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We present a comprehensive study on the conformational behavior of diversely substituted 4-fluorotetrahydrothiopyran derivatives. Through quantum chemical simulations including DFT as well as NBO and NPA analysis, we elucidate the pivotal role of electrostatic interactions, occasionally complemented by hyperconjugative interactions, in stabilizing axial fluorine conformers. Less polar conformers were occasionally obtained, attributed to the interplay of electrostatic and hyperconjugative interactions. Experimental validation through NMR spectroscopy aligns with the computational analysis, thus providing a coherent understanding of the structural dynamics of these compounds.

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Structural changes induced by water play a pivotal role in chemistry and biology but remain challenging to predict, measure, and control at molecular level. Here we explore size-governed gas-phase water aggregation in the flexible molecule 4-hydroxy-2-butanone, modeling the conformational adaptability of flexible substrates to host water scaffolds and the preference for sequential droplet growth. The experiment was conducted using broadband rotational spectroscopy, rationalized with quantum chemical calculations. Two different isomers were observed experimentally from the di- to the pentahydrates (4-hydroxy-2-butanone-(H2O)n=2-5), including the 18O isotopologues for the di- and trihydrates. Interestingly, to accommodate water molecules effectively, the heavy atom skeleton of 4-hydroxy-2-butanone reshapes in every observed isomer and does not correspond to the stable conformer of the free monomer. All solvates initiate from the alcohol group (proton donor) but retain the carbonyl group as secondary binding point. The water scaffolds closely resemble those found in the pure water clusters, balancing between the capability of 4-hydroxy-2-butanone for steering the orientation and position of the water molecules and the ability of water to modulate the monomer's conformation. The present work thus provides an accurate molecular description on how torsionally flexible molecules dynamically adapt to water along progressing solvation.

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Coarse-grained molecular dynamics simulations are performed to understand the behavior of diblock polyelectrolytes in solutions of divalent salt by studying the conformations of chains over a wide range of salt concentrations. The polymer molecules are modeled as bead spring chains with different charged fractions and the counterions and salt ions are incorporated explicitly. Upon addition of a divalent salt, the salt cations replace the monovalent counterions, and the condensation of divalent salt cations onto the polyelectrolyte increases, and the chains favor to collapse. The condensation of ions changes with the salt concentration and depends on the charged fraction. Also, the degree of collapse at a given salt concentration changes with the increasing valency of the counterion due to the bridging effect. As a quantitative measure of the distribution of counterions around the polyelectrolyte chain, we study the radial distribution function between monomers on different polyelectrolytes and the counterions inside the counterion worm surrounding a polymer chain at different concentrations of the divalent salt. Our simulation results show a strong dependence of salt concentration on the conformational properties of diblock copolymers and indicate that it can tune the self-assembly behaviors of such charged polyelectrolyte block copolymers.

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The molecular aggregation of a galactomannan (NSAP-25) from Sophora alopecuroides L. seeds was investigated, where three polydisperse systems were confirmed during particle size analysis, indicating existence of different aggregates composed of random coil chains revealed by circular dichroism. Morphologically, NSAP-25 aggregate of various sizes (200-1200 nm) was possibly multi-stranded and formed by ellipsoid-like particles (20-60 nm) composed of compact coil chain, exhibiting extended amorphous structure with chain-like branches intertwined. Hence, NSAP-25 aggregation was inevitable, which exerted an unignorable effect on augmenting flexibility (ß↓, γ↓, α↓ and Lp/ML↓) and compactness (ρ↓, df↑ and C∞↓) of branched random coil chain based on macromolecular analysis, especially when concentration increased. Moreover, it could be relevant to thermokinetic behavior of random nucleation and subsequent growth (A2 model and negative ΔS*) as well as good thermal stability (IPDT, ITS, t0.05, Tm and Tp), thus conferring potential applications for NSAP-25 in food and pharmaceutical industries.

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The introduction of fluorine atoms into molecules and materials across many fields of academic and industrial research is now commonplace, owing to their unique properties. A particularly interesting feature is the impact of fluorine substitution on the relative orientation of a C-F bond when incorporated into organic molecules. In this Review, we will be discussing the conformational behavior of fluorinated aliphatic carbo- and heterocyclic systems. The conformational preference of each system is associated with various interactions introduced by fluorine substitution such as charge-dipole, dipole-dipole, and hyperconjugative interactions. The contribution of each interaction on the stabilization of the fluorinated alicyclic system, which manifests itself in low conformations, will be discussed in detail. The novelty of this feature will be demonstrated by presenting the most recent applications.

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The synthesis of phenyl-resorcinarenes and pyrogallolarenes is known to produce a conformational mixture of cone and chair isomers. Depending on the synthesis conditions the composition of the conformational mixture is variable; however, the cone conformer is the greatest proportion of phenyl-resorcin[4]arenes and chair conformer of pyrogallol[4]arenes. The experimental evidence suggests that phenyl-substituted resorcinarene and pyrogallolarene exist as a dynamic boat in solution.

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Gaining an understanding of the conformational behavior of fluorinated compounds would allow for expansion of the current molecular design toolbox. In order to facilitate drug discovery efforts, a systematic survey of a series of diversely substituted and protected fluorinated piperidine derivatives has been carried out using NMR spectroscopy. Computational investigations reveal that, in addition to established delocalization forces such as charge-dipole interactions and hyperconjugation, solvation and solvent polarity play a major role. This work codifies a new design principle for conformationally rigid molecular scaffolds.

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A polysaccharide (PFPP) from purple passion fruit peel was optimally extracted, with the highest yield (10.05%, w/w) obtained under 35 °C extraction temperature, 240 W ultrasonic power, 65:1 mL/g liquid-to-solid ratio, 0.6% (w/v) ammonium oxalate, 30 min extraction time and pH 2.0. According to composition analyses, pectic PFPP and its fractions (PFPP-10, -15 and -20) were revealed as linear homogalacturonans interrupted by rhamnogalacturonan I in different lengths and extensities, where low esterification degrees (35.35-39.66%) were indicated via FT-IR. Furthermore, based on macromolecular models, comprehensive analyses on macromolecular and conformational characterizations of PFPP fractions were conducted quantitatively through, e.g., shape factor (1.42-1.79), Mark-Houwink-Sakurada exponent (0.55-0.74), conformational power-law exponent (0.52-0.58), fractal dimension (1.72-1.94) and persistence length (6.73-13.47 nm). Therefore, different semi-flexible coil conformations were proposed schematically, where lower molecular-weight PFPP fractions were less flexible. This could provide a molecular basis for precise re-utilizations of PFPP in food and pharmaceutical industries.

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Mixed Langmuir films of type 1 alpha-(α-) and keto-mycolic acids (MAs) were investigated to understand the roles of α-methyl trans-cyclopropane containing keto-MA in determining the physical and chemical properties of the monolayers. Surface pressure (π) vs. mean molecular area (A) isotherms were measured at constant mole fractions defined as the ratio of the keto-MA molarity to the total molarity of α-MA and keto-MA (Xketo) at 25 °C and 37 °C. A and the elastic modulus (E) of the mixed monolayer were compared for different Xketo at fixed π values. In keto-MA rich monolayers, A values were much larger than values of the combined areas of α-MA and keto-MA, while the E values were close to those of solid keto-MA monolayers. A and E were also plotted against the mole fraction of α-methyl trans-cyclopropane containing keto-MA, which showed that the α-methyl trans-cyclopropane group stabilized the W-form conformation of mycolic acids in monolayers, and rendered them solid state. Furthermore, a comparison of the experimental results and the α-methyl trans-cyclopropane content in cell-wall MAs from various strains indicated that the ratio of trans-cyclopropane content was important in determining the nature of the mixed MA layer.

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The transcription factor FOXP3 is required for the development and function of regulatory T cells. Here, we studied the dynamics of FOXP3 in the presence and absence of DNA target sequence. Multiple molecular dynamics (MD) simulations were employed to investigate the role of DNA in enhancing the stability of FOXP3 via protein-DNA interactions, and to study the structural transition in protein at three different temperatures (300, 350, and 400 K). Results indicate that FOXP3 is stabilized by DNA even though the temperature rises up to 400 K. FOXP3 is found to undergo significant conformational change at a higher temperature, however, DNA provides greater rigidity and lower overall conformational flexibility, resulting in the global stabilization of FOXP3. The conformational restriction of FOXP3-DNA complex is probed with essential dynamics (ED). Free-energy landscape analysis at high temperature shows the presence of metastable intermediates, suggesting the reason behind the observed thermal stability. Secondary structural snapshots clearly indicate the presence of non-native interactions between DNA and protein. This study increases our understanding of the dynamic behaviors and the interaction mechanism of FOXP proteins and DNA at the atomic level and offers a model for studying the structural biology of transcriptional regulation. Communicated by Ramaswamy H. Sarma.

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We study the conformational behavior of spherical polyelectrolyte brushes in the presence of monovalent and trivalent counterions in a confined environment. The confinement is exerted by two parallel walls on the brushes. The enhancement of the confinement induces the extension of grafted chains. For the monovalent case, the increase of the charge fraction leads to extended brush conformation for different slit width (distance between two walls) but collapsed brush in the presence of trivalent counterions is observed. The confinement does not affect electrostatic correlation between trivalent counterions and charged monomers. However, it was found that narrow slit width contributes to stronger electrostatic correlation for the monovalent case. This is because more monovalent counterions are inside the brush at strong confinement, but almost all trivalent counterions are trapped into the brush independently of the slit width. The diffusion of counterions under the confinement is related to the electrostatic correlation. Our simulations also reveal that the brush thickness depends on the slit width nonlinearly.

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Complete and unambiguous 1 H NMR chemical shift assignment of α-cedrene (2) and cedrol (9), as well as for α-pipitzol (1), isocedrol (10), and the six related compounds 3-8 has been established by iterative full spin analysis using the PERCH NMR software (PERCH Solutions Ltd., Kuopio, Finland). The total sets of coupling constants are described and correlated with the conformational equilibria of the five-membered ring of 1-10, which were calculated using the complete basis set method. Copyright © 2015 John Wiley & Sons, Ltd.

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The conformational behavior of the wild-type endonucleases I-DmoI and two of its mutants has been studied in the presence and in the absence of DNA target sequences by means of extended molecular dynamics simulations. Our results show that in the absence of DNA, the three protein forms explore a similar essential conformational space, whereas when bound to the same DNA target sequence of 25 base pairs, they diversify and restrain the subspace explored. In addition, the differences in the essential subspaces explored by the residues near the catalytic site for both the bound and unbound forms are discussed in background of the experimental protein activity.

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