Charge Penetration Research Articles

Assessing Ion-Water Interactions in the AMOEBA Force Field Using Energy Decomposition Analysis of Electronic Structure Calculations.

AMOEBA is a molecular mechanics force field that addresses some of the shortcomings of a fixed partial charge model, by including permanent atomic point multipoles through quadrupoles, as well as many-body polarization through the use of point inducible dipoles. In this work, we investigate how well AMOEBA formulates its non-bonded interactions, and how it implicitly incorporates quantum mechanical effects such as charge penetration (CP) and charge transfer (CT), for water-water and water-ion interactions. We find that AMOEBA's total interaction energies, as a function of distance and over angular scans for the water dimer and for a range of water-monovalent cations, agree well with an advanced density functional theory (DFT) model, whereas the water-halides and water-divalent cations show significant disagreement with the DFT result, especially in the compressed region when the two fragments overlap. We use a second-generation energy decomposition analysis (EDA) scheme based on absolutely localized molecular orbitals (ALMOs) to show that in the best cases AMOEBA relies on cancellation of errors by softening of the van der Waals (vdW) wall to balance permanent electrostatics that are too unfavorable, thereby compensating for the missing CP effect. CT, as another important stabilizing effect not explicitly taken into account in AMOEBA, is also found to be incorporated by the softened vdW interaction. For the water-halides and water-divalent cations, this compensatory approach is not as well executed by AMOEBA over all distances and angles, wherein permanent electrostatics remains too unfavorable and polarization is overdamped in the former while overestimated in the latter. We conclude that the DFT-based EDA approach can help refine a next-generation AMOEBA model that either realizes a better cancellation of errors for problematic cases like those illustrated here, or serves to guide the parametrization of explicit functional forms for short-range contributions from CP and/or CT.

A Universal and Straightforward Approach to Include Penetration Effects in Electrostatic Interaction Energy Estimation.

To compensate for the lack of the explicit treatment of charge penetration in classical force fields, we propose a new charge-distribution model based on a promolecule augmented with point charges (aug-PROmol). It relies on a superposition of spherical atomic electron densities obtained for each chemical element from SCF energy optimized atomic orbitals. Atomic densities are further rescaled by partial point charges computed from fits to the molecular electrostatic potential. Aug-PROmol was tested on the S66 benchmark dataset extended to nonequilibrium geometries (J. Chem. Theory Comput., 2011, 7, 3466). The model does not need any additional parametrization other than point charges. Despite its simplicity, aug-PROmol approximates the electrostatic energy with good agreement (RMSE=0.76 kcal mol(-1) to DFT-SAPT with B3LYP/aug-cc-pVTZ).

Noncovalent Interactions and Impact of Charge Penetration Effects in Linear Oligoacene Dimers and Single Crystals

Noncovalent interactions determine in large part the thermodynamic aspects of molecular packing in organic crystals. Using a combination of symmetry-adapted perturbation theory (SAPT) and classical multipole electrostatics, we describe the interaction potential energy surfaces for dimers of the oligoacene family, from benzene to hexacene, including up to 5000 configurations for each system. An analysis of these surfaces and a thorough assessment of dimers extracted from the reported crystal structures underline that high-order interactions (i.e., three-body nonadditive interactions) must be considered in order to rationalize the details of the crystal structures. A comparison of the SAPT electrostatic energy with the multipole interaction energy demonstrates the importance of the contribution of charge penetration, which is shown to account for up to 50% of the total interaction energy in dimers extracted from the experimental single crystals; in the case of the most stable cofacial model dimers, this con...

A theoretical study of π-stacking interactions in C-substituted tetrazoles

The π-stacking effects of benzene ring (Ben) with 1H- and 2H-tetrazole derivatives (1H-TZ-X and 2H-TZ-X) substituted at C5 (where X is Cl, COH, NO, NO2, CN, NH2, OH, OCH3, SH and H) has been investigated by the quantum mechanical calculations at the M06-2X/6-311++G** level. The results indicate the 1H-TZ-X||Ben complexes (|| donates π-stacking interaction) are more stable than 2H-TZ-X||Ben while in unstacked forms, 1H-TZ-X is less stable than 2H-TZ-X. All substituents enhance the π-stacking interaction relative to the unsubstituted ones and enhancement is higher for the electron-withdrawing substituents (EWSs). Also, investigation of the local and direct effect of substituents in stacking interaction showed that all substituents regardless of whether are electron donating or electron withdrawing have an additive effect in π-stacking interaction. Excellent correlations were found between the binding energies of the complexes and combination of substituent constant terms. The results showed that the electrostatic interaction alone is not responsible for stacking stabilization but charge penetration is important. Furthermore, analysis of aromaticity, AIM, ESP and NPA were investigated to obtain aromaticity index, non-bonding interactions, chemical reactivity and polarity (dipole moment), respectively.

Development of an efficient numerical model for shaped charge analysis

The process of shaped charge jet formation, fragmentation, and penetration in rolled-homogenous armor steel target plates was investigated using the explicit, nonlinear Lagrangian finite element method. The investigation was conducted in two dimensions utilizing an axisymmetric configuration for a shaped charge with a 40 mm cone diameter. The results obtained using numerical simulations were compared to the experimental results obtained from tests. In addition, the dynamic behavior of the jet was compared to the visual data obtained from X-rays to confirm jet formation and fragmentation predictions. The advanced features of the developed shaped charge model include adaptive remeshing to follow the high deformation pattern of the jet, appropriate constitutive material models and equations of state to account for high strain rate, and restart files to allow the simulation to be performed in stages.

Method for Slater-Type Density Fitting for Intermolecular Electrostatic Interactions with Charge Overlap. I. The Model.

The effects of charge overlap, or charge penetration, are neglected in most force fields and interaction terms in QM/MM methods. The effects are however significant at intermolecular distances near the van der Waals minimum. In the present study, we propose a method to evaluate the intermolecular Coloumb interaction using Slater-type functions, thus explicitly modeling the charge overlap. The computational cost of the method is low, which allows it to be used in large systems with most force fields as well as in QM/MM schemes. The charge distribution is modeled as a distributed multipole expansion up to quadrupole and Slater-type functions of angular momentum up to L = 1. The exponents of the Slater-type functions are obtained using a divide-and-conquer method to avoid the curse of dimensionality that otherwise is present for large nonlinear optimizations. A Levenberg-Marquardt algorithm is applied in the fitting process. A set of parameters is obtained for each molecule, and the process is fully automated. Calculations have been performed in the carbon monoxide and the water dimers to illustrate the model. Results show a very good accuracy of the model with relative errors in the electrostatic potential lower than 3% over all reasonable separations. At very short distances where the charge overlaps is the most significant, errors are lower than 8% and lower than 3.5% at distances near the van der Waals minimum.

Experimental and numerical investigation on heavy-caliber shaped-charge penetration in thick concrete target

The independent developed software EXPLOSION-2D was adopted to simulate the heavy-caliber shaped-charge forming, and the laws of heavy-caliber shaped-charge forming were obtained and the influence of blasting height for shaped charge penetration thickness concrete target was simulated. Based on the performance parameters of the penetrators, two kinds of shaped-charge structures which had good penetration effect were selected to penetrate in the thick concrete target. According to the simulation results the best shaped-charge structure which could penetrate the thick concrete target well was designed and the corresponding experiments were carried out. The concrete target after the experiment was cut to evaluate the concrete target damage in different location by the inside damage of concrete target and the hole diameters of different location were measured. The test conditions were simulated by the EXPLOSION-2D software and the simulation results was compared with the experimental results. The comparison results show that the numerical simulation technology can evaluate the damage of concrete target effectively.

Fabrication of 3D foam-like hybrid carbon materials of porous carbon/graphene and its electrochemical performance

In this work, we report the direct fabrication of 3D foam-like carbon materials by ambient pressure chemical vapour deposition on Ni foams, and followed by a simply chemical etching. By controlling growth temperature, microstructures of the 3D foam-like carbon materials can be adjusted from 3D porous carbon, free-standing 3D hybrid carbon materials composed of porous carbon and graphene, to free-standing 3D hollow graphene. The free-standing 3D hybrid carbon materials, in which porous carbon tightly adhered to the inner surface of hollow graphene, are found to be promising alternatives for the electrode materials of energy storage devices because of their interconnected hierarchical porous structures and high electrical conductivity, which provide a more favorable path for charge penetration and transportation. A binder-free supercapacitor assembled by 3D hybrid carbon materials exhibits good capacitance performance and high rate capability.

Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles.

We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short-range charge penetration correction modifying the charge-charge, charge-dipole and charge-quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry-Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono- and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER-HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration-corrected polarizable force fields highlighting the mandatory need of non-spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short-range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio- or bioinorganic systems in periodic boundary conditions.

Assessment of Empirical Models versus High-Accuracy Ab Initio Methods for Nucleobase Stacking: Evaluating the Importance of Charge Penetration.

Molecular mechanics (MM) force field models have been demonstrated to have difficulty reproducing certain potential energy surfaces of π-stacked complexes. Here, we examine the performance of the AMBER and CHARMM models relative to high-quality ab initio data across systematic helical parameter scans and typical B-DNA geometries for π-stacking energies of nucleobase dimers. These force fields perform best for typical B-DNA geometries (mean absolute error < 1 kcal mol(-1)), whereas errors typically approach ∼2 kcal mol(-1) for broader potential scans, with maximum errors > 10 kcal mol(-1) relative to high-quality ab initio reference interaction energies. The adequate performance of MM models near minimum energy structures is accomplished through cancellation of errors in various energy terms, whereas large errors at short intermolecular distances are caused by large MM electrostatics errors due to a lack of explicit terms modeling charge penetration effects.

Analysis for Evaluating the Impact of PEVs on New-Town Distribution System in Korea

This paper analyzes the impact of Plug-in Electric vehicles(PEVs) on power demand and voltage change when PEVs are connected to the domestic distribution system. Specifically, it assesses PEVs charging load by charging method in accordance with PEVs penetration scenarios, its percentage of total load, and voltage range under load conditions. Concretely, we develop EMTDC modelling to perform a voltage distribution analysis when the PEVs charging system by their charging scenario was connected to the distribution system under the load condition. Furthermore we present evaluation algorithm to determine whether it is possible to adjust it such that it is in the allowed range by applying ULTC when the voltage change rate by PEVs charging scenario exceed its allowed range. Also, detailed analysis of the impact of PEVs on power distribution system was carried out by calculating existing electric power load and additional PEVs charge load by each scenario on new-town in Korea to estimate total load increases, and also by interpreting the subsequent voltage range for system circuits and demonstrating conditions for countermeasures. It was concluded that total loads including PEVs charging load on new-town distribution system in Korea by PEVs penetration scenario increase significantly, and the voltage range when considering ULTC, is allowable in terms of voltage tolerance range up to a PEVs penetration of 20% by scenario. Finally, we propose the charging capacity of PEVs that can delay the reinforcement of power distribution system while satisfying the permitted voltage change rate conditions when PEVs charging load is connected to the power distribution system by their charging penetration scenario.

Bringing macromolecules into cells and evading endosomes by oxidized carbon nanoparticles.

A great challenge exists in finding safe, simple, and effective delivery strategies to bring matters across cell membrane. Popular methods such as viral vectors, positively charged particles and cell penetrating peptides possess some of the following drawbacks: safety issues, lysosome trapping, limited loading capacity, and toxicity, whereas electroporation produces severe damages on both cargoes and cells. Here, we show that a serendipitously discovered, relatively nontoxic, water dispersible, stable, negatively charged, oxidized carbon nanoparticle, prepared from graphite, could deliver macromolecules into cells, without getting trapped in a lysosome. The ability of the particles to induce transient pores on lipid bilayer membranes of cell-sized liposomes was demonstrated. Delivering 12-base-long pyrrolidinyl peptide nucleic acids with d-prolyl-(1S,2S)-2-aminocyclopentanecarboxylic acid backbone (acpcPNA) complementary to the antisense strand of the NF-κB binding site in the promoter region of the Il6 gene into the macrophage cell line, RAW 264.7, by our particles resulted in an obvious accumulation of the acpcPNAs in the nucleus and decreased Il6 mRNA and IL-6 protein levels upon stimulation. We anticipate this work to be a starting point in a new drug delivery strategy, which involves the nanoparticle that can induce a transient pore on the lipid bilayer membrane.

Thermodynamics of small alkali metal halide cluster ions: comparison of classical molecular simulations with experiment and quantum chemistry.

We evaluate the ability of selected classical molecular models to describe the thermodynamic and structural aspects of gas-phase hydration of alkali metal halide ions and the formation of small water clusters. To understand the effect of many-body interactions (polarization) and charge penetration effects on the accuracy of a force field, we perform Monte Carlo simulations with three rigid water models using different functional forms to account for these effects: (i) point charge nonpolarizable SPC/E, (ii) Drude point charge polarizable SWM4-DP, and (iii) Drude Gaussian charge polarizable BK3. Model predictions are compared with experimental Gibbs free energies and enthalpies of ion hydration, and with microscopic structural properties obtained from quantum DFT calculations. We find that all three models provide comparable predictions for pure water clusters and cation hydration but differ significantly in their description of anion hydration. None of the investigated classical force fields can consistently and quantitatively reproduce the experimental gas-phase hydration thermodynamics. The outcome of this study highlights the relation between the functional form that describes the effective intermolecular interactions and the accuracy of the resulting ion hydration properties.

Modeling Charge Penetration Effects in Water-Water Interactions

This report introduces Gaussian electrostatic models (GEMs) to account for charge penetration effects in water-water interactions, allowing electrostatic interactions to be accurately described. Three different Gaussian electrostatic models, GEM-3S, GEM-5S, and GEM-6S are designed with s-type Gaussian functions. The coefficients and exponents of the Gaussian functions are optimized using the electrostatic potential (ESP) fitting procedure based on that of the MP2/aug-cc-pVTZ method. The electrostatic energies of ten different water dimers that were calculated with GEM-6S agree well with the results of symmetry-adapted perturbation theory (SAPT), indicating that this designed model can be effectively applied to future water models.

Autodyn-2D Simulation of Shaped Charge Jet Formation and Penetration Mechanism into Multi-Layered Shielded Target

In this work, the shaped charge jet formation depends on different parameters which can has effect on jet behavior such as jet velocity, breakup and penetration. Jet radius or liner thickness, shell thickness, liner material density, α angle and stand-off distance are evaluated in purpose to investigate their effect on performance of shaped charge jet velocity and jet breakup phenomena, also we investigate the effect of stand-off distance on shaped charge jet penetration into steel target. We also studied the performance of some protective shields materials in order to assure more protection for vehicle structure against shaped charge jet penetration. For that, different materials were used as armors such as: kevlar epoxy, polyethylene, glass epoxy, steel-1006 and Al2O3 ceramic. These protective shields were evaluated in order to show their performance against shaped charge penetration into target. To do so, adopted explicit dynamic analyzing program Autodyn basing on finite element were used to simulate shaped charge jet formation and penetration. Autodyn-2D simulationshighlight the efficiency of our work comparing with the experiments done in literature and Birkhoff’s theory. In other terms, increasing in shell thickness, alpha angle and liner densityenhance jet breakup time, protective shields layered armor of steel-1006, steel 1006 with polyethylene and steel-1006 with Al2O3ceramic give more protection for structure against shaped charge jet penetration comparing with others armors.

Screened Electrostatic Interactions in Molecular Mechanics.

In a typical application of molecular mechanics (MM), the electrostatic interactions are calculated from parametrized partial atomic charges treated as point charges interacting by radial Coulomb potentials. This does not usually yield accurate electrostatic interactions at van der Waals distances, but this is compensated by additional parametrized terms, for example Lennard-Jones potentials. In the present work, we present a scheme involving radial screened Coulomb potentials that reproduces the accurate electrostatics much more accurately. The screening accounts for charge penetration of one subsystem's charge cloud into that of another subsystem, and it is incorporated into the interaction potential in a way similar to what we proposed in a previous article (J. Chem. Theory Comput. 2010, 6, 3330) for combined quantum mechanical and molecular mechanical (QM/MM) simulations, but the screening parameters are reoptimized for MM. The optimization is carried out with electrostatic-potential-fitted partial atomic charges, but the optimized parameters should be useful with any realistic charge model. In the model we employ, the charge density of an atom is approximated as the sum of a point charge representing the nucleus and inner electrons and a smeared charge representing the outermost electrons; in particular, for all atoms except hydrogens, the smeared charge represents the two outermost electrons in the present model. We find that the charge penetration effect can cause very significant deviations from the popular point-charge model, and by comparison to electrostatic interactions calculated by symmetry-adapted perturbation theory, we find that the present results are considerably more accurate than point-charge electrostatic interactions. The mean unsigned error in electrostatics for a large and diverse data set (192 interaction energies) decreases from 9.2 to 3.3 kcal/mol, and the error in the electrostatics for 10 water dimers decreases from 1.7 to 0.5 kcal/mol. We could have decreased the average errors further, but at the cost of sometimes significantly overestimating the screening; instead we chose a more conservative (safer) parametrization that systematically underestimates the screening (which by definition means it improves over point charges) and only occasionally overestimates it. Despite this conservative choice, we find that the screened MM method is even more accurate for the electrostatics than unscreened QM/MM calculations. This new method is easy to implement in any MM program, and it can be used to develop more physical force fields for molecular simulations.

Charging and characterization of non-patterned organic micro electret arrays

This paper presents the charging and characterization of an organic micro electret array for vibration energy harvesting. Micro sized electrets with stable and high surface potential are essential for the long-term effectiveness of micro electrostatic power generators which harvest low-level vibration energy. In this study, a localized corona charging method to obtain micro sized electret areas on non-patterned macro sized dielectric thin film has been proposed to solve the problem of low charging efficiency and fast charge decay of micro sized electrets. This method involves using a shadow mask to transfer charge patterns and a triode corona charging configuration to facilitate charge penetration. Charging efficiency of 93.6% is achieved on an electret area of 100 µm × 100 µm, and 87% of its initial surface potential remains on the shrunken area of 50 µm × 50 µm after 240 days of storage. A technique combining SEM surface topography and non-contact measurement of the average surface potential has been developed to map the charge distribution on locally charged dielectric thin film and measure the surface potential on the micro sized charged area by incorporating the layout characteristic of a micro electret array.

Improved parameterization of interatomic potentials for rare gas dimers with density-based energy decomposition analysis.

We examine interatomic interactions for rare gas dimers using the density-based energy decomposition analysis (DEDA) in conjunction with computational results from CCSD(T) at the complete basis set (CBS) limit. The unique DEDA capability of separating frozen density interactions from density relaxation contributions is employed to yield clean interaction components, and the results are found to be consistent with the typical physical picture that density relaxations play a very minimal role in rare gas interactions. Equipped with each interaction component as reference, we develop a new three-term molecular mechanical force field to describe rare gas dimers: a smeared charge multipole model for electrostatics with charge penetration effects, a B3LYP-D3 dispersion term for asymptotically correct long-range attractions that is screened at short-range, and a Born-Mayer exponential function for the repulsion. The resulted force field not only reproduces rare gas interaction energies calculated at the CCSD(T)/CBS level, but also yields each interaction component (electrostatic or van der Waals) which agrees very well with its corresponding reference value.

Polymer-based devices for the label-free detection of DNA in solution: low DNA concentrations yield large signals.

Poly (N-isopropylacrylamide-co-N-(3-aminopropyl) methacrylamide hydrochloride) microgel-based optical devices (etalons) have been shown to change their optical properties in the presence of single-stranded DNA. We hypothesize that this is due to the negatively charged DNA penetrating through the Au overlayer of the etalon, resulting in cross-linking and collapse of the positively charged microgels. We have shown that this technology is capable of detecting micromolar concentrations of target DNA in solutions containing two and four base pair mismatch sequences without the use of labels. Furthermore, the device's response increases as the concentration of DNA decreases, which is unique for sensing strategies. We point out that coupling this transduction mechanism to DNA amplification strategies could result in extremely low detection limits.

Uniform Design on the Forward Annular Shaped Charge of Torpedo Tandem Warhead

By using LS-DYNA 3D software, the structure of forward annular shaped charge of torpedo tandem warhead is optimized in the simulation with uniform design method. During the simulation of annular shaped charge penetration into the plate underwater, the liner opening angle,liner thickness,charge height and charge angle are taken as factors, while the penetration depth is taken as index. The optimized structure parameters resulted form simulation can be used in the design of torpedo.