Computational Spectroscopy and Reaction Dynamics

Physico- and bio-chemical processes on the femto- to picosecond time scale are ideally suited to be investigated with all-atom simulations. They include, amongst others, vibrational relaxation, ligand migration in sterically demanding environments (proteins, ices), or vibrational spectra. By comparing with experimental data, the results can be used to obtain an understanding of the mechanisms underlying the observations. Furthermore, most of these processes are sensitive to the intermolecular interactions. Therefore, detailed refinement of such interaction potentials is possible

Computational Two-Dimensional Infrared Spectroscopy without Maps : N-Methylacetamide in Water

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 similar to 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 SO fs range) followed by one or two longer time scales. In the case of three time scales, the intermediate one is approximate to 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 tau(1) = 50-100 fs range, the correlation time tau(c) 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

Structure and Dynamics of an Electrolyte Confined in Charged Nanopores

Molecular 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 <i>diffuse charge</i> and with <i>local charges</i> are considered (in both cases, two surface charge densities are considered, −0.9 e/nm² and −1.8 e/nm²). 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. <i>Langmuir</i>, <b>2008</b>, <i>24</i>, 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

Atomistic simulations of reactive processes in the gas- and condensed-phase

This review focuses on force-field-based approaches to investigate – through computer simulations – reactive processes in chemical and biological systems. Both, reactions in the gas-phase and in condensed-phase environments are discussed and opportunities and the potential for further developments are pointed out. Where available, results are compared with alternative methods and the advantages and drawbacks of the methods are compared. Particular applications include vibrationally and electronically induced (photo)dissociation of small molecules, proton transfer in the gas- and condensed phase and ligand un- and re-binding in proteins

Design and Piezoelectric Energy Harvesting Properties of a Ferroelectric Cyclophosphazene Salt

Cyclophosphazenes offer a robust and easily modifiable platform for a diverse range of functional systems that have found applications in a wide variety of areas. Herein, for the first time, it reports an organophosphazene-based supramolecular ferroelectric [(PhCH2 NH)6 P3 N3 Me]I, [PMe]I. The compound crystallizes in the polar space group Pc and its thin-film sample exhibits remnant polarization of 5 µC cm-2 . Vector piezoresponse force microscopy (PFM) measurements indicated the presence of multiaxial polarization. Subsequently, flexible composites of [PMe]I are fabricated for piezoelectric energy harvesting applications using thermoplastic polyurethane (TPU) as the matrix. The highest open-circuit voltages of 13.7 V and the maximum power density of 34.60 µW cm-2 are recorded for the poled 20 wt.% [PMe]I/TPU device. To understand the molecular origins of the high performance of [PMe]I-based mechanical energy harvesting devices, piezoelectric charge tensor values are obtained from DFT calculations of the single crystal structure. These indicate that the mechanical stress-induced distortions in the [PMe]I crystals are facilitated by the high flexibility of the layered supramolecular assembly

Molecular Engineering of Rigid Hydrogels Co-assembled from Collagenous Helical Peptides Based on a Single Triplet Motif

The potential of ultra-short peptides to self-assemble into well-ordered functional nanostructures makes them promising minimal components for mimicking the basic ingredient of nature and diverse biomaterials. However, selection and modular design of perfect de novo sequences are extremely tricky due to their vast possible combinatorial space. Moreover, a single amino acid substitution can drastically alter the supramolecular packing structure of short peptide assemblies. Here, we report the design of rigid hybrid hydrogels produced by sequence engineering of a new series of ultra-short collagen-mimicking tripeptides. Connecting glycine with different combinations of proline and its post-translational product 4-hydroxyproline, the single triplet motif, displays the natural collagen-helix-like structure. Improved mechanical rigidity is obtained via co-assembly with the non-collagenous hydrogelator, fluorenylmethoxycarbonyl (Fmoc) diphenylalanine. Characterizations of the supramolecular interactions that promote the self-supporting and self-healing properties of the co-assemblies are performed by physicochemical experiments and atomistic models. Our results clearly demonstrate the significance of sequence engineering to design functional peptide motifs with desired physicochemical and electromechanical properties and reveal co-assembly as a promising strategy for the utilization of small, readily accessible biomimetic building blocks to generate hybrid biomolecular assemblies with structural heterogeneity and functionality of natural materials

Mapping the deformability of natural and designed cellulosomes in solution

International audienceBackground Natural cellulosome multi-enzyme complexes, their components, and engineered ‘designer cellulosomes’ (DCs) promise an efficient means of breaking down cellulosic substrates into valuable biofuel products. Their broad uptake in biotechnology relies on boosting proximity-based synergy among the resident enzymes, but the modular architecture challenges structure determination and rational design.Results We used small angle X-ray scattering combined with molecular modeling to study the solution structure of cellulosomal components. These include three dockerin-bearing cellulases with distinct substrate specificities, original scaffoldins from the human gut bacterium Ruminococcus champanellensis (ScaA, ScaH and ScaK) and a trivalent cohesin-bearing designer scaffoldin (Scaf20L), followed by cellulosomal complexes comprising these components, and the nonavalent fully loaded Clostridium thermocellum CipA in complex with Cel8A from the same bacterium. The size analysis of R g and D max values deduced from the scattering curves and corresponding molecular models highlight their variable aspects, depending on composition, size and spatial organization of the objects in solution.Conclusions Our data quantifies variability of form and compactness of cellulosomal components in solution and confirms that this native plasticity may well be related to speciation with respect to the substrate that is targeted. By showing that scaffoldins or components display enhanced compactness compared to the free objects, we provide new routes to rationally enhance their stability and performance in their environment of action