Questions tagged [transition-state]

For questions about determining/optimizing transitions states of chemical reactions

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What is best way to get lowest adsorption site at subsurface of high entropy alloys?

I am currently studying diffusion of oxygen in high entropy alloys. I want to calculate the activation energy from an adsorption site on the surface to the subsurface. I placed the oxygen atom below ...
Nana Kofi Boakye's user avatar
2 votes
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Error: Cannot open GBW file: TS.gbw

I have a problem with calculating Transition State using NEB-TS. Here is my input file: ...
Jots's user avatar
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6 votes
1 answer
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Example of single reaction with multiple transition states

I was working with nudged elastic band (NEB) to model some reactions, and someone asked what would happen if there are multiple pathways between the reactant and product (minima on the PES). This led ...
S R Maiti's user avatar
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4 votes
1 answer
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Syntax Error in ORCA

I keep getting the following error for my orca code: [file orca_main/maininp1.cpp, line 17547]: ERROR: expect a '$', '!', '%', '*' or '[' in the input [file ...
znc204's user avatar
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How do you make sure the reaction is diffusion limited (Gaussian)?

I am investigating the mechanism of hydrogen transfer between a hydroperoxyl radical and an aromatic hydroxyl group donating it. The problem is that I cannot find transition state structure. So far, I'...
farmaceut's user avatar
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4 votes
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Is it possible to generate atom-mapped xyz files from reaction SMILES for NEB?

There are SMILES that represent reactions happening (e.g. C=C.O>>CCO representing water addition to ethylene). And I know that there are atom-mapping ...
S R Maiti's user avatar
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5 votes
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ORCA failed during NEB-TS ONIOM [closed]

Thanks in advance for any help provided. I was trying to find the transition state of a diels alder reaction and considering my system's bulkiness I wanted to try a NEB calculation considering part of ...
Laura Marcon's user avatar
4 votes
1 answer
113 views

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

I am attempting to implement an algorithm for transition state finding (in Python, but that's not important). The algorithm is called BITSS (Binary Image-pair Transition State Search). It defines a ...
S R Maiti's user avatar
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4 votes
1 answer
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How does ORCA treat intermediates in Nudged Elastic Band (NEB) calculations

I'm trying to run a quite complicated NEB optimization with (hopefully) one intermediate structure. But before losing time, I was wondering: how does ORCA treat that intermediate? does ORCA optimize ...
Andrea Pellegrini's user avatar
5 votes
3 answers
349 views

Gibbs free energy modification after finishing NEB?

I have finished the NEB calculation, but it seems all the energy I got is Internal energy instead of Gibbs free energy, so do I need to do Gibbs free energy modification? Is there any standard ...
Jack's user avatar
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7 votes
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What are the output files generated by an NEB calculation?

I just used Orca for the first time. Can someone address me a valid guide to understand all the files in the directory? I'd like to perform a Nudged Elastic Band (NEB) calculation, but I'm stuck ...
Andrea Pellegrini's user avatar
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How do you perform parallelization of NEB-TS in ORCA? [closed]

I have tried running a NEB-TS calculation in orca with %pal nprocs 32, but I get an error saying ...
カイル's user avatar
9 votes
1 answer
132 views

Reaction rate estimation for relatively complex reactions

I am looking for a summary of your favorite methods to estimate a reaction rate constant for a “complex” polyatomic reaction (requiring a cell of ~100 atoms) from ab initio methods (the one I have in ...
Barbaud Julien's user avatar
7 votes
1 answer
658 views

Gaussian: Transition state convergence question

I am running a TS computation in Gaussian 16. It performs several steps. At the end of each there is a summary on whether Maximum Force, ...
Bpi's user avatar
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7 votes
1 answer
275 views

Vibrational frequency analysis for NEB result through Maestro

I have ran a Nudged Elastic Band (NEB) calculation using QuantumEspresso through Maestro to find the potential transition state. Within Maestro there is an option where you can select for NEB type ...
KAJ226's user avatar
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8 votes
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Troubleshooting mechanistic calculation: Transition state energy and intermediate energy too close [closed]

I'm studying a mechanism of aromatic substitution of fluorine which proceeds via an intermediate. I'm searching for a transition state using a relaxed surface scan, then I optimize the TS and perform ...
Roman's user avatar
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12 votes
1 answer
277 views

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

What are some of the biggest open-questions / challenges in Condensed Phase theory and computation? What efforts are being done to answer them? I realize Condensed Phase chemistry is a huge field, but ...
epalos's user avatar
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9 votes
1 answer
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Energy decomposition analysis (EDA) at transition state

I am trying to understand the interaction between the nucleophile and the substrate for some SN2 reactions (e.g. $\ce{I- +CH3Cl->CH3I + Cl-}$) at the transition states. Now, it seems that EDA would ...
S R Maiti's user avatar
  • 6,851
8 votes
1 answer
162 views

Isotopes in Reaction Kinetics by Transition State Theory

Can kinetic isotope effects be handled in density functional theory level calculations? My intuition says that in the context of molecular dynamics simulations that they can be, but can transition ...
Tristan Maxson's user avatar
10 votes
1 answer
171 views

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

In computational chemistry when using transition state theory we often use standard states for all involved structures. However, sometimes people argue that it should be corrected for concentration (...
DSVA's user avatar
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17 votes
1 answer
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Benchmark transition state geometries in condensed phases

I'm seeking references/benchmarks for transition state geometries of reactions in condensed phases like crystals, zeolites, or surfaces. Basically the system just needs to be considered big, yet ...
Cody Aldaz's user avatar
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13 votes
1 answer
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TS-search with explicit solvent

I'm looking for an advice how the best to set up the system and optimize a transition state with explicit solvent. I believe that solvent molecules are participating in the reaction by specific ...
Dmitry Eremin's user avatar
19 votes
3 answers
322 views

Correct jobs sequence for transition-state (TS) search

I've seen many papers analyzing reaction pathway using a small basis set like 6-31G* for all optimization steps and later single point calculations in bigger one (like 6-311++G**). What is the correct ...
Dmitry Eremin's user avatar