The interplay between aromatic stacking and hydrogen bonding in nucleobases has been investigated via high-level quantum chemical calculations. The experimentally observed stacking arrangement between consecutive bases in DNA and RNA/DNA double helices is shown to enhance their hydrogen bonding ability as opposed to gas phase optimized complexes. This phenomenon results from more repulsive electrostatic interactions as is demonstrated in a model system of cytosine stacked offset-parallel with substituted benzenes. Therefore, the H-bonding capacity of the N3 and O2 atoms of cytosine increases linearly with the electrostatic repulsion between the stacked rings. The local hardness, a density functional theory-based reactivity descriptor, appears to be a key index associated with the molecular electrostatic potential (MEP) minima around H-bond accepting atoms, and is inversely proportional to the electrostatic interaction between stacked molecules. Finally, the MEP minima on surfaces around the bases in experimental structures of DNA and RNA–DNA double helices show that their hydrogen bonding capacity increases when taking more neighboring (intra-strand) stacking partners into account.
The present work focuses on the influence of aromatic stacking on the ability of an aromatic nitrogen base to accept a hydrogen bond. Substituent effects were studied at the MP2 level for 10 complexes of a substituted benzene stacked with pyridine in a parallel offset conformation. The interaction energies between each substituted benzene and pyridine were analyzed in terms of Hartree-Fock, correlation, and electrostatic contributions. It appears that the basicity of pyridine is directly related to the electrostatic interaction between the cycles. It increases with increasing electron donating character of the benzene substituents. Also, density functional theory based descriptors such as global and local hardnesses and the benzene ring polarizability are found to adequately predict the interaction energy. These findings may be important in the study of DNA/ RNA chains.
The present work reports ab initio molecular dynamics simulations, based on density functional theory using the PBE functional, of Li(+)- Na(+)- and K(+)-montmorillonites, considering three types of isomorphic substitutions in the montmorillonite layer: tetrahedral (T(sub)), octahedral (O(sub)) and both (OT(sub)). These simulations allow us to evaluate the effect of each type of substitution on the inner- outer-sphere complex formation of the alkali cations. It is observed that, for the three kinds of substituted montmorillonites, K(+) remains bound to the surface confirming its role as swelling inhibitor. In contrast, Li(+) tends to hydrate and coordinate to 4 water molecules in all cases, except for OT(sub), for which one of the two Li(+) cations remains bound to the oxygens close to the substituted tetrahedral site. Finally, Na(+) presents an intermediate behaviour, binding to the surface in T(sub) montmorillonite but being hydrated in O(sub). These simulations show that the hydration/adsorption behaviour of alkali cations in the swelling process of montmorillonite depends on the affinity of the cation for water and the surface, as well as on the type of substitution that controls the negative charge on surface oxygen atoms.
This work analyzes the adsorption of RNA/DNA nucleobases on the external surfaces of Na + -montmorillonite by using periodic plane wave calculations based on the PBE functional. The adsorption energies were corrected by a posteriori added empirical term to account for purely dispersive interactions. Adsorption has been considered either on the side comprising the Na + counterion or on the opposite side, where only siloxane bonds are present. Different orientations of the nucleobases (parallel and orthogonal to the surface plane) have been considered. The results show that guanine and cytosine, for which the metal cation interacts with two basic centers (N and O), are the ones with larger adsorption energies (-27.6 kcal mol -1 for G O6N7 and -27.0 kcal mol -1 for C O2N3 ). The remaining three bases present smaller adsorption energies (-21.7 for T π(O4) , -21.2 for U π(O4) and -20.2 kcal mol -1 for A N3 ). On the other hand, adsorption of the nucleobase on the surface free from Na + , either in a face-to-face or orthogonal orientation, was found to be sizable for all bases (from -3.7 to -11.3 kcal mol -1 ), due to the stabilizing effect of dispersion interactions.
Ribonucleases (RNases) catalyze the cleavage of the phosphodiester bond in RNA up to 10 15 -fold, as compared with the uncatalyzed reaction. High resolution crystal structures of these enzymes in complex with 3-mononucleotide substrates demonstrate the accommodation of the nucleophilic 2-OH group in a binding pocket comprising the catalytic base (glutamate or histidine) and a charged hydrogen bond donor (lysine or histidine). Ab initio quantum chemical calculations performed on such Michaelis complexes of the mammalian RNase A (EC 3.1.27.5) and the microbial RNase T 1 (EC 3.1.27.3) show negative charge build up on the 2-oxygen upon substrate binding. The increased nucleophilicity results from stronger hydrogen bonding to the catalytic base, which is mediated by a hydrogen bond from the charged donor. This hitherto unrecognized catalytic dyad in ribonucleases constitutes a general mechanism for nucleophile activation in both enzymic and RNAcatalyzed phosphoryl transfer reactions.RNases have been the subject of landmark research in areas ranging from basic protein chemistry to enzymology to protein folding and crystallography. These enzymes catalyze the intramolecular nucleophilic displacement of the 5Ј-leaving group by the attacking 2Ј-hydroxyl group in RNA, forming a 2Ј,3Ј-cyclophosphate (see Fig. 1). The nucleophilic attack occurs inline, in a postulated trigonal bipyramidal transition state, implying a catalytic base and acid on either side of the scissile bond (1, 2). X-ray crystallographical and site-directed mutagenesis experiments have provided substantial insight in the structure-function relationship of two unrelated families of ribonucleases. RNase A, (bovine pancreatic ribonuclease A) (EC 3.1.27.5) (3) and RNase T 1 , (EC 3.1.27.3) (4, 5) (and references therein) are the best characterized members of the mammalian and the microbial enzymes, respectively. The mammalian enzymes depend on two histidines for acid/base catalysis, whereas a histidine/glutamic acid pair is found in the microbial enzymes (6).The active site of RNase T 1 is composed of the side chains of Tyr-38, His-40, Glu-58, Arg-77, His-92, and Phe-100 (see Fig. 2a). With the exception of Arg-77, all these amino acids have been shown to take part in catalysis (5). Both the His-40 and Glu-58 side chains are in the direct vicinity of the 2Ј-nucleophile. pH dependence studies have shown Glu-58 to be unprotonated and His-40 to be protonated at the onset of catalysis, proving that Glu-58 is the catalytic base accepting a proton from the 2Ј-nucleophile (7). The protonated His-92 located at the opposite side of the active site functions as the catalytic acid. Removal of the His-40 side chain leads to a 6500-fold decrease in the second-order rate constant k cat /K m suggesting an important catalytic role for this residue in the wild type enzyme. His-40 is believed to polarize the 2Ј-hydroxyl group and to properly orientate Glu-58 toward the substrate (8, 9). However, the actual role of this residue is not totally clarified at present. Despite the l...
Silica and silica based materials are widely used in chemistry and materials science due to their importance in many technological fields. The properties of these materials, which are crucial for their applications, are mainly determined by the presence of hydrogen bonding between surface silanols. Here, we present ab initio molecular dynamics simulations (AIMD) on different surfaces derived from the crystallographic α-quartz (100) and the α-cristobalite (001) and (101) faces, both free and at the interface with liquid water. The focus was on studying whether water adsorption can disrupt the H-bond pattern at the pristine free silica surface and how deep the perturbation due to the contact with the surface affects the structure of the water multilayer. Results highlight that the water phase is over structured at the interface with silica, as compared to water bulk. Furthermore, an apparent counterintuitive behavior has been observed for quartz (100) and cristobalite (001) surfaces: the interaction with water does not cleave the pre-existent H-bonds between the surface silanol groups. On the contrary, in several cases, it is observed that SiOH···OHSi H-bonds are even strengthened, as the result of a mutual cooperative H-donor/H-acceptor enhancement between silanols and water molecules, which may alter the adsorption capability of these silica surfaces.
Adsorption and disproportionation of dinitrogen tetraoxide on sodium-, potassium-, and rubidium-exchanged zeolites X with Si/Al ratio of 1.18 were studied using density functional theory calculations with periodic boundary conditions. It is found that the stabilization and activation of most of the N2O4 isomers confined in the zeolitic cage does not follow Lewis acidity difference of the extraframework cations. This is also observed for the energetics of the N2O4 disproportionation reaction resulting in formation of a space-separated NO+···NO3 - ion pair. The reaction energy increases in the row NaX < RbX < KX. The strength of perturbations and, therefore, the low-frequency shift of the N−O stretching frequency of the adsorbed NO+ cations correlate well with the basicity of the zeolite (RbX > KX > NaX). However, this factor is not the relevant reactivity parameter for the N2O4 disproportionation in the cationic forms of zeolites. The higher activity for the disproportionation as well as the stronger molecular adsorption of N2O4 on RbX and KX zeolites as compared to that on NaX is ascribed to the features analogous to the molecular recognition characteristics of supramolecular systems. The steric properties of the zeolite cage and the mobility of the extraframework cations induced by adsorption are essential to shape the optimum configuration of the active site for N2O4 disproportionation.
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