SUBJECTS stacking interactions

The DNA-carbon nanotube interaction is a complicated and dynamic process. Many studies on this subject have been pursued through a series of techniques, including molecular dynamic simulation, microscopy, circular dichroism, and optical spectroscopy.57,58 Although the detailed mechanism is not fully understood at present, several physical factors have been proposed to be driving DNA-carbon nanotube interactions,46,59-61 such as entropy loss due to confinement of the DNA backbone, van der Waals and hydrophobic (rr-stacking) interactions, electronic interactions between DNA and carbon nanotubes, and nanotube deformation. A recent UV optical spectroscopy study of the ssDNA-SWNT system demonstrated experimentally that... 

A MCFC stack interacts with other system components and causes an interdependency between them. To investigate transient behavior, the plant is assumed to be at steady state corresponding to rated power and subjected to a sudden variation in power demand. This chapter has developed the control system with an adaptive minimum variance controller and based on the simulation study, the resulting controller is robust enough to stabilize the system for different operating conditions. 

Over the past decade, there have been numerous books and arti-cles " reviewing ab initio and density functional theory (DFT) computations of hydrogen bonding and other weak noncovalent interactions. In fact, the very first chapter of this entire review series examines basis sets for noncovalent interactions between atoms and/or molecules," while a chapter in the second volume reviews ab initio methods for hydrogen bonding." Three thematic issues of Chemical Reviews have been dedicated to van der Waals interactions (Vol. 88, No. 6, 1988 Vol. 94, No. 7, 1994 and Vol. 100, No. 11, 2000). Two articles in the centennial issue of the Journal of Physical Chemistry discuss weakly bound clusters and solvation." " It is also worth noting that 7i-type stacking interactions are very topical at the moment and are the subject not only of a separate chapter in this volume of Reviews in Computational Chemistry" but also of a special issue of Physical Chemistry Chemical Physics (Vol. 10, No. 19, 2008). 

Thermostabilization of double-stranded DNA is provided by base pairing (1) and base stacking (see Reference 27 and references therein) complemented by positive supercoiling by reverse gyrase [in hyperthermophiles (8, 9, 28)] and by stabilization via interactions with histone-like proteins (29, 30). The relative contribution of base paring and base stacking into the thermostability of double-stranded DNA has been a subject of extensive studies for more than four decades (1, 27, 31). We will consider here this question, based on the results of recent experimental and computational works (31, 32). 

Especially the weak interaction patterns like van der Waals forces, weak hydrogen bonds (i.e. those with bond energies less than about 10 kJ mol ) and n-n stackings are often discussed in the light of hydrophobic effects. Such effects are strongly system-dependent, they can hardly be understood in an ad hoc fashion, and are thus subject of constant debate (see Refs. [199, 200] for examples and Ref. [201] for a review). 

To pursue the idea of specific TCNE-allyl interactions, we suppose in Fig. 19 that each TCNE has a strong contact (J) with one MP and a weaker one (J < J) with the other. This results in a dimerized stack if J and J alternate precisely when the unit cell is doubled and there is no reason for an enlarged thermal ellipsoid. A more promising hypothesis is that J and J do not alternate precisely, so that sometimes two TCNE form strong contacts with the same MgP, to give trimers in Fig. 19. MgP sites with two weak (J ) contacts are monomers. There are equal numbers of J and J, but now the distribution is random, subject to the constraint that no more than two successive J or J can occur. 

Let us consider the phase obtained when the tube is sufhciently long (or when there are many interacting tubes) and is subject to attractive interactions leading to compaction. In this phase, the tube is stretched out locally with nearby sections parallel to one another (or the tubes are stacked parallel to one another in a periodic arrangement) and does not have the richness we associate with protein native-state structures. Returning to the protein, one may ask whether some structures are the analogs of those found in this so-called semicrystalline phase. 

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