Polymer Chemistry Mixture

cheminformatics

chemistry

polymer

This article delves into the utilization of molecular dynamics simulations with tools such as pymatgen, lammps, and openFF. It discusses interatomic potentials and force field generation processes in organic chemistry. Additionally, it covers accessing density data from multiple sources.

Published

January 28, 2022

http://www.cheminfo.org/

interatomic potentials:

https://www.ctcms.nist.gov/potentials/

https://zhuanlan.zhihu.com/p/351829537

https://www.ctcms.nist.gov/potentials/system/C-H-O/

https://atb.uq.edu.au/index.py?tab=structure_search

https://github.com/dwsideriusNIST/LAMMPS_Examples

opensmog smog2.provides force field generation tool

run simulation under given temperature, pressure and get density

openmm

generate force field on the fly:

from openff.toolkit.topology import Molecule

molecule = Molecule.from_smiles(‘c1ccccc1’)

https://www.catalysis-hub.org

pymatgen contains polymer generator to lammps:

pymatgen.io.lammps.utils

simulating reaction in molecular dynamics:

https://www.reacter.org

implemented in lammps fix bond/react method

random.randomvoidmail@erine.email (pending approval)

seen polymer names on lammps demo website:

https://lammps.org/pictures.html#reactphoto

https://docs.lammps.org/Intro_features.html

If you are a new computational chemist I would advise you to use ASE, it is not only useful for nanoparticles, I’m using it nearly every day.

patent:

https://bulkdata.uspto.gov/

http://chemdataextractor.org/results/26088052-3833-41ea-98f1-0a8a3fb2c341

https://www.zhihu.com/question/50559712

moltemplate, packmol

vmd: lammps data file visualization

build input file for lammps:

https://atomsk.univ-lille.fr/

get retrosynthesis training data on picture search engines

octa: predict polymer properties

https://octa.jp/references/examples/

Link: [5]http://oexchange.org/spec/0.8/rel/related-target

You can try [33]https://spaya.ai/ it is a retro-synthetic analysis

[37]Http://www.orgsyn.org/

[41]Http://www.orgsyn.org/

[45]Http://www.organic-chemistry.org/

Try this interesting blog: [49]http://totallysynthetic.com/blog/

And also this website: [50]http://chemistrybydesign.oia.arizona.edu/

[54]http://www.chemspider.com/

[58]https://pubchem.ncbi.nlm.nih.gov/search

Organic Syntheses Website: <[62]http://www.orgsyn.org

Organic Chemistry Portal: <[63]http://www.organic-chemistry.org/abstracts

Chemsynthesis: [64]http://www.chemsynthesis.com

ChemExper: [65]https://www.chemexper.com

Pub Chem compound: [67]http://pubchem.ncbi.nlm.nih.gov

E-molecules: [68]http://www.emolecules.com

Chemspider: [69]http://www.chemspider.com

Reaxys: [70]https://www.reaxys.com/

SciFinder: [71]http://www.cas.org,

STN: [72]https://stnweb.cas.org/

[76]http://www.chemspider.com

[80]https://www.vulcanchem.com/

https://moltemplate.org

https://chemdataextractor.org

gromacs: creating polymer structure

http://www.gromacs.org/Documentation_of_outdated_versions/How-tos/Polymers

latest gromacs documentation:

https://manual.gromacs.org/documentation/

online organic chemistry textbook:

https://www2.chemistry.msu.edu/faculty/reusch/virttxtjml/intro1.htm

openbabel can only run normally on x86 platforms. so do other cheminfo packages.

sources of organic synthesis

https://www.organic-chemistry.org

http://www.orgsyn.org

What is matsci.org?

matsci.org is a community forum for the discussion of anything materials science, with a focus on computational materials science research. Its members are typically from academic research institutions and universities.

People that currently help run matsci.org include maintainers of the following codes and collaborations:

OVITO

GULP

DL_POLY

OPTIMADE

pyiron

hiphive

ASE

MPDS

iFermi

LAMMPS

MaRDA

exciting

JARVIS

and members of the following research groups:

Hacking Materials Group

Persson Group

Materials Virtual Lab

Materials Intelligence

translate bigsmiles into smiles

polymer database:

PolyInfo and NIST Synthetic Polymer MALDI Recipes database

USPEX

chemdraw chemoffice indraw spaya.ai

reaxys scifinder-n

marvin sketch pka

https://github.com/PKUMDL-AI/AutoSynRoute

polymer simulation:

material studio

amsterdam modeling suite

cp2k orca

https://orcaforum.kofo.mpg.de/app.php/portal

chemistry in stack exchange:

https://chemistry.stackexchange.com/

polymer retrosynthesis using retro*:

seq2seq-retro mlp-retro polyretro-uspto

deepchem, chempy(inorganic)

avogadro: import openbabel files

odachi: decompose target molecular into source molecular, highlight the potential bond

rdkit: python chemistry informatic

polymer informatic

ab initio chemistry:

lammps, quantum espresso, nwchem, gamess, uspex

from https://www.webmol.net:

Gamess, Gaussian, MolPro, Mopac, NWChem, Orca, PQS, PSI, Q-Chem, TeraChem, Tinker, Quantum Expresso, and VASP