Grand challenges in quantum‐classical modeling of molecule–surface interactions
暂无分享,去创建一个
[1] 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.
[2] V. Harmandaris,et al. Properties of short polystyrene chains confined between two gold surfaces through a combined density functional theory and classical molecular dynamics approach , 2012 .
[3] K. Fichthorn,et al. A Force Field for the Interaction of Water with TiO2 Surfaces , 2011 .
[4] Alexander D. MacKerell,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.
[5] Tiffany R. Walsh,et al. Ab initio derived force‐field parameters for molecular dynamics simulations of deprotonated amorphous‐SiO2/water interfaces , 2012 .
[6] K. Burke,et al. Generalized Gradient Approximation Made Simple [Phys. Rev. Lett. 77, 3865 (1996)] , 1997 .
[7] H. Berendsen,et al. A consistent empirical potential for water–protein interactions , 1984 .
[8] Alexander D. MacKerell,et al. Development of an empirical force field for silica. Application to the quartz-water interface. , 2006, The journal of physical chemistry. B.
[9] S. Grimme. Density functional theory with London dispersion corrections , 2011 .
[10] K. Kremer,et al. A hierarchical dualscale study of bisphenol-A-polycarbonate on a silicon surface: structure, dynamics and impurity diffusion , 2011 .
[11] A. Shluger,et al. Interaction of organic molecules with the TiO2 (110) surface: ab inito calculations and classical force fields. , 2006, The journal of physical chemistry. B.
[12] Nico F A van der Vegt,et al. Modelling molecule-surface interactions--an automated quantum-classical approach using a genetic algorithm. , 2011, Physical chemistry chemical physics : PCCP.
[13] W. Knoll,et al. Superstructures of cyclodextrin derivatives on Au(111): A combined random planting molecular dynamics approach , 1997 .
[14] Nico F. A. van der Vegt,et al. Development of Classical Molecule-Surface Interaction Potentials Based on Density Functional Theory Calculations: Investigation of Force Field Representability , 2012 .
[15] S. C. Parker,et al. Modelling of the thermal dependence of structural and elastic properties of calcite, CaCO3 , 1996 .
[16] K. Burke,et al. Perdew, Burke, and Ernzerhof Reply: , 1998 .
[17] A. Becke,et al. Density-functional exchange-energy approximation with correct asymptotic behavior. , 1988, Physical review. A, General physics.
[18] Peter A. Kollman,et al. AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions , 1981 .
[19] Alexander D. MacKerell,et al. An all-atom empirical energy function for the simulation of nucleic acids , 1995 .
[20] Burke,et al. Generalized Gradient Approximation Made Simple. , 1996, Physical review letters.
[21] S. C. Parker,et al. Surface–water interactions in the dolomite problem , 2001 .
[22] 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..
[23] David Quigley,et al. Derivation of an accurate force-field for simulating the growth of calcium carbonate from aqueous solution : a new model for the calcite-water interface , 2010 .
[24] T. Walsh,et al. Hydrolysis of the amorphous silica surface. I. Structure and dynamics of the dry surface , 2000 .
[25] Ruth Pachter,et al. Nature of molecular interactions of peptides with gold, palladium, and Pd-Au bimetal surfaces in aqueous solution. , 2009, Journal of the American Chemical Society.
[26] T. Walsh,et al. Facet Selectivity of Binding on Quartz Surfaces: Free Energy Calculations of Amino-Acid Analogue Adsorption , 2012 .
[27] W. L. Jorgensen,et al. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .
[28] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[29] Claudia Ambrosch-Draxl,et al. Van der Waals Interactions Between Organic Adsorbates and at Organic/Inorganic Interfaces , 2010 .
[30] Isaac Tamblyn,et al. Molecular adsorption on metal surfaces with van der Waals density functionals , 2012, Physical Review B.
[31] Chris Oostenbrink,et al. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6 , 2004, J. Comput. Chem..
[32] L Delle Site,et al. Polymers near metal surfaces: selective adsorption and global conformations. , 2002, Physical review letters.
[33] Robert A Latour,et al. Molecular simulation of protein-surface interactions: Benefits, problems, solutions, and future directions (Review) , 2008, Biointerphases.
[34] Wang,et al. Generalized gradient approximation for the exchange-correlation hole of a many-electron system. , 1996, Physical review. B, Condensed matter.
[35] Oleg Borodin,et al. Molecular Dynamics Study of the Influence of Solid Interfaces on Poly(ethylene oxide) Structure and Dynamics , 2003 .
[36] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[37] Kurt Kremer,et al. BPA-PC on a Ni111 surface: the interplay between adsorption energy and conformational entropy for different chain-end modifications. , 2004, Journal of the American Chemical Society.
[38] Shen Li,et al. A density functional for sparse matter , 2009, Journal of physics. Condensed matter : an Institute of Physics journal.
[39] P. Cummings,et al. Investigating the quartz (1010)/water interface using classical and ab initio molecular dynamics. , 2011, Langmuir : the ACS journal of surfaces and colloids.
[40] Peter A. Kollman,et al. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules , 1995 .
[41] B. Lundqvist,et al. RPBE-vdW Description of Benzene Adsorption on Au(111) , 2010 .
[42] Kieron Burke,et al. Nonlocality of the density functional for exchange and correlation: Physical origins and chemical consequences , 1998 .
[43] Berk Hess,et al. Competing adsorption between hydrated peptides and water onto metal surfaces: from electronic to conformational properties. , 2008, Journal of the American Chemical Society.
[44] J. Garrido,et al. Peptide adsorption on a hydrophobic surface results from an interplay of solvation, surface, and intrapeptide forces , 2008, Proceedings of the National Academy of Sciences.
[45] O. Borodin,et al. A molecular dynamics simulation and quantum chemistry study of poly(dimethylsiloxane)–silica nanoparticle interactions , 2007 .
[46] Wilfred F. van Gunsteren,et al. An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase , 2001, J. Comput. Chem..
[47] D. Quigley,et al. Computational techniques at the organic-inorganic interface in biomineralization. , 2008, Chemical reviews.
[48] V. Mavrantzas,et al. Atomistic Simulation of Alkanethiol Self-Assembled Monolayers on Different Metal Surfaces via a Quantum, First-Principles Parametrization of the Sulfur−Metal Interaction , 2007, The Journal of Physical Chemistry C.
[49] Colin L. Freeman,et al. Interactions of Organic Molecules with Calcite and Magnesite Surfaces , 2009 .
[50] Richard A. Vaia,et al. Accurate Simulation of Surfaces and Interfaces of Face-Centered Cubic Metals Using 12−6 and 9−6 Lennard-Jones Potentials , 2008 .
[51] Luigi Delle Site,et al. Interaction of Hydrated Amino Acids with Metal Surfaces: A Multiscale Modeling Description , 2007 .
[52] Katrin Tonigold,et al. Adsorption of small aromatic molecules on the (111) surfaces of noble metals: A density functional theory study with semiempirical corrections for dispersion effects. , 2010, The Journal of chemical physics.
[53] Stefano Corni,et al. Simulation of Peptide–Surface Recognition , 2011 .
[54] Parr,et al. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.
[55] Vincenzo Carravetta,et al. Peptide-TiO2 surface interaction in solution by ab initio and molecular dynamics simulations. , 2006, The journal of physical chemistry. B.
[56] David E. Goldberg,et al. Genetic Algorithms in Search Optimization and Machine Learning , 1988 .
[57] W Michael Brown,et al. Efficient hybrid evolutionary optimization of interatomic potential models. , 2010, The Journal of chemical physics.
[58] B. Lundqvist,et al. Influence of van der Waals forces on the adsorption structure of benzene on silicon studied using de , 2008, 0803.2818.
[59] Gideon Schreiber,et al. Protein–surface interactions: challenging experiments and computations , 2009, Journal of molecular recognition : JMR.
[60] W. L. Jorgensen,et al. The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.
[61] Lucio Colombi Ciacchi,et al. A Classical Potential to Model the Adsorption of Biological Molecules on Oxidized Titanium Surfaces. , 2011, Journal of chemical theory and computation.
[62] K. Imamura,et al. On the adsorption of proteins on solid surfaces, a common but very complicated phenomenon. , 2001, Journal of bioscience and bioengineering.
[63] Gábor Csányi,et al. Development of a classical force field for the oxidized Si surface: application to hydrophilic wafer bonding. , 2007, The Journal of chemical physics.
[64] Pavel Hobza,et al. Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories. , 2010, Chemical reviews.
[65] Yingkai Zhang,et al. Comment on “Generalized Gradient Approximation Made Simple” , 1998 .
[66] Kurt Kremer,et al. Dual-scale modeling of benzene adsorption onto Ni(111) and Au(111) surfaces in explicit water. , 2005, Chemphyschem : a European journal of chemical physics and physical chemistry.
[67] J. Nicholas,et al. Structure and dynamics of the water/MgO interface , 1996 .
[68] Andrei V. Bandura,et al. Derivation of Force Field Parameters for TiO2−H2O Systems from ab Initio Calculations , 2003 .
[69] V. Harmandaris,et al. Properties of Benzene Confined between Two Au(111) Surfaces Using a Combined Density Functional Theory and Classical Molecular Dynamics Approach , 2011 .
[70] Peter T. Cummings,et al. Simulations of the Quartz(1011)/Water Interface: A Comparison of Classical Force Fields, Ab Initio Molecular Dynamics, and X-ray Reflectivity Experiments , 2011 .
[71] Colin L. Freeman,et al. New Forcefields for Modeling Biomineralization Processes , 2007 .
[72] A. Tkatchenko,et al. Benzene adsorbed on Si(001): The role of electron correlation and finite temperature , 2012 .
[73] Stephen C. Parker,et al. Molecular-dynamics simulation of MgO surfaces in liquid water using a shell-model potential for water , 1998 .
[74] J. Harding,et al. The challenge of biominerals to simulations , 2006 .
[75] Kurt Kremer,et al. Dual-resolution coarse-grained simulation of the bisphenol-A-polycarbonate/nickel interface. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.