Physical Chemistry Chemical Physics

doi: 10.1039/b820249bpmid: N/A

doi: 10.1039/b820250hpmid: N/A

doi: 10.1039/b820251fpmid: N/A

Bénichou, O.; Loverdo, C.; Moreau, M.; Voituriez, R.

doi: 10.1039/b811447cpmid: 19039339

Various examples of biochemical reactions in cells, such as DNA/protein interactions, reveal that in extremely diluted regimes reaction paths are not always simple brownian trajectories. They can rather be qualified as intermittent, since they combine slow diffusion phases on one hand and a second mode of faster transport on the other hand, which can be either a faster diffusion mode, as in the case of DNA-binding proteins, or a ballistic mode powered by molecular motors in the case of intracellular transport. In this article, we introduce simple theoretical models which permit to calculate explicitly the reaction rates for reactions limited by intermittent transport. This approach shows quantitatively that intermittent reaction pathways are actually very efficient, since they permit to significantly increase the reaction rates, which could explain why they are observed so often. Moreover, we give theoretical arguments which suggest that intermittent transport could also be useful for in vitro chemistry. Indeed, we show that intermittent transport naturally pops up in the context of reaction at interfaces, where reactants combine surface diffusion phases and bulk excursions, and could permit to enhance reactivity. In this case, adjusting chemically the affinity of reactants with the interface makes possible to optimize the reaction rate.

Nadykto, Alexey B.; Yu, Fangqun; Herb, Jason

doi: 10.1039/b807415apmid: 19039340

The role of the ion sign in the binary H2SO4–H2O nucleation remains unclear despite significant progress in both theory and instrumentation achieved within the last decade. In order to advance the understanding of ion nucleation phenomena, a quantum-chemical study of binary sulfuric acid–water ionic clusters nucleating in the atmosphere has been carried out. We found a profound sign effect caused by the pronounced difference in the structure and properties of clusters formed over core ions of different sign. The sign preference is found to be controlled by two somewhat competing factors: hydration and sulfuric acid attachment. While hydration of cations is clearly favorable, the affinity of sulfuric acid, which largely controls the nucleation intensity, to negative ions is much higher than that to positive ions. The presence of a very large difference in the affinity of sulfuric acid between positive and negative ions suggests that nucleation of negative ions is likely favorable.

Yan, Shihai; Joo Cho, Seung; Joo Lee, Sang; Kang, Sunwoo; Paek, Kyungsoo; Yong Lee, Jin

doi: 10.1039/b805821kpmid: 19039341

Host molecules effectively prefer to recognize F− ion rather than H2O through the upper rim, utilizing strong C–H (N–H)⋯F− interactions. The electropositive field space (“electropositive field space”) at the lower rim of the host molecules can also act as a good binding site for small anions such as F−. The electron withdrawing substituent at the para-position (X) makes the C(N)–Ha⋯F− and C(N)–Ha⋯O interactions much enhanced. The calculated vibrational frequencies and NMR chemical shifts are consistent with experimental trends.

Martín-Calvo, Ana; García-Pérez, Elena; Manuel Castillo, Juan; Calero, Sofia

doi: 10.1039/b807470dpmid: 19039342

We use Monte Carlo simulations to study the adsorption and separation of the natural gas components in IRMOF-1 and Cu-BTC metal–organic frameworks. We computed the adsorption isotherms of pure components, binary, and five-component mixtures analyzing the siting of the molecules in the structure for the different loadings. The bulk compositions studied for the mixtures were 50 : 50 and 90 : 10 for CH4–CO2, 90 : 10 for N2–CO2, and 95 : 2.0 : 1.5 : 1.0 : 0.5 for the CH4–C2H6–N2–CO2–C3H8 mixture. We choose this composition because it is similar to an average sample of natural gas. Our simulations show that CO2 is preferentially adsorbed over propane, ethane, methane and N2 in the complete pressure range under study. Longer alkanes are favored over shorter alkanes and the lowest adsorption corresponds to N2. Though IRMOF-1 has a significantly higher adsorption capacity than Cu-BTC, the adsorption selectivity of CO2 over CH4 and N2 is found to be higher in the latter, proving that the separation efficiency is largely affected by the shape, the atomic composition and the type of linkers of the structure.

Noei, Heshmat; Qiu, Hengshan; Wang, Yuemin; Löffler, Elke; Wöll, Christof; Muhler, Martin

doi: 10.1039/b811029hpmid: 19039343

The interaction of water with ZnO nanoparticles has been studied by means of diffuse reflectance infrared spectroscopy (DRIFTS) and ultra-high vacuum FTIR spectroscopy (UHV-FTIRS). Exposing clean ZnO powder to water at 323 K leads to both molecular and dissociative adsorption of H2O forming a number of hydroxyl species. All the OH bands are clearly identified by the adsorption of D2O showing the expected isotopic shifts. According to the vibrational and thermal stability data obtained from single crystal surfaces, the OH species observed on ZnO nanoparticles are identified as follows: (1) OH group (3620 cm−1) on the polar O–ZnO(0001̄) surface formed via dissociation of water on oxygen vacancy sites; (2) partial dissociation of water on the mixed-terminated ZnO(101̄0) surface yielding coexistent H2O (∼3150 and 3687 cm−1) and OH species (3672 cm−1), where the molecularly adsorbed H2O is further identified by the characteristic scissoring mode at 1617 cm−1; (3) isolated OH species (3639 and 3656 cm−1) formed on the mixed-terminated ZnO(101̄0) surface; (4) interaction of water with defects forming hydroxyl (or O–H⋯O) species (3564 and 3448 cm−1).

Ruth, Albert A.; Lynch, Kieran T.

doi: 10.1039/b809591dpmid: 19039344

An improvement of conventional attenuated total reflection (ATR) spectroscopy is demonstrated by applying an incoherent broadband light source (short-arc Xe-lamp) in a cavity-enhanced evanescent-wave absorption method. With this novel approach the absorption spectra of several metallo-octaethyl porphyrins (palladium (PdOEP), platinum (PtOEP) and zinc (ZnOEP)) in thin acetone solution layers and on a fused silica (FS) surface are studied between ≈390 and 625 nm. The time dependence of the evaporation process of the solution on the FS surface is described. The maximum sensitivity of the setup is estimated at approximately 2 × 10−5 per pass, which translates into a minimal detectable surface density of less than 2 × 10−3 monolayers for the porphyrins studied (based on the strong absorption in the Soret bands). Changes of surface and solution spectra are characterised and discussed on the basis of observed band broadenings and spectral shifts. For Pd- and PtOEP the changes of spectral feature can be interpreted with respect to J-aggregate formation supported by polarization dependent measurements. The reason for an observed blue-shift of ca. 10 nm for the Soret band in ZnOEP in combination with a large red-shift of the Q-bands (11 nm for Q1 and 18 nm for Q2) is discussed.

Huang, Chen; Carter, Emily A.

doi: 10.1039/b810407gpmid: 19039345

One obstacle in orbital-free density functional theory (OF-DFT) is the lack of accurate and transferable local pseudopotentials (LPSs). In this work, we build high quality LPSs by inverting Kohn–Sham (KS) equations on bulk valence electron densities to obtain an atom-centered local pseudopotential. With this approach, we build LPSs for Mg, Al, and Si, and then test them in KS DFT calculations of static bulk properties for several Mg, Al, and Si bulk structures as well as β″-Al3Mg. Our Mg, Al, and Si LPSs produce correct ground state properties and phase orderings. These LPSs are then tested in KS-DFT calculations of surface energies for several low-index Mg and Al surfaces, point defect properties in hexagonal-close-packed (hcp) Mg, face-centered cubic (fcc) Al, and diamond Si, and stacking fault energies in fcc Al. All of these LPS results agree quantitatively with the results from nonlocal pseudopotentials with errors less than or equal to 40 meV per atom. Finally, we perform OF-DFT calculations for various Mg and Al structures, employing the Wang–Govind–Carter (WGC) nonlocal kinetic energy density functional (KEDF). The OF-DFT results generally agree well with the corresponding KS-DFT results. With our new Mg and Al LPSs and the WGC KEDF, OF-DFT now provides a practical method for accurate, large-scale first principles simulations of main group metals and their alloys.