Questions tagged [transition-state]
For questions about determining/optimizing transitions states of chemical reactions
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How to fix Gaussian Error link l801.exe and l701.exe?
I was working on my transition state calculation on Gaussian and I come across this 2 error link on my calculation. One of them is
SCF Error SCF Error SCF Error SCF Error SCF Error SCF Error SCF ...
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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'...
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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 ...
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ORCA failed during NEB-TS ONIOM
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 ...
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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 ...
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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 ...
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3
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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 ...
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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 ...
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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 ...
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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 ...
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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, ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 (...
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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 ...
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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 ...
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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 ...
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