Base pairing in water

Most proton transfer reactions are fast they have been carefully studied by relaxation methods. A system consisting of a conjugate acid-base pair in water is a three-state cyclic equilibrium as shown in Scheme IV. [The symbolism is that used by Bemasconi. ... 

An interesting question then arises as to why the dynamics of proton transfer for the benzophenone-i V, /V-dimethylaniline contact radical IP falls within the nonadiabatic regime while that for the napthol photoacids-carboxylic base pairs in water falls in the adiabatic regime given that both systems are intermolecular. For the benzophenone-A, A-dimethylaniline contact radical IP, the presumed structure of the complex is that of a 7t-stacked system that constrains the distance between the two heavy atoms involved in the proton transfer, C and O, to a distance of 3.3A (Scheme 2.10) [20]. Conversely, for the napthol photoacids-carboxylic base pairs no such constraints are imposed so that there can be close approach of the two heavy atoms. The distance associated with the crossover between nonadiabatic and adiabatic proton transfer has yet to be clearly defined and will be system specific. However, from model calculations, distances in excess of 2.5 A appear to lead to the realm of nonadiabatic proton transfer. Thus, a factor determining whether a bimolecular proton-transfer process falls within the adiabatic or nonadiabatic regimes lies in the rate expression Eq. (6) where 4>(R), the distribution function for molecular species with distance, and k(R), the rate constant as a function of distance, determine the mode of transfer. 

The definition of pH is pH = —log[H+] (which will be modified to include activity later). Ka is the equilibrium constant for the dissociation of an acid HA + H20 H30+ + A-. Kb is the base hydrolysis constant for the reaction B + H20 BH+ + OH. When either Ka or Kb is large, the acid or base is said to be strong otherwise, the acid or base is weak. Common strong acids and bases are listed in Table 6-2, which you should memorize. The most common weak acids are carboxylic acids (RC02H), and the most common weak bases are amines (R3N ). Carboxylate anions (RC02) are weak bases, and ammonium ions (R3NH+) are weak acids. Metal cations also are weak acids. For a conjugate acid-base pair in water, Ka- Kb = Kw. For polyprotic acids, we denote the successive acid dissociation constants as Kal, K, K, , or just Aj, K2, A"3, . For polybasic species, we denote successive hydrolysis constants Kbi, Kb2, A"h3, . For a diprotic system, the relations between successive acid and base equilibrium constants are Afa Kb2 — Kw and K.a Kbl = A w. For a triprotic system the relations are A al KM = ATW, K.d2 Kb2 = ATW, and Ka2 Kb, = Kw. 

Rini, M., et al.. Real-time observation of bimodal proton transfer in acid-base pairs in water. Science, 2003, 301, 349-352. 

As discussed above, hydrogen bond interaction does not operate effectively in water that has large relative permittivity. Indeed, nucleobases can not form hydrogen-bonded complementary base pairs in water [9]. As the hydrogen bond is essential to the base-base interaction, an effective approach to the design and construction of stable and predictable nucleobase assemblies is to make the microenvironment of the nucleobase more hydrophobic (lower permittivity). The use of an air/water interface is one of the effective approaches for this purpose. 

Sawada T, Fujita M (2010) A single Watson-Crick G C base pair in water aqueous hydrogen bonds in hydrophobic cavities. J Am Chem Soc 132 7194-7201. doi 10.1021/ja 101718c... 

Danilov VI, Zheltovsky NV, Slyusarchuk ON, Poltev VI, Alderfer JL (1997) The study of the stability of Watson-Crick nucleic acid base pairs in water and dimethyl sulfoxide eom-puter simulation by the Monte Carlo method. J Biomol Struct Dyn 15(l) 69-80... 

Owing to the increasing efficiency of computational methods, it has become possible to investigate base pairs in the gas phase and solution simulated by super-molecular approaches with up to six water molecules [98IJQ37, 98JPC(A) 10374, 98JPC(B)9109, 99JST107]. In the cytosine-isocytosine Watson-Crick base pair. 

Conjugate acid-base pairs in the dissociation of acetic acid in water... 

Other molecules and ions besides water may show amphiprotic behavior. Write the two proton transfer equilibria that demonstrate the amphiprotic character of (a) HC03" (b) HP042-, and identify the conjugate acid-base pairs in each equilibrium. 

The trp repressor presents an unusual variation for interaction with the base pairs in its operator. Except for the arginine-guanine interaction, the interactions are mediated by a water molecule (see fig. 30.27c). For example, a threonine hydroxyl group makes a hydrogen bond with a water molecule, which in turn makes two hydrogen bonds with an adenine. 

For each of the compounds in the Acid-Base Properties of Salts activity (eChapter 15.14), write the reaction that takes place when the compound is placed in water. Identify the conjugate base pairs in each reaction. 

In the Bransted-Lowry theory, every acid-base reaction creates its conjugate acid-base pair. In the above reaction HCl is an acid which, after giving up a proton, becomes a conjugate base, Cl . Similarly, water is a base which, after accepting a proton, becomes a conjugate acid, the hydronium ion. 

The SCF-MI method was also employed to study the influence of hydration on the WC cytosine-guanine base pair, investigating the ability to reproduce the hydration pattern present in the real system (the base pair in the DNA framework) [33]. The calculated water positions around the base pair were compared to those predicted by a knowledge-based approach employing crystallographic data [34]. The correspondence between averaged... 

Ammonia is a pungent gas at room temperature. Its main use is in the production of fertilizers and explosives. It is very soluble in water. It forms a basic solution that is used in common products, such as glass cleaners. Identify the conjugate acid-base pairs in the reaction between aqueous ammonia and water. 

Fig. 20.5 a, b. Schematic representation of hydration of a G-T wobble base pair in the Z-DNA type crystal structure of d(CGCGTG). Hydrogen-bonding distances to water molecules (W) and C(l )- -C(l ) distances given in A units. Left hydration is only by water molecules right hydration involves a cluster [Mg(H20)6]2+ [683]... 

Since the separation between adjacent base pairs - 3.4 A is comparable to the 2.8 to 3.5 A in water... water hydrogen bonding, the water molecules associated with one base pair can hydrogen bond to water molecules bound to adjacent base pairs. In this manner, extended filaments and nets composed of water molecules in the first hydration layer can be built up which cover minor and major grooves. 

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