Molecular Dynamics Simulations in First-Semester General Chemistry: Visualizing Gas Particle Motion and Making Connections to Mathematical Gas Law Relationships

Implementation of a freely available molecular dynamics (MD) software program in a general chemistry class to assist students in learning the relationship among particle motion, macroscopic properties, and mathematical gas laws is described. In this activity, students acquire skills in data analysis while developing a deeper understanding of the origin of macroscopic physical properties of gases. The activity is easy to implement and does not require significant expertise in computational chemistry on the part of the instructor

Molecular dynamics simulations of apo and holo forms of fatty acid binding protein 5 and cellular retinoic acid binding protein II reveal highly mobile protein, retinoic acid ligand, and water molecules

Structural and dynamic properties from a series of 300 ns molecular dynamics, MD, simulations of two intracellular lipid binding proteins, iLBPs, (Fatty Acid Binding Protein 5, FABP5, and Cellular Retinoic Acid Binding Protein II, CRABP-II) in both the apo form and when bound with retinoic acid reveal a high degree of protein and ligand flexibility. The ratio of FABP5 to CRABP-II in a cell may determine whether it undergoes natural apoptosis or unrestricted cell growth in the presence of retinoic acid. As a result, FABP5 is a promising target for cancer therapy. The MD simulations presented here reveal distinct differences in the two proteins and provide insight into the bindingmechanism. CRABP-II is a much larger, more flexible protein that closes upon ligand binding, where FABP5 transitions to an open state in the holo form. The traditional understanding obtained from crystal structures of the gap between two β-sheets of the β-barrel common to iLBPs and the α-helix cap that forms the portal to the binding pocket is insufficient for describing protein conformation (open vs. closed) or ligand entry and exit. When the high degree of mobility between multiple conformations of both the ligand and protein are examined via MD simulation, a new mode of ligand motion that improves understanding of binding dynamics is revealed

Conversation among Physical Chemists: Strategies and Resources for Remote Teaching and Learning Catalyzed by a Global Pandemic

In the midst of a global pandemic in spring 2020, physical chemistry faculty gathered to share strategies and resources for teaching remotely. During this conversation, instructors created a shared document compiling the challenges they faced in spring 2020 and ways to improve teaching and learning in the physical chemistry classroom and laboratory when institutions reopened in the fall. We present a content analysis of the shared document that provides a snapshot of physical chemists’ thoughts at that moment in June 2020. The themes that emerged from our analysis are assessment, choice of learning objectives, course management, opportunities, resources, student motivation, and wellbeing. We have summarized the numerous strategies, resources, and implementation ideas that were shared by participants, many of which we believe will remain in use when traditional in-person instruction resumes. Finally, the conversation connected physical chemists, strengthening our community. Continued community engagement has occurred through further synchronous conversations, asynchronous conversations on our Slack workspace, and the creation of the repository PChem Inspired Pedagogical Electronic Resource (PIPER)

Factors affecting the number and type of student research products for chemistry and physics students at primarily undergraduate institutions: A case study.

For undergraduate students, involvement in authentic research represents scholarship that is consistent with disciplinary quality standards and provides an integrative learning experience. In conjunction with performing research, the communication of the results via presentations or publications is a measure of the level of scientific engagement. The empirical study presented here uses generalized linear mixed models with hierarchical bootstrapping to examine the factors that impact the means of dissemination of undergraduate research results. Focusing on the research experiences in physics and chemistry of undergraduates at four Primarily Undergraduate Institutions (PUIs) from 2004–2013, statistical analysis indicates that the gender of the student does not impact the number and type of research products. However, in chemistry, the rank of the faculty advisor and the venue of the presentation do impact the number of research products by undergraduate student, whereas in physics, gender match between student and advisor has an effect on the number of undergraduate research products. This study provides a baseline for future studies of discipline-based bibliometrics and factors that affect the number of research products of undergraduate students

Using Modified Long Chain Fatty Acids to Explore Protein Dynamics in an Intracellular-Lipid Binding Protein

Intracellular lipid-binding proteins (iLBPs) play a critical role in lipid availability and in signaling pathways making them possible therapeutic targets. One specific iLBP of interest is FABP5, a fatty acid binding protein that binds to naturally-occurring retinoic acid and activates the peroxisome proliferator-activated receptor β/δ causing cell growth and proliferation. Competitive-binding to FABP5 by other long-chain fatty acid ligands may reduce unwanted overgrowth of cells. Recently, an increase in computational studies of FABP5 has provided insight into the binding process. The focus of this chapter is the role of ligand starting conformation on protein dynamics. A series of nine ~1 μs molecular dynamics (MD) simulations were conducted on two modified long-chain fatty acids docked into FABP5. The ways in which undergraduate students performed the research in this project will also be discussed

Molecular dynamics simulations of <i>apo</i> and <i>holo</i> forms of fatty acid binding protein 5 and cellular retinoic acid binding protein II reveal highly mobile protein, retinoic acid ligand, and water molecules

<p>Structural and dynamic properties from a series of 300 ns molecular dynamics, MD, simulations of two intracellular lipid binding proteins, iLBPs, (Fatty Acid Binding Protein 5, FABP5, and Cellular Retinoic Acid Binding Protein II, CRABP-II) in both the apo form and when bound with retinoic acid reveal a high degree of protein and ligand flexibility. The ratio of FABP5 to CRABP-II in a cell may determine whether it undergoes natural apoptosis or unrestricted cell growth in the presence of retinoic acid. As a result, FABP5 is a promising target for cancer therapy. The MD simulations presented here reveal distinct differences in the two proteins and provide insight into the binding mechanism. CRABP-II is a much larger, more flexible protein that closes upon ligand binding, where FABP5 transitions to an open state in the holo form. The traditional understanding obtained from crystal structures of the gap between two β-sheets of the β-barrel common to iLBPs and the α-helix cap that forms the portal to the binding pocket is insufficient for describing protein conformation (open vs. closed) or ligand entry and exit. When the high degree of mobility between multiple conformations of both the ligand and protein are examined via MD simulation, a new mode of ligand motion that improves understanding of binding dynamics is revealed.</p

On the structure of water and chloride ion interactions with a peptide backbone in solution

The arrangement of water and chloride ions around a model peptide (glycyl-L-prolyl-glycine-NH2) was investigated using Molecular Dynamics (MD) simulations and complementary Empirical Potential Structure Refinement (EPSR) simulations which adapt the modelled structure to reproduce experimentally measured neutron diffraction data. The results are in good qualitative agreement and show a common picture for all hydrogen-containing amine and amide groups: namely that there are two common chloride interactions observed – a direct contact between Cl and peptide backbone and a water-mediated interaction. The geometry of this mediation depends on the distance between chloride and nitrogen and hints towards two distinct modes of interaction between water and the ion, either along one of the O–H bonds or along the water dipole.Postprint (published version

The Value of Peer Mentoring Networks for Developing Leaders and Inspiring Change

A peer-mentoring network, funded by the National Science Foundation ADVANCE program, profoundly impacted the career trajectory of five women chemistry faculty at predominantly undergraduate institutions. By providing each other support, encouragement, information, and accountability, we advanced our careers, became leaders in our own right, and implemented change at our institutions. To extend this benefit to more women STEM faculty, we have developed and implemented a model to support 74 faculty and administrators representing 51 institutions across the country

Controlling The Radical 5-exo-trig Cyclization, And Selective Synthesis Of Seco-iso-cyclopropylfurano[e]indoline (seco-iso-cfi) And Seco-cyclopropylthiophene[e]indoline (seco-cti) Dna Alkylating Subunit Of The Duocarmycins

The free radical cyclization of benzofuran bromo-allylic chloride 6 in toluene produced an unpredicted mixture of 6-benzyloxy-N-t-Boc-3-(chloromethyl)furano[e]indoline (1) and 7-benzyloxy-N-Boc-3-(chloromethyl)furano[f]quinoline (2). DFT calculations indicated that the indoline radical (6B), formed from 5-exo-trig closure of intermediate 6A, was less polar than the corresponding quinoline radical (6C). Based on this result, we report herein that cyclization of chlorides 6-8 in a polar aromatic solvent consistently and exclusively produced the indoline product in good yield (74-83%). (C) 2013 Elsevier Ltd. All rights reserved