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1. An Asynchronous,Concerted Mechanism for Cytochrome P450-Catalyzed Dehydrogenation:A Combined Deuterium Labeling and QM/MM Study NSTL国家科技图书文献中心

Alicia M.Kirk |  Jeanette E.Stok... -  《ACS catalysis》 - 2025,15(2) - 1274~1286 - 共13页

摘要: simulations and QM/MM(ONIOM)modeling,CYP199A4-catalyzed | Cytochromes P450(P450s)commonly catalyze |  hydroxylation but can also be responsible for dehydrogenation |  reactions,important in drug metabolism and biosynthesis | ;the mechanism of the latter transformation remains
关键词: cytochrome P450 |  CYP199A4 |  dehydrogenation |  QM/MM |  ONIOM |  enantioselective |  PCET

2. DFT and QM/MM Study of interactions of NSAIDs and Beta‐Blockers with DNA NSTL国家科技图书文献中心

Işılay Öztürk |  Toomas Tamm... -  《Chemistry Select》 - 2025,10(10) - n/a~n/a - 共13页

摘要: QM/MM simulations to observe interactions between |  QM/MM results, showing agreement with the QM model |  understanding the applicability of QM models to large systems |  findings demonstrate that QM models can effectively | Abstract This study investigated the
关键词: DFT ‐ QM/MM |  DNA‐nucleobase binding energies |  Noncovalent interactions |  Beta‐blockers |  NSAIDs

3. QM/MM investigation of the discriminatory pre-transfer editing mechanism operated by Lysyl-tRNA synthetase NSTL国家科技图书文献中心

Ion, Bogdan F. |  Aboelnga, Mohamed M.... -  《Journal of Biomolecular Structure and Dynamics》 - 2025,43(8) - 4004~4012 - 共9页

摘要: quantum mechanics/molecular mechanics (QM/MM | Aminoacyl-tRNA synthetases (aaRSs) are |  essential enzymes that remarkable facilitate the |  aminoacylation process during translation. With a high fidelity | , the mischarged tRNA is prevented through
关键词: Aminoacyl-tRNA synthetase |  LYSRS |  LYSU |  multi-scale |  molecular dynamics |  catalytic mechanism |  QM/MM

4. A Closer Look at the FeS Heme Bonds in Azotobacter vinelandii Bacterioferritin: QM/MM and Local Mode Analysis NSTL国家科技图书文献中心

Freindorf, Marek |  Kraka, Elfi -  《Journal of Computational Chemistry》 - 2025,46(1) - n/a~n/a - 共11页

摘要:Using the QM/MM methodology and a local mode |  analysis, we investigated a character and a strength of |  FeS bonds of heme groups in oxidized and reduced |  forms of Bacterioferritin from Azotobacter vinelandii | . The strength of the FeS bonds was correlated with a
关键词: bacterioferritin |  heme group |  local mode analysis |  QM/MM |  vibrational spectroscopy

5. Mechanism of Ampicillin Hydrolysis by New Delhi Metallo‐β‐Lactamase 1: Insight From QM/MM MP2 Calculation NSTL国家科技图书文献中心

Rui Lai |  Hui Li -  《Journal of Computational Chemistry》 - 2025,46(1) - n/a~n/a - 共12页

摘要: effective treatment of bacterial infections. QM/MM MP2 | ABSTRACT The New Delhi metallo‐β‐lactamase 1 |  (NDM‐1) can hydrolyze nearly all clinically important |  β‐lactam antibiotics, narrowing the options for |  calculations are performed to reveal the mechanism of
关键词: catalytic mechanism |  kinetic isotope effect |  MP2 |  NDM‐1 |  QM/MM

6. A Robust and Versatile QM/MM Interface for Molecular Dynamics in GROMOS NSTL国家科技图书文献中心

Peter Poliak |  Patrick Bleiziffer... -  《Journal of Computational Chemistry》 - 2025,46(5) - n/a~n/a - 共16页

摘要: and molecular mechanics (QM/MM) within molecular |  enhanced implementation of the QM/MM interface in the |  the QM/MM interface or the MD program itself. The |  improved QM/MM interface enables more advanced |  allows the modeling of QM regions as a part of bigger
关键词: density functional theory |  embedding schemes |  link‐atom scheme |  semiempirical methods |  solvated amino acids |  SPC water

7. Stereo- and Regioselective Metabolism of the Omeprazole Enantiomers by CYP2C19: Insights from Binding Free Energy and QM/MM Calculations in a Curtin-Hammett Framework NSTL国家科技图书文献中心

Xia, Songyan |  Hirao, Hajime -  《ACS catalysis》 - 2025,15(4) - 3284~3294 - 共11页

摘要: (QM/MM) calculations to investigate the stereo- and | Omeprazole, a widely used drug for acid | -related disorders, is administered as a racemic mixture |  of its R- and S-enantiomers. The therapeutic |  efficacy of omeprazole is influenced by the differential
关键词: cytochrome P450 |  drug metabolism |  omeprazole |  the Curtin-Hammett principle |  selectivity |  QM/MM |  thermodynamic integration

8. Electrostatic Edge:Decrypting the Near-Perfect Catalytic Efciency of Fumarase NSTL国家科技图书文献中心

Ritwika Chatterjee |  Reena Balhara... -  《ACS catalysis》 - 2025,15(3) - 1739~1752 - 共14页

摘要: cluster models,and QM/MM calculations.A carbanionic |  by employing DFT calculations,MD simulations,QM | Fumarase is among the most profcient enzymes |  and provides a 1015 fold rate enhancement in |  catalyzing the reversible hydration/dehydration reaction of
关键词: fumarase |  alkene hydration |  QM/MM |  electric feld |  electrostatic preorganization

9. End Group Effects on Anion Binding in Tetraglycine Peptide: A Computational Study NSTL国家科技图书文献中心

Monalisha Sarma |  Manash Pratim Sarmah... -  《Chemistry,an Asian journal》 - 2025,20(1) - e202400880.1~e202400880.10 - 共10页

摘要: mechanics (QM/MM) methods. Symmetry‐adapted perturbation | Abstract The importance of anions in various |  processes has led to a search for molecules that can |  effectively recognize and interact with these anions. This |  study explores how the tetraglycine [(Gly)4] peptide
关键词: DFT |  molecular dynamics |  noncovalent interactions |  ONIOM(QM/MM) |  peptide receptor

10. Effect of pH on azobenzene-4,4'-dicarboxylate/α-CD complex formation. Synthesis, kinetic study and molecular modeling simulations NSTL国家科技图书文献中心

Vettorazzi M. |  Sancho M.I.... -  《Journal of Molecular Liquids》 - 2025,417 - 共9页

摘要:/Molecular Mechanics (QM/MM) calculations were employed | © 2024 Elsevier B.V.The current study focuses |  on the molecular behavior of the azobenzene-4,4 | '-dicarboxylate/α-CD pseudorotaxane and how it is affected by |  changes in pH. A combination of experimental
关键词: Azobenzene |  Formation rate constants |  Molecular dynamics simulation |  Pseudorotaxane |  QM/MM |  α-cyclodextrin
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