Electrostatic Potential Values Research Articles

Theoretical Investigation of Noncovalent Interactions between Low-Rank Coal and Water

The high moisture content of low-rank coals (LRCs) is associated with the noncovalent interactions between coal and water, such as hydrogen bonding and van der Waals attraction. In this study, the molecular model of lignite was constructed and its electrostatic potential (ESP) on a van der Waals surface was analyzed. The mechanism of water absorption on the hydrophilic or hydrophobic sites of the lignite surface was investigated based on the atoms in molecules analysis and reduced density gradient analysis of seven typical lignite···water complexes. The regions with the most negative and positive ESP values were associated with oxygen in oxygen functional groups, and hydrogen was associated with smaller electronegativity. The typical hydrogen bonds O–H···O were formed between water and oxygen functional groups, whereas the weaker hydrogen bonds C–H···O were formed between water and the skeleton components of lignite, such as the benzene ring and methyl and methylene groups. Oxygen functional groups were r...

A combined crystallographic analysis and ab initio calculations to interpret the reactivity of functionalized hexavanadates and their inhibitor potency toward Na+/K+-ATPase

In vitro influence of five synthesized functionalized hexavanadates (V6) on commercial porcine cerebral cortex Na+/K+-ATPase activity has been studied. Dose dependent Na+/K+-ATPase inhibition was obtained for all investigated compounds. Calculated half maximal inhibitory concentration IC50 values, in mol/L, for Na+/K+-ATPase were 7.6×10−5, 1.8×10−5, 2.9×10−5, 5.5×10−5 for functionalized hexavanadates (V6) with tetrabutylammonium (TBA) [V6–CH3][TBA]2, [V6–NO2][TBA]2, [V6–OH][TBA]2 and [V6–C3][TBA]2 respectively. [V6–OH][Na]2 inhibited Na+/K+-ATPase activity up to 30% at maximal investigated concentration 1×10−3mol/L. This reactivity has been interpreted using a study of the non-covalent interactions of functionalized hexavanadate hybrids through Cambridge Structural Database (CSD) analysis. Bibliographic searching has led to 18 different structures and 99 contacts. We have observed that C–H⋯O contacts consolidate the structures. We have also performed density functional theory (DFT) calculations and have determined electrostatic potential values at the molecular surface on a series of functionalized V6. These results enlightened their chemical reactivity and their potential biological applications such as the inhibition of the ATPase.

Sequential Halogen Bonding with Ditopic Donors: σ-Hole Evolutions upon Halogen Bond Formation

The halogen bonding ability of ditopic halogen bond donors can be assessed from the maximum value of the molecular surface electrostatic potential, called σ-hole, at the two halogen atoms. We show here that in N,N′-diodo-dimethylhydantoin (DIH), the halogen bonding (XB) ability of the two nitrogen-bound iodine atoms does not parallel the calculated σ-hole amplitude. The cocrystallization of DIH with a series of para-substituted pyridines, noted Py-R (R = pyrrolidinyl, NMe2, Me, H, CO2Me, CF3, CN), affords bis-adducts DIH·(Py-R)2 with the more electron-rich pyridines, while mono-adducts DIH·(Py-R) are favored with the more electron-poor pyridines (R = CO2Me, CF3, CN). Analysis of the structural characteristics of these mono- and bis-adducts, combined with theoretical calculations, demonstrates that the formation of a first N–I···N′Py-R XB deeply modifies the XB ability (and associated σ-hole) of the second uncoordinated iodine atom. Under these conditions, the latter might associate through I···O XB to the...

Removal of oxygen functional groups in lignite by hydrothermal dewatering: An experimental and DFT study

Hydrothermal dewatering (HTD) is a promising method for in-depth upgrading of lignite because of its comprehensive modifications, including dehydration, deoxygenation, carbonization, and surface modification. The oxygen functional groups in XiMeng lignite before and after HTD was quantitatively determined using the 13C direct polarization/magic angle spinning technique. After HTD, the amounts of carboxyl, alcoholic hydroxyl, ether, and carbonyl groups decreased, whereas those of phenolic hydroxyl were unchanged. The simplified molecular model of lignite was constructed and the electrostatic potential (ESP), bond order, and bond dissociation enthalpy (BDE) of the lignite molecule were investigated using density functional theory. The oxygen functional groups contributed to regions with a large absolute ESP value. These regions also exhibited strong hydrophilicity because of the formation of hydrogen bonds with water. Bond order and BDE analyses are consistent with the experimental results. The hydrothermal treatment began with the cleavage of phOCH3, followed by the cleavage of CC bonds in carbonyl and carboxyl, and ended with the cleavage of the CO bonds in alcoholic hydroxyl (phCH2OH) and CH3OCH3. All these bonds had BDEs lower than 90kcal/mol. The cleavage of CO bond in phenolic hydroxyl (phOH) was the most difficult because it has the highest BDE value of 113.4kcal/mol. The raw coal had inferior slurryability with a solid concentration of 48.49%. After HTD at 300°C, the surface property of lignite was significantly improved and the solid concentration of upgraded coal significantly increased to 59.14%.

Orbit limited theory in the solar wind - κ distributions

When a solid object is immersed into ionized gas it gets brought to a certain value of electrostatic potential and surrounded by a space charge region called ?plasma sheath?. Through this region, particles are attracted or repelled from the surface of the charge collecting object. For collisionless plasma, this process is described by the so-called orbit limited theory, which explains how the collection of particles is determined by the collector geometry and plasma velocity distribution function (VDF). In this article, we provide explicit expressions for orbit-limited currents for generalized Lorentzian (?) distributions. This work is useful to describe the charging processes of objects in non-collisional plasmas like the solar wind, where the electrons VDF is often observed to exhibit quasi power-law populations of suprathermal particles. It is found that these ?suprathermals? considerably increase the charge collection. Since the surface charging process that determines the value of electrostatic potential is also affected by the plasma VDF, calculation of the collector potential in the solar wind is described along with some quantitative predictions. [Projekat Ministarstva nauke Republike Srbije, br. 176002] <br><br><font color="red"><b> This article has been corrected. Link to the correction <u><a href="http://dx.doi.org/10.2298/SAJ1795071E">10.2298/SAJ1795071E</a><u></b></font>

A Feasibility Study of Ion Balance Measurement by Partial Surfaces

This paper reports a feasibility study of the ion balance measurement by the partial surfaces. The partial surfaces were exposed under the dc corona ionizer which could be varied ion balance. The appearance of electrostatic potential, which is caused by the imbalance of positive and negative ions, was measured by the high impedance electrostatic voltmeter. The result from these partial surfaces was compared with the standard test method which is using the 6″×6″ charged plate. The average voltages of all segments of the partial surfaces are correlated to the electrostatic potential values which were measured by the standard 6″×6″ charged plate. Moreover, the partial surfaces offer the fine-grained level of results. It validates that the precision of the ion balance measurement can be improved by the partial surfaces.

New solutions for charge distribution on conductor surface

In the paper, a problem of electrostatics for charge distribution on a conductor surface is analytically solved for three new particular cases of conducting surfaces with complicated shape and specified value of electrostatic potential. The exact analytical expressions for surface charge density for the bodies are obtained. All the solutions are represented in a clear view of 3D graphs. It is shown that the proposed method of electrostatic problem for conductors allows to obtain infinitely many numerical solutions for the problem but only several special cases can be solved analytically.

A systematic structural study of halogen bonding versus hydrogen bonding within competitive supramolecular systems.

As halogen bonds gain prevalence in supramolecular synthesis and materials chemistry, it has become necessary to examine more closely how such interactions compete with or complement hydrogen bonds whenever both are present within the same system. As hydrogen and halogen bonds have several fundamental features in common, it is often difficult to predict which will be the primary interaction in a supramolecular system, especially as they have comparable strength and geometric requirements. To address this challenge, a series of molecules containing both hydrogen- and halogen-bond donors were co-crystallized with various monotopic, ditopic symmetric and ditopic asymmetric acceptor molecules. The outcome of each reaction was examined using IR spectroscopy and, whenever possible, single-crystal X-ray diffraction. 24 crystal structures were obtained and subsequently analyzed, and the synthon preferences of the competing hydrogen- and halogen-bond donors were rationalized against a background of calculated molecular electrostatic potential values. It has been shown that readily accessible electrostatic potentials can offer useful practical guidelines for predicting the most likely primary synthons in these co-crystals as long as the potential differences are weighted appropriately.

Crystal Engineering with Iodoethynylnitrobenzenes: A Group of Highly Effective Halogen-Bond Donors

The benefits of employing a “double activation” strategy for promoting effective practical co-crystal synthesis through halogen bonding was explored in a systematic supramolecular synthetic study of iodoethynylnitrobenzenes. The positive electrostatic potential on the iodine atom was enhanced through a combination of an sp-hybridized carbon atom and one or more electron-withdrawing nitro groups. Three model compounds, 1-(iodoethynyl)-4-nitrobenzene (4N-I), 1-(iodoethynyl)-3-nitrobenzene (3N-I), and 1-(iodoethynyl)-3,5-dinitrobenzene (3,5DN-I) were synthesized and characterized, and calculated molecular electrostatic surface potential values on the halogen-bond donor site were about 20–40 kJ/mol higher than those observed for previously well-established halogen-bond donors. The ability of these molecules to drive co-crystal formation was evaluated through a total of 45 co-crystallization experiments with 15 different acceptor molecules. IR spectroscopic data for the resulting products showed that each reac...

Quantitative Analyses of Molecular Surface Electrostatic Potentials in Relation to Hydrogen Bonding and Co-Crystallization

The important role that electrostatic potentials computed on molecular surfaces can have in designing new materials via co-crystallization is discussed and illustrated. The locally most positive and most negative values of the surface electrostatic potential identify and rank sites for hydrogen bonding (complementing Etter’s rules), halogen bonding, and other types of noncovalent interactions. It is shown that the primary interactions are often better viewed as involving small regions rather than specific atoms. Recent applications of cocrystallization as a means of reducing the hazard associated with energetic materials are briefly examined.

36 Electrostatic properties of Rho-dependent and Rho-independent terminators

Electrostatic properties of genome DNA are important to its interactions with different proteins, in particular – RNA polymerase.It was shown earlier that higher electrostatic potential values and ...

Mixtures of ions and amphiphilic molecules in slit-like pores: A density functional approach.

We investigate microscopic structure and thermodynamic properties of a mixture that contains amphiphilic molecules and charged hard spheres confined in slit-like pores with uncharged hard walls. The model and the density functional approach are the same as described in details in our previous work [Pizio et al., J. Chem. Phys. 140, 174706 (2014)]. Our principal focus is in exploring the effects brought by the presence of ions on the structure of confined amphiphilic particles. We have found that for some cases of anisotropic interactions, the change of the structure of confined fluids occurs via the first-order transitions. Moreover, if anions and cations are attracted by different hemispheres of amphiphiles, a charge at the walls appears at the zero value of the wall electrostatic potential. For a given thermodynamic state, this charge is an oscillating function of the pore width.

Comparison of Methods for Computation of Electron Optical System Potential Distribution

To calculate the electrostatic field of electron gun was used software ANSYS. ANSYS is based on FEM. Model of electron gun is complicated enough, so we used submodeling. Test precision of calculated electrostatic field potential values was used simple immersion lens. The computed values by FEM using submodeling were in comparison with values computed in analytical way. They were very close, when the finite element size of submodel was four times smaller than the element size of coarse model. Ill.10, bibl. 4. (in Lithuanian; summaries in Lithuanian, English, Russian).

Synthesis, spectral, X-ray single structure, DFT calculations and antimicrobial activities of [Co(II)X2 (dmphen)] (X = Br and SCN−)

Two tetrahedral mononuclear complexes with a general formula [CoX2(dmphen)](1–2) (where dmphen is 2,9-dimethyl-1,10-phenanthroline and 1 (X=Br), 2 (X=NCS)) have been synthesized. These complexes are characterized by elemental analysis, IR, UV–visible, TG/DTA and by X-ray diffraction. The calculated electrostatic potential surface of 2 has shown that the electrostatic potential values around sulfur atom is anistropically distributed; the potential values along C–S bond is less negative than the corresponding values in the π-region of S atom. This agrees with the observed geometrical arrangement of C–H⋯S–C hydrogen bonding interactions, the avg. of H⋯S–C angle is 81°. Antimicrobial properties of cobalt(II) complexes was also assessed. Cobalt complexes exhibited significant antibacterial activity against different gram negative and positive human pathogens. The absorption spectrum of these complexes in acetone was modeled by time-dependent density functional theory (TD-DFT).

Conformational analysis, X-ray crystallographic, FT-IR, FT-Raman, DFT, MEP and molecular docking studies on 1-(1-(3-methoxyphenyl) ethylidene) thiosemicarbazide

Conformational analysis, X-ray crystallographic, FT-IR, FT-Raman, DFT, MEP and molecular docking studies on 1-(1-(3-methoxyphenyl) ethylidene) thiosemicarbazide (MPET) are investigated. From conformational analysis the examination of the positions of a molecule taken and the energy changes is observed. The docking studies of the ligand MPET with target protein showed that this is a good molecule which docks well with target related to HMG-CoA. Hence MPET can be considered for developing into a potent anti-cholesterol drug. MEP assists in optimization of electrostatic interactions between the protein and the ligand. The MEP surface displays the molecular shape, size and electrostatic potential values. The optimized geometry of the compound was calculated from the DFT–B3LYP gradient calculations employing 6-31G (d, p) basis set and calculated vibrational frequencies are evaluated via comparison with experimental values.

Experimental and theoretical studies on the molecular properties of ciprofloxacin, norfloxacin, pefloxacin, sparfloxacin, and gatifloxacin in determining bioavailability.

The aim of this investigation is to identify, by in silico and in vitro methods, the molecular determinants, e.g., solubility in an aqueous medium and lipophilic properties, which have an effect on the bioavailability of five selected fluoroquinolones. These properties were estimated by analysis of the electrostatic potential pattern and values of free energy of solvation as well as the partition coefficients of the studied compounds. The study is based on theoretical quantum-chemical methods and a simple experimental shake-flask technique with two immiscible phases, n-octanol and phosphate buffer. The solvation free energy values of compounds in both environments appeared to be negative. The wide range of electrostatic potential from negative to positive demonstrates the presence of dipole–dipole intermolecular interactions, while the high electron density at various sites indicates the possibility of hydrogen bond formation with solvent molecules. High partition coefficient values, obtained by summing the atomic contributions, did not take various correction factors into account and therefore were not accurate. Theoretical partition coefficient values based on more accurate algorithms, which included these correction factors (fragmental methods), yielded more accurate values. Theoretical methods are useful tools for predicting the bioavailability of fluoroquinolones.

Fluorine as a hydrogen-bond acceptor: experimental evidence and computational calculations.

Hydrogen-bonding interactions play an important role in many chemical and biological systems. Fluorine acting as a hydrogen-bond acceptor in intermolecular and intramolecular interactions has been the subject of many controversial discussions and there are different opinions about it. Recently, we have proposed a correlation between the propensity of fluorine to be involved in hydrogen bonds and its (19)F NMR chemical shift. We now provide additional experimental and computational evidence for this correlation. The strength of hydrogen-bond complexes involving the fluorine moieties CH2F, CHF2, and CF3 was measured and characterized in simple systems by using established and novel NMR methods and compared to the known hydrogen-bond complex formed between acetophenone and p-fluorophenol. Implications of these results for (19)F NMR screening are analyzed in detail. Computed values of the molecular electrostatic potential at the different fluorine atoms and the analysis of the electron density topology at bond critical points correlate well with the NMR results.

Generative topographic mapping of binding pocket of β2 receptor and three‐way partial least squares modeling of inhibitory activities

The visualization and characterization of protein pockets is the starting point for many structure‐based drug design projects. The size and shape of protein pockets dictate 3D geometry of ligands that can strongly inhibit the following biological events. Thus, a minimal requirement for inhibition is that a molecule sterically binds the active site with some allowance for induced fit. Methods for direct display of active sites in a protein have become prevalent in recent years.In this study, a new mapping method, generative topographic mapping, is investigated to describe the 3D surface of protein pocket. The β2 receptor protein is used as a benchmark. By mapping the molecular surface points and assigning the associated molecular electrostatic potential (MEP) values, the original 3D structure of the active site is well reproduced by the 2D latent map in generative topographic mapping. The distributions of MEP values of two 2D latent maps derived from the inhibitor and the β2 receptor protein are well complemented. Using three‐way partial least squares modeling, a predictive model linking the inhibitory activity and their MEP values can be constructed, which was not feasible in the previous spherical self‐organizing map studies. The resulting regression coefficient matrix of the three‐way partial least squares model has many insights for understanding the structural requirements for β2 inhibitory activity. Copyright © 2014 John Wiley & Sons, Ltd.

Computational study of the intramolecular proton transfer between 6-hydroxypicolinic acid tautomeric forms and intermolecular hydrogen bonding in their dimers

This paper is a density functional theory (DFT) calculation of intramolecular proton transfer (IPT) in 6-hydroxypicolinic acid (6HPA, 6-hydroxypyridine-2-carboxylic acid) tautomeric forms. The transition state for the enol-to-keto transition is reported in the gas phase and in four different solvents. The planar and non-planar dimer forms of 6HPA keto and enol, respectively, were also studied in the gas phase The IPT reactions and dimerization processes were studied at the B3LYP/6-31++G(d) level of the theory. The influence of the solvent on the tautomerization reaction of 6HPA was examined using the conductor-polarizable continuum model (CPCM). The IPT reaction in the gas phase is almost the same as in solution. The calculated dimerization energies show that the stability of 6HPA tautomer dimer structures is directly affected by the distance of intermolecular hydrogen bonding and electrostatic potential (ESP) value in the tautomer dimer.

Discovery of σ-hole interactions involving ylides

The positive electrostatic potentials (σ-hole) have been found in ylides CH2XH3 (X = P, As, Sb) and CH2YH2 (Y = S, Se, Te), on the outer surfaces of group VA and VIA atoms, approximately along the extensions of the C-X and C-Y bonds, respectively. These electrostatic potentials suggest that the above ylides can interact with nucleophiles to form weak, directional noncovalent interactions similar to halogen bonding interactions. MP2 calculations have confirmed the formation of CH2XH3···HM complexes (X = P, As, Sb; M = BeH, ZnH, MgH, Li, Na). The interaction energies, interaction distances, topological properties (electron density and its Laplacian), and energy properties (kinetic electron energy density and potential electron energy density) at the X(1)···H(10) bond critical points are all correlated with the most negative electrostatic potential value of HM, indicating that electrostatic interactions play an important role in these weak X···H interactions. Similar to the halogen bonding interactions, weak interactions involving ylides may be significant in several areas such as organic synthesis, crystal engineering, and design of new materials.