Simulation of Adsorption Processes at Metallic Interfaces: An Image Charge Augmented QM/MM Approach.

A novel method for including polarization effects within hybrid quantum mechanics/molecular mechanics (QM/MM) simulations of adsorbate-metal systems is presented. The interactions between adsorbate (QM) and metallic substrate (MM) are described at the MM level of theory. Induction effects are additionally accounted for by applying the image charge formulation. The charge distribution induced within the metallic substrate is modeled by a set of Gaussian charges (image charges) centered at the metal atoms. The image charges and the electrostatic response of the QM potential are determined self-consistently by imposing the constant-potential condition within the metal. The implementation is embedded in a highly efficient Gaussian and plane wave framework and is naturally suited for periodic systems. Even though the electronic properties of the metallic substrate are not taken into account explicitly, the augmented QM/MM scheme can reproduce characteristic polarization effects of the adsorbate. The method is assessed through the investigation of structural and electronic properties of benzene, nitrobenzene, thymine, and guanine on Au(111). The study of small water clusters adsorbed on Pt(111) is also reported in order to demonstrate that the approach provides a sizable correction of the MM-based interactions between adsorbate and substrate. Large-scale molecular dynamics (MD) simulations of a water film in contact with a Pt(111) surface show that the method is suitable for simulations of liquid/metal interfaces at reduced computational cost.

[1]  M. McGrath,et al.  Vapor–liquid equilibria of water from first principles: comparison of density functionals and basis sets , 2006 .

[2]  K. B. Tarmyshov,et al.  Interface between platinum(111) and liquid isopropanol (2-propanol): a model for molecular dynamics studies. , 2007, The Journal of chemical physics.

[3]  A. Michaelides,et al.  General model for water monomer adsorption on close-packed transition and noble metal surfaces. , 2003, Physical review letters.

[4]  Walter Thiel,et al.  QM/MM studies of enzymes. , 2007, Current opinion in chemical biology.

[5]  Gregory K. Schenter,et al.  Excited States of the Bacteriochlorophyll b Dimer of Rhodopseudomonas viridis: A QM/MM Study of the Photosynthetic Reaction Center That Includes MM Polarization , 1995 .

[6]  D. Chandler,et al.  Hydrogen-bond kinetics in liquid water , 1996, Nature.

[7]  Hao Hu,et al.  Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods. , 2008, Annual review of physical chemistry.

[8]  Stewart K. Reed,et al.  Electrochemical interface between an ionic liquid and a model metallic electrode. , 2007, The Journal of chemical physics.

[9]  A. De Vita,et al.  Supramolecular self-assembly driven by electrostatic repulsion: The 1D aggregation of rubrene pentagons on Au111. , 2010, ACS nano.

[10]  G. Henkelman,et al.  A grid-based Bader analysis algorithm without lattice bias , 2009, Journal of physics. Condensed matter : an Institute of Physics journal.

[11]  M. Sullivan,et al.  Adsorption studies of C6H6 on Cu (111), Ag (111), and Au (111) within dispersion corrected density functional theory. , 2012, The Journal of chemical physics.

[12]  Minoru Sakurai,et al.  Study of the Opsin Shift of Bacteriorhodopsin: Insight from QM/MM Calculations with Electronic Polarization Effects of the Protein Environment , 2001 .

[13]  A. Michaelides,et al.  Interfacial water: a first principles molecular dynamics study of a nanoscale water film on salt. , 2009, The Journal of chemical physics.

[14]  L. Nilsson,et al.  Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K , 2001 .

[15]  C. Farina,et al.  Subtleties in energy calculations in the image method , 2009, 0903.4497.

[16]  T. Yokoyama,et al.  Quantitative analysis of long-range interactions between adsorbed dipolar molecules on Cu(111). , 2007, Physical review letters.

[17]  N. Marzari,et al.  Maximally localized generalized Wannier functions for composite energy bands , 1997, cond-mat/9707145.

[18]  P Mark,et al.  298KでのTIP3P,SPC及びSPC/E水モデルの構造及び動力学 , 2001 .

[19]  Erik L. G. Wernersson,et al.  On the effect of image charges and ion-wall dispersion forces on electric double layer interactions. , 2006, The Journal of chemical physics.

[20]  Michele Parrinello,et al.  Quickstep: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach , 2005, Comput. Phys. Commun..

[21]  Pablo G Debenedetti,et al.  A computational investigation of thermodynamics, structure, dynamics and solvation behavior in modified water models. , 2008, The Journal of chemical physics.

[22]  P. Taberna,et al.  On the molecular origin of supercapacitance in nanoporous carbon electrodes. , 2012, Nature materials.

[23]  S. F. Boys,et al.  The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors , 1970 .

[24]  Victor Guallar,et al.  QM/MM methods: looking inside heme proteins biochemistry. , 2010, Biophysical chemistry.

[25]  David T. Limmer,et al.  Hydration of metal surfaces can be dynamically heterogeneous and hydrophobic , 2013, Proceedings of the National Academy of Sciences.

[26]  S. Goedecker,et al.  Relativistic separable dual-space Gaussian pseudopotentials from H to Rn , 1998, cond-mat/9803286.

[27]  J. Ilja Siepmann,et al.  Influence of surface topology and electrostatic potential on water/electrode systems , 1995 .

[28]  Christopher J. R. Illingworth,et al.  Classical polarization in hybrid QM/MM methods. , 2006, The journal of physical chemistry. A.

[29]  Alessandro Laio,et al.  An Efficient Linear-Scaling Electrostatic Coupling for Treating Periodic Boundary Conditions in QM/MM Simulations. , 2006, Journal of chemical theory and computation.

[30]  Teter,et al.  Separable dual-space Gaussian pseudopotentials. , 1996, Physical review. B, Condensed matter.

[31]  Joost VandeVondele,et al.  Gaussian basis sets for accurate calculations on molecular systems in gas and condensed phases. , 2007, The Journal of chemical physics.

[32]  G. Wannier.  The Structure of Electronic Excitation Levels in Insulating Crystals , 1937 .

[33]  D. Nordlund,et al.  Structure and bonding of water on Pt(111). , 2002, Physical review letters.

[34]  F. Zerbetto,et al.  Modeling the stability and the motion of DNA nucleobases on the gold surface. , 2005, Langmuir : the ACS journal of surfaces and colloids.

[35]  M. Scheffler,et al.  The interaction of a point charge with a metal surface: theory and calculations for (111), (100) and (110) aluminium surfaces , 1995 .

[36]  B. D. Kay,et al.  A unique vibrational signature of rotated water monolayers on Pt(111): predicted and observed. , 2011, The Journal of chemical physics.

[37]  Stefan Grimme,et al.  Semiempirical GGA‐type density functional constructed with a long‐range dispersion correction , 2006, J. Comput. Chem..

[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]  A. Michaelides,et al.  Ice nanoclusters at hydrophobic metal surfaces. , 2007, Nature materials.

[40]  D. F. Ogletree,et al.  Metal- and hydrogen-bonding competition during water adsorption on Pd(111) and Ru(0001). , 2009, Journal of the American Chemical Society.

[41]  M. W. Finnis,et al.  The interaction of a point charge with an aluminium (111) surface , 1991 .

[42]  Lev Kantorovich,et al.  Electrostatic energy calculation for the interpretation of scanning probe microscopy experiments , 2000 .

[43]  H. Ogasawara,et al.  Chemical bonding of water to metal surfaces studied with core-level spectroscopies , 2010 .

[44]  Stefano Corni,et al.  Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces , 2008, J. Comput. Chem..

[45]  W. J. Orville-Thomas.  Atoms in Molecules — a Quantum Theory , 1996 .

[46]  Teodora Todorova,et al.  Molecular dynamics simulation of liquid water: hybrid density functionals. , 2006, The journal of physical chemistry. B.

[47]  D. A. Dunnett.  Classical Electrodynamics , 2020, Nature.

[48]  S. Goedecker,et al.  Multiscale approach for simulations of Kelvin Probe force microscopy with atomic resolution , 2012, 1203.5401.

[49]  Burke,et al.  Generalized Gradient Approximation Made Simple. , 1996, Physical review letters.

[50]  J. V. Lenthe,et al.  State of the Art in Counterpoise Theory , 1994 .

[51]  Wanda Andreoni,et al.  Decanethiols on gold: The structure of self-assembled monolayers unraveled with computer simulations , 2003 .

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

[53]  N. Bartelt,et al.  Pentagons and heptagons in the first water layer on Pt(111). , 2010, Physical review letters.

[54]  Matthias Krack,et al.  Pseudopotentials for H to Kr optimized for gradient-corrected exchange-correlation functionals , 2005 .

[55]  Foiles,et al.  Embedded-atom-method functions for the fcc metals Cu, Ag, Au, Ni, Pd, Pt, and their alloys. , 1986, Physical review. B, Condensed matter.

[56]  S. Grimme,et al.  A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. , 2010, The Journal of chemical physics.

[57]  M. McGrath,et al.  Spatial correlation of dipole fluctuations in liquid water , 2007 .

[58]  Alexander L. Shluger,et al.  QM/MM method for metal–organic interfaces , 2010, J. Comput. Chem..

[59]  R. Friesner,et al.  Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis. , 2005, Annual review of physical chemistry.

[60]  Chandler,et al.  Effect of environment on hydrogen bond dynamics in liquid water. , 1996, Physical review letters.

[61]  Ivano Tavernelli,et al.  Structure and Dynamics of Liquid Water from ab Initio Molecular Dynamics-Comparison of BLYP, PBE, and revPBE Density Functionals with and without van der Waals Corrections. , 2012, Journal of chemical theory and computation.

[62]  D. Griffiths.  Introduction to Electrodynamics , 2017 .

[63]  Stewart K. Reed,et al.  Water at an electrochemical interface--a simulation study. , 2008, Faraday discussions.

[64]  O. Borodin,et al.  On the Influence of Surface Topography on the Electric Double Layer Structure and Differential Capacitance of Graphite/Ionic Liquid Interfaces , 2011 .

[65]  Stefano Corni,et al.  GolP: An atomistic force‐field to describe the interaction of proteins with Au(111) surfaces in water , 2009, J. Comput. Chem..

[66]  F. Bocquet,et al.  Polarization effects in noncontact atomic force microscopy: A key to model the tip-sample interaction above charged adatoms , 2011 .

[67]  Michele Parrinello,et al.  A hybrid Gaussian and plane wave density functional scheme , 1997 .

[68]  Alessandro Laio,et al.  An Efficient Real Space Multigrid QM/MM Electrostatic Coupling. , 2005, Journal of chemical theory and computation.

[69]  Francois Gygi,et al.  Water confined in nanotubes and between graphene sheets: a first principle study. , 2008, Journal of the American Chemical Society.

[70]  S. Haq,et al.  Water adsorption and the wetting of metal surfaces , 2009 .