Water interactions with hydrophobic groups: assessment and recalibration of semiempirical molecular orbital methods.

In this work, we present a study of the ability of different semiempirical methods to describe intermolecular interactions in water solution. In particular, we focus on methods based on the Neglect of Diatomic Differential Overlap approximation. Significant improvements of these methods have been reported in the literature in the past years regarding the description of non-covalent interactions. In particular, a broad range of methodologies has been developed to deal with the properties of hydrogen-bonded systems, with varying degrees of success. In contrast, the interactions between water and a molecule containing hydrophobic groups have been little analyzed. Indeed, by considering the potential energy surfaces obtained using different semiempirical Hamiltonians for the intermolecular interactions of model systems, we found that none of the available methods provides an entirely satisfactory description of both hydrophobic and hydrophilic interactions in water. In addition, a vibrational analysis carried out in a model system for these interactions, a methane clathrate cluster, showed that some recent methods cannot be used to carry out studies of vibrational properties. Following a procedure established in our group [M. I. Bernal-Uruchurtu, M. T. C. Martins-Costa, C. Millot, and M. F. Ruiz-López, J. Comput. Chem. 21, 572 (2000); W. Harb, M. I. Bernal-Uruchurtu, and M. F. Ruiz-López, Theor. Chem. Acc. 112, 204 (2004)], we developed new parameters for the core-core interaction terms based on fitting potential energy curves obtained at the MP2 level for our model system. We investigated the transferability of the new parameters to describe a system, having both hydrophilic and hydrophobic groups, interacting with water. We found that only by introducing two different sets of parameters for hydrophilic and hydrophobic hydrogen atom types we are able to match the features of the ab initio calculated properties. Once this assumption is made, a good agreement with the MP2 reference is achieved. The results reported in this work provide therefore a direction for future developments of semiempirical approaches that are still required to investigate chemical processes in biomolecules and in large disordered systems.

[1]  Arshad Khan,et al.  Theoretical studies of CH4(H2O)20, (H2O)21, (H2O)20, and fused dodecahedral and tetrakaidecahedral structures: How do natural gas hydrates form? , 1999 .

[2]  Walter Thiel,et al.  Semiempirical quantum-chemical methods in computational chemistry , 2005 .

[3]  Martin Korth,et al.  Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields , 2010 .

[4]  E. Coitiño,et al.  AM1 study of hydrogen bonded complexes of water , 1989 .

[5]  G. Monard,et al.  Importance of Polarization and Charge Transfer Effects to Model the Infrared Spectra of Peptides in Solution. , 2011, Journal of chemical theory and computation.

[6]  M. Ruiz‐López,et al.  An improved semiempirical method for hydrated systems , 2004 .

[7]  Jonathan Tennyson,et al.  A database of water transitions from experiment and theory (IUPAC Technical Report) , 2014 .

[8]  Manuel F. Ruiz-López,et al.  Calibration of the Quantum/Classical Hamiltonian in Semiempirical QM/MM AM1 and PM3 Methods , 2000 .

[9]  Jirí Cerný,et al.  Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations , 2007, J. Comput. Chem..

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

[11]  Manuel F. Ruiz-López,et al.  Basic ideas for the correction of semiempirical methods describing H-bonded systems , 2000 .

[12]  Pavel Hobza,et al.  On the performance of the semiempirical quantum mechanical PM6 and PM7 methods for noncovalent interactions , 2013 .

[13]  M. Ruiz‐López,et al.  Can semi-empirical models describe HCl dissociation in water? , 2007 .

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

[15]  W. Thiel,et al.  Extension of the MNDO formalism tod orbitals: Integral approximations and preliminary numerical results , 1992 .

[16]  Hong Wang,et al.  Towards a quantum mechanical force field for carbohydrates: a reparametrized semi-empirical MO approach. , 2004 .

[17]  M. Dewar,et al.  Ground States of Molecules. 38. The MNDO Method. Approximations and Parameters , 1977 .

[18]  J. Stewart Optimization of parameters for semiempirical methods I. Method , 1989 .

[19]  Pavel Hobza,et al.  A reliable docking/scoring scheme based on the semiempirical quantum mechanical PM6-DH2 method accurately covering dispersion and H-bonding: HIV-1 protease with 22 ligands. , 2010, The journal of physical chemistry. B.

[20]  Joost VandeVondele,et al.  Linear Scaling Self-Consistent Field Calculations with Millions of Atoms in the Condensed Phase. , 2012, Journal of chemical theory and computation.

[21]  J. Max,et al.  Isotope effects in liquid water by infrared spectroscopy. III. H2O and D2O spectra from 6000 to 0 cm(-1). , 2009, The Journal of chemical physics.

[22]  János G. Ángyán,et al.  The origin of the problems with the PM3 core repulsion function , 1997 .

[23]  J. Pople,et al.  Self‐consistent molecular orbital methods. XX. A basis set for correlated wave functions , 1980 .

[24]  G. Monard,et al.  Combining a genetic algorithm with a linear scaling semiempirical method for protein–ligand docking , 2009 .

[25]  A. Schäfer,et al.  Fully optimized contracted Gaussian basis sets of triple zeta valence quality for atoms Li to Kr , 1994 .

[26]  K. Merz,et al.  Simulation of liquid water using semiempirical Hamiltonians and the divide and conquer approach. , 2005, The journal of physical chemistry. A.

[27]  Julio Daniel Carvalho Maia,et al.  GPU Linear Algebra Libraries and GPGPU Programming for Accelerating MOPAC Semiempirical Quantum Chemistry Calculations. , 2012, Journal of chemical theory and computation.

[28]  J. Stewart Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements , 2007, Journal of molecular modeling.

[29]  E. Dartois,et al.  Methane clathrate hydrate FTIR spectrum - Implications for its cometary and planetary detection , 2008 .

[30]  Claude Millot,et al.  Improving description of hydrogen bonds at the semiempirical level: water–water interactions as test case , 2000 .

[31]  D. York,et al.  Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions:  H, O, and P Atoms. , 2007, Journal of chemical theory and computation.

[32]  I. Csizmadia,et al.  Ab initio and density functional study of the conformational space of 1C4 α‐L‐fucose , 1997 .

[33]  William L. Jorgensen,et al.  Ab Initio Study Of Hydrogen-Bonded Complexes Of Small Organic Molecules With Water , 1998 .

[35]  James J. P. Stewart,et al.  Application of the PM6 method to modeling proteins , 2009, Journal of molecular modeling.

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

[37]  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.

[38]  Pavel Hobza,et al.  A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods. , 2010, Journal of chemical theory and computation.

[39]  Pavel Hobza,et al.  Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods. , 2012, Journal of chemical theory and computation.

[40]  J. Pople,et al.  Approximate Self-Consistent Molecular Orbital Theory. I. Invariant Procedures , 1965 .

[41]  Gábor I. Csonka,et al.  Analysis of the core‐repulsion functions used in AM1 and PM3 semiempirical calculations: Conformational analysis of ring systems , 1993, J. Comput. Chem..

[42]  G. Corongiu,et al.  Van der Waals Interaction Energies of Helium, Neon, and Argon with Naphthalene , 2001 .

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

[44]  B. Militzer,et al.  Hydrogen storage in molecular clathrates. , 2007, Chemical reviews.

[45]  J. Dannenberg Hydrogen bonds: a comparison of semiempirical and ab initio treatments , 1997 .

[46]  Giacinto Scoles,et al.  Intermolecular forces in simple systems , 1977 .

[47]  Eamonn F. Healy,et al.  Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model , 1985 .

[48]  Michael J. Frisch,et al.  MP2 energy evaluation by direct methods , 1988 .

[49]  Alfredo Mayall Simas,et al.  RM1: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I , 2006, J. Comput. Chem..

[50]  S. Grimme,et al.  Density functional theory with dispersion corrections for supramolecular structures, aggregates, and complexes of (bio)organic molecules. , 2007, Organic & biomolecular chemistry.

[51]  William L. Jorgensen,et al.  PDDG/PM3 and PDDG/MNDO: Improved semiempirical methods , 2002, J. Comput. Chem..

[52]  Xin Wu,et al.  Semiempirical Quantum Chemical Calculations Accelerated on a Hybrid Multicore CPU-GPU Computing Platform. , 2012, Journal of chemical theory and computation.

[53]  C. Koh,et al.  Towards a fundamental understanding of natural gas hydrates. , 2002, Chemical Society reviews.

[54]  Pavel Hobza,et al.  A halogen-bonding correction for the semiempirical PM6 method , 2011 .

[55]  Walter Thiel,et al.  OMx-D: semiempirical methods with orthogonalization and dispersion corrections. Implementation and biochemical application. , 2008, Physical chemistry chemical physics : PCCP.

[56]  Bodo Martin,et al.  Dispersion treatment for NDDO‐based semiempirical MO techniques , 2006 .

[57]  Walter Thiel,et al.  Extension of MNDO to d Orbitals: Parameters and Results for the Second-Row Elements and for the Zinc Group , 1996 .

[58]  I. H. Hillier,et al.  Semi-empirical molecular orbital methods including dispersion corrections for the accurate prediction of the full range of intermolecular interactions in biomolecules. , 2007, Physical chemistry chemical physics : PCCP.

[59]  James J. P. Stewart,et al.  Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters , 2012, Journal of Molecular Modeling.

[60]  Teodoro Laino,et al.  Semiempirical self-consistent polarization description of bulk water, the liquid-vapor interface, and cubic ice. , 2011, The journal of physical chemistry. A.

[61]  B. C. Garrett,et al.  Self-consistent polarization neglect of diatomic differential overlap: application to water clusters. , 2008, The Journal of chemical physics.

[62]  Walter Thiel,et al.  Specific Reaction Path Hamiltonian for Proton Transfer in Water: Reparameterized Semiempirical Models. , 2013, Journal of chemical theory and computation.