The two-dimensional infrared spectrum of NMAH and NMAD in H2O and D2O is computed on the basis of force field parametrizations ranging from standard point charge (PC) to more elaborate multipolar (MTP) representations of the electrostatics. For the latter, the nonbonded parameters (MTP and van der Waals) were optimized to reproduce thermodynamic data. The frequency trajectory and frequency-frequency correlation function (FFCF) are determined from explicit frequency calculations on ∼10(6) snapshots without using a more traditional "mapping" approach. This allows us to both sample configurations and compute observables in a consistent fashion. In agreement with experiment, the FFCF shows one very rapid time scale (in the 50 fs range) followed by one or two longer time scales. In the case of three time scales, the intermediate one is ≈0.5 ps or shorter, whereas the longest time scale can extend up to 2 or 3 ps. All interaction models lead to three time scales in the FFCF when fitted to an empirical parametrized form. When two time scales are assumed-as is usually done in the analysis of experimental data-and the short time scale is fixed to the τ1 = 50-100 fs range, the correlation time τc from the simulations ranges from 0.7 to 1 ps, which agrees quite well with experimentally determined values. The major difference between MTP and PC models is the observation that the later decay times in the FFCF are longer for simulations with MTPs. Also, the amplitude of the FFCF is reduced when simulations are carried out with MTPs. Overall, however, PC-based models perform well compared to those based on MTPs for NMAD in D2O and can be recommended for such investigations in the context of peptide and protein simulations.

Realization of a self-assembled, nontoxic and eco-friendly piezoelectric device with high-performance, sensitivity and reliability is highly desirable to complement conventional inorganic and polymer based materials. Hierarchically organized natural materials such as collagen have long been posited to exhibit electromechanical properties that could potentially be amplified via molecular engineering to produce technologically relevant piezoelectricity. Here, by using a simple, minimalistic, building block of collagen, we fabricate a peptide-based piezoelectric generator utilising a radically different helical arrangement of Phe-Phe-derived peptide, Pro-Phe-Phe and Hyp-Phe-Phe, based only on proteinogenic amino acids. The simple addition of a hydroxyl group increases the expected piezoelectric response by an order of magnitude (d35 = 27 pm V−1). The value is highest predicted to date in short natural peptides. We demonstrate tripeptide-based power generator that produces stable max current >50 nA and potential >1.2 V. Our results provide a promising device demonstration of computationally-guided molecular engineering of piezoelectricity in peptide nanotechnology.

Gramicidin A (gA) is the simplest known natural channel, and important progress in improving conduction activity has previously been obtained with modified natural gAs. However, simple artificial systems mimicking the gA functions are unknown. Here we show that gA can be mimicked using a simple synthetic triazole or 'T-channel' forming compound (TCT), having similar constitutional functions as the natural gAs. As in gA channels, the carbonyl moieties of the TCT, which point toward the T-channel core and surround the transport direction, are solvated by water. The net-dipolar alignment of water molecules along the chiral pore surfaces influences the conduction of protons/ions, envisioned to diffuse along dipolar hydrophilic pathways. Theoretical simulations and experimental assays reveal that the conduction through the T-channel, similar to that in gA, presents proton/water conduction, cation/anion selectivity and large open channel-conductance states. T-channels--associating supramolecular chirality with dipolar water alignment--represent an artificial primitive mimic of gA.

Diphenylalanine (FF) represents the simplest peptide building block that self-assembles into ordered nanostructures with interesting physical properties. Among self-assembled peptide structures, FF nanotubes display notable stiffness and piezoelectric parameters (Young’s modulus = 19–27 GPa, strain coefficient d 33 = 18 pC/N). Yet, inorganic alternatives remain the major materials of choice for many applications due to higher stiffness and piezoelectricity. Here, aiming to broaden the applications of the FF motif in materials chemistry, we designed three phenyl-rich dipeptides based on the β,β-diphenyl-Ala-OH (Dip) unit: Dip-Dip, cyclo-Dip-Dip, and tert-butyloxycarbonyl (Boc)-Dip-Dip. The doubled number of aromatic groups per unit, compared to FF, produced a dense aromatic zipper network with a dramatically improved Young’s modulus of ∼70 GPa, which is comparable to aluminum. The piezoelectric strain coefficient d 33 of ∼73 pC/N of such assembly exceeds that of poled polyvinylidene-fluoride (PVDF) polymers and compares well to that of lead zirconium titanate (PZT) thin films and ribbons. The rationally designed π–π assemblies show a voltage coefficient of 2–3 Vm/N, an order of magnitude higher than PVDF, improved thermal stability up to 360 °C (∼60 °C higher than FF), and useful photoluminescence with wide-range excitation-dependent emission in the visible region. Our data demonstrate that aromatic groups improve the rigidity and piezoelectricity of organic self-assembled materials for numerous applications.

This paper reports on a molecular dynamics study of aqueous electrolyte solutions confined in hydrophobic nanopores. We examined for the first time the effect of the size and polarizability of the ions on the structure and dynamics of the confined electrolyte solution by considering the series of sodium halides (NaX with X = F, Cl, Br, and I). We also address the effect of pore size by varying the diameter of the nanochannel. As far as structural properties are concerned, the behavior of the NaF electrolyte solution significantly differs from that of the other sodium halide solutions. Because of their small size, Na and F in NaF are found to be significantly solvated by water. In addition, due to steric and hydrophobic effects [ Chandler D. Chandler D. Nature2005437640.], Cl, Br, and I tend to be repelled from the regions where the density of water is larger. Ion-specific effects on the dynamics of water and ions are found to be minimized when the electrolyte solution is confined at the nanoscale in comparison to bulk water and the water−air interface. For instance, both the data for water and the ionic species indicate that the ratio of the self-diffusivity for the confined solution to that for the bulk is independent of the nature of the anion F, Cl, Br, and I. Moreover, while the average solvation times for Na in NaF and Na in NaX (X = Cl, Br, I) significantly differ for bulk electrolyte solutions, they turn out to be very similar for the confined solutions. Such a leveling of the dynamical properties of the electrolyte solutions due to confinement is also observed on the pairing of the anions and cations.

We report oriented immobilization of proteins using the standard hexahistidine (His6)-Ni2+:NTA (nitrilotriacetic acid) methodology, which we systematically tuned to give control of surface coverage. Fluorescence microscopy and surface plasmon resonance measurements of self-assembled monolayers (SAMs) of red fluorescent proteins (TagRFP) showed that binding strength increased by 1 order of magnitude for each additional His6-tag on the TagRFP proteins. All TagRFP variants with His6-tags located on only one side of the barrel-shaped protein yielded a 1.5 times higher surface coverage compared to variants with His6-tags on opposite sides of the so-called β-barrel. Time-resolved fluorescence anisotropy measurements supported by polarized infrared spectroscopy verified that the orientation (and thus coverage and functionality) of proteins on surfaces can be controlled by strategic placement of a His6-tag on the protein. Molecular dynamics simulations show how the differently tagged proteins reside at the surface in “end-on” and “side-on” orientations with each His6-tag contributing to binding. Also, not every dihistidine subunit in a given His6-tag forms a full coordination bond with the Ni2+:NTA SAMs, which varied with the position of the His6-tag on the protein. At equal valency but different tag positions on the protein, differences in binding were caused by probing for Ni2+:NTA moieties and by additional electrostatic interactions between different fractions of the β-barrel structure and charged NTA moieties. Potential of mean force calculations indicate there is no specific single-protein interaction mode that provides a clear preferential surface orientation, suggesting that the experimentally measured preference for the end-on orientation is a supra-protein, not a single-protein, effect.

Atomistic simulations of dioxygen (O(2)) dynamics and migration in nitric oxide-bound truncated Hemoglobin N (trHbN) of Mycobacterium tuberculosis are reported. From more than 100 ns of simulations the connectivity network involving the metastable states for localization of the O(2) ligand is built and analyzed. It is found that channel I is the primary entrance point for O(2) whereas channel II is predominantly an exit path although access to the protein active site is also possible. For O(2) a new site compared to nitric oxide, from which reaction with the heme group can occur, was found. As this site is close to the heme iron, it could play an important role in the dioxygenation mechanism as O(2) can remain there for hundreds of picoseconds after which it can eventually leave the protein, while NO is localized in Xe2. The present study supports recent experimental work which proposed that O(2) docks in alternative pockets than Xe close to the reactive site. Similar to other proteins, a phenylalanine residue (Phe62) plays the role of a gate along the access route in channel I. The most highly connected site is the Xe3 pocket which is a "hub" and free energy barriers between the different metastable states are ≈1.5 kcal mol(-1) which allows facile O(2) migration within the protein.

International audienceMolecular Dynamics simulations are used to investigate the structure and dynamics of an aqueous electrolyte (NaCl) confined within a nanomembrane, which consists of a nanopore with a diameter 3 nm having a negatively charged surface. Both nanomembranes with a diffuse charge and with local charges are considered (in both cases, two surface charge densities are considered, -0.9 e/nm(2) and -1.8 e/nm(2)). For all nanomembranes, significant layering of water and ions in the vicinity of the nanomembrane surface is observed. While the distribution of water and chloride ions is nearly insensitive to the nanomembrane charge and type, the arrangement of sodium cations within the nanomembrane depends on the system being considered. The water and ion density profiles in the nanomembranes are compared with the predictions of a modified Poisson-Boltzmann equation in which charge image, solvation effects, and dispersion interactions with the surface are taken into account [Huang et al. Langmuir, 2008, 24, 1442]. The self-diffusion coefficient for a given species is smaller than its bulk counterpart and is at most 75% of the bulk value. While the self-diffusion coefficients for water and sodium cations decrease with decreasing the overall negative charge of the nanomembrane, the self-diffusion coefficient for the chloride anions is nearly independent of the nanomembrane type and charge. We also estimate the dynamics of the confined aqueous electrolyte by calculating time correlation functions which allow estimating solvation, ion pairing, and residence times