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■ Abbreviation / Long Form : QM/MM / quantum mechanics/molecular mechanics

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Total Number of Papers: 1391
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Abbreviation:   QM/MM  (>> Co-occurring Abbreviation)
Long Form:   quantum mechanics/molecular mechanics
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No. Year Title Co-occurring Abbreviation
2020 A Potent Host Defense Peptide Triggers DNA Damage and Is Active against Multidrug-Resistant Gram-Negative Pathogens. BCP, CD, HDP, TUNEL
2020 Accelerated Computation of Free Energy Profile at Ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference Potential. 3. Gaussian Smoothing on Density-of-States. CV, DOS, PMF
2020 Accurate Description of Cation-pi Interactions in Proteins with a Nonpolarizable Force Field at No Additional Cost. LJ, NBFIX, PMFs
2020 Accurate Diels-Alder Energies and Endo Selectivity in Ionic Liquids Using the OPLS-VSIL Force Field. BMIM, FEP/MC, OPLS-VSIL
2020 An assessment of water placement algorithms in quantum mechanics/molecular mechanics modeling: the case of rhodopsins' first spectral absorption band maxima. ---
2020 Assessing the validity of DLPNO-CCSD(T) in the calculation of activation and reaction energies of ubiquitous enzymatic reactions. CBS, DFs, DFT
2020 Assessment of the Cruzain Cysteine Protease Reversible and Irreversible Covalent Inhibition Mechanism. ITC, MD, T. cruzi
2020 Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes. bR, DFTB, FMO, LC, LC-TD-DFTB, LH, ppR, Rh, TD
2020 Bioengineering of Cytochrome P450 OleTJE: How Does Substrate Positioning Affect the Product Distributions? ---
10  2020 Bioluminescent Nanoluciferase-Furimamide Complex: A Theoretical Study on Different Protonation States. CT, ESs, MD, TDDFT
11  2020 Both Configuration and QM Region Size Matter: Zinc Stability in QM/MM Models of DNA Methyltransferase. ---
12  2020 Calculation of Linear and Non-linear Electric Response Properties of Systems in Aqueous Solution: A Polarizable Quantum/Classical Approach with Quantum Repulsion Effects. ---
13  2020 Catalysis by the Non-Heme Iron(II) Histone Demethylase PHF8 Involves Iron Center Rearrangement and Conformational Modulation of Substrate Orientation. 2OG, MD
14  2020 Caught in the Hinact : Crystal Structure and Spectroscopy Reveal a Sulfur Bound to the Active Site of an O2 -stable State of [FeFe] Hydrogenase. IR, NRVS, RR, XAS
15  2020 Chlorination versus hydroxylation selectivity mediated by the non-heme iron halogenase WelO5. ---
16  2020 Combined Machine Learning and Molecular Modelling Workflow for the Recognition of Potentially Novel Fungicides. FS-LM-RF
17  2020 Comparison of Free-Energy Methods to Calculate the Barriers for the Nucleophilic Substitution of Alkyl Halides by Hydroxide. DFT, EE, MCC, NMA, PMF, SCC-DFTB
18  2020 Computational and Spectroscopic Characterization of the Photocycle of an Artificial Rhodopsin. ABP, RPSB
19  2020 Computational Modeling of the Disulfide Cross-Linking Reaction. DFT
20  2020 Computational Study on the Charge Transport and Optical Spectra of Anthracene Derivatives in Aggregates. FlAnt, OLETs, PCM
21  2020 Counterion-Mediated Crossing of the Cyanine Limit in Crystals and Fluid Solution: Bond Length Alternation and Spectral Broadening Unveiled by Quantum Chemistry. DFT, MD
22  2020 Critical evaluation of anharmonicity and configurational averaging in QM/MM modelling of equilibrium isotope effects. EIE
23  2020 Current Status of AMOEBA-IL: A Multipolar/Polarizable Force Field for Ionic Liquids. QM
24  2020 Degradation mechanism for Zearalenone ring-cleavage by Zearalenone hydrolase RmZHD: A QM/MM study. ZEN
25  2020 Degradation mechanism of biphenyl and 4-4'-dichlorobiphenyl cis-dihydroxylation by non-heme 2,3 dioxygenases BphA: A QM/MM approach. BphA
26  2020 Delocalization effects in singlet fission: Comparing models with two and three interacting molecules. ---
27  2020 Density Functional Theory-Based Quantum Mechanics/Coarse-Grained Molecular Mechanics: Theory and Implementation. DFT
28  2020 Design and SAR Analysis of Covalent Inhibitors Driven by Hybrid QM/MM Simulations. EGFR, FAAH
29  2020 Design, synthesis, anti-tobacco mosaic viral and molecule docking simulations of urea/thiourea derivatives of 2-(piperazine-1-yl)-pyrimidine and 1-(4-Fluoro/4-Chloro phenyl)-piperazine and 1-(4-Chloro phenyl)-piperazine - A study. FTIR, NMR, TMV
30  2020 Determinants of the Lead(II) Affinity in pbrR Protein: A Computational Study. ---
31  2020 DFFR: A New Method for High-Throughput Recalibration of Automatic Force-Fields for Drugs. DFFR, DFT/SCRF
32  2020 DFTB/MM Molecular Dynamics Simulations of the FMO Light-Harvesting Complex. DFTB, FMO
33  2020 Dynamic Structure and Stability of DNA Duplexes Bearing a Dinuclear Hg(II)-Mediated Base Pair. QM
34  2020 Efficient Analytic Second Derivative of Electrostatic Embedding QM/MM Energy: Normal Mode Analysis of Plant Cryptochrome. EE
35  2020 Elucidating the role of structural fluctuations, and intermolecular and vibronic interactions in the spectroscopic response of a bacteriophytochrome. ---
36  2020 Embedded Mean-Field Theory for Solution-Phase Transition-Metal Polyolefin Catalysis. EMFT, MD
37  2020 Enabling Control over Mechanical Conformity and Luminescence in Molecular Crystals: Interaction Engineering in Action. ---
38  2020 Environmental Effects on Guanine-Thymine Mispair Tautomerization Explored with Quantum Mechanical/Molecular Mechanical Free Energy Simulations. GT, WC-like, wG-T
39  2020 Evaluating QM/MM Free Energy Surfaces for Ranking Cysteine Protease Covalent Inhibitors. ---
40  2020 Examining sterically demanding lysine analogs for histone lysine methyltransferase catalysis. SAM
41  2020 Exchange Repulsion in Quantum Mechanical/Effective Fragment Potential Excitation Energies: Beyond Polarizable Embedding. CIS, EFP
42  2020 Excimer Intermediates en Route to Long-Lived Charge-Transfer States in Single-Stranded Adenine DNA as Revealed by Nonadiabatic Dynamics. ---
43  2020 Experimental and theoretical affinity and catalysis studies between halogenated phenols and peroxidases: Understanding the bioremediation potential. 2,4-DCP, 4-BP, DFT, HRP
44  2020 Exploring Chloride Selectivity and Halogenase Regioselectivity of the SalL Enzyme through Quantum Mechanical/Molecular Mechanical Modeling. ---
45  2020 Exploring the Chemoselectivity towards Cysteine Arylation by Cyclometallated AuIII Compounds: New Mechanistic Insights. DFT, HR-LC-ESI-MS
46  2020 Extending scaled-interaction adaptive-partitioning QM/MM to covalently bonded systems. AP, PES
47  2020 Facile Synthesis and Metabolic Incorporation of m-DAP Bioisosteres Into Cell Walls of Live Bacteria. m-CYT, m-DAP, MD, PG, TP
48  2020 Formation of an unusual glutamine tautomer in a blue light using flavin photocycle characterizes the light-adapted state. BLUF, PCET
49  2020 Insight into the Catalytic Mechanism of GH11 Xylanase: Computational Analysis of Substrate Distortion Based on a Neutron Structure. ES
50  2020 Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires. ATP, cAMP, ES, MD
51  2020 Mechanistic Insights into the Oxidative Rearrangement Catalyzed by the Unprecedented Dioxygenase ChaP Involved in Chartreusin Biosynthesis. PCET, VOC
52  2020 Mechanistic Insights into the Oxidative Ring Expansion from Penicillin N to Deacetoxycephalosporin C Catalyzed by a Nonheme Iron(II) and alpha-KG-Dependent Oxygenase. DAOC, DAOCS, PEN N
53  2020 Mechanistic study of the ATP hydrolysis reaction in dynein motor protein. ATP
54  2020 Modeling the Hydrolysis of Iron-Sulfur Clusters. ---
55  2020 Molecular mechanism of Be2+-ion binding to HLA-DP2: tetrahedral coordination, conformational changes and multi-ion binding. CBD, MD, TCR
56  2020 Monophenolase and catecholase activity of Aspergillus oryzae catechol oxidase: insights from hybrid QM/MM calculations. ---
57  2020 Multiple Reaction Pathways in the Morphinone Reductase-Catalyzed Hydride Transfer Reaction. MR, TPS
58  2020 Multiscale computation delivers organophosphorus reactivity and stereoselectivity to immunoglobulin scavengers. DFT-b, Ig
59  2020 N2H2 binding to the nitrogenase FeMo cluster studied by QM/MM methods. ---
60  2020 On-the-fly determination of active region centers in adaptive-partitioning QM/MM. AC, AP, MD
61  2020 Orientation of Ligand Field for Dangling Manganese in Photosynthetic Oxygen-Evolving Complex of Photosystem II. ---
62  2020 Potential of Mean Force Calculations for an SN2 Fluorination Reaction in Five Different Imidazolium Ionic Liquid Solvents Using Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulations. FF, ILs, NCI, PM6
63  2020 Protein Matrix Control of Reaction Center Excitation in Photosystem II. DLPNO, PSII
64  2020 QM and QM/MM umbrella sampling MD study of the formation of Hg(II)-thymine bond: Model for evaluation of the reaction energy profiles in solutions with constant pH. ---
65  2020 Quantum mechanical/molecular mechanical trajectory surface hopping molecular dynamics simulation by spin-flip time-dependent density functional theory. SF-TDDFT
66  2020 Red, Orange, Green: Light- and Temperature-Dependent Color Tuning in a Cyanobacteriochrome. CBCRs, RR, UV-vis
67  2020 Redox Properties of Native and Damaged DNA from Mixed Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations. 8-oxoG
68  2020 Reduced scaling extended multi-state CASPT2 (XMS-CASPT2) using supporting subspaces and tensor hyper-contraction. SS-CASPT2, XMS-CASPT2
69  2020 Role of Microsolvation and Quantum Effects in the Accurate Prediction of Kinetic Isotope Effects: The Case of Hydrogen Atom Abstraction in Ethanol by Atomic Hydrogen in Aqueous Solution. DFT, KIE, MP-VTST
70  2020 Role of Structural Dynamics in Selectivity and Mechanism of Non-heme Fe(II) and 2-Oxoglutarate-Dependent Oxygenases Involved in DNA Repair. 2OG, m3C, MD
71  2020 Simulating the Nonadiabatic Relaxation Dynamics of 4-(N,N-Dimethylamino)benzonitrile (DMABN) in Polar Solution. DMABN, LE, RICT, SOS, TICT
72  2020 Solid-state effect on luminescent properties of thermally activated delayed fluorescence molecule with aggregation induced emission: A theoretical perspective. AIE, HR, PCM, TADF, THF, TVCF
73  2020 Solvation Free Energies and Adsorption Energies at the Metal/Water Interface from Hybrid Quantum-Mechanical/Molecular Mechanics Simulations. ---
74  2020 Stabilization of the Triplet Biradical Intermediate of 5-Methylcytosine Enhances Cyclobutane Pyrimidine Dimer (CPD) Formation in DNA. 5mC, CPD
75  2020 Steady-State Kinetics of Enzyme-Catalyzed Hydrolysis of Echothiophate, a P-S Bonded Organophosphorus as Monitored by Spectrofluorimetry. OP
76  2020 Substitution effect on luminescent property of thermally activated delayed fluorescence molecule with aggregation induced emission: A QM/MM study. AIE, D-A-D, DMAC, ISC, OLEDs, PCM, PFBP, RISC, RMSD, SOC, TADF
77  2020 The Impact of Electron Correlation on Describing QM/MM Interactions in the Attendant Molecular Dynamics Simulations of CO in Myoglobin. MbCO, MD
78  2020 Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase. EPR
79  2020 Two-Photon Absorption Cross-Sections in Fluorescent Proteins Containing Non-canonical Chromophores Using Polarizable QM/MM. FPs, nCCs, PE
80  2020 Ultrafast Backbone Protonation in Channelrhodopsin-1 Captured by Polarization Resolved Fs Vis-pump-IR-Probe Spectroscopy and Computational Methods. ChR
81  2020 Using Atomic Confining Potentials for Geometry Optimization and Vibrational Frequency Calculations in Quantum-Chemical Models of Enzyme Active Sites. ---
82  2020 What Is the Structure of the E4 Intermediate in Nitrogenase? DFT
83  2020 Why is CarH photolytically active in comparison to other B12-dependent enzymes? AdoCbl, Cbls, PESs
84  2019 A full additive QM/MM scheme for the computation of molecular crystals with extension to many-body expansions. ---
85  2019 A noniterative mean-field QM/MM-type approach with a linear response approximation toward an efficient free-energy evaluation. FT, LRA, MC-MOZ-SCF, RSHE, SFE
86  2019 A QM/MM study on ethene and benzene oxidation using silica-supported chromium trioxide. ---
87  2019 A unique activation-promotion mechanism of the influenza B M2 proton channel uncovered by multiscale simulations. BM2, CpHMD
88  2019 a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement. ARM
89  2019 Ab initio quantum mechanics/molecular mechanics method with periodic boundaries employing Ewald summation technique to electron-charge interaction: Treatment of the surface-dipole term. PBC
90  2019 Acceleration of Mechanistic Investigation of Plant Secondary Metabolism Based on Computational Chemistry. DFT, MD
91  2019 Adaptive Partitioning QM/MM for Molecular Dynamics Simulations: 6. Proton Transport through a Biological Channel. CLC
92  2019 Analytic gradient for the QM/MM-Ewald method using charges derived from the electrostatic potential: Theory, implementation, and application to ab initio molecular dynamics simulation of the aqueous electron. ---
93  2019 Anharmonic Vibrational Analysis of Biomolecules and Solvated Molecules Using Hybrid QM/MM Computations. MD, P450nor, PES, VSCF
94  2019 Assessment of MC-PDFT Excitation Energies for a Set of QM/MM Models of Rhodopsins. ARM, CASSCF, MC-PDFT
95  2019 Assessment of Multi-Scale Approaches for Computing UV-Vis Spectra in Condensed Phases: Toward an Effective yet Reliable Integration of Variational and Perturbative QM/MM Approaches. MD
96  2019 Binding and Catalytic Mechanisms of Veratryl Alcohol Oxidation by Lignin Peroxidase: A Theoretical and Experimental Study. LiP, SQM, VA
97  2019 Carcinogenic Metabolic Activation Process of Naphthalene by the Cytochrome P450 Enzyme 1B1: A Computational Study. ---
98  2019 Catalytic mechanism of the PrhA (V150L/A232S) double mutant involved in the fungal meroterpenoid biosynthetic pathway: a QM/MM study. ---
99  2019 Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology. ---
100  2019 Computational insight into the interaction of oxaliplatin with insulin. MD