Use a sufficient vacuum slab

Oct 13, 2025 by pynkocean.com 128 views

Introduction

In computational chemistry, the transition state (TS) is a crucial concept in understanding chemical reactions. It represents the highest energy point on the potential energy surface (PES) where the reactants are converted into products. The Constrained Intrinsic Reaction Coordinate with Nudged Elastic Band (CI-NEB) method is a popular approach for finding the TS. However, when using this method, it is not uncommon to encounter two imaginary frequencies in the transition state. In this article, we will discuss what to do when you get two imaginary frequencies in the transition state obtained using CI-NEB.

What are Imaginary Frequencies?

Imaginary frequencies are a common issue in computational chemistry, particularly when dealing with TS. They occur when the Hessian matrix, which is used to calculate the vibrational frequencies, has a negative eigenvalue. This negative eigenvalue indicates that the system is unstable, and the frequency is imaginary. In the context of TS, imaginary frequencies can be a sign of a problem with the TS geometry or the reaction path.

Why Do We Get Two Imaginary Frequencies in CI-NEB?

There are several reasons why you might get two imaginary frequencies in the transition state obtained using CI-NEB. Some possible reasons include:

Insufficient vacuum slab: If the vacuum slab is not sufficient, the periodic boundary conditions can lead to artificial interactions between the slab and the vacuum, resulting in imaginary frequencies.
Incorrect TS geometry: If the TS geometry is not correct, it can lead to imaginary frequencies. This can be due to a variety of reasons, including incorrect optimization or a flawed reaction path.
Reaction path issues: If the reaction path is not correct, it can lead to imaginary frequencies. This can be due to a variety of reasons, including a flawed TS or incorrect optimization.

What to Do When You Get Two Imaginary Frequencies?

So, what do you do when you get two imaginary frequencies in the transition state obtained using CI-NEB? Here are some steps you can follow:

1. Check the Vacuum Slab

First, check the vacuum slab to ensure that it is sufficient. If the vacuum slab is not sufficient, try increasing it to see if the imaginary frequencies disappear.

2. Check the TS Geometry

Next, check the TS geometry to ensure that it is correct. If the TS geometry is not correct, try optimizing it again or using a different optimization method.

3. Check the Reaction Path

Then, check the reaction path to ensure that it is correct. If the reaction path is not correct, try using a different reaction path or optimizing the TS again.

4. Use a Different Method

If none of the above steps work, try using a different method, such as the nudged elastic band (NEB) method or the climbing image nudged elastic band (CI-NEB) method.

5. Use a Different Basis Set

Finally, try using a different basis set to see if the imaginary frequencies disappear.

Example: CO+O -> CO2 Step on 3X3 Pt(111)

Let's consider an example where we are trying to find the TS for the CO+O -> CO2 step on 3X3 Pt(111) with sufficient vacuum slab. We use the CI-NEB method to find the TS, but we get two imaginary frequencies. We follow the steps above to try and resolve the issue.

Step 1: Check the Vacuum Slab

We check the vacuum slab to ensure that it is sufficient. We find that the vacuum slab is indeed sufficient, so we move on to the next step.

Step 2: Check the TS Geometry

We check the TS geometry to ensure that it is correct. We find that the TS geometry is not correct, so we try optimizing it again using a different optimization method.

Step 3: Check the Reaction Path

We check the reaction path to ensure that it is correct. We find that the reaction path is not correct, so we try using a different reaction path.

Step 4: Use a Different Method

We try using a different method, such as the NEB method, but we still get two imaginary frequencies.

Step 5: Use a Different Basis Set

Finally, we try using a different basis set, and we find that the imaginary frequencies disappear.

Conclusion

In conclusion, getting two imaginary frequencies in the transition state obtained using CI-NEB is a common issue in computational chemistry. However, by following the steps above, you can try and resolve the issue. Remember to check the vacuum slab, TS geometry, and reaction path, and try using a different method or basis set if necessary. With patience and persistence, you can find the correct TS and get the desired results.

References

Density Functional Theory (DFT): A popular approach for finding the TS.
VASP: A popular software package for performing DFT calculations.
Computational Chemistry: The field of study that deals with the use of computers to simulate and predict chemical behavior.
Geometry Optimization: The process of finding the minimum energy geometry of a molecule.
Transition State: The highest energy point on the potential energy surface where the reactants are converted into products.
Frequently Asked Questions (FAQs) about Two Imaginary Frequencies in Transition State Obtained by CI-NEB Method =============================================================================================

Q: What are imaginary frequencies in the context of transition state?

A: Imaginary frequencies are a common issue in computational chemistry, particularly when dealing with transition state. They occur when the Hessian matrix, which is used to calculate the vibrational frequencies, has a negative eigenvalue. This negative eigenvalue indicates that the system is unstable, and the frequency is imaginary.

Q: Why do we get two imaginary frequencies in CI-NEB method?

A: There are several reasons why you might get two imaginary frequencies in the transition state obtained using CI-NEB. Some possible reasons include:

Insufficient vacuum slab: If the vacuum slab is not sufficient, the periodic boundary conditions can lead to artificial interactions between the slab and the vacuum, resulting in imaginary frequencies.
Incorrect TS geometry: If the TS geometry is not correct, it can lead to imaginary frequencies. This can be due to a variety of reasons, including incorrect optimization or a flawed reaction path.
Reaction path issues: If the reaction path is not correct, it can lead to imaginary frequencies. This can be due to a variety of reasons, including a flawed TS or incorrect optimization.

Q: What should I do when I get two imaginary frequencies in CI-NEB method?

A: When you get two imaginary frequencies in CI-NEB method, follow these steps:

Check the vacuum slab: Ensure that the vacuum slab is sufficient.
Check the TS geometry: Ensure that the TS geometry is correct.
Check the reaction path: Ensure that the reaction path is correct.
Use a different method: Try using a different method, such as the nudged elastic band (NEB) method or the climbing image nudged elastic band (CI-NEB) method.
Use a different basis set: Try using a different basis set to see if the imaginary frequencies disappear.

Q: Can I use a different optimization method to resolve the issue?

A: Yes, you can try using a different optimization method to resolve the issue. Some popular optimization methods include:

BFGS: A quasi-Newton optimization method that is widely used in computational chemistry.
L-BFGS: A limited-memory BFGS optimization method that is efficient and widely used.
CG: A conjugate gradient optimization method that is efficient and widely used.

Q: Can I use a different basis set to resolve the issue?

A: Yes, you can try using a different basis set to resolve the issue. Some popular basis sets include:

6-31G: A split-valence basis set that is widely used in computational chemistry.
6-311G: A split-valence basis set that is widely used in computational chemistry.
cc-pVTZ: A correlation-consistent basis set that is widely used in computational chemistry.

Q: Can I use a different software package to resolve the issue?

A: Yes, you can try using a different software package to resolve the issue. Some popular software packages include:

VASP: A popular software package for performing DFT calculations.
Gaussian: A popular software package for performing quantum chemistry calculations.
CP2K: A popular software package for performing DFT calculations.

Q: How can I prevent getting two imaginary frequencies in CI-NEB method?

A: To prevent getting two imaginary frequencies in CI-NEB method, follow these best practices:

Use a sufficient vacuum slab: Ensure that the vacuum slab is sufficient to prevent artificial interactions between the slab and the vacuum.
Optimize the TS geometry correctly: Ensure that the TS geometry is correct to prevent imaginary frequencies.
Use a correct reaction path: Ensure that the reaction path is correct to prevent imaginary frequencies.
Use a different method or basis set: Try using a different method or basis set to see if the imaginary frequencies disappear.

Conclusion

In conclusion, getting two imaginary frequencies in the transition state obtained using CI-NEB method is a common issue in computational chemistry. However, by following the steps above and using best practices, you can try and resolve the issue. Remember to check the vacuum slab, TS geometry, and reaction path, and try using a different method or basis set if necessary. With patience and persistence, you can find the correct TS and get the desired results.