We report calculations of the Raman and Raman optical activity (ROA) spectra of methyl-β-D-glucose utilizing density functional theory combined with molecular dynamics (MD) simulations to provide an explicit hydration environment. This is the first report of such combination of MD simulations with ROA ab initio calculations. We achieve a significant improvement in accuracy over the more commonly used gas phase and polarizable continuum model (PCM) approaches, resulting in an excellent level of agreement with the experimental spectrum. Modeling the ROA spectra of carbohydrates has until now proven a notoriously difficult challenge due to their sensitivity to the effects of hydration on the molecular vibrations involving each of the chiral centers. The details of the ROA spectrum of methyl-β-D-glucose are found to be highly sensitive to solvation effects, and these are correctly predicted for the first time including those originating from the highly sensitive low frequency vibrational modes. This work shows that a thorough consideration of the role of water is pivotal for understanding the vibrational structure of carbohydrates and presents a new and powerful tool for characterizing carbohydrate structure and conformational dynamics in solution.

We demonstrate that nanotubular networks formed by enzyme-triggered self-assembly of Fmoc-L3 (9-fluorenylmethoxycarbonyl-tri-leucine) show significant charge transport. FT-IR, fluorescence spectroscopy and wide angle X-ray scattering (WAXS) data confirm formation of beta-sheets that are locked together viapi-stacking interactions. Molecular dynamics simulations confirmed the pi-pi stacking distance between fluorenyl groups to be 3.6-3.8 A. Impedance spectroscopy demonstrated that the nanotubular xerogel networks possess minimum sheet resistances of 0.1 MOmega/sq in air and 500 MOmega/sq in vacuum (pressure: 1.03 mbar) at room temperature, with the conductivity scaling linearly with the mass of peptide in the network. These materials may provide a platform to interface biological components with electronics.

Imidazole is a small but important molecule occurring as a structure fragment in systems from amino acids, over ionic liquids, to synthetic polymers. Here we focus on the structure and dynamics of imidazole in water at ambient conditions, using both radial and spatial distribution functions. Molecular dynamics simulations were carried out for various imidazole concentrations, using a traditional point-charge potential and a high-rank multipolar potential. The difference in the description of the electrostatics leads to sizable quantitative differences (e.g., the diffusion coefficient) but also qualitative differences in the local structure. In contrast to a point-charge potential, the multipolar potential favors hydrogen-bonded chainlike imidazole dimers over stacked dimers.

Rigid body molecular dynamics simulations were carried out on pure liquid imidazole at four different temperatures and at 1 atm. Imidazole, which is important both in life science and materials science, is one of the simplest molecules to possess both a lone pair and a π system. These two features are known to benefit from multipolar electrostatics. Here the electrostatic interaction is governed by atomic multipole moments obtained from topologically partitioned ab initio electron densities. The non-electrostatic terms are modeled with Lennard-Jones parameters adjusted to fit the experimental liquid density. All σ values are incrementally increased by one single scaling factor. We report on how the presence of multipolar electrostatics influences the local structure, dynamics and thermodynamics of the liquid compared to electrostatics by atomic point charges. The point charge force field exaggerates the number of π-stacked dimers in the liquid, and underestimates the number of hydrogen-bonded dimers. The effect of the temperature on the local structure of liquid imidazole was analysed using radial and spatial distribution functions.

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. The importance of multipole moments when describing water and hydrated amino acid cluster geometryPaul Popelier To cite this version:Paul Popelier.

Digital rock technology and pore-scale physics have become increasingly relevant topics in a wide range of porous media with important applications in subsurface engineering. This technology relies heavily on images of pore space and pore-level fluid distribution determined by X-ray microcomputed tomography (micro-CT). Digital images of pore space (or pore-scale fluid distribution) are typically obtained as gray-level images that first need to be processed and segmented to obtain the binary images that uniquely represent rock and pore (including fluid phases). This processing step is not trivial. Rock complexity, image quality, noise, and other artifacts prohibit the use of a standard processing workflow. Instead, an array of strategies of increasing sophistication has been developed. Typical processing pipelines consist of filtering, segmentation, and postprocessing steps. For each step, various choices and different options exist. This makes selection and validation of an optimum processing pipeline difficult. Using Darcy-scale quantities as a benchmark is not a good option because of rock heterogeneity and different scales of observation. Here, we present a conceptual workflow where noisy images are derived from a ground truth by systematically including typical image artifacts and noise. Artifacts and noise are not simply added to the images. Instead, tomographic forward projection and reconstruction steps are used to incorporate the artifacts in a physically correct way. A proof of concept of this workflow is demonstrated by comparing seven different image-segmentation pipelines ranging from absolute thresholding to a machine-learning approach (Trainable Weka Segmentation). The Trainable Weka Segmentation showed the best performance of the tested methods.

We build on previous work [S. Y. Liem and P. L. A. Popelier, J. Chem. Theory Comput. 4, 353 (2008)], where for the first time, a high-rank multipolar electrostatic potential was used in molecular dynamics simulations of liquid water at a wide range of pressures and temperatures, and using a multipolar Ewald summation. Water is represented as a rigid body, with atomic multipole moments defined by quantum chemical topology partitioning its gas phase electron density. The effect of the level of theory on the local structure of liquid water is systematically addressed. Values for Lennard-Jones (LJ) parameters are optimized, for both oxygen and hydrogen atoms, against bulk properties. The best LJ parameters were then used in a set of simulations at 30 different temperatures (1 atm) and another set at 11 different pressures (at 298 K). Inclusion of the hydrogen LJ parameters significantly increases the self-diffusion coefficient. The behavior of bulk properties was studied and the local water structure analyzed by both radial and spatial distribution functions. Comparisons with familiar point-charge potentials, such as TIP3P, TIP4P, TIP5P, and simple point charge, show the benefits of multipole moments.

We examine the performance of the general AMBER force field (GAFF) and the CHARMM general force field (CGenFF) within the context of capturing the liquid–vapor saturation properties of naphthalene derivatives. Molecular simulation is employed to construct phase diagrams for naphthalene, tetralin, trans-decalin, quinolone, 1-methylnaphthalene, 1-naphthol, indole, benzo­[b]­furan, and benzo­[b]­thiophene over a range of temperatures that spans from room temperature to the critical point. A general histogram-based approach introduced by Rane and co-workers (J. Chem. Theory Comput. 2013, 9, 2552) is used to calculate saturated densities, vapor pressures, and enthalpies of vaporization. Results for GAFF and CGenFF are compared to experimental data, available correlations, and literature results for the transferable potentials for phase equilibria force field (TraPPE). GAFF and CGenFF provide reasonable descriptions for the saturation properties of the naphthalene derivatives studied. Specifically, GAFF and CGenFF capture the critical temperature to within average errors of 5.6 and 6.3%, respectively, and the boiling temperature to within average errors of 4.0 and 4.4%, respectively. The models generally produce estimates of the critical temperature and boiling temperature that are low relative to experiment. The two models provide a relatively consistent description of the six molecules studied containing two fused six-membered rings, whereas their description of the three molecules examined containing fused five- and six-membered rings often differs appreciably. In terms of an overall comparison, our results do not indicate that one force field clearly outperforms the other.