Diffusion small molecules

WW Brandt. Model calculation of the temperature dependence of small molecule diffusion in high polymers. J Phys Chem 63 1080-1084, 1959. 

In principle, the interaction of small molecules within a swollen polymer is one of the easiest situation to be proven, due to the large difference in size of species involved. Changes in the small molecule diffusivity will occur as a result of specific interactions between the diffusant and the polymeric matrix. 

The presence of a covalent acyl-enzyme intermediate in the catalytic reaction of the serine proteases made this class of enzymes an attractive candidate for the initial attempt at using subzero temperatures to study an enzymatic mechanism. Elastase was chosen because it is easy to crystallize, diffracts to high resolution, has an active site which is accessible to small molecules diffusing through the crystal lattice, and is stable in high concentrations of cryoprotective solvents. The strategy used in the elastase experiment was to first determine in solution the exact conditions of temperature, organic solvent, and proton activity needed to stabilize an acyl-enzyme intermediate for sufficient time for X-ray data collection, and then to prepare the complex in the preformed, cooled crystal. Solution studies were carried out in the laboratory of Professor A. L. Fink, and were summarized in Section II,A,3. Briefly, it was shown that the chromophoric substrate -carbobenzoxy-L-alanyl-/>-nitrophenyl ester would react with elastase in both solution and in crystals in 70 30 methanol-water at pH 5.2 to form a productive covalent complex. These... 

An additional condition may be imposed, even when a cofactor-independent enzyme is used, if a mediator molecule is involved in the electron transfer process, as is often the case with oxidases. Laccases, for example, may employ small-molecule diffusible mediator compounds in their redox cycle to shuttle electrons between the redox center of the enzyme and the substrate or electrode (Scheme 3.1) [1, 2]. Similarly, certain dehydrogenases utiHze pyrroloquinoline quinone. In biocatalytic systems, mediators based on metal complexes are often used. 

A small molecule diffuses faster than a larger one. Therefore the effectiveness is greater for molecules of greater mass. 

Dialysis is the process in which small molecules diffuse across a semipermeable membrane that has pore sizes large enough to pass small molecules but not large ones. A microdialysis probe has a semipermeable membrane attached to the shaft of a hypodermic needle, which can be inserted into an animal. Fluid is pumped through the probe from the inlet to the outlet. Small molecules from the animal diffuse into the probe and are rapidly transported to the outlet. Fluid exiting the probe (dialysate) can be analyzed by liquid chromatography. 

You can demonstrate the size of colloidal particles with a dialysis experiment in which two solutions are separated by a semipermeable membrane that has pores with diameters of 1—5 nm.3 Small molecules diffuse through these pores, but large molecules (such as proteins or colloids) cannot. (Collecting biological samples by microdialysis was discussed at the opening of Chapter 25.)... 

Large molecules remain trapped inside a dialysis bag, whereas small molecules diffuse through the membrane in both directions. 

The relatively new method of fluorescence correlation spectroscopy (FCS) is based on the fact that molecules with different molecular weights (usually) exhibit different diffusion times in solution. Thus, small molecules diffuse faster than larger ones. To determine K- values, one component must be labeled with a fluorescent dye. Due to the different molecular weights of the uncomplexed, labeled component and the complex, the diffusion times of the free and complexed molecule differ. This fact allows determining the distribution of free and complexed molecules in the solution. After measuring the distribution in different mixtures with varying ligand concentrations, the K- value can be calculated [44]. 

In this technique, the enzyme solution is put inside a dialysis bag which is then immersed in a solution of substrate, or cofactors. Small molecules can diffuse through the wall of the bag and react in the presence of the enzyme, while products, if also small molecules, diffuse into the outside solution, where they may be recovered. This technique has been used in syntheses with sialyl aldolase, Kdo-synthetase, the common aldolase, a mixture of hexokinase and pyruvate kinase, a-(2— 6) sialyl transferase,26 a mixture of pyruvate kinase and adenylate kinase,27 and CMP-Neu5Ac synthetase.28... 

Let us note the diffusion behaviour of small molecules, that is unreacted MMA, in the PMMA gel matrix. Using the vinyl peak of the unreacted MMA, PGSE 3H NMR measurements on the small molecule diffusion are performed for PMMA gel samples A1-A4 with varying A. The experimental data lie on a straight line in the A range from 60 to 500 ms, and the slope of the plots is independent of the diffusion time A. This clearly shows that the diffusion of the small molecule is a single mode and not restricted. The diffusion coefficient of MMA (D) as obtained from the slope of the straight line is also independent of the polymer concentration for samples A1-A4, D (10 9 m2 s ) 1.4,1.5,1.5 and 1.4, respectively. The... 

Small solutes such as urea and sodium caprylate often coexist with protein macromolecules in solutions. When these small molecules diffuse the protein solution, the diffusivity of the molecules decreases with increasing protein... 

Figure 4-5. Cel filtration. Cel filtration depends on the fact that small molecules diffuse into the pores of the gel filtration matrix more readily than larger ones. The large excluded molecules are carried by the flow of elution medium...

Figure 26-18 is a diagram of a dialysis module in which analyte ions or small molecules diffuse from the sample solution through a membrane into a reagent stream, which often contains a species that reacts with the analyte to form a colored product, which can then be determined photometrically. Large molecules, which interfere in the determination, remain in the original stream and are carried to waste. The membrane is supported between two Teflon plates in which complementary channels have been cut to accommodate the two stream flows on opposite sides of the membrane. The transfer of smaller species through the membrane is usually incomplete (often less than 50%). Thus, successful quantitative analysis requires close control of temperature and flow rates for both samples and standards. Such control is easily accomplished in automated flow-injection systems. 

Dialysis is considered the reference method when studying protein binding of drugs (45) but is also useful for protein removal prior to plasma analysis. Dialysis is a classical separation method that uses semipermeable membranes to separate compounds by molecular weight. The protein sample is exposed to a buffer solution separated by the membrane. After the system is allowed to come to equilibrium, the small molecules diffuse to similar concentrations on both sides, while the sample side contains all of the protein... 

The best-known application of dialysis is the use of artificial kidneys to remove waste products from the blood of persons with kidney disease. Hollow-fiber cellulosic membranes are employed, and blood is passed through the fibers while saline solution is circulated on the outside. Urea and other small molecules diffuse through the membrane to the external solution, while proteins and cells are retained in the blood. The dialyzing solution has added salts and glucose to prevent loss of these materials from the blood. 

The rate constant for the binding of RNA polymerase holoenzyme to a promoter on a long DNA molecule is greater than that for the collision of two small molecules in solution. Since small molecules diffuse through solutions more rapidly than large ones, how can this be true ... 

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