Message-Passing Neural Networks for Molecular Property Prediction Using Chemprop
06 May 2022 | | Contributor(s):: Kevin Greenman
Chemprop is an open-source implementation of a directed message passing neural network (D-MPNN) that has been demonstrated to be successful in predicting a variety of molecular properties, including solvation properties, optical properties, infrared spectra, and toxicity....
11 Apr 2022 | | Contributor(s):: Kevin Greenman
Demo of the Chemprop message-passing neural network package for the Hands-on Data Science and Machine Learning Training Series
Applied Thermal Measurement at the Nanoscale
09 Feb 2022 | | Contributor(s):: Zhen Chen, Chris Dames
This book aims to serve as a practical guide for novices to design and conduct measurements of thermal properties at the nanoscale using electrothermal techniques. An outgrowth of the authors’ tutorials for new graduate students in their own labs, it includes practical details on...
CHEM 870 Tutorial 01a: Getting to know nanoHUB and Ab-initio Calculations
20 Dec 2021 | | Contributor(s):: Nicole Adelstein
The goal of these activities is for you to get comfortable with running electronic structure calculations. We will be using the ORCA GUI housed on nanoHUB to start. ORCA can be run from the command line too.
CHEM 870: Computational Methods in Chemistry - Electronic Structure
Computational Methods in Chemistry is a course that introduces the theory and practice (skills) necessary to perform electronic structure calculations.
CHEM 870 Tutorial 2: Exploring nanoHUB – Ionization Energies and Missing Correlation
The goal of these activities is to explore more capabilities of nanoHUB, including calculating the ionization energy. In addition, you will learn to estimate the missing correlation energy in ab-initio Hartree-Fock calculations.See background information in slides from Lecture 6: Open Shell,...
CHEM 870 Tutorial 3: Gaussian, Charge Density and Spin Density
There are many goals of this tutorial:To learn to run Gaussian, one of the most ubiquitous computational chemistry software packages in the world.To create text input files and submit simulations from the command line (like an old-school computational researcher), rather than relying on...
CHEM 870 Tutorial 4: Basis Sets, Geometry Optimization, and Configuration Interaction
The main goal of these activities is to see the effect of the choice of basis set has on molecular geometry and bond strength (the dissociation energy). Including configuration interaction (or coupled-clusters) also improves a basis set, so is also explored in these activities.
CHEM 870 Tutorial 5: Normal Modes and IR Spectroscopy
The main goal of these activities is to calculate the infrared absorbance spectra of N2, O2, and CO2. CO2 is a green house gas, while the diatomics make up the majority of gases in our atmosphere. Much of this tutorial is taken from material and spectra (“Figure 2”) by Tom Shattuck at...
CHEM 870 Tutorial 6: Binding Energy, DFT, and CO2 Capture
The main goal of these activities is to calculate the binding energy of CO2 to linker molecules in metal organic frameworks (MOFs). CO2 is a greenhouse gas. One necessary component of combating climate change is removing CO2 from the atmosphere. We will use density functional theory (DFT)...
IWCN 2021: Density Functional Theory Modeling of Chemical Reactions at Interfaces
15 Jul 2021 | | Contributor(s):: Namita Narendra, Jessica Wang, James Charles, Tillmann Christoph Kubis
In this work, we introduce a DFT-based method to predict energies of solute molecules in bulk solution and in various distances to solvent/air interfaces. The solute and all solvent molecules (~1400 atoms) are explicitly considered, and their electrons solved self-consistently in density...
Particle Size and Spectral Analysis of AgNO3 and Cu: Design Challenge Activity
17 Jun 2021 | | Contributor(s):: John H. Hitchcock, NNCI Nano
When the traditional silver nitrate reduction by copper is performed, students are often puzzled by the black appearance of the silver when it first is observed. In this activity, students will research two questions about the reaction, develop a viable system of gathering data, and investigate...
Optical and Thermodynamic Properties of Gold Metal Nanoparticles - Effect of Chemical Functionalization
27 May 2021 | | Contributor(s):: Baudilio Tejerina, George C. Schatz, Marcelo Carignano
This laboratory is intended to introduce the student to the use of semiempirical electronic structure methods. In particular, the semiempirical methods will be applied to the study of metallic clusters and the interaction of the clusters with discrete molecular systems such as pyridine.
Carbon Nanotube Fracture
27 May 2021 | | Contributor(s):: Christine M Aikens, George C. Schatz, Marcelo Carignano
Due to their mechanical properties, carbon nanotubes (CNTs) hold promise as nanoreinforcements in a variety of composites. As a result, numerous theoretical and experimental studies have been performed in order to understand the behavior of CNTs under axial tension. Whereas quantum mechanical...
Exploring Surface Energy of Polymers by Contact Angle Estimation
03 Dec 2020 | | Contributor(s):: Fred Okoh, NNCI Nano
Students will qualitatively and quantitatively estimate contact angles of polymers and compare their surface energy. They will use a variety of polymer sheets onto which they will place drops of water. After observing the shape of the drop, they will take digital photographs of the drop, print...
Modeling Nanotechnology Project
03 Dec 2020 | | Contributor(s):: Ayesha Denny, NNCI Nano
Students will explore products that have been developed or enhanced by incorporation of nanotechnology. They will choose a product to investigate and then determine how this nano-product works, e.g. the science and engineering of the product. Their final part of the project will be to...
To See or Not to See? Hydrophobic and Hydrophilic Surfaces
03 Dec 2020 | | Contributor(s):: Jenny Willis, NNCI Nano
This activity can be completed as a separate one or in conjunction with the lesson Superhydrophobicexpialidocious: Learning about hydrophobic surfaces found at: https://www.nnci.net/node/5895. The activity is a visual demonstration of the difference between hydrophobic and hydrophilic...
"Turning Fruit Juice into Graphene Quantum Dots" Supplementary Lesson Plans: Going Atomic
15 Nov 2020 | | Contributor(s):: Susan P Gentry, Rachel Altovar
Expanding on the pre-existing resource on nanoHUB: “Turning Fruit Juice into Graphene Quantum Dots” this resource expands on the concepts in the experimental guide to give a comprehensive overview of materials pertaining to concepts and ideas within the...
MODULE 3 - Structures: "Turning Fruit Juice into Graphene Quantum Dots" Supplementary Lesson Plans: Going Atomic
In MODULE 3- Structures in the "Turning Fruit Juice into Graphene Quantum Dots" Supplementary Lesson Plans, crystal structures and systems are investigated. This module relates back to graphene and how its structure relates back to its unique properties in comparison to other forms of...