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Theory and Experiment:. Student Explorations in the Collection and Interpretation of Thermochemical and Spectroscopic Data. James B. Foresman York College of PA York PA 17405 USA [email protected] http://goose.ycp.edu/~jforesma. Molecular Modeling Exercises.

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Theory and Experiment:

Student Explorations in the Collection and Interpretation of

Thermochemical and Spectroscopic Data

James B. Foresman

York College of PA

York PA 17405 USA

[email protected]

http://goose.ycp.edu/~jforesma



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Molecular Modeling Exercises

Context: Laboratory Setting

(so time to solution is a consideration)


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Molecular Modeling Exercises

Focus: Visualizing Chemistry

(linking benchtop to molecular level)


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Molecular Modeling Exercises

Outcome: Understanding Computer Models and Programs

(both the mechanics of using the tools and realizing the strengths and limitations of the models)


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The Software:

Create

Process

Visualize


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The Software:

Create

Process

Visualize

HyperChem

Spartan

PCModel

Chem3D

GaussView

WebMO

MOE

Cache

Many Others


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The Software:

Create

Process

Visualize

HyperChem

Spartan

PCModel

Chem3D

GaussView

WebMO

MOE

Cache

Many Others

HyperChem

Spartan

PCModel

Chem3D

Gaussian

ADF

Jaguar

Gamess

Many Others


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The Software:

Create

Process

Visualize

HyperChem

Spartan

PCModel

Chem3D

GaussView

WebMO

MOE

Cache

Many Others

HyperChem

Spartan

PCModel

Chem3D

Gaussian

ADF

Jaguar

Gamess

Many Others

HyperChem

Spartan

PCModel

Chem3D

GaussView

Molekel

gOpenMol

T3D, MOE

Many Others


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Example: Phenolphthalein Color Change

Acid-Base titrations are routinely performed

in introductory courses.

Why does the solution containing the

indicator turn pink?








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Compare theoretical

uv/VIS spectra of the

two forms

H2In

In2-


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Compare

HOMO and

LUMO

Orbitals of

the two

forms

HOMO

Of

Protonated

form


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Compare

HOMO and

LUMO

Orbitals of

the two

forms

LUMO

Of

Protonated

form


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Compare

HOMO and

LUMO

Orbitals of

the two

forms

HOMO

Of

Dianion

form


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Compare

HOMO and

LUMO

Orbitals of

the two

forms

LUMO

Of

Dianion

form


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Example: Heat of Solution

Students can use a primitive device to

measure the temperature change when a

solid is added to water.

potassium nitrate  endothermic DH=+35 kJ

potassium acetate  exothermic DH=-15 kJ

Why? What factors are involved?


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Example: Heat of Solution

www.gaussian.com


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Example: Comparing Azulene and Naphthalene

Students can measure heats of combustion.

Also they can compare IR, uv-VIS, and NMR

spectra of these two isomers.

What electronic details account for the

differences that are observed?



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Example: Comparing Azulene and Naphthalene

azulene naphthalene

Heats of

Combustion

[kJ/mol]

-5291 -5156

DHiso = -135 kJ/mol


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DHiso Theoretical and Experimental Estimates

Huckel -46 kJ/mol

AM1 -177

HF/6-31G(d) -181

B3LYP/6-31G(d) -141

CBS-Q -147


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DHiso Theoretical and Experimental Estimates

Huckel -46 kJ/mol

AM1 -177

HF/6-31G(d) -181

B3LYP/6-31G(d) -141

CBS-Q -147

Gas phase Expt-148


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Example: Electronic Spectrum of a Vanadium Complex

Students prepare and obtain the uv-VIS

spectrum of vanadyl acetylacetonate and

attempt to classify the transitions as:

d-d

d-ligand

ligand-ligand

ligand-metal







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load gaussian output file into Molekel and

examine optimized B3LYP LANL2DZ distances ...


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load gaussian cubes into

Molekel, subtract ground

from excited state for this

d-d transition






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Example: 2-Nitroaniline C-13 NMR Spectrum

Students can obtain the carbon and proton NMR

spectra of this compound and make assignments

based on comparisons to nitrobenzene and aniline.

Use theory to explain any differences in the

predictions made by substituent additivity.



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Example: Sulfur Hexafluoride Intermolecular Forces

Students collect PVT data for a sample of

SF6 at high pressures (critical temp is 45 oC)

Second Virial Coefficients are examined:

comparison is made to:

literature reference

model potentials


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Several model potentials can be tested and

then B(T) is graphed according to this

equation:


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Example: Isoflurane Conformers and VCD Spectra

Students work as a team to explore the various

rotational and optical isomers of this

flexible small molecule. IR and VCD spectra are

obtained for each.

Comparison is made to literature spectra

(no VCD instrument yet)

Application of Boltzmann Distribution function

Exercise suggested by the paper:

Biedermann, Cheeseman, Frisch, Schurig, Gutman, Agranat, J. Org. Chem. 1999, 64, 3878




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MOE

conformational

search ...

results are

exported

to a database

containing

structures and

energies



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Thanks

  • Carl Salter, Moravian College

  • Don Clarke, Fordham University

  • Wayne Anderson, Bloomsburg University

  • Hans Peter Luthi, ETH Zurich

  • Stefan Portmann, CSCS/ETH Zurich


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