Atomistic molecular dynamics simulations of chemical force microscopy

Chemical force microscopy and related force measurement techniques have emerged as powerful tools for studying fundamental interactions central to understanding adhesion and tribology at the molecular scale. However, detailed interpretation of these interactions requires knowledge of chemical and physical processes occurring in the region of the tip-sample junction that experiments cannot provide, such as atomic-scale motions and distribution of forces. In an effort to address some of these open issues, atomistic molecular dynamics simulations were performed modeling a chemical force microscope stylus covered with a planar C12 alkylthiolate self-assembled monolayer (SAM) interacting with a solid wall. A complete loading-unloading sequence was simulated under conditions of near-constant equilibrium, approximating the case of infinitely slow tip motion. In the absence of the solid wall, the stylus film existed in a fluid state with structural and dynamic properties similar to those of the analogous planar SAM at an elevated temperature. When the wall was brought into contact with the stylus and pressed against it, a series of reversible changes occurred culminating with solidification of the SAM film at the largest compressive force. During loading, the chemical composition of the contact changed, as much of the film's interior was exposed to the wall. At all tip heights, the distribution of forces within the contact zone was uneven and subject to large local fluctuations. Analysis using the Johnson-Kendall-Roberts, Derjaguin-Muller-Toporov, and Hertz contacts mechanics models revealed significant deviations from the simulation results, with the JKR model providing best overall agreement. Some of the discrepancies found would be overlooked in an actual experiment, where, unlike the simulations, contact area is not separately known, possibly producing a misleading or incorrect interpretation of experimental results. These shortcomings may be improved upon by using a model that correctly accounts for the finite thickness of the compliant components and nonlinear elastic effects.     

Self-assembling structures of long-chain phenyl glucoside influenced by the introduction of double bonds

Four long-chain phenyl glucoside amphiphiles possessing a saturated or unsaturated long alkyl chain group as the self-assembling unit of a highly organized molecular architecture were synthesized. Their self-assembling properties were investigated by EF-TEM, SEM, CD, FT-IR, and XRD. Compound 2 possessing one double bond in the lipophilic portion showed twisted helical fibers, which formed a bilayered structure with a 3.59 nm period, while compound 3 showed the helical ribbons and left-handed nanotubular structures with 150-200 nm inner diameters and ca. 20 nm of wall. Very interestingly, compound 4 possessing three double bonds showed a nanotubular structure with ca. 70 nm of inner diameter through a helical ribbon, which formed a loose bilayered structure with 4.62 nm. These results indicate that self-assembling properties strongly depend on the number of cis double bonds.     

The synthesis of peptides and proteins containing non-natural amino acids

Methods for the incorporation of non-natural amino acids into proteins have advanced significantly over recent years and in this tutorial review we aim to give a general overview of the area. These techniques offer the possibility of modulating the structures and functions of proteins and thus permit the generation of novel designed systems for both biocatalytic and mechanistic studies. Four complementary approaches are discussed in detail along with examples of their application. The advantages and disadvantages of each technique are also discussed.     

A CONVENIENT IRRADIATION CELL FOR FERRIOXALATE ACTINOMETRY

Abstract— A calibrated volumetric optical cuvette is described which both simplifies the technique and improves the precision of potassium ferrioxalate actinometry. The cuvette is used both for irradiation of the actinometer solution and for in situ dilution and chemical developing of the irradiated aliquot. The technique permits all but one manipulation to be carried out in total darkness, thus protecting the actinometer solutions from ambient light. The method can be extended to any actinometric procedure and the volumetric cuvettes are very useful in a variety of other spectrophotometric applications.     

Coulomb interaction in the one-dimensional free-electron model

In the limiting case of the free-electron theory where the electron motion is constricted to one dimension, the one-dimensional Coulomb potential gives rise to divergent interaction integrals. It is shown that a proposal by Olszewski to remove the divergenses by first evaluating the integrals in the three-dimensional case and then passing to the limit of one dimension only is incorrect, and that convergent integrals may only be obtained by suitably modifying the original one-dimensional Coulomb potential between particles.

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Zusammenfassung In dem Grenzfall des Modells der Freien Elektronen, in dem die Elektronenbewegung auf eine Dimension eingeschrÄnkt ist, ergibt das eindimensionale Coulombpotential divergente Wechselwirkungsintegrale. Es wird gezeigt, da\ ein Vorschlag von Olszewski zur Aufhebung der Divergenz durch übergang von dreidimensionalen zum eindimensionalen Integral falsch ist. Konvergente Integrale können nur durch geeignete VerÄnderung des ursprünglichen eindimensionalen Coulombpotentials erhalten werden.

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Résumé Dans le cas limite de la théorie de l'électron libre à une dimension, le potentiel coulombien donne lieu à des intégrales d'interaction divergentes. On montre que la proposition d'Oszewski pour éliminer les divergences, en évaluant d'abord les intégrales tridimensionnelles et en passant à la limite à une dimension, est incorrecte et que des intégrales convergentes ne peuvent Être obtenues qu'en modifiant le potentiel coulombien unidimensionnel entre particules.

     

SCF-π-electron calculations using orthogonalised atomic orbitals

Modifications of the SCF-LCAO-π-MO method analysed in the previous paper are described in which provision is made for the incorporation of Variable Bond Order and Variable Electronegativity procedures. A comparison is made with the results of other π-electron calculations and values are reported for twenty hydrocarbon systems.     

Collision-induced dissociations of substituted benzyl anions: Deprotonated 2-Phenyl-1,3-dithiane

Deprotonated 2-phenyl-1,3-dithiane undergoes competitive losses of H˙, C₃H₆ C₂H₄S, C₃H₄S, C₇H₆S, C₁₀H₁₀ and C₁₀H₁₀S upon collisional activation. The elimination of H occurs from the phenyl ring. The loss of C₃H₆ occurs by simple cleavage of the dithiane ring. All other processes involve specific proton transfer followed by either cleavage or internal nucleophilic displacement.     

An efficient synthesis of cyercene A

An efficient approach to the total synthesis of the marine derived polypropionate cyercene A is described. A key feature of the synthesis is the development of methodology for the diastereoselective Wadsworth-Emmons type condensation of a functionalised γ-pyrone unit.