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QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin-Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches
quantum mechanical (QM, TPSS-D3/def2-TZVP DFT-D3) and molecular mechanics (MM, AMBER solvent methods (COSMO for DFT-D3; GB and PB for MM). Large-scale DFT-D3 optimizations of DFT-D3 over the ...
CF - Fyzikální chemie a teoretická chemie
- 2014 •
- Jx •
- Link
Rok uplatnění
Jx - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)
Výsledek na webu
A combined quantum and molecular mechanical study of the O2 reductive cleavage in the catalytic cycle of multicopper oxidases
Using QM/MM calculations, the key intermediates of the reaction cycle of multicopper oxidases have been structurally characterized and the reaction mechanism proposed....
CF - Fyzikální chemie a teoretická chemie
- 2005 •
- Jx
Rok uplatnění
Jx - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)
Comparison of CAP and DFT-Spread DMT for High Speed Transmission Over 50m SI-POF
and initial experimentation regarding the comparison of CAP and DFT-Spread DMT for transmission over 50m of 1-mm SI-POF. It is shown that CAP and DFT-Spread DMT fiber (SI-POF). Among these schemes, ...
JA - Elektronika a optoelektronika, elektrotechnika
- 2016 •
- D •
- Link
Rok uplatnění
D - Stať ve sborníku
Výsledek na webu
A novel Cu(II)-based DNA-intercalating agent: Structural and biological insights using biophysical and in silico techniques
with ethidium bromide) and theoretical (DFT, molecular docking simulation, and QM/MM...
Condensed matter physics (including formerly solid state physics, supercond.)
- 2023 •
- Jimp •
- Link
Rok uplatnění
Jimp - Článek v periodiku v databázi Web of Science
Výsledek na webu
Reaction Mechanism of O-GlcNAc Transferase Explored By QM/MM Molecular Dynamics
were investigated at the DFT QM/MM level. The sophisticated theoretical approaches such as hybrid QM/MM DFT Carr-Parinello ab initio molecular dynamics combined with a string......
Physical chemistry
- 2016 •
- O
Rok uplatnění
O - Ostatní výsledky
Effect of Al-Si-Al and Al-Si-Si-Al Pairs in the ZSM-5 Zeolite Framework on the Al-27 NMR Spectra. A Combined High-Resolution Al-27 NMR and DFT/MM Study
The effect of the presence of Al-O-Si-O-Al and Al-O-Si-O-Si-O-Al sequences in the ZSM-5 zeolite framework on the local geometry of AlO4- tetrahedra and the Al-27 NMR parameters was investigated employing Al-27 3Q MAS NMR spectroscopy and DFT...
CF - Fyzikální chemie a teoretická chemie
- 2009 •
- Jx
Rok uplatnění
Jx - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)
On the reliability of the corrected semiempirical quantum chemical method (PM6-DH2) for assigning the protonation states in HIV-1 protease/inhibitor complexes
complexes is presented. We use a QM/MM approach in which the large QM part (the ligand using MM/GB method. This approach is applied to two model systems, the carboxylate pairs in HIV-1 protease/inhibitor complexes. The computationa...
CF - Fyzikální chemie a teoretická chemie
- 2011 •
- Jx •
- Link
Rok uplatnění
Jx - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)
Výsledek na webu
QM/MM Calculations with deMon2k
in the context of constrained-DFT/MM calculations. Each of these implementations is described sacrificing necessary accuracy. Powerful Quantum Mechanical/Molecular Mechanical (QM/MM it efficient while retaining accuracy, t...
CF - Fyzikální chemie a teoretická chemie
- 2015 •
- Jx •
- Link
Rok uplatnění
Jx - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)
Výsledek na webu
Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM
Hybrid QM/MM methods combine the rigor of quantum mechanical (QM) calculations with the low computational cost of empirical molecular mechanical (MM) treatment allowing. Catalysis by RNA enzymes (ribozymes) has only recently begun t...
CF - Fyzikální chemie a teoretická chemie
- 2009 •
- Jx
Rok uplatnění
Jx - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)
Ab Initio Calculations in Chemistry after 28 Years
discussed: DFT, electron correlation, attainable accuracy and reliability of calculations, relativistic effects, QM/MM and combined QM and molecular dynamics......
CF - Fyzikální chemie a teoretická chemie
- 2008 •
- Jx
Rok uplatnění
Jx - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)
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