Partial Charge Model Research Articles

Anaerobic microbial transformation of halogenated aromatics and fate prediction using electron density modeling.

Halogenated homo- and heterocyclic aromatics including disinfectants, pesticides and pharmaceuticals raise concern as persistent and toxic contaminants with often unknown fate. Remediation strategies and natural attenuation in anaerobic environments often build on microbial reductive dehalogenation. Here we describe the transformation of halogenated anilines, benzonitriles, phenols, methoxylated, or hydroxylated benzoic acids, pyridines, thiophenes, furoic acids, and benzenes by Dehalococcoides mccartyi strain CBDB1 and environmental fate modeling of the dehalogenation pathways. The compounds were chosen based on structural considerations to investigate the influence of functional groups present in a multitude of commercially used halogenated aromatics. Experimentally obtained growth yields were 0.1 to 5 × 10(14) cells mol(-1) of halogen released (corresponding to 0.3-15.3 g protein mol(-1) halogen), and specific enzyme activities ranged from 4.5 to 87.4 nkat mg(-1) protein. Chlorinated electron-poor pyridines were not dechlorinated in contrast to electron-rich thiophenes. Three different partial charge models demonstrated that the regioselective removal of halogens is governed by the least negative partial charge of the halogen. Microbial reaction pathways combined with computational chemistry and pertinent literature findings on Co(I) chemistry suggest that halide expulsion during reductive dehalogenation is initiated through single electron transfer from B12Co(I) to the apical halogen site.

On combining Thole's induced point dipole model with fixed charge distributions in molecular mechanics force fields.

The Thole induced point dipole model is combined with three different point charge fitting methods, Merz-Kollman (MK), charges from electrostatic potentials using a grid (CHELPG), and restrained electrostatic potential (RESP), and two multipole algorithms, distributed multipole analysis (DMA) and Gaussian multipole model (GMM), which can be used to describe the electrostatic potential (ESP) around molecules in molecular mechanics force fields. This is done to study how the different methods perform when intramolecular polarizability contributions are self-consistently removed from the fitting done in the force field parametrization. It is demonstrated that the polarizable versions of the partial charge models provide a good compromise between accuracy and computational efficiency in describing the ESP of small organic molecules undergoing conformational changes. For the point charge models, the inclusion of polarizability reduced the the average root mean square error of ESP over the test set by 4-10%.

Correlation between alkaline-earth-metal dopants and threshold voltage (Vth) stability of solution-processed gallium indium oxide thin film transistors

We examined solution-processed alkaline-earth-metal doped gallium indium oxide (GIO) thin film transistors (TFT) and studied the relationship between the dopant species and the threshold voltage (Vth) stability. As the atomic number of the dopant increases, the amount of oxygen vacancies, which act as the major defect sites, decreased and the Vth stability is enhanced. The electron trapping times and total defect sites were quantitatively calculated. Particularly, Sr-doped GIO TFT show the highest Vth stability under positive gate bias and the origin of Vth stability enhancement is deduced by using the partial charge model and reaction kinetics.

The SAMPL4 hydration challenge: evaluation of partial charge sets with explicit-water molecular dynamics simulations.

We used blind predictions of the 47 hydration free energies in the SAMPL4 challenge to test multiple partial charge models in the context of explicit solvent free energy simulations with the general AMBER force field. One of the partial charge models, IPolQ-Mod, is a fast continuum solvent-based implementation of the IPolQ approach. The AM1-BCC, restrained electrostatic potential (RESP) and IpolQ-Mod approaches all perform reasonably well (R(2)>0.8), while VCharge, though faster, gives less accurate results (R(2) of 0.5). The AM1-BCC results are more accurate than those of RESP for tertiary amines and nitrates, but the overall difference in accuracy between these methods is not statistically significant. Interestingly, the IPolQ-Mod method is found to yield partial charges in very close agreement with RESP. This observation suggests that the success of RESP may be attributed to its fortuitously approximating the arguably more rigorous IPolQ approach.

Atomistic simulations of Cu2O bulk and Cu/Cu2O interface properties by using a new interatomic potential

In this paper, we propose a simple interatomic model for Cu2O bulk and Cu/Cu2O interface properties. The energetic scheme followed here is based on the fixed partial charge model in which the covalent contribution compensates the electrostatic forces in the total cohesive energy. The new interatomic potential is constructed by using the Lennard–Jones functional form for the non-bonded interactions (Cu–Cu and O–O) and the Morse functional form for the Cu–O bonded interaction. From literature, the existing Morse parameters for the Cu–O system overestimate the energetic cohesion between the metal and oxygen at the equilibrium interatomic distance. To address this energy excess we proceed by a new potential parameterization in order to obtain a good relative ratio between the covalent and electrostatic parts in the global energy. The new interatomic potential developed in this study successfully reproduces the bulk cohesive energy and the Cu2O(111) surface energy. The Cu2O(111) surface energy is found to be in very good agreement with the predicted ab initio value despite producing slightly different atomic relaxation effects. The behavior of the atomic relaxation on the Cu2O(111) surface shows that the relaxed surface is less reactive compared to the expected one after energy minimization. These results are consolidated by studying the bonding of the Cu(111)/Cu2O(111) oriented interface. The calculated Cu(111)/Cu2O(111) interface properties are found to be consistent with the physical concept of interface adhesion. This interface example is also studied in order to capture the interfacial elastic behavior as a function of applied stress normal to the interface plane. The results display an unexpected dependence between the interfacial excess energy and tensile stresses by defining a new interfacial transverse tensor characterizing the dimension of the perturbed interface region. This is a promising result since the misfit strain may play a major role in redefining the elastic tensors of a heterogeneous interface.

Assessing the Performance of MM/PBSA and MM/GBSA Methods. 3. The Impact of Force Fields and Ligand Charge Models

Here, we systematically investigated how the force fields and the partial charge models for ligands affect the ranking performance of the binding free energies predicted by the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) approaches. A total of 46 small molecules targeted to five different protein receptors were employed to test the following issues: (1) the impact of five AMBER force fields (ff99, ff99SB, ff99SB-ILDN, ff03, and ff12SB) on the performance of MM/GBSA, (2) the influence of the time scale of molecular dynamics (MD) simulations on the performance of MM/GBSA with different force fields, (3) the impact of five AMBER force fields on the performance of MM/PBSA, and (4) the impact of four different charge models (RESP, ESP, AM1-BCC, and Gasteiger) for small molecules on the performance of MM/PBSA or MM/GBSA. Based on our simulation results, the following important conclusions can be obtained: (1) for short time-scale MD simulations (1 ns or less), the ff03 force field gives the best predictions by both MM/GBSA and MM/PBSA; (2) for middle time-scale MD simulations (2-4 ns), MM/GBSA based on the ff99 force field yields the best predictions, while MM/PBSA based on the ff99SB force field does the best; however, longer MD simulations, for example, 5 ns or more, may not be quite necessary; (3) for most cases, MM/PBSA with the Tan's parameters shows better ranking capability than MM/GBSA (GB(OBC1)); (4) the RESP charges show the best performance for both MM/PBSA and MM/GBSA, and the AM1-BCC and ESP charges can also give fairly satisfactory predictions. Our results provide useful guidance for the practical applications of the MM/GBSA and MM/PBSA approaches.

Nanopatterned zinc titanate thin films prepared by the evaporation-induced self-assembly process

Nanopatterned thin films prepared by the evaporation-induced self-assembly process have up to now been limited to a few transition metal oxides (i.e. Al2O3, TiO2 and ZrO2). Here we describe the formation of zinc titanate nanoperforated thin films with different Zn/Ti ratios using the dipcoating process. Atomic force microscopy and scanning electron microscopy reveal that the structure consists of well-ordered pseudohexagonal nanoperforations in the range of 30nm in diameter separated by 25nm wide metal oxide ridges, while the film thickness is close to 2nm. For films with a zinc precursor content up to 50mol%, the well-organized structure of the thin film can be maintained, while at higher Zn contents the nanostructure is gradually becoming more disordered, which we have shown is consistent with the partial charge model. Grazing incidence X-ray diffraction measurements on the films calcined at 700°C indicate that the anatase phase of the pure TiO2 films is gradually consumed at the expense of a newly formed Zn2Ti3O8 phase upon increasing the Zn/Ti ratio in the starting precursor solution. The unique combination of the nanostructure with the zinc titanate composition grants these nanopatterned thin films significant application prospects in for instance optics and catalysis.

Binding Free Energy Estimation for Protein-Ligand Complex Based on MM-PBSA with Various Partial Charge Models

An accurate estimation of binding free energy between protein and ligand, is one of the most important issues in the drug discovery process. However, it is an arduous and hard process to obtain accurate energy, especially the experimentally relevant free energies for protein-ligand in solution, including a proper treatment of the long-range electrostatics and solvation effects that are involved in optimization of atomic net charges and so on. In this study, the impacts of the various atomic net charge models were considered, and their effects on binding free energy profiles also were investigated. The methods were tested on: the 30 structurally diverse ligands of diverse protein complexes, the 14 structurally diverse ligands of the protein kinase B (PKB) and the 10 structurally diverse ligands of the cyclin-dependent kinases 2 (CDK2) with measured affinities. The tested charges were calculated based on AM1 (Austin Method, version 1) - BCC (bond charge correction), MNDO (modified neglect of diatomic differential overlay), PM5 (Parameterisation Model, version 5), MUL (Mulliken), CM2 (Charge Model 2), CM3 (Charge Model 3), RESP (restrained electrostatic potential) and QM/MM (quantum mechanics/molecular mechanics) models. Our findings showed that the MNDO charge model was best propitious for PKB system and QM/MM for CDK2, whereas none of any given models was suited for the diverse ligands of diverse protein complexes. The trends of MM-PBSA binding free energies using all charge models were in good accord with experimental results for CDK2 but not for PKB in most cases. Considering the above results, particular attention should be paid to the ligand-charge and maybe protein-charge during the estimation of accurate binding free energies in drug design.

On the nature of heptavalent technetium in concentrated nitric and perchloric acid

The speciation of Tc(+7) was performed in HClO4 and HNO3 by 99-Tc NMR, UV–Vis and XAFS spectroscopy. The speciation of Tc(+7) depends on the concentration and strength of the acid. Pertechnetic acid, HTcO4, forms above 8M HClO4 while in concentrated HNO3, [TcO4]− is still the predominant species. EXAFS spectroscopy shows that the structure of HTcO4 in HClO4 is similar to the one in H2SO4. The reactivity of Tc(+7) was analyzed in the frame of the partial charge model. The partial charge calculated on the Tc atoms (ΔTc) indicates that HTcO4 (ΔTc=+057) is more electrophilic than [TcO4]− (ΔTc=+0.52). The difference in the oxidizing properties between [TcO4]− and HTcO4 is given from the reaction of these species with 12M HCl(aq). In 13M sulfuric acid HTcO4 is reduced to Tc(+5) while [TcO4]− is not reduced in 6M H2SO4.

Molecular dynamics of excited state intramolecular proton transfer: 3-hydroxyflavone in solution

The ultrafast enol-keto photoisomerization in the lowest singlet excited state of 3-hydroxyflavone is investigated using classical molecular dynamics in conjunction with empirical valence bond (EVB) potentials for the description of intramolecular interactions, and a molecular mechanics and variable partial charge model, dependent on transferring proton position, for the description of solute-solvent interactions. A parallel multi-level genetic program was used to accurately fit the EVB potential energy surfaces to high level ab initio data. We have studied the excited state intramolecular proton transfer (ESIPT) reaction in three different solvent environments: methylcyclohexane, acetonitrile, and methanol. The effects of the environment on the proton transfer time and the underlying mechanisms responsible for the varied time scales of the ESIPT reaction rates are analyzed. We find that simulations with our EVB potential energy surfaces accurately reproduce experimentally determined reaction rates, fluorescence spectra, and vibrational frequency spectra in all three solvents. Furthermore, we find that the ultrafast ESIPT process results from a combination of ballistic transfer, and intramolecular vibrational redistribution, which leads to the excitation of a set of low frequency promoting vibrational modes. From this set of promoting modes, we find that an O-O in plane bend and a C-H out of plane bend are present in all three solvents, indicating that they are fundamental to the ultrafast proton transfer. Analysis of the slow proton transfer trajectories reveals a solvent mediated proton transfer mechanism, which is diffusion limited.

The growth mechanism of zinc oxide and hydrozincite: a study using electron microscopies and in situ SAXS

The growth mechanism of ZnO is investigated by a combination of electron microscopy and in situ small-angle X-ray scattering (SAXS). The particles are prepared by the precipitation of zinc nitrate with urea. Depending on the reaction conditions, ZnO, hydrozincite, or a mixture of both phases is detected in our system. The molecular precursors and complexation reactions of the formation process are numerically predicted by the partial-charge model. The condensation and complexation reactions lead to the formation of nanoparticle building units up to a size of 10 nm. Afterwards, the nanoparticles immediately self-assemble into micro-sized particles.

What is the “best” atomic charge model to describe through-space charge-transfer excitations?

We investigate the efficiency of several partial atomic charge models (Mulliken, Hirshfeld, Bader, Natural, Merz-Kollman and ChelpG) for investigating the through-space charge-transfer in push-pull organic compounds with Time-Dependent Density Functional Theory approaches. The results of these models are compared to benchmark values obtained by determining the difference of total densities between the ground and excited states. Both model push-pull oligomers and two classes of "real-life" organic dyes (indoline and diketopyrrolopyrrole) used as sensitisers in solar cell applications have been considered. Though the difference of dipole moments between the ground and excited states is reproduced by most approaches, no atomic charge model is fully satisfactory for reproducing the distance and amount of charge transferred that are provided by the density picture. Overall, the partitioning schemes fitting the electrostatic potential (e.g. Merz-Kollman) stand as the most consistent compromises in the framework of simulating through-space charge-transfer, whereas the other models tend to yield qualitatively inconsistent values.

Understanding the Surface Potential of Water

We have resolved the inconsistency in quantifying the surface potential at the liquid-vapor interface when using explicit ab initio electronic charge density and effective atomic partial charge models of liquid water. This is related, in part, to the fact that the resulting electric potentials from partial-charge models and ab initio charge distributions are quite different except for those regions of space between the molecules. We show that the electrostatic surface potential from a quantum mechanical charge distribution compares well to high-energy electron diffraction and electron holography measurements, as opposed to the comparison with electrochemical measurements. We suggest that certain regions of space be excluded when comparing computed surface potentials with electrochemical measurements. This work describes a novel interpretation of ab initio computed surface potentials through high-energy electron holography measurements as useful benchmarks toward a better understanding of electrochemistry.

A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets

We report here a new and fast approach [Transferable Partial Atomic Charge Model (TPACM4)-upto four bonds] for deriving the partial atomic charges of small molecules for use in protein/DNA-ligand docking and scoring. We have created a look-up table of 5302 atom types to cover the chemical space of C, H, O, N, S, P, F, Cl, and Br atoms in small molecules together with their quantum mechanical RESP fit charges. The atom types defined span diverse plausible chemical environments of each atom in a molecule. The partial charge on any atom in a given molecule is then assigned by a reference to the look-up table. We tested the sensitivity of the TPACM4 partial charges in estimates of hydrogen bond dimers energies, solvation free energies and protein-ligand binding free energies. An average error ±1.11 kcal/mol and a correlation coefficient of 0.90 is obtained in the calculated protein-ligand binding free energies vis-à-vis an RMS error of ±1.02 kcal/mol and a correlation coefficient of 0.92 obtained with RESP fit charges in comparison to experiment. Similar accuracies are realized in predictions of hydrogen bond energies and solvation free energies of small molecules. For a molecule containing 50-55 atoms, the method takes on the order of milliseconds on a single processor machine to assign partial atomic charges. The TPACM4 programme has been web-enabled and made freely accessible at http://www.scfbio-iitd.res.in/software/drugdesign/charge.jsp.

ChemInform Abstract: Influence of Inorganic and Organic Additives on the Tailored Synthesis of Iron Oxides.

The influence of the inorganic anions, chloride, phosphate, sulphate and perchlorate and the organic molecules, n-butyl dihydrogen phosphate, 1-naphthyl disodium orthophosphate, methylphosphonic acid, phenylphosphonic acid, methylenediphosphonic acid and 1,2-ethylenediphosphonic acid, on the synthesis of iron oxides by the forced hydrolysis of aqueous FeIII solutions has been studied by electron microscopy, electron and X-ray diffraction and infrared and X-ray photoelectron spectroscopies. Haematite (α-Fe2O3) was formed in the presence of the inorganic additives. The presence of chloride and perchlorate resulted in rhombohedral crystals comprising {10text-decoration:overline14} or {10text-decoration:overline12} faces, respectively. Phosphate gave spindle-shaped crystals elongated along the c axis with stabilised faces of {hki0} form. Sulphate behaved in a similar manner but the effect was less pronounced. Computer simulations of relaxed crystal faces predicted the following order of surface energies; {10text-decoration:overline12} < {10text-decoration:overline10} < {0001} < {1text-decoration:overline210} < {10text-decoration:overline14} < {10text-decoration:overline11}. Infrared and X-ray photoelectron spectroscopies confirmed the presence of chloride, phosphate or sulphate, but not perchlorate, on the crystal surfaces. The phosphate and sulphate were bound in a bidentate manner. The organic additives, except for the diphosphonates, produced the oxyhydroxide. Iepidocrocite (γ-FeOOH), with no morphological modifications. Prismatic haematite was formed in the presence of methylenediphosphonic acid whereas 1,2-ethylenediphosphonic acid gave akaganeite (β-FeOOH). The results are discussed in terms of stereochemical and geometric interactions between adsorbed additives and selective crystal faces. Predictions of the complexation and hydrolysis behaviour of FeIII-additive species, using the partial charge model (J. Livage, M. Henry and C. Sanchez, Prog. Solid State Chem., 1988, 18, 259; N. J. Reeves and S. Mann, to be published) were in agreement with the experimental data.

Evaluation of the Affinity of Some Toxic Elements to Schwertmannite in Natural Streams Contaminated with Acid Mine Drainage

In order to evaluate fixation potential of schwertmannite for fluvial transport of various toxic elements, we examined bottom precipitates and stream waters collected from the rivers contaminated with acid mine drainage (AMD), which arose from the abandoned Nishinomaki mine (Shimonita, Gunma, Japan). Mineralogical and morphological observations revealed that schwertmannite was the main mineral of the precipitates. The affinity of various toxic ions to schwertmannite was evaluated on the basis of (1) apparent solid–liquid partition coefficients (Kd’s) between precipitates and stream waters, (2) coprecipitation behaviors during schwertmannite formation in a laboratory test, and (3) consideration on coprecipitation processes using partial charge model (PCM). As a result, oxyanions of V, As, Mo and Sb, Kd’s of which were relatively large (>104 (ml g−1)), were considered to be immobilized by schwertmannite precipitates. A laboratory test also demonstrated that these ions except Mo coprecipitated with schwertmannite. In addition, partial charges and average electronegativities predicted on the basis of PCM suggested that the oxyanions of V, As, Mo, and Sb could create stable inner sphere complexes with schwertmannite embryos, which results in their high affinity to schwertmannite. On the other hand, cationic ions of Mn, Cu, Zn, Sr, Cs, and U, Kd’s of which were relatively small (<104 (ml g−1)), were thought to have a tendency to flow downstream without uptake by schwertmannite precipitates. All these results suggested that schwertmannite has high fixation potential for fluvial transport of various toxic oxyanions in AMD-contaminated rivers.

ChemInform Abstract: Chemical Design of Highly Water-Soluble Ti, Nb, and Ta Precursors for Multi-Component Oxides.

Novel citric acid based Ti, Nb and Ta precursors that are highly stable in the presence of water were developed. No alkoxides of Ti, Nb and Ta were utilized in the preparation, instead much less moisture-sensitive metallic Ti, NbCl5 and TaCl5 were chosen as starting chemicals for Ti, Nb and Ta, respectively. The feasibility of these chemicals as precursors is demonstrated in the powder synthesis of BaTi 4O9, Y3NbO7 and LiTaO3. The waterresistant Ti precursor was employed as a new source of water-soluble Ti in the amorphous citrate method, and phase pure BaTi4O9 in powdered form was successfully synthesized at 800 °C. The Pechini-type polymerizable complex method using the water-resistant Nb and Ta precursors was applied to the synthesis of Y 3NbO7 and LiTaO3, and both the powder materials in their pure form were successfully synthesized at reduced temperatures, viz. 500-700 °C. The remarkable retardation of hydrolysis of these water-resistant precursors is explained in terms of the partial charge model theory.

Full spectroscopic characterization of an hydrolytically stable and colored Ti(IV)-precursor in solution

The orange-colored and hydrolytically stable compound {[Ti2O(bhmpc)(Hbhmpc)(H2bhmpc)].C4H8O2.HX}2 (with H3bhmpc = 2,6-bis(hydroxymethyl)-p-cresol and X = OEt or CCl3) has been studied by a combination of single crystal X-ray diffraction data, U.V.-vis. spectroscopy, IR and Raman spectroscopies, 1H, 13C and 17O solution NMR spectroscopies, electron density and statistical thermodynamics modeling. We observed that the molecular structure found in the solid state is conserved in solution. Based on X-ray diffraction data, we also propose a complete and non-ambiguous assignment for the fully resolved 1H and 13C solution NMR spectra through the use of 2D-techniques (COSY, ROESY, HSQC, HMBC) and 1H relaxation time measurements. The ability of the partial charge model introduced more than 20 years ago by J. Livage's group to reproduce observed 13C NMR chemical shifts in solution is demonstrated. Statistical thermodynamic modeling between Ti(OR)4 (monomers, trimers or tetramers) has shown that complexation was in all cases under entropy control. Possible applications of this soluble and stable precursor to the sol–gel processing of hybrid organic–inorganic are addressed.

Synthesis and characterization of silicate polymers

In this work an inorganic polymer is developed based on Elkem microsilica and potassium hydroxide. Using experimental data and the partial charge model a model for the gelation is suggested based on the hydrolysis and condensation reactions occurring during synthesis. In addition the optimal composition of the binder system was determined using compressive strength test and solubility experiments. Based on partial charge calculations and experimental data for the hydroxide concentration and the viscosity obtained in this study it is suggested that the polymerization of the inorganic polymer is determined by the concentration of silica species. It was found that the alkalinity has a crucial effect on the condensation process. The optimal potassium hydroxide concentration used in the synthesis of the inorganic polymer was found to be around 3.5 M, which resulted in a compressive strength of the product in the region of 50 MPa.

Application of Static Charge Transfer within an Ionic‐Liquid Force Field and Its Effect on Structure and Dynamics

The effects of linear scaling of the atomic charges of a reference potential on the structure, dynamics, and energetics of the ionic liquid 1,3-dimethylimidazolium chloride are investigated. Diffusion coefficients that span over four orders of magnitude are observed between the original model and a scaled model in which the ionic charges are +/-0.5 e. While the three-dimensional structure of the liquid is less affected, the partial radial distribution functions change markedly--with the positive result that for ionic charges of +/-0.7 e, an excellent agreement is observed with ab initio molecular dynamics data. Cohesive energy densities calculated from these partial-charge models are also in better agreement with those calculated from the ab initio data. We postulate that ionic-liquid models in which the ionic charges are assumed to be +/-1 e overestimate the intermolecular attractions between ions, which results in overstructuring, slow dynamics, and increased cohesive energy densities. The use of scaled-charge sets may be of benefit in the simulation of these systems--especially when looking at properties beyond liquid structure--thus providing an alternative to computationally expensive polarisable force fields.