Peptoids as a Chiral Stationary Phase for Liquid Chromatography: Insights from Molecular Dynamics Simulations.

Peptoids are peptide regioisomers with attractive structural tunability in terms of sequence and three-dimensional arrangement. Peptoids are foreseen to have a great potential for many diverse applications, including their utilization as a chiral stationary phase in chromatography. To achieve chiral recognition, a chiral side chain is required to allow specific interactions with a given enantiomer from a racemic mixture. One of the most studied chiral stationary phases, built with (S)-N-1-phenylethyl (Nspe) units, was shown to be successful in resolving racemic mixtures of binaphthyl derivatives. However, there is currently no description at the atomic scale of the factors favoring its enantioselectivity. Here, we take advantage of steered molecular dynamics simulations to mimic the elution process at the atomic scale and present evidence that the predominantly right-handed helical conformation of Nspe peptoids and their ability to form stronger hydrogen bonds with the (S) enantiomer are responsible for the chiral recognition of the popular chiral probe 2,2'-bihydroxy-1,1'-binaphthyl.

Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics.

Coarse-grained models have long been considered indispensable tools in the investigation of biomolecular dynamics and assembly. However, the process of simulating such models is arduous because unconventional force fields and particle attributes are often needed, and some systems are not in thermal equilibrium. Although modern molecular dynamics programs are highly adaptable, software designed for preparing all-atom simulations typically makes restrictive assumptions about the nature of the particles and the forces acting on them. Consequently, the use of coarse-grained models has remained challenging. Moltemplate is a file format for storing coarse-grained molecular models and the forces that act on them, as well as a program that converts moltemplate files into input files for LAMMPS, a popular molecular dynamics engine. Moltemplate has broad scope and an emphasis on generality. It accommodates new kinds of forces as they are developed for LAMMPS, making moltemplate a popular tool with thousands of users in computational chemistry, materials science, and structural biology. To demonstrate its wide functionality, we provide examples of using moltemplate to prepare simulations of fluids using many-body forces, coarse-grained organic semiconductors, and the motor-driven supercoiling and condensation of an entire bacterial chromosome.

Design Rules to Maximize Charge-Carrier Mobility along Conjugated Polymer Chains.

The emergence of polymeric materials displaying high charge-carrier mobility values despite poor interchain structural order has spawned a renewal of interest in the identification of structure-property relationships pertaining to the transport of charges along conjugated polymer chains and the subsequent design of optimized architectures. Here, we present the results of intrachain charge transport simulations obtained by applying a robust surface hopping algorithm to a phenomenological Hamiltonian parametrized against first-principles simulations. Conformational effects are shown to provide a clear signature in the temperature-dependent charge-carrier mobility that complies with recent experimental observations. We further contrast against molecular crystals the evolution with electronic bandwidth and electron-phonon interactions of the room-temperature mobility in polymers, showing that intrachain charge-carrier mobility values in excess of 100 cm2/(V s) can be achieved through a proper chemical engineering of the backbones.

3D to 2D reorganization of silver-thiol nanostructures, triggered by solvent vapor annealing.

Metal-organic composites are of great interest for a wide range of applications. The control of their structure remains a challenge, one of the problems being a complex interplay of covalent and supramolecular interactions. This paper describes the self-assembly, thermal stability and phase transitions of ordered structures of silver atoms and thiol molecules spanning from the molecular to the mesoscopic scale. Building blocks of molecularly defined clusters formed from 44 silver atoms, each particle coated by a monolayer of 30 thiol ligands, are used as ideal building blocks. By changing solvent and temperature it is possible to tune the self-assembled 3D crystals of pristine nanoparticles or, conversely, 2D layered structures, with alternated stacks of Ag atoms and thiol monolayers. The study investigates morphological, chemical and structural stability of these materials between 25 and 300 °C in situ and ex situ at the nanoscale by combining optical and electronic spectroscopic and scattering techniques, scanning probe microscopies and density-functional theory (DFT) calculations. The proposed wet-chemistry approach is relatively cheap, easy to implement, and scalable, allowing the fabricated materials with tuned properties using the same building blocks.

Surface-Induced Phase of Tyrian Purple (6,6'-Dibromoindigo): Thin Film Formation and Stability.

The appearance of surface-induced phases of molecular crystals is a frequently observed phenomenon in organic electronics. However, despite their fundamental importance, the origin of such phases is not yet fully resolved. The organic molecule 6,6'-dibromoindigo (Tyrian purple) forms two polymorphs within thin films. At growth temperatures of 150 °C, the well-known bulk structure forms, while at a substrate temperature of 50 °C, a surface-induced phase is observed instead. In the present work, the crystal structure of the surface-induced polymorph is solved by a combined experimental and theoretical approach using grazing incidence X-ray diffraction and molecular dynamics simulations. A comparison of both phases reveals that π-π stacking and hydrogen bonds are common motifs for the intermolecular packing. In-situ temperature studies reveal a phase transition from the surface-induced phase to the bulk phase at a temperature of 210 °C; the irreversibility of the transition indicates that the surface-induced phase is metastable. The crystallization behavior is investigated ex-situ starting from the sub-monolayer regime up to a nominal thickness of 9 nm using two different silicon oxide surfaces; island formation is observed together with a slight variation of the crystal structure. This work shows that surface-induced phases not only appear for compounds with weak, isotropic van der Waals bonds, but also for molecules exhibiting strong and highly directional hydrogen bonds.

Time-resolved, in situ DRIFTS/EDE/MS studies on alumina-supported rhodium catalysts: effects of ceriation and zirconiation on rhodium-CO interactions.

The effects of ceria and zirconia on the structure-function properties of supported rhodium catalysts (1.6 and 4 wt % Rh/γ-Al2O3) during CO exposure are described. Ceria and zirconia are introduced through two preparation methods: 1) ceria is deposited on γ-Al2O3 from [Ce(acac)3] and rhodium metal is subsequently added, and 2) through the controlled surface modification (CSM) technique, which involves the decomposition of [M(acac)x] (M=Ce, x=3; M=Zr, x=4) on Rh/γ-Al2O3. The structure-function correlations of ceria and/or zirconia-doped rhodium catalysts are investigated by diffuse reflectance infrared Fourier-transform spectroscopy/energy-dispersive extended X-ray absorption spectroscopy/mass spectrometry (DRIFTS/EDE/MS) under time-resolved, in situ conditions. CeOx and ZrO2 facilitate the protection of Rh particles against extensive oxidation in air and CO. Larger Rh core particles of ceriated and zirconiated Rh catalysts prepared by CSM are observed and compared with Rh/γ-Al2O3 samples, whereas supported Rh particles are easily disrupted by CO forming mononuclear Rh geminal dicarbonyl species. DRIFTS results indicate that, through the interaction of CO with ceriated Rh particles, a significantly larger amount of linear CO species form; this suggests the predominance of a metallic Rh phase.

Development and testing of a compact basis set for use in effective core potential calculations on rhodium complexes.

We present a set of effective core potential (ECP) basis sets for rhodium atoms which are of reasonable size for use in electronic structure calculations. In these ECP basis sets, the Los Alamos ECP is used to simulate the effect of the core electrons while an optimized set of Gaussian functions, which includes polarization and diffuse functions, is used to describe the valence electrons. These basis sets were optimized to reproduce the ionization energy and electron affinity of atomic rhodium. They were also tested by computing the electronic ground state geometry and harmonic frequencies of [Rh(CO)(2) µ-Cl](2) , Rh(CO)(2) ClPy, and RhCO (neutral and its positive, and negative ions) as well as the enthalpy of the reaction of [Rh(CO)(2) µ-Cl](2) with pyridine (Py) to give Rh(CO)(2) ClPy, at different levels of theory. Good agreement with experimental values was obtained. Although the number of basis functions used in our ECP basis sets is smaller than those of other ECP basis sets of comparable quality, we show that the newly developed ECP basis sets provide the flexibility and precision required to reproduce a wide range of chemical and physical properties of rhodium compounds. Therefore, we recommend the use of these compact yet accurate ECP basis sets for electronic structure calculations on molecules involving rhodium atoms.