1st- or 2nd-year students of biophysics in the context of an undergraduate physical chemistry course. We use a graphical web interface to overcome the steep learning barriers associated with command line interactions in commonly used molecular dynamics protocols. The web interface (VIKING) also handles communication with computing hardware in the background, so that students with limited or no programming experience can launch and analyze the simulations easily. A collaboration between the VIKING support team and responsible teachers is required to set up VIKING. We also present a solution in which simulations can be launched on students’ own computers, if some command line knowledge can be expected. The laboratory can also be repurposed for students of various backgrounds (physics, chemistry, biology, or engineering) and scholastic levels (undergraduate or graduate).

Physical Chemistry in Context: Using Quantum Mechanics to Understand the Greenhouse Effect

The concepts taught in an undergraduate physical chemistry course are directly related to the molecular processes governing climate change, yet the connections between quantum mechanical molecular properties and global warming are rarely made explicit. To improve student knowledge about climate change, we developed a three-part activity that computationally and experimentally explores blackbody radiation, the greenhouse effect, and the relationship between IR absorption properties and global warming potentials for the anthropogenic greenhouse gases defined in the Paris Agreement. The activities addressed the traditional learning objectives of a quantum-focused physical chemistry course by exploring topics such as the quantized nature of energy in Planck’s Law, the selection rules for rovibrational transitions, and discrepancies between theoretical models and observed experimental results. However, our approach was unique in that each concept was addressed within the context of the atmospheric phenomena related to climate change. A previously published climate science survey instrument was administered pre- and postactivity to assess student learning gains. The average percent of correct responses on this survey increased from 44% to 68% as a result of completing the activities.

Understanding the electrochemical sensors’ figures of merit using a H2O2 sensitive, low-cost ferrite powder first generation electrode

The development of electrochemical sensors capable of quantifying either chemical, biological, or environmental parameters of interest endorses both the increased academic and educational relevance of electrochemistry. As a result, understanding quantitative electrochemical sensing characterization and performance analysis through analytical figures of merit stands as a curricular requirement from both a theoretical and methodological standpoint as it involves the development of several skills which are highly transferable into further electrochemical education and professional practices. On the other hand, due to popular fields of applications such as non-invasive wearable electrochemical sensors for monitoring electrolytes in sweat on high-performance athletes, students are well-aware of its potential, increasing their willingness to partake in electrochemical activities. Addressing the aforementioned, the experience described herein is divided into two main sections. Firstly, a theoretical introduction regarding electrochemical sensors and electrochemical performance validation techniques known as electroanalytical figures of merit are proposed. Secondly, a hands-on experience using a H2O2sensitive ferrite powder working electrode is carried out by performing voltammetric and chronoamperometric techniques so that students develop a basic understanding of the redox processes occurring at the working electrode surface and obtain analytical performance parameters that allow conclusions to be drawn regarding the ferrite powder sensing capabilities towards H2O2 reduction. As for implementation requirements, the proposed four-hour laboratory protocol is suitable for graduate/upper-level undergraduate physical or analytical chemistry courses and, due to its length, is recommended to be conducted in groups of two to three students.

That’s So Cool. Using a Flame to Freeze Water. The Vapor-Absorption Refrigerator and How It Works

The design and operation of the vapor-absorption refrigerator (VAR) are described using the principles and tools typically covered in upper-division undergraduate physical chemistry courses. The objective is to enable students to understand in detail how this device works and how it compares with more typical vapor-compression refrigerators. Calculations of the thermodynamics and heat flow relating to the refrigeration cycles are presented, leading to the calculation of the coefficient of performance. Two types of VARs are examined, one using LiBr/water solution as the absorbing medium and water as the refrigerant, which relies on the hygroscopic nature of aqueous solutions of LiBr. The second uses water as the absorber and ammonia as the refrigerant. The device described, the Crosley IcyBall, was a popular and inexpensive home refrigerator requiring no electricity. It is an example of a VAR operating in a single-cycle mode.

Faculty beliefs about the purposes for teaching undergraduate physical chemistry courses

We report the results of a phenomenographic analysis of faculty beliefs about the purposes for teaching upper-division physical chemistry courses in the undergraduate curriculum. A purposeful sampling strategy was used to recruit a diverse group of faculty for interviews. Collectively, the participating faculty regularly teach or have taught physical chemistry courses in 16 different chemistry departments in the United States. While faculty agreed that the goal of teaching physical chemistry was to help students develop robust conceptual knowledge of the subject matter within thermodynamics, statistical mechanics, quantum mechanics, spectroscopy, chemical kinetics, and other major topics, some articulated strong beliefs about epistemic and social learning goals. An understanding of the relations between different ways of thinking about teaching upper-division physical chemistry courses offers practitioners with alternative perspectives that may help them expand their awareness of the purposes for teaching physical chemistry in the undergraduate curriculum. Furthermore, knowledge of faculty beliefs about their teaching provides educational researchers and curriculum developers with an understanding about the potential opportunities or barriers for helping faculty align their beliefs and goals for teaching with research-based instructional strategies. We discuss our findings with the intention to expand faculty awareness of the discourse on physical chemistry education to include various perspectives of the purpose for teaching upper-division physical chemistry courses.

Assessing chemistry one class at a time

Education Before changes in a curriculum can be proposed, it is necessary to assess the current state of the course. Fox and Roehrig did exactly that when surveying undergraduate physical chemistry courses in the United States. Data were collected about issues such as depth versus breadth of content

Nationwide Survey of the Undergraduate Physical Chemistry Course

A nationwide survey of the undergraduate physical chemistry course was conducted to investigate the depth and breadth of content that is covered, how content is delivered, how student understanding is assessed, and the experiences and beliefs of instructors. The survey was administered to instructors of physical chemistry (N = 331) at American Chemical Society certified colleges and universities in the United States. The majority of instructors (N = 187) provided contact information, allowing responses to be associated with their institution. The goal of this preliminary study is to provide an awareness of the current state of physical chemistry courses across the United States. Several relationships regarding the course curriculum were investigated such as depth versus breadth of course content, and goal for understanding versus types of assessment questions. Also, several relationships regarding instructor beliefs and experiences were investigated such as degree of teacher preparation experience versus ...

A Game-Based Approach to an Entire Physical Chemistry Course

We designed, implemented, and evaluated a game-based learning approach to increase student motivation and achievement for an undergraduate physical chemistry course. By focusing only on the most important game aspects, the implementation was realized with a production ratio of 1:8 (study load in hours divided by production effort in hours). Student motivation was found to increase significantly: compared to the traditional lecture format, self-study time was estimated to increase more than 3-fold to 4.6 h per week on average by the students. The failure rate in the final examination was also reduced, mainly because of bonus points that students could receive upon successful participation in the game. However, there is some indication that application of game-based learning might not improve higher-order thinking skills.

Use of JANAF Tables in Equilibrium Calculations and Partition Function Calculations for an Undergraduate Physical Chemistry Course

The usefulness of the JANAF tables is demonstrated with specific equilibrium calculations. An emphasis is placed on the nature of standard chemical potential calculations. Also, the use of the JANAF tables for calculating partition functions is examined. In the partition function calculations, the importance of the zero of energy is highlighted.

Using a Spreadsheet To Solve the Schrödinger Equations for the Energies of the Ground Electronic State and the Two Lowest Excited States of H2

We have designed an exercise suitable for a lab or project in an undergraduate physical chemistry course that creates a Microsoft Excel spreadsheet to calculate the energy of the S0 ground electronic state and the S1 and T1 excited states of H2. The spreadsheet calculations circumvent the construction and diagonalization of the Fock matrix and thus can be accomplished by any undergraduate chemistry student with basic calculus skills. The wave functions of the S0, S1, and T1 states of H2 are constructed from the symmetry-adapted bonding and antibonding molecular orbitals (MO). All quantum mechanical integrals are estimated using the Monte Carlo integration method. Due to the stochastic nature of the spreadsheet calculations, 25 runs were carried out to obtain the mean energy of the S0, S1, and T1 electronic states of H2. The accuracy of the spreadsheet calculations is comparable to that of the HF/STO-3G calculations. The atomic and molecular orbitals and the energy components can be easily calculated and plotted for better visualization and understanding of essential quantum chemical concepts. This spreadsheet can also be adapted to tackle a wider range of quantum chemistry problems with different levels of complexity.

Solid-State NMR Spectroscopy for the Physical Chemistry Laboratory

Solid-state nuclear magnetic resonance (NMR) spectroscopy finds growing application to inorganic and organic materials, biological samples, polymers, proteins, and cellular membranes. However, this technique is often neither included in laboratory curricula nor typically covered in undergraduate courses. On the other hand, spectroscopy and molecular structure taught in second-semester undergraduate physical chemistry courses meet the minimal background prerequisites for interpreting data obtained in many solid-state NMR experiments. A solid-state 2H NMR experiment is described in which the student obtains and interprets the spectrum of a powder sample of hexamethylbenzene-d18 using a solution NMR spectrometer as found in many undergraduate institutions. A quadrupolar-echo pulse sequence is applied to the sample to obtain the 2H NMR spectrum. The spectrum of a randomly oriented powder sample consists of two spectral branches with broad shoulders. The quadrupolar frequencies corresponding to the nuclear spin transitions are interpreted in terms of molecular mobility in the solid state, that is, 3-fold rotation of the methyl groups and 6-fold rotation of the hexamethylbenzene ring. In this way, students discover that solid substances may have significant molecular motions. This undergraduate investigation employing solid-state 2H NMR provides an informative exposure to state-of-the-art research techniques by using facilities that are already in place at many undergraduate institutions. Furthermore, it demonstrates a real-life manifestation of quantum mechanics as explained in physical chemistry courses, as well as fundamentals of molecular motions such as rotation of aromatic ring compounds and methyl groups in the solid state.

The Particle in a Box Redux: Improved Experimental Conditions for the Laser Synthesis of Linear Polyynes

The one-dimensional, particle-in-a-box model is an integral part of most undergraduate physical chemistry courses. Linear polyynes can be synthesized and are found to serve as real-world examples of the particle-in-a-box model. An improved set of experimental conditions for the laser synthesis of linear polyynes has been determined. Specifically, a Nd:YAG laser operating at 532 nm and 20 mJ/pulse for 5 min can produce sufficient polyynes to be detected with a UV–vis spectrophotometer. Students can use the experimental wavelength and the eigenvalue expression for the particle in a box to calculate the length of the box and compare it to the length of the molecule with good results. The lower laser energy used here is important because it enables a less costly laser to be used for the experiment, which will enable more instructors to incorporate the experiment into their curriculum.

Cyclic Polyynes as Examples of the Quantum Mechanical Particle on a Ring

Many quantum mechanical models are discussed as part of the undergraduate physical chemistry course to help students understand the connection between eigenvalue expressions and spectroscopy. Typical examples covered include the particle in a box, the harmonic oscillator, the rigid rotor, and the hydrogen atom. This article demonstrates that cyclic polyynes, C10, C14, and C18, effectively illustrate the quantum mechanical model for rotation in two dimensions: the particle on a ring. The exercise presented can be used to facilitate a classroom discussion on the particle-on-a-ring model or it can be used as a homework assignment. In either case, students compare a wavelength calculated from the eigenvalue expression for the particle on a ring to a UV–vis spectrum calculated via molecular modeling software. Spartan is used to perform a density functional theory calculation on the cyclic polyynes. Discussion focuses on how the particle-on-a-ring model works, its limitations, and how the model could be improved.

Reviews of Workbook for Organic Chemistry: Supplemental Problems and Solutions and Physical Organic Chemistry: A Guided Inquiry Workbook

I this review, I consider supplemental course materials Workbook for Organic Chemistry: Supplemental Problems and Solutions by Jerry Jenkins and Physical Organic Chemistry: A Guided Inquiry Workbook by Kelly Butler. As the organic workbook is for undergraduates and the physical organic workbook is for advanced undergraduates and graduate students, I will begin with the organic workbook. Quite simply, for students (and instructors) seeking additional problems to supplement a traditional undergraduate organic course, Jenkins’s workbook is superb. The paper format provides students plenty of opportunity to draw molecules while solving problems. For instructors interested in online homework, W. H. Freeman has also placed these problems in WebAssign. Nearly all current organic texts contain an assortment of problems for students to solve. Virtually all of these texts provide a supplemental “solutions manual” of worked solutions to the text problems. In addition, many texts supplement the traditional paper problems and solutions manuals with online problems, often with learning “hints” and guided solutions. So one might then question the need for additional problems as presented in Jenkins’s workbook. As Jenkins writes in his preface, “[B]etter performing students, however, consistently ask for additional exercises. It is the purpose of this manual, then, to provide Supplemental Problems and Solutions that reinforce and extend those textbook exercises.” Jenkins has succeeded in this task of providing additional problems; most are suited for better performing students. The workbook is organized in two parts: problems and solutions to problems. The problem chapters are arranged by functional group, following the sequence of most organic texts by beginning with alkanes and ending with amines. Each functional group chapter is presented in a standard format of general information followed by reactions, syntheses, and mechanisms. The reaction sections present problems in the form of reactant(s), reagent(s), and students then draw the product(s). The syntheses sections present starting and product molecules and students then provide a sequence of reagent(s) and intermediate product(s) to afford the transformation. The mechanism sections present reactant(s), reagent(s), and product(s) and direct students to outline a detailed step-by-step mechanism using electron-pushing arrow formalism. In addition to the functional group chapters, there are chapters on basics (hybridization, formulas, physical properties, acids and bases, resonance), stereochemistry and NMR (proton only). The preface also includes TIPS (To Improve Problem Solving) on mechanism arrows, equilibrium versus resonance arrows, hydrogen nomenclature, state of association and dissociation, and a listing of common abbreviations introductory students are likely to encounter. The solution chapters mirror the format of the problem chapters and provide straightforward and detailed solutions for each problem in the problem chapters. Some of the solutions also provide explanatory notes. While Jenkins’s workbook is successful in providing additional problems for better performing students, the target audience could be expanded to include “poorer performing students” with only slight adjustments. The poorer performing students are often the least motivated to work “supplemental” problems, but perhaps are the most in need of supplemental work. Because the workbook solutions contain minimal explanatory notes, and the synthesis solutions none at all, poorer students are likely to find the problems frustrating for lack of explanation to help them along and as a result, not use them at all. More detailed explanatory notes might help develop the chemical insight poorer students often lack, enabling them to at least get started on the problems rather than giving up for not knowing where to begin. For example, in the syntheses sections before presenting the solution, the author might provide some analysis of the functional groups and their arrangement in the synthetic target versus the starting molecule, along with short explanatory notes on how the various transformations and arrangements may be achieved, then present a solution to the problem. Aside from this shortcoming, the workbook provides plenty of problem-solving practice in all the topics undergraduates are likely to undertake in their organic course sequence, and for this, the workbook is a valuable contribution. As Butler writes in the author’s notes, Physical Organic Chemistry: A Guided Inquiry Workbook is “intended for use in an introductory graduate or an advanced undergraduate physical organic chemistry course in conjunction with a textbook.” The workbook is written using the process-oriented, guided-inquiry learning (POGIL) approach by providing activities for students working in small, self-managed groups. The success of the POGIL approach for courses in general and organic chemistry is well documented. A quick review of the literature indicates sparse POGIL use in graduate-level and upper-level undergraduate chemistry courses. While many upper-level courses employ small

Students' understanding of mathematical expressions in physical chemistry contexts: An analysis using Sherin’s symbolic forms

Undergraduate physical chemistry courses require students to be proficient in calculus in order to develop an understanding of thermodynamics concepts. Here we present the findings of a study that examines student understanding of mathematical expressions, including partial derivative expressions, in two undergraduate physical chemistry courses. Students participated in think-aloud interviews and responded to a set of questions involving mixed second partial derivatives with either abstract symbols or thermodynamic variables. The findings describe students’ ability to transfer mathematics knowledge to chemistry problems and how students use symbolic forms described by Sherin (2001) to make sense of mathematical expressions in physical chemistry contexts.

Teaching crystallography to undergraduate physical chemistry students

Teaching goals, laboratory experiments and homework assignments are described for teaching crystallography as part of two undergraduate physical chemistry courses. A two-week teaching module is suggested for introductory physical chemistry, including six to eight classroom sessions, several laboratory experiences and a 3 h computer-based session, to acquaint undergraduate physical chemistry students with crystals, diffraction patterns, the mathematics of structure determination by X-ray diffraction, data collection, structure solution and the chemical insights available from crystal structure information. Student projects and laboratory work for three to four weeks of an advanced physical chemistry course are presented. Topics such as symmetry operators, space groups, systematic extinctions, methods of solving the phase problem, the Patterson map, anomalous scattering, synchrotron radiation, crystallographic refinement, hydrogen bonding and neutron diffraction all lead to the goal of understanding and evaluating a crystallographic journal article. Many of the ideas presented here could also be adapted for inorganic chemistry courses.

Nanotechnology Provides a New Perspective on Chemical Thermodynamics

A small mechanical device, the atomic force microscope, measuring a force and the distance over which this force is applied, can be used on a single polysaccharide molecule to obtain the Gibbs energy of a conformational change within the polysaccharide. This well-defined conformational change within certain types of polysaccharide molecules is analogous to a chemical reaction with an equilibrium constant, Gibbs energy, enthalpy, and entropy applying to the individual molecule. Normally these thermodynamic properties for a substance would be obtained by measuring a heat of reaction and heat capacity and the measurements would be done on a large collection of molecules. It is now possible, with the new tools of nanotechnology, to do this measurement mechanically and on just one molecule. Single-molecule stretching is a fundamentally different way of measuring thermodynamic properties that links, in a simple and remarkable way, the physics of springs and forces with chemical reactions and equilibria. These concepts can be used in undergraduate physical chemistry courses to fascinate students about new ways of understanding physical chemistry and of measuring thermodynamic properties that arise from the techniques of nanotechnology.

Maple-Assisted Template for Automatic Calculation of Second Order AA'XX' NMR Spectra

This paper presents the creation of a template for the interpretation and simulation of second order AA'XX' NMR-spectra, starting from the core information offered in a regular undergraduate physical chemistry course.

Ab Initio Determinations of Photoelectron Spectra Including Vibronic Features. An Upper-Level Undergraduate Physical Chemistry Laboratory

We present a first-principles determination of the photoelectron spectra of water and hypochlorous acid as a laboratory exercise accessible to students in an undergraduate physical chemistry course. This paper demonstrates the robustness and user-friendliness of software developed for the Franck–Condon factor calculation. While the calculator is suitable for determining multiple types of electronic spectra, the paper focuses on photoelectron work. Because it is based upon ionization, photoelectron spectroscopy is an intuitively satisfying electronic technique that offers undergraduate students a glimpse into the abstract and often confusing concept of vibronic structure. While experimental application of this method is both expensive and challenging, it is ideally suited to theoretical determination. The vibrational envelopes of water and hypochlorous acid demonstrate the salient features of electronic spectroscopy.The ground state photoelectron spectra of these compounds are used as teaching examples; we also examine the unique pedagogical advantages of the laboratory.

Simulação do equilíbrio: o método de Monte Carlo

We make several simulations using the Monte Carlo method in order to obtain the chemical equilibrium for several first-order reactions and one second-order reaction. We study several direct, reverse and consecutive reactions. These simulations show the fluctuations and relaxation time and help to understand the solution of the corresponding differential equations of chemical kinetics. This work was done in an undergraduate physical chemistry course at UNIFIEO.