Response properties of embedded molecules through the polarizable embedding model

The polarizable embedding (PE) model is a fragment-based quantum-classical approach aimed at accurate inclusion of environment effects in quantum-mechanical response property calculations. The aim of this tutorial is to give insight into the practical use of the PE model. Starting from a set of molecular structures and until you arrive at the final property, there are many crucial details to consider in order to obtain trustworthy results in an efficient manner. To lower the threshold for new users wanting to explore the use of the PE model, we describe and discuss important aspects related to its practical use. This includes directions on how to generate input files and how to run a calculation.

[1]  C. E. Dykstra Efficient calculation of electrically based intermolecular potentials of weakly bonded clusters , 1988 .

[2]  J. Olsen,et al.  Linear and nonlinear response functions for an exact state and for an MCSCF state , 1985 .

[3]  John B. Shoven,et al.  I , Edinburgh Medical and Surgical Journal.

[4]  L. Onsager Electric Moments of Molecules in Liquids , 1936 .

[5]  U. Ryde,et al.  Conformational Dependence of Isotropic Polarizabilities. , 2011, Journal of chemical theory and computation.

[6]  Jacob Kongsted,et al.  The polarizable embedding coupled cluster method. , 2011, Journal of Chemical Physics.

[7]  Jacob Kongsted,et al.  Local electric fields and molecular properties in heterogeneous environments through polarizable embedding. , 2016, Physical chemistry chemical physics : PCCP.

[8]  C. Cappelli,et al.  Integrated QM/polarizable MM/continuum approaches to model chiroptical properties of strongly interacting solute–solvent systems , 2016 .

[9]  Jógvan Magnus Haugaard Olsen,et al.  Averaged Solvent Embedding Potential Parameters for Multiscale Modeling of Molecular Properties. , 2016, Journal of chemical theory and computation.

[10]  P. C. Hariharan,et al.  The influence of polarization functions on molecular orbital hydrogenation energies , 1973 .

[11]  Jacob Kongsted,et al.  The multi-configuration self-consistent field method within a polarizable embedded framework. , 2013, The Journal of chemical physics.

[12]  Christian Ochsenfeld,et al.  A convergence study of QM/MM isomerization energies with the selected size of the QM region for peptidic systems. , 2009, The journal of physical chemistry. A.

[13]  Jógvan Magnus Haugaard Olsen,et al.  Nuclear Magnetic Shielding Constants from Quantum Mechanical/Molecular Mechanical Calculations Using Polarizable Embedding: Role of the Embedding Potential. , 2014, Journal of chemical theory and computation.

[14]  Jacob Kongsted,et al.  Automated Fragmentation Polarizable Embedding Density Functional Theory (PE-DFT) Calculations of Nuclear Magnetic Resonance (NMR) Shielding Constants of Proteins with Application to Chemical Shift Predictions. , 2017, Journal of chemical theory and computation.

[15]  Jógvan Magnus Haugaard Olsen,et al.  Convergence of environment polarization effects in multiscale modeling of excitation energies , 2014 .

[16]  Jógvan Magnus H. Olsen,et al.  Multipole moments for embedding potentials: Exploring different atomic allocation algorithms , 2016, J. Comput. Chem..

[17]  Jacob Kongsted,et al.  Statistical mechanically averaged molecular properties of liquid water calculated using the combined coupled cluster/molecular dynamics method. , 2006, The Journal of chemical physics.

[18]  Jógvan Magnus Haugaard Olsen,et al.  Analysis of computational models for an accurate study of electronic excitations in GFP. , 2015, Physical chemistry chemical physics : PCCP.

[19]  W. L. Jorgensen Quantum and statistical mechanical studies of liquids. 10. Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water , 2002 .

[20]  Jógvan Magnus Haugaard Olsen,et al.  The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein. , 2017, Journal of chemical theory and computation.

[21]  Jacob Kongsted,et al.  Polarizable embedding with a multiconfiguration short-range density functional theory linear response method. , 2015, The Journal of chemical physics.

[22]  Kenneth Ruud,et al.  A density matrix-based quasienergy formulation of the Kohn-Sham density functional response theory using perturbation- and time-dependent basis sets. , 2008, The Journal of chemical physics.

[23]  Petr Kulhánek,et al.  Evaluating boundary dependent errors in QM/MM simulations. , 2009, The journal of physical chemistry. B.

[24]  J. Kongsted,et al.  Modeling magnetic circular dichroism within the polarizable embedding approach , 2018, Theoretical Chemistry Accounts.

[25]  Christian Ochsenfeld,et al.  Convergence of Electronic Structure with the Size of the QM Region: Example of QM/MM NMR Shieldings. , 2012, Journal of chemical theory and computation.

[26]  Jacob Kongsted,et al.  Molecular Properties through Polarizable Embedding , 2011 .

[27]  Pär Söderhjelm,et al.  How accurate can a force field become? A polarizable multipole model combined with fragment-wise quantum-mechanical calculations. , 2009, The journal of physical chemistry. A.

[28]  Jacob Kongsted,et al.  Damped Response Theory in Combination with Polarizable Environments: The Polarizable Embedding Complex Polarization Propagator Method. , 2014, Journal of chemical theory and computation.

[29]  B. Thole Molecular polarizabilities calculated with a modified dipole interaction , 1981 .

[30]  Jacopo Tomasi,et al.  A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics , 1997 .

[31]  U. Singh,et al.  A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the CH3Cl + Cl− exchange reaction and gas phase protonation of polyethers , 1986 .

[32]  J. G. Snijders,et al.  A discrete solvent reaction field model within density functional theory , 2003 .

[33]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[34]  Christine M Isborn,et al.  Electronic Absorption Spectra from MM and ab initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein. , 2012, Journal of chemical theory and computation.

[35]  J. Pople,et al.  Self—Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian—Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules , 1972 .

[36]  Trygve Helgaker,et al.  Recent advances in wave function-based methods of molecular-property calculations. , 2012, Chemical reviews.

[37]  M. Swart,et al.  DRF90: a polarizable force field , 2006 .

[38]  M. Levitt,et al.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.

[39]  Walter Thiel,et al.  Convergence in the QM‐only and QM/MM modeling of enzymatic reactions: A case study for acetylene hydratase , 2013, J. Comput. Chem..

[40]  Frank Jensen,et al.  Basis Set Convergence of Nuclear Magnetic Shielding Constants Calculated by Density Functional Methods. , 2008, Journal of chemical theory and computation.

[41]  Olav Vahtras LoProp for Dalton , 2014 .

[42]  F. Jensen Unifying General and Segmented Contracted Basis Sets. Segmented Polarization Consistent Basis Sets. , 2014, Journal of chemical theory and computation.

[43]  Pär Söderhjelm,et al.  Protein Influence on Electronic Spectra Modeled by Multipoles and Polarizabilities. , 2009, Journal of chemical theory and computation.

[44]  Luca Frediani,et al.  The Dalton quantum chemistry program system , 2013, Wiley interdisciplinary reviews. Computational molecular science.

[45]  T. Martínez,et al.  The charge transfer problem in density functional theory calculations of aqueously solvated molecules. , 2013, The journal of physical chemistry. B.

[46]  Jógvan Magnus Haugaard Olsen,et al.  PERI-CC2: A Polarizable Embedded RI-CC2 Method. , 2012, Journal of chemical theory and computation.

[47]  F. Jensen,et al.  Electrostatic Potential of Insulin: Exploring the Limitations of Density Functional Theory and Force Field Methods. , 2013, Journal of chemical theory and computation.

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

[49]  Jacob Kongsted,et al.  Solvation Effects on Electronic Transitions: Exploring the Performance of Advanced Solvent Potentials in Polarizable Embedding Calculations. , 2011, Journal of chemical theory and computation.

[50]  M. Karplus,et al.  A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations , 1990 .

[51]  Heather J. Kulik,et al.  How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase , 2015, The journal of physical chemistry. B.

[52]  Christine M Isborn,et al.  Convergence of Computed Aqueous Absorption Spectra with Explicit Quantum Mechanical Solvent. , 2017, Journal of chemical theory and computation.

[53]  Jógvan Magnus Haugaard Olsen,et al.  Relativistic Polarizable Embedding. , 2017, Journal of chemical theory and computation.

[54]  J. Tomasi,et al.  Quantum mechanical continuum solvation models. , 2005, Chemical reviews.

[55]  Kurt V. Mikkelsen,et al.  On the importance of excited state dynamic response electron correlation in polarizable embedding methods , 2012, J. Comput. Chem..

[56]  Jógvan Magnus Haugaard Olsen,et al.  Open-ended response theory with polarizable embedding: multiphoton absorption in biomolecular systems. , 2016, Physical chemistry chemical physics : PCCP.

[57]  Chris-Kriton Skylaris,et al.  Electrostatic embedding in large-scale first principles quantum mechanical calculations on biomolecules. , 2011, The Journal of chemical physics.

[58]  Daniel Wüstner,et al.  Embedding beyond electrostatics-The role of wave function confinement. , 2016, The Journal of chemical physics.

[59]  Hui Li,et al.  Note: FixSol solvation model and FIXPVA2 tessellation scheme. , 2012, The Journal of chemical physics.

[60]  Kenneth Ruud,et al.  Polarizable density embedding: a new QM/QM/MM-based computational strategy. , 2015, The journal of physical chemistry. A.

[61]  Jógvan Magnus Haugaard Olsen,et al.  A QM/MM and QM/QM/MM study of Kerr, Cotton-Mouton and Jones linear birefringences in liquid acetonitrile. , 2018, Physical chemistry chemical physics : PCCP.

[62]  Jógvan Magnus Haugaard Olsen PyFraME: Python tools for Fragment-based Multiscale Embedding , 2018 .

[63]  M. Gordon,et al.  Solvent effects on optical properties of molecules: a combined time-dependent density functional theory/effective fragment potential approach. , 2008, The Journal of chemical physics.

[64]  Jógvan Magnus Haugaard Olsen,et al.  Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials. , 2015, Journal of chemical theory and computation.

[65]  Jógvan Magnus Haugaard Olsen,et al.  Modeling Electronic Circular Dichroism within the Polarizable Embedding Approach. , 2017, Journal of chemical theory and computation.

[66]  J. Kongsted,et al.  Energy flow in the cryptophyte PE545 antenna is directed by bilin pigment conformation. , 2013, The journal of physical chemistry. B.

[67]  J. Kongsted,et al.  Lanczos-driven coupled-cluster damped linear response theory for molecules in polarizable environments. , 2014, The Journal of chemical physics.

[68]  N. Handy,et al.  A new hybrid exchange–correlation functional using the Coulomb-attenuating method (CAM-B3LYP) , 2004 .

[69]  Tsuyoshi Murata,et al.  {m , 1934, ACML.

[70]  P ? ? ? ? ? ? ? % ? ? ? ? , 1991 .

[71]  J. Kongsted,et al.  Electronic Energy Transfer in Condensed Phase Studied by a Polarizable QM/MM Model. , 2009, Journal of chemical theory and computation.

[72]  C. Cramer,et al.  Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics. , 1999, Chemical reviews.

[73]  J. Tomasi,et al.  Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects , 1981 .

[74]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[75]  Frank Jensen,et al.  Polarization consistent basis sets: Principles , 2001 .

[76]  Kurt V. Mikkelsen,et al.  Linear Response Properties of Liquid Water Calculated Using CC2 and CCSD within Different Molecular Mechanics Methods , 2004 .

[77]  Roland Lindh,et al.  Local properties of quantum chemical systems: the LoProp approach. , 2004, The Journal of chemical physics.

[78]  Jógvan Magnus H. Olsen,et al.  An averaged polarizable potential for multiscale modeling in phospholipid membranes , 2017, J. Comput. Chem..

[79]  Jógvan Magnus Haugaard Olsen Development of Quantum Chemical Methods towards Rationalization and Optimal Design of Photoactive Proteins , 2012 .

[80]  John Z. H. Zhang,et al.  Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein-molecule interaction energy , 2003 .

[81]  S. Schneider,et al.  Ribose-protonated DNA base excision repair: a combined theoretical and experimental study. , 2014, Angewandte Chemie.

[82]  Jacob Kongsted,et al.  Excited States in Solution through Polarizable Embedding , 2010 .

[83]  Susanne Hertz,et al.  Advances in Quantum Chemistry , 2019, Quantum Systems in Physics, Chemistry and Biology - Theory, Interpretation, and Results.

[84]  Kenneth Ruud,et al.  GEN1INT: A unified procedure for the evaluation of one‐electron integrals over Gaussian basis functions and their geometric derivatives , 2011 .

[85]  Jacob Kongsted,et al.  Polarizable Density Embedding: A Solution to the Electron Spill-Out Problem in Multiscale Modeling. , 2017, The journal of physical chemistry letters.

[86]  Jacob Kongsted,et al.  Computational Approach for Studying Optical Properties of DNA Systems in Solution. , 2016, Journal of chemical theory and computation.

[87]  Francesco Aquilante,et al.  Calculation of protein-ligand interaction energies by a fragmentation approach combining high-level quantum chemistry with classical many-body effects. , 2009, The journal of physical chemistry. B.

[88]  Gemechis D Degaga,et al.  Quantum chemistry as a tool to assess energetic and spectroscopic properties of C1 and C2 hydrocarbons in MOF-74-Mg , 2018, Theoretical Chemistry Accounts.

[89]  Jacob Kongsted,et al.  Excited states in large molecular systems through polarizable embedding. , 2016, Physical chemistry chemical physics : PCCP.