Dear all
My major is based on the experimental. I rare often go to get help from software.
I am looking for the software to simulate the possibility of chemical reaction between POLYMERS. The reaction was not reported yet in any paper. I tried to find somehow similar reaction between two polymers with similar functional groups. But, not successful. I tried to use MD simulation, but interaction parameters are completely unknown. Again, I tried to use the interaction parameters between two similar MOLECULES (and not polymers).
I am wondering if there any software to simulate the reaction properties including the possibility of the formation of the chemical bond, decomposition of the bond, equilibrium constant, the heat of reaction, is it equilibrium one or not, how the Temperature, pH, ionic strength, time …. Affect the reaction.
I don’t mind if the results come with some error since my synthesized polymer and my reaction not reported at all, although basically, it is very simple for the reaction between two functional groups. It is the reaction of –COOH with an amine (but both of them are a polymer).
It would be nice if I can design my polymers only with the 3-4 monomer (oligomer) and then try to see the results.
I don’t mind, I pay for software. The high cost is also OK. But, I am a Chemical Engineer, and my knowledge about chemistry is poor. I can get professional chemistry help.
Best regards
Rajabzadeh k. Saeid, Associate Professor
E-mail: [email protected]; Personal E-Mail: [email protected] Web:
https://scholar.google.com/citations?user=r3z6D68AAAAJ&hl=en
https://www.researchgate.net/profile/Saeid_Rajabzadeh
https://www.scopus.com/authid/detail.uri?authorId=24467099200
http://www.researcherid.com/rid/K-5083-2017
orcid.org/0000-0003-2883-4587
Hello Sir,
Most of the above mentioned e.g: (formation of bond, decomposition of the bond, equilibrium constant, heat of reaction) can be pretty much done in any Quantum Chemistry software which includes DFT (Density functional theory). A list of these software is given here along with the licensing information: https://en.wikipedia.org/wiki/List_of_quantum_chemistry_and_solid-state_physics_software
By popular opinion Gaussian (Commercial) is probably the most user friendly and can be used as a black box (although I do not recommend that) even by people who are unaware of the fundamentals. Other softwares, like Turbomole (Commercial), GAMESS and ORCA are also equally good options.
Aside from the price of the softwares, I think the most important aspect is also to invest and/or to mange good computational resources. For most standard DFT calculations good CPU facility is a must.
I agree with Turbasu Sengupta and would add from my side few points:
1) description of "what has to be modelled" is still rather incomplete. Depending on it one would stick to sequence of DFT optimisations or to DFT-MD. Important part is size of the system, while systems around 100 nonhydrogen atoms can be handled rather fast and effective, 300 could already be a nasty problem. It can be simplified in few ways - QM/MM approach where chemically interacting groups (the one that have bond break and bond formation) are described with DFT and the rest of the system is handled with much cheaper approsch. Alternative to this could be semiempirical approach, however i would recommend to look not on canonical semiempirics but on Tight-Binding approaches (namely DFTB and GFN-XTB, both software are free) or may be "QM" method of Laikov (abbreviation should not be misunderstood with "quantum mechanics", it is available only in "Priroda" software that is free but has its own drawbacks). Among software for DFT-MD i would mention Terachem and periodic software like QuantumEspresso, VASP, Wien2K, CP2K, CPMD.
2) Its true that some software in quantum chemistry is pretty black-box, and entrance barrier to the field might be rather low. However "self-study" of this field quite often results in calculations that looks ok to the authors but are absolutely awkward, meaningless and facepalmy to the experts. I would really recommend to find someone who is knowing what he is doing and collaborate with this person/department (i do not suggest myself while i have enough of my own projects and this one is out of my sphere of interest, its just a friendly advice)
Hi Turbasu Sengupta and Dimitry Sharapa;
I appreciate very much your kind answer. You shared your valuable time with me.
I have a professor with experience in MD using MS beside myself. But, my case looks very complicated. It is challenging. I can access a cluster with 200 CPU.
It looks I need another person with Profesdionality in QD.
Thanks thanks and thanks
Dear Prof. Saeid Rajabzadeh,
For your purpose, I think "Schrödinger Suites" software, also, is a good choice.
About the software:
... With GPU-accelerated molecular dynamics simulations using the extremely efficient MD engine Desmond1, and the commercial OPLS3e force-field2,3, accurate prediction of polymer properties through atomistic simulation becomes feasible for even desktop computers. The Materials Science Suite provides chemical structure and polymer builders, a chemically adaptable cross-linking simulation module (Crosslink Polymers), automated thermophysical and mechanical response simulation modules (e.g. Thermophysical Properties, and Stress Strain), and analysis tools (e.g. MS MD Trajectory Analysis) allowing users to efficiently analyze single or multiple systems. Overall, the Materials Science Suite provides a unique and powerful advantage to both experienced polymer modelers and new-to-modeling scientists and engineers...
Best Regards
Khodadadi
Dear Saeid,
If you're looking at reactions in such large systems, using ab initio MD with DFT or DFTB is probably not going to be feasible. You may try to use ReaxFF, which has been developed specifically for dealing with chemical reactions in large complex systems. Some applications specifically to polymers:
https://www.scm.com/doc/Tutorials/Advanced/ReaxFF_polymers_bond_boost.html (looking at cross-linking polymers, no absolute reaction rates)
https://www.scm.com/doc/Tutorials/Advanced/ReaxFF_polymers_mechanical_properties.html (mechanical properties of epoxy polymers)
Kind regards,
Fedor
in chemdraw 3D you can find a large calcul methods witch could help you
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