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Dan O'Leary

@doleary47.bsky.social
371 followers 598 following 48 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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Dan O'Leary @doleary47.bsky.social · 28/08/2026
Calculate IEs over user-defined temp range with both Bigeleisen-Mayer and Enthalpy-Entropy partitioning, and with tunnelling corrections for KIEs. Developed @pomonacollege.bsky.social in collaboration with Prof. Gianmarc Grazioli and his intrepid team of students @sanjosestate.bsky.social 🧪⚛️⚗️
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Dan O'Leary @doleary47.bsky.social · 28/08/2026
Do you calculate isotope effects using electronic structure calculations? Our program PyQuiverHS uses a browser-based workflow to make IE calculations easy. 📄Read the paper (open access): onlinelibrary.wiley.com/doi/10.1002/... 🌐Try PyQuiverHS: www.isotope-effects.com #chemsky #compchemsky
onlinelibrary.wiley.com
PyQuiverHS: A Web Tool for Computing Isotope Effects
PyQuiverHS has been developed as a freely available and open-source web tool, hosted at www.isotope-effects.com for calculating variable-temperature kinetic and equilibrium isotope effects with Bigel...
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Dan O'Leary @doleary47.bsky.social · 14/08/2026
Co-authored with @pomonacollege.bsky.social students, our chapter, "Multicolor 3D Printed Orbital Models across the Chemistry Curriculum" joins a terrific lineup in this @pubs.acs.org symposium series volume. Check it out! doi.org/10.1021/bk-2... #chemsky #compchemsky #3Dprint 🧪⚗️🥳
doi.org
3D Printing for Chemical Education: Tools for Active Learning
Integrate 3D Printing into Your Chemistry Classroom and Laboratory. Three-dimensional printing technology offers chemistry educators new ways to engage stu
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Dan O'Leary @doleary47.bsky.social · 20/06/2026
Excited to share this set of 40 multicolor 3D-printed molecular orbital models for second-semester 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
pubs.acs.org
3D-Printed Multicolor Molecular Orbital Models for a Second-Semester Organic Chemistry Course
We have developed a set of multicolor 3D-printed molecular orbital models associated with topics taught in a second semester organic chemistry course at Pomona College. The set includes the following: (1) π molecular orbitals (MOs) in benzene; (2) water sp- and p-type lone pair orbitals; (3) valence bond and π-MO models of amide stability and reactivity; (4) formaldehyde (neutral, H+, and Li+ complexes) sp- and p-type lone pair and π/π* orbitals; (5) orbital interactions and the Bürgi–Dunitz angle in a cyanohydrin transition state; (6) acetaldehyde enolate π-MOs; (7) orbital interactions in an enolate alkylation transition state; (8) orbital interactions in a lithium enolate aldol transition state; (9) benzyne πHOMO and π*LUMO orbitals; (10) n−σ* orbital interaction in the water dimer intermolecular hydrogen bond; (11) peptide α-helix structure and n−σ* orbital interaction in an intramolecular i, i + 4 hydrogen bond; (12) anomeric effect (nO–σ*CO orbital interaction) in a carbohydrate model compound. The models provide insights regarding aspects of π molecular orbital theory, stability, reactivity, and mechanistic “arrow pushing”. A hobby-grade five-color 3D fused deposition modeling (FDM) printer is used to make the models, which are sized to provide compact take-home class handouts and kits for each student. The models are fabricated with orbital bisections and text annotations to enhance information content. Student perceptions of this set of 3D-printed molecular models and their use in the classroom are generally favorable. 3D Manufacturing Format (3MF) model files are available in the Supporting Information for this article.
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Dan O'Leary @doleary47.bsky.social · 08/05/2025
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.
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Dan O'Leary @doleary47.bsky.social · 01/05/2025
The animation pairs with this slide:
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Dan O'Leary @doleary47.bsky.social · 01/05/2025
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 🧪🎉
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Dan O'Leary @doleary47.bsky.social · 28/04/2025
Dan and Cecil the Sagehen.
A chemistry professor and Cecil the Sagehen, mascot of Pomona College.
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Dan O'Leary @doleary47.bsky.social · 28/04/2025
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 🧪
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Dan O'Leary @doleary47.bsky.social · 19/04/2025
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.
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Dan O'Leary @doleary47.bsky.social · 18/04/2025
Workflow for models previously used in the classroom: pubs.acs.org/doi/10.1021/...
pubs.acs.org
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.
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Dan O'Leary @doleary47.bsky.social · 18/04/2025
3D print of an alanine derived alpha helix showing a hydrogen bond orbital interaction between two amino acids at the i and i+4 positions.
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Dan O'Leary @doleary47.bsky.social · 18/04/2025
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 🧪
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Dan O'Leary @doleary47.bsky.social · 15/04/2025
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Dan O'Leary @doleary47.bsky.social · 15/04/2025
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 🧪⚗️🧪
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Dan O'Leary @doleary47.bsky.social · 02/04/2025
Thank you! I'll share this link with students tomorrow.
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Dan O'Leary @doleary47.bsky.social · 02/04/2025
Workflow: pubs.acs.org/doi/10.1021/...
pubs.acs.org
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.
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Dan O'Leary @doleary47.bsky.social · 02/04/2025
3D printed d-orbital models.3D printed d-orbital models.
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Dan O'Leary @doleary47.bsky.social · 02/04/2025
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 🧪⚗️🧪
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Dan O'Leary @doleary47.bsky.social · 31/03/2025
Very cool!
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Dan O'Leary @doleary47.bsky.social · 26/03/2025
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!
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Dan O'Leary @doleary47.bsky.social · 26/03/2025
Thanks! We have some peptide systems coming up that you might like too.
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Dan O'Leary @doleary47.bsky.social · 26/03/2025
All set to the music of Georgian-Russian composer and chemist Alexander Borodin, an early investigator of the aldol reaction. 🎶🎵🧪🧬⚗️
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Dan O'Leary @doleary47.bsky.social · 26/03/2025
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
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Dan O'Leary @doleary47.bsky.social · 21/03/2025
Workflow and 3mf files: pubs.acs.org/doi/10.1021/...
pubs.acs.org
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 regardin...
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Dan O'Leary @doleary47.bsky.social · 21/03/2025
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.
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Dan O'Leary @doleary47.bsky.social · 21/03/2025
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.
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Dan O'Leary @doleary47.bsky.social · 21/03/2025
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.
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Dan O'Leary @doleary47.bsky.social · 06/03/2025
Our workflow is outlined here: pubs.acs.org/doi/10.1021/...
pubs.acs.org
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 regardin...
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Dan O'Leary @doleary47.bsky.social · 06/03/2025
Plastic 3D prints of a transition state for an enolate alkylation reaction.Plastic 3D prints of the pi molecular orbitals for the enolate of acetaldehyde.
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Dan O'Leary @doleary47.bsky.social · 06/03/2025
A few 3D prints from this week's organic chemistry class: an NBO enolate alkylation transition state and a pi MO model for the enolate of acetaldehyde. We reviewed the SN2 reaction and noted the larger "on-C" orbital of the nucleophilic pi2 MO! #ChemSky #CompChemSky #3DP #3Dprint #3DModels #prusa 🧪
Plastic 3D prints of a transition state for an enolate alkylation reaction.Plastic 3D prints of the pi molecular orbitals for the enolate of acetaldehyde.
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Reposted by Dan O'Leary
Conway Group @conway-group.bsky.social · 15/02/2025
If you are attending the Spring ACS Meeting in San Diego, please come and join us on Monday night for a showcase of UCLA research and to meet UCLA students, postdocs, faculty, alumni, and friends! All ACS attendees are welcome! #ChemSky
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Reposted by Dan O'Leary
Vittorio Saggiomo @vsaggiomo.bsky.social · 12/02/2025
We're back!!! First preprint of the year (3 more on the way). Here, we used microalgae to produce a 3D printable resin: Squeeze the oil from the microalgae, a couple of simple reactions (#chemsky), mixy mixy and there you have a strong bioresin. chemrxiv.org/engage/chemr...
from microagae to a 3D printed designstarting from microalgae oil, we performed two reactions, mix the resulting product with more components and the print and mechanical test the objects. 3D printed tests, the classical rook and one hexagon with the name of the group (BNT)
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Dan O'Leary @doleary47.bsky.social · 11/02/2025
We made these enantiomer keychains for students last spring, and a co-worker converted smaller prints into earrings. I like your CPK earrings!
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Dan O'Leary @doleary47.bsky.social · 08/02/2025
Correction: Howard Whitlock, Jr.
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Reposted by Dan O'Leary
Stieber Lab @stieberlab.bsky.social · 07/02/2025
Happy National Periodic Table Day with this community artwork our Chemunity group created last semester! #chemsky
Periodic table artwork in hallway made from hand painted white tiles with various designs by different people and element symbols and numbers. Tiles are on a black background. Above the table it says “welcome to the chemistry and biochemistry department “ in white font
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Dan O'Leary @doleary47.bsky.social · 07/02/2025
A 3D printed molecular model of the molecule twistane.
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Dan O'Leary @doleary47.bsky.social · 07/02/2025
To share this history with members of our community, I created a 3D printed keychain of twistane and its calculated electron electron density surface. Folks with Pomona College connections will understand the "47" situated just behind the structure! #chemsky #compchemsky #3DP #3Dprint #3DModels 🧪
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Dan O'Leary @doleary47.bsky.social · 07/02/2025
Corwin Hansch! He shared this story with me when I was getting started in the department in 1994. Corwin is known for his pioneering work in quantitative structure activity relationships (QSAR) and for educating generations of Pomona College students. I'm fortunate to have known him.
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Dan O'Leary @doleary47.bsky.social · 07/02/2025
It is chiral and exclusively contains twist cyclohexane rings within its structure, hence the name. The chirality of the sculpture matches the image in the paper, published by Harold Whitlock at U. Wisconsin. So who at Pomona showed Fig. 1 to the design team?
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Dan O'Leary @doleary47.bsky.social · 07/02/2025
The synthesis of twistane had just been reported in JACS. The faculty member thought it sufficiently interesting to represent the field. Indeed, the molecule has fascinating symmetry properties.
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Dan O'Leary @doleary47.bsky.social · 07/02/2025
What's on your chemistry building? When Seaver North Laboratory @pomonacollege.bsky.social was being built in the 1960’s, the architects asked a faculty member what sort of sculpture would be emblematic of the field of chemistry.
A sculpture of the molecule twistane on the front of a building at Pomona College.
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Reposted by Dan O'Leary
Paul Robustelli @paulrobustelli.bsky.social · 31/01/2025
Proud to share: "Ensemble docking for intrinsically disordered proteins" from Dartmouth undergrad Anjali Dhar 24' and grad student Tommy Sisk. We present ensemble docking strategies for IDPs that, remarkably, seem to work! www.biorxiv.org/content/10.1... Code: github.com/paulrobustel...
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Dan O'Leary @doleary47.bsky.social · 31/01/2025
Water lone pair 3D orbital prints made their NBO debut in organic chemistry today at pomonacollege.bsky.social! #ChemSky #CompChemSky #3DP #3Dprint #3DModels 🧪
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Dan O'Leary @doleary47.bsky.social · 31/01/2025
Beautiful! Co-author Michelle Garcia designed that set for an independent project in my computational chemistry course.
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Dan O'Leary @doleary47.bsky.social · 30/01/2025
Awesome, can't wait to see them! #chemsky
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Dan O'Leary @doleary47.bsky.social · 28/01/2025
I'm a chemistry professor at Pomona College. Recent pub: pubs.acs.org/doi/10.1021/...
pubs.acs.org
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 regardin...
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Dan O'Leary @doleary47.bsky.social · 27/01/2025
Thank you, Lily!
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Dan O'Leary @doleary47.bsky.social · 27/01/2025
This was our first paper, which is a "how to" guide for print preparation: pubs.acs.org/doi/10.1021/...
pubs.acs.org
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 prepa...
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Dan O'Leary @doleary47.bsky.social · 27/01/2025
Thank you! It's been enjoyable working with students on this project, I'll share your message with them :)
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