Molecular Dynamics Simulations of Metal Ion Binding to the His‐tag Motif

In our previous study, we have observed that the chelation of various metal ions to the His‐tag motifs mostly involves the i and i+2 His residues for Ni²⁺, Cu²⁺, Zn²⁺ and Co²+. In the present study, various 200 ps molecular dynamics simulations were further conducted to investigate the chelating pathway of various metal ions to the His‐tag motif with 6 His residues (His‐tag6) and the binding affinities of these metal binding pockets towards these metal ions. The results indicate that His‐tag6 with the chelated metal ion located in positions His(2,4) or His(3,5) exhibits the strongest affinity for Ni²+ and Cu²+.K⁺ was found to be preferred to chelate in His(1,3) and His(3,5) coordinations. However, Fe³+ was found to have higher affinity towards His(1,3) and His(2,4) binding pockets. Our results also suggest that Ni²⁺ exhibits the highest binding affinity towards His‐tag6 over the other metal ions. Most of the structural variations of the His‐tag6 motif were from the Histidyl side chains during metal ion binding. In addition, there is an inverse linear correlation between the final chelated distance and the charge/volume ratio of metal ion. There is a negative correlation between the metal binding affinity and the averaged potential energy generated from the MD simulations.     

Atomistic Simulations of COSAN: Amphiphiles without a Head‐and‐Tail Design Display “Head and Tail” Surfactant Behavior

Cobaltabisdicarbollide (COSAN) anions have an unexpectedly rich self‐assembly behavior, which can lead to vesicles and micelles without having a classical surfactant molecular architecture. This was rationalized by the introduction of new terminology and novel driving forces. A key aspect in the interpretation of COSAN behavior is the assumption that the most stable form of these ions is the transoid rotamer, which lacks a “hydrophilic head” and a “hydrophobic tail”. Using implicit solvent DFT calculations and MD simulations we show that in water, 1) the cisoid rotamer is the most stable form of COSAN and 2) this cisoid rotamer has a well‐defined hydrophilic polar region (“head”) and a hydrophobic apolar region (“tail”). In addition, our simulations show that the properties of this rotamer in water (interfacial affinity, micellization) match those expected for a classical surfactant. Therefore, we conclude that the experimental results for the COSAN ions can now be understood in terms of its amphiphilic molecular architecture.     

The Effect of Fluoro Substitution upon the β‐Hairpin Fold of a β‐Tetrapeptide in Methanol

The importance of β‐peptides lies in their ability to mimic the conformational behavior of α‐peptides, even with a much shorter chain length, and in their resistance to proteases. To investigate the effect of substitution of β‐peptides on their dominant fold, we have carried out a molecular‐dynamics (MD) simulation study of two tetrapeptides, Ac‐(2R,3S)‐β^2,3hVal(αMe)‐(2S)‐β²hPhe‐(R)‐β³hLys‐(2R,3S)‐β^2,3‐Ala(αMe)‐NH₂, differing in the substitution at the C_α of Phe2 (pepF with F, and pepH with H). Three simulations, unrestrained (UNRES), using ³J‐coupling biasing with local elevation in combination with either instantaneous (INS) or time‐averaging (AVE) NOE distance restraining, were carried out for each peptide. In the unrestrained simulations, we find three (pepF) and two (pepH) NOE distance bound violations of maximally 0.22 nm that involve the terminal residues. The restrained simulations match both the NOE distance bounds and ³J‐values derived from experiment. The fluorinated peptide shows a slightly larger conformational variability than the non‐fluorinated one.     

Molecular Dynamics Simulation of Ester‐Linked Hen Egg White Lysozyme Reveals the Effect of Missing Backbone Hydrogen Bond Donors on the Protein Structure

The three‐dimensional structure of a protein is stabilized by a number of different atomic interactions. One of these is hydrogen bonding. Its influence on the spatial structure of the hen egg white lysozyme is investigated by replacing peptide bonds (except those of the two proline residues) by ester bonds. Molecular dynamics simulations of native and ester‐linked lysozyme are compared with the native crystal structure and with NOE distance bounds derived from solution NMR experiments. The ester‐linked protein shows a slight compaction while losing its native structure. However, it does not unfold completely. The structure remains compact due to its hydrophobic core and a changed network of hydrogen bonds involving side chains.     

Formation of Long,Multicenter π‐[TCNE]22− Dimers in Solution: Solvation and Stability Assessed through Molecular Dynamics Simulations

Purely organic radical ions dimerize in solution at low temperature, forming long, multicenter bonds, despite the metastability of the isolated dimers. Here, we present the first computational study of these π‐dimers in solution, with explicit consideration of solvent molecules and finite temperature effects. By means of force‐field and ab initio molecular dynamics and free energy simulations, the structure and stability of π‐[TCNE]₂^2? (TCNE=tetracyanoethylene) dimers in dichloromethane have been evaluated. Although the dimers dissociate at room temperature, they are stable at 175 K and their structure is similar to the one in the solid state, with a cofacial arrangement of the radicals at an interplanar separation of approximately 3.0 Å. The π‐[TCNE]₂^2? dimers form dissociated ion pairs with the NBu₄⁺ counterions, and their first solvation shell comprises approximately 20 CH₂Cl₂ molecules. Among them, the eight molecules distributed along the equatorial plane of the dimer play a key role in stabilizing the dimer through bridging C?H???N contacts. The calculated free energy of dimerization of TCNE ^{. ?} in solution at 175 K is ?5.5 kcal mol^?1. These results provide the first quantitative model describing the pairing of radical ions in solution, and demonstrate the key role of solvation forces on the dimerization process.     

The Propensity of α‐Aminoisobutyric Acid (=2‐Methylalanine; Aib) to Induce Helical Secondary Structure in an α‐Heptapeptide: A Computational Study

We present a molecular‐dynamics simulation study of an α‐heptapeptide containing an α‐aminoisobutyric acid (=2‐methylalanine; Aib) residue, Val¹‐Ala²‐Leu³‐Aib⁴‐Ile⁵‐Met⁶‐Phe⁷, and a quantum‐mechanical (QM) study of simplified models to investigate the propensity of the Aib residue to induce 3₁₀/α‐helical conformation. For comparison, we have also performed simulations of three analogues of the peptide with the Aib residue being replaced by L ‐Ala, D ‐Ala, and Gly, respectively, which provide information on the subtitution effect at C(α) (two Me groups for Aib, one for L ‐Ala and D ‐Ala, and zero for Gly). Our simulations suggest that, in MeOH, the heptapeptide hardly folds into canonical helical conformations, but appears to populate multiple conformations, i.e., C₇ and 3₁₀‐helical ones, which is in agreement with results from the QM calculations and NMR experiments. The populations of these conformations depend on the polarity of the solvent. Our study confirms that a short peptide, though with the presence of an Aib residue in the middle of the chain, does not have to fold to an α‐helical secondary structure. To generate a helical conformation for a linear peptide, several Aib residues should be present in the peptide, either sequentially or alternatively, to enhance the propensity of Aib‐containing peptides towards the helical conformation. A correction of a few of the published NMR data is reported.     

Equilibrium Swelling of an Epoxy‐Resin in Contact with Water – A Molecular Dynamics Simulation Study

Full Paper: We have studied the equilibrium swelling of an idealized model network based on a realistic epoxy‐resin in contact with water using the molecular dynamics simulation method. We use a novel method to measure the water chemical potential inside the network as function of water concentration. The equality of the water chemical potential computed in this fashion with the bulk water chemical potential under the same thermodynamic conditions determines the equilibrium water content and the swelling ratio. We study the dependence of the water content as function of temperature and as function of the size of the atomic partial charges.

Schematic representation of the simulation volume. Spheres represent epoxy units with n = 0. The dashed lines represent curing agent units with m = 5.     

An Unprecedented Process of Peroxide Ion Formation and its Localization in the Crystal Structure of Strontium Peroxy‐HydroxyapatiteSr10(PO4)6(O2)x(OH)2–2x.

Formation of strontium peroxy‐hydroxyapatite solid solution Sr₁₀(PO₄)₆(O₂)_x(OH)_2–2x was studied on annealing the hydroxyapatite in the temperature range 900–1350 °C in oxygen, air, and argon atmosphere. The redox process was found to display unprecedented features: (i) the peroxide content increased with raising temperature, (ii) the peroxide content remained substantial even at a low oxygen pressure of 1.013 Pa, (iii) the peroxide content was extremely persistent, and even at a temperature of 1350 °C in oxygen atmosphere the peroxide groups substituted more than two‐third of the original hydroxide groups. Chemical processes consistent with these features are suggested. In the UV/Vis spectrum, an absorption peak at 300 nm was recorded, which was attributed to an electronic transition in the peroxide ion, since its intensity depended linearly on the peroxide content. In the Raman spectra, a weak band at 765–770 cm^–1 was ascribed to symmetric stretching vibrations of O₂^2–. The structures of the compounds were refined from powder X‐ray diffraction data using the Rietveld method supported by a maximum entropy method (MEM) electron density calculation. The peroxide ions are localized in the center of the hexagonal channel. At high concentration they tend to order with the associated vacancies along the channels. As a consequence, the width of the channel sections varies, the PO₄ tetrahedra tilt, and the remote strontium atoms are displaced leading to changes in their coordination. Generally, the peroxide for hydroxide substitution manifests itself in the reduction of the overall channel diameter (and its volume), while the volume occupied by out‐of‐channel ions remains the same.     

Vibrational Spectroscopic Study on Ion Solvation and Ion Association of Lithium Tetrafluoroborate in 4‐Ethoxymethyl‐ethylene Carbonate

应用红外及拉曼光谱研究了不同浓度的四氟硼酸锂在4-乙氧甲基-碳酸乙烯酯溶剂中的离子溶剂化和离子缔合现象。环形变谱带和羰基伸缩振动谱带的分裂,以及骨架环振动谱带的迁移和分裂表明,锂离子与溶剂分子间存在着较强的相互作用,这种相互作用是通过溶剂羰基氧原子实现的。利用光谱拟合技术定量计算了表观溶剂化数。随着电解质锂盐浓度的增加,溶剂化数逐渐由4.32降至1.26。此外,四氟硼酸根v1谱带的分裂表明在高浓度溶液中存在着光谱自由的四氟硼酸根、直接接触离子对和离子对二聚体。     

Characterization of the polymorphic states of copper(II)‐bound Aβ(1–16) peptides by computational simulations

Understanding the polymorphic states of metal amyloid β (Aβ) interactions helps to elucidate metal‐mediated events in the pathogenesis of Alzheimer's disease. Systematic investigations on the effects of metal ions such as Cu²⁺ and Zn²⁺ on the structural and thermodynamic properties of Aβ at the molecular lever seem desirable. In this study, a set of new AMBER force field parameters was developed to model various Cu²⁺ coordination spheres of Aβ. These parameters including force constants and partial charges obtained using restrained electrostatic potential method were then validated in replica‐exchange molecular dynamics simulations on six Cu²⁺‐Aβ(1–16) systems. The Cu²⁺ coordination geometry differs depending on the Cu²⁺ binding fashions. The structural analyses reveal that Aβ(1–16) prefers turn conformations, which provides a geometrical favor to establish multiple Cu²⁺ coordination modes in solution at physiological pH. The relative stability of different Cu²⁺‐Aβ(1–16) complexes was estimated by free energy calculations. The Cu²⁺ ligands in the most stable Cu²⁺‐Aβ(1–16) structure involve Glu³, His⁶, His¹³ and His¹⁴ in terms of MM/3D‐RISM (molecular mechanics/three‐dimensional reference interaction site model). The solvation free energy and conformational entropy calculated by 3D‐RISM method suggest that the binding of Cu²⁺ within Aβ(1–16) is a spontaneous process. The overlap of the preparation free energy distributions demonstrates the heterogeneous states of Aβ(1–16) conformations that are ready for Cu²⁺ binding whereas the populations of such polymorphic states may shift at differing pH. © 2013 Wiley Periodicals, Inc.     

α‐Cyclodextrin Host–Guest Binding: A Computational Study of the Different Driving Forces

Free‐energy differences govern the equilibrium between bound and unbound states of a host and its guest molecules. The understanding of the underlying entropic and enthalpic contributions, and their complex interplay are crucial for the design of new drugs and inhibitors. In this study, molecular dynamics (MD) simulations were performed with inclusion complexes of α‐cyclodextrin (αCD) and three monosubstituted benzene derivatives to investigate host–guest binding. αCD Complexes are an ideal model system, which is experimentally and computationally well‐known. Thermodynamic integration (TI) simulations were carried out under various conditions for the free ligands in solution and bound to αCD. The two possible orientations of the ligand inside the cavity were investigated. Agreement with experimental data was only found for the more stable orientation, where the substituent resides inside the cavity. The better stability of this conformation results from stronger Van der Waals interactions and a favorable antiparallel host–guest dipole–dipole alignment. To estimate the entropic contributions, simulations were performed at three different temperatures (250, 300, and 350 K) and using positional restraints for the host. The system was found to be insensitive to both factors, due to the large and symmetric cavity of αCD, and the nondirectional nature of the host–guest interactions.     

Solvent‐Modulated Influence of Intramolecular Hydrogen‐Bonding on the Conformational Properties of the Hydroxymethyl Group in Glucose and Galactose: A Molecular Dynamics Simulation Study

Intramolecular hydrogen‐bonding (H‐bonding) is commonly regarded as a major determinant of the conformation of (bio)molecules. However, in an aqueous environment, solvent‐exposed H‐bonds are likely to represent only a marginal (possibly adverse) conformational driving as well as steering force. For example, the hydroxymethyl rotamers of glucose and galactose permitting the formation of an intramolecular H‐bond with the adjacent hydroxyl group are not favored in water but, in the opposite, least populated. This is because the solvent‐exposed H‐bond is dielectrically screened as well as subject to intense H‐bonding competition by the water molecules. In the present study, the effect of a decrease in the solvent polarity on this rotameric equilibrium is probed using molecular dynamics simulation. This is done by considering six physical solvents (H₂O, DMSO , MeOH , CHC l₃, CC l₄, and vacuum), along with 19 artificial water‐like solvent models for which the dielectric permittivity and H‐bonding capacity can be modulated independently via a scaling of the O–H distance and of the atomic partial charges. In the high polarity solvents, the intramolecular H‐bond is observed, but arises as an opportunistic consequence of the proximity of the H‐bonding partners in a given rotameric state. Only when the polarity of the solvent is decreased does the intramolecular H‐bond start to induce a conformational pressure on the rotameric equilibrium. The artificial solvent series also reveals that the effects of the solvent permittivity and of its H‐bonding capacity mutually enhance each other, with a slightly larger influence of the permittivity. The hydroxymethyl conformation in hexopyranoses appears to be particularly sensitive to solvent‐polarity effects because the H‐bond involving the hydroxymethyl group is only one out of up to five H‐bonds capable of forming a network around the ring.     

Numerical Simulation of the Pressure Denaturation of a Helical β‐Peptide Heptamer Solvated in Methanol

The effect of elevated pressure on the conformational behavior of a β‐peptide heptamer ( 1 ) in MeOH solution was considered. The response of the peptide to elevated pressure was probed by means of molecular dynamics (MD) simulations, and described in atomic terms. The most‐striking features of the response are that the region of the ‘unfolded’ state of the peptide accessible at elevated pressure is narrow, and that thermal and pressure denaturation produce similar ‘unfolded’ states in the case of 1 .     

Separation,Quantification and Structural Study of (+)‐Catechin and (–)‐Epicatechin by Ion Mobility Mass Spectrometry Combined with Theoretical Algorithms

Two catechin epimers and their non‐covalent complexes with γ‐cyclodextrin were studied by using ion mobility coupled with mass spectrometry (IM‐MS). Rapid separation of complexes was achieved with the peak‐to‐peak resolution reaching 0.86 after optimization of IM condition. Collision cross section (CCS) was measured to explore the structural difference of complexes. A gap of 11.75 Ų between two complexes was found. Molecular modeling and theoretical CCS calculation were adopted to explain the measurement results. Two binding ways of both complexes were found and the calculated CCS corresponds accurately to the measured CCS. Quantification of catechins in mixtures was performed and the relative error was less than 15%, indicating the effectiveness of quantification by IM‐MS.     

Host/Guest Simulation of Fluorescent Probes Adsorbed into Low‐Density Polyethylene, 1. Excimer Formation of 1,3‐Di(1‐pyrenyl)propane

Molecular dynamics and Rotational Isomer State/Monte Carlo techniques with a Dreiding 1.01 Force Field are employed to study the excimer formation of isolated 1,3‐di(1‐pyrenyl)propane and the probe adsorbed into a low‐density polyethylene (LDPE) matrix model. The probability of formation of each molecular conformer at several temperatures was calculated using these theoretical techniques. Conformational statistical analysis of the four torsion angles (ϕ₁, ϕ₂, θ₁, θ₂) of Py3MPy showed that the angles —C—C^ar— (ϕ₁, ϕ₂) present two states c ^± = ±90°; and the angles —C—C— (θ₁, θ₂), the three trans states = 180°, g ^± = ±60°. The correlation of θ₁–θ₂ torsion angles showed that the most probable pairs were g⁺g^– and g^–g⁺ for the excimer‐like specimens, although these angles are distorted because of interactions with the polymer matrix. The temperature dependence of the excimer‐formation probability revealed that this process was thermodynamically controlled in the isolated case. When the probe was adsorbed into the LDPE matrix, the excimer formation process was reversed at T = 375 K. At T >  375 K, the behavior was similar to the isolated case but, at T < 375 K, excimer formation probability increased with temperature as found experimentally by steady‐state fluorescence spectroscopy. This temperature was coincident with the onset of the LDPE melting process, determined experimentally by thermal analysis.     

Core–Shell Hollow Microspheres of Magnetic Iron Oxide@Amorphous Calcium Phosphate: Synthesis Using Adenosine 5′‐Triphosphate and Application in pH‐Responsive Drug Delivery

Drug nanocarriers with magnetic targeting and pH‐responsive drug‐release behavior are promising for applications in controlled drug delivery. Magnetic iron oxides show excellent magnetism, but their application in drug delivery is limited by low drug‐loading capacity and poor control over drug release. Herein, core–shell hollow microspheres of magnetic iron oxide@amorphous calcium phosphate (MIO@ACP) were prepared and investigated as magnetic, pH‐responsive drug nanocarriers. Hollow microspheres of magnetic iron oxide (HMIOs) were prepared by etching solid MIO microspheres in hydrochloric acid/ethanol solution. After loading a drug into the HMIOs, the drug‐loaded HMIOs were coated with a protective layer of ACP by using adenosine 5′‐triphosphate (ATP) disodium salt (Na₂ATP) as stabilizer, and drug‐loaded core–shell hollow microspheres of MIO@ACP (HMIOs/drug/ACP) were obtained. The as‐prepared HMIOs/drug/ACP drug‐delivery system exhibits superparamagnetism and pH‐responsive drug‐release behavior. In a medium with pH 7.4, drug release was slow, but it was significantly accelerated at pH 4.5 due to dissolution of the ACP shell. Docetaxel‐loaded core–shell hollow microspheres of MIO@ACP exhibited high anticancer activity.     

Systematic Dielectric and NMR Study of the Ionic Liquid 1‐Alkyl‐3‐Methyl Imidazolium

The dynamic behaviors of ionic liquid samples consisting of a series of 1‐alkyl‐3‐methylimidazolium cations and various counteranionic species are investigated systematically over a wide frequency range from 1 MHz to 20 GHz at room temperature using dielectric relaxation (DR) and nuclear magnetic resonance (NMR) spectroscopies. DR spectra for the ionic liquids are reasonably deconvoluted into two or three relaxation modes. The slowest relaxation times are strongly dependent upon sample viscosity and cation size, whereas the relaxation times of other modes are almost independent of these factors. We attribute the two slower relaxation modes to the rotational relaxation modes of the dipolar cations because the correlation times of the cations evaluated using longitudinal relaxation time (T₁ ¹³C NMR) measurements corresponded to the dielectric relaxation times. On the other hand, the fastest relaxation mode is presumably related to the inter‐ion motions of ion‐pairs formed between cationic and anionic species. In the case of the ionic liquid bis(trifluoromethanesulfonyl)imide, the system shows marked dielectric relaxation behavior due to rotational motion of dipolar anionic species in addition to the relaxation modes attributed to the dipolar cations.     

Atomistic Characterisation of Li+ Mobility and Conductivity in Li7−xPS6−xIx Argyrodites from Molecular Dynamics Simulations,Solid‐State NMR,and Impedance Spectroscopy

The atomistic mechanisms of Li⁺ ion mobility/conductivity in Li_7?xPS_6?xI_x argyrodites are explored from both experimental and theoretical viewpoints. Ionic conductivity in the title compound is associated with a solid–solid phase transition, which was characterised by low‐temperature differential scanning calorimetry, ⁷Li and ¹²⁷I NMR investigations, impedance measurements and molecular dynamics simulations. The NMR signals of both isotopes are dominated by anisotropic interactions at low temperatures. A significant narrowing of the NMR signal indicates a motional averaging of the anisotropic interactions above 177±2 K. The activation energy to ionic conductivity was assessed from both impedance spectroscopy and molecular dynamics simulations. The latter revealed that a series of interstitial sites become accessible to the Li⁺ ions, whilst the remaining ions stay at their respective sites in the argyrodite lattice. The interstitial positions each correspond to the centres of tetrahedra of S/I atoms, and differ only in terms of their common corners, edges, or faces with adjacent PS₄ tetrahedra. From connectivity analyses and free‐energy rankings, a specific tetrahedron is identified as the key restriction to ionic conductivity, and is clearly differentiated from local mobility, which follows a different mechanism with much lower activation energy. Interpolation of the lattice parameters as derived from X‐ray diffraction experiments indicates a homogeneity range for Li_7?xPS_6?xI_x with 0.97≤x≤1.00. Within this range, molecular dynamics simulations predict Li⁺ conductivity at ambient conditions to vary considerably.     

Radical Desorption Kinetics in Emulsion Polymerization, 2 – Brownian Dynamics Simulation of Radical Desorption in Non‐Homogeneous Particles

One of the most important events in free‐radical emulsion polymerization is desorption of radicals from the polymer particles to the aqueous phase. Desorption takes place by diffusion of radicals inside the particle toward the surface and transfer to the aqueous phase. The rate of desorption can be determined theoretically for homogeneous spherical particles. For more complex cases, analytical solutions become difficult or impossible to obtain and a numerical approach is better suited for estimating desorption rate coefficients. In this paper, Brownian dynamics simulation is used for the estimation of desorption rate coefficients in emulsion polymerization systems of increased complexity, in particular for non‐homogeneous polymer particles.