Molecular tuning

Table 1 Amino acids observed as calciiun-binding ligands in 567 EF-hand sequences. (Reproduced from J.J. Falke, S.K. Drake, A.L. Flazard, O.B. Peersen, Molecular tuning of ion binding to calcium signalling proteins. Q, Rev. Biophys. 27(3) 219-90 by permission of Cambridge University Press)...

Falke, J.J.,Drake, S.K.,Hazard, A.L., Peersen,O.B. 1994. Molecular tuning ofion binding to calcium... 

Figure B3.3.12. Sulphur atoms in liquid iron at the Earth s core conditions, simnlated by first-principle Car-Parrinello molecular dynamics, (a) Initial conditions, showing a mannally-prepared initial cluster of snlphur atoms, (b) A short tune later, indicating spontaneous dispersal of the snlphur atoms, which mingle with the surroundmg iron atoms. Thanks are dne to D Alfe and M J Gillan for this figure. For fiirtlier details see [210. 211].

The parameter /r tunes the stiffness of the potential. It is chosen such that the repulsive part of the Leimard-Jones potential makes a crossing of bonds highly improbable (e.g., k= 30). This off-lattice model has a rather realistic equation of state and reproduces many experimental features of polymer solutions. Due to the attractive interactions the model exhibits a liquid-vapour coexistence, and an isolated chain undergoes a transition from a self-avoiding walk at high temperatures to a collapsed globule at low temperatures. Since all interactions are continuous, the model is tractable by Monte Carlo simulations as well as by molecular dynamics. Generalizations of the Leimard-Jones potential to anisotropic pair interactions are available e.g., the Gay-Beme potential [29]. This latter potential has been employed to study non-spherical particles that possibly fomi liquid crystalline phases. 

In adtiiijon Lo inolccnlar mnch an jcs calcnlatjoii s, HypcrChcin can perform various quantum mechanical calciilaLion s. These calculations are more universal than molecular mechanics, but are also more tune consuming and less empirical. 

Electronic transitions in molecules in supersonic jets may be investigated by intersecting the jet with a tunable dye laser in the region of molecular flow and observing the total fluorescence intensity. As the laser is tuned across the absorption band system a fluorescence excitation spectrum results which strongly resembles the absorption spectrum. The spectrum... 

A particularly useful property of the PX monomer is its enthalpy of formation. Conventional means of obtaining this value, such as through its heat of combustion, are, of course, excluded by its reactivity. An experimental attempt was made to obtain this measure of chemical reactivity with the help of ion cyclotron resonance a value of 209 17 kJ/mol (50 4 kcal/mol) was obtained (10). Unfortunately, the technique suffers from lack of resolution in addition to experimental imprecision. It is perhaps better to rely on molecular orbital calculations for the formation enthalpy. Using a semiempirical molecular orbital technique, which is tuned to give good values for heat of formation on experimentally accessible compounds, the heat of formation of /5-xylylene has been computed to be 234.8 kj/mol (56.1 kcal/mol) (11). 

Because of the tunabiUty, dye lasers have been widely used in both chemical and biological appHcations. The wavelength of the dye laser can be tuned to the resonant wavelength of an atomic or molecular system and can be used to study molecular stmcture as well as the kinetics of a chemical reaction. If tunabiHty is not required, a dye laser is not the preferred instmment, however, because a dye laser requires pumping with another laser and a loss of overall system efficiency results. 

Membranes are also used to separate gases, for example, the production of N2 and O2 from air and the recovery of hydrogen from ammonia plant purge gas. The working principle is a membrane that is chemically tuned to pass a molecular type. 

SFG [4.309, 4.310] uses visible and infrared lasers for generation of their sum frequency. Tuning the infrared laser in a certain spectral range enables monitoring of molecular vibrations of adsorbed molecules with surface selectivity. SFG includes the capabilities of SHG and can, in addition, be used to identify molecules and their structure on the surface by analyzing the vibration modes. It has been used to observe surfactants at liquid surfaces and interfaces and the ordering of interfacial... 

In these reactions the system is tuned, for example by adjustment of the reaction temperature and time and modification of the catalyst structure to maximize the quantity of the desired dimers produced, and to minimize the production of higher molecular weight oligomers and polymers. In other reactions it is the opposite... 

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