Molecular Graphics Software Research Articles

Teaching protein structure and function through molecular visualization.

The function of proteins is governed by their three-dimensional structure. This structure is determined by the chemical characteristics and atomic interactions of amino acids. Students of biochemistry, with a particular focus on protein chemistry, benefit from looking at protein structures and understanding how proteins are built and fold. Due to their three-dimensional nature, static two-dimensional representations in textbooks can be limiting to student learning. Here, we developed a series of tutorials that introduce students to molecular graphics software. The students are challenged to apply the software to look at proteins and to get a deeper understanding of how amino acid properties are linked to structure. We also familiarize students with some of the latest tools in computational structural biology. Students performed the tutorials with visual enthusiasm and reported general satisfaction in being able to visualize theoretical concepts learned during lectures. We further stimulated student engagement by allowing space for self-exploration. We share the tutorial instructions for other teachers to build on them, and we also offer suggestions for further improvement based on student feedback. In summary, we present a series of tutorials aimed at students of an advanced course in protein biochemistry to enable them to explore the universe of protein structures and how those relate to function.

A Semester-Long Learning Path Teaching Computational Skills via Molecular Graphics in PyMOL

ABSTRACT Structural biology describes biological processes at the molecular level and is an integral part of undergraduate study programs in molecular biosciences. Students are often fascinated by the visualizations created by molecular graphics software, which allow them to see the molecular world for the first time. Today, molecular visualization and structural analysis do not require expensive high-end computers but can be performed on the students' own laptops and are therefore highly suited for active learning approaches. We have designed a semester-long learning path that integrates molecular graphics and structural analysis using PyMOL into an undergraduate course in biomolecular structure and function. Compared to stand-alone PyMOL introductions, the semester-long learning path allows for an improved pedagogical design. The path progressively introduces more advanced functions in relevant scientific contexts and allows for spaced repetition. Advanced analysis functions in PyMOL are available only via the command line, so the learning path also teaches basic scripting and serves as an accessible introduction to computational thinking because a few lines of code can produce stunning results. Student surveys carried out at the end of the course suggest that the learning path supported the ability to perform structural analysis to a high degree. Moreover, a simulated exam showed that almost all students were able to carry out basic visualization tasks using PyMOL scripts, while three-quarters could undertake advanced structural analysis after following the course. In summary, integration of molecular graphics software with teaching of structural biochemistry allows a hands-on approach to analyzing molecular mechanisms and introduces biologically oriented students to computational thinking.

Molcontroller: A VMD Graphical User Interface Featuring Molecule Manipulation.

Visual Molecular Dynamics (VMD) is one of the most widely used molecular graphics software in the community of theoretical simulations. So far, however, it still lacks a graphical user interface (GUI) for molecular manipulations when doing some modeling tasks. For instance, translation or rotation of a selected molecule(s) or part(s) of a molecule currently only can be achieved using tcl scripts. Here, we use the Tcl/Tk toolkit to develop a user-friendly GUI for VMD, named Molcontroller, which is featured by allowing users to quickly and conveniently perform various molecular manipulations. This GUI might be helpful for improving the modeling efficiency of VMD users.

Cosolvent Analysis Toolkit (CAT): a robust hotspot identification platform for cosolvent simulations of proteins to expand the druggable proteome

Cosolvent Molecular Dynamics (MD) simulations are increasingly popular techniques developed for prediction and characterization of allosteric and cryptic binding sites, which can be rendered “druggable” by small molecule ligands. Despite their conceptual simplicity and effectiveness, the analysis of cosolvent MD trajectories relies on pocket volume data, which requires a high level of manual investigation and may introduce a bias. In this work, we present CAT (Cosolvent Analysis Toolkit): an open-source, freely accessible analytical tool, suitable for automated analysis of cosolvent MD trajectories. CAT is compatible with commonly used molecular graphics software packages such as UCSF Chimera and VMD. Using a novel hybrid empirical force field scoring function, CAT accurately ranks the dynamic interactions between the macromolecular target and cosolvent molecules. To benchmark, CAT was used for three validated protein targets with allosteric and orthosteric binding sites, using five chemically distinct cosolvent molecules. For all systems, CAT has accurately identified all known sites. CAT can thus assist in computational studies aiming at identification of protein “hotspots” in a wide range of systems. As an easy-to-use computational tool, we expect that CAT will contribute to an increase in the size of the potentially ‘druggable’ human proteome.

CAPLIB: A New Program Library for the Modeling and Analysis of Icosahedrally Symmetric Viral Capsids.

A new program library named “CAPLIB” was developed for the modeling and analysis of icosahedrally symmetric virus capsids. CAPLIB is equipped with the mathematical data of 60 rotation matrices of icosahedral symmetry, 15 planes bisecting the entire capsid structure, and a table summarizing how the 60 asymmetric units (cells) are partitioned by the planes. CAPLIB contains the function to determine the cell numbers of atoms from the atomic positions and the function to determine the rotation axes and angles from the rotation matrices. Using CAPLIB, it is possible to generate the structure of any selected protein unit within the entire capsid by rotating a single protein unit structure. CAPLIB can classify Protein Data Bank files of capsids with the directions of rotation axes, rotate the protein structure onto the standard position, and perform various deformations of the entire capsid. The interface to the molecular graphics software, PyMOL, was also developed for efficient modeling of capsids.

FRET-Based Trilateration Applied to the Mapping of CaM within the Ryanodine Receptor

We have carried out trilaterations, based on simulated annealing calculations and time-resolved FRET measurements, to map the location of calmodulin (CaM) within the ryanodine receptor (RyR) Ca2+ channel. Fluorescence lifetime (FLT) detection of FRET allows resolving multiple distances for each FRET pair, which are represented by Gaussian distance distributions fitted to the FRET data. Our improved general trilateration approach takes into account the distance distributions from multiple FRET pairs, and shows the location of the acceptor probe as a probability distribution in the format of an MRC/CCP4-format density map. This map can be displayed using common molecular graphics software. A more specialized approach takes into account the four-fold symmetry of the RyR channels in calculating the predicted FRET from a donor with known location to symmetrically located FRET acceptors. Several single-cysteine variants of the 12-kDa FK506-binding protein (FKBP) were labeled with FRET donor (Alexa Fluor 488), and targeted to RyR1 and RyR2. Effective average positions of the donors were calculated from simulated annealing, constrained by the FKBP atomic structure and by the RyR1 and RyR2 cryo-EM maps. Four single-cysteine variants of CaM, two N-lobe and two C-lobe sites, were labelled with fluorescence acceptor (Alexa Fluor 568). FRET from the FKBP donors to the CaM acceptor was measured via FLT detection. The FRET-based trilateration has allowed us to resolve the location of the N- and C-lobes of CaM within the RyR1 and RyR2 cryo-EM maps. A shift in the location of CaM dependent on resting or contracting [Ca2+] is observed. The upgraded methodology is setup for determining the structure-function relationship of other RyR modulators. This work was supported by NIH grants R01 HL92097 (RLC) and R37 AG26160 (DDT), and by American Heart Association Postdoctoral Fellowship 16POST31010019 (RTR).

PyMOL mControl: Manipulating molecular visualization with mobile devices

Viewing and manipulating three-dimensional (3D) structures in molecular graphics software are essential tasks for researchers and students to understand the functions of molecules. Currently, the way to manipulate a 3D molecular object is mainly based on mouse-and-keyboard control that is usually difficult and tedious to learn. While gesture-based and touch-based interactions are increasingly popular in interactive software systems, their suitability in handling molecular graphics has not yet been sufficiently explored. Here, we designed the gesture-based and touch-based interaction methods to manipulate virtual objects in PyMOL utilizing the motion and touch sensors in a mobile device. Three fundamental viewing controls-zooming, translation and rotation-and frequently used functions were implemented. Results from a pilot user study reveal that task performances on viewing controls using a mobile device are slightly reduced as compared to mouse-and-keyboard method. However, it is considered to be more suitable for oral presentations and equally suitable for education scenarios such as school classes. Overall, PyMOL mControl provides an alternative way to manipulate objects in molecular graphic software with new user experiences. The software is freely available at http://cbbio.cis.umac.mo/mcontrol.html. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(1):76-83, 2017.

Improved FRET-Based Trilateration Methods Applied to the Mapping of Calmodulin within the Ryanodine Receptor

We have used improved trilateration methods, simulated annealing calculations, and time-resolved FRET measurements to map the location of calmodulin (CaM) within the ryanodine receptor (RyR) Ca2+ channel. Our previous published FRET trilateration method used distances from confocal microscopy measurements, where the distance uncertainties were calculated based on measurement precision (Svensson et al. 2014 Biophys J. 107, 2037-48). Fluorescence lifetime (FLT) detection of FRET allows resolving multiple distances for each FRET pair, which are represented by Gaussian distance distributions fitted to the FRET data. Our new generic trilateration approach takes into account the Gaussian distance distribution and shows the FRET probability distributions as an MRC/CCP4-format density map, which can be displayed using common molecular graphics software. A more specialized approach takes into account the four-fold symmetry of the RyR channels in calculating the predicted FRET from a donor with known location to symmetrically located FRET acceptors. Five single-cysteine variants of the 12-kDa FK506-binding protein (FKBP) were labeled with FRET donor, Alexa Fluor 488, and targeted to RyR. Effective average positions of the donors were calculated from simulated annealing, constrained by the RyR cryo-EM map and by the FKBP atomic structure. Four single-cysteine variants of CaM, two N-lobe and two C-lobe sites, were labelled with a fluorescence acceptor, Alexa Fluor 568. FRET from the FKBP donors to the CaM acceptor was measured via FLT. FRET-based trilateration has allowed us to resolve both the location of the N- and C-lobes of CaM within the RyR cryo-EM map. A shift in the location of CaM dependent on resting or contracting [Ca2+] is observed. This work was supported by NIH grants R01 HL092097 (RLC), and R37 AG26160 (DDT) and by a Postdoctoral Fellowship from the American Heart Association (RTR).

Do we see what we should see? Describing non-covalent interactions in protein structures including precision.

The power of X-ray crystal structure analysis as a technique is to 'see where the atoms are'. The results are extensively used by a wide variety of research communities. However, this 'seeing where the atoms are' can give a false sense of security unless the precision of the placement of the atoms has been taken into account. Indeed, the presentation of bond distances and angles to a false precision (i.e. to too many decimal places) is commonplace. This article has three themes. Firstly, a basis for a proper representation of protein crystal structure results is detailed and demonstrated with respect to analyses of Protein Data Bank entries. The basis for establishing the precision of placement of each atom in a protein crystal structure is non-trivial. Secondly, a knowledge base harnessing such a descriptor of precision is presented. It is applied here to the case of salt bridges, i.e. ion pairs, in protein structures; this is the most fundamental place to start with such structure-precision representations since salt bridges are one of the tenets of protein structure stability. Ion pairs also play a central role in protein oligomerization, molecular recognition of ligands and substrates, allosteric regulation, domain motion and α-helix capping. A new knowledge base, SBPS (Salt Bridges in Protein Structures), takes these structural precisions into account and is the first of its kind. The third theme of the article is to indicate natural extensions of the need for such a description of precision, such as those involving metalloproteins and the determination of the protonation states of ionizable amino acids. Overall, it is also noted that this work and these examples are also relevant to protein three-dimensional structure molecular graphics software.

Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets

BackgroundProtein structures provide a valuable resource for rational drug design. For a protein with no known ligand, computational tools can predict surface pockets that are of suitable size and shape to accommodate a complementary small-molecule drug. However, pocket prediction against single static structures may miss features of pockets that arise from proteins' dynamic behaviour. In particular, ligand-binding conformations can be observed as transiently populated states of the apo protein, so it is possible to gain insight into ligand-bound forms by considering conformational variation in apo proteins. This variation can be explored by considering sets of related structures: computationally generated conformers, solution NMR ensembles, multiple crystal structures, homologues or homology models. It is non-trivial to compare pockets, either from different programs or across sets of structures. For a single structure, difficulties arise in defining particular pocket's boundaries. For a set of conformationally distinct structures the challenge is how to make reasonable comparisons between them given that a perfect structural alignment is not possible.ResultsWe have developed a computational method, Provar, that provides a consistent representation of predicted binding pockets across sets of related protein structures. The outputs are probabilities that each atom or residue of the protein borders a predicted pocket. These probabilities can be readily visualised on a protein using existing molecular graphics software. We show how Provar simplifies comparison of the outputs of different pocket prediction algorithms, of pockets across multiple simulated conformations and between homologous structures. We demonstrate the benefits of use of multiple structures for protein-ligand and protein-protein interface analysis on a set of complexes and consider three case studies in detail: i) analysis of a kinase superfamily highlights the conserved occurrence of surface pockets at the active and regulatory sites; ii) a simulated ensemble of unliganded Bcl2 structures reveals extensions of a known ligand-binding pocket not apparent in the apo crystal structure; iii) visualisations of interleukin-2 and its homologues highlight conserved pockets at the known receptor interfaces and regions whose conformation is known to change on inhibitor binding.ConclusionsThrough post-processing of the output of a variety of pocket prediction software, Provar provides a flexible approach to the analysis and visualization of the persistence or variability of pockets in sets of related protein structures.

EPR Spectroscopic Distance Measurements of the KCNE1 Membrane Protein in Micelles and Lipid Bilayers

Distance measurements between two strategically placed nitroxide spin labels can provide pertinent structural information on complicated biological systems such as membrane proteins. Distances of approximately 8 A - 25 A can be determined by measuring line broadening due to dipolar coupling using continuous wave (CW)-EPR spectroscopy. The short range distances can be measured between isotopically coupled nuclear spins and nitroxide electronic spin labels up to a distance of about 8 A using Electron Spin Echo Envelope Modulation (ESEEM) and long range distances of 20 A - 70A between two nitroxide electronic spin labels using Double Electron Electron Resonance (DEER). The transmembrane domain (TMD) of KCNE1 binds to the pore domain of the KCNQ1 channel modulating the channel's gating. In order to characterize the structural properties of the TMD of KCNE1, double cysteine mutants were prepared for TMD of KCNE1 and further modified by the addition of a MTSL nitroxide spin label. The purified proteins were reconstituted into LMPG detergent micelles and POPC/POPG bilayer vesicles. Dipolar broadening CW-EPR experiments were performed on the double mutants F53C-L63C, F56C-S64C, L59C-Y65C, and L59C-S64C at 225K; and DEER experiments on double mutants V50C-S68C, V47C-I66C at 80K. Molecular Dynamics Modeling study was performed on these mutants using nanoscale molecular dynamics (NAMD) with the molecular graphics software VMD. A 1 ns molecular dynamics simulation was ran for each double mutants and distance distribution was obtained by analyzing the trajectory data file using VMD. The distance distributions obtained from dipolar broadening CW EPR and DEER are in good agreement with NAMD/VMD and MMM modeling results.

Reflections on the past 25 years

1.1. Molecular graphics software: vector graphics were rapidly superseded by raster graphics, and workstations and personal computers became more or less indistinguishable. Visualization of molecular structures on your own laptop has reached a level of quality and performance that was simply unimaginable at the end of the eighties, and essentially at no cost: programs and plugins such as RasMol, Chime, JMol, and PyMOL are probably the best known examples. 1.2. Building of small molecules: writing Z-matrices by hand and manipulating real wireframe or ball-and-stick models was customary. Today Java molecular editors allow students and their mentors to draw literally any molecule on an electronic board and convert it to a 3D structure using programs such as CORINA. The former nightmare of formats interconversion appears to be history thanks to programs like OpenBabel and storage of chemical notations has been simplified with SMILES. The downside is that many users do not even know what is inside their files! 1.3. Homology modeling of proteins, structural comparisons, cavity and tunnel detection, binding site characterization, ligand docking, in silico protein–protein complex formation, etc. are operations that can be easily (and many times reliably) done by any interested user.

Interacting with the biomolecular solvent accessible surface via a haptic feedback device

BackgroundFrom the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation.ResultsA haptic rendering application for biomolecular visualisation has been developed that allows the user to gain three-dimensional awareness of the shape of a biomolecule. By using a water molecule as the probe, modelled as an oxygen atom having hard-sphere interactions with the biomolecule, the process of exploration has the further benefit of being able to determine regions on the molecular surface that are accessible to the solvent. This gives insight into how awkward it is for a water molecule to gain access to or escape from channels and cavities, indicating possible entropic bottlenecks. In the case of liver alcohol dehydrogenase bound to the inhibitor SAD, it was found that there is a channel just wide enough for a single water molecule to pass through. Placing the probe coincident with crystallographic water molecules suggests that they are sometimes located within small pockets that provide a sterically stable environment irrespective of hydrogen bonding considerations.ConclusionBy using the software, named HaptiMol ISAS (available from ), one can explore the accessible surface of biomolecules using a three-dimensional input device to gain insights into the shape and water accessibility of the biomolecular surface that cannot be so easily attained using conventional molecular graphics software.

Interactive graphics return to protein science

Visualization of molecular images is an important means of interpreting structural and other data and of communicating scientific results in the field of protein science. Long-time readers of the journal Protein Science will recall that early issues of the journal were accompanied by a floppy disk containing graphical images in the pioneering kinemage format developed by David C. Richardson and Jane S. Richardson (The kinemage: A tool for scientific communication, Protein Science (1992) 1, 3-9.). Unfortunately, kinemages disappeared from Protein Science a decade ago. In this issue, a Commentary by Li and Palmer (Protein Science (2009) 18, 678-681) returns interactive computer graphics to Protein Science. This article incorporates interactive figures, based on the open-source Jmol package (http://jmol.sourceforge.net/), that are viewable using any World-Wide-Web browser through embedded links within the electronic version of the paper. These figures are of two types. First, authors can generate figures specially designed to enhance the information presented in the article (see below). Second, any Protein Data Bank (PDB) code quoted in the manuscript will be linked to the FirstGlance in Jmol viewer (http://molvis.sdsc.edu/fgij/index.htm). This will allow the reader to immediately and interactively visualize the structure in question. No additional files or programs need to be downloaded or installed on a reader's computer in order to view these figures. The molecular images can be manipulated, either using command options provided within the figures (which requires no knowledge of Jmol) or by opening the Jmol console window (which requires a modicum of familiarity with molecular graphics packages). Jmol has been adopted by a number of other journals and organizations, including ACS Chemical Biology, Biochemical Journal, and the International Union of Crystallography, as a platform for “enhanced” figures. The level of interactivity provided by Jmol is the major benefit over animations or embedded movies; of course, animations and movies prepared in standard formats, using for example other molecular graphics software packages, also can be included as supplementary material to a paper in Protein Science. Interactive figures in Protein Science are prepared by incorporating user-generated Jmol scripts and hyertext markup language (html) content into html templates. This hybrid approach simplifies the process of generating figures for new users, but provides flexibility for more expert authors. We emphasize that this initiative is continuing to be developed. The commentary of Li and Palmer is intended to provide readers with a flavor of the system that we have in mind. Feedback is welcome. During the initial “learning phase”, authors wishing to include interactive figures in their papers in Protein Science should contact the Editor for additional information. The re-incorporation of interactive graphics into Protein Science is a long-awaited return of the journal to its roots and an exciting opportunity for authors to augment the usefulness of their papers for readers.

Parity alternation of linear ground-state hydrogenated cationic carbon clusters HC nSi + ( n = 1–10)

Making use of molecular graphics software, we have designed numerous models of HC n Si + ( n = 1–10), and by means of the B3LYP density functional method, performed geometry optimization and calculation on vibrational frequency. The ground-state isomers of HC n Si + ( n = 1–10) are found to be linear with the Si and H atom located at the ends of the C n chain. When n is even, the C n chain is polyacetylene-like whereas when n is odd, the C n chain displays a structure that fades into a cumulenic-like arrangement towards the Si end. According to the results of mass spectrometric investigation available in the literature, the intensities of even- n HC n Si + are more intense than those of odd- n HC n Si +, implying that the former are more stable than the latter. We detect trends of odd/even alternation in electronic configuration, the highest vibrational frequency, ionization potential, incremental binding energy as well as in certain bond length and certain atomic charge of the linear ground-state structures of the HC n Si + ( n = 1–10) clusters. The calculation results reveal that the even- n cationic clusters are more stable than the odd- n ones.

Parity alternation of linear ground-state hydrogenated cationic carbon clusters HC n+ ( n = 1–10)

Making use of molecular graphics software, we have designed numerous models of HC n + ( n = 1–10) cationic clusters, and performed geometry optimization and vibrational frequency calculation by means of the B3LYP density functional method. The linear ground-state isomers of HC n + ( n = 1–10) are found to be linear with the hydrogen atom located at one end of the carbon chain. When n is odd, the carbon chain is polyacetylene-like in configuration whereas when n is even, the carbon chain displays a polyacetylene-like structure that fades into a cumulenic-like arrangement towards the carbon end. We detected trends of odd/even alternation in electronic configuration, energy difference, ionization potential as well as in certain bond length and certain atomic charge of the linear ground-state HC n + ( n = 1–10) isomers. The results reveal that the odd- n cationic clusters are more stable than the even- n ones; they match the relative yields of HC n + clusters as revealed in mass spectrometric investigations.

A density functional study of the structures and energies of C nN 5− ( n = 1–13) clusters

We designed numerous models of C n N 5 − ( n = 1–13) using molecular graphics software. Geometry optimization and calculation of vibration frequency were carried out by means of the B3LYP density functional approach. After comparison of structure stability, we found that the ground-state structure of CN 5 − shows a N 4CN chain configuration whereas those of C n N 5 − ( n = 2–13) contain a planar pentagonal ring compose of nitrogen and carbon atoms when n ≤ 8, and of carbon atoms only when 9 ≤ n. For odd- n ground-state isomers with 1 < n ≤ 9, one carbon atom of the ring is bonded to a nitrogen atom and the other carbon atom(s) are bonded to a cyano (–CN) group. When n is even and with 2 ≤ n ≤ 10, all the carbon atom(s) within the ring are bonded to a cyano group. When n = 11–13, one of the carbon atoms of the ring is bonded to a straight NC 2–, NC 3– and NC 4– chain, respectively, while the other carbon atoms of the ring are each bonded to a cyano group. The NC 2– and NC 4– chains show cumulenic-like structures whereas the NC 3– chain shows polyacetylene-like structure. According to total energies, the C n N 5 − with even n are more stable than those with odd n, matching the peak patterns observed in the mass spectra of C n N 5 −. The trend of such odd/even alternation can be explained based on concepts of bonding characters, energy differences, electron affinities, and incremental binding energies.

The Protein Society: Celebrating 20 years in 2006—The founding and early years

A person is clearly identified as “old” when he begins to get requests to write a history of an organization with which he has been associated for many years. So it was not exactly a surprise when The Protein Society requested that I write a history of the Society and its journal upon the occasions of the 20th yearly American Symposium of The Protein Society and my announced retirement as Editor of Protein Science, since I have been active in both throughout their entire histories and am certifiably at an age that most of the attendees of the 20th Symposium will consider advanced.

Parity alternation in the linear ground-state beryllium-doped carbon clusters BeC n− ( n = 1–8)

Making use of molecular graphics software, we designed numerous models of BeC n − ( n = 1–8). Geometry optimization and calculation on vibration frequency were carried out by the B3LYP density functional method. After comparison of structure stability, we found that the ground-state isomers of BeC n − ( n = 1–8) are linear with the beryllium atom located at one end of the C n chain, except that the linear BeC 5 − isomer is slightly higher in energy than the planar cyclic BeC 5 − isomer. When n is even, the C n chain of BeC n − ( n = 1–8) is polyacetylene-like whereas when at odd n, the carbon chain is cumulene-like. The BeC n − ( n = 1–8) with even n are found to be more stable than those with odd n, and the result is in good accord with the relative intensities of BeC n − ( n = 1–8) observed in mass spectrometric studies. In this paper, we provide satisfactory explanation for such trend of even/odd alternation based on concepts of bonding nature, electronic configuration, electron affinity, incremental binding energy, and dissociation channels.

A New Exploration of the Torsional Energy Surface of n-Pentane Using Molecular Models and Molecular Modeling Software

This article presents a computational experiment about the conformational analysis of n-pentane that can be performed by advanced undergraduate or beginning graduate students. Initially, the four main conformers were determined using molecular models, and their relative stabilities were estimated by the steric repulsions. The structures of these conformers were drawn in molecular graphics software and were optimized utilizing a force field. Vibrational frequencies were also calculated. The results obtained in this study were compared to benchmark calculations and to other force fields. Conformations were also located by conformational search software. From an estimation of the entropy, it was possible to calculate the Gibbs free energy, the relative population of each conformer, and average 3JHH coupling constants. This experiment exposes the students to several important concepts and techniques such as exploration of the conformational potential energy surface by molecular models or computational techniq...