Dan O'Leary
@doleary47.bsky.social
330 followers 580 following 44 posts
I'm a professor of chemistry at Pomona College in Claremont, California. I teach general and organic chemistry, NMR spectroscopy, and computational chemistry. My research interests span these realms + the history of science + 3D printing pedagogies.
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doleary47.bsky.social
Pleased to share this set of ~35 multicolor 3D-printed molecular orbital models for organic chemistry classrooms, developed with students @pomonacollege.bsky.social. Article and 3D print files (no paywall): pubs.acs.org/doi/10.1021/...
#ChemSky #CompChemSky #3DP #3Dprint #3DModels 🧪
Multicolor 3D-Printed Molecular Orbital Models for a First-Semester Organic Chemistry Course
We have developed a set of multicolor 3D-printed structural and molecular orbital models for use in a first-semester organic chemistry course. These models provide visual and tactile insights regarding aspects of organic structure, reactivity, and mechanistic “arrow pushing”. The set includes: 1. orbital models of σ and π bonding in methane and ethylene, 2. σCH–σ*CH hyperconjugation in staggered and eclipsed ethane conformations, 3. LUMO accessibility in SN2 electrophiles and HOMO–LUMO orbital interactions in SN2 transition states, 4. E2 transition state structure and orbital interactions in β-hydrogen removal and π bond formation, 5. σCH–pC hyperconjugation in the ethyl cation, 6. transition state structure and σCH–pC orbital interactions in a carbocation 1,2-hydride shift, 7. late and early, respectively, Br• and Cl• H atom radical abstraction transition state structures and SOMO orbitals, 8. bromonium ion structure and LUMO orbital, 9. protonated epoxide ion and neutral epoxide structures and LUMO orbitals, 10. transition state structure and orbital interactions in a hydroboration reaction, 11. transition state structure and orbital interactions in the lithium aluminum hydride reduction of formaldehyde, and 12. π molecular orbitals in 1,3-butadiene. The prints are made with hobby-grade 5-color 3D fused deposition modeling (FDM) printers and sized to provide compact take-home class handouts for each student or projected in-class with a document camera. Models are fabricated with orbital or electron density surface bisections and text annotations to enhance information content. Student perceptions of this set of 3D-printed molecular models are generally favorable and have improved their understanding of course materials.
pubs.acs.org
doleary47.bsky.social
I worked with this program for 20 years. It only funded students interested in chemistry and chemical engineering careers. I'm saddened to see it terminated.
doleary47.bsky.social
The animation pairs with this slide:
doleary47.bsky.social
Fischer's discovery of the configuration of (+)-glucose, described differently in organic textbooks, remains for me a must tell story as the semester winds down. Symmetry tests are timeless. This animation illustrates the end group interchange for sorting glucose (3) and mannose (4). #chemsky 🧪🎉
doleary47.bsky.social
Dan and Cecil the Sagehen.
A chemistry professor and Cecil the Sagehen, mascot of Pomona College.
doleary47.bsky.social
The final 3D orbital print of the semester is a sweet one! Organic chemistry students @pomonacollege.bsky.social received a model illustrating the anomeric effect. An unexpected bonus (scroll down) was a visit by Cecil the Sagehen! ##chemsky #compchemsky #3dp 🧪
doleary47.bsky.social
Thanks! We've been approaching this from a DIY point of view, with hopes of enabling others to do the same. That said, it would be interesting to learn more about marketability. HGS Maruzen remains my favorite molecular model company.
doleary47.bsky.social
Workflow for models previously used in the classroom:
pubs.acs.org/doi/10.1021/...
Multicolor 3D-Printed Molecular Orbital Models for a First-Semester Organic Chemistry Course
We have developed a set of multicolor 3D-printed structural and molecular orbital models for use in a first-semester organic chemistry course. These models provide visual and tactile insights regarding aspects of organic structure, reactivity, and mechanistic “arrow pushing”. The set includes: 1. orbital models of σ and π bonding in methane and ethylene, 2. σCH–σ*CH hyperconjugation in staggered and eclipsed ethane conformations, 3. LUMO accessibility in SN2 electrophiles and HOMO–LUMO orbital interactions in SN2 transition states, 4. E2 transition state structure and orbital interactions in β-hydrogen removal and π bond formation, 5. σCH–pC hyperconjugation in the ethyl cation, 6. transition state structure and σCH–pC orbital interactions in a carbocation 1,2-hydride shift, 7. late and early, respectively, Br• and Cl• H atom radical abstraction transition state structures and SOMO orbitals, 8. bromonium ion structure and LUMO orbital, 9. protonated epoxide ion and neutral epoxide structures and LUMO orbitals, 10. transition state structure and orbital interactions in a hydroboration reaction, 11. transition state structure and orbital interactions in the lithium aluminum hydride reduction of formaldehyde, and 12. π molecular orbitals in 1,3-butadiene. The prints are made with hobby-grade 5-color 3D fused deposition modeling (FDM) printers and sized to provide compact take-home class handouts for each student or projected in-class with a document camera. Models are fabricated with orbital or electron density surface bisections and text annotations to enhance information content. Student perceptions of this set of 3D-printed molecular models are generally favorable and have improved their understanding of course materials.
pubs.acs.org
doleary47.bsky.social
Biomolecular 3D orbital prints were featured this week in organic chemistry @pomonacollege.bsky.social! Class members went home with a student-designed alpha helix model showing i, i+4 N-H---O=C hydrogen bond orbital overlap. #chemsky #compchemsky #3dp 🧪
doleary47.bsky.social
Monday's 3D print for my organic chemistry class @pomonacollege.bsky.social: an orbital interaction that partly defines the water dimer hydrogen bond. Orbital phases displayed in Pomona-Pitzer colors, appropriate for admitted students day! ELO warming the space. #chemsky #compchemsky #3dp 🧪⚗️🧪
doleary47.bsky.social
Thank you! I'll share this link with students tomorrow.
doleary47.bsky.social
Do-It-Yourself 5-Color 3D Printing of Molecular Orbitals and Electron Density Surfaces
This report outlines an approach for preparing 5-color 3D printed plastic models of molecular orbitals and electron density surfaces using a hobby-grade 3D printer. Instructions are provided for preparing 3D orbital and electron density surface (EDS) models using solid or mesh representations in ground state and transition state structures. We show that the information content of 3D orbital and surface models can be enhanced with text annotation, bisection, strut and dashed bond placement, and composite orbital-EDS model constructions. Example prints illustrate orbital concepts in organic and inorganic chemistry, such as the ethyl cation (σ–p hyperconjugation), methane (hybridization and C–H bonding), ethane (σ–σ* hyperconjugation in the staggered and eclipsed conformations), 2-hydroxytetrahydropyran (the anomeric effect/n−σ* hyperconjugation), the water dimer (hydrogen bonding/n−σ* overlap), ethylene, 1,3-butadiene, and benzene (π molecular orbitals), Re2Cl82–, and U2(COT)2 (metal–metal quadruple bonds). Transition state models illustrate orbital interactions in the SN2 reaction of cyanide with methyl, ethyl, and isopropyl chloride and in a hydroboration reaction of BH3 with propene. Composite EDS models of methyl and isopropyl chloride (for exploring their relative reactivities as SN2 electrophiles) and methylcyclohexane (visualizing 1,3-diaxial interactions) are described. Student perceptions of a multicolor 3D orbital print used in an introductory organic chemistry laboratory course are reported.
pubs.acs.org
doleary47.bsky.social
These 3D-printed d-orbital models are ready to parachute into an active learning-based general chemistry class @pomonacollege.bsky.social. Some assembly required! #3dp #chemsky #compchemsky 🧪⚗️🧪
doleary47.bsky.social
Thank you for sharing! In some years, a friend on the music faculty will provide students with a brief synopsis of Borodin's musical contributions. One year, he even collaborated with a student in the class and performed a piano piece written by a very young Borodin. That was a fun class!
doleary47.bsky.social
Thanks! We have some peptide systems coming up that you might like too.
doleary47.bsky.social
All set to the music of Georgian-Russian composer and chemist Alexander Borodin, an early investigator of the aldol reaction. 🎶🎵🧪🧬⚗️
doleary47.bsky.social
The aldol reaction was front and center in today's organic class! The orbital prints are a Houk group transition state for a lithium enolate + aldehyde reaction and a @pomonacollege.bsky.social student-designed Burgi-Dunitz print. #chemsky #3dp #compchemsky
doleary47.bsky.social
Poster: Hiwot Endeshaw and Jaylyn Gonzalez, "Development of 3D-Printed Molecular Orbital Teaching Models for Advanced Topics in Chemistry and Biologically Relevant Systems", Monday 3/24, 12:00 PM - 2:00 PM, Hall B2/C SD Convention Center, Poster Board #441.
doleary47.bsky.social
Talk: Daniel O'Leary, "3D-Printed Molecular Orbitals and Transition State Structures for a First-Semester Organic Chemistry Course", Sunday 3/23, 8:25-8:45 AM, Hall B-1, Room 2, SD Convention Center.
doleary47.bsky.social
Happy to be participating in the "3D Printing in Chem Ed" symposium at #ACSSpring2025! Attendees will receive a Burgi-Dunitz orbital model designed by a @pomonacollege.bsky.social student. If you miss the talk, visit their poster and pick one up! Details are below. #ChemSky #CompChemSky #3DP 🧪
A chemical reaction between cyanide and formaldehyde and molecular models showing the angle of attack (Burgi-Dunitz) of the nucleophile in the reaction transition state.