Development of Classical Force Fields for Interfaces between Single Molecules and Au.

Interfaces between metals and organic materials play an essential role in molecular surface science, photovoltaics, or molecular electronics. Modeling the evolution of interface geometry over sufficiently long timescales requires an accurate parameterization of the relevant metal-molecule interactions. Here, we describe a method for calculating interface parameters from reference density functional theory calculations of small metal-molecule complexes. We apply this method to develop a parameter set for a series of metal-molecule-metal junctions. We study the dynamics of short oligophenyls with amine, methyl-sulfide, or direct Au-C links, which are bonded to Au(111) via small adatom structures. Nanosecond classical molecular dynamics simulations using the generated parameter set reveal insight into molecular degrees of freedom not accessible from ab initio molecular dynamics simulations.

[1]  H. Vázquez,et al.  Calculation of Energy Level Alignment and Interface Electronic Structure in Molecular Junctions beyond DFT , 2021, The Journal of Physical Chemistry C.

[2]  Hyunhak Jeong,et al.  Understanding the Conductance Dispersion of Single-Molecule Junctions , 2020, The Journal of Physical Chemistry C.

[3]  Zhi Li,et al.  Molecular Electronics: Toward the Atomistic Modeling of Conductance Histograms , 2019, The Journal of Physical Chemistry C.

[4]  H. Vázquez,et al.  Crossover in the inelastic electron tunneling spectra of conjugated molecules with direct Au-C links. , 2019, Physical chemistry chemical physics : PCCP.

[5]  A. Pecchia,et al.  Nanoscale morphology and electronic coupling at the interface between indium tin oxide and organic molecular materials. , 2018, Nanoscale.

[6]  H. Vázquez,et al.  Direct Au-C contacts based on biphenylene for single molecule circuits. , 2018, Physical chemistry chemical physics : PCCP.

[7]  H. Shigekawa,et al.  The effect of nitrogen lone-pair interaction on the conduction in a single-molecule junction with amine-Au bonding , 2018, Scientific Reports.

[8]  A. Tkatchenko,et al.  Modeling Nonreactive Molecule-Surface Systems on Experimentally Relevant Time and Length Scales: Dynamics and Conductance of Polyfluorene on Au(111). , 2018, The journal of physical chemistry letters.

[9]  N. Renaud,et al.  Signatures of Conformational Dynamics and Electrode-Molecule Interactions in the Conductance Profile During Pulling of Single-Molecule Junctions. , 2018, The journal of physical chemistry letters.

[10]  T. Kawai,et al.  Stretching-Induced Conductance Variations as Fingerprints of Contact Configurations in Single-Molecule Junctions. , 2017, Journal of the American Chemical Society.

[11]  Shiling Yuan,et al.  The properties of asphaltene at the oil-water interface: A molecular dynamics simulation , 2017 .

[12]  I. Yarovsky,et al.  Understanding and Designing the Gold-Bio Interface: Insights from Simulations. , 2016, Small.

[13]  M. Hybertsen,et al.  Structure-Property Relationships in Atomic-Scale Junctions: Histograms and Beyond. , 2016, Accounts of chemical research.

[14]  Colin Nuckolls,et al.  Chemical principles of single-molecule electronics , 2016 .

[15]  G. Cuniberti,et al.  Modeling of Solvent Effects in the Electrical Response of π-Stacked Molecular Junctions , 2015 .

[16]  Y. Leng,et al.  Gold/Benzenedithiolate/Gold Molecular Junction: A Driven Dynamics Simulation on Structural Evolution and Breaking Force under Pulling , 2015 .

[17]  J. Neaton,et al.  Single-molecule diodes with high rectification ratios through environmental control. , 2015, Nature nanotechnology.

[18]  N. N. Medvedev,et al.  Structure of dimers of glycyrrhizic acid in water and their complexes with cholesterol: Molecular dynamics simulation , 2015, Journal of Structural Chemistry.

[19]  G. Cuniberti,et al.  Interplay between Mechanical and Electronic Degrees of Freedom in π-Stacked Molecular Junctions: From Single Molecules to Mesoscopic Nanoparticle Networks , 2015 .

[20]  C. Lambert,et al.  Interplay between quantum interference and conformational fluctuations in single-molecule break junctions. , 2015, Nanoscale.

[21]  Fredrik Westerlund,et al.  Single-molecule electronics: from chemical design to functional devices. , 2014, Chemical Society reviews.

[22]  M. Steigerwald,et al.  Trimethyltin-mediated covalent gold-carbon bond formation. , 2014, Journal of the American Chemical Society.

[23]  J. Olmos-Asar,et al.  Monolayer protected gold nanoparticles: the effect of the headgroup-Au interaction. , 2014, Physical chemistry chemical physics : PCCP.

[24]  Chengbu Liu,et al.  Toward the development of the potential with angular distortion for halogen bond: a comparison of potential energy surfaces between halogen bond and hydrogen bond. , 2014, The journal of physical chemistry. A.

[25]  Wilfred F van Gunsteren,et al.  Practical Aspects of Free-Energy Calculations: A Review. , 2014, Journal of chemical theory and computation.

[26]  J. Mendieta,et al.  fireball/amber: An Efficient Local-Orbital DFT QM/MM Method for Biomolecular Systems. , 2014, Journal of chemical theory and computation.

[27]  Klaus Schulten,et al.  Rapid parameterization of small molecules using the force field toolkit , 2013, J. Comput. Chem..

[28]  M. Hybertsen,et al.  Length-dependent thermopower of highly conducting Au-C bonded single molecule junctions. , 2013, Nano letters.

[29]  L. Venkataraman,et al.  Correlating structure, conductance, and mechanics of silver atomic-scale contacts. , 2013, ACS nano.

[30]  Amaury de Melo Souza,et al.  Atomistic simulations of highly conductive molecular transport junctions under realistic conditions. , 2013, Nanoscale.

[31]  C. Iacovella,et al.  Structural Origins of Conductance Fluctuations in Gold-Thiolate Molecular Transport Junctions. , 2013, The journal of physical chemistry letters.

[32]  Tiffany R Walsh,et al.  GolP-CHARMM: First-Principles Based Force Fields for the Interaction of Proteins with Au(111) and Au(100). , 2013, Journal of chemical theory and computation.

[33]  R. K. Mishra,et al.  Thermodynamically consistent force fields for the assembly of inorganic, organic, and biological nanostructures: the INTERFACE force field. , 2013, Langmuir : the ACS journal of surfaces and colloids.

[34]  E. Leiva,et al.  Anchoring sites to the STM tip can explain multiple peaks in single molecule conductance histograms. , 2013, Physical chemistry chemical physics : PCCP.

[35]  M. Askerka,et al.  Theoretical prediction of S-H bond rupture in methanethiol upon interaction with gold. , 2012, The journal of physical chemistry. A.

[36]  M. Hybertsen,et al.  Linker dependent bond rupture force measurements in single-molecule junctions. , 2012, Journal of the American Chemical Society.

[37]  C. Iacovella,et al.  Large-scale atomistic simulations of environmental effects on the formation and properties of molecular junctions. , 2012, ACS nano.

[38]  C. Lambert,et al.  Single molecular conductance of tolanes: experimental and theoretical study on the junction evolution dependent on the anchoring group. , 2012, Journal of the American Chemical Society.

[39]  Pramod C. Nair,et al.  An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0. , 2011, Journal of chemical theory and computation.

[40]  Severin T. Schneebeli,et al.  Highly conducting π-conjugated molecular junctions covalently bonded to gold electrodes. , 2011, Journal of the American Chemical Society.

[41]  Kangnian Fan,et al.  CO oxidation catalyzed by a single gold atom: benchmark calculations and the performance of DFT methods. , 2011, Physical chemistry chemical physics : PCCP.

[42]  Severin T. Schneebeli,et al.  In situ formation of highly conducting covalent Au-C contacts for single-molecule junctions. , 2011, Nature nanotechnology.

[43]  Shoji Takada,et al.  On easy implementation of a variant of the replica exchange with solute tempering in GROMACS , 2011, J. Comput. Chem..

[44]  M. Hybertsen,et al.  Mechanics and chemistry: single molecule bond rupture forces correlate with molecular backbone structure. , 2011, Nano letters.

[45]  Yong‐Hoon Kim,et al.  Conformational and conductance fluctuations in a single-molecule junction: Multiscale computational study , 2010 .

[46]  Guoli Zhang,et al.  Breaking mechanism of single molecular junctions formed by octanedithiol molecules and Au electrodes. , 2009, Journal of the American Chemical Society.

[47]  F. Flores,et al.  Modelling energy level alignment at organic interfaces and density functional theory. , 2009, Physical chemistry chemical physics : PCCP.

[48]  M. Steigerwald,et al.  Frustrated rotations in single-molecule junctions. , 2009, Journal of the American Chemical Society.

[49]  M. Ratner,et al.  Stochastic modulation in molecular electronic transport junctions: molecular dynamics coupled with charge transport calculations. , 2008, Nano letters.

[50]  M. Steigerwald,et al.  Contact chemistry and single-molecule conductance: a comparison of phosphines, methyl sulfides, and amines. , 2007, Journal of the American Chemical Society.

[51]  Yuyuan Tian,et al.  Single molecule junctions formed via Au-thiol contact: stability and breakdown mechanism. , 2007, Journal of the American Chemical Society.

[52]  M. Ford,et al.  Adsorption of Amine Compounds on the Au(111) Surface: A Density Functional Study , 2007 .

[53]  S. Louie,et al.  Amine-gold linked single-molecule circuits: experiment and theory. , 2007, Nano letters.

[54]  S. Louie,et al.  Renormalization of molecular electronic levels at metal-molecule interfaces. , 2006, Physical review letters.

[55]  M. Steigerwald,et al.  Single-molecule circuits with well-defined molecular conductance. , 2006, Nano letters.

[56]  J. Wells,et al.  Interaction between benzenedithiolate and gold: classical force field for chemical bonding. , 2005, The Journal of chemical physics.

[57]  P. M. Anderson,et al.  Developing a force field for simulation of poly(ethylene oxide) based upon ab initio calculations of 1,2-dimethoxyethane , 2005 .

[58]  A. Fazzio,et al.  How do gold nanowires break? , 2001, Physical review letters.

[59]  D. Sánchez-Portal,et al.  The SIESTA method for ab initio order-N materials simulation , 2001, cond-mat/0104182.

[60]  William L. Jorgensen,et al.  OPLS ALL-ATOM MODEL FOR AMINES : RESOLUTION OF THE AMINE HYDRATION PROBLEM , 1999 .

[61]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[62]  D. van der Spoel,et al.  GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .

[63]  P. Morse.  Diatomic Molecules According to the Wave Mechanics. II. Vibrational Levels , 1929 .

[64]  M. Paulsson,et al.  Conductance of alkanedithiol single-molecule junctions: a molecular dynamics study. , 2009, Nano letters.

[65]  Xiaofan Luo,et al.  Molecular Electronics , 2009 .

[66]  A. Daniel Boese,et al.  Predicting the binding energies of H-bonded complexes: A comparative DFT study , 1999 .

[67]  Jean-Paul Ryckaert,et al.  Molecular dynamics of liquid alkanes , 1978 .

[68]  Jean-Paul Ryckaert,et al.  Molecular dynamics of liquid n-butane near its boiling point , 1975 .