Intermolecular potentials for simulations of collisions of SiNCS+ and (CH3)2SiNCS+ ions with fluorinated self-assembled monolayers

Abstract Analytical potential energy functions were developed for interactions of SiNCS+ and (CH3)2SiNCS+ ions with perfluorinated self-assembled monolayer (F-SAM) surfaces. Two model compounds were used to represent an F-SAM: CF4 and nine chains of perfluorobutane forming a miniSAM structure. Density functional theory plus dispersion (DFT-D) calculations were carried out to compute intermolecular potential energy curves (IPECs) for these systems. The applied DFT-D method (specifically, B97-D) was successfully tested against high-level wavefunction calculations performed on the smallest system investigated. The IPECs calculated at the B97-D level were fitted to analytical potentials of the Buckingham type. The calculations show that the parameters obtained from the fits involving CF4 are transferable to the miniSAM system, provided the fittings are conducted with caution, thus corroborating that CF4 is a good model for parameterizing intermolecular potentials for interactions of gases with F-SAM surfaces.

[1]  Henry F. Schaefer,et al.  In pursuit of the ab initio limit for conformational energy prototypes , 1998 .

[2]  B. S. Day,et al.  Theoretical study of the effect of surface density on the dynamics of Ar + alkanethiolate self-assembled monolayer collisions. , 2006, The journal of physical chemistry. A.

[3]  B. S. Day,et al.  Packing density and structure effects on energy-transfer dynamics in argon collisions with organic monolayers. , 2005, The Journal of chemical physics.

[4]  Antonio Vila,et al.  AIM study on the influence of fluorine atoms on the alkyl chain , 2003 .

[5]  J. Barker,et al.  Identifying trapping desorption in gas–surface scattering , 2000 .

[6]  D. Nesbitt,et al.  Dynamics of CO2 scattering off a perfluorinated self-assembled monolayer. Influence of the incident collision energy, mass effects, and use of different surface models. , 2009, The journal of physical chemistry. A.

[7]  J. Futrell,et al.  Effect of the surface on charge reduction and desorption kinetics of soft landed peptide ions , 2009, Journal of the American Society for Mass Spectrometry.

[8]  Hans-Joachim Werner,et al.  Extrapolating MP2 and CCSD explicitly correlated correlation energies to the complete basis set limit with first and second row correlation consistent basis sets. , 2009, The Journal of chemical physics.

[9]  J. Pople,et al.  Møller–Plesset theory for atomic ground state energies , 1975 .

[10]  P. Kollman,et al.  An approach to computing electrostatic charges for molecules , 1984 .

[11]  R. Cooks,et al.  Ion/surface reactions, surface-induced dissociation and surface modification resulting from hyperthermal collisions of OCNCO+, OCNCS+, (CH3)2SiNCO+, and (CH3)2SiNCS+ with a fluorinated self-assembled monolayer surface , 1997 .

[12]  Cheng Chang,et al.  Properties of atoms in molecules: atomic volumes , 1987 .

[13]  W. T. Elam,et al.  Preparative soft and reactive landing of multiply charged protein ions on a plasma-treated metal surface. , 2005, Analytical chemistry.

[14]  P. Kollman,et al.  Atomic charges derived from semiempirical methods , 1990 .

[15]  W. Hase,et al.  A Hamiltonian with a Subset of Normal Modes for Studying Mode-Specific Energy Transfer in Intermolecular Collisions† , 2001 .

[16]  Hans W. Horn,et al.  ELECTRONIC STRUCTURE CALCULATIONS ON WORKSTATION COMPUTERS: THE PROGRAM SYSTEM TURBOMOLE , 1989 .

[17]  Donald G. Truhlar,et al.  Basis-set extrapolation , 1998 .

[18]  A. Nakajima,et al.  Soft-landing isolation of vanadium-benzene sandwich clusters on a room-temperature substrate using n-alkanethiolate self-assembled monolayer matrixes. , 2006, The journal of physical chemistry. B.

[19]  T. Yan,et al.  Dynamics of energy transfer in collisions of O(3P) atoms with a 1-decanethiol self-assembled monolayer surface. , 2006, The journal of physical chemistry. B.

[20]  W. Hase,et al.  ENERGY TRANSFER IN RARE GAS COLLISIONS WITH SELF-ASSEMBLED MONOLAYERS , 1997 .

[21]  D. Troya,et al.  Theoretical study of the dynamics of hyperthermal collisions of Ar with a fluorinated alkanethiolate self-assembled monolayer. , 2008, Physical chemistry chemical physics : PCCP.

[22]  Marco Häser,et al.  Auxiliary basis sets to approximate Coulomb potentials , 1995 .

[23]  P. Demirev,et al.  Characterization of intact microorganisms by MALDI mass spectrometry. , 2001, Mass spectrometry reviews.

[24]  Wesley D. Allen,et al.  The heat of formation of NCO , 1993 .

[25]  W. T. Elam,et al.  Preparative soft and reactive landing of gas-phase ions on plasma-treated metal surfaces. , 2005, Analytical chemistry.

[26]  J. Laskin,et al.  Helical peptide arrays on self-assembled monolayer surfaces through soft and reactive landing of mass-selected ions. , 2008, Angewandte Chemie.

[27]  W. Hase,et al.  A QM/MM model for O( 3 P) reaction with an alkyl thiolate self-assembled monolayer , 2000 .

[28]  U. Heiz,et al.  Imaging size-selected silicon clusters with a low-temperature scanning tunneling microscope , 2000 .

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

[30]  J. Laskin,et al.  In situ reactivity and TOF-SIMS analysis of surfaces prepared by soft and reactive landing of mass-selected ions. , 2010, Analytical chemistry.

[31]  D. Troya,et al.  Theoretical study of the dynamics of F+alkanethiol self-assembled monolayer hydrogen-abstraction reactions. , 2010, The Journal of chemical physics.

[32]  Muthu B. J. Wijesundara,et al.  Preparation of chemical gradient surfaces by hyperthermal polyatomic ion deposition: A new method for combinatorial materials science , 2001 .

[33]  W. Hase,et al.  Chemical Dynamics Simulations of CO2 in the Ground and First Excited Bend States Colliding with a Perfluorinated Self-Assembled Monolayer , 2010 .

[34]  R. Cooks,et al.  Ion/surface reactions and ion soft-landing. , 2005, Physical chemistry chemical physics : PCCP.

[35]  A. Nakajima,et al.  Soft-landing isolation of gas-phase-synthesized transition metal-benzene complexes into a fluorinated self-assembled monolayer matrix , 2008 .

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

[37]  K. Rademann,et al.  Bimodal Distribution in the Fragmentation Behavior of Small Antimony Clusters Sb + x ( x = 3-12) Scattered from a Highly Oriented Pyrolitic Graphite Surface , 1999 .

[38]  Martin W. Feyereisen,et al.  Use of approximate integrals in ab initio theory. An application in MP2 energy calculations , 1993 .

[39]  A. Nakajima,et al.  Thermal and Hyperthermal Collision-Energy Depositions of Transition Metal−Benzene Sandwich Complexes onto a Self-Assembled n-Octadecanethiol Monolayer , 2008 .

[40]  G. Whitesides,et al.  Self-assembled monolayers of thiolates on metals as a form of nanotechnology. , 2005, Chemical reviews.

[41]  Brian D. Wladkowski,et al.  The SN2 Identity Exchange Reaction F- + CH3F .fwdarw. FCH3 + F-: Definitive ab Initio Predictions , 1994 .

[42]  Janet E. Jones.  On the determination of molecular fields. —II. From the equation of state of a gas , 1924 .

[43]  C David Sherrill,et al.  An Assessment of Density Functional Methods for Potential Energy Curves of Nonbonded Interactions: The XYG3 and B97-D Approximations. , 2010, Journal of chemical theory and computation.

[44]  W. Hase,et al.  Intermolecular potential to represent collisions of protonated peptide ions with fluorinated alkane surfaces. , 2005, The journal of physical chemistry. B.

[45]  Richard D. Smith,et al.  Retrieval of DNA Using Soft-Landing after Mass Analysis by ESI-FTICR for Enzymatic Manipulation , 1999 .

[46]  D. Bakowies.  Accurate extrapolation of electron correlation energies from small basis sets. , 2007, The Journal of chemical physics.

[47]  R. Cooks,et al.  Soft landing of ions onto self-assembled hydrocarbon and fluorocarbon monolayer surfaces 1 1 Dedicat , 1999 .

[48]  W. Hase,et al.  Effect of surface stiffness on the efficiency of surface-induced dissociation , 2001 .

[49]  W. Hase,et al.  Chemical Dynamics Simulations of CO2 Scattering off a Fluorinated Self-Assembled Monolayer Surface , 2007 .

[50]  C. Sherrill.  Frontiers in electronic structure theory. , 2010, The Journal of chemical physics.

[51]  W. Alexander,et al.  Theoretical study of the Ar-, Kr-, and Xe-CH4, -CF4 intermolecular potential-energy surfaces. , 2006, The journal of physical chemistry. A.

[52]  S. Sinnott,et al.  Effects of unique ion chemistry on thin-film growth by plasma-surface interactions. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[53]  Richard F. W. Bader.  A quantum theory of molecular structure and its applications , 1991 .

[54]  Inelastic scattering dynamics of Ar from a perfluorinated self-assembled monolayer surface. , 2007, The journal of physical chemistry. A.

[55]  S. Barlow,et al.  Preparation and in situ characterization of surfaces using soft landing in a Fourier transform ion cyclotron resonance mass spectrometer. , 2005, Analytical chemistry.

[56]  J. Futrell,et al.  Soft-landing of peptides onto self-assembled monolayer surfaces. , 2006, The journal of physical chemistry. A.

[57]  M. Ara,et al.  Characterization of alkyl monolayer covalently bonded to Si(111) and soft-landing of vanadium-benzene sandwich clusters onto the alkyl monolayer substrate , 2009 .

[58]  R. Bader,et al.  Theoretical analysis of hydrocarbon properties. 1. Bonds, structures, charge concentrations, and charge relaxations , 1987 .

[59]  R. Cooks,et al.  In situ SIMS analysis and reactions of surfaces prepared by soft landing of mass-selected cations and anions using an ion trap mass spectrometer , 2009, Journal of the American Society for Mass Spectrometry.

[60]  F. Claeyssens,et al.  Immobilization of large size-selected silver clusters on graphite , 2006 .

[61]  A. Varandas.  Extrapolating to the one-electron basis-set limit in electronic structure calculations. , 2007, The Journal of chemical physics.

[62]  A. Nakajima,et al.  Soft-Landing Experiments of Cr(benzene)2 Sandwich Complexes onto a Carboxyl-Terminated Self-Assembled Monolayer Matrix , 2009 .

[63]  R. Bader.  Atoms in molecules : a quantum theory , 1990 .

[64]  T. Darden,et al.  Simple Formulas for Improved Point-Charge Electrostatics in Classical Force Fields and Hybrid Quantum Mechanical/Molecular Mechanical Embedding. , 2008, International journal of quantum chemistry.

[65]  S. Sibener,et al.  Role of Surface Intramolecular Dynamics in the Efficiency of Energy Transfer in Ne Atom Collisions with a n-Hexylthiolate Self-Assembled Monolayer† , 2003 .

[66]  Martin Head-Gordon,et al.  Quadratic configuration interaction. A general technique for determining electron correlation energies , 1987 .

[67]  Holger Patzelt,et al.  RI-MP2: optimized auxiliary basis sets and demonstration of efficiency , 1998 .

[68]  Kirk A. Peterson,et al.  Benchmark calculations with correlated molecular wave functions. IV. The classical barrier height of the H+H2→H2+H reaction , 1994 .

[69]  T. Dunning,et al.  Electron affinities of the first‐row atoms revisited. Systematic basis sets and wave functions , 1992 .

[70]  D. Troya,et al.  Classical trajectory study of collisions of Ar with alkanethiolate self-assembled monolayers: potential-energy surface effects on dynamics. , 2005, The Journal of chemical physics.

[71]  K. Song,et al.  An analytical potential energy function to model protonated peptide soft-landing experiments. The CH3NH3+/CH4 interactions. , 2008, Physical chemistry chemical physics : PCCP.

[72]  R. Cooks,et al.  Soft landing of polyatomic ions for selective modification of fluorinated self-assembled monolayer surfaces , 1998 .

[73]  George L. Barnes,et al.  Energy transfer, unfolding, and fragmentation dynamics in collisions of N-protonated octaglycine with an H-SAM surface. , 2009, Journal of the American Chemical Society.

[74]  Trygve Helgaker,et al.  Quantitative quantum chemistry , 2008 .

[75]  R. Parr.  Density-functional theory of atoms and molecules , 1989 .

[76]  Trygve Helgaker,et al.  Basis-set convergence in correlated calculations on Ne, N2, and H2O , 1998 .

[77]  Francisco B. Pereira,et al.  A new genetic algorithm to be used in the direct fit of potential energy curves to ab initio and spectroscopic data , 2008 .

[78]  T. Lee,et al.  Experimental and theoretical studies of the effect of mass on the dynamics of gas/organic-surface energy transfer. , 2008, The Journal of chemical physics.

[79]  Ilya G. Kaplan,et al.  Intermolecular interactions : physical picture, computational methods, model potentials , 2006 .

[80]  R. Cooks,et al.  Chiral enrichment of serine via formation, dissociation, and soft-landing of octameric cluster ions , 2004, Journal of the American Society for Mass Spectrometry.

[81]  D. Troya,et al.  Experimental and theoretical study of CO collisions with CH3- and CF3-terminated self-assembled monolayers. , 2009, The Journal of chemical physics.

[82]  Miquel Duran,et al.  How does basis set superposition error change the potential surfaces for hydrogen-bonded dimers? , 1996 .

[83]  Jan M. L. Martin.  Ab initio total atomization energies of small molecules — towards the basis set limit , 1996 .

[84]  W. Hase,et al.  Dynamics of energy transfer in peptide-surface collisions. , 2002, Journal of the American Chemical Society.

[85]  J. Laskin,et al.  Soft-landing of peptide ions onto self-assembled monolayer surfaces: an overview. , 2008, Physical chemistry chemical physics : PCCP.

[86]  M. Rodgers,et al.  Chemical Dynamics Simulations of Energy Transfer in Collisions of Protonated Peptide−Ions with a Perfluorinated Alkylthiol Self-Assembled Monolayer Surface , 2008 .

[87]  T. Windus,et al.  Ab initio and analytic intermolecular potentials for Ar-CF4. , 2006, The journal of physical chemistry. A.

[88]  R. Cooks,et al.  Ion soft-landing into liquids: Protein identification, separation, and purification with retention of biological activity , 2004, Journal of the American Society for Mass Spectrometry.

[89]  J. Laskin,et al.  Soft-Landing of CoIII(salen)+ and MnIII(salen)+ on Self-Assembled Monolayer Surfaces† , 2010 .

[90]  Atanu Sengupta,et al.  Surface-enhanced Raman spectroscopy of soft-landed polyatomic ions and molecules. , 2007, Analytical chemistry.

[91]  O. Borodin,et al.  A Quantum Chemistry Based Force Field for Perfluoroalkanes and Poly(tetrafluoroethylene) , 2002 .

[92]  R. Cooks,et al.  Soft-Landing of Polyatomic Ions at Fluorinated Self-Assembled Monolayer Surfaces , 1997, Science.

[93]  Stefan Grimme,et al.  Accurate description of van der Waals complexes by density functional theory including empirical corrections , 2004, J. Comput. Chem..

[94]  R. Buckingham,et al.  The Classical Equation of State of Gaseous Helium, Neon and Argon , 1938 .

[95]  Xiche Hu,et al.  Vectorization of the general Monte Carlo classical trajectory program VENUS , 1991 .

[96]  G. Schatz,et al.  Theoretical studies of hyperthermal O(3P) collisions with hydrocarbon self-assembled monolayers. , 2004, The Journal of chemical physics.

[97]  J. Almlöf,et al.  Integral approximations for LCAO-SCF calculations , 1993 .

[98]  K. Kern,et al.  Electrospray ion beam deposition: soft-landing and fragmentation of functional molecules at solid surfaces. , 2009, ACS nano.

[99]  W. Hase,et al.  Comparisons of models for simulating energy transfer in ne-atom collisions with an alkyl thiolate self-assembled monolayer , 2002 .

[100]  G. Siuzdak,et al.  Mass spectrometry and viral analysis. , 1996, Chemistry & biology.

[101]  D. Schwenke.  The extrapolation of one-electron basis sets in electronic structure calculations: how it should work and how it can be made to work. , 2005, The Journal of chemical physics.

[102]  T. Yan,et al.  Origin of the Boltzmann translational energy distribution in the scattering of hyperthermal Ne atoms off a self-assembled monolayer , 2000 .

[103]  Zheng Ouyang,et al.  Preparing Protein Microarrays by Soft-Landing of Mass-Selected Ions , 2003, Science.