Combinational simulations of free energy of polymer solution

It is conceptually proposed that the total entropy of polymer solution is contributed from two distinct parts: the positional and the oomformational. The former can be represented analytically, while the latter can be simulated with the random self-avoiding walk model on the simple cubic lattice for multichain systems. The obtained results indicated that both the conformational entropy and the mixing heat are consistent with the scaling laws wry well.     

Strong phenyl-perfluorophenyl π-π stacking and C-H?F-C hydrogen bonding interactions in the crystals of the corresponding aromatic aldimines

The X-ray diffraction analysis of two co-crystals, 1·2 (aldimines 1 and 2) and 3·4 (aldimines 3 and 4), reveals that there are strong phenyl-perfluorophenyl π-π stacking and intermolecular hydrogen bonding interactions. The new perfluoroaryl-aryl face-to-face interaction of the crystalline aldimines provides a design motif for a new class of self-assembling system.     

Simultaneous prediction of binding free energy and specificity for PDZ domain–peptide interactions

Interactions between protein domains and linear peptides underlie many biological processes. Among these interactions, the recognition of C-terminal peptides by PDZ domains is one of the most ubiquitous. In this work, we present a mathematical model for PDZ domain–peptide interactions capable of predicting both affinity and specificity of binding based on X-ray crystal structures and comparative modeling with Rosetta. We developed our mathematical model using a large phage display dataset describing binding specificity for a wild type PDZ domain and 91 single mutants, as well as binding affinity data for a wild type PDZ domain binding to 28 different peptides. Structural refinement was carried out through several Rosetta protocols, the most accurate of which included flexible peptide docking and several iterations of side chain repacking and backbone minimization. Our findings emphasize the importance of backbone flexibility and the energetic contributions of side chain-side chain hydrogen bonds in accurately predicting interactions. We also determined that predicting PDZ domain–peptide interactions became increasingly challenging as the length of the peptide increased in the N-terminal direction. In the training dataset, predicted binding energies correlated with those derived through calorimetry and specificity switches introduced through single mutations at interface positions were recapitulated. In independent tests, our best performing protocol was capable of predicting dissociation constants well within one order of magnitude of the experimental values and specificity profiles at the level of accuracy of previous studies. To our knowledge, this approach represents the first integrated protocol for predicting both affinity and specificity for PDZ domain–peptide interactions.     

Thermal conductivity and interfacial energy of solid Bi solution in the Bi–Al–Zn eutectic system

The equilibrated grain boundary groove shapes for solid Bi solution (Bi–6.1 at.%Zn–0.38 at.%Al) in equilibrium with the Bi–Al–Zn eutectic liquid have been observed from quenched sample with a radial heat flow apparatus. The Gibbs–Thomson coefficient, solid–liquid interfacial energy and grain boundary energy of solid Bi solution have been determined from the observed grain boundary groove shapes. The variations of thermal conductivity with temperature for solid Bi solution (Bi–6.1 at.%Zn–0.38 at.%Al) has been measured up to five degree below the melting temperature by using radial heat flow technique. The ratio of thermal conductivity of equilibrated Bi–Al–Zn eutectic liquid phase to solid Bi solution (Bi–6.1 at.%Zn–0.38 at.%Al) phase has also been measured with a Bridgman type growth apparatus at the melting temperature.     

Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge

Herein, we report the absolute binding free energy calculations of CBClip complexes in the SAMPL5 blind challenge. Initial conformations of CBClip complexes were obtained using docking and molecular dynamics simulations. Free energy calculations were performed using thermodynamic integration (TI) with soft-core potentials and Bennett’s acceptance ratio (BAR) method based on a serial insertion scheme. We compared the results obtained with TI simulations with soft-core potentials and Hamiltonian replica exchange simulations with the serial insertion method combined with the BAR method. The results show that the difference between the two methods can be mainly attributed to the van der Waals free energies, suggesting that either the simulations used for TI or the simulations used for BAR, or both are not fully converged and the two sets of simulations may have sampled difference phase space regions. The penalty scores of force field parameters of the 10 guest molecules provided by CHARMM Generalized Force Field can be an indicator of the accuracy of binding free energy calculations. Among our submissions, the combination of docking and TI performed best, which yielded the root mean square deviation of 2.94 kcal/mol and an average unsigned error of 3.41 kcal/mol for the ten guest molecules. These values were best overall among all participants. However, our submissions had little correlation with experiments.     

The intricacies of the stacking interaction in a pyrrole–pyrrole system

Extensive calculations of potential energy surfaces for parallel-displaced configurations of pyrrole–pyrrole systems have been carried out by the use of a dispersion-corrected density functional. System geometries associated with the energy minima have been found. The minimum interaction energy has been calculated as ?5.38 kcal/mol. However, bonding boundaries appeared to be relatively broad, and stacking interactions can be binding even for ring centroid distances larger than 6 Å. Though the contribution of the correlation energy to intermolecular interaction in pyrrole dimers appeared to be relatively small (around 1.6 smaller than it is in a benzene–benzene system), this system’s minimum interaction energy is lower than those calculated for benzene–benzene, benzene–pyridine and even pyridine–pyridine configurations. The calculation of the charges and energy decomposition analysis revealed that the specific charge distribution in a pyrrole molecule and its relatively high polarization are the significant source of the intermolecular interaction in pyrrole dimer systems.     

Relative substituent position on the strength of π-π stacking interactions

It was observed that the relative position of the arene substituents has a profound influence on the strength of π-π stacking in the 9-benzyl-substituted triptycene system. A new series of model compounds (3a-i) capable of revealing quantitatively π-π stacking interactions was studied. This series of compounds (3a-i) has an ortho-substituted methyl group in one of the two interacting arenes and the syn/anti ratios were determined and compared to a series previously studied compounds (4a-i) that have a para methyl group on the corresponding arene. A greater than 50% increase in the strength of π-π stacking interactions was observed with the methyl group in the ortho position comparing to that in the para position. No difference in π-π stacking interactions was observed when the other aromatic ring was a pentafluorobenzoate group.     

CH-anion versus anion-π interactions in the crystal and in solution of pentafluorobenzyl phosphonium salts

A series of phosphonium salts with pentafluorobenzyl substituents have been synthesized and were investigated in the crystal as well as in solution. The solid state structures of 1a, 1b and 2d reveal the presence of anion-π as well as CH-anion interactions. The two attractive, yet competitive forces seem to act in concert and a directing effect of the CH interaction on the relative position between anion and π-system is observed. The search for anion-π interactions in solution failed. Only CH-anion interactions proved to be important in solution.     

Alkylsulfate-based ionic liquids in the liquid–liquid extraction of aromatic hydrocarbons

The (liquid + liquid) equilibrium data (LLE) for the extraction of toluene from heptane with different ionic liquids (ILs) based on the alkylsulfate anion (R-SO₄) was determined at T = 313.2 K and atmospheric pressure. The effect of more complex R-SO₄ anions on capacity of extraction and selectivity in the liquid–liquid extraction of toluene from heptane was studied. The ternary systems were formed by {heptane + toluene + 1,3-dimethylimidazolium methylsulfate ([mmim][CH₃SO₄]), 1-ethyl-3-methylimidazolium hydrogensulfate ([emim][HSO₄]), 1-ethyl-3-methylimidazolium methylsulfate ([emim][CH₃SO₄]), or 1-ethyl-3-methylimidazolium ethylsulfate ([emim][C₂H₅SO₄])}. The degree of quality of the experimental LLE data was ascertained by applying the Othmer–Tobias correlation. The phase diagrams for the ternary systems were plotted, and the tie lines correlated with the NRTL model compare satisfactorily with the experimental data.     

A threshold for charge transfer in aromatic interactions? A quantitative study of pi-stacking interactions

[structure: see text] Attractive interactions between substituted arenes in the parallel displaced configuration have been quantitatively studied using triptycene-derived molecular conformational reporters. Charge-transfer bands are observed for models where the interactions are between strong donor and acceptors. Substituent effects on the strength of the aromatic interaction follow opposite trends for strongly electron-deficient arenes and mildly perturbed arenes. The free energy of interactions for models with strong electron donors and acceptors does not follow a linear correlation in the Hammett plot. Electrostatic models alone do not account for the nonlinearity of the free energy-substituents plot.     

The oxidation of aromatic amines in the presence of “electron-rich” aromatic systems

The oxidation of aromatic amines to the corresponding nitro substituents is performed under mild, nonacidic conditions in the presence of highly nucleophilic aromatic systems such as indoles and furans.     

Regioselective Friedel–Crafts deacylations of polycyclic aromatic ketones in the pyrene series

1,3,6,8-tetrabenzoylpyrene (1,3,6,8-Bz ₄ PY) and 1,3,6-tribenzoylpyrene (1,3,6-Bz ₃ PY) were synthesized and their crystal structures were determined. The Friedel–Crafts deacylations in PPA of 1,3,6,8-Bz ₄ PY (at 120–200 °C) and of 1,3,6-Bz ₃ PY (at 80–160 °C) have been studied. The mono-deacylation of 1,3,6-Bz ₃ PY was regioselective and led to three dibenzoylpyrenes in the following order of relative amounts: 1,8-Bz ₂ PY > 1,6-Bz ₂ PY > 1,3-Bz ₂ PY. 1,3,6,8-Bz ₄ PY was resistant to deacylation at 120–160 °C. The deacylations of 1,3,6,8-Bz ₄ PY at 200 °C gave the polycyclic aromatic ketone (PAK) 8H-dibenzo[def,qr]chrysen-8-one (DBCO) via an intramolecular Scholl reaction. Two plausible pathways of the Friedel–Crafts deacylation of 1,3,6,8-Bz ₄ PY to give DBCO are proposed. A density functional theory (DFT) B3LYP/6-311(d,p) computational study of the conformational spaces of 1,3,6-Bz ₃ PY and 1,3,6,8-Bz ₄ PY was performed. The estimated energy barriers of formation of dibenzoylpyrenes by deacylation of 1,3,6-Bz ₃ PY increase in the following order: 1,8-Bz ₂ PY < 1,3-Bz ₂ PY < 1,6-Bz ₂ PY. A mechanism of the Friedel–Crafts deacylation of 1,3,6-Bz ₃ PY in PPA via the respective O-protonated ketone and σ-complexes is presented.     

Hydrophobic and electrostatic interactions in the mixture hydrolyzed polyacrylamide–N-dodecylpyridinium chloride (AD37–DPC) in aqueous solution

The interactions of oppositely charged polyelectrolyte and surfactant (anionic polyacrylamide AD37 and dodecylpyridinium chloride DPC, respectively) in aqueous solution were studied at 25 °C by measurement of viscosity and conductivity. The system was investigated in aqueous medium in the absence and presence of NaCl. The AD37 interacts strongly with the DPC surfactant of the opposite charge. The interactions are electrostatic and hydrophobic. Thus, they are manifested in the formation of hydrophobic aggregates. The critical aggregation concentration (CAC) is much lower than the critical micellar concentration (CMC) of the surfactant alone. However, the value of the saturation concentration X ₂ is higher. The ionic strength of the medium after addition of salt explains an important part of these interactions. In fact, the electrolyte charge affects the CMC and the CAC values.     

Characterization and manipulation of the photosystem Ⅱ-semiconductor interfacial molecular interactions in solar-to-chemical energy conversion

Semi-artificial photosynthesis interfacing catalytic protein machinery with synthetic photocatalysts exhibits great potential in solar-to-chemical energy conversion. However, characterizing and manipulating the molecular integration structure at the biotic-abiotic interface remain a challenging task. Herein,the biointerface molecular integration details of photosystem II(PSII)-semiconductor hybrids, including the PSII orientation, interfacial microdomains, and overall structure modulation, are s...     

Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host–guest challenges

We calculate the absolute binding free energies of tetra-methylated octa-acids host–guest systems as a part of the SAMPL6 blind challenge (receipt ID vq30p). We employed two different free energy simulation methods, i.e., the umbrella sampling (US) and double decoupling method (DDM). The US method was used with the weighted histogram analysis method (WHAM) (US-WHAM scheme). In the DDM scheme, Hamiltonian replica-exchange method (HREM) was combined with the Bennett acceptance ratio (BAR) (HREM-BAR scheme). We obtained initial binding poses via molecular docking using GalaxyDock-HG program, which is developed for the SAMPL challenge. The root mean square deviation (RMSD) and the mean absolute deviations (MAD) using US-WHAM scheme were 1.33 and 1.02 kcal/mol, respectively. The MAD was the top among all submissions, however the correlation with respect to experiment was unexceptional. While the RMSD and MAD via HREM-BAR scheme were greater than US-WHAM scheme, (i.e., 2.09 and 1.76 kcal/mol), their correlations were slightly better than US-WHAM. The correlation between the two methods was high. Further discussion on the DDM method can be found in a companion paper by Han et al. (receipt ID 3z83m) in the same issue.     

Unexpectedly low affinity of aromatic disulfides for π-stacking interactions of the arene-polyfluoroarene type

1,2,3,4,5-Pentafluorodiphenyl disulfide (1) was synthesized from C₆F₅SCl and C₆H₅SSiMe₃ in quantitative yield. The homo-crystals of disulfide 1 and co-crystals of 1,1′,2,2′,3,3′,4,4′,5,5′-decafluorodiphenyl disulfide (2) with naphthalene (stoichiometry 1:2, complex 4) and diphenyl disulfide (3) with octafluoronaphthalene (stoichiometry 2:1, complex 5) were prepared followed by XRD characterization. In the crystal lattice of 1, face-to-face and face-to-edge Ph_H/Ph_F orientations of neighboring rings were observed together with face-to-edge Ph_F/Ph_F orientations. For the face-to-face Ph_H/Ph_F orientation, the large offset of Ph_H and Ph_F groups excludes their π-stacking interaction which is very non-typical of the field. The crystal lattice of 4 reveals standard π-stacking interactions of the arene-polyfluoroarene type. While in the lattice of 4 each Ph_F ring interacts alternating with naphthalenes, in 5 two disulfides 3 are bridged by one octafluoronaphthalene with only one of the Ph_H rings of each disulfide interacting with the polyfluoroarene π-system. The large offset of neighboring molecules excludes however their π-stacking interactions in complex 5. An attempt to prepare 2/3 co-crystals failed.     

Protein–polysaccharide associative interactions in the design of tailor-made colloidal particles

This article reviews some recent advances in the use of diverse protein–polysaccharide associative interactions in the design of colloidal particles having potential to be used for both fortification of food colloids with health-promoting bioactive compounds with better control of their physical stability and breakdown within the gastrointestinal tract. Protein–polysaccharide associative interactions are discussed in the following aspects: (i) the formation of micro- and nanoparticles for the delivery of health promoting ingredients (nutraceuticals); (ii) the controlled gastrointestinal fate of colloidal particles; (iii) the formation of biopolymer-based particles as fat replacers; and (iv) the behavior of colloidal particles as stabilizers of emulsions and foams. The first aspect concerns soluble protein–polysaccharide complex particles (electrostatic nanocomplexes, complex coacervates, covalent conjugates), mixed hydrogel particles, and nanoemulsion-based delivery systems.     

Enthalpy parameters of molecular interactions of dl-α-alanyl-dl-α-alanine with polyhydric alcohols in the aqueous solution

Russian Journal of General Chemistry - Integral enthalpies of dissolution Δsol H m of DL-α-alanyl-DL-α-alanine in aqueous solutions of glycerol, ethylene glycol, 1,2-propylene...     

Calculation of the molecular exchanging energy of binary surfactants system on the surface monolayer of aqueous solution

By using the binary anionic/cationic surfactants system CH3(CH2)nOSO_3/CH3(CH2)nN (CH3)3 as an ex-ample, the molecular exchanging energy (ε) of adsorption on the surface monolayer of aqueous solu-tion has been studied. ε can be obtained with two methods. One is from the relationship between ε and the molecule interaction parameter (β). This relationship is founded by considering that the adsorption of mixed surfactants on the surface monolayer of solution satisfies the dimensional crystal model condition under which β can be obtained by testing the surface tension of solution. The other is directly from the molecular structure of surfactants with the Lennard-Jones formula. The results for the studied system show that these two methods coincide well.