CHARMM force field generation for a cationic thiophene oligomer with ffTK

Author:

Kıbrıs Erman,Barbak Nehir Nalıncı,Irmak Nuran ElmacıORCID

Funder

Türkiye Bilimsel ve Teknolojik Araştirma Kurumu

Publisher

Springer Science and Business Media LLC

Subject

Computational Theory and Mathematics,Inorganic Chemistry,Organic Chemistry,Physical and Theoretical Chemistry,Computer Science Applications,Catalysis

Reference21 articles.

1. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) Charmm: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4 (2):187–217. https://doi.org/10.1002/jcc.540040211. https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.540040211

2. Carreon AC, Santos WL, Matson JB, So RC (2014) Cationic polythiophenes as responsive dna-binding polymers. Polym. Chem. 5:314–317. https://doi.org/10.1039/C3PY01069D

3. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Petersson GA, Nakatsuji H, Li X, Caricato M, Marenich AV, Bloino J, Janesko BG, Gomperts R, Mennucci B, Hratchian HP, Ortiz JV, Izmaylov AF, Sonnenberg JL, Williams-Young D, Ding F, Lipparini F, Egidi F, Goings J, Peng B, Petrone A, Henderson T, Ranasinghe D, Zakrzewski VG, Gao J, Rega N, Zheng G, Liang W, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Throssell K, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark MJ, Heyd JJ, Brothers EN, Kudin KN, Staroverov VN, Keith TA, Kobayashi R, Normand J, Raghavachari K, Rendell AP, Burant JC, Iyengar SS, Tomasi J, Cossi M, Millam JM, Klene M, Adamo C, Cammi R, Ochterski JW, Martin RL, Morokuma K, Farkas O, Foresman JB, Fox DJ (2016) Gaussian0~9 Revision A.02. Gaussian Inc. Wallingford CT

4. Galindo-Murillo R, Robertson JC, Zgarbová M, Šponer J, Otyepka M, Jurecka P, Cheatham TE (2016) Assessing the current state of amber force field modifications for dna. J Chem Theory Comput 12(8):4114–4127. https://doi.org/10.1021/acs.jctc.6b00186. PMID: 27300587

5. Ho HA, Béra-Abérem M, Leclerc M (2005) Optical sensors based on hybrid dna/conjugated polymer complexes. Chemistry 11(6):1718–1724. https://doi.org/10.1002/chem.200400537. https://onlinelibrary.wiley.com/doi/abs/10.1002/chem.200400537

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