Opsin does not absorb visible light, but when it bonded with 11-cis-retinal by its lysine side-chain to from rhodopsin, the new molecule has a very broad absorption band in the visible region of the spectrum. By removing the oxygen atom form the retinal and two hydrogen atom form the free amino group of the lysine, the linkage show on the picture above is formed, and it is called Schiff base.
Photoreceptor proteins are light-sensitive proteins involved in the sensing and response to light in a variety of organisms. Photoreceptor proteins can be find in both animals and plants. Hence, they can, indeed, be considered as “star actors” in the pursuit to understand, in general terms, the atomic details of the dynamics of functional conformational transitions [i.e., (partial) un/folding] in these proteins required for their functioning.
At 25 o C, the concentrations of both hydronium and hydroxide ions equal 1.0 * 10 -7 . The ion product of water, K w, is the equilibrium condition for the self-ionization of water and is express as follows: This equation is derived from the equilibrium condition for the self-ionization of water, K w . It brings the three equations for pH, pOH, and K w together to show that they are all related to each other and either one can be found if the other two are known.
The first step in calculating the pH of an aqueous solution of any weak acid or base is to notice whether the initial concentration is high or low relative to 10 -7 M (the concentration of hydronium and hydroxide ions in water due to the autoionization of water). Remember that, for the first dissociation, x = [H 3 O + ] = [C 6 H 7 O 7 - ], so you can plug in the first value of x in for the initial concentrations of C 6 H 7 O 7 - and H 3 O + .
Basically, if system A is in thermal equilibrium with system C and system B is also in thermal equilibrium with system C, system A and system B are in thermal equilibrium with each other. In 1872 James Clerk Maxwell wrote: "If when two bodies are placed in thermal communication, one of the two bodies loses heat, and the other gains heat, that body which gives out heat is said to have a higher temperature than that which receives heat from it."
One of the principal triumphs of the theory of quantum mechanics in chemistry (see Chapter 8) has been its ability to predict the kinds of atoms that will bond together, and the three-dimensional structures and reactivities of the molecules that result. The angle in the water molecule is 104.5°, and the angle in hydrogen sulfide is 92.1°; the four atoms connected to the central carbon in methane and methyl alcohol are directed to the four corners of a tetrahedron.
Classically, the Franck–Condon principle is the approximation that an electronic transition is most likely to occur without changes in the positions of the nuclei in the molecular entity and its environment. The quantum mechanical formulation of this principle is that the intensity of a vibronic transition is proportional to the square of the overlap integral between the vibrational wavefunctions of the two states that are involved in the transition.
where k is a proportionality constant, Io is the incident light intensity, is the molar absorptivity, b is the path length, and c is the concentration of the substrate. Fluorescence commonly occurs from a transition from the lowest vibrational level of the first excited electronic state to the one of the vibrational levels of the electronic ground state.
The inner product of the product of a scalar and the first vector times the second vector is equal to the product of the scalar times the inner product of the first vector times the second vector. The inner product of the vector sum of vector 1 and vector 2 times vector 3 is equal to the sum of the inner product of vector 1 times vector 3 and the inner product of vector 2 times vector 3.
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