A polarizable dipole–dipole interaction model for evaluation of the interaction energies for NH···OC and CH···OC hydrogen‐bonded complexes

In this article, a polarizable dipole–dipole interaction model is established to estimate the equilibrium hydrogen bond distances and the interaction energies for hydrogen‐bonded complexes containing peptide amides and nucleic acid bases. We regard the chemical bonds N? H, C?O, and C? H as bond dipoles. The magnitude of the bond dipole moment varies according to its environment. We apply this polarizable dipole–dipole interaction model to a series of hydrogen‐bonded complexes containing the N? H···O?C and C? H···O?C hydrogen bonds, such as simple amide‐amide dimers, base‐base dimers, peptide‐base dimers, and β‐sheet models. We find that a simple two‐term function, only containing the permanent dipole–dipole interactions and the van der Waals interactions, can produce the equilibrium hydrogen bond distances compared favorably with those produced by the MP2/6‐31G(d) method, whereas the high‐quality counterpoise‐corrected (CP‐corrected) MP2/aug‐cc‐pVTZ interaction energies for the hydrogen‐bonded complexes can be well‐reproduced by a four‐term function which involves the permanent dipole–dipole interactions, the van der Waals interactions, the polarization contributions, and a corrected term. Based on the calculation results obtained from this polarizable dipole–dipole interaction model, the natures of the hydrogen bonding interactions in these hydrogen‐bonded complexes are further discussed. © 2013 Wiley Periodicals, Inc.     

On the calculations of interaction energies and induced electric properties within the polarizable continuum model

In this work we investigate the influence of a polarizable environment on the interaction energies and the interaction-induced (excess) static electric dipole properties for the selected model hydrogen-bonded complexes. The excess properties were estimated for water and hydrogen fluoride dimers using the supermolecular approach and assuming the polarizable continuum model (PCM) as a representation of the polarizable environment. We analyze in this context the performance of the counterpoise correction and the consequences of various possible monomer cavity choices. The polarizable environment reduces the absolute magnitudes of interaction energies and interaction-induced dipole moments, whereas an increase is observed for the absolute magnitudes of induced polarizabilities and first hyperpolarizabilities. Our results indicate that the use of either monomeric (MC) or dimeric (DC) cavities in calculations of monomer properties does not change qualitatively the resultant excess properties. We conclude that the DC scheme is more consistent with the definition of the interaction energy and consequently also the interaction-induced property, whereas the MC scheme corresponds to the definition of stabilization energy. Our results indicate also a good performance of the counterpoise correction scheme for the self-consistent methods in the case of all studied properties.     

Molecular dynamics study of polarizable ion models for molten AgBr

Three different polarizable ion models for molten AgBr have been studied by molecular dynamics simulations. The three models are based on a rigid ion model (RIM) with a pair potential of the type proposed by Vashishta and Rahman for alpha-AgI, to which the induced dipole polarization of the ions is added. In the first (PIM1) the dipole moments are only induced by the local electric field, while in the other two (PIM1s and PIM2s) a short-range overlap induced polarization opposes the electrically induced dipole moments. In the PIM1 and the PIM1s only the anions are assumed polarizable, while in the PIM2s both species are polarizable. Long molecular dynamics simulations show that the PIM2s is an unphysical model since, for some improbable but possible critical configurations, the ions become infinitely polarized. The results of using the PIM1, the PIM1s, as well as those of the simple RIM, have been compared for the static structure and ionic transport properties. The PIM1 reproduces the broad main peak of the total structure factor present in the neutron diffraction data, although the smoothed three-peak feature of this broad peak is slightly overestimated. The structural results for the PIM1s are intermediate between those for the RIM and the PIM1, but fail to reproduce the experimental features within the broad principal peak. Concerning the ionic transport properties, the value of the conductivity obtained using PIM1 is in good agreement with experimental values, while the self-diffusion coefficients and the conductivity for the PIM1s are lower than the corresponding values using the PIM1 and the RIM.     

Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model

A polarizable empirical force field based on the classical Drude oscillator has been developed for the aliphatic alcohol series. The model is optimized with emphasis on condensed-phase properties and is validated against a variety of experimental data. Transferability of the developed parameters is emphasized by the use of a single electrostatic model for the hydroxyl group throughout the alcohol series. Aliphatic moiety parameters were transferred from the polarizable alkane parameter set, with only the Lennard-Jones parameters on the carbon in methanol optimized. The developed model yields good agreement with pure solvent properties with the exception of the heats of vaporization of 1-propanol and 1-butanol, which are underestimated by approximately 6%; special LJ parameters for the oxygen in these two molecules that correct for this limitation are presented. Accurate treatment of the free energies of aqueous solvation required the use of atom-type specific O(alcohol)-O(water) LJ interaction terms, with specific terms used for the primary and secondary alcohols. With respect to gas phase properties the polarizable model overestimates experimental dipole moments and quantum mechanical interaction energies with water by approximately 10 and 8 %, respectively, a significant improvement over 44 and 46 % overestimations of the corresponding properties in the CHARMM22 fixed-charge additive model. Comparison of structural properties of the polarizable and additive models for the pure solvents and in aqueous solution shows significant differences indicating atomic details of intermolecular interactions to be sensitive to the applied force field. The polarizable model predicts pure solvent and aqueous phase dipole moment distributions for ethanol centered at 2.4 and 2.7 D, respectively, a significant increase over the gas phase value of 1.8 D, whereas in a solvent of lower polarity, benzene, a value of 1.9 is obtained. The ability of the polarizable model to yield changes in dipole moment as well as the reproduction of a range of condensed phase properties indicates its utility in the study of the properties of alcohols in a variety of condensed phase environments as well as representing an important step in the development of a comprehensive force field for biological molecules.     

Automation of AMOEBA polarizable force field parameterization for small molecules

A protocol to generate parameters for the AMOEBA polarizable force field for small organic molecules has been established, and polarizable atomic typing utility, Poltype, which fully automates this process, has been implemented. For validation, we have compared with quantum mechanical calculations of molecular dipole moments, optimized geometry, electrostatic potential, and conformational energy for a variety of neutral and charged organic molecules, as well as dimer interaction energies of a set of amino acid side chain model compounds. Furthermore, parameters obtained in gas phase are substantiated in liquid-phase simulations. The hydration free energy (HFE) of neutral and charged molecules have been calculated and compared with experimental values. The RMS error for the HFE of neutral molecules is less than 1 kcal/mol. Meanwhile, the relative error in the predicted HFE of salts (cations and anions) is less than 3% with a correlation coefficient of 0.95. Overall, the performance of Poltype is satisfactory and provides a convenient utility for applications such as drug discovery. Further improvement can be achieved by the systematic study of various organic compounds, particularly ionic molecules, and refinement and expansion of the parameter database.     

Electric dipole moments in polar solvents. II. Tetraisoamylammonium nitrate ion pairs in chlorobenzene. Effect of mutual polarization of the ions

The dielectric constant and conductivity of dilute solutions of tetraisoamylammonium nitrate in chlorobenzene are measured between –34.6° and 99.0°C to give association constants for the formation of ion pairs (K _A) and triple ions, and electric dipole moments. The quantityK _A as a function of temperature is reproduced by the Denison-Ramsey-Fuoss treatment for unolarized ion pairs [Eq. (2)] with a distance of closest approach of 4.90 Å. The dielectric data are reproduced by Onsager's equation with an inherent (gas-phase) dipole moment of the ion pairs of 14.2±0.3 D. Other methods of calculation lead to consistent dipole moments, confirming that the mutual polarization of the ions is important. The energetics of ionic association is considered on the basis that the ion pair may be treated as a polarizable dipole in a spherical cavity.     

Molecular dynamics study of polarizable point dipole models for molten sodium iodide

The structure, the ionic transport properties, and the dynamics of long-wavelength charge-density fluctuations, for two polarizable point dipole models of molten NaI, have been studied by molecular dynamics simulations. These models are based on a rigid ion potential to which the induced dipole polarization of the anions is added. The polarization is added in such a way that point dipoles are induced on the anions by both local electric field and short-range damping interactions that oppose the electrically induced dipole moments. The two polarizable ion models differ only in the range of the damping polarization interactions. The influence of the induced anion polarization on the different properties of simulated molten NaI is discussed.     

Structure and dynamics of the aqueous liquid-vapor interface: a comprehensive particle-based simulation study

This research addresses a comprehensive particle-based simulation study of the structural, dynamic, and electronic properties of the liquid-vapor interface of water utilizing both ab initio (based on density functional theory) and empirical (fixed charge and polarizable) models. Numerous properties such as interfacial width, hydrogen bond populations, dipole moments, and correlation times will be characterized with identical schemes to draw useful conclusions on the strengths and weakness of the proposed models for interfacial water. Our findings indicate that all models considered in this study yield similar results for the radial distribution functions, hydrogen bond populations, and orientational relaxation times. Significant differences in the models appear when examining both the dipole moments and surface relaxation near the aqueous liquid-vapor interface. Here, the ab initio interaction potential predicts a significant decrease in the molecular dipole moment and expansion in the oxygen-oxygen distance as one approaches the interface in accordance with recent experiments. All classical polarizable interaction potentials show a less dramatic drop in the molecular dipole moment, and all empirical interaction potentials studied yield an oxygen-oxygen contraction as the interface is approached.     

Structure, thermodynamics, and liquid-vapor equilibrium of ethanol from molecular-dynamics simulations using nonadditive interactions

We present a molecular-dynamics simulation study of the bulk and liquid-vapor interfacial properties of ethanol using a polarizable force field based on the fluctuating charge (FQ) formalism, as well as the nonpolarizable CHARMM22 force field. Both models are competitive with respect to the prediction of ambient liquid properties such as liquid density, enthalpy of vaporization, dielectric constant, and self-diffusion constants. The polarizable model predicts an average condensed-phase dipole moment of 2.2 D associated with an induced liquid-phase dipole moment of 0.6 D; though qualitatively in agreement with earlier nonadditive models as well as recent Car-Parinello calculations, the current FQ model underestimates the condensed-phase dipole moment. In terms of liquid structure, both models are in agreement with recent neutron-diffraction results of liquid ethanol structure, although the polarizable model predicts the hydroxyl-hydrogen-hydroxyl-hydrogen structure factor in closer agreement with the experimental data. In terms of interfacial properties, both models predict ambient surface tension to within 4% of the experimental value of 22.8 dyncm, while overestimating the surface excess entropy by almost a factor of 2. Both models display the characteristic preferential orientation of interfacial molecules. The polarizable model allows for a monotonic variation of the average molecular dipole moment from the bulk value to that of the vapor phase. Consequently, there is a dramatic difference in the surface potential predicted by the polarizable and nonpolarizable models. The polarizable model estimates a surface potential of -209+/-3 mV, while the nonpolarizable model yields a value of -944+/-10 mV. Finally, based on the vapor-liquid equilibrium simulation data from several temperatures, we estimate the critical properties of both models. As observed with other FQ models for associating fluids (such as water and methanol), and counter to what one would anticipate by modeling more physically the electrostatic response to local environment, the current FQ model underestimates the critical temperature and overestimates the critical density of ethanol; moreover, the FQ model is, in this respect, equivalent to the underlying fixed-charge model. These results further suggest the need to revisit polarizable models in terms of quantitative vapor-liquid equilibrium prediction.     

Molecular dynamics study of polarization effects on AgI

Three different models of AgI are studied by molecular dynamics simulations. The first one is the rigid ion model (RIM) with the effective pair potential of the Vashishta and Rahman form and the parametrization proposed by Shimojo and Kobayashi. The other two are polarizable ion models in which the induced polarization effects have been added to the RIM effective pair potential. In one of them (PIM1), only the anions are assumed to be polarizable by the local electric field. In the other one (PIM2s), the silver polarization is also included, and a short-range overlap-induced polarization opposes the electrically induced dipole moments. This short-range polarization is proved to be necessary to avoid overpolarization when both species are assumed to be polarizable. The three models reproduce the superionic character of alpha-AgI at 573 K and the liquid behavior of molten AgI at 923 K. The averaged spatial distribution of the cations in the alpha-phase obtained for PIM1 appears to be in better agreement with experimental data analysis. The PIM1 also reproduces the structure factor prepeak at about 1 A(-1) observed from neutron diffraction data of molten AgI. The three models retain in the liquid phase the superionic character of alpha-AgI, as the mobility of the cations is significantly larger than that for the anions. The ionic conductivity for the polarizable ion models is in better agreement with experimental data for alpha-AgI and molten AgI.     

单十二烷基磷酸酯辅助共轭亚油酸的囊泡化研究

以共轭亚油酸(CLA)为模型脂肪酸,与安全、温和的阴离子表面活性剂单十二烷基磷酸酯(MLP)进行复配,动态激光光散射和透射电镜表征结果表明,CLA在中性至弱酸性环境中仍然能够囊泡化.通过pH滴定曲线研究了CLA和MLP 2种分子的荷电物种随pH值的变化规律,据此分析各物种间的相互作用,并推断经MLP辅助CLA能够在中性至弱酸性环境中囊泡化的动因是CLA-MLP间的氢键或离子-偶极作用.     

Attraction of iodide ions by the free water surface, revealed by simulations with a polarizable force field based on Drude oscillators

Recent theoretical and experimental studies have shown that polarizable anions, such as iodide and bromide, preferentially accumulate close to the surface of electrolyte solutions. This finding is in sharp contrast to the previously prevailing idea that salts are dielectrically excluded from the free water surface and opens up new avenues for research in specific salt effects. In this work, we have verified the ability of a recently introduced polarizable water model, SWM4-DP, to reproduce this behavior, by simulations of a NaI/water slab, corresponding to a 1.2 M solution. The water and ion polarizabilities are modeled by classical Drude oscillator particles. As revealed by the simulations, a double layer is formed close to the free water surface, with the iodide ions located closer to the interface and the sodium ions at a neighboring, interior layer. Near the surface, all solution species acquire an induced dipole moment, that is perpendicular to the surface and points toward the exterior. The double charge layer causes ordering of water at a subsurface region. Simulations with a simpler system of a single iodide ion in a water slab show that the surface position is stabilized by induced charge interactions; in contrast, the charge-dipole interactions between the iodide permanent charge and the water permanent dipole moment favor the bulk position. Thus, the polarizabilities of ion and water are essential for explaining the increased preference of iodide for the air-water interface, in accordance with other studies.     

Polarizable simulations with second order interaction model (POSSIM) force field: Developing parameters for protein side‐chain analogues

A previously introduced polarizable simulations with second‐order interaction model (POSSIM) force field has been extended to include parameters for small molecules serving as models for peptide and protein side‐chains. Parameters have been fitted to permit reproducing many‐body energies, gas‐phase dimerization energies, and geometries and liquid‐phase heats of vaporization and densities. Quantum mechanical and experimental data have been used as the target for the fitting. The POSSIM framework combines accuracy of a polarizable force field and computational efficiency of the second‐order approximation of the full‐scale induced point dipole polarization formalism. The resulting parameters can be used for simulations of the parameterized molecules themselves or their analogues. In addition to this, these force field parameters are currently being used in further development of the POSSIM fast polarizable force field for proteins. © 2012 Wiley Periodicals, Inc.     

Key role of the polarization anisotropy of water in modeling classical polarizable force fields

We have evaluated the extent to which classical polarizable force fields, based either on the chemical potential equalization principle or on distributed polarizabilities in the framework of the Sum of Interactions Between Fragments Ab initio computed (SIBFA), can reproduce the ab initio polarization energy and the dipole moment of three distinct water oligomers: bifurcated chains, transverse hydrogen-bonded chains, and longitudinal hydrogen-bonded chains of helical shape. To analyze the many-body polarization effect, chains of different size, i.e., from 2 to 12 water monomers, have been considered. Although the dipole moment is a well-defined quantity in both classical polarizable models and quantum mechanical methods, polarization energy can be defined unequivocally only in the former type of approaches. In this study we have used the Kitaura-Morokuma (KM) procedure. Although the KM approach is on the one hand known to overestimate the polarization energy for strongly interacting molecules, on the other hand it can account for the many-body polarization effectively, whereas some other procedures do not. Our data show that, if off-centered lone pair polarizabilities are explicitly represented, classical polarizable force fields can afford a close agreement with the ab initio results, both in terms of polarization energy and in terms of dipole moment.