Dissipative Catalysis with a Molecular Machine

We report on catalysis by a fuel‐induced transient state of a synthetic molecular machine. A [2]rotaxane molecular shuttle containing secondary ammonium/amine and thiourea stations is converted between catalytically inactive and active states by pulses of a chemical fuel (trichloroacetic acid), which is itself decomposed by the machine and/or the presence of additional base. The ON‐state of the rotaxane catalyzes the reduction of a nitrostyrene by transfer hydrogenation. By varying the amount of fuel added, the lifetime of the rotaxane ON‐state can be regulated and temporal control of catalysis achieved. The system can be pulsed with chemical fuel several times in succession, with each pulse activating catalysis for a time period determined by the amount of fuel added. Dissipative catalysis by synthetic molecular machines has implications for the future design of networks that feature communication and signaling between the components.     

Investigation of binding event perturbations caused by elevated QCM-D oscillation amplitude

We report measurements with the quartz crystal microbalance with dissipation monitoring (QCM-D) technique, with focus on how the shear oscillation amplitude of the sensor surface influences biorecognition binding events. Technically, this is made as reported recently (M. Edvardsson, M. Rodahl, B. Kasemo, F. H??k, Anal. Chem., 2005, 77(15), 4918-4926) by operating the QCM in dual frequency mode; one harmonic (n = n1) is utilized for continuous excitation of the QCM-D sensor at resonance at variable driving amplitudes (1-10 V), while the second harmonic (n not equaln(1)) is used for combined f and D measurements. By using one harmonic as a "probe" and the other one as an "actuator", elevated amplitudes can be used to perturb - or activate - binding reactions in a controlled way, while simultaneously maintaining the possibility of probing the adsorption and/or desorption events in a non-perturbative manner using combined f and D measurements. In this work we investigate the influence of oscillation amplitude variations on the binding of NeutrAvidin-modified polystyrene beads (slashed circle approximately 200 nm) to a planar biotin-modified lipid bilayer supported on an SiO2-modified QCM-D sensor. These results are further compared with data on an identical system, except that the NeutrAvidin-biotin recognition was replaced by fully complementary DNA hybridization. Supported by micrographs of the binding pattern, the results demonstrate that there exists, for both systems, a unique critical oscillation amplitude, A(c), below which binding is unaffected by the oscillation, and above which binding is efficiently prevented. Associated with A(c), there is a critical crystal radius, r(c), defining the central part of the crystal where binding is prevented. From QCM-D data, A(c) for the present system was estimated to be approximately 6.5 nm, yielding a value of r(c) of approximately 3 mm--the latter number was nicely confirmed by fluorescent- and dark-field micrographs of the crystal. Furthermore, the fact that A(c) is observed to be identical for the two types of biorecognition reactions suggests that it is neither the strength, nor the number of contact points, that determine the amplitude at which binding is prevented. Rather, particle size seems to be the determining parameter.     

Exploring the potential energy surface of retinal, a comparison of the performance of different methods

The ground state structure of retinal has been investigated. We found that DFT and CASSCF produce different results for the bond length alternation in a model system of retinal. Quantum mechanics/molecular mechanics calculations including the closest surrounding amino acids have been performed, using DFT and CASSCF to calculate the structure of retinal in the protein cavity. The planarity of the retinal molecule is affected by the surrounding protein. DFT and CASSCF produce different twist angles. The difference between CASSCF and DFT appears to be related to the positively charged nitrogen of the Schiff base, which leads to different pi-bond orders produced by the two methods.     

Cubic phase nanoparticles (Cubosome): principles for controlling size, structure, and stability

Methods and compositions for producing lipid-based cubic phase nanoparticles were first discovered in the 1990s. Since then a number of studies have been presented, but little is known about how to control key properties such as particle size, morphology, and stability of cubic phase dispersions. In the present work we give examples of how these properties can be tuned by composition and processing conditions. Importantly we show that stable particle dispersions with consistent size and structure can be produced by a simple processing scheme comprising a homogenization and heat treatment step.     

Decoupling of diffusion from structural relaxation and spatial heterogeneity in a supercooled simple liquid

We report a molecular dynamics simulation of a simple monatomic glass-forming liquid. It is shown that transition to deeper minima in the energy landscape under supercooling results in the formation of icosahedrally structured domains with distinctly slow diffusion which grow with cooling in a low-dimensional manner and percolate around T(c), the critical temperature of the mode-coupling theory. Simultaneously, a sharp slowing down of the structural relaxation relative to diffusion is observed. It is concluded that this effect cannot be accounted for by the spatial variation in atomic mobility. The low-dimensional clustering is discussed as a possible mechanism of fragility.     

Femtosecond photomagnetic switching of spins in ferrimagnetic garnet films

We demonstrate that intense laser pulses can be used to directly control the spins in ferrimagnetic garnet films. Through an ultrafast and nonthermal photomagnetic effect the magnetocrystalline anisotropy is modified to create a new long-lived equilibrium orientation for the magnetization. Simultaneously, the magnetization is rotated into this new state by precession in a strong transient optically generated magnetic field. All take place within the 100 fs duration of a single laser pulse, thus demonstrating the feasibility of photomagnetic switching on the femtosecond time scale.     

Aromatic allylation via diazotization: variation of the allylic moiety and a short route to a benzazepine derivative

A continued study of the recently discovered diazotizative allylation (DiazAll) reaction of aniline derivatives is reported. Several allyl reagents, commonly used in radical allylation reactions, were evaluated, and some of these reagents resulted in allylation when used in the DiazAll reaction. The best result was obtained with allyl bromide. Substituted allylic bromides gave the corresponding allyl aromatic compounds in poor to excellent yields. In comparison with an established method for aromatic allylation, the DiazAll reaction performed well and was superior when a more complex allylic bromide was used. Finally, a new allylation-bromocyclization reaction was demonstrated and used in the synthesis of a known inhibitor of phenylethanolamine N-methyltransferase (PNMT), an enzyme involved in the biosynthesis of adrenaline.     

Synthetic aperture imaging using sources with finite aperture: deconvolution of the spatial impulse response

A method for ultrasonic synthetic aperture imaging using finite-sized transducers is introduced that is based on a compact, linear, discrete model of the ultrasonic measurement system developed using matrix formalism. Using this model a time-domain algorithm for deconvolution of the transducer's spatial impulse responses (SIRs) is developed that is based on a minimum mean square error (MMSE) criterion. The algorithm takes the form of a spatiotemporal filter that compensates for the SIRs associated with a finite-sized transducer at every point of the processed image. A major advantage of the proposed method is that it can be used for any transducer, provided that its associated SIRs are known. This is in contrast to the synthetic aperture focusing technique (SAFT), which treats the transducer as a point source. The performance of the method is evaluated with simulations and experiments, performed in water using a linear phased array. The results obtained using the proposed method are compared to those obtained with a classical time-domain SAFT algorithm. For a finite aperture source, it is clearly shown that the resolution obtained using the proposed method is superior to that obtained using the SAFT algorithm.     

Factors influencing the determination of analyte ion surface partitioning coefficients in electrosprayed droplets

The observed response in mass spectrometry utilizing electrospray as a sample introduction technique can be affected by a number of factors. In this study a series of two-electrolyte systems was investigated and the mass spectrometric responses were modeled by the use of droplet surface partitioning coefficients and instrumental response factors according to a recently reported method (Sjöberg et al., Anal. Chem. 2001, 73, 23–28). The partitioning coefficient and the instrumental response factor were found to be affected by the chosen experimental conditions. Experimental parameters that were investigated include spray position relative to the orifice, spray potential, nebulizer and curtain gas flow rates, ionic strength, and organic content of the sprayed solution. The time history of the generated droplets turned out to be of importance to both the partitioning coefficients and the instrumental response factor. For example, a general increase in the surface partitioning coefficients for the tetrapentylammonium ion was initially observed when the spray was aiming closer to the sampling orifice. Furthermore, it was shown with a small amount of deuterium labeled electrolyte that the total ionic strength and not just the electrolyte concentration influence the instrumental response factor.