Upper-level Physical Chemistry Research Articles

Investigating the Clough, Lutz, and Jirgensons Rule for the pH Dependence of Optical Rotation of Amino Acids

Students in an upper-level physical chemistry course used a polarimeter to measure the molar optical rotation of different optically active amino acids to confirm the Clough, Lutz, and Jirgensons (CLJ) rule. This rule states that an amino acid is in the l-configuration if the molar optical rotation becomes more positive upon the addition of acid or the acid is of the d-configuration if the optical rotation becomes more negative in an acidified solution. Students demonstrated this rule for known configurations of amino acids and then applied this rule to determine the configuration of an amino acid with an unknown configuration.

Integrating Primary Research into the Teaching Lab: Benefits and Impacts of a One-Semester CURE for Physical Chemistry

Many chemistry laboratory exercises follow a given protocol with known results. Such traditional laboratories rarely give students an accurate representation of how research is conducted, the scientific practices involved in research, and the ownership that accompanies developing and carrying out an independent project. Several laboratory reforms have sought to overcome these limitations, including the creation of course-based undergraduate research experiences (CUREs). The CURE design is meant to emulate authentic research in the teaching laboratory by having students perform novel experiments with unknown results. In this article, we describe our implementation of a CURE for an upper-level physical chemistry laboratory course. Our students carried out novel research using molecular dynamics simulations, isothermal titration calorimetry, and stopped-flow kinetics to study ligand binding to the protein human serum albumin. We studied the effects of the CURE laboratory redesign via a mixed-methods approach...

Computational Study of Environmental Effects on Torsional Free Energy Surface of N-Acetyl-N′-methyl-l-alanylamide Dipeptide

We propose an articulated computational experiment in which both quantum mechanics (QM) and molecular mechanics (MM) methods are employed to investigate environment effects on the free energy surface for the backbone dihedral angles rotation of the small dipeptide N-acetyl-N′-methyl-l-alanylamide. This computation exercise is appropriate for an upper-level physical chemistry course. The purposes are (i) to show the importance of solvent effects on the free energy surface of molecules in solution and (ii) to compare different computational chemistry tools in terms of computation complexity versus detail of information obtained from calculus. The QM section is divided in three parts: in vacuo, implicit solvent, and explicit solvent calculations. Similarly, also the MM section is divided in three parts: molecular mechanics, molecular dynamics, and adaptive biasing force molecular dynamics. QM and MM sections can be proposed by the instructor as different and complementary parts of the experiment or as independent QM or MM class lessons. Together, the two sections can be used to set up a computational chemistry laboratory exercise targeted to the study of solvent effects on molecular properties.

A Primer in Monte Carlo Integration Using Mathcad

The essentials of Monte Carlo integration are presented for use in an upper-level physical chemistry setting. A Mathcad document that aids in the dissemination and utilization of this information is described and is available in the Supporting Information. A brief outline of Monte Carlo integration is given, along with ideas and pedagogy for optimum use of the Mathcad document in relation to application of this technique to quantum mechanical calculations to which undergraduate chemistry students are typically exposed.

The Belousov–Zhabotinskii Reaction: Improving the Oregonator Model with the Arrhenius Equation

Oscillating chemical reactions (OCRs) have been known since 1828, with the Belousov–Zhabotinskii (BZ) reaction the most studied example. Initially, OCRs were considered to be special cases due to the small number detected and because the oscillatory behavior did not seem to agree with the second law of thermodynamics. However, OCRs have become increasingly important not only in chemistry, but also in biology as they are the foundation of several significant phenomena: glycolysis, nerve signal transmission, heartbeats, and so forth. The BZ reaction has been examined both experimentally and theoretically. Temporal oscillations appear in both cases, but discrepancies are found between experimental results and theoretical calculations. This article addresses the discrepancies by describing (i) a simple, clear, and inexpensive experimental procedure for carrying out the reaction and determining the oscillation period and (ii) an innovative methodology that includes the effect of temperature on the original model using the Arrhenius equation. The equations resulting from this approach can easily be solved with the help of MATLAB. In addition, a user-friendly graphical interface has been developed that highlights the effects on the oscillating system caused by changes in different parameters. The effect of the temperature generated during the reaction is also analyzed. This analysis discloses temperature variations: a relevant issue that the theoretical model does not envisage. The exercise is appropriate for upper-level physical chemistry students.

ATR–FTIR Spectroscopy in the Undergraduate Chemistry Laboratory. Part I: Fundamentals and Examples

Attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy is a useful technique for measuring the infrared spectra of solids and liquids as well as probing adsorption on particle surfaces. Several examples of the use of FTIR-ATR spectroscopy in different undergraduate chemistry laboratory courses are presented here. These examples include measuring the infrared spectra of solid and liquid organic compounds commonly used as unknowns and of inorganic solids synthesized by students. The use of ATR-FTIR spectroscopy in the upper-level physical chemistry laboratories will be discussed in Part II where a new experiment involving the adsorption of ions from solution onto oxide particle surfaces is introduced. In addition to the implementation of ATR-FTIR spectroscopy into the undergraduate curriculum, students involved in undergraduate research can use this technique to get high-quality publishable data on a number of interdisciplinary chemically-relevant interesting research projects.

ATR–FTIR Spectroscopy in the Undergraduate Chemistry Laboratory. Part II: A Physical Chemistry Laboratory Experiment on Surface Adsorption

Attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy is a useful technique for measuring the infrared spectra of solids and liquids as well as probing adsorption on particle surfaces. The use of FTIR-ATR spectroscopy in organic and inorganic chemistry laboratory courses as well as in undergraduate research was presented in Part I as well as background information and the fundamentals of the ATR-FTIR technique. In Part II, the use of ATR-FTIR spectroscopy in the upper-level physical chemistry laboratories is discussed. A new experiment involving the adsorption of ions from solution onto oxide particle surfaces is introduced. In this laboratory experiment, students use ATR-FTIR spectroscopy to determine the Langmuir adsorption constant, Kads, for sulfate ion adsorbed on 2 particles at pH = 3. A thin film of oxide particles deposited onto the ZnSe ATR element is exposed to solutions of different sulfate concentrations. The infrared spectrum of adsorbed sulfate can be measured in this way. This experiment, which can be easily implemented into an upper-level chemistry curriculum, introduces students to several concepts including surface adsorption, oxide surface chemistry, and environmental interfacial processes.

The Incorporation of a Single-Crystal X-ray Diffraction Experiment into the Undergraduate Physical Chemistry Laboratory

Recent advances in detector technology and computing methods have made it possible to incorporate X-ray diffraction methods for routine analysis into the undergraduate chemistry curriculum. At the W. M. Keck Foundation Center for Molecular Structure (CMolS) at CSU Fullerton, we have integrated a two-week laboratory for determining crystal structures of organic molecules into the upper-level physical chemistry laboratory course. During this two-week experiment, students prepare a single-crystal sample of an organic substance, collect and integrate diffraction data, then refine a direct-methods structure solution. The laboratory successfully introduces the elementary concepts of X-ray diffraction and crystal structure determination. The refinement results serve as an excellent segue to discussions on the physical properties of crystals, packing interactions, thermal motions, and chirality, which can be expanded into an undergraduate course on X-ray crystallography.

Beginning Calculations in Physical Chemistry (Johnson, Barry R.; Scott, Stephen K.)

This workbook is designed to complement rather than supplement existing textbooks. Its format is one of examples followed by closely coordinated exercises that can be worked directly on the pages of the text itself. The first six chapters present material at a level typically covered in (or before) the first year general chemistry course and the final two chapters move into more sophisticated areas at the level considered in upper-level physical chemistry courses.