Homology model of the rainbow trout estrogen receptor (rtERα) and docking of endocrine disrupting chemicals (EDCs)‖

A model for rainbow trout (Oncorhynchus mykiss) estrogen receptor (rtERα) was built by homology with the human estrogen receptor (hERα). A high level of sequence conservation between the two receptors was found with 64% and 80% of identity and similarity, respectively. Selected endocrine disrupting chemicals were docked into the ligand binding domain (LBD) of rtERα and the corresponding free binding energies Δ(ΔG_bind) values were calculated. A Quantitative Structure-Activity Relationship (QSAR) model between the relative binding affinity data and the Δ(ΔG_bind) values was derived in order to predict which further organic pollutants are likely to bind to rtERα.

     

Scalar Relativistic Density Functional Theoretical Investigation of Higher Complexation Ability of Substituted 1,10‐Phenanthroline over Bipyridine Towards Am3+/Eu3+ Ions

The better selectivity of Am³⁺ over Eu³⁺ ion with N‐based CyMe4‐BTPhen compared to CyMe4‐BTBP for experimentally observed [ML₂(NO₃)]²⁺ complexes was demonstrated using scalar relativistic DFT in conjunction with Born‐Haber thermodynamic cycle and COSMO solvation model. The calculated free energy of extraction, ΔG_ext reveals strong dependence on the hydration free energies of Am³⁺ and Eu³⁺ ions and week dependence to the difference in Gibbs free energy of solvation of the ligand or metal‐ligand complexes. Further, for the first time, we have computed the effect of co‐anion species ([M(NO₃)₅]^2–) on ΔG_ext of Am³⁺ and Eu³⁺ ions with CyMe4‐BTPhen and CyMe4‐BTBP, which adds a positive contribution and thus reduces the ΔG_ext. The calculated values of ΔΔΔG_ext (= ΔΔG_ext,L1 – ΔΔG_ext,L2, ΔΔG_ext = ΔG_ext,M1 – ΔG_ext,M2) can be used to avoid the very sensitive metal ion solvation energy, effect of co‐anionic species and thus provides a robust approach to determine the selectivity between two metal ions towards different competitive ligands. The natural population analysis (NPA), molecular orbital analysis, Mayer bond order analysis, and bond character analysis using Bader's quantum theory of atoms in molecules indicates slightly more covalency for complexes of Am³⁺ ion that are correlated to the experiental selectvity of Am³⁺ ion over Eu³⁺ ion and hence might be useful in the design and development of next generation extractants.     

Structures and Dynamic Solution Behavior of Cationic,Two‐Coordinate Gold(I)–π‐Allene Complexes

A family of seven cationic gold complexes that contain both an alkyl substituted π‐allene ligand and an electron‐rich, sterically hindered supporting ligand was isolated in >90 % yield and characterized by spectroscopy and, in three cases, by X‐ray crystallography. Solution‐phase and solid‐state analysis of these complexes established preferential binding of gold to the less substituted C?C bond of the allene and to the allene π face trans to the substituent on the uncomplexed allenyl C?C bond. Kinetic analysis of intermolecular allene exchange established two‐term rate laws of the form rate=k₁[complex]+k₂[complex][allene] consistent with allene‐independent and allene‐dependent exchange pathways with energy barriers of ΔG^≠₁=17.4–18.8 and ΔG^≠₂=15.2–17.6 kcal mol^?1, respectively. Variable temperature (VT) NMR analysis revealed fluxional behavior consistent with facile (ΔG^≠=8.9–11.4 kcal mol^?1) intramolecular exchange of the allene π faces through η¹‐allene transition states and/or intermediates that retain a staggered arrangement of the allene substituents. VT NMR/spin saturation transfer analysis of [{P(tBu)₂o‐binaphthyl}Au(η²‐4,5‐nonadiene) ]⁺SbF₆^? ( 5 ), which contains elements of chirality in both the phosphine and allene ligands, revealed no epimerization of the allene ligand below the threshold for intermolecular allene exchange (ΔG^≠_298K=17.4 kcal mol^?1), which ruled out the participation of a η¹‐allylic cation species in the low‐energy π‐face exchange process for this complex.     

Density functional theory investigation of the binding interactions between phosphoryl,carbonyl, imino,and thiocarbonyl ligands and the pentaaqua nickel(II) complex: Coordination affinity and associated parameters

Density Functional Theory (UB3LYP/6‐311++G(d,p)) calculations of the affinity of the pentaaqua nickel(II) complex for a set of phosphoryl [O?P(H)(CH₃)(PhR)], imino [HN?C(CH₃)(PhR)], thiocarbonyl [S?C(CH₃)(PhR)] and carbonyl [O?C(CH₃)(PhR)] ligands were performed, where R?NH₂, OCH₃, OH, CH₃, H, Cl, CN, and NO₂ is a substituent at the para‐position of a phenyl ring.The affinity of the pentaaqua nickel(II) complex for these ligands was analized and quantified in terms of interaction enthalpy (ΔH), Gibbs free energy (ΔG²⁹⁸), geometric and electronic parameters of the resultant octahedral complexes. The ΔH and ΔG²⁹⁸ results show that the ligand coordination strength increases in the following order: carbonyl < thiocarbonyl < imino < phosphoryl. This coordination strength order is also observed in the analysis of the metal‐ligand distances and charges on the ligand atom that interacts with the Ni(II) cation. The electronic character of the substituent R is the main parameter that affects the strength of the metal‐ligand coordination. Ligands containing electron‐donating groups (NH₂, OCH₃, OH) have more exothermic ΔH and ΔG²⁹⁸ than ligands with electron‐withdrawing groups (Cl, CN, NO₂). The metal‐ligand interaction decomposed by means of the energy decomposition analysis (EDA) method shows that the electronic character of the ligand modulates all the components of the metal‐ligand interaction. The absolute softness of the free ligands is correlated with the covalent contribution to the instantaneous interaction energy calculated using the EDA method. © 2013 Wiley Periodicals, Inc.     

Thermodynamic activation parameters for viscous flow of dilute aqueous solutions of ethylenediamine,trimethylenediamine and N,N-dimethyltrimethylenediamine

The density and the viscosity data have been used to determine the thermodynamic activation parameters, free energies (ΔG ^?), enthalpies (ΔH ^?) and entropies (ΔS ^?), for viscous flow of the systems; water (W) + ethylenediamine (ED), W + trimethylenediamine (TMD) and W + N,N-dimethyltrimethylenediamine (DMTMD) in the temperature range of 303.15–323.15 K over the composition range of 0 ≤ X ₂ ≤ 0.45, where X ₂ is the mole fraction of diamines. On addition of diamines to water, ΔG ^?, ΔH ^? and ΔS ^? values increase sharply, pass through a maximum and then decline. The heights of maximum in the ΔG ^? versus X ₂ curve vary as, W + DMTMD > W + TMD > W + ED. For all systems, the excess properties, ΔG ^{? E} , ΔH ^{? E} and ΔS ^{? E} are positive. The observed increase in thermodynamic values may be due to combined effect of hydrophobic hydration of diamines and water–diamine interaction as a result of hydrophilic effect.     

Thermodynamics of Sr(NO3)2 and Cd(NO3)2 in aquo-organic solvents from conductance data

The ion-solvent interaction of Sr(NO₃)₂ and Cd(NO₃)₂ in 10, 20 and 30 wt.% organic solvent (dioxane, glycol, methyl alcohol)-water mixtures at different temperatures has been studied using electrolytic conductivity data. The dissociation constant of the ion-pair Sr(NO₃)⁺ and Cd(NO₃)⁺ has been calculated along with ΔG⁰_t, ΔG⁰_t(cl) and ΔG⁰_t(ch). The ion pairs interact with the solvents and the interaction is of the order dioxane+water>methyl alcohol+water>glycol+water.     

Role played by the head size of some non‐ionic surfactants on their adsorption onto montmorillonite clay

Sorption behavior of polyoxethylene(n)monooleate series [Ol(EO)_n] onto montmorillonite clay was studied at 25°C to investigate the influence of the surfactant's head size on the sorption process. All the tested surfactants exhibited L‐shaped isotherms that means a strong interaction between the adsorbent and the adsorbate. Also, all the obtained isotherms ended with a drastic increase in the isotherm slope at nearly constant equilibrium concentration. This abrupt increase reflected the fairly high affinity of the tested surfactants to the clay surface at high bulk concentration region. The maximum amount adsorbed at the plateau region, Γ_max, was calculated according to the Langmuir adsorption theory and followed the order: Ol(EO)₁₄ > Ol(EO)₂₀ < Ol(EO)₄₀ < Ol(EO)₈₀. In case of short ethylene oxide (EO) chain, Γ_max decreased with the increase in the chain length; but a reverse result was obtained in case of surfactants with longer EO chain length (20 to 80 units). The free energy of adsorption, ΔG°_ad, had negative values indicating the spontaneous adsorption of surfactant molecules onto clay. The values of ΔG°_ad increased with increasing EO units from 14 to 20 units and decreased with further elongation in the EO chain from 20 to 80 units. Copyright © 2004 John Wiley & Sons, Ltd.     

Untersuchungen an molekülkomplexen von n-σ-TYP MITT. I. über freie enthalpie—kraftkonstantenkorrelationen von molekülkomplexen des jods m

Linear correlations have been found between the ΔG⁰ values of the molecular complexes R₁R₂R₃PO/I₂, R₁R₂SO/I₂ and R₁R₂SeO/I₂ and the PO, SO and SeO valence force constants, respectively. The nature of the correlation is determined by the ZO donor bond and not by the donor atom, where Z is P, S or Se. The change on ΔG⁰ values for an equal change in the ZO valence force constants increases in the order R₁R₂SO/I₂?R₁R₂R₃PO/I₂ < R₁ R₂SeO/I₂. Seleninyl complexes with I₂ are more stable than the analogous thionyl complexes. From ΔG⁰—f_zo correlation deductions can be made about the nature of the ZO donor bond and ΔG⁰ values can be evaluated from vibrational spectra. A linear correlation exists between the ΔG⁰ values of corresponding thionyl and seleninyl complexes which is of the same form as the correlation between the valence force constants of analogous thionyl and seleninyl compounds.     

New insight into the substituent effects on the hydrolytic deamination of saturated and unsaturated cytosine

Ab initio calculations were carried out to understand the effect of electron donating groups (EDG) and electron withdrawing groups (EWG) at the C5 position of cytosine (Cyt) and saturated cytosine (H₂Cyt) of the deamination reaction. Geometries of the reactants, transition states, intermediates, and products were fully optimized at the B3LYP/6-31G(d,p) level in the gas phase as this level of theory has been found to agree very well with G3 theories. Activation energies, enthalpies, and Gibbs energies of activation along with the thermodynamic properties (ΔE, ΔH, and ΔG) of each reaction were calculated. A plot of the Gibbs energies of activation (ΔG^‡) for C5 substituted Cyt and H₂Cyt against the Hammett σ-constants reveal a good linear relationship. In general, both EDG and EWG substituents at the C5 position in Cyt results in higher ΔG^‡ and lower σ values compared to those of H₂Cyt deamination reactions. C5 alkyl substituents ( H,  CH₃,  CH₂CH₃,  CH₂CH₂CH₃) increase ΔG^‡ values for Cyt, while the same substituents decrease ΔG^‡ values for H₂Cyt which is likely due to steric effects. However, the Hammett σ-constants were found to decrease at the C5 position of cytosine (Cyt) and saturated cytosine (H2Cyt) on the deamination reaction. Both ΔG^‡ and σ values decrease for the substituents Cl and Br in the Cyt reaction, while ΔG^‡ values increase and σ decrease in the H₂Cyt reaction. This may be due to high polarizability of bromine which results in a greater stabilization of the transition state in the case of bromine compared to chlorine. Regardless of the substituent at C5, the positive charge on C4 is greater in the TS compared to the reactant complex for both the Cyt and H₂Cyt. Moreover, as the charges on C4 in the TS increase compared to reactant, ΔG^‡ also increase for the C5 alkyl substituents ( H,  CH₃,  CH₂CH₃,  CH₂CH₂CH₃) in Cyt, while ΔG^‡ decrease in H₂Cyt. In addition, analysis of the frontier MO energies for the transition state structures shows that there is a correlation between the energy of the HOMO–LUMO gap and activation energies.     

Sels de Pyrylium. XVIII. Etude par RMN du Carbone-13 de Sels d'Aminopyrylium et des Barrières de Rotation dans quelques Cations N,N-Diméthylaminopyrylium

The C-2—N bond of 2-N,N-dimethylaminopyrylium cations has a partial π character due to the conjugation of the nitrogen lone-pair with the ring. The values of ΔG^≠, ΔH^≠, ΔS^≠ parameters related to the corresponding hindered rotation have been determined by ¹³C NMR total bandshape analysis. This conjugation decreases the electrophilic character of carbon C-4 so that the displacement of the alkoxy group is no longer possible. Such a hindered rotation also exists in 4-N,N-dimethylaminopyrylium cations and the corresponding ΔG^≠ parameters have been evaluated. Comparison of these two cationic species shows that hindered rotation around the C—N bond is larger in position 4 than in position 2. Furthermore, the barrier to internal rotation around the C-2? N bond decreases with increasing electron donating power of the substituent at position 4. ΔG^≠ values decreases from 19.1 kcal mol^?1 (79.9 kJ mol^?1) to 12.6 kcal mol^?1 (52.7 kJ mol^?1) according to the following sequence for the R-4 substituents: -C₆H₅, -CH₃, -OCH₃, -N(CH₃)₂.     

Thermodynamic studies of sitting-atop (SAT) complexation of uranyl and free base meso -tetraarylporphyrins

The interaction of uranyl with meso-tetraphenylporphyrin and its para-substituted derivatives (H₂t(4-X)pp, X : H, Br, Cl, CH(CH₃)₂, OCH₃, CH₃) in chloroform produced 1 : 1 sitting-atop (SAT) complexes ((uranyl)H₂t(4-X)pp). Formation constants were calculated by computer fitting of complex absorbance versus mole ratio data to appropriate equations and found to decrease with temperature increase. Thermodynamic parameters, ΔG ⁰, ΔH ⁰ and ΔS ⁰ were obtained. The formation constants vary with changing of the substituent on the aryl rings of H₂t(4-X)pp in the following order: (uranyl)H₂t(4-OCH₃)pp?>?(uranyl)H₂t(4-CH₃)pp?>?(uranyl)H₂t(4-CH(CH₃)₂)pp?>?(uranyl)H₂tpp?>?(uranyl)H₂t(4-Br)pp?>?(uranyl)H₂t(4-Cl)pp.     

Optimal scaling factors for CM1 and CM3 atomic charges in RM1-based aqueous simulations

Scaling factors for atomic charges derived from the RM1 semiempirical quantum mechanical wavefunction in conjunction with CM1 and CM3 charge models have been optimized by minimizing errors in absolute free energies of hydration, ΔG_hyd, for a set of 40 molecules. Monte Carlo statistical mechanics simulations and free energy perturbation theory were used to annihilate the solutes in gas and in a box of TIP4P water molecules. Lennard–Jones parameters from the optimized potentials for liquid simulations‐all atom (OPLS–AA) force field were utilized for the organic compounds. Optimal charge scaling factors have been determined as 1.11 and 1.14 for the CM1R and CM3R methods, respectively, and the corresponding unsigned average errors in ΔG_hyd relative to experiment were 2.05 and 1.89 kcal/mol. Computed errors in aniline and two derivatives were particularly large for RM1 and their removal from the data set lowered the overall errors to 1.61 and 1.75 kcal/mol for CM1R and CM3R. Comparisons are made to the AM1 method which yielded total errors in ΔG_hyd of 1.50 and 1.64 kcal/mol for CM1A*1.14 and CM3A*1.15, respectively. This work is motivated by the need for a highly efficient yet accurate quantum mechanical (QM) method to study condensed‐phase and enzymatic chemical reactions via mixed QM and molecular mechanical (QM/MM) simulations. As an initial test, the Menshutkin reaction between NH₃ and CH₃Cl in water was computed using a RM1/TIP4P‐Ew/CM3R procedure and the resultant ΔG^?, ΔG_rxn, and geometries were in reasonable accord with other computational methods; however, some potentially serious shortcomings in RM1 are discussed. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Polarized Raman scattering of concentrated solutions of poly(dimethyl siloxane) in benzene

Raman depolarization (ρ) measurements have been made over the temperature range 20 > T > 60°C for solutions of poly(dimethyl siloxane) (mol wt 7.7 × 10⁴ and 2.0 × 10⁴) for several concentrations up to 100%. The band studied was the highly polarized methyl stretch at 2907 cm^?1. Computer calculations of the probability p_t of a rotational isomer being trans allow the ρ values to be related to ΔG, the free energy of mixing. ΔG is plotted as a function of concentration and minima are observed at 60 ± 3% (mol wt = 7.7 × 10⁴) and 70 ± 3% (mol wt = 2 × 10⁴).     

Molecular electrostatic potentials and partial atomic charges from correlated wave functions: Applications to the electronic ground and excited states of 3-methylindole

Procedures have been developed to generate molecular electrostatic potentials based on correlated wave function from ab initio or semiempirical electronic structure programs. A new algorithm for point-wise sampling of the potential is described and used to obtain partial atomic charges via a linear, least squares fit between classical and quantum mechanical electrostatic potentials. The proposed sampling algorithm is efficient and promises to introduce less rotational variance in the potential derived partial charges than algorithms applied previously. Electrostatic potentials and fitted atomic charges from ab initio (HF/6–31G* and MP2/6-31G*) and semiempirical (INDO/S; HF, SECI, and SDCI) wave functions are presented for the electronic ground (S₀) and excited (¹L_b, ¹L_a) states of 3-methylindole. © 1992 by John Wiley & Sons, Inc.     

Spectroscopic and Molecular Docking Approaches for Investigation of Interaction of Phellopterin with Human Serum Albumin

The mechanism of interaction between human serum albumin (HSA) and natural product phellopterin (PL) from Angelica dahurica was investigated by spectroscopic techniques with molecular docking under simulated physiological conditions. The experimental results showed that the fluorescence of HSA was regularly quenched by PL, and the quenching constants (K_SV) decreased with increasing temperature, which indicated that the quenching mechanism was a static quenching procedure. The binding constants (K_A) were larger than 10^?5 M^?1 and the number of binding sites (n) was approximate to 1 at different temperatures, which indicated that the binding affinity was hige and there was just one main binding site in HSA for PL. According to thermodynamic parameters from Van't Hoff equation, the binding process of PL with HSA was spontaneous and exothermic process due to ΔG < 0, and the electrostatic force played major role in the binding between PL and HSA according to ΔH < 0 and ΔS > 0. The binding distance (r) was calculated to be about 3.35 nm, which implied that the energy transfer from HSA to PL occurred with high possibility according to the theory of Förster's non-radiation energy transfer. The microenvironment and conformation of HSA changed with the addition of PL based on the results of synchronous and three-dimensional fluorescence methods. The molecular docking analysis revealed the binding locus of PL to HSA in subdomain IIIA (Sudlow's site II).     

Extraction and preconcentration capacity of bifunctionalized diamine-thiol polysiloxane immobilized ligand system towards some divalent cations

Porous solid bi-organofunctionalized diamine-thiol polysiloxane immobilized ligand system of the general formula P-(CH₂)₃- X, (where P represents [Si-O]_n siloxane network and X represents a mixture of diamine; -NH(CH)₂NH₂ and thiol; -SH functional groups) has been prepared by hydrolytic polycondensation of TEOS with a mixture of 3-mercaptopropyltrimethoxysilane and 3- (2-aminoethylimino)propyltrimethoxysilane agents. The ligand system was evaluated for extraction and preconcentartion of a series of divalent metal ions from aqueous solutions including: Co²⁺, Ni²⁺, Cu²⁺, Zn²⁺, Cd²⁺ and Pb²⁺. Both batch and dynamic methods were used to examine maximum sorption capacity. The maximum binding capacity followed the sequence; Cu²⁺ > Pb²⁺ > Cd²⁺ > Ni²⁺ > Zn²⁺ > Co²⁺ at pH 5.5. Measurement of variation of sorption of metal ions with temperature yielded negative values of ΔG° and positive values of ΔS° and ΔH° indicating a spontaneous and endothermic process of binding metal ions to the ligand system.     

Spectroscopic investigations of hematoxylin–Eu(III) complex interacting with Herring-sperm DNA

The interaction of HE–Eu(III) complex (HE?=?hematoxylin) with Herring-sperm DNA (hsDNA) has been studied by absorption spectra, fluorescence, and viscosity measurements in physiological buffer (pH?=?7.40). The binding constant of HE–Eu(III) complex to hsDNA was obtained by double reciprocal method at 298 and 310?K and the corresponding thermodynamic parameters (Δ_r Hm??=?8.55?×?10⁴?J?mol^?1, Δ_r Gm??=??3.01?×?10⁴?J?mol^?1, Δ_r Sm??=?387.95?J?mol^?1?K^?1) were calculated, showing that the interaction between HE–Eu(III) complex and hsDNA was driven mainly by entropy. The value of K indicated that the binding mode of HE–Eu(III) complex with DNA was not classical intercalation. These results were further supported by viscosity method and competitive binding experiment. Scatchard analysis suggests that the interaction mode was a mixed binding, which contains partial intercalation and groove binding.     

Thermodynamic studies of the binding interactions of surfactin analogues to lipid vesicles Application of isothermal titration calorimetry

Isothermal titration calorimetry was applied for studying the binding interactions of cyclic and linear surfactins with different ionic charge (z= −2 and −3) and lipid chain length (n=14 and 18) to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidyl-choline (POPC) vesicles in 10mMTris buffer at pH8.5with 150mMNaCl at 25°C. Surfactin analogues interacted spontaneously (ΔG _D ^w→b < 0) with POPC vesicles. The binding reactions were endothermic (ΔH _D ^w→b > 0) and entropy-driven process (ΔS _D ^w→b > 0). Moreover, significant differences in the binding constant values (K) ranging from 6.6·10³ to 9.6·10⁴ M⁻¹ show that cyclic structure and the increase of lipid chain length are favourable on the surfactin binding affinity to POPC vesicles, whereas the rise of the number of negative charges has an opposite effect.     

Radical polymerization of N-vinylpyrrolidone in the presence of syndiotactic poly(methacrylic acid) templates

Radical polymerization of N-vinylpyrrolidone along poly(methacrylic acid) templates of high syndiotatic content was followed dilatometrically in dimethylformamide, which was used as solvent. The effects of template concentration, template molar mass, and temperature on polymerization rate and average molar mass of the formed polyvinylpyrrolidone (PVP) were examined. Template concentrations were varied around the critical concentration for homogeneous segmental distribution, C^*. Below this concentration, template coils can act as separate microreactors wherein growing PVP radicals exhibit maximum rate enhancement, i. e., relative rate ν_R = ν_R,max. In the free solution, blank polymerization occurs, i. e., ν_R = 1. Consequently, ν_R can be approximated by the equation ν_R = ?ν_R,max + (1 ? ?), where ? represents the volume fraction occupied by template coils. The slight increase in UR and PVP molar mass with the template chain length is supposed to be caused by the influence of translational diffusion on the termination step. Over the investigated temperature range of 50–70°C, the activation energy and entropy were almost identical for blank and template polymerization. An expected decrease of ΔE^≠ and ΔS^≠ in template systems is supposed to be compensated by the effects of desolvation of the template macromolecules during the propagation step.