Works matching Quantum mechanics/molecular mechanics

Results: 409

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/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

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

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

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

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

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

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

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

Improving the Catalytic Power of the DszD Enzyme for the Biodesulfurization of Crude Oil and Derivatives.

Published in:

Chemistry - A European Journal, 2017, v. 23, n. 68, p. 17231, doi. 10.1002/chem.201704057

By:

Ferreira, Pedro;
Sousa, Sérgio F.;
Fernandes, Pedro A.;
Ramos, Maria João

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

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

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

Concerted Asynchronous Hula-Twist Photoisomerization in the S65T/H148D Mutant of Green Fluorescent Protein.

Published in:

Angewandte Chemie, 2014, v. 126, n. 33, p. 8793, doi. 10.1002/ange.201405303

By:

Zhang, Qiangqiang;
Chen, Xuebo;
Cui, Ganglong;
Fang, Wei ‐ Hai;
Thiel, Walter

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

Theoretical Insights into Catalytic Mechanism of Protein Arginine Methyltransferase 1.

Published in:

PLoS ONE, 2013, v. 8, n. 8, p. 1, doi. 10.1371/journal.pone.0072424

By:

Zhang, Ruihan;
Li, Xin;
Liang, Zhongjie;
Zhu, Kongkai;
Lu, Junyan;
Kong, Xiangqian;
Ouyang, Sisheng;
Li, Lin;
Zheng, Yujun George;
Luo, Cheng

Publication type:

Article

Concerted Asynchronous Hula-Twist Photoisomerization in the S65T/H148D Mutant of Green Fluorescent Protein.

Published in:

Angewandte Chemie International Edition, 2014, v. 53, n. 33, p. 8649, doi. 10.1002/anie.201405303

By:

Zhang, Qiangqiang;
Chen, Xuebo;
Cui, Ganglong;
Fang, Wei‐Hai;
Thiel, Walter

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

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

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

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

Deep Generative Models for Molecular Science.

Published in:

Molecular Informatics, 2018, v. 37, n. 1/2, p. 1, doi. 10.1002/minf.201700133

By:

Jørgensen, Peter B.;
Schmidt, Mikkel N.;
Winther, Ole

Publication type:

Article

Study of the Wilcox torsion balance in solution for a Tröger's base derivative with hexyl-and heptyl substituents using a combined molecular mechanics and quantum chemistry approach.

Published in:

Journal of Molecular Modeling, 2019, v. 25, n. 3, p. N.PAG, doi. 10.1007/s00894-019-3935-5

By:

Heßelmann, Andreas;
Ferraro, Federica

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

Simulation of mechanical parameters of graphene using the DREIDING force field.

Published in:

Acta Mechanica, 2018, v. 229, n. 6, p. 2343, doi. 10.1007/s00707-018-2115-5

By:

Korobeynikov, S. N.;
Alyokhin, V. V.;
Babichev, A. V.

Publication type:

Article

Implementation of atomic basis set composed of 1s Gaussian and 1s Slater-type orbitals to carry out quantum mechanics molecular calculations.

Published in:

Journal of Computational Chemistry, 1999, v. 20, n. 6, p. 604, doi. 10.1002/(SICI)1096-987X(19990430)20:6<604::AID-JCC6>3.0.CO;2-O

By:

Cesco, J. C.;
Denner, C. C.;
Giubergia, G. O.;
Rosso, A. E.;
Pérez, J. E.;
Ortiz, F. S.;
Taurian, O. E.;
Contreras, R. H.

Publication type:

Article

A QM/MM study of the associative mechanism for the phosphorylation reaction catalyzed by protein kinase A and its D166A mutant.

Published in:

Journal of Computer-Aided Molecular Design, 2014, v. 28, n. 11, p. 1077, doi. 10.1007/s10822-014-9786-3

By:

Pérez-Gallegos, Ayax;
Garcia-Viloca, Mireia;
González-Lafont, Àngels;
Lluch, José

Publication type:

Article

Design and experimental investigation on longitudinal-torsional composite horn considering the incident angle of ultrasonic wave.

Published in:

International Journal of Advanced Manufacturing Technology, 2019, v. 105, n. 1-4, p. 325, doi. 10.1007/s00170-019-04220-0

By:

Zhao, Bo;
Bie, Wenbo;
Wang, Xiaobo;
Chen, Fan;
Chang, Baoqi

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

Quantum Mechanical Study on the Blue-Shifting Hydrogen-Bond between 3-Aminophenol and CHX3 (X ═ F, Cl).

Published in:

Bulletin of the Korean Chemical Society, 2015, v. 36, n. 1, p. 111, doi. 10.1002/bkcs.10028

By:

Lee, So Young;
Kang, Hyuk

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

Curvature and thermal corrections in tree-level CPT-Violating Leptogenesis.

Published in:

European Physical Journal C -- Particles & Fields, 2020, v. 80, n. 6, p. 1, doi. 10.1140/epjc/s10052-020-8109-1

By:

Mavromatos, Nick E.;
Sarkar, Sarben

Publication type:

Article

Modeling bicarbonate formation in an alkaline solution with multi-level quantum mechanics/molecular dynamics simulations.

Published in:

Molecular Physics, 2025, v. 123, n. 7/8, p. 1, doi. 10.1080/00268976.2024.2375370

By:

Bobell, Benjamin;
Boyn, Jan-Niklas;
Martirez, John Mark P.;
Carter, Emily A.

Publication type:

Article

Matter Density and Relativistic Models of Wave Function Collapse.

Published in:

Journal of Statistical Physics, 2014, v. 154, n. 1/2, p. 623, doi. 10.1007/s10955-013-0814-9

By:

Bedingham, Daniel;
Dürr, Detlef;
Ghirardi, GianCarlo;
Goldstein, Sheldon;
Tumulka, Roderich;
Zanghì, Nino

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 mixed quantum mechanics/molecular mechanics (QM/MM) method for large-scale modeling of chemistry in protein environments.

Published in:

Journal of Computational Chemistry, 2000, v. 21, n. 16, p. 1442, doi. 10.1002/1096-987X(200012)21:16<1442::AID-JCC3>3.0.CO;2-O

By:

Murphy, R. B.;
Philipp, D. M.;
Friesner, R. A.

Publication type:

Article