Questions tagged [reaction-mechanism]

Questions about reaction mechanisms.

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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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9 votes
3 answers
620 views

Can AMBER be used for a molecular dynamics simulation of a Diels-Alder reaction?

I am studying a Diels-Alder reaction of cyclopentadiene and maleic anhydride. I know that AMBER can be used to run MD simulations on proteins, however would I be able to use these small molecules to ...
Joel Daniel's user avatar
4 votes
1 answer
129 views

Perovskite formation energy from precursors

I would like to find a robust way to compute formation energies of perovskites from their precursors in solution at the DFT level of theory. I have been looking at the literature and I have only been ...
Paul Logan's user avatar
3 votes
1 answer
105 views

How to model TS for given a small biomolecular system?

In this paper (e.g. doi:10.1021/cs500093h and other applied QM/MM studies), it is demonstrated several transition states, intermediates, and products of given set of biomolecules (several residues, ...
làntèrn's user avatar
  • 231
8 votes
1 answer
674 views

Calculating enthalpy of a chemical reaction using DFT

Let's say we have a decomposition reaction $\tag{1}A \rightarrow B + C$ how would I go about calculating the Enthalpy of this chemical reaction using VASP. I am gonna describe what I am thinking below ...
Parmeet Singh EP 066's user avatar
15 votes
3 answers
2k views

Can DFT simulate chemical reactions?

I was wondering, can you simulate the chemical reaction between two or more molecules using DFT? If not, what numerical method is usually used for this?
Carlos Andrés del Valle's user avatar
7 votes
1 answer
173 views

Is It possible to do microkinetic modelling for liquid phase reactions, in the presence of a catalyst?

As from the title, I want to do NEB-TS for chemical reactions in the liquid phase, and use the information to calculate reaction rates/kinetic rates. I know that the NEB-TS is possible in the liquid ...
compuchem4all's user avatar
5 votes
0 answers
93 views

Methods to study reaction mechanisms in solid state reactions and identifying intermediates [closed]

An example of a solid state reaction: sintering of an initial powder of reactants leading to a product. Densification of the sintered powder giving a highly pure product powder. What methods (ab ...
Hitanshu Sachania's user avatar
9 votes
1 answer
129 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
11 votes
1 answer
138 views

Combustion models. How does one determine the most relevant reactions?

I am not entirely sure if this is better suited to Chemistry.SE or Matter modelling, but hey, you guys are nicer. I am fascinated by just how complicated combustion processes are. I was watching an ...
Ingolifs's user avatar
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7 votes
1 answer
269 views

Can the dehydrogenation energy be negative?

I am studying the dehydrogenation of a cyclohexane ring containing $\ce{B-N}$ on the adjacent position. or simply we can think about $\ce{H3N-BH3}$. If we release one $\ce{H2}$ molecule from it then ...
astha's user avatar
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8 votes
0 answers
85 views

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
  • 2,373
10 votes
1 answer
195 views

A concern about IRC results

I've run an IRC (intrinsic reaction coordinates) calculation from my TS (transition state) and got two minima for each side. I am concerned about them. One of them took about 100 steps to be achieved ...
Roman's user avatar
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10 votes
0 answers
154 views

Calculating single electron transfer [closed]

I'm thinking about doing some computational research about pyrazoline oxidation in chlorinated solvents under light. I've found plausible mechanism (article) that involves single electron transfer ...
Roman's user avatar
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4 votes
1 answer
138 views

Using double-hybrid functional instead of MP2 to avoid basis set dependence

I'm investigating reaction mechanism and I want to calculate energies of my reagents, products and TS on a higher level of theory than I use for the geometries and frequencies. I'm thinking about MP2, ...
Roman's user avatar
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8 votes
0 answers
62 views

Reaction mechanism elucidation methodology [closed]

I'm studying a mechanism of fluorine substitution in my molecule (the project isn't that much about actual research as learning computational chemistry). There are two $\ce{C6F5}$ rings and I want to ...
Roman's user avatar
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