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Quantum Chemistry for Engineers: Nanohub Nanoscience Projects

by Marcelo Carignano, Tomekia Simeon, Baudilio Tejerina, George C. Schatz

Version 16
by Marcelo Carignano
Version 33
by Michael Anderson

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[[Image(quant-eng-l4.jpg)]]
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4 Electronic structure calculations play a major role in science and engineering, providing valuable information about molecular structure, thermodynamic and spectroscopic properties, and for modeling chemical reactivity and catalysis. The teaching of electronic structure theory at the undergraduate level is a common activity in chemistry departments (usually as part of a physical chemistry curriculum that is taught to junior-level students), and often some of the students are from engineering. Traditionally the material covered in such courses emphasizes fundamental concepts, such as the postulates of quantum mechanics, and simple applications, such as the particle in box, harmonic oscillator, and the hydrogen atom. Sometimes there is a computational component in which an electronic structure code is used to study small molecule properties. Such material is reasonable for chemistry majors, but does not serve engineering students very well.
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At Northwestern University we have developed curricular materials for teaching junior-level engineering students that include projects with an engineering emphasis. These projects use the '''NUITNS''' program package at nanohub.org, which is an integrated package for electronic structure computation and molecular property visualization. '''NUITNS''' provides a user environment where the interface for defining the nature of the calculations and for visualizing the results is straightforward enough that the students can focus on the physical content of their calculations, basically making quantum mechanics “come alive” for solving problems that have real-world connections.
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At Northwestern University we have developed curricular materials for teaching junior-level engineering students that include projects with an engineering emphasis. These projects use the '''NUITNS''' program package at nanoHUB.org, which is an integrated package for electronic structure computation and molecular property visualization. '''NUITNS''' provides a user environment where the interface for defining the nature of the calculations and for visualizing the results is straightforward enough that the students can focus on the physical content of their calculations, basically making quantum mechanics “come alive” for solving problems that have real-world connections.
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'''NUITNS''' includes the following components:
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[http://nanohub.org/resources/nuitns NUITNS] includes the following components:
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* [https://nanohub.org/tools/qclab QC-Lab] : electronic structure calculations based on the GAMESS electronic structure program (also includes the '''MacMolPlt''' and '''Molden''' programs for building and display of molecules)
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* [https://nanohub.org/tools/qclab QC-Lab] : electronic structure calculations based on the GAMESS electronic structure program (also includes the !MacMolPlt and Molden programs for building and display of molecules)
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13 * [https://nanohub.org/resources/CNDO CNDO/INDO] : electronic structure calculations based on semiempirical methods
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* [https://nanohub.org/resources/uvspec] UV-Spec: electronic structure and the prediction of electronic spectra based on semi-empirical methods
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* [https://nanohub.org/resources/uvspec UV-Spec] : electronic structure and the prediction of electronic spectra based on semi-empirical methods
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* [http://nanohub.org/resources/MolST] Molecular Structure Tracer: visualization of molecular structure
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* [http://nanohub.org/resources/MolST MolST] Molecular Structure Tracer: visualization of molecular structure
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* [https://nanohub.org/resources/tedvis] Theoretical Visualization of Electron Density: visualization of electron density
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* [https://nanohub.org/resources/tedvis TEDVis] Theoretical Visualization of Electron Density: visualization of electron density
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Among these components, QC-Lab provides the most extensive functionality for doing electronic structure calculations. Figure 1 shows a snapshot of the QC-Lab interface, which includes facilities for inputting or building molecular structures, defining parameters for using a variety of electronic structure methods and basis functions, and selecting many different properties to calculate. The output from such calculations can be used (via the \MacMolPlt and Molden programs) to display molecular orbitals, electron densities, vibrational normal modes, various kinds of spectra, and many other properties. QC-Lab can accommodate density functional and wave function-based electronic structure theories, as well as semiempirical calculations based on methods like PM3. The CNDO/INDO and UV-Spec codes provide additional functionality for doing semiempirical calculations based on methods like INDO/S that are relevant to the determination of electronic spectra.
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Among these components, '''QC-Lab''' provides the most extensive functionality for doing electronic structure calculations.
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The figure below shows a snapshot of the QC-Lab interface, which includes facilities for inputting or building molecular structures, defining parameters for using a variety of electronic structure methods and basis functions, and selecting many different properties to calculate. The output from such calculations can be used (via the !MacMolPlt and Molden programs) to display molecular orbitals, electron densities, vibrational normal modes, various kinds of spectra, and many other properties. '''QC-Lab''' can accommodate density functional and wave function-based electronic structure theories, as well as semiempirical calculations based on methods like PM3. The '''CNDO/INDO''' and '''UV-Spec''' codes provide additional functionality for doing semiempirical calculations based on methods like INDO/S that are relevant to the determination of electronic spectra.
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[[Image(nuitns-qclab.jpg)]]
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We have developed five assignments in which students can use various components of NUITNS in applications that show the capabilities, and occasionally failures, of quantum mechanics to describe real-world problems. These include:
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a) the thermodynamics and thermochemistry associated with methanol, including studies of solvation effects and combustion modeling,
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We have developed five assignments in which students can use various components of '''NUITNS''' in applications that show the capabilities, and occasionally failures, of quantum mechanics to describe real-world problems. These include:
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b) the optical and chemical properties of doped nanodiamonds (substitutional and endohedral doping effects for diamondoid structures)
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'''a)''' The thermodynamics and thermochemistry associated with methanol, including studies of solvation effects and combustion modeling,
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c) retinal isomerization (calculating isomerization energies for chomophores involved in vision),
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'''b)''' The optical and chemical properties of doped nanodiamonds (substitutional and endohedral doping effects for diamondoid structures)
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d) the structures and optical properties of silver nanoparticles (calculating electronic spectra of gold clusters as models of nanoparticles),
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'''c)''' Retinal isomerization (calculating isomerization energies for chomophores involved in vision),
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e) carbon nanotube mechanical properties (determining stress-strain behavior of individual carbon nanotubes).
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'''d)''' The structures and optical properties of silver nanoparticles (calculating electronic spectra of gold clusters as models of nanoparticles),
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The first two of these assignments are described in a paper by T. Simeon, C. Aikens, B. Tejerina and G. C. Schatz (J. Chem. Ed, submitted, 2010). The other three assignments are presented in files that are linked below. These assignments provide opportunities for the students to gain experience in building molecules, testing different electronic structure models and basis sets, calculating thermodynamic, mechanical and spectroscopic properties, making comparisons with experiment, and ultimately to assess the quality of the results.
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'''e)''' Carbon nanotube mechanical properties (determining stress-strain behavior of individual carbon nanotubes).
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The first two of these assignments are described in a paper by T. Simeon, C. Aikens, B. Tejerina and
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G. C. Schatz (''J. Chem. Ed", submitted, 2010'). The other three assignments are presented in files that are linked below. These assignments provide opportunities for the students to gain experience in building molecules, testing different electronic structure models and basis sets, calculating thermodynamic, mechanical and spectroscopic properties, making comparisons with experiment, and ultimately to assess the quality of the results.
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43 Links to other documents:
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1. Retinal isomerization project
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2. Au nanoparticle spectrum project. Also included are four input files:
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== 1. [https://nanohub.org/topics/RetinalIsomerization Retinal isomerization project] ==
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Au4_Tetrahedral.xyz, Au20.xyz, Au20_Py_Vertex.xyz, Au20_Py_Surface.xyz
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== 2. [https://nanohub.org/topics/OpticalandthermodynamicpropertiesofgoldmetalnanoparticlesEffectofchemicalfunctionalization Au nanoparticle spectrum project] ==
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3. Carbon nanotube mechanical property project
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== 3. [https://nanohub.org/topics/CarbonNanotubeFracture Carbon nanotube mechanical property project] ==

nanoHUB.org, a resource for nanoscience and nanotechnology, is supported by the National Science Foundation and other funding agencies. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.