Publications

Principal References

The principle references for pDynamo are:

    • The second edition of the book M. J. Field, A Practical Introduction to the Simulation of Molecular Systems published by Cambridge University Press in 2007 [Amazon UK, Amazon US, CUP].

    • The paper M. J. Field, The pDynamo Library for Molecular Simulations using Hybrid Quantum Mechanical and Molecular Mechanical Potentials, J. Chem. Theo. Comp. 4, 1151–1161 (2008) [Link]. This paper provides a general introduction to pDynamo and its QC models and hybrid potentials.

Those for fDynamo are:

    • The first edition of the book M. J. Field, A Practical Introduction to the Simulation of Molecular Systems published by Cambridge University Press in 1999 [Amazon UK].

    • The paper M. J. Field, M. Albe, C. Bret, F. Proust-De Martin and A. Thomas, The Dynamo Library for Molecular Simulations using Hybrid Quantum Mechanical and Molecular Mechanical Potentials, J. Comp. Chem. 21, 1088–1100 (2000) [Link]. This paper described the semi-empirical QC and hybrid potential capabilities of fDynamo but much of what was said is also applicable to pDynamo.

Readers who use either pDynamo or fDynamo in their work are requested to cite the corresponding references.

Research Articles

Examples of studies performed wholly or partially with fDynamo or pDynamo include:

2020

  • J. Woodhouse, G. la Nass-Kovacs, N. Coquelle, L. M. Uriarte, V. Adam, T. R. M. Barends, M. Byrdin, E. de la Mora, R. B. Doak, M. Feliks, M. Field, F. Fieschi, V. Guillon, S. Jakobs, Y. Joti, P. Macheboeuf, K. Motomura, K. Nass, S. Owada, C. M. Roome, C. Ruckebusch, G. Schiro, R. L. Shoeman, M. Thepaut, T. Togashi, K. Tono, M. Yabashi, M. Cammarata, L. Foucar, D. Bourgeois, M. Sliwa, J.-P. Colletier, I. Schlichting and M. Weik. Photoswitching mechanism of a fluorescent protein revealed by time-resolved serial femtosecond crystallography and transient absorption spectroscopy. Nat. Comm. 11, 741 (2020) [Link].

2019

  • M. Hoias Teixeira, F. Curtolo, S. Camilo, M. Field, P. Zheng, H. Li and G. Arantes. Modelling the hydrolysis of iron-sulfur clusters. J. Chem. Inf. Mod. 60, 653–660 (2019) [Link].

2018

  • N. Coquelle, M. Sliwa, J. Woodhouse, G. Schiro, V. Adam, A. Aquila, T. R. M. Barends, S. Boutet, M. Byrdin, R. B. Doak, M. Feliks, F. Fieschi, L. Foucar, V. Guillon, M. Hilpert, M. Hunter, S. Jakobs, J. E. Koglin, G. Kovacsova, B. Levy, M. Liang, K. Nass, J. Ridard, J. S. Robinson, C. M. Roome, C. Ruckebusch, M. Thepaut, M. Cammarata, I. Demachy, M. J. Field, R. L. Shoeman, D. Bourgeois, J.-P. Colletier, I. Schlichting and M. Weik. Chromophore Twisting in the Excited State of a Fluorescent Protein Captured by Time-Resolved Serial Femtosecond Crystallography. Nat. Chem. 10, 31–27 (2018) [Link].

2017

  • N. Bhattacharjee, M. Feliks, M. M. Shaik and M. J. Field. Catalytic Mechanism of Peptidoglycan Deacetylase: A Computational Study. J. Phys. Chem. B 121, 89–99 (2017) [Link].

  • M. M. Shaik, N. Bhattacharjee, M. Feliks, K. K. S. Ng and M. J. Field. Norovirus RNA-Dependent RNA Polymerase: A Computational Study of Metal-Binding Preferences. Proteins 8, 1435–1445 (2017) [Link].

  • M. J. Field. An Algorithm for Adaptive QC/MM Simulations. J. Chem. Theor. Comp. 9, 2342–2351 (2017) [Link].

2016

  • N. Bhattacharjee, M. J. Field, J.-P. Simorre, M. Arthur and C. M. Bougault. Hybrid Potential Simulation of the Acylation of Enterococcus faecium L,D-Transpeptidase by Carbapenems. J. Phys. Chem. B 120, 4767–4781 (2016) [Link].

  • A. Aleksandrov, A. Palencia, S. Cusack and M. J. Field. Aminoacetylation Reaction Catalyzed by Leucyl-tRNA Synthetase Operates via a Self-Assisted Mechanism Using a Conserved Residue and the Aminoacyl Substrate. J. Phys. Chem. B 120, 4388–4398 (2016) [Link].

  • M. Bacchi, E. Veinberg, M. J. Field, J. Niklas, T. Matsui, D. M. Tiede, O. G. Poluektov, M. Ikeda-Saito, M. Fontecave and V. Artero. Artificial Hydrogenases based on Cobaloximes and Heme Oxygenase. ChemPlusChem 81, 1083–1089 (2016) [Link].

  • M. Feliks, C. Lafaye, X. Shu, A. Royant and M. J. Field. Structural Determinants of Improved Fluorescence in a Family of Bacteriophytochrome-Based Infrared Fluorescent Proteins: Insights from Continuum Electrostatic Calculations and Molecular Dynamics Simulations. Biochemistry 55, 4263–4274 (2016) [Link].

2015

  • R. Zhang, A. Bhattacharjee, M. J. Field and D. Salahub. Multiple Proton Relay Routes in the Reaction Mechanism of RNAP II. Proteins 83, 268–281 (2015) [Link].

  • P. Zheng, G. M. Arantes, M. J. Field and H. Li. Force-Induced Chemical Reactions on the Metal Centre in a Single Metalloprotein Molecule. Nat. Commun. 6, 7569 (2015) [Link].

  • M. Feliks and M. J. Field. Pcetk: a pDynamo-based Toolkit for Protonation State Calculations in Proteins. J. Chem. Inf. Mod. 55, 2288–2296 (2015) [Link].

2014

  • T. Wymore, M. J. Field, P. Langan, J. C. Smith and J. M. Parks. Hydrolysis of DFP and the Nerve Agent (S)-Sarin by DFPase Proceeds along Two Different Reaction Pathways: Implications for Engineering Bioscavengers. J. Phys. Chem. B 118, 4479–4489 (2014) [Link].

  • W. Crous, M. J. Field and K. J. Naidoo. Simple Link Atom Saccharide Hybrid (SLASH) Treatment for Glycosidic Bonds at the QM/MM Boundary. J. Chem. Theor. Comput. 10, 1727–1738 (2014) [Link].

  • A. Aleksandrov, E. Zverena and M. J. Field. The Mechanism of Citryl-Coenzyme A Formation Catalyzed by Citrate Synthase. J. Phys. Chem. B 118, 4505–4513 (2014) [Link].

  • M. Bacchi, G. Berggren, J. Niklas, E. Veinberg, M. W. Mara, M. L. Shelby, O. G. Poluektov, L. X. Chen, D. M. Tiede, C. Cavazza, M. J. Field, M. Fontecave and V. Artero. Cobaloxime-Based Artificial Hydrogenases. Inorg. Chem. 53, 8071–8082 (2014) [Link].

  • M. Sanchez-Martinez, M. J. Field and R. Crehuet. Enzymatic Minimum Free Energy Path Calculations Using Swarms of Trajectories. J. Phys. Chem. B 119, 1103–1113 (2014) [Link].

2013

    • A. Baggioli, O. Crescenzi, M. J. Field, F. Castiglione and G. Raos. Computational 17O-NMR Spectroscopy of Organic Acids and Peracids: Comparison of Solvation Models. Phys. Chem. Chem. Phys. 15, 1130–1140 (2013) [Link].

    • M. Feliks, B. M. Martins and G. M. Ullmann. Catalytic Mechanism of the Glycyl Radical Enzyme 4-Hydroxyphenylacetate Decarboxylase from Continuum Electrostatic and QC/MM Calculations. J. Am. Chem. Soc. 135, 14574–14585 (2013) [Link].

    • A. Aleksandrov and M. J. Field. Mechanism of Activation of Elongation Factor Tu by Ribosome: Catalytic Histidine Activates GTP by Protonation. RNA 19, 1218–1225 (2013) [Link].

    • G.M. Arantes, A. Bhattacharjee and M. J. Field. Homolytic Cleavage of FeS Bonds in Rubredoxin under Mechanical Stress. Angew. Chem. Int. Ed. 52, 8144–8146 (2013) [Link].

    • M. Sanchez-Martinez, E. Marcos, R. Tauler, M. J. Field and R. Crehuet. Conformational Compression and Barrier Height Heterogeneity in the N-Acetylglutatmate Kinase. J. Phys. Chem. B 117, 14261–14272 (2013) [Link].

2012

    • A. Aleksandrov and M. J.Field. A Hybrid Elastic Band String Algorithm for Studies of Enzymatic Reactions. Phys. Chem. Chem. Phys. 14, 12544–12553 (2012) [Link].

2011

    • A. Aleksandrov and M. J. Field. Efficient Solvent Boundary Potential for Hybrid Potential Simulations. Phys. Chem. Chem. Phys. 13, 10503–10509 (2011) [Link].

    • A. Roy, M. J. Field, V. Adam and D. Bourgeois. The Nature of Transient Dark States in a Photoactivatable Fluorescent Protein. J. Am. Chem. Soc. 133, 18586–18589 (2011) [Link].

2010

    • E. Marcos, M. J. Field and R. Crehuet. Pentacoordinated Phosphorus Revisited by High-Level QM/MM Calculations. Proteins: Structure, Function and Bioinformatics 78, 2405–2411 (2010) [Link].

2009

    • S. Roy, S. Goedecker, M. J. Field and E. Penev. A Minima-Hopping Study of All-Atom Protein Folding and Structure Prediction. J. Phys. Chem. B 113, 7315–7321 (2009) [Link].

    • M. Lelimousin, V. Adam, G. U. Nienhaus, D. Bourgeois and M. J. Field. Photoconversion of the Fluorescent Protein EosFP: A Hybrid Potential Simulation Study Reveals Intersystem Crossings. J. Am. Chem. Soc. 131, 16814–16823 (2009) [Link].

2008

    • I. Fernandez Galván and M. J. Field. Improving the Efficiency of the NEB Reaction Path Finding Algorithm. J. Comp. Chem. 29, 2008, 139–143 (2008) [Link].

    • I. Fernandez Galván, A. Volbeda, J. C. Fontecilla-Camps and M. J. Field. A QM/MM Study of Proton Transport Pathways in a Nickel-Iron Hydrogenase. Proteins: Structure, Function and Bioinformatics 73, 195–203 (2008) [Link].

    • G. M. Arantes. The Catalytic Acid in the Dephosphorylation of the Cdk2-pTpY/CycA Protein Complex by Cdc25B Phosphatase. J. Phys. Chem. B 112, 15244–15247 (2008) [Link].

    • G. M. Arantes and M. C. C. Ribeiro. A Microscopic View of Substitution Reactions Solvated by Ionic Liquids. J. Chem. Phys. 128, 114503 (2008) [Link].

2007

    • S. Keinan, X. Hu, D. N. Beratan and W. Yang. Designing Molecules with Optimal Properties using the Linear Combination of Atomic Potentials Approach in an AM1 Semiempirical Framework. J. Phys. Chem. A 111 176–181 (2007) [Link].

    • R. Crehuet and M. J. Field. A Transition Path Sampling Study of the Reaction Catalyzed by the Enzyme Chorismate Mutase. J. Phys. Chem. B 111, 5708–5718 (2007) [Link].

    • T. Wymore, D. W. Deerfield II and J. Hempel. Mechanistic Implications of the Cysteine-Nicotinamide Adduct in Aldehyde Dehydrogenase Based on Quantum Mechanical/Molecular Mechanical Simulations. Biochemistry 46, 9495–9506 (2007) [Link].

    • P. Amara, I. Fernandez Galván, J. C. Fontecilla-Camps and M. J. Field. The Enamine Intermediate May Not Be Universal to Thiamine Catalysis. Angew. Chemie Intl. Ed. 46, 9019–9022 (2007) [Link].

2006

    • A. Thomas and M. J. Field. A Comparative QM/MM Simulation Study of the Reaction Mechanisms of Human and Plasmodium falciparum HG(X)PRTases. J. Am. Chem. Soc. 128, 10096–10102 (2006) [Link].

    • G. M. Arantes and M. Loos. Specific Parametrisation of a Hybrid Potential to Simulate Reactions in Phosphatases. Phys. Chem. Chem. Phys. 8, 347–353 (2006) [Link].

    • G. M. Arantes. Free-Energy Profiles for Catalysis by a Dual-Specificity Phosphatase. Biochemical Journal 399, 343-350 (2006) [Link].

2005

    • R. Crehuet, A. Thomas and M. J. Field. An Implementation of the Nudged-Elastic-Band Algorithm and Application to the Reaction Mechanism of HGXPRTase from Plasmodium Falciparum. J. Mol. Graph. Model. 24, 102–110 (2005) [Link].

2004

    • N. Diaz and M. J. Field. Insights into the Phosphoryl-Transfer Mechanism of cAMP-Dependent Protein Kinase from Quantum Chemical Calculations and Molecular Dynamics Simulations. J. Am. Chem. Soc. 126, 529–542 (2004) [Link].

    • T. Wymore, J. Hempel, S. S. Cho, A. D. MacKerell Jr., H. B. Nicholas Jr. and D. W. Deerfield II. Molecular Recognition of Aldehydes by Aldehyde Dehydrogenase and Mechanism of Nucleophile Activation. Proteins: Structure, Function and Genetics 57, 758–771 (2004) [Link].

2003

    • P. Amara and M. J. Field. Evaluation of an Ab Initio QM/MM Hybrid-Potential Link-Atom Method. Theor. Chem. Accts. 109, 43–52 (2003) [Link].

    • T. Wymore, D. W. Deerfield II, M. J. Field, J. Hempel and H. B. Nicholas, Jr. Initial Catalytic Events in Class 3 Aldehyde Dehydrogenase: MM and QM/MM Simulations. Chemico-Biological Interactions 143/144, 75–84 (2003) [Link].

    • M. Oliva, O. Dideberg and M. J. Field. Understanding the Molecular Mechanims of Active-Site Serine Penicillin-Recognizing Proteins: A Molecular Dynamics Simulations Study. Proteins: Structure, Function and Genetics 53, 88–100 (2003) [Link].

    • E. Pellegrini and M. J. Field. Development and Testing of a de novo Drug-Design Algorithm. J. Comput. Aided Mol. Design 17, 621–41 (2003) [Link].

2002

    • E. Pellegrini and M. J. Field. A Generalized Born Solvation Model for Macromolecular Hybrid-Potential Calculations. J. Phys. Chem. A 106, 1316–1326 (2002) [Link].

    • A. Thomas and M. J. Field. Reaction Mechanism of the HGXPRTase from Plasmodium falciparum: A Hybrid Potential Quantum Mechanical/Molecular Mechanical Study. J. Am. Chem. Soc. 124, 12432–12438 (2002) [Link].

2001

    • S. Martí, J. Andrés, V. Moliner, E. Silla, I. Tuñón, J. Bertrán and M. J. Field. Insights into Enzyme Catalysis: The Chorismate Mutase Case. J. Am. Chem. Soc. 123, 1709–1712 (2001) [Link].

2000

    • C. Bret, M. J. Field and L. Hemmingsen. A Chemical Potential Equalization Model for Treating Polarization in Molecular Mechanical Force Fields. Mol. Phys. 98, 751–763 (2000) [Link].

    • F. Proust-De Martin, R. Dumas and M. J. Field. A Hybrid-Potential Free-Energy Study of the Isomerization Step of the Acetohydroxy Acid Isomeroreductase Reaction. J. Am. Chem. Soc. 122, 7688–7697 (2000) [Link].

1999

    • A. Thomas, D. Jourand, C. Bret, P. Amara and M. J. Field. Is There a Covalent Intermediate in the Viral Neuraminidase Reaction? A Hybrid-Potential Free-Energy Study. J. Am. Chem. Soc. 121, 9693–9702 (1999) [Link].