标题
Nucleic acid reactivity: Challenges for next-generation semiempirical quantum models
作者
关键词
-
出版物
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 36, Issue 18, Pages 1370-1389
出版商
Wiley
发表日期
2015-05-06
DOI
10.1002/jcc.23933
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- Recent Advances toward a General Purpose Linear-Scaling Quantum Force Field
- (2014) Timothy J. Giese et al. ACCOUNTS OF CHEMICAL RESEARCH
- Nucleic Acid Catalysis: Metals, Nucleobases, and Other Cofactors
- (2014) W. Luke Ward et al. CHEMICAL REVIEWS
- Mechanistic Insights into RNA Transphosphorylation from Kinetic Isotope Effects and Linear Free Energy Relationships of Model Reactions
- (2014) Haoyuan Chen et al. CHEMISTRY-A EUROPEAN JOURNAL
- Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions
- (2014) Timothy J. Giese et al. Journal of Chemical Theory and Computation
- Quantum Mechanical Calculation of Noncovalent Interactions: A Large-Scale Evaluation of PMx, DFT, and SAPT Approaches
- (2014) Amanda Li et al. Journal of Chemical Theory and Computation
- Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods
- (2014) Ming Huang et al. Journal of Chemical Theory and Computation
- Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications
- (2014) Michael Gaus et al. Journal of Chemical Theory and Computation
- Linear free energy relationships in RNA transesterification: theoretical models to aid experimental interpretations
- (2014) Ming Huang et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- On the performance of the semiempirical quantum mechanical PM6 and PM7 methods for noncovalent interactions
- (2013) Jiří Hostaš et al. CHEMICAL PHYSICS LETTERS
- A Caveat on SCC-DFTB and Noncovalent Interactions Involving Sulfur Atoms
- (2013) Riccardo Petraglia et al. Journal of Chemical Theory and Computation
- A Variational Linear-Scaling Framework to Build Practical, Efficient Next-Generation Orbital-Based Quantum Force Fields
- (2013) Timothy J. Giese et al. Journal of Chemical Theory and Computation
- Critical Test of Some Computational Chemistry Methods for Prediction of Gas-Phase Acidities and Basicities
- (2013) Eve Toomsalu et al. Journal of Chemical Theory and Computation
- Accuracy of Quantum Chemical Methods for Large Noncovalent Complexes
- (2013) Robert Sedlak et al. Journal of Chemical Theory and Computation
- Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2'-O-transphosphorylation
- (2013) H. Gu et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Calculations on Noncovalent Interactions and Databases of Benchmark Interaction Energies
- (2012) Pavel Hobza ACCOUNTS OF CHEMICAL RESEARCH
- Parametrization and Benchmark of DFTB3 for Organic Molecules
- (2012) Michael Gaus et al. Journal of Chemical Theory and Computation
- Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters
- (2012) James J. P. Stewart JOURNAL OF MOLECULAR MODELING
- Improved Electronic Properties from Third-Order SCC-DFTB with Cost Efficient Post-SCF Extensions
- (2012) Steve Kaminski et al. JOURNAL OF PHYSICAL CHEMISTRY A
- Extended Polarization in Third-Order SCC-DFTB from Chemical-Potential Equalization
- (2012) Steve Kaminski et al. JOURNAL OF PHYSICAL CHEMISTRY A
- Activated Ribonucleotides Undergo a Sugar Pucker Switch upon Binding to a Single-Stranded RNA Template
- (2012) Na Zhang et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- General Acid–Base Catalysis Mediated by Nucleobases in the Hairpin Ribozyme
- (2012) Stephanie Kath-Schorr et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Biological Phosphoryl-Transfer Reactions: Understanding Mechanism and Catalysis
- (2011) Jonathan K. Lassila et al. Annual Review of Biochemistry
- Benchmarking Semiempirical Methods for Thermochemistry, Kinetics, and Noncovalent Interactions: OMx Methods Are Almost As Accurate and Robust As DFT-GGA Methods for Organic Molecules
- (2011) Martin Korth et al. Journal of Chemical Theory and Computation
- DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB)
- (2011) Michael Gaus et al. Journal of Chemical Theory and Computation
- Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods
- (2011) Jan Řezáč et al. Journal of Chemical Theory and Computation
- Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles
- (2011) Marie Zgarbová et al. Journal of Chemical Theory and Computation
- A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
- (2010) Stefan Grimme et al. JOURNAL OF CHEMICAL PHYSICS
- Reparameterization of RNA χ Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine
- (2010) Ilyas Yildirim et al. Journal of Chemical Theory and Computation
- Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields
- (2010) Martin Korth Journal of Chemical Theory and Computation
- Glycosidic Bond Conformation Preference Plays a Pivotal Role in Catalysis of RNA Pseudouridylation: A Combined Simulation and Structural Study
- (2010) Jing Zhou et al. JOURNAL OF MOLECULAR BIOLOGY
- Accurate Proton Affinity and Gas-Phase Basicity Values for Molecules Important in Biocatalysis
- (2010) Adam Moser et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Ring Puckering: A Metric for Evaluating the Accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB Carbohydrate QM/MM Simulations
- (2010) Christopher B. Barnett et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Do the hairpin and VS ribozymes share a common catalytic mechanism based on general acid-base catalysis? A critical assessment of available experimental data
- (2010) T. J. Wilson et al. RNA
- Accurate dipole polarizabilities for water clusters n=2–12 at the coupled-cluster level of theory and benchmarking of various density functionals
- (2009) Jeff R. Hammond et al. JOURNAL OF CHEMICAL PHYSICS
- Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes
- (2009) Jan Řezáč et al. Journal of Chemical Theory and Computation
- A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods
- (2009) Martin Korth et al. Journal of Chemical Theory and Computation
- CAN SEMIEMPIRICAL QUANTUM MODELS CALCULATE THE BINDING ENERGY OF HYDROGEN BONDING FOR BIOLOGICAL SYSTEMS?
- (2009) FENG FENG et al. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY
- Empirically corrected DFT and semi-empirical methods for non-bonding interactions
- (2009) Michael E. Foster et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Ab initio and ABEEM/MM fluctuating charge model studies of dimethyl phosphate anion in a microhydrated environment
- (2009) Fang-Fang Wang et al. THEORETICAL CHEMISTRY ACCOUNTS
- Solvent Structure and Hammerhead Ribozyme Catalysis
- (2008) Monika Martick et al. CHEMISTRY & BIOLOGY
- Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems (www.begdb.com): A Users Manual and Examples
- (2008) Jan Řezáč et al. COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS
- Application of the PM6 method to modeling proteins
- (2008) James J. P. Stewart JOURNAL OF MOLECULAR MODELING
- Mechanistic Characterization of the HDV Genomic Ribozyme: Solvent Isotope Effects and Proton Inventories in the Absence of Divalent Metal Ions Support C75 as the General Acid
- (2008) Andrea L. Cerrone-Szakal et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now