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Experimental structure determination in the

undergraduate curriculum

Creating data-rich integrated laboratory exercises

Dean H. Johnston PDS/OVCS 2011

Why now? (what has changed?)

•  Access to crystallographic databases •  Computing power

–  rapid structure solution / refinement – high quality graphical displays

•  Instrumentation –  low maintenance – high level of automation

Status and Future Potential of Crystallography (USNC/Cr 1976)

•  “It seems apparent that the major use of crystallography in most undergraduate chemistry curricula is simply the dissemination of certain crystallographic results.”

•  “In almost no case was there evidence that any information was given to students about how to evaluate the reliability of these results.”

Searching “education and ______”

Structural Data Continuum

idealized experimental

VSEPR Computed Textbook Database Laboratory

•  Most instruction in structural chemistry at the undergraduate level uses either idealized geometries (i.e. VSEPR) or selected bond distances and bond angles (average values)

•  Students are disconnected from the experimental sources of structural data, and therefore unaware of the associated uncertainty in such measurements

Crystallography in the Curriculum •  General Chemistry (1st or 2nd year) •  Inorganic Chemistry (2nd or 3rd year) •  Biochemistry (3rd or 4th year) •  Stand-alone crystallography course

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•  General Chemistry (1st or 2nd year) •  Inorganic Chemistry (2nd or 3rd year) •  Biochemistry (3rd or 4th year) •  Stand-alone crystallography course “many contexts exist in which crystallography can be incorporated in undergraduate education with minimal disruption to current courses, and should be included in curricula of all undergraduate programs in the physical and life sciences”

Crystallography Education Policies for the Physical and Life Sciences, ACA & USNC/Cr

Crystallography in the Curriculum Questions / Potential Issues •  Curriculum

–  If we add (crystallography), what do we take out?

– What do we want to teach our students? – What do we want our students to learn?

•  Faculty time: – data collection, data analysis, and data

distribution is too time consuming – can’t “babysit” the instrument

insert favorite subject here

Our Context •  Otterbein University

–  3000 total students –  primarily undergraduate institution (PUI)

•  Chemistry Department –  six full-time faculty in Chemistry / Biochemistry –  around ten majors per year

•  General Chemistry –  enrollment of 75-80 students –  diverse majors including chemistry, biology

allied health, equine science, etc.

General Chemistry

General Chemistry Lab

Goal –  to develop an integrated multi-week

laboratory activity that reinforces concepts of molecular geometry, intermolecular forces, unit cells and crystal packing using experimental data (both databases and student-generated)

General Chemistry Lab

1 Battle, G. M.; Allen, F. H.; Ferrence, G. M. J. Chem. Educ. 2010, 87, 813-818. 2 Crystals @ Otterbein: http://crystals.otterbein.edu

•  Student groups assigned an amino acid •  Cambridge Database VSEPR activity1 •  Crystal packing / unit cell activity2 •  Crystallization of amino acid (multi-week) •  (X-ray analysis of amino acid samples) •  Analysis of experimental X-ray data

using Mercury and Mogul

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Amino Acid List

•  L-alanine •  DL-alanine •  L-asparagine •  L-cysteine •  L-glutamine •  L-histidine

•  L-methionine •  DL-methionine •  L-serine •  DL-serine •  L-threonine •  L-valine

Amino acids were chosen based on the number of entries in the Cambridge Database and availability / cost.

CSD VSEPR Tutorial

Figures from Battle, G. M.; Allen, F. H.; Ferrence, G. M. J. Chem. Educ. 2010, 87, 813-818.

Crystal Packing Crystallography •  All samples were

mounted and run on a Bruker SMART X2S benchtop diffractometer

Data Analysis •  Students used Mercury to analyze:

– overall structure (atoms, connectivity) – geometry (compared to VSEPR predictions

and physical model built using model kit) – hydrogen bonding network – unit cell packing and number of molecules

per unit cell – calculated density (compare to reference) – structure “validation” (Mogul)

Validation / Mogul Analysis

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Questions / Potential Issues •  Curriculum: what do we take out?

– most of the material was already in place – modified existing exercises to incorporate

experimental data (CSD / student samples)

•  Faculty time: –  level of automation of the SMART X2S

allowed data collection, structure solution, and distribution (on CDs) with minimal intervention

Inorganic Chemistry

Inorganic Student Projects •  sophomore-level inorganic chemistry

course with integrated laboratory •  enrollment between 10 and 20 students •  final three weeks of term

– select a synthetic procedure (Inorg. Synth.) – determine equipment, reagent needs – get approval, order reagents – make compound(s), characterize

Inorganic Student Projects

[Cu(tmhd)2]

tris(3-nitro-acetylacetonate) cobalt(III)

Inorganic Student Projects

tricarbonyltris(pyridine)molybdenum(0)

Inorganic Student Projects (C12H18N2)[Mo6Cl14]•1.5 C3H6O

(C6H10N2)[Mo6Cl14]•3 DMF

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(C12H18N2)[Mo6Cl14]•1.5 C3H6O Organic Chemistry (!)

Acta Cryst. (2011). E67, o2735

Acta Cryst. (2011). E67, o2276

Conclusions •  Crystallography provides a rich source of

data that we can use to teach fundamental concepts of chemical structure, bonding, intermolecular forces, crystal packing, and critical analysis at the undergraduate level

•  Advances in single crystal XRD instrumentation have made experimental crystallography accessible and feasible for teaching (and research) at primarily undergraduate institutions

Acknowledgements •  Allen Hunter (YSU) •  Otterbein Students •  Chem Department,

Otterbein University •  Greg Ferrence (ISU) •  Matt Zeller (YSU) •  ACA 2010 Summer

School faculty

•  National Science Foundation (DUE #0942850)

Web Resources

• All materials available online at: – http://crystals.otterbein.edu – http://symmetry.otterbein.edu