Molybdenum disulfide (MoS2) of single- and few-layer thickness was exfoliated on SiO2/Si substrate and characterized by Raman spectroscopy. The number of S−Mo−S layers of the samples was independently determined by contact-mode atomic force microscopy. Two Raman modes, E12g and A1g, exhibited sensitive thickness dependence, with the frequency of the former decreasing and that of the latter increasing with thickness. The results provide a convenient and reliable means for determining layer thickness with atomic-level precision. The opposite direction of the frequency shifts, which cannot be explained solely by van der Waals interlayer coupling, is attributed to Coulombic interactions and possible stacking-induced changes of the intralayer bonding. This work exemplifies the evolution of structural parameters in layered materials in changing from the three-dimensional to the two-dimensional regime.

/pdf/anomalous-lattice-vibrations-of-single-and-few-layer-mos2-1w8dp2s904.pdf

Anomalous lattice vibrations of single- and few-layer MoS2.

Single molecules of double-stranded DNA (dsDNA) were stretched with force-measuring laser tweezers. Under a longitudinal stress of approximately 65 piconewtons (pN), dsDNA molecules in aqueous buffer undergo a highly cooperative transition into a stable form with 5.8 angstroms rise per base pair, that is, 70% longer than B form dsDNA. When the stress was relaxed below 65 pN, the molecules rapidly and reversibly contracted to their normal contour lengths. This transition was affected by changes in the ionic strength of the medium and the water activity or by cross-linking of the two strands of dsDNA. Individual molecules of single-stranded DNA were also stretched giving a persistence length of 7.5 angstroms and a stretch modulus of 800 pN. The overstretched form may play a significant role in the energetics of DNA recombination.

/pdf/overstretching-b-dna-the-elastic-response-of-individual-16c6cujz0e.pdf

Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules

Combined quantum-mechanics/molecular-mechanics (QM/MM) approaches have become the method of choice for modeling reactions in biomolecular systems. Quantum-mechanical (QM) methods are required for describing chemical reactions and other electronic processes, such as charge transfer or electronic excitation. However, QM methods are restricted to systems of up to a few hundred atoms. However, the size and conformational complexity of biopolymers calls for methods capable of treating up to several 100,000 atoms and allowing for simulations over time scales of tens of nanoseconds. This is achieved by highly efficient, force-field-based molecular mechanics (MM) methods. Thus to model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region (e.g., substrates and co-factors in an enzymatic reaction) and an MM treatment for the surroundings (e.g., protein and solvent). The resulting schemes are commonly referred to as combined or hybrid QM/MM methods. They enable the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.

QM/MM Methods for Biomolecular Systems

Ordered mesoporous materials in catalysis

1. Introduction 46372. Theoretical Methodologies and Simulation Tools 46402.1. Ab Initio Quantum Chemistry 46412.2. Molecular Dynamics 46422.2.1. Classical Molecular Dynamics and MonteCarlo Simulations46432.2.2. Empirical Valence Bond Models 46442.2.3. Ab Initio Molecular Dynamics (AIMD) 46452.3. Poisson−Boltzmann Theory 46452.4. Nonequilibrium Statistical Mechanical IonTransport Modeling46462.5. Dielectric Saturation 46473. Transport Mechanisms 46483.1. Proton Conduction Mechanisms 46483.1.1. Homogeneous Media 46483.1.2. Heterogeneous Systems (ConfinementEffects)46553.2. Mechanisms of Parasitic Transport 46613.2.1. Solvated Acidic Polymers 46613.2.2. Oxides 46654. Phenomenology of Transport inProton-Conducting Materials for Fuel-CellApplications46664.1. Hydrated Acidic Polymers 46664.2. PBI−H

/pdf/transport-in-proton-conductors-for-fuel-cell-applications-3gvrtpo4jv.pdf

Transport in proton conductors for fuel-cell applications: simulations, elementary reactions, and phenomenology.

The nature of the species formed when water interacts with Bronsted acid sites in a microporous solid acid catalyst, HSAPO-34, was studied by powder neutron diffraction and infrared spectroscopy. Previous infrared and computational studies had failed to unambiguously establish whether water is protonated to form hydronium (H3O+) ions or is merely hydrogen-bonded to acid sites inside the zeolite. Our experiments clearly showed that both species are present: An H3O+ ion is found in the eight-ring channel of the zeolite and a second water molecule is hydrogen-bonded to an acid site on the six-ring.

https://science.sciencemag.org/content/sci/271/5250/799.full.pdf

On the Nature of Water Bound to a Solid Acid Catalyst

TITANIUM occurs widely in the Earth's crust, traces of it being present in most rocks, soils and clays. It is estimated that titanosilicate minerals alone number more than 100; but, remarkably, in only one of these does the Ti(IV) ion take up fivefold coordination. This is in fresnoite1 (Ba2TiSi2O8), which contains square-pyramidal TiO5 polyhedra. In the course of a programme2–11 to produce new microporous and mesoporous solid catalysts, we have discovered an unusual non-centrosymmetric, tetragonal layered solid (Na4Ti2Si8O22·4H2O), designated JDF-L1, which promises to have interesting applications in materials chemistry. This material contains five-coordinate Ti(IV) ions in the form of TiO5 square pyramids in which each of the vertices of the base is linked to SiO4 tetrahedra [TiO·O4(SiO3)4] to form continuous sheets. The structure was solved by applying ab initio methods to data obtained by X-ray absorption spectroscopy and powder X-ray diffraction. The interlamellar Na+ ions of JDF-L1 are replaceable by protonated amines, and after treatment with a mixture of dilute acid and hydrogen peroxide the parent solid selectively oxidizes phenol to quinone. These results indicate that the material should have useful catalytic, intercalation and ion-exchange properties analogous to those of aluminosilicate clays.

Synthesis and structure of a layered titanosilicate catalyst with five-coordinate titanium

The structure of acid sites in cobalt-substituted aluminophosphates (AlPOs) catalysts has been investigated, with EXAFS spectroscopy. Data obtained, using in situ methods, for the Co K-edge spectra of cobalt-substituted AlPO-5, AlPO-18, AlPO-36, and APSO-44 in as-prepared, calcined, and reduced states yield the local structure of the Co ions. Whereas the as-prepared materials clearly contain Co(II) ions in regular four-coordinated sites, complex behavior is exhibited by their calcined analogues, with essentially complete oxidation of Co(II) to Co(III) in CoAlPO-18, with the local coordination of the high-spin Co(III) being distorted. By contrast incomplete oxidation of the Co(II) is observed for CoAlPO-5 and CoAlPO-36. A combination of EXAFS data analysis with the results of computer modeling studies suggests that this behavior is interpretable in terms of the formation of oxygen vacancies by dehydroxylation which lead to undercoordinated Lewis acid, Co(II) sites. IR data of the reduced samples reveal the...

X-ray absorption spectroscopic study of Bronsted, Lewis, and redox centers in cobalt-substituted aluminum phosphate catalysts

One of the disappointments to emerge from the recent intensive study of low-dimensional solids has been the increasing realization that relatively few of the investigated systems exhibit genuine one-or two-dimensional behaviour. Measured electronic and optical properties of crystalline and amorphous low-dimensional solids signify that there is significant interchain or interlayer perturbation. One possible way of eliminating such perturbation in so-called one-dimensional systems is to accommodate individual chains within the pores of a host dielectric material, which, preferentially, should itself be crystalline and well ordered. Here we report the use of combined high-resolution electron microscopy and computer simulation, to achieve the successful incorporation of chains of selenium into a synthetic mordenite, a zeolite which has one-dimensional channels (diameter ∼7 A) running parallel to its c-axis. Remarkably, the uptake of selenium, which converts the white mordenite into an orange colour, occurs in a patchwise fashion leading to domains of occupied channels. The incorporation is readily accomplished thermally, and can be effected with a range of other zeolitic hosts, including ZSM-5, ZSM-23 and zeolites L and Y.

J. M. Thomas

Papers

On the Nature of Water Bound to a Solid Acid Catalyst

Synthesis and structure of a layered titanosilicate catalyst with five-coordinate titanium

X-ray absorption spectroscopic study of Bronsted, Lewis, and redox centers in cobalt-substituted aluminum phosphate catalysts

Isolating individual chains of selenium by incorporation into the channels of a zeolite

L3/L2 white-line intensity ratios in the electron energy-loss spectra of 3d transition-metal oxides