Relevant bibliographies by topics / Characterisation of molecular clusters; Quantum-mechanics (QM) calculations; molecular-mechanics (MM) calculations

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'Characterisation of molecular clusters; Quantum-mechanics (QM) calculations; molecular-mechanics (MM) calculations'

Author: Grafiati
Published: 4 June 2021
Last updated: 2 February 2022

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Journal articles on the topic "Characterisation of molecular clusters; Quantum-mechanics (QM) calculations; molecular-mechanics (MM) calculations"

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Calixto, Ana R., Natércia F. Brás, Pedro A. Fernandes, and Maria J. Ramos. "Reaction Mechanism of Human Renin Studied by Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations." ACS Catalysis 4, no. 11 (2014): 3869–76. http://dx.doi.org/10.1021/cs500497f.

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Yamamoto, Masao, Shin Nakamura, and Takumi Noguchi. "Protonation structure of the photosynthetic water oxidizing complex in the S0 state as revealed by normal mode analysis using quantum mechanics/molecular mechanics calculations." Physical Chemistry Chemical Physics 22, no. 42 (2020): 24213–25. http://dx.doi.org/10.1039/d0cp04079g.

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Kurczab, Rafał. "The evaluation of QM/MM-driven molecular docking combined with MM/GBSA calculations as a halogen-bond scoring strategy." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 73, no. 2 (2017): 188–94. http://dx.doi.org/10.1107/s205252061700138x.

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The combination of quantum mechanics/molecular mechanics-driven (QM/MM) molecular docking with binding free-energy calculations was successfully used to reproduce the X-ray geometries of protein–ligand complexes with halogen bonding. The procedure involves quantum-polarized ligand docking (QPLD) to obtain the QM-derived ligand atomic charges in the protein environment at the B3PW91/cc-pVTZ level and the MM/GBSA (generalized-Born/surface area) algorithm to calculate the binding free energies of resultant complexes. The performance was validated using a set of 106 X-ray complexes and compared wi
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Lodola, Alessio, Marco Mor, Jitnapa Sirirak, and Adrian J. Mulholland. "Insights into the mechanism and inhibition of fatty acid amide hydrolase from quantum mechanics/molecular mechanics (QM/MM) modelling." Biochemical Society Transactions 37, no. 2 (2009): 363–67. http://dx.doi.org/10.1042/bst0370363.

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FAAH (fatty acid amide hydrolase) is a promising target for the treatment of several central nervous system and peripheral disorders. Combined QM/MM (quantum mechanics/molecular mechanics) calculations have elucidated the role of its unusual catalytic triad in the hydrolysis of oleamide and oleoylmethyl ester substrates, and have identified the productive inhibitor-binding orientation for the carbamoylating compound URB524. These are potentially crucial insights for designing new covalent inhibitors of this drug target.
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Ho, Junming, Yihan Shao, and Jin Kato. "Do Better Quality Embedding Potentials Accelerate the Convergence of QM/MM Models? The Case of Solvated Acid Clusters." Molecules 23, no. 10 (2018): 2466. http://dx.doi.org/10.3390/molecules23102466.

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This study examines whether the use of more accurate embedding potentials improves the convergence of quantum mechanics/molecular mechanics (QM/MM) models with respect to the size of the QM region. In conjunction with density functional theory calculations using the ωB97X-D functional, various embedding potentials including the TIP3P water model, the effective fragment potential (EFP), and semi-empirical methods (PM6, PM7, and DFTB) were used to simulate the deprotonation energies of solvated acid clusters. The calculations were performed on solvated neutral (HA) and cationic (HB+) acids clust
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Cao, Lili, Octav Caldararu, and Ulf Ryde. "Protonation and Reduction of the FeMo Cluster in Nitrogenase Studied by Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations." Journal of Chemical Theory and Computation 14, no. 12 (2018): 6653–78. http://dx.doi.org/10.1021/acs.jctc.8b00778.

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Kamiński, Radosław, Katarzyna N. Jarzembska, and Sławomir Domagała. "CLUSTERGEN: a program for molecular cluster generation from crystallographic data." Journal of Applied Crystallography 46, no. 2 (2013): 540–43. http://dx.doi.org/10.1107/s0021889813002173.

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A new program,CLUSTERGEN, for molecular cluster generation is introduced.CLUSTERGENprovides the quantum mechanics/molecular mechanics (QM/MM) input files for program packages such asADF[Baerendset al.(2012). Vrije Universiteit, Amsterdam, The Netherlands] andGAUSSIAN[Frischet al.(2009). Gaussian Inc., Pittsburgh, Pennsylvania, USA]. Additionally, it prints out a standardCRYSTAL[Dovesiet al.(2009). University of Turin, Italy] input and, in general, facilitates file-format manipulation. TheCLUSTERGENprogram is supported by an extensive manual and a user-friendly graphical interface. The code is
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Jin, Xinsheng, Tong Zhu, John Z. H. Zhang, and Xiao He. "A systematic study on RNA NMR chemical shift calculation based on the automated fragmentation QM/MM approach." RSC Advances 6, no. 110 (2016): 108590–602. http://dx.doi.org/10.1039/c6ra22518g.

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Cummins, Peter L., and Jill E. Gready. "Coupled semiempirical quantum mechanics and molecular mechanics (QM/MM) calculations on the aqueous solvation free energies of ionized molecules." Journal of Computational Chemistry 20, no. 10 (1999): 1028–38. http://dx.doi.org/10.1002/(sici)1096-987x(19990730)20:10<1028::aid-jcc5>3.0.co;2-7.

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Chandorkar, Shreya, Shampa Raghunathan, Tanashree Jaganade, and U. Deva Priyakumar. "Multiscale Modeling of Wobble to Watson–Crick-Like Guanine–Uracil Tautomerization Pathways in RNA." International Journal of Molecular Sciences 22, no. 11 (2021): 5411. http://dx.doi.org/10.3390/ijms22115411.

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Energetically unfavorable Watson–Crick (WC)-like tautomeric forms of nucleobases are known to introduce spontaneous mutations, and contribute to replication, transcription, and translation errors. Recent NMR relaxation dispersion techniques were able to show that wobble (w) G•U mispair exists in equilibrium with the short-lived, low-population WC-like enolic tautomers. Presently, we have investigated the wG•U → WC-like enolic reaction pathway using various theoretical methods: quantum mechanics (QM), molecular dynamics (MD), and combined quantum mechanics/molecular mechanics (QM/MM). The previ
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Dissertations / Theses on the topic "Characterisation of molecular clusters; Quantum-mechanics (QM) calculations; molecular-mechanics (MM) calculations"

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Haldar, Susanta. "Teoretická studie nekovalentních interakcí, od malých molekul k biomolekuklám." Doctoral thesis, 2015. http://www.nusl.cz/ntk/nusl-347456.

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xv Abstract The aim of this thesis is to investigate the accurate stabilization energy and binding free energy in various non-covalent complexes spanned from small organic molecules to biomolecules. Non-covalent interactions such as H-bonds, π...π stacking and halogen bonds are mainly responsible for understanding of most biological processes, such as small molecule interactions with surface, protein-ligand binding in the cell machinery, etc. In the thesis, different non-covalent complexes such as graphene…electron donor- acceptor complexes, DNA base pair interaction with silica surface, etc,
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Book chapters on the topic "Characterisation of molecular clusters; Quantum-mechanics (QM) calculations; molecular-mechanics (MM) calculations"

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Chung, Lung Wa, Xin Li, and Keiji Morokuma. "Modeling Enzymatic Reactions in Metalloenzymes and Photobiology by Quantum Mechanics (QM) and Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations." In Quantum Biochemistry. Wiley-VCH Verlag GmbH & Co. KGaA, 2010. http://dx.doi.org/10.1002/9783527629213.ch3.

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Conference papers on the topic "Characterisation of molecular clusters; Quantum-mechanics (QM) calculations; molecular-mechanics (MM) calculations"

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Solis-Calero, C., PA Morais, FF Maia Jr, VN Freire, and HF Carvalho. "Explaining SARS-CoV-2 3CL Mpro binding to peptidyl Michael acceptor and a ketone-based inhibitors using Molecular fractionation with conjugate caps method." In VIII Simpósio de Estrutura Eletrônica e Dinâmica Molecular. Universidade de Brasília, 2020. http://dx.doi.org/10.21826/viiiseedmol2020185.

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The main protease SARS-CoV-2 3CL Mpro (3CL-Mpro) is an attractive target for developing antiviral inhibitors due to its essential role in processing the polyproteins translated from viral coronavirus RNA. In this work, it was obtained non-covalent complexes of this protease with two distinct ligands, a peptidyl Michael acceptor (N3) and a ketone-based compound (V2M). The complexes were modeled from processed crystallographic data (PDB id: 6LU7 and 6XHM respectively) using combined quantum mechanics/molecular mechanics (QM/MM) calculations. The QM region was treated at the PBE-def2-SV(P) level,
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You might also be interested in the extended bibliographies on the topic 'Characterisation of molecular clusters; Quantum-mechanics (QM) calculations; molecular-mechanics (MM) calculations' for particular source types:
Journal articles
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