Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM.

scientific article published in May 2006

Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM. is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1021/CT050289G
P8608Fatcat IDrelease_xdf4br6iwvgl5okgkgnxze2wyi
P698PubMed publication ID26626688
P5875ResearchGate publication ID215656228

P50authorJohn A. MontgomeryQ51630599
Thom VrevenQ64495234
P2093author name stringKeiji Morokuma
Michael J Frisch
István Komáromi
K Suzie Byun
Stefan Dapprich
P433issue3
P921main subjectquantum mechanicsQ944
P304page(s)815-826
P577publication date2006-05-01
P1433published inJournal of Chemical Theory and ComputationQ1768377
P1476titleCombining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM.
P478volume2

Reverse relations

cites work (P2860)
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Q54993477A quantum mechanical computational method for modeling electrostatic and solvation effects of protein.
Q46704195A study of the binding energies of efavirenz to wild-type and K103N/Y181C HIV-1 reverse transcriptase based on the ONIOM method
Q56421693A supramolecular porphyrin–ferrocene–fullerene triad
Q46567783A theoretical study of nitric oxide adsorption and dissociation on copper-exchanged zeolites SSZ-13 and SAPO-34: the impact of framework acid-base properties
Q40027168A two-layer ONIOM study of thiophene cracking catalyzed by proton- and cation-exchanged FAU zeolite
Q57278610A variational formulation of the polarizable continuum model
Q52641554An acidic pH independent piperazine-TPE AIEgen as a unique bioprobe for lysosome tracing.
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Q48110381An insight to the molecular interactions of the FDA approved HIV PR drugs against L38L↑N↑L PR mutant
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Q58699233Applications of Potential Energy Surfaces in the Study of Enzymatic Reactions
Q38210222Applications of density functional theory to iron-containing molecules of bioinorganic interest
Q38280096Applications of quantum mechanical/molecular mechanical methods to the chemical insertion step of DNA and RNA polymerization
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Q35081707Calculated vibrational properties of pigments in protein binding sites
Q57397719Carotenoids as a Shortcut for Chlorophyll Soret-to-Q Band Energy Flow
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Q39646923Characterisation of tri-ruthenium dihydride complexes through the computation of NMR parameters
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Q41095160Chemical feasibility of the general acid/base mechanism of glmS ribozyme self-cleavage
Q56782332Cisplatin cytotoxicity: a theoretical study of induced mutations
Q47292361Co+-H interaction inspired alternate coordination geometries of biologically important cob(I)alamin: possible structural and mechanistic consequences for methyltransferases
Q37397707Color tuning in short wavelength-sensitive human and mouse visual pigments: ab initio quantum mechanics/molecular mechanics studies.
Q92932302Comparative Computational Approach To Study Enzyme Reactions Using QM and QM-MM Methods
Q36706730Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints
Q37133235Comparison of calculated and experimental isotope edited FTIR difference spectra for purple bacterial photosynthetic reaction centers with different quinones incorporated into the QA binding site
Q35877348Computational Prediction of One-Step Synthesis of Seven-membered Fused Rings by (5+2) Cycloaddition Utilising Cycloalkenes
Q44712236Computational evidence for structural consequences of kiteplatin damage on DNA.
Q38164447Computational modelling of oxygenation processes in enzymes and biomimetic model complexes
Q90534455Conformational diversity induces nanosecond-timescale chemical disorder in the HIV-1 protease reaction pathway
Q91450648Conformations and Binding Properties of Thiametoxam and Clothianidin Neonicotinoid Insecticides to Nicotinic Acetylcholine Receptors: The Contribution of σ-Hole Interactions
Q60799131Conversion of Methyl Mercaptan to Hydrocarbons over H-ZSM-5 Zeolite: DFT/BOMD Study
Q57391526Copper–amyloid-β complex may catalyze peroxynitrite production in brain: evidence from molecular modeling
Q51621832Correlation regions within a localized molecular orbital approach.
Q42620886Covalent inhibitors of fatty acid amide hydrolase: a rationale for the activity of piperidine and piperazine aryl ureas.
Q90470987Cyclic Changes in Active Site Polarization and Dynamics Drive the 'Ping-pong' Kinetics in NRH:Quinone Oxidoreductase 2: An Insight from QM/MM Simulations
Q101216905Demystifying the catalytic pathway of Mycobacterium tuberculosis isocitrate lyase
Q51641598Dioxygen Binding in the Active Site of Histone Demethylase JMJD2A and the Role of the Protein Environment.
Q28740931Double mutation in photosystem II reaction centers and elevated CO2 grant thermotolerance to mesophilic cyanobacterium
Q34721063Double-lock ratchet mechanism revealing the role of alphaSER-344 in FoF1 ATP synthase
Q33786653Drawing the Retinal Out of Its Comfort Zone: An ONIOM(QM/MM) Study of Mutant Squid Rhodopsin
Q60777668Electrochemical and Catalytic Studies of a Manganese(III)Complex with a Tetradentate Schiff-Base Ligand Encapsulated in NaY Zeolite
Q27316298Elucidation of Enzymatic Mechanism of Phenazine Biosynthetic Protein PhzF Using QM/MM and MD Simulations
Q51601126Evaluating the enthalpic contribution to ligand binding using QM calculations: effect of methodology on geometries and interaction energies.
Q53084565Exploring chemical reaction mechanisms through harmonic Fourier beads path optimization.
Q41816835Exploring the full catalytic cycle of rhodium(i)-BINAP-catalysed isomerisation of allylic amines: a graph theory approach for path optimisation.
Q49979464Exploring what prompts ITIC to become a superior acceptor in organic solar cell by combining molecular dynamics simulation with quantum chemistry calculation.
Q46401634Exposing the G-quadruplex to electric fields: the role played by telomeres in the propagation of DNA errors
Q30356246Factors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations.
Q37337277Fighting Cancer with Transition Metal Complexes: From Naked DNA to Protein and Chromatin Targeting Strategies
Q44943134Formation of a thymine-Hg(II)-thymine metal-mediated DNA base pair: proposal and theoretical calculation of the reaction pathway
Q42185455Full-Quantum chemical calculation of the absorption maximum of bacteriorhodopsin: a comprehensive analysis of the amino acid residues contributing to the opsin shift
Q44431189Gaining insight into the chemistry of lipoxygenases: a computational investigation into the catalytic mechanism of (8R)-lipoxygenase
Q51095984Genetically introduced hydrogen bond interactions reveal an asymmetric charge distribution on the radical cation of the special-pair chlorophyll P680.
Q28741210H-bond network around retinal regulates the evolution of ultraviolet and violet vision
Q43569323Halogen bonding in ligand-receptor systems in the framework of classical force fields
Q37596616Histidine Orientation Modulates the Structure and Dynamics of a de Novo Metalloenzyme Active Site
Q30370777Human 3-hydroxyanthranilate 3,4-dioxygenase () dynamics and reaction, a multilevel computational study.
Q36238170Hybrid dynamics simulation engine for metalloproteins
Q41788791Hydrogen bonding and spin density distribution in the Qb semiquinone of bacterial reaction centers and comparison with the Qa site.
Q36595184Hydrogen bonding between the Q(B) site ubisemiquinone and Ser-L223 in the bacterial reaction center: a combined spectroscopic and computational perspective
Q64256621Insight into Structural Characteristics of Protein-Substrate Interaction in Pimaricin Thioesterase
Q59757976Insight into the reaction mechanism of cis,cis-muconate lactonizing enzymes: a DFT QM/MM study
Q38714551Interstrand DNA covalent binding of two dinuclear Ru(ii) complexes. Influence of the extra ring of the bridging ligand on the DNA interaction and cytotoxic activity
Q45527739Investigation of the hydroxylation mechanism of noncoupled copper oxygenases by ab initio molecular dynamics simulations.
Q39900733Is it possible to reverse aged acetylcholinesterase inhibited by organophosphorus compounds? Insight from the theoretical study.
Q38210405Learning from photobiology how to design molecular devices using a computer
Q47986931Ligand-induced conformational preorganization of loops of c-MYC G-quadruplex DNA and its implications in structure-specific drug design
Q42938333Link atom bond length effect in ONIOM excited state calculations
Q35052399MSCALE: A General Utility for Multiscale Modeling.
Q28082151Mathematical and computational modeling in biology at multiple scales
Q33652126Matrix metalloproteinase 2 (MMP2) inhibition: DFT and QM/MM studies of the deprotonation-initialized ring-opening reaction of the sulfoxide analogue of SB-3CT.
Q33638905Matrix metalloproteinase 2 inhibition: combined quantum mechanics and molecular mechanics studies of the inhibition mechanism of (4-phenoxyphenylsulfonyl)methylthiirane and its oxirane analogue.
Q37160459Mechanism of spectral tuning going from retinal in vacuo to bovine rhodopsin and its mutants: multireference ab initio quantum mechanics/molecular mechanics studies.
Q49852856Mechanism of ultrafast non-reactive deactivation of the retinal chromophore in non-polar solvents.
Q88342046Mechanistic Explanation of the Weak Carbonic Anhydrase's Esterase Activity
Q48023868Mechanistic insights on the reduction of glutathione disulfide by protein disulfide isomerase
Q44298845Mechanistic investigation of methanol to propene conversion catalyzed by H-beta zeolite: a two-layer ONIOM study
Q28816938MoD-QM/MM Structural Refinement Method: Characterization of Hydrogen Bonding in the Oxytricha nova G-Quadruplex
Q57278584Modeling environment effects on spectroscopies through QM/classical models
Q48052827Modeling the archetype cysteine protease reaction using dispersion corrected density functional methods in ONIOM-type hybrid QM/MM calculations; the proteolytic reaction of papain
Q40440496Modifications of the chromophore of Spinach aptamer based on QM:MM calculations
Q26743663Molecular docking as a popular tool in drug design, an in silico travel
Q62631468Molecular insight on the non-covalent interactions between carbapenems and l,d-transpeptidase 2 from Mycobacterium tuberculosis: ONIOM study
Q36467657Molecular modeling of the reaction pathway and hydride transfer reactions of HMG-CoA reductase.
Q52838984Molecular recognition of thiaclopride by Aplysia californica AChBP: new insights from a computational investigation.
Q64107374Mutation Spectrum in TPO Gene of Bangladeshi Patients with Thyroid Dyshormonogenesis and Analysis of the Effects of Different Mutations on the Structural Features and Functions of TPO Protein through Approach
Q89588813Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets
Q51358728ONIOM approach for non-adiabatic on-the-fly molecular dynamics demonstrated for the backbone controlled Dewar valence isomerization.
Q55421368On the Difference Between Additive and Subtractive QM/MM Calculations.
Q60960944On the Inhibition Mechanism of Glutathione Transferase P1 by Piperlongumine. Insight From Theory
Q44453688On the optical absorption of the anionic GFP chromophore in vacuum, solution, and protein.
Q90403990Palladium-catalyzed regioselective and stereo-invertive ring-opening borylation of 2-arylaziridines with bis(pinacolato)diboron: experimental and computational studies
Q38179927Pharmacoinformatic approaches to understand complexation of dendrimeric nanoparticles with drugs
Q50863670Photoprotection and triplet energy transfer in higher plants: the role of electronic and nuclear fluctuations.
Q34152194Post-protein binding metal-mediated coupling of an acridine orange-based fluorophore.
Q35531910Preparation of multi-coloured different sized fluorescent gold clusters from blue to NIR, structural analysis of the blue emitting Au7 cluster, and cell-imaging by the NIR gold cluster.
Q48059931Probing the remarkable thermal kinetics of visual rhodopsin with E181Q and S186A mutants.
Q64915256QM Cluster or QM/MM in Computational Enzymology: The Test Case of LigW-Decarboxylase.
Q88586255QM/MM Investigation for Protonation States in a Bilin Reductase PcyA-Biliverdin IXɑ Complex
Q88726360QM/MM Simulations with the Gaussian Electrostatic Model: A Density-based Polarizable Potential
Q34289671QM/MM Studies of the Matrix Metalloproteinase 2 (MMP2) Inhibition Mechanism of (S)-SB-3CT and its Oxirane Analogue
Q34334374QM/MM Study of Dehydro and Dihydro β-Ionone Retinal Analogues in Squid and Bovine Rhodopsins: Implications for Vision in Salamander Rhodopsin
Q58486657QM/MM description of platinum–DNA interactions: comparison of binding and DNA distortion of five drugs
Q45934645QM/MM investigation into binding of square-planar platinum complexes to DNA fragments.
Q57971613QM/MM-Methoden für biomolekulare Systeme
Q46529065QM/QM studies for Michael reaction in coronavirus main protease (3CL Pro).
Q51896520QM:QM electronic embedding using Mulliken atomic charges: energies and analytic gradients in an ONIOM framework.
Q51549381QM:QM embedding using electronic densities within an ONIOM framework: energies and analytic gradients.
Q57015760Quantum Mechanics/Molecular Mechanics Studies on the Mechanism of Action of Cofactor Pyridoxal 5′-Phosphate in Ornithine 4,5-Aminomutase
Q35643920Quantum mechanical/molecular mechanical structure, enantioselectivity, and spectroscopy of hydroxyretinals and insights into the evolution of color vision in small white butterflies
Q37129262Quantum mechanics/molecular mechanics electrostatic embedding with continuous and discrete functions
Q34624976Quantum mechanics/molecular mechanics investigation of the mechanism of phosphate transfer in human uridine-cytidine kinase 2.
Q37417927Quantum mechanics/molecular mechanics simulation of the ligand vibrations of the water-oxidizing Mn4CaO5 cluster in photosystem II.
Q38775359Raman optical activity of tetra-alanine in the poly(l-proline) II type peptide conformation
Q36598084Rate of hydrolysis in ATP synthase is fine-tuned by α-subunit motif controlling active site conformation
Q48042543Reaction Mechanism of Mycobacterium Tuberculosis Glutamine Synthetase Using Quantum Mechanics/Molecular Mechanics Calculations
Q37479261Recent developments of the quantum chemical cluster approach for modeling enzyme reactions
Q36103096Requirement for transient metal ions revealed through computational analysis for DNA polymerase going in reverse
Q33557324Revealing the role of the product metal in DNA polymerase β catalysis
Q92941158Roles of Closed- and Open-Loop Conformations in Large-Scale Structural Transitions of l-Lactate Dehydrogenase
Q57163600Self-healing mechanism of metallopolymers investigated by QM/MM simulations and Raman spectroscopy
Q31033197Simulation of Raman optical activity of multi-component monosaccharide samples.
Q36800693Spectral tuning in visual pigments: an ONIOM(QM:MM) study on bovine rhodopsin and its mutants.
Q36753144Spin trapping of hydroperoxyl radical by a cyclic nitrone conjugated to β-cyclodextrin: a computational study
Q51134892Study of mutation and misfolding of Cu-Zn SOD1 protein.
Q45903781Substrate recognition by norovirus polymerase: microsecond molecular dynamics study.
Q37632316Subsystem-based theoretical spectroscopy of biomolecules and biomolecular assemblies
Q90442542Surprising solvent-induced structural rearrangements in large [N···I+···N] halogen-bonded supramolecular capsules: an ion mobility-mass spectrometry study
Q35211506Synthesis, crystal structure and biological activity of 2-hydroxyethylammonium salt of p-aminobenzoic acid
Q35872631Targeting druggable enzymome by exploiting natural medicines: An in silico-in vitro integrated approach to combating multidrug resistance in bacterial infection
Q92999293The Driving Force for the Acylation of β-Lactam Antibiotics by L,D-Transpeptidase 2: Quantum Mechanics/Molecular Mechanics (QM/MM) Study
Q37638321The MOD-QM/MM Method: Applications to Studies of Photosystem II and DNA G-Quadruplexes
Q27679688The Mechanism of the Amidases: MUTATING THE GLUTAMATE ADJACENT TO THE CATALYTIC TRIAD INACTIVATES THE ENZYME DUE TO SUBSTRATE MISPOSITIONING
Q54102696The catalytic formation of leukotriene C4: a critical step in inflammatory processes.
Q62631444The catalytic role of water in the binding site of l,d-transpeptidase 2 within acylation mechanism: A QM/MM (ONIOM) modelling
Q49010422The computational prediction of Raman and ROA spectra of charged histidine tautomers in aqueous solution.
Q39917513The contribution of computational studies to organometallic catalysis: descriptors, mechanisms and models
Q35377798The entropic contributions in vitamin B12 enzymes still reflect the electrostatic paradigm
Q52575993The mechanism of a green fluorescent protein proton shuttle unveiled in the time-resolved frequency domain by excited state ab initio dynamics.
Q51180497The multi-configuration self-consistent field method within a polarizable embedded framework.
Q53393935The small-molecule inhibitor selectivity between IKKα and IKKβ kinases in NF-κB signaling pathway.
Q41678580The structural and energetic aspects of substrate binding and the mechanism of action of the DapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) investigated using a hybrid QM/MM method
Q90666288Theoretical Investigation of the Structural Characteristics in the Active State of Akt1 Kinase
Q37366654Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.
Q37483257Theoretical studies of structure, function and reactivity of molecules--a personal account
Q46823435Theoretical study on the mechanism of a ring-opening reaction of oxirane by the active-site aspartic dyad of HIV-1 protease.
Q46344194Triplet-triplet energy transfer in artificial and natural photosynthetic antennas
Q90402218Uncovering dark multichromophoric states in Peridinin-Chlorophyll-Protein
Q51786495Using the ONIOM hybrid method to apply equation of motion CCSD to larger systems: benchmarking and comparison with time-dependent density functional theory, configuration interaction singles, and time-dependent Hartree-Fock.
Q43120251Vibrational analysis on the revised potential energy curve of the low-barrier hydrogen bond in photoactive yellow protein.
Q39721582Visible and ultraviolet spectroscopy of gas phase protein ions.
Q34326045Zwitterionic versus canonical amino acids over the various defects in zeolites: a two-layer ONIOM calculation
Q37714218pH-dependent coordination of Pb2+ to metallothionein2: structures and insight into lead detoxification

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