ChemShell—a modular software package for QM/MM simulations

ChemShell is a modular computational chemistry package with a particular focus on hybrid quantum mechanical/molecular mechanical (QM/MM) simulations. A core set of chemical data handling modules and scripted interfaces to a large number of quantum chemistry and molecular modeling packages underpin a flexible QM/MM scheme. ChemShell has been used in the study of small molecules, molecular crystals, biological macromolecules such as enzymes, framework materials including zeolites, ionic solids, and surfaces. We outline the range of QM/MM coupling schemes and supporting functions for system setup, geometry optimization, and transition‐state location (including those from the open‐source DL‐FIND optimization library). We discuss recently implemented features allowing a more efficient treatment of long range electrostatic interactions, X‐ray based quantum refinement of crystal structures, free energy methods, and excited‐state calculations. ChemShell has been ported to a range of parallel computers and we describe a number of options including parallel execution based on the message‐passing capabilities of the interfaced packages and task‐farming for applications in which a number of individual QM, MM, or QM/MM calculations can performed simultaneously. We exemplify each of the features by brief reference to published applications.

[1]  K. Sen,et al.  Peroxo-iron mediated deformylation in sterol 14alpha-demethylase catalysis. , 2010, Journal of the American Chemical Society.

[2]  Marco Bocola,et al.  A conclusive mechanism of the photoinduced reaction cascade in blue light using flavin photoreceptors. , 2008, Journal of the American Chemical Society.

[3]  H. Senn,et al.  QM/MM Methods for Biological Systems , 2006 .

[4]  Walter Thiel,et al.  A combined QM/MM study on the reductive half-reaction of xanthine oxidase: substrate orientation and mechanism. , 2009, Journal of the American Chemical Society.

[5]  Gregory J O Beran,et al.  Prediction of organic molecular crystal geometries from MP2-level fragment quantum mechanical/molecular mechanical calculations. , 2012, The Journal of chemical physics.

[6]  W Smith,et al.  DL_POLY_2.0: a general-purpose parallel molecular dynamics simulation package. , 1996, Journal of molecular graphics.

[7]  Walter Thiel,et al.  QM/MM methods for biomolecular systems. , 2009, Angewandte Chemie.

[8]  Walter Thiel,et al.  Linear scaling geometry optimisation and transition state search in hybrid delocalised internal coordinates , 2000 .

[9]  Paul Sherwood,et al.  Zeolite structure and reactivity by combined quantum-chemical- classical calculations , 1999 .

[10]  Walter Thiel,et al.  Solvent Boundary Potentials for Hybrid QM/MM Computations Using Classical Drude Oscillators: A Fully Polarizable Model. , 2012, Journal of chemical theory and computation.

[11]  W. A. Brown,et al.  An embedded cluster study of the formation of water on interstellar dust grains. , 2009, Physical chemistry chemical physics : PCCP.

[12]  W. Thiel,et al.  Implementation of surface hopping molecular dynamics using semiempirical methods , 2008 .

[13]  Qian Peng,et al.  Quantum chemical insights into the aggregation induced emission phenomena: A QM/MM study for pyrazine derivatives , 2012, J. Comput. Chem..

[14]  Julian D. Gale,et al.  The General Utility Lattice Program (GULP) , 2003 .

[15]  M. Waller,et al.  51V NMR chemical shifts from quantum-mechanical/molecular-mechanical models of vanadium bromoperoxidase. , 2008, The journal of physical chemistry. B.

[16]  W. Thiel,et al.  Long-Range Electrostatic Effects in QM/MM Studies of Enzymatic Reactions: Application of the Solvated Macromolecule Boundary Potential. , 2011, Journal of chemical theory and computation.

[17]  S. C. Rogers,et al.  QUASI: A general purpose implementation of the QM/MM approach and its application to problems in catalysis , 2003 .

[18]  M. Bühl,et al.  Modeling Molecular Crystals by QM/MM: Self-Consistent Electrostatic Embedding for Geometry Optimizations and Molecular Property Calculations in the Solid. , 2012, Journal of chemical theory and computation.

[19]  M. Elstner,et al.  The protonation state of Glu181 in rhodopsin revisited: interpretation of experimental data on the basis of QM/MM calculations. , 2010, The journal of physical chemistry. B.

[20]  Walter Thiel,et al.  QM/MM Free-Energy Perturbation Compared to Thermodynamic Integration and Umbrella Sampling:  Application to an Enzymatic Reaction. , 2006, Journal of chemical theory and computation.

[21]  Walter Thiel,et al.  Enzymatic Hydroxylation in p-Hydroxybenzoate Hydroxylase:  A Case Study for QM/MM Molecular Dynamics. , 2005, Journal of chemical theory and computation.

[22]  P. Sherwood,et al.  The Growth of Copper Clusters over ZnO: the Competition between Planar and Polyhedral Clusters , 2008 .

[23]  W. Thiel,et al.  Influence of the LOV domain on low-lying excited states of flavin: a combined quantum-mechanics/molecular-mechanics investigation. , 2009, The journal of physical chemistry. B.

[24]  W. Thiel,et al.  Hydrogen bonding regulates the monomeric nonradiative decay of adenine in DNA strands. , 2011, Angewandte Chemie.

[25]  You Lu,et al.  Monomeric adenine decay dynamics influenced by the DNA environment , 2012, J. Comput. Chem..

[26]  Johannes Kästner,et al.  Locating Instantons in Many Degrees of Freedom. , 2011, Journal of chemical theory and computation.

[27]  K. Travis,et al.  Novel potentials for modelling defect formation and oxygen vacancy migration in Gd2Ti2O7 and Gd2Zr2O7 pyrochlores , 2012 .

[28]  Alexey A. Sokol,et al.  Zinc oxide: A case study in contemporary computational solid state chemistry , 2008, J. Comput. Chem..

[29]  Dongqi Wang,et al.  Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: a combined QM/MM study. , 2009, Journal of the American Chemical Society.

[30]  Marco Bocola,et al.  A QM/MM study on the fast photocycle of blue light using flavin photoreceptors in their light-adapted/active form. , 2010, Physical chemistry chemical physics : PCCP.

[31]  H. Senn,et al.  Insight into enzymatic C-F bond formation from QM and QM/MM calculations. , 2005, Journal of the American Chemical Society.

[32]  M. Waller,et al.  51V NMR chemical shifts calculated from QM/MM models of peroxo forms of vanadium haloperoxidases. , 2009, The journal of physical chemistry. B.

[33]  W. Thiel,et al.  QM/MM nonadiabatic decay dynamics of 9H-adenine in aqueous solution. , 2011, Chemphyschem : a European journal of chemical physics and physical chemistry.

[34]  S. Shaik,et al.  A single-site mutation (F429H) converts the enzyme CYP 2B4 into a heme oxygenase: a QM/MM study. , 2012, Journal of the American Chemical Society.

[35]  W. Thiel,et al.  Quantum refinement of protein structures: implementation and application to the red fluorescent protein DsRed.M1. , 2010, The journal of physical chemistry. B.

[36]  P. Sherwood,et al.  Hybrid QM/MM embedding approach for the treatment of localized surface states in ionic materials , 2004 .

[37]  Walter Thiel,et al.  Photoinduced nonadiabatic dynamics of 9H-guanine. , 2009, Chemphyschem : a European journal of chemical physics and physical chemistry.

[38]  Walter Thiel,et al.  Toward accurate barriers for enzymatic reactions: QM/MM case study on p-hydroxybenzoate hydroxylase. , 2008, The Journal of chemical physics.

[39]  Walter Thiel,et al.  DL-FIND: an open-source geometry optimizer for atomistic simulations. , 2009, The journal of physical chemistry. A.

[40]  S. Shaik,et al.  How Do Perfluorinated Alkanoic Acids Elicit Cytochrome P450 to Catalyze Methane Hydroxylation? An MD and QM/MM Study. , 2013, RSC advances.

[41]  Walter Thiel,et al.  Assessment of semiempirical methods for the photoisomerisation of a protonated Schiff base , 2009 .

[42]  Yong Wang,et al.  P450 enzymes: their structure, reactivity, and selectivity-modeled by QM/MM calculations. , 2010, Chemical reviews.

[43]  Alexey A. Sokol,et al.  Characterization of hydrogen dissociation over aluminium-doped zinc oxide using an efficient massively parallel framework for QM/MM calculations , 2011, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[44]  P. Sherwood,et al.  Activation of carbon dioxide over zinc oxide by localised electrons. , 2012, Chemphyschem : a European journal of chemical physics and physical chemistry.

[45]  H. Senn,et al.  Finite-temperature effects in enzymatic reactions - Insights from QM/MM free-energy simulations , 2009 .

[46]  Walter Thiel,et al.  Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations. , 2010, The Journal of chemical physics.

[47]  Walter Thiel,et al.  Efficiency and Accuracy of the Generalized Solvent Boundary Potential for Hybrid QM/MM Simulations: Implementation for Semiempirical Hamiltonians. , 2008, Journal of chemical theory and computation.

[48]  W. Thiel,et al.  QM/MM studies of xanthine oxidase: variations of cofactor, substrate, and active-site Glu802. , 2010, The journal of physical chemistry. B.

[49]  M. Vincent,et al.  Computer simulation of zeolite structure and reactivity using embedded cluster methods , 1997 .

[50]  Frank Neese,et al.  Toward identification of the compound I reactive intermediate in cytochrome P450 chemistry: a QM/MM study of its EPR and Mössbauer parameters. , 2005, Journal of the American Chemical Society.

[51]  Walter Thiel,et al.  Exploiting QM/MM Capabilities in Geometry Optimization:  A Microiterative Approach Using Electrostatic Embedding. , 2007, Journal of chemical theory and computation.

[52]  Walter Thiel,et al.  A General Boundary Potential for Hybrid QM/MM Simulations of Solvated Biomolecular Systems. , 2009, Journal of chemical theory and computation.