Molecules, mechanically

Singh U C and P A Kollman 1986. A Combined Ab Initio Quantum Mechanical and Molecule Mechanical Method for Carrying out Simulations on Complex Molecular Systems Applicatior to the CHsQ + Cr Exchange Reaction and Gas Phase Protonation of Polyethers. Journal Computational Chemistry 7 718-730. 

Finer, J. T., Simmons, R. M., and Spndich, J. A., 1994. Single myosin molecule mechanics Piconewton forces and nanometer steps. Nature 368 113-119. 

FIGURE 5.3 Different types of functional readouts of agonism. Receptors need not mediate cellular response but may demonstrate behaviors such as internalization into the cytoplasm of the cell (mechanism 1). Receptors can also interact with membrane proteins such as G-proteins (mechanism 2) and produce cytosolic messenger molecules (mechanism 3), which can go on to mediate gene expression (mechanism 4). Receptors can also mediate changes in cellular metabolism (mechanism 5). 

This all seemed very reasonable at the time, but subsequent work was not consistent with it. A small but measurable amount of 180 exchange was reported for some amides in reasonably concentrated HC1 media,277,278 and for at least one amide the amount of exchange decreased with increasing acidity,277 which is the opposite of what would be expected with the Scheme 14 one-water-molecule mechanism taking over from the equation (74) three-water-molecule mechanism as the acidity increased. Also, the solvent deuterium isotope effect was found to be close to unity for at least one amide,278 a result that has since been confirmed,279 which is not what would be expected on the basis of either a three- or a one-water-molecule process.280 Because of this it was decided to reexamine the lactam hydrolysis data subsequent to the publication of the excess acidity analysis of the H NMR results for these,268 a new study appeared with rate constant data for four of these molecules in aqueous H2S04 media obtained by UV spectroscopy at several temperatures,281 and this was included too.282... 

One example was reported by Tolman and coworkers (78) who found that the copper(I) complex C Tp112 (TpR2=tris(3-(R2)-5-methylpyrazol-l-yl)hydroborate) promotes NO disproportionation via a weakly bound CuITpR2(NO) intermediate (formally a MNO 11 species). The products are N20 and a copper(II) nitrito complex (Eq. (36)). The rate law established the reaction to be first-order in copper complex concentration and second-order in [NO], and this was interpreted in terms of establishment of a pre-equilibrium between NO and the Cu(I) precursor and the Cux(NO) adduct, followed by rate-limiting electrophilic attack of a second NO molecule (mechanism B of Scheme 5) (78b). 

Although there is very little data on the mechanistic aspects of the biosynthetic enzymes, it is thought that their reaction mechanisms are very similar to those of the mammalian heme oxygenases. Indirect evidence that the mechanism of action of the biosynthetic enzymes is similar to that of the mammalian heme oxygenases was provided by 0-labeling studies showing that the biosynthesis of phycocyanobilin occurred via a two-molecule mechanism (141, 142) comparable to that of the mammalian heme oxygenases (8). 

The last chapter, by Y. Takagi Y. Ikeda, and K. Taira is focused on ribozyme (RNA molecules) mechanisms. The biological functions of RNA molecules depend on their adoption of given three-dimensional structures, the presence of charged phosphodiester bonds playing an important role. Some ribozymes utilize metal ions as catalysts while others use the metal ions to maintain appropriate three-dimensional structures. All the examples reported in this chapter demonstrate that the mechanisms exploited by naturally existing ribozymes appear to be more diverse than originally expected. 

H. Dietz and M. Rief Exploring the Energy Landscape of GFP by Single-Molecule Mechanical Experiments. Proc. Natl. Acad. Sci. USA 101, 16192 (2004). 

Lee H, Scherer NF, Messersmith PB. Single-molecule mechanics of mussel adhesion. Proc Natl Acad Sci USA 2006 103 12999-13003. 

A similar photooxidation pathway was found for Mg(ll)TPP. It reacted readily with molecular oxygen to give the corresponding 15,16-dihydrobiliverdin, similar to the one shown for Mg(II)OEP in Scheme 1. Further studies have proposed that the photooxygenation of metallo-me o-tetrasubstituted porphyrins proceeds via a one-molecule mechanism involving only one oxygen molecule. Most likely, the first intermediates formed upon photooxygenation are short-lived peroxides. Such compounds are very unstable and a possible dioxetane structure is shown in formula 31. 

An examination of the hexenes formed from the radiolysis of solid n-hexane seems to indicate the presence of charge localization. The experimental data are shown in Table V. The five isomeric hexenes formed include all the possibilities if no isomerization of the n-hexane carbon skeleton takes place. Two ion molecule mechanisms are postulated for the formation of these hexenes the necessity of two mechanisms will be justified in the next section. The first is an internal hydrogen abstraction reaction which is analogous to reaction 1 in Table IV except that it is intramolecular. It can be written as ... 

Under the conditions of the experiments, reaction (4-12) was unimportant. The excited-molecule mechanism led to the prediction... 

The mercury-photosensitized decomposition of 1,1-difluoroethene, and of ( )- and (Z)-1.2-difluoroethene, proceeds by elimination of hydrogen fluoride via an excited molecule mechanism to produce fluoroacetylene (12).55... 

J. T. Finer, R. M. Simmons, and J. A. Spudich, Single Myosin Molecule Mechanics Piconewton Forces and Nanometre Steps , Nature, 368, 113-119 (1994). 

Ion-molecule reactions have also proved fertile ground for both theoretical studies and experiment. Here there are mainly two typical ion-molecule mechanisms stripping reactions such as... 

The techniques involved are single-molecule spectroscopy including optical (fluorescence) methods and single-molecule mechanical manipulation including scanning probe techniques (e.g., force measurements). 

As a general comment about the dynamic mechanical relaxational behavior of this polymer, the results are consistent with dielectric data [210] and with the fact that no glass transition phenomenon is observed, at least in the range of temperature studied. This is striking in an amorphous polymer. It is likely that the residual part of the molecule mechanically active above the temperature of the ft relaxation is only a small one, and this is the reason for the low loss observed in the a zone. 

D Autreaux B, Toledano MB (2007) ROS as signalling molecules mechanisms that generate specificity in ROS homeostasis. Nat Rev Mol Cell Biol 8 813-824... 

The Whitesides-Mitchell experiment80 can be interpreted by BPR using the nitrogen as pivot. The experiment rules out, for this particular molecule, mechanisms discussed by Muetterties78 as alternatives... 

Butcher RA, Schreiber SL. Using genome-wide transcriptional profiling to elucidate small-molecule mechanism. Curr. Opin. Chem. Biol. 2005 9 25-30. 

In the case of trimethylamine, an excited molecule mechanism has been invok-ed o o8. The formation of methane can be explained by the abstraction reactions of methyl radicals but the mechanism of hydrogen formation is uncertain. At low... 

The vapour phase photolysis of ethylene sulfide at 2537 A results in the formation of ethylene, which comprises at least 95 % of the total products at short conversions minor products are Hj, CH4 and C2H2 . The overall reaction appears to proceed via an excited molecule mechanism and ( 2114) extrapolates to ca. 1.9 at low pressures. The primary formation of ethylene can be explained by the following sequence... 

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