Octahedral point-charge model and its application to fragment molecular orbital calculations of chemical shifts

Abstract To obtain chemical shifts in large molecular systems accurately with a low computational cost, we developed an octahedral point-charge model that mimics the electrostatic potential due to charge distributions. The point-charges in this model are defined to reproduce the multipole moments calculated using the revised distributed multipole analysis. The accuracy of charge representations was tested on formamide. The octahedral point-charge model was used in the fragment molecular orbital method and applied to NMR calculation of a β-sheet polypeptide. The maximum errors relative to conventional ab initio NMR calculation were 0.13, 0.73, and 0.09 ppm for 13 C, 15 N, and 1 H, respectively.

[1]  Christian Ochsenfeld,et al.  Convergence of Electronic Structure with the Size of the QM Region: Example of QM/MM NMR Shieldings. , 2012, Journal of chemical theory and computation.

[2]  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.

[3]  K. Kitaura,et al.  Fragment-Molecular-Orbital-Method-Based ab Initio NMR Chemical-Shift Calculations for Large Molecular Systems , 2010 .

[4]  Donald E. Williams,et al.  Representation of the molecular electrostatic potential by a net atomic charge model , 1981 .

[5]  Xiao He,et al.  Fragment density functional theory calculation of NMR chemical shifts for proteins with implicit solvation. , 2012, Physical chemistry chemical physics : PCCP.

[6]  K. Kitaura,et al.  Fragment molecular orbital method: an approximate computational method for large molecules , 1999 .

[7]  D. Grant,et al.  The calculation of 13C chemical shielding tensors in ionic compounds utilizing point charge arrays obtained from Ewald lattice sums , 2001 .

[8]  Todd A. Keith,et al.  Calculation of magnetic response properties using a continuous set of gauge transformations , 1993 .

[9]  György G. Ferenczy Charges derived from distributed multipole series , 1991 .

[10]  P. Kollman,et al.  How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000 .

[11]  K. Merz,et al.  Protein NMR chemical shift calculations based on the automated fragmentation QM/MM approach. , 2009, The journal of physical chemistry. B.

[12]  Kazuo Kitaura,et al.  Extending the power of quantum chemistry to large systems with the fragment molecular orbital method. , 2007, The journal of physical chemistry. A.

[13]  Anthony J Stone,et al.  Distributed Multipole Analysis:  Stability for Large Basis Sets. , 2005, Journal of chemical theory and computation.

[14]  M. Alderton,et al.  Distributed multipole analysis , 2006 .

[15]  Robert J.P. Williams,et al.  Structural information from NMR secondary chemical shifts of peptide α C−H protons in proteins , 1983 .

[16]  H. Sekino,et al.  Evaluation of NMR Chemical Shift by Fragment Molecular Orbital Method , 2007 .

[17]  G. Wagner Prospects for NMR of large proteins , 1993, Journal of biomolecular NMR.

[18]  Mark S. Gordon,et al.  Electrostatic energy in the effective fragment potential method: Theory and application to benzene dimer , 2007, J. Comput. Chem..

[19]  M. Bühl,et al.  The DFT route to NMR chemical shifts , 1999, J. Comput. Chem..

[20]  D A Dougherty,et al.  Cation-pi interactions in aromatics of biological and medicinal interest: electrostatic potential surfaces as a useful qualitative guide. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[21]  K. Kitaura,et al.  Systematic study of the embedding potential description in the fragment molecular orbital method. , 2010, The journal of physical chemistry. A.

[22]  Cioslowski General and unique partitioning of molecular electronic properties into atomic contributions. , 1989, Physical review letters.

[23]  Anthony J. Stone,et al.  Distributed multipole analysis, or how to describe a molecular charge distribution , 1981 .

[24]  György G. Ferenczy,et al.  Transferable net atomic charges from a distributed multipole analysis for the description of electrostatic properties: a case study of saturated hydrocarbons , 1993 .

[25]  G. Otting,et al.  Pathway of chymotrypsin evolution suggested by the structure of the FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F) , 1997, Nature Structural Biology.

[26]  Kurt Wüthrich,et al.  1H‐nmr parameters of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H‐Gly‐Gly‐X‐L‐Ala‐OH , 1979 .

[27]  E. Oldfield,et al.  Methods for computing nuclear magnetic resonance chemical shielding in large systems. Multiple cluster and charge field approaches , 1993 .

[28]  J. Tossell,et al.  Nuclear magnetic shieldings and molecular structure , 1993 .

[29]  Xiao He,et al.  Automated Fragmentation QM/MM Calculation of Amide Proton Chemical Shifts in Proteins with Explicit Solvent Model. , 2013, Journal of chemical theory and computation.

[30]  R. S. Mulliken Electronic Population Analysis on LCAO–MO Molecular Wave Functions. I , 1955 .

[31]  Qiang Cui,et al.  Combining implicit solvation models with hybrid quantum mechanical/molecular mechanical methods: A critical test with glycine , 2002 .

[32]  Spencer R Pruitt,et al.  Fragmentation methods: a route to accurate calculations on large systems. , 2012, Chemical reviews.

[33]  Toyokazu Ishida Low-barrier hydrogen bond hypothesis in the catalytic triad residue of serine proteases: correlation between structural rearrangement and chemical shifts in the acylation process. , 2006, Biochemistry.

[34]  Shinichiro Nakamura,et al.  Ab initio NMR chemical shift calculations on proteins using fragment molecular orbitals with electrostatic environment , 2007 .

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

[36]  R. J. Williams,et al.  Assignment of proton resonances, identification of secondary structural elements, and analysis of backbone chemical shifts for the C102T variant of yeast iso-1-cytochrome c and horse cytochrome c. , 1990, Biochemistry.

[37]  R. Ditchfield,et al.  Self-consistent perturbation theory of diamagnetism , 1974 .

[38]  U. Rothlisberger,et al.  Nuclear magnetic resonance chemical shifts from hybrid DFT QM/MM calculations , 2004 .

[39]  M. Karplus,et al.  Molecular Properties from Combined QM/MM Methods. 2. Chemical Shifts in Large Molecules , 2000 .

[40]  Kazuo Kitaura,et al.  Exploring chemistry with the fragment molecular orbital method. , 2012, Physical chemistry chemical physics : PCCP.

[41]  T. Exner,et al.  Toward the Quantum Chemical Calculation of NMR Chemical Shifts of Proteins. 2. Level of Theory, Basis Set, and Solvents Model Dependence. , 2012, Journal of chemical theory and computation.

[42]  Peter Pulay,et al.  Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations , 1990 .

[43]  L. E. Chirlian,et al.  Atomic charges derived from electrostatic potentials: A detailed study , 1987 .

[44]  Mark S. Gordon,et al.  General atomic and molecular electronic structure system , 1993, J. Comput. Chem..