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1. Full Text MMPBSA.py: An efficient program for end-state free energy calculations
by Miller III, Bill R and McGee, T. Dwight and Swails, Jason M and Homeyer, Nadine and Gohlke, Holger and Roitberg, Adrian E
Journal of Chemical Theory and Computation, ISSN 1549-9618, 09/2012, Volume 8, Issue 9, pp. 3314 - 3321
MM-PBSA is a post-processing end-state method to calculate free energies of molecules in solution. MMPBSA.py is a program written in Python for streamlining... 
CONTINUUM SOLVENT | DOCKING | DNA | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | QM/MM | BINDING | MOLECULAR-MECHANICS
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2. Full Text Cover Feature: Photochemical Formation of Cyclobutane Pyrimidine Dimers in DNA through Electron Transfer from a Flanking Base (ChemPhysChem 13/2018)
by Lee, Wook and Matsika, Spiridoula
ChemPhysChem, ISSN 1439-4235, 07/2018, Volume 19, Issue 13, pp. 1550 - 1550
The Cover Feature illustrates a new photo‐induced triplet pathway for cyclobutane pyrimidine dimer (CPD) formation in DNA. Similar to quenching or repair... 
QM/MM | electron transfer | photochemistry | DNA | exciplex
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3. Full Text Quantum mechanics/molecular mechanics simulation of the ligand vibrations of the water-oxidizing MnM4CaO5 cluster in photosystem II
by Nakamura, Shin and Noguchi, Takumi
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 11/2016, Volume 113, Issue 45, pp. 12727 - 12732
FTIR | Water oxidation | QM/MM | Carboxylate ligand | Photosynthesis
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4. Full Text Theoretical perspective of the excited state intramolecular proton transfer for a compound with aggregation induced emission in the solid phase
by Lin, Lili and Fan, Jianzhong and Cai, Lei and Wang, Chuan-Kui
RSC Advances, ISSN 2046-2069, 09/2017, Volume 7, Issue 7, pp. 4489 - 4496
In this study, we have investigated the excited state intramolecular proton transfer (ESIPT) for the diphenylethylene-modified 2-(2-hydroxyphenyl)benzothiazole... 
CHEMISTRY, MULTIDISCIPLINARY | QM/MM | SINGLE
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5. Full Text DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB)
by Gaus, Michael and Cui, Qiang and Elstner, Marcus
Journal of Chemical Theory and Computation, ISSN 1549-9618, 04/2011, Volume 7, Issue 4, pp. 931 - 948
The self-consistent-charge density-functional tight-binding method (SCC-DFTB) is an approximate quantum chemical method derived from density functional theory... 
PHOSPHORYL TRANSFER | MOLECULAR-MODEL | CARBONIC-ANHYDRASE | WATER DIMER | SEMIEMPIRICAL METHODS | COMPLEX MATERIALS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | PROTON-TRANSFER | FORCE-FIELDS | BACTERIORHODOPSIN | QM/MM SIMULATIONS
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6. Full Text Theoretical perspective of the excited state intramolecular proton transfer for a compound with aggregation induced emission in the solid phase
by Lin, Lili and Fan, Jianzhong and Cai, Lei and Wang, Chuan-Kui
RSC Advances, ISSN 2046-2069, 2017, Volume 7, Issue 70, pp. 44089 - 44096
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7. Full Text A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs Dedicated to the memory of Professor Ivano Bertini
by Kumbhar, Sadhana and Johannsen, Silke and Sigel, Roland K.O and Waller, Mark P and Müller, Jens
Journal of Inorganic Biochemistry, ISSN 0162-0134, 2013, Volume 127, pp. 203 - 210
A series of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations was performed on models of a DNA duplex with artificial silver(I)-mediated... 
Metal-mediated base pairs | DNA | QM/MM | Nucleobases
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8. Full Text Density functionals for surface science: Exchange-correlation model development with Bayesian error estimation
by Wellendorff, Jess and Lundgaard, Keld T and Møgelhøj, Andreas and Petzold, Vivien and Landis, David D and Nørskov, Jens K and Bligaard, Thomas and Jacobsen, Karsten W and SLAC National Accelerator Lab., Menlo Park, CA (United States)
Physical Review B - Condensed Matter and Materials Physics, ISSN 1098-0121, 06/2012, Volume 85, Issue 23
A methodology for semiempirical density functional optimization, using regularization and cross-validation methods from machine learning, is developed. We... 
ADSORPTION ENERGETICS | PHYSICS, CONDENSED MATTER | ENERGY | PHYSICS, APPLIED | THERMOCHEMISTRY | MATERIALS SCIENCE, MULTIDISCIPLINARY | 1ST PRINCIPLES | GENERALIZED GRADIENT APPROXIMATION | CO ADSORPTION | QM/MM METHODS | M06 SUITE | DER-WAALS INTERACTIONS | ELECTRONIC-STRUCTURE
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9. Full Text Evolution of the Excitonic State of DNA Stacked Thymines: Intrabase ππ∗ → S0 Decay Paths Account for Ultrafast (Subpicosecond) and Longer (>100 ps) Deactivations
by Conti, Irene and Garavelli, Marco
Journal of Physical Chemistry Letters, ISSN 1948-7185, 05/2018, Volume 9, Issue 9, pp. 2373 - 2379
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10. Full Text How To Break the Janus Effect of H 2 O 2 in Biocatalysis? Understanding Inactivation Mechanisms To Generate more Robust Enzymes
by Zhao, ZeXin and Lan, Dongming and Tan, Xiyu and Hollmann, Frank and Bornscheuer, Uwe T and Yang, Bo and Wang, Yonghua
ACS Catalysis, 2019, pp. 2916 - 2921
epoxidation | multiscale MD | inactivation | lipase | QM/MM MD
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11. Full Text Catalytic Control in the Facile Proton Transfer in Taxadiene Synthase
by Freud, Yehoshua and Ansbacher, Tamar and Major, Dan Thomas
ACS Catalysis, ISSN 2155-5435, 11/2017, Volume 7, Issue 11, pp. 7653 - 7657
QM/MM simulations | enzyme catalysis | proton transfer | chemical control | lyase
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12. Full Text On the calculation of magnetic properties of nucleic acids in liquid water with the sequential QM/MM method
by Colherinhas, G and Oliveira, L.B.A and Castro, M.A and Fonseca, T.L and Coutinho, K and Canuto, S
Journal of Molecular Liquids, ISSN 0167-7322, 11/2019, Volume 294, p. 111611
We present calculations of nuclear magnetic shieldings of the nucleic acids adenine, cytosine, guanine e thymine in liquid water environment in normal... 
Solvent effect | Sequential QM/MM method | Magnetic properties
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13. Full Text Parameterization of DFTB3/3OB for sulfur and phosphorus for chemical and biological applications
by Gaus, Michael and Lu, Xiya and Elstner, Marcus and Cui, Qiang
Journal of Chemical Theory and Computation, ISSN 1549-9618, 04/2014, Volume 10, Issue 4, pp. 1518 - 1537
We report the parametrization of the approximate density functional tight binding method, DFTB3, for sulfur and phosphorus. The parametrization is done in a... 
PHOSPHATE | CATALYTIC PROMISCUITY | FUNCTIONAL-TIGHT-BINDING | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | HYDROLYSIS | CHEMISTRY, PHYSICAL | PARAMETRIZATION | EXTENSION | GAUSSIAN-3 | SCC-DFTB METHOD | QM/MM ANALYSIS | HYPERVALENT MOLECULES
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14. Full Text Hydrolysis of Guanosine Triphosphate (GTP) by the Ras center dot GAP Protein Complex: Reaction Mechanism and Kinetic Scheme
by Khrenova, MG and Grigorenko, BL and Kolomeisky, AB and Nemukhin, AV
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 10/2015, Volume 119, Issue 40, pp. 12838 - 12845
Molecular mechanisms of the hydrolysis of guanosine triphosphate (GTP) to guanosine diphosphate (GDP) and inorganic phosphate (Pi) by the Ras center dot GAP... 
P21(RAS) | ACTIVATING PROTEIN | CATALYZED-HYDROLYSIS | FTIR | QM/MM METHODS | CHEMISTRY, PHYSICAL | INTERMEDIATE | STATE | SIMULATION
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15. Full Text The ONIOM Method and Its Applications
by Chung, Lung Wa and Sameera, W.M.C and Ramozzi, Romain and Page, Alister J and Hatanaka, Miho and Petrova, Galina P and Harris, Travis V and Li, Xin and Ke, Zhuofeng and Liu, Fengyi and Li, Hai-Bei and Ding, Lina and Morokuma, Keiji
Chemical Reviews, ISSN 0009-2665, 2015, Volume 115, Issue 12, pp. 5678 - 5796
BOND-DISSOCIATION ENTHALPIES | GREEN FLUORESCENT PROTEIN | DIELS-ALDER REACTIONS | QUANTUM MECHANICS/MOLECULAR MECHANICS | POTENTIAL-ENERGY SURFACES | DENSITY-FUNCTIONAL-THEORY | AB-INITIO QM/MM | MOLECULAR-DYNAMICS SIMULATIONS | ELECTRONIC-STRUCTURE CALCULATIONS | WALLED CARBON NANOTUBES | CHEMISTRY, MULTIDISCIPLINARY | Quantum Theory | Carbohydrates - chemistry | Nucleic Acids - chemistry | Solutions | Organic Chemicals - chemistry | Molecular Structure | Proteins - chemistry | Molecular Dynamics Simulation | Molecular mechanics | Chemical properties | Research | Catalysis | Organic compounds | Electric properties | Excited state chemistry
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16. QM/MM and MD studies of the first proton transfer for O2 activation in the catalytic cycle of cytochrome P450cin
by Liu, Feng-Jiao and Song, Jin-Shuai and Lu, Qian-Qian and Wei, Jing and Zhang, Min-Yi and Huang, Jing and Li, Chun-Sen
Jiegou Huaxue, ISSN 0254-5861, 12/2018, Volume 37, Issue 12, pp. 1907 - 1915
Proton transfer | P450cin | QM/MM | CYP176A1
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17. Full Text Solvation Free Energy Calculations with Quantum Mechanics/Molecular Mechanics and Machine Learning Models
by Zhang, Pan and Shen, Lin and Yang, Weitao
Journal of Physical Chemistry B, ISSN 1520-6106, 01/2019, Volume 123, Issue 4, pp. 901 - 908
For exploration of chemical and biological systems, the combined quantum mechanics and molecular mechanics (QM/MM) and machine learning (ML) models have been... 
DISTRIBUTIONS | APPROXIMATION | QM/MM METHODS | PROGRESS | CHEMISTRY | CHEMISTRY, PHYSICAL | POTENTIALS | COMPUTATIONS | MOLECULAR-DYNAMICS SIMULATIONS | SURFACES | WATER
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18. Full Text Combining quantum mechanics methods with molecular mechanics methods in ONIOM
by Vreven, Thom and Byun, K. Suzie and Komáromi, István and Dapprich, Stefan and Montgomery, John A and Morokuma Jr, Keiji and Frisch, Michael J
Journal of Chemical Theory and Computation, ISSN 1549-9618, 2006, Volume 2, Issue 3, pp. 815 - 826
The purpose of this paper is 2-fold. First, we present several extensions to the ONIOM(QM: MM) scheme. In its original formulation, the electrostatic... 
SCHEME | FIELD | QM/MM METHODS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | DYNAMICS | CHEMISTRY, PHYSICAL | SYSTEMS | ATOMS | GEOMETRY OPTIMIZATION | SIMULATIONS | MODEL
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19. Full Text QM/MM methods for biomolecular systems
by Senn, Hans Martin and Thiel, Walter
Angewandte Chemie - International Edition, ISSN 1433-7851, 02/2009, Volume 48, Issue 7, pp. 1198 - 1229
Combined quantum-mechanics/molecular-mechanics (QM/MM) approaches have become the method of choice for modeling reactions in biomolecular systems.... 
QM/MM calculations | Theoretical chemistry | Enzyme catalysis | Molecular simulations | POLARIZABLE FORCE-FIELD | P-HYDROXYBENZOATE HYDROXYLASE | enzyme catalysis | theoretical chemistry | COMBINED AB-INITIO | CHEMISTRY, MULTIDISCIPLINARY | TRANSITION-STATE STABILIZATION | CHORISMATE MUTASE REACTION | POTENTIAL-ENERGY SURFACE | MOLECULAR-DYNAMICS SIMULATIONS | QUANTUM-MECHANICS/MOLECULAR-MECHANICS | DENSITY-FUNCTIONAL THEORY | molecular simulations | ELECTRON CORRELATION METHODS | Enzymes - chemistry | Quantum Theory | Biocatalysis | Models, Biological | Computer Simulation
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