20 votes

Correct jobs sequence for transition-state (TS) search

A common and not quite unreasonable approach is to do molecular structure optimisations at a low level, establish the path(s) at this level, and obtain better energies at a higher level. It really ...
Martin - マーチン's user avatar
11 votes
Accepted

Correct jobs sequence for transition-state (TS) search

J1 Freq (6-31G*); J2 TS_search (6-31G*); J3 Freq (6-31G*); is good because it let's you optimize the saddle point and then get the thermodynamic data For the single-point correction don't ...
Cody Aldaz's user avatar
  • 8,017
10 votes

What are some of the biggest theoretical and computational challenges in Condensed Phase Chemistry?

The Monte Carlo Sign Problem For classical systems, Monte Carlo works extremely well. Quantum Monte Carlo is very powerful, but there are many interesting systems that suffer from the sign problem, ...
taciteloquence's user avatar
8 votes
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What are the output files generated by an NEB calculation?

This question is bit too broad for a specific answer. The most common types of files that are generated by Orca are: *.gbw files are binary wavefunction files, ...
S R Maiti's user avatar
  • 6,851
7 votes

Benchmark transition state geometries in condensed phases

Not really sure about benchmarks for solid state TS geometries. A couple of scattered piece of references are: (i) This paper by Ceder's group has several related TS barriers: aip.scitation.org/doi/...
gogo's user avatar
  • 1,247
7 votes
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TS-search with explicit solvent

Explicit solvent can be of importance, like you mention, whenever strong coordination or hydrogen bonding is involved. For example, transition metals often coordinate to solvent and not including them ...
Cody Aldaz's user avatar
  • 8,017
7 votes
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Isotopes in Reaction Kinetics by Transition State Theory

The canonical transition state theory expression for the thermal rate constant, with tunneling correction, is $$ k(T) = \kappa(T) \frac{k_\mathrm{B}T}{hc^\circ}\exp [-\Delta^\ddagger G/RT]$$ which is ...
Antonio de Oliveira-Filho's user avatar
7 votes

Is it ok to start from an identity matrix Hessian guess for optimisation?

This is a difficult question to answer, because it really depends what you mean by "OK". There is certainly no fundamental problem with an initial guess Hessian which is the identity matrix, ...
Phil Hasnip's user avatar
  • 7,262
5 votes

Reaction rate estimation for relatively complex reactions

Relatively big systems can be treated with fragmentation methods that allow one to reduce the cost of the overall computation by using the most accurate and/or expensive approach on the most relevant ...
Antonio de Oliveira-Filho's user avatar
5 votes
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Gaussian: Transition state convergence question

Are you doing an opt and freq calculation? In Gaussian, the opt keyword uses an approximate ...
Tyberius's user avatar
  • 15.5k
5 votes

Example of single reaction with multiple transition states

Perhaps the simplest example is the transition between cis and trans diazene, N2H2. Both are planar structures, with the two hydrogens either on the same or opposite sides of the central N=N. There ...
Frank Jensen's user avatar
  • 1,776
4 votes

Syntax Error in ORCA

You shouldn't have a * after the name of the coordinate file; the line should just be: * xyzfile -2 1 filename.xyz It also ...
isolated matrix's user avatar
4 votes
Accepted

Vibrational frequency analysis for NEB result through Maestro

Based on what you have said, a phonon calculation is likely what you want. You should see imaginary frequencies in the output if you do infact have a transition state. You may need stricter ...
Tristan Maxson's user avatar
4 votes
Accepted

How does ORCA treat intermediates in Nudged Elastic Band (NEB) calculations

As far as I know, there's no method available for optimizing intermediates with NEB. Same goes for multiple TS. CI-NEB only has one climbing image, which will converge towards the highest point on the ...
Kexanone's user avatar
  • 523
4 votes

Gibbs free energy modification after finishing NEB?

I think the first question you have to ask is whether you can get an accurate free energy for your reaction barrier in VASP. If you have a reaction with a small molecule on an oxide surface under ...
lamycel's user avatar
  • 121
3 votes
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Energy decomposition analysis (EDA) at transition state

Very interesting question. I have no experience doing EDA, but as I'll probably need to do it in the future, I used your question as a starting point to learn more about it. I did some research, but ...
ksousa's user avatar
  • 4,108
2 votes
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How do you make sure the reaction is diffusion limited (Gaussian)?

I solved the problem by reducing maxstep to 1 and using notrust and calcfc. The proposed ...
farmaceut's user avatar
  • 556
2 votes
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Gibbs free energy modification after finishing NEB?

To get the Gibbs Free energy from the internal energy, you have to consider the configurational entropy. I anticipate you need the Gibbs Free energy to calculate the activation barrier as a function ...
Tara Mishra's user avatar
2 votes

Gibbs free energy modification after finishing NEB?

It depends on why you've made the NEB. If to find a possible reaction coordinate, you can use the ∆E as an indicator. Another thing is that you can't perform the "traditional" ...
Andrea Pellegrini's user avatar
2 votes

Correcting thermodynamic data for concentration, what concentration is best to use?

TLDR: The rate constant calculated by transition state theory depends on the standard-state (gas-phase: ideal gas at a partial pressure of 1 atm or any state concentration (1 cm$^3$ molecule$^{-1}$ or ...
Antonio de Oliveira-Filho's user avatar
2 votes

Correct jobs sequence for transition-state (TS) search

If you're using Gaussian you can also use the QST2 and QST3 methods: the first uses reagents and products as input and try to think of a reaction coordinate to find the MEP; the former uses reagent, ...
Andrea Pellegrini's user avatar

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