Polarizable Point Research Articles

Clusters of classical water models

The properties of clusters can be used as tests of models constructed for molecular simulation of water. We searched for configurations with minimal energies for a small number of molecules. We identified topologically different structures close to the absolute energy minimum of the system by calculating overlap integrals and enumerating hydrogen bonds. Starting from the dimer, we found increasing number of topologically different, low-energy arrangements for the trimer(3), the tetramer(6), the pentamer(6), and the hexamer(9). We studied simple models with polarizable point dipole. These were the BSV model [J. Brodholt et al., Mol. Phys. 86, 149 (1995)], the DC model [L. X. Dang and T. M. Chang, J. Chem. Phys. 106, 8149 (1997)], and the GCP model [P. Paricaud et al., J. Chem. Phys. 122, 244511 (2005)]. As an alternative the SWM4-DP and the SWM4-NDP charge-on-spring models [G. Lamoureux et al., Chem. Phys. Lett. 418, 245 (2006)] were also investigated. To study the impact of polarizability restricted to the plane of the molecule we carried out calculations for the SPC-FQ and TIP4P-FQ models, too [S. W. Rick et al., J. Chem. Phys. 101, 6141 (1994)]. In addition to them, justified by their widespread use even for near critical or surface behavior calculations, we identified clusters for five nonpolarizable models of ambient water, SPC/E [H. J. C. Berendsen et al., J. Phys. Chem. 91, 6269 (1987)], TIP4P [W. L. Jorgensen et al., J. Chem. Phys. 79, 926 (1983)], TIP4P-EW [H. W. Horn et al., J. Chem. Phys. 120, 9665 (2004)], and TIP4P/2005 [J. L. F. Abascal and C. Vega, J. Chem. Phys. 123, 234505 (2005)]. The fifth was a five-site model named TIP5P [M. W. Mahoney and W. L. Jorgensen, J. Chem. Phys. 112, 8910 (2000)]. To see the impact of the vibrations we studied the flexible SPC model. [K. Toukan and A. Rahman, Phys. Rev. B 31, 2643 (1985)]. We evaluated the results comparing them with experimental data and quantum chemical calculations. The position of the negative charge in the models plays a crucial role. In this respect models with SPC geometry provided structures different from the TIP4P-type potentials, including polarizable ones. The TIP4P variants form configurations similar to one another. Results for TIP4P-EW and for TIP4P/2005 were especially close to each other in every respect. This is also true for the BSV and the DC pair. The charge-on-spring models (SWM4-DP and SWM4-NDP) are also very similar to each other, despite the sign exchange of charges on the spring particle and the oxygen. The spherical polarization of water is crucial. Due to the planar polarization of the SPC-FQ and the TIP4P-FQ models, they prefer planar arrangements contrary to other polarizable models and quantum chemical calculations. The tetrahedral geometry of TIP5P stabilizes additional clusters with peculiar geometries and small O-O distances. Inclusion of vibrations causes only insignificant changes in the characteristic geometries but decreases the internal energy relative to its reference rigid version. Comparing with quantum mechanical calculations the GCP model provided the best overall results.

Resonance in Interacting Induced-Dipole Polarizing Force Fields: Application to Force-Field Derivatives

The Silberstein model of the molecular polarizability of diatomic molecules, generalized by Applequist et al. for polyatomic molecules, is analyzed. The atoms are regarded as isotropically polarizable points located at their nuclei, interacting via the fields of their induced dipoles. The use of additive values for atom polarizabilities gives poor results, in some cases leading to artificial predictions of absorption bands. The molecular polarizability of methane and its derivative are computed. The agreement with experimental mean molecular polarizabilities is within 1–5%. A hypothesis is indispensable for a suitable representation of polarizability derivative.

Diffraction Effects in the Propagation of Radiation in Polarizable Layers

The very low transmission of light through holes smaller than the wavelength has been found to be enhanced for subwavelength apertures in metallic surfaces with periodic corrugations. This effect has been attributed to the interaction of light with surface plasmons. Similar effects obtained subsequently for non-metallic surfaces have been attributed to evanescent waves on the surface produced by the diffracted Bloch waves from different points in the array. We present an exact solution of Maxwell's equations in the discrete dipole approximation (DDA) for a periodic array of polarizable point dipoles in a layer. Metallic as well as non metallic layers are described. When the wavelength is smaller than the lattice period there is a Bragg's scattered wave, while for subwavelength conditions an evanescent wave on the surface appears. The transmission/reflection coefficients are found to oscillate as a function of frequency, with resonances occurring in a broad range of frequencies depending on the polarizability, at which the evanescent field is enhanced. A detailed study is presented for nanostructured arrays. We find that this model agrees with features observed in experiments through hole arrays supporting the role played by diffraction during light transmission through such arrays without invoking surface plasmons and providing a base to analyze more complex geometries.

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.

Theoretical analysis of the electronic asymmetry of the special pair in the photosynthetic reaction center: Effect of structural asymmetry and protein environment

We have studied the effect of structural differences and protein environment on electronic asymmetry of the special pair (SP) and the special pair cation radical in the bacterial photosynthetic reaction center with density functional theory. The electronic asymmetry has been found to derive from the difference in the orientation of methyl ester groups of SP halves. Due to the protein polarity enhancement with polarizable continuum model and point charge model, one electron oxidation is more significantly biased to the L-side bacteriochlorophyll a (SP L) in the both models.

SERS effect in CO physisorbed on homogeneous and core-shell nanoparticle aggregates

Surface Enhanced Raman Scattering (SERS) is studied for a simple molecule (CO) physisorbed on a nanoparticle belonging to a nanoparticle aggregate, with well defined composition and architecture, in order to assess the effect of metal nanostructure on the Raman enhancement. The approach involves explicit consideration of the molecule, with due allowance for the characteristics of its radiated field, which are believed to be particularly important elements in determining enhancement from complex-shape aggregates. The electrodynamic problem for a nonresonant polarizable point dipole in the presence of an aggregate of spherical scatterers has been resolved numerically, extending to a multi-particle system the treatment put forward by Kerker.

Self ordering threshold and superradiant backscattering to slow a fast gas beam in a ring cavity with counter propagating pump

We study the dynamics of a fast gaseous beam in a high Q ring cavity counter propagating a strong pump laser with large detuning from any particle optical resonance. As spontaneous emission is strongly suppressed the particles can be treated as polarizable point masses forming a dynamic moving mirror. Above a threshold intensity the particles exhibit spatial periodic ordering enhancing collective coherent backscattering which decelerates the beam. Based on a linear stability analysis in their accelerated rest frame we derive analytic bounds for the intensity threshold of this selforganization as a function of particle number, average velocity, kinetic temperature, pump detuning and resonator linewidth. The analytical results agree well with time dependent simulations of the N-particle motion including field damping and spontaneous emission noise. Our results give conditions which may be easily evaluated for stopping and cooling a fast molecular beam.

Repair Reactions of Pyrimidine-Derived Radicals by Aliphatic Thiols

Pyrimidinyl radicals of various structures (Pyr*) were generated in aqueous and alcohol-containing solutions by means of pulse radiolysis to determine the rate constants of their repair reactions by different thiols (RSH = cysteamine, 2-mercaptoethanol, cysteine, and penicillamine): Pyr* + RSH --> PyrH + RS*. C5-OH and C6-OH adduct radicals of the pyrimidines react with thiols with k9 = (1.2-10.0) x 10(6) dm3 mol(-1) s(-1). Similar repair rate constants were found for uracil- and thymine-derived N1-centered radicals, k31 = (1.5-6.1) x 10(6) dm3 mol(-1) s(-1). However, pyrimidine radical anions protonated at their C6 position and C6-uracilyl radicals, with carbonyl groups at their C5 position, react with thiols faster, with k24 = (0.5-7.6) x 10(7) dm3 mol(-1) s(-1) and k14 = (1.4-4.8) x 10(7) dm3 mol(-1) s(-1), respectively. Quantum chemical calculations, at the B3LYP/6-31G(d,p) and self-consistent reaction field polarizable continuum model level point to the combined effects of the energy gap between interacting molecular orbitals, charge distribution within different pyrimidine-derived radicals, and the coefficients of the atomic orbitals as the possible reasons for the differences in the rate constants of repair.

On the cloaking effects associated with anomalous localized resonance

Regions of anomalous localized resonance, such as occurring near superlenses, are shown to lead to cloaking effects. This occurs when the resonant field generated by a polarizable line or point dipole acts back on the polarizable line or point dipole and effectively cancels the field acting on it from outside sources. Cloaking is proved in the quasistatic limit for finite collections of polarizable line dipoles that all lie within a specific distance from a coated cylinder having a shell permittivity where is the permittivity of the surrounding matrix, and is the core permittivity. Cloaking is also shown to extend to the Veselago superlens outside the quasistatic regime: a polarizable line dipole located less than a distance d /2 from the lens, where d is the thickness of the lens, will be cloaked due to the presence of a resonant field in front of the lens. Also a polarizable point dipole near a slab lens will be cloaked in the quasistatic limit.

Electromagnetic response of a point-dipole crystal

We study the electromagnetic response of a cubic array of polarizable and resonant point dipoles. We show, that in addition to the formation of photonic and polaritonic bands and gaps in the dispersion of transverse waves, the array allows for bulk and surface plasmon wave propagation, as well as negative refraction in a polaritonic band, and subwavelength lensing. We suggest experimental arrangements for demonstration of these effects, both at microwave and optical frequencies.

Monte Carlo simulation of polarizable systems: Early rejection scheme for improving the performance of adiabatic nuclear and electronic sampling Monte Carlo simulations

An early rejection scheme for trial moves in adiabatic nuclear and electronic sampling Monte Carlo simulation (ANES-MC) of polarizable intermolecular potential models is presented. The proposed algorithm is based on Swendsen–Wang filter functions for prediction of success or failure of trial moves in Monte Carlo simulations. The goal was to reduce the amount of calculations involved in ANES-MC electronic moves, by foreseeing the success of an attempt before making those moves. The new method was employed in Gibbs ensemble Monte Carlo (GEMC) simulations of the polarizable simple point charge-fluctuating charge (SPC-FQ) model of water. The overall improvement in GEMC depends on the number of swap attempts (transfer molecules between phases) in one Monte Carlo cycle. The proposed method allows this number to increase, enhancing the chemical potential equalization. For a system with 300 SPC-FQ water molecules, for example, the fractions of early rejected transfers were about 0.9998 and 0.9994 at 373 and 423 K, respectively. This means that the transfer moves consume only a very small part of the overall computing effort, making GEMC almost equivalent to a simulation in the canonical ensemble.

Fugacity Coefficients of Saturated Water from Molecular Simulation

We apply isothermal−isobaric Monte Carlo molecular simulation to measure the vapor-phase fugacity coefficients and equation of state of three fixed-charge models of water: SPC/E, MSPC/E, and TIP3P. State conditions correspond to the experimental vapor−liquid saturation pressures for temperatures between 292.65 and 386.85 K. The results are compared to the experimental data for water vapor. We also examine properties as given by the application of the virial equation of state, using values of the second virial coefficients computed by us or that have been previously reported (in some cases up to third virial coefficients) for the models simulated here. The models show significant deviation from ideal-gas behavior, considerably more than seen experimentally, and a second-order virial treatment does not fully characterize the behavior. This deviation from experiment is consistent with the expected failings of fixed-charge models developed for liquid phases, when applied to the vapor. A virial-equation treatment of a fluctuating-charge model (TIP4P/fq) and the polarizable point charge model (PPC) indicates that the vapor-phase properties of these models will be much more in line with experimental fugacities and densities along the coexistence line.

Microstructure of Water At the Level of Three-particle Correlation Functions As Predicted by Classical Intermolecular Models

We compared the microscopic structure of liquid water at ambient conditions predicted by six classical intermolecular potential models. Applying their accepted acronyms were the SPC (Simple Point Charge), SPC/E (SPC extended), MSPC/E (SPC/E modified), TIP4P (Transferable Intermolecular Potential, four point charges), TIP5P (TIP, five point charges), and the PPC (Polarizable Point Charge) intermolecular potential models. Configurations of computer simulations were used to study the structure at the level of partial three-particle correlation functions. We created contour maps for visual evaluation, calculated overlap integrals of the three-particle correlation functions of the models to quantify their similarity, and determined their distance-dependent three-particle entropy contribution. The SPC/E and the TIP4P water models generate quite similar structures, while the SPC and the MSPC/E pair exhibit the largest discrepancies. The structure of the PPC is the most ordered and the SPC structure is the most disordered among the studied interaction models.

Combining ab initio and density functional theories with semiempirical methods

For large reactive systems, the calculation of energies can be simplified by treating the active part with a high-level quantum mechanical (QM) (ab initio or density functional) approach and the environment with a less sophisticated semiempirical (SE) approach, as an improvement over the widely used hybrid quantum mechanical/molecular mechanical (QM/MM) methods. An example is the interaction between an active region of an enzyme and its immediate environment. One such method is the original “Our-own-N-layer Integrated molecular Orbital+Molecular Mechanics (ONIOM)” approach. In this paper, the interaction between the QM and SE region is described explicitly by two different schemes. In the iterative QM/SE schemes (QM/SE-I), the electrostatic interaction and polarization effects are introduced explicitly for both the QM and SE atoms by a self-consistent procedure based on either polarizable point charges or the electron density. In the noniterative QM/SE scheme, based on the ONIOM model (QM/SE-O), the exchange (Pauli repulsion) and charge transfer effects are taken into account at the SE level, in addition to the explicit electrostatic interaction and polarization between the two regions. Test calculations are made on a number of model systems (including small polar or charged molecules interacting with water and proton transfer reactions in the presence of polar molecules or an extended hydrogen-bond network). The quantitative accuracy of the results depend on several parameters, such as the charge-scaling/normalization factors for the SE charge and the QM/SE van der Waals parameters, which can be chosen to optimize the result. For the QM/SE-O approach, the results are more sensitive to the quality of the SE level (e.g., self-consistent-charge density-functional-tight-binding vs AM1) than the explicit interaction between QM and SE atoms.

D-RESP: Dynamically Generated Electrostatic Potential Derived Charges from Quantum Mechanics/Molecular Mechanics Simulations

A scheme is proposed for calculating electrostatic potential (ESP) derived charges from mixed quantum mechanics/ molecular mechanics (QM/MM) molecular dynamics simulations. These charges are fitted to the electrostatic field due to the quantum charge density evaluated on the MM atoms close to the QM system and are restrained to the corresponding Hirshfeld value by a quadratic penalty function. The D-RESP charges estimated by this procedure reproduce the field due to the charge density polarized by the environment and can be obtained as a function of time along a finite temperature molecular dynamics trajectory with essentially no computational overhead with respect to a standard QM/MM calculation. The fluctuation of the D-RESP values in a finite temperature run provide information about the importance of polarization effects and thus allow for a direct comparison of the relative performance of polarizable versus non polarizable point charge models. Moreover, the D-RESP charges estimated by this procedure can be used as a simple and straightforward indicator of the chemical state of the system.

Charge redistribution and polarization energy of organic molecular crystals

We present an approach to electronic polarization in molecular solids treated as a set of quantum systems interacting classically. Individual molecules are dealt with rigorously as quantum-mechanical systems subject to classical external fields created by all other molecules and, possibly, external sources. Self-consistent equations are derived for induced dipoles and for atomic charges whose redistribution in external fields is given explicitly by an atom-atom polarizability tensor. Electronic polarization is studied in two representative organic molecular crystals, anthracene and perylenetetracarboxylic acid dianhydride (PTCDA), and contrasted to previous results for systems of polarizable points. The stabilization energies of the neutral lattice, of isolated anions and cations, and of cation-anion pairs are found. Charge redistribution on ions is included. The dielectric tensors of crystals are successfully related to gas-phase properties and provide consistency checks on polarization energies. The procedure is generally applicable to organic crystals in the limit of no intermolecular overlap.

Equations of state and phase coexistence properties for simulated water

There is a practical need in modeling both ambient and high-temperature water near and above the critical point with a single transferable intermolecular potential. Thermodynamic properties for two water potentials, the simple point charge (SPC/E) and the polarizable point charge (PPC) models, are examined with the aid of molecular dynamics simulations. Analytical equations of state, liquid–vapor coexistence properties and critical point parameters are given. The effect of applying an external electric field to the system on the coexistence properties is investigated. A shift of the critical point of water to higher temperature and pressure is observed, a result similar to that of the introduction of an electrolyte to water.

Self-diffusion process in water: Spatial picture of single-particle density fluctuations

A computer simulation methodology with which to study the single-particle dynamics in complex molecular liquids is presented. Molecular dynamics simulations of liquid water are performed in the temperature range of 238–473 K using the polarizable point charge (PPC) potential. The self part of the van Hove density–density correlation function is calculated. Using the Gaussian approximation of the van Hove function the mean self-diffusion coefficient for the PPC potential is calculated. The singularity temperature for supercooled PPC water, Ts=218 K, estimated from the self-diffusion data appears to agree well with most estimates for real water. In order to elucidate the spatial picture of the single-particle molecular density in this complex liquid and its time evolution, we explicitly resolve the self van Hove function in the local frame of water molecules. The self-diffusion tensor is introduced and numerically evaluated from this spatial (separation and direction dependent) self van Hove function. The fluctuations of the single-particle molecular density in liquid water appear to be spatially anisotropic (nonspherical). At low temperatures these dynamical heterogeneities in liquid water tend to increase.

Polarization Force Fields for Peptides Implemented in ECEPP2 and MM2

The empirical conformational energy program for peptides (ECEPP2) and molecular mechanics (MM2) have been used for the simulation of the For-Gly-NH2 backbone. I propose two different methods for the calculation of the polarization energy term: the polarization procedure by non-interacting induced dipoles (NID) which assumes scalar isotropic point polarizabilities and the polarization scheme by interacting induced dipoles (ID) which calculates tensor effective anisotropic point polarizabilities (method of Applequist). I present a comparative study of ECEPP2 and MM2 + polarization. I discuss molecular mechanics results including the total energy differences, partitional analyses of the total steric energies and torsion dihedral angles. The γ global and the α, β and Δ local minima are stabilized by intramolecular hydrogen bonds. Although ECEPP2-based calculations rather under or over-estimate the relative energy of some local minima, the ID polarization energy term represents a significant correction to the total relative energy.

Effects of the polarizability and water density constraint on the structure of water near charged surfaces: Molecular dynamics simulations

To understand how the inclusion of explicit polarizability into water interaction potential changes the structure of water next to a charged metallic surface we compared the results from the simulations using polarizable point charge model and simple point charge model. To study the effect of density constraints we also performed simulations of water next to hydrophobic walls and metal walls. In these simulations the water density was not predetermined, but regulated itself during the run.