Ab initio and ABEEM/MM fluctuating charge model studies of dimethyl phosphate anion in a microhydrated environment

Wang, Fangfang; Zhao, Dong‐Xia; Gong, Liutang

doi:10.1007/s00214-009-0592-2

Cited by 17 publications

(5 citation statements)

References 73 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Ab initio computational methods have previously proven to be useful in investigating OP micro-hydration and include studies of the dihydrogen phosphate (DHP) and dimethyl phosphate (DMP) anion [14][15][16], bisphosphonates [17][18][19], phosphate [20], polyphosphate anions [21], DMMP [22,23], the G-agent simulant diisopropyl fluorophosphate (DIFP), and Sarin [22]. Recently we reported ab initio studies of adsorption energetics for the micro-hydrated Sarin•nH 2 O (n=1-4) clusters, confirming that the primary interaction was hydrogen bonding between the Sarin P=O group and water [24].…”

Section: Introductionmentioning

confidence: 99%

Infrared signature of micro-hydration in the organophosphate Sarin: an ab initio study

Alam

Pearce

2015

J Mol Model

View full text Add to dashboard Cite

The infrared (IR) spectra of micro-hydrated Sarin•(H2O)n clusters containing between one and four explicit waters have been studied using ab initio density functional theory (DFT) methods. The phosphate group P=O bond vibration region (∼1270 to 1290 cm(-1)) revealed the largest frequency variation with hydration, with a frequency red shift reflecting the direct hydrogen bond formation between the P=O of Sarin and water. Small variations to the P-F stretch (∼810 to 815 cm(-1)) and the C-O-P vibrational modes (∼995 to 1004 cm(-1)) showed that the water interactions with these functional groups were minor, and that the structures of Sarin were not extensively perturbed in the hydrated complexes. Increasing the number of explicit hydration waters produced only small vibrational changes in the lowest free energy complexes. These minor changes were consistent with a single water-phosphate hydrogen bond being the dominant structure, though a second water-phosphate hydrogen bond was observed in some complexes and was identified by an additional red shift of the P=O bond vibration. The H2O•H2O vibrational modes (∼3450 to 3660 cm(-1)) increased in complexity with higher hydration levels and reflect the extended hydrogen bonding networks formed between the explicit waters in the hydrated Sarin clusters. Graphical Abstract Ab initio studies of the infrared signature for micro-hydrated Sarin.

show abstract

Section: Introductionmentioning

confidence: 99%

Infrared signature of micro-hydration in the organophosphate Sarin: an ab initio study

Alam

Pearce

2015

J Mol Model

View full text Add to dashboard Cite

show abstract

“…Based on the atom-bond electronegativity equalization method (ABEEM) [69][70][71] fused into MM, Yang et al [72][73][74] have established a new generation of polarization molecular force field, that is, the ABEEMrp/MM fluctuating charge model. It has been applied successfully to the water system [72,73], ion solvation [75][76][77], organic molecules [78], peptides [79], and nucleic acid [74,75].…”

Section: Introductionmentioning

confidence: 99%

Mg2+/Ca2+ binding to DNA bases: a quantum chemical method and ABEEMσπ/MM fluctuating charge model study

Gong

et al. 2012

Theor Chem Acc

Self Cite

View full text Add to dashboard Cite

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.

show abstract

“…Because the polarizable force field can reflect the response of the electron density to an electrostatic field of condense phase environment, it has been developed quickly and used widely since the 1970s. On the basis of the atom-bond electronegativity equalization method (ABEEM) − fused into molecular mechanics (MM), Yang et al − have developed a new polarization force field, that is, the ABEEM/MM fluctuating charge model. It has been applied successfully to the water system, , ion−water system, − organic molecules, peptides, and nucleic acid systems. − Recently, the ABEEM/MM model has been used to perform dynamics simulation for proteins…”

Section: Introductionmentioning

confidence: 99%

A Systemic Investigation of Hydrogen Peroxide Clusters (H₂O₂)_n (n = 1−6) and Liquid-State Hydrogen Peroxide: Based on Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics and Molecular Dynamics

Yang

2011

J. Phys. Chem. A

View full text Add to dashboard Cite

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.

show abstract

Ab initio and ABEEM/MM fluctuating charge model studies of dimethyl phosphate anion in a microhydrated environment

Cited by 17 publications

References 73 publications

Infrared signature of micro-hydration in the organophosphate Sarin: an ab initio study

Infrared signature of micro-hydration in the organophosphate Sarin: an ab initio study

Mg2+/Ca2+ binding to DNA bases: a quantum chemical method and ABEEMσπ/MM fluctuating charge model study

A Systemic Investigation of Hydrogen Peroxide Clusters (H₂O₂)_n (n = 1−6) and Liquid-State Hydrogen Peroxide: Based on Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics and Molecular Dynamics

Contact Info

Product

Resources

About

Ab initio and ABEEM/MM fluctuating charge model studies of dimethyl phosphate anion in a microhydrated environment

Cited by 17 publications

References 73 publications

Infrared signature of micro-hydration in the organophosphate Sarin: an ab initio study

Infrared signature of micro-hydration in the organophosphate Sarin: an ab initio study

Mg2+/Ca2+ binding to DNA bases: a quantum chemical method and ABEEMσπ/MM fluctuating charge model study

A Systemic Investigation of Hydrogen Peroxide Clusters (H2O2)n (n = 1−6) and Liquid-State Hydrogen Peroxide: Based on Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics and Molecular Dynamics

Contact Info

Product

Resources

About

A Systemic Investigation of Hydrogen Peroxide Clusters (H₂O₂)_n (n = 1−6) and Liquid-State Hydrogen Peroxide: Based on Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics and Molecular Dynamics