Zobrazeno 1 - 10
of 13
pro vyhledávání: '"Filip Ryjáček"'
Publikováno v:
Phys. Chem. Chem. Phys.. 7:2006-2017
Altogether 13 keto and enol tautomers of uracil and 13 keto and enol tautomers of thymine were studied theoretically in the gas phase, in a microhydrated environment (1 and 2 water molecules) and in a water environment. Bulk water was described using
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ce47b5140b71fe409f17ce3aaf77d48a
https://doi.org/10.1039/b501499a
https://doi.org/10.1039/b501499a
Publikováno v:
The Journal of Physical Chemistry B. 108:2087-2097
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::455f62a32f2e3047b4f839348ddcfb14
https://doi.org/10.1021/jp036090m
https://doi.org/10.1021/jp036090m
Autor:
Semen A Trygubenko, Martin Kabeláč, Filip Ryjáček, Tomas Kubar, Michal Hanus, Tetyana V. Bogdan, Pavel Hobza
Publikováno v:
Journal of the American Chemical Society. 125:7678-7688
Altogether eight keto and enol tautomers of guanine were studied theoretically in the gas phase, in a microhydrated environment (1 and 2 water molecules) and in bulk water. The structures of isolated, as well as mono- and dihydrated tautomers were de
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::74ed08f9434e3576800404ae676700b5
https://doi.org/10.1021/ja034245y
https://doi.org/10.1021/ja034245y
Autor:
Nad'a Špačková, Filip Lankaš, Luc Van Meervelt, Pavel Hobza, Thomas E. Cheatham, Filip Ryjáček, Jiří Šponer
Publikováno v:
Journal of the American Chemical Society. 125:1759-1769
An extended set of nanosecond-scale molecular dynamics simulations of DNA duplex sequences in explicit solvent interacting with the minor groove binding drug 4',6-diamidino-2-phenylindole (DAPI) are investigated for four different and sequence specif
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2a57d523630052f3e76cde64121c254a
https://doi.org/10.1021/ja025660d
https://doi.org/10.1021/ja025660d
Publikováno v:
The Journal of Physical Chemistry A. 105:1197-1202
The potential energy surface (PES) of the 9-methyladenine···1-methylthymine (mA···mT) nucleic acid base pair was investigated using molecular dynamics/quenching method utilizing the Cornell et al. (Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gou
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::fb24d340acf64fc39dd4b0c094062ff5
https://doi.org/10.1021/jp003078a
https://doi.org/10.1021/jp003078a
Publikováno v:
Physical Chemistry Chemical Physics. 2:4906-4909
The dynamical structure of the adenine···thymine nucleic acid base pair exposed to a small number of water molecules (from 1 to 216) was determined using molecular dynamics simulations with Cornell et al. force field (W. D. Cornell, P. Cieplak, C.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::64026061738b41f50e23c385f710069b
https://doi.org/10.1039/b007167f
https://doi.org/10.1039/b007167f
Publikováno v:
Chemical Physics Letters. 313:393-398
Ab initio calculations are described for bonded and stacked structures of adenine⋯2,4-difluorotoluene. Stabilization energies are determined with inclusion of correlation energy at the MP2/6-31G ∗ (0.25) level. Stacked structures of the pair are
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::c1c634adc8a192f4543eae7e33b30841
https://doi.org/10.1016/s0009-2614(99)01013-1
https://doi.org/10.1016/s0009-2614(99)01013-1
Publikováno v:
ResearcherID
Correlated ab initio as well as semiempirical quantum chemical calculations and molecular dynamics simulations were used to study the intercalation of cationic ethidium, cationic 5-ethyl-6-phenylphenanthridinium and uncharged 3,8-diamino-6-phenylphen
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2cb2c49f094d56cd36c983f8c02b5f2b
https://pubmed.ncbi.nlm.nih.gov/16294358
https://pubmed.ncbi.nlm.nih.gov/16294358
Publikováno v:
Journal of computational chemistry. 24(15)
The Cornell et al. empirical potential (Cornell et al., J Am Chem Soc 1995, 117, 5197) was modified by the introduction of nonplanarity of the amino group in guanine, adenine, and cytosine. Reparameterization was performed for 12 bond parameters of t
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::89c145fea623d74eb9a0e9a86c3b7254
https://pubmed.ncbi.nlm.nih.gov/14515371
https://pubmed.ncbi.nlm.nih.gov/14515371
Autor:
Jiří Šponer, Marcus Elstner, Filip Ryjáček, Pavel Hobza, Martin Kabeláč, David Řeha, and Sándor Suhai, Judit E. Šponer
Publikováno v:
Journal of the American Chemical Society. 124(13)
Properties of isolated intercalators (ethidium (E), daunomycin (D), ellipticine (EL), and 4,6'-diaminide-2-phenylindole (DAPI)) and their stacking interactions with adenine...thymine (AT) and guanine...cytosine (GC) nucleic acid base pairs were inves
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9645d6c6acfbbe3dde0527dba354b521
https://pubmed.ncbi.nlm.nih.gov/11916422
https://pubmed.ncbi.nlm.nih.gov/11916422