A polarizable force field (PFF) using multiple fluctuating charges per atom, ABEEMσπ PFF, is presented in this work. The fluctuating partial charges are obtained from the electronegativity equalization principle applied to the decomposition scheme of atom-bond regions into multiple charge sites: atomic, lone-pair electron, and σ and π bond regions. These multiple partial charges per atom should better account for the polarization effect than single atomic charge in other PFFs. To evaluate the PFF, structural and energetic properties for some organic and biochemical systems, including rotational barriers; binding energies of base pairs; a base−base interaction in a B-DNA decamer; and interaction energies of ten stationary conformers of a water dimer, peptides, and bases with water molecules, have been calculated and compared with the experimental data or ab initio MP2 results. Molecular dynamics simulations using the PFF have been performed for crambin and BPTI protein systems. Better performances in modeling root-mean-square deviations of backbone bond lengths, bond angles, key dihedral angles, the coordinate root-mean-square shift of atoms, and the distribution of hydrogen bonds have been observed in comparison with other PFFs. These results indicate that the fluctuating charge force field, ABEEMσπ/MM, is accurate and reliable and can be applied to wide ranges of organic and biomolecular systems.

Hydrogen peroxide (HP) clusters (H(2)O(2))(n) (n = 1-6) and liquid-state HP have been systemically investigated by the newly constructed ABEEM/MM fluctuating charge model. Because of the explicit description of charge distribution and special treatment of the hydrogen-bond interaction region, the ABEEM/MM potential model gives reasonable properties of HP clusters, including geometries, interaction energies, and dipole moments, when comparing with the present ab initio results. Meanwhile, the average dipole moment, static dielectric constant, heats of vaporization, radial distribution function, and diffusion constant for the dynamic properties of liquid HP at 273 K and 1 atm are fairly consistent with the available experimental data. To the best of our knowledge, this is the first theoretical investigation of condensed HP. The properties of HP monomer are studied in detail involving the structure, torsion potentials, molecular orbital analysis, charge distribution, dipole moment, and vibrational frequency.

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The interactions of Mg 2? and Ca 2? binding to adenine, cytosine, guanine, and thymine at various binding sites were studied by a high-level quantum chemical method and ABEEMrp/MM fluctuating charge model. The geometries and binding energies of M 2? -bases complexes were determined at CCSD(T)/6-311 ??G(2d,2p)//MP2/6-311 ??G(2d,2p) level of theory, with the basis set superposition error corrections for the binding energy calculations. In comparison with the ab initio results, an accurate classical metal cation-base interaction potential was constructed and parameterized in terms of ABEEMrp/ MM model. It is revealed that Mg 2? /Ca 2? prefers to bind with bases at the bidentate position (between two nitrogen atoms or oxygen and nitrogen atoms in purine and pyrimidine), where the binding energy is the largest. Moreover, the distance between M 2? and the base increases from Mg 2? to Ca 2? , while the binding energy of Mg 2? -base is greater than that of Ca 2? -base. The ABEEMrp/MM potential gives reasonable geometries and binding energies compared with the present quantum chemical calculations, and the overall percentage RMSDs are 1.4 and 1.6% for geometries and binding energies, respectively. Furthermore, the transferability of the parameters of the new potential is validated by investigation of Mg 2? /Ca 2? binding to tautomer of bases, and results from our potential also show quite good consistency with those of MP2/6-311 ??G(2d,2p)//B3LYP/6-311 ??G(d,p) method, with the overall percentage RMSDs of 2.2 and 4.7% for geometries and binding energies, respectively. This work will serve as a basis for further investigations of the mechanisms of cation effects on the structure and property of nucleic acids.

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