Understanding Conformational Properties and Role of Hydrogen Bonds in Glycosaminoglycans-Interleukin8 Complexes in Aqueous Medium by Molecular Dynamics Simulation

Atomistic molecular dynamics simulations were performed under ambient conditions to explore the conformational features and binding affinities of hexameric glycosaminoglycans (GAGs) with chemokine Interleukin8 (IL8) in an aqueous medium. We tried to understand the role of hydrogen bonds (HBs) involving conserved water in mediating the interactions. The Luzar-Chandler model was adopted to study the kinetics of HB breaking and formation concerning different water-mediated HBs. The conformational flexibilities of bound GAGs are due to the flexible glycosidic linkages than the occasional/rare ring pucker conformation. The free energy landscape constructed with ϕ, and ψ, depicted that different conformational minima associated with the glycosidic linkage flexibility of the GAGs in bound states are separated by energy barriers. The binding affinities of IL8 towards GAGs are favored through the electrostatic and non-polar solvation interactions. 4-different types of conserved water were explored in the solvent-mediated binding of GAGs with IL8. The average lifetime of the IL8-GAG direct HB pairs was ∼ten times less than the IL8-GAG-shared water HBs. This is due to the rapid establishment of HB breaking and reformation kinetics involving water of a shared layer. We find that despite the highly negatively charged surface of GAGs, the IL8 surface populated by non-cationic amino acids could serve as a promising binding site in addition to the cationic surface of the protein.     

Slow motion in [ring‐fluoro]polycarbonate by CODEX

Chain dynamics in [ring‐fluoro]polycarbonate (an A‐B alternating copolymer that has a single fluorine substituent on every fourth main chain ring) have been characterized by centerband only detection of exchange (CODEX) and rotating‐frame ¹³C spin‐lattice relaxation. The slow motions detected by CODEX are facilitated by a mechanically active lattice reorganization that permits a flip of the fluorinated ring about its C₂ axis. Nonfluorinated rings undergo small‐amplitude reorientations and C₂ flips, both of which are fast and not CODEX active. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 1062–1066, 2008     

杯[4]吡咯在不同溶液中的分子动力学模拟研究

运用分子动力学(MD)模拟方法对杯[4]吡咯与不同溶剂之间的相互作用能、杯[4]吡咯在不同溶液中的构象变化以及杯[4]吡咯与溶剂分子之间的氢键相互作用进行了计算研究.模拟发现,杯[4]吡咯与不同溶剂间的相互作用能受溶剂分子偶极矩和杯[4]吡咯-溶剂分子间氢键相互作用影响.杯[4]吡咯在不同溶液中的构象发生翻转的主导因素是杯[4]吡咯与溶剂分子间形成氢键相互作用,溶剂分子的偶极矩不是杯[4]吡咯发生构象转化的主要因素.     

Intramolecular Dynamics of Lanthanide(III) Tetraoxadiaza Macrocycle Complexes in Solution as Studied by NMR

¹H and ¹³C NMR and ¹H NMR relaxation spectroscopy (RS)measurements are reported for the CDCl₃ and CD₂Cl₂ solutions of [La(NO₃)₃(diaza-18-crown-6)] ({bf I}), [Pr(NO₃)₃(diaza-18-crown-6)] ({bf II}) and [Nd(NO₃)₃(diaza-18-crown-6)] ({bf III}) complexes. Temperature dependencies of the ¹H NMR spectra of II have been analyzed using the dynamic NMR methods for multi-site exchange. Enantiomeric isomer interconversion in II is characterized by H = 21.5 ± 4 kJ mol^-1. Studies of the values of the lanthanide-induced shifts and the longitudinal relaxation rate enhancement revealed that the structure of complexes in solution is similar to that reported for the [La(NO₃)₃(18-crown-6)] complex in the crystal state. Nevertheless, it appears that the principal values of the molar paramagnetic susceptibility tensor (_i) significantly differ in complexes II and III. The possible reasons for the different characteristics of these complexes are discussed.     

Logic Gating by Macrocycle Displacement Using a Double‐Stranded DNA [3]Rotaxane Shuttle

Molecular interlocked systems with mechanically trapped components can serve as versatile building blocks for dynamic nanostructures. Here we report the synthesis of unprecedented double‐stranded (ds) DNA [2]‐ and [3]rotaxanes with two distinct stations for the hybridization of the macrocycles on the axle. In the [3]rotaxane, the release and migration of the “shuttle ring” mobilizes a second macrocycle in a highly controlled fashion. Different oligodeoxynucleotides (ODNs) employed as inputs induce structural changes in the system that can be detected as diverse logically gated output signals. We also designed nonsymmetrical [2]rotaxanes which allow unambiguous localization of the position of the macrocycle by use of atomic force microscopy (AFM). Either light irradiation or the use of fuel ODNs can drive the threaded macrocycle to the desired station in these shuttle systems. The DNA nanostructures introduced here constitute promising prototypes for logically gated cargo delivery and release shuttles.     

Choline Chloride as a Nano-Crowder Protects HP-36 from Urea-Induced Denaturation: Insights from Solvent Dynamics and Protein-Solvent Interactions

Urea at sufficiently high concentration unfolds the secondary structure of proteins leading to denaturation. In contrast, choline chloride (ChCl) and urea, in 1 : 2 molar ratio, form a deep eutectic mixture, a liquid at room temperature, protecting proteins from denaturation. In order to get a microscopic picture of this phenomenon, we perform extensive all-atom molecular dynamics simulations on a model protein, HP-36. Based on our calculation of Kirkwood-Buff integrals, we analyze the relative accumulation of urea and ChCl around the protein. Additional insights are drawn from the translational and rotational dynamics of solvent molecules and hydrogen bond auto-correlation functions. In the presence of urea, water shows slow subdiffusive dynamics around the protein owing to a strong interaction of water with the backbone atoms. Urea also shows subdiffusive motion. The addition of ChCl further slows down the dynamics of urea, restricting its accumulation around the protein backbone. Adding to this, choline cations in the first solvation shell of the protein show the strongest subdiffusive behavior. In other words, ChCl acts as a nano-crowder by excluding urea from the protein backbone and thereby slowing down the dynamics of water around the protein. This prevents the protein from denaturation and makes it structurally rigid, which is supported by the smaller radius of gyration and root mean square deviation values of HP-36.     

Complexation of M3+ Lanthanide Cations by Calix[4]arene-CMPO Ligands: A Molecular Dynamics Study in Methanol Solution and at a Water/Chloroform Interface

Abstract

We report a molecular dynamics study on the 1:1 M³⁺ lanthanide (La³⁺, Eu³⁺ and Yb³⁺) inclusion complexes of an important extractant molecule L: a calix[4]arene-tetraalkyl ether substituted at the wide rim by four NH-C(O)-CH₂-P(O)Ph₂ arms. The M(NO₃)₃ and MCl₃ complexes of L are compared in methanol solution and at a water / chloroform interface. In the different environments the coordination sphere of M³⁺ involves the four phosphoryl oxygens and three to four loosely bound carbonyl oxygens of the CMPO-like arms. Based on free energy simulations, we address the question of ion binding selectivity in pure liquid phases and at the liquid-liquid interface where L and the complexes are found to adsorb. According to the simulations, the enhancement of M³⁺ cation extraction in the presence of the calixarene platform, examined by comparing L to the (CMPO)₄ “ligand” at the interface, is related to the fact that (i) the (CMPO)₄Eu(NO₃)₃ complex is more hydrophilic than the LEu(NO₃) one and (ii) the free CMPO ligands spread at the interface, and are therefore less organized for cation capture than L.     

Ab Initio Molecular Dynamics Study of Hydrogen Cleavage by a Lewis Base [tBu3P] and a Lewis Acid [B(C6F5)3] at the Mesoscopic Level—Dynamics in the Solute–Solvent Molecular Clusters

With the help of state‐of‐the‐art ab initio molecular dynamics methods, we investigated the reaction pathway of the {tBu₃P + H₂ + B(C₆F₅)₃} system at the mesoscopic level. It is shown that: i) the onset of H₂ activation is at much larger boron???phosphorus distances than previously thought; ii) the system evolves to the product in a roaming‐like fashion because of quasi‐periodic nuclear motion along the asymmetric normal mode of P???H?H???B fragment; iii) transient configurations of a certain type are present despite structural interference from the solvent; iv) transient‐state configurations with sub‐picosecond lifetime have potentially interesting infrared activity in the organic solvent (toluene) as well as in the gas phase. The presented results should be helpful for future experimental and theoretical studies of frustrated Lewis pair (FLP) activity.     

Simulation of the Mechanical Unfolding of the Ubiquitin by Pulling in Different Directions with Constant Speed

Mechanical extension of the ubiquitin with constant speed in five different directions is simulated on coarse-grained Go-like and all-atom models. The anisotropy of the mechanical resistance of the protein is observed in agreement with experimental data. Differences and similarities between the results obtained for two models are discussed. It is shown that the unfolding begins from the rupture of contacts between residues located in the vicinity of points of the external load application.     

Modular construction of pyrido[24]crown-8-based templates in the self-assembly of cross-linked [n]catenanes

Starting from the versatile 4-bromopyrido[24]crown-8 building block, novel ditopic and tritopic receptors have been synthesized and shown to be appropriate hosts for bis(4-formylbenzyl)ammonium hexafluorophosphate. Association constants (per binding site) for the corresponding [3]- and [4]pseudorotaxanes, assembled from these components, were determined to be 2753  M^?1 and 723  M^?1, respectively. Mechanical bond formation was attempted utilizing dynamic imine bond formation between the formyl groups of the bound dibenzylammonium threads and p-phenylenediamine.     

Five‐State Molecular Shuttling of a Pair of [2]Rotaxanes: Distinct Outputs in Response to Acid and Base Stimuli

In this study we synthesized two acid‐/base‐controllable [2]rotaxanes featuring aminodiazobenzene and aminocoumarin units, respectively, as chromophores and dibenzo[24]crown‐8 and dibenzo[25]crown‐8 units, respectively, as their macrocyclic components. Each [2]rotaxane contained N‐alkylarylamine (ammonium) and N,N‐dialkylamine (ammonium) centers as binding sites for their crown ether components. The absorption patterns of the chromophores were dependent on the position of the encircling macrocyclic component and the degree of protonation, with three distinct states (under acidic, neutral, and basic conditions) evident for each [2]rotaxane. The mixed [2]rotaxane system displayed stepwise and independent molecular shuttling behavior based on the degree of protonation of the amino groups in response to both the amount and strength of added acids or bases; as such, the system provided five different absorption signals as outputs that could be read using UV/Vis spectroscopy.     

Shuttling dynamics in an acid-base-switchable [2]rotaxane.

Molecular shuttles are an intriguing class of rotaxanes which constitute prototypes of mechanical molecular machines and motors. By using stopped-flow spectroscopic techniques in acetonitrile solution, we investigated the kinetics of the shuttling process of a dibenzo[24]crown-8 ether (DB24C8) macrocycle between two recognition sites or "stations"--a secondary ammonium (-NH2+-)/amine (-NH-) center and a 4,4'-bipyridinium (bipy2+) unit--located on the dumbbell component in a [2]rotaxane. The affinity for DB24C8 decreases in the order -NH2+- > bipy2+ > -NH-. Hence, shuttling of the DB24C8 macrocycle can be obtained by deprotonation and reprotonation of the ammonium station, reactions which are easily accomplished by addition of base and acid to the solution. The rate constants were measured as a function of temperature in the range 277-303 K, and activation parameters for the shuttling motion in both directions were determined. The effect of different counterions on the shuttling rates was examined. The shuttling from the -NH2+- to the bipy2+ station, induced by the deprotonation of the ammonium site, is considerably slower than the shuttling in the reverse direction, which is, in turn, activated by reprotonation of the amine site. The results show that the dynamics of the shuttling processes are related to the change in the intercomponent interactions and structural features of the two mutually interlocked molecular components. Our observations also indicate that the counterions of the cationic rotaxane constitute an important contribution to the activation barrier for shuttling.     

Dual‐Mode Controlled Self‐Assembly of TiO2 Nanoparticles Through a Cucurbit[8]uril‐Enhanced Radical Cation Dimerization Interaction

The realization of controllable multicomponent self‐assembly through reversible supramolecular interactions is a challenging goal, and is an important strategy for the fabrication of switchable nanomaterials. Herein we show that the self‐assembly of TiO₂ nanoparticles (NP) functionalized with methyl viologen can be controlled both by light irradiation and chemical reduction through cucurbit[8]uril‐enhanced radical cation dimerization interactions. Moreover, the controlled assembly and disassembly of this system are accompanied by switchable photocatalytic activity of the TiO₂ NPs, which shows potential application as a novel smart and recyclable photocatalyst.     

Electron Localization Dynamics in the Triplet Excited State of [Ru(bpy)3]2+ in Aqueous Solution

Hybrid DFT/classical molecular dynamics of the long‐lived triplet excited state of [Ru(bpy)₃]²⁺ (bpy=2,2′‐bipyridine) in aqueous solution is used to investigate the solvent‐mediated electron localization and dynamics in the triplet metal‐to‐ligand charge‐transfer (MLCT) state. Our studies reveal a solvent‐induced breaking of the coordination symmetry with consequent localization of the photoexcited electron on one or two bipyridine units for the entire length of our simulation, which amounts to several picoseconds. Frequent electronic “hops” between the ligands constituting the pair are observed with a characteristic time of approximately half a picosecond.     

Increased Halide Recognition Strength by Enhanced Intercomponent Preorganisation in Triazolium Containing [2]Rotaxanes

Three triazolium‐based [2]rotaxanes containing different sized axle and macrocycle components were synthesised in good yields (40–57 %) through chloride anion templation. The anion recognition properties of the interlocked receptor systems were investigated using ¹H NMR titration experiments: all three rotaxanes display impressive selectivities for halide anions over the more basic oxoanion acetate. The rotaxanes incorporating shorter, more rigid axle components with aryl‐substituted triazolium groups display substantially higher anion binding affinities than those with longer, bis‐alkyl‐substituted heterocycles, which is attributed to the increased intercomponent preorganisation afforded by the smaller axle component. Computational DFT and molecular dynamics simulations composed of unconstrained and umbrella sampling simulations corroborate the experimental observations.     

Paramagnetic Properties and Moderately RapidConformational Dynamics in the Cobalt(II) Calix[4]arene Complex by NMR

¹H NMR measurements are reported for the CD₂Cl₂/CDCl₃ solutions of the Co(II) calix[4]arenetetraphosphineoxide complex (I). Temperature dependences of the ¹H NMR spectra of I have been analyzed using the line shape analysis, taking into account the temperature variation of paramagnetic chemical shifts, within the frame of the dynamic NMR method. Conformational dynamics of the 2:1 Co(II) calix[4]arene complexes was conditioned by the pinched cone ↔pinched cone interconversion of I (with activation Gibbs energy ΔG^≠(298K) = 40 ± 3 kJ/mol. Due to substantial temperature dependence of paramagnetic shifts, complex I can be used as model compound for designing an NMR thermosensor reagent for local temperature monitoring.     

Correlation between Dynamic Heterogeneity and Local Structure in a Room‐Temperature Ionic Liquid: A Molecular Dynamics Study of [bmim][PF6]

The complex dynamics of a room‐temperature ionic liquid, 1‐n‐butyl‐3‐methylimidazolium hexafluorophosphate ([bmim][PF₆]), is studied using equilibrium classical molecular dynamics simulations in the temperature range of 250–450 K. The activation energies for the self‐diffusion of ions are around 30–34 kJ mol^?1, with that of the anion a little higher than that for the cation. The electrical conductivity of the liquid is calculated and good agreement with experiments is obtained. Structural relaxation is studied through the decay of coherent (total density–density correlation) and incoherent (self part of density–density correlation) intermediate scattering functions over a range of temperatures and wave vectors relevant to the system. The relaxation data are used to identify and characterize two processes, α and β. The dependence of the two relaxation times on temperature and wave vector is obtained. The dynamical heterogeneity of the ions determined through the non‐Gaussian parameter indicates the motion of the cation to be more heterogeneous than that of the anion. The faster ones among the cations are coordinated to faster anions, while slower cations are surrounded predominantly by slower anions. Thus, the dynamical heterogeneity in this ionic liquid is shown to have structural signatures.