Works matching Quantum mechanics/molecular mechanics

Results: 384

Multiscale modelling: hybrid quantum mechanics/molecular mechanics as an example and some recent developments.

Published in:

Current Science (00113891), 2017, v. 112, n. 7, p. 1455, doi. 10.18520/cs/v112/i07/1455-1462

By:

Ghosh, Debashree

Publication type:

Article

Electrostatic effects in enzyme catalysis: a quantum mechanics/molecular mechanics study of the nucleophilic substitution reaction in haloalkane dehalogenase.

Published in:

Theoretical Chemistry Accounts: Theory, Computation, & Modeling, 2004, v. 112, n. 4, p. 327, doi. 10.1007/s00214-004-0592-1

By:

Soriano, Alejandro;
Silla, Estanislao;
Tuñón, Iñaki;
Marti, Sergio;
Moliner, Vicent;
Bertrán, Juan

Publication type:

Article

Cover Feature: Quantum Mechanics/Molecular Mechanics Studies of the Mechanism of Cysteine Proteases Inhibition by Dipeptidyl Nitroalkenes (Chem. Eur. J. 9/2020).

Published in:

Chemistry - A European Journal, 2020, v. 26, n. 9, p. 1891, doi. 10.1002/chem.201905164

By:

Arafet, Kemel;
González, Florenci V.;
Moliner, Vicent

Publication type:

Article

Quantum Mechanics/Molecular Mechanics Studies of the Mechanism of Cysteine Proteases Inhibition by Dipeptidyl Nitroalkenes.

Published in:

Chemistry - A European Journal, 2020, v. 26, n. 9, p. 2002, doi. 10.1002/chem.201904513

By:

Arafet, Kemel;
González, Florenci V.;
Moliner, Vicent

Publication type:

Article

A quantum mechanics/molecular mechanics study on the hydrolysis mechanism of New Delhi metallo-β-lactamase-1.

Published in:

Journal of Computer-Aided Molecular Design, 2013, v. 27, n. 3, p. 247, doi. 10.1007/s10822-012-9630-6

By:

Zhu, Kongkai;
Lu, Junyan;
Liang, Zhongjie;
Kong, Xiangqian;
Ye, Fei;
Jin, Lu;
Geng, Heji;
Chen, Yong;
Zheng, Mingyue;
Jiang, Hualiang;
Li, Jun-Qian;
Luo, Cheng

Publication type:

Article

Structure and electronic properties of hydrated mesityl oxide: a sequential quantum mechanics/molecular mechanics approach.

Published in:

Theoretical Chemistry Accounts: Theory, Computation, & Modeling, 2012, v. 131, n. 5, p. 1, doi. 10.1007/s00214-012-1214-y

By:

Damasceno, Marcus;
Costa Cabral, Benedito;
Coutinho, Kaline

Publication type:

Article

Quantum Mechanics/Molecular Mechanics Simulations for Chiral-Selective Aminoacylation: Unraveling the Nature of Life.

Published in:

Computation, 2024, v. 12, n. 12, p. 238, doi. 10.3390/computation12120238

By:

Ando, Tadashi;
Tamura, Koji

Publication type:

Article

Quantum Mechanics/Molecular Mechanics Study on Caspase-2 Recognition by Peptide Inhibitors.

Published in:

Acta Chimica Slovenica, 2020, v. 67, n. 3, p. 876, doi. 10.17344/acsi.2020.5847

By:

Mitrasinovic, Petar M.

Publication type:

Article

Reaction Mechanism of Mycobacterium Tuberculosis Glutamine Synthetase Using Quantum Mechanics/Molecular Mechanics Calculations.

Published in:

Chemistry - A European Journal, 2016, v. 22, n. 27, p. 9218, doi. 10.1002/chem.201600305

By:

Moreira, Cátia;
Ramos, Maria J.;
Fernandes, Pedro Alexandrino

Publication type:

Article

Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs.

Published in:

Chemistry - A European Journal, 2016, v. 22, n. 8, p. 2562, doi. 10.1002/chem.201503802

By:

Quesne, Matthew G.;
Borowski, Tomasz;
de Visser, Sam P.

Publication type:

Article

Quantum Mechanics/Molecular Mechanics Studies on the Mechanism of Action of Cofactor Pyridoxal 5′-Phosphate in Ornithine 4,5-Aminomutase.

Published in:

Chemistry - A European Journal, 2014, v. 20, n. 36, p. 11390, doi. 10.1002/chem.201402759

By:

Pang, Jiayun;
Scrutton, Nigel S.;
Sutcliffe, Michael J.

Publication type:

Article

New Insights into the Nature of Observable Reaction Intermediates in Cytochrome P450 NO Reductase by Using a Combination of Spectroscopy and Quantum Mechanics/Molecular Mechanics Calculations.

Published in:

Chemistry - A European Journal, 2014, v. 20, n. 6, p. 1602, doi. 10.1002/chem.201302443

By:

Riplinger, Christoph;
Bill, Eckhard;
Daiber, Andreas;
Ullrich, Volker;
Shoun, Hirofumi;
Neese, Frank

Publication type:

Article

Back Cover: Quantum Mechanics/Molecular Mechanics Study on the Oxygen Binding and Substrate Hydroxylation Step in AlkB Repair Enzymes (Chem. Eur. J. 2/2014).

Published in:

Chemistry - A European Journal, 2014, v. 20, n. 2, p. 612, doi. 10.1002/chem.201490003

By:

Quesne, Matthew G.;
Latifi, Reza;
Gonzalez‐Ovalle, Luis E.;
Kumar, Devesh;
de Visser, Sam P.

Publication type:

Article

Quantum Mechanics/Molecular Mechanics Study on the Oxygen Binding and Substrate Hydroxylation Step in AlkB Repair Enzymes.

Published in:

Chemistry - A European Journal, 2014, v. 20, n. 2, p. 435, doi. 10.1002/chem.201303282

By:

Quesne, Matthew G.;
Latifi, Reza;
Gonzalez‐Ovalle, Luis E.;
Kumar, Devesh;
de Visser, Sam P.

Publication type:

Article

An investigation into the hydrogen bond of poly (p-phenylene benzobisoxazole)/carboxylic carbon nanotube composites, insight from quantum mechanics/molecular mechanics simulation.

Published in:

Polymer Composites, 2015, v. 36, n. 8, p. 1454, doi. 10.1002/pc.23051

By:

Hu, Kun;
Zhuang, Qixin;
Liu, Xiaoyun;
Han, Zhewen

Publication type:

Article

Insight into the isomerization mechanism of retinal proteins from hybrid quantum mechanics/molecular mechanics simulations.

Published in:

WIREs: Computational Molecular Science, 2022, v. 12, n. 1, p. 1, doi. 10.1002/wcms.1562

By:

Sen, Saumik;
Kar, Rajiv K.;
Borin, Veniamin A.;
Schapiro, Igor

Publication type:

Article

Development and application of quantum mechanics/molecular mechanics methods with advanced polarizable potentials.

Published in:

WIREs: Computational Molecular Science, 2021, v. 11, n. 4, p. 1, doi. 10.1002/wcms.1515

By:

Nochebuena, Jorge;
Naseem‐Khan, Sehr;
Cisneros, G. Andrés

Publication type:

Article

Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms.

Published in:

WIREs: Computational Molecular Science, 2017, v. 7, n. 2, p. n/a, doi. 10.1002/wcms.1281

By:

Sousa, Sérgio Filipe;
Ribeiro, António J. M.;
Neves, Rui P. P.;
Brás, Natércia F.;
Cerqueira, Nuno M. F. S. A.;
Fernandes, Pedro A.;
Ramos, Maria João

Publication type:

Article

Adaptive quantum mechanics/molecular mechanics methods.

Published in:

WIREs: Computational Molecular Science, 2016, v. 6, n. 4, p. 369, doi. 10.1002/wcms.1255

By:

Zheng, Min;
Waller, Mark P.

Publication type:

Article

Quantum mechanics and mixed quantum mechanics/molecular mechanics simulations of model nerve agents with acetylcholinesterase.

Published in:

Theoretical Chemistry Accounts: Theory, Computation, & Modeling, 2003, v. 109, n. 3, p. 160, doi. 10.1007/s00214-002-0424-0

By:

Hurley, M.M.;
Wright, J.B.;
Lushington, G.H.;
White, W.E.

Publication type:

Article

Quantum Mechanics/Molecular Mechanics Simulations Show Saccharide Distortion is Required for Reaction in Hen Egg‐White Lysozyme.

Published in:

Chemistry - A European Journal, 2019, v. 25, n. 3, p. 764, doi. 10.1002/chem.201805250

By:

Limb, Michael A. L.;
Suardíaz, Reynier;
Grant, Ian M.;
Mulholland, Adrian J.

Publication type:

Article

Evolution from S3 to S4 States of the Oxygen‐Evolving Complex in Photosystem II Monitored by Quantum Mechanics/Molecular Mechanics (QM/MM) Dynamics.

Published in:

Chemistry - A European Journal, 2018, v. 24, n. 42, p. 10820, doi. 10.1002/chem.201801709

By:

Narzi, Daniele;
Capone, Matteo;
Bovi, Daniele;
Guidoni, Leonardo

Publication type:

Article

Structural Protein Effects Underpinning Cognitive Developmental Delay of the PURA p.Phe233del Mutation Modelled by Artificial Intelligence and the Hybrid Quantum Mechanics–Molecular Mechanics Framework.

Published in:

Brain Sciences (2076-3425), 2022, v. 12, n. 7, p. N.PAG, doi. 10.3390/brainsci12070871

By:

López-Rivera, Juan Javier;
Rodríguez-Salazar, Luna;
Soto-Ospina, Alejandro;
Estrada-Serrato, Carlos;
Serrano, David;
Chaparro-Solano, Henry Mauricio;
Londoño, Olga;
Rueda, Paula A.;
Ardila, Geraldine;
Villegas-Lanau, Andrés;
Godoy-Corredor, Marcela;
Cuartas, Mauricio;
Vélez, Jorge I.;
Vidal, Oscar M.;
Isaza-Ruget, Mario A.;
Arcos-Burgos, Mauricio

Publication type:

Article

Assessing Configurational Sampling in the Quantum Mechanics/Molecular Mechanics Calculation of Temoporfin Absorption Spectrum and Triplet Density of States.

Published in:

Molecules, 2018, v. 23, n. 11, p. 2932, doi. 10.3390/molecules23112932

By:

De Vetta, Martina;
Baig, Omar;
Steen, Dorika;
Nogueira, Juan J.;
González, Leticia;
Lin, Hai;
Truhlar, Donald G.

Publication type:

Article

Quantum Mechanics/Molecular Mechanics Studies on the Relative Reactivities of Compound I and II in Cytochrome P450 Enzymes.

Published in:

International Journal of Molecular Sciences, 2018, v. 19, n. 7, p. 1974, doi. 10.3390/ijms19071974

By:

Luis, Josep M.;
Solà, Miquel;
Postils, Verònica;
Saint-André, Maud;
Timmins, Amy;
de Visser, Sam P.;
Li, Xiao-Xi;
Wang, Yong

Publication type:

Article

A Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) Study on Ornithine Cyclodeaminase (OCD): A Tale of Two Iminiums.

Published in:

International Journal of Molecular Sciences, 2012, v. 13, n. 10, p. 12994, doi. 10.3390/ijms131012994

By:

Ion, Bogdan F.;
Bushnell, Eric A. C.;
De Luna, Phil;
Gauld, James W.

Publication type:

Article

On electrostatic interactions of adenosine triphosphate–insulin‐degrading enzyme revealed by quantum mechanics/molecular mechanics and molecular dynamics.

Published in:

Quantitative Biology, 2024, v. 12, n. 4, p. 414, doi. 10.1002/qub2.61

By:

Somin, Sarawoot;
Kulasiri, Don;
Samarasinghe, Sandhya

Publication type:

Article

Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods.

Published in:

International Reviews in Physical Chemistry, 2010, v. 29, n. 1, p. 65, doi. 10.1080/01442350903495417

By:

Ranaghan, Kara E.;
Mulholland, Adrian J.

Publication type:

Article

A Quantum Mechanics/Molecular Mechanics Study of the Protein-Ligand Interaction for Inhibitors of HIV-1 Integrase.

Published in:

Chemistry - A European Journal, 2007, v. 13, n. 27, p. 7715, doi. 10.1002/chem.200700040

By:

Alves, Cláudio N.;
Martí, Sergio;
Castillo, Raquel;
Andrés, Juan;
Moliner, Vicent;
Tuñón, Iñaki;
Silla, Estanislao

Publication type:

Article

A disappearing act performed by magnesium: the nucleotide exchange mechanism of Ran GTPase by quantum mechanics/molecular mechanics studies.

Published in:

Theoretical Chemistry Accounts: Theory, Computation, & Modeling, 2016, v. 135, n. 8, p. 1, doi. 10.1007/s00214-016-1953-2

By:

Mooney, Maura C.;
Xu, Yongtao;
McClory, James;
Huang, Meilan

Publication type:

Article

Use of quantum mechanics/molecular mechanics-based FEP method for calculating relative binding affinities of FBPase inhibitors for type-2 diabetes.

Published in:

Theoretical Chemistry Accounts: Theory, Computation, & Modeling, 2012, v. 131, n. 2, p. 1, doi. 10.1007/s00214-012-1096-z

By:

Rathore, R.;
Reddy, R.;
Kondapi, A.;
Reddanna, P.;
Reddy, M.

Publication type:

Article

MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations.

Published in:

Journal of Computational Chemistry, 2023, v. 44, n. 4, p. 516, doi. 10.1002/jcc.27018

By:

Cárdenas, Gustavo;
Lucia‐Tamudo, Jesús;
Mateo‐delaFuente, Henar;
Palmisano, Vito F.;
Anguita‐Ortiz, Nuria;
Ruano, Lorena;
Pérez‐Barcia, Álvaro;
Díaz‐Tendero, Sergio;
Mandado, Marcos;
Nogueira, Juan J.

Publication type:

Article

CO bonding in hexa‐ and pentacoordinate carboxy‐neuroglobin: A quantum mechanics/molecular mechanics and local vibrational mode study.

Published in:

Journal of Computational Chemistry, 2022, v. 43, n. 25, p. 1725, doi. 10.1002/jcc.26973

By:

Freindorf, Marek;
Delgado, Alexis Antoinette Ann;
Kraka, Elfi

Publication type:

Article

The Driving Force for the Acylation of β‐Lactam Antibiotics by L,D‐Transpeptidase 2: Quantum Mechanics/Molecular Mechanics (QM/MM) Study.

Published in:

ChemPhysChem, 2019, v. 20, n. 9, p. 1126, doi. 10.1002/cphc.201900173

By:

Ibeji, Collins U.;
Lawal, Monsurat M.;
Tolufashe, Gideon F.;
Govender, Thavendran;
Naicker, Tricia;
Maguire, Glenn E. M.;
Lamichhane, Gyanu;
Kruger, Hendrik G.;
Honarparvar, Bahareh

Publication type:

Article

The Reaction Mechanism of Cytochrome P450 NO Reductase: A Detailed Quantum Mechanics/Molecular Mechanics Study.

Published in:

ChemPhysChem, 2011, v. 12, n. 17, p. 3192, doi. 10.1002/cphc.201100523

By:

Riplinger, Christoph;
Neese, Frank

Publication type:

Article

Quantum Mechanics/Molecular Mechanics Study on the Photoreactions of Dark- and Light-Adapted States of a Blue-Light YtvA LOV Photoreceptor.

Published in:

Angewandte Chemie International Edition, 2017, v. 56, n. 32, p. 9341, doi. 10.1002/anie.201703487

By:

Chang, Xue-Ping;
Gao, Yuan-Jun;
Fang, Wei-Hai;
Cui, Ganglong;
Thiel, Walter

Publication type:

Article

Quantum Mechanics/Molecular Mechanics Study on the Photoreactions of Dark- and Light-Adapted States of a Blue-Light YtvA LOV Photoreceptor.

Published in:

Angewandte Chemie, 2017, v. 129, n. 32, p. 9469, doi. 10.1002/ange.201703487

By:

Chang, Xue ‐ Ping;
Gao, Yuan ‐ Jun;
Fang, Wei ‐ Hai;
Cui, Ganglong;
Thiel, Walter

Publication type:

Article

Implementation of a quantum mechanics/molecular mechanics approach in the parallel density functional program ParaGauss and applications to model copper thiolate clusters.

Published in:

Theoretical Chemistry Accounts: Theory, Computation, & Modeling, 2003, v. 109, n. 6, p. 285, doi. 10.1007/s00214-003-0432-8

By:

Kerdcharoen, Teerakiat;
Birkenheuer, Uwe;
Krüger, Siren;
Woiterski, André;
Rösch, Notker

Publication type:

Article

Hydration structure of Na+, K+, F−, and Cl− in ambient and supercritical water: A quantum mechanics/molecular mechanics study.

Published in:

International Journal of Quantum Chemistry, 2014, v. 114, n. 15, p. 1006, doi. 10.1002/qua.24597

By:

Ma, Haibo

Publication type:

Article

Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. II. Application of the local basis equation.

Published in:

Journal of Computational Chemistry, 2013, v. 34, n. 10, p. 862, doi. 10.1002/jcc.23209

By:

Ferenczy, György G.

Publication type:

Article

Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. Part I. Application of the Huzinaga equation.

Published in:

Journal of Computational Chemistry, 2013, v. 34, n. 10, p. 854, doi. 10.1002/jcc.23210

By:

Ferenczy, György G.

Publication type:

Article

A quantum mechanics/molecular mechanics study of the reaction mechanism of the hepatitis C virus NS3 protease with the NS5A/5B substrate.

Published in:

Proteins, 2007, v. 66, n. 2, p. 444, doi. 10.1002/prot.21190

By:

Oliva, Carolina;
Rodríguez, Alejandro;
González, Miguel;
Yang, Wei

Publication type:

Article

A quantum mechanics/molecular mechanics (QM/MM) investigation on the mechanism of adsorptive removal of heavy metal ions by lignin: single and competitive ion adsorption.

Published in:

Cellulose, 2017, v. 24, n. 8, p. 3131, doi. 10.1007/s10570-017-1329-3

By:

Karezani, Edris;
Hallajisani, Ahmad;
Asgarpour Khansary, Milad

Publication type:

Article

Valence Bond-Based Hybrid Quantum Mechanics Molecular Mechanics Approaches and Proper Inclusion of the Effect of the Surroundings.

Published in:

Israel Journal of Chemistry, 2014, v. 54, n. 8/9, p. 1189, doi. 10.1002/ijch.201400038

By:

Shurki, Avital;
Sharir‐Ivry, Avital

Publication type:

Article

STUDIES OF QUANTUM MECHANICS/MOLECULAR DOCKING ON ZANUBRUTINIB AS POTENTIAL REPURPOSED AGAINST COVID-19.

Published in:

Bulletin of the Chemical Society of Ethiopia, 2022, v. 36, n. 2, p. 479, doi. 10.4314/bcse.v36i2.19

By:

Mahani, Nosrat Madadi;
Mohammadi, Sayed Zia

Publication type:

Article

Insights Into Guanine Radical Cation Deprotonation Using the Quantum Mechanics and Quantum Mechanics/Molecular Mechanics (ABEEM) Methods.

Published in:

International Journal of Quantum Chemistry, 2024, v. 124, n. 19, p. 1, doi. 10.1002/qua.27491

By:

Wang, Yue;
Liu, Cui;
Gong, Lidong;
Yang, Zhongzhi

Publication type:

Article

Evaluation of binding and antagonism/downregulation of brilanestrant molecule in estrogen receptor-α via quantum mechanics/molecular mechanics, molecular dynamics and binding free energy calculations.

Published in:

Journal of Biomolecular Structure & Dynamics, 2020, v. 38, n. 1, p. 219, doi. 10.1080/07391102.2019.1574605

By:

Chinnasamy, Kalaiarasi;
Saravanan, Manjula;
Poomani, Kumaradhas

Publication type:

Article

Biological Applications of Hybrid Quantum Mechanics/Molecular Mechanics Calculation.

Published in:

2012

By:

Kang, Jiyoung;
Hagiwara, Yohsuke;
Tateno, Masaru

Publication type:

Journal Article

Biological Applications of Hybrid Quantum Mechanics/Molecular Mechanics Calculation.

Published in:

Journal of Biomedicine & Biotechnology, 2012, v. 2012, p. 1, doi. 10.1155/2012/236157

By:

Kang, Jiyoung;
Hagiwara, Yohsuke;
Tateno, Masaru

Publication type:

Article

Glycosaminoglycan Monosaccharide Blocks Analysis by Quantum Mechanics, Molecular Dynamics, and Nuclear Magnetic Resonance.

Published in:

BioMed Research International, 2014, v. 2014, p. 1, doi. 10.1155/2014/808071

By:

Samsonov, Sergey A.;
Theisgen, Stephan;
Riemer, Thomas;
Huster, Daniel;
Teresa Pisabarro, M.

Publication type:

Article