Electrostatic Potential Charges Research Articles

Tripleurin XIIc: Peptide Folding Dynamics in Aqueous and Hydrophobic Environment Mimic Using Accelerated Molecular Dynamics.

Peptaibols are a special class of fungal peptides with an acetylated N-terminus and a C-terminal 1,2-amino alcohol along with non-standard amino acid residues. New peptaibols named tripleurins were recently identified from a strain of the filamentous fungal species Trichoderma pleuroti, which is known to cause green mould disease on cultivated oyster mushrooms. To understand the mode of action of these peptaibols, the three-dimensional structure of tripleurin (TPN) XIIc, an 18-mer peptide, was elucidated using an enhanced sampling method, accelerated MD, in water and chloroform solvents. Non-standard residues were parameterized by the Restrained Electrostatic Potential (RESP) charge fitting method. The dihedral distribution indicated towards a right-handed helical formation for TPN XIIc in both solvents. Dihedral angle based principal component analysis revealed a propensity for a slightly bent, helical folded conformation in water solvent, while two distinct conformations were revealed in chloroform: One that folds into highly bent helical structure that resembles a beta-hairpin and another with an almost straight peptide backbone appearing as a rare energy barrier crossing event. The hinge-like movement of the terminals was also observed and is speculated to be functionally relevant. The convergence and efficient sampling is addressed using Cartesian PCA and Kullback-Leibler divergence methods.

Solvation Free Energy Calculation Using a Fixed-Charge Model: Implicit and Explicit Treatments of the Polarization Effect.

In this work, IPolQ-Mod charges and the reference potential scheme are used to calculate the solvation free energies of a set of organic molecules. Both methods could capture the phase transfer of a solute with accompanying polarization cost utilizing a fixed-charge model. The IPolQ-Mod charges, which are the average of two charge sets fitted in a vacuum state and a condensed phase, take account of the polarization effect implicitly. For the reference potential method, the quantum mechanics polarization corrections are calculated explicitly by thermodynamic perturbation. The polarization effect captured by the IPolQ-Mod charges is an approximation to that of the reference potential method theoretically. In the present study, the reference potential method shows a slight improvement over the classical restrained electrostatic potential (RESP) charges, which perform pretty well in predicting the solvation free energy. However, IPolQ-Mod(MP2) shows a poor agreement with the experimental data. Compared with IPolQ-Mod(MP2), IPolQ-Mod(M06-2X) or IPolQ-Mod(ωB97X) is found to give more appropriate prediction of the molecule's dipole and the solvation free energies calculated by IPolQ-Mod(M06-2X) or IPolQ-Mod(ωB97X) are more compatible with those of the RESP charges. If the other force field parameters remain unchanged, M06-2X or ωB97X is recommended to derive the IPolQ-Mod charges.

Studies on optical, electrical, mechanical and theoretical investigation of 4-nitro-benzoic acid (3-ethoxy-2-hydroxy-benzylidene)-hydrazide: A novel Schiff base organic NLO material

New organic non-centrosymmetric Schiff base material 4-Nitro-benzoic acid (3-ethoxy-2-hydroxy-benzylidene)-hydrazide was synthesized and grown as single crystal by slow evaporation solution growth technique. Single crystal X-ray diffraction reveals the noncentrosymmetric nature of the grown crystal with space group Pna21. The nonlinear efficiency of the grown material was studied by Kurtz-Perry powder technique and found to be 0.7 times that of KDP. The photoluminescence emission of the grown crystal shows emission at 360 nm. The mechanical stability of the crystal was examined by Vicker's microhardness study and the yield strength of the material was calculated. Low dielectric constant at higher frequencies was observed from dielectric measurements. Reduction in charge carriers when the sample was illuminated by halogen lamp proves the negative photoconductivity of the sample. In addition, quantum chemical calculations were carried out using density functional theory for the NEH molecule optimized at B3LYP/6-31 + G (d, p) basis set to calculate its frontier molecular orbital, electrostatic potential and Mulliken charge analysis.

Hidroksi- ve Sülfonamid- Azobenzen Platin (II) Komplekslerinin Yapısal, Spektroskopik ve Anti-Kanser Özellikleri: DFT ve Moleküler Yerleştirme Çalışmaları

The three platinum (II) complexes ([Pt(L1)(DMSO)Cl], [Pt(L2)(DMSO)Cl] and [Pt(L2)2]) bearing the bidentate ligands sulphonamide-((E)-2-(4-methylphenylsulfonamido)-2′,6′-difluoroazobenzene, HL1) and hydroxy-azo-2,6-difluorobenzene ((E)-2-((2,6-difluorophenyl)diazenyl)phenol, HL2) were optimized with the optimum levels of B3LYP/6-31+G(d) and B3LYP/LANL2DZ/6-31+G(d) level. The structural parameters (bond lengths and ligand angles), IR and 1H, 13C and 19F-NMR spectra obtained from the optimized structures were compared with the experimental data and the results were found to be consistent with the experimental results. Experimental inhibition activities against A2780 and A2780CP70 cancer cells were compared with quantum chemical parameters such as HOMO energy (EHOMO), LUMO energy (ELUMO), LUMO-HOMO energy vacancy (DE), hardness (h), softness (s), electronegativity (c) and chemical potential (m). The relationship between the molecular structure with the biological activity was examined and ELUMO order was found to be compatible with the experimental inhibition efficiency ranking. Molecular electrostatic potential (MEP) maps were studied of ligands and complexes exhibiting anti-cancer properties and for ligands and complexes, regions of attachment to cancer cells were determined. In addition, electrostatic potential (ESP) charges obtained from MEP maps of ligands and complexes were ranked according to their ease of binding to the cancer cell. The obtained ranking was found to be in accordance with the experimental inhibition efficiency order. For studied ligands and complexes, molecular docking studies were carried out with the Hex.8.0.0 program. The target proteins (PDB ID: 4M5W and 5FI4, respectively) corresponding to the A2780 and A2780CP70 cell lines were selected in the literature. The interaction energies of 4M5W and 5FI4 target proteins with HL1 and HL2 ligands were calculated to be -300.02, -240.80 and -336.64, -247.04 kJ/mol, respectively. The binding energies between the complexes and 4M5W and 5FI4 target proteins were calculated to be -387.52, -285.44, -364.88 and -399.63, -297.8, -385.323 kJ/mol. According to these results, the experimental and calculated inhibition efficiency order was found to be compatible.

Predicting Relative Binding Affinity Using Nonequilibrium QM/MM Simulations.

Calculating binding free energies with quantum-mechanical (QM) methods is notoriously time-consuming. In this work, we studied whether such calculations can be accelerated by using nonequilibrium (NE) molecular dynamics simulations employing Jarzynski's equality. We studied the binding of nine cyclic carboxylate ligands to the octa-acid deep-cavity host from the SAMPL4 challenge with the reference potential approach. The binding free energies were first calculated at the molecular mechanics (MM) level with free energy perturbation using the generalized Amber force field with restrained electrostatic potential charges for the host and the ligands. Then the free energy corrections for going from the MM Hamiltonian to a hybrid QM/MM Hamiltonian were estimated by averaging over many short NE molecular dynamics simulations. In the QM/MM calculations, the ligand was described at the semiempirical PM6-DH+ level. We show that this approach yields MM → QM/MM free energy corrections that agree with those from other approaches within statistical uncertainties. The desired precision can be obtained by running a proper number of independent NE simulations. For the systems studied in this work, a total simulation length of 20 ps was appropriate for most of the ligands, and 36-324 simulations were necessary in order to reach a precision of 0.3 kJ/mol.

Investigations over optical properties of boron complexes of benzothiazolines.

Quantum chemical analyses over benzothiazolines and their boron complexes are performed. In calculations, M06-2X method was selected with 6-31 + G(d,p) level. Structural and spectral (IR and NMR) characterization of studied compounds are done in detail. Quantum chemical descriptors (QCDs) are calculated to investigate the optical properties. Furthermore, molecular electrostatic potential (MEP) maps of the studied compounds are calculated by using electro-static potential (ESP) charges. According to QCDs and MEP maps, NLO properties of boron complexes are more than those of benzothiazolines and (Z)-2-((pyridin-2-ylmethylene)amino) benzenethiolatebutane-1,3-bis(olate)boron(III), complex (7), has the most NLO activity in studied compounds. Finally, solvent effect on NLO activity are investigated by calculating UV-vis spectrum in gas phase (ε = 1), toluene (ε = 2.3741), chloroform (ε = 4.7113), methanol (ε = 32.613), water (ε = 78.3553) and n-methylformamide-mixture (ε = 181.56). According to these spectra results, NLO activity mainly increases with increasing of polarizability of media.

Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations.

In QM/MM calculations, it is essential to handle electrostatic interactions between the QM and MM subsystems accurately and efficiently. To achieve maximal efficiency, it is convenient to adopt a hybrid scheme, where the QM electron density is used explicitly in the evaluation of short-range QM/MM electrostatic interactions, while a multipolar representation for the QM electron density is employed to account for the long-range QM/MM electrostatic interactions. In order to avoid energy discontinuity at the cutoffs, which separate the short- and long-range QM/MM electrostatic interactions, a switching function should be utilized to ensure a smooth potential energy surface. In this study, we benchmarked the accuracy of such hybrid embedding schemes for QM/MM electrostatic interactions using different multipolar representations, switching functions and cutoff distances. For test systems (neutral and anionic oxyluciferin in MM (aqueous and enzyme) environments), the best accuracy was acquired with a combination of QM electrostatic potential (ESP) charges and dipoles and two switching functions (long-range electrostatic corrections (LREC) and Switch) in the treatment of long-range QM/MM electrostatics. It allowed us to apply a 10Å distance cutoff and still obtain QM/MM electrostatics/polarization energies within 0.1 kcal/mol and time-dependent density functional theory (TDDFT)/MM vertical excitation energies within 10−3 eV from theoretical reference values.

Physicochemical studies on proton transfer reaction between methyl[5-(propylthio)-1H-benzoimidazole-2-yl]carbamate (albendazole, ABZ) with 2,4,6- trinitrophenol (picric acid, PA) in chloroform

In this study, a new proton transfer complex between albendazole drug (ABZ), methyl [5-(propylthio)-1H-benzoimidazole-2-yl]carbamate and picric acid (PA) has been synthesized and characterized in chloroform and solid state by different physicochemical methods. In chloroform, the proton transfer complex exhibited an absorption maxima at 409 nm. In addition, the complex was formed in a 1:1 molecular composition. The formation constant, spectroscopic physical parameters and enthalpy of formation confirmed that, the formed complex has high stability. The solid-state complex was also found in a 1:1 stoichiometric ratio from elemental analysis and was isolated as yellow crystals. Changes in vibrational mode wavenumbers and chemical shifts in infrared and 1H NMR spectra were found in comparison with the reactants, confirming the complex formation. Furthermore, TG/DTA analysis provided information about changes in material properties as a function of temperature. Density functional theory (DFT) at B3LYP/6-31G (d,p) level of the theory was employed to support the experimental results. The optimized structures of reactants and the new complex, their geometrical parameters, reactivity parameters, molecular electrostatic potential maps (MEP) and natural atomic charges from natural bond orbital (NBO) analysis were calculated. It has been concluded from the investigated computational analysis that the presence of many hydrogen bonds in the formed complex beside charge transfer interaction are certainly responsible for its high stability. Time-dependent functional theory (TD-DFT) at the same was applied to explain the origin of the recorded electronic transition in chloroform. A good consistency was found between experimental and theoretical results.

Quantum mechanical studies on dioxin‐imprinted polymer precursor composites: Fundamental insights to enhance the binding strength and selectivity of biomarkers

We present a benchmark study of binding energies for dioxin-imprinted polymer complexes. A density functional theory approach was used for screening the polymerization precursors in the rational design of molecularly imprinted polymers (MIPs). Tetrachlorodibenzo-p-dioxin (TCDD) was taken as an imprinted molecule. The geometry optimization, natural bond orbital charge, and molecular electrostatic potential of TCDD and acrylamide (AM) were studied at the M062X level and 6-31G(d,p) belonging to one of the hybrid density functional theories. The results of molecular electrostatic potential and natural bond orbital charge analysis were comparable. Among the studied functional monomers-AM, methacrylic acid (MAA), itaconic acid, and vinyl pyridine-AM was confirmed as the best functional monomer, because the strongest interaction (the maximum number of hydrogen bonds and the lowest binding energy) occurs between TCDD and AM. The stability property was excellent when the ratio of TCDD and AM was 1:4. The polarizable continuum model was used for solvent calculations. Computational results showed that acetonitrile plays an important role in the MIP formation, as it seems to control the size and the shape of the cavity. The atoms in molecule and Becke surface method have also been applied to understand the nature and strength of the hydrogen bonding interactions in complexes. TCDD-AM complexes were found involving C-O···Cl and N-H···Cl hydrogen bonds. Good correlations have been established between hydrogen bond lengths versus atoms in molecule topological parameter like electron density ρ(r) and its Laplacian ▽2 ρ(r) at the bond critical points. On ground of theoretical results, a series of MIPs were synthesized. The MIP prepared using TCDD as the template, the functional monomer (AM), and the cross-linker (TRIM) in acetonitrile solvent exhibited the highest adsorption capacity for TCDD. The maximum binding capacity of TCDD on the MIP was 3.7μg/mg. This research work can provide a theoretical reference for the fabrication and characterization of novel TCDD-MIPs for environmental applications.

Benchmark of different charges for prediction of the partitioning coefficient through the hydrophilic/lipophilic index.

A few different theoretical methods for assigning the partial atomic charges were benchmarked for calculation of the hydrophilic/lipophilic index (HLI). The coefficients were selected to produce the best correlation of the HLI values with the experimental octanol-water partition. Different parameters were checked in calculations of partial charges to get the best performance of the HLI values obtained. Thus, four partitioning schemes (Coulson, Mulliken, Merz-Kollman, Ford-Wang) were benchmarked for calculations of atomic charges with six semiempirical methods (AM1, PM3, RM1, PM6, PM6-D3H4, PM7). Moreover, five distinct types of partial atomic charges (Mulliken, Hirshfeld, Löwdin, CHELPG, NPA), obtained at the Hartree-Fock and DFT levels of theory with three basis sets, were tested for their ability to produce the HLI values with the best correlation to experimental logP coefficients of 50 mono-charged organic anions. In the case of the semiempirical methods, the best correlation between the HLI and logP values (the correlation coefficient r = 0.9216) was obtained with the AM1 Ford-Wang parametric electrostatic potential charges. The Mulliken and Coulson charges calculated with the PM7 method can be used as an alternative to AM1, with the r values of 0.9107 and 0.8984, respectively. In the case of the DFT, the PBE/def2-TZVP natural population analysis charges produce the best correlation (r = 0.9220). Nevertheless, in spite of a marginally lower performance (r = 0.9159), the NPA charges computed at the PBE/def2-SVP level are more robust and can be regarded as the optimum choice for calculating the HLI values. Graphical abstract The hydrophilic/lipophilic index (HLI).

Prediction of Henry's law constant of CO2 in ionic liquids based on SEP and Sσ-profile molecular descriptors

Nowadays, greenhouse gas CO2 emissions have caused serious global warming problems. Unique properties of ionic liquids (ILs), such as negligible vapor pressure, good thermal and chemical stability, high gas dissolution capacity, etc., have made them highly promising in capturing CO2. Although researchers have done a lot of experimental work using ILs to capture CO2, time-consuming and high experimental economic costs have led to a strong interest in establishing predictive models. In this work, 297 experimental data points including 16 cations and 9 anions for 34 ILs are collected and the structures of cations and anions are optimized by quantum chemistry. Then the electrostatic potential surface area (SEP) and charge distribution area (Sσ-profile) descriptors are calculated and used to predict the Henry's law constant (HLC) of CO2 in ILs. Three new models, namely, the multiple linear regression (MLR), support vector machine (SVM), and extreme learning machine (ELM) are finally developed based on the above-calculated descriptors. Results show that the ELM model with AARD = 3.22% for the entire data set is the most valid and powerful one to predict the HLC of CO2.

Parametrization of Molybdenum Cofactors for the AMBER Force Field.

Molybdenum-containing enzymes have been receiving significant attention from the scientific community since they participate in important biological processes and in the global biogeochemical cycles of carbon, nitrogen, and sulfur. Molecular modeling studies of these metalloproteins with classical force fields are, however, often hampered by the "missing parameter" problem. In this article, a set of parameters have been determined for the AMBER force field from nine different molybdenum cofactors. All of these cofactors were optimized and parametrized using a bonded model approach. All of the bonds and angles involving the Mo ion were parametrized. The Restrained Electrostatic Potential charges of the coordination sphere of each cofactor were also determined. Finally, we demonstrated the stability of our parameters in a showcase of nine enzymes. The parameters presented in this work provide a valuable resource for the molecular simulation community as they extend the range of metal ions that can be studied using classical approaches while also providing a starting point for subsequent parametrization of similar metal centers. All of the developed parameters can be found in the Supporting Information .

An investigation about the structures, thermodynamics and kinetics of the formic acid involved molecular clusters

Despite the very important role of atmospheric aerosol nucleation in climate change and air quality, the detailed aerosol nucleation mechanism is still unclear. Here we investigated the formic acid (FA) involved multicomponent nucleation molecular clusters including sulfuric acid (SA), dimethylamine (DMA) and water (W) through a quantum chemical method. The thermodynamics and kinetics analysis was based on the global minima given by Basin-Hopping (BH) algorithm coupled with Density Functional Theory (DFT) and subsequent benchmarked calculations. Then the interaction analysis based on ElectroStatic Potential (ESP), Topological and Atomic Charges analysis was made to characterize the binding features of the clusters. The results show that FA binds weakly with the other molecules in the cluster while W binds more weakly. Further kinetic analysis about the time evolution of the clusters show that even though the formic acid’s weak interaction with other nucleation precursors, its effect on sulfuric acid dimer steady state concentration cannot be neglected due to its high concentration in the atmosphere.

Analysis on molecular, spectroscopic and electronic behavior of 4,4'-(butane-1,4-diyl)bis(1-((1-(4-chlorobenzyl)-1H-1,2,3-triazol-5-yl)methyl)-3-methyl-1H-1,2,4-triazol-5(4H)-one): A theoretical approach

In this study, 4,4'-(butane-1,4-diyl)bis(1-((1-(4-chlorobenzyl)-1H-1,2,3-triazol-5-yl)methyl)-3-methyl-1H-1,2,4-triazol-5(4H)-one) was synthesized and characterized by FT-IR, 1H NMR and 13C NMR. In addition, quantum chemical calculations of the structure, vibrational frequencies, gauge including atomic orbital 1H and 13C chemical shift values were carried out using the density functional B3LYP method with the 6-311++G(d,p) basis set. To investigate nonlinear optical properties of the compound, the dipole moment, the polarizability and the first hyperpolarizability were computed using the density functional B3LYP and Hartree-Fock methods with the 6-311++G(d,p) basis set. Besides, density functional theory calculations of the molecular electrostatic potential, frontier orbitals and atomic charges of the compound were carried out at the B3LYP/6-311++G(d,p) level of theory.

Using machine learning and quantum chemistry descriptors to predict the toxicity of ionic liquids

Large-scale application of ionic liquids (ILs) hinges on the advancement of designable and eco-friendly nature. Research of the potential toxicity of ILs towards different organisms and trophic levels is insufficient. Quantitative structure-activity relationships (QSAR) model is applied to evaluate the toxicity of ILs towards the leukemia rat cell line (ICP-81). The structures of 57 cations and 21 anions were optimized by quantum chemistry. The electrostatic potential surface area (SEP) and charge distribution area (Sσ-profile) descriptors are calculated and used to predict the toxicity of ILs. The performance and predictive aptitude of extreme learning machine (ELM) model are analyzed and compared with those of multiple linear regression (MLR) and support vector machine (SVM) models. The highest R2 and the lowest AARD% and RMSE of the training set, test set and total set for the ELM are observed, which validates the superior performance of the ELM than that of obtained by the MLR and SVM. The applicability domain of the model is assessed by the Williams plot.

New Cu (II), Co(II) and Ni(II) complexes of chalcone derivatives: Synthesis, X-ray crystal structure, electrochemical properties and DFT computational studies

The reaction of nickel(II), copper(II) and cobalt(II) with 4-hydroxy-3-[(2E)-3-(1H-indol-3-yl)prop-2-enoyl]-6-methyl-2H-pyran-2-one (HL) leads to a series of new complexes: Ni(L)2(NH3), Cu(L)2(DMF)2 and Co(L)2(H2O). The crystal structure of the Cu(L)2(DMF)2 complex have been determined by X-ray diffraction methods. The Cu(II) lying on an inversion centre is coordinated to six oxygen atoms forming an octahedral elongated. Additionally, the electrochemical behavior of the metal complexes were investigated by cyclic voltammetry at a glassy carbon electrode (GC) in CH3CN solutions, showing the quasi-reversible redox process ascribed to the reduction of the MII/MI couples. The X-ray single crystal structure data of the complex was matched excellently with the optimized monomer structure of the desired compound; Hirschfeld surface analysis supported the packed crystal lattice 3D network intermolecular forces. HOMO/LUMO energy level and the global reactivity descriptors quantum parameters are also calculated. The electrophilic and nucleophilic potions in the complex surface are theoretically evaluated by molecular electrostatic potential and Mulliken atomic charges analysis.

Extension of the Mott–Gurney Law for a Bilayer Gap

Steady drift states of an electron flow in a planar gap filled with a bilayer dielectric have been considered. Exact mathematical formulas have been derived that describe the distributions of the electrostatic potential and space charge limited electron flow current (extended Mott–Gurney law for a bilayer diode).

Theoretical and conceptual density functional theory (DFT) study on selectivity of 4-hydroxyquinazoline electrophilic aromatic nitration

In common with other aza-heterocycles, 4-hydroxyquinazoline and their derivatives are important pharmacophores and versatile lead molecule used in several specific biological activities. The potency of these compounds depends on the nature and/or position of their substituents. In this paper, we report a theoretical study of the most probable nitration reaction centers of 4-hydroxyquinazoline for electrophilic attack, the mono and di-nitration was also discussed. In parallel, a computational study has been performed in gas by using the B3LYP/6311 G(d) level. The stability of the four nitro isomers is rationalized by means of the global index and local reactivity indices. Their molecular electrostatic potential (MEP) and Milliken charge were explored. Molecular geometries and NMR H spectra was examined. In addition, stationary points of reactant, transition state and intermediate were optimized in water condensed phase at the same level. The relative energies of the regioisomeric δ-complexes confirm that the substitution at C6 (6-nitro σ-complexes) is favored in these conditions, what was in agreement with our others calculating results (in gas).

Zinc–Phosphorus Complex Working as an Atomic Valve for Colloidal Growth of Monodisperse Indium Phosphide Quantum Dots

Growth of monodisperse indium phosphide (InP) quantum dots (QDs) represents a pressing demand in display applications, as size uniformity is related to color purity in display products. Here, we report the colloidal synthesis of InP QDs in the presence of Zn precursors in which size uniformity is markedly enhanced as compared to the case of InP QDs synthesized without Zn precursors. Nuclear magnetic resonance spectroscopy, X-ray photoelectron spectroscopy, and mass spectrometry analyses on aliquots taken during the synthesis allow us to monitor the appearance of metal–phosphorus complex intermediates in the growth of InP QDs. In the presence of zinc carboxylate, intermediate species containing Zn–P bonding appears. The Zn–P intermediate complex with P(SiMe3)3 exhibits lower reactivity than that of the In–P complex, which is corroborated by our prediction based on density functional theory and electrostatic potential charge analysis. The formation of a stable Zn–P intermediate complex results in lower reac...

Molecular dynamics simulation study of binding affinity of thieno[2,3-b]benzo[1,8]naphthyridine derivatives to DNA

DNA binding position and binding affinity of drugs are important information that helps medicinal chemists in synthesis of new drugs. We used molecular docking and molecular dynamics simulation to reveal binding strength of thieno[2,3-b]benzo[1,8]naphthyridine derivatives to DNA. Molecular docking showed that molecules with more steric hindrance select groove position in DNA structure. Other molecules are intercalated between base pairs of GC and AT. Restrained electrostatic potential (RESP) charges, root mean square deviation (RMSD), and total potential analyses were performed. RMSD and total potential analyses showed that all simulations have stability for MMGBSA analysis. Binding affinity of all drugs was derived via MMGBSA analysis. Thermodynamics analysis showed that binding affinity of groove binding drugs is less than that of intercalating ones. Also, it was found that a linear relationship exists between RESP charges and ΔG pred. Additionally, our results demonstrated the highest affinity for molecules carrying substituent groups of–OCH3 and–CH3.