Podcast
Questions and Answers
Which of the following features is NOT a characteristic of the ORCA program system?
Which of the following features is NOT a characteristic of the ORCA program system?
Avogadro is only compatible with Windows operating systems.
Avogadro is only compatible with Windows operating systems.
False
Name one primary application area for Avogadro.
Name one primary application area for Avogadro.
Computational chemistry
ORCA runs completely from the ______.
ORCA runs completely from the ______.
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Match the following software tools with their primary functionality:
Match the following software tools with their primary functionality:
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Which of the following characteristics describes Avogadro?
Which of the following characteristics describes Avogadro?
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Avogadro is exclusively used for creating molecular visualizations.
Avogadro is exclusively used for creating molecular visualizations.
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What is the purpose of atomic coordinates in quantum mechanics simulations?
What is the purpose of atomic coordinates in quantum mechanics simulations?
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The _____ tool in Avogadro allows users to measure distances between atoms.
The _____ tool in Avogadro allows users to measure distances between atoms.
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Match the terms related to ORCA input files with their definitions:
Match the terms related to ORCA input files with their definitions:
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Which menu option in Avogadro is used for quick geometry optimization?
Which menu option in Avogadro is used for quick geometry optimization?
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To draw a bond in Avogadro, you should left click and drag.
To draw a bond in Avogadro, you should left click and drag.
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Which software is specialized in spectroscopic properties?
Which software is specialized in spectroscopic properties?
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What is the primary use of the ORCA software?
What is the primary use of the ORCA software?
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All the quantum mechanics software listed has a free version available.
All the quantum mechanics software listed has a free version available.
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What does DFT stand for in quantum mechanics?
What does DFT stand for in quantum mechanics?
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________ is used to calculate Boltzmann-weighted chemical shifts and coupling constants.
________ is used to calculate Boltzmann-weighted chemical shifts and coupling constants.
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Match the following quantum mechanics software with their primary focus:
Match the following quantum mechanics software with their primary focus:
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Which of the following quantum mechanics programs is free?
Which of the following quantum mechanics programs is free?
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Geometry optimization is a technique used to find the stable configuration of a molecule.
Geometry optimization is a technique used to find the stable configuration of a molecule.
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What is the main purpose of using atomic coordinates in simulations?
What is the main purpose of using atomic coordinates in simulations?
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Study Notes
Introduction to Quantum Chemistry Simulations with ORCA
- This course series introduces quantum chemistry simulations using the ORCA software.
- The presenter is Xin Yang.
Course Outline
- 10:00 - 10:20: Introduction to Computational Chemistry.
- 10:20 - 10:35: Hands-on Session 1: Setting up an ORCA calculation.
- 10:35 - 11:10: Basics of Quantum Mechanical Simulation.
- 11:10 - 11:45: Hands-on Session 2: Geometry optimization and frequency calculation.
- 11:45 - 12:00: Calculations of Molecular Properties.
- 12:00 - 12:15: Hands-on Session 3: Prediction of UV/Vis Spectra.
- 12:15 - 12:30: Wrap-up Lecture.
Microscopic vs. Macroscopic
- The diagram shows different time and length scales for simulation.
- Electrons, quantum mechanics, and atoms are at the microscopic level.
- Continua, segments, and grids are at the macroscopic level.
Computational Chemistry
- Branch of chemistry using mathematical models and computations to predict and solve chemical problems.
- It uses mathematical approximations and computer programs to solve chemical problems.
- The text provides examples of quantum mechanical and molecular mechanical methods, as well as those founded on empirical/statistical/machine learning.
Why Computational Chemistry?
- Assists experimental chemists by avoiding tedious, time-consuming, costly, and sometimes dangerous experiments (e.g., drug design).
- Investigates unstable molecules, analyzes quantities not experimentally observable (e.g., atomic charges), and rectifies experimental findings (e.g., determining if a methylene radical is linear or bent).
- Aids in calculating certain quantities more accurately than experiments, thereby enhancing understanding of chemical phenomena (e.g., solubility, enthalpy formation, reaction mechanisms).
Computational Quantum Chemistry
- Solves the Schrödinger equation for molecular systems, employing the Hamiltonian operator to find wavefunctions and energy levels of the system.
- Typical system sizes range from 1 to ~ 50 atoms for ab initio methods, ~100 atoms for DFT methods, and larger than DFT for semi-empirical methods.
Quantum Mechanical Methods (Ab initio)
- Include Hartree-Fock, Post-Hartree Fock, and Multireference methods.
- Applicable to any system in principle, but computationally expensive.
- Typically used for small systems (normally < 50 atoms).
- Scaling is proportional to Nn where n = 2, 3, 4, 5, 6...
Quantum Mechanical DFT Methods
- Total energy of a system is dependent on electron density.
- The method involves a single determinant method, considers electron correlation, and is less dependent on basis set quality.
- Exact functional form is unknown; the results might vary depending on the chosen functional.
Reaction Mechanism Calculations
- The calculations are useful to understand regioselectivity in polymer initiation steps encompassing geometry optimization, thermochemistry, transition state search, and intrinsic reaction coordinate.
IR Spectra
- Calculated directly in ORCA and QM codes.
- Predictions include only fundamental transitions ; higher transitions , e.g., double bonds are not included.
- Scaling factors are used to correct calculated frequencies.
UV-Vis Spectra
- TD-DFT method is used to predict the spectra.
- The experimental and calculated values of absorption peaks and wavelength are provided in the data.
NMR Spectra
- NMR shifts depend on conformers.
- Sometimes a conformer search or Boltzmann weighting is required.
- Calculations produce Boltzmann-weighted chemical shifts and coupling constants.
- Includes magnetic shielding constants (chemical shifts), and spin-spin coupling constants.
QM Simulation Software
- This table lists QM software packages, their description, and pricing.
ORCA
- Ab initio, DFT, and semi-empirical SCF-MO package.
- Developed by Frank Neese et al.
- Features Robustness, open-source, cross-platform capabilities, as well as ease of installation and active development.
Avogadro
- Free, open-source molecular editor and visualization tool.
- Designed for use in Mac, Windows, and Linux environments.
- Offers high-quality rendering and a powerful plugin architecture.
- Ideal for computational chemistry, molecular modeling, bioinformatics, material science, and related areas.
Hands-on Session #1
- Students will perform an ORCA calculation using pre-prepared input files.
- Instructions include logging into the Vidi Portal, loading modules in a terminal window, inspecting the input file structure (.h2.inp), and submitting ORCA jobs via the command line.
Hands-on Session #2
- Students prepare input files with Avogadro.
- Visualize results with Molden and Avogadro while focusing on geometry convergence, bond distance changes, and molecular orbitals along with normal modes and IR spectra.
Geometry Optimization
- A geometry optimization process minimizes the overall energy of a system by altering atomic coordinates.
- The goal is to find local minimum energy points, but the calculation may not always reach the global minimum.
Stationary Points
- A point in the potential energy surface of a molecule where the gradient vector is zero.
- Important in determining whether a point is a minimum (stable structure), a saddle point (transition state), or other points (e.g. higher-order saddle points).
Frequency Calculations
- Used to characterize stationary points (e.g., minima, transition states).
- Predicts vibrational spectra (e.g., IR, Raman).
- Determines thermodynamic properties (e.g., zero-point energy, finite temperature corrections).
Calculation of Vibrational Frequencies
- The vibrations are represented by normal modes.
- The calculation of vibrational frequencies uses a mass-weighted Hessian matrix.
- The normal modes are independent in harmonic oscillator approximation.
Calculation of Vibrational Frequencies
- The vibrational modes of a molecule can be expressed as normal modes.
- Linear molecules follow the 3N - 5 rule for normal modes, while non-linear molecules follow the 3N - 6 rule.
- The calculation of normal vibrational modes is based on the harmonic oscillator approximation.
- Frequency calculation depends on minimum or saddle point to apply the vibrational partition function.
Sample ORCA Output & Thermodynamics
- The ORCA output provides comprehensive thermodynamic data including internal energy (U), enthalpy (H), entropy (S), Gibbs free energy (G) that are derived via electronic calculations.
- The parameters of the thermodynamic cycles are associated with vibrational frequency, rotational states, and kinetic energy terms of the system.
Energies
- Absolute energies are less accurate due to approximations related to Schrödinger equation solution.
- Relative energies have more precise calculations as errors are canceled out.
- Calculations should employ same Hamiltonian and basis sets to provide stable and precise relative energies of the investigated systems.
Hands-on Session #3
- Students examine ORCA output of 2-propenal.
- Students predict its UV-Vis spectrum.
Excited States Calculations
- TD-DFT is the simplest and widely used method for computing excited states.
- STEOM-CCSD yields higher accuracy but is computationally more expensive.
Solvation
- Traditional gas-phase calculations are deficient when describing solutions.
- Explicit solvation models use explicit solvent molecules, while Implicit models estimate solvent effect via parameters.
Implicit Solvation
- CPCM employs a conductor-like polarizable continuum model where the solvent is treated as a continuum.
- SMD uses the full solute electron density to compute the cavity dispersion contribution instead of using the cavity area.
Relativistic Corrections
- Important for systems with heavy elements.
- Includes corrections like mass-velocity, Darwin, indirect relativistic effects, and spin-orbit coupling using methods such as RECPs and Zero-Order Regular Approximation (ZORA) or DKH calculations.
ORCA Specific DFT Settings
- Optimized DFT calculation settings are outlined, which include RI-J approximation to enhance computational speed.
Basis Sets
- Describes the characteristics and requirements of various types of basis functions such as STO-3G, DZ, and TZ.
- Details on these atomic orbital functions, their construction, and their role in creating molecular orbitals.
Polarization and Diffuse Functions
- Describes polarization functions as higher-order angular momentum functions.
- Discusses diffuse functions, which are crucial for systems involving anions, excited states, and regions far from the nucleus.
Effective Core Potentials
- Describes effective core potentials or ECPs.
- ECPs are used instead of explicitly representing core electrons in systems containing heavy elements in order to speed up calculations without significant loss of accuracy.
Common Job Types
- The most frequently used calculation types in ORCA software are covered.
- Examples include single-point energy calculations, geometry optimization, and frequency calculations.
Other Tasks/Interesting Features
- Calculations of ground-state properties (charge distributions, orbitals, spectroscopic data like EPR, Mössbauer).
- Calculations of excited states, their properties, and spectral data (absorption and CD spectra).
Wrapping Up
- Summarizes the required inputs for the simulations.
- Describes various calculation results that can be obtained based on the utilized input and calculation settings.
Running ORCA on Ada and Terra
- This section provides useful tips for running the ORCA calculations on ADA and Terra.
- Recommendations include consulting the user guide, creating directories for each calculation, using batch systems, and specifying the appropriate number of cores for parallel processing in the input files.
Need Help?
- Provides contact information for the HPRC Helpdesk.
- Instructions on getting assistance via the website, email, and phone.
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Description
Test your knowledge on the features and functionalities of the ORCA program and Avogadro. This quiz covers compatibility, primary applications, and software tools matching. Challenge yourself to see how well you know these chemical modeling tools!
