A self-consistent MoD-WM/MM structural refinement method: characterization of hydrogen bonding in the orytricha nova G-1uar

Journal Article · Tue Jan 01 00:00:00 EST 2008 · J. Comp. and Theoretical Chemistry

OSTI ID:956657

Batista, Enrique R ^[1]; Newcomer, Micharel B ^[2]; Raggin, Christina M ^[2]; Gascon, Jose A ^[2]; Loria, J Patrick ^[2]; Batista, Victor S ^[2]

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1. Los Alamos National Laboratory
2. YALE UNIV

This paper generalizes the MoD-QM/MM hybrid method, developed for ab initio computations of protein electrostatic potentials [Gasc6n, l.A.; Leung, S.S.F.; Batista, E.R.; Batista, V.S. J. Chem. Theory Comput. 2006,2, 175-186], as a practical algorithm for structural refinement of extended systems. The computational protocol involves a space-domain decomposition scheme for the formal fragmentation of extended systems into smaller, partially overlapping, molecular domains and the iterative self-consistent energy minimization of the constituent domains by relaxation of their geometry and electronic structure. The method accounts for mutual polarization of the molecular domains, modeled as Quantum-Mechanical (QM) layers embedded in the otherwise classical Molecular-Mechanics (MM) environment according to QM/MM hybrid methods. The method is applied to the description of benchmark models systems that allow for direct comparisons with full QM calculations, and subsequently applied to the structural characterization of the DNA Oxytricha nova Guanine quadruplex (G4). The resulting MoD-QM/MM structural model of the DNA G4 is compared to recently reported highresolution X-ray diffraction and NMR models, and partially validated by direct comparisons between {sup 1}H NMR chemical shifts that are highly sensitive to hydrogen-bonding and stacking interactions and the corresponding theoretical values obtained at the density functional theory DFT QM/MM (BH&H/6-31 G*:Amber) level in conjunction with the gauge independent atomic orbital (GIAO) method for the ab initio self consistent-field (SCF) calculation of NMR chemical shifts.

• Research Organization: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC52-06NA25396
• OSTI ID: 956657
• Report Number(s): LA-UR-08-07980; LA-UR-08-7980; TRN: US201016%%2342
• Journal Information: J. Comp. and Theoretical Chemistry, Journal Name: J. Comp. and Theoretical Chemistry
• Country of Publication: United States
• Language: English

Related Subjects

74 ATOMIC AND MOLECULAR PHYSICS
ALGORITHMS
BENCHMARKS
CHEMICAL BONDS
CHEMICAL SHIFT
DECOMPOSITION
DENSITY
DNA
ELECTRONIC STRUCTURE
ELECTROSTATICS
FRAGMENTATION
FUNCTIONALS
GEOMETRY
GUANINE
HYDROGEN
INTERACTIONS
NUCLEAR MAGNETIC RESONANCE
POLARIZATION
POTENTIALS
PROTEINS
RELAXATION
STRUCTURAL MODELS
X-RAY DIFFRACTION