Molecular function utilization

Nonadiabatic transitions definitely play crucial roles for molecules to manifest various functions. The theory of nonadiabatic transition is very helpful not only to comprehend the mechanisms, but also to design new molecular functions and enhance their efficiencies. The photochromism that is expected to be applicable to molecular switches and memories is a good example [130]. Photoisomerization of retinal is well known to be a basic mechanism of vision. In these processes, the NT type of nonadiabatic transitions play essential roles. There must be many other similar examples. Utilization of the complete reflection phenomenon can also be another candidate, as discussed in Section V.C. In this section, the following two examples are cosidered (1) photochromism due to photoisomerization between cyclohexadiene (CHD) and hexatriene (HT) as an example of photoswitching molecular functions, and (2) hydrogen transmission through a five-membered carbon ring. 

Consequently, the molecular wave function utilizing the px orbital can be expressed as... 

In this chapter, it will be described how we have utilized endogenous and engineered Zn2+ binding sites to explore the structure and molecular function of Na+/Cl -depen-dent neurotransmitter transporters. The work has not only allowed the definition of the first structural constraints in the tertiary structure of this class of transporters, but also provided new insight into both conformational changes accompanying substrate translocation and mechanisms governing conformational isomerization in the translocation cycle. In the chapter, we will also review the theoretical and practical basis for... 

Lysozyme and Antibodies To fully appreciate how proteins function in a cell, it is helpful to have a three-dimensional view of how proteins interact with other cellular components. Fortunately, this is possible using on-line protein databases and the three-dimensional molecular viewing utilities Chime and Protein Explorer. If you have not yet installed the Chime plug-in on your computer, go to www.mdlchime.com/chime and follow the instructions for your operating system and browser. Once chime is installed, go to the Protein Data Bank (www.rcsb.org/pdb). 

Polymer Backbone Motion. Alternate descriptions of molecular motion utilize an effectively non-exponential autocorrelation function to describe polymer dynamics. One formalism is the use of a log-/2 distribution of correlation times in place of a single correlation time(14). Such a description may simulate the various time scales for overall and internal motions in polymers. 

Figure 7.3 Oxygen-oxygen radial density distribution for liquid water. The smooth curve is the experimental result of Head-Gordon and Hura (2002) the dots are the data, collected in bins of width 0.05 A, from ab initio molecular dynamics utilizing the rPBE electron density functional. The estimated temperature is 314 K for the latter case, slightly higher than that of the experiments at 300 K. See Asthagiri et al. (2003c).

Biologists attribute molecular intelligence to the process of evolution. However, molecular intelligence might better be evaluated with intended function in mind since Nature may have optimized a particular molecular function on the basis of an entirely different set of criteria. Consider BR as an example. The photonic properties of BR are a byproduct of evolution rather than a primary feature essential for survival of Halobacteria, Before these properties can be optimally exploited for construction of a photonic device, it is often necessary to modify the structure of BR. For example, Vsevolodov and Dyukova utilized BR with a synthetic chromophore (5-keto BR) [41] and Hampp et al... 

Our analysis of the possible role of the ERP suggests another attribute of intelligent materials that is, modular design of molecular functions. The ability of bacteriorhodopsin to bind protons from the cytoplasm upon light stimulation serves as a critical step in proton translocation. The same event in rhodopsin, however, may serve an entirely different function it triggers the cyclic GMP cascade. Thus, Nature could well have utilized a common design for vision and for photosynthesis (85). The same design principle may be implemented with completely different types of molecules or materials. On the other hand, the same molecular event may be exploited for different purposes. 

Yu, C. Mosbach, K. Molecular imprinting utilizing an amide functional group for hydrogen bonding leading to highly efficient polymers. J. Org. Chem. 1997, 62, 4057-4064. 

In this chapter we briefly note the improbability of a protein comprised of 20 different amino acids in specified sequence. Then we step through the details whereby a protein of specified sequence comes into being, and, like the accountant, sum up the cost in terms of the biological energy currency, adenosine triphosphate (ATP), that is, in terms of the number of ATP molecules consumed in the production of a protein of unique sequence. Such an essentially ordinary exercise requires inclusion in this book in order to remove unnecessary mystery of protein production, to provide an example whereby molecular machines utilize energy to produce biological structure, and to place in perspective the ease with which new protein-based machines evolve when functioning by the consilient mechanism. 

The nitrogen atom of a Schiff base or oxime can coordinate to various metal ions (alkali metal, alkaline earth metal, transition metal, heavy metal ion). In particular, chelates such as salen (bis(salicylidene)ethylenediamine), saloph (bis(salicylidene)-o-phenylenediamine), and salamo (bis(salicylideneaminooxy)ethane) afford stable metal complexes, which are utilized for a variety of molecular functions such as catalysis of organic reactions, magnetism, luminescence, etc. °... 

Studies ofconnexin function utilizing molecular methodology... 

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