atomistica.online
MOLECULAR MODELING COURSE
Introduction to Single-Point Energy Calculations
What is a Single-Point Energy Calculation
At the core of the computational modeling of molecular and periodic structures is the desire to understand and predict the behavior of molecules and crystals just by knowing their structure. One of the most fundamental properties of molecules and periodic structures is their energy. A single-point energy calculation provides the total energy of a molecule or periodic structure at a specific geometric arrangement of its atoms without modifying this geometry.
Why is it Important?
Benchmarking: Before delving into more complex calculations or simulations, researchers often use single-point energy calculations to benchmark or compare different methods or basis sets.
Insight into Reactivity: By calculating the energy of different molecular configurations, one can gain insight into potential reaction pathways and the stability of molecular structures.
Basis for Advanced Calculations: Many advanced molecular modeling techniques, like molecular dynamics or transition state searches, use energy calculations as a foundational component.
How Does it Work?
Molecular Geometry Input: The user provides a specific geometric configuration of the molecule. This can be obtained from experimental data, guessed based on chemical intuition, or derived from previous calculations.
Choice of Method: Depending on the system and the specifics of the study, a quantum mechanical method (like Hartree-Fock, DFT, or post-Hartree-Fock methods) and a basis set are chosen.
Calculation: The electronic structure program then calculates the total energy of the molecule in its given configuration without changing its geometry.
Output: The result is the total energy of the molecule for that specific geometry.
Points to Remember:
A single-point energy calculation provides only the energy of the given molecular geometry. It does not offer any information about whether this geometry is a minimum (stable species), a transition state, or a higher energy structure.
The accuracy of the result heavily depends on the chosen method and basis set.
While the geometry isn’t optimized in a single-point calculation, understanding the energy of various configurations is crucial for many advanced applications.
Practical Part
Overview
In this practical exercise, we will calculate the single-point energy of an ibuprofen molecule. The single-point energy calculation can take seconds to hours, depending on the method. This exercise will apply a high-speed semiempirical method called GFN2-xTB. This method is derived from density functional theory (DFT), and was created to produce reliable molecular geometries and frequencies with a wide coverage of the periodic system of elements. The mentioned GFN2-xTB is one of the so-called extended tight binding methods and is implemented in the xTB program developed by Prof. Stefan Grimme and coworkers.
Running calculations with the xTB program is easy, but it requires users to use a command prompt and write commands, sometimes additional input files, that instruct the xTB program what to do with your molecular structure. These commands and input files are logical, intuitive, and very well-documented (). However, the command prompt and the xTB commands may be repealing for those unfamiliar or less experienced with command-line interfaces (beginners and/or experimentally oriented early-stage researchers). This is where tools of atomistica.online kicks in, in this particular case, the online xtb calculator.
Online xtb calculator acts as a mediator between the user and the xTB program. Online xtb calculator is a user-friendly interface that allows you to run many xTB calculations on our server directly from your web browser, so there is no need to install or maintain anything. You only have to upload your molecular structure in .xyz format and set up calculations using a simple interface. In addition, you will be provided with the structure of ibuprofen.
Procedure
Step 1 – Download molecular structure of ibuprofen in .xyz format by pressing the button bellow:
3D molecular structure of ibuprofen:
Step 2 – Open “Online xtb calculator” to calculate the energy of downloaded structures
Step 3 – Upload your structure
Step 4 – Select task: Energy
Step 5 – Select method: GFN2-xTB (this is ultra-fast semiempirical method derived from the DFT method)
Step 6 – Press “RUN XTB” button
Step 7 – Congratulations for your first atomistic calculation 🙂 In the output section, navigate to the bottom and read the total energy of a molecule
Step 8 – Write down the energy of a molecule .txt file
Step 9 – Repeat everything, using different methods, GFN1-xTB and GFN0-xTB, read the obtained energies and write them in .txt file
Step 10 – Compare the obtained results
Results
Using the provided geometry, you should obtain the results close to numbers given in the Table.
Table - Single point energies of Ibuprofen
| Method | Energy of ibuprofen [Eh] |
|---|---|
| GFN2-xTB | -45.171881396267 |
| GFN1-xTB | -46.630482269072 |
| GFN0-xTB | -43.992887622745 |
Conclussions
- Different methods will give different values of energy for the same molecular geometry. Comparisons are valid only if calculations are made using the same method. This is frequently called, the same level of theory.
- In case of the quantum mechanical calculations, the magnitude of energy depends on the number of electrons. The higher the number of electrons, the higher will be the magnitude (providing that you use the same level of theory for calculations)
- It’s crucial to remember that the absolute values of quantum mechanical energies often don’t have a direct physical meaning. Instead, differences in energy (like between two different structures or reactions) are what provide meaningful insights.
- While single-point energy calculations are generally less computationally demanding than other types of calculations, the cost can still vary significantly based on the method, basis set, and size of the molecule.
Single-point energy calculations provide information only for the specific geometry inputted. They don’t indicate if the given geometry is the most stable or if there might be a lower-energy configuration.