Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents

The self-assembly of cyclic D,L-alpha-peptides into hollow nanotubes is a crucial mechanistic step in their application as antibacterial and drug-delivery agents. To understand this process, molecular dynamics (MD) simulations were performed on dimers of cyclic peptides formed from cyclo [(-L-Trp-D-N-MeLeu-)4-]2 and cyclo [(-L-Trp-D-Leu-)4-]2 subunits in nonpolar (nonane) and polar (water) solvent. The dimers were observed to be stable only in nonpolar solvent over the full 10 ns length of the MD trajectory. The behavior of the dimers in different solvents is rationalized in terms of the intersubunit hydrogen bonding, hydrogen bonding with the solvent, and planarity of the rings. It is shown that the phi and psi dihedral angles of a single uncapped ring in nonane lie in the beta-sheet region of the Ramachandran plot, and the ring stays in a flat conformation. Steered MD (SMD) simulations based on Jarzynski's equality were performed to obtain the potential of mean force as a function of the distance between the two rings of the capped dimer in nonane. It is also shown that a single peptide subunit prefers to reside close to the nonane/water interface rather than in bulk solvent because of the amphiphilic character of the peptide ring. The present MD results build the foundation for using MD simulations to study the mechanism of the formation of cyclic peptide nanotubes in lipid bilayers.     

Replica exchange molecular dynamics simulations of amyloid peptide aggregation

The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant temperature molecular dynamics (CTMD). During the aggregation process the energetic and structural properties are essentially the same in REMD and CTMD. A condensation stage toward disordered aggregates precedes the beta-sheet formation. Two order parameters, borrowed from anisotropic fluid analysis, are used to monitor the aggregation process. The order parameters do not depend on the peptide sequence and length and therefore allow to compare the amyloidogenic propensity of different peptides     

Polymer brushes in solvents of variable quality: molecular dynamics simulations using explicit solvent

The structure and thermodynamic properties of a system of end-grafted flexible polymer chains grafted to a flat substrate and exposed to a solvent of variable quality are studied by molecular dynamics methods. The macromolecules are described by a coarse-grained bead-spring model, and the solvent molecules by pointlike particles, assuming Lennard-Jones-type interactions between pairs of monomers (epsilon(pp)), solvent molecules (epsilon(ss)), and solvent monomer (epsilon(ps)), respectively. Varying the grafting density sigma(g) and some of these energy parameters, we obtain density profiles of solvent particles and monomers, study structural properties of the chain (gyration radius components, bond orientational parameters, etc.), and examine also the profile of the lateral pressure P( parallel)(z), keeping in the simulation the normal pressure P( perpendicular) constant. From these data, the reduction of the surface tension between solvent and wall as a function of the grafting density of the brush has been obtained. Further results include the stretching force on the monomer adjacent to the grafting site and its variation with solvent quality and grafting density, and dynamic characteristics such as mobility profiles and chain relaxation times. Possible phase transitions (vertical phase separation of the solvent versus lateral segregation of the polymers into "clusters," etc.) are discussed, and a comparison to previous work using implicit solvent models is made. The variation of the brush height and the interfacial width of the transition zone between the pure solvent and the brush agrees qualitatively very well with corresponding experiments.     

Transient molecular dynamics simulations of liquid viscosity for nonpolar and polar fluids

A transient molecular dynamics (TMD) method for obtaining fluid viscosity is extended to multisite, force-field models of both nonpolar and polar liquids. The method overlays a sinusoidal velocity profile over the peculiar particle velocities and then records the transient decay of the velocity profile. The viscosity is obtained by regression of the solution of the momentum equation with an appropriate constitutive equation and initial and boundary conditions corresponding to those used in the simulation. The transient velocity decays observed appeared to include both relaxation and retardation effects. The Jeffreys viscoelastic model was found to model accurately the transient responses obtained for multisite models for n-butane, isobutane, n-hexane, water, methanol, and 1-hexanol. TMD viscosities obtained for saturated liquids over a wide range of densities agreed well for the polar fluids, both with nonequilibrium molecular dynamics (NEMD) results using the same force-field models and with correlations based on experimental data. Viscosities obtained for the nonpolar fluids agreed well with the experimental and NEMD results at low to moderate densities, but underpredicted experimental values at higher densities where shear-thinning effects and viscous heating may impact the TMD simulations.     

Reactivity of ferrocenium cations with molecular oxygen in polar organic solvents: Decomposition, redox reactions and stabilization

The behaviour of chemically or electrochemically generated ferrocenium cations has been studied in some polar organic solvents (DMF, DMSO, acetonitrile, acetone, methylene chloride) under molecular oxygen. Adducts between oxygen and ferrocenium species can differently evolve according to the solvent (oxidizable or not) and the absence or the presence of another reagent. A rapid decomposition of ferrocenium cations is observed in the absence of another substrate. In the presence of some substrates and antioxidants, the stability of ferrocenium cations towards molecular oxygen notably increases and in some cases redox reactions take place with formation of ferrocene.     

Polarizability response in polar solvents: molecular-dynamics simulations of acetonitrile and chloroform

The relaxation of the many-body polarizability in liquid acetonitrile and chloroform at room temperature was studied by molecular-dynamics simulations. The collective polarizability induced by intermolecular interactions was included using first- and all-orders dipole-induced-dipole models and calculated considering both molecule-centered and distributed site polarizabilities. The anisotropic response was analyzed using a separation scheme that allows a decomposition of the total response in terms of orientational and collision-induced effects. We found the method effective in approximately separating the contributions of these relaxation mechanisms, although the orientational-collision-induced interference makes a non-negligible contribution to the total response. In both liquids the main contribution to the anisotropic response is due to orientational dynamics, but intermolecular collision-induced (or translational) effects are important, especially at short times. We found that higher-order interaction-induced effects were essentially negligible for both liquids. Larger differences were found between the center-center and site-site models, with the latter showing faster polarizability relaxation and better agreement with experiment. Isotropic and anisotropic spectra were computed from the corresponding time correlation functions. The lowest-frequency contributions are largely suppressed in the isotropic spectra and their overall shape is similar to the purely collision-induced contribution to the anisotropic spectra, but with an amplitude which is smaller by a factor of approximately 5 in acetonitrile and approximately 3 in chloroform.     

Slip length of water on graphene: limitations of non-equilibrium molecular dynamics simulations

Data for the flow rate of water in carbon nanopores is widely scattered, both in experiments and simulations. In this work, we aim at precisely quantifying the characteristic large slip length and flow rate of water flowing in a planar graphene nanochannel. First, we quantify the slip length using the intrinsic interfacial friction coefficient between water and graphene, which is found from equilibrium molecular dynamics (EMD) simulations. We then calculate the flow rate and the slip length from the streaming velocity profiles obtained using non-equilibrium molecular dynamics (NEMD) simulations and compare with the predictions from the EMD simulations. The slip length calculated from NEMD simulations is found to be extremely sensitive to the curvature of the velocity profile and it possesses large statistical errors. We therefore pose the question: Can a micrometer range slip length be reliably determined using velocity profiles obtained from NEMD simulations? Our answer is "not practical, if not impossible" based on the analysis given as the results. In the case of high slip systems such as water in carbon nanochannels, the EMD method results are more reliable, accurate, and computationally more efficient compared to the direct NEMD method for predicting the nanofluidic flow rate and hydrodynamic boundary condition.     

Self-assembly of molecular capsules in polar solvents

[structure: see text] We present a novel type of molecular capsule formed by self-organization of calix[4]arenes with several oppositely charged functional groups located at their upper rims. In highly polar solvents, the complementary half-spheres form stable 1:1 complexes with association constants of up to 7 x 10(5) M(-)(1) in methanol. The cavity inside the capsules is large enough for the inclusion of small aliphatic or (hetero)aromatic guest molecules.     

The influence of aqueous versus glassy solvents on protein dynamics: vibrational echo experiments and molecular dynamics simulations

Spectrally resolved infrared stimulated vibrational echo measurements are used to measure the vibrational dephasing of the CO stretching mode of carbonmonoxy-hemoglobin (HbCO), a myoglobin mutant (H64V), and a bacterial cytochrome c(552) mutant (Ht-M61A) in aqueous solution and trehalose glasses. The vibrational dephasing of the heme-bound CO is significantly slower for all three proteins embedded in trehalose glasses compared to that of aqueous protein solutions. All three proteins exhibit persistent but notably slower spectral diffusion when the protein surface is fixed by the glassy solvent. Frequency-frequency correlation functions (FFCFs) of the CO are extracted from the vibrational echo data to reveal that the structural dynamics, as sensed by the CO, of the three proteins in trehalose and aqueous solution are dominated by fast (tens of femtoseconds), motionally narrowed fluctuations. MD simulations of H64V in dynamic and "static" water are presented as models of the aqueous and glassy environments. FFCFs are calculated from the H64V simulations and qualitatively reproduce the important features of the experimentally extracted FFCFs. The suppression of long time scale (picoseconds to tens of picoseconds) frequency fluctuations (spectral diffusion) in the glassy solvent is the result of a damping of atomic displacements throughout the protein structure and is not limited to structural dynamics that occur only at the protein surface. The analysis provides evidence that some dynamics are coupled to the hydration shell of water, supporting the idea that the bioprotection offered by trehalose is due to its ability to immobilize the protein surface through a thin, constrained layer of water.     

Perfect wetting along a three-phase line: theory and molecular dynamics simulations

Wetting behavior along a three-phase equilibrium has been obtained by density gradient theory (DGT) and molecular dynamics simulations for a type-II equal size Lennard-Jones mixture. In order to perform a consistent comparison between both methodologies, the molecular parameters of this type of mixture were defined from the global phase diagram of equal size Lennard-Jones mixtures. We have found excellent agreement between predictions from the DGT (coupled to a Lennard-Jones equation for the bulk phases) and simulations results for both the phase and interface behavior, in the whole temperature, pressure, and concentration ranges. For all conditions explored in this work, this type-II mixture shows a three-phase equilibrium composed by a bulk immiscible liquid phase (L1) and a bulk gas phase (G) separated by a second immiscible liquid phase (L2). A similar phase distribution is obtained from the interfacial concentration profile in the whole range of conditions used in this work. This type of structure is a clear evidence that L2 completely wets the GL1 interface. The wetting behavior is also confirmed by the values and evolution of the interfacial tensions. In summary, this kind of type-II mixture does not show wetting transitions and exhibits a permanent perfect wetting in all the thermodynamic conditions explored here.     

Understanding the Hofmeister effect in interactions between chaotropic anions and lipid bilayers: molecular dynamics simulations

A set of all-atom molecular dynamics simulations have been performed to better understand critical phenomena regarding a Hofmeister series of anions and lipid bilayers. The simulations isolate the effect of anion size and show clear differences in the interactions with the dipolar phoshpatidylcholine headgroup. Cl- anions penetrate into the headgroup region of the bilayer, but the simulations confirm theories which predict that larger anions penetrate more deeply, into a more heterogeneous and hydrophobic molecular region. That anion size leads to such differences in partitioning in the bilayer provides atomic-level support to hypotheses inspired by several experimental studies. The ability of larger anions to bury deep within the bilayer is correlated with a less well-structured hydration shell, shedding of which upon penetration incurs a smaller penalty for the larger anions than for Cl-.     

Self-organization of spheroidal molecular assemblies in polar solvents

[reaction: see text] We report a number of 1:1 noncovalent complexes composed of a symmetrical trisphosphonate and various symmetrical trisammonium or trisamidinium compounds. The spheroidal complexes show high thermodynamic stability, with association constants Ka reaching 10(6) M(-1) in methanol and in some cases even exceeding 10(3) M(-1) in water. The observed Ka values correlate well with the different degree of preorganization of the complexation partners.     

Rotational reorientation dynamics of oxazine 750 in polar solvents

The rotational reorientation dynamics of oxazine 750 (OX750) in the first (with pump pulse at 660 nm) and a higher excited state (with pump pulse at 400 nm) in different polar solvents have been investigated using femtosecond time-resolved stimulated emission pumping fluorescence depletion (FS TR SEP FD) spectroscopy. In both excited states, three different anisotropy decay laws have been observed for OX750 in different solvents. Only in acetone and formamide could the anisotropy decays of OX750 be described by single-exponential functions, whereas the anisotropy decays have been found to exhibit biexponential behavior in other solvents. The slower anisotropy decay observed in all of the solvents has been assigned to the overall rotational relaxation of OX750 molecules, and a quantitative analysis of this time constant has been performed using the Stokes-Einstein-Debye hydrodynamic theory and the extended charge distribution model developed by Alavi and Waldeck. In both methanol and ethanol, a faster anisotropy decay on the order of picoseconds and a slower anisotropy decay on the hundreds of picoseconds time scale are observed. The most likely explanation for the faster anisotropy involves the rotation of the transition dipole moment in the excited state of OX750 resulting from the electron transfer (ET) reaction taking place from the alcoholic solvents to the OX750 chromophore. As a possible explanation, the wobbling-in-the-cone model has been used to analyze the biexponential anisotropy decays of OX750 in dimethylformamide (DMF) and dimethyl sulfoxide (DMSO). The observed faster anisotropy decays on the hundreds of femtoseconds time scale in DMF and DMSO are ascribed to the wobbling-in-the-cone motion of the ethyl group of OX750, which is sensitive to the strength of the hydrogen bond formed between the solvent and the protonation site of OX750.     

Density functional theory for efficient ab initio molecular dynamics simulations in solution

We present a density functional for first-principles molecular dynamics simulations that includes the electrostatic effects of a continuous dielectric medium. It allows for numerical simulations of molecules in solution in a model polar solvent. We propose a smooth dielectric model function to model solvation into water and demonstrate its good numerical properties for total energy calculations and constant energy molecular dynamics.     

Mechanism of rhodamine 6G molecular aggregation in montmorillonite colloid

Stopped-flow mixing device and visible absorption spectroscopy were used for the analysis of dye rhodamine 6G (R6G) molecular aggregation in the colloids based on Na-saturated montmorillonite. Two stages of the reaction were identified: The first stage was very short and taking only several seconds, involving the adsorption of R6G cations and their initial aggregation on the surface of colloid particles. The initially formed J-aggregates exhibited similar spectral properties as monomeric form of R6G. In the second stage, initially formed aggregates converted to sandwich-type H-aggregates absorbing light at significantly lower wavelengths and adsorbed monomers. The aggregate rearrangement took several hours. Monomers, with the spectral properties identical to R6G solution, were also identified as a component in complex spectra using principal component analysis (PCA) and multivariate curve resolution (MCR). Partial bleaching of the dye was also proven. Reaction kinetics of the rearrangement of the aggregates followed the model considering a complex mechanism of the molecular aggregation. Data fits using stretched-exponential function led to the determination of rate constants, which had been in the range 10^?3?4×10^?3s^?1.      

Microsecond molecular dynamics simulations of the kinetic pathways of gas hydrate formation from solid surfaces

In this paper, we report microsecond molecular dynamics simulations of the kinetic pathway of CO(2) hydrate formation triggered by hydroxylated silica surfaces. Our simulation results show that the nucleation of the CO(2) hydrate is a three-stage process. First, an icelike layer is formed closest to the substrates on the nanosecond scale. Then, on the submicrosecond timescale, a thin layer with intermediate structure is induced to compensate for the structure mismatch between the icelike layer and the final stable CO(2) hydrate. Finally, on the microsecond timescale, the nucleation of the first CO(2) hydrate motif layer is generated from the intermediate structure that acts as nucleation seeds. We also address the effects of the distance between two surfaces.